Programming Multi-Component Self-Assembly Using Dipolar Interaction and Molecular Shape By Yi Xue B.S. University of Science and Technology of China Thesis Submitted in Partial Fulfillment of Requirements for the Degree of Doctor of Philosophy in the Department of Chemistry at Brown University Providence, Rhode Island May 2014 © Copyright 2014 by Yi Xue This dissertation by Yi Xue is accepted in its present form by the Department of Chemistry as satisfying the dissertation requirement for the Degree of Doctor of Philosophy Date___________ _____________________________ Matthew B. Zimmt, Advisor Recommended to the Graduate Council by Date__________ _____________________________ J. William Suggs, Reader Date___________ _____________________________ Lai-Sheng Wang, Reader Approved by the Graduate Council Date___________ _____________________________ Peter M. Weber Dean of the Graduate School iii Curriculum Vitae Yi Xue was born on November 10th, 1985 in Beijing, China. He went to the Second High School Attached to Beijing Normal University in 2001. Three years later, Yi started his undergraduate study in the Department of Chemistry at University of Science and Technology of China and graduated with B.S. degree in chemistry in 2008. Yi was admitted to the Department of Chemistry at Brown University in August 2008 and began to work toward his PhD degree under the supervision of Professor Matthew B. Zimmt. His research involved supramolecular 2-D self-assembly of organic molecules. His peer-viewed scientific publications include: 1. Yi Xue, Min-Kyoung Kim, Tereza Pašková and Matthew Zimmt, The in's and out's of monolayer morphology control using alkadiyne side chain, Manuscript in preparation 2. Min-Kyoung Kim, Yi Xue, Tereza Pašková and Matthew Zimmt Monolayer patterning using ketone dipoles, Phys.Chem.Chem.Phys, 2013, DOI: 10.1039/C3CP50808K 3. Yi Xue, Matthew Zimmt, Patterned monolayer self-assembly programmed by side chain shape: four-component gratings, J. Am. Chem. Soc. 2012, 134, 4513-4516. 4. Yi Xue, Matthew Zimmt, Tetris in monolayers: patterned self-assembly using side chain shape, Chem. Commun. 2011,47, 8832-8834. 5. Wenjun Tong, Yi Xue and Matthew Zimmt, Morphology Control and Monolayer Patterning with CF(2) Groups: An STM Study, J. Phys. Chem. C 2010, 114, 20783-2079 iv 6. Benxia li, Yi Xie and Yi Xue, Controllable synthesis of CuS nanostructures from self-assembled precursors with biomolecule assistance, J. Phys. Chem. C 2007, 111, 12181-12187. v Acknowledgment I truly enjoy this five years’ graduate life at Brown. First of all, I would like to express my gratefulness to my advisor, Professor Matthew B. Zimmt. There is an old Chinese proverb, “give a man a fish and you feed him for a day. Teach a man to fish and you feed him for a lifetime”. Professor Zimmt is the man who “teach me to fish” – not only I have learned a lot of useful knowledge and skills from him, but he also played an irreplaceable role in shaping my critical thinking ability, which would have a significant, positive impact on both my future career and life. Professor Zimmt is a man of logic and is a role model of real scientist. I admire his enthusiasm, curiosity and criticalness towards science. He is indeed a venerable mentor who really cares his students. He always sacrifices his own free time to facilitate his students’ research and study. I greatly appreciate the valuable scientific suggestions he made to my dissertation and all the grammar mistakes he has fixed for me. Professor Zimmt is also a kind-hearted and righteous person. Besides research, he also helped me in adapting life in U.S. by teaching me American culture and some useful daily life tricks. I really feel lucky to have him to be my advisor and I would definitely miss the joyful time in the Zimmt group. I would like to express my deep gratitude to my fiancée and my other half, Qiyao Zhang. We have been through a lot together these four years. Without her, I cannot make it to this stage. I want to thank her for always been supportive, keep encouraging me and cheered me up during my darkest and most depressed time. Qiyao is a very smart girl and she has a heart of an angel. Not only she took care of me in my daily life, she also helped me a lot in my career and greatly improved my working efficiency. Although I am not a man of many words and I rarely express my emotions, here I want to tell you, Qiyao, I vi love you forever and you are a part of my soul. I truly appreciate the support, encouragement and trust from you and your parents. I am very grateful to my committee members, Professor J. William Suggs and Professor Lai-Sheng Wang. They gave me a lot of help in improving my original research proposal and my dissertation. They are very nice people and I really appreciate their support in my graduate research and study. We had some valuable discussions in the past few years and I have learned many useful knowledge and ideas from our communications. I would also like to thank Professor Christopher T. Seto. I have learned a lot from our joint group meetings during the last three years. Professor Seto is like my second advisor in the department and I greatly appreciate the knowledge he taught me. Thanks to his strict training, I have a much better understanding in organic chemistry. And his suggestions helped me refined my presentation skills. I want to thank all previous and current Zimmt group members. It is always a happy experience to work and hang out with my colleagues. I thank Dr. Wenjun Tong and Dr. Xiaoliang Wei for teaching me a lot of skills and tricks in organic synthesis and scanning tunneling microscopy. I thank Dr. Yaqi Wang for the helpful discussion in my research as well as jogging together in our spare time. I also had a wonderful time with my current colleagues, Yan Yang and Jian He. They are both kind-hearted people and are very supportive to me. Yan is a smart, knowledgeable and humorous girl who always brings happiness to the lab. While Jian is always calm and well-tempered and I am especially impressed by his broad and deep knowledge in organic chemistry. I thank Min Kyoung (Michelle) Kim for her diligence. Michelle helped me synthesized several important compounds for my research projects. I thank Tereza Pašková for her assistance vii in STM experiments and reorganization of our STM room. Also I want to thank Professor Vlastimil Fidler for the helpful suggestions he provided during our group meetings. I wish everyone of you succeed in your study/research and future career. I would like to thank all my friends at Brown, including but not limited to: Xiang Sun, Michael Zompa, Dongguo Li, Dr. Binbin Wu, Dr. Hao Tu, Chi-Cheung Su, Ronald Okoth, Rui Zhang, Jie Guang, Yiming Chen, etc. They make my life at Brown full of fun. Last but not least, I want to express my very special thanks to my mom, Xiaomin Duan, and dad, Qinglin Xue. Thank you for raising me up and educating me to be an upright and honest person. Thank you for the years of your unconditional support in my study and career. And thank you for your encouragement that helped me to overcome many difficulties. I love you forever and I will make you proud. viii Table of Contents Chapter 1 Introduction.................................................................................................................. 1 1.1 Top-down and bottom-up approaches in nanofabrication...................................................... 1 1.2 Supramolecular self-assembly ............................................................................................... 2 1.3 Self-assembled monolayers.................................................................................................... 7 1.4 Multi-component self-assembled monolayers ..................................................................... 12 1.5 Scanning tunneling microscopy ........................................................................................... 14 1.6 Research objectives and thesis overview ............................................................................. 18 References .................................................................................................................................. 20 Chapter 2 Morphology Control of Self-Assembled Monolayer using Dipolar Interactions . 30 2.1 Introduction .......................................................................................................................... 30 2.2 STM sample preparation and acquisition protocols ............................................................. 31 2.3 Building blocks and morphologies of the monolayer .......................................................... 32 2.3.1 1-D tapes ....................................................................................................................... 33 2.3.2 Side chain registration .................................................................................................. 35 2.3.3 Odd-even effect............................................................................................................. 36 2.3.4 Corner-to-corner (C-2-C) morphology ......................................................................... 38 2.4 Monolayer patterning using CF2 dipoles.............................................................................. 39 2.4.1 Single component self-assembled monolayers: A-[172,F-9,9]2 and A-[172,F-10,10]2 .......... 41 2.4.2 Self-assembled monolayers of single component A-[152,F-8,8]2 and A-[152,F-9,9]2 ......... 48 2.4.3 Self-assembled monolayers of CF2 mixtures ................................................................ 51 2.5 Monolayer patterning using ketone dipoles ......................................................................... 55 2.5.1 Self-assembled monolayers of single component A-[172,C=O-9]2 and A-[172,C=O-10]2 ..... 58 2.5.2 Self-assembled monolayers of A-[172,C=O-9]2 and A-[172,C=O-10]2 1:1 mixture .............. 61 2.5.3 Self-assembled monolayer of A-[172,F-9,9]2 and A-[172,C=O-10]2 1:1 mixture.................. 64 2.6 Molecular Mechanics (MM) simulation of monolayer properties ....................................... 66 2.6.1 MM minimized monolayer sections and unit cells ....................................................... 67 2.6.2 Self-assembly energies (SAEs) determination from MM simulations ......................... 74 2.7 Conclusion ........................................................................................................................... 78 References .................................................................................................................................. 79 Chapter 3 Molecular Shape Control of Self-Assembled Monolayer Morphology ................. 82 3.1 Introduction .......................................................................................................................... 82 3.2 STM sample preparation and acquisition protocols ............................................................. 84 ix 3.3 Self-Assembly of shape self-complementary compounds ................................................... 85 3.3.1 Self-assembly of single component diyne monolayers: molecule 1 and molecule 2 .... 86 3.3.2 Self-assembly of molecule 7 and molecule 8................................................................ 91 3.4 Pairwise shape-complementary compounds: 2-components self-assembly......................... 93 3.4.1 Attempted self-assembly with single components: A-23 (3) and A-23 (4) .................. 96 3.4.2 Self-assembly of mixed monolayers of molecule 3 and 4 ............................................ 97 3.4.3 Self-assembly of shape self-incommensurate molecules 5 and 6 ................................ 99 3.5 Pairwise shape-complementary compounds: 4-component self-assembly ....................... 102 3.5.1 System design ............................................................................................................ 103 3.5.2 Self-assembly of S1,S2, D1, D2 mixtures .................................................................. 105 3.5.3 Four-component self-assembly: minus one component............................................. 111 3.6 Molecular Mechanics (MM) simulations of monolayer unit cell properties ..................... 113 3.7 Introducing H-bonding into shape based self-assembly .................................................... 121 3.8 Conclusion ......................................................................................................................... 126 References ................................................................................................................................ 128 Chapter 4 Monolayer Quality of Molecular Shape Directed Self-Assembly ........................ 132 4.1 Introduction ........................................................................................................................ 132 4.2 STM sample preparation and acquisition protocols ........................................................... 133 4.3 Domain interfaces .............................................................................................................. 135 4.3.1 Examples of 120°interface ......................................................................................... 135 4.3.2 Examples of enantiotopic interface ............................................................................. 137 4.3.3 "Slip" interfaces .......................................................................................................... 140 4.4 Occurrence frequency of different interfaces: a statistical study ....................................... 145 4.5 Proposed model for domain interfaces and energetic simulations ..................................... 148 4.5.1 Tapes assembled by "in" and "out" diyne compounds................................................ 148 4.5.2 Evaluation of tape stacking energetics ........................................................................ 152 4.6 Defects in S1, S2, D1, D2 four-component system ........................................................... 159 4.7 Conclusion ......................................................................................................................... 163 References ................................................................................................................................ 165 Chapter 5 Syntheses and Spectral Data .................................................................................. 168 5.1 Syntheses of anthracene core (1,5-bis(chloromethyl)anthracene) ..................................... 168 5.2 Syntheses of CF2 derivatives.............................................................................................. 173 5.3 Syntheses of ketone derivatives ......................................................................................... 181 x 5.4 Syntheses of diyne derivatives ........................................................................................... 188 5.4.1 Syntheses of symmetrically substituted 1,5-anthracene derivatives ........................... 188 5.4.2 Syntheses of four-component system S1, S2, D1 and D2 .......................................... 197 References ................................................................................................................................ 211 Chapter 6 Conclusions and Future Prospects ......................................................................... 212 6.1 Conclusions ........................................................................................................................ 212 6.1.1 Monolayer patterning using CF2 and ketone dipoles .................................................. 212 6.1.2 Programming self-assembled monolayer using side chain shape ............................... 213 6.1.3 Correlations between side chain shape and monolayer defect densities ..................... 214 6.2 Future prospects ................................................................................................................. 215 6.2.1 Multi-component self-assembly.................................................................................. 215 6.2.2 Polymerization of monolayers .................................................................................... 216 References ................................................................................................................................ 218 xi List of Figures Figure 1-1 Top-down and bottom-up approach ............................................................................... 1 Figure 1-2 IBM logo assembled from 35 xenon atoms on Ni (110) surface using STM tip ........... 3 Figure 1-3 Cross sectional scheme of a typical lipid bilayer formed by self-assembly ................... 4 Figure 1-4 Design scheme and AFM images of DNA origami ...................................................... 6 Figure 1-5 Illustration of chemisorbed and physisorbed monolayer ............................................... 7 Figure 1-6 STM images of TMA self-assembled monolayer ........................................................ 10 Figure 1-7 Structure and STM image of self-assembled monolayers of [18]DBA derivative ...... 11 Figure 1-8 STM image of a four-component monolayer assembled from a mixture solution of bisDBA-C12, COR, ISA, and TRI................................................................................ 13 Figure 1-9 Schematic drawing of the operation principle of a STM ............................................. 15 Figure 1-10 Illustration drawing of the STM image acquired in constant current mode. .............. 16 Figure 1-11 Structure and STM image of HOPG .......................................................................... 17 Figure 1-12 STM image and schematic illustration of interdigitated packing of 1,5-substituted anthracene derivative .................................................................................................... 18 Figure 2-1 CPK model of A-[17]2.................................................................................................. 33 Figure 2-2 A-[17]2 surface enantiomers......................................................................................... 33 Figure 2-3 Two distinct AA 1-D tapes assembled by A-[17]2 ....................................................... 34 Figure 2-4 1-D AA* tape assembled by A-[17]2 ........................................................................... 34 Figure 2-5 ω↔2, ω↔1 and ω↔3 side chain registration with A-[17]2 ......................................... 36 Figure 2-6 Odd-even effect on monolayer morphology: 1,5-bis(2-(alkylthio)ethyl)anthracenes . 37 Figure 2-7 C-2-C morphology monolayers from A-[17]2 - AA ω↔2 and AA* ω↔3 .................. 38 Figure 2-8 Polymorphism and herringbone morphology induced by ether "concave regions" ..... 40 Figure 2-9 Comparison between A-[172,10]2 and A-[172,F-10,10]2 ..................................................... 41 Figure 2-10 Structures of A-[172,F-9,9]2 and A-[172,F-10,10]2 ............................................................. 41 Figure 2-11 ω↔2 packing of A-[172,F-9,9]2 and A-[172,F-10,10]2 generates dipolar repulsions ........ 42 Figure 2-12 ω↔3 packing of A-[172,F-9,9]2 and A-[172,F-10,10]2 generates dipolar attractions ........ 43 Figure 2-13 STM images of the monolayer assembled by A-[172,F-9,9]2 ........................................ 43 Figure 2-14 CF2 dipole alignment for ω↔3 and ω↔1 packing of A-[172,F-9,9]2 ............................ 45 Figure 2-15 STM images of the monolayer assembled by A-[172,F-10,10]2 ..................................... 46 Figure 2-16 CF2 dipole alignment in ω↔3 and ω↔1 packing of A-[172,F-10,10]2 ........................... 47 Figure 2-17 Structures of A-[152,F-9,9]2 and A-[152,F-8,8]2................................................................ 48 Figure 2-18 STM images of the monolayer assembled by A-[152,F-8,8]2 and A-[152,F-9,9]2 ............. 49 xii Figure 2-19 ω↔2 and ω↔3 packing of A-[152,F-9,9]2 .................................................................... 50 Figure 2-20 ω↔2 packing of CF2 dipolar complementary pairs ................................................... 51 Figure 2-21 STM image of the monolayer assembled by a 1:1 solution mixture of A-[172,F-9,9]2 and A-[172,F-10,10]2 .......................................................................................................... 52 Figure 2-22 STM image of the monolayer assembled by a 1:1 solution mixture of A-[152,F-8,8]2 and A-[152,F-9,9]2 ............................................................................................................ 54 Figure 2-23 Structures of A-[172,C=O-9]2 and A-[172,C=O-10]2 .......................................................... 56 Figure 2-24 2 and 3 packing of A-[172,C=O-10]2 ................................................................. 57 Figure 2-25 2 and 3 packing of A-[172,C=O-9]2 .................................................................. 57 Figure 2-26 STM images of A-[17C=O-9]2 monolayer ..................................................................... 58 Figure 2-27 STM images of A-[17C=O-10]2 monolayer .................................................................. 60 Figure 2-28 2 packing of ketone dipolar complementary pair ............................................... 61 Figure 2-29 STM images of the monolayer assembled by a 1:1 solution mixture of A-[172,C=O-9]2 and A-[172,C=O-10]2 ......................................................................................................... 62 Figure 2-30 2 packing of A-[172,F-9,9]2 and A-[172,C=O-10]2 ...................................................... 64 Figure 2-31 STM scan of the monolayer formed by a 1:1 solution mixture of A-[172,F-9,9]2 and A- [172,C=O-10]2 .................................................................................................................... 65 Figure 2-32 3 packed AA* and 2 packed AA morphology of A-[172,F-9,9]2 ..................... 67 Figure 2-33 3 packed AA* and 2 packed AA morphology of A-[172,F-10,10]2 .................. 68 Figure 2-34 3 packed AA* and 2 packed AA morphology of A-[152,F-8,8]2 ..................... 68 Figure 2-35 3 packed AA* and 2 packed AA morphology of A-[152,F-9,9]2 ..................... 69 Figure 2-36 2 packed AB morphology of A-[172,F-10,10]2/A-[172,F-9,9]2 patterned monolayer .. 69 Figure 2-37 2 packed AB morphology of A-[152,F-8,8]2/A-[152,F-9,9]2 patterned monolayer ... 70 Figure 2-38 3 packed AA* and 2 packed AA morphology of A-[172,C=O-9]2 ................... 70 Figure 2-39 3 packed AA* and 2 packed AA morphology of A-[172,C=O-10]2 .................. 71 Figure 2-40 2 packed AB morphology of A-[172,C=O-10]2/A-[172,C=O-9]2 patterned monolaye . 71 Figure 2-41 2 packed AB morphology of A-[172,C=O-10]2/A-[172,F-9,9]2 patterned monolayer . 72 Figure 3-1 Straight side chain vs "kinked" side chain ................................................................... 82 Figure 3-2 Packing of molecules with compatible shapes ............................................................. 83 Figure 3-3 Packing of molecule with incompatible shapes ........................................................... 83 Figure 3-4 Molecule 1 designed to self-pack with ω↔2 registration ........................................... 86 Figure 3-5 A-[252-CC12,14]2 (molecule 1)..................................................................................... 86 Figure 3-6 A-[242-CC12,14]2 (molecule 2)..................................................................................... 86 xiii Figure 3-7 STM image and CPK model of monolayer assembled from molecule 1 ..................... 88 Figure 3-8 STM image and CPK model of monolayer assembled from molecule 2 ..................... 90 Figure 3-9 A-[292-CC14,16]2 (molecule 7)..................................................................................... 91 Figure 3-10 A-[232-CC11,13]2 (molecule 8) .................................................................................. 91 Figure 3-11 STM image and CPK model of monolayer assembled from molecule 7 ................... 92 Figure 3-12 STM image and CPK model of monolayer assembled from molecule 8 ................... 93 Figure 3-13 A-[232-CC7,9]2 (molecule 3) ..................................................................................... 94 Figure 3-14 A-[232-CC15,17]2 (molecule 4) ................................................................................... 94 Figure 3-15 Non-dense packing of 3 and 4 due to the position of the side chain diyne ‘‘kink’’ ... 95 Figure 3-16 Intended monolayer packing morphology of molecules 3 and 4 ............................... 96 Figure 3-17 A typical STM image of 3 at phenyloctane-HOPG interface. ................................... 96 Figure 3-18 STM image and CPK model of 1 : 1 mixture monolayer of 3 and 4 ......................... 98 Figure 3-19 A-[252-CC10,12]2 (molecule 5) .................................................................................. 99 Figure 3-20 A-[252-CC14,16]2 (molecule 6) .................................................................................. 99 Figure 3-21 STM image and CPK model of 1 : 1 mixture monolayer of 5 and 6 ....................... 100 Figure 3-22 Non-dense packing of 5 and 6 due to the position of the side chain diyne ‘‘kink’’ . 101 Figure 3-23 4 component system S1, S2, D1, D2 and the side shape selection rule ................... 104 Figure 3-24 Simulated monolayer section containing a complete unit cell ................................ 104 Figure 3-25 A 20nm x 20nm STM image of the monolayer assembled from a phenyloctane solution of S1, D1, D2, and S2 ................................................................................... 105 Figure 3-26 A 43nm x 43nm STM image of the monolayer assembled from a solution of S1, D1, D2, and S2 at air- HOPG interface ............................................................................. 107 Figure 3-27 A 140nm x 140nm STM image of the monolayer assembled from a solution of S1, D1, D2, and S2 at air- HOPG interface....................................................................... 109 Figure 3-28 STM image of the monolayer assembled from a phenyl‐octane solution lacking S2 but containing S1, D1 and D2 ..................................................................................... 112 Figure 3-29 Proposed packing of [312-CC13,15] chain (S1) and [272-CC17,19] chain (D2)........ 113 Figure 3-30 MM minimized ω↔10 packing for single component 3.......................................... 118 Figure 3-31 MM minimized ω↔2/10 packing for single component 3 ...................................... 118 Figure 3-32 MM minimized ω↔14 packing for single component 5.......................................... 119 Figure 3-33 MM minimized ω↔2/14 packing for single component 5 ...................................... 119 Figure 3-34 Proposed monolayer morphology of molecule 5 and diynoic acid mixture ............. 122 Figure 3-35 Illustration scheme of self-stacking lamellas formed by single component pentacosa- 14,16-diynoic acid ...................................................................................................... 122 xiv Figure 3-36 A 15nm x 15nm STM image of the monolayer assembled from a phenyl‐octane solution containing 1:2 ratio of molecule 5 and diynoic acid ..................................... 123 Figure 3-37 A 50nm x 50nm STM image of the monolayer assembled from a phenyl‐octane solution containing 1:2 ratio of molecule 5 and diynoic acid ..................................... 124 Figure 4-1 A-[252-CC12,14]2, “out”............................................................................................. 133 Figure 4-2 A-[232-CC11,13]2, “in” ............................................................................................... 133 Figure 4-3 CPK models of 120°domain interfaces ..................................................................... 136 Figure 4-4 100nm x 100nm STM scan of A-[252-CC12,14]2 and 100nm x 100nm STM scan of A- [292-CC14,16]2 ............................................................................................................. 136 Figure 4-5 STM scan of an enantiotopic interface within A-[232-CC11,13]2 monolayer............. 138 Figure 4-6 STM scan of an enantiotopic interface within S1, S2, D1, D2 four-component monolayer ................................................................................................................... 139 Figure 4-7 A 26nm x 26nm STM scan of A-[232-CC11,13]2 showing a slip interface ................ 140 Figure 4-8 A 50nm x 50nm STM scan of A-[232-CC11,13]2 exhibiting five slip interfaces........ 141 Figure 4-9 A 50nm x 50nm STM scan of A-[232-CC7,9]2 (3) and A-[232-CC15,17]2 (4) mixture showing a slip interface .............................................................................................. 142 Figure 4-10 160nm x 160nm STM scan of A-[252-CC12,14]2 and A-[232-CC11,13]2 ................. 143 Figure 4-11 150nm x 150nm STM scan of A-[252-CC10,12]2/A-[252-CC14,16]2 pair and 80nm x 80nm STM scan of A-[232-CC7,9]2/A-[232-CC15,17]2 pair (right) ............................ 144 Figure 4-12 A large monolayer domain of A-[252-CC12,14]2 observed by STM ........................ 147 Figure 4-13 The "up-down-up" vertical profile of an "in" diyne compound ............................... 149 Figure 4-14 The "up-up-up" vertical profile of an "out" diyne compound .................................. 149 Figure 4-15 "Triangle-wave" shaped tape periphery of an "in" diyne compound ...................... 150 Figure 4-16 "Square-wave" shaped tape periphery of an "out" diyne compound........................ 150 Figure 4-17 Tape stacking for different slip displacements for "in" diyne A-[232-CC11,13]2 and "out" diyne A-[252-CC12,14]2 monolayer sections ..................................................... 151 Figure 4-18 Minimized monolayer sections of A-[252-CC12,14]2 and A-[232 CC11,13]2 ............ 153 Figure 4-19 Minimized monolayer sections of A-[292-CC14,16]2 ............................................... 156 Figure 4-20 STM images and their corresponded CPK models of type 1 enantiotopic interface and type 2 enantiotopic interface ....................................................................................... 157 Figure 4-21 Regular morphology, "transition" and slip interface of 3 and 4 mixture ................. 159 Figure 4-22 Two consecutive STM scans (43nm x 43nm) of S1, S2, D1, D2 four-component monolayer ................................................................................................................... 160 Figure 4-23 Minimized monolayer sections of defect morphology and regular morphology ..... 161 xv Figure 4-24 A atypical slip interface in four-component system and its attempt CPK model .... 162 Scheme 5-1 Synthetic scheme for A-[172-F10,10]2 ........................................................................ 173 Scheme 5-2 Synthetic scheme for A-[172-C=O9,9]2 ..................................................................... 181 Scheme 5-3 Synthetic scheme for A-[252-C≡C12,14]2 ................................................................... 188 Scheme 5-4 Synthetic scheme for compound S1 and D2 ............................................................ 197 Scheme 5-5 Synthetic scheme for compound S2 and D1 ............................................................ 207 Figure 6-1 Proposed 5-component system with a horizontal expansion of 40nm ....................... 216 Figure 6-2 Topochemical polymerization of diacetylenes ........................................................... 216 Figure 6-3 H-bond may increase structural flexibility of the monolayer thus enable the polymerization ............................................................................................................ 217 xvi List of Tables Table 2-1 Measured unit cell parameters vs simulated unit cell parameters ................................. 72 Table 2-2 Self-Assembly Energies of Molecules with C=O or CF2 containing side chains .......... 75 Table 3-1 Measured unit cell parameters vs simulated unit cell parameters ............................... 114 Table 3-2 Calculated SAE for diyne systems .............................................................................. 117 Table 4-1 Occurrence frequency for different types of domain interfaces .................................. 146 Table 4-2 Molecular mechanics SAE for different types of interfaces ........................................ 155 Table 4-3 Patterns of anthracene column shifts and column compositions across the interface . 163 xvii Chapter 1 Introduction 1.1 Top-down and bottom-up approaches in nanofabrication Top-down and bottom-up are two distinct approaches to manufacturing devices. The top-down approach usually involves building something by starting with a larger block of material and carving away its composition. Sculpting (Figure 1, left) is a typical top-down manufacturing approach since the detailed shape and patterns of the sculpture are carved out from rough and bulky stones (or ice, sands, etc.). In contrast, with the bottom-up approach, the device is built by adding together smaller parts and building blocks. LEGO® toys are one example of the bottom-up approach - complicated models are assembled from numerous small "standard" LEGO® pieces (Figure 1, right). [1] Figure 1. Top-down approach (left): a sculpture carved from a bulk stone ; Bottom-up approach (left): [2] excavator model assembled from 1123 small LEGO® pieces [Figures from Ref. 1 and Ref.2] 1 In nanotechnology, top-down and bottom-up are two approaches employed by scientists and engineers for fabrication of small devices at micro- and nanometer scales[3-10]. In top-down nanofabrication, externally controlled tools are used to shape materials into the desired patterns and structures. Similar to sculpting, the detailed shapes and structures are generated from starting materials with larger dimensions. Various lithography techniques, such as photolithography[11-17], electron beam lithography[18-21], soft lithography[22-24] and scanning probe lithography[6, 7, 25] are used in the top-down approach. Currently, photolithography techniques are well developed and are used widely to manufacture microchips with feature sizes as small as 22 nm[26]. On the other hand, bottom-up approaches seek to have molecular or atomic components built up into larger and more complex assemblies based on various mechanisms and technologies[27-32]. Basically, this area of nanofabrication uses atoms or small molecules as the building blocks of multi-level structures. The process is much like building a LEGO® model on the nano- and microscale. The intrinsic nature of the bottom-up approach endows it with great potential to fabricate nanostructures with molecular or even atomic resolution. 1.2 Supramolecular self-assembly In LEGO® model, the individual pieces are assembled into desired shapes and patterns by our hands. However, when the building blocks shrink down to the sizes of molecules and atoms, the objects become too small for us to easily handle them manually. Scanning probing microscopy (SPM) is demonstrated to be a pivotal tool for 2 manipulating single atoms and molecules[33-38]. The technology was first developed by researchers at IBM as they astounded the scientific community by positioning 35 xenon atoms on a nickel (110) surface to assemble the company logo (Figure 2) [33]. Although SPM technology provides a way to precisely position and manipulate molecules and atoms, the low throughput and demanding experimental conditions (ultra-high vacuum and cryogenic temperatures) limits its practical application in mass-production of nano- and microscale devices. Figure 2. IBM logo assembled from 35 xenon atoms on Ni (110) surface using STM tip. Each letter is 50Å from top to bottom. [Adapted from Ref. 33 with permission of the Nature Publishing Group] Instead of manipulating molecules and atoms one by one, another strategy for micro- and nanoscle assembly is to pre-code the information for the individual components so that the components could assemble into the desired structures by themselves. Here the “codes” could be shapes[39-42], charges[43-45], dipoles[46-50] and etc[51-56]. These characteristics determine the interactions among the individual components and direct them to assemble into organized structures and patterns. Since 3 this process is autonomous without external direction, the process is defined as self- assembly[57-68]. Figure 3. Cross sectional scheme of a typical lipid bilayer formed by self-assembly. Self-assembly processes are common in nature. A typical example is the formation of the lipid bilayer of the cellular membrane[69, 70] . Figure 3 displays a schematic cross sectional profile of a phospholipid bilayer. The phospholipid molecule is composed of two major parts: a hydrophilic phosphate head and two hydrophobic fatty acid tales. This structure promotes hydrophilic - hydrophobic interactions[71] that direct phospholipids self-assemble into bilayers in the biological system. In the bilayer structure, the hydrophilic phosphate heads point "out" toward the water environment on both sides of the bilayer and the hydrophobic tails are contained within the bilayer to avoid energetically unfavorable interactions with the surrounding water. The self-assembled bilayer structure is held up by non-covalent forces that do not involve formation of strong chemical bonds (e.g. covalent bonds) between individual molecules. These forces are categorized as supramolecular interactions[72]. Typical 4 supramolecular interactions include hydrogen bonding, coordination bonding, hydrophilic - hydrophobic interactions, van der Waals interactions, dipolar interactions, pi - pi interactions and etc. These relatively weak (compared to covalent bonds) and reversible interactions are the dominant forces that direct molecular self-assembly[60]. Inspired by self-assembly in nature, scientists and engineers employ designed molecular self-assemblies to create desired structures and patterns at micro- and nanoscale[58, 59, 61-68] . This could result in the creation of previously unachieved nanostructures and nanodevices[51, 61, 66, 67]. One very successful example of designed molecular self-assembly is DNA Origami[51-56] developed by Paul Rothemund[51]. In his research, structures were fabricated by raster-filling the desired shape with a long (7- kilobase) single "scaffold" DNA strand whose conformation was directed using over 200 short oligonucleotide "staple strands" (Figure 4, left). The necessary sequences of all the short staple strands were calculated using computer program. Once the DNA strands were synthesized and mixed, the staple and scaffold strands self-assembled without “external guidance”, directed by Watson - Crick base paring. The resulting DNA self- assembled structures are roughly 100 nm in diameter and approximate desired shapes such as squares, disks, five-pointed stars and smiley faces with a spatial resolution of 6 nm (Figure 4, right). 5 Figure 4. Left: Design scheme of DNA origami, the black line represents a long "scaffold" DNA strand and the colored lines correspond to short "staple" DNA strands; Right: AFM images of self-assembled DNA structures.[Adapted from Ref. 51 with permission of the Nature Publishing Group] Molecular self-assembly provides a promising approach for mass production of various nanostructured materials and devices on a large scale at a low cost. Potential applications of self-assembled nano devices and materials include drug delivery[73-77], sensors[78-82], and electronics[78, 79, 82] . These applications require reliable and facile strategy to control the self-assembly of molecules into precise 2D or 3D structures. At this point in time, spatial resolution and component complexity are still two major challenges in the research field of molecular self-assembly. 6 1.3 Self-assembled monolayers Self-assembled monolayers are 2D molecular self-assemblies formed spontaneously on solid surfaces[83-87]. Compared to their 3D self-assembly counterparts, the 2D self-assembled monolayers have much less structural complexity. Furthermore, thanks to the invention of scanning tunneling microscopy, the structural details of 2D self-assembled monolayers can be determied down to the atomic scale[87]. Thus self- assembled monolayers are perfect models for studying and exploring the fundamental principles of molecular self-assembly. Self-assembled monolayers may be categorized as two types: the first type is chemisorbed monolayers such as thiol derivatives on gold surfaces[87] and silane derivatives on silicon surfaces[86] (Figure 5, left). In these monolayers, the molecules are anchored to the surface by the strong chemical bonds between functional groups and surface atoms (e.g. sulfur-gold bond). The second type is physisorbed monolayers such as alkanes and aromatic derivatives on solid substrate such as highly oriented pyrolytic graphite (HOPG)[84, 85]. In these systems, the molecules are weakly absorbed to surfaces via van der Waals forces with no restriction of chemical bonds. Figure 5. Left: Illustration of a chemisorbed monolayer in which the molecules are anchored to the [88] substrate by chemical bonds ; Right: Illustration of a physisorbed monolayer [Figures from Ref. 82]. 7 Physisorbed self-assembled monolayers are prepared by depositing molecules onto solid substrate using various techniques including, but not limited to, 1. Direct drop-casting[89, 90]: the compounds are dissolved in a high boiling solvent (e.g. 1-phenyloctane, 1,2,4-trichlorobenzene, tetradecane, 1- nonanol and etc.) and the solution is directly deposited onto the solid substrate. The monolayer forms at the liquid-solid interface. 2. Solvent evaporation[91]: the solution (e.g. water, chloroform, toluene and etc.) of compounds is directly deposited onto the solid substrate, then the solvent is evaporated over time. The monolayer forms at the liquid- solid and at the air-solid interfaces. 3. Langmuir-Blodgett trough[92]: a solution of compounds deposited onto the surface of a given sub-phase (usually water) forms a monolayer at the air-liquid interface. The monolayer is compressed and a solid substrate is inserted into the liquid vertically. The monolayer is transferred onto the solid substrate (air-solid interface) by pulling the substrate vertically out of the liquid at a certain speed. 4. Organic molecular beam deposition (OMBD)[93]: the monolayer is prepared by evaporation of purified solid compounds in a temperature controlled oven under high vacuum (10-5 mbar - 10-9 mbar) or ultra high vacuum (<10-9 mbar). Popular choice of substrates for physisorbed self-assembled monolayers are Au(111)[94], Ag(111)[94], MoS2, MoSe2[95] and HOPG[89, 90]. Among various combinations of 8 preparation techniques and substrates, direct drop-casting on HOPG is used very frequently for STM studies on physisorbed monolayers of organic molecules. The drop- casting method is easy to carry out and does not require expensive and complicated infrastructure (e.g. cryogenic, ultra high vacuum). HOPG's high conductivity, stability under ambient condition, easy preparation of clean atomically flat surfaces (peeling by adhesive tapes) and high affinity for alkylated compounds[96, 97] make it an excellent substrate for assembly of organic monolayers and acquisition of high quality STM data. Just like their 3D self-assembly counterparts, the structures and morphologies of 2D self-assembled monolayers are dictated by supramolecular interactions such as hydrogen bonding[89, 93], dipole-dipole interactions[47, 48, 50], van der Waals interactions[42, 98, 99] , metal - ligand coordination[100, 101], etc. The self-assembled monolayer of trimesic acid (TMA) is an excellent example of 2D supramolecular assembly directed by hydrogen bonding[93]. The TMA molecule has three carboxylic acids groups that act as both strong hydrogen bond donor and acceptor. STM experiments show that TMA forms at least two different structures on graphite surface (Figure 6). The “honeycomb” structure is composed of sixfold rings of trimesic acid molecules with perfectly pairwise arrangements of the carboxylic acid group hydrogen bonds (Figure 6, left). The second structure, called "flower", can be considered as a "squeezed" honeycomb structure with a non-pairwise (trimeric) hydrogen bonding arrangement for one of the three carboxylic acid groups on each TMA molecule (Figure 6, right). 9 Figure 6. Left: STM image (top) and schematic picture (below) of the honeycomb structured TMA self- assembled monolayer; Right: STM image (top) and schematic picture (below) of the flower structured TMA self-assembled monolayer. [Adapted from Ref. 93 with permission of Wiley-VCH] In the absence of strong directional interactions such as hydrogen bonding or metal - ligand coordination, van der Waals interactions can play a dominant role in directing self-assembly of organic molecules on graphite. Close packing of alkyl chains is a common means of providing the necessary van der Waals interactions[96-99, 102]. Figure 7 shows a 2D self-assembly of a Dehydrobenzo[18]annulene ([18]DBA) derivative that is stabilized by interdigitation of alkyl chains[98]. The molecule has a triangular [18]DBA core that is hexa-substituted with decyl chains (Figure 7, bottom). The [18]DBA cores appears as bright triangles with a zigzag alignment in STM images (Figure 7, top left). 10 The authors' interpretation is that at two sides of each triangular core (yellow lines), the molecules are linked by interdigitated alkyl chains, with the remaining two alkyl chains at the third side (yellow circles) located between the zigzag rows (Figure 7, top right). Figure 7. Top left: STM image (13nm x 13nm) of [18]DBA derivative assembled at trichlorobenzene- HOPG interface; Top right: schematic model of the self-assembled monolayer structure; Bottom: molecular structure of [18]DBA derivative. [Adapted from Ref. 98 with permission of the American Chemical Society] 11 1.4 Multi-component self-assembled monolayers Building a functional nano-device will require precise assembly of multiple components. The controlled self-assembly of multi-component monolayers with well- defined structure remains an actively explored challenge. Monolayer assembled from a mixture of different molecules can exhibit: (1) phase segregation; (2) random mixing (doping); or (3) cocrystallization. Random mixing may provide statistical control of the monolayer composition[103, 104] . However, to achieve repeatable patterns and high spatial resolution, cocrystallization of multiple components is preferred. In a cocrystallized system, spacings between the components are defined by crystal structure, thus the spatial resolution could reach molecular level. In 1996, Rabe and Müllen’s research groups were the first to develop compositionally patterned, two-component monolayer by cocrystallization of 5- alkoxyisophthalic acids and 2,5-dimethylpyrazine at liquid – HOPG interface[105]. The 2D molecular assembly is directed by strong hydrogen bonding between the carboxylic acid group and the nitrogen atom of the diazine. Since that report, numerous two-[105-115] and even three-[116, 117] component 2D self-assembled structure have been developed. However, examples of four-component self-assembled monolayers are still very rare. De Feyter and co-workers reported one successful four-component 2D crystal self- assembled from a solution mixture of coronene (COR), isophthalic acid (ISA), triphenylene (TRI) and alkyl chain substituted dehydrobenzo[12]annulene (DBA) derivatives (Figure 8)[89]. The assembly strategy is based on the structural properties of low-density nanoporous networks and their ability to host guest species. In the four- 12 component self-assembled monolayer, coronene "guest" molecules fill vacancies within a "host" structures built from six hydrogen-bonded isophthalic acid molecules; these heteroclusters fit into the hexagonal nanoporous network of the DBA derivative (Figure 8, top right). Figure 8. Top left: STM image of a four-component monolayer assembled from a mixture solution of -6 -4 -3 -4 bisDBA-C12 (3.8 x 10 M), COR (4.5 x 10 M), ISA (2.5 x 10 M), and TRI (6.0 x 10 M); Top right: Tentative model of the self-assembled monolayer structure; Bottom: molecular structures of the four components. [Adapted from Ref. 89 with permission of Wiley-VCH] Advances in the design and assembly of such complex, multi-component structures at surfaces depends critically on the ability to verify assembly. The invention of scanning tunneling microscopy (STM) made it possible to visualize surfaces structures 13 with atomic level resolution and it serve as an essential tool in investigating detailed morphologies and the dynamics of self-assembled monolayers. 1.5 Scanning tunneling microscopy The invention of scanning tunneling microscopy (STM) in 1982 initiated the development of a whole family of scanning probe microscopy (SPM) techniques that include atomic force microscopy (AFM), scanning capacitance microscopy (SCM), magnetic force microscopy (MFM) and others. Unlike optical and electron microscopy which characterize surfaces by "seeing", the SPM techniques characterize surfaces by "feeling": an image of the sample is obtained by raster scanning a probe (usually a sharp tip) over the surface, with the probe-surface interaction recorded as a function of probe position. The probe-surface interaction in STM is the tunneling current generated between the probe and sample surface, thus the name, scanning tunneling microscopy. Figure 9 illustrates the operation principle of an STM. An atomically sharp metal tip is brought into close proximity to the surface sample (the sample must be conductive or adsorbed on a conductive sample). By applying a small voltage bias, Vbias, between the tip and sample, electrons are able to tunnel from the sample to the tip or vice versa depending on the polarity ("+" or "-") of the bias. The tip is moved by a piezoelectric scanner to raster scan across the surface. Due to the exponential decay of the tunneling current, It, with increasing tip - sample distance, z[118], the magnitude of It (usually 10 pA to 1 nA) is extremely sensitive to z. This sensitivity leads to a high lateral and vertical resolution: the outermost atom at the tip-apex collects around 90% of the current[118]. 14 The STM operation is computer-controlled, with the scanning parameters, e.g. Vbias, It, and scanning speed, set via an user interface. Figure 9. Schematic drawing of the operation principle of a STM. Tip positioning with atomic precision is controlled by piezoelectric materials. The tunneling current is recorded while the probe (a sharp tip with only one or few atoms at the apex) is rafter scanning the surface. The scanning trial is indicated by red dashed lines. There are two basic operating modes for STM: constant current mode and constant height mode. In constant current mode (Figure 10), the measured tunneling current It is compared to a preset current Iset using a feedback loop. The controller (computer) provides a correction voltage to the piezoelectric scanner to adjust the z position of the tip in order to return It to the Iset value. The correction feedback signal (i.e. z position) is recorded together with the x - y positions of the tip while raster 15 scanning the surface. The resulting STM image provides a height profile of the sample. In constant height mode, the z-position of the tip is kept constant and the tunneling current is recorded as the probe raster scans the sample surface. In this case, the STM image provides a current profile of the sample. Generally, the constant-current mode yields better resolution and the constant-height mode allows faster scanning. Figure 10. Left: Illustration scheme of constant current operating mode of STM. The tip would keep adjusting its distance from surface to maintain a constant tunneling current during the raster scanning. Right: Illustration drawing of the STM image acquired in constant current mode. Different colors (or contrast) refer to different height. HOPG is one frequently used as a substrate in studies of self-assembled monolayers and is also a good example for interpretation of STM images. Figure 11 provides a 3nm x 3nm constant height STM image of an HOPG surface. The image consists of bright (yellow) and dark (red) region. The bright yellow color indicates a 16 higher tunneling current and the dark color indicates low tunneling current. The STM image provides a spatial map of the electron density (i.e. density of state) of the surface sample[118]. The structure of HOPG (Figure 11, left) shows two types of surface carbon atoms; one with a neighboring layer’s carbon atom directly underneath (α) and one without a neighboring atom in the plane below (β). The electron density of the HOPG surface varies slightly for these two types of carbon atoms. The registration of α atoms with the atoms in the next layer is believed to stabilize the valence electrons on these atoms[119, 120]. In contrast, the electrons of β atoms lack this interaction. Thus, these electrons lie at slightly higher energy. For this reason the tunneling current is larger between β atoms and the tip and the STM image of HOPG displays periodicity for every other atom. [121] Figure 11. Left: 3D perspective (top) and top view of HOPG structure . Right: 3nm x 3nm constant height STM image of HOPG surface. The measured distance between neighboring bright dots is 0.25nm. The yellow hexagons in both left and right indicate the same unit. [Left Figure from Ref. 121] 17 1.6 Research objectives and thesis overview This thesis develops methods for supramolecular patterning of physisorbed self- assembled monolayers. The goal is to develop reliable and robust molecular recognition strategies that direct sets of molecules to assemble multi-component monolayers with pre-designed patterns of composition (compositional patterning). In my research, STM has been extensively exploited to investigate the structure and morphology of the monolayers. The systems we studied are mostly 1,5-disubstituted anthracene derivatives on HOPG substrate. Our group's previous studies[41, 42, 47, 48, 102, 111, 122-124] showed that 1,5-substituted anthracene bearing linear side chains self-assemble monolayers with interdigitated packing of side chains (Figure 12). Figure 12. STM image (left) and schematic illustration (right) of interdigitated packing of 1,5-substituted anthracene derivative. [Left Figure from Ref. 123] Supramolecular interactions between neighboring molecules can be tuned by tailoring the compositions and structures of their side chains. Our strategy for multi- 18 component monolayer patterning is to outfit different molecules with side chains that generate complementary interactions (e.g. chain length[102, 111], dipolar interactions[47, 48, 50, 111, 123, 124] , chain shapes[41, 42]) so that molecules recognize their "designed" neighbors. In Chapter 2, we investigate the potency of dipolar interactions produced by CF2 and ketone groups for dipolar patterning of multi-component monolayers. A series of C=O and CF2 incorporated 1,5-substituted anthracene derivatives were prepared and their monolayers investigated using STM. In Chapter 3, we introduce "kink" shapes into the side chains through the use of conjugated diyne groups and study their impact on monolayer morphology. Side chains with complementary "kink" shapes are exploited to direct self-assembly of multi-component monolayers. Chapter 4 analyzes the defects in monolayers assembled by 1,5-substituted anthracene derivatives with "kinked" side chains. 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Zimmt, Journal of Colloid and Interface Science 2012, 387, 221. [123] W. Tong, Y. Wei, K. W. Armbrust, M. B. Zimmt, Langmuir 2009, 25, 2913. [124] Y. Wei, W. Tong, C. Wise, X. Wei, K. Armbrust, M. Zimmt, J Am Chem Soc 2006, 128, 13362. 29 Chapter 2 Morphology Control of Self-Assembled Monolayer Using Dipolar Interactions 2.1 Introduction Self-assembly of compositionally patterned, multi-component monolayers requires adequate driving force to direct each component to adsorb next to its design neighbors with the intended geometry[1-8]. Intermolecular interactions such as van der Waals[9, 10], hydrogen bonding[5, 8, 11], dipole-dipole[12, 13] and coordination bonding[14, 15] have been exploited to facilitate and stabilize multi-component assembly of designed supramolecular structures. By carefully designing and optimizing sets of molecules with complementary supramolecular interactions, self-assembly of complicated patterns, on nano to micron length scales, have been achieved. A successful example is DNA Origami[16-21], which utilizes designed Watson-Crick base pairing to fold multiple DNA strands into desired 2-D and 3-D shapes. Previous research from our group reported the self-assembly of compositionally patterned, multi-component monolayers directed by dipolar interactions between the side chains of 1,5-substituted anthracene derivatives[22, 23] . The patterning strategy incorporated ether dipoles into the side chains so that packing of identical side chains produced repulsive dipole-dipole interactions, whereas packing of dipolar complementary side chains produced attractive dipole-dipole interactions. The 30 enthalpic preference arising from packing of dipolar complementary side chain pairs directed the self-assembly of patterned, multi-component monolayers. Although the prior studies demonstrated that the dipolar patterning strategy works, the small magnitude of the ether dipoles (1.2D) limited their utility in monolayer patterning. In addition, subtle geometric features associated with the ether group produced complex monolayer polymorphism[24][25][26, 27]. In an effort to surmount these problems, this work explores whether the dipole moments and geometric features of CF2 and ketone groups are more potent directors of dipolar patterning in the self- assembly of multi-component, 1,5-substituted anthracene monolayers. 2.2 STM sample preparation and acquisition protocols Scanning tunneling microscopy data was acquired using a Digital Instruments NanoScope STM interfaced to a Digital Instruments NanoScope IIIa controller. Data collected from at the solution ‐ graphite or air ‐ graphite interfaces (HOPG, ZYB grade, Momentive Performance, Strongsville, OH) used mechanically cut 87/13 Pt/Rh tips (0.25 mm, Omega Engineering, Stamford, CT) or 80/20 Pt/Ir tips (0.25 mm, Goodfellow, Oakdale, PA). Concentrated solutions for each compound were prepared by dissolving 2‐4 mg of compound in 400 - 600 μL of phenyl octane (Aldrich, 98% or Alfa Aesar, 98%) at 20 °C and then filtered (Anatop Plus 0.02 μm filters, Whatman). The concentration of these initial solutions was, typically, 5 - 10 mM. The initial solutions were diluted to 0.05 - 2 mM for STM imaging. A drop (3 - 5 μL) of a diluted solution was deposited on a recently cleaved HOPG surface. To increase the domain sizes of monolayers, some 31 samples were annealed at 30 - 40°C for 0.5 ‐ 2 hours before imaging. “Dry” monolayers were prepared by rinsing a preformed monolayer with 1‐2 mL of cold ethanol or cold tetradecane. The sample was then dried in air prior to imaging. The STM tip was engaged through the solution (or in air) and scanned in constant height or constant current mode. Tip scan velocities were in the range 0.20 – 1.2 μm/s. Multiple samples were prepared and imaged to evaluate monolayer morphology and unit cells. Thermal drift distortions in the data were corrected using a program developed by Dr. Wenjun Tong[24]. The program solves for the x- and y‐thermal drift velocities by comparing consecutively captured images obtained using opposite slow scan directions. This correction is valid if thermal drift velocities remain relatively constant in consecutive scans. Reported unit cell parameters are averages of thermal drift corrected STM data from three or more independently prepared and scanned sets of samples. STM scanner x‐ and y‐calibration was performed prior to monolayer formation using thermal drift corrected HOPG images (5 or 10 nm scale). 2.3 Building blocks and morphologies of the monolayer Like the pieces of a jigsaw puzzle, individual molecules are the fundamental building blocks of 2-D self-assembled monolayers. The molecules used in this thesis’ monolayer studies are 1,5-substituted anthracenes, an example of which is 1,5- bis(pentadecyloxymethyl)anthracene A-[17]2 (Figure 1). 32 Figure 1. CPK model of A-[17]2 The planer molecule A-[17]2 has C2h symmetry. It is prochiral and has two enantiotopic faces. A-[17]2 molecules can absorb onto a flat surface using either of the two enantiotopic faces, thus generating a pair of surface (2-D) enantiomers. We refer to the different 2-D surface enantiomers as A or A* (Figure 2). Figure 2. A-[17]2 surface enantiomers 2.3.1 1-D tapes Molecules are the 0-D building blocks of 2-D monolayers. Another useful way to view 2-D monolayers is as assemblies of numerous, tightly packed "1-D tapes". Each 1-D tape consists of (nearly) linear assemblies of individual molecules. Each molecule within 33 a 1-D tape makes side chain - side chain contacts with two adjacent molecules of the tape (Figure 3). In Figure 3a, the tape molecules’ side chains make contact via their odd- position atoms (edges), which lie closer to the anthracenes’ center rings. We refer to these as interior-interior edge contacts. In Figure 3b, tape molecules’ side chains make contact via their even-position atoms (edges), which lie closer to the anthracenes’ exterior rings. We refer to these as exterior-exterior edge contacts. In both 1-D tapes, all molecules absorbs to the surface using the same enantiotopic faces, A, thus these tapes are categorized as AA tapes. Within linear AA tapes, all adjacent molecules make contacts using the same side chain edge contacts. Figure 3. Two distinct AA 1-D tapes assembled by A-[17]2 Figure 4. 1-D AA* tape assembled by A-[17]2 34 Figure 4 shows another type of linear, 1-D tape in which adjacent molecules make contact using different side chain edges; one molecule's interior edge is in contact with its tape neighbor’s exterior edge. These interior-exterior edge contacts in a linear tape require adjacent molecules to adsorb to the surface using different enantiotopic faces, A and A*. The resulting 1-D tapes are categorized as AA* tapes. 2.3.2 Side chain registration Close packing of the 1-D tapes containing 1,5-substituted anthracene derivatives produces the 2-D monolayers observed by STM. In most cases, the packed tapes align to produce monolayers that exhibit columns of anthracene cores that alternate with columns of interdigitated, aliphatic side chains (lamellae)[22, 23, 26-29]. Previous monolayer studies of 1,5-[linear alkyl side chain] substituted anthracene compounds revealed that side chain contacts, within tapes and usually between tapes, align the terminal heavy atom (ωth-position) of each linear side chain in registration with the heavy atom at the 2-position of the neighboring side chains[29] (Figure 5a). We defined this "standard packing morphology" as "ω↔2 packing". The ω↔2 packing is a balance between steric repulsion and van der Waals attraction: It avoids steric repulsions between the ω- methyl group and anthracene hydrogens that arise in ω↔1 packing (Figure 5b). At the same time, it provides each side chain with greater van der Waals contacts and stabilization than ω↔3 packing (Figure 5c). 35 Figure 5. (a) ω↔2, (b) ω↔1 and (c) ω↔3 side chain registration with A-[17]2 2.3.3 Odd-even effect The preference for ω↔2 packing induces an interesting odd-even effect on monolayer morphology. Figure 6 shows the odd-even system studied by Dr. Yanhu Wei[29]. With 1,5-bis(2-(alkylthio)ethyl)anthracene compounds bearing odd length side chains (15 heavy atoms, Figure 6 left), ω↔2 packing forces all molecules within a 1-D tape to adsorb to the surface using the same enantiotopic face. Most monolayers assembled from 1,5-[odd length-side chain]anthracenes adsorb all tapes and, thus, all molecules within a domain via the same enantiotopic face. As a result, anthracenes within adjacent columns of the monolayer are aligned parallel to each other. As the 1-D 36 building blocks in this 2-D monolayer are AA tapes, this monolayer is said to exhibit AA morphology. Figure 6. Odd-even effect on monolayer morphology: 1,5-bis(2-(alkylthio)ethyl)anthracenes (Ref. [29]) By contrast, ω↔2 packing of 1,5-[even length-side chain] anthracenes (14 heavy atoms, Figure 6 right) forces adjacent molecules within the 1-D tapes to adsorb via opposite enantiotopic faces to the surface. This yields nearly perpendicular alignment of anthracene cores within adjacent columns. As the 1-D building blocks in this 2-D monolayer are AA* tapes, this monolayer is said to exhibit AA* morphology. 37 2.3.4 Corner-to-corner (C-2-C) morphology The simplest 2-D self-assembled monolayers are formed by stacking of identical 1-D tapes. However, different packing modes of the same 1D‐tapes generate different monolayer morphologies. For the "standard morphology", intertape side chain alignment (registration) is identical to intratape side chain alignment (registration). This produces a “corner-to-corner” morphology (C-2-C) in which anthracene cores from adjacent 1-D tapes contact each other at their H-3/H-4 corners (Figure 7). The resulting anthracene columns alternate with alkyl columns consisting of ω↔# registered side chains. C-2-C morphology can form by stacking either AA or AA* tapes. Figure 6 in 2.3.3 presents examples of C-2-C AA morphology (left) and C-2-C AA* morphology (right). Figure 7. C-2-C morphology monolayers from A-[17]2 - AA ω↔2 (top), AA* ω↔3 (below) 38 The side chain of molecule A-[17]2 bears odd number heavy atoms. ω↔2 registration of the side chain requires the terminal C-C bond of one side chain align parallel to the C-O bond from the neighboring side chain (Figure 7 top right, the bonds are marked with red color). This generates a AA type tape as well as the monolayer morphology. Once the ω↔2 packed side chains are shifted by one CH2 group apart along the horizontal (i.e. side chain) direction, the ω-position heavy atom of the side chain aligns with 3-position heavy atoms of the neighboring chains. However, the terminal C-C bond is no longer parallel to the adjacent C-C bonds of neighboring chains (Figure 7, middle right). In order to form ω↔3 side chain packing with parallel aligned C-C bonds, the neighboring molecule need to flip over to absorb to the surface via a different enantiotopic face and consequently generates an AA* morphology (Figure 7, bottom right). Thus, for odd length alkyl side chain, ω↔2 packing produces AA monolayer morphology while ω↔3 packing produces AA* monolayer morphology. 2.4 Monolayer patterning using CF2 dipoles[30] In the absence of overwhelming dipolar or steric interactions, ω↔2 packing is observed in the tapes and monolayers assembled by 1,5-[linear alkyl side chain] anthracenes. Dr. Wenjun Tong and Dr. Yanhu Wei's research[24][25] demonstrated that the dipole moments of side chain ether groups (1.2 - 1.3 D) can generate moderate dipole - dipole repulsions and attractions that, in some cases, destabilize ω↔2 packing and drive alternative packing. Ether oxygen atoms have smaller van der Waals radii than CH2 groups. The ether groups create "concave" regions within the side chain that 39 promote alternate stacking alignments, in which anthracene hydrogen atoms fit into the ether concave regions. As a result, monolayers assembled by anthracenes bearing ether side chains exhibit a variety of morphologies and, in some cases, polymorphism (Figure 8)[26, 27]. Figure 8. (a) Polymorphism induced by ether "concave regions", the cyan bar marks the "head-to-head" morphology and the black bar marks "corner-to-corner" morphology (Ref[26]); (b) an alternate "herringbone" morphology induced by ether “concave regions” (Ref[27]). In an attempt to avoid the problems of small dipole moment and polymorphism, this research investigated the CF2 group as an alternative to the ether group for dipolar interactions and monolayer patterning. Compared to an ether group, the CF 2 group has a larger dipole moment of 2.2 D, and the van der Waals radius of CF2 is slightly larger than that of a CH2 group (Figure 9). Consequently, CF2 groups may provide stronger dipolar attractions and repulsions than ether groups, and at the same time, avoid alternate tape packing and side chain misalignments found for ethers. 40 2,10 2,F-10,10 Figure 9. Comparison between ether compound A-[17 ]2 and CF2 compound A-[17 ]2 To test the CF2 group’s ability to control tape packing and monolayer structure, four 1,5-disubstituted anthracenes bearing CF2 containing side chains were synthesized and their monolayer morphologies characterized using STM. All four compounds , A- [172,F-9,9]2, A-[172,F-10,10]2, A-[152,F-8,8]2 and A-[152,F-9,9]2 have odd-length side chains with the CF2 groups positioned at either the (ω+1)/2 or (ω+3)/2 positions of the side chains. 2.4.1 Single component self-assembled monolayers: A-[172,F-9,9]2 and A-[172,F-10,10]2 2,F-9,9 2,F-10,10 Figure 10. Structures of A-[17 ]2 and A-[17 ]2 41 A-[172,F-9,9]2 and A-[172,F-10,10]2 have 17 heavy atom-long side chains with the CF2 dipole located at the (ω+1)/2 position of the A-[172,F-9,9]2 side chain or at the (ω+3)/2 position of the A-[172,F-10,10]2 side chain. ω↔2 packing of either single component produces AA tapes in which the CF2 dipoles within contacting side chains are adjacent (out of registration by one side chain position) and aligned anti-parallel (Figure 11). This alignment generates dipolar repulsions that destabilize ω↔2 packing of the side chains. 2,F-9,9 2,F-10,10 Figure 11. ω↔2 packing of A-[17 ]2 and A-[17 ]2 generates dipolar repulsions By contrast, ω↔3 packing of either single component, A-[172,F-9,9]2 or A-[172,F- 10,10 ]2, generates dipolar attractions between CF2 groups in adjacent side chains. For A- [172,F-10,10]2, ω↔3 packing yields collinear CF2 dipoles (Figure 12, bottom); for A-[172,F- 9,9 ]2, ω↔3 packing yields parallel aligned CF2 dipoles spaced by one CH2 group (out of registration by two side chain positions, Figure 12, top). These dipolar attractions come at the cost of reduced van der Waals interactions between the terminal methyl group and the benzylic CH2O within neighboring chains. ω↔3 packed 1-D tapes exhibit an AA* morphology. The different alignment of anthracene cores for ω↔2 (AA) and ω↔3 42 (AA*) side chain packing serves are a major criterion for identifying the side chain alignment and tape packing morphology in STM experiments. 2,F-9,9 2,F-10,10 Figure 12. ω↔3 packing of A-[17 ]2 and A-[17 ]2 generates dipolar attractions 2,F-9,9 Figure 13. (a) constant current STM image (14 nm x 14 nm) of the monolayer assembled by A-[17 ]2 at the phenyloctane - HOPG interface (0.1 nA, 1000 mV, 7.6 Hz, 3mM). (b) 30nm x 30nm STM scan 2,F-9,9 (constant current) of A-[17 ]2 monolayer(0.1 nA, 850 mV, 10.2 Hz, 3mM). Both scans reveal different anthracene alignments within neighboring aryl columns (yellow). 43 Phenyl octane solutions of either A-[172,F-9,9]2 or of A-[172,F-10,10]2 assemble stable monolayers with defect free domain sizes ranging from 30 nm x 30 nm to 80 nm x 80 nm. Figure 13a shows a 14 nm x 14 nm section of a monolayer assembled by A-[172,F- 9,9 ]2 at the phenyloctane-HOPG interface. The bright yellow columns (one marked by a cyan arrow) consist of corner-to-corner packed (C-2-C) anthracenes. The STM image reveals nearly perpendicular alignment of anthracenes in adjacent aromatic columns. This indicates that the monolayer is comprised of AA* tapes rather than the AA tapes expected for ω↔2 packing of odd length alkyl side chains. CPK models of two A-[172,F-9,9]2 molecule are superposed at the top right of Fig. 13a. An interesting pattern of broad, zigzag dark “furrows” (yellow arrow) is present near the center of each aliphatic lamella. The furrows correspond to the locations of the lower conductivity[31, 32] CF2 groups. As illustrated in Figures 12 and 14, ω↔3 packing of A-[172,F-9,9]2 positions CF2 groups from adjacent side chains out of registration by two side chain positions. Thus, the regions of low tunneling due to CF 2 groups should appear as wide or zigzag shaped dark columns for 3 packing. By contrast, ω↔1 packing of A-[172,F-9,9]2 would generate collinearly aligned CF2 columns (Figure. 14), which should appear as thin and straight low tunneling regions in the STM images. The width and zigzag shape of the furrows in Figure 13a support ω↔3 packing rather than ω↔1 packing. 44 2,F-9,9 Figure 14. CF2 dipole alignment for ω↔3 and ω↔1 packing of A-[17 ]2 The morphology of a crystalline 2-D monolayer can be characterized by a 2-D unit cell. The measured unit cell parameters for the A-[172,F-9,9]2 monolayer (green box in Figure 13a) are a = 5.54 ± 0.22 nm, b = 0.95 ± 0.06 nm, α = 87 ± 4 °, which are in fair agreement with calculated value of a = 6.08 nm, b = 0.94 nm, α = 90 ° (see chapter 2, section 2.6 for details of the calculation). Domains with AA* unit cell repeats extending 30-80nm along both unit cell axes are observed readily in A-[172,F-9,9]2 monolayers (Figure 13b), indicating that ω↔3, AA* is the preferred assembly morphology for A- [172,F-9,9]2 at the phenyloctane-HOPG interface. The fact that ω↔3, AA* is the dominant morphology in A-[172,F-9,9]2 monolayers suggests that the combination of dipolar attractions and reduced van der Waals contact for ω↔3 packing provides a lower 45 energy state than the combination of dipolar repulsions and better van der Waals contact in ω↔2 packing. 2,F-10,10 Figure 15. (a) constant height STM image (10 nm x 10 nm) of the monolayer assembled by A-[17 ]2 at the phenyloctane - HOPG interface (0.1 nA, 850 mV, 15 Hz, 3mM). (b) 30nm x 30nm STM scan 2,F-10,10 (constant height) of A-[17 ]2 monolayer (0.1 nA, 800 mV, 7.6 Hz, 3mM). Both scans reveal alternation in the appearance of anthracene columns. Figure 15a displays a 10 nm x 10 nm monolayer section of the monolayer self- assembled by A-[172,F-10,10]2 at the phenyloctane-HOPG interface. This high resolution STM image reveals C-2-C aligned, "six-dot domino" patterns of the anthracene cores. The anthracenes in adjacent aryl columns exhibit nearly perpendicular anthracene long axis orientations, indicating that A-[172,F-10,10]2 assembles AA* morphology tapes and monolayers, similar to A-[172,F-9,9]2. The unit cell parameters for the monolayer are a = 5.64 ± 0.19 nm, b = 0.96 ± 0.05 nm, α = 91 ± 3 °, which are in fair agreement with calculated values of a = 6.08 nm, b = 0.94 nm, α = 90 °. 46 A linear, "dark furrow" attributable to the CF2 groups is present at the center of each aliphatic lamella. In contrast to the wide, zigzag shaped furrows in A-[172,F-9,9]2 monolayers (Figure 15a), the furrows in A-[172,F-10,10]2 monolayers appear as thin straight lines, which is consistent with ω↔3 packing of A-[172,F-10,10]2 (Figure 16). By contrast, ω↔1 packing positions the CF2 groups in a zigzag alignment. Again, the narrow width and linear shape of CF2 furrows indicate ω↔3 registration, rather than ω↔1 registration, of the A-[172,F-10,10]2 side chains. 2,F-10,10 Figure 16. CF2 dipole alignment in ω↔3 and ω↔1 packing of A-[17 ]2 An interesting pattern of "dark spots" could be observed at the corners of each anthracene core. These spots lie next to the terminal methyl groups of the neighboring side chains (Figure 15a, CPK overlay). These dark spots are additional evidence 47 supporting assembly of ω↔3 packed AA* tapes: ω↔3 packing generates vacancies between the chain terminus and the adjacent anthracenes, each vacancy lowers the local conductivity and appears as a dark spot in the STM image. Figure 15b shows 30 nm x 30 nm a large scan of A-[172,F-10,10]2. The perpendicular anthracene orientations of adjacent aryl columns generate distinctive, albeit poorly resolved, STM patterns consistent with AA* morpholoyg. No AA morphology was observed in A-[172,F-10,10]2 monolayers, thus confirming that A-[172,F-10,10]2 forms ω↔3 packing with dipolar attraction rather than ω↔2 packed tapes with dipolar repulsion. 2.4.2 Self-assembled monolayers of single component A-[152,F-8,8]2 and A-[152,F-9,9]2 2,F-9,9 2,F-8,8 Figure 17. Structures of A-[15 ]2 and A-[15 ]2 Another pair of CF2 incorporated anthracene derivatives with shorter side chains, A-[152,F-8,8]2 and A-[152,F-9,9]2 were prepared to study the CF2 group’s role in controlling monolayer morphology. A single CF2 group at the (ω+1)/2 or the (ω+3)/2 position of odd length, ω = 15 side chains generates dipolar repulsions between ω↔2 packed side 48 chains. Again, a switch to ω↔1 or ω↔3 packing generates dipolar attractions. Thus, A- [152,F-8,8]2 and A-[152,F-9,9]2 are expected to assemble ω↔1 or ω↔3 packed, AA* monolayers rather than ω↔2 packed, AA monolayers. Figure 18. (a) Constant current STM image (12 nm x 12 nm) of the monolayer assembled on HOPG by A- 2,F-8,8 [15 ]2 in phenyl octane (0.12 nA, 780 mV, 8.7 Hz, 3mM). The * marks aryl columns whose dot patterns resemble the typical anthracene core. (b) constant current STM image (13 nm x 13 nm) of the 2,F-9,9 AA*, C-2-C monolayer assembled on HOPG by A-[15 ]2 in phenyl octane (0.1 nA, 800 mV, 10.2 Hz, 3mM). The monolayers assembled by A-[152,F-8,8]2 and A-[152,F-9,9]2 are less stable compared to those of A-[172,F-10,10]2 and A-[172,F-9,9]2. The domains disappeared and reformed rapidly during the scanning, making it difficult to adjust collection parameters and optimize monolayer resolution. Figure 18 provides the best STM images that have been captured for A-[152,F-8,8]2 (Figure 18a) and A-[152,F-9,9]2 (Figure 18b). The monolayer assembled by A-[152,F-8,8]2 exhibits two distinct patterns for the anthracenes in neighboring aryl columns. The C-2-C aligned "six-dots domino" patterns for anthracene 49 cores are barely discernible in the aryl columns marked with asterisks. The neighboring aryl columns appear narrower compared to the asterisk columns, however, the structure of the columns are unrecognizable due to the poor resolution of the image. The pattern alternation within the aryl columns offers weak evidence in support of an AA* tape based monolayer. The green box marks the monolayer unit cell. The experimental parameters a = 5.45 ± 0.28, b = 0.98 ± 0.11, α = 89 ± 5 ° are in decent agreement with the calculated values (chapter 2, 2.6.1) a = 5.55, b = 0.94, α = 90 °. 2,F-9,9 Figure 19. ω↔2 and ω↔3 packing of A-[15 ]2 Neighboring aryl columns in monolayers assembled by A-[152,F-9,9]2 exhibit a slight pattern alternation. This alternation is so subtle that it can not serve as a strong evidence to discern the AA or AA* morphology of the monolayer. However, the A-[152,F- 9,9 ]2 monolayer does exhibit thin, linear shaped “dark furrows” at the center of aliphatic lamellas. As Figure 19 shows, ω↔3 AA* packing generates collinearly aligned, parallel 50 CF2 groups, whereas ω↔2 AA packing produces a zigzag alignment of the CF2 groups in adjacent side chains. The observation of thin, linear "dark furrows" serves as weak evidence for assembly of ω↔3 packed, AA* morphology in monolayers of A-[152,F-9,9]2. 2.4.3 Self-assembled monolayers of CF2 mixtures The results in sections 2.4.1 and 2.4.2 demonstrated that dipolar interactions between CF2 groups at the (ω+1)/2 or (ω+3)/2 position of odd length side chains switch the monolayer morphology from “normal” ω↔2 AA packing to ω↔3 AA* packing. On the other hand, the side chains in the two molecule pairs (A-[172,F-10,10]2 / A-[172,F-9,9]2) and (A-[152,F-8,8]2 / A-[152,F-9,9]2) were designed to be dipolar complementary. The ω↔3 packing of each single component monolayer generates dipolar attractions at the cost of reduced van der Waals contact. In contrast, ω↔2 packing of compositionally patterned monolayers (AB, vide infra) by each complementary pair affords parallel, collinearly aligned CF2 dipoles in addition to optimal side chain van der Waals interactions (Figure 20). Figure 20. ω↔2 packing of CF2 dipolar complementary pairs 51 Ideally, ω↔2 packing of the complementary pairs should afford higher stabilization than the ω↔3 packing of each single component. Thus, we expect a 1:1 solution mixture of A-[172,F-10,10]2 / A-[172,F-9,9]2 or A-[152,F-8,8]2 / A-[152,F-9,9]2 to assemble ω↔2, AA patterned monolayers. In this morphology, the composition of a 1-D tape alternates between the two dipolar complementary molecules with both molecules adsorbing via the same enantiotopic face. We refer to this as an AB tape (as distinct from AA, AA* or AB* tapes). Figure 21. Constant current STM image (13 nm x 13 nm) of the monolayer assembled on HOPG by a 1:1 2,F-9,9 2,F-10,10 solution mixture of A-[17 ]2 and A-[17 ]2 in phenyl octane (0.12 nA, 850 mV, 7.6 Hz, total concentration: 2mM). Figure 21 shows a 11.5nm x 11.5nm section of C-2-C monolayer assembled from 1:1 solution mixtures of A-[172,F-10,10]2 and A-[172,F-9,9]2. The monolayer exhibits a morphology with parallel aligned anthracenes in all aryl columns. The observed 52 morphology is consistent with self-assembly of a patterned monolayer built from ω↔2 packed, AB tapes whose composition alternates between A-[172,F-10,10]2 and A-[172,F-9,9]2. The anthracenes’ characteristic "six-dots domino" patterns are evident in Figure 21. The distance between the two CF2 groups within a molecule of A-[172,F-10,10]2 is longer than the corresponding distance in A-[172,F-9,9]2. Supposedly, the composition of each aryl column could be determined based on the spacing alternations between the "dark furrows" attributed to CF2 groups. Unfortunately, "dark furrows" are not evident in this particular image, making it difficult to assign the aryl column composition. The unit cell of the patterned monolayer contains one molecule of each compound (green box). Its parameters a = 5.58 ± 0.15 nm, b = 0.95 ± 0.06 nm, α = 81 ± 3 ° are in reasonable agreement with expectations for an ω↔2 packed, AB tape, C-2-C morphology (a = 5.87 nm, b = 0.96 nm, α = 83 °, chapter 2, 2.6.1). As no AA* (or AB*) domains were observed in monolayers prepared from 1:1 solution mixtures of A-[172,F-10,10]2 and A-[172,F-9,9]2, the formation free energy of the compositionally AB patterned monolayer must be significantly more favorable than the ω↔3 packed AA* monolayer formed by either single component. In stark contrast to the unstable monolayers assembled by single component solutions of A-[152,F-8,8]2 or A-[152,F-9,9]2, monolayers assembled from 1:1 solution mixtures of A-[152,F-8,8]2 and A-[152,F-9,9]2 are robust, persistent and easily imaged. The monolayer exhibits C-2-C morphology with parallel aligned anthracenes in all aryl columns (Figure 22). The anthracene cores appear as yellow rectangles, with the long axes of anthracenes oriented from bottom left to top right. In the monolayers formed 53 by each single component, anthracene columns exhibit shape alternations along the direction of 1-D tapes, suggesting AA* morphology. However, in this two-component mixture monolayer, the anthracene long-axis alignment is the same in all columns. Thus the mixture monolayer assembles AB type, ω↔2 packed 1-D tapes whose composition alternates between A-[152,F-8,8]2 and A-[152,F-9,9]2. Figure 22. Constant current STM image (15 nm x 15 nm) of the monolayer assembled on HOPG by a 1:1 2,F-8,8 2,F-9,9 solution mixture of A-[15 ]2 (anthracene columns marked as "8") and A-[15 ]2 (anthracene columns marked as "9") in phenyl octane (0.12 nA, 780 mV, 7.6 Hz, total concentration: 2mM). The "dark furrows" attributed to CF2 groups are evident in the middle of each aliphatic lamella. The spacings between the "furrows" alternate between 2.6nm and 2.8nm, in which the shorter spacing corresponds to CF2 distance of A-[152,F-8,8]2 and longer spacing corrensponds to CF2 distance of A-[152,F-9,9]2. This distance alternation further confirms a compositionally patterned AB morphology formed by A-[152,F-8,8]2 and 54 A-[152,F-9,9]2 mixture. The unit cell (green box) contains one molecule of A-[152,F-8,8]2 and one of A-[152,F-9,9]2. The unit cell parameters a = 5.37 ± 0.17 nm, b = 1.01 ± 0.07 nm, α = 80 ± 5 ° are in good agreement with the results of molecular mechanics simulation (a = 5.36 nm, b = 0.96 nm, α = 82 °, chapter 2, 2.6.1). The experimental results from 1:1 solution mixture of A-[172,F-10,10]2 / A-[172,F-9,9]2 or of A-[152,F-8,8]2 / A-[152,F-9,9]2 demonstrate that the CF2 dipolar interaction is an effective tool for directing molecular recognition. The CF2 group placed in the complementary side chains produces parallel, collinear alignments of their CF 2 dipoles in ω↔2 packed morphology. The simultaneously optimized dipolar and van der Waals interactions drive the formation of compositionally patterned mixture monolayers. The selectivity between the dipolar complementary pair is so strong that no single component domains have been observed from the mixture monolayers. 2.5 Monolayer patterning using ketone dipoles[33] The large dipole moment of the CF2 group makes it effective at directing patterned self-assembly of multi-component monolayers. Incorporating multiple CF2 units per side chain would allow design and implementation of multiple complementary side chain pairs and facilitate self-assembly of greater complexity monolayers directed by dipolar patterning. Unfortunately, the CF2 unit is difficult to synthesize in high yield and incorporating multiple copies per side chain is synthetically challenging. 55 2,C=O-9 2,C=O-10 Figure 23. Structures of A-[17 ]2 and A-[17 ]2 The ketone functional group, which is a synthetic precursor of the CF 2 unit, has an even larger dipole moment (2.6 D). If strong dipolar interactions between CF 2 groups were the dominant driving force for directing molecular recognition in the A-[172,F-10,10]2 / A-[172,F-9,9]2 system, it is reasonable to assume that ketone groups could also be highly effective and practical functional groups for directing multi-component dipolar patterning. Conversely, the ketone carbonyl group (C=O) is significantly larger than a CH2 or CF2 group. Steric repulsions involving C=O groups may impede side chain packing and reduce the van der Waals contact of the neighboring side chains. To evaluate the potential of ketone groups in dipolar patterning, two 1,5-disubstituted anthracenes bearing mono-ketone side chains A-[172,C=O-9]2 and A-[172,C=O-10]2 (Figure 23) were synthesized and the morphologies of their single- and two-component monolayers were characterized by STM. Similar to their CF2 counterparts A-[172,F-9,9]2 and A-[172,F-10,10]2, the two 1,5-disubstituted anthracene derivatives employed in this study have 17 heavy atom long side chains ( = 17) and are designed to be “self-repulsive”, with a carbonyl group (C=O) at either the (+3)/2 or (+1)/2 (i.e. n=9 or n=10) position of the side 56 chain. As indicated in Figures 24 and 25, if the “benefit” of a switch from dipolar repulsion (2 packing) to dipolar attraction (3 packing) exceeds the “cost” of reduced van der Waals interactions with 3 packing, then single component solutions of A-[172,C=O-9]2 or A-[172,C=O-10]2 will assemble 3 packed, AA* monolayers rather than 2 packed, AA monolayers. Figure 24. 2 and 3 packing of A-[17 2,C=O-10 ]2 Figure 25. 2 and 3 packing of A-[17 2,C=O-9 ]2 57 2.5.1 Self-assembled monolayers of single component A-[172,C=O-9]2 and A-[172,C=O-10]2 C=O-9 Figure 26. (a) 10.8nm x 10.8nm constant current image (0.1nA, 800mV, 10.2 Hz, 2mM) of A-[17 ]2 assembled at the HOPG - phenyl octane interface. (b) 30nm x 30nm constant current image (0.1 nA, C=O-9 800mV, 7.6 Hz, 2mM) of A-[17 ]2. Figure 26a displays a 10.8nm x 10.8nm section of the C-2-C monolayer assembled by A-[172,C=O-9]2 at the phenyloctane - HOPG interface. The anthracene columns (bright yellow) exhibit alternating patterns: anthracenes in columns 1, 3 and 5 (from left to right) appear as bright yellow rectangles with their long axes aligned from bottom left to top right. Each anthracene in columns 2 and 4 appears as a bright yellow oval, within which a central long axis (dark line) is aligned nearly vertical and almost perpendicular to the anthracenes in the adjacent columns. This alternating appearance of anthracene columns is consistent with an 1 or 3 packed, AA* morphology of the A-[172,C=O-9]2 monolayer (Figure 25, bottom). A few anthracenes in column 1, 3 and 5 exhibit the atomic resolution "six-dots domino" pattern. However, for anthracenes in 58 column 2 and 4, only four or five dots are visible, with two or one dot appearing indistinct. Similar to the STM images of CF2 derivatives, the STM image of A-[172,C=O-9]2 also exhibits "dark furrows" near the middle of the aliphatic lamellas. These furrows mark the locations of the low conductivity ketone groups. CPK models overlays are placed at the bottom of the image. The side chain alignments, ketone positions and anthracene orientations of the STM image are in good agreement with the 3 packed CPK models. Only the AA* anthracene morphology is observed in these STM experiments, indicating that 3 packing of the A-[172,C=O-9]2 side chains is preferred over an 2 packed morphology; the ketone groups at the (+1)/2 position of odd length side chains destabilize the 2 side chain packing. The A-[172,C=O-9]2 monolayer unit cell (Figure 26a, green box) contains two molecules, each adsorbed via a different enantiotopic face. The measured unit cell parameters a = 6.01 ± 0.13 nm, b = 0.99 ± 0.04 nm, α = 74 ± 3 ° are in decent agreement with the calculated values (a = 6.12 nm, b = 0.94 nm, α = 79.6 °). Figure 26b display a 30nm x 30nm STM scan in which the AA* morphology is still distinguishable. 59 2,C=O-10 Figure 27. (a) 15nm x 6.6nm monolayer section assembled from 1mM A-[17 ]2 in phenyloctane (constant current, 0.1nA, 1200mV, 12.2Hz). To enhance the STM image resolution, a drop (~1μL) of phenyloctane solution containing 5μM C60 fullerene was applied to a previously assembled monolayer. 2,C=O-10 (b) 10.4nm x 10.4 nm constant current image (0.10 nA, 800mV, 12.2 Hz) of 2mM A-[17 ]2. Figure 27a displays a 15nm x 6.6nm section of the C-2-C monolayer assembled by A-[172,C=O-10]2 at the phenyloctane - HOPG interface. Although the image lacks atomic resolution, the rectangular shape of the anthracene cores could be distinguished. The monolayer exhibits alternating patterns in the columns indicative of an 1 or 3 packed AA* morphology: the long axes of anthracenes in columns 1, 3 and 5 (from left to right) align from bottom right to top left, while the long axes of anthracenes in columns 2 and 4 align from bottom left to top right. The anthracenes from adjacent columns are almost perpendicular to each other. "Dark furrows" from the C=O groups are observed at the middle for each aliphatic lamella. The linear shape of these "furrows" is in good agreement with the 3 packed AA* morphology of A-[172,C=O-10]2 (Figure 24, bottom). 60 Figure 27b shows another STM scan of A-[172,C=O-10]2 with CPK overlays. In this image, neighboring anthracene columns exhibit one of two distinct yellow dot patterns, with the same pattern repeating every other column. The characteristic "six-dots domino" anthracene STM patterns are discernible and are well matched with the CPK overlays. The unit cell (green box) contains two molecules absorbed via different enantiotopic faces. The measured unit cell parameters, a=5.86±0.11nm, b=1.00±0.04nm, α=77±6° , are in decent agreement with molecular mechanics minimized results (a=6.04nm, b=0.93nm, α=81.0°). Again, only the AA* morphology is observed in STM experiments, indicating that the dipolar interactions of ketone groups at the (+3)/2 position of odd length side chains are strong enough to switch the monolayer from 2 packing to 3 packing. 2.5.2 Self-assembled monolayers of A-[172,C=O-9]2 and A-[172,C=O-10]2 1:1 mixture Figure 28. 2 packing of ketone dipolar complementary pair Single component monolayers of A-[172,C=O-9]2 or of A-[172,C=O-10]2 assemble 3 packed side chains with C=O dipolar attractions at the cost of reduced van der Waals interactions. Just like their CF2 counterpart, A-[172,C=O-9]2 and A-[172,C=O-10]2 were designed as a dipolar complementary pair. As shown in Figure 28, the dipolar C=O 61 groups of A-[172,C=O-9]2 and A-[172,C=O-10]2 can attain a collinear, parallel alignment and 2 packed side chains by assembling an AB packed, patterned monolayer. This compositionally patterned, 2 packed morphology affords stabilizing dipolar interactions and optimal side chain van der Waals interactions. The compositionally patterned mixture monolayer has parallel alignment of the anthracenes' long axis in all columns. As both single component monolayers exhibit AA* morphology, the observation of parallel aligned anthracenes in adjacent columns (AB morphology) can distinguish the two component mixed monolayer from single component monolayers. 2,C=O-9 Figure 29. (a) 12.6 nm x 12.6 nm constant current image (0.1 nA, 700mV, 7.6 Hz) of 1mM A-[17 ]2 2,C=O-10 and A-[17 ]2. (b) 10.0 nm x 10.0 nm constant current image (0.1 nA, 850mV, 12 Hz) of 1mM A- 2,C=O-9 2,C=O-10 [17 ]2 (the anthracene columns are marked as "9") and A-[17 ]2 (the anthracene columns are marked as "10"). The spacings between ketone "furrows" alternate between 3.0nm and 2.7nm. Figure 29 displays STM scans of monolayer sections assembled by a 1:1 mixture of A-[172,C=O-9]2 and A-[172,C=O-10]2 at the phenyloctane - HOPG interface. Figure 29a shows the monolayer has all anthracenes' long axes aligned from bottom left to top 62 right. The "six-dots domino" STM patterns of anthracene are evident in all aryl columns of Figure 29b (black boxes). Also visible are low tunneling C=O “dark spots” at the middle of the aliphatic lamellae. The collinear alignment of the "dark spots" matches the predicted alignment of ketone groups for an 2 packed AB morphology (Figure 28). The measured unit cell (Figure 29a, green box) parameters a = 5.70 ± 0.10 nm, b = 0.92 ± 0.03 nm, α = 85 ± 4 ° are in good agreement with the calculated values (a = 5.85 nm, b = 0.96 nm, α = 81.4 °). The measured unit cell a-parameter of the mixed monolayer is 0.16 to 0.30nm smaller than the unit cell a-parameter of the single component, 3 monolayers. The shorter unit cell a-parameter in the mixed monolayer is consistent with the shorter aryl column spacing in 2 packing morphology (compared to 3 packing, 2 packing reduces the spacing between adjacent aryl columns by one CH2 unit ~ 0.13 nm). The compositions of the molecules comprising each anthracene column can be identified using the distance between the two flanking C=O groups ("dark spots" in Figure 29b). The measured distances alternate between 3.0nm and 2.7nm. The wider separations correspond to A-[172,C=O-10]2 columns and the narrower separations correspond to A-[172,C=O-9]2 columns. The analysis above confirms self-assembly of a compositionally patterned two- component (AB) monolayer. The dipolar ketone groups, like their CF 2 counterparts, are effective in directing patterned multi-component self-assembly based. 63 2.5.3 Self-assembled monolayer of A-[172,F-9,9]2 and A-[172,C=O-10]2 1:1 mixture Figure 30. 2 packing of A-[17 2,F-9,9 2,C=O-10 ]2 and A-[17 ]2 We have demonstrated that solution mixtures of A-[172,C=O-9]2 / A-[172,C=O-10]2 and solution mixtures of A-[172,F-9,9]2 / A-[172,F-10,10]2 assemble compositionally patterned, two component (AB) monolayers. As both pairs of compounds have identical chain length (=17) and have dipolar functional groups, C=O or CF2, at either the 9th or 10th position of the side chain, it was of interest to investigate whether a compositionally patterned AB monolayer could be assembled from dipolar complementary pairs with different dipolar functional groups (Figure 30). To test this, we prepared phenyloctane solution containing 1:1 mixture of A-[172,F-9,9]2 and A-[172,C=O- 10 ]2 and characterized its monolayer by STM. Figure 31 displays a 11.0nm x 11.0nm section of the monolayer assembled from 1:1 mixture solution of A-[172,C=O-10]2 and A-[172,F-9,9]2. The STM image provides atomic resolution of the anthracene cores. The high tunneling “six-dots domino” patterns (white ovals) are evident and long axes of all anthracenes are parallel to each other (AA morphology). As single component solutions of either compound assemble 3 packed AA* monolayers, the observed parallel aligned anthracenes in all columns of the A-[172,C=O-10]2 and A-[172,F-9,9]2 mixed monolayer suggests assembly of an 2 packed, 64 AB patterned morphology driven by complementary dipolar interactions of the C=O and CF2 groups. 2,F-9,9 2,C=O-10 Figure 31. STM scan of the monolayer formed by a mixture of A-[17 ]2 and A-[17 ]2 at the phenyl octane - HOPG interface. 11.0nm x 11.0 nm constant current image (0.1 nA, 1300mV, 7.6 Hz) of 2,F-9,9 2,C=O-10 1mM A-[17 ]2 and A-[17 ]2. Although low tunneling “dark furrows” could be observed at the middle of aliphatic lamellas, the contrast is too weak for precise measurement of furrow spacings. Thus it is difficult to determine the exact column composition on this STM image and the CPK models are superimposed arbitrarily. The measured unit cell parameters a = 5.76 ± 0.14 nm, b = 0.92 ± 0.04 nm,  = 86 ± 3 o are in decent agreement with the molecular mechanics minimized values (a = 5.84 nm, b = 0.96 nm,  = 84 o) and are almost the same as the measured unit cell parameters of the ketone mixture. The experimental results confirm that C=O and CF2 dipoles are interchangeable in directing 65 2-D self-assembly, and this compatibility allows them to form compositionally patterned, multi-component monolayers. 2.6 Molecular Mechanics (MM) simulation of monolayer properties As part of the effort to understand how molecular structure impacts the supramolecular morphology of self-assembled monolayers, simulations of monolayer sections on graphene sheets were performed using HyperChem 8.0. Molecular mechanics minimizations were performed on monolayer sections consisting of four to six anthracene columns, each of which contains four to six molecules. The HOPG surface was modeled as a single layer, graphene sheet that was at least 10 - 20% larger than the monolayer section. Atomic charges on the molecules were assigned using Mulliken population analysis of AM1 calculations. The side chains of molecules were configured to lie in the same plane as the anthracene core (x-y plane). The molecules’ x-y planes were aligned parallel to the graphene sheet, with a starting position close to (but not in contact with) the sheet. Prior to minimization, the atoms in the single layered graphene sheet were set as “fixed atoms” within Hyperchem. This prevented the graphene atoms from moving and the sheet from curling during minimizations. Minimizations were run until the MM energy of the sample decreased less than 10 -5 kcal/mole in 24 hours. MM minimization studies of A-[172,F-9,9]2, A-[172,F-10,10]2, A-[152,F-9,9]2 and A-[152,F-8,8]2 monolayer sections were performed by Dr. Wenjun Tong[24][30]. 66 2.6.1 MM minimized monolayer sections and unit cells The MM minimizations were performed on the following monolayer sections: 2 packed AA morphology of A-[172,F-9,9]2, A-[172,F-10,10]2, A-[152,F-9,9]2, A-[152,F-8,8]2, A- [172,C=O-9]2 and A-[172,C=O-10]2 single component monolayers; 3 packed AA* morphology of A-[172,F-9,9]2, A-[172,F-10,10]2, A-[152,F-9,9]2, A-[152,F-8,8]2, A-[172,C=O-9]2 and A- [172,C=O-10]2 single component monolayers; 2 packed AB morphology of A-[172,F-9,9]2 / A-[172,F-10,10]2 mixed monolayer; 2 packed AB morphology of A-[152,F-8,8]2 / A-[152,F- 9,9 ]2 mixed monolayer; 2 packed AB morphology of A-[172,C=O-9]2 / A-[172,C=O-10]2 mixed monolayer; 2 packed AB morphology of A-[172,F-9,9]2 / A-[172,C=O-10]2 mixed monolayer. Figures 32 to 41 present CPK models of the minimized monolayer sections (vide infra) following deletion of the graphene sheet used in the minimizations. . a) 3 packed AA* and (b) 2 packed AA morphology of A-[17 [24][30] 2,F-9,9 Figure 32 ]2 67 . (a) 3 packed AA* and (b) 2 packed AA morphology of A-[17 [24][30] 2,F-10,10 Figure 33 ]2 . (a) 3 packed AA* and (b) 2 packed AA morphology of A-[15 [24][30] 2,F-8,8 Figure 34 ]2 68 . (a) 3 packed AA* and (b) 2 packed AA morphology of A-[15 [24][30] 2,F-9,9 Figure 35 ]2 . 2 packed AB morphology of A-[17 [24][30] 2,F-10,10 2,F-9,9 Figure 36 ]2/ A-[17 ]2 patterned monolayer 69 . 2 packed AB morphology of A-[15 [24][30] 2,F-8,8 2,F-9,9 Figure 37 ]2 / A-[15 ]2 patterned monolayer Figure 38. (a) 3 packed AA* and (b) 2 packed AA morphology of A-[17 2,C=O-9 ]2 70 Figure 39. (a) 3 packed AA* and (b) 2 packed AA morphology of A-[17 2,C=O-10 ]2 Figure 40. 2 packed AB morphology of A-[17 2,C=O-10 2,C=O-9 ]2 / A-[17 ]2 patterned monolayer 71 Figure 41. 2 packed AB morphology of A-[17 2,C=O-10 2,F-9,9 ]2 / A-[17 ]2 patterned monolayer Compound Experimental Unit Cell Parameters Simulation Unit Cell Parameters a (nm) b (nm) α (o) a (nm) b (nm) α (o) A-[172,F-9,9]2 5.54±0.22 0.95±0.06 87±4 6.08 0.94 90 A-[172,F-10,10]2 5.64±0.19 0.96±0.05 91±3 6.08 0.94 90 A-[172,F-9,9]2 + 5.48±0.15 0.95±0.06 81±3 5.87 0.96 83 A-[172,F-10,10]2 A-[152,F-8,8]2 5.45±0.28 0.98±0.11 89±5 5.55 0.94 90 A-[152,F-9,9]2 5.22±0.34 1.01±0.16 91±5 5.58 0.94 90 A-[152,F-8,8]2 + 5.37±0.17 1.01±0.07 80±5 5.36 0.96 82 A-[152,F-9,9]2 A-[172,C=O-9]2 6.01±0.13 0.99±0.04 74±3 6.12 0.94 80 A-[172,C=O-10]2 5.86±0.11 1.00±0.04 77±6 6.04 0.93 81 A-[172,C=O-9]2 + 5.70±0.10 0.92±0.03 85±4 5.85 0.96 81 A-[172,C=O-10]2 A-[172,F-9,9]2 + 5.76±0.14 0.92±0.04 86±3 5.84 0.96 84 A-[172,C=O-10]2 Table 1. Measured unit cell parameters vs simulated unit cell parameters Table 1 lists the unit cell parameters from STM experiments and from MM simulations. The measured unit cell a-parameters for each 2-component monolayer are 72 0.06 - 0.30nm smaller than the a-parameters of the corresponded single component monolayer[34], which is in qualitative agreement with ω↔2 side chain packing of two- component monolayers and ω↔3 side chain packing of single component monolayers. All ω↔3 pack monolayer sections from MM simulation exhibit regular C-2-C morphology, in which the H-4 of anthracene core lie in between H-4 and H-3 of anthracene core from the adjacent tape so that the aromatic hydrogens at the corners of anthracenes are in close contact with their neighbors (the simulations of ω↔2 packed monolayers of anthracene-diyne derivatives display similar features, see Chapter 3). Interestingly, all ω↔2 packed monolayer sections from MM simulation display an "irregular" C-2-C morphology: instead of pointing H-4 into H-4 and H-3, the H-4 and H-3 of anthracene core point toward H-3 and H-4 of anthracene core from the adjacent tape, or to say, H-4↔H-3 and H-3↔H-4. Compare to regular C-2-C morphology, the H- 3 and H-4 in irregular C-2-C morphology are slightly separated apart from the adjacent aromatic hydrogens. This subtle difference may originate from the steric effect of CF 2 and C=O group: both CF2 and C=O group are bulkier than CH2 group which impede the approach of adjacent side chains. The steric repulsion in between adjacent side chains may slightly separate their anthracene cores. For ω↔3 packing, the vacancy between the anthracene and terminal CH3 group provides flexibility for anthracene core to bend toward its neighbor so that the aromatic hydrogens are in close contact (i.e. H-4 into H-4 and H-3). For ω↔2 packing, the terminal CH3 group is closer to the anthracene which may impede the mobility of the anthracene core. As a result, H-3 and H-4 from adjacent 73 anthracene cores are slightly separated apart to produce a H-3↔H-4 / H-4↔H-3 morphology. 2.6.2 Self-assembly energies (SAEs) determination from MM simulations The adiabatic self-assembly energy (SAE) represents the energy change for assembly of a particular monolayer morphology from isolated molecules in their lowest energy equilibrium geometries. The SAE calculation protocol was established by Dr. Wenjun Tong: Following minimization, the graphene sheet is deleted and the monolayer section’s energy is determined with a single point MM energy calculation. Next, a single molecule from an interior position of the monolayer section is shifted so that it no longer interacts with other molecules in the section. A single point MM energy calculation is performed for this “shifted” assembly. Subtracting the intact monolayer section’s energy from the “shifted” assembly energy affords the “vertical” extraction energy (VEE) of the shifted molecule. Next, the strain energy of the shifted molecule is determined as the shifted molecule’s MM energy in the monolayer minimized geometry minus its MM energy after minimization in isolation. The shifted molecule’s SAE is calculated as its strain energy minus half of its VEE; as the VEE reflects the interactions of the shifted molecule with its neighbors, the VEE value needs to be halved when calculating the SAE per shifted molecule. The self-assembly energy excluding electrostatic contributions (SAE’) was determined from the same set of structures (molecule and morphology) except that electrostatic terms were excluded from the single point energy calculations. The 74 electrostatic contribution per dipolar group was calculated as [VEE(all terms) - VEE(excluding electrostatic terms)]/4. The factor of four arises from the presence of two identical dipolar groups in each molecule and because the VEE must be attributed equally between the extracted molecule and its neighbors. Table 2 lists SAE for single/multi component monolayers of A-[172,F-9,9]2, A-[172,F- 10,10 ]2, A-[172,C=O-9]2 and A-[172,C=O-10]2. The SAE calculations for monolayers assembled by A-[172,F-9,9]2 and A-[172,F-10,10]2 were performed by Dr. Wenjun Tong. With Without Electrostatic electrostatic electrostatic contribution contributions contributions per dipolar group SAE kcal/mol SAE’ kcal/mol (kcal/mole) Single Component Monolayer A-[17C=O-10]2 -AA* ω↔3 -24.9 -22.2 -1.4 A-[17C=O-10]2 -AA ω↔2 -22.3 -23.7 0.7 A-[17C=O-9]2 -AA* ω↔3 -22.9 -21.6 -0.6 A-[17C=O-9]2 -AA ω↔2 -20.5 -22.6 1.1 A-[17F-10,10]2 -AA* ω↔3 -24.8 -23.1 -0.8 A-[17F-10,10]2 -AA ω↔2 -21.8 -23.4 0.7 A-[17F-9,9]2 -AA* ω↔3 -23.9 -23.3 -0.3 A-[17,F-9,9]2 -AA ω↔2 -21.6 -23.7 1.0 Two Component Monolayer (ω↔2 packed) A-[17C=O-9]2 + A-[17C=O-10]2 -25.4 -23.1 -1.1 A-[17F-9,9]2 + A-[17F-10,10]2 -25.9 -24.4 -0.8 A-[17F-9,9]2 + A-[17C=O-10]2 -25.6 -23.4 -1.1 Table 2. Self-Assembly Energies of Molecules with C=O or CF2 containing side chains The SAE calculations for each single compound’s monolayer predict the 3 packed, C-2-C morphology is 2.4 – 3.0 kcal/mol more stable than its 2 packed C-2-C morphology. The predictions agree qualitatively with the experimental results since no 2, AA morphology has been observed in the STM experiments. 75 The simulation results demonstrate that dipolar group positions do have evident impacts on the dipolar interactions. Table 2 shows that the electrostatic terms (column 4) provide more stabilization (dipolar attraction) in collinear dipole alignment (A-[172,F- 10,10 ]2, A-[172,C=O-10]2) than for zigzag dipole alignment (parallel but two side chain positions out of registration - A-[172,F-9,9]2, A-[172,C=O-9]2) in 3 packed, C-2-C morphology. The parallel, collinearly aligned C=O groups are 0.8 kcal/mol more stabilizing than the zigzag aligned C=O groups. Similarly, collinearly aligned CF 2 groups afford 0.5 kcal/mol more stabilization than the zigzag aligned CF 2 group. The electrostatic stabilization per dipolar group for A-[172,C=O-10]2 is larger than that of A- [172,F-10,10]2, suggesting that collinear C=O groups generate more dipolar attraction than collinear CF2 groups. This is in qualitative agreement with that the larger C=O dipole moment: (C=O) =2.6 D > (CF2) = 2.1 D. Dipolar repulsion between anti-parallel C=O and CF2 groups in 2 packed chains destabilizes the 2 packed morphologies. This is confirmed by the positive value of electrostatic terms in the 2 packed morphologies (Table 2, column 4). Replacing C=O or CF2 dipolar repulsions within 2 packed chains by attractive interactions within 3 packed chains provides considerable electrostatic driving force in favor of 3 packing, which is 4.2 kcal/mol for A-[17C=O-10]2, 3.4 kcal/mol for A- [17C=O-9]2, 3.0 kcal/mol for A-[17F-10,10]2 and 2.6 kcal/mol for A-[17F-9,9]2. The result predicts that ketone dipolar interactions generate stronger dipolar driving forces than the CF2 dipolar interactions. 76 The SAE’ values in Table 2 (column 3) are the stabilization energies without dipolar interactions. The SAE’ values indicate that, in the absence of electrostatic terms, 2 packing is 0.2 – 1.5 kcal/mol more stabilizing than 3 packing. This is consistent with the fact that 2 packing offer more van der Waals contacts for side chains than 3 packing. As the net effect, the combined contribution of dipolar attraction in 3 packing and dipolar repulsion in 2 packing override the more favourable van der Waals contacts in 2 packing. The SAE calculations also predict that compositionally patterned, 2 packed, C-2-C monolayers assembled from dipolar complementary pairs (A-[17C=O-9]2/A-[17C=O- 10 ]2, A-[17F-9,9]2/A-[17F-10,10]2 and A-[17F-9,9]2/A-[17C=O-10]2) are 0.6 – 2.5 kcal/mol more stable than 3 packed single component monolayers. The simultaneous realization of optimal van der Waals and dipolar alignments provides strong driving force for the assembly of compositionally patterned monolayers from the CF2 and ketone dipolar complementary pairs. Although the SAE value provides energetic evaluations of molecule - molecule interactions within the monolayers, this oversimplified model does not provide any information about molecule – substrate interactions and molecule – solvent interactions. Thus, the SAE simulation could only be used as a rough estimation and the calculated results should be treated more qualitatively than quantitatively. 77 2.7 Conclusion The dipolar attractions and repulsions produced by CF2 and ketone functional group are proved to be effective tools in directing self-assembly of single- and multi- component 1,5-substituted anthracenes monolayers. Placing CF2 and ketone groups at (ω+1)/2 or (ω+3)/2 position of the side chain generates dipolar repulsions between ω↔2 packed side chains. The combined effect of dipolar interactions (repulsion in the 2 packed morphology; attraction in the 3 packed morphology) drives self- assembly of atypical, 3 morphology in single component monolayers. Side chains with CF2/ketone groups at (ω+1)/2 are dipolar complementary to the side chains with CF2/ketone groups at (ω+3)/2 position. 1:1 mixing of two 1,5-substituted anthracenes bearing dipolar complementary side chains (e.g. A-[172,F-9,9]2 + A-[172,F-10,10]2, A-[152,F-9,9]2 + A-[152,F-8,8]2, A-[172,C=O-9]2 + A-[172,C=O-10]2 and A-[172,F-9,9]2 + A-[172,C=O-10]2) promotes self-assembly of compositionally patterned, 2 packed two-component monolayers. The formation of two-component monolayers are driven by the simultaneous optimization of van der Waals contact (2 packing of side chains) and dipolar interactions (parallel, collinear alignment of dipolar groups). The observation of parallel aligned anthracenes in neighboring aryl columns, along with the unit cell parameters of the two-component monolayers and the spacing of low tunneling furrows arising from the ketone or CF2 groups confirm self-assembly of compositionally patterned, two- component monolayers with AB morphology. The dipolar complementary side chain pairs can comprise of either the same (e.g. A-[172,F-9,9]2 + A-[172,F-10,10]2) or different dipoles (e.g. A-[172,F-9,9]2 + A-[172,C=O-10]2). 78 References [1] K. EichhorstGerner, A. Stabel, G. Moessner, D. Declerq, S. Valiyaveettil, V. Enkelmann, K. Mullen, J. P. Rabe, Angewandte Chemie-International Edition in English 1996, 35, 1492. [2] P. Qian, H. Nanjo, T. Yokoyama, T. M. Suzuki, Chem Commun 1999, 1197. [3] K. E. Plass, K. M. Engle, K. A. Cychosz, A. J. Matzger, Nano Lett 2006, 6, 1178. [4] C. A. Palma, J. Bjork, M. Bonini, M. S. Dyer, A. Llanes-Pallas, D. Bonifazi, M. Persson, P. Samori, J Am Chem Soc 2009, 131, 13062. [5] X. 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Zimmt, Physical Chemistry Chemical Physics 2013. [34] The a-parameter of single component monolayer of A-[152,F-9,9]2 appear to be smaller than that of the two-component monolayer. Since the poor resolution produces large uncertainties in the unit cell parameters, the a-parameter of A-[152,F-9,9]2 may be inaccurate. 81 Chapter 3 Molecular Shape Control of Self-Assembled Monolayer Morphology 3.1 Introduction Supramolecular interactions play a vital role in controlling morphology and stability of self-assembled monolayers[1-4]. Strong directional interactions such as hydrogen bonding and metal coordination have been exploited in constructing 2-D and 3-D self-assemblies[5-12]. In the absence of these strong interactions, weaker supramolecular interactions such as dipolar interactions and Van der Waals force could also direct self-assembly of neutral organic molecules[1, 13-15] . In Chapter 2, we demonstrated that dipolar interactions involving CF2 or ketone groups can be used to control monolayer morphology. In this chapter, we introduce a new strategy that is based intrinsically on Van der Waals interaction, using molecular shape [16] to control monolayer structures and molecular recognition. Figure 1. Straight side chain (left) vs "kinked" side chain (right) In previous systems studied by our research group, anthracene cores were substituted by straight alkyl chains (Figure 1, left) on their 1 and 5 position [17-22]. These straight chains resemble "I" shaped tetrominos from the Tetris game. The relatively 82 smooth shape of straight alkyl chains endows freedom for closely packed molecules to slide, thus allowing various metastable defect morphologies such as lamella displacement and molecule dislocations[23][24][21]. Moreover, it is difficult to use straight alkyl chains to provide molecular recognition during self-assembly of multi-components since these chains are always able to pack effectively with a duplicate copy. In an attempt to overcome these disadvantages, we "kinked" the side chain shape by introducing conjugated diyne[25-33] units within the interiors of aliphatic chains. An alkadiyne side chain’s kinked shape resembles a "Z" tetromino (Figure 1, right) and places shape constraints on molecule packing. Figure 2. Packing of molecules with compatible shapes Figure 3. Packing of molecule with incompatible shapes Just as in the Tetris game, both the diyne "kinks" and alkyl straight sections of adjacent molecules need to fit correctly (Figure 2) in order to achieve densely packed monolayer morphologies[16]. If substantial driving force and stability are associated with 83 dense packing, molecules will “choose the right neighbors” based on compatible shapes. Conversely, packing of shape-incompatible molecules (Figure 3) will generate vacancies (red circles in Figure 3) which will destabilize self-assembly of such monolayer structures. 3.2 STM sample preparation and acquisition protocols Scanning tunneling microscopy data was acquired using a Digital Instruments NanoScope STM interfaced to a Digital Instruments NanoScope IIIa controller. Data collected from the solution ‐ graphite or air ‐ graphite interfaces (HOPG, ZYB grade, Momentive Performance, Strongsville, OH) used mechanically cut 87/13 Pt/Rh tips (0.25 mm, Omega Engineering, Stamford, CT) or 80/20 Pt/Ir tips (0.25 mm, Goodfellow, Oakdale, PA). Concentrated solutions for each compound were prepared by dissolving 2‐4 mg of compound in 400 - 600 μL of phenyl octane (Aldrich, 98% and Alfa Aesar, 98%) at 20 °C and then filtered (Anatop Plus 0.02 μm filters, Whatman). These initial solutions, which normally had concentrations of 5 - 10 mM, were diluted to 0.05 - 2 mM for STM imaging. A solution drop (3 - 5 μL) was deposited on a recently cleaved HOPG surface. To increase the domain sizes of monolayers, some samples were annealed at 30 - 40°C for 0.5 ‐ 2 hours before imaging. “Dry” monolayers were prepared by rinsing a preformed monolayer with 1‐2 mL of cold ethanol or cold tetradecane and then dried in air prior to imaging. The STM tip was engaged through the solution (or in air) and scanned in constant height or constant current mode. Tip scan velocities were in the range 0.20 – 1.2 μm/s. Multiple samples were prepared and imaged to evaluate monolayer morphology and unit cells. Thermal drift distortions in the data were 84 corrected using a program developed by Dr. Wenjun Tong[23]. The program solves for x and y‐thermal drift velocities in consecutively captured images obtained using opposite slow scan directions. This correction is valid if thermal drift velocities are reasonably constant in consecutive scans. Reported unit cell parameters are averages of thermal drift corrected STM data from three or more independently prepared and scanned sets of samples. STM scanner x‐ and y‐calibration was performed prior to monolayer formation using thermal drift corrected HOPG images (5 or 10 nm scale). 3.3 Self-Assembly of shape self-complementary compounds[34] The first investigations sought to assess whether anthracenes bearing side chains with diyne groups assemble stable physisorbed monolayers. For this study, four molecules were prepared; A-[252-CC12,14]2 (molecule 1), A-[242-CC12,14]2 (molecule 2), A-[292-CC14,16]2 (molecule 7) and A-[232-CC12,14]2 (molecule 8). These molecules were designed to pack so that (i) the first C(sp) of one chain could lie in registration with the fourth C(sp) of an identical neighbor and (ii) the nth-heavy atom of each chain would lie in registration with the (w+2-n)th heavy atom of the adjacent chain. We refer to these diyne compounds as shape self-complementary (Figure 4) and we define these diyne "kinks" as lying at the side chain center (actually center of the side chain lamella). 85 Figure 4. Molecule 1 designed to self-pack with ω↔2 registration 3.3.1 Self-assembly of single component diyne monolayers: molecule 1 and molecule 2 2 12,14 Figure 5. A-[25 -CC ]2 (molecule 1) 2 12,14 Figure 6. A-[24 -CC ]2 (molecule 2) Molecule 1 has two identical side chains containing 25 heavy atoms, with a 12- position diyne groups at the center of the aliphatic side chains. Multiple STM scans reveal that molecule 1 readily assembles stable monolayers in which the crystalline unit cell repeats for 100’s of nanometers along both unit cell axes. Figure 7 shows a 13.6nm x 8.6nm section of a monolayer formed by 1 at the phenyloctane-HOPG interface. The bright yellow columns (one marked by a cyan arrow) consist of corner-to-corner packed 86 (C-2-C) anthracenes adsorbed via the same enantiotopic face (i.e., an AA pattern, see Chapter 2, Section 2.3). This high resolution scan reveals the anthracene cores as "six- dot dominos" and the diyne regions appear as straight, four-dots lines. The measured length of the four-dot line is 0.75nm, which corresponds to the length of -CH2-CC-CC- CH2- unit. The sizes of the terminal two dots are similar to the sizes of the dots produced by CH2 hydrogens, while the middle two dots are slightly bigger. Thus, the four-dot line patterns are combine contribution from both diyne unit (two-dots pattern at the center which resembles HOMO of diyne) and its neighboring CH2 hydrogens (the two terminal dots). The diyne groups serve as good chemical markers[35] for characterizing the monolayer morphology. In the STM image, the four dot patterns are positioned at the center of the aliphatic lamella, in good agreement with the proposed morphology. The long axes of the aryl cores and the axes of the diyne group are oriented from bottom left to top right. The long axes of the anthracenes are aligned at 32±3° from the column repeat (red or cyan arrow). The diyne groups are aligned at 48° from the column repeat. The monolayer unit cell is indicated by the green box on the top left. The measured unit cell parameters for the molecule 1 monolayer are a=3.76±0.04nm, b=0.95±0.02nm, α=90.1±1.7°, which are in good agreement with molecular mechanics simulated values of a = 3.79 nm, b = 0.94 nm, α = 88.6 ° (see section 3.6 for detail). 87 Figure 7. (a) Constant height STM image (0.85 V, 0.1 nA, 13.6 nm x 8.0 nm) of molecule 1 at the phenyloctane—HOPG interface (solution concentration: 0.2mM) with a CPK model overlay. (b) CPK model of the simulated monolayer. [Figure form Ref. 34] Previous studies revealed that anthracenes substituted with straight alkyl chains at their 1- and 5-positions assemble monolayers with ω↔2 packing of side chains in the aliphatic lamellae (the last heavy atom, , of each side chain packes in registration with the 2nd heavy atom of the two adjacent side chains, see Chapter 2, Section 2.3). 2 packing provides the optimal balance of van der Waals attraction and steric repulsion between neighboring side chains. These studies revealed that the 2 packing preference generates an odd-even effect on the monolayer morphology. Side chains containing an odd number of heavy atoms promote assembly of an AA monolayer morphology, in which all anthracenes in all columns adsorb to HOPG via the same enantiotopic face. STM images revealed parallel aligned anthracenes in the two columns 88 flanking each 2 packed, odd length aliphatic lamella (image). By contrast, side chains containing an even number of heavy atoms promote assembly of AA* morphology monolayers. In the AA* morphology, anthracenes in the two columns flanking the 2 packed, even length aliphatic lamella adsorb via opposite enantiotopic faces; STM images reveal a (roughly) perpendicular long axis alignment of the anthracenes in these two flanking columns (see Chapter 2, 2.3 for detailed explanation). For molecule 1, 2 packing of odd length side chains and the central location of the diyne group both promote AA packing. To evaluate diyne group's role in directing the self-assembled morphology, molecule 2 was prepared and studied by STM. Molecule 2 has a diyne group at the same side chain location (12-position) as molecule 1 but has only 24-heavy atoms in its side chains, an even number and one heavy atom shorter than for molecule 1. If ω↔2 packing of the even length side chains controls the morphology, then STM images of molecule 2 should exhibit AA* monolayers, with perpendicular long-axis alignments of anthracene cores in neighboring aryl columns. Alternatively, if the diyne groups "kinks" control side chain packing, the terminal methyl groups in molecule 2 will be forced to lie in registration with the 3-position of adjacent chains, 3 packing, and forego one CH2 group's van der Waals interaction with both flanking diyne chains. 3 packing generate vacancies between the terminal methyl groups and anthracene cores (red circles in Figure 8b) but produces tight packing of the diyne "kinks". An 3 packed monolayer of 2 will exhibit AA morphology, with parallel aligned anthracenes in adjacent aryl columns, and should yield STM images that are similar to the monolayer assembled by molecule 1. 89 Figure 8. (a) Constant height STM image (0.6 V, 0.1 nA, 15 nm x 8.8 nm) of molecule 2 at the phenyloctane-HOPG interface (solution concentration: 0.2mM) with a CPK model overlay. (b) CPK model of the simulated monolayer, red circles indicated vacancies generated by ω↔3 packing. [Figure form Ref. 34] Figure 8 displays a high resolution STM image of the monolayer self-assembled by molecule 2. The anthracene cores appear as rectangular shapes, albeit without atomic resolution. The anthracene cores within adjacent aryl columns are parallel aligned (long axes extending from bottom left to top right) indicating an AA morphology. The experimental unit cell parameters, a=3.72±0.02nm, b=0.95±0.03nm, α=91.3±2.5°, are indistinguishable from those of molecule 1 monolayers. The experimental evidence suggests that shape constraints imposed by the diyne kinks within molecule 2 drive assembly of monolayer morphology with optimal side chain shape alignment but non- optimal side chain registration (i.e. ω↔3). Shape (i.e. the diyne “kink”) is a more potent director of side chain packing than loss of one CH2 van der Waals interaction. 90 3.3.2 Self-assembly of molecule 7 and molecule 8 2 14,16 Figure 9. A-[29 -CC ]2 (molecule 7) 2 11,13 Figure 10. A-[23 -CC ]2 (molecule 8) A-[292-CC14,16]2 (7) and A-[232-CC12,14]2 (8) were prepared to investigate further that the self-assembly of shape self-complementary diyne compounds. Both molecules are symmetrically substituted, with side chains at the anthracene's 1- and 5- position that contain diyne groups located at side chain “center”. It is worth noting that diyne groups in molecule 7 lie at even side chain positions (i.e. 14th heavy atom), which affords roughly parallel alignment of the diyne groups and the anthracene core long axis. This topological feature of molecule 7 is analogous to those in molecules 1 and 2. By contrast, molecule 8 has the diyne groups at odd side chain positions (i.e. 11th heavy atom), which aligns the diyne groups nearly perpendicular to the anthracene core long axis. An STM image of the monolayer assembled by molecule 7 at the phenyloctane - HOPG interface (Fig. 11) clearly exhibits atomic resolution of (i) the anthracene cores ("six-dot" dominos aligned from bottom left to top right), (ii) the side chain alkyl sections (the straight lines of dots next to the anthracenes) and the diynes (diagonal 91 lines of four dots at the side chain centers). A closer examination of the four-dots pattern reveals that the middle two dots are slightly bigger than the terminal ones (Figure 11, right), which is in consistent with the previous STM observation of molecule 1. Molecule 7 assembled the same ω↔2 registered, AA morphology monolayers as molecule 1. This is the only morphology we have observed for molecule 7, as well as for molecules 1 and 2. Apparently, the stacking of diyne kinks plays an important role in directing monolayer assembly even for molecules with higher "aspect ratio" (i.e. longer side chains). The measured unit cell parameters of the molecule 7 monolayer (Fig. 11 green box) a=4.35±0.04nm, b=0.97±0.02nm, α=85.5±3.2° are in good agreement with MM simulated values (a=4.30nm, b=0.94nm, α=88.6°, see section 3.6) Figure 11. (a) Constant current STM image (0.85 V, 0.12 nA, 15 nm x 11.3 nm) of molecule 7 at the phenyloctane-HOPG interface (solution concentration: 0.1mM) with a CPK model overlay. (b) CPK model of the simulated monolayer. 92 Molecule 8 also assembles stable monolayer at phenyloctane-HOPG interface. Anthracenes within adjacent columns are parallel aligned (Fig 12). The diynes (Figure 12a, red bar) are aligned (almost) perpendicular to the anthracenes' long axis (Figure 12a, blue bar), as expected from their odd side chain positions. The STM derived unit cell parameters are a=3.56±0.03nm, b=0.98±0.02nm, α=86.5±2.7°. Figure 12. (a) Constant current STM image (0.80 V, 0.1 nA, 15.3 nm x 10.9 nm) of molecule 8 at the phenyloctane-HOPG interface (solution concentration: 0.4mM) with a CPK model overlay. (b) CPK model of the simulated monolayer. 3.4 Pairwise shape-complementary compounds: 2-components self-assembly[34] The studies in Chapter 3.3 confirmed that shape self-complementary diyne compounds assemble stable monolayers in which the diynes kinks direct molecule 93 stacking and monolayer morphology. To explore the application of diyne kinks' as a tool for building molecular recognition into monolayer self-assembly, we have designed and prepared compounds in which the diyne kink is shifted away from side chain center. Figures 13 and 14 shows two molecules investigated in this study. These two molecules are isomers of shape self-complementary diyne molecule 8. In comparison with the side chain centralized diyne groups in 8, molecule 3 has its diyne groups shifted towards the anthracene core by 4 carbons. By contrast, molecule 4 has its diyne groups shifted away from the anthracene core by 4 carbons. 2 7,9 Figure 13. A-[23 -CC ]2 (molecule 3) 2 15,17 Figure 14. A-[23 -CC ]2 (molecule 4) As illustrated in Figure 15, the off center diyne kinks within molecule 3 reduce, substantially, the van der Waals contacts between adjacent side chains in a single component monolayer. The off center diyne kinks within molecule 4 produce similarly poor packing contacts. The optimal packing of single component monolayers composed of either 3 or 4 includes large vacancies (indicated by red circles in Figure 15). These vacancies significantly reduce van der Waals interactions between adjacent side chains (see more detail section 3.6). Non-densely packed morphologies are likely to be less 94 thermodynamically robust. Moreover, the exposure of the inner side chains allows solvent molecules to interact with the loosely packed monolayers, which would further destabilize the self-assembled structure. In contrast to the shape self-complementary diyne side chains, these off center diyne designs produce weak packing of identical side chains. We refer to these off center alkadiyne chains as ‘‘shape self-incommensurate’’. Figure 15. Non-dense packing of 3 and 4 due to the position of the side chain diyne ‘‘kink’’. [Figure form Ref. 34] In contrast to the shape self-complementary design of molecules 1, 2, 7 and 8, the shape self-incommensurate side chains of 3 and of 4 are pairwise shape- complementary. As shown in Figure 16, replacing molecule 3's neighbor with molecule 4 yields a densely packed tape, with ω↔2 side chain registration and proper alignment of the diyne kinks. Stacking these tapes should form a dense packed monolayer. If this occurs, side chain shape can function as a molecular recognition element in monolayers. 95 Figure 16. Intended monolayer packing morphology of molecules 3 and 4 3.4.1 Attempted self-assembly with single components: A-23 (3) and A-23 (4) Figure 17. A typical STM image of 3 at phenyloctane-HOPG interface. 50 nm x 50 nm, 0.10 nA, 0.8 V. Single component solutions of molecule 3 or of molecule 4 in phenyloctane (0.2 - 0.5 mM) were deposited on HOPG and imaged using STM. No identifiable monolayers have been observed during repetitive imaging attempts (Fig. 17). This is sharp contrast to the rapid monolayer assembly from was able to form by the same chain length, but shape self-complementary diyne compound 8 (see 3.3.2). The failure to observe 96 monolayers of pure 3 or pure 4 supports the description of the [232;CC-7,9] side chain and of the [232;CC-15,17] side chain as shape self-incommensurate. 3.4.2 Self-assembly of mixed monolayers of molecule 3 and 4. In stark contrast to the negative STM results from single component solutions of 3 or 4, a 1 : 1 mixture of 3 and 4 in phenyl-octane rapidly assembles a highly stable monolayer. Columns of anthracenes and of diynes (diagonal line of four dots) are readily discernible in an atomic resolution STM scan (Fig. 18). The proximity of nearest diyne columns to the intervening anthracene column identifies the molecules assembling the intervening aryl column. For molecule 3, the diynes are close to anthracene core, whereas for molecule 4 the diynes are further from the aryl core. Based on these diyne positions, the columns of molecule 3 and molecule 4 can be assigned unambiguously (cyan arrows). The STM data indicates 3.6 nm separation of nearest anthracene columns, with diyne columns centered 1.3 and 2.3 nm from the closest and next closest anthracene columns, respectively. All anthracenes within the same domain are aligned parallel and the diynes are aligned perpendicular to the anthracenes' long axis, as expected for their odd side chain positions (7-position for molecule 3; 15-position for molecule 4). The STM derived unit cell parameters of this monolayer are a = 7.16±0.07 nm, b = 0.95±0.02 nm and α = 83.5±3.3°, which is in good agreement with the simulated values (a = 7.21 nm, b = 0.93 nm and α = 78.5°, see section 3.6). The inclusion of one molecule each of 3 and 4 in the unit cell produces a longer a-axis and a larger unit cell area than from single component diyne monolayers described in 3.3. 97 Figure 18. (a) Constant height STM image (0.8 V, 0.1 nA, 18.5 nm x 10.9 nm) of a 1 : 1 mixture (total concentration: 0.5mM) of 3 and 4 at the phenyloctane-HOPG interface. (b) CPK model of the simulated monolayer section of 3 and 4. [Figure form Ref. 34] In addition to assembling monolayer from solution containing stoichiometric ratio (1:1) of 3 and 4, monolayers assembled from solutions with component ratio of 2:1 and 1:2 (total concentration were maintained at 0.5mM) were also studied by STM. Of all studied samples, the AB patterned morphology displayed in Figure 18 is the only morphology that has been observed in STM experiments. The successful self-assembly of compositionally patterned monolayer from 3 and 4 mixture demonstrate that the kinked side chain shape provide high fidelity in molecular recognition. The off-centered kink shape effectively impede packing of the same side chains, thus instead of producing randomly mixed monolayers, the system favors co-crystallized AB morphology with densely packed side chains. 98 3.4.3 Self-assembly of shape self-incommensurate molecules 5 and 6 A pair of molecules with 25 heavy atoms, self-incommensurate diyne side chains were designed and prepared to confirm diynes’ ability to confer molecular recognition in monolayer assembly. Figures 19 and 20 show the structures of molecules 5 and 6. Compared to their shape self-complementary isomer, molecule 1, molecules 5 and 6 have their diyne groups shifted by 2 carbons toward/away from the aryl core. As the diynes are at even side chain positions, both compounds’ diyne kinks are aligned roughly parallel to the anthracene core's long axis. 2 10,12 Figure 19. A-[25 -CC ]2 (molecule 5) 2 14,16 Figure 20. A-[25 -CC ]2 (molecule 6) A 1:1 mixture of 5 and 6 in phenyloctane solution assembled stable and molecularly-resolved monolayers. In the STM images (Figure 21), all anthracenes are aligned parallel and oriented from bottom left to top right. The diyne columns in Fig. 21 exhibit STM contrast and appear as low resolution "streaks" aligned orthogonal to the aliphatic columns. The STM data indicates a 3.8nm spacing between closest anthracene columns and that the diyne "streaks" are centered 1.6 and 2.2 nm from each 99 neighboring anthracene column. This is in perfect match with MM minimized monolayer section, which suggests a 3.8nm anthracene spacing and 1.6 and 2.1 nm distances between the centers of the aryl and diyne columns. The measured STM data can be used to identify columns as molecule 5 or 6 based on the diyne - anthracene spacing. The CPK overlay in Fig. 21a closely matches the STM data. The STM derived parameters for this two molecule unit cell are a = 7.55±0.05 nm, b = 0.96±0.03 nm and α = 88.3±2.7°, which are in good agreement with MM simulated values (a = 7.60 nm, b = 0.93 nm and α = 88.8°, see section 3.6). Figure 21. (a) Constant current STM image (0.8 V, 0.15 nA, 15.6 nm x 13.7 nm) of a 1 : 1 mixture (total concentration: 0.2 mM) of 5 and 6 at the phenyloctane-HOPG interface. (b) CPK model of the simulated monolayer section of 5 and 6. 100 The compositionally patterned morphology in Figure 21 is the only morphology observed in STM experiments. Although for 5 and 6 diyne kinks only off-centered by two CH2 groups, this side chain shape based molecular recognition strategy still shows its reliability in controlling monolayer morphology. Controlled STM experiments were performed with phenyloctane solutions containg single component 5 and 6. The concentration of each single component was maintained as same to the optimized total concentration of the two-component solution (0.2 mM). The results show that neither compound forms detectable monolayer at this condition. Figure 22. Non-dense packing of 5 and 6 due to the position of the side chain diyne ‘‘kink’’ Figure 22 shows the optimal side chain packing of single component 5 and 6. For molecule 5, the diyne "kink" shifts towards anthracene core, which generates a shorter 101 "inner" part of side chain (from diyne to anthracene) and longer "outer" part of side chain (from diyne to terminal). This shape effectively impedes close packing of the same side chains (Figure 22, top). As Figure 22 shows, optimal of packing of [252-CC10,12] chain produces a ω↔2/14 morphology: the intra-tape packing adapts ω↔2 registration while the inter-tape packing adapts ω↔14 registration. This morphology produces small intra-tape vacancies and at the same time generates large inter-tape vacancies (Figure 22 top, red ellipses). For molecule 6, packing of [252-CC14,16] chain produces ω↔5 morphology, which leaves vacancies in between anthracene cores and side chain terminals (Figure 22 bottom, red ellipses). In section 3.3 we demonstrated that stable ω↔3 morphology could be form by packing of [242-CC12,14] chain, hence single component 6 ([252-CC14,16] chain) is likely to form ω↔5 packed monolayer. However, this morphology was not observed at our experimental condition (phenyloctane-HOPG interface, 0.2 mM concentration). One possible reason is that the concentration used in the STM experiments was too low for the formation of loosely packed ω↔5 morphology. A higher solution concentration may facilitate the monolayer assembly of single component 6. 3.5 Pairwise shape-complementary compounds: 4-component self-assembly[36] There are numerous literature examples of monolayers self-assembled from two or three molecular components. However, four-component self-assembled monolayers are still rare. Development of reliable approaches for designing monolayers with 102 increased structural and compositional complexity remains an important and unsolved challenge. The successful demonstration of 2-component self-assembly directed by alkadiyne side chain shape (Chaptere 3.3) identifies pairwise self-incommensurate diyne side chains as a useful strategy for increasing structural complexity of self-assembled monolayers. To further exam and challenge this strategy's reliability in directing multi- component self-assembly, we designed a self-assembly system containing four distinct molecular component. In this study, four anthracenes bearing a total of six different diyne side chains were prepared and their self-assembly on graphite was studied. 3.5.1 System design The four molecular structures are shown in Figure 23. Side chain shape was modulated using both chain length (23, 27, and 31 heavy atoms) and diyne “kink” displacement. Two molecules with C2h symmetry are referred to as molecule S1 (A-[312- CC13,15]2 ) and S2 (A-[272-CC9,11]2); the letter "S" denotes an anthracene symmetrically substituted with two identical side chains. The other two molecules have lower Ch symmetry; D1 (A-[312-CC17,19][232-CC9,11]) and D2 (A-[272-CC17,19]-[232-CC13,15]). These molecules are dissymmetric (D), bearing two different alkadiyne side chains at their 1- and 5-postions. are having their anthracene cores dissymmetrically substituted. As shown in Figure 23, the 31 length chains of S1 form shape complementary pairs with the 31 length chains of D1, the 27 length chains of S2 form shape complementary pairs with the 27 length chain of D2, and the 23 length chains of D1 form shape comple- mentary pairs with the 23 length chains of D2. 103 Figure 23. 4 component system S1, S2, D1, D2 and the shape selection rule for the side chains. Based on the designed shape selection, self-assembly should yield a monolayer whose column compositions exhibit a [repeating sequence] of ..D1]-[S1-D1-D2-S2-D2- D1]-[S1-.. The proposed six molecule unit cell should contain one copy each of S1, S2 and two copies of both D1 and D2. Figure 24 displays a simulated section of monolayer containing the designed unit cell. The unit cell possesses a long horizontal expansion (distance from one S1 to next S1) of 23.5nm. Figure 24. Simulated monolayer section containing a complete unit cell 104 This four component system has six distinct side chains along with two enantiotopic faces per molecule. In a system with such complexity, molecules randomly picking their neighbors could generate an enormous number of different repeating sequences; determining the exact number of possible sequences is a complicated cyclic permutation problem and will not be discussed here. Prof. Zimmt has calculated a lower limit[37] on the number of unique, six-molecule repeat sequences to be 6 × 104. With this number of different possibilities, the designed unit cell can determine the monolayer morphology only if the molecular shape selection affords strong driving force. 3.5.2 Self-assembly of S1,S2, D1, D2 mixtures Figure 25. Constant current image (0.85 V, 0.1 nA, 20 nm × 20 nm) of the monolayer assembled from a phenyloctane solution of S1, D1, D2, and S2 (total concentration: 2mM). Red arrows mark diyne columns. [Figure form Ref. 36] 105 Figure 25 displays a monolayer region assembled on HOPG from a phenyloctane solution containing S1, S2, D1, D2 with a ratio of 1:1:2:2 (the stoichiometric ratio of the unit cell). The anthracene cores appear as (nearly) horizontally oriented, six-dot dominos with high tunneling contrast. Anthracenes within adjacent columns are parallel to each other, indicating adsorption to HOPG via the same enantiotopic face. The measured spacings between the four anthracene columns crossing the green rectangle are 3.8, 3.3, and 4.4 nm, which are in good agreement with spacings obtained from MM simulation: 3.92 nm for S2-D2, 3.35 nm for D2-D1, and 4.48 nm for D1-S1. The diyne moieties (indicated by red arrows) also shows moderate contrast in this image. The compositions of the anthracene columns were easily assigned based on anthracene- anthracene column spacings and anthracene-diyne column spacings. A CPK model overlay exhibits remarkable matching of both the anthracene and diyne groups with the experimental STM image. The green box identifies the asymmetric unit of the unit cell ("half" unit cell). Its measured parameters are a = 11.5 ± 0.4 nm, b = 0.93 ± 0.05 nm, α = 91 ± 3°, the a-parameter matches perfectly with the MM simulated value (see Figure 24, half of the horizontal expansion of the unit cell is 11.75nm). 106 Figure 26. Constant height STM image (0.85 V, 0.04 nA, 43 nm × 43 nm) of the monolayer assembled from a solution of S1, D1, D2, and S2 at air- HOPG interface (total concentration: 1.2mM). Cyan (red) arrows mark anthracene (diyne) columns. The unit cell (green rectangle) parameters are a = 23.0 ± 0.9 nm, b = 0.95 ± 0.06 nm, α = 90 ± 5°. The anthracene column spacings are ∼3.8 nm for S2/D2, ∼3.3 nm for D1/D2, and ∼4.4 nm for D1/S1. [Figure form Ref. 36] The robustness of the 4-component physisorbed monolayer was tested by , rinsing the graphite substrate after monolayer self-assembly at the phenyloctane-HOPG interface. In the rinsing experiment, a 3 μL drop of the phenyloctane solution containing 0.2 mM S1/S2 and 0.4 mM D1/D2 was applied to HOPG and annealed at 40 °C for two hours. The sample was rinsed with 2 mL of cold ethanol to remove the phenyloctane solution and then air-dried for one hour. Figure 26 shows an STM image of the “dry” monolayer captured after rinsing and drying. The intact and repeating monolayer 107 pattern demonstrates that the 4-component system is robust enough to survive both solvent washing and the drying process. At the length scale of this image (43nm x 43nm), it is not possible to see the internal structure of the molecules. Fortunately, the edges of the diyne columns exhibit STM contrast ("railway tracks" indicated by red arrows) and the anthracene columns (bright columns indicated by cyan arrows) can be distinguished from the aliphatic columns. The measured spacings between anthracene columns, 4.4nm for S1-D1, 3.3nm for D1-D2 and 3.8nm for D2-S2, agree perfectly with the spacings derived from Figure 25 and the simulated data (see section 3.6). As noted for Fig 24, the composition of each column is assigned based on spacings between anthracene and diyne features. A complete unit cell (green box) of the four component monolayer can be visualized in this large monolayer section. The 23nm long unit cell contains six molecules in the order S1-D1-D2-S2-D2-D1. A packing defect can be observed near the bottom of a D2 column (Fig. 25, lower left). Interestingly, this defect is absent from the next STM scan. Details of this defect would be discussed in Chapter 4 (see section 4.6). 108 Figure 27. Constant current image (0.85 V, 0.040 nA, 140 nm × 140 nm) of the monolayer assembled from a phenyloctane solution containing 0.2mM S1/S2 and 0.4mM D1/D2 at the air-HOPG interface. The phenyloctane - HOPG interface was rinsed with ethanol and air dried prior to STM imaging. The colored bars mark columns of S1 (red), D1 (green), D2 (yellow), and S2 (blue). [Figure form Ref. 36] Figure 27 displays a 140 nm × 140 nm STM scan at the air-HOPG interface after rinsing and drying the self-assembled four component monolayer. Although the diyne columns are not detected reliably at this scan scale, three different spacings (long, medium and short) between the anthracene columns (diagonal dotted lines) are distinguishable. Based on the proposed model and STM scans in Figure 25 and 26, the 109 widest column spacing is assigned as S1-D1; the medium column spacing is assigned as D2-S2 and the narrowest column spacing is assigned as D1-D2. The pattern of spacings allowed the composition of each anthracene column to be assigned: S1 - red bar, D1 - green bar, D2 - yellow bar and S2 - blue bar. In constructing Fig. 26, a single unit cell repeat of bars (red-green-yellow-blue- yellow-green-red) was marked on the image. This repeat was then superimposed on the remaining anthracene columns without modification. The perfect alignment of this unit cell repeat and the anthracene columns along the red line demonstrates that the designed, shape-based neighbor selection persists without error for at least 160 nm (>7 unit cells) in the direction perpendicular to the anthracene columns. By contrast, the regularity of patterns in the vertical direction (along the anthracene column) is interrupted by various defects including (i) interfaces between enantiomeric domains (solid white lines), (ii) 120 degree interfaces between domains related by graphite’s 3- fold symmetry (black line), and (iii) single and clusters of improperly aligned/adsorbed molecules (see detailed description in Chapter 4, section 4.6). Despite, these defects a complete domain at the center of the image (between the upper solid white and dashed white lines) contains more than 2000 molecules assembled according to the designed selectivities of differently shaped, alkadiyne side chains. 110 3.5.3 Four-component self-assembly: minus one component To test the fidelity of alkadiyne shape-based molecular recogition, we performed control experiments in which a phenyloctane solution lacking one of the four components was applied to HOPG. Doing so would cause either (i) the molecules failed to form stable monolayer; or (ii) the molecules still managed to form a monolayer by "forcing" side chains to select unintended neighbors. When S1, D1, or D2 was the compound excluded from solutions of the other [38] three compounds , no STM detectable monolayers were observed. The images captured from these systems resemble the "blank" image of Figure 17, indicating that the 3-component systems, D1-D2-S2, S1-D2-S2 and S1-D1-S2 do not form stable packing morphologies. In each case, at least one side chain from the missing compound is required to confer monolayer stability. The four or five side chains present in these three, 3-components solution do not provide an adequate, alternative shape match for the missing chain (or chains). The 3-component mixture lacking S2 did assemble highly irregular monolayers comprised of small domains (less than 30nm x 30nm) with frequent disruptions along and perpendicular to the anthracene columns[39]. The monolayers exhibit various spacing patterns, and more than one set of spacing patterns, between anthracene columns. Figure 28 shows a typical STM image of a monolayer assembled from a S1, D1, D2 mixture with a ratio of 1:2:2 (total concentration: 5mM). Two spacings are evident at the top of the image: the longer one of 4.4nm, indicated by cyan arrows, is in agreement with S1-D1 spacing; a shorter one of 3.3nm, indicated by red arrows, matches the D1-D2 spacing. Compared to the 4-component system, the S2- 111 D2 spacing of 3.8nm was missing. The primary pattern of column repeats (top of the image) is 4.4nm, 4.4 nm, 3.3 nm. Figure 28. Constant height STM image of the monolayer (0.80V, 0.07nA, 30nm × 30nm) assembled from a phenyl‐octane solution lacking S2 but containing 1mM concentration of S1 and 2mM concentration of D1 and D2. [Figure form Ref. 35 supporting information] Investigation of all side chain packing mismatches revealed that the [312;CC-13,15] side chain of S1 can pack with the [272-CC9,11] side chain of D2 to form a meta-stable packing morphology (Figure 29). This S1-D2 mismatch produces a 4.4nm spacing that is the same as the S1-D1. This unintended packing provides a full complement of van der Waals contacts for the [272-CC9,11] side chain. However, the [312-CC13,15] side chain of S1 lacks van der Waals contacts with four CH2 groups (Figure 29, red ellipse). This 112 analysis assigns the observed, 3-component monolayer as having a ‐[S1‐(4.4nm)‐D1‐(3.3nm)‐ D2‐(4.4nm)]‐ packing morphology. 2 13,15 2 17,19 Figure 29. Proposed packing between [31 -CC ] chain of S1 and [27 -CC ] chain of D2 Although the control experiments showed a meta-stable morphology can be formed by mismatched S1 / D2 packing in three-component monolayers, the absence of observed -[4.4nm - 3.3nm - 4.4nm]- repeats in monolayers formed from all four compounds suggests greater stability (selectivity) of the intended D2-S2 side chain packing compared to the unintended D2-S1 contacts. The frequent breaks observed in the S1-D1-D2 system, compared to the large domains and pattern coherence in the monolayer assembled by all four components, also indicates reduced stability and robustness. 3.6 Molecular Mechanics (MM) simulations of monolayer unit cell properties Molecular mechanics simulation of monolayer sections has proven to be a useful tool for estimation of unit cell parameters and stabilization energies of self-assembled 113 monolayers[40-46]. Our simulation studies were performed using HyperChem 8.0. Molecular mechanics minimizations were performed on monolayer sections consisting of 4 - 6 anthracene columns, each of which contains 4 - 6 molecules. The HOPG surface was modeled as a single layer, graphene sheet that was at least 10 - 20% larger than the monolayer section. Atomic charges were assigned using Mulliken population analysis of AM1 calculations. The side chains of molecules were configured to lie in the same plane as the anthracene core (x-y plane). The molecules’ x-y planes were aligned parallel to the graphene sheet, with a starting position close to (but not in contact with) the sheet. Prior to minimization, the atoms in the single layered graphene sheet were set as “fixed atoms” within Hyperchem. This prevented the graphene atoms from moving and the sheet from curling during minimizations. Minimizations were run until the MM energy of the sample decreased less than 10 -5 kcal/mole in 24 hours. Compound Experimental Unit Cell Parameters Simulation Unit Cell a (nm) b (nm) α (o) b (nm) α (o) a (nm) Parameters 1 (A-[252-C≡C12,14]2) 3.76±0.04 0.95±0.02 90.1±1.7 3.79 0.94 88.6 2 (A-[242-C≡C12,14]2) 3.72±0.02 0.95±0.03 91.3±2.5 3.79 0.91 91.1 7 (A-[292-C≡C14,16]2) 4.35±0.04 0.97±0.02 85.5±3.2 4.30 0.94 88.6 8 (A-[232-C≡C11,13]2) 3.56±0.03 0.98±0.02 86.5±2.7 3.59 0.95 84.2 3 (A-[232-C≡C7,9]2) + 7.16±0.07 0.95±0.02 83.5±3.3 7.21 0.93 78.5 4 (A-[232-C≡C15,17]2) 5 (A-[252-C≡C10,12]2) + 7.55±0.05 0.96±0.03 88.3±2.7 7.60 0.93 88.8 6 (A-[252-C≡C14,16]2) S1+S2+D1+D2 23.0±0.9 0.95±0.06 90 ± 5 24.3 0.95 84.5 Table 1. Measured unit cell parameters vs simulated unit cell parameters. Table 1 lists the unit cell parameters from STM experiments and from MM simulations. As most calculated unit cell parameters are in good agreement with 114 experimental values, the results in Table 1 demonstrate that MM simulations produce reasonable predictions of the monolayer morphologies. The MM simulation predicts the same unit cell parameters for 1 and 2, this is confirmed by the indistinguishable unit cell parameters measured by STM experiments. This convergent further proves that [242- C≡C12,14]2 side chains of 2 adapt ω↔3 packing rather than ω↔2. The experimental data also shows that a-parameter of 1 (A-[252-C≡C12,14]2) is 0.20 nm longer than a- parameter of 8 (A-[232-C≡C11,13]2), which is roughly corresponds to the length of two CH2 units. Similarly, the measured a-parameter of 7 (A-[292-C≡C14,16]2) is 0.59 nm longer than a-parameter of 1 (A-[252-C≡C12,14]2), which is roughly corresponds to the length of four CH2 units. The measured a-parameters of the two-component monolayers are very close to 2x values of the a-parameters of their single-component counterparts with same chain length. This indicates that shifting diyne "kinks" off the side chain center does not disrupt the propagation angle of the side chain. The self-assembly energy (SAE) for each monolayer morphology was calculated using the protocol established by Dr. Wenjun Tong[23]. The SAE values were determined using monolayer sections minimized on a graphene sheet. The protocol to determine the SAE contains mulitple steps. First, the graphene sheet was deleted, the monolayer section was saved and its MM energy, Emonolayer, was determined using a single point MM calculation. Next, a single molecule from an interior position of the monolayer section was shifted far away from the monolayer so that it would no longer interact with other molecules in the section. A single point MM energy E1 was calculated for this shifted configuration. Subtracting the intact monolayer section’s energy, Emonolayer, from 115 E1 affords the vertical extraction energy, Evertical, for that single molecule within the monolayer. After calculating single point MM energy of just the shifted molecule, Emolecule, molecular mechanics was used to determine the molecule’s lowest energy structure and energy, Erelax. The strain energy Estrain of the single molecule within the monolayer section was determined as: Estrain = Emolecule - Erelax In the last step, SAE per molecule was calculated as: SAE = Estrain - 1/2Evertical Since Evertical reflects the interactions of the shifted molecule with its neighbors, it needs to be halved for the SAE calculation. It is important to note that the calculated SAE provide a rough estimate of molecule - molecule interactions within the monolayers. Interactions of the monolayer with HOPG and the solvent are not included in the SAE. For each monolayer section, an average SAE value was determined for all interior molecules with the same structure (4 - 8 molecules depending on section size and composition). Table 2 summarizes the calculated SAE for each system. 116 SAE (kcal/mol) Strain Energy (kcal/mol) Shape self-complementary molecules A-[232-CC11,13]2 (molecule 8) -27.00 1.30 A-[242-CC12,14]2 (molecule 2) -31.25 1.18 A-[252-CC12,14]2 (molecule 1) -33.72 1.23 A-[292-CC14,16]2 (molecule 7) -38.52 1.37 Shape self-incommensurate molecules A-[232-CC7,9]2 (molecule 3, ω↔10, -20.10 1.23 Figure 15 top) A-[232-CC7,9]2 (molecule 3, ω↔2/10, -17.52 1.15 Figure) A-[232-CC15,17]2 (molecule 4, ω↔10, -19.50 1.10 Figure) -30.50 (3) 1.02 (3) Molecule 3 and 4 mixture -30.52 (4) 1.00 (4) 2 10,12 A-[25 -CC ]2 (molecule 5, ω↔14 -18.11 0.95 Figure) A-[252-CC10,12]2 (molecule 5, ω↔2/14 -20.84 1.07 Figure) A-[252-CC14,16]2 (molecule 6, ω↔5, -29.27 1.01 Figure) Molecule 5 and 6 mixture -35.48 (5) 1.02 (5) -35.42 (6) 1.08 (6) Table 2. Calculated SAE for diyne systems Interestingly, both molecules in the 2-component monolayer sections exhibited more negative SAE values than the shape self-complementary counterpart with the same side chain length: -30.5 kcal/mole for 3 and 4 in the mixed monolayer versus -27.0 kcal/mole for 8 and -35.4 kcal/mole for 5 and 6 in the mixed monolayer versus -33.7 kcal/mole for 1. These observations are surprising as their identical chain lengths produce the same numbers of contacts between neighboring chains. The calculated strain energies are smaller for both molecules in the two-component monolayers 117 compared to the single molecule in the one-component monolayer. Perhaps, the off- center position of the diyne kinks in the two-component monolayers affords closer side chain contacts and larger calculated SAE values. The calculated unit cell b-axis lengths (Table 1) are, in fact, slightly smaller for the two-component mixtures than for the one- component monolayer with the same length side chain. This may be the origin of the mixtures’ more negative SAE values. As the experimental b-axis lengths do not show the same trend, the relevance of this calculated result is not certain. Figure 30. MM minimized ω↔10 packing for single component 3 Figure 31. MM minimized ω↔2/10 packing for single component 3 118 We proposed two possible morphologies for single component monolayer of molecule 3. In the first morphology (Figure 30) the [232-CC7,9] chain adapts ω↔10 packing, which produces vacancy between the anthracene core and side chain terminal and at same time gain inter- and intra-tape vdW contacts between the outer parts of alkadiyne chain. In the second morphology (Figure 31) the alkadiyne chain adapts a mixed ω↔2 (for intra-tape contact) and ω↔10 packing (for inter-tape contact). This ω↔2/10 morphology generates large vacancies in both inter- and intra-tape contacts. MM minimization shows that the SAE of ω↔10 morphology is 2.5 kcal/mol more stable than SAE of ω↔2/10 morphology. Thus we define ω↔10 as the optimal side chain packing for single component 3. Figure 32. MM minimized ω↔14 packing for single component 5 Figure 33. MM minimized ω↔2/14 packing for single component 5 119 Similarly, there are also two possible packing morphologies for single component 5. The first morphology (Figure 32) adapts ω↔14 packing that produces vacancy between the anthracene core and side chain terminal and at same time gain inter- and intra-tape vdW contacts between the outer parts of the [252-CC10,12] chain. While the second morphology (Figure 33) adapts alternating ω↔2/14 side chain packings that generates relatively small vacancies in intra-tape contacts and large vacancies in inter- tape contact. In contrast the SAE results of single component 3, for molecule 5 the ω↔2/14 morphology is actually more stable than ω↔14 morphology (SAE favored by 2.7 kcal/mol). Therefore the optimal side chain packing for single component 5 is ω↔2/14 (Figure 33). The calculated results reveal that the SAE values for both components in the A- 23 mixture, 3 and 4, are 10 kcal/mol more negative than SAE of single component monolayer of 3 or 4. The much more negative SAE for the mixture is consistent with its much greater side chain contact and with the absence of STM detectable monolayers from pure solutions of 3 or 4. On the other hand, the SAE values for 5 and 6 mixture is 15 kcal/mol more negative than SAE of single component 5 (ω↔2/14 ) and 6 kcal/mol more negative than SAE of single component 6 (ω↔5). This well explains the experimental result that only co-crystallization morphology was observed for the 5 and 6 mixtures. The SAE of ω↔5 (-29.27 kcal/mol) packed molecule 6 is close to the SAE of ω↔3 packed molecule 2 (-31.25 kcal/mol), however, molecule 2 forms stable monolayer at phenyloctane interface that was not observed for molecule 6. One 120 possible explanation might be that for less stable ω↔5 morphology, higher solution concentration is required to drive the formation of self-assembled monolayer. 3.7 Introducing H-bonding into shape based self-assembly The above studies have shown that the kinked shape of alkadiyne side chains are an effective tool for programming complex supramolecular structure in self-assembled monolayers. The molecules used in those systems contained only alkadiyne chains and an anthracene core, thus the dominant interactions between molecules were van der Waals interactions. In this study, we have designed and prepared a 2-component monolayer system whose assembly is determined by two important intermolecular interactions, van der Waals interaction and hydrogen bonding. Molecule 5 from A-25 mixture was used as one of the components. Instead of molecule 6, pentacosa-14,16-diynoic acid was prepared as molecule 5's side chain shape complementary partner. The proposed packing morphology, illustrated in Figure 34, interdigitates the side chains of molecule 5 with the alkadiyne part of the diynoic acid. The terminal carboxyl group of the diynoic acid is expected to form a pair of hydrogen bonds with an acid from a neighboring column. In this design, the dimers formed by diynoic acid pairs fulfill molecule 6's role. 121 Figure 34. Proposed monolayer morphology of molecule 5 and diynoic acid mixture A primary concern with this system is whether the diynoic acid will form self- stacked monolayers by itself[25-27, 30, 32, 33] (Figure 35). This could result in a phase separation of 1-component and 2-component monolayer domains or, in the worst case, completely prevent assembly of the desired co-crystal morphology. Figure 35. Illustration scheme of self-stacking lamellas formed by single component pentacosa-14,16- diynoic acid 122 Figure 36. Constant current STM image of the monolayer (0.80V, 0.1nA, 15 nm × 15 nm) assembled from a phenyl‐octane solution containing 1:2 ratio of molecule 5 and diynoic acid (total concentration: 0.5 mM). The carboxylic acid moieties displayed as dark furrows. Initial STM experiments showed self-assembly of stable, two-component monolayers with large size domains. Figure 36 displays a typical scan of the monolayer assembled from a phenyloctane solution containing molecule 5 and diynoic acid at 1:2 ratio (total concentration: 0.5 mM). The anthracene moieties appear as bright yellow columns with high tunneling contrast (blue arrows). Between anthracene columns, two diyne columns with lower STM contrast are visible (red arrows). The STM image exhibits dark furrows between two adjacent diyne columns (yellow arrows). These furrows mark [29, 47] the locations of low tunneling carboxyl groups . The large spacing between closest anthracene columns (7.3 nm), the presence of two diyne columns between closest 123 anthracene columns and the low tunneling carboxyl group furrow are qualitatively consistent with assembly of the intended morphology. Similar tunneling patterns of the anthracenes in adjacent columns suggest an AA morphology. However, more detailed studies are required to elucidate the details of monolayer packing. Figure 37 shows a larger scan (50nm x 50nm) of the monolayer. The dark furrows of carboxyl group are not evident in this image. However, the anthracenes (blue arrows) and diynes (red arrows) still show decent contrast. Given the spacing (7.3 nm) between anthracene columns and double diyne columns character, we could confirm that the monolayer in this image has the same morphology as in Figure 36. Figure 37. Large scale STM image of the monolayer (constant current, 0.80V, 0.1nA, 50 nm × 50 nm) assembled from a phenyl‐octane solution containing 1:2 ratio of molecule 5 and diynoic acid (total concentration: 0.5 mM). 124 Similar length scale scans at various positions on the graphite substrate revealed no evidence of other morphologies from this two-component system. There appears to be strong preference for co-crystal formation over pure diynoic acid domain. When comparing our proposed co-crystal morphology (Figure 34) with the self-stacking diynoic acid morphology (Figure 35), it reveals that the co-crystallization of two-component not only stabilizes molecule 5, the single component of which could not form detectable monolayer, but also strengthen the hydrogen bonding between diynoic acid as well. In the self-stacking lamellas of diynoic acid, the close packing of the alkadiyne chains impedes the formation of second hydrogen bond due to the electrostatic repulsion. Consequently each diynoic acid molecule is paired with its neighbor from adjacent lamellas via one hydrogen bond. However, in the co-crystallization morphology, the spacing between the diynoic acids within the same lamella is further separated by the shape-complementary alkadiyne chains of molecule 5. The larger spacing effectively reduced electrostatic repulsion in between the –COOH groups thus enable the formation of a second hydrogen bond. Each diynoic acid molecule in the 2D co-crystal is stabilized by two hydrogen bonds as well as van der Waals contact of alkadiyne chains. The simultaneous stabilization of both molecule 5 (by vdW contact between shape- complementary chains) and pentacosa-14,16-diynoic acid (by both vdW contact of shape-complementary chains and H-bondings) serves as a strong diving force to direct self-assembly of compositionally patterned two-component monolayer. 125 3.8 Conclusion Conjugated diyne units introduce distinct “kinks” in the side chains of 1,5- substituted anthracene derivaties. These kinks place shape constraints on molecule packing and monolayer packing density. Diyne kinks positioned near side chain center allow (nearly) optimal packing of identical alkadiyne side chains. Such alkadiyne side chains are ‘‘shape self-complementary’’ (A-[232-CC11,13]2, A-[242-CC12,14]2, A-[252- CC12,14]2 and A-[292-CC14,16]2). By contrast, placement of the diyne kink far from side chain center inhibits packing of identical side chains, rendering these alkadiyne chains ‘‘shape self-incommensurate’’ (A-[232-CC7,9]2, A-[232-CC15,17]2, A-[252-CC10,12]2, A- [252-CC14,16]2, A-[312-CC13,15]2, A-[272-CC9,11]2, A-[312-CC17,19][232-CC9,11] and A- [272-CC17,19]-[232-CC13,15]). The self-assembly of complex, supramolecular structure in monolayers can be programmed by employing pairs of molecules outfitted with shape self-incommensurate, but pairwise shape-complementary side chains. In our research, compositionally patterned two-component (A-[232-CC7,9]2 + A-[232-CC15,17]2, and A- [252-CC10,12]2 + A-[252-CC14,16]2) and four-component (A-[312-CC13,15]2 + A-[272- CC9,11]2 + A-[312-CC17,19][232-CC9,11] + A-[272-CC17,19]-[232-CC13,15]) self-assembled monolayers were successfully prepared. 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Ogawa, Acs Nano 2012, 6, 3876. [46] A. Osnis, C. N. Sukenik, D. T. Major, J Phys Chem C 2012, 116, 770. [47] A. Gesquiere, M. M. Abdel-Mottaleb, S. De Feyter, F. C. De Schryver, M. Sieffert, K. Mullen, A. Calderone, R. Lazzaroni, J. L. Bredas, Chemistry-a European Journal 2000, 6, 3739. 131 Chapter 4 Monolayer Quality of Molecular Shape Directed Self- Assembly 4.1 Introduction Self-assembled monolayers with designed composition and structure have potential nano-electronics applications, e.g., in organic thin film transistors[1-15] or photovoltaic cells[16-25]. Among the challenges to be addressed prior to use in such applications are high fidelity self-assembly of monolayers with prescribed nano- structure and of extended domains with low defect densities. Monolayer quality has been improved and defect density has been reduced by various methods, including the use of Langmuir-Blodgett techniques[26, 27] , annealing[28, 29] and utilizing capillary forces[30]. As a complement to these preparative methods, one expects that the structures of the molecules used for self-assembly should exert considerable impact on monolayer quality[31]. In Chapter 3, we reported that conjugated diyne ‘‘kinks’’ within the side chains of 1,5-substituted anthracene derivatives functioned as shape-based molecular recognition elements for controlled assembly of multi-component monolayers[29, 32] . A subtlety exists in the Tetris-like shape matching that affords molecular recognition. Diyne “kinks” that start at even side chain positions bend the side chain away from the anthracene center of symmetry (i.e. “out”, Figure 1). By contrast, diyne “kinks” that start at odd side chain positions bend the side chain toward the anthracene center of symmetry (i.e. “in”, Figure 2). STM studies of numerous 1,5- 132 alkadiyne substituted anthracene monolayers revealed that this subtle difference of odd versus even diyne position exerts large effects on the domain size and defect density within the resulting self-assembled monolayers. The influence of diyne position derives from the “in” versus “out” shape of the side chains relative to the anthracene cores. This chapter describes the various defects observed in 1,5-alkadiyne substituted anthracene monolayers and investigates the impact of diyne orientation ("in" versus "out") on monolayer domain size and defect density. 2 12,14 Figure 1. A-[25 -CC ]2, “out” 2 11,13 Figure 2. A-[23 -CC ]2, “in” 4.2 STM sample preparation and acquisition protocols Scanning tunneling microscopy data was acquired using a Digital Instruments NanoScope STM interfaced to a Digital Instruments NanoScope IIIa controller. Data collected from the solution ‐ graphite or air ‐ graphite interfaces (HOPG, ZYB grade, Momentive Performance, Strongsville, OH) used mechanically cut 87/13 Pt/Rh tips (0.25 mm, Omega Engineering, Stamford, CT) or 80/20 Pt/Ir tips (0.25 mm, Goodfellow, 133 Oakdale, PA). Concentrated solutions of each compound were prepared by dissolving 2‐4 mg of compound in 400 - 600 μL of phenyl octane (Aldrich, 98% and Alfa Aesar, 98%) at 20 °C and then filtered (Anatop Plus 0.02 μm filters, Whatman). These initial solutions normally had concentration of 5 - 10 mM. The initial solutions were diluted to 0.05 - 2 mM for STM imaging. A drop (3 - 5 μL) of the diluted solution was deposited on a recently cleaved HOPG surface. To increase the domain sizes of monolayers, some samples were annealed at 30 - 40°C for 0.5 ‐ 2 hours before imaging. “Dry” monolayers were prepared by rinsing a preformed monolayer with 1‐2 mL of cold ethanol or cold tetradecane. The sample was dried in air prior to imaging. The STM tip was engaged through the solution (or in air) and scanned in constant height or constant current mode. Tip scan velocities were in the range 0.20 – 1.2 μm/s. Multiple samples were prepared and imaged to evaluate monolayer morphology and unit cells. Thermal drift distortions in collected data were corrected using a program developed by Dr. Wenjun Tong[33]. The program solves for the x- and y‐thermal drift velocities in consecutive images captured using opposite slow scan directions. This correction is valid if thermal drift velocities remain relatively constant in consecutive scans. Reported unit cell parameters are averages of thermal drift corrected STM data from three or more independently prepared and scanned sets of samples. STM scanner x‐ and y‐calibration was performed prior to monolayer formation using thermal drift corrected HOPG images (5 or 10 nm scale). 134 4.3 Domain interfaces Monolayers self-assembled on HOPG from many compounds containing long aliphatic chains, including 1,5-alkadiyne substituted anthracenes, display multiple domains exhibiting different orientations of the alkyl lamella [34-39]. The interfaces between different domains are one of the most common defects in the monolayers on HOPG. In the STM studies of monolayers controlled by diyne shapes, three types of domain interfaces have been observed: (i) interfaces with ~ 120° angle between domain alkyl lamellae; (ii) interfaces between enantiomeric domains with 5-15° angle between the two domains’ alkyl lamellae and (iii) slip interfaces formed by molecules adsorbed via the same enantiotopic faces and a 0° angle between domain alkyl lamellae. The first two types of domain interfaces were observed frequently in previous studies of 1,5-alkyl substituted anthracenes. The third interface type, observed infrequently in monolayers assembled 1,5-alkyl substituted anthracenes, is observed frequently in monolayers assembled by certain types of 1,5-alkadiyne substituted anthracenes. 4.3.1 Examples of 120° interface 120° domain interfaces are observed commonly within closed packed alkyl chain monolayers on HOPG. Alkyl chains physisorbed to an HOPG surface tend to access an all-trans conformation, with the chain axis parallel to the graphite lattice direction ([100], [010] and [110]). As shown in Figure 3, alkyl chains in each domain are aligned along the directions compatible with the 3-fold symmetry of the HOPG substrate (red arrows). As 135 a result, alkyl lamella/anthracene columns in one domain can orient at 120° with respect to alkyl lamella/anthracene columns in neighboring domains. Figure 3. CPK models of 120° domain interfaces. The red arrows indicate the directions of HOPG's 3-fold symmetry axes; the yellow lines indicate directions of the alkyl lamellae and the anthracene column repeats. 2 12,14 2 Figure 4. 100nm x 100nm STM scan of A-[25 -CC ]2 (left) and 100nm x 100nm STM scan of A-[29 - 14,16 CC ]2 (right) exhibiting 120° domain interfaces. 136 Figure 4 show the typical interface observed in A-[252-CC12,14]2 (left) and A-[292- CC14,16]2 (right). The anthracene columns within adjacent domains provide a convenient way to measure the angle between such domains. In this case, the measured angles are 131° for A-[252-CC12,14]2 and 113° for A-[292-CC14,16]2, which are in reasonable agreement with the theoretical value of 120°. Since these large scale images are not drift corrected, the small angular deviations from 120° may result from image distortion induced by thermal drift. There is another source of deviation from 120°. Two adjacent domains may contain the same or opposite anthracene surface enantiomers. The direction of the anthracene repeat (which is identical to the aliphatic chain lamella repeat) usually deviates by a few degrees, to as many as 10°, off of perpendicular to the mean side chain direction. The sense of the deviation from 90° is opposite within enantiotopic domains. As it is the mean side chain direction that tends to line up with the underlying HOPG axis, the angle between anthracene repeats can be slightly larger or smaller than 120° if adjacent “120°” domains contain opposite anthracene surface enantiomers. 4.3.2 Examples of enantiotopic interface Interfaces between domains containing different surface enantiomers also form with nearly parallel mean side chain directions. We refer to these as enantiotopic interfaces[40]. Observation of numerous STM images indicate that enantiotopic interfaces usually are characterized by a small intersection angle (2° - 5°) between the anthracene repeat axes within the enantiotopic domains. Figure 5 shows an example of 137 this interface from an A-[232-CC11,13]2 monolayer on HOPG. The domain interface is indicated by a yellow solid line and two surface anthracene enantiomers are indicated with blue borders. The long axis of anthracenes within the left domain are oriented by +50° relative to the interface line whereas the long axis of anthracenes within the right domain are oriented by -50° relative to the interface. The side chain alignment of the left domain (blue dashed line) is only varied by 2° relative to side chain alignment of the right domain (red dashed line). All these evidence indicate that other than doing an in- plane rotation (indicated by black border in Figure 5), the molecules from the left domain adsorb to the HOPG using the opposite enantiotopic faces to the molecules from the right domain. These enantiotopic domains resemble glide reflections of each other. The two domains are mirror images and contain surface (2D) enantiomers. 2 11,13 Figure 5. 13.2nm x 13.2nm STM scan of A-[23 -CC ]2. The yellow line indicates an enantiotopic domain interface, blue and red dashed lines indicate side chain alignment of molecules from left and right domain, respectively. The black lines indicate the anthracene column repeats. 138 Figure 6 displays an enantiotopic interface from the four-component monolayer assembled by S1,S2,D1,D2. Once again, the mirrored long axis alignments of the anthracenes (red ovals) and small angle between side chains (blue dashed lines) identify the top and bottom domains are surface enantiomers to each other. The anthracene column repeats in the two domains are 8°off of parallel. Figure 6. 14nm x 14nm STM scan of S1, S2, D1, D2 four-component mixture. The yellow line indicates an enantiotopic domain interface. The black lines indicate the anthracene column repeats. In many large scale STM images (>100 nm), the feature resolution is insufficient to enough to identify, unambiguously, the long axis orientations of anthracenes. In most cases, an enantiotopic interface can be identified by the small angular deviation of anthracene columns on opposite sides of the interface. 139 4.3.3 "Slip" interfaces The "slip" interface is a rare type of domain interface that has been observed with greater frequency in certain 1,5-alkadiyne substituted anthracene monolayers[41]. Figure 7 shows a slip interface within an A-[232-CC11,13]2 monolayer. The anthracene columns (red arrow) in one domain terminate at the interface and align collinearly with the diyne columns (blue arrow) within the neighboring domain. In contrast to the enantiotopic interfaces, the domains on either side of the slip interface exhibit identical morphology, with all molecules adsorbed to HOPG via the same enantiotopic face (long axis of anthracenes are indicated by yellow bars). As a result, the domain on one side of the interface looks like a horizontal shift or slip of the domain on the other side. Thus, we refer to this type of interface as "slip" interface. 2 11,13 Figure 7. 26nm x 26nm scan of A-[23 -CC ]2 showing a slip interface near the top. 140 Slip interfaces are the most common domain interface found in A-[232-CC11,13]2 monolayers. The frequency (number / unit area) of slip interfaces is much higher than that of 120° or of enantiotopic interfaces. Figure 8 shows a representative scan of an A- [232-CC11,13]2 monolayer formed by drop-casting. In this 50nm x 50nm monolayer section, a total of five slip interfaces (indicated by yellow arrows) are present. The frequent anthracene column breaks associated with "slips" greatly reduce the average domain size within A-[232-CC11,13]2 monolayers. 2 11,13 Figure 8. 50nm x 50nm STM scan of A-[23 -CC ]2 exhibiting five slip interfaces. A survey of STM scans from 1,5-alkadiyne anthracene monolayers revealed that slip interfaces appear with moderate frequency for A-[232-CC11,13]2 (molecule 8), in the two component mixture of A-[232-CC7,9]2 (molecule 3) and A-[232-CC15,17]2 (molecule 141 4), and in the four component mixture of A-[312;CC-13,15]2 (S1), A-[272;CC-9,11]2 (S2), A- [312;CC-17,19]-[232;CC-9,11] (D1) and A-[272;CC-17,19]-[232;CC-13,15] (D2). All the above compounds have "in" type diyne side chains, with the diyne groups located at side chain odd positions. Figure 9 displays a slip interface (top right, dashed line) in the two-component monolayer formed by molecule 3 and molecule 4. The identity of each aryl column can be determined from the anthracene-anthracene column spacings and anthracene-diyne column spacings. At the slip interface, anthracene columns of 4 (red arrow) from one domain align collinearly with the diyne columns (blue arrow) of the adjacent domain. The bottom left of the scan contains an enantiotopic interface, which is identified by the small angle between anthracene columns in the domains above and below the interface. 2 7,9 2 15,17 Figure 9. 50nm x 50nm STM scan of A-[23 -CC ]2 (3) and A-[23 -CC ]2 (4) mixture showing a slip interface at top region (yellow dashed line). 142 A second set of dinye compounds exhibit no detectable slip interfaces in their self-assembled monolayers. This group of compounds, A-[252-CC12,14]2, A-[292- CC14,16]2, and the mixture of A-[252-CC10,12]2 and A-[252-CC14,16]2 have “out” type diyne side chains, with the diyne group located at even side chain positions. The most common domain interfaces observed in these "out" diyne systems are 120° and enantiotopic interfaces. Without the disruption arising from slip interfaces, monolayers of "out" diynes generally have larger average domain sizes and lower defect densities (better self-assembly qualities) than the monolayers of "in" diynes. Figures 10 and 11 contrast one and two component monolayers assembled by "out" and "in" diynes. Each of these samples was prepared by drop-casting without subsequent annealing. 2 12,14 2 11,13 Figure 10. 160nm x 160nm STM scan of A-[25 -CC ]2 (left) and A-[23 -CC ]2 (right) Figure 10 exhibits large scale monolayer sections of A-[252-CC12,14]2 (left) and A- [232-CC11,13]2 (right) assembled at the phenyloctane-HOPG interface. The image of A- [252-CC12,14]2 (left) contains no 120o, enantiotopic or slip interfaces defect-free 143 monolayer within a 160nm x 160nm area. Although some contaminations (large spots with high contrast) appeared at the bottom of the image, the anthracene moieties under the contaminations appear as collinearly continued columns. Thus, all diyne molecules in this image belong to a single domain. By contrast, the 160nm x 160nm monolayer section of A-[232-CC11,13]2 exhibits frequent breaks along the anthracene columns in the center region. The anthracene columns from one domain terminate at the center of the side chain lamellae of the neighboring domain, which matches the position of the mid-chain diyne groups (not visible). The anthracene columns on both sides of each interface are parallel to each other. These observations identify the disruptions as slip interfaces. 2 10,12 2 14,16 Figure 11. 150nm x 150nm STM scan of A-[25 -CC ]2/A-[25 -CC ]2 pair (left) and 80nm x 80nm 2 7,9 2 15,17 STM scan of A-[23 -CC ]2/A-[23 -CC ]2 pair (right). Figure 11 displays two-component monolayers assembled from an "out" diyne pair A-[252-CC10,12]2/A-[252-CC14,16]2 (left) and "in" diyne pair A-[232-CC7,9]2/A-[232- CC15,17]2 (right). The two-component monolayer formed by the "out" diyne pair 144 contains a single domain, with absolutely no column breaks or obvious defects in the 160nm x 160nm STM scan. This contrasts with the multiple column breaks in the smaller scale image of the two-component monolayer assembled by the "in" diyne pair, (four slip interfaces within 80nm x 80nm). These images establish that diyne side chain location has a significant impact on monolayer domain size and defect density. 4.4 Occurrence frequency of different interfaces: a statistical study Section 4.3 introduced the different types of domain interfaces observed in 1,5- alkadiyne substituted anthracene monolayers. Based on the collected data, 120° interfaces and enantiotopic interfaces are found in both "in" and "out" diyne monolayers. Slip interfaces, however, appear to be unique to the monolayers formed by "in" diyne compounds and to be the dominant defects in those monolayers. A semi- quantitative study of domain interface occurrence frequency was performed for A-[232- CC11,13]2 ("in"), A-[252-CC12,14]2 ("out") and A-[292-CC14,16]2 ("out") monolayers. In these experiments, monolayer samples were prepared by the drop casting method. The concentration of the phenyloctane solution (normally between 0.1 - 0.5 mM) were optimized for each compound to get the most extensive monolayer coverage with a minimum of multilayer formation. The drop cast samples were scanned at 20°C at the phenyloctane-HOPG interface. About 30 images of 100nm x 100nm monolayer sections were captured for each type of monolayer[42]. To ensure independence of the monolayer samples, the HOPG substrate was moved slightly after each capture, so that the next scanned region was (at least) a few tens of micrometers away from the prior 145 scanned region. The average density of each interface type (number/104 nm2) is listed in Table 1. Mean number of domain interfaces per 104 nm2 of monolayer Compound slip enantiotopic 120° A-[232-CC11,13]2 8.7 0.7 1.1 A-[252-CC12,14]2 0.0 0.4 1.2 A-[292-CC14,16]2 0.0 0.9 1.1 Table 1. Occurrence frequency for different types of domain interfaces The statistical study confirmed that monolayers assembled from "out" diyne compounds (A-[252-CC12,14]2 and A-[292-CC14,16]2) have significantly longer range order (fewer interfaces) than monolayers assembled from "in" diynes (A-[232-CC11,13]2). For these three systems, the A-[252-CC12,14]2 monolayer has the best overall "self-assembly quality" (1.6 domain interfaces per 104 nm2). The A-[292-CC14,16]2 monolayers contain roughly twice the density of enantiotopic interfaces than found in A-[252-CC12,14]2). Still, A-[292-CC14,16]2 assembles reasonably high quality monolayers, with 2 domain interfaces per 104 nm2. No slip interfaces were found in monolayers from either "out" diyne compound. The "in" diyne compound A-[232-CC11,13]2 assembles much "worse" monolayer with 10.5 domain interfaces per 104 nm2. It is worth noting that 83% of the domain disruptions for A-[232-CC11,13]2 are slip interfaces. The STM study of A-[252-CC12,14]2 monolayer demonstrated that large single domains formed readily without annealing treatment. Figure 12 shows a remarkably large domain observed in an A-[252-CC12,14]2 monolayer. This image was assembled from sixteen 100nm x 100nm STM scans of contiguous regions. The actual relative position of each image is estimated based on the continuity of the domain interfaces. 146 The center region contains a single large domain that spans at least 0.4 m along both unit cell axis directions; parallel and “perpendicular” to the anthracene columns. The domain is terminated by a 120° interface on the left, a 120° interface on the right, and an enantiotopic interface at the lower left corner. The positioning limit of the STM scanner prevented further scans of the region above the top of the image. The anthracene columns near this top region show no signs of discontinuation. It is reasonable to assume that the domain extended beyond the region that was captured. 2 12,14 Figure 12. A large monolayer domain of A-[25 -CC ]2 observed by STM. This image was assembled from sixteen adjacent 100nm x 100nm STM scans. 147 4.5 Proposed model for domain interfaces and energetic simulations The "slip" domain interfaces observed in STM experiment exhibit two distinct features: (i) the anthracene columns within neighboring domain are parallel; (ii) at the interface, every, or every other, anthracene column within one domain aligns collinearly with a diyne column from the adjacent domain. Based on the observed STM alignments, we investigated possible models for molecule stacking at the interfaces and evaluated the energetics for the different interface structures using molecular mechanics simulations. 4.5.1 Tapes assembled by "in" and "out" diyne compounds The two-dimensional monolayers self-assembled by 1,5-disubstituted anthracenes can be envisioned as a stack of numerous one-dimensional tapes (see chapter 2, 2.3). Within a single domain, all pairs of adjacent tapes stack with the same relative alignment. As this tape stacking alignment occurs with high probability, one presumes it affords optimal supramolecular interactions. By contrast, the interfaces between adjacent domains are characterized by lower probability, "improper" stacking (meta-stable) of the tapes constituting the interface. For an "in" diyne compound, e.g. A-[232-CC11,13]2 (Fig. 13), the odd-position diyne groups span the centerline of the molecule (blue dashed line) and place the side chain’s inner and outer alkyl segments on opposite sides of the centerline. This results in an "up-down-up" of zigzag shape of the molecule. 148 Figure 13. The "up-down-up" vertical profile of an "in" diyne compound In contrast, the diyne groups in an "out" diyne compound (A-[252-CC12,14]2) extend away from the centerline and position the outer alkyl segment of the side chain furthest from the centerline, resulting in an "up-up-up" steps shape of the molecule (Figure 14). Figure 14. The "up-up-up" vertical profile of an "out" diyne compound The distinctly different shapes of the "in" and "out" diyne compounds have significant impact on their 1-D tapes' structures. Figures 15 and 16 show examples of the 1-D tapes assembled by A-[232-CC11,13]2 and A-[252-CC12,14]2, respectively. The upper and lower peripheries of two adjacent tapes are indicated by yellow and red lines. The zigzag shape of the "in" diyne compound produces a "triangle-wave" shaped tape periphery (Fig. 15). The alternating bumps and notches yield a slight vertical height modulation along the tape. In the dominant monolayer morphology, the anthracenes’ bumps (~0.5nm in height) within one tape fit into gaps between the terminal methyl groups and anthracenes of an adjacent tape; the bumps and notches generated by the diyne groups (~0.7nm in height) fit into the diyne features within the neighboring tapes. This dominant tape stacking creates anthracene columns and diyne columns within a 149 domain. Figure 15. "Triangle-wave" shaped tape periphery of an "in" diyne compound For an "out" diyne compound A-[252-CC12,14]2 (Figure 16), the tapes have a "square-wave" shaped periphery, with an extended, vertical height modulation along the tape. This dominant tape stacking of “out” diyne compounds produces anthracene columns and diyne columns within a domain. Figure 16. "Square-wave" shaped tape periphery of an "out" diyne compound Figure 17 illustrates various slip displacements along the interface of two neighboring tapes for A-[232-CC11,13]2 (left) and A-[252-CC12,14]2 (right). Traces (red, yellow) of the “slipped” tapes’ peripheries are sketched under the corresponding CPK models. The top image in each column displays the preferred tape stacking alignment, with the presence of uninterrupted anthracene and diyne columns (Fig. 17a and 17d). In the middle images (Fig. 17b and 17e), the lower portion of the monolayer sections has been shifted by about 0.7nm to the right, while maintaining van der Waals contact between the tapes at the interface. For both A-[232-CC11,13]2 and A-[252-CC12,14]2, these slipped stacking alignments establish large vertical separations between large sections of the two interface tapes. An additional 1nm shift to the right of the lower domains (Fig. 17c and 17f), reestablishes close contacts between the tape peripheries of 150 A-[232-CC11,13]2; the anthracene "bumps" of one tape fit into the diyne "notches" of the adjacent tape. In stark contrast, large vertical separations persist for slipped stacking of tapes within the A-[252-CC12,14]2 monolayer. 2 11,13 Figure 17. Tape stacking for different slip displacements for "in" diyne A-[23 -CC ]2 (left, a-c) and 2 12,14 "out" diyne A-[25 -CC ]2 (right, d-f) monolayer sections. The above analysis reveals that the slip interfaces of "in" diyne compounds have their origins in the "triangle-wave" shaped periphery tape of the “in” diyne tapes. The optimal tape stacking fits anthracene "bumps" into methyl-anthracene "notches" and diyne "bumps" into diyne "notches". However, the similarity in shapes and spacings of the two bump/notch features of the tape periphery supports a second pairing of bumps and notches. This second, meta-stable stacking fits anthracene "bumps" into diyne "notches". The resulting "slipped" tape stacking is in good agreement with the STM data, in which the anthracene columns collinearly aligned with diyne columns from adjacent 151 domain. The tape alignment options of the “out” diyne compounds are more constrained. The "out" diyne compounds’ "square-wave" periphery produces only one stacking alignment with extensive tape - tape van der Waals contacts. This inhibits slipping of adjacent tapes and explains the absence of slip domain interfaces within "out" diyne systems. 4.5.2 Evaluation of tape stacking energetics Molecular mechanics simulations were performed to quantify the energies of normal morphology, slip interface and enantiotopic interface tape stacking and domain interfaces. Monolayer sections consisting of four to six 1-D tapes, with four to six molecules per tape, were stacked in a geometry that resembled STM visualized morphologies (i.e. normal, slip or enantiotopic). Molecular mechanics minimizations (HyperChem 8.0) were performed on these monolayer sections in proximity to a single layer graphene sheet 10 - 20% larger than the monolayer section. The x-y planes of molecules were aligned parallel to the graphene sheet, with a starting position close to, but not in contact with, the surface. Prior to the minimization, the atoms in the single layered graphene sheet were set as “fixed atoms” which prevented their moving during the optimization. Atomic charges on atoms of each molecule were assigned using a Mulliken population analysis of AM1 minimized structures. Molecular mechanics minimizations were run until the MM energy of the sample decreased less than 10-4 kcal/mole in 24 hours. The relative stability of the different types of interfaces were assessed based on the self-assembly energies (SAE) of the interfacial molecules. The SAE 152 values were calculated using a method analogous to that described in Chapter 3, section 3.5. 2 12,14 2 11,13 Figure 18. Minimized monolayer sections of A-[25 -CC ]2 (left) and A-[23 CC ]2 (right). (a) A- 2 12,14 2 12,14 2 12,14 [25 -CC ]2 normal morphology; (b) A-[25 -CC ]2 slip interface; (c) A-[25 -CC ]2 enantiotopic 2 11,13 2 11,13 2 11,13 interface; (d) A-[23 CC ]2 normal morphology; (e) A-[23 CC ]2 slip interface; (f) A-[23 CC ]2 enantiotopic interface. Figure 18 displays molecular mechanics minimized monolayer sections of A-[252- CC12,14]2 (left) and A-[232 CC11,13]2 (right). Different tape stackings produce, from top to bottom, normal morphology, slip interface and enantiotopic interface. SAE values were averaged (Table 2) for molecules at the interface of the two interface tapes (but excluding molecules that are on the left or right periphery of the simulations). For A-[232 CC11,13]2, the calculated SAE value for molecules at the slip interface is 1.94 kcal/mole 153 higher than for the normal tape stacking morphology. The relative probability of slip interfaces can be estimated using this energy and the Boltzmann equation, where Nreg and Nslip relate to the surface densities of normal-stacked and slip- stacked tapes, respectively. If one assumes no entropic difference between these two stacking morphologies (i.e. assuming greg = gslip), the equation reduces to where E = SAEreg – SAEslip = -1.94 kcal/mol. At the experimental temperature, T = 293K, this simple calculation predicts Nreg/Nslip  28 or one slip interface for every 29 tapes at equilibrium. This corresponds to one slip interface every 28nm along the anthracene column direction. The statistical study in section 4.4 found 8.7 slip interfaces per 1002 nm2 or an average occurrence of one slip interface every 12 nm along the anthracene columns. The slip interface frequency calculated using molecular mechanics simulation (3.6 per 100nm) is 40% as large as the observed slip interface frequency (8.7 per 100nm). The discrepancy may originate from numerous factors. First, the monolayers assembled by drop casting may not be in thermal equilibrium. Monolayer assembly kinetics may influence the probabilities of different tape stacking arrangements. Our observation that room temperature annealing (days) and thermal annealing (1-2 hours at 35oC) reduces the observed slip interface density, by as much as a factor of 2, suggests that drop casting of A-[232-CC11,13]2 might not produce 154 equilibrated monolayers immediately. Next, the SAE model’s simplicity also contributes to the discrepancy. The model considers molecular interactions within the monolayer, but it completely ignores solvent-monolayer and monolayer-HOPG interactions. Third, our simulations may not reproduce monolayer structures with sufficient accuracy or take into account all slip interface structures. As an example of the latter point, the simulated slip interfaces run parallel to the tapes, whereas some observed slip interfaces align skew to the tapes. The SAE for A-[232-CC11,13]2 at the enantiotopic interface is 2.95 kcal/mole higher than within normally packed domains. At 293 K, the simulation and simplified Boltzmann model predict an enantiotopic interface occurrence frequency of one per every 160 tapes or one every 150nm along the anthracene columns direction. This is in good agreement with the statistical observation of one enantiotopic interface every 140 nm. SAE (kcal/mol) Vertical Extraction Strain Energy (kcal/mol) Energy (kcal/mol) A-[232 CC11,13]2 - normal -27.00 -28.30 1.30 A-[232 CC11,13]2 - slip -25.06 (+1.94) -26.62 1.56 A-[232 CC11,13]2 - enantiotopic -24.05 (+2.95) -25.38 1.33 A-[252-CC12,14]2 - normal -33.72 -34.95 1.23 A-[252-CC12,14]2 - slip -28.35 (+5.37) -30.00 1.65 A-[252-CC12,14]2 - enantiotopic -29.32 (+4.40) -30.42 1.10 A-[292-CC14,16]2 - normal -38.52 -39.89 1.37 A-[292-CC14,16]2 - slip -31.87 (+6.65) -33.08 1.21 A-[292-CC14,16]2 - enantiotopic 1 -29.85 (+8.67) -31.05 1.20 A-[292-CC14,16]2 - enantiotopic 2 -28.97 (+9.55) -30.14 1.17 3 and 4 mixture - normal -30.50 (3) -31.52 (3) 1.02 (3) -30.52 (4) -31.52 (4) 1.00 (4) 3 and 4 mixture - slip -24.74 (3) (+5.76) -25.82 (3) 1.08 (3) -29.69 (4) (+0.83) -30.70 (4) 1.01 (4) Table 2. Molecular mechanics SAE for different types of interfaces. 155 The molecular mechanics SAE values for A-[252-CC12,14]2 indicate a high energetic cost for assembly of slip- and of enantiotopic interfaces. The calculated results and simplified Boltzmann model predict one slip interface every 9μm and one enantiotopic interface every 1.7μm. The predicted low frequency of A-[252-CC12,14]2 slip interfaces agrees with the failure to detect any slip domain interfaces in STM experiments. However, the experimental occurrence frequency of enantiotopic interfaces (one per every 240nm) is about eight times higher than the predicted value. Again, this discrepancy may arise from the simplified SAE model, from inadequate modeling of interface structures and from failure to achieve thermally equilibrated monolayers. A-[252-CC12,14]2 has longer side chains than A-[232-CC11,13]2 and adsorbs more strongly to the HOPG surface. Thus, A-[252-CC12,14]2 will encounter larger kinetic barriers to desorption and higher energy morphologies in drop cast monolayers may be more highly over represented and decay to equilibrium levels more slowly than in A- [232-CC11,13]2 monolayers. 2 14,16 Figure 19. Minimized monolayer sections of A-[29 -CC ]2. (a) normal morphology; (b) slip interface; (c) type 1 enantiotopic interface; (d) type 2 enantiotopic interface. 156 Figure 19 displays minimized monolayer sections (normal, slip and enantiotopic) of A-[292-CC14,16]2. The two types of enantiotopic interfaces (Figure 19c and 19d) are proposed based on actual STM data. As Figure 20 shows, the left image corresponds to type 1 enantiotopic interface in Figure 19c, in which anthracene columns with different enantiotopic faces point to each other at the interface. The right image corresponds to type 2 enantiotopic interface in Figure 19d, in which anthracene columns discontinued at the diyne moieties of the neighboring domain. Figure 20. STM images and their corresponded CPK models of type 1 enantiotopic interface (left) and type 2 enantiotopic interface (right). The calculated SAE values (Table 2) indicate extremely large energetic costs to assemble either the slip (6.7 kcal/mol) or enantiotopic (8.7 kcal/mol and 9.6 kcal/mol) interfaces. The high energy of the slip interface is not inconsistent with the failure to 157 detect this morphology in STM images of A-[292-CC14,16]2. However, the high energy of the enantiotopic interface is not consistent with 0.9 enantiotopic interfaces found per 100nm along the A-[292-CC14,16]2 anthracene columns. It is possible that the huge vacancy at the A-[292-CC14,16]2 enantiotopic interface accommodates and is stabilized by solvent molecules, thus lowering the actual energetic cost. Additionally, the kinetic barriers to equilibration will be larger for A-[292-CC14,16]2 than for A-[252-CC12,16]2 and, in the absence of thermal annealing, may produce a much higher density of interfaces than expected at equilibrium. If this latter explanation is important, it is difficult to understand why slip interfaces are not observed in this system. Figure 21 presents minimized monolayer sections representing normal (21a) and slip (21c) monolayer morphologies for the “in” diyne molecule pair 3 and 4. The simulated slip interface was aligned based on observed STM data (e.g. section 4.3.3 Figure 9), in which anthracene columns containing 4 in one domain align collinearly with every other diyne column across the interface. The tape periphery are presented below each CPK model and based on the stacking between adjacent periphery, the "transition" morphology between normal and slip is proposed in Figure 21b. The SAE values (Table 2) reveal that the slip interface affords 4 only slightly less stabilization, by 0.83kcal/mol, than the normal morphology. However, this tape alignment creates large vacancies adjacent to one side chain of 3, which destabilizes the SAE of 4 by 5.76kcal/mol relative to the normal morphology. For the 1:1 mixed monolayer, the energetic cost to form the slip interface is the average of these two destabilization, 3.3kcal/mol. In qualitative accord with the simulations, the “in”-diyne 158 mixed monolayer of 3 and 4 produced a lower frequency of slip-interfaces than did the “in”-diyne monolayer of A-[232-CC11,13]2. However, the predicted slip-interface frequency for 3 / 4 monolayers (about one slip per every 280nm) was 7-fold smaller than the experimental result (one slip per 40nm; 10 independent STM images). Figure 21. (a) regular morphology; (b) "transition" morphology between normal and slip; (c) slip interface of 3 and 4 mixture 4.6 Defects in S1, S2, D1, D2 four-component system Some atypical defects have been observed in the S1, S2, D1, D2 four-component system. Figure 22 displays two consecutively captured images of the 4-component 159 monolayer[29]. The left image is a Figure 25 from Chapter 3, section 3.4.2. The right image is an STM scan collected immediately after the previous scan. A defect is present in the left most D2 column of the left scan (red oval). Figure 22. Two consecutive STM scans (43nm x 43nm) of S1, S2, D1, D2 four-component monolayer The diyne columns on either side of the defect are intact. The distance between the diynes in D2’s two side chains is 0.3 nm larger than for any of the other molecules (see Figure 24 in Chapter 3, section 3.4.1). Thus, the defect cannot be substitution of D1, S1 or S2 molecules for D2 molecules. The defect appears to be two D2 molecules rotated by 180° relative to an axis normal to the monolayer. This orientation directs D2's [232-CC13,15] chain toward the S2 column (left) and its [272-CC17,19] chain toward the D1 column (right). The diyne kinks in both D2 side chains are equidistant from the chain termini. This maintains collinear alignments within both diyne columns flanking the D2 core. However, the anthracene cores of the two rotated D2 molecules are shifted toward S2 by four CH2 units, or 0.51nm, which is in good agreement with the defect 160 observed in the STM scan. Molecular mechanics minimized models of the defect (left) and the intact monolayer (right) are reproduced in Figure 23. To avoid steric repulsion between the displaced D2 anthracene cores and the side chains of S2, the outer alkyl segments of three adjacent S2 molecules have been flipped into a gauche conformation that extends them away from the anthracene and the graphite). The overall MM energy of the defect monolayer (left) is 11.5 kcal/mole higher than of the intact monolayer energy (right). Figure 23. Minimized monolayer sections of defect morphology (left) and regular morphology (right) Interestingly, the D2 column defect is absent in the next STM scan of the same region (Figure 22, right). As the scans were recorded at the air-HOPG interface, this change could not be attributed to molecule exchange with solution. One possible explanation is that the high energy defect is "repaired" by tip-molecule interaction during the scan. Alternatively, the “dry” monolayer may contain sufficient numbers of mobile (non-imageable) molecules for the tip to promote exchange and repair during scanning. 161 Figure 24. A atypical slip interface in four-component system (top) and its attempt CPK model (bottom) The STM image in Figure 24a is a magnification around white dashed line region of Figure 26 in Chapter 3, 3.5.2[29]. Anthracene columns (“line of dots”) are marked with red (S1), blue (S2), green (D1) and yellow (D2) bars. And the interface is marked with white dashed line aligned from bottom left to top right. The measured angle between anthracene columns and interface is 79°. Interestingly, the columns marked with red and yellow still maintain the collinear alignment when across the interface. In contrast, anthracene columns marked with blue and green exhibit a small shift when across the interface. Table 3 summarizes the patterns of the anthracene columns shifts and column compositions across the interface. Here we assume the bottom domain is fixed and the column shifts are performed by top domain. 162 Table 3. Patterns of anthracene column shifts and column compositions across the interface The pattern in Table 3 reveals that the top domain could be produced by shifting bottom domain to the right with a distance of D2-S2-D2 (pointed by arrows in Table 3). According to the MM minimized unit cell of four-component monolayer, this distance is equal to 7.84nm (see Chapter 3, Section 3.5.1, Figure 24). The attempted CPK model based on this analysis is provided in Figure 24b. The model is generated by shifting upper region of a monolayer section 7.84nm to the right (the shift distance should produce collinearly aligned S1 amd D2 anthracene columns) along the 1-D tape direction. The patterns of anthracene columns shifts and column compositions match perfectly with the STM image. The model also demonstrates that the 79° angle between interface and anthracene columns is originated from the expansion direction of the 1-D tape (83° to the anthracene columns). Since the interface is generated by domain shift along the 1-D tape, the defect could be considered as an "atypical" slip interface in the four- component monolayer. 4.7 Conclusion Conjugated diyne ‘‘kinks’’ functioned as shape-based molecular recognition elements in directing single- and multi-component self-assembly 1,5-substituted anthracene derivatives. Diyne “kinks” incorporated at even side chain positions 163 produces "out" type 1,5-alkadiyne substituted anthracene derivatives (A-[252-CC12,14]2, A-[292-CC14,16]2, A-[252-CC10,12]2 and A-[252-CC14,16]2) by bending the outer part of side chain away from the anthracene center of symmetry. Diyne “kinks” incorporated at odd side chain positions produces "in" type 1,5-alkadiyne substituted anthracene derivatives (A-[232-CC11,13]2, A-[232-CC7,9]2, A-[232-CC15,17]2, A-[312-CC13,15]2, A-[272- CC9,11]2, A-[312-CC17,19][232-CC9,11] and A-[272-CC17,19]-[232-CC13,15]) by bending the outer part of side chain toward the anthracene center of symmetry. This subtle difference of odd versus even diyne position exerts large impacts on the domain size and defect density within the resulting self-assembled monolayers. "Out" diyne derivatives readily assemble monolayers with large domain sizes that could cover up to 1 µm2. By contrast, monolayers assembled from "in" diyne derivatives exhibits high occurrence frequency of slip interfaces that disrupt the anthracene columns. 1-D tape periphery analysis and molecular mechanics simulation studies revealed that the slip interfaces of "in" diyne monolayers are generated by meta-stable stacking of 1-D tapes that fits anthracene "bumps" into diyne "notches". This correlation between molecular shape and monolayer defect density may serve as a useful guide in improving self- assembly quality of the monolayers. 164 References [1] J. Collet, O. Tharaud, A. Chapoton, D. Vuillaume, Appl Phys Lett 2000, 76, 1941. [2] I. Kymissis, C. D. Dimitrakopoulos, S. Purushothaman, Ieee Transactions on Electron Devices 2001, 48, 1060. [3] A. Salleo, M. L. Chabinyc, M. S. Yang, R. A. Street, Appl Phys Lett 2002, 81, 4383. [4] M. Halik, H. Klauk, U. Zschieschang, G. Schmid, S. Ponomarenko, S. Kirchmeyer, W. Weber, Adv Mater 2003, 15, 917. [5] T. Kawase, T. Shimoda, C. Newsome, H. 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Work-up (the following procedure must be carried out in a well-functioning hood with extreme caution): The mixture was cooled with ice-bath. The dark brown precipitate was collected by filtration and was washed with benzene. The filtrate was air-dried and then was boiled with HNO3 (6N, 150mL). The solution was cooled to room temperature and was diluted with water. The crude product was used for the next step without purification. 168 Preparation of anthraquinone-1,5-dicarboxylic acid: Crude 1,5- dicyanoanthraquinone (5.0g) and concentrated sulfuric acid (70mL) were added to a 250mL two-neck flask at 0°C. Then ice-cold water (12mL) was slowly added to the flask. A thermometer was inserted into the flask to monitor the temperature. The mixture was stirred at 165°C for 1.5 hours and then was cooled to room temperature. Work-up: The mixture was cooled with ice-bath and diluted with ice-cold water (700mL). The light brown precipitate was collected by filtration and then dissolved with 15% NaHCO3, solution. The insoluble impurities were get rid of by filtration. HCl (6N) was added dropwise to the solution until the solution turned acidic. The crude product was collected by filtration and washed with water. The product (light brown solid) was then dried in an 80°C oven and was used for the next step without purification. Preparation of anthracene-1,5-dicarboxylic acid: The crude anthraquinone-1,5- dicarboxylic acid (5.0g) and 170mL of 20% NH4OH were added into a 500mL flask with stir. The di-acid dissolved and formed a reddish-brown solution. Zinc powder (11.0g, 168mmol) was added to the solution and the mixture was refluxed until the red color discharged (7 hours). Work-up: The mixture was cooled to room temperature and was filtered to get rid of the zinc powder. Glacial acetic acid was added to the filtered solution until the 169 solution turned acid. The crude product (yellow precipitate) was collected by filtration and was washed with water. The product (yellow solid) was then dried in an 80°C oven and was used for the next step without purification. Preparation of dimethyl anthracene-1,5-dicarboxylate: KOH pellets (2.7g, 48mmol) were crushed into fine powders and were added into a flask containing 100mL dimethyl sulfoxide. The solution was stirred for 30 minutes and crude anthracene-1,5- dicarboxylic acid (4.2g) was added into the flask. The mixture was stirred for 15 minutes and iodomethane (3.0 mL, 48mmol) was added dropwise. The reaction mixture was then stirred overnight. Work-up and purification: The reaction mixture was poured into ice-water (1L in total). Orange solid was crushed out and was collected by filtration. The filtrate (crude product) was washed with water and air dried. The crude product was purified by double recrystallization with ethyl acetate and then with benzene, affording 3.1g of pure dimethyl anthracene-1,5-dicarboxylate (yellow, needle like crystals, 10mmol, yield over 4 steps: 45%). 1H‐NMR (300MHz, CDCl3): δ 9.66 (s, 2H), 8.30 (m, 4H), 7.55 (dd, 2H, J = 8.2 and 7.0Hz), 4.06 (s, 6H). 170 Preparation of anthracene-1,5-diyldimethanol: Lithium aluminum hydride (0.9g, 24mmol) and THF (250mL from a newly opened bottle) were added to a 500mL flame- dried flask under nitrogen atmosphere. The flask was cooled to 0°C with ice bath and stirred for 40 minutes. Dimethyl anthracene-1,5-dicarboxylate solid (1.1g, 3.8mmol) was added slowly into the flask. The reaction mixture was stirred for 6 hours (0°C to room temperature). Work-up and purification: The reaction mixture was cooled to 0°C with ice bath. 0.9mL ice-cold water was added to the mixture dropwise, followed by addition of 0.9mL 15% NaOH solution and 2.7mL of ice-cold water. The mixture was warmed up to room temperature with rapid stirring and was diluted with 100mL THF. The solid precipitate was filtered and the solvent (THF) was removed under reduced pressure using a rotary evaporator. To extract the solid within the filtrate, all solid filtrate was transferred into a Soxhlet extractor and was reflux with toluene for 12 hours. The combined product from solution and filtrate afforded 0.83g (almost pure) anthracene-1,5-diyldimethanol (pale yellow solid, 3.5mmol, yield: 92%). 1H‐NMR (300MHz, DMSO): δ 8.70 (s, 2H), 8.03 (d, 2H, J = 8.1Hz), 7.56 (d, 2H, J = 5.6Hz), 7.47 (dd, 2H, J = 8.0 and 7.0Hz), 5.38 (t, 2H, J = 5.6Hz), 5.10 (d, 4H, J = 5.6Hz). 171 Preparation of 1,5-bis(chloromethyl)anthracene: Benzene (200mL) and anthracene‐1,5‐diyldimethanol (0.77g, 3.2mmol) was added to a 500mL two-neck, flame-dried flask. The mixture was stirred and thionyl chloride (24ml, 329mmol) was added to the flask by syringe. The reaction mixture was refluxed under nitrogen for 7.5 hours. Work-up and purification: The reaction mixture was cooled to room temperature. The solvent was removed under reduced pressure using a rotary evaporator. The crude product was purified by recrystallization with benzene, affording 0.65g pure 1,5- bis(chloromethyl)anthracene (yellow, needle like crystal, 2.4mmol, yield: 75%). 1H‐NMR (300MHz, CDCl3): δ 8.77 (s, 2H), 8.12 (d, 2H, J = 9.0Hz), 7.59 (d, 2H, J = 6.0Hz), 7.48 (dd, 2H, J = 8.0 and 7.0Hz), 5.20 (s, 4H). 172 5.2 Syntheses of CF2 derivatives Scheme 1. Synthetic scheme for A-[172-F10,10]2: 173 Preparation of (((7-bromoheptyl)oxy)methyl)benzene: Benzyl alcohol (1.30ml, 12.6mmol) was added to a flame‐dried flask containing DMF (12ml) under nitrogen. Sodium hydride (60% dispersion in oil, 604.3mg, 20.2mmol) was added to the mixture with continuous stirring. A solution of 1,7-dibromoheptane (4.3ml, 25mmol) in DMF was added dropwise and the mixture was stirred for one day. Work-up and purification: The reaction was quenched by adding 2.5% HCl until acidic. The mixture was extracted with Et2O. The organic layer was washed with 5% HCl, water, brine and dried with anhydrous sodium sulfate. The resulting solution was filtered and concentrated under reduced pressure. The crude product was purified by flash chromatography (50% DCM/Hexane), affording 1.69g pure (((7- bromoheptyl)oxy)methyl)benzene (5.9mmol, yield: 47%) 1 H NMR (400MHz, CDCl3): δ 7.33 (m, 5H), 4.54 (s, 2H), 3.51 (t, 2H, J=6.4Hz), 3.43 (t, 2H, J=6.8Hz), 1.89 (m, 2H), 1.62 (m, 4H), 1.46 (m, 4H). Preparation of 8-(benzyloxy)octanenitrile: (((7- bromoheptyl)oxy)methyl)benzene (1.69g, 5.9mmol) was added to a flame-dried flask containing DMF (20ml) under nitrogen. Potassium cyanide (0.65g, 10 mmol) was immediately added and the mixture was stirred for one day. Work-up and purification: Saturated sodium carbonate solution was added to the reaction mixture. The mixture was extracted with Et2O. The organic layer was washed with saturated sodium bicarbonate solution three times, then with water, brine 174 and dried with anhydrous sodium sulfate (all aqueous layers were collected in a dedicated cyanide waste container). The resulting solution was filtered and concentrated under reduced pressure. The crude product was purified by flash chromatography (40% DCM/Hexane), affording 1.11g pure 8-(benzyloxy)octanenitrile (4.8mmol, yield: 81%) 1 H NMR (300MHz, CDCl3): δ 7.32 (m, 5H), 4.52 (s, 2H), 3.49 (t, 2H, J=6.6Hz), 2.34 (t, 2H, J=7.0Hz), 1.64 (m, 6H), 1.45 (m, 4H). Preparation of (((8,8-difluoropentadecyl)oxy)methyl)benzene Preparation of Grignard reagent BrMg(CH2)6CH3: Magnesium turnings (1.11g, 46.3mmol) were added to a microwave tube. The tube was sealed, degassed and refilled with nitrogen. A solution of 1-bromoheptane (2.4ml, 15 mmol) in Et2O (5ml) was added by syringe. Any immediate pressure built up was released. The tube was placed into a microwave reactor (Smith Creator) at 120°C for 1 hour to induce Grigard formation (the solution turned dark after irradiation). Grignard reaction with nitrile: A solution of 8-(benzyloxy)octanenitrile (1.11g, 4.8mmol) in Et2O (20ml) was added into a flame-dried two-neck flask and cooled to 0°C. The previously prepared Grignard reagent was added to the flask by syringe. After complete addition, the mixture was stirred and heated at reflux for 5 hours then cooled to room temperature. The reaction was quenched by adding 2.5% HCl and the mixture was stirred overnight to let hydrolysis complete. 175 Work-up and purification: The mixture was extracted with Et2O. The organic layer was washed with 5% HCl, water, brine and then dried with anhydrous sodium sulfate. The resulting solution was filtered and concentrated under reduced pressure. The crude product was purified by flash chromatography (20% Hexane/DCM), affording 1.00g pure 1-(benzyloxy)pentadecan-8-one (3.0mmol, yield: 63%). 1 H NMR (400MHz, CDCl3): δ 7.32 (m, 5H), 4.52 (s, 2H), 3.49 (t, 2H, J=6.4Hz), 2.40 (t, 4H, J=7.4Hz), 1.65 (m, 6H), 1.30 (m, 14H), 0.91 (t, 3H, J=6.4Hz). Preparation of (((8,8-difluoropentadecyl)oxy)methyl)benzene: 1- (benzyloxy)pentadecan-8-one (1.00g, 3.0mmol), Deoxo‐Fluor® (50% in THF, 7ml) and dry DCM (10ml) were added to a Teflon flask. A few drops of methanol were added to the mixture. The Teflon flask was sealed immediately in the bomb and put into a 100°C oven for two days. Work-up and purification: The reaction mixture was poured into saturated sodium carbonate solution. The mixture was extracted with DCM. The organic layer was washed with saturated sodium carbonate solution and with saturated nickel (II) chloride solution to remove the sulfur impurities generated by the Deoxo‐Fluor® reaction. The organic layer was washed with water and brine and then dried with anhydrous sodium sulfate. The resulting solution was filtered and concentrated under reduced pressure. The crude product was purified by flash chromatography (30% DCM/Hexane) affording 0.46g pure (((8,8-difluoropentadecyl)oxy)methyl)benzene (1.3mmol, yield: 43%). 176 1 H NMR (400MHz, CDCl3): δ 7.36 (m, 5H), 4.58 (s, 2H), 3.55 (t, 2H, J=6.4Hz), 1.87 (m, 4H), 1.71 (m, 2H), 1.41 (m, 18H), 0.98 (t, 3H, J=6.6Hz). 13 C NMR (100MHz, CDCl3): δ 139.19, 128.77, 128.03, 127.90, 125.78 (t, 1 JCF=239.0Hz), 73.31, 70.83, 36.81(t, 2JCF=24.5Hz), 36.78(t, 2JCF=25.0Hz), 32.21, 30.21, 29.89, 29.86, 29.73, 29.59, 26.56, 23.13, 22.85 (t, 3JCF=5.0Hz), 22.80 (t, 3JCF=5.0Hz), 14.56. Preparation of 8,8-difluoropentadecan-1-ol: Pd/C (10%, 0.21g) and (((8,8- difluoropentadecyl)oxy)methyl)benzene (0.46g, 1.3mmol) were added to the reaction bottle with ethanol (100ml). The bottle was sealed, degassed and refilled with hydrogen (50psi). The mixture was shaken for 3 days. Work-up and purification: The reaction mixture was filtered thru Celite® 521 and concentrated under reduced pressure. The crude product was purified by flash chromatography (100% DCM) affording 0.23g pure 8,8-difluoropentadecan-1-ol (0.86mmol, yield: 66%) 1 H NMR (300MHz, CDCl3): δ 3.64 (t, 2H, J=7.5Hz), 1.71 (m, 6H), 1.35 (m, 18H), 0.89 (t, 3H, J=6.0Hz). 13 C NMR (75MHz, CDCl3): δ 125.39 (t, 1JCF=239.0Hz), 62.88, 36.32 (t, 2JCF=25.0Hz), 36.26 (t, 2JCF=25.0Hz), 32.68, 31.68, 29.36, 29.18, 29.05, 25.58, 22.59, 22.41, 22.33, 22.27, 14.02. 177 Preparation of 1,5-bis(((8,8-difluoropentadecyl)oxy)methyl)anthracene (A-[172- F10,10]2): Sodium hydride (60% dispersion in oil, 0.051g, 0.96mmol) and 8,8- difluoropentadecan1-ol (0.23g, 0.86mmol) were added to a microwave tube. The tube was sealed, degassed and refilled with nitrogen. THF (3ml) was added by syringe to the tube. Any immediate pressure build up was released. The tube was placed into a microwave reactor (Smith Creator) at 120°C for 40 minutes. A solution of 1,5-- bis(chloromethyl)anthracene (0.053g 0.21mmol) in THF (2ml) was added by syringe to the tube. The tube was placed in the Smith Creator at 130°C for four hours. Work-up and purification: 2.5% HCl was added to reaction mixture until acidic. The mixture was extracted with Et2O. The organic layer was washed with water, brine and dried with anhydrous sodium sulfate. The resulting solution was filtered and concentrated under reduced pressure. The crude product was purified by flash chromatography (40% DCM/Hexane), affording 0.10g pure 1,5-bis(((8,8- difluoropentadecyl)oxy)methyl)anthracene (0.14mmol, yield: 65%). A-[172-F10,10]2 Spectral Data: 1 H NMR (400MHz, CDCl3): δ 8.73 (s, 2H), 8.03 (d, 2H, J=8.2Hz), 7.52 (d, 2H, J=6.2Hz), 7.44 (dd, 2H, J=6.8 and 6.8Hz), 5.10 (s, 4H), 3.61 (t, 4H, J=6.4 Hz), 1.72 (m, 8H), 1.31 (m, 40H), 0.92 (t, 6H, J=6.8Hz). 13 C NMR (100MHz, CDCl3): δ 133.91, 132.06, 129.79, 129.26, 125.74, 125.46 (t, 1 JCF=238.0 Hz), 124.77, 123.54, 71.73, 70.37, 36.30 (t, 2JCF=25.0 Hz), 36.26 (t, 2JCF=25.0 178 Hz), 31.70, 29.78, 29.72, 29.38, 29.22, 29.08, 26.16, 22.63, 22.35 (t, 3JCF=4.5 Hz), 22.30 (t, 3 JCF=5.0 Hz), 14.09. m/s (FAB) m/z Calcd for M+ (C46H70F4O2) 730.5, found 730.7; (M+Na)+ (C46H70F4O2Na) 753.5, found 753.7. HRMS Calcd for (M+Na)+ 753.5210, found 753.5225. A-[172-F9,9]2, A-[152-F9,9]2 and A-[152-F8,8]2 were prepared using similar procedures. Their spectral data are provided below: A-[172-F9,9]2 Spectral Data: 1 H NMR (400MHz, CDCl3): δ 8.73 (s, 2H), 8.02 (d, 2H, J=8.4Hz), 7.51 (d, 2H, J=6.4Hz), 7.44 (dd, 2H, J=7.2 and 6.4Hz), 5.10 (s, 4H), 3.62 (t, 4H, J=6.2 Hz), 1.71 (m, 8H), 1.35 (m, 40H), 0.91 (t, 6H, J=6.8Hz). 13 C NMR (100MHz, CDCl3): δ 133.89, 132.04, 129.81, 129.23, 125.70, 125.45 (t, 1 JCF=238.0 Hz), 124.75, 123.55, 71.75, 70.35, 36.33 (t, 2JCF=25.0 Hz), 36.28 (t, 2JCF=25.0 Hz), 31.62, 29.84, 29.75, 29.33, 29.20, 29.11, 26.24, 22.53, 22.36 (t, 3JCF=6.0 Hz), 22.29 (t, 3 JCF=5.5 Hz), 14.15. m/s (FAB) m/z Calcd for M+ (C46H70F4O2) 730.5, not found; (M+Na)+ (C46H70F4O2Na) 753.5, found 753.5. HRMS Calcd for (M+Na)+ 753.5210, not found. 179 A-[152-F9,9]2 Spectral Data: 1 H NMR (400MHz, CDCl3): δ 8.72 (s, 2H), 8.03 (d, 2H, J=8.2Hz), 7.53 (d, 2H, J=6.4Hz), 7.45 (dd, 2H, J=6.8 and 6.6Hz), 5.10 (s, 4H), 3.61 (t, 4H, J=6.4 Hz), 1.71 (m, 8H), 1.33 (m, 32H), 0.89 (t, 6H, J=6.6Hz). 13 C NMR (100MHz, CDCl3): δ 133.86, 132.05, 129.78, 129.28, 125.80, 125.43 (t, 1 JCF=239.0 Hz), 124.80, 123.54, 71.76, 70.30, 36.28 (t, 2JCF=26.0 Hz), 36.19 (t, 2JCF=25.0 Hz), 31.60, 29.69, 29.21, 29.08, 26.12, 22.52, 22.33 (t, 3JCF=5.0 Hz), 22.29 (t, 3JCF=4.5 Hz), 14.09. m/s (FAB) m/z Calcd for M+ (C42H62F4O2) 674.5, found 674.4; (M+Na)+ (C42H62F4O2Na) 697.5, found 697.4. HRMS Calcd for (M+Na)+ 697.4584, found 697.4568. A-[152-F8,8]2 Spectral Data: 1 H NMR (400MHz, CDCl3): δ 8.73 (s, 2H), 8.02 (d, 2H, J=8.0Hz), 7.52 (d, 2H, J=6.4Hz), 7.44 (dd, 2H, J=7.2 and 6.8Hz), 5.10 (s, 4H), 3.62 (t, 4H, J=6.4 Hz), 1.73 (m, 8H), 1.33 (m, 32H), 0.91 (t, 6H, J=6.8Hz). 13 C NMR (100MHz, CDCl3): δ 133.85, 132.01, 129.83, 129.27, 125.70, 125.50 (t, 1 JCF=240.0 Hz), 124.77, 123.56, 71.77, 70.34, 36.30 (t, 2JCF=25.0 Hz), 36.22 (t, 2JCF=25.0 Hz), 31.63, 29.84, 29.70, 29.35, 26.25, 22.74, 22.37 (t, 3JCF=5.0 Hz), 22.26 (t, 3JCF=5.5 Hz), 14.12. m/s (FAB) m/z Calcd for M+ (C42H62F4O2) 674.5, found 675.1; (M+Na)+ (C42H62F4O2Na) 697.5, found 698.1. HRMS Calcd for (M+Na)+ 697.4584, found 697.4565. 180 5.3 Syntheses of ketone derivatives The following syntheses of ketone derivatives are performed by Ms. Min Kyoung Kim Scheme 2. Synthetic scheme for A-[172-C=O9,9]2: 181 Preparation of 7-(benzyloxy)heptanal Preparation of 7-(benzyloxy)heptan-1-ol: 1,7-heptane-diol (5.0g, 37.8mmol) was added to a flame-dried flask, followed by 20mL of dry THF under nitrogen with magnetic stirring. The solution was cooled down to 0°C, and sodium hydride (0.97g, 40.6mmol) was added 10mL of dry DMF was then added. After one hour of equilibration, benzyl bromide (4.0mL, 33.8mmol) was added at 0°C. The solution was stirred at room temperature for 18 hours. Work-up: 2.5% HCl was added until the mixture turned acidic. The crude product was extracted using ethyl acetate (3 X 30 mL). The organic layer was washed with 2.5% HCl, water, brine and then dried over sodium sulfate. The solvent was removed under reduced pressure using a rotary evaporator. The crude product was used for the next step without purification. Preparation of 7-(benzyloxy)heptanal: Crude 7-(benzyloxy)heptan-1-ol (4.89g) and TEMPO (45mg, 0.29mmol) were dissolved in methylene chloride. The solution was cooled down to 0°C, and potassium bromide (0.26g, 2.2mmol) was dissolved in 1mL water and then was added to the reaction flask. The reaction mixture was stirred at 0°C for 5 minutes, then 1M NaClO solution (22mL, pH~8; pH adjustment with NaHCO3) was added dropwise. Then the solution was stirred at room temperature for 10 minutes. Work-up and purification: The reaction was quenched with 0.5M HCl. The crude product was extracted using methylene chloride (3 X 30 mL). The organic layer was washed with 0.5M HCl, water, brine and then dried over sodium sulfate. The solvent 182 was removed under reduced pressure using a rotary evaporator. The crude product was purified by flash column chromatography (10% ethyl acetate/90% hexanes), affording 2.36g of 7-(benzyloxy)heptanal (colorless liquid, 10.7mol, yield over two steps: 32%). This compound was reported previously[1-3]. Preparation of 6-(2-octyl-1,3-dioxolan-2-yl)hexan-1-ol Preparation of Grignard reagent: Magnesium turnings (1.64g, 68mmol) and a magnetic stir bar were placed in a dry 20-mL microwave tube, which was sealed after the addition. The microwave tube was then dried over vacuum for one hour then charged with nitrogen. 1-bromooctane (3.74mL, 21.7mmol) was added at 0°C, followed by 10mL of dry diethyl ether. The mixture was stirred at 0°C for about 5 minutes and then was stirred at room temperature until the solution turned dark. Then the tube was placed in a microwave reactor at 100°C for 1 hour. Preparation of 1-(benzyloxy)pentadecan-7-ol:7-(benzyloxy)heptanal (2.36g, 10.7mmol) was added to a flame-dried two-neck flask with a water condenser under nitrogen. The freshly prepared grignard reagent was added to the flask at 0°C followed by20mL of dry diethyl ether. The solution was refluxed for 5 hours. Work-up: The reaction was quenched by adding 2.5% HCl (15mL). The crude product was extracted using methylene chloride (3 X 30 mL). The organic layer was washed with 2.5% HCl, water, brine and then dried over sodium sulfate. The solvent was removed under reduced pressure using a rotary evaporator. The crude product was used for the next step without purification. 183 Preparation of 1-(benzyloxy)pentadecan-7-one: Crude 1- (benzyloxy)pentadecan-7-ol (4.0g) and TEMPO (24mg, 0.16 mmol) were dissolved in methylene chloride. The solution was cooled down to 0°C, and potassium bromide (0.14g, 1.2mmol) was dissolved in 1mL water and then was added to the reaction flask. The reaction mixture was stirred at 0°C for 5 minutes, then 1M NaClO solution (18mL, pH~8; pH adjustment with NaHCO3) was added dropwise. The reaction mixture was stirred at room temperature for 30 minutes. Work-up: The reaction was quenched by adding 0.5M HCl. The crude product was extracted using methylene chloride (3 X 30 mL). The organic layer was washed with 0.5M HCl, 0.1M NaI solution, saturated Na2S2O3 solution, water and brine then dried over sodium sulfate. The solvent was removed under reduced pressure using a rotary evaporator. The crude product was used for the next step without purification. Preparation of 1-hydroxypentadecan-7-one : 0.27g palladium/carbon powder and a stir bar were placed in a round-bottom flask. The flask was flushed with nitrogen for 10 minutes then 120mL of ethanol and crude 1-(benzyloxy)pentadecan-7-one (3.0g) was added. The reaction mixture was then charged with a hydrogen balloon and stirred at room temperature for 20 hours. The palladium/carbon was then filtered out using celite. The solvent was removed under reduced pressure using a rotary evaporator. The crude product was used for the next step without purification. Preparation of 6-(2-octyl-1,3-dioxolan-2-yl)hexan-1-ol: Crude 1- hydroxypentadecan-7-one (4.0g), p-toluenesulfonic acid (0.23g, 1.2mmol), ethylene 184 glycol (2.2mL, 0.40mol), benzene (140mL) were placed in a round-bottom flask. The reaction mixture was refluxed for 20 hours with a Dean-Stark trap. Work-up and purification: The reaction mixture was extracted using ethyl acetate (3 X 30 mL). The organic layer was washed with saturated NaHCO3 solution, water and brine then dried over sodium sulfate. The solvent was removed under reduced pressure using a rotary evaporator. The crude product was purified by flash column chromatography (20/80 ethyl acetate/hexanes then 30/ 70 ethyl acetate in hexanes), affording 1.72g pure 6-(2-octyl-1,3-dioxolan-2-yl)hexan-1-ol (white solid, 6.0mmol, yield over 4 steps: 56%) 1 H NMR (300MHz, CDCl3): δ 3.89 (s, 4H), 3.59 (t, J=7.5Hz, 2H), 1.53 (m, 6H), 1.30 (m, 18H), 0.85 (t, J=6Hz, 3H). 13 C NMR (75 MHz, CDCl3): δ 111.84, 64.82, 63.12, 62.77, 37.10, 36.98, 32.64, 32.48, 31.83, 29.90, 29.65, 29.53, 29.21, 25.67, 23.81, 23.73, 14.04. Preparation of 1,1'-((anthracene-1,5- diylbis(methylene))bis(oxy))bis(pentadecan-7-one) (i.e. A-[172-C=O9,9]2) Step 1: Sodium hydride (19mg, 0.80mmol) was added to a flame-dried microwave tube under argon atmosphere. 6-(2-octyl-1,3-dioxolan-2-yl)hexan-1-ol (0.20g, 0.69mmol) was dissolved in 6mL dry THF and was added into the microwave tube using a syringe. Then the tube was placed in a microwave reactor at 130°C for 1 hour. 1,5- bis(chloromethyl)anthracene (50mg, 0.18mmol) was dissolved in 2mL of dry THF and 185 was added to the mixture. The reaction mixture was placed in the microwave reactor at 130°C for 5 hours. The reaction mixture was quenched with water and was extracted using methylene chloride (3 X 15mL). The organic layer was washed with 0.5M HCl, water, and brine. The solvent was removed under reduced pressure using a rotary evaporator. Step 2: The resulting crude product (0.25g) was placed in a round-bottom flask with 4.3mg pyridinium p-toluenesulfonate, 9mL acetone and 1mL of water. The reaction mixture was refluxed for 3 hours. Work-up and purification: Acetone was evaporated under reduced pressure using a rotary evaporator. 40mL of methylene chloride was used to extract the crude product. The organic layer was then washed with water, saturated NaHCO3 solution, and brine. The solvent was removed under reduced pressure using a rotary evaporator. The crude product was purified by flash column chromatography (100% methylene chloride then 95/5 methylene chloride/ethyl acetate), affording 15mg pure 1,1'-((anthracene- 1,5-diylbis(methylene))bis(oxy))bis(pentadecan-7-one) (yellow solid, 0.022mmol, yield over two steps: 11%) 1 H NMR (300MHz, CDCl3): δ 8.73 (s, 2H), 8.02 (d, J=6Hz, 2H), 7.54 (d, J=6Hz, 2H), 7.45 (dd, J=6Hz and 5Hz, 2H), 5.10 (s, 4H), 3.62 (t, J=6Hz, 4H), 2.37 (m, 8H), 1.64 (m, 8H), 1.40 (m, 32H), 0.89 (t, J=6Hz, 6H). 186 13 C NMR (75 MHz, CDCl3): δ 210.55, 134.02, 132.05, 129.89, 128.95, 125.70, 124.53, 122.97, 71.70, 70.35, 43.01, 42.96, 32.24, 30.03, 29.80, 29.55, 29.24, 29.14, 26.11, 23.95, 23.69, 22.76, 15.01. m/s (FAB) m/z Calcd for (M+Na)+ (C46H70O4Na) 709.5, found 709.2. A-[172-C=O10,10]2 was synthesized using similar procedure, the spectral data are listed below: 1,1'-((anthracene-1,5-diylbis(methylene))bis(oxy))bis(pentadecan-8-one): 1 H NMR (300MHz, CDCl3): δ 8.72 (s, 2H), 8.03 (d, J=9Hz, 2H), 7.52 (d, J=6Hz, 2H), 7.47 (dd, J=6Hz and 6Hz, 2H), 5.09 (s, 4H), 3.60 (t, J=6Hz, 4H), 2.35 (m, 8H), 1.64 (m, 8H), 1.35 (m, 32H), 0.89 (t, J=6Hz, 6H). 13 C NMR (75 MHz, CDCl3): δ 211.73, 133.89, 132.04, 129.77, 129.26, 125.73, 124.76, 123.52, 71.71, 70.41, 42.82, 42.75, 31.69, 29.76, 29.23, 29.19, 29.10, 26.13, 23.89, 23.79, 22.62, 14.09. m/s (FAB) m/z Calcd for (M+Na)+ (C46H70O4Na) 709.5, found 709.5. 187 5.4 Syntheses of diyne derivatives 5.4.1 Syntheses of symmetrically substituted 1,5-anthracene derivatives A-[252- C≡C12,14]2, A-[252-C≡C10,12]2, A-[252-C≡C14,16]2, A-[242-C≡C12,14]2, A-[232-C≡C11,13]2, A-[232- C≡C7,9]2, A-[232-C≡C15,17]2 and A-[292-C≡C14,16]2. Scheme 3. Synthetic scheme for A-[252-C≡C12,14]2: 188 Preparation of undec-2-yn-1-ol: Propargyl alcohol (0.9 mL, 15.5 mmol) was added to a flame-dried flask containing THF (25 mL) and HMPA (10 mL, 60 mmol). The solution was cooled to -78°C under argon atmosphere and magnetic stirring. n-butyl lithium (13.5 mL of 2.3M solution in hexane, 31 mmol) was added to the flask by syringe. The temperature was raised to -30°C and maintained for 45 mins. 1-bromooctane (2.7mL, 15.7 mmol) was added dropwise at -30°C. The solution was then stirred at room temperature for 15 hrs. Work-up and purification: The reaction was quenched by adding satured NH4Cl aqueous solution (25 mL). The mixture was extracted with EA (3 X 30 mL). The organic layer was wash with water, brine then dried over MgSO4. The solvent removed under reduced pressure using a rotary evaporator. The crude product was purified by flash column chromatography (8% EA/hexanes then 15EA/hexanes) afforded pure undec-2- yn-1-ol 1.59g (9.5mmol, yield: 61%). 1 H NMR (300MHz, CDCl3): δ 4.26 (s, 2H), 2.22 (t, J=7.5Hz, 2H), 1.77 (s, 1H), 1.51 (m, 2H), 1.34 (m, 10H), 0.89 (t, J=6.0Hz, 3H). Preparation of undec-10-yn-1-ol (acetylene zipper reaction): 1,3- diaminopropane (25 mL) was added to a flame-dried two-neck flask under argon by syringe. Lithium (0.35g, 50 mmol) was added to the flask and the mixture (a dark blue solution) was heated and stirred in an oil bath at 70°C. After stir for 3 hrs the blue color discharged and a milky white suspension was formed. The mixture was cooled to room 189 temperature and potassium tert-butoxide (3.36 g, 30 mmol) was added all at once, affording a yellow solution. After stirring for 15 mins undec-2-yn-1-ol (1.26 g, 7.5 mmol) was added in one portion. The reaction was stirred for 10hrs at room temperature. Work-up and purification: The mixture was poured into ice-water (100mL) then extract with EA (3 X 50mL). The organic layer was washed with 0.5M HCl solution, water, brine then dried with MgSO4. The solvent was removed under reduced pressure and the crude product was purified by flash column chromatography (25% EA/hexanes) afforded pure undec-10-yn-1-ol 1.15g (6.8 mmol, yield: 91%). 1 H NMR (400MHz, CDCl3): δ 3.66 (t, J=6.6Hz, 2H), 2.20 (td, J=7.2Hz and 2.5Hz, 2H), 1.96 (t, J=2.6Hz, 1H), 1.56 (m, 4H), 1.38 (m, 10H). Preparation of 1,5-bis((undec-10-yn-1-yloxy)methyl)anthracene: Undec-10-yn- 1-ol (0.25g, 1.5mmol) was added to a flame-dried two-neck flask containing 1:1 DMF:THF solution (5mL) under nitrogen. The solution was cooled to 0°C with magnetic stirring and sodium hydride was added all at once. After stirring for 10 mins, 1,5-- bis(chloromethyl)anthracene (0.12g 0.44mmol) was added in once portion (0°C). The mixture was then stirred at room temperature for 15 hrs. Work-up and purification: The reaction was quenched by slowly adding ice-water. The mixture was then extract with DCM (3 X 20mL). The organic layer was washed with 0.5M HCl solution, water, brine then dried with MgSO4. The solvent was removed under reduced pressure and the crude product was purified by flash column chromatography 190 (40% DCM/hexanes) afforded pure 1,5-bis((undec-10-yn-1-yloxy)methyl)anthracene 0.12g (0.23 mmol, yield: 52%). 1 H NMR (300MHz, CDCl3): δ 8.72 (s, 2H), 8.03 (d, J=6.0Hz, 2H), 7.52 (d, J=6.0Hz, 2H), 7.44 (dd, J=9.0Hz and 6.0Hz, 2H), 5.09 (s, 4H), 3.61 (t, J=7.5Hz, 4H), 2.16 (td, J=7.5Hz and 3.0Hz, 4H), 1.94 (t, J=3.0Hz, 2H), 1.68 (m, 4H), 1.47 (m, 24H). Preparation of 1-iodododec-1-yne: 1-dodecyne (1.1mL, 5 mmol) was added to a flame-dried two-neck flask containing THF (10 mL) under argon atmosphere and magnetic stirring. The mixture was cooled to -20°C and n-butyl lithium (2.2 mL of 2.3M solution in hexane, 5 mmol) was slowly added to the flask. The mixture was stirred for 1 hr at -20°C, then, the temperature was cooled to -40°C and iodine (1.40 g, 5.5 mmol) solution in 5 mL of THF was added by syringe. The reaction mixture was warmed to room temperature and stirred for 12 hrs. Work-up and purification: The reaction was quenched by adding saturated Na2S2O3 solution. The mixture was then extracted by hexanes (3 X 20 mL). The organic phase was washed with saturated Na2S2O3 solution, water, and brine then dried over MgSO4. The solvent was removed under reduced pressure and the crude product was purified by flash column chromatography (100% hexanes) afforded pure 1-iodododec-1- yne 1.34g (4.6mmol, yield: 92%). 1 H NMR (300MHz, CDCl3): δ 2.37 (t, J=7.5Hz, 2H), 1.53 (m, 2H), 1.36 (m, 14H), 0.91 (t, J=7.5 Hz, 3H). 191 Preparation of 1,5-bis((tricosa-10,12-diyn-1-yloxy)methyl)anthracene (Cadiot- Chodkiewicz cross-coupling reactions): To a two-neck flask under argon were added 1,5-bis((undec-10-yn-1-yloxy)methyl)anthracene (0.12g, 0.23mmol), 1-iodododec-1-yne (0.16g, 0.55mmol) and pyrrolidine (3mL). The mixture was cooled to 0°C and copper iodide (0.017g, 0.09mmol) was added all at once. The reaction mixture was stirred at room temperature for 12 hrs. Work-up and purification: The reaction was quenched by adding satured NH 4Cl aqueous solution (20 mL). The mixture was extracted with DCM (3 X 20mL). The organic phase was washed with water and brine then dried over MgSO4. The solvent was removed under reduced pressure and the crude product was purified by flash column chromatography (30% DCM/hexanes) afforded pure 1,5-bis((tricosa-10,12-diyn-1- yloxy)methyl)anthracene 0.12g (0.14mmol, yield: 61%). 1 H NMR (300MHz, CDCl3): δ 8.73 (s, 2H), 8.04 (d, J=9.0Hz, 2H), 7.53 (d, J=9.0Hz, 2H), 7.44 (dd, J=9.0Hz and 6.0Hz, 2H), 5.10 (s, 4H), 3.61 (t, J=6.0Hz, 4H), 2.24 (m, 8H), 1.67 (m, 4H), 1.53 (m, 8H), 1.40 (m, 48H), 0.90 (t, J=6.0Hz, 6H). 13 C NMR (75MHz, CDCl3): δ 133.94, 132.07, 129.80, 129.26, 125.74, 124.75, 123.54, 77.57, 77.22, 71.72, 70.45, 66.99, 65.26, 31.90, 29.82, 29.57, 29.48, 29.41, 29.38, 29.31, 29.10, 29.00, 28.86, 28.82, 28.36, 28.33, 28.25, 26.27, 22.68, 19.20, 14.12. m/s (FAB) m/z Calcd for (M+Na)+ (C62H90O2Na) 889.7, found 889.9. HRMS Calcd for (M+Na)+ 889.6839 found 889.6821. 192 A-[242-C≡C12,14]2, A-[232-C≡C11,13]2, A-[232-C≡C7,9]2, A-[232-C≡C15,17]2, A-[292- C≡C14,16]2, A-[252-C≡C10,12]2 and A-[252-C≡C14,16]2 were prepared using similar procedures. Their spectral data are provided below: A-[242-C≡C12,14]2 spectral data: 1,5-bis((docosa-10,12-diyn-1-yloxy)methyl)anthracene 1 H NMR (300MHz, CDCl3): δ 8.73 (s, 2H), 8.04 (d, J=9.0Hz, 2H), 7.52 (d, J=6.0Hz, 2H), 7.44 (dd, J=9.0Hz and 6.0Hz, 2H), 5.10 (s, 4H), 3.61 (t, J=6.0Hz, 4H), 2.24 (m, 8H), 1.67 (m, 4H), 1.53 (m, 8H), 1.40 (m, 44H), 0.90 (t, J=6.0Hz, 6H). 13 C NMR (75MHz, CDCl3): δ 133.95, 132.07, 129.80, 129.26, 125.73, 124.74, 123.54, 77.57, 77.23, 71.71, 70.45, 66.94, 65.27, 31.92, 29.80, 29.55, 29.46, 29.40, 29.40, 29.33, 29.07, 28.98, 28.84, 28.80, 28.33, 28.21, 26.20, 22.05, 19.01, 13.97. m/s (FAB) m/z Calcd for (M+Na)+ (C60H86O2Na) 861.7, found 861.3. HRMS Calcd for (M+Na)+ 861.6526 found 861.6530. A-[232-C≡C11,13]2 spectral data: 1,5-bis((henicosa-9,11-diyn-1-yloxy)methyl)anthracene 1 H NMR (300MHz, CDCl3): δ 8.73 (s, 2H), 8.04 (d, J=9.0Hz, 2H), 7.53 (d, J=9.0Hz, 2H), 7.45 (dd, J=9.0Hz and 6.0Hz, 2H), 5.10 (s, 4H), 3.61 (t, J=6.0Hz, 4H), 2.24 (m, 8H), 1.67 (m, 4H), 1.53 (m, 8H), 1.38 (m, 40H), 0.90 (t, J=6.0Hz, 6H). 193 13 C NMR (75MHz, CDCl3): δ 133.93, 132.06, 129.80, 129.26, 125.74, 124.75, 123.54, 77.57, 77.51, 71.72, 70.40, 67.82, 65.29, 31.88, 29.80, 29.45, 29.28, 29.25, 29.12, 29.05, 28.87, 28.77, 28.37, 28.33, 26.24, 22.68, 19.22, 19.19, 14.12. m/s (FAB) m/z Calcd for (M+Na)+ (C58H82O2Na) 833.6, found 833.5. HRMS Calcd for (M+Na)+ 833.6213 found 861.6221. A-[232-C≡C7,9]2 spectral data: 1,5-bis((henicosa-5,7-diyn-1-yloxy)methyl)anthracene 1 H NMR (300MHz, CDCl3): δ 8.70(s, 2H), 8.05 (d, J=9.0Hz, 2H), 7.52 (d, J=6.0Hz, 2H), 7.44 (dd, J=9.0Hz and 6.0Hz, 2H), 5.09 (s, 4H), 3.64 (t, J=6.0Hz, 4H), 2.26 (m, 8H), 1.80 (m, 4H), 1.66 (m, 4H), 1.50 (m, 4H), 1.28 (m, 40H), 0.90 (t, J=7.5Hz, 6H). 13 C NMR (75MHz, CDCl3): δ 133.76, 132.05, 129.74, 129.32, 125.73, 124.79, 123.64, 77.68, 77.22, 71.70, 69.67, 65.66, 65.24, 31.93, 29.68, 29.65, 29.63, 29.49, 29.36, 29.11, 28.87, 28.36, 28.05, 27.96, 25.17, 22.70, 19.20, 18.98, 14.12. m/s (FAB) m/z Calcd for (M+Na)+ (C58H82O2Na) 833.6, found 833.8. HRMS Calcd for (M+Na)+ 833.6213 not found. A-[232-C≡C15,17]2 spectral data: 1,5-bis((henicosa-13,15-diyn-1-yloxy)methyl)anthracene 194 1 H NMR (300MHz, CDCl3): δ 8.72(s, 2H), 8.03 (d, J=6.0Hz, 2H), 7.52 (d, J=6.0Hz, 2H), 7.44 (dd, J=9.0Hz and 6.0Hz, 2H), 5.10 (s, 4H), 3.61 (t, J=6.0Hz, 4H), 2.26 (m, 8H), 1.68 (m, 4H), 1.54 (m, 8H), 1.28 (m, 40H), 0.91 (t, J=7.5Hz, 6H). 13 C NMR (75MHz, CDCl3): δ 133.95, 132.06, 129.80, 129.24, 125.69, 124.74, 123.52, 77.55, 77.21, 71.70, 70.53, 65.25, 64.67, 31.00, 29.85, 29.59, 29.57, 29.56, 29.46, 29.25, 29.09, 28.86, 28.61, 28.35, 28.05, 26.30, 22.17, 19.21, 13.92. m/s (FAB) m/z Calcd for (M+Na)+ (C58H82O2Na) 833.6, found 833.9. HRMS Calcd for (M+Na)+ 833.6213 found 861.6248. A-[292-CC14,16]2 spectral data (this compound is prepared by Ms. Min Kyoung Kim): 1 H NMR (400MHz, CDCl3): δ 8.73 (s, 2H), 8.04 (d, J=8.4Hz, 2H), 7.53 (d, J=6.8Hz, 2H), 7.45 (dd, J=15.2Hz and 8.4Hz, 2H), 5.10 (s, 4H), 3.62 (t, J=5.2Hz, 4H), 2.26 (m, 8H), 1.68 (m, 4H), 1.53 (m, 9H), 1.28 (m, 59H), 0.90(t, J=6.8Hz 10H). 13 C NMR (100 MHz, CDCl3): δ 133.93, 132.06, 129.80, 129.27, 125.73, 124.75, 123.54, 77.59, 77.23, 71.72, 70.53, 65.24, 31.94, 29.85, 29.65, 29.53, 29.50, 29.46, 29.37, 29.12, 28.87, 28.37, 26.31, 22.71, 19.23, 14.15. m/s (MALDI) m/z calcd for (M+H)+ (C70H107O2) 979.83, found no molecular ion peak. 195 A-[252-CC14,16]2 spectral data (this compound is prepared by Ms. Min Kyoung Kim): 1 H NMR (300MHz, CDCl3): δ 8.73 (s, 2H), 8.04 (d, J=9.0Hz 2H), 7.53 (d, J=6.0Hz, 2H), 7.44 (dd, J=15.0Hz and 9.0Hz, 2H), 5.10 (s, 4H), 3.61 (t, J=6.0Hz, 4H), 2.26 (m, 9H), 1.65 (m, 4H), 1.60 (m, 52H), 0.90 (t, J=6.0Hz 9H) 13 C NMR (75 MHz, CDCl3): δ 133.92, 132.05, 129.79, 129.27, 125.73, 124.75, 123.54, 77.58, , 71.73, 70.51, 65.24, 31.84, 29.85, 29.59, 29.54, 29.46, 29.17, 28.87, 28.36, 26.31, 22.67, 19.22, 14.13. m/s (MALDI) m/z calcd for (M+H)+ (C62H91O2) 867.70, found867. A-[252-CC10,12]2 spectral data (this compound is prepared by Ms. Min Kyoung Kim): 1 H NMR (300MHz, CDCl3): δ 8.73 (s, 2H), 8.04 (d, J=9.0Hz, 2H), 7.52 (d, J=6.0Hz, 2H), 7.45 (dd, J=15.0Hz and 9.0Hz, 2H), 5.10 (s, 4H), 3.60 (t, J=6.0Hz, 4H), 2.26 (m, 8H), 1.65 (m, 6H), 1.50 (m, 53H) 0.90 (t, J=6.0Hz, 7H). 13 C NMR (75 MHz, CDCl3): δ 133.88, 132.05, 129.78, 125.79, 124.78, 123.55, 77.61, 71.74, 70.31, 65.27, 65.24, 31.94, 29.76, 29.65, 29.51, 29.38, 28.88, 28.79, 28.37, 28.24, 26.13, 22.72, 19.23, 19.17, 14.16. m/s (MALDI) m/z calcd for (M+H)+ (C62H91O2) 867.70, found867. 196 5.4.2 Syntheses of four-component system S1 (A-[312;CC-13,15]2), S2 (A-[272;CC-9,11]2), D1 (A-[312;CC-17,19]-[232;CC-9,11]) and D2 (A-[272;CC-17,19]-[232;CC-13,15]) Scheme 4. Synthetic scheme for compound S1 and D2: 197 Preparation of dodec-2-yn-1-ol: Propargyl alcohol (1.0 mL, 17.2 mmol) was added to a flame-dried flask containing THF (25 mL) and HMPA (5 mL, 60 mmol) under argon atmosphere with magnetic stirring. The solution was cooled to -78°C and n-butyl lithium (13.5 mL of 2.3M solution in hexane, 31 mmol) was added to the flask by syringe. The temperature was raised to -30°C and maintained for 45 mins. 1- bromononane (3.4mL, 18.0 mmol) was added dropwise at -30°C. The solution was then stirred at room temperature for 15 hrs. Work-up and purification: The reaction was quenched by adding saturated NH 4Cl aqueous solution (25 mL). The mixture was extracted with EA (3 X 30 mL). The organic layer was washed with water, brine and then dried over MgSO4. The solvent was removed under reduced pressure using a rotary evaporator. The crude product was purified by flash column chromatography (8% EA/hexanes then 15% EA/hexanes) affording pure dodec-2-yn-1-ol 2.10 g (11.5 mmol, yield: 66%). 1 H NMR (300MHz, CDCl3): δ 4.26 (s, 2H), 2.23 (t, J=7.5Hz, 2H), 1.78 (s, 1H), 1.50 (m, 2H), 1.32 (m, 12H), 0.89 (t, J=6.0Hz, 3H). 13 C NMR (75 MHz, CDCl3): δ 86.57, 78.15, 51.23, 31.75, 29.30, 29.17, 29.10, 28.87, 28.55, 22.75, 18.75, 14.05. HRMS (FAB): m/z Calcd for (M+Na)+ (C12H22ONa) 205.1568, found 205.1559. 198 Preparation of dodec-11-yn-1-ol (alkyne zipper reaction): 1,3-diaminopropane (30 mL) was added by syringe to a flame-dried two-neck flask under argon. Lithium (0.40g, 57 mmol) was added to the flask and the mixture (a dark blue solution) was heated and stirred in an oil bath at 70°C. After stirring 4 hrs, the blue color discharged and a milky white suspension formed. The mixture was cooled to room temperature and potassium tert-butoxide (3.81 g, 34 mmol) was added all at once, affording a yellow solution. After stirring for 15 mins, dodec-2-yn-1-ol (2.10 g, 11.5 mmol) was added in one portion. The reaction was stirred for 1.5hrs at room temperature. Work-up and purification: The mixture was poured into ice-water (100mL) then extracted with EA (3 X 50mL). The organic layer was washed with 0.5M HCl solution, water, brine and then dried with MgSO4. The solvent was removed under reduced pressure and the crude product was purified by flash column chromatography (25% EA/hexanes) affording pure dodec-11-yn-1-ol 1.89g (10.3 mmol, yield: 90%). 1 H NMR (300MHz, CDCl3): δ 3.65 (t, J=6.5Hz, 2H), 2.22 (td, J=7.0Hz and 3.0Hz, 2H), 1.97 (t, J=2.5Hz, 1H), 1.57 (m, 4H), 1.35 (m, 12H). 13 C NMR (75 MHz, CDCl3): δ 85.02, 68.30, 62.91, 32.50, 29.57, 29.53, 29.40, 29.12, 28.70, 28.55, 27.00, 18.50. HRMS (FAB): m/z Calcd for (M+Na)+ (C12H22ONa) 205.1568, found 205.1563 199 Preparation of Hexadec-15-yn-1-ol The procedures employed were the same as to prepare dodec-11-yn-1-ol. The spectral data are: 1 H NMR (300MHz, CDCl3): δ 3.64 (t, J=6.0Hz, 2H), 2.20 (td, J=6.0Hz and 3.0Hz, 2H), 1.94 (t, J=3.0Hz, 1H), 1.55 (m, 4H), 1.27 (m, 20H). 13 C NMR (75 MHz, CDCl3): δ 84.80, 68.02, 63.03, 32.80, 29.62, 29.59, 29.58, 29.49, 29.45, 29.43, 29.10, 28.76, 28.55, 28.49, 25.74, 18.39. HRMS (FAB): m/z Calcd for (M+Na)+ (C16H30ONa) 261.2194, found 261.2190. Preparation of 1,5-bis((dodec-11-yn-1-yloxy)methyl)anthracene (compound 2, synthetic precursor to S1) and 1-(chloromethyl)-5-((dodec-11-yn-1- yloxy)methyl)anthracene (compound 1, synthetic precursor to D2): Dodec-11-yn-1-ol (0.29g, 1.6mmol) was added to a flame-dried two-neck flask containing 1:1 THF/DMF (7mL) under argon. The solution was cooled to 0°C and sodium hydride (60% in mineral oil, 64mg, 1.6mmol) was added all at once. After stirring at room temperature for 30 mins, 1,5-bis(chloromethyl)anthracene (0.27g 1.0 mmol) was added in once portion (0°C). The mixture was then stirred at room temperature for 15 hrs. Work-up and purification: The reaction was quenched by slowly adding ice-water. The mixture was extracted with DCM (3 X 30mL). The organic layer was washed with 0.5M HCl solution, water, brine and then dried with MgSO4. The solvent was removed 200 under reduced pressure and the crude product was purified by flash column chromatography (20% DCM/hexanes then 50% DCM/Hexanes) affording compound 1 (mono substituted) 0.13g (0.30 mmol, yield: 30%) and compound 2 (disubstituted) 0.20g (0.35 mmol, yield: 35%) Spectral data for 1,5-bis((dodec-11-yn-1-yloxy)methyl)anthracene (2): 1 H NMR (300MHz, CDCl3): δ 8.73 (s, 2H), 8.04 (d, J=9.0Hz, 2H), 7.53 (d, J=6.0Hz, 2H), 7.44 (dd, J=9.0Hz and 6.0Hz, 2H), 5.10 (s, 4H), 3.61 (t, J=6.0Hz, 4H), 2.18 (td, J=6.0Hz and 3.0Hz, 4H), 1.96 (t, J=3.0Hz, 2H), 1.68 (m, 4H), 1.53 (m, 4H), 1.38 (m, 24H). 13 C NMR (75MHz, CDCl3): δ 133.93, 132.06, 129.80, 129.27, 125.73, 124.75, 123.54, 84.84, 71.72, 70.51, 68.07, 29.84, 29.55, 29.44, 29.42, 29.09, 28.75, 28.50, 26.30, 18.41. HRMS (FAB): m/z Calcd for (M+Na)+ (C40H54O2Na) 589.4022, found 589.4018. Spectral data for 1-(chloromethyl)-5-((dodec-11-yn-1-yloxy)methyl)anthracene (1): 1 H NMR (300MHz, CDCl3): δ 8.77 (s, 1H), 8.72 (s, 1H), 8.08 (s, 1H), 8.06 (s, 1H), 7.52 (m, 4H), 5.21 (s, 2H), 5.10 (s, 2H), 3.60 (t, J=7.5Hz, 2H), 2.18 (td, J=6.0Hz and 3.0Hz, 2H), 1.95 (t, J=3.0Hz, 1H), 1.70 (m, 2H), 1.46 (m, 14H). 201 13 C NMR (75MHz, CDCl3): δ 132.80, 132.67, 132.33, 132.06, 131.78, 130.71, 129.69, 129.18, 127.39, 126.63, 125.32, 124.69, 124.16, 121.46, 83.28, 71.74, 70.44, 68.04, 44.95, 30.03, 29.82, 29.52, 29.39, 29.05, 28.73, 28.47, 26.25, 18.43. HRMS (FAB): m/z Calcd for (M+Na)+ (C28H33ClONa) 443.2118, found 443.2109. Preparation of 1-((dodec-11-yn-1-yloxy)methyl)-5-((hexadec-15-yn-1- yloxy)methyl)anthracene (compound 3, synthetic precursor to D2): Hexadec-15-yn-1-ol (0.14g, 0.6mmol) was added to a flame-dried two-neck flask containing 1:1 THF/DMF (3mL) under argon. The solution was cooled to 0°C and sodium hydride (60% in mineral oil, 24mg, 0.6mmol) was added all at once. After stirring at room temperature for 1 hour, 1-(chloromethyl)-5-((dodec-11-yn-1-yloxy)methyl)anthracene (compound 1, 0.13g, 0.3mmol) solution in 1:1 THF/DMF (2mL) was added in one portion (0°C). The mixture was then stirred at 40°C for 15 hrs. Work-up and purification: The reaction was quenched by slowly adding ice-water. The mixture was extracted with DCM (3 X 20mL). The organic layer was washed with 0.5M HCl solution, water, brine and then dried with MgSO4. The solvent was removed under reduced pressure and the crude product was purified by flash column chromatography (30% DCM/hexanes) affording 0.12g of compound 3 (0.20 mmol, yield: 66%). 202 1 H NMR (300MHz, CDCl3): δ 8.72 (s, 2H), 8.03 (d, J=6.0Hz, 2H), 7.52 (d, J=6.0Hz, 2H), 7.44 (dd, J=9.0Hz and 6.0Hz, 2H), 5.10 (s, 4H), 3.61 (t, J=6.0Hz, 4H), 2.19 (td, J=6.0Hz and 3.0Hz, 4H), 1.96 (s, 2H), 1.68 (m, 4H), 1.52 (m, 4H), 1.38 (m, 32H). 13 C NMR (75MHz, CDCl3): δ 133.92, 132.06, 129.79, 129.28, 125.75, 124.76, 123.56, 84.85, 71.74, 70.54, 70.50, 68.11, 68.10, 29.87, 29.86, 29.66, 29.65, 29.57, 29.52, 29.46, 29.16, 29.12, 29.11, 28.81, 28.81, 28.77, 28.76, 28.52, 26.33, 18.43. HRMS (FAB): m/z Calcd for (M+Na)+ (C44H62O2Na) 645.4648, found 645.4633. Preparation of 1-iodoheptadec-1-yne: 1-heptadecyne (1.18g, 5 mmol) was added to a flame-dried two-neck flask containing THF (15 mL) under argon atmosphere. The mixture was cooled to -20°C and n-butyl lithium (2.2 mL of 2.3M solution in hexane, 5 mmol) was slowly added to the flask. The mixture was stirred for 1 hr at -20°C, then, the temperature was cooled to -40°C and iodine (1.32 g, 5.2 mmol) solution in 5 mL of THF was added by syringe. The reaction mixture was warmed to room temperature and stirred for 16 hrs. Work-up and purification: The reaction was quenched by adding saturated Na2S2O3 solution. The mixture was then extracted with hexanes (3 X 30 mL). The organic phase was washed with saturated Na2S2O3 solution, water, brine and then dried over MgSO4. The solvent was removed under reduced pressure and the crude product was 203 purified by flash column chromatography (100% hexanes) affording pure 1- iodoheptadec-1-yne 1.72g (4.7mmol, yield: 95%). 1 H NMR (300MHz, CDCl3): δ 2.26 (t, J=6.0Hz, 2H), 1.51 (m, 2H), 1.28 (m, 24H), 0.90 (t, J=6.0Hz, 3H). 13 C NMR (75MHz, CDCl3): δ 94.88, 65.26, 31.95, 29.71, 29.68, 29.63, 29.51, 29.40, 29.36, 29.10, 28.87, 28.80, 28.50, 22.73, 20.84, 20.60, 14.17. HRMS (EI) m/z Calcd for M+ (C17H31I) 362.1470, found 362.1482. Preparation of 1-iodonon-1-yne The procedure employed was the same as to prepare 1-iodoheptadec-1-yne. The spectral data are: 1 H NMR (300MHz, CDCl3): δ 2.25 (t, J=4.5Hz, 2H), 1.53 (m, 2H), 1.28 (m, 8H), 0.91 (t, J=6.0Hz, 3H). 13 C NMR (75MHz, CDCl3): δ 96.10, 64.55, 31.59, 29.80, 29.53, 28.87, 28.55, 22.02, 14.15. HRMS (EI) m/z Calcd for M+ (C9H15I) 250.0218 found 250.0225. 204 Preparation of 1,5-bis((nonacosa-11,13-diyn-1-yloxy)methyl)anthracene (compound S1) (Cadiot-Chodkiewicz cross-coupling reactions): To a two-neck flask under argon were added compound 2 (0.20g, 0.35mmol), 1-iodoheptadec-1-yne (0.29g, 0.80mmol) and pyrrolidine (5mL). The mixture was cooled to 0°C and copper iodide (12mg, 0.07mmol) was added all at once. The reaction mixture was stirred at room temperature for 12 hrs. Work-up and purification: The reaction was quenched by adding saturated NH 4Cl aqueous solution (15 mL). The mixture was extracted with DCM (3 X 20mL). The organic phase was washed with water, brine and then dried over MgSO4. The solvent was removed under reduced pressure and the crude product was purified by flash column chromatography (30% DCM/hexanes) affording compound S1 0.20g (0.19mmol, yield: 55%). 1 H NMR (300MHz, CDCl3): δ 8.73 (s, 2H), 8.04 (d, J=6.0Hz, 2H), 7.53 (d, J=6.0Hz, 2H), 7.45 (dd, J=6.0Hz and 6.0Hz, 2H), 5.10 (s, 4H), 3.62 (t, J=4.5Hz, 4H), 2.25 (m, 8H), 1.66 (m, 4H), 1.55 (m, 8H), 1.50 (m, 12H), 1.40 (m, 60H), 0.91 (t, J=4.5Hz, 6H). 13 C NMR (75MHz, CDCl3): δ 133.93, 132.06, 129.80, 129.27, 125.73, 124.75, 123.54, 77.58, 77.56, 71.73, 70.50, 65.27, 65.26, 31.95, 29.85, 29.84, 29.72, 29.70, 29.68, 29.64, 29.56, 29.51, 29.44, 29.40, 29.13, 29.13, 29.09, 29.09, 28.89, 28.85, 28.85, 28.38, 26.30, 26.30, 22.72, 19.23, 14.16. MS (MALDI) m/z Calcd for (M+H)+ (C74H115O2) 1035.89, found 1035.98. 205 Preparation of 1-((henicosa-11,13-diyn-1-yloxy)methyl)-5-((pentacosa-15,17- diyn-1-yloxy)methyl)anthracene (compound D2): To a two-neck flask under argon were added compound 3 (0.12g, 0.20mmol), 1-iodonon-1-yne (0.13g, 0.50mmol) and pyrrolidine (3mL). The mixture was cooled to 0°C and copper iodide (7mg, 0.04mmol) was added all at once. The reaction mixture was stirred at room temperature for 12 hrs. Work-up and purification: The reaction was quenched by adding saturated NH 4Cl aqueous solution (10 mL). The mixture was extracted with DCM (3 X 20mL). The organic phase was washed with water and brine and then dried over MgSO4. The solvent was removed under reduced pressure and the crude product was purified by flash column chromatography (30% DCM/hexanes) affording compound D2 0.10g (0.12mmol, yield: 60%). 1 H NMR (300MHz, CDCl3): δ 8.73 (s, 2H), 8.03 (d, J=6.0Hz, 2H), 7.53 (d, J=9.0Hz, 2H), 7.44 (dd, J=6.0Hz and 6.0Hz, 2H), 5.10 (s, 4H), 3.61 (t, J=6.0Hz, 4H), 2.26 (m, 8H), 1.65 (m, 4H), 1.56 (m, 8H), 1.38 (m, 48H), 0.90 (t, J=7.5Hz, 6H). 13 C NMR (75MHz, CDCl3): δ 133.90, 132.05, 129.79, 129.27, 125.75, 124.76, 123.55, 77.59, 77.47, 71.73, 70.54, 70.48, 65.23, 65.22, 31.71, 31.62, 29.86, 29.65, 29.57, 29.51, 29.44, 29.41, 29.14, 29.09, 28.89, 28.84, 28.80, 28.37, 26.32, 26.30, 22.65, 19.23, 14.17, 14.12. LRMS (FAB) m/z Calcd for (M+Na)+ (C62H90O2Na) 890, found 890. HRMS (FAB) m/z Calcd for (M+Na)+ , 889.6839, not found. 206 Compound D1 (A-[312;CC-17,19]-[232;CC-9,11]) and S2 (A-[272;CC-9,11]2) were prepared using similar procedures as for D2 and S1. Scheme 5. Synthetic scheme for compound S2 and D1: 207 The spectral data for D1, S2 and other important synthetic intermediates are provided below: Spectral data for S2: 1,5-bis((pentacosa-7,9-diyn-1-yloxy)methyl)anthracene 1 H NMR (300MHz, CDCl3): δ 8.73 (s, 2H), 8.04 (d, J=6.0Hz, 2H), 7.53 (d, J=6.0Hz, 2H), 7.46 (dd, J=6.0Hz and 6.0Hz, 2H), 5.10 (s, 4H), 3.61 (t, J=6.0Hz, 4H), 2.24 (m, 8H), 1.69 (m, 4H), 1.55 (m, 8H), 1.50, (m, 12H), 1.40 (m, 44H), 0.91 (t, J=6.0Hz, 6H). 13 C NMR (75MHz, CDCl3): δ 133.87, 132.06, 129.78, 129.28, 125.79, 124.80, 123.54, 77.62, 77.41, 71.74, 70.25, 65.33, 65.25, 31.96, 29.72, 29.71, 29.68, 29.65, 29.51, 29.40, 29.39, 29.13, 29.13, 28.89, 28.62, 28.38, 28.29, 25.80, 25.79, 22.73, 19.23, 19.13, 14.16. MS (MALDI) m/z Calcd for (M+H)+ (C66H99O2) 924.77, found 924.71. Spectral data for D1: 1-((henicosa-7,9-diyn-1-yloxy)methyl)-5-((nonacosa-15,17-diyn-1- yloxy)methyl)anthracene 1 H NMR (300MHz, CDCl3): δ 8.72 (s, 2H), 8.04 (d, J=9.0Hz, 2H), 7.52 (d, J=6.0Hz, 2H), 7.47 (dd, J=6.0Hz and 6.0Hz, 2H), 5.10 (s, 4H), 3.61 (m, 4H), 2.24 (m, 8H), 1.66 (m, 4H), 1.53 (m, 8H), 1.40 (m, 56H), 0.90 (t, J=6.0Hz, 6H). 208 13 C NMR (75MHz, CDCl3): δ 133.91, 133.84, 132.05, 132.04, 129.79, 129.76, 129.31, 129.25, 125.78, 125.76, 124.81, 124.75, 123.56, 123.52, 77.63, 77.62, 77.59, 71.74, 70.54, 70.24, 65.30, 65.22, 31.94, 29.86, 29.64, 29.51, 29.51, 29.37, 29.14, 29.13, 28.88, 28.88, 28.62, 28.37, 28.37, 28.28, 26.33, 25.80, 22.73, 22.72, 19.23, 19.13, 14.17. LRMS (FAB) m/z Calcd for (M+Na)+ (C66H98O2Na) 946, found 946. HRMS Calcd for (M+Na)+ 945.7465, not found. Spectral data for compound 5 (synthetic precursor to S2): 1,5-bis((oct-7-yn-1-yloxy)methyl)anthracene 1 H NMR (300MHz, CDCl3): δ 8.73 (s, 2H), 8.04 (d, J=6.0Hz, 2H), 7.53 (d, J=6.0Hz, 2H), 7.45 (dd, J=9.0Hz and 6.0Hz, 2H), 5.10 (s, 4H), 3.62 (t, J=7.5Hz, 4H), 2.17 (td, J=6.0Hz and 3.0Hz, 4H), 1.95 (t, J=3.0Hz, 2H), 1.69 (m, 4H), 1.42 (m, 12H). 13 C NMR (75MHz, CDCl3): δ 133.88, 132.06, 129.79, 129.28, 125.78, 124.79, 123.54, 84.68, 71.74, 70.30, 68.15, 29.71, 28.55, 28.42, 25.82, 18.33. HRMS (FAB): m/z Calcd for (M+Na)+ (C32H38O2Na) 477.2770, found 477.2758. Spectral data for compound 4 (synthetic precursor to D1): 1-(chloromethyl)-5-((oct-7-yn-1-yloxy)methyl)anthracene 209 1 H NMR (300MHz, CDCl3): δ 8.75 (s, 1H), 8.71 (s, 1H), 8.08 (s, 1H), 8.05 (s, 1H), 7.53 (m, 4H), 5.19 (s, 2H), 5.09 (s, 2H), 3.61 (t, J=6.0Hz, 2H), 2.18 (td, J=6.0Hz and 3.0Hz, 2H), 1.97 (t, J=3.0Hz, 1H), 1.70 (m, 2H), 1.42 (m, 6H). 13 C NMR (75MHz, CDCl3): δ 133.95, 132.78, 132.27, 132.02, 130.63, 130.01, 129.29, 128.92, 127.41, 126.12, 125.23, 124.68, 124.14, 123.17, 84.70, 71.70, 70.30, 68.20, 44.96, 29.71, 28.55, 28.43, 25.82, 18.35. HRMS (FAB): m/z Calcd for (M+Na)+ (C24H25ClONa) 387.1492, found 387.1497. Spectral data for compound 6 (synthetic precursor to D1): 1-((hexadec-15-yn-1-yloxy)methyl)-5-((oct-7-yn-1-yloxy)methyl)anthracene 1 H NMR (300MHz, CDCl3): δ 8.73 (s, 2H), 8.04 (d, J=9.0Hz, 2H), 7.53 (d, J=9.0Hz, 2H), 7.44 (dd, J=9.0Hz and 6.0Hz, 2H), 5.10 (s, 4H), 3.61 (t, J=7.5Hz, 4H), 2.18 (m, 4H), 1.95 (m, 2H), 1.71 (m, 4H), 1.55 (m, 4H), 1.43 (m, 8H), 1.32 (m, 16H). 13 C NMR (75MHz, CDCl3): δ 133.92, 133.84, 132.05, 129.80, 129.77, 129.32, 129.26, 125.78, 124.81, 124.75, 123.58, 123.52, 84.87, 84.69, 71.74, 70.54, 70.30, 68.18, 68.10, 29.87, 29.86, 29.72, 29.71, 29.65, 29.55, 29.52, 29.16, 28.81, 28.56, 28.53, 28.52, 28.42, 26.34, 25.83, 25.82, 18.44, 18.34. HRMS (FAB): m/z Calcd for (M+Na)+ (C40H54O2Na) 589.4022, found 589.4031. 210 References [1] L. Trottet, H. Owen, P. Holme, J. Heylings, I. P. Collin, A. P. Breen, M. N. Siyad, R. S. Nandra, A. F. Davis, Int J Pharm 2005, 304, 63. [2] D. K. Mohapatra, D. Bhattasali, M. K. Gujar, M. I. Khan, K. S. Shashidhara, Eur J Org Chem 2008, 6213. [3] J. S. Yadav, C. S. Reddy, Org Lett 2009, 11, 1705. 211 Chapter 6 Conclusions and Future Prospects 6.1 Conclusions 6.1.1 Monolayer patterning using CF2 and ketone dipoles The large dipole moments of CF2 and ketone are effective tool in directing self- assembly of single- and multi-component monolayers. Placing CF2 and ketone groups at (ω+1)/2 or (ω+3)/2 position of the side chain generates dipolar repulsions between ω↔2 packed side chains and would direct monolayer assemble into atypical ω↔3 morphology. Side chains with CF2/ketone groups at (ω+1)/2 are dipolar complementary to the side chains with CF2/ketone groups at (ω+3)/2 position. 1:1 mixing of two 1,5- substituted anthracenes bearing dipolar complementary side chains (e.g. A-[172,F-9,9]2 + A-[172,F-10,10]2, A-[152,F-9,9]2 + A-[152,F-8,8]2, A-[172,C=O-9]2 + A-[172,C=O-10]2 and A-[172,F-9,9]2 + A-[172,C=O-10]2) promotes self-assembly of compositionally patterned, 2 packed two- component monolayers. The formation of two-component monolayers are driven by the simultaneous optimization of van der Waals contact (2 packing of side chains) and dipolar interactions (parallel, collinear alignment of dipolar groups). Furthermore, the dipolar interactions generate by CF2 and ketone groups are interchangeable. The dipolar complementary side chain pairs can comprise of either the same (e.g. A-[172,F-9,9]2 + A- [172,F-10,10]2) or different dipoles (e.g. A-[172,F-9,9]2 + A-[172,C=O-10]2). 212 6.1.2 Programming self-assembled monolayer using side chain shape Conjugated diyne units introduce distinct “kinks” in the side chains of 1,5- substituted anthracene derivaties. These kinks place shape constraints on molecule packing and monolayer packing density. Diyne kinks positioned near side chain center allow (nearly) optimal packing of identical alkadiyne side chains. Such alkadiyne side chains are ‘‘shape self-complementary’’ (A-[232-CC11,13]2, A-[242-CC12,14]2, A-[252- CC12,14]2 and A-[292-CC14,16]2). By contrast, placement of the diyne kink far from side chain center inhibits packing of identical side chains, rendering these alkadiyne chains ‘‘shape self-incommensurate’’ (A-[232-CC7,9]2, A-[232-CC15,17]2, A-[252-CC10,12]2, A- [252-CC14,16]2, A-[312-CC13,15]2, A-[272-CC9,11]2, A-[312-CC17,19][232-CC9,11] and A- [272-CC17,19]-[232-CC13,15]). The self-assembly of complex, supramolecular structure in monolayers can be programmed by employing pairs of molecules outfitted with shape self-incommensurate, but pairwise shape-complementary side chains. In our research, compositionally patterned two-component (A-[232-CC7,9]2 + A-[232-CC15,17]2, and A- [252-CC10,12]2 + A-[252-CC14,16]2) and four-component (A-[312-CC13,15]2 + A-[272- CC9,11]2 + A-[312-CC17,19][232-CC9,11] + A-[272-CC17,19]-[232-CC13,15]) self-assembled monolayers were successfully prepared. This strategy for side chain shape based patterning of monolayers should be scalable to unit cells of sufficient length. The intrinsic nature of this molecular recognition strategy is based on optimal van der Waals contacts of alkadiyne side chains, which are weaker supramolecular interactions comparing to strong directional interactions such as H-bondings and metal- coordinations. However, mixing of pentacosa-14,16-diynoic acid with its shape 213 complementary 1,5-alkadiyne-disubstituted anthracene A-[252-CC10,12]2 produces compositionally patterned two-component monolayer instead of single component diynoic acid monolayer. This observation reveals that the side chain shape based molecular recognition strategy provides high fidelity in directing self-assembly even when strong H-bondings are involved. 6.1.3 Correlations between side chain shape and defect densities within self- assembled monolayers Diyne “kinks” incorporated at even side chain positions produces "out" type 1,5- alkadiyne substituted anthracene derivatives (A-[252-CC12,14]2, A-[292-CC14,16]2, A-[252- CC10,12]2 and A-[252-CC14,16]2) by bending the outer part of side chain away from the anthracene center of symmetry. Diyne “kinks” incorporated at odd side chain positions produces "in" type 1,5-alkadiyne substituted anthracene derivatives (A-[232-CC11,13]2, A-[232-CC7,9]2, A-[232-CC15,17]2, A-[312-CC13,15]2, A-[272-CC9,11]2, A-[312-CC17,19][232- CC9,11] and A-[272-CC17,19]-[232-CC13,15]) by bending the outer part of side chain toward the anthracene center of symmetry. This subtle difference of odd versus even diyne position exerts large impacts on the domain size and defect density within the resulting self-assembled monolayers. "Out" diyne derivatives readily assemble monolayers with large domain sizes that could cover up to 1 µm2. By contrast, monolayers assembled from "in" diyne derivatives exhibits high occurrence frequency of slip interfaces that disrupt the anthracene columns. 1-D tape periphery analysis and molecular mechanics simulation studies revealed that the slip interfaces of "in" diyne 214 monolayers are generated by meta-stable stacking of 1-D tapes that fits anthracene "bumps" into diyne "notches". This correlation between molecular shape and monolayer defect density may serve as a useful guide in improving self-assembly quality of the monolayers. 6.2 Future prospects 6.2.1 Multi-component self-assembly Kinked side chain shape shows high fidelity in directing self-assembly of multi- component monolayers. By far we have successfully prepared compositionally pattern, four-component self-assembled monolayer using the side chain shape based molecular recognition strategy. A mixture of S1, S2, D1 and D2 formed monolayer with a repeating pattern of -[S1-D1-D2-S2-D2-D1]-. The unit cell contain six molecules and reaches a horizontal expansion of 24 nm (distance from one S1 to next S1). For the application of using monolayers as template to graft polymers and nanoparticles, controlled long composition spacing (~50nm) is desired. One possible strategy to further increase the horizontal expansion of the unit cell is to input more components into the self-assembly system. When designing a multi-component monolayer system using side chain shape strategy, there must present two and only two symmetrically substituted anthracenes in order to generate a complete repeating unit. This requirement originates from the C2h symmetry introduced by 1,5-symmetrically substituted anthracenes. Based on this rule, we could design self-assembled monolayer systems with more components by increasing numbers of dissymmetrically substituted anthracenes . For example, D1 and 215 D2 could be redesigned to be connected with a third dissymmetrically substituted anthracene D3. This design generates a repeating pattern of -[S1-D1-D3-D2-S2-D2-D3- D1]-. If the average chain length of D3 is 4 nm, the distance between two S1 could be further separated to 40 nm (Figure 1). Figure 1. Proposed 5-component system with a horizontal expansion of 40nm. 6.2.1 Polymerization of monolayers Diacetylene compounds are well-known for their capability of single-crystal-to- single-crystal topochemical polymerization[1-11] (Figure 2). The polymerization could be initiated by UV irradiation[8, 12], heat[7, 9] or voltage pulse from STM tip[12-15]. 216 Figure 2. Topochemical polymerization of diacetylenes The polymerized 2-D monolayer would have stronger physical absorption to the substrate thus would be more robust and reliable when using as a template for grafting polymers and nanoparticles. However, by far our attempt UV polymerizations of interdigitated diyne monolayers (e.g. single-component monolayer of A-[252-CC12,14]2, two-component monolayer of A-[232-CC7,9]2 and A-[232-CC15,17]2) have failed. One possible reason might be that the interdigitated structure is too rigid thus the molecules within the monolayer has little flexibility. The transition from monomer monolayer to polymer monolayer might generates significant steric tension into the system which prevents polymerization. The future attempt of monolayer polymerization would focus on the two- component monolayer formed by A-[252-CC10,12]2 and pentacosa-14,16-diynoic acid. 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