Accurate and efficient calculation of the desorption energy of small molecules from graphene

Journal of Physical Chemistry C

Volumn 119, Issue 4, 2015, Pages 1867-1879

  Conti, Simone ^a   Cecchini, Marco ^a  

^a UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ADSORBATES; ADSORPTION; COMPUTATION THEORY; DENSITY FUNCTIONAL THEORY; DESIGN FOR TESTABILITY; DESORPTION; GRAPHENE; QUANTUM THEORY; TEMPERATURE PROGRAMMED DESORPTION;

ALIPHATIC HYDROCARBONS; COMPUTATIONAL PREDICTIONS; EMPIRICAL FORCE FIELDS; MOLECULAR ADSORPTION; NANOSTRUCTURED CARBON MATERIALS; QUANTITATIVE AGREEMENT; SEMI-EMPIRICAL METHODS; SEMI-EMPIRICAL QUANTUM MECHANICS;

BINDING ENERGY;

EID: 84949115574     PISSN: 19327447     EISSN: 19327455     Source Type: Journal    
DOI: 10.1021/jp5104774     Document Type: Article

References (85)

1. Westervelt, R. M. Graphene nanoelectronics. Science 2008, 320 (5874), 324-325.
2. Scheuermann, G. M.; Rumi, L.; Steurer, P.; Bannwarth, W.; Mülhaupt, R. Palladium nanoparticles on graphite oxide and its functionalized graphene derivatives as highly active catalysts for the Suzuki-Miyaura coupling reaction. J. Am. Chem. Soc. 2009, 131 (23), 8262-8270.
3. Schedin, F.; Geim, A. K.; Morozov, S. V.; Hill, E. W.; Blake, P.; Katsnelson, M. I.; Novoselov, K. S. Detection of individual gas molecules adsorbed on graphene. Nature Mater. 2007, 6 (9), 652-655.
4. Dua, V.; Surwade, S. P.; Ammu, S.; Rao Agnihotra, S.; Jain, S.; Roberts, K. E.; Park, S.; Ruoff, R. S.; Manohar, S. K. All-organic vapor sensor using inkjet-printed reduced graphene oxide. Angew. Chem., Int. Ed. 2010, 49 (12), 2154-2157.
5. Martin, P. Graphene-based nanomaterials for energy storage. Energy Environ. Sci. 2011, 4 (3), 668-674.
6. Kamat, P. V. Graphene-based nanoassemblies for energy conversion. J. Phys. Chem. Lett. 2011, 2 (3), 242-251.
7. Dimitrakakis, G. K.; Tylianakis, E.; Froudakis, G. E. Pillared graphene: a new 3D network nanostructure for enhanced hydrogen storage. Nano Lett. 2008, 8 (10), 3166-3170.
8. Chen, W.; Duan, L.; Zhu, D. Adsorption of polar and nonpolar organic chemicals to carbon nanotubes. Environ. Sci. Technol. 2007, 41 (24), 8295-8300.
9. Daohui, L.; Baoshan, X. Adsorption of phenolic compounds by carbon nanotubes: role of aromaticity and substitution of hydroxyl groups. Environ. Sci. Technol. 2008, 42 (19), 7254-7259.
10. Ciesielski, A.; Palma, C.-A.; Bonini, M.; Samorì, P. Towards supramolecular engineering of functional nanomaterials: Pre-programming multi-component 2d self-assembly at solid-liquid interfaces. Adv. Mater. 2010, 22 (32), 3506-3520.
11. Ciesielski, A.; Samorì, P. Graphene via sonication assisted liquid-phase exfoliation. Chem. Soc. Rev. 2014, 43 (1), 381-398.
12. Geim, A. K. Graphene: status and prospects. Science 2009, 324 (5934), 1530-1534.
13. Novoselov, K. S.; Fal'ko, V. I.; Colombo, L.; Gellert, P. R.; Schwab, M. G.; Kim, K. A roadmap for graphene. Nature 2012, 490 (7419), 192-200.
14. Ciesielski, A.; Haar, S.; El Gemayel, M.; Yang, H.; Clough, J.; Melinte, G.; Gobbi, M.; Orgiu, E.; Nardi, M. V.; Ligorio, G.; Palermo, V.; Koch, N; Ersen, O.; Casiraghi, C.; Samorì, P. Harnessing the liquid-phase exfoliation of graphene using aliphatic compounds: A supramolecular approach. Angew. Chem., Int. Ed. 2014, 53, 10355-10361.
15. Haar, S.; Ciesielski, A.; Clough, J.; Yang, H.; Mazzaro, R.; Richard, F.; Conti, S.; Merstorf, N.; Cecchini, M.; Morandi, V.; Casiraghi, C.; Samorì., P. A supramolecular strategy to leverage the liquid-phase exfoliation of graphene in presence of surfactants: unraveling the role of the length of fatty acids. Small 2014, DOI: 10.1002/smll.201402745.
16. Redhead, P. A. Thermal desorption of gases. Vacuum 1962, 12 (4), 203-211.
17. Paserba, K. R.; Gellman, A. J. Effects of conformational isomerism on the desorption kinetics of n-alkanes from graphite. J. Chem. Phys. 2001, 115 (14), 6737-6751.
18. Tait, S. L.; Dohnálek, Z.; Campbell, C. T.; Kay, B. D. n-alkanes on MgO (100). II. chain length dependence of kinetic desorption parameters for small n-alkanes. J. Chem. Phys. 2005, 122 (16), 164708.
19. Tait, S. L.; Dohnálek, Z.; Campbell, C. T.; Kay, B. D. n-alkanes on Pt (111) and on C (0001)/Pt (111): Chain length dependence of kinetic desorption parameters. J. Chem. Phys. 2006, 125 (23), 234308.
20. Kysilka, J.; Rubeš, M.; Grajciar, L.; Nachtigall, P.; Bludskỳ, O. Accurate description of argon and water adsorption on surfaces of graphene-based carbon allotropes. J. Phys. Chem. A 2011, 115 (41), 11387-11393.
21. Thierfelder, C.; Witte, M.; Blankenburg, S.; Rauls, E.; Schmidt, W. G. Methane adsorption on graphene from first principles including dispersion interaction. Surf. Sci. 2011, 605 (7), 746-749.
22. Rubeš, M.; Kysilka, J.; Nachtigall, P.; Bludskỳ, O. DFT/CC investigation of physical adsorption on a graphite (0001) surface. Phys. Chem. Chem. Phys. 2010, 12 (24), 6438-6444.
23. 2, and NO on graphene: A first-principles study. Phys. Rev. B 2008, 77 (12), 125416.
24. Chan, K. T.; Neaton, J. B.; Cohen, M. L. First-principles study of metal adatom adsorption on graphene. Phys. Rev. B 2008, 77 (23), 235430.
25. Ershova, O. V.; Lillestolen, T. C.; Bichoutskaia, E. Study of polycyclic aromatic hydrocarbons adsorbed on graphene using density functional theory with empirical dispersion correction. Phys. Chem. Chem. Phys. 2010, 12 (24), 6483-6491.
26. Björk, J.; Hanke, F.; Palma, C.-A.; Samorì, P.; Cecchini, M.; Persson, M. Adsorption of aromatic and anti-aromatic systems on graphene through π-π stacking. J. Phys. Chem. Lett. 2010, 1 (23), 3407-3412.
27. Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H - Pu. J. Chem. Phys. 2010, 132 (15), 154104.
28. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. Development and use of quantum mechanical molecular models. 76. AM1: A new general purpose quantum mechanical molecular model. J. Am. Chem. Soc. 1985, 107 (13), 3902-3909.
29. Stewart, J. J. P. Optimization of parameters for semiempirical methods I. Method. J. Comput. Chem. 1989, 10 (2), 209-220.
30. Stewart, J. J. P. Optimization of parameters for semiempirical methods II. Applications. J. Comput. Chem. 1989, 10 (2), 221-264.
31. Rocha, G. B.; Freire, R. O.; Simas, A. M.; Stewart, J. J. P. RM1: A reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I. J. Comput. Chem. 2006, 27 (10), 1101-1111.
32. Stewart, J. J. P. Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements. J. Mol. Model. 2007, 13 (12), 1173-1213.
33. McNamara, J. P.; Hillier, I. H. Semi-empirical molecular orbital methods including dispersion corrections for the accurate prediction of the full range of intermolecular interactions in biomolecules. Phys. Chem. Chem. Phys. 2007, 9 (19), 2362-2370.
34. Řezáč, J.; Fanfrlík, J.; Salahub, D.; Hobza, P. Semiempirical quantum chemical PM6 method augmented by dispersion and H-bonding correction terms reliably describes various types of non-covalent complexes. J. Chem. Theory Comput. 2009, 5 (7), 1749-1760.
35. Foster, M. E.; Sohlberg, K. A new empirical correction to the AM1 method for macromolecular complexes. J. Chem. Theory Comput. 2010, 6 (7), 2153-2166.
36. Korth, M.; Pitonak, M.; Rezac, J.; Hobza, P. A transferable H-bonding correction for semiempirical quantum-chemical methods. J. Chem. Theory Comput. 2009, 6 (1), 344-352.
37. Korth, M. Third-generation hydrogen-bonding corrections for semiempirical QM methods and force fields. J. Chem. Theory Comput. 2010, 6 (12), 3808-3816.
38. Řezáč, J.; Hobza, P. Advanced corrections of hydrogen bonding and dispersion for semiempirical quantum mechanical methods. J. Chem. Theory Comput. 2011, 8 (1), 141-151.
39. Stewart, J. J. P. Optimization of parameters for semiempirical methods VI: More modifications to the NDDO approximations and re-optimization of parameters. J. Mol. Model. 2013, 19 (1), 1-32.
40. Gordeev, E. G.; Polynski, M. V.; Ananikov, V. P. Fast and accurate computational modeling of adsorption on graphene: a dispersion interaction challenge. Phys. Chem. Chem. Phys. 2013, 15 (43), 18815-18821.
41. Jorgensen, W. L.; Tirado-Rives, J. The OPLS potential functions for proteins: Energy minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 1988, 110 (6), 1657-1666.
42. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 1996, 118 (45), 11225-11236.
43. Jorgensen, W. L.; McDonald, N. A. Development of an all-atom force field for heterocycles. properties of liquid pyridine and diazenes. J. Mol. Struct.: THEOCHEM 1998, 424 (1), 145-155.
44. McDonald, N. A.; Jorgensen, W. L. Development of an all-atom force field for heterocycles. Properties of liquid pyrrole, furan, diazoles, and oxazoles. J. Phys. Chem. B 1998, 102 (41), 8049-8059.
45. Rizzo, R. C.; Jorgensen, W. L. OPLS all-atom model for amines: resolution of the amine hydration problem. J. Am. Chem. Soc. 1999, 121 (20), 4827-4836.
46. Price, M. L. P.; Ostrovsky, D.; Jorgensen, W. L. Gas-phase and liquid-state properties of esters, nitriles, and nitro compounds with the OPLS-AA force field. J. Comput. Chem. 2001, 22 (13), 1340-1352.
47. Watkins, E. K.; Jorgensen, W. L. Perfluoroalkanes: Conformational analysis and liquid-state properties from ab initio and Monte Carlo calculations. J. Phys. Chem. A 2001, 105 (16), 4118-4125.
48. Kaminski, G. A.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J. Phys. Chem. B 2001, 105 (28), 6474-6487.
49. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and testing of a general amber force field. J. Comput. Chem. 2004, 25 (9), 1157-1174.
50. Wang, J.; Wang, W.; Kollman, P. A.; Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations. J. Mol. Graphics Modell. 2006, 25 (2), 247-260.
51. Vanommeslaeghe, K.; Hatcher, E.; Acharya, C.; Kundu, S.; Zhong, S.; Shim, J.; Darian, E.; Guvench, O.; Lopes, P.; Vorobyov, I.; Mackerell, A. D., Jr. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J. Comput. Chem. 2010, 31 (4), 671-690.
52. Ponder, J. W.; Case, D. A. Force fields for protein simulations. Adv. Protein Chem. 2003, 66, 27-86.
53. MacKerell, A. D.; Feig, M.; Brooks, C. L. Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comput. Chem. 2004, 25 (11), 1400-1415.
54. Halgren, T. A. Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. J. Comput. Chem. 1996, 17 (5-6), 490-519.
55. Halgren, T. A. Merck molecular force field. II. MMFF94 van der waals and electrostatic parameters for intermolecular interactions. J. Comput. Chem. 1996, 17 (5-6), 520-552.
56. Halgren, T. A. Merck molecular force field. III. Molecular geometries and vibrational frequencies for MMFF94. J. Comput. Chem. 1996, 17 (5-6), 553-586.
57. Halgren, T. A.; Nachbar, R. B. Merck molecular force field. IV. Conformational energies and geometries for MMFF94. J. Comput. Chem. 1996, 17 (5-6), 587-615.
58. Halgren, T. A. Merck molecular force field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules. J. Comput. Chem. 1996, 17 (5-6), 616-641.
59. Ulbricht, H.; Zacharia, R.; Cindir, N.; Hertel, T. Thermal desorption of gases and solvents from graphite and carbon nanotube surfaces. Carbon 2006, 44 (14), 2931-2942.
60. Zacharia, R.; Ulbricht, H.; Hertel, T. Interlayer cohesive energy of graphite from thermal desorption of polyaromatic hydrocarbons. Phys. Rev. B 2004, 69 (15), 155406.
61. Thrower, J.; Friis, E. E.; Skov, A. L.; Nilsson, L.; Andersen, M.; Ferrighi, L.; Jørgensen, B.; Baouche, S.; Balog, R.; Hammer, B. Interaction between coronene and graphite form temperature-programmed desorption and DFT-vdW calculations: Importance of entropic effects and insights into graphite interlayer binding. J. Phys. Chem., Part C: Nanomater., Interfaces Hard Matter 2013, 117 (26), 13520-13529.
62. Chai, J.-D.; Head-Gordon, M. Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections. Phys. Chem. Chem. Phys. 2008, 10 (44), 6615-6620.
63. Grimme, S. Density functional theory with london dispersion corrections. Wiley Interdisciplinary Rev.: Comput. Mol. Sci. 2011, 1 (2), 211-228.
64. Boys, S. F.; Bernardi, F. The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Mol. Phys. 1970, 19 (4), 553-566.
65. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenberg, J. L.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Montgomery, J. A.;, Jr., Peralta, J. E.; Ogliaro, F.; Bearpark, M.; Heyd, J. J.; Brothers, E.; Kudin, K. N.; Staroverov, V. N.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Rega, N.; Millam, J. M.; Klene, M.; Knox, J. E.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Zakrzewski, V. G.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Dapprich, S.; Daniels, A. D.; Ö Farkas, Foresman, J. B.; Ortiz, J. V.; Cioslowski, J.; Fox, D. J.. Gaussian 09, Revision A.02. Gaussian Inc.: Wallingford CT, 2009.
66. J. J. P. Stewart. MOPAC2012. http://openmopac.net., Computational Chemistry: Colorado Springs, CO, 2012.
67. http://marge.uochb.cas.cz/rezac/h4correction/index.html.
68. http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english.
69. Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. CHARMM: the biomolecular simulation program. J. Comput. Chem. 2009, 30 (10), 1545-1614.
70. Vanommeslaeghe, K.; MacKerell, A. D., Jr. Automation of the CHARMM General Force Field (CGenFF) I: Bond perception and atom typing. J. Chem. Inf. Model. 2012, 52 (12), 3144-3154.
71. Vanommeslaeghe, K.; Prabhu Raman, E.; MacKerell, A. D., Jr. Automation of the CHARMM General Force Field (CGenFF) II: Assignment of bonded parameters and partial atomic charges. J. Chem. Inf. Model. 2012, 52 (12), 3155-3168.
72. Van Der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. GROMACS: fast, flexible, and free. J. Comput. Chem. 2005, 26 (16), 1701-1718.
73. Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. GROMACS: A message-passing parallel molecular dynamics implementation. Comput. Phys. Commun. 1995, 91 (1), 43-56.
74. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 2008, 4 (3), 435-447.
75. Sousa da Silva, A. W.; Vranken, W. F. ACPYPE - Antechamber python parser interface. BMC research notes 2012, 5 (1), 367.
76. Byrd, R. H.; Lu, P.; Nocedal, J.; Zhu, C. A limited memory algorithm for bound constrained optimization. SIAM J. Sci. Comput. 1995, 16 (5), 1190-1208.
77. Zhu, C.; Byrd, R. H.; Lu, P.; Nocedal, J. Algorithm 778: L-BFGS-B: Fortran subroutines for large-scale bound-constrained optimization. ACM Trans. Math. Software (TOMS) 1997, 23 (4), 550-560.
78. Ribeiro, A. A. S. T.; Horta, B. A. C.; de Alencastro, R. B. MKTOP: A program for automatic construction of molecular topologies. J. Braz. Chem. Soc. 2008, 19 (7), 1433-1435.
79. Kurtz, H. A.; Stewart, J. J. P.; Dieter, K. M. Calculation of the nonlinear optical properties of molecules. J. Comput. Chem. 1990, 11 (1), 82-87.
80. Hostaš, J.; Řezáč, J.; Hobza, P. On the performance of the semiempirical quantum mechanical PM6 and PM7 methods for noncovalent interactions. Chem. Phys. Lett. 2013, 568, 161-166.
81. Israelachvili, J. N.. Intermolecular and surface forces, 3rd ed.; Academic Press: San Diego, CA, 2011.
82. Clayden, J., Greeves, N., and Warren, S. Organic Chemistry; Oxford University Press: Oxford, U.K., 2012.
83. Cioslowski, J.; Liu, G.; Moncrieff, D. Theoretical thermochemistry of homolytic C-C and C-Cl bond dissociations in unbranched perchloroalkanes. J. Phys. Chem. A 1998, 102 (48), 9965-9969.
84. Zitko, V.. Chlorinated para ffi ns. In The Handbook of Environmental Chemistry: Anthropogenie Compounds; Hutzinger, O., Ed.; Springer: Berlin, 1980.
85. CHIRON: The Biomarker Catalogue; http://www.chiron.no; Chiron AS: Trondheim, Norway, 2008.