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Alikhani ME, Madebène B, Silvi B. Microsolvation of cobalt, nickel, and copper atoms with ammonia: a theoretical study of the solvated electron precursors. J Mol Model 2024; 30:220. [PMID: 38902588 DOI: 10.1007/s00894-024-06019-7] [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: 03/01/2024] [Accepted: 06/10/2024] [Indexed: 06/22/2024]
Abstract
CONTEXT The s-block metals dissolved in ammonia form metal-ammonia complexes with diffuse electrons which could be used for redox catalysis. In this theoretical paper, we investigated the possibility of the d-bloc transition metals (Mn, Fe, Co, Ni, and Cu) solvated by ammonia. It has been demonstrated that both Mn and Fe atoms undergo into an oxidative reaction with NH3 forming an inserted species, HMNH2. On the contrary, the Co, Ni, and Cu atoms can accommodate four NH3, via the coordination bond, to form the first solvation sphere within C2v, D2d, and Td point groups, respectively. Addition of a fifth NH3 constitute the second solvation shell by forming hydrogen bond with the other NH3s. Interestingly, M(NH3)4 (M = Co, Ni, and Cu) is a so-called solvated electron precursor and should be considered as a monocation M(NH3)4+ kernel in tight contact with one electron distributed over its periphery. This nearly free electron could be used to capture a CO2 molecule and engages in a reduction reaction. METHODS Geometry optimization of the stationary points on the potential energy surface was performed using density functional theory - CAM-B3LYP functional including the GD3BJ dispersion contribution - in combination with the 6-311 + + G(2d, 2p) basis set for all the atoms. All first-principles calculations were performed using the Gaussian 09 quantum chemical packages. The natural electron configuration of transition atom engaged in the compounds has been found using the natural bond orbital (NBO) method. We used the EDR (electron delocalization range) approach to analyze the structure of solvated electrons in real space. We also used the electron localization function (ELF) to measure the degree of electronic localization within a chemical compound. The EDR and ELF analyses are done using the TopMod and Multiwfn packages, respectively.
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Affiliation(s)
| | - Bruno Madebène
- Sorbonne Université CNRS, MONARIS, UMR8233, F-75005, Paris, France
| | - Bernard Silvi
- Sorbonne Université CNRS, LCT, UMR7616, F-75005, Paris, France
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2
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Da-yang TE, Lai CH. Potential energy surfaces of the Cu2+(NH3)n=1−10 clusters in solvent phase: A DFT study. Chem Phys 2023. [DOI: 10.1016/j.chemphys.2023.111902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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3
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Structures, Binding and Clustering Energies of Cu2+(MeOH)n=1-8 Clusters and Temperature Effects : A DFT Study. Polyhedron 2023. [DOI: 10.1016/j.poly.2023.116343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
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4
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Da-yang TE, Fifen JJ, Conradie J, Conradie MM. Structures, temperature effect, binding and clustering energies of Cu2+(MeOH)n=1-8 clusters and extrapolations. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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5
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Transition metal atoms grafted on the nanodiamonds surface: Identification and guest–host spin–spin interactions. MENDELEEV COMMUNICATIONS 2022. [DOI: 10.1016/j.mencom.2022.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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6
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Da-yang TE, Fifen JJ, Malloum A, Lahmar S, Nsangou M, Conradie J. Structures of the solvated copper(ii) ion in ammonia at various temperatures. NEW J CHEM 2020. [DOI: 10.1039/c9nj05169d] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigated theoretically the structures and relative stabilities of the solvated copper(ii) ion in ammonia, Cu2+(NH3)n, n = 1–10.
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Affiliation(s)
| | - Jean Jules Fifen
- Department of Physics
- Faculty of Science
- The University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Alhadji Malloum
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
- Department of Physics
| | - Souad Lahmar
- Laboratoire de Spectroscopie Atomique Moléculaire et Applications
- Faculté des Sciences de Tunis
- Université de Tunis El Manar
- Tunis
- Tunisia
| | - Mama Nsangou
- University of Maroua
- Maroua
- Cameroon
- Department of Physics
- Faculty of Science
| | - Jeanet Conradie
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
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7
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Coskuner-Weber O. Revisiting Cu(II) Bound Amyloid-β40 and Amyloid-β42 Peptides: Varying Coordination Chemistries. JOURNAL OF THE TURKISH CHEMICAL SOCIETY, SECTION A: CHEMISTRY 2018. [DOI: 10.18596/jotcsa.424144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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8
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Sahu P, Ali SM, Shenoy KT, Mohan S. Molecular Facts on the Structure and Dynamics of Electrolyte Species in Cu-Cl Cycle for Hydrogen Generation: An Insight from Molecular Dynamic Simulations. J Phys Chem B 2018; 122:4115-4130. [PMID: 29569915 DOI: 10.1021/acs.jpcb.8b01650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Cu complex, which is the key chemical species in well-known Cu-Cl hybrid thermochemical cycles and also in numerous metal hydrometallurgical and sedimentary deposit processes, displays a wide variety of structural and dynamical characteristics that are further complicated by the presence of multiple oxidation states of Cu ions with different coordination chemistries, therefore they are difficult to explore from experiments alone. In this article, an attempt has been made to understand the coordination behavior of the Cu complex using MD simulations. The study provides compelling evidence of the experimentally observed multiple stoichiometries of Cu ions, i.e., 1:6:0, 1:5:1, and 1:4:2 for Cu+:H2O:Cl- and 1:6:0 for Cu2+:H2O:Cl-. The presence of the anionic Cu complex, [Cu+Cl2]-·2H2O, [Cu+Cl2]-·3H2O, [Cu2+Cl3]-·H2O, and [Cu2+Cl3]-·2H2O, was captured in the presence of excess chloride ions. Furthermore, the probability distribution profiles have been estimated to determine the most possible complex in the considered systems. The results establish structural and dynamical reformation of the Cu complex with change in the salt concentration or variation in the solvent medium in which they are dissolved. Moreover, the structure and kinetics of the Cu ions in the Cu-Cl electrolyzer have been explored over a large range of the electric field by extending the simulated systems for varied strengths of the electric fields. It has been observed that with an increase in the strength of the electric field, the water molecules lose their coordination strength with central Cu ions, which, on the other hand, results in a significant change in the structure of the captured complex. The diffusion dynamics of the ions is altered while applying the electric field, which is furthermore modified while increasing the strength of electric field beyond a critical limit. In fact, the diffusion mechanism of the ions was seen to be transformed from Brownian-like to linear motion and then to hopping diffusion with the increasing strength of the electric field. To the best of our knowledge, this is the first time when the multiple oxidation states of the Cu ion are explored using MD simulations, and the coexisting pictures of the multiple coordinations and the solvent effects have been clearly revealed. Also to date, the present article is the first one to report the insights of the structure and the dynamics of the ions in the Cu-Cl electrolyzer over a wide range of the electric field. The present studies will be very helpful in understanding the mechanism involved in numerous metal hydrometallurgical and sedimentary deposit processes and to comprehend the analogies involved in the electrode reactions of the Cu-Cl cycle for hydrogen generation.
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Affiliation(s)
- Pooja Sahu
- Chemical Engineering Division , Bhabha Atomic Research Center , Mumbai , Maharashtra 400085 , India.,Department of Chemical Science , Homi Bhabha National Institute , Mumbai , Maharashtra 400094 , India
| | - Sk Musharaf Ali
- Chemical Engineering Division , Bhabha Atomic Research Center , Mumbai , Maharashtra 400085 , India.,Department of Chemical Science , Homi Bhabha National Institute , Mumbai , Maharashtra 400094 , India
| | - K T Shenoy
- Chemical Engineering Division , Bhabha Atomic Research Center , Mumbai , Maharashtra 400085 , India
| | - S Mohan
- Chemical Engineering Division , Bhabha Atomic Research Center , Mumbai , Maharashtra 400085 , India
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9
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Formation of chelate structure between His-Met dipeptide and diaqua-cisplatin complex; DFT/PCM computational study. J Biol Inorg Chem 2018; 23:363-376. [DOI: 10.1007/s00775-018-1536-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 01/23/2018] [Indexed: 02/01/2023]
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10
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Study on electronic properties, thermodynamic and kinetic parameters of the selected platinum(II) derivatives interacting with guanine. J Inorg Biochem 2017; 172:100-109. [DOI: 10.1016/j.jinorgbio.2017.04.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 04/06/2017] [Accepted: 04/08/2017] [Indexed: 11/23/2022]
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11
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Šebesta F, Burda JV. Side Reactions with an Equilibrium Constraint: Detailed Mechanism of the Substitution Reaction of Tetraplatin with dGMP as a Starting Step of the Platinum(IV) Reduction Process. J Phys Chem B 2017; 121:4400-4413. [PMID: 28394593 DOI: 10.1021/acs.jpcb.7b01427] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two possible pathways of the substitution reaction within the reduction process of the PtIV(DACH)Cl4 by dGMP are compared: associative reaction course and autocatalytic Basolo-Pearson mechanisms. Since two forms: single-protonated and fully deprotonated phosphate group of dGMP are present in equilibrium at neutral and mildly acidic solutions, consideration of a side reactions scheme with acido-basic equilibrium-constraint is a very important model for obtaining reliable results. The examined complexes are optimized at the B3LYP-GD3BJ/6-31G(d) level with the COSMO implicit solvation model and Klamt's radii used for cavity construction. Energy characteristics and thermodynamics for all reaction branches are determined using the B3LYP-GD3BJ/6-311++G(2df,2pd)/IEF-PCM/scaled-UAKS level with Wertz's entropy corrections. Rate constants are estimated for each individual branch according to Eyring's transition state theory (TST), averaged according to equilibrium constraint and compared with available experimental data. The determined reaction barriers of the autocatalytic pathway fairly correspond with experimental values. Furthermore, autocatalytic reaction of tetraplatin and its two analogues complexes [PtIV(en)Cl4 and PtIV(NH3)2Cl4] are explored and compared with measured data in order to examined general reaction descriptors.
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Affiliation(s)
- Filip Šebesta
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University , Ke Karlovu 3, 121 16 Prague 2, Czech Republic
| | - Jaroslav V Burda
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University , Ke Karlovu 3, 121 16 Prague 2, Czech Republic
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12
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Structure and properties of a copper-mediated nucleobase pair from density functional theory investigation. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.03.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Zábojníková T, Cajzl R, Kljun J, Chval Z, Turel I, Burda JV. Interactions of the "piano-stool" [ruthenium(II)(η(6) -arene)(quinolone)Cl](+) complexes with water; DFT computational study. J Comput Chem 2016; 37:1766-80. [PMID: 27185047 DOI: 10.1002/jcc.24373] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 02/23/2016] [Accepted: 02/24/2016] [Indexed: 12/12/2022]
Abstract
Full optimizations of stationary points along the reaction coordinate for the hydration of several quinolone Ru(II) half-sandwich complexes were performed in water environment using the B3PW91/6-31+G(d)/PCM/UAKS method. The role of diffuse functions (especially on oxygen) was found crucial for correct geometries along the reaction coordinate. Single-point (SP) calculations were performed at the B3LYP/6-311++G(2df,2pd)/DPCM/saled-UAKS level. In the first part, two possible reaction mechanisms-associative and dissociative were compared. It was found that the dissociative mechanism of the hydration process is kinetically slightly preferred. Another important conclusion concerns the reaction channels. It was found that substitution of chloride ligand (abbreviated in the text as dechlorination reaction) represents energetically and kinetically the most feasible pathway. In the second part the same hydration reaction was explored for reactivity comparison of the Ru(II)-complexes with several derivatives of nalidixic acid: cinoxacin, ofloxacin, and (thio)nalidixic acid. The hydration process is about four orders of magnitude faster in a basic solution compared to neutral/acidic environment with cinoxacin and nalidixic acid as the most reactive complexes in the former and latter environments, respectively. The explored hydration reaction is in all cases endergonic; nevertheless the endergonicity is substantially lower (by ∼6 kcal/mol) in basic environment. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Tereza Zábojníková
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague 2, 121 16, Czech Republic
| | - Radim Cajzl
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague 2, 121 16, Czech Republic
| | - Jakob Kljun
- Faculty of Chemistry and Chemical Technologyn University of Ljubljana, Večna pot 113, Ljubljana, 1000, Slovenia
| | - Zdeněk Chval
- Department of Laboratory Methods and Information Systems, Faculty of Health and Social Studies, University of South Bohemia, J. Boreckého 27, České Budějovice, 370 11, Czech Republic
| | - Iztok Turel
- Faculty of Chemistry and Chemical Technologyn University of Ljubljana, Večna pot 113, Ljubljana, 1000, Slovenia
| | - Jaroslav V Burda
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague 2, 121 16, Czech Republic
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14
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Lu N, Bu Y, Wang H. Intensified effects of multi-Cu modification on the electronic properties of the modified base pairs containing hetero-ring-expanded pyrimidine bases. Phys Chem Chem Phys 2016; 18:2913-23. [PMID: 26733396 DOI: 10.1039/c5cp06133d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Novel DNA base pair derivatives (A2CunU, A2CunC, G3CunU, and G3CunC) are designed by aromatic expansion of pyrimidine bases with four kinds of hetero-rings (denoted by nC and nU, n = 1, 2, 3, and 4) and metal-decoration through Cu replacement of hydrogens in the Watson-Crick hydrogen bond region. Their structures and properties are calculated for examining the cooperative effects of the two modification ways. The calculated results reveal that multiple Cu decoration makes up the deficiencies of size-expansion, and exhibits not only increase of structural stability and reduction of ionization potentials, but also ideal shrink of the HOMO-LUMO gaps, notable enhancement of interbase coupling as well as remarkable redshifts of π → π* transitions for all M-x modified base pairs. The decrease extents of the gaps and ionization potentials follow the same order G3CunU > G3CunC > A2CunU > A2CunC, and in each series (denoted by different n), the gaps, ionization potentials and first π → π* transition energies have an order of 4 < 1 < 2 < 3. The Cu d orbitals function as bridges for π electron delocalization on the conjugated aromatic rings of two bases, leading to an enhancement of transverse electronic communication, as verified by spin density delocalization, orbital composition changes, redshift of the π → π* transition and also advocated by the electron-sharing indexes such as delocalization index, Mayer bond orders and multicenter bonding. Electron localization function ELF-π isosurfaces above the molecular plane further suggested that effective longitudinal conduction is closely relevant with the bicyclic domain involving good electron delocalization and strong π-π stacking between layers. This work presents theoretical evidence for the cooperative effects of metal decoration and ring-expansion modifications on the electronic properties of the modified base pairs and also proves that the base pairs designed here could be competent building blocks for the DNA-based nanowires with improved electron activity and excellent conductivity.
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Affiliation(s)
- Nan Lu
- College of Chemistry and Material Science, Shandong Agricultural University, Taian 271018, P. R. China and School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China.
| | - Yuxiang Bu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China.
| | - Huatian Wang
- College of Chemistry and Material Science, Shandong Agricultural University, Taian 271018, P. R. China
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15
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Gridnev ID, Osipov VY, Aleksenskii AE, Vul’ AY, Enoki T. Combined Experimental and DFT Study of the Chemical Binding of Copper Ions on the Surface of Nanodiamonds. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2014. [DOI: 10.1246/bcsj.20130345] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ilya D. Gridnev
- Department of Chemistry, Graduate School of Science, Tohoku University
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16
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Wise O, Coskuner O. New force field parameters for metalloproteins I: Divalent copper ion centers including three histidine residues and an oxygen-ligated amino acid residue. J Comput Chem 2014; 35:1278-89. [DOI: 10.1002/jcc.23622] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 02/06/2014] [Accepted: 03/23/2014] [Indexed: 01/04/2023]
Affiliation(s)
- Olivia Wise
- Department of Chemistry; The University of Texas at San Antonio, One UTSA Circle; San Antonio Texas 78249
- Neurosciences Institute; The University of Texas at San Antonio, One UTSA Circle; San Antonio Texas 78249
| | - Orkid Coskuner
- Department of Chemistry; The University of Texas at San Antonio, One UTSA Circle; San Antonio Texas 78249
- Neurosciences Institute; The University of Texas at San Antonio, One UTSA Circle; San Antonio Texas 78249
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17
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Tsipis AC. DFT/TDDFT insights into the chemistry, biochemistry and photophysics of copper coordination compounds. RSC Adv 2014. [DOI: 10.1039/c4ra04921g] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Highlighting the recent progress in DFT/TDDFT application to coordination chemistry of copper.
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Affiliation(s)
- Athanassios C. Tsipis
- Laboratory of Inorganic and General Chemistry
- Department of Chemistry
- University of Ioannina
- 451 10 Ioannina
- Greece
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18
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Kumar R, Obrai S, Mitra J, Sharma A. DFT studies of structural and some spectral parameters of copper(II) complexes with N,N,N',N″-tetrakis (2-hydroxyethyl/propyl) ethylenediamine and tris(2-hydroxyethyl)amine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 115:244-249. [PMID: 23835057 DOI: 10.1016/j.saa.2013.06.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 05/25/2013] [Accepted: 06/04/2013] [Indexed: 06/02/2023]
Abstract
The structures and some spectral parameters of three copper(II) complexes; [Cu(THEEN)(H2O)](PIC)2 (1), [Cu(THPEN)] (PIC)2 C3H8O (2) and [Cu(TEAH3)(PIC)] (PIC)⋅(H2O) (3), previously synthesized and characterized by X-ray diffraction, are here computationally studied by using density functional theory (DFT) in its hybrid form B3LYP. In these complexes, THEEN is N,N,N',N″-tetrakis(2-hydroxyethyl) ethylenediamine and THPEN is N,N,N',N″-tetrakis(2-hydroxypropyl) ethylenediamine, tetrapodal ligands and TEAH3 is tris(2-hydroxyethyl)amine, a tripodal ligand. The primary coordination sphere of copper(II) ion in complexes (1), (2) and (3) are optimized, structural parameters are calculated, vibrational bands are assigned and energy gaps of frontier orbital (HOMO-LUMO) have been calculated with B3LYP/6-31G/LANL2DZ level of theory using DMSO as solvent. The calculated geometric and spectral results reproduced the experimental data with well agreement. Theoretical calculated molecular orbitals (HOMO-LUMO) and their energies have been calculated that suggest charge transfer occurs within the complexes.
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Affiliation(s)
- Rakesh Kumar
- Department of Chemistry, Dr. B.R. Ambedkar National Institute of Technology, Jalandhar 144 011, Punjab, India
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19
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Tang S, Gong T, Fu Y. Mechanistic study of copper-catalyzed intramolecular ortho-C-H activation/carbon-nitrogen and carbon-oxygen cyclizations. Sci China Chem 2012. [DOI: 10.1007/s11426-012-4795-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Tamasi G, Mangani S, Cini R. Copper(I)-alkyl sulfide and -cysteine tri-nuclear clusters as models for metallo proteins: a structural density functional analysis. J Biomol Struct Dyn 2012; 30:728-51. [DOI: 10.1080/07391102.2012.689703] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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21
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Romancová I, Chval Z, Předota M. Influence of the Environment on the Specificity of the Mg(II) Binding to Uracil. J Phys Chem A 2012; 116:1786-93. [DOI: 10.1021/jp208823f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ingrid Romancová
- Institute
of Physics
and Biophysics, Faculty of Science, University of South Bohemia, Branišovská 31, CZ-370
05 České Budějovice, Czech Republic
| | - Zdeněk Chval
- Department of Laboratory
Methods and Information Systems, Faculty of Health and
Social Studies, University of South Bohemia, J. Boreckého 27, CZ-370 11 České Budějovice,
Czech Republic
| | - Milan Předota
- Institute
of Physics
and Biophysics, Faculty of Science, University of South Bohemia, Branišovská 31, CZ-370
05 České Budějovice, Czech Republic
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Marino T, Russo N, Toscano M, Pavelka M. Theoretical investigation on DNA/RNA base pairs mediated by copper, silver, and gold cations. Dalton Trans 2011; 41:1816-23. [PMID: 22159156 DOI: 10.1039/c1dt11028d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
B3LYP density functional based computations were performed in order to characterize the interactions present in some Cu(+), Ag(+), and Au(+) metal ion-mediated DNA and RNA base pairs from both structural and electronic points of view. Examined systems involve as ligands canonical Watson-Crick, Hoogsteen and Wobble base pairs. Two artificial Hoogsteen base pairs were also taken into account. Binding energy values indicate that complexes involving silver cations are less stable than those in which copper or gold are present, and propose a similar behaviour for these two latter ions. The nature of the bond linking metal ions and bases was described by the NBO analysis that suggests metal coordinative interactions to be covalent. An evaluation of the dispersion contributions for the investigated systems was performed with the B3LYP-D3 functional.
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Affiliation(s)
- Tiziana Marino
- Dipartimento di Chimica, Ponte P. Bucci Cubo 14C, Università degli Studi della Calabria, 87036 Arcavacata di Rende (CS), Italy.
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Chval Z, Futera Z, Burda JV. Comparison of hydration reactions for “piano-stool” RAPTA-B and [Ru(η6− arene)(en)Cl]+ complexes: Density functional theory computational study. J Chem Phys 2011; 134:024520. [DOI: 10.1063/1.3515534] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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24
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van Duin ACT, Bryantsev VS, Diallo MS, Goddard WA, Rahaman O, Doren DJ, Raymand D, Hermansson K. Development and validation of a ReaxFF reactive force field for Cu cation/water interactions and copper metal/metal oxide/metal hydroxide condensed phases. J Phys Chem A 2010; 114:9507-14. [PMID: 20707333 PMCID: PMC4224311 DOI: 10.1021/jp102272z] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
To enable large-scale reactive dynamic simulations of copper oxide/water and copper ion/water interactions we have extended the ReaxFF reactive force field framework to Cu/O/H interactions. To this end, we employed a multistage force field development strategy, where the initial training set (containing metal/metal oxide/metal hydroxide condensed phase data and [Cu(H(2)O)(n)](2+) cluster structures and energies) is augmented by single-point quantum mechanices (QM) energies from [Cu(H(2)O)(n)](2+) clusters abstracted from a ReaxFF molecular dynamics simulation. This provides a convenient strategy to both enrich the training set and to validate the final force field. To further validate the force field description we performed molecular dynamics simulations on Cu(2+)/water systems. We found good agreement between our results and earlier experimental and QM-based molecular dynamics work for the average Cu/water coordination, Jahn-Teller distortion, and inversion in [Cu(H(2)O)(6)](2+) clusters and first- and second-shell O-Cu-O angular distributions, indicating that this force field gives a satisfactory description of the Cu-cation/water interactions. We believe that this force field provides a computationally convenient method for studying the solution and surface chemistry of metal cations and metal oxides and, as such, has applications for studying protein/metal cation complexes, pH-dependent crystal growth/dissolution, and surface catalysis.
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Affiliation(s)
- Adri C T van Duin
- Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
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Rahaman O, van Duin ACT, Bryantsev VS, Mueller JE, Solares SD, Goddard WA, Doren DJ. Development of a ReaxFF Reactive Force Field for Aqueous Chloride and Copper Chloride. J Phys Chem A 2010; 114:3556-68. [DOI: 10.1021/jp9090415] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Obaidur Rahaman
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, Material and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, and Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742
| | - Adri C. T. van Duin
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, Material and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, and Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742
| | - Vyacheslav S. Bryantsev
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, Material and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, and Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742
| | - Jonathan E. Mueller
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, Material and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, and Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742
| | - Santiago D. Solares
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, Material and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, and Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742
| | - William A. Goddard
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, Material and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, and Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742
| | - Douglas J. Doren
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, Material and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, and Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742
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Pontikis G, Borden J, Martínek V, Florián J. Linear energy relationships for the octahedral preference of Mg, Ca and transition metal ions. J Phys Chem A 2009; 113:3588-93. [PMID: 19323489 DOI: 10.1021/jp808928f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The geometry, atomic charges, force constants, and relative energies of the symmetric and distorted M(2+)(H(2)O)(4)(F(-))(2), M(3+)(H(2)O)(4)(F(-))(2), M(2+)(H(2)O)(3)(F(-))(2), and M(3+)(H(2)O)(3)(F(-))(2) metal complexes, M = Mg, Ca, Co, Cu, Fe, Mn, Ni, Zn, Cr, V, were calculated by using the B3LYP/TZVP density functional method in both gas phase and aqueous solution, modeled using the polarized continuum model. The deformation energy associated with moving one water ligand 12 degrees from the initial "octahedral" arrangement, in which all O-M-O, O-M-F, and F-M-F angles are either 90 degrees or 180 degrees, was calculated to examine the angular ligand flexibility. For all M(2+)(H(2)O)(4)(F(-))(2) complexes, this distortion increased the energy of the complex in proportion to the electrostatic potential-derived (ESP) charge of the metal, and in proportion to D(-10), where D is the distance from the distorted ligand to its closest neighbor. The octahedral stability was further examined by calculating the energies for the removal of a water ligand from the octahedral complex to form a square-pyramidal or trigonal-bipyramidal complex. The octahedral preference, defined as the negative of the corresponding binding energy of the ligand, was found to linearly correlate with the ESP charge of the metal in both the gas phase and aqueous solution. The obtained results indicate that quantum-mechanical covalent effects are of secondary importance for both the flexibility and the octahedral preference of M(2+)(H(2)O)(4)(F(-))(2) and M(3+)(H(2)O)(4)(F(-))(2) complexes. This conclusion and supporting data are important for the development of consistent molecular mechanical force fields of the studied metal ions.
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Affiliation(s)
- George Pontikis
- Department of Chemistry, Loyola University Chicago, Chicago, Illinois 60626, USA
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Zhao J, Ng CMD, Chu IK, Siu KWM, Hopkinson AC. Methionine, α-methylmethionine and S-methylcysteine radical cations: generations and dissociations in the gas phase. Phys Chem Chem Phys 2009; 11:7629-39. [DOI: 10.1039/b905615g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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28
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Pavelka M, Burda JV. Computational study of redox active centres of blue copper proteins: a computational DFT study. Mol Phys 2008. [DOI: 10.1080/00268970802672684] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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29
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Siu CK, Ke Y, Guo Y, Hopkinson AC, Siu KWM. Dissociations of copper(II)-containing complexes of aromatic amino acids: radical cations of tryptophan, tyrosine, and phenylalanine. Phys Chem Chem Phys 2008; 10:5908-18. [PMID: 18818845 DOI: 10.1039/b807692h] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dissociations of two types of copper(II)-containing complexes of tryptophan (Trp), tyrosine (Tyr), or phenylalanine (Phe) are described. The first type is the bis-amino acid complex, [Cu(II)(M)(2)].(2+), where M = Trp, Tyr, or Phe; the second [Cu(II)(4Cl-tpy)(M)].(2+), where 4Cl-tpy is the tridendate ligand 4'-chloro-2,2':6',2''-terpyridine. Dissociations of the Cu(ii) bis-amino acid complexes produce abundant radical cation of the amino acid, M.(+), and/or its secondary products. By contrast, dissociations of the 4Cl-tpy-bearing ternary complexes give abundant M.(+) only for Trp. Density functional theory (DFT) calculations show that for Tyr and Phe, amino-acid displacement reactions by H(2)O and CH(3)OH (giving [Cu(II)(4Cl-tpy)(H(2)O)].(2+) and [Cu(II)(4Cl-tpy)(CH(3)OH)].(2+)) are energetically more favorable than dissociative electron transfer (giving M.(+) and [Cu(I)(4Cl-tpy)](+)). The fragmentation pathway common to all these [Cu(II)(4Cl-tpy)(M)].(2+) ions is the loss of NH(3). DFT calculations show that the loss of NH(3) proceeds via a "phenonium-type" intermediate. Dissociative electron transfer in [Cu(II)(4Cl-tpy)(M-NH(3))].(2+) results in [M-NH(3)].(+). The [Phe-NH(3)] (+) ion dissociates facilely by eliminating CO(2) and giving a metastable phenonium-type ion that rearranges readily into the styrene radical cation.
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Affiliation(s)
- Chi-Kit Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, Canada
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Pavelka M, Shukla MK, Leszczynski J, Burda JV. Theoretical Study of Hydrated Copper(II) Interactions with Guanine: A Computational Density Functional Theory Study. J Phys Chem A 2008; 112:256-67. [DOI: 10.1021/jp074891+] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Riihimäki ES, Martínez JM, Kloo L. Molecular Dynamics Simulations of Cu(II) and the PHGGGWGQ Octapeptide. J Phys Chem B 2007; 111:10529-37. [PMID: 17696524 DOI: 10.1021/jp072672i] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interaction between Cu2+ and the copper-binding octapeptide region in the human prion protein has been investigated by molecular dynamics simulations. In total four different nonbonded and bonded models were used in the study. Charge sets containing atomic partial charges were developed for these models. Out of the considered models, the bonded model performed physically in the most correct way. The simulations with the bonded model showed that the water molecules in the axial position are very labile. The tryptophan indole ring can remain in a stable position on top of the equatorial coordination plane of copper without water mediation. Strong aromatic interaction was observed between the imidazole and indole rings. The nonbonded models showed a tendency for water-mediated interaction between the copper ion and different carbonyl oxygen atoms. In the case of the bonded model, a carbonyl group could also interact directly with the copper ion in one of the apical position.
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Affiliation(s)
- Eva-Stina Riihimäki
- Inorganic Chemistry, Department of Chemistry, Royal Institute of Technology, 100 44 Stockholm, Sweden
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Safi Z, Lamsabhi AM. Gas-phase reactivity of 2,7-dimethyl-[1,2,4]-triazepine thio derivatives toward Cu+ cation: a DFT study. J Phys Chem A 2007; 111:2213-9. [PMID: 17388292 DOI: 10.1021/jp068642h] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The gas-phase interactions of 2,7-dimethyl-[1,2,4]-triazepine and its thio derivatives with Cu+ were studied through the use of high-level density functional theory (DFT) calculations. The structure of all possible tautomers and their conformers was optimized at the B3LYP/6-31G(d) level of theory. Final energies were obtained at the B3LYP/6-311+G(2df,2p) level. It has been found that the direct association of Cu+ occurs at the oxygen atom attached to position 3 in the case of the dioxo derivative and at the sulfur atom in all other cases. For the dithio derivatives, the global minimum of the PES corresponds to the structure in which the metal ion bridges between the heteroatom at position 3 and the nitrogen atom at position 4 of the corresponding enolic tautomer, forming a four-membered ring structure; for the dioxo derivative, this conformer competes with the ketone tautomer. Moreover, the isomerization processes leading from the most stable adduct to the other stable conformers were investigated. Among all the considered compounds, the 3,5-dithiotriazepines-Cu+ is found to be the one that associates Cu+ more tightly in the gas phase. The calculated Cu+ binding energies show a good correlation with the experimental proton affinities.
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Affiliation(s)
- Zaki Safi
- Department of Chemistry, Faculty of Science, Al-Azhar University of Gaza, Gaza, Palestine
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Knoll EH, Friesner RA. Localized Orbital Corrections for the Calculation of Ionization Potentials and Electron Affinities in Density Functional Theory. J Phys Chem B 2006; 110:18787-802. [PMID: 16986869 DOI: 10.1021/jp0619888] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper describes the extension of a previously reported empirical localized orbital correction model to the correction of ionization potential energies (IP) and electron affinities (EA) for atoms and molecules of first and second row elements. The B3LYP localized orbital correction version of the model (B3LYP-LOC) uses 22 heuristically determined parameters that improve B3LYP DFT IP and EA energy calculations on the G2 data set of 134 molecules from a mean absolute deviation (MAD) from experiment of 0.137 to 0.039 eV. The method significantly reduces the number of outliers and overall MAD to error levels below that achieved with G2 wave function based theory; furthermore, the new model has zero additional computational cost beyond standard DFT calculations. Although the model is heuristic and is based on a multiple linear regression to experimental errors, each of the parameters is justified on physical grounds, and each provides insight into the fundamental limitations of DFT, most importantly the failure of current DFT methods to accurately account for nondynamical electron correlation.
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Affiliation(s)
- Eric H Knoll
- Department of Chemistry, Columbia University, Havemeyer Hall, MC 3110, New York, New York 10025, USA
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