1
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Pausch A. Consistent Analytical Second Derivatives of the Kohn-Sham DFT Energy in the Framework of the Conductor-Like Screening Model through Gaussian Charge Distributions. J Chem Theory Comput 2024; 20:3169-3183. [PMID: 38557008 DOI: 10.1021/acs.jctc.4c00052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The use of implicit solvation models such as the conductor-like screening model (COSMO) in quantum chemical calculations is very common, as both a rough estimate of solvation effects as well as a general tool for stabilizing ionic molecular structures. In order to generate a smooth potential energy surface as well as consistent gradients, it is necessary to apply the Gaussian charge model (GCM) for the COSMO charges. This work introduces an efficient implementation for consistent analytical second derivatives of the electronic energy with COSMO-GCM in the framework of the Kohn-Sham density functional theory. This is used to investigate the infrared spectroscopy of amino acids in aqueous solution, where the impact of pH on the molecular structure and vibrational spectra is examined. Furthermore, the structure and stability of selected all-metal aromatic cluster ions are assessed.
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Affiliation(s)
- Ansgar Pausch
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
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2
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Varandas AJC. From six to eight Π-electron bare rings of group-XIV elements and beyond: can planarity be deciphered from the "quasi-molecules" they embed? Phys Chem Chem Phys 2022; 24:8488-8507. [PMID: 35343978 DOI: 10.1039/d1cp04130d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ab initio molecular orbital theory is used to study the structures of six and eight π-electron bare rings of group-XIV elements, and even larger [n]annulenes up to C18H18, including some of their mono-, di-, tri-, and tetra-anions. While some of the above rings are planar, others are nonplanar. A much spotlighted case is cyclo-octatetraene (C8H8), which is predicted to be nonplanar together with its heavier group-XIV analogues Si8H8 and Ge8H8, with the solely planar members of its family having the stoichiometric formulas C4Si4H8 and C4Ge4H8. A similar situation arises with the six π-electron bare rings, where benzene and substituted ones up to C3Si3H6 or so are planar, while others are not. However, the explanations encountered in the literature find support in ab initio calculations for such species, often rationalized from distinct calculated features. Using second-order Møller-Plesset perturbation theory and, when affordable (particularly tetratomics, which may allow even higher levels), the coupled-cluster method including single, double, and perturbative triple excitations, a common rationale is suggested based on a novel concept of quasi-molecules or the (3+4)-atom partition scheme. Any criticism of tautology is therefore avoided. The same analysis has also been successfully applied to even larger [n]annulenes, to their mixed family members involving silicon and germanium atoms, and to the C18 carbon ring. Furthermore, it has been extended to annulene anions to check the criteria of the popular Hückel rule for planarity and aromaticity. Exploratory work on cycloarenes is also reported. Besides a partial study of the involved potential energy surfaces, equilibrium geometries and harmonic vibrational frequencies have been calculated anew, for both the parent and the actual prototypes of the quasi-molecules.
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Affiliation(s)
- A J C Varandas
- School of Physics and Physical Engineering, Qufu Normal University, 273165 Qufu, China.,Department of Physics, Universidade Federal do Esp rito Santo, 29075-910 Vitória, Brazil.,Department of Chemistry, and Chemistry Centre, University of Coimbra, 3004-535 Coimbra, Portugal.
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3
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Abstract
We have proven that Baird's rule can also be applied to a series of all-metal species with both σ- and π-aromaticity.
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Affiliation(s)
- Dandan Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM)
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry and Department of Chemistry
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
| | - Dariusz W. Szczepanik
- Institute of Computational Chemistry and Catalysis and Department of Chemistry
- University of Girona
- Girona
- Spain
- K. Guminski Department of Theoretical Chemistry
| | - Jun Zhu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM)
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry and Department of Chemistry
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
| | - Miquel Solà
- Institute of Computational Chemistry and Catalysis and Department of Chemistry
- University of Girona
- Girona
- Spain
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4
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Islas R, Oyarzún DP, Cantero-López P. Analysis of the aromaticity in extended systems formed from isoelectronic Al42− and C42+ aromatic clusters. Struct Chem 2018. [DOI: 10.1007/s11224-018-1120-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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5
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Boldyrev AI, Wang LS. Beyond organic chemistry: aromaticity in atomic clusters. Phys Chem Chem Phys 2016; 18:11589-605. [DOI: 10.1039/c5cp07465g] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We describe joint experimental and theoretical studies carried out collaboratively in the authors' labs for understanding the structures and chemical bonding of novel atomic clusters, which exhibit aromaticity.
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6
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Mercero JM, Boldyrev AI, Merino G, Ugalde JM. Recent developments and future prospects of all-metal aromatic compounds. Chem Soc Rev 2015; 44:6519-34. [PMID: 26058731 DOI: 10.1039/c5cs00341e] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The usefulness of aromaticity/antiaromaticity concepts to foresee structural stability patterns and salient features of the electronic structure of small inorganic and all-metal rings has been put forward. A critical revision of the advances made in the theoretical methods to assess the aromaticity/antiaromaticity of these compounds has also been made. In particular, the performance of local versus non-local indices has been reviewed. Finally, the passivation of these rings has been put forward as a key issue in order to prevent them from collapsing into larger aggregates and to provide them protection against the environment.
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Affiliation(s)
- Jose M Mercero
- IZO-SGI SGiker, Euskal Herriko Unibertsitatea (UPV/EHU), P.K. 1072, 20080 Donostia, Euskadi, Spain
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7
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Perić M, Andjelković L, Zlatar M, Daul C, Gruden-Pavlović M. DFT investigation of the influence of Jahn–Teller distortion on the aromaticity in square-planar arsenic and antimony clusters. Polyhedron 2014. [DOI: 10.1016/j.poly.2014.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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8
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9
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Badri Z, Pathak S, Fliegl H, Rashidi-Ranjbar P, Bast R, Marek R, Foroutan-Nejad C, Ruud K. All-Metal Aromaticity: Revisiting the Ring Current Model among Transition Metal Clusters. J Chem Theory Comput 2013; 9:4789-96. [DOI: 10.1021/ct4007184] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zahra Badri
- CEITEC − Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ−62500 Brno, Czech Republic
- School
of Chemistry, College of Science, University of Tehran, Tehran, Iran
| | - Shubhrodeep Pathak
- Raman Center for Atomic, Molecular and Optical Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
| | - Heike Fliegl
- Centre for Theoretical and Computational
Chemistry, Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, N−0315 Oslo, Norway
| | | | - Radovan Bast
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), CNRS/Université de Toulouse 3 (Paul Sabatier), 118 route de Narbonne, F−31062 Toulouse, France
- Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, AlbaNova University Center, S-10691 Stockholm, Sweden
| | - Radek Marek
- CEITEC − Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ−62500 Brno, Czech Republic
- National Center
for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, CZ−62500 Brno, Czech Republic
| | - Cina Foroutan-Nejad
- National Center
for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, CZ−62500 Brno, Czech Republic
| | - Kenneth Ruud
- Centre
for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø—The Arctic University of Norway, N-9037 Tromsø, Norway
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10
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Sokolov AY, Magers DB, Wu JI, Allen WD, Schleyer PVR, Schaefer HF. Free Cyclooctatetraene Dianion: Planarity, Aromaticity, and Theoretical Challenges. J Chem Theory Comput 2013; 9:4436-43. [DOI: 10.1021/ct400642y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Alexander Yu. Sokolov
- Center for Computational Quantum
Chemistry, The University of Georgia, Athens, Georgia 30602, United States
| | - D. Brandon Magers
- Center for Computational Quantum
Chemistry, The University of Georgia, Athens, Georgia 30602, United States
| | - Judy I. Wu
- Center for Computational Quantum
Chemistry, The University of Georgia, Athens, Georgia 30602, United States
| | - Wesley D. Allen
- Center for Computational Quantum
Chemistry, The University of Georgia, Athens, Georgia 30602, United States
| | - Paul v. R. Schleyer
- Center for Computational Quantum
Chemistry, The University of Georgia, Athens, Georgia 30602, United States
| | - Henry F. Schaefer
- Center for Computational Quantum
Chemistry, The University of Georgia, Athens, Georgia 30602, United States
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11
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Foroutan-Nejad C. Al4(2-); the anion-π interactions and aromaticity in the presence of counter ions. Phys Chem Chem Phys 2012; 14:9738-48. [PMID: 22684037 DOI: 10.1039/c2cp40511c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The influence of presence of counter ions and π-complexation with benzene on the bonding and magnetic properties of Al(4)(2-), the most studied all-metal cluster, is studied here. It is shown that complexation by either counter ions or benzene decreases the delocalization index between Al atoms and the magnitude of bond magnetizability, that is a Quantum Theory of Atoms in Molecules, QTAIM, -based magnetic index of aromaticity. Benzene forms two types of π-complexes with the Al(4) framework; CH-π (T-shaped) complexes and parallel π-π stacking (PPS) complexes. It is shown that variation in the π-charge of the Al(4) framework affects the relative stability of the T-shaped/PPS complexes. Free Al(4)(2-) forms a stable T-shaped anion-π complex with benzene but in the presence of cations, formation of PPS complexes is more favourable, energetically. It is suggested that this property could be used for designing molecular switches and tuneable anion sensors.
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Affiliation(s)
- Cina Foroutan-Nejad
- School of Chemistry, College of Science, University of Tehran, Tehran, Iran.
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12
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Islas R, Poater J, Matito E, Solà M. Molecular structures of M2N22− (M and N = B, Al, and Ga) clusters using the gradient embedded genetic algorithm. Phys Chem Chem Phys 2012; 14:14850-9. [DOI: 10.1039/c2cp42210g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Badri Z, Foroutan-Nejad C, Rashidi-Ranjbar P. Method/basis set dependence of NICS values among metallic nano-clusters and hydrocarbons. Phys Chem Chem Phys 2012; 14:3471-81. [DOI: 10.1039/c2cp23205g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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14
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Foroutan-Nejad C, Badri Z, Shahbazian S, Rashidi-Ranjbar P. The Laplacian of Electron Density versus NICSzz Scan: Measuring Magnetic Aromaticity among Molecules with Different Atom Types. J Phys Chem A 2011; 115:12708-14. [DOI: 10.1021/jp203681x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Zahra Badri
- School of Chemistry, College of Science, University of Tehran, Tehran, Iran
| | - Shant Shahbazian
- Department of Chemistry, Faculty of Sciences, Shahid Beheshti University, G.C., Evin, Tehran, Iran
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15
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Dominikowska J, Palusiak M. Cyclooctatetraene dianion-an artifact? J Comput Chem 2011; 32:1441-8. [DOI: 10.1002/jcc.21730] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 11/09/2010] [Accepted: 11/10/2010] [Indexed: 11/08/2022]
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16
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Chakraborty A, Giri S, Duley S, Anoop A, Bultinck P, Chattaraj PK. Aromaticity in all-metal annular systems: the counter-ion effect. Phys Chem Chem Phys 2011; 13:14865-78. [DOI: 10.1039/c1cp21430f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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17
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Poater J, Feixas F, Bickelhaupt FM, Solà M. All-metal aromatic clusters M42− (M = B, Al, and Ga). Are π-electrons distortive or not? Phys Chem Chem Phys 2011; 13:20673-81. [DOI: 10.1039/c1cp22759a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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18
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Aromaticity and electronic delocalization in all-metal clusters with single, double, and triple aromatic character. Theor Chem Acc 2010. [DOI: 10.1007/s00214-010-0805-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Feixas F, Jiménez-Halla JOC, Matito E, Poater J, Solà M. A Test to Evaluate the Performance of Aromaticity Descriptors in All-Metal and Semimetal Clusters. An Appraisal of Electronic and Magnetic Indicators of Aromaticity. J Chem Theory Comput 2010. [DOI: 10.1021/ct100034p] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ferran Feixas
- Institut de Química Computacional and Departament de Química, Universitat de Girona, Campus de Montilivi, 17071 Girona, Catalonia, Spain and Institute of Physics, University of Szczecin, 70-451 Szczecin, Poland
| | - J. Oscar C. Jiménez-Halla
- Institut de Química Computacional and Departament de Química, Universitat de Girona, Campus de Montilivi, 17071 Girona, Catalonia, Spain and Institute of Physics, University of Szczecin, 70-451 Szczecin, Poland
| | - Eduard Matito
- Institut de Química Computacional and Departament de Química, Universitat de Girona, Campus de Montilivi, 17071 Girona, Catalonia, Spain and Institute of Physics, University of Szczecin, 70-451 Szczecin, Poland
| | - Jordi Poater
- Institut de Química Computacional and Departament de Química, Universitat de Girona, Campus de Montilivi, 17071 Girona, Catalonia, Spain and Institute of Physics, University of Szczecin, 70-451 Szczecin, Poland
| | - Miquel Solà
- Institut de Química Computacional and Departament de Química, Universitat de Girona, Campus de Montilivi, 17071 Girona, Catalonia, Spain and Institute of Physics, University of Szczecin, 70-451 Szczecin, Poland
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20
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21
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JimÉnez-halla JOC, Matito E, Blancafort L, Robles J, Solà M. Tuning aromaticity in trigonal alkaline earth metal clusters and their alkali metal salts. J Comput Chem 2009; 30:2764-76. [DOI: 10.1002/jcc.21291] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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22
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Nguyen MT, Matus MH, Ngan VT, Grant DJ, Dixon DA. Thermochemistry and Electronic Structure of Small Boron and Boron Oxide Clusters and Their Anions. J Phys Chem A 2009; 113:4895-909. [DOI: 10.1021/jp811391v] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Minh Tho Nguyen
- Department of Chemistry, The University of Alabama, Shelby Hall, Tuscaloosa, Alabama 35487-0336, Department of Chemistry, University of Leuven, B-3001 Leuven, Belgium, and Unidad de Servicios de Apoyo en Resolución Analítica, Universidad Veracruzana, A. P. 575, Xalapa, Ver., Mexico
| | - Myrna H. Matus
- Department of Chemistry, The University of Alabama, Shelby Hall, Tuscaloosa, Alabama 35487-0336, Department of Chemistry, University of Leuven, B-3001 Leuven, Belgium, and Unidad de Servicios de Apoyo en Resolución Analítica, Universidad Veracruzana, A. P. 575, Xalapa, Ver., Mexico
| | - Vu Thi Ngan
- Department of Chemistry, The University of Alabama, Shelby Hall, Tuscaloosa, Alabama 35487-0336, Department of Chemistry, University of Leuven, B-3001 Leuven, Belgium, and Unidad de Servicios de Apoyo en Resolución Analítica, Universidad Veracruzana, A. P. 575, Xalapa, Ver., Mexico
| | - Daniel J. Grant
- Department of Chemistry, The University of Alabama, Shelby Hall, Tuscaloosa, Alabama 35487-0336, Department of Chemistry, University of Leuven, B-3001 Leuven, Belgium, and Unidad de Servicios de Apoyo en Resolución Analítica, Universidad Veracruzana, A. P. 575, Xalapa, Ver., Mexico
| | - David A. Dixon
- Department of Chemistry, The University of Alabama, Shelby Hall, Tuscaloosa, Alabama 35487-0336, Department of Chemistry, University of Leuven, B-3001 Leuven, Belgium, and Unidad de Servicios de Apoyo en Resolución Analítica, Universidad Veracruzana, A. P. 575, Xalapa, Ver., Mexico
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23
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Chattaraj PK, Giri S. Electrophilicity index within a conceptual DFT framework. ACTA ACUST UNITED AC 2009. [DOI: 10.1039/b802832j] [Citation(s) in RCA: 152] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Giri S, Roy DR, Duley S, Chakraborty A, Parthasarathi R, Elango M, Vijayaraj R, Subramanian V, Islas R, Merino G, Chattaraj PK. Bonding, aromaticity, and structure of trigonal dianion metal clusters. J Comput Chem 2009; 31:1815-21. [PMID: 19921693 DOI: 10.1002/jcc.21452] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Santanab Giri
- Department of Chemistry and Center for Theoretical Studies, IIT Kharagpur, Kharagpur 721 302, India
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Affiliation(s)
- Dmitry Yu. Zubarev
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300
| | - Alexander I. Boldyrev
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300
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26
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Lambrecht DS, Fleig T, Sommerfeld T. Reply to “Comment on ‘Instability of the Al42− ‘All-Metal Aromatic’ Ion and Its Implications’”. J Phys Chem A 2008. [DOI: 10.1021/jp803587v] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel S. Lambrecht
- Institut für Theoretische und Computerchemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Timo Fleig
- Institut für Theoretische und Computerchemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Thomas Sommerfeld
- Department of Chemistry and Physics, Southeastern Louisiana University, SLU 10878, Hammond, Louisiana 70402
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