1
|
Garg S, Kaur N, Goel N, Molayem M, Grigoryan VG, Springborg M. Properties of Naked Silver Clusters with Up to 100 Atoms as Found with Embedded-Atom and Density-Functional Calculations. Molecules 2023; 28:molecules28073266. [PMID: 37050029 PMCID: PMC10096883 DOI: 10.3390/molecules28073266] [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: 03/03/2023] [Revised: 03/27/2023] [Accepted: 03/31/2023] [Indexed: 04/14/2023] Open
Abstract
The structural and energetic properties of small silver clusters Agn with n = 2-100 atoms are reported. For n = 2-100 the embedded atom model for the calculation of the total energy of a given structure in combination with the basin-hopping search strategy for an unbiased structure optimization has been used to identify the energies and structures of the three energetically lowest-lying isomers. These optimized structures for n = 2-11 were subsequently studied further through density-functional-theory calculations. These calculations provide additional information on the electronic properties of the clusters that is lacking in the embedded-atom calculations. Thereby, also quantities related to the catalytic performance of the clusters are studied. The calculated properties in comparison to other available theoretical and experimental data show a good agreement. Previously unidentified magic (i.e., particularly stable) clusters have been found for n>80. In order to obtain a more detailed understanding of the structural properties of the clusters, various descriptors are used. Thereby, the silver clusters are compared to other noble metals and show some similarities to both copper and nickel systems, and also growth patterns have been identified. All vibrational frequencies of all the clusters have been calculated for the first time, and here we focus on the highest and lowest frequencies. Structural effects on the calculated frequencies were considered.
Collapse
Affiliation(s)
- Shivangi Garg
- Theoretical and Computational Chemistry Group, Department of Chemistry, Centre of Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Navjot Kaur
- Department of Chemistry, Faculty of Science, SGT University, Gurugram 122505, India
| | - Neetu Goel
- Theoretical and Computational Chemistry Group, Department of Chemistry, Centre of Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Mohammad Molayem
- Physical and Theoretical Chemistry, Department of Chemistry, University of Saarland, 66123 Saarbrücken, Germany
| | - Valeri G Grigoryan
- Physical and Theoretical Chemistry, Department of Chemistry, University of Saarland, 66123 Saarbrücken, Germany
| | - Michael Springborg
- Laboratory of Theoretical Chemistry, Department of Chemistry, Namur Institute of Structured Matter (NISM), University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| |
Collapse
|
2
|
Mirdha RH, Naskar P, Chaudhury P. Structural transformation in $$(\hbox {MgO})_{{{n}}}$$ clusters using a gradient-only strategy and its comparison with a full Hessian-based calculation. INDIAN JOURNAL OF PHYSICS 2021; 95:561-570. [DOI: 10.1007/s12648-020-01724-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 11/25/2019] [Indexed: 07/19/2023]
|
3
|
Ghorai S, Naskar P, Chaudhury P. An investigation on the structure, spectroscopy, and thermodynamic aspects of clusters: A combined Parallel tempering and
DFT
based study. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 2020; 120. [DOI: 10.1002/qua.26270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/21/2020] [Indexed: 07/19/2023]
Affiliation(s)
- Sankar Ghorai
- Department of ChemistryUniversity of Calcutta Kolkata India
| | - Pulak Naskar
- Department of ChemistryUniversity of Calcutta Kolkata India
| | | |
Collapse
|
4
|
Ghosh K, Sharma R, Chaudhury P. Structure elucidation and construction of isomerisation pathways in small to moderate-sized (6-27) MgO nanoclusters: an adaptive mutation simulated annealing based analysis with quantum chemical calculations. Phys Chem Chem Phys 2020; 22:9616-9629. [PMID: 32324181 DOI: 10.1039/c9cp06947j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Determination of global minimum structures and elucidation of reaction paths or minimum energy paths between low-lying minima are of great chemical importance. To that end, we have used our own Adaptive Mutation Simulated Annealing method to determine the global minimum and the minimum energy paths for various isomerisation reactions for small to moderate-sized (MgO)n (n = 6-27) clusters, using the Born-Mayer potential with suitable parameter values. The minimum energy structures obtained by us match well with previously reported data and are used as guess structures for further optimisation at the DFT level (using the B3LYP functional and DGDZVP basis set). Our optimised structures are found to match very well with the further DFT optimised structures, where the comparison is done by determining the root mean square deviation values as well as the radial distribution function profiles. A scheme is proposed to determine the minimum energy paths for isomerisation reactions for some cluster sizes where the transition state/s obtained by us, at very low computational cost, match well with those obtained from further optimisation using DFT calculations. We have shown the efficacy of our method in determining the reaction pathways, even for cases that involve multi-step reactions.
Collapse
Affiliation(s)
- Kuntal Ghosh
- Department of Chemistry, St. Xavier's College, 30 Mother Teresa Sarani, Kolkata - 700016, India.
| | - Rahul Sharma
- Department of Chemistry, St. Xavier's College, 30 Mother Teresa Sarani, Kolkata - 700016, India.
| | - Pinaki Chaudhury
- Department of Chemistry, University of Calcutta, Kolkata - 700009, India.
| |
Collapse
|
5
|
Tangarife E, Romero AH, Mejía-López J. A charge optimized many-body potential for iron/iron-fluoride systems. Phys Chem Chem Phys 2019; 21:20118-20131. [PMID: 31482890 DOI: 10.1039/c9cp01927h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A classical interatomic potential for iron/iron-fluoride systems is developed in the framework of the charge optimized many-body (COMB) potential. This interatomic potential takes into consideration the effects of charge transfer and many-body interactions depending on the chemical environment. The potential is fitted to a training set composed of both experimental and ab initio results of the cohesive energies of several Fe and FeF2 crystal phases, the two fluorine molecules F2 and the F2-1 dissociation energy curve, the Fe and FeF2 lattice parameters of the ground state crystalline phase, and the elastic constants of the body centered cubic Fe structure. The potential is tested in an NVT ensemble for different initial structural configurations as the crystal ground state phases, F2 molecules, iron clusters, and iron nanospheres. In particular, we model the FeF2/Fe bilayer and multilayer interfaces, as well as a system of square FeF2 nanowires immersed in an iron solid. It has been shown that there exists a reordering of the atomic positions for F and Fe atoms at the interface zone; this rearrangement leads to an increase in the charge transfer among the atoms that make the interface and put forward a possible mechanism of the exchange bias origin based on asymmetric electric charge transfer in the different spin channels.
Collapse
Affiliation(s)
- E Tangarife
- Centro de Investigación en Nanotecnología y Materiales Avanzados CIEN-UC, Facultad de Física, Pontificia Universidad Católica de Chile, CEDENNA, Santiago, Chile.
| | | | | |
Collapse
|
6
|
Structural changes upon electronic excitation in 1,2-dimethoxybenzene from rotationally resolved electronic spectroscopy of various isotopologues. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.01.074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
7
|
Yen TW, Lai SK. The subtlety of resolving orbital angular momenta in calculating Hubbard U parameters in the density functional tight-binding theory and its delicacy is illustrated by the calculated magnetic properties of carbon clusters. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2334-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Affiliation(s)
- Guillermo Avendaño-Franco
- Department of Physics and Astronomy, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Aldo H. Romero
- Department of Physics and Astronomy, West Virginia University, Morgantown, West Virginia 26506, United States
| |
Collapse
|
10
|
Panosetti C, Krautgasser K, Palagin D, Reuter K, Maurer RJ. Global Materials Structure Search with Chemically Motivated Coordinates. NANO LETTERS 2015; 15:8044-8048. [PMID: 26444084 DOI: 10.1021/acs.nanolett.5b03388] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Identification of relevant reaction pathways in ever more complex composite materials and nanostructures poses a central challenge to computational materials discovery. Efficient global structure search, tailored to identify chemically relevant intermediates, could provide the necessary first-principles atomistic insight to enable a rational process design. In this work we modify a common feature of global geometry optimization schemes by employing automatically generated collective curvilinear coordinates. The similarity of these coordinates to molecular vibrations enhances the generation of chemically meaningful trial structures for covalently bound systems. In the application to hydrogenated Si clusters, we concomitantly observe a significantly increased efficiency in identifying low-energy structures and exploit it for an extensive sampling of potential products of silicon-cluster soft landing on Si(001) surfaces.
Collapse
Affiliation(s)
- Chiara Panosetti
- Department Chemie, Technische Universität München , Lichtenbergstr. 4, D-85748 Garching, Germany
| | - Konstantin Krautgasser
- 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, United States
| |
Collapse
|
11
|
Curotto E. Ion-Stockmayer clusters: Minima, classical thermodynamics, and variational ground state estimates of Li+(CH3NO2)n(n= 1–20). J Chem Phys 2015; 143:214301. [DOI: 10.1063/1.4936587] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- E. Curotto
- Department of Chemistry and Physics, Arcadia University, Glenside, Pennsylvania 19038-3295, USA
| |
Collapse
|
12
|
|
13
|
Hanson-Heine MW, Besley NA. Spectroscopic and structural analysis of mixed carbon dioxide and fluorinated methane clusters. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.08.056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
14
|
Yen TW, Lai SK. Use of density functional theory method to calculate structures of neutral carbon clusters Cn (3 ≤ n ≤ 24) and study their variability of structural forms. J Chem Phys 2015; 142:084313. [PMID: 25725737 DOI: 10.1063/1.4908561] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In this work, we present modifications to the well-known basin hopping (BH) optimization algorithm [D. J. Wales and J. P. Doye, J. Phys. Chem. A 101, 5111 (1997)] by incorporating in it the unique and specific nature of interactions among valence electrons and ions in carbon atoms through calculating the cluster's total energy by the density functional tight-binding (DFTB) theory, using it to find the lowest energy structures of carbon clusters and, from these optimized atomic and electronic structures, studying their varied forms of topological transitions, which include a linear chain, a monocyclic to a polycyclic ring, and a fullerene/cage-like geometry. In this modified BH (MBH) algorithm, we define a spatial volume within which the cluster's lowest energy structure is to be searched, and introduce in addition a cut-and-splice genetic operator to increase the searching performance of the energy minimum than the original BH technique. The present MBH/DFTB algorithm is, therefore, characteristically distinguishable from the original BH technique commonly applied to nonmetallic and metallic clusters, technically more thorough and natural in describing the intricate couplings between valence electrons and ions in a carbon cluster, and thus theoretically sound in putting these two charged components on an equal footing. The proposed modified minimization algorithm should be more appropriate, accurate, and precise in the description of a carbon cluster. We evaluate the present algorithm, its energy-minimum searching in particular, by its optimization robustness. Specifically, we first check the MBH/DFTB technique for two representative carbon clusters of larger size, i.e., C60 and C72 against the popular cut-and-splice approach [D. M. Deaven and K. M. Ho, Phys. Rev. Lett. 75, 288 (1995)] that normally is combined with the genetic algorithm method for finding the cluster's energy minimum, before employing it to investigate carbon clusters in the size range C3-C24 studying their topological transitions. An effort was also made to compare our MBH/DFTB and its re-optimized results carried out by full density functional theory (DFT) calculations with some early DFT-based studies.
Collapse
Affiliation(s)
- T W Yen
- Complex Liquids Laboratory, Department of Physics, National Central University, Chungli 320, Taiwan
| | - S K Lai
- Complex Liquids Laboratory, Department of Physics, National Central University, Chungli 320, Taiwan
| |
Collapse
|
15
|
Neogi SG, Chaudhury P. Structure, electronic properties and vibrational spectra of (MgF2)nclusters through a combination of genetic algorithm and DFT-based approach. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1059508] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
16
|
Jiang S, Huang T, Liu YR, Xu KM, Zhang Y, Lv YZ, Huang W. Theoretical study of temperature dependence and Rayleigh scattering properties of chloride hydration clusters. Phys Chem Chem Phys 2014; 16:19241-9. [DOI: 10.1039/c4cp02618g] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
17
|
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]
|
18
|
Liu YR, Wen H, Huang T, Lin XX, Gai YB, Hu CJ, Zhang WJ, Huang W. Structural Exploration of Water, Nitrate/Water, and Oxalate/Water Clusters with Basin-Hopping Method Using a Compressed Sampling Technique. J Phys Chem A 2014; 118:508-16. [DOI: 10.1021/jp4109128] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yi-Rong Liu
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
| | - Hui Wen
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
| | - Teng Huang
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
| | - Xiao-Xiao Lin
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
| | - Yan-Bo Gai
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
| | - Chang-Jin Hu
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
| | - Wei-Jun Zhang
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
- School of Environmental Science & Optoelectronic Technology, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Wei Huang
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
- School of Environmental Science & Optoelectronic Technology, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| |
Collapse
|
19
|
Jiang S, Liu YR, Huang T, Wen H, Xu KM, Zhao WX, Zhang WJ, Huang W. Study of Cl−(H2O)n(n= 1-4) using basin-hopping method coupled with density functional theory. J Comput Chem 2013; 35:159-65. [DOI: 10.1002/jcc.23477] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 09/24/2013] [Accepted: 10/06/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Shuai Jiang
- Laboratory of Atmospheric Physico-Chemistry; Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences; Hefei Anhui 230031 China
| | - Yi-Rong Liu
- Laboratory of Atmospheric Physico-Chemistry; Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences; Hefei Anhui 230031 China
| | - Teng Huang
- Laboratory of Atmospheric Physico-Chemistry; Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences; Hefei Anhui 230031 China
| | - Hui Wen
- Laboratory of Atmospheric Physico-Chemistry; Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences; Hefei Anhui 230031 China
| | - Kang-Ming Xu
- Laboratory of Atmospheric Physico-Chemistry; Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences; Hefei Anhui 230031 China
| | - Wei-Xiong Zhao
- Laboratory of Atmospheric Physico-Chemistry; Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences; Hefei Anhui 230031 China
| | - Wei-Jun Zhang
- Laboratory of Atmospheric Physico-Chemistry; Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences; Hefei Anhui 230031 China
- School of Environmental Science and Optoelectronic Technology; University of Science and Technology of China; Hefei Anhui 230026 China
| | - Wei Huang
- Laboratory of Atmospheric Physico-Chemistry; Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences; Hefei Anhui 230031 China
- School of Environmental Science and Optoelectronic Technology; University of Science and Technology of China; Hefei Anhui 230026 China
| |
Collapse
|
20
|
Ganguly Neogi S, Chaudhury P. Structural, spectroscopic aspects, and electronic properties of (TiO2)nclusters: A study based on the use of natural algorithms in association with quantum chemical methods. J Comput Chem 2013; 35:51-61. [DOI: 10.1002/jcc.23465] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 07/27/2013] [Accepted: 09/16/2013] [Indexed: 12/21/2022]
Affiliation(s)
- Soumya Ganguly Neogi
- Department of Chemistry; University of Calcutta; 92, A.P.C. Road Kolkata 700 009 India
| | - Pinaki Chaudhury
- Department of Chemistry; University of Calcutta; 92, A.P.C. Road Kolkata 700 009 India
| |
Collapse
|
21
|
Structural and spectroscopic studies of carbon dioxide clusters: a combined genetic algorithm and DFT based study. Struct Chem 2013. [DOI: 10.1007/s11224-013-0360-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
22
|
Mella M, Curotto E. Quantum simulations of the hydrogen molecule on ammonia clusters. J Chem Phys 2013; 139:124319. [PMID: 24089779 DOI: 10.1063/1.4821648] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mixed ammonia-hydrogen molecule clusters [H2-(NH3)n] have been studied with the aim of exploring the quantitative importance of the H2 quantum motion in defining their structure and energetics. Minimum energy structures have been obtained employing genetic algorithm-based optimization methods in conjunction with accurate pair potentials for NH3-NH3 and H2-NH3. These include both a full 5D potential and a spherically averaged reduced surface mimicking the presence of a para-H2. All the putative global minima for n ≥ 7 are characterized by H2 being adsorbed onto a rhomboidal ammonia tetramer motif formed by two double donor and two double acceptor ammonia molecules. In a few cases, the choice of specific rhombus seems to be directed by the vicinity of an ammonia ad-molecule. Diffusion Monte Carlo simulations on a subset of the species obtained highlighted important quantum effects in defining the H2 surface distribution, often resulting in populating rhomboidal sites different from the global minimum one, and showing a compelling correlation between local geometrical features and the relative stability of surface H2. Clathrate-like species have also been studied and suggested to be metastable over a broad range of conditions if formed.
Collapse
Affiliation(s)
- Massimo Mella
- Dipartimento di Scienze ed Alta Tecnologia, Università degli Studi dell'Insubria, via Valleggio 11, 22100 Como, Italy
| | | |
Collapse
|
23
|
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]
|
24
|
Rondina GG, Da Silva JLF. Revised Basin-Hopping Monte Carlo Algorithm for Structure Optimization of Clusters and Nanoparticles. J Chem Inf Model 2013; 53:2282-98. [DOI: 10.1021/ci400224z] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Gustavo G. Rondina
- Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, 13560-970, São
Carlos, SP, Brazil
| | - Juarez L. F. Da Silva
- Instituto de Química de São Carlos, Universidade de São Paulo, Caixa Postal 780, 13560-970, São
Carlos, SP, Brazil
| |
Collapse
|
25
|
Neogi SG, Chaudhury P. Structure and spectroscopic aspects of water-halide ion clusters: A study based on a conjunction of stochastic and quantum chemical methods. J Comput Chem 2012; 34:471-91. [DOI: 10.1002/jcc.23156] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 09/01/2012] [Accepted: 09/07/2012] [Indexed: 01/17/2023]
|
26
|
Do H, Besley NA. Structural optimization of molecular clusters with density functional theory combined with basin hopping. J Chem Phys 2012; 137:134106. [DOI: 10.1063/1.4755994] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
27
|
Neogi SG, Chaudhury P. Structure and spectroscopy of water-fluoride microclusters: A combined genetic algorithm and DFT-based study. J Comput Chem 2011; 33:629-39. [DOI: 10.1002/jcc.21994] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 10/14/2011] [Accepted: 10/15/2011] [Indexed: 01/14/2023]
|
28
|
Nandy S, Sharma R, Bhattacharyya S. Solving symmetric eigenvalue problem via genetic algorithms: Serial versus parallel implementation. Appl Soft Comput 2011. [DOI: 10.1016/j.asoc.2011.02.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
29
|
Lubombo C, Curotto E, Janeiro Barral PE, Mella M. Thermodynamic properties of ammonia clusters (NH3)n n=2–11: Comparing classical and quantum simulation results for hydrogen bonded species. J Chem Phys 2009; 131:034312. [DOI: 10.1063/1.3159398] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
30
|
Genetic Algorithms in Application to the Geometry Optimization of Nanoparticles. ALGORITHMS 2009. [DOI: 10.3390/a2010410] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
31
|
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
| |
Collapse
|
32
|
Rogan J, García G, Ramírez M, Muñoz V, Alejandro Valdivia J, Andrade X, Ramírez R, Kiwi M. The structure and properties of small Pd clusters. NANOTECHNOLOGY 2008; 19:205701. [PMID: 21825744 DOI: 10.1088/0957-4484/19/20/205701] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The zero-temperature minimal energy structure of small free-standing Pd clusters (14≤N≤21, where N is the number of atoms in the cluster), their characteristics and their magnetic configurations are investigated. Results obtained using five different phenomenological many-body potentials (implemented in combination with a genetic algorithm search) are refined by means of various density functional theory (DFT) techniques. The agreement and differences between the results obtained with our procedure, using these five potentials, are displayed in detail. While phenomenological potentials yield values that approach the minimal energies of larger clusters, as compared with DFT results, they fail to predict the right symmetry group for some of the clusters with N>14. We find that the minimal energy configurations are not necessarily associated with high symmetry of the atomic arrangement. Actually, several cases of previously overlooked low symmetry structures turn out to have lower energies than more symmetric ones.
Collapse
Affiliation(s)
- José Rogan
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago 1, Chile
| | | | | | | | | | | | | | | |
Collapse
|
33
|
Avilés MW, McCandless ML, Curotto E. Stereographic projection path integral simulations of (HCl)n clusters (n=2–5): Evidence of quantum induced melting in small hydrogen bonded networks. J Chem Phys 2008; 128:124517. [DOI: 10.1063/1.2837802] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
34
|
Francisco E, Martín Pendás A, Blanco MA. Global optimization of ionic Mg(n)F(2n) (n=1-30) clusters. J Chem Phys 2007; 123:234305. [PMID: 16392918 DOI: 10.1063/1.2138688] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The global optimization basin-hopping (BH) method has been used to locate the global minima (GM) of Mg(n)F(2n) (n=1-30) clusters using a Born-Mayer-type potential. Some of the GM were particularly difficult to find, requiring more than 1.5 x 10(4) BH steps. We have found that both the binding energy per MgF2 unit and the effective volume of the GM isomers increase almost linearly with n, and that cluster symmetry decreases with cluster size. The data derived from the BH runs reveal a growing density of local minima just above the GM as n increases. Despite this, the attraction basin around each GM is relatively large, since after all their atomic coordinates are randomly displaced by values as high as 2.0 bohrs, the perturbed structures, upon reoptimization, relax back to the GM in more than 50% of the cases (except for n=10 and 11). The relative stabilities derived from energy second differences suggest that n=8,10,13,15, and 20 are probably the magic numbers for these systems. Mass spectrum experiments would be very useful to clarify this issue.
Collapse
Affiliation(s)
- E Francisco
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, E-33006 Oviedo, Spain.
| | | | | |
Collapse
|
35
|
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]
|
36
|
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.
Collapse
Affiliation(s)
- Seth T Call
- Department of Computer Science, Utah State University, Logan, Utah 84322-0300, USA
| | | | | |
Collapse
|
37
|
Rogan J, García G, Loyola C, Orellana W, Ramírez R, Kiwi M. Alternative search strategy for minimal energy nanocluster structures: The case of rhodium, palladium, and silver. J Chem Phys 2006; 125:214708. [PMID: 17166041 DOI: 10.1063/1.2402168] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An alternative strategy to find the minimal energy structure of nanoclusters is presented and implemented. We use it to determine the structure of metallic clusters. It consists in an unbiased search, with a global minimum algorithm: conformational space annealing. First, we find the minima of a many-body phenomenological potential to create a data bank of putative minima. This procedure assures us the generation of a set of cluster configurations of large diversity. Next, the clusters in this data bank are relaxed by ab initio techniques to obtain their energies and geometrical structures. The scheme is successfully applied to magic number 13 atom clusters of rhodium, palladium, and silver. We obtained minimal energy cluster structures not previously reported, which are different from the phenomenological minima. Moreover, they are not always highly symmetric, thus casting some doubt on the customary biased search scheme, which consists in relaxing with density functional theory global minima chosen among high symmetry structures obtained by means of phenomenological potentials.
Collapse
Affiliation(s)
- José Rogan
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago 1, Chile
| | | | | | | | | | | |
Collapse
|
38
|
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.
Collapse
|
39
|
Avilés MW, Gray PT, Curotto E. Stereographic projection path-integral simulations of (HF)n clusters. J Chem Phys 2006; 124:174305. [PMID: 16689569 DOI: 10.1063/1.2192773] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We perform several quantum canonical ensemble simulations of (HF)(n) clusters. The HF stretches are rigid, and the stereographic projection path-integral method is employed for the simulation in the resulting curved configuration space. We make use of the reweighted random series techniques to accelerate the convergence of the path-integral simulation with respect to the number of path coefficients. We develop and test estimators for the total energy and heat capacity based on a finite difference approach for non-Euclidean spaces. The quantum effects at temperatures below 400 K are substantial for all sizes. We observe interesting thermodynamic behaviors in the quantum simulations of the octamer and the heptamer.
Collapse
Affiliation(s)
- Michael W Avilés
- Department of Chemistry and Physics, Arcadia University, Glenside, Pennsylvania 19038, USA
| | | | | |
Collapse
|
40
|
An approach based on genetic algorithms and DFT for studying clusters: (H2O)n (2⩽n⩽13) cluster analysis. Chem Phys 2006. [DOI: 10.1016/j.chemphys.2005.10.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
41
|
|
42
|
Schmitt M, Krügler D, Böhm M, Ratzer C, Bednarska V, Kalkman I, Meerts WL. A genetic algorithm based determination of the ground and excited (1Lb) state structure and the orientation of the transition dipole moment of benzimidazole. Phys Chem Chem Phys 2006; 8:228-35. [PMID: 16482265 DOI: 10.1039/b512686j] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structure of benzimidazole has been determined in the electronic ground and excited states using rotationally resolved electronic spectroscopy. The rovibronic spectra of four isotopomers and subsequently the structure of benzimidazole have been automatically assigned and fitted using a genetic algorithm based fitting strategy. The lifetimes of the deuterated isotopomers have been shown to depend on the position of deuteration. The angle of the transition dipole moment with the inertial a-axis could be determined to be -30 degrees. Structures and transition dipole moment orientation have been calculated at various levels of theory and were compared to the experimental results.
Collapse
Affiliation(s)
- Michael Schmitt
- Heinrich-Heine-Universität, Institut für Physikalische Chemie, D-40225 Düsseldorf, Germany.
| | | | | | | | | | | | | |
Collapse
|
43
|
Pav DM, Curotto E. Parallel tempering simulations of the 13-center Lennard-Jones dipole-dipole cluster (muD=0-->0.5 a.u.). J Chem Phys 2005; 123:144301. [PMID: 16238385 DOI: 10.1063/1.2049279] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigate the thermodynamic behavior of the thirteen center uniform Lennard-Jones dipole-dipole cluster [(LJDD)(13)] for a wide range of dipole moment strengths. We find a relatively wide range of potential parameters where solid-solid coexistence manifests itself. Using structural characterization methods we determine the shape of the few isomers that contribute to the solid-solid coexistence region. The thermal distributions of the size of the net dipole moment are broad even at the coldest temperatures of the simulation where the (LJDD)(13) cluster is solid.
Collapse
Affiliation(s)
- Dawn M Pav
- Department of Chemistry and Physics, Arcadia University, Glenside, Pennsylvania 19038, USA
| | | |
Collapse
|
44
|
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
| |
Collapse
|
45
|
|
46
|
Pu J, Truhlar DG. Use of Block Hessians for the Optimization of Molecular Geometries. J Chem Theory Comput 2004; 1:54-60. [DOI: 10.1021/ct0400020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jingzhi Pu
- Department of Chemistry and Supercomputing Institute, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| |
Collapse
|
47
|
Oppenheimer CA, Curotto E. Parameter space minimization methods: Applications to Lennard-Jones–dipole-dipole clusters. J Chem Phys 2004; 121:6226-39. [PMID: 15446915 DOI: 10.1063/1.1786916] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The morphology of the uniform Lennard-Jones-dipole-dipole cluster with 13 centers (LJDD)13 is investigated over a relatively wide range of values of the dipole moment. We introduce and compare several necessary modifications of the basin-hopping algorithm for global optimization to improve its efficiency. We develop a general algorithm for T=0 Brownian dynamics in curved spaces, and a graph theoretical approach necessary for the elimination of dissociated states. We find that the (LJDD)13 cluster has icosahedral symmetry for small to moderate values of the dipole moment. As the dipole moment increases, however, its morphology shifts to an hexagonal antiprism, and eventually to a ring.
Collapse
Affiliation(s)
- Craig A Oppenheimer
- Department of Chemistry and Physics, Arcadia University, Glenside, Pennsylvania 19038-3295, USA
| | | |
Collapse
|
48
|
Nigra P, Freeman DL, Sabo D, Doll JD. On the encapsulation of nickel clusters by molecular nitrogen. J Chem Phys 2004; 121:475-82. [PMID: 15260569 DOI: 10.1063/1.1757435] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The structures and energetic effects of molecular nitrogen adsorbates on nickel clusters are investigated using an extended Huckel model coupled with two models of the adsorbate-nickel interaction. The potential parameters for the adsorbates are chosen to mimic experimental information about the binding strength of nitrogen on both cluster and bulk surface phases of nickel. The first model potential is a simple Lennard-Jones interaction that leads to binding sites in holes defined by sets of near-neighbor nickel atoms. The second model potential has a simple three-body form that forces the model nitrogen adsorbates to bind directly to single nickel atoms. Significant rearrangement of the core nickel structures are found in both models. A disconnectivity graph analysis of the potential energy surfaces implies that the rearrangements arise from low transition state barriers and the small differences between available isomers in the nickel core.
Collapse
Affiliation(s)
- Pablo Nigra
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, USA
| | | | | | | |
Collapse
|
49
|
|
50
|
Marim L, Lemes M, Dal Pino A. Ground-state of silicon clusters by neural network assisted genetic algorithm. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/j.theochem.2003.08.123] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|