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Jara-Cortés J, Matta CF, Hernández-Trujillo J. A fast approximate extension of the interacting quantum atoms energy decomposition to excited states. J Comput Chem 2022; 43:1068-1078. [PMID: 35470908 DOI: 10.1002/jcc.26863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/25/2022] [Accepted: 03/23/2022] [Indexed: 11/11/2022]
Abstract
An approach is developed for the fast calculation of the interacting quantum atoms energy decomposition (IQA) from the information contained in the first order reduced density matrix only. The proposed methodology utilizes an approximate exchange-correlation density from Density Matrix Functional Theory without the need to evaluate the correlation-exchange contribution directly. Instead, weight factors are estimated to decompose the exact Vxc into atomic and pairwise contributions. In this way, the sum of the IQA contributions recovers the energy obtained from the electronic structure calculation. This method can, hence, be applied to obtain atomic contributions in excited states on the same footing as in their ground states using any method that delivers the reduced first-order density matrix. In this way, one can locate chromophores from first principles quantum chemical calculations. Test calculations on the ground and excited states of a set of small molecules indicate that the scaled atomic contributions reproduce vertical electronic transition energies calculated exactly. This approach may be useful to extend the applicability of the IQA approach in the study of large photochemical systems especially when the calculations of the second order reduced density matrices is prohibitive or not possible.
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Affiliation(s)
- Jesús Jara-Cortés
- Unidad Académica de Ciencias Básicas e Ingenierías, Universidad Autónoma de Nayarit, Tepic, Mexico
| | - Chérif F Matta
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, Canada
| | - Jesús Hernández-Trujillo
- Departamento de Física y Química Teórica, Facultad de Química, UNAM. Circuito Escolar, Ciudad Universitaria, Mexico City, Mexico
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2
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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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3
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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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Geldof D, Krishtal A, Geerlings P, Van Alsenoy C. Partitioning of Higher Multipole Polarizabilities: Numerical Evaluation of Transferability. J Phys Chem A 2011; 115:13096-103. [DOI: 10.1021/jp2076897] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- D. Geldof
- Department of Chemistry, University of Antwerp, Universiteitsplein 1, B2610 Antwerp, Belgium
| | - A. Krishtal
- Department of Chemistry, University of Antwerp, Universiteitsplein 1, B2610 Antwerp, Belgium
| | - P. Geerlings
- Algemene Chemie, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - C. Van Alsenoy
- Department of Chemistry, University of Antwerp, Universiteitsplein 1, B2610 Antwerp, Belgium
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5
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Lee Warren G, Davis JE, Patel S. Origin and control of superlinear polarizability scaling in chemical potential equalization methods. J Chem Phys 2008; 128:144110. [PMID: 18412426 DOI: 10.1063/1.2872603] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Many common chemical potential equalization (muEq) methods are known to suffer from a superlinear scaling of the polarizability with increasing molecular size that interferes with model transferability and prevents the straightforward application of these methods to large, biochemically relevant molecules. In the present work, we systematically investigate the origins of this scaling and the mechanisms whereby some existing methods successfully temper the scaling. We demonstrate several types of topological charge constraints distinct from the usual single molecular charge constraint that can successfully achieve linear polarizability scaling in atomic charge based equilibration models. We find the use of recently employed charge conservation constraints tied to small molecular units to be an effective and practical approach for modulating the polarizability scaling in atomic muEq schemes. We also analyze the scaling behavior of several muEq schemes in the bond representation and derive closed-form expressions for the polarizability scaling in a linear atomic chain model; for a single molecular charge constraint these expressions demonstrate a cubic dependence of the polarizability on molecular size compared with linear scaling obtainable in the case of the atom-atom charge transfer (AACT) and split-charge equilibration (SQE) schemes. Application of our results to the trans N-alkane series reveals that in certain situations, the AACT and SQE schemes can become unstable due to an indefinite Hessian matrix. Consequently, we discuss sufficient criteria for ensuring stability within these schemes.
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Affiliation(s)
- G Lee Warren
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA.
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Wheatley RJ, Tulegenov AS, Bichoutskaia * E. Intermolecular potentials from supermolecule and monomer calculations. INT REV PHYS CHEM 2007. [DOI: 10.1080/014423504200207772] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
| | - Akyl S. Tulegenov
- a School of Chemistry , University of Nottingham , Nottingham NG7 2RD, UK
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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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8
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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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Eilmes A, Munn RW. Microscopic calculation of the energetics of charged states in amorphous polyethylene. J Chem Phys 2004; 120:7779-83. [PMID: 15267692 DOI: 10.1063/1.1689953] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Polarization energies are calculated for a single excess charge on a polyethylene chain in amorphous polyethylene using (i) local segment and nonlocal distributed molecular polarizabilities, (ii) material structures simulated by both general-purpose and specialist Monte Carlo software, and (iii) uniform and Gaussian distributions of charge with different extents of charge delocalization. Local and distributed response lead to results that are essentially the same except that they correspond to different mean polarizabilities. With increasing delocalization of the charge along the chain, the polarization energies shift to higher values and the width of their distribution decreases, the differences being more pronounced for the uniform distribution. The polarization energies for charges delocalized over 10-20 methylene units form a distribution some 14 eV wide centered around 1 eV, narrowing significantly for more homogeneous polymer melts. The calculations are relevant to trapping of charge in polyethylene. They also yield the microscopic variation in the potential along the polymer chain caused by the polarization energy difference, and so may provide useful inputs to theories of electronic conduction in polymer materials.
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Affiliation(s)
- A Eilmes
- Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland
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11
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Eilmes A, Munn RW, Góra A. Microscopic calculation of the energetics of ions in polyethylene. J Chem Phys 2003. [DOI: 10.1063/1.1623182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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12
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Eilmes A, Munn RW, Mavrantzas VG, Theodorou DN, Góra A. Microscopic calculation of the static electric susceptibility of polyethylene. J Chem Phys 2003. [DOI: 10.1063/1.1623181] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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13
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Eilmes A. Segment polarizabilities for microelectrostatic calculations in poly(ethylene oxide). Chem Phys Lett 2003. [DOI: 10.1016/j.cplett.2003.10.096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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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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17
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Munn RW. Microscopic theory of linear and nonlinear optical and dielectric response in polymer materials. J Chem Phys 2001. [DOI: 10.1063/1.1350638] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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K?dzierski P, Sokalski WA. Analysis of the transferability of atomic multipoles for amino acids in modeling macromolecular charge distribution from fragments. J Comput Chem 2001. [DOI: 10.1002/jcc.1068] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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in het Panhuis M, Munn RW. Analysis of linear and quadratic optical response of mixed Langmuir–Blodgett films of stearic acid and 5-CT. J Chem Phys 2000. [DOI: 10.1063/1.1323724] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [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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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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22
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Graña AM, Mosquera RA. Transferability in aldehydes and ketones. II. Alkyl chains. J Chem Phys 2000. [DOI: 10.1063/1.481966] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Celebi N, Ángyán JG, Dehez F, Millot C, Chipot C. Distributed polarizabilities derived from induction energies: A finite perturbation approach. J Chem Phys 2000. [DOI: 10.1063/1.480845] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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24
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Chelli R, Procacci P, Righini R, Califano S. Electrical response in chemical potential equalization schemes. J Chem Phys 1999. [DOI: 10.1063/1.480198] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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26
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Graña AM, Mosquera RA. The transferability of the carbonyl group in aldehydes and ketones. J Chem Phys 1999. [DOI: 10.1063/1.478568] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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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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