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Lourenço MP, Hostaš J, Herrera LB, Calaminici P, Köster AM, Tchagang A, Salahub DR. GAMaterial-A genetic-algorithm software for material design and discovery. J Comput Chem 2023; 44:814-823. [PMID: 36444916 DOI: 10.1002/jcc.27043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/26/2022] [Accepted: 11/06/2022] [Indexed: 11/30/2022]
Abstract
Genetic algorithms (GAs) are stochastic global search methods inspired by biological evolution. They have been used extensively in chemistry and materials science coupled with theoretical methods, ranging from force-fields to high-throughput first-principles methods. The methodology allows an accurate and automated structural determination for molecules, atomic clusters, nanoparticles, and solid surfaces, fundamental to understanding chemical processes in catalysis and environmental sciences, for instance. In this work, we propose a new genetic algorithm software, GAMaterial, implemented in Python3.x, that performs global searches to elucidate the structures of atomic clusters, doped clusters or materials and atomic clusters on surfaces. For all these applications, it is possible to accelerate the GA search by using machine learning (ML), the ML@GA method, to build subsequent populations. Results for ML@GA applied for the dopant distributions in atomic clusters are presented. The GAMaterial software was applied for the automatic structural search for the Ti6 O12 cluster, doping Al in Si11 (4Al@Si11 ) and Na10 supported on graphene (Na10 @graphene), where DFTB calculations were used to sample the complex search surfaces with reasonably low computational cost. Finally, the global search by GA of the Mo8 C4 cluster was considered, where DFT calculations were made with the deMon2k code, which is interfaced with GAMaterial.
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Affiliation(s)
- Maicon Pierre Lourenço
- Departamento de Química e Física - Centro de Ciências Exatas, Naturais e da Saúde - CCENS - Universidade Federal do Espírito Santo, Espírito Santo, Brazil
| | - Jiří Hostaš
- Department of Chemistry, Department of Physics and Astronomy, CMS Centre for Molecular Simulation, IQST Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, Calgary, Alberta, Canada
| | - Lizandra Barrios Herrera
- Department of Chemistry, Department of Physics and Astronomy, CMS Centre for Molecular Simulation, IQST Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, Calgary, Alberta, Canada
| | | | | | - Alain Tchagang
- Digital Technologies Research Centre, National Research Council of Canada, Ottawa, Ontario, Canada
| | - Dennis R Salahub
- Department of Chemistry, Department of Physics and Astronomy, CMS Centre for Molecular Simulation, IQST Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, Calgary, Alberta, Canada
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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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Prudente FV, Marques JMC, Pereira FB. Solvation of Li+ by argon: how important are three-body forces? Phys Chem Chem Phys 2017; 19:25707-25716. [DOI: 10.1039/c7cp04549b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A global geometry search on a new potential energy surface for Li+Arn clusters revealed that three-body interactions must be included to reproduce ab initio structures and accurate energetic features.
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Affiliation(s)
| | | | - Francisco 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
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Brandon D, Poirier B. Accurate calculations of bound rovibrational states for argon trimer. J Chem Phys 2014; 141:034302. [DOI: 10.1063/1.4887459] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Drew Brandon
- Department of Chemistry and Biochemistry, and Department of Physics, Texas Tech University, Box 41061, Lubbock, Texas 79409-1061, USA
| | - Bill Poirier
- Department of Chemistry and Biochemistry, and Department of Physics, Texas Tech University, Box 41061, Lubbock, Texas 79409-1061, USA
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Marques JMC, Llanio-Trujillo JL, Albertí M, Aguilar A, Pirani F. Microsolvation of the potassium ion with aromatic rings: comparison between hexafluorobenzene and benzene. J Phys Chem A 2013; 117:8043-53. [PMID: 23869742 DOI: 10.1021/jp405295b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We employ a recently developed methodology to study structural and energetic properties of the first solvation shells of the potassium ion in nonpolar environments due to aromatic rings, which is important to understand the selectivity of several biochemical phenomena. Our evolutionary algorithm is used in the global optimization study of clusters formed of K(+) solvated with hexafluorobenzene (HFBz) molecules. The global intermolecular interaction for these clusters has been decomposed in HFBz-HFBz and in K(+)-HFBz contributions, using a potential model based on different decompositions of the molecular polarizability of hexafluorobenzene. Putative global minimum structures of microsolvation clusters up to 21 hexafluorobenzene molecules were obtained and compared with the analogous K(+)-benzene clusters reported in our previous work (J. Phys. Chem. A 2012, 116, 4947-4956). We have found that both K(+)-(Bz)n and K(+)-(HFBz)n clusters show a strong magic number around the closure of the first solvation shell. Nonetheless, all K(+)-benzene clusters have essentially the same first solvation shell geometry with four solvent molecules around the ion, whereas the corresponding one for K(+)-(HFBz)n is completed with nine HFBz species, and its structural motif varies as n increases. This is attributed to the ion-solvent interaction that has a larger magnitude for K(+)-Bz than in the case of K(+)-HFBz. In addition, the ability of having more HFBz than Bz molecules around K(+) in the first solvation shell is intimately related to the inversion in the sign of the quadrupole moment of the two solvent species, which leads to a distinct ion-solvent geometry of approach.
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Affiliation(s)
- J M C Marques
- Departamento de Química, Universidade de Coimbra, 3004-535 Coimbra, Portugal.
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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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Marques JMC, Llanio-Trujillo JL, Albertí M, Aguilar A, Pirani F. Alkali-ion microsolvation with benzene molecules. J Phys Chem A 2012; 116:4947-56. [PMID: 22515316 DOI: 10.1021/jp302136u] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The target of this investigation is to characterize by a recently developed methodology, the main features of the first solvation shells of alkaline ions in nonpolar environments due to aromatic rings, which is of crucial relevance to understand the selectivity of several biochemical phenomena. We employ an evolutionary algorithm to obtain putative global minima of clusters formed with alkali-ions (M(+)) solvated with n benzene (Bz) molecules, i.e., M(+)-(Bz)(n). The global intermolecular interaction has been decomposed in Bz-Bz and in M(+)-Bz contributions, using a potential model based on different decompositions of the molecular polarizability of benzene. Specifically, we have studied the microsolvation of Na(+), K(+), and Cs(+) with benzene molecules. Microsolvation clusters up to n = 21 benzene molecules are involved in this work and the achieved global minimum structures are reported and discussed in detail. We observe that the number of benzene molecules allocated in the first solvation shell increases with the size of the cation, showing three molecules for Na(+) and four for both K(+) and Cs(+). The structure of this solvation shell keeps approximately unchanged as more benzene molecules are added to the cluster, which is independent of the ion. Particularly stable structures, so-called "magic numbers", arise for various nuclearities of the three alkali-ions. Strong "magic numbers" appear at n = 2, 3, and 4 for Na(+), K(+), and Cs(+), respectively. In addition, another set of weaker "magic numbers" (three per alkali-ion) are reported for larger nuclearities.
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Affiliation(s)
- J M C Marques
- Departamento de Química, Universidade de Coimbra, 3004-535 Coimbra, Portugal.
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Marques JMC, Pais AACC, Abreu PE. On the use of big-bang method to generate low-energy structures of atomic clusters modeled with pair potentials of different ranges. J Comput Chem 2011; 33:442-52. [DOI: 10.1002/jcc.21987] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2011] [Revised: 10/11/2011] [Accepted: 10/12/2011] [Indexed: 01/02/2023]
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Abreu P, Marques J, Pereira F. Electronic structure calculations on the Ar–C6H12 interaction: Application to the microsolvation of the chair conformer. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.02.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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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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Albertí M, Pirani F. Features of Ar Solvation Shells in Neutral and Ionic Clustering: The Competitive Role of Two-Body and Many-Body Interactions. J Phys Chem A 2011; 115:6394-404. [DOI: 10.1021/jp202995s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Margarita Albertí
- IQTCUB, Departament de Química Física, Universitat de Barcelona, Barcelona, Spain
| | - Fernando Pirani
- Dipartimento di Chimica, Università di Perugia, Perugia, Italy
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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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Marques JMC, Llanio-Trujillo JL, Abreu PE, Pereira FB. How Different Are Two Chemical Structures? J Chem Inf Model 2010; 50:2129-40. [DOI: 10.1021/ci100219f] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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
| | - J. L. Llanio-Trujillo
- 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
| | - P. E. Abreu
- 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
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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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Heatwole EM, Prezhdo OV. Analytic dynamics of the Morse oscillator derived by semiclassical closures. J Chem Phys 2009; 130:244111. [DOI: 10.1063/1.3154143] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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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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