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The Linear Scaling Semiempirical LocalSCF Method and the Variational Finite LMO Approximation

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Linear-Scaling Techniques in Computational Chemistry and Physics

Abstract

When dealing with large biological systems speed determines the utility of the computational method. Therefore in order to bring quantum-mechanical (QM) methods to computational studies of biomolecules it is necessary to significantly reduce their resource requirement. In this light semiempirical QM methods are particularly encouraging because of their modest computational cost combined with potentially high accuracy. However, even semiempirical methods are frequently found to be too demanding for typical biological applications which require extensive conformational sampling. Significant speed up is obtained in the linear scaling LocalSCF method which is based on the variational finite localized molecular orbital (VFL) approximation. The VFL provides an approximate variational solution to the Hartree-Fock-Roothaan equation by seeking the density matrix and energy of the system in the basis of compact molecular orbitals using constrained atomic orbital expansion (CMO). Gradual release of the expansion constraints leads to determination of the theoretically most localized solution under small non-orthogonality of CMOs. Validation tests confirm good agreement of the LocalSCF method with matrix diagonalization results on partial atomic charges, dipole moment, conformational energies, and geometry gradients while the method exhibits low computer memory and CPU time requirements. We observe stable dynamics when using the LocalSCF method.

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Abbreviations

AM1:

Austin model 1

AO:

Atomic orbital

B3LYP:

Becke 3-term correlation, Lee-Yang-Parr exchange functional

CC:

Coupled cluster

CI:

Configuration interaction

CMO:

Constrained expansion molecular orbital

CPU:

Central processing unit

DFT:

Density functional theory;

HF/6-31G*:

Hartree-Fock method using Pople 6-31G* basis set

HOF:

Heat of formation

LMO:

Localized molecular orbital

LocalSCF:

Local self consistent field

MD:

Molecular dynamics

MO:

Molecular orbital

MP2:

Second-order Moller-Plesset perturbation theory

NDDO:

Neglect of diatomic differential overlap

NPT:

Constant number of particles, pressure, and temperature

NVE:

Constant number of particles, volume, and energy

NVT:

Constant number of particles, volume and temperature

PBC:

Periodic boundary condition

PM3:

Parametric method 3

PM5:

Parametric method 5

QM:

Quantum mechanics

RAM:

Random access memory

SBP:

Spherical boundary potential

SCF:

Self-consistent field

VFL:

Variational finite localized molecular orbital approximation

References

  1. Goedecker S (1999) Linear scaling electronic structure methods Rev Mod Phys 71:1085–1123

    Article  CAS  Google Scholar 

  2. Goedecker S, Scuseria GE (2003) Linear scaling electronic structure methods in chemistry and physics Comp Sci Eng 5:14–21

    Article  CAS  Google Scholar 

  3. McCammon JA, Gelin BR, Karplus M (1977) Dynamics of folded proteins Nature 267:585–590

    Article  CAS  Google Scholar 

  4. Anikin NA, Anisimov VM, Bugaenko VL et al. (2004) LocalSCF method for semiempirical quantum-chemical calculation of ultralarge biomolecules J Chem Phys 121:1266–1270

    Article  CAS  Google Scholar 

  5. Anisimov VM, Bugaenko VL (2009) QM/QM docking method based on the variational finite localized molecular orbital approximation J Comp Chem 30:784–798

    Article  CAS  Google Scholar 

  6. Szabo A, Ostlund NS (1996) Modern quantum chemistry, Dover, New York, NY

    Google Scholar 

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

    Article  CAS  Google Scholar 

  8. Hall GG (1951) The molecular orbital theory of chemical valency. VIII. A method of calculating ionization potentials Proc Roy Soc, London A205:541–552

    Google Scholar 

  9. Greengard LF (1988) The rapid evaluation of potential fields in particle systems, MIT Press, Cambridge, MA

    Google Scholar 

  10. Stewart JJP (1996) Application of localized molecular orbitals to the solution of semiempirical self-consistent field equations Int J Quant Chem 58:133–146

    Article  CAS  Google Scholar 

  11. Dixon SL, Merz KM Jr (1996) Semiempirical molecular orbital calculations with linear system size scaling J Chem Phys 104:6643–6649

    Article  CAS  Google Scholar 

  12. Lee T-S, York DM, Yang W (1996) Linear-scaling semiempirical quantum calculations for macromolecules J Chem Phys 105:2744–2750

    Article  CAS  Google Scholar 

  13. Yang W, Lee T-S (1995) A density-matrix divide-and-conquer approach for electronic structure calculations of large molecules J Chem Phys 103:5674–5678

    Article  CAS  Google Scholar 

  14. Anisimov VM, Bugaenko VL, Bobrikov VV (2006) Validation of linear scaling semiempirical localSCF method J Chem Theory Comput 2:1685–1692

    Article  CAS  Google Scholar 

  15. Tuckerman ME, Martyna GJ (2000) Understanding modern molecular dynamics: Techniques and applications J Phys Chem B 104:159–178

    Article  CAS  Google Scholar 

  16. Berman HM, Westbrook J, Feng Z, et al. (2000) The protein data bank Nucl Acids Res 28:235–242

    Article  CAS  Google Scholar 

  17. Bugaenko VL, Bobrikov VV, Andreyev AM, et al. (2005) LocalSCF, Fujitsu Ltd, Tokyo

    Google Scholar 

  18. White CA, Head-Gordon M (1994) Derivation and efficient implementation of the fast multipole method J Chem Phys 101:6593–6605

    Article  Google Scholar 

  19. Stewart JJP (1989) Optimization of parameters for semiempirical methods I. Method. J. Comp. Chem. 10:209–220

    Article  CAS  Google Scholar 

  20. Stewart JJP (2002) Mopac 2002, Fujitsu Ltd, Tokyo

    Google Scholar 

  21. 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

    Article  CAS  Google Scholar 

  22. Dewar MJS, Zoebisch EG, Healy EF, et al. (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

    Article  CAS  Google Scholar 

  23. Anisimov VM, Bugaenko VL, Cavasotto CN (2009) Quantum mechanical dynamics of charge transfer in ubiquitin in aqueous solution Chem Phys Chem 10:3194–3196

    Article  CAS  Google Scholar 

  24. Altoè P, Stenta M, Bottoni A, et al. (2007) A tunable QM/MM approach to chemical reactivity, structure and physico-chemical properties prediction Theor Chem Acc 118:219–240

    Article  Google Scholar 

  25. Hoover WG (1985) Canonical dynamics: Equilibrium phase-space distributions Phys Rev A 31:1695–1697

    Article  Google Scholar 

  26. Harvey SC, Tan RKZ, Cheatham III TE (1998) The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition J Comp Chem 19:726–740

    Article  CAS  Google Scholar 

  27. Hummer G, Gronbech-Jensen N, Neumann M (1998) Pressure calculation in polar and charged systems using Ewald summation: Results for the extended simple point charge model of water J Chem Phys 109:2791–2797

    Article  CAS  Google Scholar 

  28. Winkler RG (2002) Virial pressure of periodic systems with long range forces J Chem Phys 117:2449–2450

    Article  CAS  Google Scholar 

  29. Martyna GJ, Tuckerman ME, Tobias DJ et al. (1996) Explicit reversible integrators for extended systems dynamics Mol Phys 87:1117–1157

    Article  CAS  Google Scholar 

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Correspondence to Victor M. Anisimov .

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Panczakiewicz, A., Anisimov, V.M. (2011). The Linear Scaling Semiempirical LocalSCF Method and the Variational Finite LMO Approximation. In: Zalesny, R., Papadopoulos, M., Mezey, P., Leszczynski, J. (eds) Linear-Scaling Techniques in Computational Chemistry and Physics. Challenges and Advances in Computational Chemistry and Physics, vol 13. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-2853-2_15

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