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Li XT, Li J, Liu SQ, Du SH, Wang SJ, Chen J, Cheng SB. Dual External Field Strategy in Regulating the Superhalogen Characteristics of the Non-Noble Metal Constituted Tantalum Oxide Clusters. J Phys Chem A 2024; 128:5298-5306. [PMID: 38917472 DOI: 10.1021/acs.jpca.4c02089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
The identification of the non-noble metal constituted TaO cluster as a potential analogue to the noble metal Au is significant for the development of tailored materials. It leverages the superatom concept to engineer properties with precision. However, the impact of incrementally integrating TaO units on the electronic configurations and properties within larger TaO-based clusters remains to be elucidated. By employing the density functional theory calculations, the global minima and low-lying isomers of the TanOn (n = 2-5) clusters were determined, and their structural evolution was disclosed. In the cluster series, Ta5O5 was found to possess the highest electron affinity (EA) with a value of 2.14 eV, based on which a dual external field (DEF) strategy was applied to regulate the electronic property of the cluster. Initially, the electron-withdrawing CO ligand was affixed to Ta5O5, followed by the application of an oriented external electric field (OEEF). The CO ligation was found to be able to enhance the Ta5O5 cluster's electron capture capability by adjusting its electron energy levels, with the EA of Ta5O5(CO)4 peaking at 2.58 eV. Subsequently, the introduction of OEEF further elevated the EA of the CO-ligated cluster. Notably, OEEF, when applied along the +x axis, was observed to sharply increase the EA to 3.26 eV, meeting the criteria for superhalogens. The enhancement of EA in response to OEEF intensity can be quantified as a functional relationship. This finding highlights the advantage of OEEF over conventional methods, demonstrating its capacity for precise and continuous modulation of cluster EAs. Consequently, this research has adeptly transformed tantalum oxide clusters into superhalogen structures, underscoring the effectiveness of the DEF strategy in augmenting cluster EAs and its promise as a viable tool for the creation of superhalogens.
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Affiliation(s)
- Xiao-Tong Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Jun Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Si-Qi Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Shi-Hu Du
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Shi-Jun Wang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Jing Chen
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Shi-Bo Cheng
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
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2
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Emami L, Hassani M, Mardaneh P, Zare F, Saeedi M, Emami M, Khabnadideh S, Sadeghian S. 6-Bromo quinazoline derivatives as cytotoxic agents: design, synthesis, molecular docking and MD simulation. BMC Chem 2024; 18:125. [PMID: 38965630 PMCID: PMC11225515 DOI: 10.1186/s13065-024-01230-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 06/24/2024] [Indexed: 07/06/2024] Open
Abstract
Based on unselectively, several side effects and drug resistance of available anticancer agents, the development and research for novel anticancer agents is necessary. In this study, a new series of quinazoline-4(3H)-one derivatives having a thiol group at position 2 of the quinazoline ring (8a-8 h) were designed and synthesized as potential anticancer agents. The Chemical structures of all compounds were characterized by 1H-NMR, 13C-NMR, and Mass spectroscopy. The antiproliferative activity of all derivatives were determined against two cancer cell lines (MCF-7 and SW480) and one normal cell lines (MRC-5) by the MTT method. Cisplatin, Erlotinib and Doxorubicin were used as positive controls. The results of in vitro screening showed that 8a with an aliphatic linker to SH group was the most potent compound with IC50 values of 15.85 ± 3.32 and 17.85 ± 0.92 µM against MCF-7 and SW480 cell lines, respectively. 8a indicated significantly better potency compared to Erlotinib in the MCF-7 cell line. The cytotoxic results obtained from testing compound 8a on the normal cell line, revealing an IC50 value of 84.20 ± 1.72 µM, provide compelling evidence of its selectivity in distinguishing between tumorigenic and non-tumorigenic cell lines. Structure-activity relationship indicated that the variation in the anticancer activities of quinazoline-4(3H)-one derivatives was affected by different substitutions on the SH position. Molecular docking and MD simulation were carried out for consideration of the binding affinity of compounds against EGFR and EGFR-mutated. The binding energy of compounds 8a and 8c were calculated at -6.7 and - 5.3 kcal.mol- 1, respectively. Compounds 8a and 8c were found to establish hydrogen bonds and some other important interactions with key residue. The DFT analysis was also performed at the B3LYP/6-31 + G(d, p) level for compounds 8a, 8c and Erlotinib. Compound 8a was thermodynamically more stable than 8c. Also, the calculated theoretical and experimental data for the IR spectrum were in agreement. The obtained results delineated that the 8a can be considered an appropriate pharmacophore to develop as an anti-proliferative agent.
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Affiliation(s)
- Leila Emami
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maryam Hassani
- Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Pegah Mardaneh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Fateme Zare
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maryam Saeedi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mina Emami
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Soghra Khabnadideh
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
- Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Sara Sadeghian
- Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
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3
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Yashmin F, Mazumder LJ, Sharma PK, Guha AK. Spodium bonding with noble gas atoms. Phys Chem Chem Phys 2024; 26:8115-8124. [PMID: 38410934 DOI: 10.1039/d3cp06184a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
The nature of the bonding between a neutral group 12 member (Zn3, Cd3 and Hg3) ring and a noble gas atom was explored using quantum chemical simulations. Natural bond orbital, quantum theory of atoms in molecules, symmetry-adapted perturbation theory, and molecular electrostatic potential surface analysis were also used to investigate the type of interaction between the noble gas atom and the metal rings (Zn3, Cd3 and Hg3). The Zn3, Cd3 and Hg3 rings are bonded to the noble gas through non-covalent interactions, which was revealed by the non-covalent interaction index. Additionally, energy decomposition analysis reveals that dispersion energy is the key factor in stabilizing these systems.
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Affiliation(s)
- Farnaz Yashmin
- Department of Chemistry, Cotton University, Panbazar, Guwahati, Assam, 781001, India.
| | - Lakhya J Mazumder
- Department of Chemistry, Cotton University, Panbazar, Guwahati, Assam, 781001, India.
| | - Pankaz K Sharma
- Department of Chemistry, Cotton University, Panbazar, Guwahati, Assam, 781001, India.
| | - Ankur K Guha
- Department of Chemistry, Cotton University, Panbazar, Guwahati, Assam, 781001, India.
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4
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Javanmard K, Farhadi S, Zabardasti A. Simultaneous adsorption of ciprofloxacin drug and methyl violet dye on boron nitride nanosheets: experimental and theoretical insights. Phys Chem Chem Phys 2023; 25:21336-21349. [PMID: 37529865 DOI: 10.1039/d3cp01793a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
In this study, hexagonal boron nitride (BN) with a sheet-like morphology is successfully synthesized by reacting borax (Na2B4O7·10H2O) and urea (CO(NH2)2) powders in air via a facile microwave-assisted method within a short reaction time (15 min). The as-prepared product is structurally characterized via Fourier transformation infrared spectroscopy (FTIR), X-ray powder diffraction (XRD), Raman spectroscopy, field emission scanning electron microscopy (FESEM), energy dispersion X-ray analyzer (EDX), transmission electron microscopy (TEM), and Brunauer-Emmett-Teller (BET) surface area measurements. The adsorption process of methyl violet (MV) as a model of organic dyes and ciprofloxacin (CIP) as a model of antibiotics onto the boron nitride nanosheets has been experimentally and theoretically studied. The BN nanosheets exhibit the maximum adsorption capacity of 320.94 mg g-1 for MV dye and 266.29 mg g-1 for CIP antibiotic. The Freundlich isotherm model was suitable to describe the adsorption equilibrium isotherm data and the pseudo second-order model reflected the adsorption kinetics well. The calculated thermodynamic parameters show that the adsorption process is spontaneous under the measured conditions. The adsorption of CIP, MV and CIP + MV molecules on the surface of BN has been investigated through DFT calculations. The charge transfer and high adsorption capacity demonstrate the potential of BN nanosheets as an adsorbent for the simultaneous removal of MV dye and CIP drug from contaminated water.
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Affiliation(s)
- Keivan Javanmard
- Department of Inorganic Chemistry, Faculty of Chemistry, Lorestan University, Khorramabad, 68151-44316, Iran.
| | - Saeed Farhadi
- Department of Inorganic Chemistry, Faculty of Chemistry, Lorestan University, Khorramabad, 68151-44316, Iran.
| | - Abedin Zabardasti
- Department of Inorganic Chemistry, Faculty of Chemistry, Lorestan University, Khorramabad, 68151-44316, Iran.
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5
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Zhang S, Wen W, Xia X, Ouyang W, Mai BX, Adrian L, Schüürmann G. Insight into the Mechanism Underlying Dehalococcoides mccartyi Strain CBDB1-Mediated B 12-Dependent Aromatic Reductive Dehalogenation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37428517 DOI: 10.1021/acs.est.3c00364] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Anaerobic bacteria transform aromatic halides through reductive dehalogenation. This dehalorespiration is catalyzed by the supernucleophilic coenzyme vitamin B12, cob(I)alamin, in reductive dehalogenases. So far, the underlying inner-sphere electron transfer (ET) mechanism has been discussed controversially. In the present study, all 36 chloro-, bromo-, and fluorobenzenes and full-size cobalamin are analyzed at the quantum chemical density functional theory level with respect to a wide range of theoretically possible inner-sphere ET mechanisms. The calculated reaction free energies within the framework of CoI···X (X = F, Cl, and Br) attack rule out most of the inner-sphere pathways. The only route with feasible energetics is a proton-coupled two-ET mechanism that involves a B12 side-chain tyrosine (modeled by phenol) as a proton donor. For 12 chlorobenzenes and 9 bromobenzenes with experimental data from Dehalococcoides mccartyi strain CBDB1, the newly proposed PC-TET mechanism successfully discriminates 16 of 17 active from 4 inactive substrates and correctly predicts the observed regiospecificity to 100%. Moreover, fluorobenzenes are predicted to be recalcitrant in agreement with experimental findings. Conceptually, based on the Bell-Evans-Polanyi principle, the computational approach provides novel mechanistic insights and may serve as a tool for predicting the energetic feasibility of reductive aromatic dehalogenation.
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Affiliation(s)
- Shangwei Zhang
- Advanced Interdisciplinary Institute of Environment and Ecology, Beijing Normal University, Zhuhai 519087, China
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Wu Wen
- Instrumentation and Service Center for Science and Technology, Beijing Normal University, Zhuhai 519087, China
| | - Xinghui Xia
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Wei Ouyang
- Advanced Interdisciplinary Institute of Environment and Ecology, Beijing Normal University, Zhuhai 519087, China
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Bi-Xian Mai
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Lorenz Adrian
- UFZ Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research, Permoserstraße 15, Leipzig 04318, Germany
- Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, Berlin 13355, Germany
| | - Gerrit Schüürmann
- UFZ Department of Ecological Chemistry, Helmholtz Centre for Environmental Research, Permoserstraße 15, Leipzig 04318, Germany
- Institute of Organic Chemistry, Technical University Bergakademie Freiberg, Leipziger Straße 29, Freiberg 09596, Germany
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6
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Ghosh A, Conradie J. The Perfluoro Cage Effect: A Search for Electron-Encapsulating Molecules. ACS OMEGA 2023; 8:4972-4975. [PMID: 36777561 PMCID: PMC9910065 DOI: 10.1021/acsomega.2c07374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/06/2023] [Indexed: 06/18/2023]
Abstract
Quantum chemical calculations have for some time predicted that perfluorinated polyhedral organic molecules should exhibit a low-energy LUMO consisting of the overlapping inward-pointing lobes of the C-F σ* orbitals. Accordingly, these molecules should be able to encapsulate an electron within the interior of their cavities. Inspired by the recent confirmation of this prediction for perfluorocubane, we have sought to identify additional perfluorinated cage molecules capable of this remarkable behavior, which we refer to as the perfluoro cage effect (PCE). Using DFT calculations with multiple well-tested exchange-correlation functionals and large STO-QZ4P basis sets, we have identified several systems including [n]prismanes (n = 3-6), [n]asteranes (n = 3-5), twistane, and two norbornadiene dimer cages that clearly exhibit the PCE. In other words, they exhibit a low-energy LUMO belonging to the total symmetric irreducible representation of the point group in question and adiabatic electron affinities ranging from somewhat under 1 eV to over 2 eV. A pronounced size effect appears to hold, with larger cages exhibiting higher electron affinities (EAs). The largest adiabatic EAs, well over 3 eV, are predicted for perfluorinated dodecahedrane and C60. In contrast, the PCE is barely discernible for perfluorinated tetrahedrane and bicyclo[1.1.1]pentane.
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Affiliation(s)
- Abhik Ghosh
- Department
of Chemistry, UiT − The Arctic University
of Norway, Tromsø N-9037, Norway
| | - Jeanet Conradie
- Department
of Chemistry, UiT − The Arctic University
of Norway, Tromsø N-9037, Norway
- Department
of Chemistry, University of the Free State, P.O. Box 339, Bloemfontein 9300, South
Africa
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7
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Mazumder LJ, Sharma R, Yashmin F, Sharma PK. Beryllium bonding with noble gas atoms. J Comput Chem 2023; 44:644-655. [PMID: 36394306 DOI: 10.1002/jcc.27028] [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: 08/07/2022] [Revised: 09/25/2022] [Accepted: 09/28/2022] [Indexed: 11/19/2022]
Abstract
Quantum chemical calculations were carried out to investigate the nature of the bonding between a neutral Be3 ring and noble gas atom. Electronic structure calculation for these complexes was carried out at different computational levels in association with natural bond orbital, quantum theory of atoms in molecules, electron localization function, symmetry adapted perturbation theory, and molecular electrostatic potential surface analysis of Be3 complexes. The Be atoms in the Be3 moiety are chemically bonded to one another, with the BeBe bond dissociation energy being ~125 kJ mol-1 . The Be3 ring interacts with the noble gases through non-covalent interactions. The binding energies of the noble gas atoms with the Be3 ring increases with increase in their atomic number. The non-covalent interaction index, density overlap region indicator and independent gradient model analyses reveal the presence of non-covalent inter-fragment interactions in the complexes. Energy decomposition analysis reveals that dispersion plays the major role towards stabilizing these systems.
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Affiliation(s)
| | - Rohan Sharma
- Department of Chemistry, Cotton University, Guwahati, Assam, India
| | - Farnaz Yashmin
- Department of Chemistry, Cotton University, Guwahati, Assam, India
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8
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Roy S, Paul S, Misra A. A Theoretical Account of the Coupling between Metal- and Ligand-centred Spins. Chemphyschem 2023; 24:e202200889. [PMID: 36622254 DOI: 10.1002/cphc.202200889] [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: 12/04/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 01/10/2023]
Abstract
This study addresses the magnetic interaction between paramagnetic metal ions and the radical ligands taking the [CuII (hfac)2 (imVDZ)] and [MII (hfac)2 (pyDTDA)] (imVDZ=1,5-dimethyl-3-(1-methyl-2-imidazolyl)-6-oxoverdazyl; hfac=(1,1,1,5,5,5)hexafluroacetylacetonate; pyDTDA=4-(2'-pyridyl)-1,2,3,5-dithiadiazolyl), (M=Cu, Ni, Co, Fe, Mn) compounds as reference systems. The coupling between the metal and ligand spins is quantified in terms of the exchange coupling constant (J) in the platform of density functional theory (DFT) and the wave function-based complete active space self-consistent field (CASSCF) method. Application of DFT and broken symmetry (BS) formalism results ferromagnetic coupling for all the transition metal complexes except the Mn(II) complex. This DFT-BS prediction of magnetic nature matches with the experimental finding for all the complexes other than the Fe(II)-pyDTDA complex, for which an antiferromagnetic coupling between high spin iron and the thiazyl ligand has been reported. However, evaluation of spin state energetics through the multiconfigurational wave function-based method produces the S=3/2 ground spin state for the iron-thiazyl in parity with experiment. Electronic structure analyses find the overlap between the metal- and ligand-based singly occupied molecular orbitals (SOMOs) to be one of the major reasons attributing to different extent of exchange coupling in the systems under investigation.
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Affiliation(s)
- Sriparna Roy
- Department of Chemistry, University of North Bengal, Siliguri, Darjeeling , 734013, India
| | - Satadal Paul
- Department of Chemistry, Bangabasi Morning College, 19 R.C Sarani, Kolkata, 700009, India
| | - Anirban Misra
- Department of Chemistry, University of North Bengal, Siliguri, Darjeeling , 734013, India
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9
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Ghosh A, Conradie J. Porphyryne. ACS OMEGA 2022; 7:40275-40278. [PMID: 36385855 PMCID: PMC9647813 DOI: 10.1021/acsomega.2c05199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 10/13/2022] [Indexed: 05/12/2023]
Abstract
Density functional theory calculations with the B3LYP*-D3 method with large STO-QZ4P basis sets unambiguously predict a singlet ground state for Zn-porphyryne. However, the calculations also predict a low singlet-triplet gap of about 0.4 eV and a high adiabatic electron affinity of 2.4 eV. Accordingly, the reactivity of porphyryne species may be dominated by electron transfer, hydrogen abstraction, and proton-coupled electron transfer processes.
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Affiliation(s)
- Abhik Ghosh
- Department
of Chemistry, UiT − The Arctic University
of Norway, N-9037 Tromsø, Norway
| | - Jeanet Conradie
- Department
of Chemistry, UiT − The Arctic University
of Norway, N-9037 Tromsø, Norway
- Department
of Chemistry, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
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10
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Kosar N, Ayub K, Gilani MA, Muhammad S, Mahmood T. Benchmark Density Functional Theory Approach for the Calculation of Bond Dissociation Energies of the M-O 2 Bond: A Key Step in Water Splitting Reactions. ACS OMEGA 2022; 7:20800-20808. [PMID: 35935283 PMCID: PMC9348009 DOI: 10.1021/acsomega.2c01331] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
A very fascinating aspect in quantum chemical research is to determine the accurate and cost-effective methods for the calculation of electronic and structural properties through a benchmark study. The current study focuses on the performance evaluation of density functional theory methods for the accurate measurement of bond dissociation energies (BDEs) of chemically important M-O2 bonds in water splitting reactions. The BDE measurement has got noteworthy attention due to its importance in all areas of chemistry. For BDE measurements of M-O2 bonds in five metal complexes with oxygen molecules, 14 density functionals (DFs) are chosen from seven classes of DFs with two series of mixed basis sets. A combination of pseudopotential and Pople basis sets [LANL2DZ & 6-31G(d) and SDD & 6-31+G(d)] are used as a series of mixed basis sets. The B3LYP-GD3BJ functional with LANL2DZ & 6-31G(d) gives outstanding results due to low deviations, error, and the best Pearson's correlation (R) between the experimental and theoretical data. Our study suggested an efficient, low-cost, precise, and accurate B3LYP-GD3BJ/LANL2DZ & 6-31G(d) level of theory for BDE of the M-O2 bond, which may be useful for chemists working in the field of energy generation and utilization.
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Affiliation(s)
- Naveen Kosar
- Department
of Chemistry, University of Management and
Technology (UMT), C11,
Johar Town, Lahore 54770, Pakistan
| | - Khurshid Ayub
- Department
of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Mazhar Amjad Gilani
- Department
of Chemistry, COMSATS University Islamabad, Lahore Campus, Lahore 54600, Pakistan
| | - Shabbir Muhammad
- Department
of Chemistry, College of Science, King Khalid
University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Tariq Mahmood
- Department
of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
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11
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Asadi L, Saadati Z, Salehpour M. Theoretical evaluation of Al-doped biphenylene nanosheet sensing properties toward gamma-butyrolactone. Struct Chem 2022. [DOI: 10.1007/s11224-022-01964-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Liang Y, Zheng W, Xie H, Zha X, Wang T. A quantum chemistry study on C–H homolytic bond dissociation enthalpies of five-membered and six-membered heterocyclic compounds. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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13
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Zhu B, Jiang J, Lu B, Li X, Zeng X. Fluoromethylsulfinyl radicals: spectroscopic characterization and photoisomerization via intramolecular hydrogen shift. Phys Chem Chem Phys 2022; 24:8881-8889. [PMID: 35362501 DOI: 10.1039/d1cp05556a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Two new sulfinyl radicals, CHF2SO˙ and CH2FSO˙, have been generated in the gas phase through homolytic cleavage of the weak S-S bonds in disulfane oxides CHF2S(O)SCF3 and CH2FS(O)SCF3 by high-vacuum flash pyrolysis (HVFP) at ca. 500 °C. The IR spectroscopy characterization of the two fluoromethylsulfinyl radicals in solid N2 (10 K), Ar (10 K), and Ne (3 K) matrices reveals the presence of two conformers for CHF2SO˙ (gauche and cis) and one conformer for CH2FSO˙ (gauche). Upon 266 nm laser irradiation, these radicals undergo both isomerization and decomposition in the matrices. In addition to the dominant formation of the elusive oxathiyl radicals CHF2OS˙ (gauche and cis) and CH2FOS˙ (gauche) via 1,2-alkyl migration, two higher-energy carbon-centered radicals ˙CF2SOH and ˙CHFSOH bearing similar molecular structures to hydroperoxyalkyl radicals (˙QOOH) form via intramolecular 1,3-hydrogen shift in the two sulfinyl radicals. Additionally, the involvement of 1,3-hydrogen shift in CHF2OS˙ and CH2FOS˙ is also indicated by the observation of the fragmentation species. The identification of these radicals by matrix-isolation IR and UV-vis spectroscopy is aided by the quantum chemical calculations at the B3LYP/6-311++G(3df,3pd) level of theory. The stability of the isomers of the two sulfinyl radicals CHF2SO˙ and CH2FSO˙ has been discussed according to the experimental observations and also based on the CCSD(T)-F12a/aug-cc-pVTZ//B3LYP/6-311++G(3df,3pd) calculated energy profiles.
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Affiliation(s)
- Bifeng Zhu
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, Shanghai, 200433, China.
| | - Junjie Jiang
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, Shanghai, 200433, China.
| | - Bo Lu
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, Shanghai, 200433, China.
| | - Xiaolong Li
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, Shanghai, 200433, China.
| | - Xiaoqing Zeng
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, Shanghai, 200433, China.
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14
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Borges-Martínez M, Montenegro-Pohlhammer N, Zhang X, Galvez-Aranda DE, Ponce V, Seminario JM, Cárdenas-Jirón G. Fullerene binding effects in Al(III)/Zn(II) Porphyrin/Phthalocyanine photophysical properties and charge transport. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 269:120740. [PMID: 34968837 DOI: 10.1016/j.saa.2021.120740] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
We evaluate the fullerene C60 binding effect; through the metal (Al) and through the ligand (Pc,TPP), on the photophysical and charge transport properties of M-porphyrin(TPP)/phthalocyanine(Pc) (M = Al(III), Zn(II)). We perform density functional theory (DFT) and time-dependent DFT calculations for the macrocycle-C60 dyads, showing that all systems studied are thermodynamically favorable. The C60 binding effect on the absorption spectrum is a red-shift of the Q and Soret (B) bands of TPPs and Pcs. The Pc-dyads show longer λ for Q bands (673 nm) than those with TPP (568 nm). AlTPP-C60 and ZnTPP-C60 show a more favorable electron injection to TiO2 than the analogs Pcs, and the regeneration of the dye is preferred in AlTPP-C60 and AlPc-C60. Zero-bias conductance is computed (10-4-10-7 G0) for the dyads using molecular junctions with Au(111)-based electrodes. When a bias voltage of around 0.6 V up to 1 V is applied, an increase in current is obtained for AlTPP-C60 (10-7 A), ZnTPP-C60 (10-7 A), and AlPc-C60 (10-8 A). Although there is not a unique trend in the behavior of the dyads, Pcs have better photophysical properties than TPPs and the latter are better in the charge transport. We conclude that AlTPP(ZnTPP)-C60 dyads are an excellent alternative for designing new materials for dye-sensitized solar cells or optoelectronic devices.
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Affiliation(s)
- Merlys Borges-Martínez
- Laboratory of Theoretical Chemistry, Faculty of Chemistry and Biology, University of Santiago de Chile (USACH), 9170022, Santiago, Chile.
| | - Nicolás Montenegro-Pohlhammer
- Laboratory of Theoretical Chemistry, Faculty of Chemistry and Biology, University of Santiago de Chile (USACH), 9170022, Santiago, Chile.
| | - Xiance Zhang
- Department of Chemical Engineering, Texas A&M University, College Station, Texas, U.S.A
| | - Diego E Galvez-Aranda
- Department of Chemical Engineering, Texas A&M University, College Station, Texas, U.S.A
| | - Victor Ponce
- Department of Chemical Engineering, Texas A&M University, College Station, Texas, U.S.A
| | - Jorge M Seminario
- Department of Chemical Engineering, Texas A&M University, College Station, Texas, U.S.A.
| | - Gloria Cárdenas-Jirón
- Laboratory of Theoretical Chemistry, Faculty of Chemistry and Biology, University of Santiago de Chile (USACH), 9170022, Santiago, Chile.
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15
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Kushvaha SK, Gorantla SMNVT, Mondal KC. Stabilization of Interstellar CSi 2 Species by Donor Base Ligands: L-CSi 2-L; L = cAAC Me, NHC Me, and PMe 3. J Phys Chem A 2022; 126:845-858. [PMID: 35119854 DOI: 10.1021/acs.jpca.1c09746] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The donor ligand bonded singlet (L)2Si2C containing a bent Si2C unit in the middle has been studied by theoretical quantum mechanical calculations (NBO, QTAIM, EDA-NOCV analyses) [L = cAAC, NHC, Me3P]. EDA-NOCV analysis suggests that this Si2C is possible to stabilize by a pair of donor base ligands. The bond dissociation energy of the Si2C fragment is endothermic (85-45 kcal/mol) with a sufficiently high intrinsic interaction energy (ΔEint = -89 to -48 kcal/mol). Fifty percent of the total stabilization energy arises from electrostatic interactions, and nearly 45% is contributed by covalent orbital interaction between Si2C and (L)2 fragments in their singlet states. 75-80% of the orbital interaction energy is contributed by two sets of σ-donation L → SiCSi ← L. The π-back-donation is only 15-10%. The dispersion energy is not negligible (3-5%). The interaction energy is highest for 1 (L = cAAC) among three compounds. Additionally, (cAAC)2Si2C-Ni(CO)3 (4) has been studied. The interaction energy between 1 and Ni(CO)3 is nearly 61 kcal/mol with the major contribution coming from donation of electron cloud from electron rich Si2C backbone to empty hybrid orbital of Ni(CO)3 fragment. A sufficiently strong π-back-donation from (OC)3Ni to Si2C has also been identified.
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Affiliation(s)
- Saroj Kumar Kushvaha
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
| | | | - Kartik Chandra Mondal
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
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16
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Villarroel E, Olea F, Araya-López C, Gajardo J, Merlet G, Cabezas R, Romero J, Quijada-Maldonado E. Diluent effects in the solvent extraction of rhenium (VII) with amine extractants in [Tf2N]-based ionic liquids: Experimental and COSMO-RS analysis. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117091] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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17
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Non-enzymatic glucose sensors based on Hexa-peri-hexabenzocoronene: A computational study. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2021.111388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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18
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Ding S, Gu W. Evaluate the potential utilization of B24N24 fullerene in the recognition of COS, H2S, SO2, and CS2 gases (environmental pollution). J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117041] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Zhang S, Adrian L, Schüürmann G. Outer-sphere electron transfer does not underpin B 12-dependent olefinic reductive dehalogenation in anaerobes. Phys Chem Chem Phys 2021; 23:27520-27524. [PMID: 34874373 DOI: 10.1039/d1cp04632b] [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
Anaerobic microbial B12-dependent reductive dehalogenation may pave a way to remediate soil, sediment, and underground water contaminated with halogenated olefins. The chemical reaction is initiated by electron transfer (ET) from supernucleophilic cob(I)alamin (B12s). However, the inherent mechanism as outer-sphere or inner-sphere route is still under debate. To clarify the possibility of an outer-sphere pathway, we calculated free energy barriers of the initial steps of all outer-sphere ET routes by Marcus theory employing density functional theory (DFT). For 18 fluorinated, chlorinated, and brominated ethenes as representative olefins, 164 of 165 reactions with free energy barriers larger than 20 kcal mol-1 are not feasible under physiological dehalogenase conditions. Moreover, electronic structure analysis of perbromoethene with an outer-sphere free energy barrier of 18.2 kcal mol-1 reveals no ET initiation down to Co⋯Br and Co⋯C distances of 3.15 Å. The results demonstrate that the B12-catalyzed reductive dechlorination of olefins in microbes should proceed through an inner-sphere ET pathway.
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Affiliation(s)
- Shangwei Zhang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China.,UFZ Department of Ecological Chemistry, Helmholtz Centre for Environmental Research, Permoserstraße 15, Leipzig 04318, Germany.
| | - Lorenz Adrian
- UFZ Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany.,Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany
| | - Gerrit Schüürmann
- UFZ Department of Ecological Chemistry, Helmholtz Centre for Environmental Research, Permoserstraße 15, Leipzig 04318, Germany. .,Technical University Bergakademie Freiberg, Institute of Organic Chemistry, Leipziger Straße 29, 09596 Freiberg, Germany.
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20
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Li S, Bodenstedt K, Kharma M, Burson CM, Alhmoud D, Moulder CA, Farvid S, Ghimire MM, Rawashdeh AMM, El Bouanani M, Omary MA. Can A Double-Doped Device Modification of A Standard Bilayer OLED Improve the Photo- And/or Electro-luminescence Efficiency? A Case Study of Architecture Design in Fluorescent Devices with A Potential Roadmap for High-Efficiency Phosphorescent Devices. COMMENT INORG CHEM 2021. [DOI: 10.1080/02603594.2021.1992399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Shan Li
- Departments of Chemistry and Materials Science and Engineering, University of North Texas, Denton, Texas, USA
| | - Kurt Bodenstedt
- Departments of Chemistry and Materials Science and Engineering, University of North Texas, Denton, Texas, USA
| | - Mustafa Kharma
- Department of Chemistry, Yarmouk University, Irbid, Jordan
- Department of Chemistry, Jordan University, Amman, Jordan
| | - Claire M. Burson
- Departments of Chemistry and Materials Science and Engineering, University of North Texas, Denton, Texas, USA
- Department of Chemistry, Southern Methodist University, Dallas, Texas, USA
| | - Dieaa Alhmoud
- Department of Chemistry, Yarmouk University, Irbid, Jordan
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts, USA
| | - Catherine A. Moulder
- Departments of Chemistry and Materials Science and Engineering, University of North Texas, Denton, Texas, USA
- Department of Chemistry, Washington State University, Pullman, Washington, USA
| | - Seyedmajid Farvid
- Departments of Chemistry and Materials Science and Engineering, University of North Texas, Denton, Texas, USA
| | - Mukunda M. Ghimire
- Department of Chemistry, Lebanon Valley College, Annville, Pennsylvania, USA
| | | | - Mohamed El Bouanani
- Departments of Chemistry and Materials Science and Engineering, University of North Texas, Denton, Texas, USA
| | - Mohammad A. Omary
- Departments of Chemistry and Materials Science and Engineering, University of North Texas, Denton, Texas, USA
- Department of Chemistry, Yarmouk University, Irbid, Jordan
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21
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Application of borophene as catechol sensor: a computational study. J Mol Model 2021; 27:310. [PMID: 34599669 DOI: 10.1007/s00894-021-04929-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 09/21/2021] [Indexed: 10/20/2022]
Abstract
The efficacy of borophene (BP) as catechol (CC) sensor was explored using density functional theory (DFT) method. All calculations were performed at B3LYP level of theory and 6-31 + G(d) basis set employing the dispersion correction term of Grimme to consider dispersion interactions. The CC molecule is adsorbed on top of BP horizontally with the adsorption energy (Eads) of about - 13.5 kcal·mol-1. The HOMO and LUMO levels of nanosheet destabilize by about 0.36 and 0.14 eV, respectively, going from bare BP to BP-CC complex. Therefore, the Eg value decreases by about 10.5% upon adsorption process, which is a reasonable energy gap change for detection of CC. The negligible difference between the work function values (Φ, defined as the minimum amount of the energy needed to remove an electron from a solid to a point in the vacuum immediately outside the solid surface) of BP and its complex with CC indicates that the BP sheet is not an appropriate Φ-type sensor (in these sensors, adsorption of a chemical changes the gate voltage and produces an electrical signal that leads to the detection of chemical agent) for CC detection. The electrical conductivity of BP becomes 72 times higher after CC adsorption. The time needed for CC desorption from BP sheet is 7.6 ns, based on conventional transition state theory, showing that BP benefits from a short recovery time. The effect of CC concentration was explored by adsorption of 2 and 3 CC molecules on top of BP nanosheet and the results showed that the sensor response does not change by increasing the CC concentration. Also, the effect of lateral dimensions of BP on the adsorption energy was explored and it was shown that Eads increases by enlargement of the nanosheet.
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22
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Liu S, Zhu P, Zou S, Ebrahimiasl S. Theoretical evaluation of central ring doped Hexa-peri-hexabenzocoronene as Gamma-butyrolactone drug sensors. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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23
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Li W, Zhao T. Hydroxyurea anticancer drug adsorption on the pristine and doped C70 fullerene as potential carriers for drug delivery. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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24
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Tsybizova A, Brenig C, Kieninger C, Kräutler B, Chen P. Surprising Homolytic Gas Phase Co-C Bond Dissociation Energies of Organometallic Aryl-Cobinamides Reveal Notable Non-Bonded Intramolecular Interactions. Chemistry 2021; 27:7252-7264. [PMID: 33560580 PMCID: PMC8251903 DOI: 10.1002/chem.202004589] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Indexed: 01/12/2023]
Abstract
Aryl-cobalamins are a new class of organometallic structural mimics of vitamin B12 designed as potential 'antivitamins B12 '. Here, the first cationic aryl-cobinamides are described, which were synthesized using the newly developed diaryl-iodonium method. The aryl-cobinamides were obtained as pairs of organometallic coordination isomers, the stereo-structure of which was unambiguously assigned based on homo- and heteronuclear NMR spectra. The availability of isomers with axial attachment of the aryl group, either at the 'beta' or at the 'alpha' face of the cobalt-center allowed for an unprecedented comparison of the organometallic reactivity of such pairs. The homolytic gas-phase bond dissociation energies (BDEs) of the coordination-isomeric phenyl- and 4-ethylphenyl-cobinamides were determined by ESI-MS threshold CID experiments, furnishing (Co-Csp 2 )-BDEs of 38.4 and 40.6 kcal mol-1 , respectively, for the two β-isomers, and the larger BDEs of 46.6 and 43.8 kcal mol-1 for the corresponding α-isomers. Surprisingly, the observed (Co-Csp 2 )-BDEs of the Coβ -aryl-cobinamides were smaller than the (Co-Csp 3 )-BDE of Coβ -methyl-cobinamide. DFT studies and the magnitudes of the experimental (Co-Csp 2 )-BDEs revealed relevant contributions of non-bonded interactions in aryl-cobinamides, notably steric strain between the aryl and the cobalt-corrin moieties and non-bonded interactions with and among the peripheral sidechains.
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Affiliation(s)
- Alexandra Tsybizova
- Laboratorium für Organische ChemieDepartment of Chemistry and Applied BiosciencesETH ZürichZürichSwitzerland
| | - Christopher Brenig
- Institute of Organic Chemistry & Center of Molecular BiosciencesUniversity of InnsbruckInnsbruckAustria
| | - Christoph Kieninger
- Institute of Organic Chemistry & Center of Molecular BiosciencesUniversity of InnsbruckInnsbruckAustria
| | - Bernhard Kräutler
- Institute of Organic Chemistry & Center of Molecular BiosciencesUniversity of InnsbruckInnsbruckAustria
| | - Peter Chen
- Laboratorium für Organische ChemieDepartment of Chemistry and Applied BiosciencesETH ZürichZürichSwitzerland
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25
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Mazumder L, Kalita AJ, Rohman SS, Kashyap C, Ullah SS, Baruah I, Boro A, Guha AK, Sharma PK. Unsupported Donor-Acceptor Complexes of Noble Gases with Group 13 Elements. ACS OMEGA 2021; 6:8656-8661. [PMID: 33817527 PMCID: PMC8015094 DOI: 10.1021/acsomega.1c00543] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
Unsupported donor-acceptor complexes of noble gases (Ng) with group 13 elements have been theoretically studied using density functional theory. Calculations reveal that heavier noble gases form thermodynamically stable compounds. The present study reveals that no rigid framework is necessary to stabilize the donor-acceptor complexes. Rather, prepyramidalization at the Lewis acid center may be an interesting alternative to stabilize these complexes. Detailed bonding analyses reveal the formation of two-center-two-electron dative bonding, where Ng atoms act as a donor.
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Affiliation(s)
- Lakhya
J. Mazumder
- Advanced Computational
Chemistry
Centre, Cotton University, Panbazar, Guwahati 781001, Assam, India
| | - Amlan J. Kalita
- Advanced Computational
Chemistry
Centre, Cotton University, Panbazar, Guwahati 781001, Assam, India
| | - Shahnaz S. Rohman
- Advanced Computational
Chemistry
Centre, Cotton University, Panbazar, Guwahati 781001, Assam, India
| | - Chayanika Kashyap
- Advanced Computational
Chemistry
Centre, Cotton University, Panbazar, Guwahati 781001, Assam, India
| | - Sabnam S. Ullah
- Advanced Computational
Chemistry
Centre, Cotton University, Panbazar, Guwahati 781001, Assam, India
| | - Indrani Baruah
- Advanced Computational
Chemistry
Centre, Cotton University, Panbazar, Guwahati 781001, Assam, India
| | - Ashapurna Boro
- Advanced Computational
Chemistry
Centre, Cotton University, Panbazar, Guwahati 781001, Assam, India
| | - Ankur K. Guha
- Advanced Computational
Chemistry
Centre, Cotton University, Panbazar, Guwahati 781001, Assam, India
| | - Pankaz K. Sharma
- Advanced Computational
Chemistry
Centre, Cotton University, Panbazar, Guwahati 781001, Assam, India
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26
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Borges-Martínez M, Montenegro-Pohlhammer N, Cárdenas-Jirón G. The bimetallic and the anchoring group effects on both optical and charge transport properties of hexaphyrin amethyrin. NEW J CHEM 2021. [DOI: 10.1039/d1nj00091h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bimetallic Cu(ii)-hexaphyrin amethyrin proposed as a molecular switch operated by the application of an external magnetic field.
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Affiliation(s)
- Merlys Borges-Martínez
- Laboratory of Theoretical Chemistry
- Faculty of Chemistry and Biology, University of Santiago de Chile (USACH)
- Santiago
- Chile
| | - Nicolás Montenegro-Pohlhammer
- Laboratory of Theoretical Chemistry
- Faculty of Chemistry and Biology, University of Santiago de Chile (USACH)
- Santiago
- Chile
| | - Gloria Cárdenas-Jirón
- Laboratory of Theoretical Chemistry
- Faculty of Chemistry and Biology, University of Santiago de Chile (USACH)
- Santiago
- Chile
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27
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Zhang S, Adrian L, Schüürmann G. Dehalococcoides-Mediated B 12-Dependent Reductive Dehalogenation of Aromatics Does Not Proceed through Outer-Sphere Electron Transfer. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:15751-15758. [PMID: 33237747 DOI: 10.1021/acs.est.0c04404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Several anaerobic bacteria can couple the reduction of aromatic halides to energy conservation. This organohalide respiration is catalyzed by enzymes containing cob(I)alamin, an activated supernucleophilic form of the coenzyme vitamin B12. However, the mechanism underlying the electron transfer (inner-sphere vs outer-sphere ET) still remains elusive. To clarify this issue, we selected 36 fluoro-, chloro-, and bromobenzenes as representative substrates and calculated their free-energy barriers at the quantum chemical density functional theory level, considering a wide range of theoretically possible outer-sphere ET mechanisms. Across all 336 reaction routes addressed, 334 routes involve free-energy barriers larger than 20 kcal/mol. For two reaction routes with highly brominated benzenes, free-energy barriers below 20 kcal/mol imply abiotic reduction as observed in experiments. Thus, microbial B12-dependent aromatic reductive dehalogenation does not proceed through an outer-sphere ET mechanism. Instead, the present study strongly suggests that microbe-catalyzed reductive dehalogenation of aromatic halides is governed by inner-sphere ET.
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Affiliation(s)
- Shangwei Zhang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Controol and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
- UFZ Department of Ecological Chemistry, Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Lorenz Adrian
- UFZ Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
- Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany
| | - Gerrit Schüürmann
- UFZ Department of Ecological Chemistry, Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
- Institute of Organic Chemistry, Technical University Bergakademie Freiberg, Leipziger Straße 29, 09596 Freiberg, Germany
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28
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Dmitrieva OA, Ivanova YB, Semeikin AS, Mamardashvili NZ. Fluorescence properties and quantum-chemical modeling of tert-butyl-substituted porphyrazines: Structural and ionization effect. SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 240:118601. [PMID: 32570041 DOI: 10.1016/j.saa.2020.118601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/13/2020] [Accepted: 06/08/2020] [Indexed: 02/08/2023]
Abstract
Synthesis and identification of tetrakis-[5,6-bis(4-tert-butylphenyl)pyrazino] porphyrazine, tetra-(4-tert-butyl)phthalocyanine and octakis-(4-tert-butylphenyl)porphyrazine were carried out. Spectrophotometric method was used to study the spectral, acidic and fluorescence properties of the synthesized compounds. It was determined that the synthesized tert-butyl-substituted porphyrazines exhibit a high sensitivity of fluorescence to the molecule ionization. To understand the features of the spectral properties the geometry optimization and an analysis of energy levels and localization of highest occupied and lowest unoccupied molecular orbitals of the studied compounds were performed on the basis of density functional theory with the BP86 functional and the def2-TZVP basis set. The effect of substituents in molecular fragments of the macrocycle on the acidic and electro-optical properties of the studied compounds is revealed. Materials with pH-tunable fluorescence were designed.
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Affiliation(s)
- O A Dmitrieva
- G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya st., 1, Ivanovo, Russia
| | - Yu B Ivanova
- G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya st., 1, Ivanovo, Russia
| | - A S Semeikin
- Ivanovo State University of Chemistry and Technology, Sheremetevsky av., 7, Ivanovo, Russia
| | - N Z Mamardashvili
- G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya st., 1, Ivanovo, Russia.
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29
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Wang L, Wu Z, Lu B, Eckhardt AK, Schreiner PR, Trabelsi T, Francisco JS, Yao Q, Xie C, Guo H, Zeng X. Spectroscopic identification of the •SSNO isomers. J Chem Phys 2020; 153:094303. [DOI: 10.1063/5.0020669] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Lina Wang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Zhuang Wu
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Bo Lu
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - André K. Eckhardt
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| | - Peter R. Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| | - Tarek Trabelsi
- Department of Earth and Environment Science and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6243, USA
| | - Joseph S. Francisco
- Department of Earth and Environment Science and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6243, USA
| | - Qian Yao
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Changjian Xie
- Institute of Modern Physics, Shaanxi Key Laboratory for Theoretical Physics Frontiers, Northwest University, Xian, Shaanxi 710127, China
| | - Hua Guo
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Xiaoqing Zeng
- Department of Chemistry, Fudan University, Shanghai 200433, China
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
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30
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Toda MJ, Mamun AA, Lodowski P, Kozlowski PM. Why is CarH photolytically active in comparison to other B12-dependent enzymes? JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2020; 209:111919. [DOI: 10.1016/j.jphotobiol.2020.111919] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 12/23/2022]
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31
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Ivanova YB, Dmitrieva OA, Khrushkova YV, Lyubimova TV, Semeikin AS, Mamardashvili NZ. Synthesis and Acid–Base, Absorption, and Fluorescence Properties
of Phthalocyanine Derivatives. RUSS J GEN CHEM+ 2020. [DOI: 10.1134/s1070363220050151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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32
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Xiao C, Ma K, Cai G, Zhang X, Vessally E. Borophene as an electronic sensor for metronidazole drug: A computational study. J Mol Graph Model 2020; 96:107539. [DOI: 10.1016/j.jmgm.2020.107539] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/12/2020] [Accepted: 01/12/2020] [Indexed: 12/17/2022]
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Dmitrieva OA, Chizhova NV, Rusanov AI, Koifman MO, Mamardashvili NZ. Spectral-Fluorescence Properties of Zn(II)-Octaphenyltetraazaporphyrins. J Fluoresc 2020; 30:657-664. [PMID: 32328856 DOI: 10.1007/s10895-020-02530-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 03/20/2020] [Indexed: 02/08/2023]
Abstract
Zn(II)-octa-(4-chlorophenyl)- and Zn(II)-octa-(4-bromophenyl)tetraazaporphyrins were synthesized by the reaction of cyclotetramerization of di-(4-chlorophenyl)- and di-(4-bromophenyl)maleonitriles with zinc(II) chloride. The obtained compounds were identified by UV-vis, IR, NMR 1H spectroscopy and mass spectrometry. Geometry optimization of the series of halogenated Zn(II)-octaaryltetraazaporphyrins was performed using the density functional method with the BP86 functional and the def2-TZVP basis set. An analysis of the distribution of molecular orbital energies in the neighborhood of highest occupied molecular orbitals (HOMO and HOMO-1) and lowest unoccupied molecular orbitals (LUMO and LUMO+1) and the width of the HOMO - LUMO energy gaps (EH-L) was performed for the studied compounds. Fluorimetric measurements of the Zn(II)-octaphenyltetraazaporphyrins in toluene were carried out and fluorescence quantum yields of studied compounds were determined and analyzed. It has been shown that the halogen on the para-position of the phenyl groups significantly affects the value of the obtained quantum yields of fluorescence emission but does not significantly affect the Stokes shifts.
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Affiliation(s)
- Olga A Dmitrieva
- G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya Str. 1, Ivanovo, Russian Federation, 153045
| | - Natalya V Chizhova
- G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya Str. 1, Ivanovo, Russian Federation, 153045
| | - Alexey I Rusanov
- Ivanovo State University of Chemistry and Technology, Sheremetevskiy Av. 7, Ivanovo, Russian Federation, 153000
| | - Mikhail O Koifman
- Ivanovo State University of Chemistry and Technology, Sheremetevskiy Av. 7, Ivanovo, Russian Federation, 153000
| | - Nugzar Z Mamardashvili
- G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya Str. 1, Ivanovo, Russian Federation, 153045.
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Chambers DR, Juneau A, Ludwig CT, Frenette M, Martin DBC. C–O Bond Cleavage of Alcohols via Visible Light Activation of Cobalt Alkoxycarbonyls. Organometallics 2019. [DOI: 10.1021/acs.organomet.9b00552] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Dana R. Chambers
- Department of Chemistry, University of California Riverside, Riverside, California 92521, United States
| | - Antoine Juneau
- Département de Chimie, Université du Québec à Montréal, Case Postale
8888, Succursale Centre-Ville, Montréal, Quebec H3C 3P8, Canada
| | - Cory T. Ludwig
- Department of Chemistry, University of California Riverside, Riverside, California 92521, United States
| | - Mathieu Frenette
- Département de Chimie, Université du Québec à Montréal, Case Postale
8888, Succursale Centre-Ville, Montréal, Quebec H3C 3P8, Canada
| | - David B. C. Martin
- Department of Chemistry, University of California Riverside, Riverside, California 92521, United States
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Rodriguez-Mackenzie AD, Arbelo-Lopez HD, Wymore T, Lopez-Garriga J. A reaction pathway to compound 0 intermediates in oxy-myoglobin through interactions with hydrogen sulfide and His64. J Mol Graph Model 2019; 94:107465. [PMID: 31670138 DOI: 10.1016/j.jmgm.2019.107465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/25/2019] [Accepted: 10/01/2019] [Indexed: 11/18/2022]
Abstract
Myoglobin (Mb) binds oxygen with high affinity as a low spin singlet complex and thus functions as an oxygen storage protein. Yet, hybrid Density Functional Theory/Molecular Mechanical (DFT/MM) calculations of oxy-Mb models predict that the O2 bond is much less resistant to breaking in the presence of hydrogen sulfide (H2S) compared with water. Specifically, a hydrogen atom from H2S can be transferred to the distal oxygen atom through homolytic cleavage of the S-H bond to form the intermediate Compound (Cpd) 0 structure and a thiyl radical. In the presence of a neutral His64 (Nε protonation, His64-ε) and H2S, only a metastable Cpd 0 would be formed as the active site is devoid of any additional proton donor to fully break the O2 bond. In contrast, the calculations predict that the triplet state is significantly favored over the open shell singlet diradical state throughout the entire reaction coordinate in the presence of H2S and a positively charged His64. Furthermore, a positively charged His64 can readily donate a proton to Cpd 0 to fully break the O2 bond resulting in a configuration analogous to reported reaction models of a hemoglobin mutant bound to H2O2 with H2S present. Typically, exotic techniques are required to generate Cpd 0 but under the conditions just described the intermediate is readily detected in UV-Vis spectra at room temperature. The effect is observed as a 2 nm red shift of the Soret band from 414 nm to 416 nm (pH 5.0, His64-εδ) and from 416 nm to 418 nm (pH 6.6, His64-ε).
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Affiliation(s)
| | - Hector D Arbelo-Lopez
- Department of Chemistry, University of Puerto Rico Mayaguez Campus, Mayaguez, 00680, Puerto Rico
| | - Troy Wymore
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, United States.
| | - Juan Lopez-Garriga
- Department of Chemistry, University of Puerto Rico Mayaguez Campus, Mayaguez, 00680, Puerto Rico.
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Sitek P, Chmielowska A, Jaworska M, Lodowski P, Szczepańska M. Theoretical study of cobalt and nickel complexes involved in methyl transfer reactions: structures, redox potentials and methyl binding energies. Struct Chem 2019. [DOI: 10.1007/s11224-019-01384-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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37
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Elucidating the mechanism of cob(I)alamin mediated methylation reactions by alkyl halides: SN2 or radical mechanism? J Catal 2019. [DOI: 10.1016/j.jcat.2019.06.036] [Citation(s) in RCA: 6] [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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38
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Halsey-Moore C, Jena P, McLeskey JT. Tuning range-separated DFT functionals for modeling the peak absorption of MEH-PPV polymer in various solvents. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2019.112506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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39
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Martynov AG, Mack J, May AK, Nyokong T, Gorbunova YG, Tsivadze AY. Methodological Survey of Simplified TD-DFT Methods for Fast and Accurate Interpretation of UV-Vis-NIR Spectra of Phthalocyanines. ACS OMEGA 2019; 4:7265-7284. [PMID: 31459828 PMCID: PMC6648833 DOI: 10.1021/acsomega.8b03500] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/11/2019] [Indexed: 05/14/2023]
Abstract
A methodological survey of density functional theory (DFT) methods for the prediction of UV-visible (vis)-near-infrared (NIR) spectra of phthalocyanines is reported. Four methods, namely, full time-dependent (TD)-DFT and its Tamm-Dancoff approximation (TDA), together with their simplified modifications (sTD-DFT and sTDA, respectively), were tested by using the examples of unsubstituted and alkoxy-substituted metal-free ligands and zinc complexes. The theoretical results were compared with experimental data derived from UV-visible absorption and magnetic circular dichroism spectroscopy. Seven popular exchange-correlation functionals (BP86, B3LYP, TPSSh, M06, CAM-B3LYP, LC-BLYP, and ωB97X) were tested within these four approaches starting at a relatively modest level using 6-31G(d) basis sets and gas-phase BP86/def2-SVP optimized geometries. A gradual augmentation of the computational levels was used to identify the influence of starting geometry, solvation effects, and basis sets on the results of TD-DFT and sTD-DFT calculations. It was found that although these factors do influence the predicted energies of the vertical excitations, they do not affect the trends predicted in the spectral properties across series of structurally related substituted free bases and metallophthalocyanines. The best accuracy for the gas-phase vertical excitations was observed in the lower-energy Q-band region for calculations that made use of range-separated hybrids for both full and simplified TD-DFT approaches. The CAM-B3LYP functional provided particularly accurate results in the context of the sTD-DFT approach. The description of the higher-energy B-band region is considerably less accurate, and this demonstrates the need for further advances in the accuracy of theoretical calculations. Together with a general increase in accuracy, the application of simplified TD-DFT methods affords a 2-3 orders of magnitude speedup of the calculations in comparison to the full TD-DFT approach. It is anticipated that this approach will be widely used on desktop computers during the interpretation of UV-vis-NIR spectra of phthalocyanines and related macrocycles in the years ahead.
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Affiliation(s)
- Alexander G. Martynov
- A.N.
Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninskii pr., 31, Building 4, 119071 Moscow, Russia
- E-mail: (A.G.M.)
| | - John Mack
- Institute
for Nanotechnology Innovation, Department of Chemistry, Rhodes University, Makhanda 6140, South Africa
- E-mail: (J.M.)
| | - Aviwe K. May
- Institute
for Nanotechnology Innovation, Department of Chemistry, Rhodes University, Makhanda 6140, South Africa
| | - Tebello Nyokong
- Institute
for Nanotechnology Innovation, Department of Chemistry, Rhodes University, Makhanda 6140, South Africa
| | - Yulia G. Gorbunova
- A.N.
Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninskii pr., 31, Building 4, 119071 Moscow, Russia
- N.S.
Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii pr., 31, 119991 Moscow, Russia
| | - Aslan Yu Tsivadze
- A.N.
Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninskii pr., 31, Building 4, 119071 Moscow, Russia
- N.S.
Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii pr., 31, 119991 Moscow, Russia
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40
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Benchmark DFT studies on C–CN homolytic cleavage and screening the substitution effect on bond dissociation energy. J Mol Model 2019; 25:47. [DOI: 10.1007/s00894-019-3930-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 01/09/2019] [Indexed: 12/28/2022]
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41
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A theoretical investigation on the aminolysis of pyromellitic and 1,4,5,8-naphthalenetetracarboxylic dianhydrides. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2018.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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42
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Chang H, Zheng W, Zheng Y, Zhu D, Wang J. The DFT study on Rh–C bond dissociation enthalpies of (iminoacyl)rhodium(III)hydride and (iminoacyl)rhodium(III)alkyl. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2018.12.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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43
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Mojica-Sánchez JP, Flores-Moreno R, Pineda-Urbina K, Gómez-Sandoval Z. Exploring the Structure, Energetic, and Magnetic Properties of Neutral Small Lithium Clusters Doped with Yttrium: Supermagnetic Atom Research. ACS OMEGA 2018; 3:11252-11261. [PMID: 31459233 PMCID: PMC6645110 DOI: 10.1021/acsomega.8b01463] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/04/2018] [Indexed: 06/10/2023]
Abstract
Density functional theory calculations based on magnetic and energetic stability criteria were performed to study a series of yttrium-doped lithium neutral clusters. A relativistic approximation was employed to properly describe the energy and multiplicity of the given clusters' fundamental states. The interaction of the 4d-Y atomic orbitals with the sp-Li states had an important role in the magnetic and energetic behavior of the selected systems. The spin density was concentrated over the yttrium atom regardless of the size of the cluster. Li7Y is a new stable superatom due to its enhanced magnetic properties.
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Affiliation(s)
- Juan Pablo Mojica-Sánchez
- Facultad
de Ciencias Químicas, Universidad
de Colima, Carretera Colima-Coquimatlán km 9, Coquimatlán, Colima Col. C.P. 28400, México
| | - Roberto Flores-Moreno
- Departamento
de Química, Grupo de Estructura de la Materia, Universidad Guadalajara, Blvd. Marcelino García Barragán 1421, Guadalajara, Jalisco C.P. 44430, México
| | - Kayim Pineda-Urbina
- Facultad
de Ciencias Químicas, Universidad
de Colima, Carretera Colima-Coquimatlán km 9, Coquimatlán, Colima Col. C.P. 28400, México
| | - Zeferino Gómez-Sandoval
- Facultad
de Ciencias Químicas, Universidad
de Colima, Carretera Colima-Coquimatlán km 9, Coquimatlán, Colima Col. C.P. 28400, México
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44
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Xu K, Hirao H. Revisiting the catalytic mechanism of Mo-Cu carbon monoxide dehydrogenase using QM/MM and DFT calculations. Phys Chem Chem Phys 2018; 20:18938-18948. [PMID: 29744484 DOI: 10.1039/c8cp00858b] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Previous density functional theory (DFT) studies have shown that the release of the produced carbon dioxide (CO2) from an active-site cluster is a thermodynamically or kinetically difficult step in the enzymatic carbon monoxide (CO) oxidation catalyzed by Mo-Cu carbon monoxide dehydrogenase (Mo-Cu CODH). To better understand the effect of the protein environment on this difficult CO2 release step as well as other reaction steps, we applied hybrid quantum mechanics and molecular mechanics (QM/MM) calculations to the Mo-Cu CODH enzyme. The results show that in the first step, the equatorial Mo[double bond, length as m-dash]O group in the active-site cluster attacks the nearby CO molecule bound to the Cu site. Afterward, a stable thiocarbonate intermediate is formed in which the CO2 molecule is embedded and the copper-S(μ-sulfido) bond is broken. A free CO2 molecule, i.e., the final product, is then released from the active-site cluster, not directly from the thiocarbonate intermediate but via a previously formed intermediate that also contains CO2 but retains the Cu-S(μ-sulfido) bond. In contrast to the previous DFT results, the calculated barrier for this process was low in our QM/MM calculations. An additional QM/MM analysis of the barrier height showed that the effect of the protein environment on this barrier lowering is not very large. We found that the reason for the low barrier obtained by QM/MM is that the barrier for CO2 release is already not high at the DFT level. These results allow us to conclude that the CO oxidation reaction passes through the formation of a thiocarbonate intermediate, and that the subsequent CO2 release is kinetically not difficult. Nevertheless, the protein environment has an important role to play in making the latter process thermodynamically favored. No low-barrier pathway for the product release could be obtained for the reaction of n-butylisocyanide, which is consistent with the experimental fact that n-butylisocyanide inhibits Mo-Cu CODH.
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Affiliation(s)
- Kai Xu
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China.
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45
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Zheng Y, Zheng W, Wang J, Chang H, Zhu D. Computational Study on N-N Homolytic Bond Dissociation Enthalpies of Hydrazine Derivatives. J Phys Chem A 2018; 122:2764-2780. [PMID: 29470086 DOI: 10.1021/acs.jpca.7b12094] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hydrazine derivatives have been regarded as the important building blocks in organic chemistry for the synthesis of organic N-containing compounds. It is important to understand the structure-activity relationship of the thermodynamics of N-N bonds, in particular, their strength as measured by using the homolytic bond dissociation enthalpies (BDEs). We calculated the N-N BDEs of 13 organonitrogen compounds by eight composite high-level ab initio methods including G3, G3B3, G4, G4MP2, CBS-QB3, ROCBS-QB3, CBS-Q, and CBS-APNO. Then 25 density functional theory (DFT) methods were selected for calculating the N-N BDEs of 58 organonitrogen compounds. The M05-2X method can provide the most accurate results with the smallest root-mean-square error (RMSE) of 8.9 kJ/mol. Subsequently, the N-N BDE predictions of different hydrazine derivatives including cycloalkylhydrazines, N-heterocyclic hydrazines, arylhydrazines, and hydrazides as well as the substituent effects were investigated in detail by using the M05-2X method. In addition, the analysis including the natural bond orbital (NBO) as well as the energies of frontier orbitals were performed in order to further understand the essence of the N-N BDE change patterns.
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Affiliation(s)
- Yuanyuan Zheng
- College of Chemistry and Chemical Engineering , Shanghai University of Engineering Science , Shanghai 201620 , China
| | - Wenrui Zheng
- College of Chemistry and Chemical Engineering , Shanghai University of Engineering Science , Shanghai 201620 , China
| | - Jiaoyang Wang
- College of Chemistry and Chemical Engineering , Shanghai University of Engineering Science , Shanghai 201620 , China
| | - Huifang Chang
- College of Chemistry and Chemical Engineering , Shanghai University of Engineering Science , Shanghai 201620 , China
| | - Danfeng Zhu
- College of Chemistry and Chemical Engineering , Shanghai University of Engineering Science , Shanghai 201620 , China
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46
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Hitzenberger M, Schuster D, Hofer TS. The Binding Mode of the Sonic Hedgehog Inhibitor Robotnikinin, a Combined Docking and QM/MM MD Study. Front Chem 2017; 5:76. [PMID: 29109946 PMCID: PMC5660280 DOI: 10.3389/fchem.2017.00076] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/25/2017] [Indexed: 12/19/2022] Open
Abstract
Erroneous activation of the Hedgehog pathway has been linked to a great amount of cancerous diseases and therefore a large number of studies aiming at its inhibition have been carried out. One leverage point for novel therapeutic strategies targeting the proteins involved, is the prevention of complex formation between the extracellular signaling protein Sonic Hedgehog and the transmembrane protein Patched 1. In 2009 robotnikinin, a small molecule capable of binding to and inhibiting the activity of Sonic Hedgehog has been identified, however in the absence of X-ray structures of the Sonic Hedgehog-robotnikinin complex, the binding mode of this inhibitor remains unknown. In order to aid with the identification of novel Sonic Hedgehog inhibitors, the presented investigation elucidates the binding mode of robotnikinin by performing an extensive docking study, including subsequent molecular mechanical as well as quantum mechanical/molecular mechanical molecular dynamics simulations. The attained configurations enabled the identification of a number of key protein-ligand interactions, aiding complex formation and providing stabilizing contributions to the binding of the ligand. The predicted structure of the Sonic Hedgehog-robotnikinin complex is provided via a PDB file as Supplementary Material and can be used for further reference.
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Affiliation(s)
- Manuel Hitzenberger
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria.,Department of Physics, Theoretical Biophysics (T38), Technical University of Munich, Munich, Germany
| | - Daniela Schuster
- Pharmaceutical Chemistry, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
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47
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Moulder CA, Cundari TR. A DFT Survey of the Effects of d‐Electron Count and Metal Identity on the Activation and Functionalization of C−H Bonds for Mid to Late Transition Metals. Isr J Chem 2017. [DOI: 10.1002/ijch.201700066] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Catherine A. Moulder
- University of North Texas, Department of Chemistry Center for Advanced Scientific Computing and Modeling (CASCaM) 1155 Union Circle #305070 Denton, Texas 76203–5017 United States
| | - Thomas R. Cundari
- University of North Texas, Department of Chemistry Center for Advanced Scientific Computing and Modeling (CASCaM) 1155 Union Circle #305070 Denton, Texas 76203–5017 United States
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48
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Filipović NR, Elshaflu H, Grubišić S, Jovanović LS, Rodić M, Novaković I, Malešević A, Djordjević IS, Li H, Šojić N, Marinković A, Todorović TR. Co(iii) complexes of (1,3-selenazol-2-yl)hydrazones and their sulphur analogues. Dalton Trans 2017; 46:2910-2924. [PMID: 28197616 DOI: 10.1039/c6dt04785h] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The first Co(iii) complexes with (1,3-selenazol-2-yl)hydrazones as an unexplored class of ligands were prepared and characterized by NMR spectroscopy and X-ray diffraction analysis. The novel ligands act as NNN tridentate chelators forming octahedral Co(iii) complexes. The impact of structural changes on ligands' periphery as well as that of isosteric replacement of sulphur with selenium on the electrochemical and electronic absorption features of complexes are explored. To support the experimental data, density functional theory (DFT) calculations were also conducted. Theoretical NMR chemical shifts, the relative energies and natural bond orbital (NBO) analysis are calculated within the DFT approach, while the singlet excited state energies and HOMO-LUMO energy gap were calculated with time-dependent density functional theory (TD-DFT). The electrophilic f- and nucleophilic f+ Fukui functions are well adapted to find the electrophile and nucleophile centres in the molecules. Both (1,3-selenazol-2-yl)- and (1,3-thiazol-2-yl)hydrazone Co(iii) complexes showed potent antimicrobial and antioxidant activity. A significant difference among them was a smaller cytotoxicity of selenium compounds.
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Affiliation(s)
- Nenad R Filipović
- Department of Chemistry and Biochemistry, Faculty of Agriculture, University of Belgrade, Nemanjina 6, Belgrade, Serbia
| | - Hana Elshaflu
- Faculty of Technology and Metallurgy, University of Belgrade, Karnegijeva 4, Belgrade, Serbia
| | - Sonja Grubišić
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, Belgrade, Serbia
| | - Ljiljana S Jovanović
- Department of Chemistry, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovića 4, Novi Sad, Serbia
| | - Marko Rodić
- Department of Chemistry, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovića 4, Novi Sad, Serbia
| | - Irena Novaković
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, Belgrade, Serbia
| | - Aleksandar Malešević
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, Serbia.
| | - Ivana S Djordjević
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, Belgrade, Serbia
| | - Haidong Li
- University of Bordeaux, Bordeaux INP, ENSCBP, Institut des Sciences Moléculaires, CNRS UMR 5255, 16 Avenue Pey-Berland, 33607 Pessac, France
| | - Nešo Šojić
- University of Bordeaux, Bordeaux INP, ENSCBP, Institut des Sciences Moléculaires, CNRS UMR 5255, 16 Avenue Pey-Berland, 33607 Pessac, France
| | - Aleksandar Marinković
- Faculty of Technology and Metallurgy, University of Belgrade, Karnegijeva 4, Belgrade, Serbia
| | - Tamara R Todorović
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, Serbia.
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49
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Wang J, Zheng W, Ding L, Wang Y. Computational study on C–B homolytic bond dissociation enthalpies of organoboron compounds. NEW J CHEM 2017. [DOI: 10.1039/c6nj02887j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The theoretical study of three hybridized C–B BDEs with different substituents can provide corresponding guidance to experimental research studies.
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Affiliation(s)
- JiaoYang Wang
- College of Chemistry and Chemical Engineering
- Shanghai University of Engineering Science
- Shanghai 201620
- China
| | - WenRui Zheng
- College of Chemistry and Chemical Engineering
- Shanghai University of Engineering Science
- Shanghai 201620
- China
| | - LanLan Ding
- College of Chemistry and Chemical Engineering
- Shanghai University of Engineering Science
- Shanghai 201620
- China
| | - YingXing Wang
- College of Chemistry and Chemical Engineering
- Shanghai University of Engineering Science
- Shanghai 201620
- China
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50
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Chernev P, Zaharieva I, Rossini E, Galstyan A, Dau H, Knapp EW. Merging Structural Information from X-ray Crystallography, Quantum Chemistry, and EXAFS Spectra: The Oxygen-Evolving Complex in PSII. J Phys Chem B 2016; 120:10899-10922. [DOI: 10.1021/acs.jpcb.6b05800] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Petko Chernev
- Institute of Chemistry and Biochemistry and ‡Department of Physics, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Ivelina Zaharieva
- Institute of Chemistry and Biochemistry and ‡Department of Physics, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Emanuele Rossini
- Institute of Chemistry and Biochemistry and ‡Department of Physics, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Artur Galstyan
- Institute of Chemistry and Biochemistry and ‡Department of Physics, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Holger Dau
- Institute of Chemistry and Biochemistry and ‡Department of Physics, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Ernst-Walter Knapp
- Institute of Chemistry and Biochemistry and ‡Department of Physics, Freie Universität Berlin, D-14195 Berlin, Germany
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