1
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Mohammadian Z, Shayesteh A. Spin-orbit coupling in low-lying electronic states of CuH. Phys Chem Chem Phys 2023; 25:30488-30500. [PMID: 37921626 DOI: 10.1039/d3cp02869k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
Potential energy curves for the low-lying electronic states of CuH have been calculated using the MRCI method with a large active space containing the 3d, 4s, 4pz and 3d' orbitals of the copper atom. All electronic states of CuH correlating with the 3d10 4s1 (2S) and 3d9 4s2 (2D) states of Cu were included, and spin-orbit corrections were calculated using the MRCI wavefunctions. Potential energy curves were obtained for individual Ω states, and the Einstein A coefficients were computed for the spin-forbidden transitions from the low-lying electronic states to the X1Σ+ ground state. Diagonal and off-diagonal elements of the spin-orbit Hamiltonian matrix were calculated for the X1Σ+, A1Σ+, 13Σ+, 23Σ+, 11Π, 13Π, 11Δ and 13Δ states, and the mixing of vibronic wavefunctions was investigated using the eigenvectors. The available experimental data on vibrational levels of the A1Σ+ excited state of CuH and CuD were combined in a multi-isotopologue Birge-Sponer plot, and the ab initio data on the unobserved vibrational levels were used for a more accurate extrapolation, resulting in a new experimental value for the equilibrium dissociation energy (De) of the CuH molecule. The De value for the ground state of CuH was determined to be 22 630 ± 250 cm-1, resulting in D0 values of 2.686 and 2.720 eV for CuH and CuD, respectively. Therefore, new experimental values for the bond dissociation enthalpies of CuH and CuD are reported to be 262.9 ± 3 and 266.2 ± 3 kJ mol-1, respectively.
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Affiliation(s)
- Zeinab Mohammadian
- School of Chemistry, College of Science, University of Tehran, Tehran, 14176, Iran.
| | - Alireza Shayesteh
- School of Chemistry, College of Science, University of Tehran, Tehran, 14176, Iran.
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2
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Beck RA, Huang Y, Petrone A, Abbott JW, Pauzauskie PJ, Li X. Electronic Structures and Spectroscopic Signatures of Noble-Gas-Doped Nanodiamonds. ACS PHYSICAL CHEMISTRY AU 2023; 3:299-310. [PMID: 37249932 PMCID: PMC10214509 DOI: 10.1021/acsphyschemau.2c00072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 05/31/2023]
Abstract
Fluorescent nanodiamonds, that is, those containing optically active defects, have attracted interest for their ability to be used as qubits; for in vivo imaging; and as sensors for spin, stress, and temperature. One of the most commonly studied nanodiamond color centers is the nitrogen vacancy. However, there is strong interest in discovering other impurity centers that provide localized midband gap transitions. Noble gas atoms have garnered attention since they have been discovered within nanodiamonds produced through high-pressure-high-temperature laser-heated diamond anvil cell synthesis methods, where they are commonly used as hydrostatic pressure media. Noble gas atoms that exist in macrosized natural or synthetic diamonds have been shown to be able to form color centers. This research uses ab initio density functional theory and cluster models to systematically study the localized electronic structure for group VIII impurities of nanodiamond, including helium, neon, argon, krypton, and xenon. An in-depth examination of the interaction between the noble gas atom and diamond lattice has been carried out. The changes to the vibrational and UV/vis absorption spectra have been analyzed. It was determined that the energetically preferred geometry is dependent on the atom size. Most noble gas defects are stabilized within the nanodiamond lattice and exist in tetrahedral interstitial positions, except for the largest noble gas studied in this work, Xe, which was determined to prefer a substitutional configuration. Both Kr and Xe are expected to be able to manifest visible/near-IR optical responses when included in the diamond lattice.
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Affiliation(s)
- Ryan A. Beck
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Yue Huang
- Department
of Materials Science and Engineering, University
of Washington, Seattle, Washington 98195, United States
| | - Alessio Petrone
- Dipartimento
di Scienze Chimiche Angelo, via Cintia, I-80126 Napoli, Italy
| | - Joseph W. Abbott
- Laboratory
of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale
de Lausanne,1015 Lausanne, Switzerland
| | - Peter J. Pauzauskie
- Department
of Materials Science and Engineering, University
of Washington, Seattle, Washington 98195, United States
| | - Xiaosong Li
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
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3
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Kenouche S, Bachir N, Martínez-Araya JI. Explaining the High Catalytic Activity in Bis(indenyl)methyl Zirconium Cation Using Combined EDA-NOCV/QTAIM Approach. Chemphyschem 2023; 24:e202200488. [PMID: 36161688 DOI: 10.1002/cphc.202200488] [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: 07/11/2022] [Revised: 09/24/2022] [Indexed: 01/20/2023]
Abstract
The main purpose of this study is to elucidate some discrepancies already observed in the catalytic activity values of some zirconocene methyl cations. The EDA-NOCV scheme was employed for a theoretical description of the interactions between an ethylene molecule and five catalysts of zirconocene methyl cation. The nature of the chemical interactions has been elucidated through the QTAIM topological analysis. The steric hindrance due to the ligands was evaluated qualitatively by means of an IRI-based analysis and quantitively through Fisher information. The findings prove that the indenyl ligand seems to favor the orbital interaction between the ethylene molecule and the metal centre of zirconocene methyl cation. Both electrostatic and orbital contributions play a crucial role in stabilising the studied complexes. Based on the NOCV deformation density contributions, the strongest orbital interaction is reached with the bis(indenyl)methyl zirconium cation, which is the only one exhibiting covalent interactions. Especially, the strong contribution of π-back donation (occurring from the occupied orbitals of the zirconium atom to the π* anti-bonding orbital of ethylene) may be a key to understand why this catalyst has a higher polymerisation yield than the other studied catalysts. This work suggests a perspective for predicting values of catalytic activity when theoretically designing novel catalysts of zirconocene type.
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Affiliation(s)
- Samir Kenouche
- Group of Modeling of Chemical Systems using Quantum Calculations, Applied Chemistry Laboratory (LCA)., University of M. Khider of Biskra, BP 145 RP, 07000, Biskra, Algeria
| | - Nassima Bachir
- Group of Modeling of Chemical Systems using Quantum Calculations, Applied Chemistry Laboratory (LCA)., University of M. Khider of Biskra, BP 145 RP, 07000, Biskra, Algeria
| | - Jorge I Martínez-Araya
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello (UNAB), Av. República 275, 8370146, Santiago, Chile
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4
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Kenouche S, Martínez-Araya JI. A combined QTAIM/IRI topological analysis of the effect of axial/equatorial positions of NH 2 and CN substituents in the [(PY 5Me 2)MoO] + complex. J Mol Graph Model 2022; 116:108273. [PMID: 35930821 DOI: 10.1016/j.jmgm.2022.108273] [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: 12/24/2021] [Revised: 05/09/2022] [Accepted: 07/08/2022] [Indexed: 12/15/2022]
Abstract
By means of the Interaction Region Indicator (IRI) and Quantum Theory of Atoms in Molecules (QTAIM), the influence exerted by NH2 (amino) and CN (cyano) as electron donor and electron acceptor substituent groups, respectively, located at para-positions of axial and equatorial pyridine rings of derivatized complexes coming from the [(PY5Me2)MoO]+ complex during the hydrogen molecular release in the gas phase was analyzed. In any case, a H-H covalent bond is forming at the transition state, with a strengthening of the electron density of 5.5% when the substituent group involved is NH2 at the para-position of the axial pyridine ring. However, there was no difference between NH2 and CN when these substituent groups are located at the para-positions of the equatorial pyridine rings. The topological properties of electron densities from the QTAIM are not perturbed by the electron donor and electron acceptor nature of the substituents, even when these substituent groups are located at the axial or equatorial pyridine rings of the Mo-based complex.
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Affiliation(s)
- Samir Kenouche
- Group of Modeling of Chemical Systems Using Quantum Calculations, Applied Chemistry Laboratory (LCA), University M. Khider of Biskra, 07000 Biskra, Algeria
| | - Jorge I Martínez-Araya
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello (UNAB), Av. República 275, 8370146, Santiago, Chile.
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5
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Shamshurin M, Gushchin A, Adonin S, Benassi E, Sokolov M. Niobium and Tantalum Halocyanide Clusters: The Complete Family. Inorg Chem 2022; 61:16586-16595. [PMID: 36162107 DOI: 10.1021/acs.inorgchem.2c01824] [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
Synthetic procedures providing straightforward access to the whole family of Nb and Ta halide clusters with terminal cyanide ligands have been developed. Corresponding [M6X12(CN)12]4- (M = Nb, Ta; X = Cl, Br) can be accessed by ligand-exchange procedures from K4Nb6X18 (X = Cl, Br) and Bu4NCN, (Et4N)2[Ta6Cl18] and Bu4NCN and from [Ta6Br12(H2O)4Br2]·4H2O and KCN in moderate to high yields (50-80%). The products were isolated as Bu4N salts. The compounds were investigated both experimentally and by quantum chemistry, revealing correlations between structural, electrochemical, electrostatic, electronic, and topological features as a function of type of metal, halide, and charge.
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Affiliation(s)
- Maxim Shamshurin
- Nikolaev Institute of Inorganic Chemistry, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 3, 630090 Novosibirsk, Russian Federation
| | - Artem Gushchin
- Nikolaev Institute of Inorganic Chemistry, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 3, 630090 Novosibirsk, Russian Federation
| | - Sergey Adonin
- Nikolaev Institute of Inorganic Chemistry, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 3, 630090 Novosibirsk, Russian Federation
| | - Enrico Benassi
- Novosibirsk State University, Ulitsa Pirogova 2, 630090 Novosibirsk, Russian Federation
| | - Maxim Sokolov
- Nikolaev Institute of Inorganic Chemistry, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 3, 630090 Novosibirsk, Russian Federation.,Novosibirsk State University, Ulitsa Pirogova 2, 630090 Novosibirsk, Russian Federation
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Nyenhuis M, Schönrath I, Kamzeeva PN, Zatsepin TS, Müller J, Doltsinis N, Aralov AV. Benzothiazole-substituted 1,3-diaza-2-oxophenoxazine as a luminescent nucleobase surrogate for silver(I)-mediated base pairing. Dalton Trans 2022; 51:13386-13395. [PMID: 35989665 DOI: 10.1039/d2dt01762h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A benzothiazole-substituted derivative (X) of 1,3-diaza-2-oxophenoxazine was evaluated with respect to its ability to engage in Ag(I)-mediated homo base pair formation in two different DNA duplexes. The metal binding was determined by a combination of temperature-dependent UV spectroscopy, CD spectroscopy, and fluorescence spectroscopy, indicating the incorporation of two Ag(I) ions to generate a dinuclear X-Ag(I)2-X base pair. Interestingly, a luminescence increase was observed upon metal binding. Theoretical luminescence spectra were calculated using time-dependent density functional theory (TDDFT) for all possible Ag(I)-mediated X : X base pair geometries to identify the species responsible for the increase in luminescence. The study shows that even bulky non-planar artificial nucleobases can be applied to form stabilizing metal-mediated base pairs.
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Affiliation(s)
- Marvin Nyenhuis
- Westfälische Wilhelms-Universität Münster, Institute for Solid State Theory and Center for Multiscale Theory and Computation, Wilhelm-Klemm-Straße 10, 48149 Münster, Germany.
| | - Isabell Schönrath
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 28/30, 48149 Münster, Germany.
| | - Polina N Kamzeeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia.
| | - Timofei S Zatsepin
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, 121205 Moscow, Russia.,Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory Str. 1-3, 119992 Moscow, Russia
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 28/30, 48149 Münster, Germany.
| | - Nikos Doltsinis
- Westfälische Wilhelms-Universität Münster, Institute for Solid State Theory and Center for Multiscale Theory and Computation, Wilhelm-Klemm-Straße 10, 48149 Münster, Germany.
| | - Andrey V Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia.
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7
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Ju P, Huang Q, Zhang R, Chen JL, Zhao F, Liu SJ, Wen HR. A tricolor-switchable stimuli-responsive luminescent binuclear Cu( i) complex with switchable NH⋯O interactions. Inorg Chem Front 2022. [DOI: 10.1039/d2qi00359g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Blue-green-yellow tricolor luminescence conversion is attributed to the loss and recovery of CH2Cl2 solvent molecules and the destruction and restoration of the orderly packing array caused by the breaking and rebuilding of NH⋯O hydrogen bonds.
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Affiliation(s)
- Peng Ju
- Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, Department of Materials, Metallurgy and Chemistry, Jiangxi University of Science and Technology, Ganzhou 341000, P.R. China
| | - Qin Huang
- Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, Department of Materials, Metallurgy and Chemistry, Jiangxi University of Science and Technology, Ganzhou 341000, P.R. China
| | - Rui Zhang
- Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, Department of Materials, Metallurgy and Chemistry, Jiangxi University of Science and Technology, Ganzhou 341000, P.R. China
| | - Jing-Lin Chen
- Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, Department of Materials, Metallurgy and Chemistry, Jiangxi University of Science and Technology, Ganzhou 341000, P.R. China
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, P.R. China
| | - Feng Zhao
- School of Chemistry and Chemical Engineering, Jiangxi Science and Technology Normal University, Nanchang 330013, P.R. China
| | - Sui-Jun Liu
- Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, Department of Materials, Metallurgy and Chemistry, Jiangxi University of Science and Technology, Ganzhou 341000, P.R. China
| | - He-Rui Wen
- Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, Department of Materials, Metallurgy and Chemistry, Jiangxi University of Science and Technology, Ganzhou 341000, P.R. China
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8
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Ison EA, Tubb JL. Energy Decomposition Analysis of Lewis Acid/Base Adducts and Frustrated Lewis Pairs: The Use of EOrb/ ESteric Ratios as a Reaction Parameter. Inorg Chem 2021; 60:13797-13805. [PMID: 34329555 DOI: 10.1021/acs.inorgchem.1c00911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The nature of bonding in classical adducts and frustrated Lewis pairs (FLPs) of oxorhenium and nitridorhenium complexes with B(C6F5)3 was investigated computationally (B3PW91-D3). These studies have revealed that the primary noncovalent interaction (NCI) in the FLPs involves lone pair/π interactions between the terminal M≡X bond and the aromatic C6F5 ring in B(C6F5)3. Energy decomposition analyses on classical adducts and FLPs reveal that these species can be defined by the ratio (EOrb/ESteric) of covalent-to-noncovalent contributions to the total interaction energy, EInt. This type of analysis reveals that values for FLPs exist in a narrow range (1.2-2.5), with values for adducts significantly outside this range. The application of this method to other main-group combinations of Lewis acids and bases that have been shown to exhibit FLP reactivity yields similar results. These data suggest that similar NCIs are present in both transition-metal and main-group FLPs, especially where Lewis acids such as B(C6F5)3 are utilized.
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Affiliation(s)
- Elon A Ison
- Department of Chemistry, North Carolina State University (NCSU), 2620 Yarbrough Drive, Raleigh, North Carolina 27695-8204, United States
| | - Joshua L Tubb
- Department of Chemistry, North Carolina State University (NCSU), 2620 Yarbrough Drive, Raleigh, North Carolina 27695-8204, United States
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9
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Martínez-Araya JI, Morell C. The density polarization reveals directions of electron displacements due to the substituent effect: Analysis performed on a metal-organic Mo-Oxo catalyst. J Comput Chem 2021; 42:1118-1125. [PMID: 33880780 DOI: 10.1002/jcc.26526] [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: 01/29/2021] [Revised: 03/13/2021] [Accepted: 03/18/2021] [Indexed: 11/09/2022]
Abstract
Some Mo-oxo complexes bearing pyridine rings have the capability for dihydrogen production from water. However, energy barrier and overall energy vary depending on the effect exerted by several substituent groups located at different positions around one or more pyridine rings which are ligands of these compounds. Based on the Karunadasa and coworkers investigation where the para-position was experimentally tested in compounds derivatised from the 2,6-bis[1,1-bis(2-pyridil)ethyl]-pyridine oxo-molybdenum complex synthesized (Karunadasa et al., Nature, 2010, 464, 1329), we tested the combined effect of electron-withdrawing and electron-donating groups simulated as perturbations represented by point-charges. Then, we used the density polarization concept, δρ(r), a local reactivity descriptor corresponding to the partially integrated linear response function, χ(r, r') (a non-local reactivity descriptor), which is able to reveal different displacements of π-electrons on molecular structures. We perturbed the para-positions in the pentadentate ligand 2,6-bis[1,1-bis(2-pyridil)ethyl]-pyridine in the Mo-based complex by means of point-charges. They were located in three different configurations of the organic ligand (trans, geminal, and cis) which could help to explain energy barriers and overall energy of reactions catalyzed by this type of Mo-complexes. Our results indicate that the trans configuration of point-charges induces the most amount of fraction of electron shifted on the complex. A Mo-based complex bearing the same trans configuration for electron-withdrawing and electron-donating substituent groups (cyano and amino, respectively), leads to a kinetically more favorable H2 release than the cis or geminal configuration of the substituent groups aforementioned.
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Affiliation(s)
- Jorge I Martínez-Araya
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello (UNAB), Santiago, Chile
| | - Christophe Morell
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280,CNRS, Université Claude Bernard Lyon 1, Villeurbanne, France
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10
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Yan Z, Li X, Chung LW. Multiscale Quantum Refinement Approaches for Metalloproteins. J Chem Theory Comput 2021; 17:3783-3796. [PMID: 34032440 DOI: 10.1021/acs.jctc.1c00148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Biomolecules with metal ion(s) (e.g., metalloproteins) play many important biological roles. However, accurate structural determination of metalloproteins, particularly those containing transition metal ion(s), is challenging due to their complicated electronic structure, complex bonding of metal ions, and high number of conformations in biomolecules. Quantum refinement, which was proposed to combine crystallographic data with computational chemistry methods by several groups, can improve the local structures of some proteins. In this study, a quantum refinement method combining several multiscale computational schemes with experimental (X-ray diffraction) information was developed for metalloproteins. Various quantum refinement approaches using different ONIOM (our own N-layered integrated molecular orbital and molecular mechanics) combinations of quantum mechanics (QM), semiempirical (SE), and molecular mechanics (MM) methods were conducted to assess the performance and reliability on the refined local structure in two metalloproteins. The structures for two (Cu- or Zn-containing) metalloproteins were refined by combining two-layer ONIOM2(QM1/QM2) and ONIOM2(QM/MM) and three-layer ONIOM3(QM1/QM2/MM) schemes with experimental data. The accuracy of the quantum-refined metal binding sites was also examined and compared in these multiscale quantum refinement calculations. ONIOM3(QM/SE/MM) schemes were found to give good results with lower computational costs and were proposed to be a good choice for the multiscale computational scheme for quantum refinement calculations of metal binding site(s) in metalloproteins with high efficiency. Additionally, a two-center ONIOM approach was employed to speed up the quantum refinement calculations for the Zn metalloprotein with two remote active sites/ligands. Moreover, a recent quantum-embedding wavefunction-in-density functional theory (WF-in-DFT) method was also adopted as the high-level method in unprecedented ONIOM2(CCSD-in-B3LYP/MM) and ONIOM3(CCSD-in-B3LYP/SE/MM) calculations, which can be regarded as novel pseudo-three- and pseudo-four-layer ONIOM methods, respectively, to refine the key Zn binding site at the coupled-cluster singles and doubles (CCSD) level. These refined results indicate that multiscale quantum refinement schemes can be used to improve the structural accuracy obtained for local metal binding site(s) in metalloproteins with high efficiency.
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Affiliation(s)
- Zeyin Yan
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xin Li
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Lung Wa Chung
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
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11
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Jasik P, Franz J, Kędziera D, Kilich T, Kozicki J, Sienkiewicz JE. Spontaneous electron emission vs dissociation in internally hot silver dimer anions. J Chem Phys 2021; 154:164301. [PMID: 33940838 DOI: 10.1063/5.0046060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Referring to a recent experiment, we theoretically study the process of a two-channel decay of the diatomic silver anion (Ag2 -), namely, the spontaneous electron ejection giving Ag2 + e- and the dissociation leading to Ag- + Ag. The ground state potential energy curves of the silver molecules of diatomic neutral and negative ions were calculated using proper pseudo-potentials and atomic basis sets. We also estimated the non-adiabatic electronic coupling between the ground state of Ag2 - and the ground state of Ag2 + e-, which, in turn, allowed us to estimate the minimal and mean values of the electron autodetachment lifetimes. The relative energies of the rovibrational levels allow the description of the spontaneous electron emission process, while the description of the rotational dissociation is treated with the quantum dynamics method as well as time-independent methods. The results of our calculations are verified by comparison with the experimental data.
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Affiliation(s)
- P Jasik
- Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, 80-233 Gdańsk, Poland
| | - J Franz
- Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, 80-233 Gdańsk, Poland
| | - D Kędziera
- Faculty of Chemistry, Nicolaus Copernicus University, 87-100 Toruń, Poland
| | - T Kilich
- Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, 80-233 Gdańsk, Poland
| | - J Kozicki
- Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, 80-233 Gdańsk, Poland
| | - J E Sienkiewicz
- Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, 80-233 Gdańsk, Poland
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12
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Guo X, Yang T, Sheong FK, Lin Z. Beyond the Nucleophilic Role of Metal–Boryl Complexes in Borylation Reactions. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00752] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Xueying Guo
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong, China
| | - Tilong Yang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong, China
| | - Fu Kit Sheong
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong, China
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong, China
| | - Zhenyang Lin
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong, China
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13
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Dong J, Sun X, Zhen N, Li Z, Liu D, Zou B, Dai Q, Chi Y, Chen SL, Poblet JM, Hu C. Oxidative detoxification of nerve agent VX simulant by polyoxoniobate: Experimental and theoretical insights. J Catal 2021. [DOI: 10.1016/j.jcat.2020.12.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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14
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Pareek M, Sunoj RB. Mechanistic insights into rhodium-catalyzed enantioselective allylic alkylation for quaternary stereogenic centers. Chem Sci 2020; 12:2527-2539. [PMID: 34164021 PMCID: PMC8179253 DOI: 10.1039/d0sc04959j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Installing quaternary stereogenic carbon is an arduous task of contemporary importance in the domain of asymmetric catalysis. To this end, an asymmetric allylic alkylation of α,α-disubstituted aldehydes by using allyl benzoate in the presence of Wilkinson's catalyst [Rh(Cl)(PPh3)3], (R)-BINOL–P(OMe) as the external ligand, and LiHMDS as the base has been reported to offer high enantioselectivity. The mechanistic details of this important reaction remain vague, which prompted us to undertake a detailed density functional theory (SMD(THF)/B3LYP-D3) investigation on the nature of the potential active catalyst, energetic features of the catalytic cycle, and the origin of high enantioselectivity. We note that a chloride displacement from the native Rh-phosphine [Rh(Cl)(PPh3)3] by BINOL–P(OMe) phosphite and an ensuing MeCl elimination can result in the in situ formation of a Rh-phosphonate [Rh(BINOL–P
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O)(PPh3)3]. A superior energetic span (δE) noted with such a Rh-phosphonate suggests that it is likely to serve as an active catalyst. The uptake of allyl benzoate by the active catalyst followed by the turnover determining C–O bond oxidative addition furnishes a Rh-π-allyl intermediate, which upon interception by (Z)-Li-enolate (derived from α,α-disubstituted aldehyde) in the enantiocontrolling C–C bond generates a quaternary stereogenic center. The addition of the re prochiral face of the (Z)-Li-enolate to the Rh-bound allyl moiety leading to the R enantiomer of the product is found to be 2.4 kcal mol−1 more preferred over the addition through its si face. The origin of the stereochemical preference for the re face addition is traced to improved noncovalent interactions (NCIs) and less distortion in the enantiocontrolling C–C bond formation transition state than that in the si face addition. Computed enantioselectivity (96%) is in very good agreement with the experimental value (92%), so is the overall activation barrier (δE of 17.1 kcal mol−1), which is in conformity with room temperature reaction conditions. The origin of high enantioselectivity in the formation of quaternary stereogenic carbon.![]()
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Affiliation(s)
- Monika Pareek
- Department of Chemistry, Indian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Raghavan B Sunoj
- Department of Chemistry, Indian Institute of Technology Bombay Powai Mumbai 400076 India
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15
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Glossman-Mitnik D, Martínez-Araya JI. KID Procedure Applied on the [(PY 5Me 2)MoO] + Complex. ACS OMEGA 2020; 5:30549-30555. [PMID: 33283103 PMCID: PMC7711706 DOI: 10.1021/acsomega.0c04450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/04/2020] [Indexed: 06/12/2023]
Abstract
The KID (Koopmans in DFT) protocol usually applies in organic molecules of the closed-shell type. We used the KID procedure on an open-shell Mo-based system for the first time to choose the most suitable density functional to compute global and local reactivity descriptors obtained from the conceptual density-functional theory (DFT). From a set of 18 density functionals, spread from the second until the fourth rung of Jacob's ladder: BLYP, BP86, B97-D, MN12-L, MN15-L, M06-L, M11-L, CAM-B3LYP, PBE0, B3LYP, N12-SX, M06-2X, MN15, MN12-SX, ωB97X-D, M11, LC-ωHPBE, and APFD, we concluded that CAM-B3LYP provides the best outcome, and in the second place, M06-2X. Because the vertical first ionization potential and vertical first electron affinity in the ground state (gs) are defined as follows I = E gs(N - 1) - E gs(N) and A = E gs(N) - E gs(N + 1), where E gs(N - 1), E gs(N), and E gs(N + 1) correspond to energies of the system bearing N, N + 1, and N - 1 electrons, along with Koopmans' theorem (KT) given by I ≈ -εHOMO (εHOMO, highest occupied molecular orbital energy) and A ≈ -εLUMO (εLUMO, lowest unoccupied molecular orbital energy), the deviation from the KT was performed by the use of the index, such that J I = |E gs(N - 1) - E gs(N) + εHOMO| and J A = |E gs(N) - E gs(N + 1) + εLUMO|, which are absolute deviations from the perspective of I and A, respectively. Furthermore, the εSOMO (SOMO: singly-occupied molecular orbital energy) leads us to another index given by |ΔSL| = |εSOMO - εLUMO|. Therefore, J HL and |ΔSL| are indexes defined to evaluate the quality of the KT when employed within the context of quantum chemical calculations based on DFT and not the Hartree-Fock theory. We propose the index that could be more suitable to choose the most proper density functional because the J HL and |ΔSL| are independent indexes.
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Affiliation(s)
- Daniel Glossman-Mitnik
- Laboratorio
Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua, Chih 31136, Mexico
| | - Jorge I. Martínez-Araya
- Departamento
de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello (UNAB), Av. República 498, Santiago 8370146, Chile
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16
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Brown CA, Abrahamse M, Ison EA. Re-Silane complexes as frustrated lewis pairs for catalytic hydrosilylation. Dalton Trans 2020; 49:11403-11411. [PMID: 32779676 DOI: 10.1039/d0dt02084b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A pathway for the catalytic hydrosilylation of carbonyl substrates with M(C6F5)3 (M = B, Al and Ga) was calculated by DFT (B3PW91-D3) and it was shown that in the case of the Al reagent, the carbonyl substrate binds irreversibly and inhibits catalysis by generating a stable carbonyl adduct. In contrast, the reduced electrophilicity of B(C6F5)3 disfavors the binding of the carbonyl substrate and increases the concentration of an activated silane adduct which is the species responsible for catalytic turnover. A similar mechanism was found for both cationic and neutral Re(iii) species. Further, it was shown by tuning the electrophilicity of the rhenium catalysts, conditions can be found that would enable the catalytic hydrosilylation of ketone and nitrile substrates that were unreactive in previously reported systems. Thus the mechanisms proposed in this work, lay the foundation for the design of new catalytic systems.
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Affiliation(s)
- Caleb A Brown
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695-8204, USA.
| | - Michael Abrahamse
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695-8204, USA.
| | - Elon A Ison
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695-8204, USA.
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17
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Wu SQ, Zhang SQ, Hong X. Understanding the mechanism and reactivity of Pd-catalyzed C-P bond metathesis of aryl phosphines: a computational study. Org Biomol Chem 2020; 18:5414-5419. [PMID: 32618317 DOI: 10.1039/d0ob00719f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Transition metal-catalyzed single bond metathesis has recently emerged as a useful strategy for functional group transfer. In this work, we explored the mechanism and reactivity profile of Pd/PhI-cocatalyzed C-P bond metathesis between aryl phosphines using density functional theory (DFT) calculations. The overall single bond metathesis involves two Pd(ii)-catalyzed C-P reductive eliminations and two Pd(0)-catalyzed C-P oxidative additions, which allows the reversible C-P bond cleavage and formation of the phosphonium cation. Distortion/interaction analysis indicates that the facile C-P bond cleavage and formation of the phosphonium cation are due to the involvement of coordinating aryl phosphine in the process. In addition, the substituent effects on the reaction kinetics and thermodynamics of metathesis were computed, which provides helpful mechanistic information for the design of related single bond metathesis reactions.
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Affiliation(s)
- Shao-Qi Wu
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, China.
| | - Shuo-Qing Zhang
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, China.
| | - Xin Hong
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, China. and State Key Laboratory of Clean Energy Utilization, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
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18
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Pareek M, Sunoj RB. Energetics of Dynamic Kinetic Asymmetric Transformation in Suzuki–Miyaura Coupling. ACS Catal 2020. [DOI: 10.1021/acscatal.9b05526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Monika Pareek
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Raghavan B. Sunoj
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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19
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Brown CA, Lilly CP, Lambic NS, Sommer RD, Ison EA. Synthesis and Reactivity of Re(III) and Re(V) Fischer Carbenes. Organometallics 2019. [DOI: 10.1021/acs.organomet.9b00600] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Caleb A. Brown
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695-8204, United States
| | - Cassandra P. Lilly
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695-8204, United States
| | - Nikola S. Lambic
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695-8204, United States
| | - Roger D. Sommer
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695-8204, United States
| | - Elon A. Ison
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695-8204, United States
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20
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Alcock LJ, Cavigliasso G, Lawes DJ, Stranger R, Hook JM, Ralph SF. Dynamic solution behaviour of metal complexes of the hexaamine cage ligand Me8tricosane. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2019.119013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Nicholas AD, Bullard RM, Wheaton AM, Streep M, Nicholas VA, Pike RD, Patterson HH. Synthesis and Luminescence of Optical Memory Active Tetramethylammonium Cyanocuprate(I) 3D Networks. MATERIALS 2019; 12:ma12081211. [PMID: 31013868 PMCID: PMC6514951 DOI: 10.3390/ma12081211] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 04/07/2019] [Accepted: 04/10/2019] [Indexed: 11/17/2022]
Abstract
The structures of three tetramethylammonium cyanocuprate(I) 3D networks [NMe4]2[Cu(CN)2]2•0.25H2O (1), [NMe4][Cu3(CN)4] (2), and [NMe4][Cu2(CN)3] (3), (Me4N = tetramethylammonium), and the photophysics of 1 and 2 are reported. These complexes are prepared by combining aqueous solutions of the simple salts tetramethylammonium chloride and potassium dicyanocuprate. Single-crystal X-ray diffraction analysis of complex 1 reveals {Cu2(CN)2(μ2-CN)4} rhomboids crosslinked by cyano ligands and D3h {Cu(CN)3} metal clusters into a 3D coordination polymer, while 2 features independent 2D layers of fused hexagonal {Cu8(CN)8} rings where two Cu(I) centers reside in a linear C∞v coordination sphere. Metallophilic interactions are observed in 1 as close Cu⋯Cu distances, but are noticeably absent in 2. Complex 3 is a simple honeycomb sheet composed of trigonal planar Cu(I) centers with no Cu…Cu interactions. Temperature and time-dependent luminescence of 1 and 2 have been performed between 298 K and 78 K and demonstrate that 1 is a dual singlet/triplet emitter at low temperatures while 2 is a triplet-only emitter. DFT and TD-DFT calculations were used to help interpret the experimental findings. Optical memory experiments show that 1 and 2 are both optical memory active. These complexes undergo a reduction of emission intensity upon laser irradiation at 255 nm although this loss is much faster in 2. The loss of emission intensity is reversible in both cases by applying heat to the sample. We propose a light-induced electron transfer mechanism for the optical memory behavior observed.
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Affiliation(s)
- Aaron D Nicholas
- Department of Chemistry, University of Maine, Orono, ME 04469, USA.
| | - Rebeka M Bullard
- Department of Chemistry, University of Maine, Orono, ME 04469, USA.
| | - Amelia M Wheaton
- Department of Chemistry, College of William and Mary, Williamsburg, VA 23187-8795, USA.
| | - Michaela Streep
- Department of Chemistry, College of William and Mary, Williamsburg, VA 23187-8795, USA.
| | | | - Robert D Pike
- Department of Chemistry, College of William and Mary, Williamsburg, VA 23187-8795, USA.
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22
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Yepes D, Jaque P, Martínez-Araya JI. Scrutinizing the substituent effect on Mo-based electrocatalysts for molecular hydrogen release through axial–equatorial decomposition: a DFT study. Phys Chem Chem Phys 2019; 21:16601-16614. [DOI: 10.1039/c9cp00670b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effect of electron-donating and -withdrawing groups is studied in terms of axial and equatorial locations at the p-pyridine rings in the [(PY5Me2)MoO]2+ for the H2 release in aqueous media. It opens a way to modify its kinetics and thermodynamics.
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Affiliation(s)
- Diana Yepes
- Departamento de Ciencias Químicas
- Facultad de Ciencias Exactas
- Universidad Andres Bello (UNAB)
- Santiago
- Chile
| | - Pablo Jaque
- Departamento de Química Orgánica y Fisicoquímica
- Facultad de Ciencias Químicas yFarmacéuticas
- Universidad de Chile (U. de Chile)
- Santiago
- Chile
| | - Jorge I. Martínez-Araya
- Departamento de Ciencias Químicas
- Facultad de Ciencias Exactas
- Universidad Andres Bello (UNAB)
- Santiago
- Chile
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23
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24
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How does binuclear zinc amidohydrolase FwdA work in the initial step of methanogenesis: From formate to formyl-methanofuran. J Inorg Biochem 2018; 185:71-79. [PMID: 29778928 DOI: 10.1016/j.jinorgbio.2018.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/05/2018] [Accepted: 05/08/2018] [Indexed: 11/22/2022]
Abstract
The initial step of methanogenesis is the fixation of CO2 to formyl-methanofuran (formyl-MFR) catalyzed by formyl-MFR dehydrogenase, which can be divided into two half reactions. Herein, the second half reaction catalyzed by FwdA (formyl-methanofuran dehydrogenase subunit A), i.e., from formate to formyl-methanofuran, has been investigated using density functional theory and a chemical model based on the X-ray crystal structure. The calculations indicate that, compared with other well-known di-zinc hydrolases, the FwdA reaction employs a reverse mechanism, including the nucleophilic attack of MFR amine on formate carbon leading to a tetrahedral gem-diolate intermediate, two steps of proton transfer from amine to formate moieties assisted by the Asp385, and the CO bond dissociation to form the formyl-MFR product. The second step of proton transfer from the amine moiety to the Asp385 is rate-limiting with an overall barrier of 21.2 kcal/mol. The two zinc ions play an important role in stabilizing the transition states and intermediates, in particular the negative charge at the formate moiety originated from the nucleophilic attack of the MFR amine. The work here appends a crucial piece in the methanogenic mechanistics and advances the understanding of the global carbon cycle.
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25
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Drougas E. Quantum mechanical studies on the singlet and triplet potential energy surface of the reactions CF 3O 2 + I, CF 3O + OI and CF 3 + OIO. Mol Phys 2018. [DOI: 10.1080/00268976.2017.1377850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Evangelos Drougas
- Laboratory of Physical Chemistry, Chemistry Department, University of Ioannina, Ioannina, Greece
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26
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Zelenay B, Besora M, Monasterio Z, Ventura-Espinosa D, White AJP, Maseras F, Díez-González S. Copper-mediated reduction of azides under seemingly oxidising conditions: catalytic and computational studies. Catal Sci Technol 2018. [DOI: 10.1039/c8cy00515j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The reduction of aryl azides in the presence of water and air and without an obvious reducing agent is reported.
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Affiliation(s)
- Benjamin Zelenay
- Department of Chemistry
- Imperial College London
- SW7 2AZ London
- UK
- Institute of Chemical Research of Catalonia (ICIQ)
| | - Maria Besora
- Institute of Chemical Research of Catalonia (ICIQ)
- The Barcelona Institute of Science and Technology
- 43007 Tarragona
- Spain
| | | | | | | | - Feliu Maseras
- Institute of Chemical Research of Catalonia (ICIQ)
- The Barcelona Institute of Science and Technology
- 43007 Tarragona
- Spain
- Departament de Química
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27
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Martínez-Araya JI, Yepes D, Jaque P. A 3D visualization of the substituent effect : A brief analysis of two components of the operational formula of dual descriptor for open-shell systems. J Mol Model 2017; 24:31. [PMID: 29282551 DOI: 10.1007/s00894-017-3565-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/04/2017] [Indexed: 10/18/2022]
Abstract
Six organometallic compounds coming from a basic Mo-based complex were analyzed from the perspective of the dual descriptor in order to detect subtle influences that a substituent group could exert on the reactive core at a long range. Since the aforementioned complexes are open-shell systems, the used operational formula for the dual descriptor is that one defined for those aforementioned systems, which was then compared with spin density. In addition, dual descriptor was decomposed into two terms, each of which was also applied on every molecular system. The obtained results indicated that components of dual descriptor could become more useful than the operational formula of dual descriptor because differences exerted by the substituents at the para position were better detected by components of dual descriptor rather than the dual descriptor by itself.
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Affiliation(s)
- Jorge I Martínez-Araya
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Av. República 498, Santiago, Chile.
| | - Diana Yepes
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Av. República 498, Santiago, Chile
| | - Pablo Jaque
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Av. República 498, Santiago, Chile
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28
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Drienovská I, Alonso-Cotchico L, Vidossich P, Lledós A, Maréchal JD, Roelfes G. Design of an enantioselective artificial metallo-hydratase enzyme containing an unnatural metal-binding amino acid. Chem Sci 2017; 8:7228-7235. [PMID: 29081955 PMCID: PMC5633786 DOI: 10.1039/c7sc03477f] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 09/01/2017] [Indexed: 01/04/2023] Open
Abstract
The design of artificial metalloenzymes is a challenging, yet ultimately highly rewarding objective because of the potential for accessing new-to-nature reactions. One of the main challenges is identifying catalytically active substrate-metal cofactor-host geometries. The advent of expanded genetic code methods for the in vivo incorporation of non-canonical metal-binding amino acids into proteins allow to address an important aspect of this challenge: the creation of a stable, well-defined metal-binding site. Here, we report a designed artificial metallohydratase, based on the transcriptional repressor lactococcal multidrug resistance regulator (LmrR), in which the non-canonical amino acid (2,2'-bipyridin-5yl)alanine is used to bind the catalytic Cu(ii) ion. Starting from a set of empirical pre-conditions, a combination of cluster model calculations (QM), protein-ligand docking and molecular dynamics simulations was used to propose metallohydratase variants, that were experimentally verified. The agreement observed between the computationally predicted and experimentally observed catalysis results demonstrates the power of the artificial metalloenzyme design approach presented here.
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Affiliation(s)
- Ivana Drienovská
- Stratingh Institute for Chemistry , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , Netherlands .
| | - Lur Alonso-Cotchico
- Departament de Química , Universitat Autònoma de Barcelona , Edifici C.n. , 08193 Cerdanyola del Vallés , Barcelona , Spain .
| | - Pietro Vidossich
- Departament de Química , Universitat Autònoma de Barcelona , Edifici C.n. , 08193 Cerdanyola del Vallés , Barcelona , Spain .
| | - Agustí Lledós
- Departament de Química , Universitat Autònoma de Barcelona , Edifici C.n. , 08193 Cerdanyola del Vallés , Barcelona , Spain .
| | - Jean-Didier Maréchal
- Departament de Química , Universitat Autònoma de Barcelona , Edifici C.n. , 08193 Cerdanyola del Vallés , Barcelona , Spain .
| | - Gerard Roelfes
- Stratingh Institute for Chemistry , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , Netherlands .
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29
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Ghattas W, Cotchico-Alonso L, Maréchal JD, Urvoas A, Rousseau M, Mahy JP, Ricoux R. Artificial Metalloenzymes with the Neocarzinostatin Scaffold: Toward a Biocatalyst for the Diels-Alder Reaction. Chembiochem 2016; 17:433-40. [DOI: 10.1002/cbic.201500445] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Wadih Ghattas
- Institute de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO); UMR 8182, CNRS, Université Paris-Sud; Bât. 420, rue du Doyen Georges Poitou 91405 Orsay Cedex France
| | - Lur Cotchico-Alonso
- Departament de Química; Universitat Autònoma de Barcelona; Edifici C.n. 08193, Cerdonyola del Vallès Barcelona Spain
| | - Jean-Didier Maréchal
- Departament de Química; Universitat Autònoma de Barcelona; Edifici C.n. 08193, Cerdonyola del Vallès Barcelona Spain
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC); UMR 9198, CEA, CNRS, Université Paris-Sud; Bât. 430, rue du Doyen Georges Poitou 91405 Orsay Cedex France
| | - Maëva Rousseau
- Institute de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO); UMR 8182, CNRS, Université Paris-Sud; Bât. 420, rue du Doyen Georges Poitou 91405 Orsay Cedex France
| | - Jean-Pierre Mahy
- Institute de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO); UMR 8182, CNRS, Université Paris-Sud; Bât. 420, rue du Doyen Georges Poitou 91405 Orsay Cedex France
| | - Rémy Ricoux
- Institute de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO); UMR 8182, CNRS, Université Paris-Sud; Bât. 420, rue du Doyen Georges Poitou 91405 Orsay Cedex France
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30
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Day PN, Pachter R, Nguyen KA, Bigioni TP. Linear and Nonlinear Optical Response in Silver Nanoclusters: Insight from a Computational Investigation. J Phys Chem A 2016; 120:507-18. [DOI: 10.1021/acs.jpca.5b09623] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Paul N. Day
- Air Force Research Laboratory, Materials and
Manufacturing Directorate Wright-Patterson Air Force Base, Ohio 45433, United States
- General Dynamics Information Technology, Inc, Dayton Ohio 45431, United States
| | - Ruth Pachter
- Air Force Research Laboratory, Materials and
Manufacturing Directorate Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Kiet A. Nguyen
- Air Force Research Laboratory, Materials and
Manufacturing Directorate Wright-Patterson Air Force Base, Ohio 45433, United States
- UES, Inc, Dayton Ohio 45432, United States
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31
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Nemykin VN, Dudkin SV, Fathi-Rasekh M, Spaeth AD, Rhoda HM, Belosludov RV, Barybin MV. Probing Electronic Communications in Heterotrinuclear Fe–Ru–Fe Molecular Wires Formed by Ruthenium(II) Tetraphenylporphyrin and Isocyanoferrocene or 1,1′-Diisocyanoferrocene Ligands. Inorg Chem 2015; 54:10711-24. [DOI: 10.1021/acs.inorgchem.5b01614] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Victor N. Nemykin
- Department of Chemistry and Biochemistry, University of Minnesota, Duluth, 1039 University Drive, Duluth, Minnesota 55812, United States
| | - Semyon V. Dudkin
- Department of Chemistry and Biochemistry, University of Minnesota, Duluth, 1039 University Drive, Duluth, Minnesota 55812, United States
| | - Mahtab Fathi-Rasekh
- Department of Chemistry and Biochemistry, University of Minnesota, Duluth, 1039 University Drive, Duluth, Minnesota 55812, United States
| | - Andrew D. Spaeth
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045, United States
| | - Hannah M. Rhoda
- Department of Chemistry and Biochemistry, University of Minnesota, Duluth, 1039 University Drive, Duluth, Minnesota 55812, United States
| | | | - Mikhail V. Barybin
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045, United States
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32
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Nechaev IV, Samofalova TV, Naumov AV, Semenov VN. Structure and IR spectra of bis(thiourea)cadmium sulfate according to quantum-chemical calculation data. RUSS J INORG CHEM+ 2015. [DOI: 10.1134/s0036023615020114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Kumar P, Kashid VS, Reddi Y, Mague JT, Sunoj RB, Balakrishna MS. A phosphomide based PNP ligand, 2,6-{Ph2PC(O)}2(C5H3N), showing PP, PNP and PNO coordination modes. Dalton Trans 2015; 44:4167-79. [DOI: 10.1039/c4dt03960b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coordination chemistry of a versatile phosphomide ligand, 2,6-{Ph2PC(O)}2(C5H3N), is described.
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Affiliation(s)
- Pawan Kumar
- Phosphorus Laboratory
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai 400 076
- India
| | - Vitthalrao S. Kashid
- Phosphorus Laboratory
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai 400 076
- India
| | - Yernaidu Reddi
- Phosphorus Laboratory
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai 400 076
- India
| | - Joel T. Mague
- Department of Chemistry
- Tulane University
- New Orleans
- USA
| | - Raghavan B. Sunoj
- Phosphorus Laboratory
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai 400 076
- India
| | - Maravanji S. Balakrishna
- Phosphorus Laboratory
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai 400 076
- India
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Doroshenko AA, Nechaev IV, Vvedenskii AV. Quantum-chemical modeling of gas-phase adsorption of the hydroxyl radical on IB metal clusters Me n (n = 2–8). RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2014. [DOI: 10.1134/s003602441409012x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Structure, fluorescence, redox properties and theoretical interpretation of heteroleptic copper(I) and silver(I) complexes of N-[(2-pyridyl)methyliden]-6-coumarin and triphenylphosphine. Inorganica Chim Acta 2014. [DOI: 10.1016/j.ica.2013.10.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Lu Q, Yu H, Fu Y. Linear correlation between the C–H activation barrier and the C–Cu/C–H bond dissociation energy gap in Cu-promoted C–H activation of heteroarenes. Chem Commun (Camb) 2013; 49:10847-9. [DOI: 10.1039/c3cc46069j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Dolg M, Cao X. Relativistic pseudopotentials: their development and scope of applications. Chem Rev 2011; 112:403-80. [PMID: 21913696 DOI: 10.1021/cr2001383] [Citation(s) in RCA: 232] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Michael Dolg
- Theoretical Chemistry, University of Cologne, Greinstrasse 4, 50939 Cologne, Germany.
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Braga AAC, Caballero A, Urbano J, Diaz-Requejo MM, Pérez PJ, Maseras F. Mechanism of Side Reactions in Alkane CH Bond Functionalization by Diazo Compounds Catalyzed by Ag and Cu Homoscorpionate Complexes-A DFT Study. ChemCatChem 2011. [DOI: 10.1002/cctc.201100082] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Oxidative desulfurization (ODS) of organosulfur compounds catalyzed by peroxo-metallate complexes of WOx–ZrO2: Thermochemical, structural, and reactivity indexes analyses. J Catal 2011. [DOI: 10.1016/j.jcat.2011.06.010] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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40
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Relativistic Pseudopotentials. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2010. [DOI: 10.1007/978-1-4020-9975-5_6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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41
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Harb M, Rabilloud F, Simon D. Optical absorption of silver clusters: A study of the effective potential core size. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.06.042] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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42
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Bell F, Holland J, Green JC, Gagné MR. Computational Studies on the Pt(II)-Catalyzed Cycloisomerization of 1,6-dienes into Bicyclopropanes: A Mechanistic Quandary Evaluated by DFT. Organometallics 2009; 28:2038-2045. [PMID: 20161262 PMCID: PMC2700740 DOI: 10.1021/om800760x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanism of the (bis(phosphanylethyl)phosphane)Pt(2+) catalyzed cyclo-isomerization reaction of 7-methyl-octa-1,6-diene to form 1-isopropylbicyclo[3.1.0]hexane was studied using computational methods. The cyclopropanation step was found to be the turnover-limiting step. The overall reaction proceeds via both a 5-exo and a 6-endo route. W conformations were shown to facilitate cyclopropanation, but do not have any influence on the rate of the 1,2-hydride shifts.
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Affiliation(s)
- Franziska Bell
- The Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, United Kingdom
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Bleiholder C, Rominger F, Gleiter R. α-Metallocenylmethylium Ions and Their Isoelectronic Congeners: A Comparison Based on DFT Calculations. Organometallics 2009. [DOI: 10.1021/om800573u] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christian Bleiholder
- Organisch-Chemisches Institut der Universität Heidelberg, Im Neuenheimer Feld 270, D-69120 Heidelberg, Germany, and Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | - Frank Rominger
- Organisch-Chemisches Institut der Universität Heidelberg, Im Neuenheimer Feld 270, D-69120 Heidelberg, Germany, and Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | - Rolf Gleiter
- Organisch-Chemisches Institut der Universität Heidelberg, Im Neuenheimer Feld 270, D-69120 Heidelberg, Germany, and Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
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44
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Chen SL, Marino T, Fang WH, Russo N, Himo F. Peptide Hydrolysis by the Binuclear Zinc Enzyme Aminopeptidase from Aeromonas proteolytica: A Density Functional Theory Study. J Phys Chem B 2008; 112:2494-500. [DOI: 10.1021/jp710035j] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shi-Lu Chen
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, AlbaNova SE-10691 Stockholm, Sweden, Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MURST, Università della Calabria, I-87030 Arcavacata di Rende (CS), Italy, and College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Tiziana Marino
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, AlbaNova SE-10691 Stockholm, Sweden, Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MURST, Università della Calabria, I-87030 Arcavacata di Rende (CS), Italy, and College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Wei-Hai Fang
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, AlbaNova SE-10691 Stockholm, Sweden, Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MURST, Università della Calabria, I-87030 Arcavacata di Rende (CS), Italy, and College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Nino Russo
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, AlbaNova SE-10691 Stockholm, Sweden, Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MURST, Università della Calabria, I-87030 Arcavacata di Rende (CS), Italy, and College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Fahmi Himo
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, AlbaNova SE-10691 Stockholm, Sweden, Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MURST, Università della Calabria, I-87030 Arcavacata di Rende (CS), Italy, and College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
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Galano A, Rodriguez-Gattorno G, Torres-García E. A combined theoretical–experimental study on the acidity of WOx-ZrO2 systems. Phys Chem Chem Phys 2008; 10:4181-8. [DOI: 10.1039/b802934b] [Citation(s) in RCA: 19] [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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46
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Feng X, Gu J, Xie Y, King RB, Schaefer HF. Homoleptic Carbonyls of the Second-Row Transition Metals: Evaluation of Hartree−Fock and Density Functional Theory Methods. J Chem Theory Comput 2007; 3:1580-7. [PMID: 26633228 DOI: 10.1021/ct7000254] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xuejun Feng
- School of Chemical and Material Engineering, Southern Yangtze University, Wuxi 214122, P. R. China, Drug Design & Discovery Center, Shanghai Institute of Materia Medica, CAS, Shanghai 201203 P. R. China, and Center for Computational Chemistry and Department of Chemistry, University of Georgia, Athens, Georgia 30602
| | - Jiande Gu
- School of Chemical and Material Engineering, Southern Yangtze University, Wuxi 214122, P. R. China, Drug Design & Discovery Center, Shanghai Institute of Materia Medica, CAS, Shanghai 201203 P. R. China, and Center for Computational Chemistry and Department of Chemistry, University of Georgia, Athens, Georgia 30602
| | - Yaoming Xie
- School of Chemical and Material Engineering, Southern Yangtze University, Wuxi 214122, P. R. China, Drug Design & Discovery Center, Shanghai Institute of Materia Medica, CAS, Shanghai 201203 P. R. China, and Center for Computational Chemistry and Department of Chemistry, University of Georgia, Athens, Georgia 30602
| | - R. Bruce King
- School of Chemical and Material Engineering, Southern Yangtze University, Wuxi 214122, P. R. China, Drug Design & Discovery Center, Shanghai Institute of Materia Medica, CAS, Shanghai 201203 P. R. China, and Center for Computational Chemistry and Department of Chemistry, University of Georgia, Athens, Georgia 30602
| | - Henry F. Schaefer
- School of Chemical and Material Engineering, Southern Yangtze University, Wuxi 214122, P. R. China, Drug Design & Discovery Center, Shanghai Institute of Materia Medica, CAS, Shanghai 201203 P. R. China, and Center for Computational Chemistry and Department of Chemistry, University of Georgia, Athens, Georgia 30602
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Durand P, Malrieu JP. Effective Hamiltonians and Pseudo-Operators as Tools for Rigorous Modelling. ADVANCES IN CHEMICAL PHYSICS 2007. [DOI: 10.1002/9780470142936.ch6] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Cundari TR, Benson MT, Lutz ML, Sommerer SO. Effective Core Potential Approaches to the Chemistry of the Heavier Elements. REVIEWS IN COMPUTATIONAL CHEMISTRY 2007. [DOI: 10.1002/9780470125854.ch3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
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50
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