Benchmark Calculations of Interaction Energies in Noncovalent Complexes and Their Applications

Chemical Reviews

Volumn 116, Issue 9, 2016, Pages 5038-5071

  Řezáč, Jan ^a   Hobza, Pavel ^a,b  

^a INSTITUTE OF ORGANIC CHEMISTRY AND BIOCHEMISTRY   (Czech Republic)

^b PALACKÝ UNIVERSITY   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEXATION; COMPUTATIONAL METHODS; QUANTUM THEORY;

APPROXIMATE METHODS; BENCHMARK CALCULATIONS; COMPUTATIONAL APPROACH; CORRELATED METHODS; INTERACTION ENERGIES; NON-COVALENT COMPLEXES; PARAMETRIZATIONS; QUANTUM MECHANICAL;

BENCHMARKING;

EID: 84962478542     PISSN: 00092665     EISSN: 15206890     Source Type: Journal    
DOI: 10.1021/acs.chemrev.5b00526     Document Type: Review

References (240)

1. Hobza, P.; Zahradník, R. Intermolecular interactions between medium-sized systems. Nonempirical and empirical calculations of interaction energies. Successes and failures Chem. Rev. 1988, 88, 871-897 10.1021/cr00088a004
2. Hobza, P.; Šponer, J. Structure, Energetics, and Dynamics of the Nucleic Acid Base Pairs: Nonempirical Ab Initio Calculations Chem. Rev. 1999, 99, 3247-3276 10.1021/cr9800255
3. Müller-Dethlefs, K.; Hobza, P. Noncovalent Interactions: A Challenge for Experiment and Theory Chem. Rev. 2000, 100, 143-168 10.1021/cr9900331
4. Hobza, P.; Zahradník, R.; Müller-Dethlefs, K. The world of non-covalent interactions: 2006 Collect. Czech. Chem. Commun. 2006, 71, 443-531 10.1135/cccc20060443
5. Černý, J.; Hobza, P. Non-covalent interactions in biomacromolecules Phys. Chem. Chem. Phys. 2007, 9, 5291-5303 10.1039/b704781a
6. Riley, K. E.; Pitoňák, M.; Jurečka, P.; Hobza, P. Stabilization and Structure Calculations for Noncovalent Interactions in Extended Molecular Systems Based on Wave Function and Density Functional Theories Chem. Rev. 2010, 110, 5023-5063 10.1021/cr1000173
7. Sherrill, C. D. In Reviews in Computational Chemistry; Lipkowitz, K. B.; Cundari, T. R., Eds.; John Wiley & Sons, Inc., 2008; pp 1-38.
8. Hohenstein, E. G.; Sherrill, C. D. Wavefunction methods for noncovalent interactions WIREs Comput. Mol. Sci. 2012, 2, 304-326 10.1002/wcms.84
9. Čížek, J. On the Correlation Problem in Atomic and Molecular Systems. Calculation of Wavefunction Components in Ursell-Type Expansion Using Quantum-Field Theoretical Methods J. Chem. Phys. 1966, 45, 4256-4266 10.1063/1.1727484
10. Bartlett, R. J.; Musiał, M. Coupled-cluster theory in quantum chemistry Rev. Mod. Phys. 2007, 79, 291-352 10.1103/RevModPhys.79.291
11. Noga, J.; Bartlett, R. J. The full CCSDT model for molecular electronic structure J. Chem. Phys. 1987, 86, 7041-7050 10.1063/1.452353
12. Raghavachari, K.; Trucks, G. W.; Pople, J. A.; Head-Gordon, M. A. A fifth-order perturbation comparison of electron correlation theories Chem. Phys. Lett. 1989, 157, 479-483 10.1016/S0009-2614(89)87395-6
13. Urban, M.; Noga, J.; Cole, S. J.; Bartlett, R. J. Towards a full CCSDT model for electron correlation J. Chem. Phys. 1985, 83, 4041-4046 10.1063/1.449067
14. Lee, Y. S.; Kucharski, S. A.; Bartlett, R. J. A coupled cluster approach with triple excitations J. Chem. Phys. 1984, 81, 5906-5912 10.1063/1.447591
15. Noga, J.; Bartlett, R. J.; Urban, M. Towards a full CCSDT model for electron correlation. CCSDT-n models Chem. Phys. Lett. 1987, 134, 126-132 10.1016/0009-2614(87)87107-5
16. 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 10.1021/ct4002762
17. Řezáč, J.; Šimová, L.; Hobza, P. CCSD[T] Describes Noncovalent Interactions Better than the CCSD(T), CCSD(TQ), and CCSDT Methods J. Chem. Theory Comput. 2013, 9, 364-369 10.1021/ct3008777
18. Bomble, Y. J.; Stanton, J. F.; Kállay, M.; Gauss, J. Coupled-cluster methods including noniterative corrections for quadruple excitations J. Chem. Phys. 2005, 123, 054101 10.1063/1.1950567
19. London, F. Some characteristics and uses of molecular force Z. Phys. Chem. B-Chem. Elem. Aufbau. Mater. 1930, 11, 222-251
20. Bloom, J. W. G.; Wheeler, S. E. Taking the Aromaticity out of Aromatic Interactions Angew. Chem. 2011, 123, 7993-7995 10.1002/ange.201102982
21. Pimentel, G.; McClellan, A. The Hydrogen Bond; W. H. Freeman & Co., 1960.
22. Arunan, E.; Desiraju, G. R.; Klein, R. A.; Sadlej, J.; Scheiner, S.; Alkorta, I.; Clary, D. C.; Crabtree, R. H.; Dannenberg, J. J.; Hobza, P. et al. Definition of the hydrogen bond (IUPAC Recommendations 2011) Pure Appl. Chem. 2011, 83, 1637-1641 10.1351/PAC-REC-10-01-02
23. Isaacs, E. D.; Shukla, A.; Platzman, P. M.; Hamann, D. R.; Barbiellini, B.; Tulk, C. A. Covalency of the Hydrogen Bond in Ice: A Direct X-Ray Measurement Phys. Rev. Lett. 1999, 82, 600-603 10.1103/PhysRevLett.82.600
24. Liu, Q.; Hoffmann, R. Theoretical Aspects of a Novel Mode of Hydrogen-Hydrogen Bonding J. Am. Chem. Soc. 1995, 117, 10108-10112 10.1021/ja00145a024
25. Klooster, W. T.; Koetzle, T. F.; Siegbahn, P. E. M.; Richardson, T. B.; Crabtree, R. H. Study of the N-H ··· H-B dihydrogen bond including the crystal structure of BH3NH3 by neutron diffraction J. Am. Chem. Soc. 1999, 121, 6337-6343 10.1021/ja9825332
26. Politzer, P.; Murray, J. S.; Clark, T. Halogen bonding and other σ-hole interactions: a perspective Phys. Chem. Chem. Phys. 2013, 15, 11178-11189 10.1039/c3cp00054k
27. Brinck, T.; Murray, J.; Politzer, P. Surface Electrostatic Potentials of Halogenated Methanes as Indicators Int. J. Quantum Chem. 1992, 44, 57-64 10.1002/qua.560440709
28. Clark, T.; Hennemann, M.; Murray, J. S.; Politzer, P. Halogen bonding: the σ-hole J. Mol. Model. 2007, 13, 291-296 10.1007/s00894-006-0130-2
29. Metrangolo, P.; Resnati, G. Halogen Bonding: A Paradigm in Supramolecular Chemistry Chem.-Eur. J. 2001, 7, 2511-2519 10.1002/1521-3765(20010618)7:12<2511::AID-CHEM25110>3.0.CO;2-T
30. Auffinger, P.; Hays, F. A.; Westhof, E.; Ho, P. S. Halogen bonds in biological molecules Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 16789-16794 10.1073/pnas.0407607101
31. Politzer, P.; Lane, P.; Concha, M. C.; Ma, Y.; Murray, J. S. An overview of halogen bonding J. Mol. Model. 2007, 13, 305-311 10.1007/s00894-006-0154-7
32. Hobza, P.; Riley, K. The Relative Roles of Electrostatics and Dispersion in the Stabilization of Halogen Bonds Phys. Chem. Chem. Phys. 2013, 15, 17742 10.1039/c3cp52768a
33. El Kerdawy, A.; Murray, J. S.; Politzer, P.; Bleiziffer, P.; Heßelmann, A.; Görling, A.; Clark, T. Directional Noncovalent Interactions: Repulsion and Dispersion J. Chem. Theory Comput. 2013, 9, 2264 10.1021/ct400185f
34. Sedlák, R.; Kolář, M. H.; Hobza, P. Polar Flattening and the Strength of Halogen Bonding J. Chem. Theory Comput. 2015, 11, 4727-4732 10.1021/acs.jctc.5b00687
35. Scheiner, S. The Pnicogen Bond: Its Relation to Hydrogen, Halogen, and Other Noncovalent Bonds Acc. Chem. Res. 2013, 46, 280-288 10.1021/ar3001316
36. Wang, W.; Ji, B.; Zhang, Y. Chalcogen Bond: A Sister Noncovalent Bond to Halogen Bond J. Phys. Chem. A 2009, 113, 8132-8135 10.1021/jp904128b
37. Bauzá, A.; Frontera, A. Aerogen Bonding Interaction: A New Supramolecular Force? Angew. Chem., Int. Ed. 2015, 54, 7340-7343 10.1002/anie.201502571
38. Kolář, M. H.; Hobza, P. Computer Modeling of Halogen Bonds and Other σ-Hole Interactions Chem. Rev. 2016, 10.1021/acs.chemrev.5b00560
39. Boys, S.; Bernardi, F. Calculation of Small Molecular Interactions by Differences of Separate Total Energies-Some Procedures with Reduced Errors Mol. Phys. 1970, 19, 553-566 10.1080/00268977000101561
40. Alvarez-Idaboy, J. R.; Galano, A. Counterpoise corrected interaction energies are not systematically better than uncorrected ones: comparison with CCSD(T) CBS extrapolated values Theor. Chem. Acc. 2010, 126, 75-85 10.1007/s00214-009-0676-z
41. Gutowski, M.; Van Duijneveldt, F. B.; Chałasiński, G.; Piela, L. Proper correction for the basis set superposition error in SCF calculations of intermolecular interactions Mol. Phys. 1987, 61, 233-247 10.1080/00268978700101101
42. Burns, L. A.; Marshall, M. S.; Sherrill, C. D. Comparing Counterpoise-Corrected, Uncorrected, and Averaged Binding Energies for Benchmarking Noncovalent Interactions J. Chem. Theory Comput. 2014, 10, 49-57 10.1021/ct400149j
43. 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 10.1021/cr00031a007
44. Mentel, L. M.; Baerends, E. J. Can the Counterpoise Correction for Basis Set Superposition Effect Be Justified? J. Chem. Theory Comput. 2014, 10, 252-267 10.1021/ct400990u
45. Halkier, A.; Klopper, W.; Helgaker, T.; Jørgensen, P.; Taylor, P. R. Basis set convergence of the interaction energy of hydrogen-bonded complexes J. Chem. Phys. 1999, 111, 9157-9167 10.1063/1.479830
46. Simon, S.; Duran, M.; Dannenberg, J. J. How does basis set superposition error change the potential surfaces for hydrogen-bonded dimers? J. Chem. Phys. 1996, 105, 11024-11031 10.1063/1.472902
47. Hobza, P.; Havlas, Z. Counterpoise-corrected potential energy surfaces of simple H-bonded systems Theor. Chem. Acc. 1998, 99, 372-377 10.1007/s002140050034
48. Dunning, T. H. Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen J. Chem. Phys. 1989, 90, 1007 10.1063/1.456153
49. Woon, D. E.; Dunning, T. H. Gaussian basis sets for use in correlated molecular calculations. IV. Calculation of static electrical response properties J. Chem. Phys. 1994, 100, 2975 10.1063/1.466439
50. Papajak, E.; Zheng, J.; Xu, X.; Leverentz, H. R.; Truhlar, D. G. Perspectives on Basis Sets Beautiful: Seasonal Plantings of Diffuse Basis Functions J. Chem. Theory Comput. 2011, 7, 3027-3034 10.1021/ct200106a
51. Woon, D. E.; Dunning, T. H., Jr. Gaussian basis sets for use in correlated molecular calculations. V. Core-valence basis sets for boron through neon J. Chem. Phys. 1995, 103, 4572-4585 10.1063/1.470645
52. Peterson, K. A.; Dunning, T. H. Accurate correlation consistent basis sets for molecular core-valence correlation effects: The second row atoms Al-Ar, and the first row atoms B-Ne revisited J. Chem. Phys. 2002, 117, 10548-10560 10.1063/1.1520138
53. Peterson, K. A.; Figgen, D.; Goll, E.; Stoll, H.; Dolg, M. Systematically convergent basis sets with relativistic pseudopotentials. II. Small-core pseudopotentials and correlation consistent basis sets for the post-d group 16-18 elements J. Chem. Phys. 2003, 119, 11113-11123 10.1063/1.1622924
54. Weigend, F. A fully direct RI-HF algorithm: Implementation, optimised auxiliary basis sets, demonstration of accuracy and efficiency Phys. Chem. Chem. Phys. 2002, 4, 4285-4291 10.1039/b204199p
55. Weigend, F.; Häser, M.; Patzelt, H.; Ahlrichs, R. RI-MP2: optimized auxiliary basis sets and demonstration of efficiency Chem. Phys. Lett. 1998, 294, 143-152 10.1016/S0009-2614(98)00862-8
56. Weigend, F.; Köhn, A.; Hättig, C. Efficient use of the correlation consistent basis sets in resolution of the identity MP2 calculations J. Chem. Phys. 2002, 116, 3175-3183 10.1063/1.1445115
57. Patkowski, K. On the accuracy of explicitly correlated coupled-cluster interaction energies - have orbital results been beaten yet? J. Chem. Phys. 2012, 137, 034103 10.1063/1.4734597
58. Jurečka, P.; Nachtigall, P.; Hobza, P. RI-MP2 calculations with extended basis sets-a promising tool for study of H-bonded and stacked DNA base pairs Phys. Chem. Chem. Phys. 2001, 3, 4578-4582 10.1039/b105892b
59. 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 10.1021/ct400057w
60. Hariharan, P. C.; Pople, J. A. The influence of polarization functions on molecular orbital hydrogenation energies Theoret. Chim. Acta 1973, 28, 213-222 10.1007/BF00533485
61. Kroon-Batenburg, L.; van Duijneveldt, F. The use of a moment-optimized DZP basis set for describing the interaction in the water dimer J. Mol. Struct.: THEOCHEM 1985, 121, 185-199 10.1016/0166-1280(85)80058-0
62. Riley, K. E.; Hobza, P. Assessment of the MP2 Method, along with Several Basis Sets, for the Computation of Interaction Energies of Biologically Relevant Hydrogen Bonded and Dispersion Bound Complexes J. Phys. Chem. A 2007, 111, 8257-8263 10.1021/jp073358r
63. Riley, K. E.; Řezáč, J.; Hobza, P. MP2.X: a generalized MP2.5 method that produces improved binding energies with smaller basis sets Phys. Chem. Chem. Phys. 2011, 13, 21121-21125 10.1039/c1cp22525a
64. Řezáč, J.; Dubecký, M.; Jurečka, P.; Hobza, P. Extensions and applications of the A24 data set of accurate interaction energies Phys. Chem. Chem. Phys. 2015, 17, 19268-19277 10.1039/C5CP03151F
65. Helgaker, T.; Klopper, W.; Koch, H.; Noga, J. Basis-set convergence of correlated calculations on water J. Chem. Phys. 1997, 106, 9639-9646 10.1063/1.473863
66. Halkier, A.; Helgaker, T.; Jørgensen, P.; Klopper, W.; Koch, H.; Olsen, J.; Wilson, A. K. Basis-set convergence in correlated calculations on Ne, N2, and H2O Chem. Phys. Lett. 1998, 286, 243-252 10.1016/S0009-2614(98)00111-0
67. Truhlar, D. G. Basis-set extrapolation Chem. Phys. Lett. 1998, 294, 45-48 10.1016/S0009-2614(98)00866-5
68. Bakowies, D. Accurate extrapolation of electron correlation energies from small basis sets J. Chem. Phys. 2007, 127, 164109 10.1063/1.2768359
69. Okoshi, M.; Atsumi, T.; Nakai, H. Revisiting the extrapolation of correlation energies to complete basis set limit J. Comput. Chem. 2015, 36, 1075-1082 10.1002/jcc.23896
70. Min, S. K.; Lee, E. C.; Lee, H. M.; Kim, D. Y.; Kim, D.; Kim, K. S. Complete basis set limit of Ab initio binding energies and geometrical parameters for various typical types of complexes J. Comput. Chem. 2008, 29, 1208-1221 10.1002/jcc.20880
71. Hylleraas, E. A. Neue Berechnung der Energie des Heliums im Grundzustande, sowie des tiefsten Terms von Ortho-Helium Eur. Phys. J. A 1929, 54, 347-366 10.1007/BF01375457
72. Kutzelnigg, W.; Klopper, W. Wave functions with terms linear in the interelectronic coordinates to take care of the correlation cusp. I. General theory J. Chem. Phys. 1991, 94, 1985-2001 10.1063/1.459921
73. Ten-no, S. Initiation of explicitly correlated Slater-type geminal theory Chem. Phys. Lett. 2004, 398, 56-61 10.1016/j.cplett.2004.09.041
74. May, A. J.; Manby, F. R. An explicitly correlated second order Møller-Plesset theory using a frozen Gaussian geminal J. Chem. Phys. 2004, 121, 4479-4485 10.1063/1.1780891
75. Klopper, W.; Manby, F. R.; Ten-No, S.; Valeev, E. F. R12 methods in explicitly correlated molecular electronic structure theory Int. Rev. Phys. Chem. 2006, 25, 427-468 10.1080/01442350600799921
76. Ten-no, S.; Noga, J. Explicitly correlated electronic structure theory from R12/F12 ansätze WIREs Comput. Mol. Sci. 2012, 2, 114-125 10.1002/wcms.68
77. Köhn, A.; Richings, G. W.; Tew, D. P. Implementation of the full explicitly correlated coupled-cluster singles and doubles model CCSD-F12 with optimally reduced auxiliary basis dependence J. Chem. Phys. 2008, 129, 201103 10.1063/1.3028546
78. Shiozaki, T.; Kamiya, M.; Hirata, S.; Valeev, E. F. Explicitly correlated coupled-cluster singles and doubles method based on complete diagrammatic equations J. Chem. Phys. 2008, 129, 071101 10.1063/1.2967181
79. Knizia, G.; Adler, T. B.; Werner, H.-J. Simplified CCSD(T)-F12 methods: Theory and benchmarks J. Chem. Phys. 2009, 130, 054104 10.1063/1.3054300
80. Köhn, A. Explicitly correlated connected triple excitations in coupled-cluster theory J. Chem. Phys. 2009, 130, 131101 10.1063/1.3116792
81. Tew, D. P.; Klopper, W.; Neiss, C.; Hättig, C. Quintuple-χ quality coupled-cluster correlation energies with triple-χ basis sets Phys. Chem. Chem. Phys. 2007, 9, 1921-1930 10.1039/b617230j
82. Adler, T. B.; Knizia, G.; Werner, H.-J. A simple and efficient CCSD(T)-F12 approximation J. Chem. Phys. 2007, 127, 221106 10.1063/1.2817618
83. Hättig, C.; Tew, D. P.; Köhn, A. Communications: Accurate and efficient approximations to explicitly correlated coupled-cluster singles and doubles, CCSD-F12 J. Chem. Phys. 2010, 132, 231102 10.1063/1.3442368
84. Peterson, K. A.; Adler, T. B.; Werner, H.-J. Systematically convergent basis sets for explicitly correlated wavefunctions: The atoms H, He, B-Ne, and Al-Ar J. Chem. Phys. 2008, 128, 084102 10.1063/1.2831537
85. Yousaf, K. E.; Peterson, K. A. Optimized auxiliary basis sets for explicitly correlated methods J. Chem. Phys. 2008, 129, 184108 10.1063/1.3009271
86. Hill, J. G.; Peterson, K. A.; Knizia, G.; Werner, H.-J. Extrapolating MP2 and CCSD explicitly correlated correlation energies to the complete basis set limit with first and second row correlation consistent basis sets J. Chem. Phys. 2009, 131, 194105 10.1063/1.3265857
87. Koch, H.; Fernández, B.; Christiansen, O. The benzene-argon complex: A ground and excited state ab initio study J. Chem. Phys. 1998, 108, 2784 10.1063/1.475669
88. Sinnokrot, M. O.; Valeev, E. F.; Sherrill, C. D. Estimates of the Ab Initio Limit for π-π Interactions: The Benzene Dimer J. Am. Chem. Soc. 2002, 124, 10887-10893 10.1021/ja025896h
89. Tsuzuki, S.; Honda, K.; Uchimaru, T.; Mikami, M.; Tanabe, K. Origin of Attraction and Directionality of the π/π Interaction: Model Chemistry Calculations of Benzene Dimer Interaction J. Am. Chem. Soc. 2002, 124, 104-112 10.1021/ja0105212
90. Hobza, P.; Šponer, J. Toward True DNA Base-Stacking Energies: MP2, CCSD(T), and Complete Basis Set Calculations J. Am. Chem. Soc. 2002, 124, 11802-11808 10.1021/ja026759n
91. Cybulski, S. M.; Lytle, M. L. The origin of deficiency of the supermolecule second-order Møller-Plesset approach for evaluating interaction energies J. Chem. Phys. 2007, 127, 141102 10.1063/1.2795693
92. Jurečka, P.; Hobza, P. On the convergence of the (ΔECCSD(T)-ΔEMP2) term for complexes with multiple H-bonds Chem. Phys. Lett. 2002, 365, 89-94 10.1016/S0009-2614(02)01423-9
93. 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, HBC6, and HSG databases J. Chem. Phys. 2011, 135, 194102 10.1063/1.3659142
94. Řezáč, 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 10.1021/ct2002946
95. Werner, H.-J.; Knowles, P. J.; Manby, F. R.; Schütz, M.; et al., MOLPRO, a package of ab initio programs, version 2010.1; 2010; http://www.molpro.net (accessed Feb 10, 2016).
96. Řezáč, J.; Hobza, P. Ab Initio Quantum Mechanical Description of Noncovalent Interactions at Its Limits: Approaching the Experimental Dissociation Energy of the HF Dimer J. Chem. Theory Comput. 2014, 10, 3066-3073 10.1021/ct500047x
97. Kállay, M.; Surján, P. R. Computing coupled-cluster wave functions with arbitrary excitations J. Chem. Phys. 2000, 113, 1359-1365 10.1063/1.481925
98. Hirata, S.; Bartlett, R. J. High-order coupled-cluster calculations through connected octuple excitations Chem. Phys. Lett. 2000, 321, 216-224 10.1016/S0009-2614(00)00387-0
99. Olsen, J. The initial implementation and applications of a general active space coupled cluster method J. Chem. Phys. 2000, 113, 7140-7148 10.1063/1.1290005
100. Kállay, M.; Surján, P. R. Higher excitations in coupled-cluster theory J. Chem. Phys. 2001, 115, 2945-2954 10.1063/1.1383290
101. Jäger, B.; Hellmann, R.; Bich, E.; Vogel, E. Ab initio pair potential energy curve for the argon atom pair and thermophysical properties of the dilute argon gas. I. Argon-argon interatomic potential and rovibrational spectra Mol. Phys. 2009, 107, 2181-2188 10.1080/00268970903213305
102. Hellmann, R.; Bich, E.; Vogel, E. Ab initio potential energy curve for the neon atom pair and thermophysical properties of the dilute neon gas. I. Neon-neon interatomic potential and rovibrational spectra Mol. Phys. 2008, 106, 133-140 10.1080/00268970701843147
103. Patkowski, K.; Szalewicz, K. Argon pair potential at basis set and excitation limits J. Chem. Phys. 2010, 133, 094304 10.1063/1.3478513
104. Raghavachari, K.; Pople, J. A.; Replogle, E. S.; Head-Gordon, M. Fifth order Moeller-Plesset perturbation theory: comparison of existing correlation methods and implementation of new methods correct to fifth order J. Phys. Chem. 1990, 94, 5579-5586 10.1021/j100377a033
105. Demovičová, L.; Hobza, P.; Řezáč, J. Evaluation of composite schemes for CCSDT(Q) calculations of interaction energies of noncovalent complexes Phys. Chem. Chem. Phys. 2014, 16, 19115-19121 10.1039/C4CP02617A
106. 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 10.1021/ct500347q
107. Douglas, M.; Kroll, N. M. Quantum electrodynamical corrections to the fine structure of helium Ann. Phys. 1974, 82, 89-155 10.1016/0003-4916(74)90333-9
108. Hess, B. A. Relativistic electronic-structure calculations employing a two-component no-pair formalism with external-field projection operators Phys. Rev. A: At., Mol., Opt. Phys. 1986, 33, 3742-3748 10.1103/PhysRevA.33.3742
109. Reiher, M. Relativistic Douglas-Kroll-Hess theory WIREs Comput. Mol. Sci. 2012, 2, 139-149 10.1002/wcms.67
110. de Jong, W. A.; Harrison, R. J.; Dixon, D. A. Parallel Douglas-Kroll energy and gradients in NWChem: Estimating scalar relativistic effects using Douglas-Kroll contracted basis sets J. Chem. Phys. 2001, 114, 48-53 10.1063/1.1329891
111. Kutzelnigg, W. The adiabatic approximation I. The physical background of the Born-Handy ansatz Mol. Phys. 1997, 90, 909-916 10.1080/00268979709482675
112. Gauss, J.; Tajti, A.; Kállay, M.; Stanton, J. F.; Szalay, P. G. Analytic calculation of the diagonal Born-Oppenheimer correction within configuration-interaction and coupled-cluster theory J. Chem. Phys. 2006, 125, 144111 10.1063/1.2356465
113. Feller, D.; Peterson, K. A.; Dixon, D. A. A survey of factors contributing to accurate theoretical predictions of atomization energies and molecular structures J. Chem. Phys. 2008, 129, 204105 10.1063/1.3008061
114. Császár, A. G.; Allen, W. D.; Schaefer, H. F. In pursuit of the ab initio limit for conformational energy prototypes J. Chem. Phys. 1998, 108, 9751-9764 10.1063/1.476449
115. Tajti, A.; Szalay, P. G.; Császár, A. G.; Kállay, M.; Gauss, J.; Valeev, E. F.; Flowers, B. A.; Vázquez, J.; Stanton, J. F. HEAT: High accuracy extrapolated ab initio thermochemistry J. Chem. Phys. 2004, 121, 11599-11613 10.1063/1.1811608
116. Bomble, Y. J.; Vázquez, J.; Kállay, M.; Michauk, C.; Szalay, P. G.; Császár, A. G.; Gauss, J.; Stanton, J. F. High-accuracy extrapolated ab initio thermochemistry. II. Minor improvements to the protocol and a vital simplification J. Chem. Phys. 2006, 125, 064108 10.1063/1.2206789
117. Harding, M. E.; Vázquez, J.; Ruscic, B.; Wilson, A. K.; Gauss, J.; Stanton, J. F. High-accuracy extrapolated ab initio thermochemistry. III. Additional improvements and overview J. Chem. Phys. 2008, 128, 114111 10.1063/1.2835612
118. Boese, A. D.; Oren, M.; Atasoylu, O.; Martin, J. M. L.; Kállay, M.; Gauss, J. W3 theory: Robust computational thermochemistry in the kJ/mol accuracy range J. Chem. Phys. 2004, 120, 4129-4141 10.1063/1.1638736
119. Karton, A.; Rabinovich, E.; Martin, J. M. L.; Ruscic, B. W4 theory for computational thermochemistry: In pursuit of confident sub-kJ/mol predictions J. Chem. Phys. 2006, 125, 144108 10.1063/1.2348881
120. Boese, A. D. Assessment of Coupled Cluster Theory and more Approximate Methods for Hydrogen Bonded Systems J. Chem. Theory Comput. 2013, 9, 4403-4413 10.1021/ct400558w
121. Harding, M. E.; Klopper, W. Benchmarking the Lithium-Thiophene Complex ChemPhysChem 2013, 14, 708-715 10.1002/cphc.201200834
122. Jankowski, P.; McKellar, A. R. W.; Szalewicz, K. Theory Untangles the High-Resolution Infrared Spectrum of the ortho-H2-CO van der Waals Complex Science 2012, 336, 1147-1150 10.1126/science.1221000
123. Taube, A. G.; Bartlett, R. J. Frozen natural orbitals: Systematic basis set truncation for coupled-cluster theory Collect. Czech. Chem. Commun. 2005, 70, 837-850 10.1135/cccc20050837
124. DePrince, A. E.; Sherrill, C. D. Accurate Noncovalent Interaction Energies Using Truncated Basis Sets Based on Frozen Natural Orbitals J. Chem. Theory Comput. 2013, 9, 293-299 10.1021/ct300780u
125. Adamowicz, L.; Bartlett, R. J. Optimized virtual orbital space for high-level correlated calculations J. Chem. Phys. 1987, 86, 6314-6324 10.1063/1.452468
126. Pitoňák, M.; Neogrády, P.; Kellö, V.; Urban, M. Optimized virtual orbitals for relativistic calculations: an alternative approach to the basis set construction for correlation calculations Mol. Phys. 2006, 104, 2277-2292 10.1080/00268970600662390
127. Kraus, M.; Pitoňák, M.; Hobza, P.; Urban, M.; Neogrády, P. Highly correlated calculations using optimized virtual orbital space with controlled accuracy. Application to counterpoise corrected interaction energy calculations Int. J. Quantum Chem. 2012, 112, 948-959 10.1002/qua.23014
128. Sæbø, S.; Pulay, P. Local configuration interaction: An efficient approach for larger molecules Chem. Phys. Lett. 1985, 113, 13-18 10.1016/0009-2614(85)85003-X
129. Sæbø, S.; Pulay, P. Local Treatment of Electron Correlation Annu. Rev. Phys. Chem. 1993, 44, 213-236 10.1146/annurev.pc.44.100193.001241
130. Hampel, C.; Werner, H.-J. Local treatment of electron correlation in coupled cluster theory J. Chem. Phys. 1996, 104, 6286-6297 10.1063/1.471289
131. Scuseria, G. E.; Ayala, P. Y. Linear scaling coupled cluster and perturbation theories in the atomic orbital basis J. Chem. Phys. 1999, 111, 8330-8343 10.1063/1.480174
132. Schütz, M.; Werner, H.-J. Local perturbative triples correction (T) with linear cost scaling Chem. Phys. Lett. 2000, 318, 370-378 10.1016/S0009-2614(00)00066-X
133. Rolik, Z.; Kállay, M. A general-order local coupled-cluster method based on the cluster-in-molecule approach J. Chem. Phys. 2011, 135, 104111 10.1063/1.3632085
134. Rolik, Z.; Szegedy, L.; Ladjánszki, I.; Ladóczki, B.; Kállay, M. An efficient linear-scaling CCSD(T) method based on local natural orbitals J. Chem. Phys. 2013, 139, 094105 10.1063/1.4819401
135. Sparta, M.; Neese, F. Chemical applications carried out by local pair natural orbital based coupled-cluster methods Chem. Soc. Rev. 2014, 43, 5032 10.1039/c4cs00050a
136. Liakos, D. G.; Sparta, M.; Kesharwani, M. K.; Martin, J. M. L.; Neese, F. Exploring the Accuracy Limits of Local Pair Natural Orbital Coupled-Cluster Theory J. Chem. Theory Comput. 2015, 11, 1525-1539 10.1021/ct501129s
137. Dubecký, S.; Mitas, L.; Jurecka, P. Noncovalent Interactions by Quantum Monte Carlo. Chem. Rev. 2016, in this issue
138. 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 10.1021/ct4006739
139. Ambrosetti, A.; Alfè, D.; DiStasio, R. A.; Tkatchenko, A. Hard Numbers for Large Molecules: Toward Exact Energetics for Supramolecular Systems J. Phys. Chem. Lett. 2014, 5, 849-855 10.1021/jz402663k
140. Grimme, S. Improved second-order Møller-Plesset perturbation theory by separate scaling of parallel- and antiparallel-spin pair correlation energies J. Chem. Phys. 2003, 118, 9095 10.1063/1.1569242
141. DiStasio, R. A., Jr.; Head-Gordon, M. Optimized spin-component scaled second-order M?ller-Plesset perturbation theory for intermolecular interaction energies Mol. Phys. 2007, 105, 1073-1083 10.1080/00268970701283781
142. Jung, Y.; Lochan, R. C.; Dutoi, A. D.; Head-Gordon, M. Scaled opposite-spin second order Møller-Plesset correlation energy: An economical electronic structure method J. Chem. Phys. 2004, 121, 9793-9802 10.1063/1.1809602
143. Grimme, S.; Goerigk, L.; Fink, R. F. Spin-component-scaled electron correlation methods WIREs Comput. Mol. Sci. 2012, 2, 886-906 10.1002/wcms.1110
144. Marchetti, O.; Werner, H.-J. Accurate Calculations of Intermolecular Interaction Energies Using Explicitly Correlated Coupled Cluster Wave Functions and a Dispersion-Weighted MP2 Method† J. Phys. Chem. A 2009, 113, 11580-11585 10.1021/jp9059467
145. 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 10.1021/jz301694b
146. 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 10.1039/c3cp51826d
147. Heßelmann, A. Improved supermolecular second order Møller-Plesset intermolecular interaction energies using time-dependent density functional response theory J. Chem. Phys. 2008, 128, 144112 10.1063/1.2905808
148. Pitoňák, M.; Heßelmann, A. Accurate Intermolecular Interaction Energies from a Combination of MP2 and TDDFT Response Theory J. Chem. Theory Comput. 2010, 6, 168-178 10.1021/ct9005882
149. Ohnishi, Y.-y.; Ishimura, K.; Ten-no, S. Interaction Energy of Large Molecules from Restrained Denominator MP2-F12 J. Chem. Theory Comput. 2014, 10, 4857-4861 10.1021/ct500738g
150. Pitoňák, M.; Neogrády, P.; Černý, J.; Grimme, S.; Hobza, P. Scaled MP3 Non-Covalent Interaction Energies Agree Closely with Accurate CCSD(T) Benchmark Data ChemPhysChem 2009, 10, 282-289 10.1002/cphc.200800718
151. Sedlák, R.; Riley, K. E.; Řezáč, J.; Pitoňák, M.; Hobza, P. MP2.5 and MP2.X: Approaching CCSD(T) Quality Description of Noncovalent Interaction at the Cost of a Single CCSD Iteration ChemPhysChem 2013, 14, 698-707 10.1002/cphc.201200850
152. Řezáč, J.; Huang, Y.; Hobza, P.; Beran, G. J. O. Benchmark Calculations of Three-Body Intermolecular Interactions and the Performance of Low-Cost Electronic Structure Methods J. Chem. Theory Comput. 2015, 11, 3065-3079 10.1021/acs.jctc.5b00281
153. Takatani, T.; Hohenstein, E. G.; Sherrill, C. D. Improvement of the coupled-cluster singles and doubles method via scaling same- and opposite-spin components of the double excitation correlation energy J. Chem. Phys. 2008, 128, 124111 10.1063/1.2883974
154. Pitoňák, M.; Řezáč, J.; Hobza, P. Spin-component scaled coupled-clusters singles and doubles optimized towards calculation of noncovalent interactions Phys. Chem. Chem. Phys. 2010, 12, 9611 10.1039/c0cp00158a
155. Wu, Q.; Yang, W. Empirical correction to density functional theory for van der Waals interactions J. Chem. Phys. 2002, 116, 515-524 10.1063/1.1424928
156. Grimme, S. Accurate description of van der Waals complexes by density functional theory including empirical corrections J. Comput. Chem. 2004, 25, 1463-1473 10.1002/jcc.20078
157. Jurečka, P.; Černý, J.; Hobza, P.; Salahub, D. Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations J. Comput. Chem. 2007, 28, 555-569 10.1002/jcc.20570
158. Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu J. Chem. Phys. 2010, 132, 154104 10.1063/1.3382344
159. Grimme, S.; Ehrlich, S.; Goerigk, L. Effect of the damping function in dispersion corrected density functional theory J. Comput. Chem. 2011, 32, 1456-1465 10.1002/jcc.21759
160. Goerigk, L.; Kruse, H.; Grimme, S. Benchmarking Density Functional Methods against the S66 and S66x8 Datasets for Non-Covalent Interactions ChemPhysChem 2011, 12, 3421-3433 10.1002/cphc.201100826
161. Grimme, S.; Hansen, A.; Brandenburg, J.; Bannwarth, C. Dispersion-Corrected Mean-Field Electronic Structure Methods. Chem. Rev. 2016, in this issue
162. Eshuis, H.; Bates, J. E.; Furche, F. Electron correlation methods based on the random phase approximation Theor. Chem. Acc. 2012, 131, 1084 10.1007/s00214-011-1084-8
163. Christensen, A.; Kubar, T.; Cui, Q.; Elstner, M. Semi-Empirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications. Chem. Rev. 2016, in this issue
164. Elstner, M.; Hobza, P.; Frauenheim, T.; Suhai, S.; Kaxiras, E. Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory based treatment J. Chem. Phys. 2001, 114, 5149 10.1063/1.1329889
165. Martin, B.; Clark, T. Dispersion treatment for NDDO-based semiempirical MO techniques Int. J. Quantum Chem. 2006, 106, 1208-1216 10.1002/qua.20856
166. McNamara, J. P.; Hillier, I. H. Semi-empirical molecular orbital methods including dispersion corrections for the accurate prediction of the full range of intermolecular interactions in biomolecules Phys. Chem. Chem. Phys. 2007, 9, 2362 10.1039/b701890h
167. Morgado, C. A.; McNamara, J. P.; Hillier, I. H.; Burton, N. A.; Vincent, M. A. Density Functional and Semiempirical Molecular Orbital Methods Including Dispersion Corrections for the Accurate Description of Noncovalent Interactions Involving Sulfur-Containing Molecules J. Chem. Theory Comput. 2007, 3, 1656-1664 10.1021/ct700072a
168. Řezáč, J.; Fanfrlík, J.; Salahub, D.; Hobza, P. Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes J. Chem. Theory Comput. 2009, 5, 1749-1760 10.1021/ct9000922
169. Korth, M.; Pitoňák, M.; Řezáč, J.; Hobza, P. A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical Methods J. Chem. Theory Comput. 2010, 6, 344-352 10.1021/ct900541n
170. Řezáč, J.; Hobza, P. Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods J. Chem. Theory Comput. 2012, 8, 141-151 10.1021/ct200751e
171. Stewart, J. J. P. Application of the PM6 method to modeling proteins J. Mol. Model. 2009, 15, 765-805 10.1007/s00894-008-0420-y
172. 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 10.1021/cr00031a008
173. Stone, A. The Theory of Intermolecular Forces, 2 nd ed.; Oxford University Press: Oxford, 2013.
174. Monkhorst, H. J.; Jeziorski, B.; Harris, F. E. Recursive scheme for order-by-order many-body perturbation theory Phys. Rev. A: At., Mol., Opt. Phys. 1981, 23, 1639-1644 10.1103/PhysRevA.23.1639
175. 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 10.1021/jp003883p
176. Heßelmann, A.; Jansen, G. First-order intermolecular interaction energies from Kohn-Sham orbitals Chem. Phys. Lett. 2002, 357, 464-470 10.1016/S0009-2614(02)00538-9
177. Heßelmann, A.; Jansen, G. Intermolecular induction and exchange-induction energies from coupled-perturbed Kohn-Sham density functional theory Chem. Phys. Lett. 2002, 362, 319-325 10.1016/S0009-2614(02)01097-7
178. Heßelmann, A.; Jansen, G. Intermolecular dispersion energies from time-dependent density functional theory Chem. Phys. Lett. 2003, 367, 778-784 10.1016/S0009-2614(02)01796-7
179. Misquitta, A. J.; Szalewicz, K. Intermolecular forces from asymptotically corrected density functional description of monomers Chem. Phys. Lett. 2002, 357, 301-306 10.1016/S0009-2614(02)00533-X
180. 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 10.1063/1.1924593
181. Szalewicz, K. Symmetry-adapted perturbation theory of intermolecular forces WIREs Comput. Mol. Sci. 2012, 2, 254-272 10.1002/wcms.86
182. Podeszwa, R.; Bukowski, R.; Szalewicz, K. Potential Energy Surface for the Benzene Dimer and Perturbational Analysis of π-π Interactions J. Phys. Chem. A 2006, 110, 10345-10354 10.1021/jp064095o
183. Tekin, A.; Jansen, G. How accurate is the density functional theory combined with symmetry-adapted perturbation theory approach for CHπ and π-π interactions? A comparison to supermolecular calculations for the acetylene-benzene dimer Phys. Chem. Chem. Phys. 2007, 9, 1680-1687 10.1039/b618997k
184. Podeszwa, R. Interactions of graphene sheets deduced from properties of polycyclic aromatic hydrocarbons J. Chem. Phys. 2010, 132, 044704 10.1063/1.3300064
185. Witte, J.; Goldey, M.; Neaton, J. B.; Head-Gordon, M. Beyond Energies: Geometries of Nonbonded Molecular Complexes as Metrics for Assessing Electronic Structure Approaches J. Chem. Theory Comput. 2015, 11, 1481-1492 10.1021/ct501050s
186. Howard, J. C.; Tschumper, G. S. Benchmark Structures and Harmonic Vibrational Frequencies Near the CCSD(T) Complete Basis Set Limit for Small Water Clusters: (H2O)n = 2, 3, 4, 5, 6 J. Chem. Theory Comput. 2015, 11, 2126-2136 10.1021/acs.jctc.5b00225
187. Řezáč, J.; Riley, K. E.; Hobza, P. Benchmark calculations of noncovalent interactions of halogenated molecules J. Chem. Theory Comput. 2012, 8, 4285-4292 10.1021/ct300647k
188. Řezáč, J.; Riley, K. E.; Hobza, P. Evaluation of the performance of post-Hartree-Fock methods in terms of intermolecular distance in noncovalent complexes J. Comput. Chem. 2012, 33, 691-694 10.1002/jcc.22899
189. Řezáč, J.; Riley, K. E.; Hobza, P. Extensions of the S66 Data Set: More Accurate Interaction Energies and Angular-Displaced Nonequilibrium Geometries J. Chem. Theory Comput. 2011, 7, 3466-3470 10.1021/ct200523a
190. Turney, J. M.; Simmonett, A. C.; Parrish, R. M.; Hohenstein, E. G.; Evangelista, F. A.; Fermann, J. T.; Mintz, B. J.; Burns, L. A.; Wilke, J. J.; Abrams, M. L. et al. Psi4: an open-source ab initio electronic structure program WIREs Comput. Mol. Sci. 2012, 2, 556-565 10.1002/wcms.93
191. Řezáč, J. Cuby-Ruby Framework for Computational Chemistry, version 4; http://cuby4.molecular.cz/ (accessed Feb 10, 2016).
192. Řezáč, J. Cuby: An integrative framework for computational chemistry J. Comput. Chemm 2016, 10.1002/jcc.24312
193. Takatani, T.; Hohenstein, E. G.; Malagoli, M.; Marshall, M. S.; Sherrill, C. D. Basis set consistent revision of the S22 test set of noncovalent interaction energies J. Chem. Phys. 2010, 132, 144104 10.1063/1.3378024
194. Zhao, Y.; Truhlar, D. G. Design of Density Functionals That Are Broadly Accurate for Thermochemistry, Thermochemical Kinetics, and Nonbonded Interactions J. Phys. Chem. A 2005, 109, 5656-5667 10.1021/jp050536c
195. Zhao, Y.; Truhlar, D. G. Benchmark Databases for Nonbonded Interactions and Their Use To Test Density Functional Theory J. Chem. Theory Comput. 2005, 1, 415-432 10.1021/ct049851d
196. Martin, J. M. L.; de Oliveira, G. Towards standard methods for benchmark quality ab initio thermochemistry-W1 and W2 theory J. Chem. Phys. 1999, 111, 1843-1856 10.1063/1.479454
197. 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 10.1039/b600027d
198. Podeszwa, R.; Patkowski, K.; Szalewicz, K. Improved interaction energy benchmarks for dimers of biological relevance Phys. Chem. Chem. Phys. 2010, 12, 5974 10.1039/b926808a
199. Molnar, L. F.; He, X.; Wang, B.; Merz, K. M., Jr Further analysis and comparative study of intermolecular interactions using dimers from the S22 database J. Chem. Phys. 2009, 131, 065102 10.1063/1.3173809
200. Gráfová, L.; Pitoňák, M.; Řezáč, J.; Hobza, P. Comparative Study of Selected Wave Function and Density Functional Methods for Noncovalent Interaction Energy Calculations Using the Extended S22 Data Set J. Chem. Theory Comput. 2010, 6, 2365-2376 10.1021/ct1002253
201. Mintz, B. J.; Parks, J. M. Benchmark Interaction Energies for Biologically Relevant Noncovalent Complexes Containing Divalent Sulfur J. Phys. Chem. A 2012, 116, 1086-1092 10.1021/jp209536e
202. Řezáč, J.; Hobza, P. A halogen-bonding correction for the semiempirical PM6 method Chem. Phys. Lett. 2011, 506, 286-289 10.1016/j.cplett.2011.03.009
203. Brahmkshatriya, P. S.; Dobeš, P.; Fanfrlík, J.; Řezáč, J.; Paruch, K.; Bronowska, A.; Lepšík, M.; Hobza, P. Quantum Mechanical Scoring: Structural and Energetic Insights into Cyclin-Dependent Kinase 2 Inhibition by Pyrazolo [1,5-a]pyrimidines Curr. Comput.-Aided Drug Des. 2013, 9, 118-129 10.2174/1573409911309010011
204. Kubillus, M.; Kubař, T.; Gaus, M.; Řezáč, J.; Elstner, M. Parameterization of the DFTB3 Method for Br, Ca, Cl, F, I, K, and Na in Organic and Biological Systems J. Chem. Theory Comput. 2015, 11, 332-342 10.1021/ct5009137
205. 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 the Benzene Dimer, the Methane Dimer, Benzene-Methane, and Benzene-H2S† J. Phys. Chem. A 2009, 113, 10146-10159 10.1021/jp9034375
206. Granatier, J.; Pitoňák, M.; Hobza, P. Accuracy of Several Wave Function and Density Functional Theory Methods for Description of Noncovalent Interaction of Saturated and Unsaturated Hydrocarbon Dimers J. Chem. Theory Comput. 2012, 8, 2282-2292 10.1021/ct300215p
207. Thanthiriwatte, K. S.; Hohenstein, E. G.; Burns, L. A.; Sherrill, C. D. Assessment of the Performance of DFT and DFT-D Methods for Describing Distance Dependence of Hydrogen-Bonded Interactions J. Chem. Theory Comput. 2011, 7, 88-96 10.1021/ct100469b
208. Bauzá, A.; Alkorta, I.; Frontera, A.; Elguero, J. On the Reliability of Pure and Hybrid DFT Methods for the Evaluation of Halogen, Chalcogen, and Pnicogen Bonds Involving Anionic and Neutral Electron Donors J. Chem. Theory Comput. 2013, 9, 5201-5210 10.1021/ct400818v
209. Karthikeyan, S.; Sedlák, R.; Hobza, P. On the Nature of Stabilization in Weak, Medium, and Strong Charge-Transfer Complexes: CCSD(T)/CBS and SAPT Calculations J. Phys. Chem. A 2011, 115, 9422-9428 10.1021/jp1112476
210. Řezáč, J.; de la Lande, A. Robust, Basis-Set Independent Method for the Evaluation of Charge-Transfer Energy in Noncovalent Complexes J. Chem. Theory Comput. 2015, 11, 528-537 10.1021/ct501115m
211. Berka, K.; Laskowski, R.; Riley, K. E.; Hobza, P.; Vondrášek, J. Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures J. Chem. Theory Comput. 2009, 5, 982-992 10.1021/ct800508v
212. Hostaš, J.; Jakubec, D.; Laskowski, R. A.; Gnanasekaran, R.; Řezáč, J.; Vondrášek, J.; Hobza, P. Representative Amino Acid Side-Chain Interactions in Protein-DNA Complexes: A Comparison of Highly Accurate Correlated Ab Initio Quantum Mechanical Calculations and Efficient Approaches for Applications to Large Systems J. Chem. Theory Comput. 2015, 11, 4086 10.1021/acs.jctc.5b00398
213. Faver, J. C.; Benson, M. L.; He, X.; Roberts, B. P.; Wang, B.; Marshall, M. S.; Kennedy, M. R.; Sherrill, C. D.; Merz, K. M. Formal Estimation of Errors in Computed Absolute Interaction Energies of Protein-Ligand Complexes J. Chem. Theory Comput. 2011, 7, 790-797 10.1021/ct100563b
214. Bryantsev, V. S.; Diallo, M. S.; van Duin, A. C. T.; Goddard, W. A. Evaluation of B3LYP, X3LYP, and M06-Class Density Functionals for Predicting the Binding Energies of Neutral, Protonated, and Deprotonated Water Clusters J. Chem. Theory Comput. 2009, 5, 1016-1026 10.1021/ct800549f
215. Anacker, T.; Friedrich, J. New accurate benchmark energies for large water clusters: DFT is better than expected J. Comput. Chem. 2014, 35, 634-643 10.1002/jcc.23539
216. Temelso, B.; Renner, C. R.; Shields, G. C. Importance and Reliability of Small Basis Set CCSD(T) Corrections to MP2 Binding and Relative Energies of Water Clusters J. Chem. Theory Comput. 2015, 11, 1439-1448 10.1021/ct500944v
217. Sedlák, R.; Janowski, T.; Pitoňák, M.; Řezáč, J.; Pulay, P.; Hobza, P. Accuracy of Quantum Chemical Methods for Large Noncovalent Complexes J. Chem. Theory Comput. 2013, 9, 3364-3374 10.1021/ct400036b
218. Grimme, S. Supramolecular Binding Thermodynamics by Dispersion-Corrected Density Functional Theory Chem.-Eur. J. 2012, 18, 9955-9964 10.1002/chem.201200497
219. Risthaus, T.; Grimme, S. Benchmarking of London Dispersion-Accounting Density Functional Theory Methods on Very Large Molecular Complexes J. Chem. Theory Comput. 2013, 9, 1580-1591 10.1021/ct301081n
220. Sure, R.; Grimme, S. Comprehensive Benchmark of Association (Free) Energies of Realistic Host-Guest Complexes J. Chem. Theory Comput. 2015, 11, 3785-3801 10.1021/acs.jctc.5b00296
221. 2 J. Chem. Phys. 1991, 94, 442-447 10.1063/1.460359
222. Barone, V.; Biczysko, M.; Bloino, J.; Puzzarini, C. Characterization of the Elusive Conformers of Glycine from State-of-the-Art Structural, Thermodynamic, and Spectroscopic Computations: Theory Complements Experiment J. Chem. Theory Comput. 2013, 9, 1533-1547 10.1021/ct3010672
223. Barone, V.; Biczysko, M.; Bloino, J.; Puzzarini, C. Accurate structure, thermodynamic and spectroscopic parameters from CC and CC/DFT schemes: the challenge of the conformational equilibrium in glycine Phys. Chem. Chem. Phys. 2013, 15, 10094-10111 10.1039/c3cp50439e
224. Riffet, V.; Bouchoux, G. Gas-phase structures and thermochemistry of neutral histidine and its conjugated acid and base Phys. Chem. Chem. Phys. 2013, 15, 6097-6106 10.1039/c3cp00043e
225. Fogueri, U. R.; Kozuch, S.; Karton, A.; Martin, J. M. The Melatonin Conformer Space: Benchmark and Assessment of Wave Function and DFT Methods for a Paradigmatic Biological and Pharmacological Molecule J. Phys. Chem. A 2013, 117, 2269-2277 10.1021/jp312644t
226. Mládek, A.; Krepl, M.; Svozil, D.; Čech, P.; Otyepka, M.; Banáš, P.; Zgarbová, M.; Jurečka, P.; Šponer, J. Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar-phosphate backbone and their comparison with modern density functional theory Phys. Chem. Chem. Phys. 2013, 15, 7295-7310 10.1039/c3cp44383c
227. Valdes, H.; Pluháčková, K.; Pitonák, M.; Řezáč, J.; Hobza, P. Benchmark database on isolated small peptides containing an aromatic side chain: comparison between wave function and density functional theory methods and empirical force field Phys. Chem. Chem. Phys. 2008, 10, 2747-2757 10.1039/b719294k
228. BEGDB: Benchmark Energy and Geometry Database. http://www.begdb.com/ (accessed Nov 20, 2013).
229. Řezáč, J.; Jurečka, P.; Riley, K. E.; Černý, J.; Valdes, H.; Pluháčková, K.; Berka, K.; Řezáč, T.; Pitoňák, M.; Vondrášek, J. Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples Collect. Czech. Chem. Commun. 2008, 73, 1261-1270 www.begdb.com 10.1135/cccc20081261
230. Goerigk, L.; Grimme, S. A General Database for Main Group Thermochemistry, Kinetics, and Noncovalent Interactions-Assessment of Common and Reparameterized (meta-)GGA Density Functionals J. Chem. Theory Comput. 2010, 6, 107-126 10.1021/ct900489g
231. Goerigk, L.; Grimme, S. Efficient and Accurate Double-Hybrid-Meta-GGA Density Functionals-Evaluation with the Extended GMTKN30 Database for General Main Group Thermochemistry, Kinetics, and Noncovalent Interactions J. Chem. Theory Comput. 2011, 7, 291-309 10.1021/ct100466k
232. Grimme, S. GMTKN30 database. http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=GMTKN30&lang=english (accessed Feb 10, 2016).
233. Minnesota Databases 2.0. http://comp.chem.umn.edu/db/ (accessed Feb 10, 2016).
234. Liakos, D. G.; Izsák, R.; Valeev, E. F.; Neese, F. What is the most efficient way to reach the canonical MP2 basis set limit? Mol. Phys. 2013, 111, 2653-2662 10.1080/00268976.2013.824624
235. TURBOMOLE, v6.5.; 2011; http://www.turbomole.com (accessed Feb 10, 2016).
236. Neese, F. The ORCA program system WIREs Comput. Mol. Sci. 2012, 2, 73-78 10.1002/wcms.81
237. Kállay, M.; Rolik, Z.; Csontos, J.; Ladjánszki, I.; Szegedy, L.; Ladóczki, B.; Samu, G. MRCC, a quantum chemical program suite; http://www.mrcc.hu (accessed Feb 10, 2016).
238. Korth, M. Third-Generation Hydrogen-Bonding Corrections for Semiempirical QM Methods and Force Fields J. Chem. Theory Comput. 2010, 6, 3808-3816 10.1021/ct100408b
239. Yang; York, D.; Cui, Q.; Elstner, M.; Yu, H. Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method: Third-Order Expansion of the Density Functional Theory Total Energy and Introduction of a Modified Effective Coulomb Interaction J. Phys. Chem. A 2007, 111, 10861-10873 10.1021/jp074167r
240. Vorlová, B.; Nachtigallová, D.; Jirásková-Vaníčková, J.; Ajani, H.; Jansa, P.; Řezáč, J.; Fanfrlík, J.; Otyepka, M.; Hobza, P.; Konvalinka, J. et al. Malonate-based inhibitors of mammalian serine racemase: Kinetic characterization and structure-based computational study Eur. J. Med. Chem. 2015, 89, 189-197 10.1016/j.ejmech.2014.10.043