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Electron density from the fragment molecular orbital method combined with density-functional tight-binding. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138900] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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2
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Electrostatic Potential Topology for Probing Molecular Structure, Bonding and Reactivity. Molecules 2021; 26:molecules26113289. [PMID: 34072507 PMCID: PMC8198923 DOI: 10.3390/molecules26113289] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/16/2021] [Accepted: 05/25/2021] [Indexed: 11/18/2022] Open
Abstract
Following the pioneering investigations of Bader on the topology of molecular electron density, the topology analysis of its sister field viz. molecular electrostatic potential (MESP) was taken up by the authors’ groups. Through these studies, MESP topology emerged as a powerful tool for exploring molecular bonding and reactivity patterns. The MESP topology features are mapped in terms of its critical points (CPs), such as bond critical points (BCPs), while the minima identify electron-rich locations, such as lone pairs and π-bonds. The gradient paths of MESP vividly bring out the atoms-in-molecule picture of neutral molecules and anions. The MESP-based characterization of a molecule in terms of electron-rich and -deficient regions provides a robust prediction about its interaction with other molecules. This leads to a clear picture of molecular aggregation, hydrogen bonding, lone pair–π interactions, π-conjugation, aromaticity and reaction mechanisms. This review summarizes the contributions of the authors’ groups over the last three decades and those of the other active groups towards understanding chemical bonding, molecular recognition, and reactivity through topology analysis of MESP.
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Kumar A, Yeole SD, Gadre SR, López R, Rico JF, Ramírez G, Ema I, Zorrilla D. DAMQT 2.1.0: A new version of the DAMQT package enabled with the topographical analysis of electron density and electrostatic potential in molecules. J Comput Chem 2016; 36:2350-9. [PMID: 26505259 DOI: 10.1002/jcc.24212] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 09/04/2015] [Accepted: 09/09/2015] [Indexed: 01/22/2023]
Abstract
DAMQT-2.1.0 is a new version of DAMQT package which includes topographical analysis of molecular electron density (MED) and molecular electrostatic potential (MESP), such as mapping of critical points (CPs), creating molecular graphs, and atomic basins. Mapping of CPs is assisted with algorithmic determination of Euler characteristic in order to provide a necessary condition for locating all possible CPs. Apart from the mapping of CPs and determination of molecular graphs, the construction of MESP-based atomic basin is a new and exclusive feature introduced in DAMQT-2.1.0. The GUI in DAMQT provides a user-friendly interface to run the code and visualize the final outputs. MPI libraries have been implemented for all the tasks to develop the parallel version of the software. Almost linear scaling of computational time is achieved with the increasing number of processors while performing various aspects of topography. A brief discussion of molecular graph and atomic basin is provided in the current article highlighting their chemical importance. Appropriate example sets have been presented for demonstrating the functions and efficiency of the code.
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Affiliation(s)
- Anmol Kumar
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, Uttar Pradesh, India
| | - Sachin D Yeole
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, Uttar Pradesh, India
| | - Shridhar R Gadre
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, Uttar Pradesh, India
| | - Rafael López
- Departamento De Química Física Aplicada, Facultad De Ciencias, Universidad Autónoma De Madrid, Madrid, E-28049, Spain
| | - Jaime F Rico
- Departamento De Química Física Aplicada, Facultad De Ciencias, Universidad Autónoma De Madrid, Madrid, E-28049, Spain
| | - Guillermo Ramírez
- Departamento De Química Física Aplicada, Facultad De Ciencias, Universidad Autónoma De Madrid, Madrid, E-28049, Spain
| | - Ignacio Ema
- Departamento De Química Física Aplicada, Facultad De Ciencias, Universidad Autónoma De Madrid, Madrid, E-28049, Spain
| | - David Zorrilla
- Departamento De Química Física, Facultad De Ciencias, Universidad De Cádiz, Cádiz, E-11501, Spain
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Kuźniarowicz P, Liu K, Aoki Y, Gu FL, Stachowicz A, Korchowiec J. Intermediate electrostatic field for the elongation method. J Mol Model 2014; 20:2277. [PMID: 24878802 PMCID: PMC4072069 DOI: 10.1007/s00894-014-2277-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 04/25/2014] [Indexed: 11/25/2022]
Abstract
A simple way to improve the accuracy of the fragmentation methods is proposed. The formalism was applied to the elongation (ELG) method at restricted open-shell Hartree-Fock (ROHF) level of theory. The α-helix conformer of polyglycine was taken as a model system. The modified ELG method includes a simplified electrostatic field resulting from point-charge distribution of the system's environment. In this way the long-distance polarization is approximately taken into account. The field attenuates during the ELG process to eventually disappear when the final structure is reached. The point-charge distributions for each ELG step are obtained from charge sensitivity analysis (CSA) in force-field atoms resolution. The presence of the intermediate field improves the accuracy of ELG calculations. The errors in total energy and its kinetic and potential contributions are reduced by at least one-order of magnitude. In addition the SCF convergence of ROHF scheme is improved.
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Affiliation(s)
- Piotr Kuźniarowicz
- Department of Molecular and Material Sciences, Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka, 816-8580 Japan
| | - Kai Liu
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, Kasuga, Fukuoka, 816-8580 Japan
| | - Yuriko Aoki
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, Kasuga, Fukuoka, 816-8580 Japan
| | - Feng Long Gu
- MOE Key Laboratory of Theoretical Chemistry of Environment; School of Chemistry and Environment, South China Normal University, Guangzhou, 510631 China
| | - Anna Stachowicz
- K. Gumiński Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Jacek Korchowiec
- K. Gumiński Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
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Hua S, Li W, Li S. The Generalized Energy-Based Fragmentation Approach with an Improved Fragmentation Scheme: Benchmark Results and Illustrative Applications. Chemphyschem 2012; 14:108-15. [DOI: 10.1002/cphc.201200867] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Indexed: 11/09/2022]
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Gordon MS, Fedorov DG, Pruitt SR, Slipchenko LV. Fragmentation Methods: A Route to Accurate Calculations on Large Systems. Chem Rev 2011; 112:632-72. [DOI: 10.1021/cr200093j] [Citation(s) in RCA: 836] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Mark S. Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames Iowa 50011, United States
| | - Dmitri G. Fedorov
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Spencer R. Pruitt
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames Iowa 50011, United States
| | - Lyudmila V. Slipchenko
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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Rahalkar AP, Yeole SD, Ganesh V, Gadre SR. Molecular Tailoring: An Art of the Possible for Ab Initio Treatment of Large Molecules and Molecular Clusters. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2011. [DOI: 10.1007/978-90-481-2853-2_10] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Hua S, Hua W, Li S. An Efficient Implementation of the Generalized Energy-Based Fragmentation Approach for General Large Molecules. J Phys Chem A 2010; 114:8126-34. [DOI: 10.1021/jp103074f] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shugui Hua
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People’s Republic of China, and Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Weijie Hua
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People’s Republic of China, and Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People’s Republic of China, and Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, S-106 91 Stockholm, Sweden
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Kavathekar R, Khire S, Ganesh V, Rahalkar AP, Gadre SR. WebMTA: A web-interface forab initiogeometry optimization of large molecules using molecular tailoring approach. J Comput Chem 2009; 30:1167-73. [DOI: 10.1002/jcc.21132] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Ganesh V. MeTA studio: a cross platform, programmable IDE for computational chemist. J Comput Chem 2009; 30:661-72. [PMID: 18711720 DOI: 10.1002/jcc.21088] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The development of a cross-platform, programmable integrated development environment (IDE), MeTA Studio, specifically tailored but not restricted to computational chemists working in the area of quantum chemistry with an emphasis on handling large molecules is presented. The IDE consists of a number of modules which include a visualizer and a programming and collaborative framework. The inbuilt viewer assists in visualizing molecules, their scalar fields, manually fragmenting a molecule, and introduces some innovative but simple techniques for handling large molecules. These include a simple Find language and simultaneous multiple camera views of the molecule. Basic tools needed to handle collaborative computing effectively are also included opening up new vistas for sharing ideas and information among computational chemists working on similar problems. MeTA Studio is an integrated programming environment that provides a rich set of application programming interfaces (APIs) which can be used to easily extend its functionality or build new applications as needed by the users. (http://code.google.com/p/metastudio/).
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Affiliation(s)
- V Ganesh
- Interdisciplinary School of Scientific Computing, University of Pune, Pune 411007, India.
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Elango M, Subramanian V, Rahalkar AP, Gadre SR, Sathyamurthy N. Structure, energetics, and reactivity of boric acid nanotubes: a molecular tailoring approach. J Phys Chem A 2008; 112:7699-704. [PMID: 18652434 DOI: 10.1021/jp802723e] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cardinality guided molecular tailoring approach (CG-MTA) [Ganesh et al. J. Chem. Phys. 2006, 125, 104019] has been effectively employed to perform ab initio calculations for large molecular clusters of boric acid. It is evident from the results that boric acid forms nanotubes, structurally similar to carbon nanotubes, with the help of an extensive hydrogen-bonding (H-bonding) network. Planar rosette-shaped hexamer of boric acid is the smallest repeating unit in such nanotubes. The stability of these tubes increases due to enhancement in the number of H-bonding interactions as the diameter increases. An analysis of molecular electrostatic potential (MESP) of these systems provides interesting features regarding the reactivity of these tubes. It is predicted that due to alternate negative and positive potentials on O and B atoms, respectively, boric acid nanotubes will interact favorably with polar systems such as water and can also form multiwalled tubes.
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Affiliation(s)
- M Elango
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai, India 600 020
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