Computing pKa values with a mixing hamiltonian quantum mechanical/molecular mechanical approach

Journal of Chemical Theory and Computation

Volumn 9, Issue 9, 2013, Pages 4257-4265

  Liu, Yang ^a   Fan, Xiaoli ^b,c   Jin, Yingdi ^a   Hu, Xiangqian ^c   Hu, Hao ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b NORTHWESTERN POLYTECHNICAL UNIVERSITY   (China)

^c DUKE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84884179993     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct400406v     Document Type: Article

References (59)

1. Marx, D. Proton transfer 200 years after von Grotthuss: Insights from ab initio simulations ChemPhysChem 2006, 7, 1848
2. Mennucci, B.; Cammi, R., Continuum Solvation Models in Chemical Physics: From Theory to Applications; John Wiley & Sons, Ltd.: West Sussex, England, 2007.
3. Warshel, A. Calculations of Enzymatic Reactions: Calculations of pKa, Proton Transfer Reactions, and General Acid Catalysis Reactions in Enzymes Biochemistry 1981, 20, 3167
4. a of Ethane J. Am. Chem. Soc. 1987, 109, 6857
5. a Difference: Phenol in Aqueous Solution J. Am. Chem. Soc. 1996, 118, 4912
6. Li, G. H.; Cui, Q. p K (a) calculations with QM/MM free energy perturbations J. Phys. Chem. B 2003, 107, 14521
7. Riccardi, D.; Schaefer, P.; Cui, Q. p K (a) calculations in solution and proteins with QM/MM free energy perturbation simulations: A quantitative test of QM/MM protocols J. Phys. Chem. B 2005, 109, 17715
8. Ghosh, N.; Cui, Q. pK(a) of residue 66 in Staphylococal nuclease. I. Insights from QM/MM simulations with conventional sampling J. Phys. Chem. B 2008, 112, 8387
9. Ghosh, N.; Prat-Resina, X.; Gunner, M. R.; Cui, Q. Microscopic pK(a) Analysis of Glu286 in Cytochrome c Oxidase (Rhodobacter sphaeroides): Toward a Calibrated Molecular Model Biochemistry 2009, 48, 2468
10. Goyal, P.; Ghosh, N.; Phatak, P.; Clemens, M.; Gaus, M.; Elstner, M.; Cui, Q. Proton Storage Site in Bacteriorhodopsin: New Insights from Quantum Mechanics/Molecular Mechanics Simulations of Microscopic pK(a) and Infrared Spectra J. Am. Chem. Soc. 2011, 133, 14981
11. Car, R.; Parrinello, M. Unified approach for molecular-dynamics and density-functional theory Phys. Rev. Lett. 1985, 55, 2471
12. Blumberger, J.; Bernasconi, L.; Tavernelli, I.; Vuilleumier, R.; Sprik, M. Electronic structure and solvation of copper and silver ions: A theoretical picture of a model aqueous redox reaction J. Am. Chem. Soc. 2004, 126, 3928
13. Blumberger, J.; Sprik, M. Free energy of oxidation of metal aqua ions by an enforced change of coordination J. Phys. Chem. B 2004, 108, 6529
14. Blumberger, J.; Sprik, M. Ab initio molecular dynamics simulation of the aqueous Ru2+/Ru3+ redox reaction: The Marcus perspective J. Phys. Chem. B 2005, 109, 6793
15. 2+ redox couple: A biased Born-Oppenheimer molecular dynamics investigation J. Chem. Phys. 2006, 124, 064507
16. VandeVondele, J.; Lynden-Bell, R.; Meijer, E. J.; Sprik, M. Density functional theory study of tetrathiafulvalene and thianthrene in acetonitrile: Structure, dynamics, and redox properties J. Phys. Chem. B 2006, 110, 3614
17. Sulpizi, M.; Sprik, M. Acidity constants from vertical energy gaps: density functional theory based molecular dynamics implementation Phys. Chem. Chem. Phys. 2008, 10, 5238
18. Cheng, J.; Sulpizi, M.; Sprik, M. Redox potentials and pK(a) for benzoquinone from density functional theory based molecular dynamics J. Chem. Phys. 2009, 131, 154504
19. Sulpizi, M.; Sprik, M. Acidity constants from DFT-based molecular dynamics simulations J. Phys. Condens. Matter 2010, 22, 284116
20. Mangold, M.; Rolland, L.; Costanzo, F.; Sprik, M.; Sulpizi, M.; Blumberger, J. Absolute pK(a) Values and Solvation Structure of Amino Acids from Density Functional Based Molecular Dynamics Simulation J. Chem. Theory Comput. 2011, 7, 1951
21. Liu, X. D.; Sprik, M.; Cheng, J. Hydration, acidity and metal complexing of polysulfide species: A first principles molecular dynamics study Chem. Phys. Lett. 2013, 563, 9
22. Kirkwood, J. G. Statistical mechanics of fluid mixtures J. Chem. Phys. 1935, 3, 300
23. Beveridge, D. L.; DiCapua, F. M., Free energy via molecular simulation: A primer. In Computer Simulation of Biomolecular Systems, van Gunsteren, W. F.; Weiner, P. K., Eds.; ESCOM: Leiden, The Netherlands, 1989; Vol. 1, pp 1.
24. Jorgensen, W. L. Free Energy Calculations: A Breakthrough for Modeling Organic Chemistry in Solution Acc. Chem. Res. 1989, 22, 184
25. Kollman, P. A. Free-energy calculations-Applications to chemical and biochemical phenomena Chem. Rev. 1993, 93, 2395
26. Hu, H.; Yang, W. T. Dual-topology/dual-coordinate free-energy simulation using QM/MM force field J. Chem. Phys. 2005, 123, 041102
27. Hu, H.; Yang, W. T. Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods Annu. Rev. Phys. Chem. 2008, 59, 573
28. Liu, S.; Pedersen, L. G. Estimation of Molecular Acidity via Electrostatic Potential at the Nucleus and Valence Natural Atomic Orbitals J. Phys. Chem. A 2009, 113, 3648
29. 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
30. Kastenholz, M. A.; Huenenberger, P. H. Computation of methodology-independent ionic solvation free energies from molecular simulations. II. The hydration free energy of the sodium cation J. Chem. Phys. 2006, 124, 224501
31. Kastenholz, M. A.; Hunenberger, P. H. Computation of methodology- independent ionic solvation free energies from molecular simulations. I. The electrostatic potential in molecular liquids J. Chem. Phys. 2006, 124, 124106
32. Reif, M. M.; Huenenbergera, P. H. Computation of methodology-independent single-ion solvation properties from molecular simulations. III. Correction terms for the solvation free energies, enthalpies, entropies, heat capacities, volumes, compressibilities, and expansivities of solvated ions J. Chem. Phys. 2011, 134, 144103
33. Zwanzig, R. W. High-temperature equation of state by a perturbation method. I. Nonpolar gases J. Chem. Phys. 1954, 22, 1420
34. Kelly, C. P.; Cramer, C. J.; Truhlar, D. G. Aqueous solvation free energies of ions and ion-water clusters based on an accurate value for the absolute aqueous solvation free energy of the proton J. Phys. Chem. B 2006, 110, 16066
35. Tissandier, M. D.; Cowen, K. A.; Feng, W. Y.; Gundlach, E.; Cohen, M. H.; Earhart, A. D.; Coe, J. V.; Tuttle, T. R. The proton's absolute aqueous enthalpy and Gibbs free energy of solvation from cluster-ion solvation data J. Phys. Chem. A 1998, 102, 7787
36. Hu, X. Q.; Hu, H.; Yang, W. T. QM4D: An Integrated and Versatile Quantum Mechanical/Molecular Mechanical Simulation Package (http://www.qm4d.info/, accessed 2012).
37. Becke, A. D. Density-functional thermochemistry. III. The role of exact exchange J. Chem. Phys. 1993, 98, 5648
38. Lee, C.; Yang, W. T.; Parr, R. G. Development of the Colle-Salvetti correlation energy formula into a functional of the electron density Phys. Rev. B 1988, 37, 785
39. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 1983, 79, 926
40. MacKerell, J., A.D.; Brooks, B.; Brooks, I., C.L.; Nilsson, L. R., B.; Won, Y.; Karplus, M., CHARMM: The energy function and its parameterization with an overview of the program. In The Encyclopedia of Computational Chemistry, Schleyer, P. v. R., Ed.; John Wiley & Sons: Chichester, U.K., 1998; Vol. 1, pp 271.
41. Hu, H.; Liu, H. Pitfall in QM/MM Molecular Dynamics Simulation of Small Solutes in Solution J. Phys. Chem. B 2013, 117, 6505
42. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. Molecular dynamics with coupling to an external bath J. Chem. Phys. 1984, 81, 3684
43. Zeng, X. C.; Hu, H.; Hu, X. Q.; Cohen, A. J.; Yang, W. T. Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: Fractional electron approach J. Chem. Phys. 2008, 128, 124510
44. Zeng, X. C.; Hu, H.; Hu, X. Q.; Yang, W. T. Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method J. Chem. Phys. 2009, 130, 164111
45. Wodrich, M. D.; Corminboeuf, C.; Schleyer, P. v. R. Systematic errors in computed alkane energies using B3LYP and other popular DFT functionals Org. Lett. 2006, 8, 3631
46. Cohen, A. J.; Mori-Sanchez, P.; Yang, W. Insights into current limitations of density functional theory Science 2008, 321, 792
47. Cohen, A. J.; Mori-Sanchez, P.; Yang, W. Challenges for Density Functional Theory Chem. Rev. 2012, 112, 289
48. Riccardi, D.; Li, G.; Cui, Q. Importance of van der Waals Interactions in QM/MM Simulations J. Phys. Chem. B 2004, 108, 6467
49. Jin, Y.; Johnson, E. R.; Hu, X.; Yang, W.; Hu, H. Contributions of Pauli Repulsions to the Energetics and Physical Properties Computed in QM/MM Methods. Submitted to J. Comput. Chem., DOI: 10.1002/jcc.23401, 2013.
50. Cui, Q.; Karplus, M. Molecular properties from combined QM/MM methods. II. Chemical shifts in large molecules J. Phys. Chem. 2000, B 104, 3721
51. Brooks, C. L., Thermodynamic calculations in biological systems. In Computer simulations of biomolecular systems, van Gunsteren, W. F.; Weiner, P. K., Eds. ESCOM: Leiden, 1989; pp 73.
52. Wang, M. L.; Hu, X. Q.; Beratan, D. N.; Yang, W. T. Designing molecules by optimizing potentials J. Am. Chem. Soc. 2006, 128, 3228
53. Keinan, S.; Hu, X.; Beratan, D. N.; Yang, W. Designing molecules with optimal properties using the linear combination of atomic potentials approach in an AM1 semiempirical framework J. Phys. Chem. A 2007, 111, 176
54. Hu, X.; Beratan, D. N.; Yang, W. A gradient-directed Monte Carlo approach to molecular design J. Chem. Phys. 2008, 129, 064102
55. Keinan, S.; Therien, M. J.; Beratan, D. N.; Yang, W. Molecular Design of Porphyrin-Based Nonlinear Optical Materials J. Phys. Chem. A 2008, 112, 12203
56. Hu, X.; Beratan, D. N.; Yang, W. A gradient-directed Monte Carlo method for global optimization in a discrete space: Application to protein sequence design and folding J. Chem. Phys. 2009, 131, 154117
57. Hu, X.; Hu, H.; Beratan, D. N.; Yang, W. A Gradient-Directed Monte Carlo Approach for Protein Design J. Comput. Chem. 2010, 31, 2164
58. Jolly, W. L. Modern Inorganic Chemistry, 2 nd Edition; McGraw-Hill: New York, 1991.
59. McMurry, J. E. Fundamentals of Organic Chemistry, 7 th Edition; Cengage Learning: Independence, KY, and Victoria, Australia, 2010.