Solvent effects on the self-assembly of 1-bromoeicosane on graphite. part II. theory

Journal of Physical Chemistry C

Volumn 113, Issue 9, 2009, Pages 3641-3649

  Ilan, Boaz ^a,b   Florio, Gina M ^b,c   Werblowsky, Tova L ^b,e   Müller, Thomas ^b,f   Hybertsen, Mark S ^d   Berne, B J ^b   Flynn, George W ^b  

^a SCHRÖDINGER INC   (United States)

^b Columbia University ^*  (United States)

^c ST JOHN'S UNIVERSITY   (United States)

^d BROOKHAVEN NATIONAL LABORATORY   (United States)

^e TOURO COLLEGE   (United States)

^f Veeco Metrology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACKBONE ANGLES; CLOSE PACKINGS; EXPLICIT SOLVENTS; GRAPHITE INTERFACES; GRAPHITE LATTICES; HEAD STRUCTURES; IMPLICIT SOLVENT MODELS; IN VACUUMS; MOLECULAR DYNAMICS SIMULATIONS; PHASE ORDERINGS; SELF- ASSEMBLIES; SOLVENT EFFECTS; SYMMETRY CONSIDERATIONS; ULTRAHIGH-VACUUM CONDITIONS; VACUUM CONDITIONS;

DYNAMICS; GRAPHITE; MOLECULAR DYNAMICS; PHASE INTERFACES; PHASE TRANSITIONS; POTENTIAL ENERGY; POTENTIAL ENERGY SURFACES; QUANTUM CHEMISTRY; VACUUM;

SOLVENTS;

EID: 65249170864     PISSN: 19327447     EISSN: 19327455     Source Type: Journal    
DOI: 10.1021/jp809218r     Document Type: Article

References (54)

1. De Feyter, S.; De Schryver, F. C. Two-dimensional supramolecular self-assembly probed by scanning tunneling microscopy. Chem. Soc. Rev. 2003, 32 (6), 393-393.
2. Giancarlo, L. C.; Fang, H. B.; Rubin, S. M.; Bront, A. A.; Flynn, G. W. Influence of the substrate on order and image contrast for physisorbed, self-assembled molecular monolayers: STM studies of functionalized hydrocarbons on graphite and MoS2. J. Phys. Chem. B 1998, 102 (50), 10255-10263.
3. Binning, G.; Rohrer, H.; Gerber, C.; Weibel, E. Surface Studies by Scanning Tunneling Microscopy. Phys. Rev. Lett. 1982, 49 (1), 57-61.
4. Giancarlo, L.; Cyr, D.; Muyskens, K.; Flynn, G. W. Scanning tunneling microscopy of molecular adsorbates at the liquid-solid interface: Functional group variations in image contrast. Langmuir 1998, 14 (6), 1465-1471.
5. Giancarlo, L. C.; Flynn, G. W. Raising flags: Applications of chemical marker groups to study self-assembly, chirality, and orientation of interfacial films by scanning tunneling microscopy. Acc. Chem. Res. 2000, 33 (7), 491-501.
6. 15COOH on graphite at the liquid-solid interface observed by scanning tunneling microscopy: Methylene unit direction of self-assembly structures. J. Phys. Chem. B 2003, 107 (1), 173-179.
7. Kampschulte, L.; Lackinger, M.; Maier, A. K.; Kishore, R. S. K.; Griessl, S.; Schmittel, M.; Heckl, W. M. Solvent induced polymorphism in supramolecular 1,3,5-benzenetribenzoic acid monolayers. J. Phys. Chem. B 2006, 110 (22), 10829-10836.
8. Lackinger, M.; Griessl, S.; Heckl, W. A.; Hietschold, M.; Flynn, G. W. Self-assembly of trimesic acid at the liquid-solid interfacesa study of solvent-induced polymorphism. Langmuir 2005, 21 (11), 4984-4988.
9. Yablon, D. G.; Giancarlo, L. C.; Flynn, G. W. Manipulating selfassembly with achiral molecules: An STM study of chiral segregation by achiral adsorbates. J. Phys. Chem. B 2000, 104 (32), 7627-7635.
10. Crystal, J.; Zhang, L. Y.; Friesner, R. A.; Flynn, G. W. Computational Modeling for scanning tunneling microscopy of physisorbed molecules via ab initio quantum chemistry. J. Phys. Chem. A 2002, 106 (9), 1802-1814.
11. Claypool, C. L.; Faglioni, F.; Goddard, W. A.; Gray, H. B.; Lewis, N. S.; Marcus, R. A. Source of image contrast in STM images of functionalized alkanes on graphite: A systematic functional group approach. J. Phys. Chem. B 1997, 101 (31), 5978-5995.
12. Faglioni, F.; Claypool, C. L.; Lewis, N. S.; Goddard, W. A. Theoretical description of the STM images of alkanes and substituted alkanes adsorbed on graphite. J. Phys. Chem. B 1997, 101 (31), 5996-6020.
13. Cheng, A.; Klein, M. L. Melting Transition of Ethylene on Graphite. Langmuir 1992, 8 (11), 2798-2803.
14. Cincotti, S.; Burda, J.; Hentschke, R.; Rabe, J. P. Calculation of Monolayer Structures of Hydrocarbon Chains on Transition-Metal Dichalcogenides - Dotriacontane on Mose2. Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys. 1995, 51 (3), 2090-2098.
15. Xie, Z. X.; Xu, X.; Tang, J.; Mao, B. W. Molecular packing in self-assembled monolayers of normal alkane on Au(111) surfaces. Chem. Phys. Lett. 2000, 323 (3-4), 209-216.
16. Florio, G. M.; Werblowsky, T. L.; Müller, T.; Berne, B. J.; Flynn, G. W. Self-assembly of small polycyclic aromatic hydrocarbons on graphite: A combined scanning tunneling microscopy and theoretical approach. J. Phys. Chem. B 2005, 109 (10), 4520-4532.
17. Müller, T.; Werblowsky, T. L.; Florio, G. M.; Berne, B. J.; Flynn, G. W. Proc. Nat. Acad. Sci. U.S.A. 2005, 102 (15), 5315-5322.
18. Krishnan, M.; Balasubramanian, S.; Clarke, S. Structure of solid monolayers and multilayers of n-hexane on graphite. Proc. Ind. Acad. Sci.-Chem. Sci. 2003, 115 (5-6), 663-677.
19. Krishnan, M.; Balasubramanian, S.; Clarke, S. An atomistic simulation study of a solid monolayer and trilayer of n-hexane on graphite. J. Chem. Phys. 2003, 118 (11), 5082-5086.
20. Arnold, T.; Dong, C. C.; Thomas, R. K.; Castro, M. A.; Perdigon, A.; Clarke, S. M.; Inaba, A. The crystalline structures of the odd alkanes pentane, heptane, nonane, undecane, tridecane and pentadecane monolayers adsorbed on graphite at submonolayer coverages and from the liquid. Phys. Chem. Chem. Phys. 2002, 4 (14), 3430-3435.
21. Kitaigorodskii, A. I., Molecular crystals and molecules; Academic Press: New York, 1973.
22. Marchenko, A.; Cousty, J. "Magic size" effect in the packing of n-alkanes on Au(111): evidence of lowered sliding force for molecules with specific length. Wear 2003, 254 (10), 941-944.
23. Zhang, H. M.; Xie, Z. X.; Mao, B. W.; Xu, X. Self-assembly of normal alkanes on the Au(111) surfaces. Chem.-Eur. J. 2004, 10 (6), 1415-1422.
24. Florio, G. M.; Ilan, B.; Müller, T.; Baker, T. A.; Rothman, A.; Werblowsky, T. L.; Flynn, G. W. Solvent Effects on the Self-Assembly of 1-Bromoeicosane on Graphite. Part I: Scanning Tunneling Microscopy. J. Phys. Chem. C 2009, 113 (9), 3631-3640.
25. Müller, T.; Flynn, G. W.; Mathauser, A. T.; Teplyakov, A. V. Temperature-programmed desorption studies of n-alkane derivatives on graphite: Desorption energetics and the influence of functional groups on adsorbate self-assembly. Langmuir 2003, 19 (7), 2812-2821.
26. Florio, G. M.; Werblowsky, T. L.; Ilan, B.; Müller, T.; Berne, B. J.; Flynn, G. W., Chain-length effects on the self-assembly of short 1-bromoalkane and n-alkane monolayers on graphite. J. Phys. Chem. C 2008.
27. Pasquarello, A.; Hybertsen, M. S.; Car, R. Theory of Si 2p corelevel shifts at the Si(001)-SiO-{2} interface. Phys. Rev. B: Condens. Matter Mater. Phys. 1996, 53 (16), 10942.
28. Yablon, D. G.; Wintgens, D.; Flynn, G. W. Odd/even effect in selfassembly of chiral molecules at the liquid-solid interface: An STM investigation of coadsorbate control of self-assembly. J. Phys. Chem. B 2002, 106 (21), 5470-5475.
29. Jorgensen, W. L. Optimized Intermolecular Potential Functions for Liquid Alcohols. J. Phys. Chem. 1986, 90 (7), 1276-1284.
30. Udier-Blagovic, M.; De Tirado, P. M.; Pearlman, S. A.; Jorgensen, W. L. Accuracy of free energies of hydration using CM1 and CM3 atomic charges. J. Comput. Chem. 2004, 25 (11), 1322-1332.
31. Hay, P. J.; Wadt, W. R. Abinitio Effective Core Potentials for Molecular Calculations - Potentials for K to Au Including the Outermost Core Orbitals. J. Chem. Phys. 1985, 82 (1), 299-310.
32. Becke, A. D. Density-Functional Thermochemistry 0.3. The Role of Exact Exchange. J. Chem. Phys. 1993, 98 (7), 5648-5652.
33. Lee, C. T.; Yang, W. T.; Parr, R. G. Development of the Colle- Salvetti Correlation-Energy Formula into a Functional of the Electron-Density. Phys. Rev. B: Condens. Matter Mater. Phys. 1988, 37 (2), 785-789.
34. Jaguar 6.5, Schrödinger, LLC, New York, NY, 2005.
35. Jorgensen, W. L. In Encyclopedia of Computational Chemistry, Schleyer, P. v. R., Ed.; Wiley: New York, 1998; Vol. 5, pp 3281-3285.
36. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. The Development and Use of Quantum-Mechanical Molecular-Models 0.76. Am1sa New General-Purpose Quantum-Mechanical Molecular-Model. J. Am. Chem. Soc. 1985, 107 (13), 3902-3909.
37. Stewart, J. J. P. Optimization of Parameters for Semiempirical Methods 0.1. Method. J. Comput. Chem. 1989, 10 (2), 209-220.
38. Steele, W. A. Physical Interaction of Gases with Crystalline Solids 0.1. Gas-Solid Energies and Properties of Isolated Adsorbed Atoms. Surf. Sci. 1973, 36 (1), 317-352.
39. Hammonds, K. D.; McDonald, I. R.; Tildesley, D. J. Computational Studies of the Structure of Monolayers of Chlorine Physisorbed on the Basal-Plane of Graphite. Mol. Phys. 1993, 78 (1), 173-189.
40. Lang, N. D.; Kohn, W. Theory of Metal-Surfaces - Induced Surface Charge and Image Potential. Phys. Rev. B: Condens. Matter Mater. Phys. 1973, 7 (8), 3541-3550.
41. Peters, G. H.; Velasco, E. Influence of Surface and Torsion Potentials on the Melting Properties of a Hexane Monolayer on a Graphite Substrate a Molecular-Dynamics Simulation Study. Mol. Phys. 1995, 84 (5), 1039-1047.
42. Schlick, T.; Fogelson, A. Tnpack - a Truncated Newton Minimization Package for Large-Scale Problems 0.1. Algorithm and Usage. ACM Trans. Math. Software 1992, 18 (1), 46-70.
43. Martyna, G. J.; Klein, M. L.; Tuckerman, M. Nose-Hoover Chainssthe Canonical Ensemble Via Continuous Dynamics. J. Chem. Phys. 1992, 97 (4), 2635-2643.
44. Nose, S. A Unified Formulation of the Constant Temperature Molecular-Dynamics Methods. J. Chem. Phys. 1984, 81 (1), 511-519.
45. Parrinello, M.; Rahman, A. Polymorphic Transitions in Single- Crystalssa New Molecular-Dynamics Method. J. Appl. Phys. 1981, 52 (12), 7182-7190.
46. Liang, W.; Whangbo, M. H.; Wawkuschewski, A.; Cantow, H. J.; Magonov, S. N. Electronic Origin of Scanning-Tunneling-Microscopy Images and Carbon Skeleton Orientations of Normal-Alkanes Adsorbed on Graphite. Adv. Mater. 1993, 5 (11), 817-821.
47. Groszek, A. J. Selective Adsorption at Graphite/Hydrocarbon Interfaces. Proc. R. Soc. London, A 1970, 314 (1519), 473-498.
48. Magonov, S. N.; Yerina, N. A. High-temperature atomic force microscopy of normal alkane C60H122 films on graphite. Langmuir 2003, 19 (3), 500-504.
49. Cincotti, S.; Rabe, J. P. Self-Assembled Alkane Monolayers on Mose2 and Mos2. Appl. Phys. Lett. 1993, 62 (26), 3531-3533.
50. Li, Y. H.; Krilov, G.; Berne, B. J. Elastic bag model for molecular dynamics simulations of solvated systems: Application to liquid water and solvated peptides. J. Phys. Chem. B 2006, 110 (26), 13256-13263.
51. Watel, G.; Thibaudau, F.; Cousty, J. Direct Observation of Long-Chain Alkane Bilayer Films on Graphite by Scanning Tunneling Microscopy. Surf. Sci. Lett. 1993, 281 (1-2), L297-L302.
52. Herwig, K. W.; Matthies, B.; Taub, H. Solvent Effects on the Monolayer Structure of Long n-Alkane Molecules Adsorbed on Graphite. Phys. Rev. Lett. 1995, 75 (17), 3154.
53. Khandkar, M. D.; Balasubramanian, S. Argon multilayers on a corrugated surface: effect of coverage on structure. Chem. Phys. Lett. 2002, 362 (1-2), 144-150.
54. 2. J. Phys. Chem. B 1999, 103 (34), 7077-7080.