Theoretical modeling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations

Accounts of Chemical Research

Volumn 46, Issue 2, 2013, Pages 596-603

  Monari, Antonio ^a,b   Rivail, Jean Louis ^a,b   Assfeld, Xavier ^a,b  

^a UNIVERSITÉ DE LORRAINE   (France)

^b CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; TRYPTOPHAN;

ARTICLE; CHEMISTRY; MOLECULAR DYNAMICS; PROTEIN MOTIF;

AMINO ACID MOTIFS; MOLECULAR DYNAMICS SIMULATION; PROTEINS; TRYPTOPHAN;

EID: 84874072956     PISSN: 00014842     EISSN: 15204898     Source Type: Journal    
DOI: 10.1021/ar300278j     Document Type: Article

References (63)

1. Monard, G.; Merz, K. M., Jr. Combined Quantum Mechanical/Molecular Mechanical Methodologies Applied to Biomolecular Systems Acc. Chem. Res. 1999, 32, 904-911
2. Lin, H.; Truhlar, D. G. QM/MM: what we have learned, where are we, and where do we go from here? Theor. Chem. Acc. 2007, 117, 185-199
3. Senn, H. M.; Thiel, W. QM/MM Methods for biomolecular systems Angew. Chem., Int. Ed. 2009, 48, 1198-1229
4. Gordon, M. S.; Fedorov, D. G.; Pruitt, S. R.; Slipchenko, L. V. Fragmentation Methods: A Route to Accurate Calculations on Large Molecular Systems Chem. Rev. 2012, 112, 632-672
5. Senn, H. M.; Thiel, W. QM/MM Methods for biomolecular systems Angew. Chem., Int. Ed. 2009, 48, 1198-1229
6. Dixon, S. L.; Merz, K. M., Jr. Semiempirical Molecular-Orbital Calculations with Linear System Size Scaling J. Chem. Phys. 1996, 104, 6643-6649
7. Daniels, A. D.; Millam, J. M.; Scuseria, G. E. Semiempirical Methods with Conjugate Gradient Density Matrix Search to Replace Diagonalization for Moleculas Systems Containing Thousand of Atoms J. Chem. Phys. 1997, 107, 425-431
8. Yang, W.; Lee, T. S. A Density Matrix Divide-and-Conquer Approach for Electronic Structure Calculations of Large Molecules J. Chem. Phys. 1995, 103, 5674-5678
9. Monard, G.; Bernal-Uruchurtu, M. I.; van der Vaart, A.; Merz, K. M., Jr.; Ruiz-López, M. F. Simulation of Liquid Water Using Semiempirical Hamiltonians and the Divide and Conquer Approach J. Phys. Chem. A 2005, 109, 3425-3432
10. Car, R.; Parrinello, M. Unified Approach for Molecular Dynamics and Density-Functional Theory Phys. Rev. Lett. 1985, 55, 2471-2474
11. Carloni, P.; Rothlisberger, U.; Parrinello, M. The Role and Perspective of Ab Initio Molecular Dynamics in the Study of Biological Systems Acc. Chem. Res. 2002, 35, 455-464
12. van Gunsteren, W. F.; Berendsen, H. J. C. Groningen Molecular Simulation (GROMOS) Library Manual; Biomos: Groningen, 1987.
13. Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; Cheatham, T. E., III; DeBolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate structural and energetic properties of molecules Comput. Phys. Commun. 1995, 91, 1-41
14. MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L., Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, W.; Wiórkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins J. Phys. Chem. B 1998, 102, 3586-3616
15. Dehez, F.; Chipot, C.; Millot, C.; ángyán, J. G. Fast and accurate determination of induction energies: reduction of topologically distributed polarizability models Chem. Phys. Lett. 2001, 338, 180-188
16. 2) J. Chem. Phys. 2002, 117, 1242-1255
17. Maseras, F.; Morokuma, K. IMOMM, a new integrated ab initio + molecular mechanics geometry optimization scheme of equilibrium structure and transition states J. Comput. Chem. 1995, 16, 1170-1179
18. - exchange-reaction and gas-phase protonation of polyethers J. Comput. Chem. 1986, 7, 718-730
19. Eurenius, K. P.; Chatfield, D. C.; Brooks, B. R. Enzyme Mechanisms with Hybrid Quantum and Molecular Mechanical Potentials. I. Theoretical Considerations Int. J. Quantum Chem. 1996, 60, 1189-1200
20. Ferré, N.; Olivucci, M. The amide bond: pitfalls and drawback of the link atom scheme J. Mol. Struct.: THEOCHEM 2003, 632, 71-82
21. Antes, I.; Thiel, W. Adjusted Connection Atoms for Combined Quantum Mechanical and Molecular Mechanical Methods J. Phys. Chem. A 1999, 103, 9290-9295
22. Swart, M. AddRemove: A New Link Model for Use in QM/MM Studies Int. J. Quantum Chem. 2003, 91, 177-183
23. DiLabio, G. A.; Hurley, M. M.; Christiansen, P. A. Simple one-electron quantum capping potentials for use in hybrid QM/MM studies of biological molecules J. Chem. Phys. 2002, 116, 9578-9584
24. Xiao, C.; Zhang, Y. Design-atom approach for quantum mechanical/molecular mechanical covalent boundary: A design-carbon atom with five valence electrons J. Chem. Phys. 2007, 127, 124102
25. Poteau, R.; Ortega, Y.; Alary, F.; Ramirez Solis, A.; Barthelat, J.-C.; Daudey, J. P. Effective Group Potentials. 1. Method J. Phys. Chem. A 2001, 105, 198-205
26. Wang, B.; Truhlar, D. G. Combined Quantum Mechanical and Molecular Mechanical Methods for Calculating Potential Energy Surfaces: Tuned and Balanced Redistributed-Charge Algorithm J. Chem. Theor. Comput. 2010, 6, 359-369
27. 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
28. Ferenczy, G. G.; Rivail, J.-L.; Surján, P. R.; Náray-Szabó, G. NDDO fragment self-consistent-field approximation for large electronic systems J. Comput. Chem. 1992, 13, 830-837
29. Théry, V.; Rinaldi, D.; Rivail, J.-L.; Maigret, B.; Ferenczy, G. G. Quantum mechanical computations on very large molecular systems: The local self-consistent field method J. Comput. Chem. 1994, 15, 269-282
30. Monard, G.; Loos, M.; Théry, V.; Baka, K.; Rivail, J. L. Hybrid Classical Quantum Force Field for Modeling Very Large Molecules Int. J. Quantum Chem. 1996, 58, 153-159
31. Antonczak, S.; Monard, G.; Ruiz-López, M. F.; Rivail, J.-L. Modeling of Peptide Hydrolysis by Thermolysin. A semiempirical and QM/MM Study J. Am. Chem. Soc. 1998, 120, 8825-8833
32. Gao, G.; Amara, P.; Alhambra, C.; Field, M. J. A Generalized Hybrid Orbital (GHO) Method for the Treatment of Boundary Atoms in Combined QM/MM Calculations J. Phys. Chem. A 1998, 102, 4714-4721
33. Pu, J.; Gao, J.; Truhlar, D. G. Combining Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) with Molecular Mechanics by the Generalized Hybrid Orbital (GHO) Method J. Phys. Chem. A 2004, 108, 5454-5463
34. Lin, H.; Truhlar, D. G. Redristributed Charge and Dipole Schemes for Combined Quantum Mechanical and Molecular Mechanical Calculations J. Phys. Chem. A 2005, 109, 3991-4004
35. Assfeld, X.; Rivail, J.-L. Quantum chemical computations on parts of large molecules: the ab initio local self consistent field method Chem. Phys. Lett. 1996, 263, 100-106
36. Moreau, Y.; Loss, P.-F.; Assfeld, X. Solvent effects on the asymmetric Diels-Alder reaction between cyclopentadiene and (-)-menthyl acrylate revisited with the three-layer hybrid local self-consistent field/molecular mechanics/self-consistent reaction field method Theor. Chem. Acc. 2004, 112, 228-239
37. Ferré, N.; Assfeld, X. Application of the local self-consistent-field method to core-ionized and core-excited molecules, polymers, and proteins: True orthogonality between ground and excited states J. Chem. Phys. 2002, 117, 4119-4125
38. Loos, P. F.; Assfeld, X. Core-ionized and core-excited states of macromolecules Int. J. Quantum Chem. 2007, 107, 2243-2252
39. Szabo, A.; Ostlund, N. S. Modern Quantum Chemistry; McGraw Hill: New York, 1989, p 144.
40. Ferré, N.; Assfeld, X.; Rivail, J.-L. Specific Force Field Determination for the Hybrid Ab Initio QM/MM LSCF Method J. Comput. Chem. 2002, 23, 610-624
41. Fornili, A.; Loos, P.-F.; Sironi, M.; Assfeld, X. Frozen core orbitals as an alternative to specific frontier bond potential in hybrid Quantum Mechanics/ Molecular Mechanics methods Chem. Phys. Lett. 2006, 427, 236-240
42. Loos, P.-F.; Fornili, A.; Sironi, M.; Assfeld, X. Removing extra frontier parameters in QM/MM methods: a tentative with the Local Self-Consistent Field Approach Comput. Lett. 2007, 4, 473-486
43. Loos, P.-F.; Assfeld, X. On The Frontier Bond Location In The QM/MM Description Of Peptides and Proteins AIP Conf. Proc. 2007, 963, 308-315
44. Ferré, N.; Assfeld, X. A new three-layer hybrid method (LSCF/MM/Madelung) devoted to the study of chemical reactivity in zeolites. Preliminary results J. Mol. Struct.: THEOCHEM 2003, 632, 83-90
45. Jensen, F. Introduction to Computational Chemistry; J. Wiley & Sons: Chichester, 2001; pp 227-229.
46. Fornili, A.; Moreau, Y.; Sironi, M.; Assfeld, X. On the Suitability of Strictly Localized Orbitals for Hybrid QM/MM Calculations J. Comput. Chem. 2006, 27, 515-523
47. Sironi, M.; Famulari, A. An orthogonal approach to determine extremely localised molecular orbitals Theor. Chem. Acc. 2000, 103, 417-422
48. Genoni, A.; Ghitti, M.; Pieraccini, S.; Sironi, M. A novel extremely localized molecular orbitals based technique for the one-electron density matrix computation Chem. Phys. Lett. 2005, 415, 256-260
49. Loos, P. F.; Assfeld, X. Self-Consistent Strictly Localized Orbitals J. Chem. Theory Comput. 2007, 3, 1047-1053
50. 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
51. Marenich, A. V.; Cramer, C. J.; Truhlar, D. G.; Guido, C. A.; Mennucci, B.; Scalmani, G.; Frisch, M. J. Practical computation of electronic excitation in solution: vertical excitation model Chem. Sci. 2011, 2, 2143-2161
52. Jacquemin, D.; Mennucci, B.; Adamo, C. Excited-state calculations with TD-DFT: from benchmarks to simulations in complex environments Phys. Chem. Chem. Phys. 2011, 13, 16987-16998
53. Mennucci, B.; Cappelli, C.; Guido, C. A.; Cammi, R.; Tomasi, J. Structures and properties of electronically excited chromophores in solution from the polarizable continuum model coupled to the TD-DFT J. Phys. Chem. A 2009, 113, 3009-3020
54. Jacquemin, D.; Perpète, E. A.; Laurent, A. D.; Assfeld, X.; Adamo, C. Spectral properties of self-assembled squaraine-tetralactam: A theoretical assessment Phys. Chem. Chem. Phys. 2009, 11, 1258-1262
55. Laurent, A. D.; Assfeld, X. Effect of the Enhanced Cyan Fluorescent Proteinic Framework on the UV/visible absorption spectra of some chromophores Interdisc. Sci. Comput. Life Sci. 2010, 2, 38-47
56. Monari, A.; Very, T.; Rivail, J.-L.; Assfeld, X. Effects of mutations on the absorption spectra of copper proteins: a QM/MM study Theor. Chem. Acc. 2012, 131, 1221
57. 2 Phys. Chem. Chem. Phys. 2012, 14, 12496-12504
58. Chantzis, A.; Very, T.; Monari, A.; Assfeld, X. Improved Treatment of Surrounding Effects: UV/vis Absorption Properties of a Solvated Ru(II) Complex J. Chem. Theory Comput. 2012, 8, 1536-1541
59. Lakowicz, J. R. Principle of Fluorescence Spectroscopy; Springer: 2006.
60. Goswani, N.; Makhal, A.; Kumar Pal, S. Toward an Alternative Intrinsic Probe for Spectroscopic Characterization of a Protein J. Phys. Chem. B 2010, 114, 15236-15243
61. Dumont, E.; Loos, P.-F.; Laurent, A. D.; Assfeld, X. Huge disulfide-linkage's electron capture variation induced by α-helix orientation J. Chem. Theory Comput. 2008, 4, 1171-1173
62. DiLabio, G. A.; Wolkow, R. A.; Johnson, E. R. Efficient silicon surface and cluster modelling using quantum capping potentials J. Chem. Phys. 2005, 122, 044708
63. Rodrigez-Ropero, F.; Zanuy, D.; Assfeld, X.; Alemán, C. Modeling an Electronic Conductor Based on Natural Peptide Sequences Biomacromolecules 2009, 10, 2338-2343