Benchmarking of DFT functionals for the hydrolysis of phosphodiester bonds

Journal of Chemical Theory and Computation

Volumn 6, Issue 8, 2010, Pages 2281-2292

  Ribeiro, António J M ^a   Ramos, Maria J ^a   Fernandes, Pedro A ^a  

^a UNIVERSITY OF PORTO   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77955561344     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct900649e     Document Type: Article

References (72)

1. Nelson, D. L.; Cox, M. M. Lehninger Principles of Biochemistry, 4th ed.; Palgrave Macmillan: 2004; pp 276-277.
2. Westheimer, F. H. Why Nature Chose Phosphates Science 1987, 235, 1173-1178.
3. Lim, C.; Karplus, M. Nonexistence of Dianionic Pentacovalent Intermediates in an Abinitio Study of the Base-Catalyzed-Hydrolysis of Ethylene Phosphate J. Am. Chem. Soc. 1990, 112, 5872-5873.
4. Dejaegere, A.; Lim, C.; Karplus, M. Dianionic Pentacoordinate Species in the Base-Catalyzed-Hydrolysis of Ethylene and Dimethyl-Phosphate J. Am. Chem. Soc. 1991, 113, 4353-4355.
5. Uchimaru, T.; Tanabe, K.; Nishikawa, S.; Taira, K. Abinitio Studies of a Marginally Stable Intermediate in the Base-Catalyzed Methanolysis of Dimethyl-Phosphate and Nonexistence of the Stereoelectronically Unfavorable Transition-State J. Am. Chem. Soc. 1991, 113, 4351-4353.
6. Lim, C.; Tole, P. Concerted Hydroxyl Ion Attack and Pseudorotation in the Base-Catalyzed-Hydrolysis of Methyl Ethylene Phosphate J. Phys. Chem. 1992, 96, 5217-5219.
7. Liang, C. X.; Ewig, C. S.; Stouch, T. R.; Hagler, A. T. Abinitio Studies of Lipid Model Species 0.1. Dimethyl-Phosphate and Methyl Propyl Phosphate Anions J. Am. Chem. Soc. 1993, 115, 1537-1545.
8. Dejaegere, A.; Liang, X. L.; Karplus, M. Phosphate Ester Hydrolysis-Calculation of Gas-Phase Reaction Paths and Solvation Effects J. Chem. Soc., Faraday Trans. 1994, 90, 1763-1770.
9. Landin, J.; Pascher, I.; Cremer, D. Ab-Initio and Semiempirical Conformation Potentials for Phospholipid Head Groups J. Phys. Chem. 1995, 99, 4471-4485.
10. Hu, C. H.; Brinck, T. Theoretical studies of the hydrolysis of the methyl phosphate anion J. Phys. Chem. A 1999, 103, 5379-5386.
11. Mercero, J. M.; Barrett, P.; Lam, C. W.; Fowler, J. E.; Ugalde, J. M.; Pedersen, L. G. Quantum mechanical calculations on phosphate hydrolysis reactions J. Comput. Chem. 2000, 21, 43-51.
12. Murashov, V. V.; Leszczynski, J. A comparison of the B3LYP and MP2 methods in the calculation of phosphate complexes J. Mol. Struct.-Theochem 2000, 529, 1-14.
13. Lopez, X.; Dejaegere, A.; Karplus, M. Solvent effects on the reaction coordinate of the hydrolysis of phosphates and sulfates: Application of Hammond and anti-Hammond postulates to understand hydrolysis in solution J. Am. Chem. Soc. 2001, 123, 11755-11763.
14. Bianciotto, M.; Barthelat, J. C.; Vigroux, A. Reactivity of phosphate monoester monoanions in aqueous solution. 1. Quantum mechanical calculations support the existence of "anionic zwitterion" MeO+(H)PO3 (2-) as a key intermediate in the dissociative hydrolysis of the methyl phosphate anion J. Am. Chem. Soc. 2002, 124, 7573-7587.
15. Bianciotto, M.; Barthelat, J. C.; Vigroux, A. Reactivity of phosphate monoester monoanions in aqueous solution. 2. A theoretical study of the elusive zwitterion intermediates RO+(H)PO32- J. Phys. Chem. A 2002, 106, 6521-6526.
16. Lopez, X.; York, D. M.; Dejaegere, A.; Karplus, M. Theoretical studies on the hydrolysis of phosphate diesters in the gas phase, solution, and RNase A Int. J. Quantum Chem. 2002, 86, 10-26.
17. Kolandaivel, P.; Kanakaraju, R. Structure, stability and interaction studies on nucleotide analogue systems Int. J. Mol. Sci. 2003, 4, 486-502.
18. Wang, Y. N.; Topol, I. A.; Collins, J. R.; Burt, S. K. Theoretical studies on the hydrolysis of mono-phosphate and tri-phosphate in gas phase and aqueous solution J. Am. Chem. Soc. 2003, 125, 13265-13273.
19. Chen, X.; Zhan, C. G. Theoretical determination of activation free energies for alkaline hydrolysis of cyclic and acyclic phosphodiesters in aqueous solution J. Phys. Chem. A 2004, 108, 6407-6413.
20. Range, K.; McGrath, M. J.; Lopez, X.; York, D. M. The structure and stability of biological metaphosphate, phosphate, and phosphorane compounds in the gas phase and in solution J. Am. Chem. Soc. 2004, 126, 1654-1665.
21. Iche-Tarrat, N.; Barthelat, J. C.; Rinaldi, D.; Vigroux, A. Theoretical studies of the hydroxide-catalyzed P-O cleavage reactions of neutral phosphate triesters and diesters in aqueous solution: Examination of the changes induced by H/Me substitution J. Phys. Chem. B 2005, 109, 22570-22580.
22. Imhof, P.; Fischer, S.; Kramer, R.; Smith, J. C. Density functional theory analysis of dimethylphosphate hydrolysis: effect of solvation and nucleophile variation J. Mol. Struct.-Theochem 2005, 713, 1-5.
23. Lopez, X.; Dejaegere, A.; Leclerc, F.; York, D. M.; Karplus, M. Nucleophilic attack on phosphate diesters: A density functional study of in-line reactivity in dianionic, monoanionic, and neutral systems J. Phys. Chem. B 2006, 110, 11525-11539.
24. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J. General performance of density functionals J. Phys. Chem. A 2007, 111, 10439-10452.
25. Cossi, M.; Scalmani, G.; Rega, N.; Barone, V. New developments in the polarizable continuum model for quantum mechanical and classical calculations on molecules in solution J. Chem. Phys. 2002, 117, 43-54.
26. Cossi, M.; Barone, V.; Mennucci, B.; Tomasi, J. Ab initio study of ionic solutions by a polarizable continuum dielectric model Chem. Phys. Lett. 1998, 286, 253-260.
27. Mennucci, B.; Tomasi, J. Continuum solvation models: A new approach to the problem of solute's charge distribution and cavity boundaries J. Chem. Phys. 1997, 106, 5151-5158.
28. Cances, E.; Mennucci, B.; Tomasi, J. A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to isotropic and anisotropic dielectrics J. Chem. Phys. 1997, 107, 3032-3041.
29. Helgaker, T.; Klopper, W.; Koch, H.; Noga, J. Basis-set convergence of correlated calculations on water J. Chem. Phys. 1997, 106, 9639-9646.
30. Halkier, A.; Helgaker, T.; Jorgensen, P.; Klopper, W.; Koch, H.; Olsen, J.; Wilson, A. K. Basis-set convergence in correlated calculations on Ne, N-2, and H2O Chem. Phys. Lett. 1998, 286, 243-252.
31. Jurecka, P.; Hobza, P. On the convergence of the (Delta E-CCSD(T)-Delta E-MP2) term for complexes with multiple H-bonds Chem. Phys. Lett. 2002, 365, 89-94.
32. Hobza, P.; Sponer, J. Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations J. Am. Chem. Soc. 2002, 124, 11802-11808.
33. Schrodinger. Jaguar, version 7.5; New York, 2008.
34. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al.Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, Revision C.02; Gaussian, Inc.: Wallingford, CT, 2004.
35. Warshel, A. Computer Modeling of Chemical Reactions in Enzymes and Solutions; Wiley-Interscience: 1997; pp 136-140.
36. Gorenstein, D. G.; Luxon, B. A.; Findlay, J. B. Stereoelectronic Effects in the Reactions of Phosphate Diesters-Abinitio Molecular-Orbital Calculations of Reaction Surfaces. 2 J. Am. Chem. Soc. 1979, 101, 5869-5875.
37. Wolfenden, R.; Ridgway, C.; Young, G. Spontaneous hydrolysis of ionized phosphate monoesters and diesters and the proficiencies of phosphatases and phosphodiesterases as catalysts J. Am. Chem. Soc. 1998, 120, 833-834.
38. Kumamoto, J.; Cox, J. R.; Westheimer, F. H. Barium Ethylene Phosphate J. Am. Chem. Soc. 1956, 78, 4858-4860.
39. Schroeder, G. K.; Lad, C.; Wyman, P.; Williams, N. H.; Wolfenden, R. The time required for water attack at the phosphorus atom of simple phosphodiesters and of DNA Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 4052-4055.
40. 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.
41. Zhao, Y.; Truhlar, D. G. Density functionals with broad applicability in chemistry Acc. Chem. Res. 2008, 41, 157-167.
42. Vosko, S. H.; Wilk, L.; Nusair, M. Accurate Spin-Dependent Electron Liquid Correlation Energies for Local Spin-Density Calculations-a Critical Analysis Can. J. Phys. 1980, 58, 1200-1211.
43. Slater, J. C. Quantum Theory of Molecular and Solids. Vol. 4: The Self-Consistent Field for Molecular and Solids; McGraw-Hill: New York, 1974.
44. Lee, C. T.; Yang, W. T.; Parr, R. G. Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron-Density Phys. Rev. B: Condens. Matter Mater. Phys. 1988, 37, 785-789.
45. Becke, A. D. Density-functional thermochemistry 0.4. A new dynamical correlation functional and implications for exact-exchange mixing J. Chem. Phys. 1996, 104, 1040-1046.
46. Becke, A. D. Density-Functional Exchange-Energy Approximation with Correct Asymptotic-Behavior Phys. Rev. A: At., Mol., Opt. Phys. 1988, 38, 3098-3100.
47. Becke, A. D. Density-Functional Thermochemistry 0.3. The Role of Exact Exchange J. Chem. Phys. 1993, 98, 5648-5652.
48. Zhao, Y.; Truhlar, D. G. Hybrid meta density functional theory methods for thermochemistry, thermochemical kinetics, and noncovalent interactions: The MPW1B95 and MPWB1K models and comparative assessments for hydrogen bonding and van der Waals interactions J. Phys. Chem. A 2004, 108, 6908-6918.
49. Perdew, J. P. Density-Functional Approximation for the Correlation-Energy of the Inhomogeneous Electron-Gas Phys. Rev. B: Condens. Matter Mater. Phys. 1986, 33, 8822-8824.
50. Perdew, J. P. Unified Theory of Exchange and Correlation Beyond the Local Density Aproximation. In Electronic Structure of Solids; Zieche, P.; Eschrig, H., Eds.; Berlin, Germany, 1991; pp 11-20.
51. Hamprecht, F. A.; Cohen, A. J.; Tozer, D. J.; Handy, N. C. Development and assessment of new exchange-correlation functionals J. Chem. Phys. 1998, 109, 6264-6271.
52. Zhao, Y.; Truhlar, D. G. Density functional for spectroscopy: No long-range self-interaction error, good performance for Rydberg and charge-transfer states, and better performance on average than B3LYP for ground states J. Phys. Chem. A 2006, 110, 13126-13130.
53. Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized gradient approximation made simple Phys. Rev. Lett. 1996, 77, 3865-3868.
54. 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.
55. Adamo, C.; Barone, V. Exchange functionals with improved long-range behavior and adiabatic connection methods without adjustable parameters: The mPW and mPW1PW models J. Chem. Phys. 1998, 108, 664-675.
56. Schmider, H. L.; Becke, A. D. Optimized density functionals from the extended G2 test set J. Chem. Phys. 1998, 108, 9624-9631.
57. Becke, A. D. Density-functional thermochemistry 0.5. Systematic optimization of exchange-correlation functionals J. Chem. Phys. 1997, 107, 8554-8560.
58. Krieger, J. B.; Chen, J. Q.; Iafrate, G. J.; Savin, A. Construction of an accurate self-interaction-corrected correlation energy functional based on an electron gas with a gap Electron Correl. Mater. Prop., [Proc. Int. Workshop], 1st 1999, 463-477.
59. Zhao, Y.; Gonzalez-Garcia, N.; Truhlar, D. G. Benchmark database of barrier heights for heavy atom transfer, nucleophilic substitution, association, and unimolecular reactions and its use to test theoretical methods J. Phys. Chem. A 2005, 109, 2012-2018.
60. Gill, P. M. W. A new gradient-corrected exchange functional Mol. Phys. 1996, 89, 433-445.
61. Lynch, B. J.; Fast, P. L.; Harris, M.; Truhlar, D. G. Adiabatic connection for kinetics J. Phys. Chem. A 2000, 104, 4811-4815.
62. Zhao, Y.; Lynch, B. J.; Truhlar, D. G. Multi-coefficient extrapolated density functional theory for thermochemistry and thermochemical kinetics Phys. Chem. Chem. Phys. 2005, 7, 43-52. (Pubitemid 40143825)
63. Kormos, B. L.; Cramer, C. J. Adiabatic connection method for X-+RX nucleophilic substitution reactions (X = F, Cl) J. Phys. Org. Chem. 2002, 15, 712-720.
64. Tao, J. M.; Perdew, J. P.; Staroverov, V. N.; Scuseria, G. E. Climbing the density functional ladder: Nonempirical meta-generalized gradient approximation designed for molecules and solids Phys. Rev. Lett. 2003, 91, 146401.
65. Dahlke, E. E.; Truhlar, D. G. Improved density functionals for water J. Phys. Chem. B 2005, 109, 15677-15683.
66. Lynch, B. J.; Zhao, Y.; Truhlar, D. G. Effectiveness of diffuse basis functions for calculating relative energies by density functional theory J. Phys. Chem. A 2003, 107, 1384-1388.
67. Handy, N. C.; Cohen, A. J. Left-right correlation energy Mol. Phys. 2001, 99, 403-412.
68. Hoe, W. M.; Cohen, A. J.; Handy, N. C. Assessment of a new local exchange functional OPTX Chem. Phys. Lett. 2001, 341, 319-328.
69. Zhao, Y.; Truhlar, D. G. A new local density functional for main-group thermochemistry, transition metal bonding, thermochemical kinetics, and noncovalent interactions J. Chem. Phys. 2006, 125, 194101.
70. Xu, X.; Goddard, W. A. The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemical properties Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 2673-2677.
71. Perdew, J. P.; Wang, Y. Accurate and Simple Analytic Representation of the Electron-Gas Correlation-Energy Phys. Rev. B: Condens. Matter Mater. Phys. 1992, 45, 13244-13249.
72. Van Voorhis, T.; Scuseria, G. E. A never form for the exchange-correlation energy functional J. Chem. Phys. 1998, 109, 400-410