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Li F, Zhang G. Effective removal of toxic heavy metal ions from wastewater using boroxine covalent organic framework. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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2
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Ramek M, Pejić J, Sabolović J. Structure prediction of neutral physiological copper(II) compounds with l-cysteine and l-histidine. J Inorg Biochem 2021; 223:111536. [PMID: 34274876 DOI: 10.1016/j.jinorgbio.2021.111536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/19/2021] [Accepted: 07/05/2021] [Indexed: 10/20/2022]
Abstract
Bis(aminoacidato)copper(II) [CuII(aa)2] coordination compounds are the physiological species of copper(II) amino acid compounds in blood plasma. Since there are no experimental data in the literature about the geometries that physiological CuII(aa)2 could form with l-cysteine (Cys), that is, for bis(l-cysteinato)copper(II) [Cu(Cys)2] and the ternary (l-histidinato)(l-cysteinato)copper(II) [Cu(His)(Cys)], this paper computationally examines the possible conformations that the two compounds could form with the Cys ligand having a protonated sulfur, as in the conventional zwitterion, which was determined to be prevailing in aqueous solution. These two amino acids can bind metals in a tridentate fashion and thus form many possible coordination patterns. Density functional calculations were performed for the conformational analyses in the gas phase and in implicitly modeled aqueous solution using a polarizable continuum model. Additionally, we examine which coordination mode, with thiol or thiolate group, is more stable. The Cys coordination via the amino N and carboxylato O atoms (a glycinato mode) is obtained as the most stable one in aqueous Cu(Cys)2, and also in Cu(His)(Cys) when the His glycinato or histaminato mode combines with the intact thiol group. Whereas the conformers with N and thiol S as the copper(II) donor atoms are predicted to be the least stable, those with the Cu-N and Cu-S(thiolate) bonding (and protonated carboxylato group) are the most stable. The differences are explained by different covalent and ionic contributions of Cu-S(thiol) vs. Cu-S(thiolate). The study can contribute to the insight into formation and reactivity of the copper(II) cysteinato complexes in solution.
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Affiliation(s)
- Michael Ramek
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria
| | - Jelena Pejić
- Institute for Medical Research and Occupational Health, Ksaverska cesta 2, HR-10000 Zagreb, Croatia
| | - Jasmina Sabolović
- Institute for Medical Research and Occupational Health, Ksaverska cesta 2, HR-10000 Zagreb, Croatia.
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Li H, Hua W, Wang Z, Liu A, Jiang J, Luo Y. Theoretical Spectroscopic Studies on Chemical and Electronic Structures of Selenocysteine and Pyrrolysine. J Phys Chem A 2020; 124:2215-2224. [PMID: 32091898 DOI: 10.1021/acs.jpca.9b10756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The chemical and electronic structures of the 21st and 22nd proteinogenic amino acid selenocysteine (Sec), pyrrolysine (Pyl), and their derivatives (deprotonated and protonated ions) were extensively characterized for the first time. Through the fragment based step-by-step research on their potential energy surface (PES), electronic energies of the most stable conformers of Sec, Pyl and the related ions were finally determined at the advanced CBS-QB3 and DSD-PBEP86-D3(BJ)/aug-cc-pVTZ levels, respectively, with the identification of many new low-energy conformers. The infrared spectra (IR) at 298 K of the most abundant conformers in different forms were scaled by comparison with the anharmonic frequency calculations and analyzed comparing with the experimental spectra of similar molecules. The characteristic soft X-ray spectra (including X-ray photoelectron spectra (XPS) and near-edge X-ray absorption fine-structure spectra (NEXAFS)) of the most stable conformers at 498 K were also simulated. In particular, the two possible protonated configurations of Pyl can be clearly distinguished by their different spectral features. Furthermore, a small binding energy intersection appeared around 293 eV at the C 1s edge between the canonical and protonated Pyl conformers, which is different from all the previous studies. This work thus filled the gap in our knowledge by providing detailed information on the chemical and electronic structures of Sec and Pyl and will be a useful guidance for future experimental research.
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Affiliation(s)
- Hongbao Li
- Institutes of Physical Science and Information Technology, Key Laboratory of Structure and Functional Regulation of Hybrid Materials, Ministry of Education. Anhui Graphene Engineering Laboratory, Anhui University, Hefei, Anhui 230601, China.,Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Weijie Hua
- Department of Applied Physics, School of Science, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Zhiqiang Wang
- Institutes of Physical Science and Information Technology, Key Laboratory of Structure and Functional Regulation of Hybrid Materials, Ministry of Education. Anhui Graphene Engineering Laboratory, Anhui University, Hefei, Anhui 230601, China
| | - Axue Liu
- Institutes of Physical Science and Information Technology, Key Laboratory of Structure and Functional Regulation of Hybrid Materials, Ministry of Education. Anhui Graphene Engineering Laboratory, Anhui University, Hefei, Anhui 230601, China
| | - Jun Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yi Luo
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
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Jiang W, Xu Q, Wei X. Use of cobalt(II) chelates of monothiol-containing ligands for the removal of nitric oxide. JOURNAL OF HAZARDOUS MATERIALS 2019; 374:50-57. [PMID: 30978630 DOI: 10.1016/j.jhazmat.2019.04.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 03/08/2019] [Accepted: 04/04/2019] [Indexed: 06/09/2023]
Abstract
It is first reported herein that cobalt(II) complexes solution of monothiol-containing multidentate ligands are used to remove low concentration of nitric oxide (NO). These chelating ligands are water-soluble amines, alcohols or acids which containing at least one -SH group, include those of cysteine, mercaptosuccinic acid, mercaptoethanesulfonate, mercaptopropionic acid and the like. These -SH compounds when coordinated with cobalt ions, forming complexes are very effective for NO removal. The results indicate that the side group (methyl, carboxyl, carboxymethyl) on α-carbon atom of ligands contribute to the denitration of the chelate solution, whereas the substituents on sulfur atom of ligands deactivate the complexation system. In addition, we have found that several monothiol compounds with simple molecule structure and low cost exhibit good performance in denitration, and some of cobalt thiol complexes are more valuable in removing NO than ferrous thiol complexes.
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Affiliation(s)
- Wei Jiang
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Qiang Xu
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xionghui Wei
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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5
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Comprehensive understanding of multiple binding of D-penicillamine with Cu2+-hexa aqua complex: a DFT approach. Struct Chem 2019. [DOI: 10.1007/s11224-019-01365-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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6
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Novel applications of perovskite oxide via catalytic peroxymonosulfate advanced oxidation in aqueous systems for trace L-cysteine detection. J Colloid Interface Sci 2019; 545:311-316. [PMID: 30897427 DOI: 10.1016/j.jcis.2019.03.045] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/11/2019] [Accepted: 03/13/2019] [Indexed: 11/23/2022]
Abstract
Perovskite oxides offer new opportunities in wastewater treatment via catalytic oxidation. Herein, we report a new application of perovskite oxides for biological detection via catalytic decolourisation and colorimetric determination. The presence of trace biomolecules in an aqueous system would interfere the decolourisation process of dyes, where the decolourisation rate is quantitatively correlated to the biomolecular concentration. In this work, trace L-cysteine (Cys) detection was demonstrated on the basis of a Ag-Ba0.5Sr0.5Co0.75Fe0.2O3-δ (Ag-BSCF)/peroxymonosulfate/textile dye system. Thiol-containing cysteine can bind to Ag, Co and Fe atoms, therefore shielding the catalytic performance of the perovskite in degradation of dye solutions. Such a cost-effective biosensor system presents an excellent linear response in Cys concentration ranging from nM to μM.
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Latrous L, Salpin JY, Haldys V, Léon E, Correia C, Lamsabhi AM. Gas-phase interactions of organotin compounds with cysteine. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:1006-1015. [PMID: 27428725 DOI: 10.1002/jms.3812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/02/2016] [Accepted: 07/12/2016] [Indexed: 06/06/2023]
Abstract
The gas-phase interactions of cysteine with di-organotin and tri-organotin compounds have been studied by mass spectrometry experiments and quantum calculations. Positive-ion electrospray spectra show that the interaction of di- and tri-organotins with cysteine results in the formation of [(R)2 Sn(Cys-H)]+ and [(R)3 Sn(Cys)]+ ions, respectively. MS/MS spectra of [(R)2 Sn(Cys-H)]+ complexes are characterized by numerous fragmentation processes, notably associated with elimination of NH3 and (C,H2 ,O2 ). Several dissociation routes are characteristic of each given organic species. Upon collision, both the [(R)3 Sn(Gly)]+ and [(R)3 Sn(Cys)]+ complexes are associated with elimination of the intact amino acid, leading to the formation of [(R)3 Sn]+ cation. But for the latter complex, two additional fragmentation processes are observed, associated with the elimination of NH3 and C3 H4 O2 S. Calculations indicate that the interaction between organotins and cysteine is predominantly electrostatic but also exhibits a considerable covalent character, which is slightly more pronounced in tri-organotin complexes. A preferred bidentate interaction of the type -η2 -S-NH2 , with sulfur and the amino group, is observed. As for the [(R)3 Sn(Cys)]+ complexes, their stability is due to the combination of the hydrogen bond taking place between the amino group and the sulfur lone pair and the interaction between the carboxylic oxygen atom and the metal. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Latifa Latrous
- Laboratoire de Chimie Analytique et Electrochimie Campus Universitaire, Faculté des Sciences de Tunis, Université de Tunis El Manar, 2092, Tunis, Tunisia.
| | - Jean-Yves Salpin
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Université d'Evry Val d'Essonne, Bâtiment Maupertuis-Boulevard François Mitterrand, 91025, Evry, France
- CNRS-UMR 8587, Evry, France
| | - Violette Haldys
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Université d'Evry Val d'Essonne, Bâtiment Maupertuis-Boulevard François Mitterrand, 91025, Evry, France
- CNRS-UMR 8587, Evry, France
| | - Emmanuelle Léon
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Université d'Evry Val d'Essonne, Bâtiment Maupertuis-Boulevard François Mitterrand, 91025, Evry, France
- CNRS-UMR 8587, Evry, France
| | - Catarina Correia
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Université d'Evry Val d'Essonne, Bâtiment Maupertuis-Boulevard François Mitterrand, 91025, Evry, France
- CNRS-UMR 8587, Evry, France
| | - Al Mokhtar Lamsabhi
- Departamento de Química, Ciencias, M-13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC Cantoblanco, 28049, Madrid, Spain
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Ash T, Debnath T, Banu T, Das AK. Exploration of Binding Interactions of Cu2+ with d-Penicillamine and its O- and Se- Analogues in Both Gas and Aqueous Phases: A Theoretical Approach. J Phys Chem B 2016; 120:3467-78. [DOI: 10.1021/acs.jpcb.5b11825] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tamalika Ash
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Tanay Debnath
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Tahamida Banu
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Abhijit K. Das
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
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Martín-Sómer A, Gaigeot MP, Yáñez M, Spezia R. A RRKM study and a DFT assessment on gas-phase fragmentation of formamide-M(2+) (M = Ca, Sr). Phys Chem Chem Phys 2015; 16:14813-25. [PMID: 24921953 DOI: 10.1039/c4cp01756k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A kinetic study of the unimolecular reactivity of formamide-M(2+) (M = Ca, Sr) systems was carried out by means of RRKM statistical theory using high-level DFT. The results predict M(2+), [M(NH2)](+) and [HCO](+) as the main products, together with an intermediate that could eventually evolve to produce [M(NH3)](2+) and CO, for high values of internal energy. In this framework, we also evaluated the influence of the external rotational energy on the reaction rate constants. In order to find a method to perform reliable electronic structure calculations for formamide-M(2+) (M = Ca, Sr) at a relatively low computational cost, an assessment of different methods was performed. In the first assessment twenty-one functionals, belonging to different DFT categories, and an MP2 wave function method using a small basis set were evaluated. CCSD(T)/cc-pWCVTZ single point calculations were used as reference. A second assessment has been performed on geometries and energies. We found BLYP/6-31G(d) and G96LYP/6-31+G(d,p) as the best performing methods, for formamide-Ca(2+) and formamide-Sr(2+), respectively. Furthermore, a detailed assessment was done on RRKM reactivity and G96LYP/6-31G(d) provided results in agreement with higher level calculations. The combination of geometrical, energetics and kinetics (RRKM) criteria to evaluate DFT functionals is rather unusual and provides an original assessment procedure. Overall, we suggest using G96LYP as the best performing functional with a small basis set for both systems.
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Affiliation(s)
- Ana Martín-Sómer
- Departamento de Química, Facultad de Ciencias, Módulo 13. Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, E-28049 Madrid, Spain.
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10
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Novikova GV, Petrov AI, Staloverova NA, Shubin AA, Dergachev ID. Complex formation of Sn(II) with L-cysteine: an IR, DTA/TGA and DFT investigation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 122:565-570. [PMID: 24334020 DOI: 10.1016/j.saa.2013.11.048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 10/27/2013] [Accepted: 11/10/2013] [Indexed: 06/03/2023]
Abstract
The novel complex of Sn(II) with L-cysteine (L-H2Cys) has been synthesized and characterized by elemental analysis, TGA and IR spectroscopy. Vibrational assignment and DFT/PBE0/def2-TZVP ab initio simulation give evidence of cysteine molecule being coordinated to Sn(II) as three-dentate chelating N,O,S-donor ligand. The four Perdew density functionals TPSS, PBE0, PBE, TPSSh have been tested to provide consistency of simulated and experimental IR spectra, the best result is provided by unweighted Hartree-Fock density functionals (PBE, TPSS). On the contrary, the Hartree-Fock weighted functionals (PBE0, TPPSh) provide the most accurate geometry optimization. Unharmonic frequencies are obtained via ab initio vibrational self-consistent field (PT2-VSCF) calculations at DFT/TPSS/Def2-TZVP level, the vibrational assignment of IR spectra has been carried out.
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Affiliation(s)
- Galina V Novikova
- Institute of Non-Ferrous Metals and Materials Science, Siberian Federal University, 79 Svobodny Prospekt, 660041 Krasnoyarsk, Russian Federation.
| | - Alexander I Petrov
- Institute of Non-Ferrous Metals and Materials Science, Siberian Federal University, 79 Svobodny Prospekt, 660041 Krasnoyarsk, Russian Federation
| | - Natalya A Staloverova
- Institute of Non-Ferrous Metals and Materials Science, Siberian Federal University, 79 Svobodny Prospekt, 660041 Krasnoyarsk, Russian Federation
| | - Alexander A Shubin
- Institute of Non-Ferrous Metals and Materials Science, Siberian Federal University, 79 Svobodny Prospekt, 660041 Krasnoyarsk, Russian Federation
| | - Ilya D Dergachev
- Institute of Non-Ferrous Metals and Materials Science, Siberian Federal University, 79 Svobodny Prospekt, 660041 Krasnoyarsk, Russian Federation
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11
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Meng L, Wu W, Zhang J. Gas Phase Conformations of Selenocysteine and Related Ions: A Comprehensive Theoretical Study. J Phys Chem A 2014; 118:1684-96. [DOI: 10.1021/jp411403w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lingbiao Meng
- Research Center of Laser
Fusion, China Academy of Engineering Physics, Mianyang 621900, China
| | - Weidong Wu
- Research Center of Laser
Fusion, China Academy of Engineering Physics, Mianyang 621900, China
| | - Jicheng Zhang
- Research Center of Laser
Fusion, China Academy of Engineering Physics, Mianyang 621900, China
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12
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Spezia R, Vuilleumier R. p of silicic acid in presence of La3+using single sweep method coupled to DFT-based molecular dynamics. Mol Phys 2013. [DOI: 10.1080/00268976.2013.848300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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13
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Khodabandeh MH, Reisi H, Davari MD, Zare K, Zahedi M, Ohanessian G. Interaction Modes and Absolute Affinities of α-Amino Acids for Mn2+: A Comprehensive Picture. Chemphyschem 2013; 14:1733-45. [DOI: 10.1002/cphc.201200964] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 02/13/2013] [Indexed: 11/07/2022]
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Matosziuk LM, Holbrook RJ, Manus LM, Heffern MC, Ratner MA, Meade TJ. Rational design of [Co(acacen)L2]+ inhibitors of protein function. Dalton Trans 2013; 42:4002-12. [PMID: 23340849 PMCID: PMC3581327 DOI: 10.1039/c2dt32565a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Cobalt(III) Schiff base complexes, such as [Co(acacen)L(2)](+), inhibit the function of Zn(II)-dependent proteins through dissociative exchange of the axial ligands with key histidine residues of the target protein. Consequently the efficacy of these compounds depends strongly on the lability of the axial ligands. A series of [Co(acacen)L(2)](+) complexes with various axial ligands was investigated using DFT to determine the kinetics and thermodynamics of ligand exchange and hydrolysis. Results showed excellent agreement with experimental data, indicating that axial ligand lability is determined by several factors: pK(a) of the axial ligand, the kinetic barrier to ligand dissociation, and the relative thermodynamic stability of the complexes before and after exchange. Hammett plots were constructed to determine if the kinetics and thermodynamics of exchange can be modulated by the addition of an electron-withdrawing group (EWG) to either the axial ligand itself or to the equatorial acacen ligand. Results predict that addition of an EWG to the axial ligand will shift the kinetics and thermodynamics so as to promote axial ligand exchange, while addition of an EWG to acacen will decrease axial ligand lability. These investigations will aid in the design of the next generation of [Co(acacen)L(2)](2+), allowing researchers to develop new, more effective inhibitors.
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Affiliation(s)
- Lauren M. Matosziuk
- Departments of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, and Radiology, Northwestern University, Evanston, Illinois 60208-3113
| | - Robert J. Holbrook
- Departments of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, and Radiology, Northwestern University, Evanston, Illinois 60208-3113
| | - Lisa M. Manus
- Departments of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, and Radiology, Northwestern University, Evanston, Illinois 60208-3113
| | - Marie C. Heffern
- Departments of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, and Radiology, Northwestern University, Evanston, Illinois 60208-3113
| | - Mark A. Ratner
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - Thomas J. Meade
- Departments of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, and Radiology, Northwestern University, Evanston, Illinois 60208-3113
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Mandal S, Das G. Structure of dipeptides having N-terminal selenocysteine residues: a DFT study in gas and aqueous phase. J Mol Model 2013; 19:2613-23. [PMID: 23494524 DOI: 10.1007/s00894-013-1808-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 02/18/2013] [Indexed: 12/18/2022]
Abstract
Over the last few decades, dipeptides as well as their analogues have served as important model systems for the computational studies concerning the structure of protein and energetics of protein folding. Here, we present a density functional structural study on a set of seven dipeptides having N-terminal selenocysteine residues (the component in the C-terminus is varied with seven different combinations viz. Ala, Phe, Glu, Thr, Asn, Arg and Sec) in gas and simulated aqueous phase using a polarizable continuum model (PCM). The molecular geometries of the dipeptides are fully optimized at B3LYP/6-311++G(d,p) level and subsequent frequency calculations confirm them as true minima. The effects of solvation and identity of the varying C-terminal residue on the energetics, structural features of the peptide planes, values of the ψ and ф dihedrals, geometry around the α-carbon atoms and theoretically predicted vibrational spectra of the dipeptides are investigated. Two types of intramolecular H-bonds, namely N…H-N and O…H-C, are found to play important roles in influencing the planarity of the peptide planes and geometry around the α-carbon atoms of the dipeptides. The identity of the varying C-terminal residue influences the values of ф, planarity of the peptide planes and geometry around the C₇ α-carbon atoms while the solvation effects are evident on the values of bond lengths and bond angles of the amide planes.
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Affiliation(s)
- Shilpi Mandal
- Department of Chemistry, North Eastern Hill University, Shillong 793022, India
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16
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Spezia R, Cimas A, Gaigeot MP, Salpin JY, Song K, Hase WL. Collision induced dissociation of doubly-charged ions: Coulomb explosion vs. neutral loss in [Ca(urea)]2+ gas phase unimolecular reactivity via chemical dynamics simulations. Phys Chem Chem Phys 2012; 14:11724-36. [PMID: 22828785 DOI: 10.1039/c2cp41379e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper we report different theoretical approaches to study the gas-phase unimolecular dissociation of the doubly-charged cation [Ca(urea)](2+), in order to rationalize recent experimental findings. Quantum mechanical plus molecular mechanical (QM/MM) direct chemical dynamics simulations were used to investigate collision induced dissociation (CID) and rotational-vibrational energy transfer for Ar + [Ca(urea)](2+) collisions. For the picosecond time-domain of the simulations, both neutral loss and Coulomb explosion reactions were found and the differences in their mechanisms elucidated. The loss of neutral urea subsequent to collision with Ar occurs via a shattering mechanism, while the formation of two singly-charged cations follows statistical (or almost statistical) dynamics. Vibrational-rotational energy transfer efficiencies obtained for trajectories that do not dissociate during the trajectory integration were used in conjunction with RRKM rate constants to approximate dissociation pathways assuming complete intramolecular vibrational energy redistribution (IVR) and statistical dynamics. This statistical limit predicts, as expected, that at long time the most stable species on the potential energy surface (PES) dominate. These results, coupled with experimental CID from which both neutral loss and Coulomb explosion products were obtained, show that the gas phase dissociation of this ion occurs by multiple mechanisms leading to different products and that reactivity on the complicated PES is dynamically complex.
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Affiliation(s)
- Riccardo Spezia
- Université d'Evry Val d'Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, UMR 8587 CNRS-CEA-UEVE, Evry, France.
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Saccoccia F, Angelucci F, Boumis G, Brunori M, Miele AE, Williams DL, Bellelli A. On the mechanism and rate of gold incorporation into thiol-dependent flavoreductases. J Inorg Biochem 2012; 108:105-11. [PMID: 22166353 PMCID: PMC3396563 DOI: 10.1016/j.jinorgbio.2011.11.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 11/04/2011] [Accepted: 11/11/2011] [Indexed: 02/08/2023]
Abstract
NADPH-dependent flavoreductases are important drug targets. During their enzymatic cycle thiolates and selenolates that have high affinity for transition metals are generated. Auranofin (AF), a gold-containing compound, is classified by the World Health Organization as an antirheumatic agent and it is indicated as the scaffold for the development of new anticancer and antiparasitic drugs. AF inhibits selenocysteine-containing flavoreductases (thioredoxin reductase and thioredoxin glutathione reductase) more effectively than non Se-containing ones (glutathione reductase); this preference has been ascribed to the high affinity of selenium for gold. We solved the 3D structure of the Se-containing Thioredoxin Glutathione Reductase from the human parasite Schistosoma mansoni complexed with Au and our results challenge this view: we believe that the relative velocity of the reaction rather than the relative affinity, depends on the presence of Sec residues, which appear to dictate AF selectivity.
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Affiliation(s)
- Fulvio Saccoccia
- Department of Biochemical Sciences “A. Rossi Fanelli,” “Sapienza” University of Rome and Istituto Pasteur-Fondazione Cenci Bolognetti, P. Le Aldo Moro 5, 00185 Rome, Italy
| | - Francesco Angelucci
- Department of Biochemical Sciences “A. Rossi Fanelli,” “Sapienza” University of Rome and Istituto Pasteur-Fondazione Cenci Bolognetti, P. Le Aldo Moro 5, 00185 Rome, Italy
- Dept. of Basic and Applied Biology, University of L’Aquila, Via Vetoio snc. loc. Coppito, I-67010 L’Aquila, Italy
| | - Giovanna Boumis
- Department of Biochemical Sciences “A. Rossi Fanelli,” “Sapienza” University of Rome and Istituto Pasteur-Fondazione Cenci Bolognetti, P. Le Aldo Moro 5, 00185 Rome, Italy
| | - Maurizio Brunori
- Department of Biochemical Sciences “A. Rossi Fanelli,” “Sapienza” University of Rome and Istituto Pasteur-Fondazione Cenci Bolognetti, P. Le Aldo Moro 5, 00185 Rome, Italy
| | - Adriana E. Miele
- Department of Biochemical Sciences “A. Rossi Fanelli,” “Sapienza” University of Rome and Istituto Pasteur-Fondazione Cenci Bolognetti, P. Le Aldo Moro 5, 00185 Rome, Italy
| | - David L. Williams
- Department of Immunology/Microbiology, Rush University Medical Center, Chicago, IL, USA
| | - Andrea Bellelli
- Department of Biochemical Sciences “A. Rossi Fanelli,” “Sapienza” University of Rome and Istituto Pasteur-Fondazione Cenci Bolognetti, P. Le Aldo Moro 5, 00185 Rome, Italy
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18
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Quantum chemical studies on the role of water microsolvation in interactions between group 12 metal species (Hg2+, Cd2+, and Zn2+) and neutral and deprotonated cysteines. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-0975-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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19
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Byun BJ, Kang YK. Conformational preferences and pK(a) value of selenocysteine residue. Biopolymers 2011; 95:345-53. [PMID: 21213257 DOI: 10.1002/bip.21581] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Revised: 12/20/2010] [Accepted: 12/22/2010] [Indexed: 12/25/2022]
Abstract
The conformational preferences of the L-selenocysteine (Sec) dipeptides with selenol and selenolate groups (Ac-Sec-NHMe and Ac-Sec(-) -NHMe, respectively) and the apparent (i.e., macroscopic) pK(a) value of the Sec residue have been studied using the dispersion-corrected density functionals M06-2X and B2PLYP-D with the implicit solvation method in the gas phase and in water. In the gas phase, the backbone-to-backbone and/or side chain-to-backbone hydrogen bonds are found to contribute in stabilizing the most preferred conformations for the Sec and Sec(-) residues, as seen for the Cys and Cys(-) residues. However, the polyproline II-like conformations prevail over the conformations with the backbone-to-backbone hydrogen bonds in water because of the weakened hydrogen bonds by the favorable direct interactions between the backbone CO and HN groups and water molecules. The Sec and Sec(-) residues are found to adopt more various conformations than the Cys and Cys(-) residues in water, although the most preferred conformations of the neutral and/or anionic forms of the two residues are similar each other in the gas phase and in water. Using the statistically weighted free energies of the Sec and Sec(-) dipeptides in the gas phase and their solvation free energies, the pK(a) value of the Sec residue is estimated to be 5.47 at 25°C, which is in good agreement with the experimental value of 5.43 ± 0.02. It is found that the lower pK(a) value of the selenol side chain for the Sec residue by ∼3 units than the thiol side chain for the Cys residue is ascribed to the higher gas-phase acidity of the Sec residue.
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Affiliation(s)
- Byung Jin Byun
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
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20
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Jeanvoine Y, Spezia R. Cu2+ binding chalcogen–chalcogen bridges: A problematic case for DFT. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Armentrout PB, Armentrout EI, Clark AA, Cooper TE, Stennett EMS, Carl DR. An Experimental and Theoretical Study of Alkali Metal Cation Interactions with Cysteine. J Phys Chem B 2010; 114:3927-37. [DOI: 10.1021/jp911219u] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- P. B. Armentrout
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, Utah
| | - Erin I. Armentrout
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, Utah
| | - Amy A. Clark
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, Utah
| | - Theresa E. Cooper
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, Utah
| | - Elana M. S. Stennett
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, Utah
| | - Damon R. Carl
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, Utah
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22
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Pesonen H, Aksela R, Laasonen K. Density Functional Complexation Study of Metal Ions with Cysteine. J Phys Chem A 2009; 114:466-73. [DOI: 10.1021/jp905733d] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Henna Pesonen
- Department of Chemistry, PO Box 3000, FIN-90014 University of Oulu, Finland, and Kemira Oyj, Espoo Research Centre, PO Box 44, FIN-02271 Espoo, Finland
| | - Reijo Aksela
- Department of Chemistry, PO Box 3000, FIN-90014 University of Oulu, Finland, and Kemira Oyj, Espoo Research Centre, PO Box 44, FIN-02271 Espoo, Finland
| | - Kari Laasonen
- Department of Chemistry, PO Box 3000, FIN-90014 University of Oulu, Finland, and Kemira Oyj, Espoo Research Centre, PO Box 44, FIN-02271 Espoo, Finland
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23
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Dudev T, Lim C. Metal-Binding Affinity and Selectivity of Nonstandard Natural Amino Acid Residues from DFT/CDM Calculations. J Phys Chem B 2009; 113:11754-64. [DOI: 10.1021/jp904249s] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Todor Dudev
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, and the Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, and the Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
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24
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Constantino E, Rimola A, Sodupe M, Rodríguez-Santiago L. Coordination of (Glycyl)nglycine (n = 1−3) to Co+ and Co2+. J Phys Chem A 2009; 113:8883-92. [DOI: 10.1021/jp901179t] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Erika Constantino
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
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25
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Jeanvoine Y, Spezia R. Mn2+-, Fe2+-, Co2+-, Ni2+-, Cu2+-, and Zn2+-Binding Chalcogen−Chalcogen Bridges: A Compared MP2 and B3LYP Study. J Phys Chem A 2009; 113:7878-87. [DOI: 10.1021/jp811460f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Yannick Jeanvoine
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, UMR 8587 CNRS, Université d’Evry Val d’Essonne, Bd F. Mitterrand, 91025 Evry Cedex, France
| | - Riccardo Spezia
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, UMR 8587 CNRS, Université d’Evry Val d’Essonne, Bd F. Mitterrand, 91025 Evry Cedex, France
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26
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Constantino E, Tortajada J, Sodupe M, Rodríguez-Santiago L. Coordination Properties of Lysine Interacting with Co(I) and Co(II). A Theoretical and Mass Spectrometry Study. J Phys Chem A 2008; 112:12385-92. [DOI: 10.1021/jp805764y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- E. Constantino
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain, and Laboratoire Analyse et Modélisation pour l’Analyse et l’Environnement, CNRS UMR 8587, Université d’Evry-Val-d’Essonne, Boulevard François Mitterrand, 91025 Evry Cedex, France
| | - J. Tortajada
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain, and Laboratoire Analyse et Modélisation pour l’Analyse et l’Environnement, CNRS UMR 8587, Université d’Evry-Val-d’Essonne, Boulevard François Mitterrand, 91025 Evry Cedex, France
| | - M. Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain, and Laboratoire Analyse et Modélisation pour l’Analyse et l’Environnement, CNRS UMR 8587, Université d’Evry-Val-d’Essonne, Boulevard François Mitterrand, 91025 Evry Cedex, France
| | - L. Rodríguez-Santiago
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain, and Laboratoire Analyse et Modélisation pour l’Analyse et l’Environnement, CNRS UMR 8587, Université d’Evry-Val-d’Essonne, Boulevard François Mitterrand, 91025 Evry Cedex, France
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27
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Spezia R, Bresson C, Auwer CD, Gaigeot MP. Solvation of Co(III)-Cysteinato Complexes in Water: A DFT-based Molecular Dynamics Study. J Phys Chem B 2008; 112:6490-9. [DOI: 10.1021/jp075774h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Riccardo Spezia
- Laboratoire Analyse et Modelisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, UMR-CNRS 8587, 91025 Evry Cedex, CEA Saclay, DEN/DPC/SECR/LSRM, 91191 Gif sur Yvette, France, CEA Marcoule, DEN/DRCP/SCPS, 3017 Bagnols sur Ceze, France, and Laboratoire de Physique Théorique de la Matiere Condensée LPTMC UMR-CNRS 7600, Université P/M Curie, 75052 Paris, France
| | - Carole Bresson
- Laboratoire Analyse et Modelisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, UMR-CNRS 8587, 91025 Evry Cedex, CEA Saclay, DEN/DPC/SECR/LSRM, 91191 Gif sur Yvette, France, CEA Marcoule, DEN/DRCP/SCPS, 3017 Bagnols sur Ceze, France, and Laboratoire de Physique Théorique de la Matiere Condensée LPTMC UMR-CNRS 7600, Université P/M Curie, 75052 Paris, France
| | - Christophe Den Auwer
- Laboratoire Analyse et Modelisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, UMR-CNRS 8587, 91025 Evry Cedex, CEA Saclay, DEN/DPC/SECR/LSRM, 91191 Gif sur Yvette, France, CEA Marcoule, DEN/DRCP/SCPS, 3017 Bagnols sur Ceze, France, and Laboratoire de Physique Théorique de la Matiere Condensée LPTMC UMR-CNRS 7600, Université P/M Curie, 75052 Paris, France
| | - Marie-Pierre Gaigeot
- Laboratoire Analyse et Modelisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, UMR-CNRS 8587, 91025 Evry Cedex, CEA Saclay, DEN/DPC/SECR/LSRM, 91191 Gif sur Yvette, France, CEA Marcoule, DEN/DRCP/SCPS, 3017 Bagnols sur Ceze, France, and Laboratoire de Physique Théorique de la Matiere Condensée LPTMC UMR-CNRS 7600, Université P/M Curie, 75052 Paris, France
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28
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Cardiano P, De Stefano C, Giuffrè O, Sammartano S. Thermodynamic and spectroscopic study for the interaction of dimethyltin(IV) with L–cysteine in aqueous solution. Biophys Chem 2008; 133:19-27. [DOI: 10.1016/j.bpc.2007.11.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Revised: 11/15/2007] [Accepted: 11/15/2007] [Indexed: 11/29/2022]
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29
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Trujillo C, Mó O, Yáñez M. A theoretical study of hydration effects on the prototropic tautomerism of selenouracils. Org Biomol Chem 2007; 5:3092-9. [PMID: 17878967 DOI: 10.1039/b708045j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The prototropic tautomerism of 2-, 4-selenouracil and 2,4-diselenouracil has been studied using density functional theory (DFT) methods, at the B3LYP/6-311 + G(3df,2p)//B3LYP/6-31G(d,p) level. The relative stability order of selenouracil tautomers does not resemble that of uracil tautomers, but it is similar to that of thiouracils, even though the energy gaps between the different tautomers of selenouracils are smaller than for thiouracils. The tautomerism activation barriers are high enough as to conclude that only the oxo-selenone or the diselenone structures should be found in the gas phase. The specific interaction with one water molecule reduces these barriers by a half, but still the oxo-selenone form is always the most stable tautomer. The addition of a second water molecule has a relatively small effect, as well as bulk effects, evaluated by means of a continuum-polarized model. For isolated 2- and 4-selenouracils, the more favorable tautomerization process corresponds to a hydrogen transfer towards the selenium atom, the activation barriers for transfer towards the oxygen atom being much higher. This situation changes when specific and bulk effects are included, and the latter process becomes the more favorable one. For 2,4-diselenouracil the more favorable tautomerization, in the gas phase, corresponds to the H shift from N1 to the Se atom at C2, while solvation effects favor the transfer from N3 to the Se atom at C4.
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Affiliation(s)
- Cristina Trujillo
- Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
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30
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Buchmann W, Spezia R, Tournois G, Cartailler T, Tortajada J. Structures and fragmentations of cobalt(II)-cysteine complexes in the gas phase. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:517-26. [PMID: 17323419 DOI: 10.1002/jms.1183] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The electronebulization of a cobalt(II)/cysteine(Cys) mixture in water/methanol (50/50) produced mainly cobalt-cationized species. Three main groups of the Co-cationized species can be distinguished in the ESI-MS spectrum: (1) the cobalt complexes including the cysteine amino acid only (they can be singly charged, for example, [Co(Cys)n- H]+ with n = 1-3 or doubly charged such as [Co + (Cys)2]2+); (2) the cobalt complexes with methanol: [Co(CH3OH)n- H]+ with n = 1-3, [Co(CH3OH)4]2+; and (3) the complexes with the two different types of ligands: [Co(Cys)(CH3OH) - H]+. Only the singly charged complexes were observed. Collision-induced dissociation (CID) products of the [Co(Cys)2]2+, [Co(Cys)2 - H]+ and [Co(Cys) - H]+ complexes were studied as a function of the collision energy, and mechanisms for the dissociation reactions are proposed. These were supported by the results of deuterium labelling experiments and by density functional theory calculations. Since [Co(Cys) - H]+ was one of the main product ions obtained upon the CID of [Co(Cys)2]2+ and of [Co(Cys)2 - H]+ under low-energy conditions, the fragmentation pathways of [Co(Cys) - H]+ and the resulting product ion structures were studied in detail. The resulting product ion structures confirmed the high affinity of cobalt(II) for the sulfur atom of cysteine.
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Affiliation(s)
- William Buchmann
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement (LAMBE), Université d'Evry-Val d'Essonne, CNRS UMR 8587, Bât. Maupertuis, Bd. F. Mitterrand, 91025 Evry Cedex, France.
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31
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Bresson C, Spezia R, Esnouf S, Solari PL, Coantic S, Den Auwer C. A combined spectroscopic and theoretical approach to investigate structural properties of Co(ii)/Co(iii) tris-cysteinato complexes in aqueous medium. NEW J CHEM 2007. [DOI: 10.1039/b707055a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Spezia R, Duvail M, Vitorge P, Cartailler T, Tortajada J, Chillemi G, D'Angelo P, Gaigeot MP. A Coupled Car-Parrinello Molecular Dynamics and EXAFS Data Analysis Investigation of Aqueous Co2+. J Phys Chem A 2006; 110:13081-8. [PMID: 17134169 DOI: 10.1021/jp064688z] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We have studied the microscopic solvation structure of Co(2+) in liquid water by means of density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations and extended X-ray absorption fine structure (EXAFS) data analysis. The effect of the number of explicit water molecules in the simulation box on the first and second hydration shell structures has been considered. Classical molecular dynamics simulations, using an effective two-body potential for Co(2+)-water interactions, were also performed to show box size effects in a larger range. We have found that the number of explicit solvent molecules has a marginal role on the first solvation shell structural parameters, whereas larger boxes may be necessary to provide a better description of the second solvation shell. Car-Parrinello simulations were determined to provide a reliable description of structural and dynamical properties of Co(2+) in liquid water. In particular, they seem to describe both the first and second hydration shells correctly. The EXAFS signal was reconstructed from Car-Parrinello simulations. Good agreement between the theoretical and experimental signals was observed, thus strengthening the microscopic picture of the Co(2+) solvation properties obtained using first-principle simulations.
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Affiliation(s)
- Riccardo Spezia
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, UMR-CNRS 8587, Université d'Evry Val d'Essonne, Boulevard F. Mitterrand, 91025 Evry Cedex, France
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