Skip to main content
SpringerLink
Log in

Semi-empirical Quantum Mechanics Computer Simulations

  • Chapter
  • First Online:
Computer Simulations in Molecular Biology

Part of the book series: Scientific Computation ((SCIENTCOMP))

  • 280 Accesses

Abstract

In this chapter, we focus on the semi-empirical quantum mechanics approaches and their use in computer simulations.

The chapter aims to introduce the semi-empirical quantum mechanics models and their use in computer simulations.

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

Access this chapter

Log in via an institution
eBook
USD 16.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 109.99
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

Institutional subscriptions

References

  • R.C. Bingham, M.J.S. Dewar, D.H. Lo, Ground states of molecules. XXV. MINDO/3. An improved version of the MINDO semi-empirical SCFMO method. J. Am. Chem. Soc. 97, 1285–1293 (1975a)

    Google Scholar 

  • R.C. Bingham, M.J.S. Dewar, D.H. Lo, Ground states of molecules. XXVI. MINDO/3. Calculations for hydrocarbons. J. Am. Chem. Soc. 97, 1294–1301 (1975b)

    Google Scholar 

  • R.C. Bingham, M.J.S. Dewar, D.H. Lo, Ground states of molecules. XXVII. MINDO/3. Calculations for CHON species. J. Am. Chem. Soc. 97, 1302–1306 (1975c)

    Google Scholar 

  • R.C. Bingham, M.J.S. Dewar, D.H. Lo, Ground states of molecules. XXVIII. MINDO/3. Calculations for compounds containing carbon, hydrogen, fluorine and chlorine. J. Am. Chem. Soc. 97, 1307–1310 (1975d)

    Google Scholar 

  • M.J.S. Dewar, W. Thiel, A semiempirical model for the two-center repulsion integrals in the NDDO approximation. Theor. Chim. Acta 46, 89–104 (1976)

    Article  Google Scholar 

  • M.J.S. Dewar, W. Thiel, Ground states of molecules. 38. the MNDO method. Approximations and parameters. J. Am. Chem. Soc. 99, 4899–4907 (1977a)

    Google Scholar 

  • M.J.S. Dewar, W. Thiel, Ground states of molecules. 39. MNDO results for molecules containing hydrogen, carbon, nitrogen, and oxygen. J. Am. Chem. Soc. 99, 4907–4917 (1977b)

    Google Scholar 

  • M.J.S. Dewar, E.G. Zoebisch, E.F. Healy, J.J.P. Stewart, 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 (1985)

    Google Scholar 

  • P.O. Dral, X. Wu, L. Spörkel, A. Koslowski, W. Weber, R. Steiger, M. Scholten, W. Thiel, Semiempirical quantum-chemical orthogonalization-corrected methods: theory, implementation, and parameters. J. Chem. Theory Comput. 12, 1082–1096 (2016)

    Article  Google Scholar 

  • T. Husch, M. Reihe, Comprehensive analysis of the neglect of diatomic differential overlap approximation. J. Chem. Theory Comput. 14(10), 5169–5179 (2018)

    Article  Google Scholar 

  • T. Husch, A.C. Vaucher, M. Reiher, Semiempirical molecular orbital models based on the neglect of diatomic differential overlap approximation. Int. J. Quantum Chem. 118, e25799 (2018)

    Article  Google Scholar 

  • H. Kayi, AM1* parameters for gold. J. Mol. Model. 16, 1029–1038 (2010)

    Article  Google Scholar 

  • H. Kayi, T. Clark, AM1* parameters for copper and zinc. J. Mol. Model. 13, 965–979 (2007)

    Article  Google Scholar 

  • H. Kayi, T. Clark, AM1* parameters for vanadium and chromium. J. Mol. Model. 15, 1253–1269 (2009a)

    Google Scholar 

  • H. Kayi, T. Clark, AM1* parameters for bromine and iodine. J. Mol. Model. 15, 295–308 (2009b)

    Google Scholar 

  • H. Kayi, T. Clark, AM1* parameters for manganese and iron. J. Mol. Model. 16, 1109–1126 (2010a)

    Google Scholar 

  • H. Kayi, T. Clark, AM1* parameters for cobalt and nickel. J. Mol. Model. 16, 29–47 (2010b)

    Google Scholar 

  • H. Kayi, T. Clark, AM1* parameters for palladium and silver. J. Mol. Model. 11, 2585–2600 (2011)

    Article  Google Scholar 

  • M. Kolb, W. Thiel, Beyond the MNDO model: methodical considerations and numerical results. J. Comput. Chem. 14, 775–789 (1993)

    Article  Google Scholar 

  • M. Korth, Third-generation hydrogen-bonding corrections for semiempirical QM methods and force fields. J. Chem. Theory Comput. 6, 3808–3816 (2010)

    Article  Google Scholar 

  • A.R. Leach, Molecular Modelling, Principles and Applications, 2nd edn. (Prentice Hall, Pearson Education Limited, Edingburgh Gate, 2001)

    Google Scholar 

  • J.A. Pople, D.L. Beveridge, P.A. Dobosh, Approximate self-consistent molecular orbital theory. V Intermediate neglect of differential overlap. J. Chem. Phys. 47(6), 2026–2033 (1967)

    Google Scholar 

  • J.A. Pople, D.P. Santry, G.A. Segal, Approximate self-consistent molecular orbital theory. II Calculations with complete neglect of differential overlap. J. Chem. Phys. 43, 136 (1965a)

    Google Scholar 

  • J.A. Pople, D.P. Santry, G.A. Segal, Approximate self-consistent molecular orbital theory. I. Invariant procedures. J. Chem. Phys. 43(10), 129–135 (1965b)

    Google Scholar 

  • J.A. Pople, G.A. Segal, Approximate self-consistent molecular orbital theory. III CNDO results for ab\(_2\) and ab\(_3\) systems. J. Chem. Phys. 44(9), 3289–3296 (1966)

    Google Scholar 

  • J. Rezác, P. Hobza, Advanced corrections of hydrogen bonding and dispersion for semiempirical quantum mechanical methods. J. Chem. Theory Comput. 8, 141–151 (2012)

    Article  Google Scholar 

  • G.B. Rocha, R.O. Freire, A.M. Simas, J.J.P. Stewart, RM1: a reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I. J. Comput. Chem. 27, 1101–1111 (2006)

    Article  Google Scholar 

  • W.J. Stevens, H. Basch, M. Krauss, Compact effective potentials and efficient shared-exponent basis sets for the first- and second-row atoms. J. Chem. Phys. 81, 6026–6033 (1984)

    Article  ADS  Google Scholar 

  • J.J.P. Stewart, Optimization of parameters for semiempirical methods I. Method. J. Comput. Chem. 10, 209–220 (1989)

    Article  Google Scholar 

  • J.J.P. Stewart, Optimization of parameters for semiempirical methods IV: extension of MNDO, AM1, and PM3 to more main group elements. J. Mol. Model. 10, 155–164 (2004)

    Article  Google Scholar 

  • J.J.P. Stewart, Optimization of parameters for semiempirical methods V: modification of NDDO approximations and application to 70 elements. J. Mol. Model. 13, 1173–1213 (2007)

    Article  Google Scholar 

  • J.J.P. Stewart, Application of the PM6 method to modeling the solid state. J. Mol. Model. 14, 499–535 (2008)

    Article  Google Scholar 

  • J.J.P. Stewart, Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters. J. Mol. Model. 19, 1–32 (2012)

    Article  Google Scholar 

  • W. Thiel, A.A. Voityuk, Extension of the MNDO formalism to \(d\)-orbitals: integral approximations and preliminary numerical results. Theor. Chim. Acta 81, 391–404 (1991)

    Article  Google Scholar 

  • W. Thiel, A.A. Voityuk, Erratum: Extension of the MNDO formalism to \(d\)-orbitals: integral approximations and preliminary numerical results. Theor. Chim. Acta 93, 315 (1996)

    Google Scholar 

  • A.A. Voityuk, N. Rösch, AM1/d parameters for molybdenum. J. Phys. Chem. A 104, 4089–4094 (2000)

    Article  Google Scholar 

  • W. Weber, W. Thiel, Orthogonalization corrections for semiempirical methods. Theor. Chem. Acc. 103, 495–506 (2000)

    Article  Google Scholar 

  • P. Winget, T. Clark, AM1* parameters for aluminum, silicon, titanium and zirconium. J. Mol. Model. 11, 439–456 (2005)

    Article  Google Scholar 

  • P. Winget, A.H.C. Horn, C. Selcuki, B. Martin, T. Clark, AM1* parameters for phosphorus, sulfur and chlorine. J. Mol. Model. 9, 408–414 (2003)

    Article  Google Scholar 

  • X. Wu, P.O. Dral, A. Koslowski, W. Thiel, Big data analysis of ab initio molecular integrals in the neglect of diatomic differential overlap approximation. J. Comput. Chem. 40(4), 638–649 (2019)

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Computer Engineering, International Balkan University, Skopje, North Macedonia

    Hiqmet Kamberaj

Authors
  1. Hiqmet Kamberaj
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hiqmet Kamberaj .

Rights and permissions

Reprints and permissions

Copyright information

© 2023 The Author(s), under exclusive license to Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Kamberaj, H. (2023). Semi-empirical Quantum Mechanics Computer Simulations. In: Computer Simulations in Molecular Biology. Scientific Computation. Springer, Cham. https://doi.org/10.1007/978-3-031-34839-6_3

Download citation

Publish with us

Policies and ethics

Search

Navigation