Citation: Jin Xin, Cramer Jacob R., Chen Qi-Wei, Liang Hai-Lin, Shang Jian, Shao Xiang, Chen Wei, Xu Guo-Qin, Gothelf Kurt V., Wu Kai. Pinning-down molecules in their self-assemblies with multiple weak hydrogen bonds of C-H…F and C-H…N[J]. Chinese Chemical Letters, ;2017, 28(3): 525-530. doi: 10.1016/j.cclet.2016.11.007 shu

Pinning-down molecules in their self-assemblies with multiple weak hydrogen bonds of C-H…F and C-H…N

Jin Xin ^a ,
Cramer Jacob R. ^b ,
Chen Qi-Wei ^a ,
Liang Hai-Lin ^a ,
Shang Jian ^a ,
Shao Xiang ^c ,
Chen Wei ^d,e ,
Xu Guo-Qin ^d,e ,
Gothelf Kurt V. ^b,, ,
Wu Kai ^a,e,,

a.
BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
b.
Danish-Chinese Centre for Self-Assembly and Function of Molecular Nanostructures on Surfaces at iNANO, Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
c.
Department of Chemical Physics, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
d.
Department of Chemistry, National University of Singapore, 117543, Singapore
e.
SPURc, 1 CREATE Way, #15-01, CREATE Tower, 138602, Singapore

Corresponding author: Gothelf Kurt V., kvg@chem.au.dk Wu Kai, kaiwu@pku.edu.cn
Received Date: 15 June 2016
Revised Date: 28 October 2016
Accepted Date: 28 October 2016
Available Online: 9 March 2016

Figures(5)

Two-dimensional self-assemblies of four partially fluorinated molecules, 1, 4-bis (2, 6-difluoropyridin-4-yl) benzene, 4, 4'-bis (2, 6-difluoropyridin-4-yl)-1, 1'-biphenyl, 4, 4'-bis (2, 6-difluoropyridin-4-yl)-1, 1':4', 1"-terphenyl and 4, 4'-bis (2, 6-difluoropyridin-3-yl)-1, 1'-biphenyl, involving weak intermolecular C-H…F and C-H…N hydrogen bonds were systematically investigated on Au (111) with low-temperature scanning tunneling microscopy. The inter-molecular connecting modes and binding sites were closely related to the backbones of the building blocks, i.e., the molecule length determines its binding sites with neighboring molecules in the assemblies while the attaching positions of the N and F atoms dictate its approaching and docking angles. The experimental results demonstrate that multiple weak hydrogen bonds such as C-H…F and C-H…N can be efficiently applied to tune the molecular orientations and the self-assembly structures accordingly.
- Fluorinated pyridyl molecules,
- Grouped hydrogen bonds,
- Molecular self-assembly,
- Molecular design,
- Scanning tunneling microscopy
1. [1]
  Cicoira F., Santato C., Rosei F.. Two-dimensional nanotemplates as surface cues for the controlled assembly of organic molecules[J]. Top. Curr. Chem., 2008,285:203-267. doi: 10.1007/978-3-540-78395-4
2. [2]
  Kudernac T., Lei S., Elemans J.A.A.W., De Feyter S.. Two-dimensional supramolecular self-assembly:nanoporous networks on surfaces[J]. Chem. Soc. Rev., 2009,38:402-421. doi: 10.1039/B708902N
3. [3]
  Liang H.L., He Y., Ye Y.C.. Two-dimensional molecular porous networks constructed by surface assembling[J]. Coord. Chem. Rev., 2009,253:2959-2979. doi: 10.1016/j.ccr.2009.07.028
4. [4]
  He Y.C., Sun W., Wang Y.. A unified model:self-assembly of trimesic acid on gold[J]. J. Phys. Chem. C, 2007,111:10138-10141. doi: 10.1021/jp072726o
5. [5]
  Theobald J.A., Oxtoby N.S., Phillips M.A., Champness N.R., Beton P.H.. Controlling molecular deposition and layer structure with supramolecular surface assemblies[J]. Nature, 2003,424:1029-1031. doi: 10.1038/nature01915
6. [6]
  Otero R., Xu W., Lukas M.. Specificity of[102_TD＄DIF]Watson-Crick base pairing on a solid surface studied at the atomic scale[J]. Angew. Chem. Int. Ed. Engl., 2008,47:9673-9676. doi: 10.1002/anie.v47:50
7. [7]
  Kannappan K., Werblowsky T.L., Rim K.T., Berne B.J., Flynn G.W.. An experimental and theoretical study of the formation of nanostructures of self-assembled cyanuric acid through hydrogen bond networks on graphite[J]. J. Phys. Chem. B, 2007,111:6634-6642. doi: 10.1021/jp0706984
8. [8]
  Xu W., Wang J.G., Jacobsen M.F.. Supramolecular porous network formed by molecular recognition between chemically modified nucleobases guanine and cytosine[J]. Angew. Chem. Int. Ed. Engl., 2010,49:9373-9377. doi: 10.1002/anie.201003390
9. [9]
  Staniec P.A., Perdigao M.A., Saywell A., Champness N.P., Beton P.H.. Hierarchical organisation on a two-dimensional supramolecular network[J]. ChemPhysChem, 2007,8:2177-2181. doi: 10.1002/(ISSN)1439-7641
10. [10]
  Kampschulte L., Werblowsky T.L., Kishore R.S.K.. Thermodynamical equilibrium of binary supramolecular networks at the liquid-solid interface[J]. J. Am. Chem. Soc., 2008,130:8502-8507. doi: 10.1021/ja801883t
11. [11]
  Vishweshwar P., Nangia A., Lynch V.M.. Recurrence of carboxylic acid-pyridine supramolecular synthon in the crystal structures of some pyrazinecarboxylic acids[J]. J. Org. Chem., 2002,67:556-565. doi: 10.1021/jo0162484
12. [12]
  Prins L.J., Reinhoudt D.N., Timmerman P.. Noncovalent synthesis using hydrogen bonding[J]. Angew. Chem. Int. Ed. Engl., 2001,40:2382-2426. doi: 10.1002/(ISSN)1521-3773
13. [13]
  Castellano R.K.. Progress toward understanding the nature and function of C-H center dot center dot center dot O interactions[J]. Curr. Org. Chem., 2004,8:845-865. doi: 10.2174/1385272043370384
14. [14]
  Lehn J.M.. Toward self-organization and complex matter[J]. Science, 2002,295:2400-2403. doi: 10.1126/science.1071063
15. [15]
  Liang H.L., Sun W., Jin X.. Two-dimensional molecular porous networks formed by trimesic acid and 4, 4'-bis (4-pyridyl) biphenyl on Au (111) through hierarchical hydrogen bonds:structural systematics and control of nanopore size and shape[J]. Angew. Chem. Int. Ed. Engl., 2011,5:7562-7566.
16. [16]
  Pawin G., Wong K.L., Kwon K.Y., Bartels L.. A homomolecular porousnetworkat a Cu (111) surface[J]. Science, 2006,313:961-962. doi: 10.1126/science.1129309
17. [17]
  Kampschulte L., Griessl S., Heckl W.M., Lackinger M.. Mediated coadsorption at the liquid-solid interface:stabilization through hydrogen bonds[J]. J. Phys.Chem. B, 2005,109:14074-14078. doi: 10.1021/jp050794+
18. [18]
  Meier C., Ziener U., Landfester K., Weihrich P.. Weak hydrogen bonds as a structural motif for two-dimensional assemblies of oligopyridines on highly oriented pyrolytic graphite:an STM investigation[J]. J. Phys. Chem. B, 2005,109:21015-21027. doi: 10.1021/jp054271d
19. [19]
  Zhang J., Li B., Cui X.F.. Spontaneous chiral resolution in supramolecular assembly of 2, 4, 6-tris (2-pyridyl)-1, 3, 5-triazine on Au (111)[J]. J. Am. Chem. Soc., 2009,131:5885-5890. doi: 10.1021/ja9001986
20. [20]
  Yang J.L., Schumann S., Hatton R.A., Jones T.S.. Copper hexadecafluorophthalocyanine (F₁₆CuPc) as an electron accepting material in bilayer small molecule organic photovoltaic cells[J]. Org. Electron., 2010,11:1399-1402. doi: 10.1016/j.orgel.2010.06.004
21. [21]
  Jiang X.X., Dai J.G., Wang H.B., Geng Y.H., Yan D.H.. Organic photovoltaic cells using hexadecafluorophthalocyaninatocopper (F₁₆CuPc) as electron acceptor material[J]. Chem. Phys. Lett., 2007,446:329-332. doi: 10.1016/j.cplett.2007.08.042
22. [22]
  Dai J.G., Jiang X.X., Wang H.B., Yang D.H.. Organic photovoltaic cell employing organic heterojunction as buffer layer[J]. Thin Solid Films, 2008,516:3320-3323. doi: 10.1016/j.tsf.2007.09.043
23. [23]
  Bao Z.N., Lovinger A.J., Brown J.. New air-stable n-channel organic thin film transistors[J]. J. Am. Chem. Soc., 1998,120:207-208. doi: 10.1021/ja9727629
24. [24]
  Gerlach A., Schreiber F., Sellner S.. Adsorption-induced distortion of F₁₆CuPc on Cu (111) and Ag (111):an[103_TD＄DIF]X-ray standing wave study[J]. Phys. Rev. B, 2005,71205425. doi: 10.1103/PhysRevB.71.205425
25. [25]
  de Oteyza D.G., El-Sayed A., Garcia-Lastra J.M.. Copper-phthalocyanine based metal-organic interfaces:the effectof fluorination, the substrate, and its symmetry[J]. J. Chem. Phys., 2010,133214703. doi: 10.1063/1.3509394
26. [26]
  Wakayama Y.. Assembly process and epitaxy of the F₁₆CuPc monolayer on Cu (111)[J]. J. Phys. Chem. C, 2007,111:2675-2678.
27. [27]
  Wakayama Y., de Oteyza D.G., Garcia-Lastra J.M., Mowbray D.J.. Solid-state reactions in binary molecular assemblies of F₁₆CuPc and pentacene[J]. ACS Nano, 2011,5:581-589. doi: 10.1021/nn102887x
28. [28]
  de Oteyza D.G., García-Lastra J.M., Corso M.. Customized electronic coupling in self-assembled donor-acceptor nanostructures[J]. Adv. Funct. Mater., 2009,19:3567-3573. doi: 10.1002/adfm.v19:22
29. [29]
  Barrena E., de Oteyza D.G., Dosch H., Wakayama Y.. 2D supramolecular selfassembly of binary organic monolayers[J]. ChemPhysChem, 2007,8:1915-1918. doi: 10.1002/(ISSN)1439-7641
30. [30]
  de Oteyza D.G., Silanes I., Ruiz-Osés M.. Balancing intermolecular and molecule-substrate interactions in supramolecular assemblies[J]. Adv. Funct. Mater., 2009,19:259-264. doi: 10.1002/adfm.v19:2
31. [31]
  Barrena E., deOteyza D.G., Sellner S.. In situ study of the growth of nanodots in organic heteroepitaxy[J]. Phys. Rev. Lett., 2006,97076102. doi: 10.1103/PhysRevLett.97.076102
32. [32]
  Huang Y.L., Chen W., Li H.. Tunable two-dimensional binary molecular networks[J]. Small, 2010,6:70-75. doi: 10.1002/smll.v6:1
33. [33]
  Shen Y.T., Deng K., Li M.. Self-assembling in fabrication of ordered porphyrins and phthalocyanines hybrid nano-arrays on HOPG[J]. CrystEngComm, 2013,15:5526-5531. doi: 10.1039/c3ce40340h
34. [34]
  Krauss T.N., Barrena E., Dosch H., Wakayama Y.. Supramolecular assembly of a 2D binary network of pentacene and phthalocyanine on Cu (100)[J]. ChemPhysChem, 2009,10:2445-2448. doi: 10.1002/cphc.v10:14
35. [35]
  Huang Y.L., Chen W., Wee A.T.S.. Molecular trapping on two-dimensional binary supramolecular networks[J]. J. Am. Chem. Soc., 2011,133:820-825. doi: 10.1021/ja106350d
36. [36]
  Rohde D., Yan C.J., Wan L.J.. C-H…F hydrogen bonding:the origin of the selfassemblies of bis (2, 2'-difluoro-1, 3, 2-dioxaborine)[J]. Langmuir, 2006,22:4750-4757. doi: 10.1021/la053138+
37. [37]
  Mu Z.C., Shu L.J., Fuchs H., Mayor M., Chi L.F.. Two dimensional chiral networks emerging from the aryl-F…H hydrogen-bond-driven self-assembly of partially fluorinated rigid molecular structures[J]. J. Am. Chem. Soc., 2008,130:10840-10841. doi: 10.1021/ja801925q
38. [38]
  Marele A.C., Corral I., Sanz P.. Some pictures of alcoholic dancing:from simple to complex hydrogen-bonded networks based on polyalcohols[J]. J. Phys. Chem. C, 2013,117:4680-4690.
39. [39]
  Sheng K., Sun Q., Zhang C., Tan Q.G.. Steering on-surface supramolecular nanostructures by tert-butyl group[J]. J. Phys. Chem. C, 2014,118:3088-3092. doi: 10.1021/jp411222m
40. [40]
  Reichert J., Marschall M., Seufert K.. Competing interactions in surface reticulation with a prochiraldicarbonitrile linker[J]. J. Phys. Chem. C, 2013,117:12858-12863.
41. [41]
  Eremtchenko M., Schaefer J.A., Tautz F.S.. Understanding and tuning the epitaxy of large aromatic adsorbates by molecular design[J]. Nature, 2003,425:602-605. doi: 10.1038/nature01901
42. [42]
  Knudsen M.M., Kalashnyk N., Masini F.. Controlling chiral organization of molecular rods on Au (111) by molecular design[J]. J. Am. Chem. Soc., 2011,133:4896-4905. doi: 10.1021/ja110052n
43. [43]
  Yokoyama T., Yokoyama S., Kamikado T., Okuno Y., Mashiko S.. Selective assembly on a surface of supramolecular aggregates with controlled size and shape[J]. Nature, 2001,413:619-621. doi: 10.1038/35098059
44. [44]
  Yokoyama T., Kamikado T., Yokoyama S., Mashiko S.. Conformation selective assembly of carboxyphenyl substituted porphyrins on Au (111)[J]. J. Chem. Phys., 2004,121:11993-11997. doi: 10.1063/1.1819877
45. [45]
  Wang Y.L., Lingenfelder M., Fabris S.. Programming hierarchical supramolecular nanostructures by molecular design[J]. J. Phys. Chem. C, 2013,117:3440-3445. doi: 10.1021/jp309566s
46. [46]
  Grill L., Dyer M., Lafferentz L.. Nano-architectures bycovalent assemblyof molecular building blocks[J]. Nat. Nanotechnol., 2007,2:687-691. doi: 10.1038/nnano.2007.346
1. [1]
  Yuting Wu , Haifeng Lv , Xiaojun Wu . Design of two-dimensional porous covalent organic framework semiconductors for visible-light-driven overall water splitting: A theoretical perspective. Chinese Journal of Structural Chemistry, 2024, 43(11): 100375-100375. doi: 10.1016/j.cjsc.2024.100375
2. [2]
  Yi Liu , Peng Lei , Yang Feng , Shiwei Fu , Xiaoqing Liu , Siqi Zhang , Bin Tu , Chen Chen , Yifan Li , Lei Wang , Qing-Dao Zeng . Topologically engineering of π-conjugated macrocycles: Tunable emission and photochemical reaction toward multi-cyclic polymers. Chinese Chemical Letters, 2024, 35(10): 109571-. doi: 10.1016/j.cclet.2024.109571
3. [3]
  Lei Wang , Jun-Jie Wu , Chang-Cun Yan , Wan-Ying Yang , Zong-Lu Che , Xin-Yu Xia , Xue-Dong Wang , Liang-Sheng Liao . Near-infrared organic lasers with ultra-broad emission bands by simultaneously harnessing four-level and six-level systems. Chinese Chemical Letters, 2024, 35(8): 109365-. doi: 10.1016/j.cclet.2023.109365
4. [4]
  Changhui Yu , Peng Shang , Huihui Hu , Yuening Zhang , Xujin Qin , Linyu Han , Caihe Liu , Xiaohan Liu , Minghua Liu , Yuan Guo , Zhen Zhang . Evolution of template-assisted two-dimensional porphyrin chiral grating structure by directed self-assembly using chiral second harmonic generation microscopy. Chinese Chemical Letters, 2024, 35(10): 109805-. doi: 10.1016/j.cclet.2024.109805
5. [5]
  Qihan Lin , Jiabin Xing , Yue-Yang Liu , Gang Wu , Shi-Jia Liu , Hui Wang , Wei Zhou , Zhan-Ting Li , Dan-Wei Zhang . taBOX: A water-soluble tetraanionic rectangular molecular container for conjugated molecules and taste masking for berberine and palmatine. Chinese Chemical Letters, 2024, 35(5): 109119-. doi: 10.1016/j.cclet.2023.109119
6. [6]
  Zixi Zou , Jingyuan Wang , Yian Sun , Qian Wang , Da-Hui Qu . Controlling molecular assembly on time scale: Time-dependent multicolor fluorescence for information encryption. Chinese Chemical Letters, 2024, 35(7): 108972-. doi: 10.1016/j.cclet.2023.108972
7. [7]
  Qinghong Pan , Huafang Zhang , Qiaoling Liu , Donghong Huang , Da-Peng Yang , Tianjia Jiang , Shuyang Sun , Xiangrong Chen . A self-powered cathodic molecular imprinting ultrasensitive photoelectrochemical tetracycline sensor via ZnO/C photoanode signal amplification. Chinese Chemical Letters, 2025, 36(1): 110169-. doi: 10.1016/j.cclet.2024.110169
8. [8]
  Fang-Yuan Chen , Wen-Chao Geng , Kang Cai , Dong-Sheng Guo . Molecular recognition of cyclophanes in water. Chinese Chemical Letters, 2024, 35(5): 109161-. doi: 10.1016/j.cclet.2023.109161
9. [9]
  Zhenzhu Wang , Chenglong Liu , Yunpeng Ge , Wencan Li , Chenyang Zhang , Bing Yang , Shizhong Mao , Zeyuan Dong . Differentiated self-assembly through orthogonal noncovalent interactions towards the synthesis of two-dimensional woven supramolecular polymers. Chinese Chemical Letters, 2024, 35(5): 109127-. doi: 10.1016/j.cclet.2023.109127
10. [10]
  Sifan Du , Yuan Wang , Fulin Wang , Tianyu Wang , Li Zhang , Minghua Liu . Evolution of hollow nanosphere to microtube in the self-assembly of chiral dansyl derivatives and inversed circularly polarized luminescence. Chinese Chemical Letters, 2024, 35(7): 109256-. doi: 10.1016/j.cclet.2023.109256
11. [11]
  Cheng-Yan Wu , Yi-Nan Gao , Zi-Han Zhang , Rui Liu , Quan Tang , Zhong-Lin Lu . Enhancing self-assembly efficiency of macrocyclic compound into nanotubes by introducing double peptide linkages. Chinese Chemical Letters, 2024, 35(11): 109649-. doi: 10.1016/j.cclet.2024.109649
12. [12]
  Xiaofei NIU , Ke WANG , Fengyan SONG , Shuyan YU . Self-assembly of [Pd₆(L)₄]⁸⁺-type macrocyclic complexes for fluorescent sensing of HSO₃^-. Chinese Journal of Inorganic Chemistry, 2024, 40(7): 1233-1242. doi: 10.11862/CJIC.20240057
13. [13]
  Zengchao Guo , Weiwei Liu , Tengfei Liu , Jinpeng Wang , Hui Jiang , Xiaohui Liu , Yossi Weizmann , Xuemei Wang . Engineered exosome hybrid copper nanoscale antibiotics facilitate simultaneous self-assembly imaging and elimination of intracellular multidrug-resistant superbugs. Chinese Chemical Letters, 2024, 35(7): 109060-. doi: 10.1016/j.cclet.2023.109060
14. [14]
  Caihong Mao , Yanfeng He , Xiaohan Wang , Yan Cai , Xiaobo Hu . Synthesis and molecular recognition characteristics of a tetrapodal benzene cage. Chinese Chemical Letters, 2024, 35(8): 109362-. doi: 10.1016/j.cclet.2023.109362
15. [15]
  Cheng-Da Zhao , Huan Yao , Shi-Yao Li , Fangfang Du , Li-Li Wang , Liu-Pan Yang . Amide naphthotubes: Biomimetic macrocycles for selective molecular recognition. Chinese Chemical Letters, 2024, 35(4): 108879-. doi: 10.1016/j.cclet.2023.108879
16. [16]
  Bing Niu , Honggao Huang , Liwei Luo , Li Zhang , Jianbo Tan . Coating colloidal particles with a well-defined polymer layer by surface-initiated photoinduced polymerization-induced self-assembly and the subsequent seeded polymerization. Chinese Chemical Letters, 2025, 36(2): 110431-. doi: 10.1016/j.cclet.2024.110431
17. [17]
  Yi Zhou , Wei Zhang , Rong Fu , Jiaxin Dong , Yuxuan Liu , Zihang Song , Han Han , Kang Cai . Self-assembly of two pairs of homochiral M₂L₄ coordination capsules with varied confined space using Tröger's base ligands. Chinese Chemical Letters, 2025, 36(2): 109865-. doi: 10.1016/j.cclet.2024.109865
18. [18]
  Yuchen Wang , Zhenhao Xu , Kai Yan . Rational design of metal-metal hydroxide interface for efficient electrocatalytic oxidation of biomass-derived platform molecules. Chinese Journal of Structural Chemistry, 2025, 44(1): 100418-100418. doi: 10.1016/j.cjsc.2024.100418
19. [19]
  Zhimin Sun , Xin-Hui Guo , Yue Zhao , Qing-Yu Meng , Li-Juan Xing , He-Lue Sun . Dynamically switchable porphyrin-based molecular tweezer for on−off fullerene recognition. Chinese Chemical Letters, 2024, 35(6): 109162-. doi: 10.1016/j.cclet.2023.109162
20. [20]
  Li Lin , Song-Lin Tian , Zhen-Yu Hu , Yu Zhang , Li-Min Chang , Jia-Jun Wang , Wan-Qiang Liu , Qing-Shuang Wang , Fang Wang . Molecular crowding electrolytes for stabilizing Zn metal anode in rechargeable aqueous batteries. Chinese Chemical Letters, 2024, 35(7): 109802-. doi: 10.1016/j.cclet.2024.109802

Get Citation

PDF

XML

Metrics

PDF Downloads(0)
Abstract views(634)
HTML views(14)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142