Recent advances toward a general purpose linear-scaling quantum force field

Accounts of Chemical Research

Volumn 47, Issue 9, 2014, Pages 2812-2820

  Giese, Timothy J ^a   Huang, Ming ^a,b   Chen, Haoyuan ^a   York, Darrin M ^a  

^a RUTGERS UNIVERSITY   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MACROMOLECULE;

CATALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; DRUG SCREENING; MACROMOLECULE; METABOLISM; PROCEDURES; QUANTUM THEORY; THEORETICAL MODEL;

CATALYSIS; COMPUTER SIMULATION; DRUG EVALUATION, PRECLINICAL; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; MODELS, THEORETICAL; QUANTUM THEORY;

EID: 84949115966     PISSN: 00014842     EISSN: 15204898     Source Type: Journal    
DOI: 10.1021/ar500103g     Document Type: Article

References (40)

1. van der Kamp, M. W.; Mulholland, A. J. Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology Biochemistry 2013, 52, 2708-2728
2. Muller, R. P.; Warshel, A. Ab initio calculations of free energy barriers for chemical reactions in solution J. Phys. Chem. 1995, 99, 17516-17524
3. Giese, T. J.; York, D. M. Charge-dependent model for many-body polarization, exchange, and dispersion interactions in hybrid quantum mechanical/molecular mechanical calculations J. Chem. Phys. 2007, 127 194101
4. Crawford, T. D. Coupled cluster calculations of vibrational raman optical activity spectra ChemPhysChem 2011, 12, 3442-3448
5. Tong, Y.; Ji, C. G.; Mei, Y.; Zhang, J. Z. H. Simulation of NMR data reveals that proteins local structures are stabilized by electronic polarization J. Am. Chem. Soc. 2009, 131, 8636-8641
6. He, X.; Wang, B.; Merz, K. M., Jr. Protein NMR chemical shift calculations based on the automated fragmentation QM/MM approach J. Phys. Chem. B 2009, 113, 10380-10388
7. Zhu, T.; He, X.; Zhang, J. Z. H. Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation Phys. Chem. Chem. Phys. 2012, 14, 7837-7845
8. Zanni, M. T.; Hochstrasser, R. M. Two-dimensional infrared spectroscopy: a promising new method for the time resolution of structures Curr. Opin. Struct. Biol. 2001, 11, 516-522
9. Xie, W.; Gao, J. Design of a next generation force field: The X-POL potential J. Chem. Theory. Comput. 2007, 3, 1890-1900
10. 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
11. Jacobson, L. D.; Herbert, J. M. An efficient, fragment-based electronic structure method for molecular systems: Self-consistent polarization with perturbative two-body exchange and dispersion J. Chem. Phys. 2011, 134 094118
12. Giese, T. J.; Chen, H.; 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
13. Duke, R. E.; Starovoytov, O. N.; Piquemal, J.; Cisneros, G. A. GEM: A molecular electronic density-based force field for molecular dynamics simulations J. Chem. Theory Comput. 2014, 10, 1361-1365 10.1021/ct500050p
14. Donchev, A. G.; Galkin, N. G.; Pereyaslavets, L. B.; Tarasov, V. I. Quantum mechanical polarizable force field (QMPFF3): Refinement and validation of the dispersion interaction for aromatic carbon J. Chem. Phys. 2006, 125 244107
15. Wollacott, A. M.; Merz, K. M., Jr. Assessment of semiempirical quantum mechanical methods for the evaluation of protein structures J. Chem. Theory Comput. 2007, 3, 1609-1619
16. 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
17. Yang, W. Electron density as the basic variable: A divide-and-conquer approach to the ab initio computation of large molecules J. Mol. Struct. 1992, 255, 461-479
18. Gordon, M. S.; Fedorov, D. G.; Pruitt, S. P.; Slipchenko, L. V. Fragmentation methods: A route to accurate calculations on large systems Chem. Rev. 2012, 112, 632-672
19. Gao, J. Toward a molecular orbital derived empirical potential for liquid simulation J. Phys. Chem. B 1997, 101, 657-663
20. 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
21. 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
22. Han, J.; Truhlar, D. G.; Gao, J. Optimization of the explicit polarization (X-Pol) potential using a hybrid density functional Theor. Chem. Acc. 2012, 131, 1161-1161
23. Giese, T. J.; Chen, H.; 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
24. Gaus, M.; Goez, A.; Elstner, M. Parametrization and benchmark of DFTB3 for organic molecules J. Chem. Theory Comput. 2013, 9, 338-354
25. Huang, M.; Giese, T. J.; Lee, T.-S.; York, D. M. Improvement of DNA and RNA sugar pucker profiles from semiempirical quantum methods J. Chem. Theory Comput. 2014, 10, 1538-1545
26. Korth, M. Third-generation hydrogen-bonding corrections for semiempirical QM methods and force fields J. Chem. Theory Comput. 2010, 6, 3808-3816
27. Garcia-Viloca, M.; Truhlar, D. G.; Gao, J. Importance of substrate and cofactor polarization in the active site of dihydrofolate reductase J. Mol. Biol. 2003, 327, 549-560
28. de Courcy, B.; Piquemal, J.; Garbay, C.; Gresh, N. Polarizable water molecules in ligand-macromolecule recognition. Impact on the relative affinities of competing pyrrolopyrimidine inhibitors for FAK kinase J. Am. Chem. Soc. 2010, 132, 3312-3320
29. Jiao, D.; Golubkov, P. A.; Darden, T. A.; Ren, P. Calculation of protein-ligand binding free energy by using a polarizable potential Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 6290-6295
30. Davies, T. G.; Bentley, J.; Arris, C. E.; Boyle, F. T.; Curtin, N. J.; Endicott, J. A.; Gibson, A. E.; Golding, B. T.; Griffin, R. J.; Hardcastle, I. R.; Jewsbury, P.; Johnson, L. N.; Mesguiche, V.; Newell, D. R.; Noble, M. E. M.; Tucker, J. A.; Wang, L.; Whitfield, H. J. Structure-based design of a potent purine-based cyclin-dependent kinase inhibitor Nat. Struct. Biol. 2002, 9, 745-749
31. Reynols, C. H.; Holloway, M. K. Thermodynamics of ligand binding and efficiency ACS Med. Chem. Lett. 2011, 2, 433-437
32. Ji, C. G.; Zhang, J. Z. H. Electronic polarization is important in stabilizing the native structures of proteins J. Phys. Chem. B 2009, 113, 16059-16064
33. Urakubo, Y.; Ikura, T.; Ito, N. Crystal structural analysis of protein-protein interactions drastically destabilized by a single mutation Protein Sci. 2008, 17, 1055-1065
34. Kobe, B.; Deisenhofer, J. A structural basis of the interactions between leucine-rich repeats and protein ligands Nature 1995, 374, 183-186
35. Kryger, G.; Harel, M.; Giles, K.; Toker, L.; Velan, B.; Lazar, A.; Kronman, C.; Barak, D.; Ariel, N.; Shafferman, A.; Silman, I.; Sussman, J. L. Structures of recombinant native and E202Q mutant human acetylcholinesterase complexed with the snake-venom toxin fasciculin-II Acta. Crystallogr. 2000, D56, 1385-1394
36. Wang, Y.; Sosa, C. P.; Cembran, A.; Truhlar, D. G.; Gao, J. Multilevel X-pol: A fragment-based method with mixed quantum mechanical representations of different fragments J. Phys. Chem. B 2012, 116, 6781-6788
37. Jurecka, P.; Šponer, J.; Černý, J.; Hobza, P. Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs Phys. Chem. Chem. Phys. 2006, 8, 1985-1993
38. Řezàč, J.; Riley, K. E.; Hobza, P. S66: A well-balanced database of benchmark interaction energies relevant to biomolecular structures J. Chem. Theory Comput. 2011, 7, 2427-2438
39. Bryantsev, V. S.; Diallo, M. S.; van Duin, A.; Goddard, W. A., III Evaluation of B3LYP, X3LYP, and M06-class density functionals for predicting the binding energies of neutral, protonated, and deprotonated water clusters J. Chem. Theory Comput. 2009, 5, 1016-1026
40. Skinner, L. B.; Huang, C.; Schlesinger, D.; Pettersson, L. G. M.; Nilsson, A.; Benmore, C. J. Benchmark oxygen-oxygen pairdistribution function of ambient water from X-ray diffraction measurements with a wide Q-range. J. Chem. Phys. 2013, 138, No. 074506.