Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions

Accounts of Chemical Research

Volumn 43, Issue 1, 2010, Pages 142-151

  Orlando, Acevedo ^a   Jorgensen, William L ^b  

^a AUBURN UNIVERSITY   (United States)

^b YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDASE; ENZYME; FATTY ACID AMIDASE; FATTY-ACID AMIDE HYDROLASE; PYRONE DERIVATIVE; SOLVENT;

ARTICLE; CHEMISTRY; COMPARATIVE STUDY; COMPUTER SIMULATION; METABOLISM; MONTE CARLO METHOD; QUANTUM THEORY; THERMODYNAMICS;

AMIDOHYDROLASES; COMPUTER SIMULATION; ENZYMES; MONTE CARLO METHOD; PYRONES; QUANTUM THEORY; SOLVENTS; THERMODYNAMICS;

EID: 75449116384     PISSN: 00014842     EISSN: None     Source Type: Journal    
DOI: 10.1021/ar900171c     Document Type: Article

References (74)

1. (a) Warshel, A.; Karplus, M. Calculation of ground and excited state potential surfaces of conjugated molecules. I. Formulation and parametrization. J. Am. Chem. Soc. 1972, 94, 5612-5625.
2. (b) Warshel, A.; Levitt, M. Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J. Mol. Biol. 1976, 103, 227-249.
3. (c) Warshel, A. Molecular dynamics simulations of biological reactions. Acc. Chem. Res. 2002, 35, 385-395.
4. a, redox reactions and solvation free energies. J. Phys. Chem. B2009, 113, 1253-1272.
5. Senn, H. M.; Thiel, W. QM/MM methods for biomolecular systems. Angew. Chem., Int. Ed. 2009, 48, 1198-1229.
6. Gao, J.; Ma, S.; Major, D. T.; Nam, K.; Pu, J.; Truhlar, D. G. Mechanisms and free energies of enzymatic reactions. Chem. Rev. 2006, 106, 3188-3209.
7. Vreven, T.; Morokuma, K. Hybrid methods: ONIOM(QM:MM) and QM/MM. Ann. Rep. Comput. Chem. 2006, 2, 35-51.
8. Acevedo, O.; Jorgensen, W. L. Solvent effects on organic reactions from QM/MM simulations. Ann. Rep. Comput. Chem. 2006, 2, 263-278.
9. (a) Jorgensen, W. L. Free energy calculations, a breakthrough for modeling organic chemistry in solution. Acc. Chem. Res. 1989, 22, 184-189.
10. (b) Kollman, P. A. Free energy calculations: Applications to chemical and biochemical phenomena. Chem. Rev. 1993, 93,2395-2417.
11. (c) Jorgensen, W. L.; Blake, J. F.; Lim, D.; Severance, D. L. Investigation of solvent effects on pericydic reactions by computer simulations. J. Chem. Soc., Faraday Trans. 1994, 90, 1727-1732.
12. (a) Kaminski, G. A.; Jorgensen, W. L. A QM/MM method based on CM1A charges: Applications to solvent effects on organic equilibria and reactions. J. Phys. Chem. B 1998, 102, 1787-1796.
13. (b) 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, 545-571.
14. (a) 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.
15. (b) Jorgensen, W. L.; Tirado-Rives, J. Potential energy functions tor atomic-level simulations of water and organic and biomolecular systems. Proc. Natl. Acad. Sci. U.S.A. 2005, 102,6665-6670.
16. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, W.; Klein, M. L. Comparison of simple potential functions tor simulating liquid water. J. Chem. Phys. 1983, 79, 926-935.
17. Jorgensen, W. L.; Tirado-Rives, J. Molecular modeling of organic and biomolecular systems using BOSS and MCPRO. J. Comput. Chem. 2005, 26, 1689-1700. (Pubitemid 43076181)
18. Thompson, J. D.; Cramer, C. J.; Truhlar, D. G. Parameterization of charge model 3 for AM1, PM3, BLYP, and B3LYP. J. Comput. Chem. 2003, 24, 1291-1304.
19. Blagović, M. U.; Morales de Tirado, P.; Pearlman, S. A.; Jorgensen, W. L. Accuracy of free energies of hydration from CM1 and CM3 atomic charges. J. Comput. Chem. 2004, 25, 1322-1332.
20. Acevedo, O.; Jorgensen, W. L. Solvent effects and mechanism for a nucleophilic aromatic substitution from QM/MM simulations. Org. Lett. 2004, 6, 2881-2884. (Pubitemid 39178031)
21. (a) Gao, J. An automated procedure tor simulating chemical reactions in solution. Application to the decarboxylation of 3-carboxybenzisoxazole in water. J. Am. Chem. Soc. 1995, 117, 8600-8607.
22. (b) Zipse, H.; Apaydin, G.; Houk, K. N. A quantum mechanical and statistical mechanical exploration of the thermal decarboxylation of Kemp's other acid (benazisoxazole-3-carboxylic acid). The influence of solvation on the transition state geometries and kinetic isotope effects of a reaction with an awesome solvent effect. J. Am. Chem. Soc. 1995, 117, 8608-8617.
23. (c) Acevedo, O.; Jorgensen, W. L. Influence of inter- and intramolecular hydrogen bonding on Kemp decarboxylations from QM/MM simulations. J. Am. Chem. Soc. 2005, 127, 8829-8834.
24. (a) Pan, D. G.; Pan, Y.-K. A QM/MM Monte Carlo simulation study of solvent effects on the decarboxylation reaction of N-carboxy-2-imidazolidinone anion in aqueous solution. J. Org. Chem. 1999, 64, 1151-1159. (Pubitemid 29098551)
25. (b) Acevedo, O.; Jorgensen, W. L. Medium effects on the decarboxylation of a biotin model in pure and mixed solvents from QM/MM simulations. J. Org. Chem. 2006, 71, 4896-4902.
26. Acevedo, O.; Jorgensen, W. L. Cope elimination: Elucidation of solvent effects from QM/MM simulations. J. Am. Chem. Soc. 2006, 128, 6141-6146.
27. Acevedo, O.; Jorgensen, W. L. Understanding rate accelerations for Diels-Alder reactions in solution using enhanced QM/MM methodology. J. Chem. Theory Comput. 2007, 3, 1412-1419.
28. Acevedo, O.; Jorgensen, W. L.; Evanseck, J. D. Elucidation of rate variations for a Diels-Alder reaction in ionic liquids from QM/MM simulations. J. Chem. Theory Comput. 2007, 3, 132-138.
29. Acevedo, O.; Squillacote, M. E. A new solvent-dependent mechanism for a triazolinedione ene reaction. J. Org. Chem. 2008, 73, 912-922.
30. Klähn, M.; Braun-Sand, S.; Rosta, E.; Warshel, A. On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions. J. Phys. Chem. B2005, 109, 15645-15650.
31. Chandrasekhar, J.; Shariffskul, S.; Jorgensen, W. L. QM/MM simulations of cycloaddition reactions in water: Contribution of enhanced hydrogen bonding at the transition state to the solvent effects. J. Phys. Chem. B2002, 106, 8078-8085.
32. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. AM1 : A new general purpose quantum mechanical molecular model. J. Am. Chem. Soc. 1985, 107, 3902-3907.
33. Stewart, J. J. P. Optimization of parameters for semiempirical methods. J. Comput. Chem. 1989, 10, 209-264.
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. Repasky, M. P.; Chandrasekhar, J.; Jorgensen, W. L. PDDG/PM3 and PDDG/MNDO: Improved semiempirical methods. J. Comput. Chem. 2002, 23, 1601-1622.
36. Sattelmeyer, K. W.; Tubert-Brohman, I.; Jorgensen, W. L. NO-MNDO: Reintroduction of the overlap matrix into MNDO. J. Chem. Theory Comput. 2006, 2, 413-419.
37. Sattelmeyer, K. W.; Tirado-Rives, J.; Jorgensen, W. L. Comparison of SCC-DFTB and NDDO-based semiempirical molecular orbital methods for organic molecules. J. Phys. Chem. A 2006, 110, 13551-13559.
38. (a) Tubert-Brohman, I.; Guimarães, C. R. W.; Repasky, M. P.; Jorgensen, W. L. Extension of the PDDG/PM3 and PDDG/MNDO semiempirical molecular orbmal methods to the halogens. J. Comput. Chem. 2003, 25, 138-150.
39. (b) TubertBrohman, I.; Guimarães, C. R. W.; Jorgensen, W. L. Extension of the PDDG/PM3 semiempirical molecular orbital method to sulfur, silicon, and phosphorus. J. Chem. Theory Comput. 2005, 1, 817-823.
40. Tirado-Rives, J.; Jorgensen, W. L. Performance of B3LYP density functional methods for a large set of organic molecules. J. Chem. Theory Comput. 2008, 4, 297-306.
41. For recent reviews, see (a) Chipot, C.; Pohorille, A In Free Energy Calculations: Theory and Applications in Chemistry and Biology, Chipot, C., Pohorille, A., Eds.; Springer-Verlag: Berlin, Germany, 2007; Springer Series in Chemical Physics, Vol.86, pp 33-75.
42. (b) Jorgensen, W. L.; Thomas, L. L. Perspective on free-energy perturbation calculations for chemical equilibria. J. Chem. Theory Comput. 2008, 4, 869-876.
43. Sheppard, A. N.; Acevedo, O. Multidimensional exploration of valley-ridge inflection points on potential energy surfaces. J. Am. Chem. Soc. 2009, 131, 2530-2540.
44. N2 reaction profiles in the gas phase and aqueous solution. J. Am. Chem. Soc. 1984, 106, 3049-3050.
45. N2 reaction in water. J. Chem. Phys. 1987, 86, 1356-1376.
46. (c) Bash, P. A.; Field, M. J.; Karplus, M. Free energy perturbation method for chemical reactions in the condensed phase. J. Am. Chem. Soc. 1987, 109, 8092-8094.
47. N2 reactions in aqueous solution. J. Am. Chem. Soc. 1988, 110, 5297-5311.
48. N2 reaction profile in water: The Menshutkin reaction. J. Am. Chem. Soc. 1991, 113, 7796-7797.
49. N2 reactions in the gas phase and solution. J. Am. Chem. Soc. 2004, 126, 9054-9058.
50. Gunaydin, H.; Acevedo, O.; Jorgensen, W. L.; Houk, K. N. Computation of accurate activation barriers for methyl-transfer reactions of sulfonium and ammonium salts in aqueous solution. J. Chem. Theory Comput. 2007, 3, 1028-1035.
51. Tomasi, J.; Persico, M. Molecular interactions in solution: An overview of methods based on continuous distributions of the solvent. Chem. Rev. 1994, 94, 2027-2094. (Pubitemid 124000195)
52. NAr reaction. J. Am. Chem. Soc. 1973, 95, 408-410.
53. N2 transition states. Can. J. Chem. 1978, 56, 2691-2699.
54. Kemp, D. S.; Paul, K. G. Physical organic chemistry of benzisoxazoles. III. Mechanism and the effects of solvents on rates of decarboxylation of benzisoxazole3-carboxylic acids. J. Am. Chem. Soc. 1975, 97, 7305-7312.
55. Rahil, J.; You, S.; Kluger, R. Solvent-accelerated decarboxylation of N-carboxy-2imidazolidinone. J. Am. Chem. Soc. 1996, 118, 12495-12498.
56. i reaction of amine oxides. J. Am. Chem. Soc. 1963, 85, 1263-1268.
57. Alexandrova, A. N.; Jorgensen, W. L. Why urea eliminates ammonia rather than hydrofyzes in aqueous solution. J. Phys. Chem. B2007, 111, 720-730.
58. Engberts, J. B. F. N. Diels-Alder reactions in water: Enforced hydrophobic interaction and hydrogen bonding. Pure Appl. Chem. 1995, 67, 823-828.
59. Taylor, M. S.; Jacobsen, E. N. Asymmetric catalysis by chiral hydrogen-bond donors. Angew. Chem., Int. Ed. 2006, 45, 1520-1543.
60. (a) Jorgensen, W. L.; Tirado-Rives, J. Monte Carlo vs molecular dynamics for conformational sampling. J. Phys. Chem. 1996, 100, 14508-14513. (Pubitemid 126796548)
61. (b) Hu, J.; Ma, A.; Dinner, A. R. Monte Carlo simulations of biomolecules: The MC module in CHARMM. J. Comput. Chem. 2006, 27, 203-216.
62. Guimarães, C. R. W.; Udier-Blagovic, M.; Jorgensen, W. L. Macrophomate synthase: QM/MM simulations address the Diels-Alder versus Michael-aldol reaction mechanism. J. Am. Chem. Soc. 2005, 127, 3577-3588. (Pubitemid 40365296)
63. Ose, T.; Watanabe, K.; Mie, T.; Honma, M.; Watanabe, H.; Yao, M.; Oikawa, H.; Tanaka, I. Insights info a natural Diels-Alder reaction from the structure of macrophomate synthase. Nature 2003, 422,185-189. (Pubitemid 36362753)
64. Wilson, E. Is the case for a Diels-Alderase dead? Chem. Eng. News 2005, May, 38.
65. Serafimov, J. M.; Gillingham, D.; Kuster, S.; Hilvert, D. The putative Diels-Alderase macrophomate synthase is an efficient aldolase. J. Am. Chem. Soc. 2008, 130, 7798-7799. (Pubitemid 351875035)
66. Cravatt, B. F.; Giang, D. K.; Mayfield, S. P.; Boger, D. L.; Lerner, R. A.; Gilula, N. B. Molecular characterization of an enzyme that degrades neuromodulator fatty-acid amides. Nature 1996, 384, 83-87.
67. Bracey, M. H.; Hanson, M. A.; Masuda, K. R.; Stevens, R. C.; Cravatt, B. F. Structural adaptations in a membrane enzyme that terminates endocannabinoid signaling. Science 2002, 298.
68. McKinney, M. K.; Cravatt, B. F. Evidence for distinct roles in catalysis for residues of the serine-serine-lysine catalytic triad of fatty acid amide hydrolase. J. Biol. Chem. 2003, 278, 37393-37399.
69. Tubert-Brohman, I.; Acevedo, O.; Jorgensen, W. L. Elucidation of hydrolysis mechanisms for fatty acid amide hydrolase and its Lys142Ala variant via QM/MM simulations. J. Am. Chem. Soc. 2006, 128, 16904-16913.
70. Zanghellini, A.; Jiang, L.; Wollacott, A. M.; Cheng, G.; Meiler, J.; Althoff, E. A.; Röthlisberger, D.; Baker, D. New algorithms and an in silico benchmark for computational enzyme design. Protein Sci. 2006, 15, 2785-2794. (Pubitemid 44833759)
71. Röthlisberger, D.; Khersonsky, O.; Wollacott, A. M.; Jiang, L.; DeChancie, J.; Betker, J.; Gallaher, J. L.; Althoff, E. A.; Zanghellini, A.; Dym, O.; Albeck, S.; Houk, K. N.; Tawfik, D. S.; Baker, D. Kemp elimination catalysts by computational enzyme design. Nature 2008, 453, 190-195.
72. Alexandrova, A. N.; Röthlisberger, D.; Baker, D.; Jorgensen, W. L. Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination. J. Am. Chem. Soc. 2008, 130, 15907-15915.
73. Alexandrova, A. N.; Jorgensen, W. L. Origin of the activity drop with the E50D variant of catalytic antibody 34E4 for Kemp elimination. J. Phys. Chem. B2009, 113, 497-504.
74. Seebeck, F. P.; Hilvert, D. Positional ordering of reacting groups contributes significantly to the efficiency of proton transfer at an antibody active site. J. Am. Chem. Soc. 2005, 127, 1307-1312.