Skip to main content
SpringerLink
Log in
Book cover

Biomolecular Simulations pp 3–27Cite as

Ab Initio, Density Functional Theory, and Semi-Empirical Calculations

  • Protocol
  • First Online:

Part of the book series: Methods in Molecular Biology ((MIMB,volume 924))

Abstract

This chapter introduces the theory and applications of commonly used methods of electronic structure calculation, with particular emphasis on methods applicable for modelling biomolecular systems. This chapter is sectioned as follows. We start by presenting ab initio methods, followed by a treatment of density functional theory (DFT) and some recent advances in semi-empirical methods. Treatment of excited states as well as basis sets are also presented.

This is a preview of subscription content, log in via an institution.

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Hartree DR (1928) The wave mechanics of an atom with a non-Coulomb central field. Part I. theory and methods. Proc Cambridge Phil Soc 24:89–110

    CAS  Google Scholar 

  2. Slater JC (1930) Note on Hartree’s method. Phys Rev 35:210–211

    Google Scholar 

  3. Fock V (1930) Näherungsmethoden zur Lösung des quantenmechanischen mehrkörperproblems. Z Phys 61:126–148

    Google Scholar 

  4. Slater JC (1929) The theory of complex spectra. Phys Rev 34:1293–1322

    CAS  Google Scholar 

  5. Löwdin PO (1962) Exchange, correlation, and spin effects in molecular and solid-state theory. Rev Mod Phys 34:80–87

    Google Scholar 

  6. Roothaan CCJ (1951) New developments in molecular orbital theory. Rev Mod Phys 23:69–89

    CAS  Google Scholar 

  7. Helgaker T, Jørgersen P, Olsen J (2000) Molecular electronic-structure theory. Wiley, Chichester

    Google Scholar 

  8. Lischka H, Dallos M, Shepard R (2002) Analytic MRCI gradient for excited states: formalism and application to the n − π∗ valence- and n − (3s, 3p) Rydberg states of formaldehyde. Mol Phys 100:1647–1658

    CAS  Google Scholar 

  9. Roos BO, Taylor PR, Siegbahn PEM (1980) A complete active space SCF method (CASSCF) using a density matrix formulated super-CI approach. Chem Phys 48:157–173

    CAS  Google Scholar 

  10. Andersson K, Malmqvist PÅ, Roos BO (1992) Second-order perturbation theory with a complete active space self-consistent field reference function. J Chem Phys 96:1218–1226

    CAS  Google Scholar 

  11. Ferré N, Olivucci M (2003) Probing the rhodopsin cavity with reduced retinal models at the CASPT2//CASSCF/AMBER Level of theory. J Am Chem Soc 125:6868–6869

    PubMed  Google Scholar 

  12. Merchán M, Serrano-Andres L (2003) Ultrafast internal conversion of excited cytosine via the lowest ππ∗ electronic singlet state. J Am Chem Soc 125:8108–8109

    PubMed  Google Scholar 

  13. Sinicropi A, Andruniow T, Ferré N, Basosi R, Olivucci M (2005) Properties of the emitting state of the green fluorescent protein resolved at the CASPT2//CASSCF/CHARMM level. J Am Chem Soc 127:11534–11535

    PubMed  CAS  Google Scholar 

  14. Ghosh A, Tangen E, Ryeng H, Taylor PR (2004) Electronic structure of high-spin iron(IV) complexes. Eur J Inorg Chem 2004:4555–4560

    Google Scholar 

  15. Ghosh A, Taylor PR (2005) Iron(IV) porphyrin difluoride does not exist: implications for DFT calculations on heme protein reaction pathways. J Chem Theory Comput 1:597–600

    CAS  Google Scholar 

  16. Jensen KP, Roos BO, Ryde U (2005) O2-binding to heme: electronic structure and spectrum of oxyheme, studied by multiconfigurational methods. J Inorg Biochem 99:45–54

    PubMed  CAS  Google Scholar 

  17. Angeli C, Pastore M, Cimiraglia R (2007) New perspectives in multireference perturbation theory: the n-electron valence state approach. Theor Chem Acc 117:743–754

    CAS  Google Scholar 

  18. Schapiro I, Ryazantsev MN, Ding WJ, Huntress MM, Melaccio F, Andruniow T, Olivucci M (2010) Computational photobiology and beyond. Aust J Chem 63:413–429

    CAS  Google Scholar 

  19. Aquilante F, De Vico L, Ferré N, Ghigo G, Malmqvist PÅ, Neogrády P, Pedersen TB, Pitoňák M, Reiher M, Roos BO, Serrano-Andrés L, Urban M, Veryazov V, Lindh R (2010) Software news and update MOLCAS 7: the next generation. J Comput Chem 31:224–247

    PubMed  CAS  Google Scholar 

  20. Čížek J (1966) 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 45:4256–4266

    Google Scholar 

  21. Kallay M, Gauss J (2004) Calculation of excited-state properties using general coupled-cluster and configuration-interaction models. J Chem Phys 121:9257–9269

    PubMed  CAS  Google Scholar 

  22. Bartlett RJ, Purvis GD (1978) Many-body perturbation theory, coupled-pair many-electron theory, and the importance of quadruple excitations for the correlation problem. Int J Quantum Chem 14:561–581

    CAS  Google Scholar 

  23. Pople JA, Binkley JS, Seeger R (1976) Theoretical models incorporating electron correlation. Int J Quantum Chem 10 S:1–19

    Google Scholar 

  24. Møller C, Plesset MS (1934) Note on an approximation treatment for many-electron systems. Phys Rev 46:618–622

    Google Scholar 

  25. Christiansen O, Koch H, Jørgensen P (1995) The second-order approximate coupled cluster singles and doubles model CC2. Chem Phys Lett 243:409–418

    CAS  Google Scholar 

  26. Hättig C, Weigend F (2000) CC2 excitation energy calculations on large molecules using the resolution of the identity approximation. J Chem Phys 113:5154–5161

    Google Scholar 

  27. Hättig C (2006) In: Grotendorst J, Blugel S, Marx D (eds) Computational nanoscience: do it yourself! NIC series, John von Neumann Institute for Computing, Jülich

    Google Scholar 

  28. Hetzer G, Pulay P, Werner HJ (1998) Multipole approximation of distant pair energies in local MP2 calculations. Chem Phys Lett 290:143–149

    CAS  Google Scholar 

  29. Schütz M (2002) A new, fast, semi-direct implementation of linear scaling local coupled cluster theory. Phys Chem Chem Phys 4:3941–3947

    Google Scholar 

  30. Ziółkowski M Jansík B Kjærgaard T Jørgensen P (2010) Linear scaling coupled cluster method with correlation energy based error control. J Chem Phys 133:014107

    PubMed  Google Scholar 

  31. Feyereisen M, Fitzgerald G, Komornicki A (1993) Use of approximate integrals in ab initio theory. An application in MP2 energy calculations. Chem Phys Lett 208:359–363

    CAS  Google Scholar 

  32. Weigend F, Häser M (1997) RI-MP2: first derivatives and global consistency. Theoret Chem Acc 97:331–340

    CAS  Google Scholar 

  33. Neese F, Schwabe T, Kossmann S, Schirmer B, Grimme S (2009) Assessment of orbital-optimized, spin-component scaled second-order many-body perturbation theory for thermochemistry and kinetics. J Chem Theory Comput 5:3060–3073

    CAS  Google Scholar 

  34. Doser B, Zienau J, Clin L, Lambrecht DS, Ochsenfeld C (2010) A linear-scaling MP2 method for large molecules by rigorous integral-screening criteria. Z Phys Chem 224:397–412

    CAS  Google Scholar 

  35. Kitaura K, Ikeo E, Asada T, Nakano T, Uebayasi M (1999) Fragment molecular orbital method: an approximate computational method for large molecules. Chem Phys Lett 313:701–706

    CAS  Google Scholar 

  36. Gordon MS, Freitag MA, Bandyopadhyay P, Jensen JH, Kairys V, Stevens WJ (2001) The effective fragment potential method: a QM-based MM approach to modeling environmental effects in chemistry. J Phys Chem A 105:293–307

    CAS  Google Scholar 

  37. Steinmann C, Fedorov DG, Jensen JH (2010) Effective fragment molecular orbital method: a merger of the effective fragment potential and fragment molecular orbital methods. J Phys Chem A 114:8705–8712

    PubMed  CAS  Google Scholar 

  38. Grimme S (2003) Improved second-order Møller–Plesset perturbation theory by separate scaling of parallel- and antiparallel-spin pair correlation energies. J Chem Phys 118:9095–9102

    CAS  Google Scholar 

  39. Jung Y, Lochan RC, Dutoi AD, Head-Gordon M (2004) Scaled opposite-spin second order Møller–Plesset correlation energy: an economical electronic structure method. J Chem Phys 121:9793–9802

    PubMed  CAS  Google Scholar 

  40. Hellweg A, Grün SA, Hättig C (2008) Benchmarking the performance of spin-component scaled CC2 in ground and electronically excited states. Phys Chem Chem Phys 10:4119–4127

    PubMed  CAS  Google Scholar 

  41. Raghavachari K, Trucks GW, Pople JA, Head-Gordon M (1989) A fifth-order perturbation comparison of electron correlation theories. Chem Phys Lett. 157:479–483

    CAS  Google Scholar 

  42. Rhee YM, Head-Gordon M (2007) Scaled second-order perturbation corrections to configuration interaction singles: efficient and reliable excitation energy methods. J Phys Chem A 111:5314–5326

    PubMed  CAS  Google Scholar 

  43. Sumowski CV, Ochsenfeld C (2009) A convergence study of QM/MM isomerization energies with the selected size of the QM region for peptidic systems. J Phys Chem A 113:11734–11741

    PubMed  CAS  Google Scholar 

  44. Casida ME (1995) In: Chong DP (ed) Recent advances in density functional methods, Part I. World Scientific, Singapore

    Google Scholar 

  45. Bauernschmitt R, Ahlrichs R (1996) Treatment of electronic excitations within the adiabatic approximation of time dependent density functional theory. Chem Phys Lett 256:454–464

    CAS  Google Scholar 

  46. Olsen J, Jørgensen P (1985) Linear and nonlinear response functions for an exact state and for an MCSCF state. J Chem Phys 82:3235–3264

    CAS  Google Scholar 

  47. Koch H, Jørgensen P (1990) Coupled cluster response functions. J Chem Phys 93:3333–3344

    CAS  Google Scholar 

  48. Head-Gordon M, Rico RJ, Oumi M, Lee TJ (1994) A doubles correction to electronic excited-states from configuration-interaction in the space of single substitutions. Chem Phys Lett 219:21–29

    CAS  Google Scholar 

  49. Head-Gordon M, Oumi M, Maurice D (1999) Quasidegenerate second-order perturbation corrections to single-excitation configuration interaction. Mol Phys 96:593–574

    CAS  Google Scholar 

  50. Schirmer J (1982) Beyond the random-phase approximation: a new approximation scheme for the polarization propagator. Phys Rev A 26:2395–2416

    CAS  Google Scholar 

  51. Lester Jr. WA, Mitas L, Hammond B (2009) Quantum Monte Carlo for atoms, molecules and solids. Chem Phys Lett 478:1–10

    CAS  Google Scholar 

  52. Valsson O, Filippi C (2010) Photoisomerization of model retinal chromophores: insight from quantum Monte Carlo and multiconfiguration perturbation theory. J Chem Theory Comput 6:1275–1292

    CAS  Google Scholar 

  53. Hättig C (2005) Structure optimizations for excited states with correlated second-order methods: CC2 and ADC(2). Adv Quantum Chem 50:37–60

    Google Scholar 

  54. Aquino AJA, Nachtigallova D, Hobza P, Truhlar DG, Hðttig C, Lischka H (2011) The charge-transfer states in a stacked nucleobase dimer complex: A benchmark study. J Comput Chem 32:1217–1227

    Google Scholar 

  55. Send R, Sundholm D (2007) Coupled-cluster studies of the lowest excited states of the 11-cis-retinal chromophore. Phys Chem Chem Phys 9:2862–2867

    PubMed  CAS  Google Scholar 

  56. Johansson MP, Sundholm D (2004) Spin and charge distribution in iron porphyrin models: a coupled cluster and density-functional study. J Chem Phys 120:3229–3236

    PubMed  CAS  Google Scholar 

  57. Send R, Kaila VRI, Sundholm D (2011) Benchmarking the coupled-cluster approximate singles and doubles method on biochromophores. J Chem Theory Comput 7:2473–2484

    CAS  Google Scholar 

  58. Silva-Junior MR, Schreiber M, Sauer SPA, Thiel W (2008) Benchmarks for electronically excited states: time-dependent density functional theory and density functional theory based multireference configuration interaction. J Chem Phys 129:104103

    PubMed  Google Scholar 

  59. Send R, Kaila VRI, Sundholm D (2011) Reduction of the virtual space for coupled-cluster calculations on large molecules and embedded systems. J Chem Phys 134:214114

    PubMed  Google Scholar 

  60. Hohenberg P, Kohn W (1964) Inhomogeneous electron gas. Phys Rev 136:B864–B871

    Google Scholar 

  61. Kohn W, Sham LJ (1965) Self-consistent equations including exchange and correlation effects. Phys Rev 140:A1133–A1138

    Google Scholar 

  62. Thomas LH (1927) The calculation of atomic fields. Proc Cambridge Phil Soc 23:542–548

    CAS  Google Scholar 

  63. Fermi E (1927) Un metodo statistico per la determinazione di alcune prioprieta dell’atomo. Rend Accad Naz Lincei 6:602–607

    CAS  Google Scholar 

  64. Ceperly DM, Alder BJ (1980) Ground state of the electron gas by a stochastic method. Phys Rev Lett 45:566–569

    Google Scholar 

  65. Vosko SJ, Wilk L, Nusair M (1980) Accurate spin-dependent electron liquid correlation energies for local spin-density calculations—a critical analysis. Can J Phys 58:1200–1211

    CAS  Google Scholar 

  66. Perdew JP, Wang Y (1992) Accurate and simple analytic representation of the electron-gas correlation energy. Phys Rev B 45:13244–13249

    Google Scholar 

  67. Perdew JP, Burke K, Ernzerhof M (1996) Generalized gradient approximation made simple. Phys Rev Lett 77:3865–3868

    PubMed  CAS  Google Scholar 

  68. Becke AD (1988) Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A 38:3098–3100

    PubMed  CAS  Google Scholar 

  69. Perdew JP (1986) Density-functional approximation for the correlation energy of the inhomogeneous electron gas. Phys Rev B 33:8822–8824

    Google Scholar 

  70. Swart M, Solà M, Bickelhaupt FM (2009) A new all-round density functional based on spin states and S N 2 barriers. J Chem Phys 131:094103

    PubMed  Google Scholar 

  71. Becke AD (1993) A new mixing of Hartree–Fock and local density-functional theories. J Chem Phys 98:1372–1377

    CAS  Google Scholar 

  72. Perdew JP, Ruzsinszky A, Csonka GI, Constantin LA, Sun J (2009) Workhorse semilocal density functional for condensed matter physics and quantum chemistry. Phys Rev Lett 103:026403

    PubMed  Google Scholar 

  73. Becke AD, Johnson ER (2005) Exchange-hole dipole moment and the dispersion interaction. J Chem Phys 122:154104

    PubMed  Google Scholar 

  74. Becke AD, Johnson ER (2005) A density-functional model of the dispersion interaction. J Chem Phys 123:154101

    PubMed  Google Scholar 

  75. Johnson ER, Becke AD (2006) Van der Waals interactions from the exchange hole dipole moment: application to bio-organic benchmark systems. Chem Phys Lett 432:600–603

    CAS  Google Scholar 

  76. Grimme S (2006) Semiempirical hybrid density functional with perturbative second-order correlation. J Chem Phys 124:034108

    PubMed  Google Scholar 

  77. Grimme S (2006) Semiempirical GGA-type density functional constructed with a long-range dispersion correction. J Comput Chem 27:1787–1799

    PubMed  CAS  Google Scholar 

  78. Grimme S, Antony J, Ehrlich S, Krieg H (2010) A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H–Pu. J Chem Phys 132:154104

    PubMed  Google Scholar 

  79. Grimme S, Ehrlich S, Goerigk L (2011) Effect of the damping function in dispersion corrected density functional theory. J Comput Chem 32:1456–1465

    PubMed  CAS  Google Scholar 

  80. Steinmann SN, Corminboeuf C (2010) A system-dependent density-based dispersion correction. J Chem Theory Comput 6:1990–2001

    CAS  Google Scholar 

  81. Siegbahn PEM, Blomberg MRA, Chen SL (2010) Significant van der Waals effects in transition metal complexes. J Chem Theory Comput 6:2040–2044

    CAS  Google Scholar 

  82. Kaila VRI, Oksanen E, Goldman A, Verkhovsky MI, Sundholm D, Wikström M (2011) A combined quantum chemical and crystallographic study on the oxidized binuclear center of cytochrome c oxidase. Biochim Biophys Acta 1807:769–778

    PubMed  CAS  Google Scholar 

  83. Rappoport D, Furche F (2006) In: Marques MAL, Ullrich CA, Nogueira F, Rubio A, Burke K, Gross EKU (eds) Time-dependent density functional theory, Springer, Berlin

    Google Scholar 

  84. Furche F, Ahlrichs R (2002) Adiabatic time-dependent density functional methods for excited state properties. J Chem Phys 117:7433–7447

    CAS  Google Scholar 

  85. Bauernschmitt R, Häser M, Treutler O, Ahlrichs R (1997) Calculation of excitation energies within time-dependent density functional theory using auxiliary basis set expansions. Chem Phys Lett 264:573–578

    CAS  Google Scholar 

  86. Casida ME, Jamorski C, Casida KC, Salahub DR (1998) Molecular excitation energies to high-lying bound states from time-dependent density-functional response theory: characterization and correction of the time-dependent local density approximation ionization threshold. J Chem Phys 108:4439–4449

    CAS  Google Scholar 

  87. Lehtonen O, Sundholm D, Send R, Johansson MP (2009) Coupled-cluster and density functional theory studies of the electronic excitation spectra of trans-1,3-butadiene and trans-2-propeniminium. J Chem Phys 131:024301

    PubMed  Google Scholar 

  88. Becke AD (1993) Density-functional thermochemistry. III. The role of exact exchange. J Chem Phys 98:5648–5652

    CAS  Google Scholar 

  89. Yanai T, Tew DP, Handy NC (2004) A new hybrid exchange? correlation functional using the Coulomb-attenuating method (CAM-B3LYP). Chem Phys Lett 393:51–57

    CAS  Google Scholar 

  90. Heyd J, Peralta JE, Scuseria GE, Martin RL (2005) Energy band gaps and lattice parameters evaluated with the Heyd-Scuseria-Ernzerhof screened hybrid functional. J Chem Phys 123:174101

    PubMed  Google Scholar 

  91. Cerón-Carrasco JP, Requena A, Marian CM (2010) Theoretical study of the low-lying excited states of β-carotene isomers by a multireference configuration interaction method. Chem Phys 373:98–103

    Google Scholar 

  92. Marian CM, Gilka N (2008) Performance of the density functional theory/multireference configuration interaction method on electronic excitation of extended π-systems. J Chem Theory Comput 4:1501–1515

    CAS  Google Scholar 

  93. Grimme S, Waletzke M (1999) A combination of Kohn–Sham density functional theory and multi-reference configuration interaction methods. J Chem Phys 111:5645–5655

    CAS  Google Scholar 

  94. Send R, Sundholm D, Johansson MP, Pawłowski F (2009) Excited-state potential-energy surfaces of polyenes and protonated Schiff bases. J Chem Theory Comput 5:2401–2414

    CAS  Google Scholar 

  95. Jacquemin D, Wathelet V, Perpète EA, Adamo C (2009) Extensive TD-DFT benchmark: singlet-excited states of organic molecules. J Chem Theory Comput 5:2420–2435

    CAS  Google Scholar 

  96. Thompson MJ, Bashford D, Noodleman L, Getzoff ED (2003) Photoisomerization and Proton Transfer in Photoactive Yellow Protein. J Am Chem Soc 125:8186–8194

    PubMed  CAS  Google Scholar 

  97. Chiba M, Fedorov DG, Kitaura K (2007) Time-dependent density functional theory based upon the fragment molecular orbital method. J Chem Phys 127:104108

    PubMed  Google Scholar 

  98. Vendrell O, Gelabert R, Moreno M, Lluch JM (2004) Photoinduced proton transfer from the green fluorescent protein chromophore to a water molecule: analysis of the transfer coordinate. Chem Phys Lett 396:202–207

    CAS  Google Scholar 

  99. Nemukhin AV, Topol IA, Burt SK (2006) Electronic excitations of the chromophore from the fluorescent protein asFP595 in solutions. J Chem Theory Comput 2:292–299

    CAS  Google Scholar 

  100. Wanko M, Hoffmann M, Strodel P, Koslowski A, Thiel W, Neese F, Frauenheim T, Elstner M (2005) Calculating absorption shifts for retinal proteins: computational challenges. J Phys Chem B 109:3606–3615

    PubMed  CAS  Google Scholar 

  101. Altun A, Yokoyama S, Morokuma K (2008) Mechanism of spectral tuning going from retinal in vacuo to bovine rhodopsin and its mutants: multireference ab initio quantum mechanics/molecular mechanics studies. J Phys Chem B 112:16883–16890

    PubMed  CAS  Google Scholar 

  102. Kaila VRI, Send R, Sundholm D (2012) The effect of protein environment on photoexcitation properties of retinal. J Phys Chem B 116:2249–2258

    Google Scholar 

  103. Dewar MJS (1975) Quantum organic chemistry. Science 187:1037–1044

    PubMed  CAS  Google Scholar 

  104. Acevedo O, Jorgensen WL (2010) Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions. Acc Chem Res 43:142–151

    PubMed  CAS  Google Scholar 

  105. Warshel A, Weiss RM (1980) An empirical valence bond approach for comparing reactions in solutions and in enzymes. J Am Chem Soc 102:6218–6226

    CAS  Google Scholar 

  106. Schmitt UW, Voth GA (1998) Multistate empirical valence bond model for proton transport in water. J Phys Chem B 102:5547–5551

    CAS  Google Scholar 

  107. Jensen F, Norrby PO (2003) Transition states from empirical force fields. Theor Chem Acc 109:1–7

    CAS  Google Scholar 

  108. Pople JA, Santry DP, Segal GA (1965) Approximate self-consistent molecular orbital theory. I. Invariant procedures. J Chem Phys 43:S129–S135

    CAS  Google Scholar 

  109. Dewar MJS, Thiel W (1977) Ground states of molecules. 38. The MNDO method. Approximations and parameters. J Am Chem Soc 99:4899–4907

    CAS  Google Scholar 

  110. Dewar MJS, Zoebisch EG, Healy EF, Stewart JJP (1985) Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model. J Am Chem Soc 107:3902–3909

    CAS  Google Scholar 

  111. Stewart JJP (1989) Optimization of parameters for semiempirical methods 1. method. J Comput Chem 10:209–220

    CAS  Google Scholar 

  112. Stewart JJP (2007) Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements. J Mol Model 13:1173–1213

    PubMed  CAS  Google Scholar 

  113. Ridley J, Zerner M (1973) Intermediate neglect of differential overlap technique for spectroscopy—pyrrole and azines. Theor Chem Acc 32:111–134

    CAS  Google Scholar 

  114. Zheng XH, Stuchebrukhov AA (2003) Electron tunneling in proteins: implementation of ZINDO model for tunneling currents calculations. J Phys Chem B 107:6621–6628

    CAS  Google Scholar 

  115. Hayashi T, Stuchebrukhov AA (2010) Electron tunneling in respiratory complex I. Proc Natl Acad Sci USA 107:19157–19162

    PubMed  CAS  Google Scholar 

  116. Ball DM, Buda C, Gillespie AM, White DP, Cundari TR (2002) Can semiempirical quantum mechanics be used to predict the spin state of transition metal complexes? an application of De Novo prediction. Inorg Chem 41:152–156

    PubMed  CAS  Google Scholar 

  117. Gorelsky SI, Lever ABP (2001) Electronic structure and spectra of ruthenium diimine complexes by density functional theory and INDO/S. Comparison of the two methods. J Organomet Chem 635:187–196

    CAS  Google Scholar 

  118. Lalia-Kantouri M, Papadopoulos CD, Quirós M, Hatzidimitriou AG (2007) Synthesis and characterization of new Co(III) mixed-ligand complexes, containing 2-hydroxy-aryloximes and α-diimines. Crystal and molecular structure of [Co(saox)(bipy)2]Br. Polyhedron 26:1292–1302

    CAS  Google Scholar 

  119. Korth M, Pitoňák M, Řezáč J, Hobza P (2010) A transferable H-bonding correction for semiempirical quantum-chemical methods. J Chem Theory Comput 6:344–352

    CAS  Google Scholar 

  120. Fanfrlík J, Bronowska AK, Řezáč J, Přenosil O, Konvalinka J, Hobza P (2010) A reliable docking/scoring scheme based on the semiempirical quantum mechanical PM6-DH2 method accurately covering dispersion and H-bonding: HIV-1 protease with 22 ligands. J Phys Chem B 114:12666–12678

    PubMed  Google Scholar 

  121. Elstner M, Porezag D, Jungnickel G, Elsner J, Haugk M, Frauenheim T, Suhai S, Seifert G (1998) Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties. Phys Rev B 58:7260–7268

    CAS  Google Scholar 

  122. Niehaus TA, Suhai S, Della Sala F, Lugli P, Elstner M, Seifert G, Frauenheim T (2001) Tight-binding approach to time-dependent density-functional response theory. Phys Rev B 63:085108

    Google Scholar 

  123. Elstner M, Cui Q, Munih P, Kaxiras E, Frauenheim T, Karplus M (2003) Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: applications to structural and energetic analysis. J Comput Chem 24:565–581

    PubMed  CAS  Google Scholar 

  124. Cui Q, Elstner M, Karplus M (2002) A theoretical analysis of the proton and hydride transfer in liver alcohol dehydrogenase (LADH). J Phys Chem B 106:2721–2740

    CAS  Google Scholar 

  125. Liu HY, Elstner M, Kaxiras E, Frauenheim T, Hermans J, Yang W (2001) Quantum mechanics simulation of protein dynamics on long timescale. Protein Struct Funct Gen 44:484–489

    CAS  Google Scholar 

  126. Dunning Jr TH (1989) Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen. J Chem Phys 90:1007–1023

    CAS  Google Scholar 

  127. Hehre WJ, Stewart RF, Pople JA (1969) Self-consistent molecular-orbital methods. I. Use of gaussian expansions of slater-type atomic orbitals. J Chem Phys 51:2657–2664

    CAS  Google Scholar 

  128. Schäfer A, Horn H, Ahlrichs R (1992) Fully optimized contracted Gaussian basis sets for atoms Li to Kr. J Chem Phys 97:2571–2577

    Google Scholar 

  129. Schäfer A, Huber C, Ahlrichs R (1994) Fully optimized contracted Gaussian basis sets of triple zeta valence quality for atoms Li to Kr. J Chem Phys 100:5829–5835

    Google Scholar 

  130. Jensen F (2001) Polarization consistent basis sets: principles. J Chem Phys 115:9113–9125

    CAS  Google Scholar 

  131. Rappoport D, Furche F (2010) Property-optimized Gaussian basis sets for molecular response calculations. J Chem Phys 133:134105

    PubMed  Google Scholar 

  132. Manninen P, Vaara J (2006) Systematic Gaussian basis-set limit using completeness-optimized primitive sets. A case for magnetic properties. J Comput Chem 27:434–445

    CAS  Google Scholar 

  133. Jensen F (2010) The optimum contraction of basis sets for calculating spin-spin coupling constants. Theor Chem Acc 126:371–382

    CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Chemistry, University of Helsinki, Helsinki, Finland

    Mikael P. Johansson, Ville R. I. Kaila & Dage Sundholm

Authors
  1. Mikael P. Johansson
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ville R. I. Kaila
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Dage Sundholm
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Dage Sundholm .

Editor information

Editors and Affiliations

  1. DSIMB, UMR-S 665, INSERM, rue Alexandre Cabanel 6, Paris, 75015, France

    Luca Monticelli

  2. , Department of Applied Physics, Aalto University, Otakaari, AALTO, FI-00076, Finland

    Emppu Salonen

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media New York

About this protocol

Cite this protocol

Johansson, M.P., Kaila, V.R.I., Sundholm, D. (2013). Ab Initio, Density Functional Theory, and Semi-Empirical Calculations. In: Monticelli, L., Salonen, E. (eds) Biomolecular Simulations. Methods in Molecular Biology, vol 924. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-017-5_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-017-5_1

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-016-8

  • Online ISBN: 978-1-62703-017-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation