Efficient and accurate fragmentation methods

Accounts of Chemical Research

Volumn 47, Issue 9, 2014, Pages 2786-2794

  Pruitt, Spencer R ^a,b   Bertoni, Colleen ^a   Brorsen, Kurt R ^a   Gordon, Mark S ^a  

^a IOWA STATE UNIVERSITY   (United States)

^b ARGONNE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84949115907     PISSN: 00014842     EISSN: 15204898     Source Type: Journal    
DOI: 10.1021/ar500097m     Document Type: Article

References (57)

1. Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S.; Windus, T. L.; Dupuis, M.; Montgomery, J. A. General Atomic and Molecular Electronic Structure System J. Comput. Chem. 1993, 14, 1347
2. Gordon, M. S.; Schmidt, M. W. Advances in Electronic Structure Theory: GAMESS a Decade Later. In Theory and Applications of Computational Chemistry; Dykstra, C. E.; Frenking, G.; Kim, K. S.; Scuseria, G. E., Eds.; Elsevier: Amsterdam, The Netherlands, 2005; pp 1167-1189.
3. Gordon, M. S.; Fedorov, S. R.; Pruitt, S. R.; Slipchenko, L. V. Fragmentation Methods: A Route to Accurate Calculations on Large Systems Chem. Rev. 2012, 112, 632
4. Stone, A. J. Distributed Multipole Analysis, or How to Describe a Molecular Charge Distribution Chem. Phys. Lett. 1981, 83, 233-239
5. Stone, A. J. The Theory of Intermolecular Forces; Oxford University Press: Oxford, U.K., 1996.
6. Amos, R. D.; Handy, N. C.; Knowles, P. J.; Rice, J. E.; Stone, A. J. Ab-initio Prediction of Properties of Carbon Dioxide, Ammonia, and Carbon Dioxide···Ammonia J. Phys. Chem. 1985, 89, 2186-2192
7. 6 and Dispersion Energy in the Effective Fragment Potential Method Mol. Phys. 2005, 103, 379-387
8. Jensen, J. H.; Gordon, M. S. An Approximate Formula for the Intermolecular Pauli Repulsion Between Closed Shell Molecules Mol. Phys. 1996, 89, 1313-1325
9. Jensen, J. H. Modeling Intermolecular Exchange Integrals between Non-orthogonal Molecular Orbitals J. Chem. Phys. 1996, 104, 7795-7796
10. Jensen, J. H.; Gordon, M. S. An Approximate Formula for the Intermolecular Pauli Repulsion between Closed Shell Molecules. II. Application to the Effective Fragment Potential Method J. Chem. Phys. 1998, 108, 4772-4782
11. Jensen, J. H. Intermolecular Exchange-Induction and Charge Transfer: Derivation of Approximate Formulas Using Non-orthogonal Localized Molecular Orbitals J. Chem. Phys. 2001, 114, 8775-8783
12. Li, H.; Gordon, M. S.; Jensen, J. H. Charge Transfer Interaction in the Effective Fragment Potential Method J. Chem. Phys. 2006, 124 214108
13. Slipchenko, L. V.; Gordon, M. S. Damping Functions in the Effective Fragment Potential Method Mol. Phys. 2009, 107, 999-1016
14. Kitaura, K.; Ikeo, E.; Asada, T.; Nakano, T.; Uebayasi, M. Fragment Molecular Orbital Method: An Approximate Computational Method for Large Molecules Chem. Phys. Lett. 1999, 313, 701-706
15. Fedorov, D. G.; Kitaura, K. The Three-Body Fragment Molecular Orbital Method for Accurate Calculations of Large Systems Chem. Phys. Lett. 2006, 433, 182-187
16. Fedorov, D. G.; Kitaura, K. Multiconfiguration self-consistent-field theory based upon the fragment molecular orbital method J. Chem. Phys. 2005, 122 054108
17. Mochizuki, Y.; Koikegami, S.; Amari, S.; Segawa, K.; Kitaura, K.; Nakano, T. Configuration Interaction Singles Method with Multilayer Fragment Molecular Orbital Scheme Chem. Phys. Lett. 2005, 406, 283-288
18. Pruitt, S. R.; Fedorov, D. G.; Kitaura, K.; Gordon, M. S. Open-Shell Formulation of the Fragment Molecular Orbital Method J. Chem. Theor. Comput. 2010, 6, 1-5
19. Pruitt, S. R.; Fedorov, D. G.; Gordon, M. S. Geometry Optimizations of Open-Shell Systems with the Fragment Molecular Orbital Method J. Phys. Chem. A 2012, 116, 4965-4974
20. Sugiki, S.; Kurita, N.; Sengoku, Y.; Sekino, H. Fragment Molecular Orbital Method with Density Functional Theory and DIIS Convergence Acceleration Chem. Phys. Lett. 2003, 382, 611-617
21. Chiba, M.; Fedorov, D.; Kitaura, K. Time-Dependent Density Functional Theory with the Multilayer Fragment Molecular Orbital Method Chem. Phys. Lett. 2007, 444, 346-350
22. Fedorov, D. G.; Kitaura, K. Second Order Møller-Plesset Perturbation Theory Based upon the Fragment Molecular Orbital Method J. Chem. Phys. 2004, 121, 2483-2490
23. Fedorov, D. G.; Kitaura, K. Coupled-Cluster Theory Based upon the Fragment Molecular-Orbital Method J. Chem. Phys. 2005, 123 134103
24. Nagata, T.; Fedorov, D. G.; Kitaura, K.; Gordon, M. S. (2009). A combined effective fragment potential-fragment molecular orbital method. I. The energy expression and initial applications J. Chem. Phys. 2009, 131, 024101-12
25. Nagata, T.; Fedorov, D. G.; Sawada, T.; Kitaura, K. Analysis of Solute-Solvent Interactions in the Fragment Molecular Orbital Method Interfaced with Effective Fragment Potentials: Theory and Application to a Solvated Griffithsin-Carbohydrate Complex J. Phys. Chem. A 2012, 116, 9088-9099
26. Fedorov, D. G.; Kitaura, K.; Li, H.; Jensen, J.; Gordon, M. S. The Polarizable Continuum Model (PCM) Interfaced with the Fragment Molecular Orbital Method (FMO) J. Comput. Chem. 2006, 27, 976-985
27. Nagata, T.; Brorsen, K.; Fedorov, D. G.; Kitaura, K.; Gordon, M. S. Fully Analytic Energy Gradient in the Fragment Molecular Orbital Method J. Chem. Phys. 2011, 134 124115
28. Brorsen, K. R.; Zahariev, F.; Nakata, H.; Gordon, M. S. Analytic gradient for fragment molecular orbital density functional theory. Manuscript in preparation.
29. Nagata, T.; Fedorov, D. G.; Ishimura, K.; Kitaura, K. Analytic Energy Gradient for Second-Order Møller-Plesset Perturbation Theory Based on the Fragment Molecular Orbital Method J. Chem. Phys. 2011, 135 044110
30. Komeiji, Y.; Nakano, T.; Fukuzawa, K.; Ueno, Y.; Inadomi, Y.; Nemoto, T.; Uebayasi, M.; Fedorov, D. G.; Kitaura, K. Fragment Molecular Orbital Method: Application to Molecular Dynamics Simulation, ' ab Initio FMO-MD' Chem. Phys. Lett. 2003, 372, 342-347
31. Komeiji, Y.; Mochizuki, Y.; Nakano, T.; Fedorov, D. G. Fragment Molecular Orbital-Based Molecular Dynamics (FMO-MD), a Quantum Simulation Tool for Large Molecular Systems J. Mol. Struct. THEOCHEM 2009, 898, 2-7
32. Nagata, T.; Fedorov, D. G.; Kitaura, K. Analytic Gradient and Molecular Dynamics Simulations Using the Fragment Molecular Orbital Method Combined with Effective Potentials Theor. Chem. Acc. 2012, 131, 1-15
33. Brorsen, K. R.; Minezawa, N.; Xu, F.; Windus, T. L.; Gordon, M. S. Fragment Molecular Orbital Molecular Dynamics with the Fully Analytic Energy Gradient J. Chem. Theor. Comput. 2012, 8, 5008-5012
34. Fedorov, D. G.; Kitaura, K., Eds.; The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems; CRC Press: Boca Raton, FL, 2009; pp 1-36.
35. Steinmann, C.; Fedorov, D. G.; Jensen, J. H. Effective Fragment Molecular Orbital Method: A Merger of the Effective Fragment Potential and Fragment Molecular Orbital Methods J. Phys. Chem. A 2010, 114, 8705-8712
36. Pruitt, S. R.; Steinmann, C.; Jensen, J. H.; Gordon, M. S. Fully Integrated Effective Fragment Molecular Orbital Method J. Chem. Theory Comput. 2013, 9, 2235-2249
37. Kumar, S.; Rosenberg, J. M.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A. Multidimensional Free-Energy Calculations Using the Weighted Histogram Analysis Method J. Comput. Chem. 1995, 16, 1339-1350
38. Choi, C. H.; Re, S.; Feig, M.; Sugita, Y. Quantum Mechanical/Effective Fragment Potential Molecular Dynamics (QM/EFP-MD) Study on Intra-molecular Proton Transfer of Glycine in Water Chem. Phys. Lett. 2012, 539, 218-221
39. Petersen, P. B.; Saykally, R. J. On the Nature of Ions at the Liquid Water Surface Annu. Rev. Phys. Chem. 2006, 57, 333-364
40. Buch, V.; Milet, A.; Vácha, R.; Jungwirth, P.; Devlin, J. P. Water Surface Is Acidic Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 7342-7347
41. Tarbuck, T. L.; Ota, S. T.; Richmond, G. L. Spectroscopic Studies of Solvated Hydrogen and Hydroxide Ions at Aqueous Surfaces J. Am. Chem. Soc. 2006, 128, 14519-14527
42. Kumar, R.; Knight, C.; Voth, G. A. Exploring the Behaviour of the Hydrated Excess Proton at Hydrophobic Interfaces Faraday Discuss. 2013, 167, 263-278
43. Wick, C. D. Hydronium Behavior at the Air-Water Interface with a Polarizable Multistate Empirical Valence Bond Model J. Phys. Chem. C 2012, 116, 4026-4038
44. Kemp, D. D.; Gordon, M. S. An Interpretation of the Enhancement of the Water Dipole Moment Due to the Presence of Other Water Molecules J. Chem. Phys. A 2008, 112, 4885-4894
45. Pruitt, S. R.; Leang, S. S.; Xu, P.; Fedorov, D. G.; Gordon, M. S. Hexamers and Witchamers: Which Hex Do You Choose? Comput. Theor. Chem. 2013, 1021, 70-83
46. Miller, Y.; Thomas, J. L.; Kemp, D. D.; Finlayson-Pitts, B. J.; Gordon, M. S.; Tobias, D. J.; Gerber, R. B. Structure of Large Nitrate-Water Clusters at Ambient Temperatures: Simulations with Effective Fragment Potentials and Force Fields with Implications for Atmospheric Chemistry J. Phys. Chem. A 2009, 113, 12805-12814
47. Xantheas, S. S.; Dunning, T. H. The Structure of the Water Trimer from ab Initio Calculations J. Chem. Phys. 1993, 98, 8037-8040
48. Xantheas, S. S. Ab Initio Studies of Cyclic Water Clusters (H2O)n n=1-6. II. Analysis of Many-Body Interactions J. Chem. Phys. 1994, 100, 7523-7534
49. Hodges, M. P.; Stone, A. J.; Xantheas, S. S. Contribution of Many-Body Terms to the Energy for Small Water Clusters: A Comparison of ab Initio Calculations and Accurate Model Potentials J. Phys. Chem. A 1997, 101, 9163-9168
50. Xantheas, S. S. Cooperativity and Hydrogen Bonding Network in Water Clusters Chem. Phys. 2000, 258, 225-231
51. Xantheas, S. S. Interaction Potentials for Water from Accurate Cluster Calculations Struct. Bonding (Berlin) 2005, 116, 119-148
52. Fedorov, D. G.; Ishimura, K.; Ishida, T.; Kitaura, K.; Pulay, P.; Nagase, S. Accuracy of the Three-Body Fragment Molecular Orbital Method Applied to Møller-Plesset Perturbation Theory J. Comput. Chem. 2007, 28, 1476-1484
53. Fedorov, D. G.; Slipchenko, L. V.; Kitaura, K. Systematic Study of the Embedding Potential Description in the Fragment Molecular Orbital Method J. Phys. Chem. A 2010, 114, 8742-8753
54. Fedorov, D. G.; Kitaura, K. Chem. Phys. Lett. 2014, 597, 99-105
55. Smith, T.; Slipchenko, L. V.; Gordon, M. S. Modeling π-π Interactions with the Effective Fragment Potential Method: The Benzene Dimer and Substituents J. Phys. Chem. A 2008, 112, 5286-5294
56. Handy, N. C.; Schaefer, H. F. On the Evaluation of Analytic Energy Derivatives for Correlated Wave Functions J. Chem. Phys. 1984, 81, 5031-5033
57. Yamaguchi, Y.; Osamura, O.; Goddard, J. D.; Schaefer, H. F. A New Dimension to Quantum Mechanics. Analytical Derivative Methods in ab Initio Molecular Electronic Structure Theory. Oxford University Press: Oxford, 1994.