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Briant M, Mestdagh JM, Gaveau MA, Poisson L. Reaction dynamics within a cluster environment. Phys Chem Chem Phys 2022; 24:9807-9835. [PMID: 35441619 DOI: 10.1039/d1cp05783a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This perspective article reviews experimental and theoretical works where rare gas clusters and helium nanodroplets are used as a nanoreactor to investigate chemical dynamics in a solvent environment. A historical perspective is presented first followed by specific considerations on the mobility of reactants within these reaction media. The dynamical response of pure clusters and nanodroplets to photoexcitation is shortly reviewed before examining the role of the cluster (or nanodroplet) degrees of freedom in the photodynamics of the guest atoms and molecules.
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Affiliation(s)
- Marc Briant
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191, Gif-sur-Yvette, France
| | | | - Marc-André Gaveau
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191, Gif-sur-Yvette, France
| | - Lionel Poisson
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405, Orsay, France.
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2
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Dhiman M, Douady J, Gervais B. Geometry, absorption and luminescence of small Ar clusters. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2049905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Mukul Dhiman
- Normandie University, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, UMR6252, Caen, France
| | - Julie Douady
- Normandie University, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, UMR6252, Caen, France
| | - Benoit Gervais
- Normandie University, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, UMR6252, Caen, France
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3
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Vitek A, Kalus R. Thermodynamics of small mercury clusters and the role of electronically excited states. A case study on Hg13. Phys Chem Chem Phys 2022; 24:6915-6925. [DOI: 10.1039/d1cp04652g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Classical Monte Carlo simulations in the isothermal-isobaric ensemble have been performed for the Hg13 cluster with the main emphasis paid to structural changes in this cluster induced by elevated temperature...
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Abstract
Many-body dispersion has gained considerable attention over the past decade, particularly for condensed phase systems. However, quantitatively accurate studies of many-body dispersion have only recently become feasible due to challenges in reliability and accuracy. Currently available methodologies for calculating many-body dispersion have been challenged, with recent evidence suggesting, for example, that dispersion-corrected density functional theory (DFT) schemes cannot consistently predict many-body dispersion accurately. This study evaluates many-body dispersion energies using a composite approach that employs singles and doubles coupled cluster theory with perturbative/noniterative triples, CCSD(T), combined with an extrapolation to the complete basis set (CBS) limit. The combined CCSD(T)/CBS approach is applied to Arn and (H2O)n, n = 3-10, clusters, and a new data set called S22(3), which includes trimers generated based on the S22 data set. In these systems, the many-body dispersion provides a very small contribution to the total interaction energy of all of the systems studied, generally 3% or less of the total interaction energy. Two-body dispersion is the dominant dispersion contribution and many-body dispersion contributes no more than 5.7% of the total dispersion energy, generally staying below 2%.
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Affiliation(s)
- Melisa Alkan
- Department of Chemistry , Iowa State University , Ames , Iowa 50011 , United States.,Ames Laboratory , Ames , Iowa 50011 , United States
| | - Peng Xu
- Department of Chemistry , Iowa State University , Ames , Iowa 50011 , United States.,Ames Laboratory , Ames , Iowa 50011 , United States
| | - Mark S Gordon
- Department of Chemistry , Iowa State University , Ames , Iowa 50011 , United States.,Ames Laboratory , Ames , Iowa 50011 , United States
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5
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Rong C, Zhao D, Yu D, Liu S. Quantification and origin of cooperativity: insights from density functional reactivity theory. Phys Chem Chem Phys 2018; 20:17990-17998. [PMID: 29927447 DOI: 10.1039/c8cp03092h] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cooperativity is a widely used chemical concept whose existence is ubiquitous in chemical and biological systems but whose quantification is still controversial and origin much less appreciated. In this work, using the interaction energy of a molecular system, which is composed of multiple copies of a building block, we propose a quantitative measurement to evaluate the cooperativity effect. This quantification approach is then applied to six molecular systems, i.e., water cluster, argon cluster, protonated water cluster, zinc atom cluster, water cluster on top of a graphene sheet, and alpha helix of glycine amino acids, each with up to 20 copies of the building block. Cooperativity is seen in all these systems. Both positive and negative cooperativity effects are observed. Employing the two energy partition schemes in density functional theory and the information-theoretic quantities such as Shannon entropy, Fisher information, information gain, etc., we then examine the origin of the cooperativity effect for these systems. Strong linear correlations between the cooperativity measure and some of these theoretical quantities have been unveiled. With these correlations, we are able to quantitatively account for their origin of cooperativity. Our results show that the interactions governing the existence and validity of the cooperativity effect are complicated. An opposite mechanism in enthalpy-entropy compensation for positive and negative cooperativity has been unveiled. These results should provide new insights and understandings from a different viewpoint about the nature and origin of cooperativity to appreciate this vastly important chemical concept.
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Affiliation(s)
- Chunying Rong
- College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha Hunan 410081, P. R. China
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6
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Aguirre NF, Díaz-Tendero S, Hervieux PA, Alcamí M, Martín F. M 3C: A Computational Approach To Describe Statistical Fragmentation of Excited Molecules and Clusters. J Chem Theory Comput 2017; 13:992-1009. [PMID: 28005371 DOI: 10.1021/acs.jctc.6b00984] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Microcanonical Metropolis Monte Carlo method, based on a random sampling of the density of states, is revisited for the study of molecular fragmentation in the gas phase (isolated molecules, atomic and molecular clusters, complex biomolecules, etc.). A random walk or uniform random sampling in the configurational space (atomic positions) and a uniform random sampling of the relative orientation, vibrational energy, and chemical composition of the fragments is used to estimate the density of states of the system, which is continuously updated as the random sampling populates individual states. The validity and usefulness of the method is demonstrated by applying it to evaluate the caloric curve of a weakly bound rare gas cluster (Ar13), to interpret the fragmentation of highly excited small neutral and singly positively charged carbon clusters (Cn, n = 5,7,9 and Cn+, n = 4,5) and to simulate the mass spectrum of the acetylene molecule (C2H2).
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Affiliation(s)
- Néstor F Aguirre
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid , 28049 Madrid, Spain
| | - Sergio Díaz-Tendero
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid , 28049 Madrid, Spain.,Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid , 28049 Madrid, Spain
| | - Paul-Antoine Hervieux
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg , 67000 Strasbourg, France
| | - Manuel Alcamí
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid , 28049 Madrid, Spain.,Instituto Madrileño de Estudios Avanzados en Nanociencias (IMDEA-Nanociencia) , 28049 Madrid, Spain
| | - Fernando Martín
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid , 28049 Madrid, Spain.,Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid , 28049 Madrid, Spain.,Instituto Madrileño de Estudios Avanzados en Nanociencias (IMDEA-Nanociencia) , 28049 Madrid, Spain
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7
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Sanz-Sanz C, Aguado A, Roncero O, Naumkin F. Non-adiabatic couplings and dynamics in proton transfer reactions of Hn (+) systems: Application to H2+H2 (+)→H+H3 (+) collisions. J Chem Phys 2016; 143:234303. [PMID: 26696058 DOI: 10.1063/1.4937138] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Analytical derivatives and non-adiabatic coupling matrix elements are derived for Hn (+) systems (n = 3-5). The method uses a generalized Hellmann-Feynman theorem applied to a multi-state description based on diatomics-in-molecules (for H3 (+)) or triatomics-in-molecules (for H4 (+) and H5 (+)) formalisms, corrected with a permutationally invariant many-body term to get high accuracy. The analytical non-adiabatic coupling matrix elements are compared with ab initio calculations performed at multi-reference configuration interaction level. These magnitudes are used to calculate H2(v(')=0,j(')=0)+H2 (+)(v,j=0) collisions, to determine the effect of electronic transitions using a molecular dynamics method with electronic transitions. Cross sections for several initial vibrational states of H2 (+) are calculated and compared with the available experimental data, yielding an excellent agreement. The effect of vibrational excitation of H2 (+) reactant and its relation with non-adiabatic processes are discussed. Also, the behavior at low collisional energies, in the 1 meV-0.1 eV interval, of interest in astrophysical environments, is discussed in terms of the long range behaviour of the interaction potential which is properly described within the triatomics-in-molecules formalism.
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Affiliation(s)
- Cristina Sanz-Sanz
- Departamento de Química Física Aplicada (UAM), Unidad Asociada IFF-CSIC, Facultad de Ciencias C-XIV, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Alfredo Aguado
- Departamento de Química Física Aplicada (UAM), Unidad Asociada IFF-CSIC, Facultad de Ciencias C-XIV, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Octavio Roncero
- Instituto de Física Fundamental, CSIC, C/ Serrano, 123, 28006 Madrid, Spain
| | - Fedor Naumkin
- Faculty of Science, UOIT, Oshawa, Ontario L1H 7K4, Canada
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Marques JMC, Pereira FB. A detailed investigation on the global minimum structures of mixed rare-gas clusters: Geometry, energetics, and site occupancy. J Comput Chem 2012; 34:505-17. [PMID: 23108580 DOI: 10.1002/jcc.23161] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 09/20/2012] [Accepted: 09/28/2012] [Indexed: 11/07/2022]
Affiliation(s)
- Jorge M C Marques
- Departamento de Química, Universidade de Coimbra, Coimbra 3004-535, Portugal.
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9
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Ma Z, Cai W, Shao X. Impact of different potentials on the structures and energies of clusters. J Comput Chem 2011; 32:3075-80. [DOI: 10.1002/jcc.21891] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Revised: 06/17/2011] [Accepted: 06/22/2011] [Indexed: 12/12/2022]
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10
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Zanuttini D, Douady J, Jacquet E, Giglio E, Gervais B. Structure and photoabsorption properties of cationic alkali dimers solvated in neon clusters. J Chem Phys 2010; 133:174503. [DOI: 10.1063/1.3490251] [Citation(s) in RCA: 8] [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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11
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Meuwly M, Doll JD. Finite-temperature quantum simulations of mixed rare gas clusters. J Chem Phys 2010; 132:234315. [PMID: 20572713 DOI: 10.1063/1.3431080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Finite-temperature quantum Monte Carlo simulations are presented for mixed neon/argon rare gas clusters containing up to n=10 atoms. For the smallest clusters (n=3) comparison with rigorous bound state calculations and experiments shows that the present approach is accurate to within fractions of wavenumbers for energies and to within a few percent or better for rotational constants. For larger cluster sizes, for which no rigorous quantum calculations are available, comparison with experiment becomes even more favorable. In all simulations accurate pair potentials for the rare gas-rare gas interactions are employed and comparison with high-level electronic structure calculations suggest that many-body interactions play a minor role. For the largest clusters investigated (Ne(4)Ar(6)) gradual melting of the neon phase is observed while the argon-phase remains structurally intact.
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Affiliation(s)
- Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
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12
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Marques J, Pereira F. An evolutionary algorithm for global minimum search of binary atomic clusters. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2009.11.059] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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13
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Schnabel S, Vogel T, Bachmann M, Janke W. Surface effects in the crystallization process of elastic flexible polymers. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.05.052] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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14
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Maerzke KA, Murdachaew G, Mundy CJ, Schenter GK, Siepmann JI. Self-Consistent Polarization Density Functional Theory: Application to Argon. J Phys Chem A 2009; 113:2075-85. [DOI: 10.1021/jp808767y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Katie A. Maerzke
- Department of Chemistry and Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, and Chemical & Materials Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Garold Murdachaew
- Department of Chemistry and Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, and Chemical & Materials Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Christopher J. Mundy
- Department of Chemistry and Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, and Chemical & Materials Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Gregory K. Schenter
- Department of Chemistry and Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, and Chemical & Materials Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - J. Ilja Siepmann
- Department of Chemistry and Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, and Chemical & Materials Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
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15
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Generation and characterization of low-energy structures in atomic clusters. J Comput Chem 2009; 31:1495-503. [DOI: 10.1002/jcc.21436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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16
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Marques JMC, Pereira FB, Leitão T. On the Use of Different Potential Energy Functions in Rare-Gas Cluster Optimization by Genetic Algorithms: Application to Argon Clusters. J Phys Chem A 2008; 112:6079-89. [DOI: 10.1021/jp711918t] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. M. C. Marques
- Departamento de Química, Universidade de Coimbra, 3004-535 Coimbra, Portugal, Instituto Superior de Engenharia de Coimbra, Quinta da Nora, 3030-199 Coimbra, Portugal, and Centro de Informática e Sistemas da Universidade de Coimbra (CISUC), 3030-290 Coimbra, Portugal
| | - F. B. Pereira
- Departamento de Química, Universidade de Coimbra, 3004-535 Coimbra, Portugal, Instituto Superior de Engenharia de Coimbra, Quinta da Nora, 3030-199 Coimbra, Portugal, and Centro de Informática e Sistemas da Universidade de Coimbra (CISUC), 3030-290 Coimbra, Portugal
| | - T. Leitão
- Departamento de Química, Universidade de Coimbra, 3004-535 Coimbra, Portugal, Instituto Superior de Engenharia de Coimbra, Quinta da Nora, 3030-199 Coimbra, Portugal, and Centro de Informática e Sistemas da Universidade de Coimbra (CISUC), 3030-290 Coimbra, Portugal
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Profant V, Poterya V, Fárník M, Slavíček P, Buck U. Fragmentation Dynamics of Size-Selected Pyrrole Clusters Prepared by Electron Impact Ionization: Forming a Solvated Dimer Ion Core. J Phys Chem A 2007; 111:12477-86. [DOI: 10.1021/jp0751561] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Václav Profant
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague 8, Czech Republic
| | - Viktoriya Poterya
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague 8, Czech Republic
| | - Michal Fárník
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague 8, Czech Republic
| | - Petr Slavíček
- Department of Physical Chemistry, Institute of Chemical Technology, Technická 5, Prague 6, Czech Republic
| | - Udo Buck
- Max-Planck-Institut für Dynamik und Selbstorganization, Bunsenstrasse 10, D-37073 Göttingen, Germany
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NAUMKIN FY, WALES DJ. Molecule-doped rare gas clusters: structure and stability of ArnNO(X2Π1/2/3/2),n≤ 25, from newab initiopotential energy surfaces of ArNO. Mol Phys 2000. [DOI: 10.1080/00268970009483285] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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19
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Faken DB, Voter AF, Freeman DL, Doll JD. Dimensional Strategies and the Minimization Problem: Barrier-Avoiding Algorithms. J Phys Chem A 1999. [DOI: 10.1021/jp9920949] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel B. Faken
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, Theoretical Division, Los Alamos National Laboratory, Mail Stop B268 Los Alamos, NM 87545, and Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881
| | - A. F. Voter
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, Theoretical Division, Los Alamos National Laboratory, Mail Stop B268 Los Alamos, NM 87545, and Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881
| | - David L. Freeman
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, Theoretical Division, Los Alamos National Laboratory, Mail Stop B268 Los Alamos, NM 87545, and Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881
| | - J. D. Doll
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, Theoretical Division, Los Alamos National Laboratory, Mail Stop B268 Los Alamos, NM 87545, and Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881
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