Leveraging symmetries of static atomic multipole electrostatics in molecular dynamics simulations

Journal of Chemical Theory and Computation

Volumn 9, Issue 12, 2013, Pages 5450-5459

  Bereau, Tristan ^a   Kramer, Christian ^b   Meuwly, Markus ^a  

^a UNIVERSITY OF BASEL   (Switzerland)

^b UNIVERSITY OF INNSBRUCK   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84890508653     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct400803f     Document Type: Article

References (59)

1. Kollman, P. A. Noncovalent interactions Acc. Chem. Res. 1977, 10, 365-371
2. Brobjer, J. T.; Murrell, J. N. A method for calculating the electrostatic energy between small polar molecules. The multipole-fitted point-charge method J. Chem. Soc. Far. Trans. 1982, 78, 1853-1870
3. Stone, A. J. The Theory of Intermolecular Forces; Clarendon Press: Oxford, 1996; Vol. 32.
4. Gray, C. Spherical tensor approach to multipole expansions. I. Electrostatic interactions Can. J. Phys. 1976, 54, 505-512
5. Stone, A. The description of bimolecular potentials, forces and torques: the S and V function expansions Mol. Phys. 1978, 36, 241-256
6. Price, S.; Stone, A.; Alderton, M. Explicit formulae for the electrostatic energy, forces, and torques between a pair of molecules of arbitrary symmetry Mol. Phys. 1984, 52, 987-1001
7. Vigné-Maeder, F.; Claverie, P. The exact multicenter multipolar part of a molecular charge distribution and its simplified representations J. Chem. Phys. 1988, 88, 4934
8. Hättig, C. Recurrence relations for the direct calculation of spherical multipole interaction tensors and Coulomb-type interaction energies Chem. Phys. Lett. 1996, 260, 341-351
9. Hättig, C. On the calculation of derivatives for Coulomb-type interaction energies and general anisotropic pair potentials Chem. Phys. Lett. 1997, 268, 521-530
10. Bereau, T.; Kramer, C.; Monnard, F. W.; Nogueira, E. S.; Ward, T. R.; Meuwly, M. Scoring multipole electrostatics in condensed-phase atomistic simulations J. Phys. Chem. B 2013, 117, 5460-5471
11. Leslie, M. DL-MULTI-A molecular dynamics program to use distributed multipole electrostatic models to simulate the dynamics of organic crystals Mol. Phys. 2008, 106, 1567-1578
12. Buckingham, A.; Fowler, P.; Hutson, J. M. Theoretical studies of van der Waals molecules and intermolecular forces Chem. Rev. 1988, 88, 963-988
13. Liem, S.; Popelier, P.; Leslie, M. Simulation of liquid water using a high-rank quantum topological electrostatic potential Int. J. Quantum Chem. 2004, 99, 685-694
14. Liem, S.; Popelier, P. High-rank quantum topological electrostatic potential: Molecular dynamics simulation of liquid hydrogen fluoride J. Chem. Phys. 2003, 119, 4560
15. Plattner, N.; Meuwly, M. The role of higher CO-multipole moments in understanding the dynamics of photodissociated carbonmonoxide in myoglobin Biophys. J. 2008, 94, 2505-2515
16. Plattner, N.; Meuwly, M. Higher order multipole moments for molecular dynamics simulations J. Mol. Model. 2009, 15, 687-694
17. Ponder, J. W.; Wu, C.; Ren, P.; Pande, V. S.; Chodera, J. D.; Schnieders, M. J.; Haque, I.; Mobley, D. L.; Lambrecht, D. S.; DiStasio, R. A., Jr; Head-Gordon, M.; Clark, G. N. I.; Johnson, M. E.; Head-Gordon, T. Current status of the AMOEBA polarizable force field J. Phys. Chem. B 2010, 114, 2549-2564
18. Kramer, C.; Gedeck, P.; Meuwly, M. Atomic multipoles: Electrostatic potential fit, local reference axis systems, and conformational dependence J. Comput. Chem. 2012, 33, 1673-1688
19. Goldstein, H.; Poole, Jr., C. P.; Safko, J. L. Classical Mechanics, 3 rd ed.; Addison-Wesley: Boston, 2001.
20. Sagui, C.; Pedersen, L. G.; Darden, T. A. Towards an accurate representation of electrostatics in classical force fields: Efficient implementation of multipolar interactions in biomolecular simulations J. Chem. Phys. 2004, 120, 73
21. Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual molecular dynamics J. Mol. Graphics 1996, 14, 33-38
22. Feller, S. E.; Zhang, Y.; Pastor, R. W.; Brooks, B. R. Constant pressure molecular dynamics simulation: The Langevin piston method J. Chem. Phys. 1995, 103, 4613
23. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Oxford University Press: New York, 1989.
24. Vanommeslaeghe, K.; Hatcher, E.; Acharya, C.; Kundu, S.; Zhong, S.; Shim, J.; Darian, E.; Guvench, O.; Lopes, P.; Vorobyov, I.; Mackerell, A. D. 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, 671-690
25. Wang, J.; Hou, T. Application of molecular dynamics simulations in molecular property prediction. 1. Density and heat of vaporization J. Chem. Theory Comp. 2011, 7, 2151-2165
26. Jorgensen, W. L.; Schyman, P. Treatment of halogen bonding in the OPLS-AA force field: Application to potent anti-HIV agents J. Chem. Theory Comp. 2012, 8, 3895-3901
27. Zacharias, M.; Straatsma, T.; McCammon, J. Separation-shifted scaling, a new scaling method for Lennard-Jones interactions in thermodynamic integration J. Chem. Phys. 1994, 100, 9025-9031
28. Boresch, S. The role of bonded energy terms in free energy simulations-Insights from analytical results Mol. Sim. 2002, 28, 13-37
29. Wood, J. H.; Boring, A. M. Improved Pauli Hamiltonian for local-potential problems Phys. Rev. B 1978, 18, 2701-2711
30. Lee, B.; Richards, F. M. The interpretation of protein structures: Estimation of static accessibility J. Mol. Biol. 1971, 55, 379-400
31. Lide, D. R. CRC Handbook of Chemistry and Physics; CRC press: Boca Raton, FL, 2012.
32. 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, 11225-11236
33. Jorgensen, W. L.; Ulmschneider, J. P.; Tirado-Rives, J. Free energies of hydration from a generalized born model and an all-atom force field J. Phys. Chem. B. 2004, 108, 16264-16270
34. Lee, M. W.; Meuwly, M. Phys. Chem. Chem. Phys. 2013, 10.1039/c3cp52713a
35. Lee, M. W.; Meuwly, M. On the role of nonbonded interactions in vibrational energy relaxation of cyanide in water J. Phys. Chem. A 2011, 115, 5053-5061
36. Lee, M. W.; Carr, J. K.; Göllner, M.; Hamm, P.; Meuwly, M. 2D IR spectra of cyanide in water investigated by molecular dynamics simulations J. Chem. Phys. 2013, 139, 054506
37. Ibrahim, M. A. Molecular mechanical study of halogen bonding in drug discovery J. Comput. Chem. 2011, 32, 2564-2574
38. Hage, K. E.; Piquemal, J.-P.; Hobaika, Z.; Maroun, R. G.; Gresh, N. Could an anisotropic molecular mechanics/dynamics potential account for sigma hole effects in the complexes of halogenated compounds? J. Comput. Chem. 2013, 1125
39. Du, L.; Gao, J.; Bi, F.; Wang, L.; Liu, C. A polarizable ellipsoidal force field for halogen bonds J. Comput. Chem. 2013, 2032
40. Riddick, J. A.; Bunger, W. B.; Sakano, T. K. Organic Solvents: Physical Properties and Methods of Purification; John Wiley and Sons: New York, 1986.
41. Gerber, P. R. Charge distribution from a simple molecular orbital type calculation and non-bonding interaction terms in the force field MAB J. Comput.-Aided Mol. Des. 1998, 12, 37-51
42. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n -alkanes J. Comput. Phys. 1977, 23, 327-341
43. Kolář, M.; Hobza, P. On extension of the current biomolecular empirical force field for the description of halogen bonds J. Chem. Theory Comp. 2012, 8, 1325-1333
44. Battistutta, R.; De Moliner, E.; Sarno, S.; Zanotti, G.; Pinna, L. A. Structural features underlying selective inhibition of protein kinase CK2 by ATP site-directed tetrabromo-2-benzotriazole Protein Sci. 2001, 10, 2200-2206
45. Bortolato, A.; Moro, S. In silico binding free energy predictability by using the linear interaction energy (LIE) method: Bromobenzimidazole CK2 inhibitors as a case study J. Chem. Inf. Model. 2007, 47, 572-582
46. MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R.; Evanseck, J.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiórkiewicz- Kuczera, J.; Yin, D.; Karplus, M. All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 1998, 102, 3586-3616
47. 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, 1400-1415
48. Boresch, S.; Tettinger, F.; Leitgeb, M.; Karplus, M. Absolute binding free energies: A quantitative approach for their calculation J. Phys. Chem. B 2003, 107, 9535-9551
49. Mobley, D. L.; Chodera, J. D.; Dill, K. A. On the use of orientational restraints and symmetry corrections in alchemical free energy calculations J. Chem. Phys. 2006, 125, 084902
50. Deng, Y.; Roux, B. Computations of standard binding free energies with molecular dynamics simulations J. Phys. Chem. B 2009, 113, 2234-2246
51. Lin, H.; Truhlar, D. G. QM/MM: What have we learned, where are we, and where do we go from here? Theor. Chem. Acc. 2007, 117, 185-199
52. Potestio, R.; Fritsch, S.; Espanol, P.; Delgado-Buscalioni, R.; Kremer, K.; Everaers, R.; Donadio, D. Hamiltonian adaptive resolution simulation for molecular liquids Phys. Rev. Lett. 2013, 110, 108301
53. Car, R.; Parrinello, M. Unified approach for molecular dynamics and density-functional theory Phys. Rev. Lett. 1985, 55, 2471
54. Gresh, N.; Claverie, P.; Pullman, A. Intermolecular interactions: Reproduction of the results of ab initio supermolecule computations by an additive procedure Int. J. Quantum Chem. 1979, 16, 243-253
55. Gresh, N.; Claverie, P.; Pullman, A. Theoretical studies of molecular conformation. Derivation of an additive procedure for the computation of intramolecular interaction energies. Comparison with ab initio SCF computations Theor. Chim. Acta 1984, 66, 1-20
56. Gresh, N.; Pullman, A.; Claverie, P. Theoretical studies of molecular conformation. II: Application of the SIBFA procedure to molecules containing carbonyl and carboxylate oxygens and amide nitrogens Theor. Chim. Acta 1985, 67, 11-32
57. Gresh, N.; Claverie, P.; Pullman, A. Intermolecular interactions: Elaboration on an additive procedure including an explicit charge-transfer contribution Int. J. Quantum Chem. 1986, 29, 101-118
58. Ren, P.; Ponder, J. W. Polarizable atomic multipole water model for molecular mechanics simulation J. Phys. Chem. B 2003, 107, 5933-5947
59. 2+ solvation using polarizable atomic multipole potential J. Phys. Chem. B 2006, 110, 18553-18559