Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applications

Journal of Physical Chemistry B

Volumn 119, Issue 3, 2015, Pages 1062-1082

  Lu, Xiya ^a   Gaus, Michael ^a   Elstner, Marcus ^b   Cui, Qiang ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b KARLSRUHE INSTITUTE OF TECHNOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; CALCULATIONS; GASES; MAGNESIUM; METAL IONS; QUANTUM THEORY; ZINC;

BIOCHEMICAL SYSTEMS; CHEMICAL AND BIOLOGICALS; CONDENSED PHASE; ENERGETIC PROPERTIES; MAIN-GROUP ELEMENTS; MEAN ABSOLUTE DEVIATIONS; PARAMETRIZATIONS; SINGLE-POINT CALCULATIONS;

DENSITY FUNCTIONAL THEORY;

ALKALINE PHOSPHATASE; MAGNESIUM; MYOSIN II; PROTON; SOLVENT; ZINC;

CHEMICAL STRUCTURE; CHEMISTRY; ENZYME ACTIVE SITE; QUANTUM THEORY;

ALKALINE PHOSPHATASE; CATALYTIC DOMAIN; MAGNESIUM; MODELS, MOLECULAR; MYOSIN TYPE II; PROTONS; QUANTUM THEORY; SOLVENTS; ZINC;

EID: 84921507266     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp506557r     Document Type: Article

References (165)

1. Lippard, S. J.; Berg, J. M. Principles of Bioinorganic Chemistry; University Science Books: Mill Valley, CA, 1994.
2. Andreini, C.; Bertini, I.; Cavallaro, G.; Holliday, G. L.; Thornton, J. M. Metal Ions in Biological Catalysis: From Enzyme Databases to General Principles J. Biol. Inorg. Chem. 2008, 13, 1205-1218
3. Waldron, K. J.; Rutherford, J. C.; Ford, D.; Robinson, N. J. Metalloproteins and Metal Sensing Nature 2009, 460, 823-830
4. 2+ on ATP Linked Enzymes and the Calculation of Gibbs Free Energy of ATP Hydrolysis J. Phys. Chem. B 2012, 114, 16137-16146
5. Steitz, T.; Steitz, J. A General 2-Metal-Ion Mechanism For Catalytic RNA Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 6498-6502
6. Parkin, G. Synthetic Analogues Relevant to the Structure and Function of Zinc Enzymes Chem. Rev. 2004, 104, 699-768
7. Maret, W.; Li, Y. Coordination Dynamics of Zinc in Proteins Chem. Rev. 2009, 109, 4682-4707
8. Lipscomb, W. N.; Strater, N. Recent Advances in Zinc Enzymology Chem. Rev. 1996, 96, 2375-2433
9. Auld, D. S. Zinc Coordination Sphere in Biochemical Zinc Sites BioMetals 2001, 14, 271-313
10. Lee, Y.-M.; Lim, C. Physical Basis of Structural and Catalytic Zn-Binding Sites in Proteins J. Mol. Biol. 2008, 379, 545-553
11. Hoops, S. C.; Anderson, K. W.; Merz, K. M., Jr. Force-Field Design for Metalloproteins J. Am. Chem. Soc. 1991, 113, 8262-8270
12. Peters, M. B.; Yang, Y.; Wang, B.; Füsti-Molnár, L.; Weaver, M. N.; Merz, K. M. Structural Survey of Zinc-Containing Proteins and Development of the Zinc AMBER Force Field (ZAFF) J. Chem. Theory Comput. 2010, 6, 2935-2947
13. Babu, C. S.; Lim, C. Empirical Force Fields for Biologically Active Divalent Metal Cations in Water J. Phys. Chem. A 2006, 110, 691-699
14. Stote, R. H.; Karplus, M. Zinc-Binding in Proteins and Solution-A Simple but Accurate Nonbonded Representation Proteins 1995, 23, 12-31
15. Duarte, F.; Bauer, P.; Barrozo, A.; Amrein, B. A.; Purg, M.; Åqvist, J.; Kamerlin, S. C. L. Force Field Independent Metal Parameters Using a Nonbonded Dummy Model J. Phys. Chem. B 2014, 118, 4351-4362
16. Gresh, N.; Cisneros, G. A.; Darden, T. A.; Piquemal, J.-P. Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy J. Chem. Theory Comput. 2007, 3, 1960-1986
17. Wu, J. C.; Piquemal, J.-P.; Chaudret, R.; Reinhardt, P.; Ren, P. Polarizable Molecular Dynamics Simulation of Zn(II) in Water Using the AMOEBA Force Field J. Chem. Theory Comput. 2010, 6, 2059-2070
18. Zhang, J.; Yang, W.; Piquemal, J.-P.; Ren, P. Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential J. Chem. Theory Comput. 2012, 8, 1314-1324
19. Yu, H. B.; Whitfield, T. W.; Harder, E.; Lamoureux, G.; Vorobyov, I.; Anisimov, V. M.; MacKerell, A. D., Jr.; Roux, B. Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field J. Chem. Theory Comput. 2010, 6, 774-786
20. Sakharov, D. V.; Lim, C. Force Fields Including Charge Transfer and Local Polarization Effects: Application to Proteins Containing Multi/Heavy Metal Ions J. Comput. Chem. 2008, 30, 191-202
21. de Courcy, B.; Piquemal, J.-P.; Gresh, N. Energy Analysis of Zn Polycoordination in a Metalloprotein Environment and of the Role of a Neighboring Aromatic Residue. What Is the Impact of Polarization? J. Chem. Theory Comput. 2008, 4, 1659-1668
22. Gresh, N.; Piquemal, J.-P.; Krauss, M. Representation of Zn(II) Complexes in Polarizable Molecular Mechanics. Further Refinements of the Electrostatic and Short-Range Contributions. Comparisons with Parallel Ab Initio Computations J. Comput. Chem. 2005, 26, 1113-1130
23. Ryde, U. Carboxylate Binding Modes in Zinc Proteins: A Theoretical Study Biophys. J. 1999, 77, 2777-2787
24. Wu, R.; Hu, P.; Wang, S.; Cao, Z.; Zhang, Y. Flexibility of Catalytic Zinc Coordination in Thermolysin and HDAC8: A Born-Oppenheimer ab Initio QM/MM Molecular Dynamics Study J. Chem. Theory Comput. 2010, 6, 337-343
25. Wu, R.; Lu, Z.; Cao, Z.; Zhang, Y. A Transferable Nonbonded Pairwise Force Field to Model Zinc Interactions in Metalloproteins J. Chem. Theory Comput. 2011, 7, 433-443
26. Plotnikov, N. V.; Kamerlin, S. C. L.; Warshel, A. Paradynamics: An Effective and Reliable Model for Ab Initio QM/MM Free-Energy Calculations and Related Tasks J. Phys. Chem. B 2011, 115, 7950-7962
27. Hu, H.; Yang, W. Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio Quantum Mechanics/Molecular Mechanics Methods Annu. Rev. Phys. Chem. 2008, 59, 573-601
28. Wu, R. B.; Cao, Z. X.; Zhang, Y. K. Computational Simulations of Zinc Enzyme: Challenges and Recent Advances Prog. Chem. 2012, 24, 1175-1184
29. Wang, L. H.; Yu, X. Y.; Hu, P.; Broyde, S.; Zhang, Y. K. A Water-Mediated and Substrate-Assisted Catalytic Mechanism for Sulfolobus solfataricus DNA Polymerase IV J. Am. Chem. Soc. 2007, 129, 4731-4737
30. Blomberg, M. R. A.; Borowski, T.; Himo, F.; Liao, R. Z.; Siegbahn, P. E. M. Quantum Chemical Studies of Mechanisms for Metalloenzymes Chem. Rev. 2014, 114, 3601-3658
31. Jonas, S.; Hollfelder, F. Mapping Catalytic Promiscuity in the Alkaline Phosphatase Superfamily Pure Appl. Chem. 2009, 81, 731-742
32. Lassila, J. K.; Zalatan, J. G.; Herschlag, D. Biological Phosphoryl Transfer Reactions: Understanding Mechanism and Catalysis Annu. Rev. Biochem. 2011, 80, 669-702
33. Duarte, F.; Amrein, B. A.; Kamerlin, S. C. L. Modeling Catalytic Promiscuity in the Alkaline Phosphatase Superfamily Phys. Chem. Chem. Phys. 2013, 15, 11160-11177
34. Dewar, M. J. S.; Thiel, W. Ground States of Molecules. 38. The MNDO Method. Approximations and Parameters J. Am. Chem. Soc. 1977, 99, 4899-4907
35. Dewar, M. J. S.; Thiel, W. Ground States of Molecules. 39. MNDO Results for Molecules Containing Hydrogen, Carbon, Nitrogen, and Oxygen J. Am. Chem. Soc. 1977, 99, 4907-4917
36. Thiel, W.; Voityuk, A. A. Extension of MNDO to d Orbitals: Parameters and Results for the Second-Row Elements and for the Zinc Group J. Phys. Chem. 1996, 100, 616-626
37. 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
38. Stewart, J. J. P. Optimization of Parameters for Semiempirical Methods I. Method J. Comput. Chem. 1989, 10, 209-220
39. Hutter, M. C.; Reimers, J. R.; Hush, N. S. Modeling the Bacterial Photosynthetic Reaction Center. 1. Magnesium Parameters for the Semiempirical AM1Method Developed Using a Genetic Algorithm J. Phys. Chem. B 1998, 102, 8080-8090
40. Stewart, J. J. P. Optimization of Parameters for Semiempirical Methods IV: Extension of MNDO, AM1, and PM3 to More Main Group Elements J. Mol. Model. 2004, 10, 155-164
41. Cai, Z.; Lopez, P.; Reimers, J. R.; Cui, Q.; Elstner, M. Application of the Computationally Efficient Self-Consistent-Charge Density-Functional Tight-Binding Method to Magnesium-Containing Molecules J. Phys. Chem. A 2007, 111, 5743-5750
42. Imhof, P.; Noé, F.; Fischer, S.; Smith, J. C. AM1/d Parameters for Magnesium in Metalloenzymes J. Chem. Theory Comput. 2006, 2, 1050-1056
43. Sorkin, A.; Truhlar, D. G.; Amin, E. A. Energies, Geometries, and Charge Distributions of Zn Molecules, Clusters, and Biocenters from Coupled Cluster, Density Functional, and Neglect of Diatomic Differential Overlap Models J. Chem. Theory Comput. 2009, 5, 1254-1265
44. Dewar, M. J. S.; Merz, K. M. AM1 Parameters for Zinc Organometallics 1988, 7, 522-524
45. Brothers, E. N.; Suarez, D.; Deerfield, D. W.; Merz, K. M. PM3-Compatible Zinc Parameters Optimized for Metalloenzyme Active Sites J. Comput. Chem. 2004, 25, 1677-1692
46. Bräuer, M.; Kunert, M.; Dinjus, E.; Klussmann, M.; Döring, M.; Görls, H.; Anders, E. Evaluation of the Accuracy of PM3, AM1 and MNDO/d as Applied to Zinc Compounds J. Mol. Struct. (Theochem) 2000, 505, 289-301
47. Stewart, J. J. P. Optimization of Parameters for Semiempirical Methods V: Modification of NDDO Approximations and Application to 70 Elements J. Mol. Model. 2007, 13, 1173-1213
48. Hou, G.; Cui, Q. QM/MM Analysis Suggests That Alkaline Phosphatase (AP) and Nucleotide Pyrophosphatase/Phosphodiesterase Slightly Tighten the Transition State for Phosphate Diester Hydrolysis Relative to Solution: Implication for Catalytic Promiscuity in the AP Superfamily J. Am. Chem. Soc. 2012, 134, 229-246
49. Hou, G.; Cui, Q. Stabilization of Different Types of Transition States in a Single Enzyme Active Site: QM/MM Analysis of Enzymes in the Alkaline Phosphatase Superfamily J. Am. Chem. Soc. 2013, 135, 10457-10469
50. López-Canut, V.; Roca, M.; Bertrán, J.; Moliner, V.; Tunón, I. Theoretical Study of Phosphodiester Hydrolysis in Nucleotide Pyrophosphatase/Phosphodiesterase. Environmental Effects on the Reaction Mechanism J. Am. Chem. Soc. 2010, 132, 6955-6963
51. López-Canut, V.; Roca, M.; Bertrán, J.; Moliner, V.; Tunón, I. Promiscuity in Alkaline Phosphatase Superfamily. Unraveling Evolution through Molecular Simulations J. Am. Chem. Soc. 2011, 133, 12050-12062
52. Elstner, M.; Porezag, D.; Jungnickel, G.; Elsner, J.; Haugk, M.; Frauenheim, T.; Suhai, S.; Seifert, G. Self-Consistent-Charge Density-Functional Tight-Binding Method for Simulations of Complex Materials Properties Phys. Rev. B 1998, 58, 7260-7268
53. Elstner, M. SCC-DFTB: What is the Proper Degree of Self-Consistency? J. Phys. Chem. A 2007, 111, 5614-5621
54. Gaus, M.; Cui, Q.; Elstner, M. Density Functional Tight Binding (DFTB): Application to Organic and Biological Molecules WIREs Comput. Mol. Sci. 2014, 4, 49-61
55. Kruger, T.; Elstner, M.; Schiffels, P.; Frauenheim, T. Validation of the Density Functional Based Tight-Binding Approximation Method for the Calculation of Reaction Energies and Other Data J. Chem. Phys. 2005, 122, 114110 1-5
56. Sattelmeyer, K. W.; Tirado-Rives, J.; Jorgensen, W. Comparison of SCC-DFTB and NDDO-Based Semiempirical Molecular Orbital Methods for Organic Molecules J. Phys. Chem. A 2006, 110, 13551-13559
57. Otte, N.; Scholten, M.; Thiel, W. Looking at Self-Consistent-Charge Density Functional Tight Binding from a Semiempirical Perspective J. Phys. Chem. A 2007, 111, 5751-5755
58. Kubar, T.; Bodrog, Z.; Gaus, M.; Köhler, C.; Aradi, B.; Frauenheim, T.; Elstner, M. Parametrization of the SCC-DFTB Method for Halogens J. Chem. Theory Comput. 2013, 9, 2939-2949
59. Zheng, G.; Witek, H. A.; Bobadova-Parvanova, P.; Irle, S.; Musaev, D. G.; Prabhakar, R.; Morokuma, K.; Lundberg, M.; Elstner, M.; Köhler, C.; Köhler, T. Parameter Calibration of Transition-Metal Elements for the Spin-Polarized Self-Consistent-Charge Density-Functional Tight-Binding (DFTB) Method: Sc, Ti, Fe, Co, and Ni J. Chem. Theory Comput. 2007, 3, 1349-1367
60. Dolgonos, G.; Aradi, B.; Moreira, N. H.; Frauenheim, T. An Improved Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) Set of Parameters for Simulation of Bulk and Molecular Systems Involving Titanium J. Chem. Theory Comput. 2010, 6, 266-278
61. Grundkötter-Stock, B.; Bezugly, V.; Kunstmann, J.; Cuniberti, G.; Frauenheim, T.; Niehaus, T. A. SCC-DFTB Parametrization for Boron and Boranes J. Chem. Theory Comput. 2012, 8, 1153-1163
62. Elstner, M.; Cui, Q.; Munih, P.; Kaxiras, E.; Frauenheim, T.; Karplus, M. Modeling Zinc in Biomolecules with the Self Consistent Charge-Density Functional Tight Binding (SCC-DFTB) Method: Applications to Structural and Energetic Analysis J. Comput. Chem. 2003, 24, 565-581
63. Moreira, N. H.; Dolgonos, G.; Aradi, B.; Da Rosa, A. L.; Frauenheim, T. Toward an Accurate Density-Functional Tight-Binding Description of Zinc-Containing Compounds J. Chem. Theory Comput. 2009, 5, 605-614
64. Cui, Q.; Elstner, M.; Kaxiras, E.; Frauenheim, T.; Karplus, M. A QM/MM Implementation of the Self-Consistent Charge Density Functional Tight Binding (SCC-DFTB) Method J. Phys. Chem. B 2001, 105, 569-585
65. Elstner, M.; Frauenheim, T.; Suhai, S. An Approximate DFT Method for QM/MM Simulations of Biological Structures and Processes J. Mol. Struct. (Theochem) 2003, 632, 29-41
66. Riccardi, D.; Schaefer, P.; Yang, Y.; Yu, H.; Ghosh, N.; Prat-Resina, X.; König, P.; Li, G.; Xu, D.; Guo, H. Development of Effective Quantum Mechanical/Molecular Mechanical (QM/MM) Methods for Complex Biological Processes J. Phys. Chem. B 2006, 110, 6458-6469
67. Cui, Q.; Elstner, M.; Karplus, M. A Theoretical Analysis of the Proton and Hydride Transfer in Liver Alcohol Dehydrogenase (LADH) J. Phys. Chem. B 2002, 106, 2721-2740
68. Yang, Y.; Yu, H.; Cui, Q. Extensive Conformational Transitions Are Required to Turn On ATP Hydrolysis in Myosin J. Mol. Biol. 2008, 381, 1407-1420
69. Riccardi, D.; Yang, S.; Cui, Q. Proton Transfer Function of Carbonic Anhydrase: Insights from QM/MM simulations Biochim. Biophys. Acta 2010, 1804, 342-351
70. Yang, Y.; Miao, Y. P.; Wang, B.; Cui, G. L.; Merz, K. M., Jr. Catalytic Mechanism of Aromatic Prenylation by NphB Biochemistry 2012, 51, 2606-2618
71. Chakravorty, D. K.; Wang, B.; Lee, C. W.; Giedroc, D. P.; Merz, K. M., Jr. Simulations of Allosteric Motions in the Zinc Sensor CzrA J. Am. Chem. Soc. 2012, 134, 3367-3376
72. Xu, D. G.; Cui, Q.; Guo, H. Quantum Mechanical/Molecular Mechanical Studies of Zinc Hydrolases Int. Rev. Phys. Chem. 2014, 33, 1-41
73. Moreira, N. H.; da Rosa, A. L.; Frauenheim, T. Covalent Functionalization of ZnO Surfaces: A Density Functional Tight Binding Study Appl. Phys. Lett. 2009, 94, 193109 1-3
74. Holthaus, S. G.; Köppen, S.; Frauenheim, T.; Ciacchi, L. C. Atomistic Simulations of the ZnO(1210)/Water Interface: A Comparison between First-Principles, Tight-Binding, and Empirical Methods J. Chem. Theory Comput. 2012, 8, 4517-4526
75. Gaus, M.; Cui, Q.; Elstner, M. DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB) J. Chem. Theory Comput. 2011, 7, 931-948
76. Yang, Y.; Yu, H.; York, D.; Cui, Q.; Elstner, M. Extension of the Self-Consistent-Charge Tight-Binding-Density-Functional (SCC-DFTB) Method: Third Order Expansion of the DFT Total Energy and Introduction of a Modified Effective Coulomb Interaction J. Phys. Chem. A 2007, 111, 10861-10873
77. Gaus, M.; Goez, A.; Elstner, M. Parametrization and Benchmark of DFTB3 for Organic Molecules J. Chem. Theory Comput. 2013, 9, 338-354
78. Gaus, M.; Lu, X.; Elstner, M.; Cui, Q. Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications J. Chem. Theory Comput. 2014, 10, 1518-1537
79. Cui, Q.; Elstner, M. Density Functional Tight Binding: Values of Semi-Empirical Methods in an Ab Initio Era Phys. Chem. Chem. Phys. 2014, 16, 14368-14377
80. Gaus, M.; Chou, C.-P.; Witek, H.; Elstner, M. Automatized Parametrization of SCC-DFTB Repulsive Potentials: Application to Hydrocarbons J. Phys. Chem. A 2009, 113, 11866-11881
81. Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized Gradient Approximation Made Simple Phys. Rev. Lett. 1996, 77, 3865-3868
82. Bodrog, Z.; Aradi, B.; Frauenheim, T. Automated Repulsive Parametrization for the DFTB Method J. Chem. Theory Comput. 2011, 7, 2654-2664
83. Becke, A. D. Density-Functional Exchange-Energy Approximation with Correct Asymptotic Behavior Phys. Rev. A 1988, 38, 3098-3100
84. Becke, A. D. Density-Functional Thermochemistry. III. The Role of Exact Exchange J. Chem. Phys. 1993, 98, 5648-5652
85. Lee, C.; Yang, W.; Parr, R. G. Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron Density Phys. Rev. B 1988, 37, 785-789
86. Curtiss, L. A.; Raghavachari, K.; Redfern, P. C.; Rassolov, V.; Pople, J. A. Gaussian-3 (G3) Theory for Molecules Containing First and Second-Row Atoms J. Chem. Phys. 1998, 109, 7764-7776
87. Curtiss, L. A.; Raghavachari, K.; Redfern, P. C.; Pople, J. A. Assessment of Gaussian-3 and Density Functional Theories for a Larger Experimental Test Set J. Chem. Phys. 2000, 112, 7374-7383
88. Curtiss, L. A.; Redfern, P. C.; Raghavachari, K. Assessment of Gaussian-3 and Density-Functional Theories on the G3/05 Test Set of Experimental Energies J. Chem. Phys. 2005, 123, 124107 1-12
89. Cheng, F.; Zhang, R.; Luo, X.; Shen, J.; Li, X.; Gu, J.; Zhu, W.; Shen, J.; Sagi, I.; Ji, R. Quantum Chemistry Study on the Interaction of the Exogenous Ligands and the Catalytic Zinc Ion in Matrix Metalloproteinases J. Phys. Chem. B 2002, 106, 4552-4559
90. Amin, E. A.; Truhlar, D. G. Zn Coordination Chemistry: Development of Benchmark Suites for Geometries, Dipole Moments, and Bond Dissociation Energies and Their Use To Test and Validate Density Functionals and Molecular Orbital Theory J. Chem. Theory Comput. 2008, 4, 75-85
91. Weaver, M. N.; Merz, K. M.; Ma, D.; Kim, H. J.; Gagliardi, L. Calculation of Heats of Formation for Zn Complexes: Comparison of Density Functional Theory, Second Order Perturbation Theory, Coupled-Cluster and Complete Active Space Methods J. Chem. Theory Comput. 2013, 9, 5277-5285
92. Hamprecht, F. A.; Cohen, A.; Tozer, D. J.; Handy, N. C. Development and Assessment of New Exchange-Correlation Functionals J. Chem. Phys. 1998, 109, 6264-6271
93. Wilson, P. J.; Bradley, T. J.; Tozer, D. J. Hybrid Exchange-Correlation Functional Determined from Thermochemical Data and Ab Initio Potentials J. Chem. Phys. 2001, 115, 9233-9242
94. Becke, A. D. Density-functional Thermochemistry. V. Systematic Optimization of Exchange-Correlation Functionals J. Chem. Phys. 1997, 107, 8554-8560
95. Schmider, H. L.; Becke, A. D. Optimized Density Functionals from the Extended G2 Test Set J. Chem. Phys. 1998, 108, 9624-9631
96. Tekarli, S. M.; Drummond, M. L.; Williams, T. G.; Cundari, T. R.; Wilson, A. K. Performance of Density Functional Theory for 3d Transition Metal-Containing Complexes: Utilization of the Correlation Consistent Basis Sets J. Phys. Chem. A 2009, 113, 8607-8614
97. Elstner, M.; Hobza, P.; Frauenheim, T.; Suhai, S.; Kaxiras, E. Hydrogen Bonding and Stacking Interactions of Nucleic Acid Base Pairs: A Density-Functional-Theory Based Treatment J. Chem. Phys. 2001, 114, 5149-5155
98. Sedlak, R.; Janowski, T.; Pitonak, M.; Rezac, J.; Pulay, P.; Hobza, P. Accuracy of Quantum Chemical Methods for Large Noncovalent Complexes J. Chem. Theory Comput. 2013, 9, 3364-3374
99. Risthaus, T.; Grimme, S. Benchmarking of London Dispersion-Accounting Density Functional Theory Methods on Very Large Molecular Complexes J. Chem. Theory Comput. 2013, 9, 1580-1591
100. Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S. CHARMM: The Biomolecular Simulation Program J. Comput. Chem. 2009, 30, 1545-1614
101. Im, W.; Berneche, S.; Roux, B. Generalized Solvent Boundary Potential for Computer Simulations J. Chem. Phys. 2001, 114, 2924-2937
102. Schaefer, P.; Riccardi, D.; Cui, Q. Reliable Treatment of Electrostatics in Combined QM/MM Simulation of Macromolecules J. Chem. Phys. 2005, 123, 014905 1-14
103. Stote, R. H.; States, D. J.; Karplus, M. On the Treatment of Electrostatic Interactions in Biomolecular Simulations J. Chem. Phys. 1991, 88, 2419-2433
104. 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, 926-935
105. Mackerell, A. D.; Bashford, D.; Bellott; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins J. Phys. Chem. B 1998, 102, 3586-3616
106. + in Liquid Water Determined from High Level ab Initio Molecular Dynamics Simulations J. Chem. Theory Comput. 2012, 8, 3526-3535
107. 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
108. Kollman, P. Free Energy Calculations: Applications to Chemical and Biochemical Phenomena Chem. Rev. 1993, 93, 2395-2417
109. Simonson, T.; Archontis, G.; Karplus, M. Free Energy Simulations Come of Age: Protein-Ligand Recognition Acc. Chem. Res. 2002, 35, 430-437
110. a Calculations with QM/MM Free Energy Perturbations J. Phys. Chem. B 2003, 107, 14521-14528
111. Smith, C. A.; Rayment, I. X-ray Structure of the Magnesium(II)·ADP·Vanadate Complex of the Dictyostelium discoideum Myosin Motor Domain to 1.9 Å Resolution Biochemistry 1996, 35, 5404-5417
112. Geeves, M. A.; Holmes, K. Structural Mechanism of Muscle Contraction Annu. Rev. Biochem. 1999, 68, 687-728
113. Rayment, I. The Structural Basis of the Myosin ATPase Activity J. Biol. Chem. 1996, 271, 15850-15853
114. Li, G.; Cui, Q. Mechanochemical Coupling in Myosin: A Theoretical Analysis with Molecular Dynamics and Combined QM/MM Reaction Path Calculations J. Phys. Chem. B 2004, 108, 3342-3357
115. Yu, H.; Ma, L.; Yang, Y.; Cui, Q. Mechanochemical Coupling in the Myosin Motor Domain. I. Insights from Equilibrium Active-Site Simulations PLoS Comput. Biol. 2007, 3, 0199-0213
116. a s of Ionizable Groups in Proteins: Atomic Detail from a Continuum Electrostatic Model Biochemistry 1990, 29, 10219-10225
117. Brooks, C. L., III; Karplus, M. Solvent Effects on Protein Motion and Protein Effects on Solvent Motion: Dynamics of the Active Site Region of Lysozyme J. Mol. Biol. 1989, 208, 159-181
118. a Analysis for the Zinc-Bound Water in Human Carbonic Anhydrase II: Benchmark for Multi-scale QM/MM Simulations and Mechanistic Implications J. Phys. Chem. A 2007, 111, 5703-5711
119. Lu, X.; Cui, Q. Charging Free Energy Calculations Using the Generalized Solvent Boundary Potential (GSBP) and Periodic Boundary Condition: A Comparative Analysis Using Ion Solvation and Oxidation Free Energy in Proteins J. Phys. Chem. B 2013, 117, 2005-2018
120. Torrie, G.; Valleau, J. Nonphysical Sampling Distributions in Monte Carlo Free-Energy Estimation: Umbrella Sampling J. Comput. Phys. 1977, 23, 187-199
121. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. The Weighted Histogram Analysis Method for Free-Energy Calculations on Biomolecules. I. The Method J. Comput. Chem. 1992, 13, 1011-1021
122. OBrien, P. J.; Lassila, J. K.; Fenn, T. D.; Zalatan, J. G.; Herschlag, D. Arginine Coordination in Enzymatic Phosphoryl Transfer: Evaluation of the Effect of Arg166 Mutations in Escherichia coli Alkaline Phosphatase Biochemistry 2008, 47, 7663-7672
123. Fischer, S.; Karplus, M. Conjugate Peak Refinement: An Algorithm for Finding Reaction Paths and Accurate Transition States in Systems with Many Degrees of Freedom Chem. Phys. Lett. 1992, 194, 252-261
124. Zhao, Y.; Truhlar, D. G. The M06 Suite of Density Functionals for Main Group Thermochemistry, Thermochemical Kinetics, Noncovalent Interactions, Excited States, and Transition Elements: Two New Functionals and Systematic Testing of Four M06-Class Functionals and 12 Other Functionals Theor. Chem. Acc. 2008, 120, 215-241
125. Grimme, S.; E, S.; Antony, J.; Krieg, H. A Consistent and Accurate Ab Initio Parameterization of Density Functional Dispersion Correction (DFT-D) for the 94 Elements H-Pu J. Chem. Phys. 2010, 132, 154104 1-19
126. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A. Gaussian 09, Revision A.1; Gaussian Inc.: Wallingford, CT, 2009.
127. Dudev, T.; Cowan, J. A.; Lim, C. Competitive Binding in Magnesium Coordination Chemistry: Water versus Ligands of Biological Interest J. Am. Chem. Soc. 1999, 121, 7665-7673
128. 2+ Ions with Nucleoside Triphosphates by Phosphorus Magnetic-Resonance Spectroscopy Nucleic Acids Res. 1975, 2, 1101-1110
129. Cohn, T. R. J.; Hughes, M. Nuclear Magnetic Resonance Spectra of Adenosine Di- and Triphosphate. II. Effect of Complexing with Divalent Metal Ions J. Biol. Chem. 1962, 237, 176-181
130. 31P-NMR Study of Monomagnesium and Dimagnesium Complexes of Adenosine 5-Triphosphate and Model Systems Biochim. Biophys. Acta 1981, 635, 63-72
131. Huang, S. L.; Tsai, M. D. Does the Magnesium(II) Ion Interact with the.Alpha.-Phosphate of ATP? An Investigation by Oxygen-17 Nuclear Magnetic Resonance Biochemistry 1982, 21, 951-959
132. Ramirez, F.; Marecek, J. Coordination of Magnesium with Adenosine 5-Diphosphate and Triphostate Biochim. Biophys. Acta 1980, 589, 21-29
133. 18O-Labeled Triphosphates J. Am. Chem. Soc. 1988, 110, 392-397
134. Liao, J. C.; Sun, S.; Chandler, D.; Oster, G. The Conformational States of Mg·ATP in Water Eur. Biophys. J. 2004, 33, 29-37
135. Stamper, C.; Bennett, B.; Edwards, T.; Holz, R. C.; Ringe, D.; Petsko, G. Inhibition of the Aminopeptidase from Aeromonas proteolytica by l-Leucinephosphonic Acid. Spectroscopic and Crystallographic Characterization of the Transition State of Peptide Hydrolysis Biochemistry 2001, 40, 7035-7046
136. Englert, M.; Xia, S.; Okada, C.; Nakamura, A.; Tanavde, V.; Yao, M.; Eom, S. H.; Konigsberg, W. H.; Soell, D.; Wang, J. Structural and Mechanistic Insights into Guanylylation of RNA-Splicing Ligase RtcB Joining RNA between 3-Terminal Phosphate and 5-OH Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 15235-15240
137. Jedrzejas, M. J.; Setlow, P. Comparison of the Binuclear Metalloenzymes Diphosphoglycerate-Independent Phosphoglycerate Mutase and Alkaline Phosphatase: Their Mechanism of Catalysis via a Phosphoserine Intermediate Chem. Rev. 2001, 101, 607-618
138. 2+)-ATP-Oxalate Complex of the Rabbit Muscle Pyruvate Kinase at 2.1 Å Resolution: ATP Binding over a Barrel Biochemistry 1998, 37, 6247-6255
139. Nakamura, T.; Zhao, Y.; Yamagata, Y.; jin Hua, Y.; Yang, W. Watching DNA Polymerase Make a Phosphodiester Bond Nature 2012, 487, 196-201
140. Schmidt, B. H.; Burgin, A. B.; Deweese, J. E.; Osheroff, N.; Berger, J. M. A Novel and Unified Two-Metal Mechanism for DNA Cleavage by Type II and IA Topoisomerases Nature 2010, 465, 641-644
141. Palermo, G.; Stenta, M.; Cavalli, A.; Dal Peraro, M.; De Vivo, M. Molecular Simulations Highlight the Role of Metals in Catalysis and Inhibition of Type II Topoisomerase J. Chem. Theory Comput. 2013, 9, 857-862
142. Chevrier, B.; Schalk, C.; DOrchymont, H.; Rondeau, J.; Moras, D.; Tarnus, C. Crystal Structure of Aeromonas Proteolytica Aminopeptidase: A Prototypical Member of the Co-Catalytic Zinc Enzyme Family Structure 1994, 2, 283-291
143. Coleman, J. E. Structure and Mechanism of Alkaline Phosphatase Annu. Rev. Biophys. Biomol. Struct. 1992, 21, 441-483
144. Marcus, Y. Ionic Radii in Aqueous Solutions Chem. Rev. 1988, 88, 1475-1498
145. Bernasconi, L.; Baerends, E. J.; Sprik, M. Long-Range Solvent Effects on the Orbital Interaction Mechanism of Water Acidity Enhancement in Metal Ion Solutions: A Comparative Study of the Electronic Structure of Aqueous Mg and Zn Dications J. Phys. Chem. B 2006, 110, 11444-11453
146. Riahi, S.; Roux, B.; Rowley, C. N. QM/MM Molecular Dynamics Simulations of the Hydration of Mg(II) and Zn(II) Ions Can. J. Chem. 2013, 91, 552-558
147. Kulik, H. J.; Marzari, N.; Correa, A. A.; Prendergast, D.; Schwegler, E.; Galli, G. Local Effects in the X-ray Absorption Spectrum of Salt Water J. Phys. Chem. B 2010, 114, 9594-9601
148. 2+ and Its Influence on the Water Hydrogen Bonding Network via Ab Initio QMCF MD Chem. Phys. Lett. 2012, 536, 39-44
149. Ikeda, T.; Boero, M.; Terakura, K. Hydration Properties of Magnesium and Calcium Ions from Constrained First Principles Molecular Dynamics J. Chem. Phys. 2007, 127, 074503 1-8
150. 2+ Hydration in Aqueous Solutions J. Phys.: Condens. Matter 1997, 9, 10065-10078
151. Rega, N.; Brancato, G.; Petrone, A.; Caruso, P.; Barone, V. Vibrational Analysis of X-ray Absorption Fine Structure Thermal Factors by Ab Initio Molecular Dynamics: The Zn(II) Ion in Aqueous Solution as a Case Study J. Chem. Phys. 2011, 134, 074504 1-10
152. Neely, J.; Connick, R. Rate of Water Exchange from Hydrated Magnesium Ion J. Am. Chem. Soc. 1970, 92, 3476-3478
153. Helm, L.; Merbach, A. Water Exchange on Metal Ions: Experiments and Simulations Coord. Chem. Rev. 1999, 187, 151-181
154. 2+ Solutions: A Study Using Incoherent Quasi-Elastic Neutron Scattering J. Phys.: Condens. Matter 1990, 2, 4297-4309
155. Douglas, B. E.; McDaniel, D. H.; Alexander, J. J. Concepts and Models of Inorganic Chemistry; John Wiley and Sons: New York, 1994.
156. Vale, R.; Milligan, R. The Way Things Move: Looking under the Hood of Molecular Motor Proteins Science 2000, 288, 88-95
157. Bustamante, C.; Keller, D.; Oster, G. The Physics of Molecular Motors Acc. Chem. Res. 2001, 34, 412-420
158. 1-ATPase Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 11339-11344
159. Strajbl, M.; Shurki, A.; Warshel, A. Converting Conformational Changes to Electrostatic Energy in Molecular Motors: The Energetics of ATP Synthase Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 14834-14839
160. McGrath, M. J.; Kuo, I.-F. W.; Hayashi, S.; Takada, S. Adenosine Triphosphate Hydrolysis Mechanism in Kinesin Studied by Combined Quantum-Mechanical/Molecular-Mechanical Metadynamics Simulations J. Am. Chem. Soc. 2013, 135, 8908-8919
161. --GDP Intermediate in Ras-GAP Decoded from FTIR Experiments by Biomolecular Simulations J. Am. Chem. Soc. 2012, 116, 12522-12534
162. Laio, A.; Gervasio, F. L. Metadynamics: A Method to Simulate Rare Events and Reconstruct the Free Energy in Biophysics, Chemistry and Material Science Rep. Prog. Phys. 2008, 71, 126601 1-22
163. W, E.; Ren, W.; Vanden-Eijnden, E. Simplified and Improved String Method for Computing the Minimum Energy Paths in Barrier-Crossing Events J. Chem. Phys. 2007, 126, 164103 1-8
164. Maragliano, L.; Fischer, A.; Vanden-Eijnden, E.; Ciccotti, G. String Method in Collective Variables: Minimum Free Energy Paths and Isocommittor Surfaces J. Chem. Phys. 2006, 125, 024106 1-15
165. Vanden-Eijnden, E.; Venturoli, M. Revisiting the Finite Temperature String Method for the Calculation of Reaction Tubes and Free Energies J. Chem. Phys. 2009, 130, 194103 1-17