Advertisement

The European Physical Journal Special Topics

, Volume 149, Issue 1, pp 127–144 | Cite as

Ab initio simulation of interface reactions as a foundation of understanding polymorphism

  • J. M. KnaupEmail author
  • C. Köhler
  • M. Hoffmann
  • P. H. König
  • T. Frauenheim
Article

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.

Keywords

Contact Angle Proton Transfer European Physical Journal Special Topic Mulliken Charge Minimum Energy Path 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. F. Jensen, Introduction to Computational Chemistry (John Wiley & Sons, New York, 1999) Google Scholar
  2. A. Szabo, S. Ostlund, Modern Quantum Chemistry (Dover Publications Inc., Mineola, New York, 1989) Google Scholar
  3. R.O. Jones, O. Gunnarsson, Rev. Mod. Phys. 61, 689 (1989) Google Scholar
  4. T. Frauenheim, G. Seifert, M. Elstner, Z. Hajnal, G. Jungnickel, D. Porezag, S. Suhai, R. Scholz, Phys. Stat. Sol. B 217, 41 (2000) Google Scholar
  5. G. Seifert, H. Eschrig, W. Bieger, Z. Phys. Chem. 267, 529 (1986) Google Scholar
  6. J.C. Slater, G.F. Koster, Phys. Rev. 94, 1498 (1954) Google Scholar
  7. M. Elstner, D. Porezag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, S. Suhai, G. Seifert, Phys. Rev. B 58, 7260 (1998) Google Scholar
  8. J.J.P. Stewart, J. Comput. Chem. 10, 209 (1989) Google Scholar
  9. M.S. Dewar, E.G. Zoebisch, E.F. Healy, J.J.P. Steward, J. Am. Chem. Soc. 107, 3902 (1985) Google Scholar
  10. A. Warshel, M. Levitt, J. Mol. Biol. 103, 227 (1976) Google Scholar
  11. M.J. Field, P.A. Bash, M. Karplus, J. Comput. Chem. 11, 700 (1990) Google Scholar
  12. J. Aaqvist, A. Warshel, Chem. Rev. 93, 2523 (1993) Google Scholar
  13. J. Gao, Acc. Chem. Res. 29, 298 (1996) Google Scholar
  14. S. Humbel, S. Sieber, K. Morokuma, J. Chem. Phys. 105, 1959 (1996) Google Scholar
  15. M. Svensson, S. Humbel, R.D.J. Froese, T. Matsubara, S. Sieber, K. Morokuma, J. Phys. Chem. 100, 19357 (1996) Google Scholar
  16. P. König, M. Hoffmann, T. Frauenheim, Q. Cui, J. Phys. Chem. B 109, 9082 (2005) Google Scholar
  17. 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) Google Scholar
  18. D. Das, K. Eurenius, E. Billings, P. Sherwood, D. Chatfield, M. Hodoscek, B. Brooks, J. Chem. Phys. 117, 10534 (2002) Google Scholar
  19. J.W. Ponder, D.A. Case, Adv. Prot. Chem. 66, 27 (2003) Google Scholar
  20. 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 Google Scholar
  21. J. Gao, D.G. Truhlar, Annu. Rev. Phys. Chem. 53, 467 (2002) Google Scholar
  22. A. Warshel, Annu. Rev. Biophys. Biomol. Struct. 32, 425 (2002) Google Scholar
  23. Q. Cui, M. Karplus, Adv. Prot. Chem. 66, 315 (2003) Google Scholar
  24. C. Lennartz, A. Schaefer, F. Terstegen, W. Thiel, J. Phys. Chem. B 106, 1758 (2002) Google Scholar
  25. V. Guallar, R.A. Friesner, J. Am. Chem. Soc. 126, 8501 (2004) Google Scholar
  26. G.A. Cisneros, H.Y. Liu, Y.K. Zhang, W.T. Yang, J. Am. Chem. Soc. 125, 10384 (2003) Google Scholar
  27. T. Woo, P. Margl, L. Deng, L. Cavallo, T. Ziegler, Catal. Today 50, 479 (1999) Google Scholar
  28. A. Maiti, M. Sierka, J. Andzelm, J. Golab, J. Sauer, J. Phys. Chem. A 104, 10932 (2000) Google Scholar
  29. C. Choi, M. Gordon, J. Am. Chem. Soc. 121, 11311 (1999) Google Scholar
  30. P. Sinclair, A. de Vries, P. Sherwood, C. Catlow, R. van Santen, J. Chem. Soc. Faraday Trans. 94, 3401 (1998) Google Scholar
  31. 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) Google Scholar
  32. I. Hillier, J. Mol. Struct. (Theochem) 463, 45 (1999) Google Scholar
  33. J. Sauer, M. Sierka, J. Comput. Chem. 21, 1470 (2000) Google Scholar
  34. J. Noell, K. Morokuma, J. Phys. Chem. 80, 2675 (1976) Google Scholar
  35. N. Lopez, G. Pacchioni, F. Maseras, F. Illas, Chem. Phys. 294, 611 (1998) Google Scholar
  36. D. Riccardi, G. Li, Q. Cui, J. Phys. Chem. B 108, 6467 (2004) Google Scholar
  37. M. Garcia-Viloca, D.G. Truhlar, J. Gao, J. Mol. Biol. 327, 549 (2003) Google Scholar
  38. A. Warshel, Annu. Rev. Biophys. Biomol. Struct. 32, 425 (2003) Google Scholar
  39. Y. Zhang, T. Lee, W. Yang, J. Chem. Phys. B 110, 46 (1999) Google Scholar
  40. J. Sauer, Chem. Rev. 89, 199 (1989) Google Scholar
  41. I. Antes, W. Thiel, J. Phys. Chem. A 103, 9290 (1999) Google Scholar
  42. G.G. Ferenczy, J.L. Rivail, P.R. Surjan, G. Naray-Szabo, J. Comput. Chem. 13, 830 (1992) Google Scholar
  43. V. Thery, D. Rinaldi, J.L. Rivail, B. Maigret, G.G. Ferenczy, J. Comput. Chem. 15, 269 (1994) Google Scholar
  44. D.M. Philipp, R.A. Friesner, J. Comput. Chem. 20, 1468 (1999) Google Scholar
  45. R.B. Murphy, D.M. Philipp, R.A. Friesner, J. Comput. Chem. 21, 1442 (2000) Google Scholar
  46. J. Gao, P. Amara, C. Alhambra, M.J. Field, J. Phys. Chem. A 102, 4714 (1998) Google Scholar
  47. J. Pu, J. Gao, D.G. Truhlar, J. Phys. Chem. A 108, 5454 (2004) Google Scholar
  48. Q. Cui, M. Elstner, E. Kaxiras, T. Frauenheim, M. Karplus, J. Phys. Chem. B 105, 569 (2001) Google Scholar
  49. 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 Google Scholar
  50. B.R. Gelin, M. Karplus, Proc. Natl. Acad. Sci. 72, 2002 (1975) Google Scholar
  51. M.J.S. Dewar, E.F. Healy, J.J.P. Stewart, J. Chem. Soc. Faraday Trans. II 80, 227 (1984) Google Scholar
  52. I.V. Ionova, E.A. Carter, J. Chem. Phys. 98, 6377 (1993) Google Scholar
  53. G. Henkelman, H. Jónsson, J. Chem. Phys. 111, 7010 (1999) Google Scholar
  54. S. Fischer, M. Karplus, Chem. Phys. Lett. 194, 252 (1992) Google Scholar
  55. J. Baker, J. Comput. Chem. 7, 385 (1986) Google Scholar
  56. C.J. Cerjan, W.H. Miller, J. Chem. Phys. 75, 2800 (1981) Google Scholar
  57. D.T. Nguyen, D.A. Case, J. Phys. Chem. 89, 4020 (1985) Google Scholar
  58. W. Quapp, Chem. Phys. Lett. 253, 286 (1996) Google Scholar
  59. H. Taylor, J. Simmons, J. Phys. Chem. 89, 684 (1985) Google Scholar
  60. D. Wales, J. Chem. Phys. 91, 7002 (1989) Google Scholar
  61. H. Jónsson, G. Mills, K.W. Jacobsen, in Classical and Quantum Dynamics in Condensed Phase Simulations (World Scientific, Singapore, 1998), p. 387 Google Scholar
  62. G. Henkelman, H. Jónsson, J. Chem. Phys. 113, 9978 (2000) Google Scholar
  63. P. Maragakis, S.A. Adreev, Y. Brumer, D.R. Reichmann, E. Kaxiras, J. Chem. Phys. 117, 4651 (2002) Google Scholar
  64. G. Henkelman, B.P. Uberuaga, H. Jónsson, J. Chem. Phys. 113, 9901 (2000) Google Scholar
  65. G.M. Torrie, J.P. Valleau, J. Comput. Phys. 23, 187 (1977) Google Scholar
  66. C. Bartels, M. Karplus, J. Comput. Chem. 18, 1450 (1997) Google Scholar
  67. E. Darve, A. Pohorille, J. Chem. Phys. 115, 9169 (2001) Google Scholar
  68. D.J. Tobias, C.L. Brooks III, J. Chem. Phys. 89, 5115 (1988) Google Scholar
  69. B. Roux, M. Karplus, Biophys. J. 59, 961 (1991) Google Scholar
  70. E.A. Cartera, G. Ciccotti, J.T. Hynesa, R. Kapralb, Chem. Phys. Lett. 156, 472 (1989) Google Scholar
  71. A. Laio, M. Parrinello, Proc. Natl. Acad. Sci. (USA) 99, 12562 (2002) Google Scholar
  72. N.K. Banavali, B. Roux, J. Am. Chem. Soc. 127, 6866 (2005) Google Scholar
  73. J.K. Hwang, A. Warshel, J. Am. Chem. Soc. 118, 11745 (1996) Google Scholar
  74. Y.R. Mo, J. Gao, J. Comput. Chem. 21, 1458 (2000) Google Scholar
  75. J. Kästner, W. Thiel, J. Chem. Phys. 124, 234106 (2006) Google Scholar
  76. P.H. König, Q. Cui (submitted) Google Scholar
  77. Z. Kurtovic, M. Marchi, D. Chandler, Mol. Phys. 78, 1155 (1993) Google Scholar
  78. M. Gao, D. Craig, V. Vogel, K. Schulten, J. Mol. Biol. 323, 939 (2002) Google Scholar
  79. K. Kreuer, S.J. Paddison, E. Spohr, M. Schuster, Chem. Rev. 104, 4637 (2004) Google Scholar
  80. A. Fersht, Structure and Mechanism in Protein Science: Guide to Enzyme Catalysis and Protein Folding (W.H. Freeman, New York, 1999) Google Scholar
  81. R.A.W. Frank, C.M. Titman, J.V. Pratap, B.F. Luisi, R.N. Perham, Science 306, 872 (2004) Google Scholar
  82. M. Elstner, T. Frauenheim, S. Suhai, J. Mol. Struct.: Theochem 632, 29 (2003) Google Scholar
  83. D. Riccardi, P. König, X. Prat-Resina, H. Yu, M. Elstner, T. Frauenheim, Q. Cui, J. Am. Chem. Soc. 128, 16302 (2006) Google Scholar
  84. A. Bondar, M. Elstner, S. Suhai, J.C. Smith, S. Fischer, Structure 12, 1281 (2004) Google Scholar
  85. Q. Cui, M. Elstner, M. Karplus, J. Phys. Chem. B 106, 2721 (2002) Google Scholar
  86. Q. Cui, M. Karplus, Adv. Prot. Chem. 66, 315 (2003) Google Scholar
  87. R. Pomès, B. Roux, Biophys. J. 75, 33 (1998) Google Scholar
  88. R. Pomès, B. Roux, Biophys. J. 71, 19 (1996) Google Scholar
  89. M.F. Schumaker, R. Pomès, B. Roux, Biophys. J. 79, 2840 (2000) Google Scholar
  90. R. Pomès, B. Roux, Biophys. J. 82, 2304 (2002) Google Scholar
  91. N. Chakrabarti, E. Tajkhorshid, B. Roux, R. Pomès, Structure 12, 65 (2004) Google Scholar
  92. A. Burykin, A. Warshel, Biophys. J. 85, 3696 (2003) Google Scholar
  93. N. Chakrabarti, B. Roux, R. Pomès, J. Mol. Biol. 343, 493 (2004) Google Scholar
  94. Y. Wu, G.A. Voth, Biophys. J. 85, 864 (2003) Google Scholar
  95. P.H. König, N. Ghosh, M. Hoffmann, M. Elstner, E. Tajkhorshid, T. Frauenheim, Q. Cui, J. Phys. Chem. A 110, 548 (2006) Google Scholar
  96. M. Hoffmann, P.H. König et al. (in preparation) Google Scholar
  97. A. Glazer, Ann. Rev. Plant Physiol. 38, 11 (1987) Google Scholar
  98. H. Komiya, T.O. Yeates, D.C. Rees, J.P. Allen, G. Feher, Proc. Natl. Acad. Sci. (USA) 85, 9012 (1988) Google Scholar
  99. P. Sebban, P. Maroti, D.K. Hanson, Biochimie 77, 677 (1995) Google Scholar
  100. M.Y. Okamura, M.L. Paddock, M.S. Graige, G. Feher, Biochim. Biophys. Acta 1458, 148 (2000) Google Scholar
  101. 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) Google Scholar
  102. C.L. Brooks, M. Karplus, J. Mol. Biol. 208, 159 (1989) Google Scholar
  103. W. Im, S. Berneche, B. Roux, J. Chem. Phys. 114, 2924 (2001) Google Scholar
  104. P. Schaefer, D. Riccardi, Q. Cui, J. Chem. Phys. 123, 014905 (2005) Google Scholar
  105. A. Remy, K. Gerwert, Nat. Struct. Biol. 10, 637 (2003) Google Scholar
  106. P. Sebban, P. Maróti, M. Schiffer, D.K. Hanson, Biochemistry 34, 8390 (1995) Google Scholar
  107. 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) Google Scholar
  108. T. Krüger, M. Elstner, P. Schiffels, T. Frauenheim, J. Chem. Phys. 122, 114110 (2005) Google Scholar
  109. J. Barz, A. Haupt, U. Vohrer, H. Hilgers, C. Oehr, Surf. Coat. Technol. 200, 453 (2005) Google Scholar
  110. C. Köhler, T. Frauenheim, Surf. Sci. 600, 453 (2006) Google Scholar
  111. C. Köhler, Z. Hajnal, P. Deák, T. Frauenheim, S. Suhai, Phys. Rev. B 64, 085333 (2001) Google Scholar
  112. C. Biloiu, I.A. Biloiu, Y. Sakai, Y. Suda, A. Ohta, J. Vac. Sci. Tech. A 22, 13 (2004) Google Scholar
  113. A. Vanhulsel, A. Dekempeneer, J. Smeets, J.P. Celis, J. Vac. Sci. Tech. A 17, 2378 (1999) Google Scholar
  114. S.L. Mayo, B.D. Olafson, W.A. Goddard III, J. Phys. Chem. 94, 8897 (1990) Google Scholar
  115. M.G. Martin, J.I. Siepmann, J. Phys. Chem. B 103, 4508 (1999) Google Scholar
  116. D.L. Schmidt, C.E. Coburn, B.M. DeKoven, G.E. Potter, G.F. Meyers, D.A. Fischer, Nature 368, 39 (1994) Google Scholar
  117. Z. Guo, F. Zhou, J. Hao, W. Liu, J. Am. Chem. Soc. 127, 15670 (2005) Google Scholar
  118. Y.L. Chen, C.A. Helm, J.N. Israelachvili, J. Phys. Chem. 95, 10736 (1991) Google Scholar
  119. P.G. de Gennes, Rev. Mod. Phys. 57, 827 (1985) Google Scholar
  120. R. Sedev, M. Fabretto, J. Ralston, J. Adhesion 80, 497 (2004) Google Scholar
  121. M.J.P. Nijmeijer, C. Bruin, A.F. Bakker, J.M.J. van Leeuwen, Phys. Rev. A 42, 6052 (1990) Google Scholar
  122. H. Yoshizawa, Y.L. Chen, J.N. Israelachvili, J. Phys. Chem. 97, 4128 (1993) Google Scholar
  123. C.F. Fan, T. Cagin, J. Chem. Phys. 103, 9053 (1995) Google Scholar
  124. M.J. de Ruijter, T.D. Blake, J. De Coninck, Langmuir 15, 7836 (1999) Google Scholar
  125. T. Werder, J.H. Walther, R.L. Jaffe, T. Halicioglu, P. Koumoutsakos, J. Phys. Chem. B 107, 1345 (2003) Google Scholar
  126. H.J.C. Berendsen, J.A. Grigera, T.P. Straatsma, J. Phys. Chem. 91, 6269 (1987) Google Scholar
  127. P.E.M. Lopes, V. Murashov, M. Tazi, E. Demchuk, A.D. MacKerell Jr., J. Phys. Chem. B 110, 2782 (2006) Google Scholar
  128. M.P. Allen, D.J. Tildesley, Computer Simulations of Liquids (Clarendon Press, Oxford, 1987) Google Scholar
  129. W. Humphrey, A. Dalke, K. Schulten, J. Mol. Graphics 14, 33 (1996), http://www.ks.uiuc.edu/Research/vmd/ Google Scholar

Copyright information

© EDP Sciences/Società Italiana di Fisica/Springer-Verlag 2007

Authors and Affiliations

  • J. M. Knaup
    • 1
    Email author
  • C. Köhler
    • 1
  • M. Hoffmann
    • 1
  • P. H. König
    • 2
  • T. Frauenheim
    • 1
  1. 1.Bremen Center for Computational Materials Science, Universität BremenBremenGermany
  2. 2.The BACTER institute, University of Wisconsin-MadisonMadisonUSA

Personalised recommendations