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Ligorio RF, Rodrigues JL, Zuev A, Dos Santos LHR, Krawczuk A. Benchmark of a functional-group database for distributed polarizability and dipole moment in biomolecules. Phys Chem Chem Phys 2022; 24:29495-29504. [PMID: 36459116 DOI: 10.1039/d2cp04052b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The extraction of functional-group properties in condensed phases is very useful for predicting material behaviors, including those of biomaterials. For this reason, computational approaches based on partitioning schemes have been developed aiming at rapidly and accurately estimating properties from chemically meaningful building blocks. A comprehensive database of group polarizabilities and dipole moments is useful not only to predict the optical properties of biomacromolecules but also to improve molecular force fields focused on simulating biochemical processes. In this work we benchmark a database of distributed polarizabilities and dipole moments for functional groups extracted from a series of polypeptides. This allows reconstruction of a variety of relevant chemical environments. The accuracy of our database was tested to predict the electro-optical properties of larger peptides and also simpler amino acids for which density functional theory calculations at the M06-HF/aug-cc-pVDZ level of theory was chosen as the reference. This approach is reasonably accurate for the diagonal components of the polarizability tensor, with errors not larger than 15-20%. The anisotropy of the polarizability is predicted with smaller efficacy though. Solvent effects were included explicitly by surrounding the database entries by a box of water molecules whose distribution was optimized using the CHARMM force field.
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Affiliation(s)
- Raphael F Ligorio
- Institut für Anorganische Chemie, Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany.
| | - Jose L Rodrigues
- Departamento de Química, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos 6627, 31270-901 Belo Horizonte, MG, Brazil
| | - Anatoly Zuev
- Institut für Anorganische Chemie, Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany.
| | - Leonardo H R Dos Santos
- Departamento de Química, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos 6627, 31270-901 Belo Horizonte, MG, Brazil
| | - Anna Krawczuk
- Institut für Anorganische Chemie, Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany.
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2
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Jabłuszewska A, Krawczuk A, Dos Santos LHR, Macchi P. Accurate Modelling of Group Electrostatic Potential and Distributed Polarizability in Dipeptides. Chemphyschem 2020; 21:2155-2165. [DOI: 10.1002/cphc.202000441] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/23/2020] [Indexed: 12/28/2022]
Affiliation(s)
- Angelika Jabłuszewska
- Faculty of Chemistry Jagiellonian University in Krakow Gronostajowa 2 30-387 Krakow Poland
| | - Anna Krawczuk
- Faculty of Chemistry Jagiellonian University in Krakow Gronostajowa 2 30-387 Krakow Poland
| | - Leonardo H. R. Dos Santos
- Departamento de Química Universidade Federal de Minas Gerais Av. Antônio Carlos 6627 31270-901 Belo Horizonte MG Brazil
| | - Piero Macchi
- Department of Chemistry, Materials and Chemical Engineering Polytechnics of Milan Via Mancinelli 7 20131 Milan Italy
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Garcia J, Podeszwa R, Szalewicz K. SAPT codes for calculations of intermolecular interaction energies. J Chem Phys 2020; 152:184109. [PMID: 32414261 DOI: 10.1063/5.0005093] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Symmetry-adapted perturbation theory (SAPT) is a method for calculations of intermolecular (noncovalent) interaction energies. The set of SAPT codes that is described here, the current version named SAPT2020, includes virtually all variants of SAPT developed so far, among them two-body SAPT based on perturbative, coupled cluster, and density functional theory descriptions of monomers, three-body SAPT, and two-body SAPT for some classes of open-shell monomers. The properties of systems governed by noncovalent interactions can be predicted only if potential energy surfaces (force fields) are available. SAPT is the preferred approach for generating such surfaces since it is seamlessly connected to the asymptotic expansion of interaction energy. SAPT2020 includes codes for automatic development of such surfaces, enabling generation of complete dimer surfaces with a rigid monomer approximation for dimers containing about one hundred atoms. These codes can also be used to obtain surfaces including internal degrees of freedom of monomers.
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Affiliation(s)
- Javier Garcia
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, USA
| | - Rafał Podeszwa
- Institute of Chemistry, University of Silesia at Katowice, Szkolna 9, Katowice, Poland
| | - Krzysztof Szalewicz
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, USA
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Shahbaz M, Szalewicz K. Evaluation of methods for obtaining dispersion energies used in density functional calculations of intermolecular interactions. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2414-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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5
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Editorial: in memoriam János G. Ángyán (1956–2017). Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2364-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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6
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Misquitta AJ, Stone AJ. ISA-Pol: distributed polarizabilities and dispersion models from a basis-space implementation of the iterated stockholder atoms procedure. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2371-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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7
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Dehez F, Ángyán JG, Gutiérrez IS, Luque FJ, Schulten K, Chipot C. Modeling Induction Phenomena in Intermolecular Interactions with an Ab Initio Force Field. J Chem Theory Comput 2015; 3:1914-26. [PMID: 26636194 DOI: 10.1021/ct700156a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
One possible road toward the development of a polarizable potential energy function relies on the use of distributed polarizabilities derived from the induction energy mapped around the molecule. Whereas such polarizable models are expected to reproduce the signature induction energy with an appreciable accuracy, it is far from clear whether they will perform equally well in the context of intermolecular interactions. To address this issue, while pursuing the ultimate goal of a "plug-and-play"-like approach, polarizability models determined quantum mechanically and consisting of atomic isotropic dipole plus charge-flow polarizabilities were combined with the classical, nonpolarizable Charmm force field. Performance of the models was probed in the challenging test cases of cation-π binding and the association of a divalent calcium ion with water, where induction effects are envisioned to be considerable. Since brute force comparison of the binding energies estimated from the polarizable and the classical Charmm potential energy functions is not justified, the individual electrostatic and induction contributions of the force field were confronted to the corresponding terms of a symmetry-adapted perturbation theory (SAPT) expansion carried out with the 6-311++G(d,p) basis set. While the quantum-mechanical and the molecular-mechanical electrostatic and damped induction contributions agree reasonably well, overall reproduction of the binding energies is plagued by an underestimated repulsion that underlines the necessity of de novo parametrization of the classical 6-12 form of the van der Waals potential. Based on the SAPT expansion, new Lennard-Jones parameters were optimized, which, combined with the remainder of the polarizable force field, yield an improved reproduction of the target binding energies.
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Affiliation(s)
- François Dehez
- Equipe de dynamique des assemblages membranaires, UMR 7565 and Equipe de modélisation quantique et cristallographique, LCM3B, UMR 7036, Nancy Université, BP 239, 54506 Vandœuvre-lès-Nancy Cedex, France, Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avgda, Diagonal 643, Barcelona 08028, Spain, and Theoretical and Computational Biophysics Group, Beckman Institute, University of Illinois at Urbana [Formula: see text] Champaign, Urbana, Illinois 61801
| | - János G Ángyán
- Equipe de dynamique des assemblages membranaires, UMR 7565 and Equipe de modélisation quantique et cristallographique, LCM3B, UMR 7036, Nancy Université, BP 239, 54506 Vandœuvre-lès-Nancy Cedex, France, Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avgda, Diagonal 643, Barcelona 08028, Spain, and Theoretical and Computational Biophysics Group, Beckman Institute, University of Illinois at Urbana [Formula: see text] Champaign, Urbana, Illinois 61801
| | - Ignacio Soteras Gutiérrez
- Equipe de dynamique des assemblages membranaires, UMR 7565 and Equipe de modélisation quantique et cristallographique, LCM3B, UMR 7036, Nancy Université, BP 239, 54506 Vandœuvre-lès-Nancy Cedex, France, Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avgda, Diagonal 643, Barcelona 08028, Spain, and Theoretical and Computational Biophysics Group, Beckman Institute, University of Illinois at Urbana [Formula: see text] Champaign, Urbana, Illinois 61801
| | - F Javier Luque
- Equipe de dynamique des assemblages membranaires, UMR 7565 and Equipe de modélisation quantique et cristallographique, LCM3B, UMR 7036, Nancy Université, BP 239, 54506 Vandœuvre-lès-Nancy Cedex, France, Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avgda, Diagonal 643, Barcelona 08028, Spain, and Theoretical and Computational Biophysics Group, Beckman Institute, University of Illinois at Urbana [Formula: see text] Champaign, Urbana, Illinois 61801
| | - Klaus Schulten
- Equipe de dynamique des assemblages membranaires, UMR 7565 and Equipe de modélisation quantique et cristallographique, LCM3B, UMR 7036, Nancy Université, BP 239, 54506 Vandœuvre-lès-Nancy Cedex, France, Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avgda, Diagonal 643, Barcelona 08028, Spain, and Theoretical and Computational Biophysics Group, Beckman Institute, University of Illinois at Urbana [Formula: see text] Champaign, Urbana, Illinois 61801
| | - Christophe Chipot
- Equipe de dynamique des assemblages membranaires, UMR 7565 and Equipe de modélisation quantique et cristallographique, LCM3B, UMR 7036, Nancy Université, BP 239, 54506 Vandœuvre-lès-Nancy Cedex, France, Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avgda, Diagonal 643, Barcelona 08028, Spain, and Theoretical and Computational Biophysics Group, Beckman Institute, University of Illinois at Urbana [Formula: see text] Champaign, Urbana, Illinois 61801
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8
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Dos Santos LHR, Krawczuk A, Macchi P. Distributed Atomic Polarizabilities of Amino Acids and their Hydrogen-Bonded Aggregates. J Phys Chem A 2015; 119:3285-98. [DOI: 10.1021/acs.jpca.5b00069] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Leonardo H. R. Dos Santos
- Department
of Chemistry and Biochemistry, University of Bern, Freiestrasse
3, 3012 Bern, Switzerland
| | - Anna Krawczuk
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland
| | - Piero Macchi
- Department
of Chemistry and Biochemistry, University of Bern, Freiestrasse
3, 3012 Bern, Switzerland
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9
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Spherical tensor multipolar electrostatics and smooth particle mesh Ewald summation: a theoretical study. J Mol Model 2014; 20:2256. [DOI: 10.1007/s00894-014-2256-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 04/22/2014] [Indexed: 10/25/2022]
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10
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Rob F, Szalewicz K. Distributed molecular polarisabilities and asymptotic intermolecular interaction energies†. Mol Phys 2013. [DOI: 10.1080/00268976.2013.808770] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Fazle Rob
- a Department of Physics and Astronomy , University of Delaware , Newark , DE , 19716 , USA
| | - Krzysztof Szalewicz
- a Department of Physics and Astronomy , University of Delaware , Newark , DE , 19716 , USA
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11
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Affiliation(s)
- A. Heßelmann
- a Lehrstuhl für Theoretische Chemie , Universität Erlangen-Nürnberg , Erlangen , Germany
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12
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Krishtal A, Geldof D, Vanommeslaeghe K, Alsenoy CV, Geerlings P. Evaluating London Dispersion Interactions in DFT: A Nonlocal Anisotropic Buckingham–Hirshfeld Model. J Chem Theory Comput 2011; 8:125-34. [DOI: 10.1021/ct200718y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- A. Krishtal
- Department of Chemistry, University of Antwerp, Universiteitsplein 1, B2610 Antwerp, Belgium
- Fachbereich Chemie, Technische Universität Kaiserslautern, Erwin Schrödinger Straße, D-67663 Kaiserslautern, Germany
| | - D. Geldof
- Department of Chemistry, University of Antwerp, Universiteitsplein 1, B2610 Antwerp, Belgium
| | - K. Vanommeslaeghe
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-629, Baltimore, Maryland 21201, United States
| | - C. Van Alsenoy
- Department of Chemistry, University of Antwerp, Universiteitsplein 1, B2610 Antwerp, Belgium
| | - P. Geerlings
- Algemene Chemie, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
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13
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Liu RF, Ángyán JG, Dobson JF. Dispersion interaction in hydrogen-chain models. J Chem Phys 2011; 134:114106. [PMID: 21428606 DOI: 10.1063/1.3563596] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We have investigated the dispersion interaction in hydrogen chain models via density functional theory-based symmetry-adapted perturbation theory using the asymptotically corrected PBE0 energy functional. The quasimetallic and the insulating prototype systems were chosen to be hydrogen chains with equally and alternately spaced H(2) units, respectively. The dependence of the dispersion energy on the chain length for quasimetallic and insulating cases has been determined for two chains arranged either in pointing or in parallel geometries. The results are compared with those previously calculated from a continuum coupled-plasmon approach [Phys. Rev. B 77, 075436 (2008)]. The interaction energy has also been modeled by pairwise summations over short fragments of the chains, demonstrating the failure of the additivity principle for the quasimetallic case, while confirming that the additivity is a qualitatively reasonable hypothesis for the insulating case.
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Affiliation(s)
- Ru-Fen Liu
- CRM2, Institut Jean Barriol, Nancy University and CNRS, 54506 Vandoeuvre-lès-Nancy, France.
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14
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Sato T, Nakai H. Local response dispersion method. II. Generalized multicenter interactions. J Chem Phys 2010; 133:194101. [DOI: 10.1063/1.3503040] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15
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Sato T, Nakai H. Density functional method including weak interactions: Dispersion coefficients based on the local response approximation. J Chem Phys 2010; 131:224104. [PMID: 20001021 DOI: 10.1063/1.3269802] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
A new method to calculate the atom-atom dispersion coefficients in a molecule is proposed for the use in density functional theory with dispersion (DFT-D) correction. The method is based on the local response approximation due to Dobson and Dinte [Phys. Rev. Lett. 76, 1780 (1996)], with modified dielectric model recently proposed by Vydrov and van Voorhis [J. Chem. Phys. 130, 104105 (2009)]. The local response model is used to calculate the distributed multipole polarizabilities of atoms in a molecule, from which the dispersion coefficients are obtained by an explicit frequency integral of the Casimir-Polder type. Thus obtained atomic polarizabilities are also used in the damping function for the short-range singularity. Unlike empirical DFT-D methods, the local response dispersion (LRD) method is able to calculate the dispersion energy from the ground-state electron density only. It is applicable to any geometry, free from physical constants such as van der Waals radii or atomic polarizabilities, and computationally very efficient. The LRD method combined with the long-range corrected DFT functional (LC-BOP) is applied to calculations of S22 weakly bound complex set [Phys. Chem. Chem. Phys. 8, 1985 (2006)]. Binding energies obtained by the LC-BOP+LRD agree remarkably well with ab initio references.
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Affiliation(s)
- Takeshi Sato
- Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan
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16
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Abstract
First-principles derivation is given for the heuristic exchange-hole model of London dispersion forces by Becke and Johnson [J. Chem. Phys. 122, 154104 (2005)]. A one-term approximation is used for the dynamic charge density response function, and it is shown that a central nonempirical ingredient of the approximate nonexpanded dispersion energy is the charge density autocorrelation function, a two-particle property, related to the exchange-correlation hole. In the framework of a dipolar approximation of the Coulomb interaction around the molecular origin, one obtains the so-called Salem-Tang-Karplus approximation to the C(6) dispersion coefficient. Alternatively, by expanding the Coulomb interaction around the center of charge (centroid) of the exchange-correlation hole associated with each point in the molecular volume, a multicenter expansion is obtained around the centroids of electron localization domains, always in terms of the exchange-correlation hole. In order to get a formula analogous to that of Becke and Johnson, which involves the exchange-hole only, further assumptions are needed, related to the difficulties of obtaining the expectation value of a two-electron operator from a single determinant. Thus a connection could be established between the conventional fluctuating charge density model of London dispersion forces and the notion of the "exchange-hole dipole moment" shedding some light on the true nature of the approximations implicit in the Becke-Johnson model.
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Affiliation(s)
- János G Angyán
- Laboratoire de Cristallographie et de Modélisation des Matériaux Minéraux et Biologiques, UMR 7036, Faculté des Sciences, Nancy Université, Vandaeuvre-lès-Nancy, France
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17
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Price SL. Toward More Accurate Model Intermolecular Potentials for Organic Molecules. REVIEWS IN COMPUTATIONAL CHEMISTRY 2007. [DOI: 10.1002/9780470125915.ch4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
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18
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Sagui C, Pomorski P, Darden TA, Roland C. Ab initio calculation of electrostatic multipoles with Wannier functions for large-scale biomolecular simulations. J Chem Phys 2006; 120:4530-44. [PMID: 15268621 DOI: 10.1063/1.1644800] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
It has long been known that accurate electrostatics is a key issue for improving current force fields for large-scale biomolecular simulations. Typically, this calls for an improved and more accurate description of the molecular electrostatic potential, which eliminates the artifacts associated with current point charge-based descriptions. In turn, this involves the partitioning of the extended molecular charge distribution, so that charges and multipole moments can be assigned to different atoms. As an alternate to current approaches, we have investigated a charge partitioning scheme that is based on the maximally localized Wannier functions. This has the advantage of partitioning the charge, and placing it around the molecule in a chemically meaningful manner. Moreover, higher order multipoles may all be calculated without any undue numerical difficulties. Tests on isolated molecules and water dimers, show that the molecular electrostatic potentials generated by such a Wannier-function based approach are in excellent agreement with the density functional-based calculations.
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Affiliation(s)
- Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA.
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19
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Torheyden M, Jansen G. A new potential energy surface for the water dimer obtained from separate fits ofab initioelectrostatic, induction, dispersion and exchange energy contributions. Mol Phys 2006. [DOI: 10.1080/00268970600679188] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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20
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Sagui C, Pedersen LG, Darden TA. Towards an accurate representation of electrostatics in classical force fields: efficient implementation of multipolar interactions in biomolecular simulations. J Chem Phys 2005; 120:73-87. [PMID: 15267263 DOI: 10.1063/1.1630791] [Citation(s) in RCA: 179] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The accurate simulation of biologically active macromolecules faces serious limitations that originate in the treatment of electrostatics in the empirical force fields. The current use of "partial charges" is a significant source of errors, since these vary widely with different conformations. By contrast, the molecular electrostatic potential (MEP) obtained through the use of a distributed multipole moment description, has been shown to converge to the quantum MEP outside the van der Waals surface, when higher order multipoles are used. However, in spite of the considerable improvement to the representation of the electronic cloud, higher order multipoles are not part of current classical biomolecular force fields due to the excessive computational cost. In this paper we present an efficient formalism for the treatment of higher order multipoles in Cartesian tensor formalism. The Ewald "direct sum" is evaluated through a McMurchie-Davidson formalism [L. McMurchie and E. Davidson, J. Comput. Phys. 26, 218 (1978)]. The "reciprocal sum" has been implemented in three different ways: using an Ewald scheme, a particle mesh Ewald (PME) method, and a multigrid-based approach. We find that even though the use of the McMurchie-Davidson formalism considerably reduces the cost of the calculation with respect to the standard matrix implementation of multipole interactions, the calculation in direct space remains expensive. When most of the calculation is moved to reciprocal space via the PME method, the cost of a calculation where all multipolar interactions (up to hexadecapole-hexadecapole) are included is only about 8.5 times more expensive than a regular AMBER 7 [D. A. Pearlman et al., Comput. Phys. Commun. 91, 1 (1995)] implementation with only charge-charge interactions. The multigrid implementation is slower but shows very promising results for parallelization. It provides a natural way to interface with continuous, Gaussian-based electrostatics in the future. It is hoped that this new formalism will facilitate the systematic implementation of higher order multipoles in classical biomolecular force fields.
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Affiliation(s)
- Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
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21
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Tsiper EV. Polarization forces in water deduced from single molecule data. PHYSICAL REVIEW LETTERS 2005; 94:013204. [PMID: 15698080 DOI: 10.1103/physrevlett.94.013204] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2004] [Indexed: 05/14/2023]
Abstract
The intermolecular electrostatic and polarization interactions in water are determined using a minimal atomic multipole model constructed with distributed polarizabilities. Hydrogen bonding and other properties of water-water interactions are reproduced by only three multipoles mu(H), mu(O), and theta(O) and two polarizabilities alpha(O) and alpha(H), which characterize a single water molecule and are deduced from single-molecule data.
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Affiliation(s)
- E V Tsiper
- School of Computational Sciences, George Mason University, Fairfax, VA 22030, USA.
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22
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Hesselmann A, Jansen G, Schütz M. Density-functional theory-symmetry-adapted intermolecular perturbation theory with density fitting: A new efficient method to study intermolecular interaction energies. J Chem Phys 2005; 122:14103. [PMID: 15638638 DOI: 10.1063/1.1824898] [Citation(s) in RCA: 476] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The previously developed DFT-SAPT approach, which combines symmetry-adapted intermolecular perturbation theory (SAPT) with a density-functional theory (DFT) representation of the monomers, has been implemented by using density fitting of two-electron objects. This approach, termed DF-DFT-SAPT, scales with the fifth power of the molecular size and with the third power upon increase of the basis set size for a given dimer, thus drastically reducing the cost of the conventional DFT-SAPT method. The accuracy of the density fitting approximation has been tested for the ethyne dimer. It has been found that the errors in the interaction energies due to density fitting are below 10(-3) kcal/mol with suitable auxiliary basis sets and thus one or two orders of magnitude smaller than the errors due to the use of a limited atomic orbital basis set. An investigation of three prominent structures of the benzene dimer, namely, the T shaped, parallel displaced, and sandwich geometries, employing basis sets of up to augmented quadruple-zeta quality shows that DF-DFT-SAPT outperforms second-order Moller-Plesset theory (MP2) and gives total interaction energies which are close to the best estimates inferred from combining the results of MP2 and coupled-cluster theory with single, double, and perturbative triple excitations.
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Affiliation(s)
- A Hesselmann
- Theoretische Organische Chemie, Institut für Organische Chemie, Universität Duisburg-Essen, Campus Essen, Universitätsstrasse 5, D-45117 Essen, Germany.
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23
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Chipot C, Ángyán JG. Continuing challenges in the parametrization of intermolecular force fields. Towards an accurate description of electrostatic and induction terms. NEW J CHEM 2005. [DOI: 10.1039/b414280m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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in het Panhuis M, Munn RW, Popelier PLA. Distributed polarizability analysis for para-nitroaniline and meta-nitroaniline: Functional group and charge-transfer contributions. J Chem Phys 2004; 120:11479-86. [PMID: 15268182 DOI: 10.1063/1.1752879] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Topological partitioning of electronic properties is used to investigate the polarizability of para-nitroaniline and meta-nitroaniline. The distributed polarizabilities for atoms are combined into total local or generalized distributed contributions for the amino, ring, and nitro functional groups; generalized distributed group contributions have not been calculated before. The local group contributions are transferable between the two molecules only when charge transfer is suppressed, but the generalized distributed contributions prove surprisingly similar in the two molecules, apparently because they treat charge-transfer contributions explicitly.
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Affiliation(s)
- M in het Panhuis
- Department of Physics, the University of Texas at Dallas, Richardson, Texas 75083, USA.
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Żuchowski PS, Bussery-Honvault B, Moszynski R, Jeziorski B. Dispersion interaction of high-spin open-shell complexes in the random phase approximation. J Chem Phys 2003. [DOI: 10.1063/1.1620496] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Angyán JG, Chipot C, Dehez F, Hättig C, Jansen G, Millot C. OPEP: a tool for the optimal partitioning of electric properties. J Comput Chem 2003; 24:997-1008. [PMID: 12720321 DOI: 10.1002/jcc.10236] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
OPEP is a suite of FORTRAN programs targeted at the optimal partitioning of molecular electric properties. It includes an interactive module for the construction of Cartesian grids of points, on which either the molecular electrostatic potential or the induction energy is mapped. The generation of distributed multipoles and polarizabilities is achieved using either the formalism of the normal equations of the least-squares problem, which restates the fitting procedure in terms of simple matrix operations, or a statistical approach, which provides a pictorial description of the distributed models of multipoles and polarizabilities, thereby allowing the pinpointing of pathological cases. Molecular symmetry is accounted for by means of local atomic frames, which are generated in an automated fashion. A Tcl/Tk graphical user interface wraps the suite of programs, thereby making OPEP a user-friendly package for building models of distributed multipoles and polarizabilities. OPEP is an open-source suite of programs distributed free of charge under the GNU general public license (GPL) at http://www.lctn.uhp-nancy.fr/Opep.
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Affiliation(s)
- János G Angyán
- Equipe de chimie et biochimie théorique, Unité Mixte de Recherche CNRS/UHP 7565, Institut nancéien de chimie moléculaire, Université Henri Poincaré--Nancy I, B.P. 239, 54506 Vandoeuvre-lès-Nancy, France
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Matta CF. Application of the quantum theory of atoms in molecules to selected physico-chemical and biophysical problems: focus on correlation with experiment. J Comput Chem 2003; 24:453-63. [PMID: 12594788 DOI: 10.1002/jcc.10208] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This article reviews how the quantum theory of atoms in molecules (QTAIM) can be used to predict experimental physico-chemical properties of molecules of biologic interest: the amino acids, the polycyclic aromatic hydrocarbons (PAH), and the opiates, for example, morphine and PEO. The predicted experimental properties are as diverse as the partial molar volumes, the free energies of hydration, the second code-letter in the genetic code, the resonance energies, and the proton spin-spin coupling constants. Recent examples of the utilization of QTAIM to construct excellent statistical models (with squared correlation coefficients (r(2)) > 0.9) correlating properties of the electron density and of the pair density to experiment are reviewed. Some new results on the solvent effects on electron delocalization are also presented.
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Affiliation(s)
- Chérif F Matta
- Lash Miller Chemical Laboratories, Chemistry Department, University of Toronto, 80 Saint George Street, Toronto, Ontario, Canada M5S 3H6.
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in het Panhuis M, Popelier PLA, Munn RW, Ángyán JG. Distributed polarizability of the water dimer: Field-induced charge transfer along the hydrogen bond. J Chem Phys 2001. [DOI: 10.1063/1.1361247] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Engkvist O, Astrand PO, Karlström G. Accurate Intermolecular Potentials Obtained from Molecular Wave Functions: Bridging the Gap between Quantum Chemistry and Molecular Simulations. Chem Rev 2000; 100:4087-108. [PMID: 11749341 DOI: 10.1021/cr9900477] [Citation(s) in RCA: 153] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- O Engkvist
- Department of Theoretical Chemistry, Chemical Centre, University of Lund, P.O.B. 124, S-221 00 Lund, Sweden
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Kosov DS, Popelier PLA. Convergence of the multipole expansion for electrostatic potentials of finite topological atoms. J Chem Phys 2000. [DOI: 10.1063/1.1288384] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Matta CF, Bader RF. An atoms-in-molecules study of the genetically-encoded amino acids: I. Effects of conformation and of tautomerization on geometric, atomic, and bond properties. Proteins 2000; 40:310-29. [PMID: 10842344 DOI: 10.1002/(sici)1097-0134(20000801)40:2<310::aid-prot110>3.0.co;2-a] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The theory of Atoms-In-Molecules (AIM) is a partitioning of the real space of a molecule into disjoint atomic constituents as determined by the topology of the electron density, rho(r). This theory identifies an atom in a molecule with a quantum mechanical open system and, consequently, all of the atom's properties are unambiguously defined. AIM recovers the basic empirical cornerstone of chemistry: that atoms and functional groups possess characteristic and additive properties that in many cases exhibit a remarkable transferability between different molecules. As a result, the theory enables the theoretical synthesis of a large molecule and the prediction of its properties by joining fragments that are predetermined as open systems. The present article is the first of a series (in preparation) that explore this possibility for polypeptides by determining the transferability of the building blocks: the amino acid residues. Transferability of group properties requires transferability of the electron density rho(r), which in turn requires the transferability of the geometric parameters. This article demonstrates that these parameters are conformation-insensitive for a representative amino acid, leucine, and that the atomic and bond properties exhibit a corresponding transferability. The effects of hydrogen bonding are determined and a set of geometrical conditions for the occurrence of such bonding is identified. The effects of transforming neutral leucine into its zwitter-ionic form on its atomic and bond properties are shown to be localized primarily to the sites of ionization.
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Affiliation(s)
- C F Matta
- Chemistry Department, McMaster University, Hamilton, Ontario, Canada
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Affiliation(s)
- D. S. Kosov
- Department of Chemistry, UMIST, Manchester, M60 1QD, England
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Reis H, Papadopoulos MG, Hättig C, Ángyán JG, Munn RW. Distributed first and second order hyperpolarizabilities: An improved calculation of nonlinear optical susceptibilities of molecular crystals. J Chem Phys 2000. [DOI: 10.1063/1.481217] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Mo Y, Gao J, Peyerimhoff SD. Energy decomposition analysis of intermolecular interactions using a block-localized wave function approach. J Chem Phys 2000. [DOI: 10.1063/1.481185] [Citation(s) in RCA: 309] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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SOETENS JEANCHRISTOPHE, JANSEN GEORG, MILLOT CLAUDE. Molecular dynamics simulation of liquid CCl4with a new polarizable potential model. Mol Phys 1999. [DOI: 10.1080/00268979909483042] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Soetens JC, Millot C, Chipot C, Jansen G, Ángyán JG, Maigret B. Effect of Polarizability on the Potential of Mean Force of Two Cations. The Guanidinium−Guanidinium Ion Pair in Water. J Phys Chem B 1997. [DOI: 10.1021/jp972113j] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jean-Christophe Soetens
- Laboratoire de Chimie Théorique, Université Henri-Poincaré-Nancy I, Unité de Recherche Associée au CNRS no 510, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France, and Institut für Theoretische Chemie, Heinrich-Heine Universität Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Claude Millot
- Laboratoire de Chimie Théorique, Université Henri-Poincaré-Nancy I, Unité de Recherche Associée au CNRS no 510, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France, and Institut für Theoretische Chemie, Heinrich-Heine Universität Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Christophe Chipot
- Laboratoire de Chimie Théorique, Université Henri-Poincaré-Nancy I, Unité de Recherche Associée au CNRS no 510, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France, and Institut für Theoretische Chemie, Heinrich-Heine Universität Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Georg Jansen
- Laboratoire de Chimie Théorique, Université Henri-Poincaré-Nancy I, Unité de Recherche Associée au CNRS no 510, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France, and Institut für Theoretische Chemie, Heinrich-Heine Universität Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - János G. Ángyán
- Laboratoire de Chimie Théorique, Université Henri-Poincaré-Nancy I, Unité de Recherche Associée au CNRS no 510, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France, and Institut für Theoretische Chemie, Heinrich-Heine Universität Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Bernard Maigret
- Laboratoire de Chimie Théorique, Université Henri-Poincaré-Nancy I, Unité de Recherche Associée au CNRS no 510, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France, and Institut für Theoretische Chemie, Heinrich-Heine Universität Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
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