Explicit polarization: A quantum mechanical framework for developing next generation force fields

Accounts of Chemical Research

Volumn 47, Issue 9, 2014, Pages 2837-2845

  Gao, Jiali ^a,b   Truhlar, Donald G ^b   Wang, Yingjie ^b   Mazack, Michael J M ^b   Löffler, Patrick ^b   Provorse, Makenzie R ^b   Rehak, Pavel ^b  

^a JILIN UNIVERSITY   (China)

^b UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

IONIC LIQUID; PROTEIN; WATER;

CHEMICAL MODEL; CHEMISTRY; MOLECULAR DYNAMICS; QUANTUM THEORY; STATIC ELECTRICITY; TEMPERATURE;

IONIC LIQUIDS; MODELS, CHEMICAL; MOLECULAR DYNAMICS SIMULATION; PROTEINS; QUANTUM THEORY; STATIC ELECTRICITY; TEMPERATURE; WATER;

EID: 84949116890     PISSN: 00014842     EISSN: 15204898     Source Type: Journal    
DOI: 10.1021/ar5002186     Document Type: Article

References (61)

1. Levitt, M.; Lifson, S. Refinement of protein conformations using a macromolecular energy minimization procedure J. Mol. Biol. 1969, 46, 269-279
2. Jorgensen, W. L.; Tirado-Rives, J. Potential energy functions for atomic-level simulations of water and organic and biomolecular systems Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6665-6670
3. MacKerell, A. D., Jr. Empirical force fields for biological macromolecules: Overview and issues J. Comput. Chem. 2004, 25, 1584-1604
4. Aida, M.; Corongiu, G.; Clementi, E. Ab initio force field for simulations of proteins and nucleic acids Int. J. Quantum Chem. 1992, 42, 1353-1381
5. Gao, J. Toward a molecular orbital derived empirical potential for liquid simulations J. Phys. Chem. B 1997, 101, 657-663
6. Xie, W.; Gao, J. Design of a next generation force field: The X-POL potential J. Chem. Theory Comput. 2007, 3, 1890-1900
7. Van der Vaart, A.; Merz, K. M., Jr. The role of polarization and charge transfer in the solvation of biomolecules J. Am. Chem. Soc. 1999, 121, 9182-9190
8. Giese, T. J.; Chen, H. Y.; Dissanayake, T.; Giambasu, G. M.; Heldenbrand, H.; Huang, M.; Kuechler, E. R.; Lee, T. S.; Panteva, M. T.; Radak, B. K.; York, D. M. A variational linear-scaling framework to build practical, efficient next-generation orbital-based quantum force fields J. Chem. Theory Comput. 2013, 9, 1417-1427
9. Giese, T. J.; Chen, H. Y.; Huang, M.; York, D. M. Parametrization of an orbital-based linear-scaling quantum force field for noncovalent interactions J. Chem. Theory Comput. 2014, 10, 1086-1098
10. Stoll, H.; Preuss, H. On the direct calculation of localized HF orbitals in molecular clusters, layers and solids Theor. Chem. Acc. 1977, 46, 11-21
11. Gordon, M. S.; Fedorov, D. G.; Pruitt, S. R.; Slipchenko, L. V. Fragmentation methods: A route to accurate calculations on large systems Chem. Rev. 2012, 112, 632-672
12. Giese, T. J.; Huang, M.; Chen, H.; York, D. M. Recent advances toward a general purpose linear-scaling quantum force field Acc. Chem. Res. 2014, 10.1021/ar500103g
13. Richard, R. M.; Lao, K. U.; Herbert, J. M. Aiming for benchmark accuracy with the many-body expansion Acc. Chem. Res. 2014, 10.1021/ar500119q
14. Gao, J.; Wang, Y. Communication: Variational many-body expansion: Accounting for exchange repulsion, charge delocalization, and dispersion in the fragment-based explicit polarization method J. Chem. Phys. 2012, 136 071101
15. Gao, J. A molecular-orbital derived polarization potential for liquid water J. Chem. Phys. 1998, 109, 2346-2354
16. Xie, W.; Song, L.; Truhlar, D. G.; Gao, J. The variational explicit polarization potential and analytical first derivative of energy: Towards a next generation force field J. Chem. Phys. 2008, 128 234108
17. Song, L.; Han, J.; Lin, Y. L.; Xie, W.; Gao, J. Explicit polarization (X-Pol) potential using ab initio molecular orbital theory and density functional theory J. Phys. Chem. A 2009, 113, 11656-11664
18. Han, J.; Mazack, M. J. M.; Zhang, P.; Truhlar, D. G.; Gao, J. Quantum mechanical force field for water with explicit electronic polarization J. Chem. Phys. 2013, 139 054503
19. Zhang, P.; Truhlar, D. G.; Gao, J. Fragment-based quantum mechanical methods for periodic systems with Ewald summation and mean image charge convention for long-range electrostatic interactions Phys. Chem. Chem. Phys. 2012, 14, 7821-7829
20. Han, J. B.; Truhlar, D. G.; Gao, J. L. Optimization of the explicit polarization (X-Pol) potential using a hybrid density functional Theor. Chem. Acc. 2012, 131, 1161-1167
21. Mazack, M. J. M.; Gao, J. Quantum mechanical force field for hydrogen fluoride with explicit electronic polarization J. Chem. Phys. 2014, 140 204501
22. IUPAC-IUB Commission on Biochemical Nomenclature Abbreviations and symbols for description of conformation of polypeptide Pure Appl. Chem. 1974, 40, 291-308
23. Xie, W.; Orozco, M.; Truhlar, D. G.; Gao, J. X-Pol potential: An electronic structure-based force field for molecular dynamics simulation of a solvated protein in water J. Chem. Theory Comput. 2009, 5, 459-467
24. Gao, J.; Amara, P.; Alhambra, C.; Field, M. J. A generalized hybrid orbital (GHO) method for the treatment of boundary atoms in combined QM/MM calculations J. Phys. Chem. A 1998, 102, 4714-4721
25. Gao, J. Hybrid quantum mechanical/molecular mechanical simulations: An alternative avenue to solvent effects in organic chemistry Acc. Chem. Res. 1996, 29, 298-305
26. Singh, U. C.; Kollman, P. A. A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: applications to the CH3Cl + Cl- exchange reaction and gas phase protonation of polyenes J. Comput. Chem. 1986, 7, 718-730
27. Xie, W.; Song, L.; Truhlar, D. G.; Gao, J. Incorporation of QM/MM buffer zone in the variational double self-consistent field method J. Phys. Chem. B 2008, 112, 14124-14131
28. Leverentz, H. R.; Gao, J. L.; Truhlar, D. G. Using multipole point charge distributions to provide the electrostatic potential in the variational explicit polarization (X-Pol) potential Theor. Chem. Acc. 2011, 129, 3-13
29. Fedorov, D. G.; Slipchenko, L. V.; Kitaura, K. Systematic study of the embedding potential description in the fragment molecular orbital method J. Phys. Chem. A 2010, 114, 8742-8753
30. Wang, B.; Yang, K. R.; Xu, X.; Isegawa, M.; Leverentz, H. R.; Truhlar, D. G. Quantum mechanical fragment methods based on partitioning atoms or partitioning coordinates Acc. Chem. Res. 2014, 10.1021/ar500068a
31. Saha, A.; Raghavachari, K. Dimers of dimers (DOD): A new fragment-based method applied to large water clusters J. Chem. Theory Comput. 2014, 10, 58-67
32. Senn, H. M.; Thiel, W. QM/MM methods for biological systems Top. Curr. Chem. 2007, 268, 173-290
33. Wang, Y. J.; Sosa, C. P.; Cembran, A.; Truhlar, D. G.; Gao, J. L. Multilevel X-Pol: A fragment-based method with mixed quantum mechanical representations of different fragments J. Phys. Chem. B 2012, 116, 6781-6788
34. Kitaura, K.; Ikeo, E.; Asada, T.; Nakano, T.; Uebayasi, M. Fragment molecular orbital method: An approximate computational method for large molecules Chem. Phys. Lett. 1999, 313, 701-706
35. Nagata, T.; Brorsen, K.; Fedorov, D. G.; Kitaura, K.; Gordon, M. S. Fully analytic energy gradient in the fragment molecular orbital method J. Chem. Phys. 2011, 134 124115
36. Fedorov, D. G.; Ishida, T.; Uebayasi, M.; Kitaura, K. The fragment molecular orbital method for geometry optimizations of polypeptides and proteins J. Phys. Chem. A 2007, 111, 2722-2732
37. Richard, R. M.; Lao, K. U.; Herbert, J. M. Approaching the complete-basis limit with a truncated many-body expansion J. Chem. Phys. 2013, 139 224102
38. Cembran, A.; Bao, P.; Wang, Y.; Song, L.; Truhlar D, G.; Gao, J. On the interfragment exchange in the X-Pol method J. Chem. Theory Comput. 2010, 6, 2469-2476
39. Gao, J.; Cembran, A.; Mo, Y. Generalized X-Pol theory and charge delocalization states J. Chem. Theory Comput. 2010, 6, 2402-2410
40. Mo, Y. R.; Bao, P.; Gao, J. L. Energy decomposition analysis based on a block-localized wavefunction and multistate density functional theory Phys. Chem. Chem. Phys. 2011, 13, 6760-6775
41. Lao, K. U.; Herbert, J. M. An improved treatment of empirical dispersion and a many-body energy decomposition scheme for the explicit polarization plus symmetry-adapted perturbation theory (XSAPT) method J. Chem. Phys. 2013, 139 034107
42. Zhang, D. W.; Xiang, Y.; Zhang, J. Z. H. New advance in computational chemistry: Full quantum mechanical ab initio computation of streptavidin-biotin interaction energy J. Phys. Chem. B 2003, 107, 12039-12041
43. Li, W.; Li, S.; Jiang, Y. Generalized energy-based fragmentation approach for computing the ground-state energies and properties of large molecules J. Phys. Chem. A 2007, 111, 2193-2199
44. Truhlar, D. G.; Dahlke, E. E.; Leverentz, H. R. Evaluation of the electrostatically embedded many-body expansion and the electrostatically embedded many-body expansion of the correlation energy by application to low-lying water hexamers J. Chem.Theory Comput. 2008, 4, 33-41
45. Hratchian, H. P.; Parandekar, P. V.; Raghavachari, K.; Frisch, M. J.; Vreven, T. QM:QM electronic embedding using Mulliken atomic charges: Energies and analytic gradients in an ONIOM framework J. Chem. Phys. 2008, 128 034107
46. Fedorov, D. G.; Kitaura, K. Second order Møller-Plesset perturbation theory based upon the fragment molecular orbital method J. Chem. Phys. 2004, 121, 2483-2490
47. Wang, B.; Truhlar, D. G. Including charge penetration effects in molecular modeling J. Chem. Theory Comput. 2010, 6, 3330-3342
48. Mo, Y.; Subramanian, G.; Gao, J.; Ferguson, D. M. Cation-π interactions: An energy decomposition analysis and its implication in δ-opioid receptor-ligand binding J. Am. Chem. Soc. 2002, 124, 4832-4837
49. Pople, J. A.; Santry, D. P.; Segal, G. A. Approximate self-consistent molecular orbital theory. I. Invariant procedures J. Chem. Phys. 1965, 43, S129-S135
50. Elstner, M.; Porezag, D.; Juugnickel, G.; Elsner, J.; Haugk, M.; Frauenheim, T.; Sukai, S.; Seifect, G. Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties Phys. Rev. B 1998, 58, 7260-7268
51. Zhang, P.; Fiedler, L.; Leverentz, H. R.; Truhlar, D. G.; Gao, J. L. Polarized molecular orbital model chemistry. 2. The PMO method J. Chem. Theory Comput. 2011, 7, 857-867
52. 2012, 8, 2983.
53. Isegawa, M.; Fiedler, L.; Leverentz, H. R.; Wang, Y. J.; Nachimuthu, S.; Gao, J. L.; Truhlar, D. G. Polarized Molecular Orbital Model Chemistry 3. The PMO Method Extended to Organic Chemistry J. Chem. Theory Comput. 2013, 9, 33-45
54. McNamara, J. P.; Sharma, R.; Vincent, M. A.; Hillier, I. H.; Morgado, C. A. The non-covalent functionalisation of carbon nanotubes studied by density functional and semi-empirical molecular orbital methods including dispersion corrections Phys. Chem. Chem. Phys. 2008, 10, 128-135
55. Zhang, P.; Bao, P.; Gao, J. L. Dipole preserving and polarization consistent charges J. Comput. Chem. 2011, 32, 2127-2139
56. Sprik, M. Hydrogen bonding and the static dielectric constant in liquid water J. Chem. Phys. 1991, 95, 6762-6769
57. Soper, A. K. The radial distribution functions of water and ice from 220 to 673 K and at pressures up to 400 MPa Chem. Phys. 2000, 258, 121-137
58. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model J. Am. Chem. Soc. 1985, 107, 3902-3909
59. Morrow, T. I.; Maginn, E. J. Molecular dynamics study of the ionic liquid 1-n-butyl-3-methylimidazolium hexafluorophosphate J. Phys. Chem. B 2002, 106, 12807-12813
60. Youngs, T. G. A.; Hardacre, C. Application of static charge transfer within an ionic-liquid force field and its effect on structure and dynamics ChemPhysChem 2008, 9, 1548-1558
61. Wendler, K.; Zahn, S.; Dommert, F.; Berger, R.; Holm, C.; Kirchner, B.; Delle Site, L. Locality and fluctuations: Trends in imidazolium-based ionic liquids and beyond J. Chem. Theory Comput. 2011, 7, 3040-3044