Accurate and Efficient Quantum Chemistry Calculations for Noncovalent Interactions in Many-Body Systems: The XSAPT Family of Methods

Journal of Physical Chemistry A

Volumn 119, Issue 2, 2015, Pages 235-252

  Lao, Ka Un ^a   Herbert, John M ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULES; CALCULATIONS; COMPLEXATION; COMPUTATION THEORY; DIMERS; DISPERSIONS; GAS HYDRATES; INTERCALATION; IONS; ITERATIVE METHODS; METHANE; MOLECULAR CRYSTALS; MONOMERS; PERTURBATION TECHNIQUES; QUANTUM CHEMISTRY;

INTERMOLECULAR INTERACTION ENERGIES; METHANE CLATHRATE HYDRATE; NON-COVALENT INTERACTION; POLARIZATION INTERACTIONS; PROTEIN-LIGAND COMPLEXES; QUANTUM CHEMISTRY CALCULATIONS; QUANTUM CHEMISTRY METHODS; SYMMETRY ADAPTED PERTURBATION THEORY;

QUANTUM EFFICIENCY;

ANTINEOPLASTIC AGENT; DNA; HUMAN IMMUNODEFICIENCY VIRUS PROTEINASE; INDINAVIR; ION; PROTEIN; PROTEINASE INHIBITOR; WATER;

CHEMICAL ANALYSIS; CHEMICAL MODEL; CHEMISTRY; DIMERIZATION; PROCEDURES; QUANTUM THEORY; STATIC ELECTRICITY;

ANTINEOPLASTIC AGENTS; CHEMISTRY TECHNIQUES, ANALYTICAL; DIMERIZATION; DNA; HIV PROTEASE; INDINAVIR; IONS; MODELS, CHEMICAL; PROTEASE INHIBITORS; PROTEINS; QUANTUM THEORY; STATIC ELECTRICITY; WATER;

EID: 84923280401     PISSN: 10895639     EISSN: 15205215     Source Type: Journal    
DOI: 10.1021/jp5098603     Document Type: Review

References (160)

1. Yakovchuk, P.; Protozanova, E.; Frank-Kamenetskii, M. D. Base-stacking and base-pairing contributions into thermal stability of the DNA double helix Nucleic Acids Res. 2006, 34, 564 - 574
2. Guvench, O.; MacKerell, A. D. Computational evaluation of protein-small molecule binding Curr. Opin. Struct. Biol. 2009, 19, 56 - 61
3. Durdagi, S.; Zhao, C.; Cuervo, J. E.; Noskov, S. Y. Atomistic models for free energy evaluation of drug binding to membrane proteins Curr. Med. Chem. 2011, 18, 2601 - 2611
4. Woodley, S. M.; Catlow, R. Crystal structure prediction from first principles Nat. Mater. 2008, 7, 937 - 946
5. Jeziorski, B.; Moszynski, R.; Ratkiewicz, A.; Rybak, S.; Szalewicz, K.; Williams, H. L. SAPT: A program for many-body symmetry-adapted perturbation theory calculations of intermolecular interaction energies. In Methods and Techniques in Computational Chemistry: METECC-94; Clementi, E., Ed.; STEF: Cagliari, 1993; Vol. B, Chapter 3, pp 79 - 129.
6. Jeziorski, B.; Moszynski, R.; Szalewicz, K. Perturbation theory approach to intermolecular potential energy surfaces of van der Waals complexes Chem. Rev. 1994, 94, 1887 - 1930
7. Szalewicz, K.; Patkowski, K.; Jeziorski, B. Intermolecular interactions via perturbation theory: From diatoms to biomolecules. In Intermolecular Forces and Clusters II; Wales, D. J., Ed.; Vol. 116 of Structure and Bonding; Springer-Verlag: Berlin, 2005; pp 43 - 117.
8. Szalewicz, K. Symmetry-adapted perturbation theory of intermolecular forces Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2012, 2, 254 - 272
9. Hohenstein, E. G.; Sherrill, C. D. Wavefunction methods for noncovalent interactions Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2012, 2, 304 - 326
10. Jansen, G. Symmetry-adapted perturbation theory based on density functional theory for noncovalent interactions Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2014, 4, 127 - 144
11. Perdew, J. P. Climbing the ladder of density functional approximations MRS Bull. 2013, 38, 743 - 750
12. 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
13. Grimme, S. Semiempirical GGA-type density functional constructed with long-range dispersion correction J. Comput. Chem. 2006, 27, 1787 - 1799
14. Grimme, S.; Antony, J.; Ehrlich, S.; 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
15. Grimme, S. Density functional theory with London dispersion corrections Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2011, 1, 211 - 228
16. Chai, J.-D.; Head-Gordon, M. Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections Phys. Chem. Chem. Phys. 2008, 10, 6615 - 6620
17. Grimme, S. Semiempirical hybrid density functional with perturbative second-order correction J. Chem. Phys. 2006, 124, 034108:1 - 16
18. Vydrov, O. A.; Van Voorhis, T. Nonlocal van der Waals density functional: The simpler the better J. Chem. Phys. 2010, 133, 244103:1 - 9
19. Mardirossian, N.; Head-Gordon, M. ωB97X-V: A 10-parameter, range-separated hybrid, generalized gradient approximation density functional with nonlocal correlation, designed by a survival-of-the-fittest strategy Phys. Chem. Chem. Phys. 2014, 16, 9904 - 9924
20. Howard, J. C.; Tschumper, G. S. Wavefunction methods for the accurate characterization of water clusters Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2014, 4, 199 - 224
21. Del Ben, M.; Schönherr, M.; Hutter, J.; VandeVondele, J. Bulk liquid water at ambient temperature and pressure from MP2 theory J. Phys. Chem. Lett. 2013, 4, 3753 - 3759 Erratum: Del Ben, M.; Schönherr, M.; Hutter, J.; VandeVondele, J. J. Phys. Chem. Lett. 2014, 5, 3066 - 3067
22. Jurečka, P.; Šponer, J.; Černý, J.; Hobza, P. Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs Phys. Chem. Chem. Phys. 2006, 8, 1985 - 1993
23. Cremer, D. Møller - Plesset perturbation theory: From small molecule methods to methods for thousands of atoms Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2011, 1, 509 - 530
24. Szabo, A.; Ostlund, N. S. The correlation energy in the random phase approximation: Intermolecular forces between closed-shell systems J. Chem. Phys. 1977, 67, 4351 - 4360
25. Tkatchenko, A.; DiStasio, R. A., Jr.; Head-Gordon, M.; Scheffler, M. Dispersion-corrected Møller - Plesset second-order perturbation theory J. Chem. Phys. 2009, 131, 094106:1 - 7
26. van Duijneveldt, F. B.; van Duijneveldt-van de Rijdt, J. G. C. M.; van Lenthe, J. H. State of the art in counterpoise theory Chem. Rev. 1994, 94, 1873 - 1885
27. Hopkins, B. W.; Tschumper, G. S. Ab initio studies of π···π interactions: The effects of quadruple excitations J. Phys. Chem. A 2004, 108, 2941 - 2948
28. Hobza, P. Calculations on noncovalent interactions and databases of benchmark interaction energies Acc. Chem. Res. 2012, 45, 663 - 672
29. Dubecký, M.; Jurečka, P.; Derian, R.; Hobza, P.; Otyepka, M.; Mitas, L. Quantum Monte Carlo methods describe noncovalent interactions with subchemical accuracy J. Chem. Theory Comput. 2013, 9, 4287 - 4292
30. Ambrosetti, A.; Alfè;, D.; DiStasio, R. A., Jr.; Tkatchenko, A. Hard numbers for large molecules: Toward exact energetics for supramolecular systems J. Phys. Chem. Lett. 2014, 5, 849 - 855
31. Řezáč, J.; Hobza, P. Describing noncovalent interactions beyond the common approximations: How accurate is the "gold standard", CCSD(T) at the complete basis set limit? J. Chem. Theory Comput. 2013, 9, 2151 - 2155
32. Šimová, L.; Řezáč, J.; Hobza, P. Convergence of the interaction energies in noncovalent complexes in the coupled-cluster methods up to full configuration interaction J. Chem. Theory Comput. 2013, 9, 3420 - 3428
33. Smith, D. G. A.; Jankowski, P.; Slawik, M.; Witek, H. A.; Patkowski, K. Basis set convergence of the post-CCSD(T) contribution to noncovalent interaction energies J. Chem. Theory Comput. 2014, 10, 3140 - 3150
34. Marshall, M. S.; Burns, L. A.; Sherrill, C. D. Basis set convergence of the coupled-cluster correction, δMP2CCSD(T): Best practices for benchmarking non-covalent interactions and the attendant revision of the S22, NBC10, and HSG databases J. Chem. Phys. 2011, 135, 194102:1 - 10
35. Yoo, S.; Aprà, E.; Zeng, X. C.; Xantheas, S. S. High-level ab initio electronic structure calculations of water clusters (H2O)16 and (H2O)17: A new global minimum for (H2O)16 J. Phys. Chem. Lett. 2010, 1, 3122 - 3127
36. Řezác, J.; Riley, K. E.; Hobza, P. S66: A well-balanced database of benchmark interaction energies relevant to biomolecular structures J. Chem. Theory Comput. 2011, 7, 2427 - 2438 Erratum: Řezác, J.; Riley, K. E.; Hobza, P. J. Chem. Theory Comput. 2014, 10, 1359 - 1360
37. Goerigk, L.; Kruse, H.; Grimme, S. Benchmarking density functional methods against the S66 and S66 × 8 datasets for non-covalent interactions ChemPhysChem 2011, 12, 3421 - 3433
38. Vydrov, O. A.; Van Voorhis, T. Benchmark assessment of the accuracy of several van der Waals density functionals J. Chem. Theory Comput. 2012, 8, 1929 - 1934
39. Lin, Y.-S.; Li, G.-D.; Mao, S.-P.; Chai, J.-D. Long-range corrected hybrid density functionals with improved dispersion corrections J. Chem. Theory Comput. 2013, 9, 263 - 272
40. Grimme, S.; Ehrlich, S.; Goerigk, L. Effect of the damping function in dispersion corrected density functional theory J. Comput. Chem. 2011, 32, 1456 - 1465
41. Pitonňák, M.; Řezác, J.; Hobza, P. Spin-component scaled coupled-clusters singles and doubles optimized towards calculation of noncovalent interactions Phys. Chem. Chem. Phys. 2010, 12, 9611 - 9614
42. Heβelmann, A. Improved supermolecular second order Møller - Plesset intermolecular interaction energies using time-dependent density functional response theory J. Chem. Phys. 2008, 128, 144112:1 - 9
43. Pitonňák, M.; Heβelmann, A. Accurate intermolecular interaction energies from a combination of MP2 and TDDFT response theory J. Chem. Theory Comput. 2010, 6, 168 - 178
44. Huang, Y.; Shao, Y.; Beran, G. J. O. Accelerating MP2C dispersion corrections for dimers and molecular crystals J. Chem. Phys. 2013, 138, 224112:1 - 8
45. Huang, Y.; Goldey, M.; Head-Gordon, M.; Beran, G. J. O. Achieving high-accuracy intermolecular interactions by combining Coulomb-attenuated second-order Møller - Plesset perturbation theory with coupled Kohn - Sham dispersion J. Chem. Theory Comput. 2014, 10, 2054 - 2063
46. Lao, K. U.; Herbert, J. M. An improved treatment of empirical dispersion and a many-body energy decomposition scheme for the explicit polarization plus symmetry-adapted perturbation theory (XSAPT) method J. Chem. Phys. 2013, 139, 034107:1 - 16 Erratum: Lao, K. U.; Herbert, J. M. J. Chem. Phys. 2014, 140, 119901
47. Chen, Z.; Li, Y.; Chen, E.; Hall, D. L.; Darke, P. L.; Culberson, C.; Shafer, J. A.; Kuo, L. C. Crystal structure at 1.9-Å resolution of human immunodeficiency virus (HIV) II protease complexed with L-735,524, an orally bioavailable inhibitor of the HIV proteases J. Biol. Chem. 1994, 269, 26344 - 26348
48. Ucisik, M. N.; Dashti, D. S.; Faver, J. C.; Merz, K. M., Jr. Pairwise additivity of energy components in protein-ligand binding: The HIV II protease-indinavir case J. Chem. Phys. 2011, 135, 085101:1 - 12
49. Gordon, M. S.; Fedorov, D. G.; Pruitt, S. R.; Slipchenko, L. V. Fragmentation methods: A route to accurate calculations on large systems Chem. Rev. 2012, 112, 632 - 672
50. Jacobson, L. D.; Richard, R. M.; Lao, K. U.; Herbert, J. M. Efficient monomer-based quantum chemistry methods for molecular and ionic clusters Annu. Rep. Comput. Chem. 2013, 9, 25 - 56
51. Jacobson, L. D.; Herbert, J. M. An efficient, fragment-based electronic structure method for molecular systems: Self-consistent polarization with perturbative two-body exchange and dispersion J. Chem. Phys. 2011, 134, 094118:1 - 17
52. Lao, K. U.; Herbert, J. M. Accurate intermolecular interactions at dramatically reduced cost: XPol+SAPT with empirical dispersion J. Phys. Chem. Lett. 2012, 3, 3241 - 3248
53. Herbert, J. M.; Jacobson, L. D.; Lao, K. U.; Rohrdanz, M. A. Rapid computation of intermolecular interactions in molecular and ionic clusters: Self-consistent polarization plus symmetry-adapted perturbation theory Phys. Chem. Chem. Phys. 2012, 14, 7679 - 7699
54. Lao, K. U.; Herbert, J. M. Symmetry-adapted perturbation theory with Kohn-Sham orbitals using non-empirically tuned, long-range-corrected density functionals J. Chem. Phys. 2014, 140, 044108:1 - 8
55. 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, 234108:1 - 9
56. Rybak, S.; Jeziorski, B.; Szalewicz, K. Many-body symmetry-adapted perturbation theory of intermolecular interactions. H2O and HF dimers J. Chem. Phys. 1991, 95, 6576 - 6601
57. Korona, T. First-order exchange energy of intermolecular interactions from coupled cluster density matrices and their cumulants J. Chem. Phys. 2008, 128, 224104:1 - 14
58. Korona, T. Second-order exchange-induction energy of intermolecular interactions from coupled cluster density matrices and their cumulants Phys. Chem. Chem. Phys. 2009, 10, 6509 - 6519
59. Korona, T. Exchange-dispersion energy: A formulation in terms of monomer properties and coupled cluster treatment of intramonomer correlation J. Chem. Theory Comput. 2009, 5, 2663 - 2678
60. Korona, T. A coupled cluster treatment of intramonomer electron correlation within symmetry-adapted perturbation theory: Benchmark calculations and a comparison with a density-functional theory description Mol. Phys. 2013, 111, 3705 - 3715
61. Williams, H. L.; Chabalowski, C. F. Using Kohn-Sham orbitals in symmetry-adapted perturbation theory to investigate intermolecular interactions J. Phys. Chem. A 2001, 105, 646 - 659
62. Jansen, G.; Heβelmann, A. Comment on "Using Kohn - Sham orbitals in symmetry-adapted perturbation theory to investigate intermolecular interactions J. Phys. Chem. A 2001, 105, 11156 - 11157
63. Misquitta, A. J.; Szalewicz, K. Intermolecular forces from asymptotically corrected density functional description of monomers Chem. Phys. Lett. 2002, 357, 301 - 306
64. Tozer, D. J.; Handy, N. C. Improving virtual Kohn-Sham orbitals and eigenvalues: Application to excitation energies and static polarizabilities J. Chem. Phys. 1998, 109, 10180 - 10189
65. Perdew, J. P.; Burke, K. Comparison shopping for a gradient-corrected density functional Int. J. Quantum Chem. 1996, 57, 309 - 319
66. Heβelmann, A.; Jansen, G. First-order intermolecular interaction energies from Kohn-Sham orbitals Chem. Phys. Lett. 2002, 357, 464 - 470
67. Heβelmann, A.; Jansen, G. Intermolecular induction and exchange-induction energies from coupled-perturbed Kohn-Sham density functional theory Chem. Phys. Lett. 2002, 362, 319 - 325
68. Misquitta, A. J.; Jeziorski, B.; Szalewicz, K. Dispersion energy from density-function theory description of monomers Phys. Rev. Lett. 2003, 91, 033201:1 - 4
69. Heβelmann, A.; Jansen, G. Intermolecular dispersion energies from time-dependent density functional theory Chem. Phys. Lett. 2003, 367, 778 - 784
70. Heβelmann, A.; Jansen, G. The helium dimer potential from a combined density functional theory and symmetry-adapted perturbation theory approach using an exact exchange-correlation potential Phys. Chem. Chem. Phys. 2003, 5, 5010 - 5014
71. Heβelmann, A.; Jansen, G.; Schütz, M. Density-functional theory symmetry-adapted intermolecular perturbation theory with density fitting: A new efficient method to study intermolecular interaction energies J. Chem. Phys. 2005, 122, 014103:1 - 17
72. Misquitta, A. J.; Szalewicz, K. Symmetry-adapted perturbation-theory calculations of intermolecular forces employing density-functional description of monomers J. Chem. Phys. 2005, 122, 214109:1 - 19
73. Misquitta, A. J.; Podeszwa, R.; Jeziorski, B.; Szalewicz, K. Intermolecular potentials based on symmetry-adapted perturbation theory with dispersion energies from time-dependent density-functional calculations J. Chem. Phys. 2005, 123, 214103:1 - 14
74. Bukowski, R.; Podeszwa, R.; Szalewicz, K. Efficient calculation of coupled Kohn-Sham dynamic susceptibility functions and dispersion energies with density fitting Chem. Phys. Lett. 2005, 414, 111 - 116
75. Podeszwa, R.; Bukowski, R.; Szalewicz, K. Density-fitting method in symmetry-adapted perturbation theory based on Kohn-Sham description of monomers J. Chem. Theory Comput. 2006, 2, 400 - 412
76. Turki, N.; Milet, A.; Rahmouni, A.; Ouamerali, O.; Moszynski, R.; Kochanski, E.; Wormer, P. E. S. Theoretical study of the OH-(H2O)2 system: Nature and importance of three-body interactions J. Chem. Phys. 1998, 109, 7157 - 7168
77. Chen, Y.; Li, H. Intermolecular interaction in water hexamer J. Phys. Chem. A 2010, 114, 11719 - 11724
78. Dahlke, E. E.; Truhlar, D. G. Electrostatically embedded many-body correlation energy, with applications to the calculation of accurate second-order Møller-Plesset perturbation theory energies for large water clusters J. Chem. Theory Comput. 2007, 3, 1342 - 1348
79. McDaniel, J. G.; Schmidt, J. R. First-principles many-body force fields from the gas phase to liquid: A "universal" approach J. Phys. Chem. B 2014, 118, 8042 - 8053
80. Lotrich, V. F.; Szalewicz, K. Symmetry-adapted perturbation theory of three-body nonadditivity of intermolecular interaction energy J. Chem. Phys. 1997, 106, 9668 - 9687
81. Lotrich, V. F.; Szalewicz, K. Symmetry-adapted perturbation theory of three-body nonadditivity in Ar trimer J. Chem. Phys. 1997, 106, 9688 - 9702
82. Lotrich, V. F.; Szalewicz, K. Perturbation theory of three-body exchange nonadditivity and application to helium trimer J. Chem. Phys. 2000, 112, 112 - 121
83. Gao, J. Toward a molecular orbital derived empirical potential for liquid simulations J. Phys. Chem. B 1997, 101, 657 - 663
84. Gao, J. A molecular-orbital derived polarization potential for liquid water J. Chem. Phys. 1998, 109, 2346 - 2354
85. Xie, W.; Gao, J. Design of a next generation force field: The X-POL potential J. Chem. Theory Comput. 2007, 3, 1890 - 1900
86. Gao, J.; Truhlar, D. G.; Wang, Y.; Mazack, M. J. M.; Löffler, P.; Provorse, M. R.; Rehak, P. Explicit polarization: A quantum mechanical framework for developing next generation force fields Acc. Chem. Res. 2014, 47, 2837 - 2845
87. Breneman, C. M.; Wiberg, K. B. Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis J. Comput. Chem. 1990, 11, 361 - 373
88. Holden, Z. C.; Richard, R. M.; Herbert, J. M. Periodic boundary conditions for QM/MM calculations: Ewald summation for extended Gaussian basis sets J. Chem. Phys. 2013, 139, 244108:1 - 13
89. 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
90. Fedorov, D. G.; Kitaura, K. Extending the power of quantum chemistry to large systems with the fragment molecular orbital method J. Phys. Chem. A 2007, 111, 6904 - 6914
91. Dahlke, E. E.; Truhlar, D. G. Electrostatically embedded many-body expansion for large systems, with applications to water clusters J. Chem. Theory Comput. 2007, 3, 46 - 53
92. Richard, R. M.; Lao, K. U.; Herbert, J. M. Aiming for benchmark accuracy with the many-body expansion Acc. Chem. Res. 2014, 47, 2828 - 2836
93. Hratchian, H. P.; Parandekar, P. V.; Raghavachari, K.; Frisch, M. J.; Vreven, T. QM:QM electronic embedding using Mulliken atomic charges: Energies and analytic gradients in an ONIOM framework J. Chem. Phys. 2008, 128, 034107:1 - 11
94. 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, 124115:1 - 13
95. Fedorov, D. G.; Ishida, T.; Uebayasi, M.; Kitaura, K. The fragment molecular orbital method for geometry optimizations of polypeptides and proteins J. Phys. Chem. A 2007, 111, 2722 - 2732
96. Hua, S.; Hua, W.; Li, S. An efficient implementation of the generalized energy-based fragmentation approach for general large molecules J. Phys. Chem. A 2010, 114, 8126 - 8134
97. Li, W.; Hua, W.; Fang, T.; Li, S. The energy-based fragmentation approach for ab initio calculations of large systems. In Computational Methods for Large Systems: Electronic Structure Approaches for Biotechnology and Nanotechnology; Reimers, J. R., Ed.; Wiley: Hoboken, NJ, 2011; pp 227 - 258.
98. Bottcher, C. J. F.; Belle, O. V.; Bordewijk, P.; Rip, A. Theory of Electric Polarization; Vol. 1 of Dielectrics in Static Fields; Elsevier: Amsterdam, 1973.
99. Jacobson, L. D.; Williams, C. F.; Herbert, J. M. The static-exchange electron-water pseudopotential, in conjunction with a polarizable water model: A new Hamiltonian for hydrated-electron simulations J. Chem. Phys. 2009, 130, 124115:1 - 18
100. Hirschfelder, J. O. Perturbation theory for exchange forces. I Chem. Phys. Lett. 1967, 1, 325 - 329
101. Hirschfelder, J. O.; Meath, W. J. Nature of intermolecular forces Adv. Chem. Phys. 1967, 12, 3 - 106
102. Jeziorski, B.; Bulski, M.; Piela, L. First-order perturbation treatment of the short-range repulsion in a system of many closed-shell atoms or molecules Int. J. Quantum Chem. 1976, 10, 281 - 297
103. Schäffer, R.; Jansen, G. Intermolecular exchange-induction energies without overlap expansion Theor. Chem. Acc. 2012, 131, 1235:1 - 10
104. Schäffer, R.; Jansen, G. Single-determinant-based symmetry-adapted perturbation theory without single-exchange approximation Mol. Phys. 2013, 111, 2570 - 2584
105. Lao, K. U.; Herbert, J. M. Breakdown of the single-exchange approximation in third-order symmetry-adapted perturbation theory J. Phys. Chem. A 2012, 116, 3042 - 3047
106. Lao, K. U.; Schäffer, R.; Jansen, G.; Herbert, J. M. Accurate description of intermolecular interactions in ionic systems using symmetry-adapted perturbation theory. Submitted for publication.
107. Fedorov, D. G.; Nagata, T.; Kitaura, K. Exploring chemistry with the fragment molecular orbital method Phys. Chem. Chem. Phys. 2012, 14, 7562 - 7577
108. Moszynski, R.; Jeziorski, B.; Ratkiewicz, A.; Rybak, S. Many-body perturbation theory of electrostatic interactions between molecules: Comparison with full configuration interaction for four-electron dimers J. Chem. Phys. 1993, 99, 8856
109. Moszyński, R.; Cybulski, S. M.; Chałasiński, G. Many-body theory of intermolecular induction interactions J. Chem. Phys. 1994, 100, 4998 - 5010
110. Williams, H. L.; Mas, E. M.; Szalewicz, K.; Jeziorski, B. On the effectiveness of monomer-, dimer-, and bond-centered basis functions in calculations of intermolecular interaction energies J. Chem. Phys. 1995, 103, 7374 - 7391
111. Wolinski, K.; Pulay, P. Second-order Møller-Plesset calculations with dual basis sets J. Chem. Phys. 2003, 118, 9497 - 9503
112. Steele, R. P.; DiStasio, R. A., Jr.; Shao, Y.; Kong, J.; Head-Gordon, M. Dual-basis second-order Møller-Plesset perturbation theory: A reduced-cost reference for correlation calculations J. Chem. Phys. 2006, 125, 074108:1 - 11
113. Hohenstein, E. G.; Sherrill, C. D. Density fitting of intramonomer correlation effects in symmetry adapted perturbation theory J. Chem. Phys. 2010, 133, 014101:1 - 12
114. van Leeuwen, R.; Baerends, E. J. Exchange-correlation potential with correct asymptotic behavior Phys. Rev. A 1994, 49, 2421 - 2431
115. Tozer, D. J.; Handy, N. C. Improving virtual Kohn-Sham orbitals and eigenvalues: Application to excitation energies and static polarizabilities J. Chem. Phys. 1998, 109, 10180 - 10189
116. Gruning, M.; Gritsenko, O. V.; van Gisbergen, S. J. A.; Baerends, E. J. Shape corrections to exchange-correlation potentials by gradient-regulated seamless connection of model potentials for inner and outer region J. Chem. Phys. 2001, 114, 652 - 660
117. Gaiduk, A. P.; Staroverov, V. N. How to tell when a model Kohn-Sham potential is not a functional derivative J. Chem. Phys. 2009, 131, 044107:1 - 7
118. Iikura, H.; Tsuneda, T.; Yanai, T.; Hirao, K. A long-range correction scheme for generalized-gradient-approximation exchange functionals J. Chem. Phys. 2001, 115, 3540 - 3544
119. Henderson, T. M.; Janesko, B. G.; Scuseria, G. E. Generalized gradient approximation model exchange holes for range-separated hybrids J. Chem. Phys. 2008, 128, 194105:1 - 9
120. Livshits, E.; Baer, R. A well-tempered density functional theory of electrons in molecules Phys. Chem. Chem. Phys. 2007, 9, 2932 - 2941
121. Rohrdanz, M. A.; Martins, K. M.; Herbert, J. M. A long-range-corrected density functional that performs well for both ground-state properties and time-dependent density functional theory excitation energies, including charge-transfer excited states J. Chem. Phys. 2009, 130, 054112:1 - 8
122. Stein, T.; Kronik, L.; Baer, R. Prediction of charge-transfer excitations in coumarin-based dyes using a range-separated functional tuned from first principles J. Chem. Phys. 2009, 131, 244119:1 - 5
123. Baer, R.; Livshits, E.; Salzner, U. Tuned range-separated hybrids in density functional theory Annu. Rev. Phys. Chem. 2010, 61, 85 - 109
124. Heβelmann, A. Comparison of intermolecular interaction energies from SAPT and DFT including empirical dispersion contributions J. Phys. Chem. A 2011, 115, 11321 - 11330
125. Grimme, S. Accurate description of van der Waals complexes by density functional theory including empirical corrections J. Comput. Chem. 2004, 25, 1463 - 1473
126. Podeszwa, R.; Pernal, K.; Patkowski, K.; Szalewicz, K. Extension of the Hartree-Fock plus dispersion method by first-order correlation effects J. Phys. Chem. Lett. 2010, 1, 550 - 555
127. Tang, K. T.; Toennies, J. P. An improved simple model for the van der Waals potential based on universal damping functions for the dispersion coefficients J. Chem. Phys. 1984, 80, 3726 - 3741
128. Williams, H. L.; Szalewicz, K.; Moszynski, R.; Jeziorski, B. Dispersion energy in the coupled pair approximation with noniterative inclusion of single and triple excitations J. Chem. Phys. 1995, 103, 4586 - 4599
129. Parrish, R. M.; Hohenstein, E. G.; Sherrill, C. D. Tractability gains in symmetry-adapted perturbation theory including coupled double excitations: CCD+ST(CCD) dispersion with natural orbital truncations J. Chem. Phys. 2013, 139, 174102:1 - 15
130. Lange, A. W.; Herbert, J. M. Both intra- and interstrand charge-transfer excited states in B-DNA are present at energies comparable to, or just above, the 1ππ∗ excitonic bright states J. Am. Chem. Soc. 2009, 131, 3913 - 3922
131. Maurer, S. A.; Beer, M.; Lambrecht, D. S.; Ochsenfeld, C. Linear-scaling symmetry-adapted perturbation theory with scaled dispersion J. Chem. Phys. 2013, 139, 184104:1 - 7
132. Fiethen, A.; Jansen, G.; Hesselmann, A.; Schütz, M. Stacking energies for average B-DNA structures from the combined density functional theory and symmetry-adapted perturbation theory approach J. Am. Chem. Soc. 2008, 130, 1802 - 1803
133. DiLabio, G. A.; Johnson, E. R. Application of 25 density functionals to dispersion-bound homomolecular dimers Phys. Chem. Chem. Phys. 2013, 15, 12821 - 12828
134. Goldey, M.; Dutoi, A.; Head-Gordon, M. Attenuated second-order Møller-Plesset perturbation theory: performance within the aug-cc-pVTZ basis Phys. Chem. Chem. Phys. 2013, 15, 15869 - 15875
135. Goldey, M.; Head-Gordon, M. Attenuating away the errors in inter- and intramolecular interactions from second-order Møller-Plesset calculations in the small aug-cc-pVDZ basis set J. Phys. Chem. Lett. 2012, 3, 3592 - 3598
136. Huang, Y.; Goldey, M.; Head-Gordon, M.; Beran, G. J. O. Achieving high-accuracy intermolecular interactions by combining Coulomb-attenuated second-order Møller-Plesset perturbation theory with coupled Kohn-Sham dispersion J. Phys. Chem. A 2014, 10, 2054 - 2063
137. Sherrill, C. D.; Takatani, T.; Hohenstein, E. G. An assessment of theoretical methods for nonbonded interactions: Comparison to complete basis set limit coupled-cluster potential energy curves for benzene dimer, the methane dimer, benzene-methane, and benzene-H2S J. Phys. Chem. A 2009, 113, 10146 - 10159
138. Helgaker, T.; Jorgensen, P.; Olsen, J. Molecular Electronic-Structure Theory; Wiley: New York, 2000.
139. Gordon, M. S.; Smith, Q. A.; Xu, P.; Slipchenko, L. V. Accurate first principles model potentials for intermolecular interactions Annu. Rev. Phys. Chem. 2013, 64, 553 - 578
140. Valeev, E. Improving on the resolution of the identity in linear R12 ab initio theories Chem. Phys. Lett. 2004, 395, 190 - 195
141. Bischoff, F. A.; Wolfsegger, S.; Tew, D. P.; Klopper, W. Assessment of basis sets for F12 explicitly-correlated molecular electronic-structure methods Mol. Phys. 2009, 107, 963 - 975
142. Hartke, B. Size-dependent transition from all-surface to interior-molecule structures in pure neutral water clusters Phys. Chem. Chem. Phys. 2003, 5, 275 - 284
143. Lagutschenkov, A.; Fanourgakis, G. S.; Niedner-Schatteburg, G.; Xantheas, S. S. The spectroscopic signature of the "all-surface" to "internally-solvated" structural transition in water clusters in the n = 17-21 size regime J. Chem. Phys. 2005, 122, 194310:1 - 9
144. Yoo, S.; Xantheas, S. S. Structures, energetics, and spectroscopic fingerprints of water clusters n = 2-24. In Handbook of Computational Chemistry; Leszczynski, J., Ed.; Springer Science + Business Media: Berlin, 2012; Chapter 21, pp 761 - 792.
145. Kazimirski, J. K.; Buch, V. Search for low energy structures of water clusters (H2O)n, n = 20-22, 48, 123, and 293 J. Phys. Chem. A 2003, 107, 9762 - 9775
146. Wang, K.; Li, W.; Li, S. Generalized energy-based fragmentation CCSD(T)-F12a method and application to the relative energies of water clusters (H2O)20 J. Chem. Theory Comput. 2014, 10, 1546 - 1553
147. Das, D.; Eurenius, K. P.; Billings, E. M.; Sherwood, P.; Chatfield, D. C.; Hodošček, M.; Brooks, B. R. Optimization of quantum mechanical molecular mechanical partitioning schemes: Gaussian delocalization of molecular mechanical charges and the double link atom method J. Chem. Phys. 2002, 117, 10534 - 10547
148. Parker, T. M.; Burns, L. A.; Parrish, R. M.; Ryno, A. G.; Sherrill, C. D. Levels of symmetry adapted perturbation theory (SAPT). I. Efficiency and performance for interaction energies J. Chem. Phys. 2014, 140, 094106:1 - 16
149. Deible, M. J.; Tuguldur, O.; Jordan, K. D. Theoretical study of the binding energy of a methane molecule in a (H2O)20 dodecahedral cage J. Phys. Chem. B 2014, 118, 8257 - 8263
150. Kumar, P.; Sathyamurthy, M. Theoretical studies of host-guest interaction in gas hydrates J. Phys. Chem. A 2011, 115, 14276 - 14281
151. Ramya, K. R.; Venkatnathan, A. Stability and reactivity of methane clathrate hydrates: Insights from density functional theory J. Phys. Chem. A 2012, 116, 7742 - 7745
152. Liu, Y.; Zhao, J.; Li, F.; Chen, Z. Appropriate description of intermolecular interactions in the methane hydrates: An assessment of DFT methods J. Comput. Chem. 2013, 34, 121 - 131
153. Weill, N.; Therrien, E.; Campagna-Slater, V.; Moitessier, N. Methods for docking small molecules to macromolecules: A user's perspective. 1. The theory Curr. Pharm. Design 2014, 20, 3338 - 3359
154. Campagna-Slater, V.; Therrien, E.; Weill, N.; Moitessier, N. Methods for docking small molecules to macromolecules: A user's perspective. 2. Applications Curr. Pharm. Design 2014, 20, 3360 - 3372
155. von Lilienfeld, O. A.; Tuckerman, M. E. Alchemical variations of intermolecular energies according to molecular grand-canonical ensemble density functional theory J. Chem. Theory Comput. 2007, 3, 1083 - 1090
156. Bryce, R. A.; Hillier, I. H. Quantum chemical approaches: Semiempirical molecular orbital and hybrid quantum mechanical/molecular mechanical techniques Curr. Pharm. Design 2014, 20, 3293 - 3302
157. Stiborova, M.; Sejbal, J.; Borek-Dohalska, L.; Aimova, D.; Poljakova, J.; Forsterova, K.; Rupertova, M.; Wiesner, J.; Hudecek, J.; Wiessler, M.; Frei, E. The anticancer drug ellipticine forms covalent DNA adducts, mediated by human cytochromes P450, through metabolism to 13-hydroxyellipticine and ellipticine N2-oxide Cancer Res. 2004, 64, 8374 - 8380
158. Benali, A.; Shulenburger, L.; Romero, N. A.; Kim, J.; von Lilienfeld, O. A. Application of diffusion Monte Carlo to materials dominated by van der Waals interactions J. Chem. Theory Comput. 2014, 10, 3417 - 3422
159. von Lilienfeld, O. A.; Tkatchenko, A. Two- and three-body interatomic dispersion energy contributions to binding in molecules and solids J. Chem. Phys. 2010, 132, 234109:1 - 11
160. Sedlak, R.; Janowski, T.; Pitonňák, M.; Řezác, J.; Pulay, P.; Hobza, P. Accuracy of quantum chemical methods for large noncovalent complexes J. Chem. Theory Comput. 2013, 9, 3364 - 3374