Semiempirical quantum-chemical methods

Wiley Interdisciplinary Reviews: Computational Molecular Science

Volumn 4, Issue 2, 2014, Pages 145-157

  Thiel, Walter ^a  

^a MAX PLANCK INSTITUT FÜR KOHLENFORSCHUNG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL ASPECTS; EXCITED-STATE DYNAMICS; HYBRID APPROACH; LINEAR SCALING; PARAMETERIZATION STRATEGIES; QUANTUM-CHEMICAL METHODS; SEMI-EMPIRICAL; SEMI-EMPIRICAL METHODS;

BENCHMARKING;

QUANTUM CHEMISTRY;

EID: 84893773262     PISSN: 17590876     EISSN: 17590884     Source Type: Journal    
DOI: 10.1002/wcms.1161     Document Type: Article

References (114)

1. Hückel E. Quantum contributions to the benzene problem. Z Phys 1931, 70:204-286.
2. Hoffmann R. An extended Hückel theory. I. Hydrocarbons. J Chem Phys 1963, 39:1397-1412.
3. Pariser R, Parr RG. A semi-empirical theory of the electronic spectra and electronic structure of complex unsaturated molecules. J Chem Phys 1953, 21:466-471.
4. Pople JA. Electron interaction in unsaturated hydrocarbons. Trans Farad Soc 1953, 49:1375-1385.
5. Pople JA, Santry DP, Segal GA. Approximate self-consistent molecular orbital theory. I. Invariant procedures. J Chem Phys 1965, 43:S129-S135.
6. 3 systems. J Chem Phys 1966, 44:3289-3296.
7. Pople JA, Beveridge DL, PA Dobosh PA. Approximate self-consistent molecular-orbital theory. V. Intermediate neglect of differential overlap. J Chem Phys 1967, 47:2026-2033.
8. Bingham RC, Dewar MJS, Lo DH. Ground states of molecules. XXV. MINDO/3. Improved version of the MINDO semiempirical SCF-MO method. J Am Chem Soc 1975, 97:1285-1293.
9. Dewar MJS, Thiel W. Ground states of molecules. 38. The MNDO method. Approximations and parameters. J Am Chem Soc 1977, 99:4899-4907.
10. Dewar MJS, 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.
11. Dewar MJS, Zoebisch E, Healy EF, Stewart JJP. Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model. J Am Chem Soc 1985, 107:3902-3909.
12. Stewart JJP. Optimization of parameters for semiempirical methods I. Method. J Comput Chem 1989, 10:209-220.
13. Stewart JJP. Optimization of parameters for semiempirical methods II. Applications. J Comput Chem 1989, 10:221-264.
14. Nanda DN, Jug K. SINDO1. A semiempirical SCF MO method for molecular binding energy and geometry. I. Approximations and parametrization. Theor Chim Acta 1980, 57:95-106.
15. Jug K, Iffert R, Schulz J. Development and parametrization of SINDO1 for second-row elements. Int J Quant Chem 1987, 32:265-277.
16. Ahlswede B, Jug K. Consistent Modifications of SINDO1: I. Approximations and parameters. J Comput Chem 1999, 20:563-571.
17. Ahlswede B, Jug K. Consistent modifications of SINDO1: II. Applications to first- and second-row elements. J Comput Chem 1999, 20:572-578.
18. Ridley J, Zerner MC. An intermediate neglect of differential overlap technique for spectroscopy: pyrrole and the azines. Theor Chim Acta 1973, 32:111-134.
19. Bacon AD, Zerner MC. An intermediate neglect of differential overlap theory for transition metal complexes: Fe, Co and Cu chlorides. Theor Chim Acta 1979, 53:21-54.
20. Voityuk AA. Intermediate neglect of differential overlap for spectroscopy. WIREs Comp Mol Sci 2013, doi:10.1002/wcms.1141.
21. Dewar MJS, Thiel W. A semiempirical model for the two-center repulsion integrals in the NDDO approximation. Theor Chim Acta 1977, 46:89-104.
22. Thiel W. Voityuk AA. Extension of the MNDO formalism to d orbitals: integral approximations and preliminary numerical results. Theor Chim Acta 1992, 81:391-404; 1996, 93:315.
23. Thiel W, Voityuk AA. Extension of MNDO to d orbitals: parameters and results for the second-row elements and for the zinc group. J Phys Chem 1996, 100:616-626.
24. Stewart JJP. Optimization of parameters for semiempirical methods V: modification of NDDO approximations and application to 70 elements. J Mol Model 2007, 13:1173-1213.
25. Stewart JJP. Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters. J Mol Model 2013, 19:1-32.
26. Repasky MP, Chandrasekhar J, Jorgensen WL. PDDG/PM3 and PDDG/MNDO: improved semiempirical methods. J Comput Chem 2002, 23:1601-1622.
27. Tubert-Brohman I, Guimaraes CRW, Repasky MP, Jorgensen WL. Extension of the PDDG/PM3 and PDDG/MNDO semiempirical molecular orbital methods to the halogens. J Comput Chem 2004, 25:138-150.
28. Korth M, Pitonak M, Rezac J, Hobza P. A transferable H-bonding correction for semiempirical quantum-chemical methods. J Chem Theory Comput 2010, 6:344-352.
29. Korth M. Empirical hydrogen-bond potential functions-an old hat reconditioned. ChemPhysChem 2011, 12:3131-3142, and references cited therein.
30. Rocha GB, Freire RO, Simas AM, Stewart JJP. RM1: A reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I. J Comput Chem 2006, 27:1101-1111.
31. Kolb M, Thiel W. Beyond the MNDO model: methodical considerations and numerical results. J Comput Chem 1993, 14:775-789.
32. Weber W. Ein neues semiempirisches NDDO-Verfahren mit Orthogonalisierungskorrekturen: Entwicklung des Modells, Parametrisierung und Anwendungen. PhD Thesis, Universität Zürich; 1996.
33. Weber W, Thiel W. Orthogonalization corrections for semiempirical methods. Theor Chem Acc 2000, 103:495-506.
34. Scholten M. Semiempirische Verfahren mit Orthogonalisierungskorrekturen: Die OM3 Methode. PhD Thesis, Universität Düsseldorf; 2003.
35. Seifert G, Eschrig H, Bieger W. An approximation variant of LCAO-Xα methods. Z Phys Chem 1986, 267:529-539.
36. Seifert G, Joswig J-O. Density functional tight-binding-an approximate DFT method. WIREs Comp Mol Sci 2012, 2:456-465.
37. Elstner M, Porezag D, Jungnickel G, Elsner J, Haugk M, Frauenheim T, Suhai S, Seifert G. Self-consistent-charge density functional method for simulations of complex materials properties. Phys Rev B 1998, 58:7260-7268.
38. Elstner M, Gaus M, Cui Q. Density functional tight binding: application to organic and biological molecules. WIREs Comp Mol Sci 2013, doi:10.1002/wcms.1156.
39. Otte N, Scholten M, Thiel W. Looking at self-consistent-charge density functional tight binding from a semiempirical perspective. J Phys Chem A 2007, 111:5751-5755.
40. Silva-Junior MR, Thiel W. Benchmark of electronically excited states for semiempirical methods: MNDO, AM1, PM3, OM1, OM2, OM3, INDO/S, and INDO/S2. J Chem Theory Comput 2010, 6:1546-1564.
41. Korth M, Thiel W. Benchmarking semiempirical methods for thermochemistry, kinetics, and noncovalent interactions: OMx methods are almost as accurate and robust as DFT-GGA methods for organic molecules. J Chem Theory Comput 2011, 7:2929-2936.
42. Thiel W. Semiempirical methods: current status and perspectives. Tetrahedron 1988, 44:7393-7408.
43. Stewart JJP. Semiempirical Molecular orbital methods. In: Lipkowitz KB, Boyd DB, eds. Reviews in Computational Chemistry, Vol 1. New York: VCH Publishers; 1990, 45-81.
44. Stewart JJP. MOPAC: a semiempirical molecular orbital program. J Comp-Aided Mol Design 1990, 4:1-103.
45. Thiel W. Perspectives on semiempirical molecular orbital theory. Adv Chem Phys 1996, 93:703-757.
46. Clark T. Quo vadis semiempirical MO theory. J Mol Struct (THEOCHEM) 2000, 530:1-10.
47. Thiel W. Semiempirical methods. In: Grotendorst J, ed. Modern methods and algorithms of quantum chemistry, NIC Series, Vol 3. Jülich, Germany: John von Neumann Institute for Computing; 2000, 261-283.
48. Bredow T, Jug K. Theory and range of modern semiempirical molecular orbital methods. Theor Chem Acc 2005, 113:1-14.
49. Thiel W. Semiempirical quantum-chemical methods in computational chemistry. In: Dykstra CE, Kim KS, Frenking G, Scuseria GE, eds. Theory and Applications of Computational Chemistry: The First 40 Years. Amsterdam: Elsevier; 2005, 559-580.
50. Bernal-Uruchurtu MI, Martins-Costa MTC, Millot C, Ruiz-Lopez MF. Improving the description of hydrogen bonds at the semiempirical level: water-water interactions as test case. J Comput Chem 2000, 21:572-581.
51. Tuttle T, Thiel W. OMx-D: Semiempirical methods with orthogonalization and dispersion corrections. Implementation and biochemical application. Phys Chem Chem Phys 2008, 10:2159-2166.
52. Grimme S. Semiempirical GGA-type density functional constructed with a long-range dispersion correction. J Comput Chem 2006, 27:1787-1799.
53. 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, 132:154104/1-19.
54. Gonzalez-Lafont A, Truong TN, Truhlar DG. Direct dynamics calculations with neglect of diatomic differential overlap molecular orbital theory with specific reaction parameters. J Phys Chem 1991, 95:4618-4627.
55. Rossi I, Truhlar DG. Parameterization of NDDO wave functions using genetic algorithms. An evolutionary approach to parameterizing potential energy surfaces and direct dynamics calculations for organic reactions. Chem Phys Lett 1995, 233:231-236.
56. Doron D, Major DT, Kohen A, Thiel W, Wu X. Hybrid quantum and classical simulations of the dihydrofolate reductase catalyzed hydride transfer reaction on an accurate semi-empirical potential energy surface. J Chem Theory Comput 2011, 7:3420-3437.
57. Wu X, Thiel W, Pezeshki S, Lin H. Specific reaction path hamiltonian for proton transfer in water: re-parameterized semi-empirical models. J Chem Theory Comput. 2013, 9:2672-2686.
58. Patchkovskii S, Thiel W. NMR chemical shifts in MNDO approximation: parameters and results for H, C, N, and O. J Comput Chem 1999, 20:1220-1245.
59. Patchkovskii S, Thiel W. Nucleus-independent chemical shifts from semiempirical calculations. J Mol Model 2000, 6:67-75.
60. Stewart JJP, Csaszar P, Pulay P. Fast semiempirical calculations. J Comput Chem 1982, 3:227-228.
61. Bakowies D, Thiel W. MNDO study of large carbon clusters. J Am Chem Soc 1991, 113:3704-3714.
62. Wu X, Koslowski A, Thiel W. Semiempirical quantum chemical calculations accelerated on a hybrid multicore CPU-GPU computing platform. J Chem Theory Comput 2012, 8:2272-2281.
63. Maia JDC, Carvalho GAU, Mangueira CP, Santana SR, Cabral LAF, Rocha GB. GPU linear algebra libraries and GPGPU programming for accelerating MOPAC semiempirical quantum chemistry calculations. J Chem Theory Comput 2012, 8:3072-3081.
64. Patchkovskii S, Thiel W. Analytical first derivatives of the energy in the MNDO half-electron open-shell treatment. Theor Chim Acta 1996, 93:87-99.
65. Patchkovskii S, Thiel W. Analytical first derivatives of the energy for small CI expansions. Theor Chem Acc 1997, 98:1-4.
66. Patchkovskii S, Thiel W. Analytical second derivatives of the energy in MNDO methods. J Comput Chem 1996, 17:1318-1327.
67. Dewar MJS, Liotard DA. An efficient procedure for calculating the molecular gradient using SCF-CI semiempirical wave functions with a limited number of configurations. J Mol Struct (THEOCHEM) 1990, 206:123-133.
68. Handy NC, Schaefer HF. On the evaluation of analytic energy derivatives for correlated wave functions. J Chem Phys 1984, 81:5031-5033.
69. Strodel P, Tavan P. A revised MRCI-algorithm. I. Efficient combination of spin adaptation with individual configuration selection coupled to an effective valence-shell Hamiltonian. J Chem Phys 2002, 117:4667-4676.
70. Koslowski A, Beck ME, Thiel W. Implementation of a general multireference configuration interaction procedure with analytic gradients in a semiempirical context using the graphical unitary group approach. J Comput Chem 2003, 24:714-726.
71. Patchkovskii S, Koslowski A, Thiel W. Generic implementation of semi-analytical CI gradients for NDDO-type methods. Theor Chem Acc 2005, 114:84-89.
72. Stewart JJP. Application of localized molecular orbitals to the solution of semiempirical self-consistent field equations. Int J Quantum Chem 1996, 58:133-146.
73. Yang W, Lee T-S. A density-matrix divide-and-conquer approach for electronic structure calculations of large molecules. J Chem Phys 1995, 103:5674-5678.
74. Lee TS, York DM, Yang W. Linear-scaling semiempirical quantum calculations for macromolecules. J Chem Phys 1996, 105:2744-2750.
75. Dixon SL, Merz KM. Semiempirical molecular orbital calculations with linear system size scaling. J Chem Phys 1996, 104:6643-6649.
76. Li X-P, Nunes RW, Vanderbilt D. Density-matrix electronic-structure method with linear system-size scaling. Phys Rev B 1993, 47:10891-10894.
77. Millam JM, Scuseria GE. Linear scaling conjugate gradient density matrix search as an alternative to diagonalization for first principles electronic structure calculations. J Chem Phys 1997, 106:5569-5577.
78. Daniels AD, Millam JM, Scuseria GE. Semiempirical methods with conjugate gradient density matrix search to replace diagonalization for molecular systems containing thousands of atoms. J Chem Phys 1997, 107:425-431.
79. Kevorkiants R. Linear Scaling Conjugate Gradient Density Matrix Search: Implementation, Validation and Application with Semiempirical MO Methods. PhD thesis, Universität Düsseldorf, 2003.
80. Warshel A, Levitt M. Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol 1976, 103:227-249.
81. Senn HM, Thiel W. QM/MM methods for biological systems. Top Curr Chem 2007, 268:173-290.
82. Senn HM, Thiel W. QM/MM methods for biomolecular systems. Angew Chem Int Ed 2009, 48:1198-1229.
83. Titmuss SJ, Cummins PL, Bliznyuk AA, Rendell AP, Gready JE. Comparison of linear scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods applied to enzyme reactions. Chem Phys Lett 2000, 320:169-176.
84. Claeyssens F, Harvey JN, Manby FR, Mata RA, Mulholland AJ, Ranaghan KE, Schütz M, Thiel S, Thiel W, Werner H-J. High-accuracy computation of reaction barriers in enzymes. Angew Chem Int Ed 2006, 45:6856-6859.
85. Tirado-Rives J, Jorgensen, WL. Performance of B3LYP density functional methods for a large set of organic molecules. J Chem Theory Comput 2008, 4:297-306.
86. 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.
87. Schreiber M, Silva-Junior MR, Sauer SPA, Thiel W. Benchmarks for electronically excited states: CASPT2, CC2, CCSD, and CC3. J Chem Phys 2008, 128:131410/1-25.
88. Silva-Junior MR, Schreiber M, Sauer SPA, Thiel W. Benchmarks for electronically excited states: time-dependent density functional theory and density functional theory based multireference configuration interaction. J Chem Phys 2008, 129:104103/1-14.
89. Senn HM, Kästner J, Breidung J, Thiel W. Finite-temperature effects in enzymatic reactions-insights from QM/MM free-energy eimulations. Can J Chem 2009, 87:1322-1337.
90. Polyak I, Reetz MT, Thiel W. QM/MM study on the mechanism of the enzymatic Baeyer-Villiger reaction. J Am Chem Soc 2012, 134:2732-2741.
91. Grimme S. Towards first principles calculation of electron impact mass spectrometry of molecules. Angew Chem Int Ed 2013, 52:6306-6312.
92. Thompson MA, Schenter GK. Excited states of the bacteriochlorophyll b dimer of Rhodopseudomonas viridis: a QM/MM study of the photosynthetic reaction center that includes MM polarization. J Phys Chem 1995, 99:6374-6386.
93. Cory MG, Zerner MC, Hu X, Schulten K. Electronic excitations in aggregates of bacteriochlorophylls. J Phys Chem B 1998, 102:7640-7650.
94. Thiel W. The MNDOC method, a correlated version of the MNDO model. J Am Chem Soc 1981, 103:1413-1420.
95. Schweig A, Thiel W. MNDOC study of excited states. J Am Chem Soc 1981, 103:1425-1431.
96. Tully JC. Molecular dynamics with electronic transitions. J. Chem. Phys. 1990, 93:1061-1071.
97. Fabiano E, Keal TW, Thiel W. Implementation of surface hopping molecular dynamics using semiempirical methods. Chem Phys 2008, 349:334-347.
98. Fabiano E, Thiel W. Nonradiative deexcitation dynamics of 9H-adenine: an OM2 surface hopping study. J Phys Chem A 2008, 112:6859-6863.
99. Lan Z, Fabiano E, Thiel W. Photoinduced nonadiabatic dynamics of pyrimidine nucleobases: on-the-fly surface-hopping study with semiempirical methods. J Phys Chem B 2009, 113:3548-3555.
100. Lan Z, Fabiano E, Thiel W. Photoinduced nonadiabatic dynamics of 9H-guanine. ChemPhysChem 2009, 10:1225-1229.
101. Lan Z, Lu Y, Fabiano E, Thiel W. QM/MM nonadiabatic decay dynamics of 9H-adenine in aqueous solution. ChemPhysChem 2011, 12:1989-1998.
102. Lu Y, Lan Z, Thiel W. Hydrogen bonding regulates the monomeric nonradiative decay of adenine in DNA strands. Angew Chem Int Ed 2011, 50:6864-6867.
103. Lu Y, Lan Z, Thiel W. Monomeric adenine decay dynamics influenced by the DNA environment. J Comput Chem 2012, 33:1225-1235.
104. Heggen B, Lan Z, Thiel W. Nonadiabatic decay dynamics of 9H-guanine in aqueous solution. Phys Chem Chem Phys 2012, 14:8137-8146.
105. Kazaryan A, Lan Z, Schäfer LV, Thiel W, Filatov M. Surface hopping excited-state dynamics study of the photoisomerization of a light-driven fluorene molecular rotary motor. J Chem Theory Comput 2011, 7:2189-2199.
106. Schönborn JB, Koslowski A, Thiel W, Hartke B. Photochemical dynamics of E-iPr-furylfulgide. Phys Chem Chem Phys 2012, 14:12193-12201.
107. Cui G, Lan Z, Thiel W. Intramolecular hydrogen bonding plays a crucial role in the photophysics and photochemistry of the GFP chromophore. J Am Chem Soc 2012, 134:1662-1672.
108. Weingart O, Lan Z, Koslowski A, Thiel W. Chiral pathways and periodic decay in cis-azobenzene photodynamics. J Phys Chem Lett 2011, 2:1506-1509.
109. Gamez JA, Weingart O, Koslowski A, Thiel W. Cooperating dinitrogen and phenyl rotations in trans-azobenzene photoisomerization. J Chem Theory Comput 2012, 8:2352-2358.
110. Cui G, Thiel W. Photoinduced ultrafast wolff rearrangement: a non-adiabatic dynamics perspective. Angew Chem Int Ed 2013, 52:433-436.
111. Dreuw A, Head-Gordon M. Failure of time-dependent density functional theory for long- range charge-transfer excited states: the zincbacterio-chlorin-bacterlochlorin and bacteriochlorophyll- spheroidene complexes. J Am Chem Soc 2004, 126:4007-4016.
112. Dreuw A, Head-Gordon M. Single-reference ab initio methods for the calculation of excited states of large molecules. Chem Rev 2005, 105:4009-4037.
113. Lan Z, Lu Y, Weingart O, Thiel W. Nonadiabatic decay dynamics of a benzylidene malononitrile. J Phys Chem A 2012, 116:1510-1518.
114. Cui G, Thiel W. Nonadiabatic dynamics of a truncated indigo model. Phys Chem Chem Phys 2012, 14:12378-12384.