Low-cost quantum chemical methods for noncovalent interactions

Journal of Physical Chemistry Letters

Volumn 5, Issue 24, 2014, Pages 4275-4284

  Brandenburg, Jan Gerit ^a   Hochheim, Manuel ^a   Bredow, Thomas ^a   Grimme, Stefan ^a  

^a UNIVERSITY OF BONN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; COMPLEXATION; COMPUTATION THEORY; COSTS; CRYSTAL STRUCTURE; HARTREE APPROXIMATION; IONS; MOLECULAR ORBITALS;

COMPUTATIONAL SAVINGS; CRYSTAL STRUCTURE PREDICTION; FIRST-PRINCIPLE DENSITY-FUNCTIONAL THEORIES; INTERMOLECULAR INTERACTIONS; LARGE-SCALE APPLICATIONS; NON-COVALENT INTERACTION; QUANTUM-CHEMICAL METHODS; SUPRAMOLECULAR HOST;

DENSITY FUNCTIONAL THEORY;

EID: 84918842958     PISSN: None     EISSN: 19487185     Source Type: Journal    
DOI: 10.1021/jz5021313     Document Type: Review

References (81)

1. Stone, A. J. The Theory of Intermolecular Forces; Oxford University Press: Oxford, U.K., 1997.
2. Hohenstein, E. G.; Sherrill, C. D. Wavefunction Methods for Noncovalent Interactions Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2012, 2, 304-326
3. Jansen, G. Symmetry-Adapted Perturbation Theory Based on Density Functional Theory for Noncovalent Interactions Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2014, 4, 127-144
4. Steed, J. W.; Atwood, J. L. Supramolecular Chemistry, 2nd ed.; Wiley-VCH: Chichester, U.K., 2009.
5. Wang, W.; Domini, O.; Reyes, C. M.; Kollman, P. A. Biomolecular Simulations: Recent Developments in Force Field, Simulation in Enzyme, Protein-Ligand, Protein-Protein, and Protein-Nucleic Acid Noncovalent Interactions Annu. Rev. Biophys. Biomol. Struct. 2001, 30, 211-243
6. Raha, K.; Merz, K. M. Large-Scale Validation of a Quantum Mechanics Based Scoring Function: Predicting the Binding Affinity and the Binding Mode of a Diverse Set of Protein-Ligand Complexes J. Med. Chem. 2005, 48, 4558-4575
7. Price, S. L. Predicting Crystal Structures of Organic Compounds Chem. Soc. Rev. 2014, 43, 2098-2111
8. Cruz-Cabeza, A. J.; Bernstein, J. Conformational Polymorphism Chem. Rev. 2014, 114, 2170-2191
9. Beran, G. J. O.; Wen, S.; Nand, K.; Huang, Y.; Heit, Y. Accurate and Robust Molecular Crystal Modeling Using Fragment-Based Electronic Structure Methods Top Curr. Chem. 2014, 345, 59-93
10. Riplinger, C.; Sandhoefer, B.; Hansen, A.; Neese, F. Natural Triple Excitations in Local Coupled Cluster Calculations with Pair Natural Orbitals J. Chem. Phys. 2013, 139, 134101
11. Thiel, W. Semiempirical Quantum-Chemical Methods Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2014, 4, 145-157
12. Bredow, T.; Jug, K. Theory and Range of Modern Semiempirical Molecular Orbital Methods Theor. Chem. Acc. 2005, 113, 1-14
13. Hennemann, M.; Clark, T. EMPIRE: A Highly Parallel Semiempirical Molecular Orbital Program: 1: Self-Constistent Field Calculation J. Mol. Model. 2014, 20, 2331
14. Kristyán, S.; Pulay, P. Can (Semi)Local Density Functional Theory Account for the London Dispersion Forces? Chem. Phys. Lett. 1994, 229, 175-180
15. Pérez-Jordá, J. M.; Becke, A. A Density-Functional Study of van der Waals Forces: Rare Gas Diatomics Chem. Phys. Lett. 1995, 233, 134-137
16. Hobza, P.; Šponer, J.; Reschel, T. Density Functional Theory and Molecular Clusters J. Comput. Chem. 1995, 16, 1315-1325
17. 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
18. Becke, A. D.; Johnson, E. R. Exchange-Hole Dipole Moment and the Dispersion Interaction J. Chem. Phys. 2005, 123, 154101
19. Tkatchenko, A.; Scheffler, M. Accurate Molecular Van Der Waals Interactions from Ground-State Electron Density and Free-Atom Reference Data Phys. Rev. Lett. 2009, 102, 073005
20. Tkatchenko, A.; DiStasio, R. A.; Car, R.; Scheffler, M. Accurate and Efficient Method for Many-Body van der Waals Interactions Phys. Rev. Lett. 2012, 108, 236402
21. Vydrov, O. A.; Van Voorhis, T. Nonlocal van der Waals Density Functional: The Simpler the Better J. Chem. Phys. 2010, 133, 244103
22. 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
23. Grimme, S. Density Functional Theory with London Dispersion Corrections Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2011, 1, 211-228
24. Burns, L. A.; Vazquez-Mayagoitia, A.; Sumpter, B. G.; Sherrill, C. D. A Comparison of Dispersion Corrections (DFT-D), Exchange-Hole Dipole Moment (XDM) Theory, and Specialized Functionals J. Chem. Phys. 2011, 134, 084107
25. 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, 5149-5155
26. Dannenberg, J. Hydrogen Bonds: A Comparison of Semiempirical and Ab Initio Treatments J. Mol. Struct.: THEOCHEM 1997, 401, 279-286
27. Csonka, G. I.; ángyán, J. G. The Origin of the Problems with the PM3 Core Repulsion Function J. Mol. Struct.: THEOCHEM 1997, 393, 31-38
28. Winget, P.; Selçuki, C.; Horn, A. H. C.; Martin, B.; Clark, T. Towards a "Next Generation" Neglect of Diatomic Differential Overlap Based Semiempirical Molecular Orbital Technique Theor. Chem. Acc. 2003, 110, 254-266
29. Korth, M. Third-Generation Hydrogen-Bonding Corrections for Semiempirical QM Methods and Force Fields J. Chem. Theory Comput. 2010, 6, 3808-3816
30. Řezáč, J.; Riley, K. E.; Hobza, P. Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Chemical Methods J. Chem. Theory Comput. 2012, 8, 141-151
31. Elstner, M.; Porezag, D.; Jungnickel, G.; Elsner, J.; Haugk, M.; Frauenheim, T.; Suhai, S.; Seifert, G. Self-Consistent-Charge Density-Functional Tight-Binding Method for Simulations of Complex Materials Properties Phys. Rev. B 1998, 58, 7260-7268
32. Gaus, M.; Cui, Q.; Elstner, M. Density Functional Tight Binding: Application to Organic and Biological Molecules Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2014, 4, 49-61
33. Seifert, G.; Joswig, J.-O. Density-Functional Tight Binding - An Approximate Density-Functional Theory method Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2012, 2, 456-465
34. Brandenburg, J. G.; Grimme, S. Accurate Modeling of Organic Molecular Crystals by Dispersion-Corrected Density Functional Tight Binding (DFTB) J. Phys. Chem. Lett. 2014, 5, 1785-1789
35. Sure, R.; Grimme, S. Corrected Small Basis Set Hartree-Fock Method for Large Systems J. Comput. Chem. 2013, 34, 1672-1685
36. Weber, W.; Thiel, W. Orthogonalization Corrections for Semiempirical Methods Theor. Chem. Acc. 2000, 103, 495-506
37. Stewart, J. J. P. Optimization of Parameters for Semiempirical Methods I. Method J. Comput. Chem. 1989, 10, 209-220
38. Ahlswede, B.; Jug, K. Consistent Modifications of SINDO1: I. Approximations and Parameters J. Comput. Chem. 1999, 20, 563-572
39. Brandenburg, J. G.; Grimme, S. Dispersion Corrected Hartree-Fock and Density Functional Theory for Organic Crystal Structure Prediction Top Curr. Chem. 2014, 345, 1-23
40. Kruse, H.; Grimme, S. A Geometrical Correction for the Inter- and Intramolecular Basis Set Superposition Error in Hartree-Fock and Density Functional Theory Calculations for Large Systems J. Chem. Phys. 2012, 136, 154101
41. Brandenburg, J. G.; Alessio, M.; Civalleri, B.; Peintinger, M. F.; Bredow, T.; Grimme, S. Geometrical Correction for the Inter- and Intramolecular Basis Set Superposition Error in Periodic Density Functional Theory Calculations J. Phys. Chem. A 2013, 117, 9282-9292
42. Igel-Mann, G.; Stoll, H.; Preuss, H. Pseudopotentials for Main Group Elements (IIIa through VIIa) Mol. Phys. 1988, 65, 1321
43. Andrae, D.; Haeussermann, U.; Dolg, M.; Stoll, H.; Preuss, H. Energy-Adjusted Ab Initio Pseudopotentials for the Second and Third Row Transition Elements Theor. Chim. Acta 1990, 77, 123-141
44. Pople, J. A.; Santry, D. P.; Segal, G. A. Approximate Self-Consistent Molecular Orbital Theory. I. Invariant Procedures J. Chem. Phys. 1965, 43, 129-135
45. Ridley, J.; Zerner, M. An Intermediate Neglect of Differential Overlap Technique for Spectroscopy: Pyrrole and Azines Theor. Chim. Acta. 1973, 32, 111-124
46. Dewar, M. J. S.; Thiel, W. Ground States of Molecules. 39. MNDO Results for Molecules Containing Hydrogen, Carbon, Nitrogen, and Oxygen J. Am. Chem. Soc. 1977, 99, 4907-4917
47. Stewart, J. J. P. Optimization of Parameters for Semiempirical Methods V: Modification of NDDO Approximations and Application to 70 Elements J. Mol. Mod. 2007, 13, 1173
48. Jug, K.; Geudtner, G.; Homann, T. MSINDO Parameterization for Third-Row Main Group Elements J. Comput. Chem. 2000, 21, 974-987
49. Scholten, M. Semiempirical Methods with Orthogonalization Corrections: The OM3Method. PhD Thesis, Heinrich-Heine-Universität Düsseldorf, Germany, 2003.
50. Stewart, J. J. P. Optimization of Parameters for Semiempirical Methods VI: More Modifications to the NDDO Approximation and Re-Optimization of Parameters J. Mol. Model. 2013, 19, 1-32
51. Bredow, T.; Geudtner, G.; Jug, K. Development of the Cyclic Cluster Method for Ionic Systems J. Comput. Chem. 2001, 22, 89-101
52. Aradi, B.; Hourahine, B.; Frauenheim, T. DFTB+, a Sparse Matrix-Based Implementation of the DFTB Method J. Phys. Chem. A 2007, 111, 5678-5684
53. Elstner, M. SCC-DFTB: What Is the Proper Degree of Self-Consistency? J. Phys. Chem. A 2007, 111, 5614-5621
54. Elstner, M. The SCC-DFTB Method and Its Application to Biological Systems Theor. Chem. Acc. 2006, 116, 316-325
55. Casimir, H. B. G.; Polder, D. The Influence of Retardation on the London-van der Waals Forces Phys. Rev. 1948, 73, 360-372
56. Johnson, E. R.; Becke, A. D. A Post-Hartree-Fock Model of Intermolecular Interactions: Inclusion of Higher-Order Corrections J. Chem. Phys. 2006, 124, 174104
57. Grimme, S.; Ehrlich, S.; Goerigk, L. Effect of the Damping Function in Dispersion Corrected Density Functional Theory J. Comput. Chem. 2011, 32, 1456-1465
58. DiStasio, R. A.; Gobre, V. V.; Tkatchenko, A. Many-Body van der Waals Interactions in Molecules and Condense Matter J. Phys.: Condensed Matter 2014, 26, 213202
59. Dobson, J. F. Beyond Pairwise Additivity in London Dispersion Interactions Int. J. Quantum Chem. 2014, 114, 1157-1161
60. Kennedy, M. R.; McDonald, A. R.; DePrince, A. E.; Marshall, M. S.; Podeszwa, R.; Sherrill, C. D. Communication: Resolving the Three-Body Contribution to the Lattice Energy of Crystalline Benzene: Benchmark Results from Coupled-Cluster Theory J. Chem. Phys. 2014, 140, 121104
61. Moellmann, J.; Grimme, S. A DFT-D3 Study of Some Molecular Crystals J. Phys. Chem. C 2014, 118, 7615-7621
62. Hostaš, J.; Řezáč, J.; Hobza, P. On the Performance of the Semiempirical Quantum Mechanical PM6 and PM7 Methods for Noncovalent Interactions Chem. Phys. Lett. 2013, 568, 161-166
63. Dovesi, R.; Orlando, R.; Erba, A.; Zicovich-Wilson, C. M.; Civalleri, B.; Casassa, S.; Maschio, L.; Ferrabone, M.; De La Pierre, M.; DArco, P. CRYSTAL14: A Program for the Ab Initio Investigation of Crystalline Solids Int. J. Quantum Chem. 2014, 114, 1287-1317
64. Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized Gradient Approximation Made Simple Phys. Rev. Lett. 1996, 77, 3865-3868
65. Stewart, J. J. P. MOPAC2012; Stewart Computational Chemistry: Colorado Springs, CO, 2012; HTTP://OpenMOPAC.net.
66. Gaus, M.; Goez, A.; Elstner, M. Parametrization and Benchmark of DFTB3 for Organic Molecules J. Chem. Theory Comput. 2013, 9, 338-354
67. Jurečka, P.; Šponer, J.; Cerny, 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
68. 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
69. Řezáč, J.; Riley, K. E.; Hobza, P. Benchmark Calculations of Noncovalent Interactions of Halogenated Molecules J. Chem. Theory Comput. 2012, 8, 4285-4292
70. 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
71. Kozuch, S.; Martin, J. M. L. Halogen Bonds: Benchmarks and Theoretical Analysis J. Chem. Theory Comput. 2013, 9, 1918-1931
72. Mu, X.; Wang, Q.; Wang, L.-P.; Fried, S. D.; Piquemal, J.-P.; Dalby, K. N.; Ren, P. Modeling Organochlorine Compounds and the -Hole Effect Using a Polarizable Multipole Force Field J. Phys. Chem. B 2014, 118, 6456-6465
73. Grimme, S. A General Quantum Mechanically Derived Force Field (QMDFF) for Molecules and Condensed Phase Simulation J. Chem. Theory Comput. 2014, 10, 4497-4514
74. Sedlak, 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
75. Grimme, S. Supramolecular Binding Thermodynamics by Dispersion Corrected Density Functional Theory Chem. - Eur. J. 2012, 18, 9955-9964
76. 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
77. Sure, R.; Antony, J.; Grimme, S. Blind Prediction of Binding Affinities for Charged Supramolecular Host-Guest Systems: Achievements and Shortcomings of DFT-D3 J. Phys. Chem. B 2014, 118, 3431-3440
78. Reilly, A. M.; Tkatchenko, A. Understanding the Role of Vibrations, Exact Exchange, and Many-Body van der Waals Interactions in the Cohesive Properties of Molecular Crystals J. Chem. Phys. 2013, 139, 024705
79. Otero-de-la-Roza, A.; Johnson, E. R. A Benchmark for Non-Covalent Interactions in Solids J. Chem. Phys. 2012, 137, 054103
80. Grimme, S.; Steinmetz, M. Effects of London Dispersion Correction in Density Functional Theory on the Structures of Organic Molecules in the Gas Phase Phys. Chem. Chem. Phys. 2013, 15, 16031-16042
81. Li, A.; Muddana, H. S.; Gilson, M. K. Quanum Mechanical Calculation of Noncovalent Interactions: A Large-Scale Evaluation of PMx, DFT, and SAPT Approaches J. Chem. Theory Comput. 2014, 10, 1563-1575