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Universal short-range ab initio atom–atom potentials for interaction energy contributions with an optimal repulsion functional form

  • Jan K. Konieczny
  • W. Andrzej Sokalski
Original Paper
Part of the following topical collections:
  1. 6th conference on Modeling & Design of Molecular Materials in Kudowa Zdrój (MDMM 2014)

Abstract

The repulsion term in conventional force fields constitutes a major source of error. Assuming that this could originate from a too simple analytical functional form, we analyzed various analytical functions using ab initio exchange component values as a reference and obtained (α + β R −1)exp(−γ R) as the optimal form to represent the repulsion term. Universal exchange, delocalization, and electrostatic penetration potentials approximating the corresponding interaction energy components defined within hybrid variation-perturbation theory (HVPT) were derived using as a reference a training set of 660 biomolecular complexes. The electrostatic multipole term was calculated using cumulative atomic multipole moments, whereas correlation contribution including dispersion term and first-order correlation correction was estimated from nonempirical D a s functions derived by Pernal et al. The resulting non-empirical atom–atom potentials (NEAAP) were tested for several urokinase–inhibitor complexes yielding improved docking results.

Keywords

Intermolecular interactions Nonempirical potentials Exchange repulsion Optimal analytical function 

Notes

Acknowledgments

This work was supported by Wroclaw Research Centre EIT+ within the project ”Biotechnologies and advanced medical technologies” - BioMed (POIG.01.01.02-02-003/08) co-financed by the European Regional Development Fund (Operational Programme Innovative Economy, 1.1.2). Partial financing by a statutory activity subsidy from Polish Ministry of Science and Higher Education for Faculty of Chemistry of Wroclaw University of Technology is also acknowledged. Calculations were performed in supercomputer centers in Wroclaw (WCSS), Poznan (PCSS), and Warsaw(ICM). The authors are indebted to Dr. Karol M. Langner from the University of Virginia at Charlottesville, VA, USA, for stimulating discussion and valuable comments.

References

  1. 1.
    Sokalski WA, Lowrey AH, Roszak S, Lewchenko V, Blaisdell J, Hariharan PC, Kaufman JJ (1986) Nonempirical atom–atom potentials for main components of intermolecular energy. J Comp Chem 7:693–700CrossRefGoogle Scholar
  2. 2.
    Gilson MK, Honig BH (1988) Energetics of charge–charge interactions in proteins. Proteins: Struct Funct Dyn 3:32–52CrossRefGoogle Scholar
  3. 3.
    Roterman I, Gilson K D, Scheraga H A (1989) A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. 1. Conformational predictions for the tandemly repeated peptide (a s na l aa s np r o)9. J Biomol Str Dyn 7:391–419CrossRefGoogle Scholar
  4. 4.
    Gresh N, Claverie P, Pullman A (1986) Intermolecular interactions: elaboration on an additive procedure including an explicit charge-transfer contribution. Int J Quantum Chem 29:101–118CrossRefGoogle Scholar
  5. 5.
    Singh UC, Kollman PA (1985) A water dimer potential based on ab initio calculations using Morokuma component analyses. J Chem Phys 83:4033–4040CrossRefGoogle Scholar
  6. 6.
    Torheyden M, Jansen G (2006) A new potential energy surface for the water dimer obtained from separate fits of ab initio electrostatic, induction, dispersion and exchange energy contributions. Mol Phys 104:2101–2138CrossRefGoogle Scholar
  7. 7.
    Parish RM, Sherill CD (2014) Spatial assignment of symmetry adapted perturbation theory interaction energy components: the atomic SAPT. J Chem Phys 141:044115CrossRefGoogle Scholar
  8. 8.
    Schmidt JR, Yu K, McDaniel JG (2015) Transferable next-generation force fields from simple liquids to complex materials. Acc Chem Res 48:548–556CrossRefGoogle Scholar
  9. 9.
    Zgarbová M, Otyepka M, Sponer J, Hobza P, Jurecka P (2010) Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations. Phys Chem Chem Phys 12:10476–10493CrossRefGoogle Scholar
  10. 10.
    Grzywa R, Dyguda-Kazimierowicz E, Sieńczyk M, Feliks M, Sokalski W A, Oleksyszyn J (2007) The molecular basis of urokinase inhibition: from the nonempirical analysis of intermolecular interactions to the prediction of binding affinity. J Mol Model 13:677–683CrossRefGoogle Scholar
  11. 11.
    Murrell JN, Teixeira JJ (1970) Dependence of exchange energy on orbital overlap. Chem Phys Lett 19:521–525Google Scholar
  12. 12.
    Sokalski WA, Chojnacki H (1978) Approximate exchange perturbation study of inter-molecular interactions in molecular complexes. Int J Quantum Chem 13:679–692CrossRefGoogle Scholar
  13. 13.
    Sokalski WA, Roszak S, Lowrey AH, Hariharan P, Walter Koski S, Kaufman JJ (1983) Crystal structure studies using ab-initio potential functions from partitioned MODPOT/VRDDO SCF energy calculations. I. N 2 and C O 2 test cases. II. Nitromethane C H 3 N O 2. Int J Quantum Chem: Quantum Chemistry Symp 17:375–391Google Scholar
  14. 14.
    Kitaura K, Morokuma K (1976) New energy decomposition scheme for molecular-interactions within Hartree–Fock approximation. Int J Quantum Chem 10:325–340CrossRefGoogle Scholar
  15. 15.
    Jeziorski B, Moszynski R, Szalewicz K (1994) Perturbation theory approach to intermolecular potential energy surfaces of van der Waals complexes. Chem Rev 94:1887–1930CrossRefGoogle Scholar
  16. 16.
    Politzer P, Murray J, Clark T (2015) Mathematical modeling and physical reality in noncovalent interactions. J Mol Model 21:52CrossRefGoogle Scholar
  17. 17.
    Sokalski WA, Roszak S, Pecul K (1988) An efficient procedure for decomposition of the SCF interaction energy into components with reduced basis set dependence. Chem Phys Lett 153:153–159CrossRefGoogle Scholar
  18. 18.
    Szefczyk B, Mulholland A, Ranaghan K, Sokalski W A (2004) Differential transition state stabilization in enzyme catalysis: quantum chemical analysis of interactions in the chorismate mutase reaction and prediction of the optimal catalytic field. J Am Chem Soc 126:16148–16159CrossRefGoogle Scholar
  19. 19.
    Langner KM, Janowski T, Gora R, Dziekonski P, Sokalski W A, Pulay P (2011) The ethidium-UA/AU intercalation site: effect of model fragmentation and backbone charge state. J Chem Theor Comp 7:2600–2609CrossRefGoogle Scholar
  20. 20.
    Sokalski WA, Poirier RA (1983) Cumulative atomic multipole representation of the molecular charge distribution and its basis set dependence. Chem Phys Lett 98:86–92CrossRefGoogle Scholar
  21. 21.
    Sokalski WA, Sawaryn A (1987) Correlated molecular and cumulative atomic multipole moments. J Chem Phys 87:526–534CrossRefGoogle Scholar
  22. 22.
    Schmidt MW, Baldridge KK, Boatz JA, Elbert S T, Gordon M S, Jensen JH, Koseki S, Matsunaga N, Nguyen KA, Su S, Windus TL, Dupuis M, Montgomery JA (1993) General atomic and molecular electronic structure system. J Comp Chem 14:1347–1363CrossRefGoogle Scholar
  23. 23.
    Sokalski WA, Shibata M, Ornstein RL, Rein R (1993) Point-charge representation of multicenter multipole moments in calculation of electrostatic properties. Theor Chim Acta 85:209–216CrossRefGoogle Scholar
  24. 24.
    Devereux M, Raghunathan S, Federov DG, Meuwly M (2014) A novel, computationally efficient multipolar model employing distributed charges for molecular dynamics simulations. J Chem Theor Comp 10:4229–4241CrossRefGoogle Scholar
  25. 25.
    Chalasinski G, Szczesniak MM (1994) Origins of structure and energetics of van der Waals clusters from ab initio calculations. Chem Rev 94:1723–1765CrossRefGoogle Scholar
  26. 26.
    Sokalski WA, Roszak S (1991) Efficient techniques for the decomposition of intermolecular interaction energy at SCF level and beyond. J Mol Struct(THEOCHEM) 234:387–400CrossRefGoogle Scholar
  27. 27.
    Podeszwa R, Pernal K, Patkowski K, Szalewicz K (2010) Extension of the Hartree–Fock plus dispersion method by first-order correlation effects. Phys Chem Lett 1:550–555CrossRefGoogle Scholar
  28. 28.
    Řezáč J, Riley KE, Hobza P (2011) S66: A well-balanced database of benchmark interaction energies relevant to biomolecular structures. J Chem Theor Comput 7:2427–2438CrossRefGoogle Scholar
  29. 29.
    Powell MJD (1964) An efficient method for finding the minimum of a function of several variables without calculating derivatives. Comp J 7:155–162CrossRefGoogle Scholar
  30. 30.
    Tafipolsky M, Engels B (2011) Accurate intermolecular potentials with physically grounded electrostatics. J Chem Theor Comp 7:1791–1803CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  1. 1.Department of Chemistry K1/W3Wrocław University of TechnologyWrocławPoland

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