1
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Li W, Ding G, Gao H, Zhuang Y, Gu X, Peijnenburg WJGM. Prediction of octanol-air partition coefficients for PCBs at different ambient temperatures based on the solvation free energy and the dimer ratio. CHEMOSPHERE 2020; 242:125246. [PMID: 31704525 DOI: 10.1016/j.chemosphere.2019.125246] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/19/2019] [Accepted: 10/27/2019] [Indexed: 06/10/2023]
Abstract
Temperature-dependent octanol-air partition coefficients (KOA) are of great importance in assessing the environmental behavior and fate of persistent organic pollutants including polychlorinated biphenyls (PCBs). Due to the tremendous amounts of time, effort and cost needed for the experimental determination of KOA, it is desirable to develop a rapid and precise predictive method to estimate KOA just based on molecular structure. In the present study, a predictive model for log KOA of PCBs at ambient temperatures was developed based on the thermodynamic relationship between KOA and the solvation free energy from air to octanol (ΔGOA). For the calculation of ΔGOA of PCBs, the optimal combination of theoretical method and basis-set was identified to be HF/MIDI!6D for both geometry optimization and energy calculation. Dimer formation could affect the partition behavior and promote the apparent KOA values of PCBs. After taking the effect of dimer formation into account, the goodness-of-fit, predictive ability, and robustness of the predictive model were significantly improved. Apparent log KOA values of PCBs at different ambient temperatures ranging from 283.15 to 303.15 K were predicted. Compared with other reported models, the model developed in the present study had not only comparable goodness-of-fit and predictive ability, but also a universal application domain and the relative independency of experimental data. Therefore, the solvation free energy method could be a promising method for the prediction of KOA.
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Affiliation(s)
- Wanran Li
- College of Environmental Science and Engineering, Dalian Maritime University, Linghai Road 1, Dalian, 116026, PR China
| | - Guanghui Ding
- College of Environmental Science and Engineering, Dalian Maritime University, Linghai Road 1, Dalian, 116026, PR China.
| | - Hong Gao
- Department of Physics, Dalian Maritime University, Linghai Road 1, Dalian, 116026, PR China
| | - Yuting Zhuang
- College of Environmental Science and Engineering, Dalian Maritime University, Linghai Road 1, Dalian, 116026, PR China
| | - Xiaoyue Gu
- College of Environmental Science and Engineering, Dalian Maritime University, Linghai Road 1, Dalian, 116026, PR China
| | - Willie J G M Peijnenburg
- Center for Safety of Substances and Products, National Institute of Public Health and the Environment, P.O. Box 1, Bilthoven, the Netherlands; Institute of Environmental Sciences (CML), Leiden University, Leiden, 2300, the Netherlands
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2
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Takeuchi H. Size-guided multi-seed heuristic method for geometry optimization of clusters: Application to benzene clusters. J Comput Chem 2018; 39:1738-1746. [PMID: 29737541 DOI: 10.1002/jcc.25349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 04/12/2018] [Accepted: 04/17/2018] [Indexed: 11/06/2022]
Abstract
Since searching for the global minimum on the potential energy surface of a cluster is very difficult, many geometry optimization methods have been proposed, in which initial geometries are randomly generated and subsequently improved with different algorithms. In this study, a size-guided multi-seed heuristic method is developed and applied to benzene clusters. It produces initial configurations of the cluster with n molecules from the lowest-energy configurations of the cluster with n - 1 molecules (seeds). The initial geometries are further optimized with the geometrical perturbations previously used for molecular clusters. These steps are repeated until the size n satisfies a predefined one. The method locates putative global minima of benzene clusters with up to 65 molecules. The performance of the method is discussed using the computational cost, rates to locate the global minima, and energies of initial geometries. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Hiroshi Takeuchi
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
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3
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Gadre SR, Yeole SD, Sahu N. Quantum chemical investigations on molecular clusters. Chem Rev 2014; 114:12132-73. [PMID: 25341561 DOI: 10.1021/cr4006632] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Shridhar R Gadre
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208 016, India
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4
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Chakrabarti D, Kusumaatmaja H, Rühle V, Wales DJ. Exploring energy landscapes: from molecular to mesoscopic systems. Phys Chem Chem Phys 2014; 16:5014-25. [PMID: 24067895 DOI: 10.1039/c3cp52603h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We review a comprehensive computational framework to survey the potential energy landscape for systems composed of rigid or partially rigid molecules. Illustrative case studies relevant to a wide range of molecular clusters and soft and condensed matter systems are discussed.
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Affiliation(s)
- Dwaipayan Chakrabarti
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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5
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Takeuchi H. Structures, stability, and growth sequence patterns of small homoclusters of naphthalene, anthracene, phenanthrene, phenalene, naphthacene, and pyrene. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.06.029] [Citation(s) in RCA: 30] [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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6
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Cao YL, Wang YS. Geometry Optimization of Ba2+(H2O)nClusters Using a Fast Hybrid Global Optimization Algorithm. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200400104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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7
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Takeuchi H. Structural Features of Small Benzene Clusters (C6H6)n (n ≤ 30) As Investigated with the All-Atom OPLS Potential. J Phys Chem A 2012; 116:10172-81. [DOI: 10.1021/jp305965r] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Hiroshi Takeuchi
- Division of Chemistry,
Graduate School of Science, Hokkaido University, 060-0810 Sapporo, Japan
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8
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Chakrabarti D, Totton TS, Kraft M, Wales DJ. A survey of the potential energy surface for the (benzene)13 cluster. Phys Chem Chem Phys 2011; 13:21362-6. [PMID: 22033556 DOI: 10.1039/c1cp22220a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We report on a survey of the potential energy surface for the 13-molecule benzene cluster, (C(6)H(6))(13), bound by an atom-atom intermolecular potential developed from first principles. The potential, which has an anisotropic repulsion term, is found to support distinct pairs of structures of C(3), C(i), and S(6) symmetry as low-lying minima, including a C(3) global minimum. The organisation of the low-lying region of the potential energy surface suggests that one of the S(6) structures is likely to act as a kinetic trap, hindering efficient relaxation to the global minimum, in agreement with the hypothesis that two isomers coexist in this system, suggested by spectroscopic experiments.
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Llanio-Trujillo JL, Marques JMC, Pereira FB. An Evolutionary Algorithm for the Global Optimization of Molecular Clusters: Application to Water, Benzene, and Benzene Cation. J Phys Chem A 2011; 115:2130-8. [DOI: 10.1021/jp1117695] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [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
| | - F. B. Pereira
- Instituto Superior de Engenharia de Coimbra, Quinta da Nora, 3030-199 Coimbra, Portugal
- Centro de Informática e Sistemas da Universidade de Coimbra (CISUC), 3030-290 Coimbra, Portugal
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10
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Dieterich JM, Hartke B. OGOLEM: Global cluster structure optimisation for arbitrary mixtures of flexible molecules. A multiscaling, object-oriented approach. Mol Phys 2010. [DOI: 10.1080/00268970903446756] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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11
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Kim S, Orendt AM, Ferraro MB, Facelli JC. Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field. J Comput Chem 2009; 30:1973-85. [PMID: 19130496 DOI: 10.1002/jcc.21189] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated computer programs for generating the molecule's force field, sampling crystal structures using a distributed parallel genetic algorithm and local energy minimization of the structures followed by the classifying, sorting, and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential.
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Affiliation(s)
- Seonah Kim
- Center for High Performance Computing, University of Utah, 155 South 1452 East Room 405, Salt Lake City, Utah 84112-0190, USA
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Lee SH, Kim JH, Chu I, Song JK. Anion clusters of naphthalene and solvents: structure, ion core, and intermolecular interactions. Phys Chem Chem Phys 2009; 11:9468-73. [DOI: 10.1039/b903626a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Takeuchi H. Development of an Efficient Geometry Optimization Method for Water Clusters. J Chem Inf Model 2008; 48:2226-33. [DOI: 10.1021/ci800238w] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Hiroshi Takeuchi
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
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14
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Takeuchi H. Geometry Optimization of Carbon Dioxide Clusters (CO2)n for 4 ≤ n ≤ 40. J Phys Chem A 2008; 112:7492-7. [DOI: 10.1021/jp802872p] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Hiroshi Takeuchi
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810
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15
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Wales DJ, Doye JPK, Miller MA, Mortenson PN, Walsh TR. Energy Landscapes: From Clusters to Biomolecules. ADVANCES IN CHEMICAL PHYSICS 2007. [DOI: 10.1002/9780470141748.ch1] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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16
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Call ST, Zubarev DY, Boldyrev AI. Global minimum structure searches via particle swarm optimization. J Comput Chem 2007; 28:1177-86. [PMID: 17299774 DOI: 10.1002/jcc.20621] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Novel implementation of the evolutionary approach known as particle swarm optimization (PSO) capable of finding the global minimum of the potential energy surface of atomic assemblies is reported. This is the first time the PSO technique has been used to perform global optimization of minimum structure search for chemical systems. Significant improvements have been introduced to the original PSO algorithm to increase its efficiency and reliability and adapt it to chemical systems. The developed software has successfully found the lowest-energy structures of the LJ(26) Lennard-Jones cluster, anionic silicon hydride Si(2)H(5) (-), and triply hydrated hydroxide ion OH(-) (H(2)O)(3). It requires relatively small population sizes and demonstrates fast convergence. Efficiency of PSO has been compared with simulated annealing, and the gradient embedded genetic algorithm.
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Affiliation(s)
- Seth T Call
- Department of Computer Science, Utah State University, Logan, Utah 84322-0300, USA
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17
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Takeuchi H. Novel Method for Geometry Optimization of Molecular Clusters: Application to Benzene Clusters. J Chem Inf Model 2006; 47:104-9. [PMID: 17238254 DOI: 10.1021/ci600336p] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A heuristic and unbiased method for searching optimal geometries of clusters of nonspherical molecules was constructed from the algorithm recently proposed for Lennard-Jones atomic clusters. In the method, global minima are searched by using three operators, interior, surface, and orientation operators. The first operator gives a perturbation on a cluster configuration by moving molecules near the center of mass of a cluster, and the second one modifies a cluster configuration by moving molecules to the most stable positions on the surface of a cluster. The moved molecules are selected by employing a contribution of the molecules to the potential energy of a cluster. The third operator randomly changes the orientations of all molecules. The proposed method was applied to benzene clusters. It was possible to find new global minima for (C6H6)11, (C6H6)14, and (C6H6)15. Global minima for (C6H6)16 to (C6H6)30 are first reported in this article.
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Affiliation(s)
- Hiroshi Takeuchi
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan.
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18
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Bazterra VE, Thorley M, Ferraro MB, Facelli JC. A Distributed Computing Method for Crystal Structure Prediction of Flexible Molecules: An Application to N-(2-Dimethyl-4,5-dinitrophenyl) Acetamide. J Chem Theory Comput 2006; 3:201-9. [DOI: 10.1021/ct6002115] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Victor E. Bazterra
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. I (1428), Buenos Aires, Argentina, and Center for High Performance Computing, University of Utah, 155 South 1452 East Rm 405, Salt Lake City, Utah 84112-0190
| | - Matthew Thorley
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. I (1428), Buenos Aires, Argentina, and Center for High Performance Computing, University of Utah, 155 South 1452 East Rm 405, Salt Lake City, Utah 84112-0190
| | - Marta B. Ferraro
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. I (1428), Buenos Aires, Argentina, and Center for High Performance Computing, University of Utah, 155 South 1452 East Rm 405, Salt Lake City, Utah 84112-0190
| | - Julio C. Facelli
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. I (1428), Buenos Aires, Argentina, and Center for High Performance Computing, University of Utah, 155 South 1452 East Rm 405, Salt Lake City, Utah 84112-0190
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19
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Alexandrova AN, Boldyrev AI, Fu YJ, Yang X, Wang XB, Wang LS. Structure of the Na(x)Cl(x+1) (-) (x=1-4) clusters via ab initio genetic algorithm and photoelectron spectroscopy. J Chem Phys 2006; 121:5709-19. [PMID: 15366994 DOI: 10.1063/1.1783276] [Citation(s) in RCA: 225] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The application of the ab initio genetic algorithm with an embedded gradient has been carried out for the elucidation of global minimum structures of a series of anionic sodium chloride clusters, Na(x)Cl(x+1) (-) (x=1-4), produced in the gas phase using electrospray ionization and studied by photoelectron spectroscopy. These are all superhalogen species with extremely high electron binding energies. The vertical electron detachment energies for Na(x)Cl(x+1) (-) were measured to be 5.6, 6.46, 6.3, and 7.0 eV, for x=1-4, respectively. Our ab initio gradient embedded genetic algorithm program detected the linear global minima for NaCl(2) (-) and Na(2)Cl(3) (-) and three-dimensional structures for the larger species. Na(3)Cl(4) (-) was found to have C(3v) symmetry, which can be viewed as a Na(4)Cl(4) cube missing a corner Na(+) cation, whereas Na(4)Cl(5) (-) was found to have C(4v) symmetry, close to a 3x3 planar structure. Excellent agreement between the theoretically calculated and the experimental spectra was observed, confirming the obtained structures and demonstrating the power of the developed genetic algorithm technique.
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21
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Alexandrova AN, Boldyrev AI. Search for the Lin0/+1/-1 (n = 5−7) Lowest-Energy Structures Using the ab Initio Gradient Embedded Genetic Algorithm (GEGA). Elucidation of the Chemical Bonding in the Lithium Clusters. J Chem Theory Comput 2005; 1:566-80. [PMID: 26641677 DOI: 10.1021/ct050093g] [Citation(s) in RCA: 187] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anastassia N. Alexandrova
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, Utah 84322-0300
| | - Alexander I. Boldyrev
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, Utah 84322-0300
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22
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Seo YS, Lee C, Lee KH, Yoon KB. 1:1 and 2:1 Charge-Transfer Complexes between Aromatic Hydrocarbons and Dry Titanium Dioxide. Angew Chem Int Ed Engl 2005; 44:910-3. [PMID: 15624219 DOI: 10.1002/anie.200461972] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- You Seok Seo
- Center for Microcrystal Assembly and Department of Chemistry, Sogang University, Seoul 121-742, Korea
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23
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Seo YS, Lee C, Lee KH, Yoon KB. 1:1 and 2:1 Charge-Transfer Complexes between Aromatic Hydrocarbons and Dry Titanium Dioxide. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200461972] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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24
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Bouvier B, Millié P, Mons M. Investigation of the Photoionization Mechanism of Small Aromatic Homoclusters. J Phys Chem A 2004. [DOI: 10.1021/jp036761g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Benjamin Bouvier
- Laboratoire Francis Perrin, URA 2453, DSM/DRECAM/SPAM, CEA Saclay, Bât. 522, 91191 Gif-sur-Yvette, France
| | - Philippe Millié
- Laboratoire Francis Perrin, URA 2453, DSM/DRECAM/SPAM, CEA Saclay, Bât. 522, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- Laboratoire Francis Perrin, URA 2453, DSM/DRECAM/SPAM, CEA Saclay, Bât. 522, 91191 Gif-sur-Yvette, France
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25
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Hennessy MH, Kelley AM. Using real-valued multi-objective genetic algorithms to model molecular absorption spectra and Raman excitation profiles in solution. Phys Chem Chem Phys 2004. [DOI: 10.1039/b315893d] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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27
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Gonzalez C, Lim EC. Evaluation of the Hartree−Fock Dispersion (HFD) Model as a Practical Tool for Probing Intermolecular Potentials of Small Aromatic Clusters: Comparison of the HFD and MP2 Intermolecular Potentials. J Phys Chem A 2003. [DOI: 10.1021/jp030587e] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Carlos Gonzalez
- Physical and Chemical Properties Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899
| | - Edward C. Lim
- Department of Chemistry and The Center for Laser and Optical Spectroscopy, The University of Akron, Akron, Ohio 44325-3601
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28
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Johnston RL, Roberts C. Genetic Algorithms for the Geometry Optimization of Clusters and Nanoparticles. SOFT COMPUTING APPROACHES IN CHEMISTRY 2003. [DOI: 10.1007/978-3-540-36213-5_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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29
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Bouvier B, Brenner V, Millié P, Soudan JM. A Model Potential Approach to Charge Resonance Phenomena in Aromatic Cluster Ions. J Phys Chem A 2002. [DOI: 10.1021/jp025794d] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Benjamin Bouvier
- CEA Saclay, DSM/DRECAM/SPAM, Laboratoire Françis Perrin, URA 2453, Bât. 522, 91191 Gif-sur-Yvette, France
| | - Valérie Brenner
- CEA Saclay, DSM/DRECAM/SPAM, Laboratoire Françis Perrin, URA 2453, Bât. 522, 91191 Gif-sur-Yvette, France
| | - Philippe Millié
- CEA Saclay, DSM/DRECAM/SPAM, Laboratoire Françis Perrin, URA 2453, Bât. 522, 91191 Gif-sur-Yvette, France
| | - Jean-Maïk Soudan
- CEA Saclay, DSM/DRECAM/SPAM, Laboratoire Françis Perrin, URA 2453, Bât. 522, 91191 Gif-sur-Yvette, France
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30
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Lee NK, Park S, Kim SK. Ab initio studies on the van der Waals complexes of polycyclic aromatic hydrocarbons. II. Naphthalene dimer and naphthalene–anthracene complex. J Chem Phys 2002. [DOI: 10.1063/1.1468642] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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31
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On the equilibrium geometries of anthracene trimer and naphthalene tetramer: comparison of the exp-6-1 and HFD structure predictions with experiment. Chem Phys Lett 2002. [DOI: 10.1016/s0009-2614(02)00528-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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32
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Vargas MC, Torres-Jim$eacute$nez J, Ruiz-Su$aacute$rez JC. Analysis of x-ray diffraction data using a hybrid stochastic optimization method. ACTA ACUST UNITED AC 2002. [DOI: 10.1088/0305-4470/35/17/304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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33
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Bazterra VE, Ferraro MB, Facelli JC. Modified genetic algorithm to model crystal structures. I. Benzene, naphthalene and anthracene. J Chem Phys 2002. [DOI: 10.1063/1.1458547] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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34
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Piuzzi F, Dimicoli I, Mons M, Millié P, Brenner V, Zhao Q, Soep B, Tramer A. Spectroscopy, dynamics and structures of jet formed anthracene clusters. Chem Phys 2002. [DOI: 10.1016/s0301-0104(01)00534-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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35
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Guimarães FF, Belchior JC, Johnston RL, Roberts C. Global optimization analysis of water clusters (H[sub 2]O)[sub n] (11≤n≤13) through a genetic evolutionary approach. J Chem Phys 2002. [DOI: 10.1063/1.1471240] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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36
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Gonzalez C, Allison TC, Lim EC. Hartree−Fock Dispersion Probe of the Equilibrium Structures of Small Microclusters of Benzene and Naphthalene: Comparison with Second-Order MØeller−Plesset Geometries. J Phys Chem A 2001. [DOI: 10.1021/jp012341k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carlos Gonzalez
- Physical and Chemistry Properties Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, and Department of Chemistry, The University of Akron, Akron, Ohio 44325-3601
| | - Thomas C. Allison
- Physical and Chemistry Properties Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, and Department of Chemistry, The University of Akron, Akron, Ohio 44325-3601
| | - Edward C. Lim
- Physical and Chemistry Properties Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, and Department of Chemistry, The University of Akron, Akron, Ohio 44325-3601
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Lilichenko M, Kelley AM. Application of artificial neural networks and genetic algorithms to modeling molecular electronic spectra in solution. J Chem Phys 2001. [DOI: 10.1063/1.1358835] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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Nakanishi H, Sugawara M. Numerical solution of the Schrödinger equation by a microgenetic algorithm. Chem Phys Lett 2000. [DOI: 10.1016/s0009-2614(00)00913-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Iwamatsu M. Global geometry optimization of silicon clusters using the space-fixed genetic algorithm. J Chem Phys 2000. [DOI: 10.1063/1.481737] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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White RP, Mayne HR. Optimal annealing schedules for two-, three-, and four-level systems using a genetic algorithm approach. J Chem Phys 2000. [DOI: 10.1063/1.481397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Gonzalez C, Lim EC. A Quantum Chemistry Study of the van der Waals Dimers of Benzene, Naphthalene, and Anthracene: Crossed (D2d) and Parallel-Displaced (C2h) Dimers of Very Similar Energies in the Linear Polyacenes. J Phys Chem A 2000. [DOI: 10.1021/jp993642l] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Carlos Gonzalez
- Physical and Chemical Properties Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899
| | - Edward C. Lim
- Department of Chemistry, The University of Akron, Akron, Ohio 44325-3601
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Doye JPK, Miller MA, Wales DJ. Evolution of the potential energy surface with size for Lennard-Jones clusters. J Chem Phys 1999. [DOI: 10.1063/1.480217] [Citation(s) in RCA: 199] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Kim W, Schaeffer MW, Lee S, Chung JS, Felker PM. Intermolecular vibrations of naphthalene trimer by ionization-detected stimulated Raman spectroscopy. J Chem Phys 1999. [DOI: 10.1063/1.479067] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Benharash P, Gleason MJ, Felker PM. Rotational Coherence Spectroscopy and Structure of Naphthalene Trimer. J Phys Chem A 1999. [DOI: 10.1021/jp984636c] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peyman Benharash
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569
| | - Michael J. Gleason
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569
| | - Peter M. Felker
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569
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Gonzalez C, Lim EC. Ab Initio and MM3 Studies of the Conformational Structures of Naphthalene Trimer: Comparison with Experiment. J Phys Chem A 1999. [DOI: 10.1021/jp984374e] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carlos Gonzalez
- Physical and Chemical Properties Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899
| | - Edward C. Lim
- Department of Chemistry, The University of Akron, Akron, Ohio 44325-3601
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Doye JPK, Wales DJ, Miller MA. Thermodynamics and the global optimization of Lennard-Jones clusters. J Chem Phys 1998. [DOI: 10.1063/1.477477] [Citation(s) in RCA: 158] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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White RP, Mayne HR. An investigation of two approaches to basin hopping minimization for atomic and molecular clusters. Chem Phys Lett 1998. [DOI: 10.1016/s0009-2614(98)00431-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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