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Mills JD, Ben-Nun M, Rollin K, Bromley MWJ, Li J, Hinde RJ, Winstead CL, Sheehy JA, Boatz JA, Langhoff PW. Atomic Spectral Methods for Ab Initio Molecular Electronic Energy Surfaces: Transitioning From Small-Molecule to Biomolecular-Suitable Approaches. J Phys Chem B 2016; 120:8321-37. [PMID: 27232159 DOI: 10.1021/acs.jpcb.6b02021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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.
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Affiliation(s)
- Jeffrey D Mills
- Air Force Research Laboratory , 10 East Saturn Boulevard, Edwards AFB, California 93524-7680, United States
| | - Michal Ben-Nun
- Predictive Science, Inc. , 9990 Mesa Rim Road #170, San Diego, California 92121, United States
| | - Kyle Rollin
- Northrup Grumman Corporation , 1 Rancho Carmel Drive, San Diego, California 92128, United States
| | - Michael W J Bromley
- School of Mathematics and Physics, The University of Queensland , Brisbane, Queensland 4072, Australia
| | - Jiabo Li
- Accelrys Inc. , 10188 Telesis Court #100, San Diego, California 92121-4779, United States
| | - Robert J Hinde
- Department of Chemistry, University of Tennessee , Knoxville, Tennessee 37996-1600, United States
| | - Carl L Winstead
- A.A. Noyes Laboratory of Chemical Physics, California Institute of Technology , Pasadena, California 91125, United States
| | - Jeffrey A Sheehy
- NASA Headquarters , 300 E Street SW, Suite 5R30, Washington, DC 201546, United States
| | - Jerry A Boatz
- Air Force Research Laboratory , 10 East Saturn Boulevard, Edwards AFB, California 93524-7680, United States
| | - Peter W Langhoff
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, MS 0365, La Jolla, California 92093-0365, United States
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Calvo F, Pahl E, Schwerdtfeger P, Spiegelman F. Diatomics-in-Molecules Modeling of Many-Body Effects on the Structure and Thermodynamics of Mercury Clusters. J Chem Theory Comput 2012; 8:639-48. [DOI: 10.1021/ct200846a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- F. Calvo
- LASIM, CNRS
UMR 5579, Université
de Lyon, 43 Bd. du 11 Novembre 1918, F69622 Villeurbanne Cedex, France
| | - E. Pahl
- Centre for Theoretical Chemistry
and Physics, Institute of Natural Science, Massey University Albany,
Private Bag 102904, North Shore City, 0745 Auckland, New Zealand
| | - P. Schwerdtfeger
- Centre for Theoretical Chemistry
and Physics, New Zealand Institute for Advanced Study, Massey University
Albany, Private Bag 102904, North Shore City, 0745 Auckland, New Zealand
and Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str.
D35032 Marburg, Germany
| | - F. Spiegelman
- LCPQ, CNRS and Université
de Toulouse (UPS), 118 Route de Narbonne, F31062 Toulouse Cedex, France
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Piecuch P, Kowalski K, Pimienta ISO, Mcguire MJ. Recent advances in electronic structure theory: Method of moments of coupled-cluster equations and renormalized coupled-cluster approaches. INT REV PHYS CHEM 2010. [DOI: 10.1080/0144235021000053811] [Citation(s) in RCA: 210] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Ritschel T, Zülicke L, Kuntz PJ. Cationic Van-der-Waals Complexes: Theoretical Study of Ar2H+ Structure and Stability. Z PHYS CHEM 2009. [DOI: 10.1524/zpch.218.4.377.29196] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
The electronic and geometric structure, stability and molecular properties of the cationic van-der-Waals complex Ar2H+ in its ground electronic state are studied by means of two ab-initio quantum-chemical approaches: conventional configuration interaction (multi-reference and coupled-cluster methods) and a diatomics-in-molecules model with ab-initio input data. To ensure consistency between the two approaches, one and the same one-electron atomic basis set (aug-cc-pVTZ by Dunning) is employed in both. The topography of the ground-state potential-energy surface is examined with respect to the nature of the binding and the stability of structures corresponding to stationary points. In accordance with most earlier theoretical work, there are two local minima at linear arrangements: a strongly bound centro-symmetric moiety, (Ar–H–Ar)+, and a weakly bound van-der-Waals complex, Ar···ArH+. These are separated by a low barrier. Only the centro-symmetric molecule is significantly stable (D
e = 0.68eV) against fragmentation into Ar + ArH+ and should have structural and dynamical relevance. A fairly simple diatomics-in-molecules model taking into account only the few lowest electronic fragment states yields a qualitatively correct description of the ground state but shows quantitative deviations from the more accurate configuration-interaction data in detail. Nevertheless, it should provide a good starting point for the treatment of larger complexes Ar
n
H+ with n > 2.
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Cooper DL, Gerratt J, Raimondi M. Modern Valence Bond Theory. ADVANCES IN CHEMICAL PHYSICS 2007. [DOI: 10.1002/9780470142943.ch6] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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Affiliation(s)
- R. Polák
- a J. Heyrovský Institute of Physical Chemistry and Electrochemistry, Czechoslovak Academy of Sciences , 121 38 , Prague 2 , Czechoslovakia
| | - P.J. Kuntz
- b Hahn-Meitner-Institut Berlin, Bereich Strahlenchemie , Glienicker Str. 100, D-1000 , Berlin 39 , F.R. Germany
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Affiliation(s)
- R. Polák
- a J. Heyroský Institute of Physical Chemistry and Electrochemistry, Czechoslovak Academy of Sciences , Dolejškova 3, 182 23 , Prague 8 , Czechoslovakia
| | - J. Vojtík
- a J. Heyroský Institute of Physical Chemistry and Electrochemistry, Czechoslovak Academy of Sciences , Dolejškova 3, 182 23 , Prague 8 , Czechoslovakia
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McGuire MJ, Piecuch P, Kowalski K, Kucharski SA, Musiał M. Renormalized Coupled-Cluster Calculations of Reactive Potential Energy Surfaces: The BeFH System. J Phys Chem A 2004. [DOI: 10.1021/jp048880h] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael J. McGuire
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, and Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland
| | - Piotr Piecuch
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, and Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland
| | - Karol Kowalski
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, and Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland
| | - Stanisław A. Kucharski
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, and Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland
| | - Monika Musiał
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, and Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland
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McGuire MJ, Kowalski K, Piecuch P. Renormalized coupled-cluster calculations of reactive potential energy surfaces: A comparison of the CCSD(T), renormalized CCSD(T), and full configuration interaction results for the collinear BeFH system. J Chem Phys 2002. [DOI: 10.1063/1.1494797] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Gadea F, Kuntz P. Application of effective hamiltonian theory to the method of diatomics-in-molecules. Mol Phys 1988. [DOI: 10.1080/00268978800100031] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Polak R, Paidarova I, Kuntz PJ. Diatomics‐in‐molecules models for H2O and H2O−. II. A self‐consistent description of the1A′,1A″,3A′, and3A″states of H2O. J Chem Phys 1987. [DOI: 10.1063/1.453074] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Perturbation non-hermitean DIM scheme for calculations of the width of autoionizing states of collision systems. Chem Phys 1986. [DOI: 10.1016/0301-0104(86)80166-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Roach AC, Kuntz PJ. Unified large basis set diatomics‐in‐molecules models for ground and excited states of H3. J Chem Phys 1986. [DOI: 10.1063/1.450582] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Diatomics-in-molecules potential energy surfaces for the collision-induced dissociation of excited by helium atoms. Chem Phys 1985. [DOI: 10.1016/0301-0104(85)80110-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Kuntz PJ. A valence-bond diatomics-in-molecules model for the formation of Na+ and Na2+ ions from the interaction of excited sodium atoms with a tungsten surface. Chem Phys 1985. [DOI: 10.1016/0301-0104(85)80056-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Polák R, Paidarová I, Kuntz PJ. Diatomics‐in‐molecules models for H2O and H2O−. I. Valence bond diatomic fragment matrices. J Chem Phys 1985. [DOI: 10.1063/1.448331] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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On the diatomic-fragment data calculation for the diatomics-in-molecules method. Applications to NH2 and NH3. Chem Phys 1984. [DOI: 10.1016/0301-0104(84)85052-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Paidarová I, Vojtík J. Diatomics-in-molecules model for penning ionization in the He(2 1S)-H2 system. Chem Phys 1984. [DOI: 10.1016/0301-0104(84)85207-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Ellison FO. Scaled diatomics‐in‐molecules (SDIM) theory. I. General theory and preliminary applications to H3and H4. J Chem Phys 1983. [DOI: 10.1063/1.445370] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Kuntz P, Chang C. Semi-empirical corrections to the mixing coefficients for the diatomics-in-molecules method. Chem Phys 1983. [DOI: 10.1016/0301-0104(83)85009-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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