Calculations of interactions in biomolecular systems: comparison of quantum and classical approaches

Authors

  • Z.G. Bazhanova
  • M.G. Khrenova
  • A.V. Nemukhin

Keywords:

quantum-chemical calculations
QM/MM
intermolecular interactions

Abstract

Methodical aspects of molecular mechanics, quantum chemistry, and combined quantum mechanics/molecular mechanics (QM/MM) approaches are discussed with respect to the intermolecular interaction calculations between some aminoacids (arginine, histidine, and serine) and water molecules. Calculations are implemented on the supercomputer SKIF-MGU «Chebyshev» by using the density functional theory to describe quantum subsystems. Some practical recommendations are formulated on the basis of numerical results.

New computational technologies

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Published

2011-06-14

Issue

Vol. 12 (2011): Issue 2.

Section

Section 1. Numerical methods and applications

Author Biographies

Z.G. Bazhanova

Lomonosov Moscow State University,
Research Computing Center
• Senior Researcher

M.G. Khrenova

Lomonosov Moscow State University,
Department of Chemistry
• Junior Researcher

A.V. Nemukhin

Lomonosov Moscow State University,
Department of Chemistry
• Professor, Head of Laboratory

References

  1. Jensen F. Introduction to computational chemistry. New York: Wiley, 2007.
  2. Grigorenko B.L., Nemukhin A.V., Topol I.A., Burt S.K. Modeling of biomolecular systems with the quantum mechanical and molecular mechanical method dased on the effective fragment potential technique: proposal of flexible fragments // J. Phys. Chem. A. 2002. 106. 10663-10672.
  3. Nemukhin A.V., Grigorenko B.L., Topol I.A., Burt S.K. Flexible effective fragment QM/MM method: validation through the challenging tests // J. Comput. Chem. 2003. 24. 1410-1420.
  4. Stephens P.J., Devlin F.J., Chabalowski C.F., Frisch M.J. Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields // J. Phys. Chem. 1994. 98. 11623-11627.
  5. Cornell W., Cieplak P., Bayly C., Gould I., Merz K., Ferguson D., Spellmeyer D., Fox T., Caldwell J., Kollman P. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules // J. Am. Chem. Soc. 1995. 117. 5179-5197.
  6. Bylaska E.J., de Jong W.A., Kowalski K., Straatsma T.P., Wang M.V. D., Apra E., Hirata T.L. W.S., Hackler M.T., Zhao Y., Fan P.-D., Harrison R.J., Dupuis M., Smith D.M. A., Nieplocha J., Tipparaju V., Krishnan M., Auer A.A., Nooijen M., Brown E., Cisnerosand G., Fann G.I., Fruchtl H., Garza J., Hirao K., Kendall R., Nichols J.A., Tsemekhman K., Wolinski K., Anchell J., Bernholdt D., Borowski P., Clark T., Clerc D., Dachsel H., Deegan M., Dyall K., Elwood В., Glendening E., Gutowski M., Hess A., affe J., Johnson B., Ju J., Kobayashi R., Kutteh R., Lin Z., Littlefield R., Meng X.L. B., Nakajima T., Ni S., Pollack L., Rosing M., Sandrone G., Stave M., Thomas H.T. G., van Lenthe J., Wong A., Zhang Z. NWChem, a computational chemistry package for parallel computers. Version 5.0. Pacific Northwest National Laboratory, Richland, Washington 99352-0999, USA. 2006.
  7. Jeffrey G.A. An introduction to hydrogen bonding. Oxford: Oxford Univ. Press, 2006.