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Atomic Spectral Methods for Ab Initio Molecular Electronic Energy Surfaces: Transitioning From Small-Molecule to Biomolecular-Suitable Approaches

Mills, Jeffrey D. and Ben-Nun, Michal and Rollin, Kyle and Bromley, Michael W. J. and Li, Jiabo and Hinde, Robert J. and Winstead, Carl L. and Sheehy, Jeffrey A. and Boatz, Jerry A. and Langhoff, Peter W. (2016) Atomic Spectral Methods for Ab Initio Molecular Electronic Energy Surfaces: Transitioning From Small-Molecule to Biomolecular-Suitable Approaches. Journal of Physical Chemistry B, 120 (33). pp. 8321-8337. ISSN 1520-6106. http://resolver.caltech.edu/CaltechAUTHORS:20160609-151403493

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Abstract

Continuing attention has addressed incorportation of the electronically dynamical attributes of biomolecules in the largely static first-generation molecular-mechanical force fields commonly employed in molecular-dynamics simulations. We describe here a universal quantum-mechanical approach to calculations of the electronic energy surfaces of both small molecules and large aggregates on a common basis which can include such electronic attributes, and which also seems well-suited to adaptation in ab initio molecular-dynamics applications. In contrast to the more familiar orbital-product-based methodologies employed in traditional small-molecule computational quantum chemistry, the present approach is based on an “ex-post-facto” method in which Hamiltonian matrices are evaluated prior to wave function antisymmetrization, implemented here in the support of a Hilbert space of orthonormal products of many-electron atomic spectral eigenstates familiar from the van der Waals theory of long-range interactions. The general theory in its various forms incorporates the early semiempirical atoms- and diatomics-in-molecules approaches of Moffitt, Ellison, Tully, Kuntz, and others in a comprehensive mathematical setting, and generalizes the developments of Eisenschitz, London, Claverie, and others addressing electron permutation symmetry adaptation issues, completing these early attempts to treat van der Waals and chemical forces on a common basis. Exact expressions are obtained for molecular Hamiltonian matrices and for associated energy eigenvalues as sums of separate atomic and interaction-energy terms, similar in this respect to the forms of classical force fields. The latter representation is seen to also provide a long-missing general definition of the energies of individual atoms and of their interactions within molecules and matter free from subjective additional constraints. A computer code suite is described for calculations of the many-electron atomic eigenspectra and the pairwise-atomic Hamiltonian matrices required for practical applications. These matrices can be retained as functions of scalar atomic-pair separations and employed in assembling aggregate Hamiltonian matrices, with Wigner rotation matrices providing analytical representations of their angular degrees of freedom. In this way, ab initio potential energy surfaces are obtained in the complete absence of repeated evaluations and transformations of the one- and two-electron integrals at different molecular geometries required in most ab inito molecular calculations, with large Hamiltonian matrix assembly simplified and explicit diagonalizations avoided employing partitioning and Brillouin–Wigner or Rayleigh–Schrödinger perturbation theory. Illustrative applications of the important components of the formalism, selected aspects of the scaling of the approach, and aspects of “on-the-fly” interfaces with Monte Carlo and molecular-dynamics methods are described in anticipation of subsequent applications to biomolecules and other large aggregates.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1021/acs.jpcb.6b02021DOIArticle
http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b02021PublisherArticle
http://pubs.acs.org/doi/full/10.1021/acs.jpcb.6b02021PublisherArticle
Additional Information:© 2016 American Chemical Society. Received: February 26, 2016. Revised: May 4, 2016. Special Issue: J. Andrew McCammon Festschrift. The financial support of the Air Force Research Laboratory (FA9300-09-C-2001, FA9300-07-M-301), the US Air Force Office of Scientific Research (F07-206-0375), the European Office of Aerospace Research and Development (FA8655-09-1-3069), the American Society of Engineering Education, and the National Research Council of the National Academy of Science is gratefully acknowledged. Access to computational facilities was provided by the National Science Foundation under the auspices of TeraGrid and XSEDE allocations. We acknowledge the valuable assistance and advice provided by Professors R. Lopez and J. F. Rico and their co-workers at various stages of the investigation, and thank Mr. W. Kalliomaa and Dr. Steve Rodgers of AFRL for continuing encouragement and support. It is a pleasure to thank Professor J. A. McCammon and other colleagues at the University of California San Diego for their hospitality and support in the Department of Chemistry and Biochemistry. The authors declare no competing financial interest.
Funders:
Funding AgencyGrant Number
Air Force Research LaboratoryFA9300-09-C-2001
Air Force Research LaboratoryFA9300-07-M-301
Air Force Office of Scientific Research (AFOSR)F07-206-0375
European Office of Aerospace Research and DevelopmentFA8655-09-1-3069
American Society for Engineering EducationUNSPECIFIED
National Research Council (USA)UNSPECIFIED
Record Number:CaltechAUTHORS:20160609-151403493
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20160609-151403493
Official Citation:Atomic Spectral Methods for Ab Initio Molecular Electronic Energy Surfaces: Transitioning From Small-Molecule to Biomolecular-Suitable Approaches Jeffrey D. Mills, Michal Ben-Nun, Kyle Rollin, Michael W. J. Bromley, Jiabo Li, Robert J. Hinde, Carl L. Winstead, Jeffrey A. Sheehy, Jerry A. Boatz, and Peter W. Langhoff The Journal of Physical Chemistry B 2016 120 (33), 8321-8337 DOI: 10.1021/acs.jpcb.6b02021
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:67804
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:10 Jun 2016 18:52
Last Modified:11 Oct 2016 18:28

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