title: Atomic Spectral Methods for Ab Initio Molecular Electronic Energy Surfaces: Transitioning From Small-Molecule to Biomolecular-Suitable Approaches.
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.
authors.affiliation: Air Force Research Laboratory , 10 East Saturn Boulevard, Edwards AFB, California 93524-7680, United States.
authors.forename: Jeffrey D
authors.initials: JD
authors.lastname: Mills
authors.affiliation: Predictive Science, Inc. , 9990 Mesa Rim Road #170, San Diego, California 92121, United States.
authors.forename: Michal
authors.initials: M
authors.lastname: Ben-Nun
authors.affiliation: Northrup Grumman Corporation , 1 Rancho Carmel Drive, San Diego, California 92128, United States.
authors.forename: Kyle
authors.initials: K
authors.lastname: Rollin
authors.affiliation: School of Mathematics and Physics, The University of Queensland , Brisbane, Queensland 4072, Australia.
authors.forename: Michael W J
authors.initials: MW
authors.lastname: Bromley
authors.affiliation: Accelrys Inc. , 10188 Telesis Court #100, San Diego, California 92121-4779, United States.
authors.forename: Jiabo
authors.initials: J
authors.lastname: Li
authors.affiliation: Department of Chemistry, University of Tennessee , Knoxville, Tennessee 37996-1600, United States.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Hinde
authors.affiliation: A.A. Noyes Laboratory of Chemical Physics, California Institute of Technology , Pasadena, California 91125, United States.
authors.forename: Carl L
authors.initials: CL
authors.lastname: Winstead
authors.affiliation: NASA Headquarters , 300 E Street SW, Suite 5R30, Washington, DC 201546, United States.
authors.forename: Jeffrey A
authors.initials: JA
authors.lastname: Sheehy
authors.affiliation: Air Force Research Laboratory , 10 East Saturn Boulevard, Edwards AFB, California 93524-7680, United States.
authors.forename: Jerry A
authors.initials: JA
authors.lastname: Boatz
authors.affiliation: Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, MS 0365, La Jolla, California 92093-0365, United States.
authors.forename: Peter W
authors.initials: PW
authors.lastname: Langhoff
mesh_terms: D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D011789:Quantum Theory