1
|
Jena NR. Manganese‐Coordinated Tyrosine Bio Materials for the Sensing of Reactive Oxygen Species. ChemistrySelect 2019. [DOI: 10.1002/slct.201900966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Nihar Ranjan Jena
- Discipline of Natural SciencesIndian Institute of Information Technology, Design and Manufacturing, Khamaria Jabalpur- 482005 India
| |
Collapse
|
2
|
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
| |
Collapse
|
3
|
Spezia R, Jeanvoine Y, Vuilleumier R. Developing polarizable potential for molecular dynamics of Cm(III)-carbonate complexes in liquid water. J Mol Model 2014; 20:2398. [DOI: 10.1007/s00894-014-2398-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 07/23/2014] [Indexed: 11/24/2022]
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Martelli F, Jeanvoine Y, Vercouter T, Beuchat C, Vuilleumier R, Spezia R. Hydration properties of lanthanoid(iii) carbonate complexes in liquid water determined by polarizable molecular dynamics simulations. Phys Chem Chem Phys 2014; 16:3693-705. [DOI: 10.1039/c3cp54001d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
6
|
Hummer AA, Rompel A. The use of X-ray absorption and synchrotron based micro-X-ray fluorescence spectroscopy to investigate anti-cancer metal compounds in vivo and in vitro. Metallomics 2013; 5:597-614. [PMID: 23558305 DOI: 10.1039/c3mt20261e] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
X-ray absorption spectroscopy (XAS) and micro-synchrotron based X-ray fluorescence (micro-SXRF) are element specific spectroscopic techniques and have been proven to be valuable tools for the investigation of changes in the chemical environment of metal centres. XAS allows the determination of the oxidation state, the coordination motif of the probed element, the identity and the number of adjacent atoms and the absorber-ligand distances. It is further applicable to nearly all types of samples independent of their actual physical state (solid, liquid, gaseous) down to μM concentrations. Micro-SXRF can provide information on the distribution and concentration of multiple elements within a sample simultaneously, allowing for the chemical state of several elements within subcellular compartments to be probed. Modern third generation synchrotrons offer the possibility to investigate the majority of the biologically relevant elements. The biological mode of action of metal-based compounds often involves interactions with target and/or transport molecules. The presence of reducing agents may also give rise to changes in the coordination sphere and/or the oxidation state. XAS and micro-SXRF are ideal techniques for investigating these issues. This tutorial review introduces the use of XAS and micro-SXRF techniques into the field of inorganic medicinal chemistry. The results obtained for platinum, ruthenium, gallium, gold and cobalt compounds within the last few years are presented.
Collapse
Affiliation(s)
- Alfred A Hummer
- Institut für Biophysikalische Chemie, Universität Wien, Althanstr. 14, 1090 Wien, Austria
| | | |
Collapse
|
7
|
Guo JJ, Wang W, Zhang YD, Yang L, Zhang SH, Zhang XQ. Solvothermal syntheses and structures of three clusters based on (1H-benzoimidazol-2-yl)-methanethiol. J COORD CHEM 2013. [DOI: 10.1080/00958972.2013.783907] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Jing Jing Guo
- a Key Laboratory of Nonferrous Metal Materials and Processing Technology, Ministry of Education, College of Chemistry and Bioengineering , Guilin University of Technology , Guilin , P.R. China
| | - Wei Wang
- a Key Laboratory of Nonferrous Metal Materials and Processing Technology, Ministry of Education, College of Chemistry and Bioengineering , Guilin University of Technology , Guilin , P.R. China
| | - Yi Dong Zhang
- a Key Laboratory of Nonferrous Metal Materials and Processing Technology, Ministry of Education, College of Chemistry and Bioengineering , Guilin University of Technology , Guilin , P.R. China
| | - Li Yang
- a Key Laboratory of Nonferrous Metal Materials and Processing Technology, Ministry of Education, College of Chemistry and Bioengineering , Guilin University of Technology , Guilin , P.R. China
| | - Shu Hua Zhang
- a Key Laboratory of Nonferrous Metal Materials and Processing Technology, Ministry of Education, College of Chemistry and Bioengineering , Guilin University of Technology , Guilin , P.R. China
| | - Xiu Qing Zhang
- a Key Laboratory of Nonferrous Metal Materials and Processing Technology, Ministry of Education, College of Chemistry and Bioengineering , Guilin University of Technology , Guilin , P.R. China
| |
Collapse
|
8
|
Tanzi L, Ramondo F, Guidoni L. Vibrational Spectra of Water Solutions of Azoles from QM/MM Calculations: Effects of Solvation. J Phys Chem A 2012; 116:10160-71. [DOI: 10.1021/jp3045059] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luana Tanzi
- Department of Physical
and Chemical Sciences, University of L’Aquila, Via Vetoio, I-67100
L’Aquila, Italy
| | - Fabio Ramondo
- Department of Physical
and Chemical Sciences, University of L’Aquila, Via Vetoio, I-67100
L’Aquila, Italy
| | - Leonardo Guidoni
- Department of Physical
and Chemical Sciences, University of L’Aquila, Via Vetoio, I-67100
L’Aquila, Italy
| |
Collapse
|
9
|
Bovi D, Mezzetti A, Vuilleumier R, Gaigeot MP, Chazallon B, Spezia R, Guidoni L. Environmental effects on vibrational properties of carotenoids: experiments and calculations on peridinin. Phys Chem Chem Phys 2011; 13:20954-64. [PMID: 21946923 DOI: 10.1039/c1cp21985e] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Carotenoids are employed in light-harvesting complexes of dinoflagellates with the two-fold aim to extend the spectral range of the antenna and to protect it from radiation damage. We have studied the effect of the environment on the vibrational properties of the carotenoid peridinin in different solvents by means of vibrational spectroscopies and QM/MM molecular dynamics simulations. Three prototypical solvents were considered: cyclohexane (an apolar/aprotic solvent), deuterated acetonitrile (a polar/aprotic solvent) and methanol (a polar/protic solvent). Thanks to effective normal mode analysis, we were able to assign the experimental Raman and IR bands and to clarify the effect of the solvent on band shifts. In the 1500-1650 cm(-1) region, seven vibrational modes of the polyene chain were identified and assigned to specific molecular vibrations. In the 1700-1800 cm(-1) region a strong progressive down-shift of the lactonic carbonyl frequency is observed passing from cyclohexane to methanol solutions. This has been rationalized here in terms of solvent polarity and solute-solvent hydrogen bond interactions. On the basis of our data we propose a classification of non-equivalent peridinins in the Peridinin-Chlorophyll-Proteins, light-harvesting complexes of dinoflagellates.
Collapse
Affiliation(s)
- Daniele Bovi
- Dipartimento di Fisica, Università di Roma LA SAPIENZA, Rome, Italy
| | | | | | | | | | | | | |
Collapse
|
10
|
Jónsson EÖ, Thygesen KS, Ulstrup J, Jacobsen KW. Ab Initio Calculations of the Electronic Properties of Polypyridine Transition Metal Complexes and Their Adsorption on Metal Surfaces in the Presence of Solvent and Counterions. J Phys Chem B 2011; 115:9410-6. [DOI: 10.1021/jp200893w] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- E. Ö. Jónsson
- CAMD, Department of Physics, Technical University of Denmark, DK - 2800 Kgs. Lyngby, Denmark
| | - K. S. Thygesen
- CAMD, Department of Physics, Technical University of Denmark, DK - 2800 Kgs. Lyngby, Denmark
| | - J. Ulstrup
- Department of Chemistry, Technical University of Denmark, DK - 2800 Kgs. Lyngby, Denmark
| | - K. W. Jacobsen
- CAMD, Department of Physics, Technical University of Denmark, DK - 2800 Kgs. Lyngby, Denmark
| |
Collapse
|
11
|
Terrier C, Vitorge P, Gaigeot MP, Spezia R, Vuilleumier R. Density functional theory based molecular dynamics study of hydration and electronic properties of aqueous La3+. J Chem Phys 2010; 133:044509. [DOI: 10.1063/1.3460813] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
12
|
Duvail M, Ruas A, Venault L, Moisy P, Guilbaud P. Molecular Dynamics Studies of Concentrated Binary Aqueous Solutions of Lanthanide Salts: Structures and Exchange Dynamics. Inorg Chem 2009; 49:519-30. [DOI: 10.1021/ic9017085] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Magali Duvail
- CEA, Nuclear Energy Division, RadioChemistry & Processes Department, F-30207 Bagnols sur Cèze, France
| | - Alexandre Ruas
- CEA, Nuclear Energy Division, RadioChemistry & Processes Department, F-30207 Bagnols sur Cèze, France
| | - Laurent Venault
- CEA, Nuclear Energy Division, RadioChemistry & Processes Department, F-30207 Bagnols sur Cèze, France
| | - Philippe Moisy
- CEA, Nuclear Energy Division, RadioChemistry & Processes Department, F-30207 Bagnols sur Cèze, France
| | - Philippe Guilbaud
- CEA, Nuclear Energy Division, RadioChemistry & Processes Department, F-30207 Bagnols sur Cèze, France
| |
Collapse
|
13
|
Chen L, Liu T, Ma C. Metal Complexation and Biodegradation of EDTA and S,S-EDDS: A Density Functional Theory Study. J Phys Chem A 2009; 114:443-54. [DOI: 10.1021/jp904296m] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Litao Chen
- State Key Laboratory Breeding Base for Green Chemistry Synthesis Technology, College of Chemical Engineering and Materials Science, Zhejiang University of Technology, Hangzhou 310014, People’s Republic of China
| | - Ting Liu
- State Key Laboratory Breeding Base for Green Chemistry Synthesis Technology, College of Chemical Engineering and Materials Science, Zhejiang University of Technology, Hangzhou 310014, People’s Republic of China
| | - Chun’an Ma
- State Key Laboratory Breeding Base for Green Chemistry Synthesis Technology, College of Chemical Engineering and Materials Science, Zhejiang University of Technology, Hangzhou 310014, People’s Republic of China
| |
Collapse
|
14
|
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
| |
Collapse
|
15
|
Tang E, Di Tommaso D, de Leeuw NH. Hydrogen transfer and hydration properties of HnPO43−n (n=0–3) in water studied by first principles molecular dynamics simulations. J Chem Phys 2009; 130:234502. [DOI: 10.1063/1.3143952] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
16
|
Duvail M, Vitorge P, Spezia R. Building a polarizable pair interaction potential for lanthanoids(III) in liquid water: A molecular dynamics study of structure and dynamics of the whole series. J Chem Phys 2009; 130:104501. [DOI: 10.1063/1.3081143] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|