Abstract.
Chemical reactions at solid/liquid or solid/gas hybrid interfaces govern the morphogenesis of growing solid state phases. In order to understand the polymorphism of solids, the understanding of the mechanisms and kinetics of these reactions is of crucial importance, as is an insight into the morphology of said surfaces on an atomistic scale. Ab initio simulations are a valuable tool to obtain these data, especially in materials design, where many possible materials for an application may have to be examined. In such cases the fabrication of all these materials for examination and characterization can be extremely time consuming and expensive. We present methods to determine surface properties and reaction energetics from ab initio simulations and demonstrate their potential using three examples: reaction energetics for the adsorption of adhesive component molecules on alumina surfaces, the functionalization of a silica surface with a fluorocarbon layer and the investigation of the wetting behavior of the functionalized surface, and the calculation of reaction energetics for a proton transfer process in the bacterial reaction centre of photosynthesis, including quantum mechanical effects as well as solvent and continuum electrostatic influences from the surrounding medium.
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References
F. Jensen, Introduction to Computational Chemistry (John Wiley & Sons, New York, 1999)
A. Szabo, S. Ostlund, Modern Quantum Chemistry (Dover Publications Inc., Mineola, New York, 1989)
R.O. Jones, O. Gunnarsson, Rev. Mod. Phys. 61, 689 (1989)
T. Frauenheim, G. Seifert, M. Elstner, Z. Hajnal, G. Jungnickel, D. Porezag, S. Suhai, R. Scholz, Phys. Stat. Sol. B 217, 41 (2000)
G. Seifert, H. Eschrig, W. Bieger, Z. Phys. Chem. 267, 529 (1986)
J.C. Slater, G.F. Koster, Phys. Rev. 94, 1498 (1954)
M. Elstner, D. Porezag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, S. Suhai, G. Seifert, Phys. Rev. B 58, 7260 (1998)
J.J.P. Stewart, J. Comput. Chem. 10, 209 (1989)
M.S. Dewar, E.G. Zoebisch, E.F. Healy, J.J.P. Steward, J. Am. Chem. Soc. 107, 3902 (1985)
A. Warshel, M. Levitt, J. Mol. Biol. 103, 227 (1976)
M.J. Field, P.A. Bash, M. Karplus, J. Comput. Chem. 11, 700 (1990)
J. Aaqvist, A. Warshel, Chem. Rev. 93, 2523 (1993)
J. Gao, Acc. Chem. Res. 29, 298 (1996)
S. Humbel, S. Sieber, K. Morokuma, J. Chem. Phys. 105, 1959 (1996)
M. Svensson, S. Humbel, R.D.J. Froese, T. Matsubara, S. Sieber, K. Morokuma, J. Phys. Chem. 100, 19357 (1996)
P. König, M. Hoffmann, T. Frauenheim, Q. Cui, J. Phys. Chem. B 109, 9082 (2005)
D. Riccardi, P. Schaefer, Y. Yang, H. Yu, N. Ghosh, X. Prat-Resina, P. König, G. Li, D. Xu, H. Guo et al., J. Phys. Chem. B 110, 6458 (2006)
D. Das, K. Eurenius, E. Billings, P. Sherwood, D. Chatfield, M. Hodoscek, B. Brooks, J. Chem. Phys. 117, 10534 (2002)
J.W. Ponder, D.A. Case, Adv. Prot. Chem. 66, 27 (2003)
C.R.A. Catlow, M. Dixon, W.C. Mackrodt, in Computer Simulations in Solids, Lect. Notes Phys., Vol. 166 (Springer-Verlag, Berlin, 1982), p. 130
J. Gao, D.G. Truhlar, Annu. Rev. Phys. Chem. 53, 467 (2002)
A. Warshel, Annu. Rev. Biophys. Biomol. Struct. 32, 425 (2002)
Q. Cui, M. Karplus, Adv. Prot. Chem. 66, 315 (2003)
C. Lennartz, A. Schaefer, F. Terstegen, W. Thiel, J. Phys. Chem. B 106, 1758 (2002)
V. Guallar, R.A. Friesner, J. Am. Chem. Soc. 126, 8501 (2004)
G.A. Cisneros, H.Y. Liu, Y.K. Zhang, W.T. Yang, J. Am. Chem. Soc. 125, 10384 (2003)
T. Woo, P. Margl, L. Deng, L. Cavallo, T. Ziegler, Catal. Today 50, 479 (1999)
A. Maiti, M. Sierka, J. Andzelm, J. Golab, J. Sauer, J. Phys. Chem. A 104, 10932 (2000)
C. Choi, M. Gordon, J. Am. Chem. Soc. 121, 11311 (1999)
P. Sinclair, A. de Vries, P. Sherwood, C. Catlow, R. van Santen, J. Chem. Soc. Faraday Trans. 94, 3401 (1998)
P. Sherwood, A.H. de Vries, M.F. Guest, G. Schreckenbach, C.R.A. Catlow, S.A. French, A.A. Sokol, S.T. Bromley, W. Thiel, A.J. Turner et al., J. Mol. Struct. (Theochem) 632, 1 (2003)
I. Hillier, J. Mol. Struct. (Theochem) 463, 45 (1999)
J. Sauer, M. Sierka, J. Comput. Chem. 21, 1470 (2000)
J. Noell, K. Morokuma, J. Phys. Chem. 80, 2675 (1976)
N. Lopez, G. Pacchioni, F. Maseras, F. Illas, Chem. Phys. 294, 611 (1998)
D. Riccardi, G. Li, Q. Cui, J. Phys. Chem. B 108, 6467 (2004)
M. Garcia-Viloca, D.G. Truhlar, J. Gao, J. Mol. Biol. 327, 549 (2003)
A. Warshel, Annu. Rev. Biophys. Biomol. Struct. 32, 425 (2003)
Y. Zhang, T. Lee, W. Yang, J. Chem. Phys. B 110, 46 (1999)
J. Sauer, Chem. Rev. 89, 199 (1989)
I. Antes, W. Thiel, J. Phys. Chem. A 103, 9290 (1999)
G.G. Ferenczy, J.L. Rivail, P.R. Surjan, G. Naray-Szabo, J. Comput. Chem. 13, 830 (1992)
V. Thery, D. Rinaldi, J.L. Rivail, B. Maigret, G.G. Ferenczy, J. Comput. Chem. 15, 269 (1994)
D.M. Philipp, R.A. Friesner, J. Comput. Chem. 20, 1468 (1999)
R.B. Murphy, D.M. Philipp, R.A. Friesner, J. Comput. Chem. 21, 1442 (2000)
J. Gao, P. Amara, C. Alhambra, M.J. Field, J. Phys. Chem. A 102, 4714 (1998)
J. Pu, J. Gao, D.G. Truhlar, J. Phys. Chem. A 108, 5454 (2004)
Q. Cui, M. Elstner, E. Kaxiras, T. Frauenheim, M. Karplus, J. Phys. Chem. B 105, 569 (2001)
G. Henkelman, G. Jóhannesson, H. Jónsson, Theoretical Methods in Condensed Phase Chemistry and Physics, in Progress in Theoretical Chemistry and Physics, Vol. 5 (Kluwer Academic Publishers, Dordrecht, 2002), pp. 269–300
B.R. Gelin, M. Karplus, Proc. Natl. Acad. Sci. 72, 2002 (1975)
M.J.S. Dewar, E.F. Healy, J.J.P. Stewart, J. Chem. Soc. Faraday Trans. II 80, 227 (1984)
I.V. Ionova, E.A. Carter, J. Chem. Phys. 98, 6377 (1993)
G. Henkelman, H. Jónsson, J. Chem. Phys. 111, 7010 (1999)
S. Fischer, M. Karplus, Chem. Phys. Lett. 194, 252 (1992)
J. Baker, J. Comput. Chem. 7, 385 (1986)
C.J. Cerjan, W.H. Miller, J. Chem. Phys. 75, 2800 (1981)
D.T. Nguyen, D.A. Case, J. Phys. Chem. 89, 4020 (1985)
W. Quapp, Chem. Phys. Lett. 253, 286 (1996)
H. Taylor, J. Simmons, J. Phys. Chem. 89, 684 (1985)
D. Wales, J. Chem. Phys. 91, 7002 (1989)
H. Jónsson, G. Mills, K.W. Jacobsen, in Classical and Quantum Dynamics in Condensed Phase Simulations (World Scientific, Singapore, 1998), p. 387
G. Henkelman, H. Jónsson, J. Chem. Phys. 113, 9978 (2000)
P. Maragakis, S.A. Adreev, Y. Brumer, D.R. Reichmann, E. Kaxiras, J. Chem. Phys. 117, 4651 (2002)
G. Henkelman, B.P. Uberuaga, H. Jónsson, J. Chem. Phys. 113, 9901 (2000)
G.M. Torrie, J.P. Valleau, J. Comput. Phys. 23, 187 (1977)
C. Bartels, M. Karplus, J. Comput. Chem. 18, 1450 (1997)
E. Darve, A. Pohorille, J. Chem. Phys. 115, 9169 (2001)
D.J. Tobias, C.L. Brooks III, J. Chem. Phys. 89, 5115 (1988)
B. Roux, M. Karplus, Biophys. J. 59, 961 (1991)
E.A. Cartera, G. Ciccotti, J.T. Hynesa, R. Kapralb, Chem. Phys. Lett. 156, 472 (1989)
A. Laio, M. Parrinello, Proc. Natl. Acad. Sci. (USA) 99, 12562 (2002)
N.K. Banavali, B. Roux, J. Am. Chem. Soc. 127, 6866 (2005)
J.K. Hwang, A. Warshel, J. Am. Chem. Soc. 118, 11745 (1996)
Y.R. Mo, J. Gao, J. Comput. Chem. 21, 1458 (2000)
J. Kästner, W. Thiel, J. Chem. Phys. 124, 234106 (2006)
P.H. König, Q. Cui (submitted)
Z. Kurtovic, M. Marchi, D. Chandler, Mol. Phys. 78, 1155 (1993)
M. Gao, D. Craig, V. Vogel, K. Schulten, J. Mol. Biol. 323, 939 (2002)
K. Kreuer, S.J. Paddison, E. Spohr, M. Schuster, Chem. Rev. 104, 4637 (2004)
A. Fersht, Structure and Mechanism in Protein Science: Guide to Enzyme Catalysis and Protein Folding (W.H. Freeman, New York, 1999)
R.A.W. Frank, C.M. Titman, J.V. Pratap, B.F. Luisi, R.N. Perham, Science 306, 872 (2004)
M. Elstner, T. Frauenheim, S. Suhai, J. Mol. Struct.: Theochem 632, 29 (2003)
D. Riccardi, P. König, X. Prat-Resina, H. Yu, M. Elstner, T. Frauenheim, Q. Cui, J. Am. Chem. Soc. 128, 16302 (2006)
A. Bondar, M. Elstner, S. Suhai, J.C. Smith, S. Fischer, Structure 12, 1281 (2004)
Q. Cui, M. Elstner, M. Karplus, J. Phys. Chem. B 106, 2721 (2002)
Q. Cui, M. Karplus, Adv. Prot. Chem. 66, 315 (2003)
R. Pomès, B. Roux, Biophys. J. 75, 33 (1998)
R. Pomès, B. Roux, Biophys. J. 71, 19 (1996)
M.F. Schumaker, R. Pomès, B. Roux, Biophys. J. 79, 2840 (2000)
R. Pomès, B. Roux, Biophys. J. 82, 2304 (2002)
N. Chakrabarti, E. Tajkhorshid, B. Roux, R. Pomès, Structure 12, 65 (2004)
A. Burykin, A. Warshel, Biophys. J. 85, 3696 (2003)
N. Chakrabarti, B. Roux, R. Pomès, J. Mol. Biol. 343, 493 (2004)
Y. Wu, G.A. Voth, Biophys. J. 85, 864 (2003)
P.H. König, N. Ghosh, M. Hoffmann, M. Elstner, E. Tajkhorshid, T. Frauenheim, Q. Cui, J. Phys. Chem. A 110, 548 (2006)
M. Hoffmann, P.H. König et al. (in preparation)
A. Glazer, Ann. Rev. Plant Physiol. 38, 11 (1987)
H. Komiya, T.O. Yeates, D.C. Rees, J.P. Allen, G. Feher, Proc. Natl. Acad. Sci. (USA) 85, 9012 (1988)
P. Sebban, P. Maroti, D.K. Hanson, Biochimie 77, 677 (1995)
M.Y. Okamura, M.L. Paddock, M.S. Graige, G. Feher, Biochim. Biophys. Acta 1458, 148 (2000)
A.D. MacKerell, D. Bashford, M. Bellott, R.L. Dunbrack, J.D. Evanseck, M.J. Field, S. Fischer, J. Gao, H. Guo, S. Ha et al., J. Phys. Chem. B 102, 3586 (1998)
C.L. Brooks, M. Karplus, J. Mol. Biol. 208, 159 (1989)
W. Im, S. Berneche, B. Roux, J. Chem. Phys. 114, 2924 (2001)
P. Schaefer, D. Riccardi, Q. Cui, J. Chem. Phys. 123, 014905 (2005)
A. Remy, K. Gerwert, Nat. Struct. Biol. 10, 637 (2003)
P. Sebban, P. Maróti, M. Schiffer, D.K. Hanson, Biochemistry 34, 8390 (1995)
J.M. Knaup, C. Köhler, T. Frauenheim, A.T. Blumenau, M. Amkreutz, P. Schiffels, B. Schneider, O.D. Hennemann, J. Phys. Chem. B 110, 20460 (2006)
T. Krüger, M. Elstner, P. Schiffels, T. Frauenheim, J. Chem. Phys. 122, 114110 (2005)
J. Barz, A. Haupt, U. Vohrer, H. Hilgers, C. Oehr, Surf. Coat. Technol. 200, 453 (2005)
C. Köhler, T. Frauenheim, Surf. Sci. 600, 453 (2006)
C. Köhler, Z. Hajnal, P. Deák, T. Frauenheim, S. Suhai, Phys. Rev. B 64, 085333 (2001)
C. Biloiu, I.A. Biloiu, Y. Sakai, Y. Suda, A. Ohta, J. Vac. Sci. Tech. A 22, 13 (2004)
A. Vanhulsel, A. Dekempeneer, J. Smeets, J.P. Celis, J. Vac. Sci. Tech. A 17, 2378 (1999)
S.L. Mayo, B.D. Olafson, W.A. Goddard III, J. Phys. Chem. 94, 8897 (1990)
M.G. Martin, J.I. Siepmann, J. Phys. Chem. B 103, 4508 (1999)
D.L. Schmidt, C.E. Coburn, B.M. DeKoven, G.E. Potter, G.F. Meyers, D.A. Fischer, Nature 368, 39 (1994)
Z. Guo, F. Zhou, J. Hao, W. Liu, J. Am. Chem. Soc. 127, 15670 (2005)
Y.L. Chen, C.A. Helm, J.N. Israelachvili, J. Phys. Chem. 95, 10736 (1991)
P.G. de Gennes, Rev. Mod. Phys. 57, 827 (1985)
R. Sedev, M. Fabretto, J. Ralston, J. Adhesion 80, 497 (2004)
M.J.P. Nijmeijer, C. Bruin, A.F. Bakker, J.M.J. van Leeuwen, Phys. Rev. A 42, 6052 (1990)
H. Yoshizawa, Y.L. Chen, J.N. Israelachvili, J. Phys. Chem. 97, 4128 (1993)
C.F. Fan, T. Cagin, J. Chem. Phys. 103, 9053 (1995)
M.J. de Ruijter, T.D. Blake, J. De Coninck, Langmuir 15, 7836 (1999)
T. Werder, J.H. Walther, R.L. Jaffe, T. Halicioglu, P. Koumoutsakos, J. Phys. Chem. B 107, 1345 (2003)
H.J.C. Berendsen, J.A. Grigera, T.P. Straatsma, J. Phys. Chem. 91, 6269 (1987)
P.E.M. Lopes, V. Murashov, M. Tazi, E. Demchuk, A.D. MacKerell Jr., J. Phys. Chem. B 110, 2782 (2006)
M.P. Allen, D.J. Tildesley, Computer Simulations of Liquids (Clarendon Press, Oxford, 1987)
W. Humphrey, A. Dalke, K. Schulten, J. Mol. Graphics 14, 33 (1996), http://www.ks.uiuc.edu/Research/vmd/
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Knaup, J., Köhler, C., Hoffmann, M. et al. Ab initio simulation of interface reactions as a foundation of understanding polymorphism. Eur. Phys. J. Spec. Top. 149, 127–144 (2007). https://doi.org/10.1140/epjst/e2007-00247-y
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DOI: https://doi.org/10.1140/epjst/e2007-00247-y