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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
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Ghorai S, Naskar P, Chaudhury P. Construction of elementary reaction paths of pure and mixed Argon-Xenon clusters : a parallel tempering based study. Struct Chem 2020. [DOI: 10.1007/s11224-019-01486-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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3
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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.
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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.
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Mirdha RH, Naskar P, Chaudhury P. Constructing transformation paths for conformational changes in (MgF 2) n clusters using a stochastic procedure. Mol Phys 2020. [DOI: 10.1080/00268976.2019.1645368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
| | - Pulak Naskar
- Department of Chemistry, University of Calcutta, Kolkata, India
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Naskar P, Talukder S, Ghosh S, Chaudhury P. Controlling the isomerization dynamics of iodide acetonitrile dimer complex by optimally designed electromagnetic field: A wave packet based approach. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 2019; 119:e25927. [DOI: 10.1002/qua.25927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
Affiliation(s)
- Pulak Naskar
- Department of ChemistryUniversity of Calcutta Kolkata India
| | - Srijeeta Talukder
- School of Chemical SciencesIndian Association for the Cultivation of Science Kolkata India
| | - Subhasree Ghosh
- Department of ChemistrySerampore College Serampore West Bengal India
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6
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Naskar P. Structural and spectroscopic aspects of SCN (-)(H 2O) n clusters and the temperature dependency of the isomers: a parallel tempering based approach. Mol Phys 2019. [DOI: 10.1080/00268976.2018.1528395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Pulak Naskar
- Department of Chemistry, University of Calcutta, Kolkata, India
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González Torres M, Villarreal-Ramírez E, Moyaho Bernal MDLA, Álvarez M, González-Valdez J, Gutiérrez Uribe JA, Leyva Gómez G, Cortez JRC. Insights into the application of polyhydroxyalkanoates derivatives from the combination of experimental and simulation approaches. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.08.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Naskar P, Roy R, Talukder S, Chaudhury P. Structural, spectroscopic and thermodynamic aspects of azide–water clusters: an approach using a conjugated prescription of stochastic and quantum chemical methods. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1465605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Pulak Naskar
- Department of Chemistry, University of Calcutta, Kolkata, India
| | - Rituparna Roy
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
| | - Srijeeta Talukder
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Kolkata, India
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9
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Ghorai S, Naskar P, Chaudhury P. Role of the vibrational contribution in Coulomb explosion of dicationic neon gas clusters: a parallel tempering based study. Phys Chem Chem Phys 2018; 20:22379-22386. [PMID: 30129648 DOI: 10.1039/c8cp03779e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The problem of Coulomb explosion in dicationic neon gas clusters has been investigated with special emphasis on the role of the vibrational contribution. The problem has been handled by describing the dicationic neon gas system with an adequate potential energy surface comprising dispersive interaction, Coulombic and polarizability containing terms. This potential energy surface, if explored for various sizes of the clusters, shows Coulombic explosion features below a certain threshold size. However this classical treatment fails to account for the correct threshold predicted from other studies including experiments. This signifies that quantum effects play an important role. With the incorporation of the vibrational contribution as the quantum effect, it is seen that reduction in the threshold value indeed occurs and the amount of decrease significantly varies with temperature. The whole study has been done using the stochastic search strategy or parallel tempering to explore the potential energy surface of the system. The stochastic strategy guarantees the achievement of a low energy solution as it is not stuck in local energy basins.
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Affiliation(s)
- Sankar Ghorai
- Department of Chemistry, University of Calcutta, 92 A P C Road, Kolkata 700 009, India.
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Ghorai S, Chaudhury P. Predicting stability limits for pure and doped dicationic noble gas clusters undergoing coulomb explosion: A parallel tempering based study. J Comput Chem 2018; 39:827-838. [PMID: 29282763 DOI: 10.1002/jcc.25156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 12/07/2017] [Accepted: 12/12/2017] [Indexed: 11/10/2022]
Abstract
We have used a replica exchange Monte-Carlo procedure, popularly known as Parallel Tempering, to study the problem of Coulomb explosion in homogeneous Ar and Xe dicationic clusters as well as mixed Ar-Xe dicationic clusters of varying sizes with different degrees of relative composition. All the clusters studied have two units of positive charges. The simulations reveal that in all the cases there is a cutoff size below which the clusters fragment. It is seen that for the case of pure Ar, the value is around 95 while that for Xe it is 55. For the mixed clusters with increasing Xe content, the cutoff limit for suppression of Coulomb explosion gradually decreases from 95 for a pure Ar to 55 for a pure Xe cluster. The hallmark of this study is this smooth progression. All the clusters are simulated using the reliable potential energy surface developed by Gay and Berne (Gay and Berne, Phys. Rev. Lett. 1982, 49, 194). For the hetero clusters, we have also discussed two different ways of charge distribution, that is one in which both positive charges are on two Xe atoms and the other where the two charges are at a Xe atom and at an Ar atom. The fragmentation patterns observed by us are such that single ionic ejections are the favored dissociating pattern. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Sankar Ghorai
- 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
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Mirdha RH, Naskar P, Chaudhury P. Mapping out reaction paths for conformational changes in (M
g
O)
n
clusters: a study based on a stochastic procedure. Struct Chem 2017. [DOI: 10.1007/s11224-017-1049-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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12
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Mirdha RH, Chaudhury P. Constructing a bunch of paths for conformational changes in size specific noble gas cluster: a study using a stochastic procedure. JOURNAL OF MATHEMATICAL CHEMISTRY 2017; 55:1916-1933. [DOI: 10.1007/s10910-017-0771-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
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Naskar P, Talukder S, Chaudhury P. An adaptive mutation simulated annealing based investigation of Coulombic explosion and identification of dissociation patterns in (CO2)n2+ clusters. Phys Chem Chem Phys 2017; 19:9654-9668. [DOI: 10.1039/c7cp00655a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this communication, we would like to discuss the advantages of adaptive mutation simulated annealing (AMSA) over standard simulated annealing (SA) in studying the Coulombic explosion of (CO2)n2+ clusters for n = 20–68, where ‘n’ is the size of the cluster.
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Affiliation(s)
- Pulak Naskar
- Department of Chemistry
- University of Calcutta
- Kolkata – 700 009
- India
| | - Srijeeta Talukder
- Department of Physical Chemistry
- Indian Association for the Cultivation of Science
- Kolkata – 700 032
- India
| | - Pinaki Chaudhury
- Department of Chemistry
- University of Calcutta
- Kolkata – 700 009
- India
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Naskar P, Chaudhury P. An investigation on the structure, spectroscopy and thermodynamic aspects of Br2((-))(H2O)n clusters using a conjunction of stochastic and quantum chemical methods. Phys Chem Chem Phys 2016; 18:16245-57. [PMID: 27251059 DOI: 10.1039/c6cp01960a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work we obtained global as well as local structures of Br2((-))(H2O)n clusters for n = 2 to 6 followed by the study of IR-spectral features and thermochemistry for the structures. The way adopted by us to obtain structures is not the conventional one used in most cases. Here we at first generated excellent quality pre-optimized structures by exploring the suitable empirical potential energy surface using stochastic optimizer simulated annealing. These structures are then further refined using quantum chemical calculations to obtain the final structures, and spectral and thermodynamic features. We clearly showed that our approach results in very quick and better convergence which reduces the computational cost and obviously using the strategy we are able to get one [i.e. global] or more than one [i.e. global and local(s)] energetically lower structures than those which are already reported for a given cluster size. Moreover, IR-spectral results and the evolutionary trends in interaction energy, solvation energy and vertical detachment energy for global structures of each size have also been presented to establish the utility of the procedure employed.
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Affiliation(s)
- Pulak Naskar
- Department of Chemistry, University of Calcutta, 92 A P C Road, Kolkata 700 009, India.
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