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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: 0] [Impact Index Per Article: 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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Ball BT, Vanovac S, Odbadrakh TT, Shields GC. Monomers of Glycine and Serine Have a Limited Ability to Hydrate in the Atmosphere. J Phys Chem A 2021; 125:8454-8467. [PMID: 34529444 DOI: 10.1021/acs.jpca.1c05466] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The role of atmospheric aerosols on climate change is one of the biggest uncertainties in most global climate models. Organic aerosols have been identified as potential cloud condensation nuclei (CCN), and amino acids are organic molecules that could serve as CCN. Amino acids make up a significant portion of the total organic material in the atmosphere, and herein we present a systematic study of hydration for two of the most common atmospheric amino acids, glycine and serine. We compute DLPNO/CCSD(T)//M08-HX/MG3S thermodynamic properties and atmospheric concentrations of Gly(H2O)n and Ser(H2O)n, where n = 1-5. We predict that serine-water clusters have higher concentrations at n = 1 and 5, while glycine-water clusters have higher concentrations at n = 2-4. However, both glycine and serine are inferred to exist primarily in their nonhydrated monomer forms in the absence of other species such as sulfuric acid.
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Affiliation(s)
- Benjamin T Ball
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Sara Vanovac
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Tuguldur T Odbadrakh
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - George C Shields
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
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Dittner M, Hartke B. Globally Optimal Catalytic Fields - Inverse Design of Abstract Embeddings for Maximum Reaction Rate Acceleration. J Chem Theory Comput 2018; 14:3547-3564. [PMID: 29883539 DOI: 10.1021/acs.jctc.8b00151] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The search for, and understanding of, good catalysts for chemical reactions is a central issue for chemists. Here, we present first steps toward developing a general computational framework to better support this task. This framework combines efficient, unbiased global optimization techniques with an abstract representation of the catalytic environment, to shrink the search space. To analyze the resulting catalytic embeddings, we employ dimensionality reduction and clustering techniques. This not only provides an inverse design approach to new catalytic embeddings but also illuminates the actual interactions behind catalytic effects. All this is illustrated here with a strictly electrostatic model for the environment and with two versions of a selected example reaction. We close with detailed discussions of future improvements of our framework.
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Affiliation(s)
- Mark Dittner
- Institute for Physical Chemistry , Christian-Albrechts-University Kiel , 24098 Kiel , Germany
| | - Bernd Hartke
- Institute for Physical Chemistry , Christian-Albrechts-University Kiel , 24098 Kiel , Germany
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Krautgasser K, Panosetti C, Palagin D, Reuter K, Maurer RJ. Global structure search for molecules on surfaces: Efficient sampling with curvilinear coordinates. J Chem Phys 2017; 145:084117. [PMID: 27586914 DOI: 10.1063/1.4961259] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Efficient structure search is a major challenge in computational materials science. We present a modification of the basin hopping global geometry optimization approach that uses a curvilinear coordinate system to describe global trial moves. This approach has recently been shown to be efficient in structure determination of clusters [C. Panosetti et al., Nano Lett. 15, 8044-8048 (2015)] and is here extended for its application to covalent, complex molecules and large adsorbates on surfaces. The employed automatically constructed delocalized internal coordinates are similar to molecular vibrations, which enhances the generation of chemically meaningful trial structures. By introducing flexible constraints and local translation and rotation of independent geometrical subunits, we enable the use of this method for molecules adsorbed on surfaces and interfaces. For two test systems, trans-β-ionylideneacetic acid adsorbed on a Au(111) surface and methane adsorbed on a Ag(111) surface, we obtain superior performance of the method compared to standard optimization moves based on Cartesian coordinates.
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Affiliation(s)
- Konstantin Krautgasser
- Department Chemie, Technische Universität München, Lichtenbergstr. 4, D-85748 Garching, Germany
| | - Chiara Panosetti
- Department Chemie, Technische Universität München, Lichtenbergstr. 4, D-85748 Garching, Germany
| | - Dennis Palagin
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Karsten Reuter
- Department Chemie, Technische Universität München, Lichtenbergstr. 4, D-85748 Garching, Germany
| | - Reinhard J Maurer
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
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Réal F, Gomes ASP, Guerrero Martínez YO, Ayed T, Galland N, Masella M, Vallet V. Structural, dynamical, and transport properties of the hydrated halides: How do At(-) bulk properties compare with those of the other halides, from F(-) to I(-)? J Chem Phys 2016; 144:124513. [PMID: 27036467 DOI: 10.1063/1.4944613] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The properties of halides from the lightest, fluoride (F(-)), to the heaviest, astatide (At(-)), have been studied in water using a polarizable force-field approach based on molecular dynamics (MD) simulations at the 10 ns scale. The selected force-field explicitly treats the cooperativity within the halide-water hydrogen bond networks. The force-field parameters have been adjusted to ab initio data on anion/water clusters computed at the relativistic Möller-Plesset second-order perturbation theory level of theory. The anion static polarizabilities of the two heaviest halides, I(-) and At(-), were computed in the gas phase using large and diffuse atomic basis sets, and taking into account both electron correlation and spin-orbit coupling within a four-component framework. Our MD simulation results show the solvation properties of I(-) and At(-) in aqueous phase to be very close. For instance, their first hydration shells are structured and encompass 9.2 and 9.1 water molecules at about 3.70 ± 0.05 Å, respectively. These values have to be compared to the F(-), Cl(-), and Br(-) ones, i.e., 6.3, 8.4, and 9.0 water molecules at 2.74, 3.38, and 3.55 Å, respectively. Moreover our computations predict the solvation free energy of At(-) in liquid water at ambient conditions to be 68 kcal mol(-1), a value also close the I(-) one, about 70 kcal mol(-1). In all, our simulation results for I(-) are in excellent agreement with the latest neutron- and X-ray diffraction studies. Those for the At(-) ion are predictive, as no theoretical or experimental data are available to date.
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Affiliation(s)
- Florent Réal
- Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, F-59000 Lille, France
| | - André Severo Pereira Gomes
- Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, F-59000 Lille, France
| | | | - Tahra Ayed
- CEISAM UMR CNRS 6230, Université de Nantes, 2 Rue de la Houssinière, BP 92208 F-44322 Nantes Cedex 3, France
| | - Nicolas Galland
- CEISAM UMR CNRS 6230, Université de Nantes, 2 Rue de la Houssinière, BP 92208 F-44322 Nantes Cedex 3, France
| | - Michel Masella
- Laboratoire de Biologie Structurale et Radiobiologie, Service de Bioénergétique, Biologie Structurale et Mécanismes, Institut de Biologie et de Technologies de Saclay, CEA Saclay, F-91191 Gif sur Yvette Cedex, France
| | - Valérie Vallet
- Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, F-59000 Lille, France
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Abburu S, Venkatraman V, Alsberg BK. TD-DFT based fine-tuning of molecular excitation energies using evolutionary algorithms. RSC Adv 2016. [DOI: 10.1039/c5ra22800j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
An evolutionary de novo design method is presented to fine-tune the excitation energies of molecules calculated using time-dependent density functional theory (TD-DFT).
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Affiliation(s)
- Sailesh Abburu
- Department of Chemistry
- Norwegian University of Science and Technology (NTNU)
- 7491 Trondheim
- Norway
| | - Vishwesh Venkatraman
- Department of Chemistry
- Norwegian University of Science and Technology (NTNU)
- 7491 Trondheim
- Norway
| | - Bjørn K. Alsberg
- Department of Chemistry
- Norwegian University of Science and Technology (NTNU)
- 7491 Trondheim
- Norway
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Supady A, Blum V, Baldauf C. First-Principles Molecular Structure Search with a Genetic Algorithm. J Chem Inf Model 2015; 55:2338-48. [DOI: 10.1021/acs.jcim.5b00243] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Adriana Supady
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195 Berlin, Germany
| | - Volker Blum
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195 Berlin, Germany
- Department of Mechanical Engineering & Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Carsten Baldauf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195 Berlin, Germany
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Dittner M, Müller J, Aktulga HM, Hartke B. Efficient global optimization of reactive force-field parameters. J Comput Chem 2015; 36:1550-61. [DOI: 10.1002/jcc.23966] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/09/2015] [Accepted: 05/15/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Mark Dittner
- Institute for Physical Chemistry, Christian-Albrechts-University; Olshausenstr. 40 24098 Kiel Germany
| | - Julian Müller
- Institute for Physical Chemistry, Christian-Albrechts-University; Olshausenstr. 40 24098 Kiel Germany
| | - Hasan Metin Aktulga
- Department of Computer Science and Engineering; Michigan State University; East Lansing Michigan 48824
- Computational Research Division; Lawrence Berkeley National Laboratory; Berkeley California 94720
| | - Bernd Hartke
- Institute for Physical Chemistry, Christian-Albrechts-University; Olshausenstr. 40 24098 Kiel Germany
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Structure, spectroscopy and electronic properties of neutral lattice-like (MgO) n clusters: a study based on a blending of DFT with stochastic algorithms inspired by natural processes. Struct Chem 2014. [DOI: 10.1007/s11224-014-0394-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Dresselhaus T, Yang J, Kumbhar S, Waller MP. Hybrid Metaheuristic Approach for Nonlocal Optimization of Molecular Systems. J Chem Theory Comput 2013; 9:2137-49. [DOI: 10.1021/ct301079m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Thomas Dresselhaus
- Organisch-Chemisches
Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße
40, 48149 Münster, Germany
| | - Jack Yang
- Organisch-Chemisches
Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße
40, 48149 Münster, Germany
| | - Sadhana Kumbhar
- Organisch-Chemisches
Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße
40, 48149 Münster, Germany
| | - Mark P. Waller
- Organisch-Chemisches
Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße
40, 48149 Münster, Germany
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13
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Raeker T, Carstensen NO, Hartke B. Simulating a Molecular Machine in Action. J Phys Chem A 2012; 116:11241-8. [DOI: 10.1021/jp305258b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tim Raeker
- Institut für Physikalische Chemie, Christian-Albrechts-Universität, Olshausenstraße
40, D-24098 Kiel, Germany
| | - Niss Ole Carstensen
- Institut für Physikalische Chemie, Christian-Albrechts-Universität, Olshausenstraße
40, D-24098 Kiel, Germany
| | - Bernd Hartke
- Institut für Physikalische Chemie, Christian-Albrechts-Universität, Olshausenstraße
40, D-24098 Kiel, Germany
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Samanta S, Qin C, Lough AJ, Woolley GA. Bidirectional photocontrol of peptide conformation with a bridged azobenzene derivative. Angew Chem Int Ed Engl 2012; 51:6452-5. [PMID: 22644657 DOI: 10.1002/anie.201202383] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Indexed: 11/07/2022]
Abstract
It goes both ways: A thiol-reactive cross-linker based on a bridged azobenzene derivative permits photoreversible control of peptide conformation on irradiation with violet (407 nm) and green (500-550 nm) light (see picture) through isomerization of the cross-linker. The large separation of the absorbance bands of the cis (yellow) and trans (red) isomers enables complete bidirectional photoswitching.
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Affiliation(s)
- Subhas Samanta
- Dept. of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
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15
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Samanta S, Qin C, Lough AJ, Woolley GA. Bidirectional Photocontrol of Peptide Conformation with a Bridged Azobenzene Derivative. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202383] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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16
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Heuristic approaches to the optimization of acceptor systems in bulk heterojunction cells: a computational study. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1191-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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Trumm M, Martínez YOG, Réal F, Masella M, Vallet V, Schimmelpfennig B. Modeling the hydration of mono-atomic anions from the gas phase to the bulk phase: The case of the halide ions F−, Cl−, and Br−. J Chem Phys 2012; 136:044509. [DOI: 10.1063/1.3678294] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Hartke B. Global optimization. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.70] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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