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Firouzi R, Sharifi Ardani S. Description of heteroaromaticity on the basis of π-electron density anisotropy. Phys Chem Chem Phys 2014; 16:11538-48. [DOI: 10.1039/c4cp01125b] [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]
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202
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Ivanova B, Spiteller M. Solid-state UV-MALDI-MS assay of transition metal dithiocarbamate fungicides. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:1163-1177. [PMID: 23881588 DOI: 10.1007/s11356-013-1837-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Accepted: 05/17/2013] [Indexed: 06/02/2023]
Abstract
The determination of transition metal containing dithiocarbamate fungicides represents a challenging aspect of analytical object. They have a low stability, low solubility and stabilize versatile coordination monomers, dimers, disulfides and/or S-oxidized derivatives. Their diverse biological activities and agricultural implementation encompass plant prevention and crop protection against a variety of plants containing fungi and diseases of 400 pathogens and 70 cultures. Nonetheless, those dithiocarbamates (DTCs) are banned for agricultural use in Europe or have expiration at years 2016-2017 because of their highly toxic degradation products and/or metabolites, in particular ethylene thiourea; they found large-scale implementations in materials research and medicine. Despite the broad interdisciplinary of DTC application, due to the above reasons, they have received little attention in the rapidly growing field of analytical chemistry, and in particular, the analytical mass spectrometry. Therefore, the study reported on qualitative, quantitative and structural analysis of ten DTCs (1-10), using the matrix assisted laser desorption/ionization (UV-MALDI)-Orbitrap-mass spectrometry (MS) contributed considerably to the implementation of the method for environmental and foodstuffs monitoring. Its ultrahigh resolving power and capacity for direct solid-state analysis, at limited number of sample pretreatment steps, at concentration levels of analytes of up to femtogram per gram resulted to achievement of a highly precise analytical information for these non-trivial objects. The presented fully validated method and technique is based on the successful ionization of DTCs embedded in three novel organic salts (M1-M3). In this regard, the reported MS and the single-crystal X-ray diffraction data as well as the quantum chemical one are able to correlate the molecular structures in condense and in the gas phase. Despite the novelty of the fundamental methodological character of the research reported, the promising metrology contributed to the applied aspect of the UV-MALDI-MS as a robust analytical method for environmental and foodstuffs monitoring, which is tested on two commercially available crop protecting products such as Mancozeb® and Antracol®, respectively.
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Affiliation(s)
- Bojidarka Ivanova
- Lehrstuhl für Analytische Chemie, Institut für Umweltforschung, Fakultät für Chemie, Universität Dortmund, Otto-Hahn-Strasse 6, 44227, Dortmund, North Rhine-Westphalia, Germany,
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203
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Kalescky R, Kraka E, Cremer D. Description of aromaticity with the help of vibrational spectroscopy: anthracene and phenanthrene. J Phys Chem A 2013; 118:223-37. [PMID: 24308602 DOI: 10.1021/jp4092514] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new approach is presented to determine π-delocalization and the degree of aromaticity utilizing measured vibrational frequencies. For this purpose, a perturbation approach is used to derive vibrational force constants from experimental frequencies and calculated normal mode vectors. The latter are used to determine the local counterparts of the vibrational modes. Next, relative bond strength orders (RBSO) are obtained from the local stretching force constants, which provide reliable descriptors of CC and CH bond strengths. Finally, the RBSO values for CC bonds are used to establish a modified harmonic oscillator model and an aromatic delocalization index AI, which is split into a bond weakening (strengthening) and bond alternation part. In this way, benzene, naphthalene, anthracene, and phenanthrene are described with the help of vibrational spectroscopy as aromatic systems with a slight tendency of peripheral π-delocalization. The 6.8 kcal/mol larger stability of phenanthrene relative to anthracene predominantly (84%) results from its higher resonance energy, which is a direct consequence of the topology of ring annelation. Previous attempts to explain the higher stability of phenanthrene via a maximum electron density path between the bay H atoms are misleading in view of the properties of the electron density distribution in the bay region.
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Affiliation(s)
- Robert Kalescky
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
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204
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Ghiasi R. Theoretical study of structure, bonding, and aromaticity of borazyne and B-substituted borazynes. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2013. [DOI: 10.1134/s0036024413130220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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205
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Saito M, Akiba T, Kaneko M, Kawamura T, Abe M, Hada M, Minoura M. Synthesis, Structure, and Reactivity of Lewis Base Stabilized Plumbacyclopentadienylidenes. Chemistry 2013; 19:16946-53. [DOI: 10.1002/chem.201303672] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Indexed: 11/06/2022]
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206
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RETRACTED ARTICLE: Experimental and theoretical study of functionalized diterpenoids of salvinorin A type and molecular factors contributing to their selectivity to κ-opioid receptors. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0866-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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207
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Simultaneous quantitation of naturally occurring insecticides, acaricides, and piscicides in rapeseed oil by UV-MALDI mass spectrometry. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2013. [DOI: 10.1007/s11694-013-9161-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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208
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Manna AK, Pati SK. Stability and electronic structure of carbon capsules with superior gas storage properties: A theoretical study. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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209
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Tanak H, Toy M. Molecular structure, vibrational spectra, NLO and MEP analysis of bis[2-hydroxy-кO-N-(2-pyridyl)-1-naphthaldiminato-кN]zinc(II). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 115:145-153. [PMID: 23832222 DOI: 10.1016/j.saa.2013.06.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 05/28/2013] [Accepted: 06/04/2013] [Indexed: 06/02/2023]
Abstract
The molecular geometry and vibrational frequencies of bis[2-hydroxy-кO-N-(2-pyridyl)-1-naphthaldiminato-кN]zinc(II) in the ground state have been calculated by using the Hartree-Fock (HF) and density functional method (B3LYP) with 6-311G(d,p) basis set. The results of the optimized molecular structure are presented and compared with the experimental X-ray diffraction. The energetic and atomic charge behavior of the title compound in solvent media has been examined by applying the Onsager and the polarizable continuum model. To investigate second order nonlinear optical properties of the title compound, the electric dipole (μ), linear polarizability (α) and first-order hyperpolarizability (β) were computed using the density functional B3LYP and CAM-B3LYP methods with the 6-31+G(d) basis set. According to our calculations, the title compound exhibits nonzero (β) value revealing second order NLO behavior. In addition, DFT calculations of the title compound, molecular electrostatic potential (MEP), frontier molecular orbitals, and thermodynamic properties were performed at B3LYP/6-311G(d,p) level of theory.
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Affiliation(s)
- Hasan Tanak
- Department of Physics, Faculty of Arts and Sciences, Amasya University, 05100 Amasya, Turkey.
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210
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Changes in ligating abilities of the singlet and triplet states of normal, abnormal and remote N-heterocyclic carbenes depending on their aromaticities. J Mol Model 2013; 19:5327-41. [DOI: 10.1007/s00894-013-2027-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 10/01/2013] [Indexed: 10/26/2022]
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211
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Role of substituents on the reactivity and electron density profile of diimine ligands: A density functional theory based study. J CHEM SCI 2013. [DOI: 10.1007/s12039-013-0469-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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212
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Ivanova B, Spiteller M. Raman Spectroscopic and Mass Spectrometric Determination of Aflatoxins. FOOD ANAL METHOD 2013. [DOI: 10.1007/s12161-013-9701-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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213
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The comparative study on interactions between ionic liquid and CO2/SO2 by a hybrid density functional approach in the gas phase. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.06.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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214
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215
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Li Q, Zheng J, Tan H, Li X, Chen G, Jia Z. Unique kinase catalytic mechanism of AceK with a single magnesium ion. PLoS One 2013; 8:e72048. [PMID: 23977203 PMCID: PMC3747045 DOI: 10.1371/journal.pone.0072048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 07/06/2013] [Indexed: 11/26/2022] Open
Abstract
Isocitrate dehydrogenase kinase/phosphatase (AceK) is the founding member of the protein phosphorylation system in prokaryotes. Based on the novel and unique structural characteristics of AceK recently uncovered, we sought to understand its kinase reaction mechanism, along with other features involved in the phosphotransfer process. Herein we report density functional theory QM calculations of the mechanism of the phosphotransfer reaction catalysed by AceK. The transition states located by the QM calculations indicate that the phosphorylation reaction, catalysed by AceK, follows a dissociative mechanism with Asp457 serving as the catalytic base to accept the proton delivered by the substrate. Our results also revealed that AceK prefers a single Mg2+-containing active site in the phosphotransfer reaction. The catalytic roles of conserved residues in the active site are discussed.
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Affiliation(s)
- Quanjie Li
- College of Chemistry, Beijing Normal University, Beijing, People’s Republic of China
| | - Jimin Zheng
- College of Chemistry, Beijing Normal University, Beijing, People’s Republic of China
| | - Hongwei Tan
- College of Chemistry, Beijing Normal University, Beijing, People’s Republic of China
- * E-mail: (HT); (GC)
| | - Xichen Li
- College of Chemistry, Beijing Normal University, Beijing, People’s Republic of China
| | - Guangju Chen
- College of Chemistry, Beijing Normal University, Beijing, People’s Republic of China
- * E-mail: (HT); (GC)
| | - Zongchao Jia
- College of Chemistry, Beijing Normal University, Beijing, People’s Republic of China
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
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216
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Stabilization of anti-aromatic and strained five-membered rings with a transition metal. Nat Chem 2013; 5:698-703. [DOI: 10.1038/nchem.1690] [Citation(s) in RCA: 200] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 05/23/2013] [Indexed: 11/08/2022]
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217
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218
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219
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Jin JL, Li HB, Lu T, Duan YA, Geng Y, Wu Y, Su ZM. Density functional studies on photophysical properties and chemical reactivities of the triarylboranes: effect of the constraint of planarity. J Mol Model 2013; 19:3437-46. [PMID: 23708610 DOI: 10.1007/s00894-013-1845-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 04/01/2013] [Indexed: 10/26/2022]
Abstract
The geometric and electronic structures, absorption spectra, transporting properties, chemical reactivity indices and electrostatic potentials of the planar three-coordinate organoboron compounds 1-2 and twisted reference compound Mes(3)B, have been investigated by employing density functional theory (DFT) and conceptual DFT methods to shed light on the planarity effects on the photophysical properties and the chemical reactivity. The results show that the planar compounds 1-2 exhibit significantly lower HOMO level than Mes(3)B, owing to the stronger electronic induction effect of boron centers. This feature conspicuously induces a blue shifted absorption for 1, although 1 seemingly possesses more extended conjugation framework than Mes(3)B. Importantly, the reactivity strength of the boron atoms in 1-2 is much lower than that in Mes(3)B, despite the fact that the tri-coordinate boron centers of 1-2 are completely naked. The interesting and abnormal phenomenon is caused by the strong p-π electronic interactions, that is, the empty p-orbital of boron center is partly filled by π-electron of the neighbor carbon atoms in 1-2, which are confirmed by the analysis of Laplacian of the electron density and natural bond orbitals. Furthermore, the negative electrostatic potentials of the boron centers in 1-2 also interpret that they are not the most preferred sites for incoming nucleophiles. Moreover, it is also found that the planar compounds 1-2 can act as promising electron transporting materials since the internal reorganization energies for electron are really small.
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Affiliation(s)
- Jun-Ling Jin
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun, China
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220
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Peng D, Yang W. Fukui function and response function for nonlocal and fractional systems. J Chem Phys 2013; 138:184108. [DOI: 10.1063/1.4803101] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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221
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Düğdü E, Ünver Y, Ünlüer D, Tanak H, Sancak K, Köysal Y, Işık Ş. Synthesis, structural characterization and comparison of experimental and theoretical results by DFT level of molecular structure of 4-(4-methoxyphenethyl)-3,5-dimethyl-4H-1,2,4-triazole. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 108:329-337. [PMID: 23490260 DOI: 10.1016/j.saa.2012.09.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 09/06/2012] [Accepted: 09/20/2012] [Indexed: 06/01/2023]
Abstract
4-(4-Methoxyphenethyl)-3,5-dimethyl-4H-1,2,4-triazole (3) was synthesized from the reaction of ethyl N'-acetylacetohydrazonate (1) with 2-(4-methoxyphenyl)ethanamine (2). The structure of the title compound 3 has been inferred through IR, (1)H/(13)C NMR, mass spectrometry, elemental analyses and combination of X-ray crystallography and theoretical methods. In addition to the molecular geometry from X-ray determination, the molecular geometry and vibrational frequencies of the title compound 3 in the ground state, were calculated using the density functional method (B3LYP) with the 6-31G(d) basis set. The calculated results show that the optimized geometry can well reproduce the crystal structure and the theoretical vibrational frequencies show good agreement with experimental values. The nonlinear optical properties are also addressed theoretically. The predicted nonlinear optical properties of 3 are greater than ones of urea. In addition, DFT calculations of molecular electrostatic potentials and frontier molecular orbitals of the title compound were carried out at the B3LYP/6-31G(d) level of theory.
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Affiliation(s)
- Esra Düğdü
- Department of Chemistry, Faculty of Sciences, Karadeniz Technical University, 61080 Trabzon, Turkey
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222
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Ivanova B, Spiteller M. A novel UV-MALDI-MS analytical approach for determination of halogenated phenyl-containing pesticides. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2013; 91:86-95. [PMID: 23453143 DOI: 10.1016/j.ecoenv.2013.01.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Revised: 01/12/2013] [Accepted: 01/16/2013] [Indexed: 06/01/2023]
Abstract
The paper highlighted the capability of the UV-MALDI mass spectrometry, employing the Orbitrap analyzer for solid-state assay of halogenated phenyl-pesticides in mixtures. It is successfully applied for the analysis of eighteen (1)-(18) molecular objects of Fenarimol (1) type and their condensation products (P5)-(P12). The full method and technique validation is performed using the dried droplet sample preparation technique on embedded analytes in novel organic matrix crystals of N-(1H-benzoimidazol-2-yl)-guanidine (M4) and (E)-phenyl-2-pyridyl ketone oxime (M5), resulting to successful ionization of the analytes. Since the sampling technique in the UV-MALDI method is a key step in the overall process impacting significantly the metrology through the reproducibility of the data, the crystallization of M4, M5 and matrix-analyte in situ morphology of the samples is controlled by single crystal X-ray diffraction. The achieved promising metrology of LODs, of 0.46ngkg(-1) (1.53ngkg(-1) LOQs), is several orders of magnitude lower than the reported ecotoxicological effect values of studied pesticides. It is confirmed by the partial validated protocol based on ESI-MS. Inasmuch that LC-MS/MS is a method of choice for foodstuffs monitoring of organic contaminations, due to its routine quantitative analytical procedures, it is often characterized with the difficulties of the chromatographic separation of the closely structured analytes at a large scale of experimental conditions, complex multi-step sampling pretreatments, which inevitably alert the variables through the systematic and random errors. In this respect, notwithstanding the complex quantitative UV-MALDI-Orbitrap-MS procedure, conceptually different from the LC-MS/MS one, its high resolving power, capability for achieving meaningful analytical qualitative, quantitative and structural information of low-molecular weight analytes, its instrumental and sampling operation flexibility, applicable for a large scale of foodstuff matrices, and operating at the analyte concentrations of up to fgg(-1) make UV-MALDI-Orbitrap-MS a perspective method of choice for an extensive implementation in the foodstuffs monitoring practice for control of the most essential task related to the assessment of the human health risks from environmental and foodstuff contaminations.
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Affiliation(s)
- Bojidarka Ivanova
- Lehrstuhl für Analytische Chemie, Institut für Umweltforschung, Fakultät für Chemie, Universität Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Nordrhein-Westfalen, Deutschland, Germany.
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223
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Alonso M, Geerlings P, De Proft F. Conformational Control in [22]- and [24]Pentaphyrins(1.1.1.1.1) by Meso Substituents and their N-Fusion Reaction. J Org Chem 2013; 78:4419-31. [DOI: 10.1021/jo4003823] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Mercedes Alonso
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels,
Belgium
| | - Paul Geerlings
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels,
Belgium
| | - Frank De Proft
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels,
Belgium
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224
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Fias S, Boisdenghien Z, Stuyver T, Audiffred M, Merino G, Geerlings P, de Proft F. Analysis of Aromaticity in Planar Metal Systems using the Linear Response Kernel. J Phys Chem A 2013; 117:3556-60. [DOI: 10.1021/jp401760j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stijn Fias
- General Chemistry, Free University of Brussels (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
| | - Zino Boisdenghien
- General Chemistry, Free University of Brussels (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
| | - Thijs Stuyver
- General Chemistry, Free University of Brussels (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
| | - Martha Audiffred
- Departamento de Física Aplicada, Centro de Investigación y de Estudios Avanzados, Unidad Mérida, Km. 6 Antigua Carretera a Progreso, Apdo.
Postal 73, Cordemex, 97310, Mérida, Yuc., México
| | - Gabriel Merino
- Departamento de Física Aplicada, Centro de Investigación y de Estudios Avanzados, Unidad Mérida, Km. 6 Antigua Carretera a Progreso, Apdo.
Postal 73, Cordemex, 97310, Mérida, Yuc., México
| | - Paul Geerlings
- General Chemistry, Free University of Brussels (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
| | - Frank de Proft
- General Chemistry, Free University of Brussels (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
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225
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Koparir M, Orek C, Koparir P, Sarac K. Synthesis, experimental, theoretical characterization and biological activities of 4-ethyl-5-(2-hydroxyphenyl)-2H-1,2,4-triazole-3(4H)-thione. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 105:522-531. [PMID: 23352922 DOI: 10.1016/j.saa.2012.12.052] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 12/10/2012] [Accepted: 12/14/2012] [Indexed: 06/01/2023]
Abstract
This work presents the characterization of 4-ethyl-5-(2-hydroxyphenyl)-2H-1,2,4-triazole-3(4H)-thione (III) by quantum chemical calculations and spectral techniques. The molecular geometry, vibrational frequencies and gauge including atomic orbital (GIAO) (1)H and (13)C NMR chemical shift values of III in the ground state have been calculated using the density functional method (B3LYP) with the 6-31G(d) basis set. The calculated results show that the optimized geometry can well reproduce the crystal structure, and the theoretical vibrational frequencies and chemical shift values show good agreement with experimental values. To determine conformational flexibility, the molecular energy profile of the title compound was obtained by DFT calculations with respect to the selected torsion angle, which was varied from -180° to +180° in steps of 10°. The energetic behavior of III in solvent media was examined using the B3LYP method with the 6-31G(d) basis set by applying the Onsager and the polarizable continuum model (PCM). The predicted nonlinear optical properties of III are greater than ones of urea. In addition, DFT calculations of molecular electrostatic potentials and frontier molecular orbitals of III were carried out at the B3LYP/6-31G(d) level of theory. The title compound was screened for antibacterial, antifungal and antioxidant activities.
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Affiliation(s)
- Metin Koparir
- Firat University, Faculty of Science, Department of Chemistry, 23119 Elazig, Turkey.
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226
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Substituted benzo[i]phenanthridines as promising topoisomerase-I non-camptothecin targeting agents: an experimental and theoretical study. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0515-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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227
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228
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Fias S, Geerlings P, Ayers P, De Proft F. σ, π aromaticity and anti-aromaticity as retrieved by the linear response kernel. Phys Chem Chem Phys 2013; 15:2882-9. [PMID: 23337925 DOI: 10.1039/c2cp43612d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The chemical importance of the linear response kernel from conceptual Density Functional Theory (DFT) is investigated for some σ and π aromatic and anti-aromatic systems. The effect of the ring size is studied by looking at some well known aromatic and anti-aromatic molecules of different sizes, showing that the linear response is capable of correctly classifying and quantifying the aromaticity for five- to eight-membered aromatic and anti-aromatic molecules. The splitting of the linear response in σ and π contributions is introduced and its significance is illustrated using some σ-aromatic molecules. The linear response also correctly predicts the aromatic transition states of the Diels-Alder reaction and the acetylene trimerisation and shows the expected behavior along the reaction coordinate, proving that the method is accurate not only at the minimum of the potential energy surface, but also in non-equilibrium states. Finally, the reason for the close correlation between the linear response and the Para Delocalisation Index (PDI), found in previous and the present study, is proven mathematically. These results show the linear response to be a reliable DFT-index to probe the σ and π aromaticity or anti-aromaticity of a broad range of molecules.
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Affiliation(s)
- Stijn Fias
- General Chemistry, Free University of Brussels, Pleinlaan 2, B-1050 Brussels, Belgium.
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229
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Inkaya E, Dinçer M, Ekici O, Cukurovali A. 1-(3-methyl-3-mesityl)-cyclobutyl-2-(5-pyridin-4-yl-2H-[1,2,4]triazol-3-ylsulfanyl)-ethanone: X-ray structure, spectroscopic characterization and DFT studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 101:218-227. [PMID: 23103463 DOI: 10.1016/j.saa.2012.09.091] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 09/08/2012] [Accepted: 09/14/2012] [Indexed: 06/01/2023]
Abstract
The triazole compound 1-(3-Methyl-3-mesityl)-cyclobutyl-2-(5-pyridin-4-yl-2H-[1,2,4]triazol-3-ylsulfanyl)-ethanone, (C23H26N4OS), was characterized by X-ray single crystal diffraction technique, IR NMR spectroscopy and quantum chemical computational methods as both experimental and theoretically. The compound crystallizes in the monoclinic space group P2(1)/c with Z=4. The molecular geometry was also optimized using density functional theory (DFT/B3LYP) method with the 6-311G(d,p) basis set in ground state and compared with the experimental data. The computed vibrational frequencies are used to determine the types of molecular motions associated with each of the experimental bands observed. The results of the calculations were applied to simulate spectra of the title compound, which show excellent agreement with observed spectra. Data of the title compound display significant structure correlation and provide the basis for future design of efficient materials having the derivatives of 1,2,4-triazole. From the optimized geometry of the molecule, vibrational frequencies, gauge-independent atomic orbital (GIAO) 1H and 13C NMR chemical shift values, molecular electrostatic potential (MEP) distribution, non-linear optical properties and frontier molecular orbitals (FMOs) of the title compound were performed at B3LYP/6-311G(d,p). On the basis of theoretical vibrational analyses, the thermodynamic properties (standard heat capacities, standard entropies, and standard enthalpy changes) of the title compound at different temperatures have been calculated, revealing the correlations between Cp,m0, Sm0, ΔHm0 and temperatures. The predicted non-linear optical properties of the title compound are much greater than those of urea. Data of the title compound display significant structure-correlation and provide the basis for future design of efficient materials having the derivatives of 1,2,4-triazole.
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Affiliation(s)
- Ersin Inkaya
- Department of Physics, Faculty of Arts and Sciences, Ondokuz Mayıs University, 55139 Kurupelit, Samsun, Turkey.
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230
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Tognetti V, Morell C, Ayers PW, Joubert L, Chermette H. A proposal for an extended dual descriptor: a possible solution when Frontier Molecular Orbital Theory fails. Phys Chem Chem Phys 2013; 15:14465-75. [DOI: 10.1039/c3cp51169c] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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231
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Mitra T, Das J, Maji M, Das R, Das UK, Chattaraj PK, Basak A. A one-pot Garratt–Braverman cyclization and Scholl oxidation route to acene–helicene hybrids. RSC Adv 2013. [DOI: 10.1039/c3ra42696c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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232
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Mala'bi T, Pogodin S, Cohen S, Agranat I. Reversible Friedel–Crafts acyl rearrangements of planar polycyclic aromatic ketones: dibenzofluorenones. RSC Adv 2013. [DOI: 10.1039/c3ra43483d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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233
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Synthesis, characterization, crystal structure and theoretical approach of (E)-2-[(3-carboxylphenylimino)methylene]phenoxyacetic acid. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2012.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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234
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Ivanova B, Spiteller M. Organosilver(i/ii) catalyzed C–N coupling reactions – phenazines. Catal Sci Technol 2013. [DOI: 10.1039/c3cy20798f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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235
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Nataraj A, Balachandran V, Karthick T. Molecular orbital studies (hardness, chemical potential, electrophilicity, and first electron excitation), vibrational investigation and theoretical NBO analysis of 2-hydroxy-5-bromobenzaldehyde by density functional method. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2012.09.047] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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236
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FEREYDUNI EHSAN, KAMAEE MAHDI, SOLEYMANI REZA, AHMADI ROYA. THE SUBSTITUTION EFFECT ON THE AROMATICITY OF SOME N-PHENYLACETAMIDE DERIVATIVES: A DFT STUDY. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2012. [DOI: 10.1142/s0219633612500903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The relative aromaticity of some N-phenylacetamide (NPA) derivatives were investigated in which the NPA was substituted by NO2, CN, CF3, Br, Cl, F, H, CH3 , and NH2 groups at two meta and para positions. For this purpose, density functional theory calculations were applied at the B3LYP/6-31+G(d,p) level to calculate the aromaticity indices including nucleus independent chemical shift (NICS), harmonic oscillator model of aromaticity (HOMA) and harmonic oscillator model of electron delocalization (HOMED). The obtained results indicated that the aromaticity of derivatives decreased in the order of NO 2 > CN > CF 3 > Br > Cl > F > H > CH 3 > NH 2 for both meta and para positions. Furthermore, the resulting order was directly related to the electron withdrawing and electron releasing strengths of the substituents. Finally, it was found that all the aromaticity indices of have a good correlation with the Hammett constant.
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Affiliation(s)
- EHSAN FEREYDUNI
- Department of Chemistry, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | - MAHDI KAMAEE
- Department of Chemistry, Shahid Chamran University, Ahvaz, Iran
| | - REZA SOLEYMANI
- Young Researchers Club, Shahre-Rey Branch, Islamic Azad University, Tehran, Iran
| | - ROYA AHMADI
- Department of Chemistry, Shahre-Rey Branch, Islamic Azad University, Tehran, Iran
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237
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Karunakaran V, Balachandran V. FT-IR, FT-Raman spectra, NBO, HOMO-LUMO and thermodynamic functions of 4-chloro-3-nitrobenzaldehyde based on ab initio HF and DFT calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 98:229-239. [PMID: 22958978 DOI: 10.1016/j.saa.2012.08.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 07/27/2012] [Accepted: 08/07/2012] [Indexed: 06/01/2023]
Abstract
FT-IR (4000-400 cm(-1)) and FT-Raman (3500-100 cm(-1)) spectral measurements of 4-chloro-3-nitrobenzaldehyde have been done. Ab initio (HF/6-311+G(d,p)) and DFT (B3LYP/6-311+G(d,p)) calculations have been performed giving energies, optimized structures, harmonic vibrational frequencies, infrared intensities and Raman activities. A detailed interpretation of the FT-IR and FT-Raman spectra of 4-chloro-3-nitrobenzaldehyde are reported on the basis of the calculated potential energy distribution. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The HOMO and LUMO energy gap reveals that the energy gap reflects the chemical activity of the molecule. The thermodynamic functions of the title compound have been performed by HF/6-311+G(d,p) and B3LYP/6-311+G(d,p). The observed and calculated wave numbers are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed spectra. Thermodynamic functions were calculated using vibrational wave numbers for different temperatures.
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Affiliation(s)
- V Karunakaran
- Research Department of Physics, Government Arts College, Ariyalur 621 713, India
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238
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Putz MV, Putz AM. DFT Chemical Reactivity Driven by Biological Activity: Applications for the Toxicological Fate of Chlorinated PAHs. STRUCTURE AND BONDING 2012. [DOI: 10.1007/978-3-642-32750-6_6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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239
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İnkaya E, Dinçer M, Korkusuz E, Yıldırım İ, Büyükgüngör O. Synthesis, spectroscopic characterization and quantum chemical computational studies on 1-acetyl-3,5-di(4-methylphenyl)-1H-pyrazole. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.06.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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240
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Orek C, Koparir P, Koparir M. N-cyclohexyl-2-[5-(4-pyridyl)-4-(p-tolyl)-4H-1,2,4-triazol-3-ylsulfanyl]-acetamide dihydrate: synthesis, experimental, theoretical characterization and biological activities. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 97:923-34. [PMID: 22906969 DOI: 10.1016/j.saa.2012.07.082] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 07/16/2012] [Accepted: 07/23/2012] [Indexed: 05/17/2023]
Abstract
The triazol compound N-cyclohexyl-2-[5-(4-pyridyl)-4-(p-tolyl)-4H-1,2,4-triazol-3-ylsulfanyl]-acetamide dihydrate has been synthesized and characterized by (1)H NMR, (13)C NMR, IR, and X-ray single-crystal determination. The molecular geometry, vibrational frequencies and gauge including atomic orbital (GIAO) (1)H and (13)C NMR chemical shift values of III in the ground state have been calculated using the density functional method (B3LYP) with the 6-31G(d) basis set. The calculated results show that the optimized geometry can well reproduce the crystal structure, and the theoretical vibrational frequencies and chemical shift values show good agreement with experimental values. The energetic behavior of III in solvent media was examined using the B3LYP method with the 6-31G(d) basis set by applying the Onsager and the polarizable continuum model (PCM). The predicted nonlinear optical properties of III are greater than ones of urea. In addition, DFT calculations of molecular electrostatic potentials, frontier molecular orbitals and thermodynamic properties of III were carried out at the B3LYP/6-31G(d) level of theory. The title compound was screened for antibacterial, antifungal and antioxidant activities.
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Affiliation(s)
- Cahit Orek
- Department of Chemistry, Faculty of Science, Firat University, 23119 Elazig, Turkey
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241
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242
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Taxak N, Dixit VA, Bharatam PV. Density functional study on the cytochrome-mediated S-oxidation: identification of crucial reactive intermediate on the metabolic path of thiazolidinediones. J Phys Chem A 2012; 116:10441-50. [PMID: 23025570 DOI: 10.1021/jp308023g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
S-Oxidation is an important cytochrome P450 (CYP450)-catalyzed reaction, and the structural and energetic details of this process can only be studied by using quantum chemical methods. Thiazolidinedione (TZD) ring metabolism involving initial S-oxidation leads to the generation of reactive metabolites (RMs) and subsequent toxicity forcing the withdrawal of the glitazone class of drugs, thus, the study of the biochemical pathway of TZD ring metabolism is a subject of interest. The S-oxidation of the TZD ring and the formation of the isocyanate intermediate (ISC) was implicated as a possible pathway; however, there are several questions still unanswered in this biochemical pathway. The current study focuses on the CYP450-mediated S-oxidation, fate of the sulfoxide product (TZDSO), ring cleavage to ISC, and formation of nucleophilic adducts. The process of S-oxidation was explored by using Cpd I (iron(IV)-oxo porphyrin, to mimic CYP450) at TZVP/6-311+G(d) basis set. The barriers were calculated after incorporating dispersion and solvent corrections. The metabolic conversion from TZDSO to ISC (studied at B3LYP/6-311++G(2df,3pd)//B3LYP/6-31+G(d)) required a novel protonated intermediate, TZDSOH(+). The effect of higher basis sets (6-311+G(d,p), aug-cc-pvqz) on this conversion was studied. TZDSOH(+) was observed to be more reactive and thermodynamically accessible than ISC, indicating that TZDSOH(+) is the actual reactive intermediate leading to toxicity of the TZD class of compounds.
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Affiliation(s)
- Nikhil Taxak
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), S. A. S. Nagar (Mohali), 160 062 Punjab, India
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243
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Jayabharathi J, Thanikachalam V, Vennila M, Jayamoorthy K. Physico-chemical studies of new luminescent chemosensor for Cu2+. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 96:677-683. [PMID: 22885080 DOI: 10.1016/j.saa.2012.06.049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 05/30/2012] [Accepted: 06/06/2012] [Indexed: 06/01/2023]
Abstract
The spectroscopic properties of (E)-2-(2-hydroxybenzylideneamino)-3-phenylpropanoic acid (HBDPPA) has been studied in a series of different solvents. As revealed by absorbance, and emission results, the molecule undergoes fast excited-state intramolecular proton transfer (ESIPT) to yield emission of the corresponding tautomeric species. A large energy barrier for interconversion of the keto-enol rotamers in the ground and excited state have been predicted on the basis of DFT calculations and also supported by HOMO-LUMO energies, PES calculation, NLO and NBO analysis. Hyperpolarizability and octupolar and dipolar components ratio confirmed that HBDPPA can be used as optoelectronic materials. The ground state equilibrium and ESIPT process of HBDPPA are essentially unaffected by the nature of the solvent. Measurements of absorption solvatochromism have been interpreted with Marcus and Reichardt-Dimroth solvent functions to estimate the transition dipoles. Good correlation exists between absorption as well as fluorescence wavenumbers obtained by the multi-component linear regression employing the Taft and Catalan solvent parameters with the experimental values. The prepared Schiff base HBDPPA can be used as a new fluorescent sensor to detect the quantity of Cu(2+) ion in any sample solution depending on the relative intensity change.
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244
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İnkaya E, Dinçer M, Ekici Ö, Cukurovali A. N′-(2-methoxy-benzylidene)-N-[4-(3-methyl-3-phenyl-cyclobutyl)-thiazol-2-yl]-chloro-acetic hydrazide: X-ray structure, spectroscopic characterization and DFT studies. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.05.059] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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245
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Beyramabadi SA, Morsali A, Vahidi SH. DFT characterization of 1-acetylpiperazinyl-dithiocarbamate ligand and its transition metal complexes. J STRUCT CHEM+ 2012. [DOI: 10.1134/s0022476612040087] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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246
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Ivanova B, Spiteller M. Coordination ability of bradykinin with ZnII- and AgI-metal ions – Experimental and theoretical study. Inorganica Chim Acta 2012. [DOI: 10.1016/j.ica.2012.06.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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247
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Jayabharathi J, Thanikachalam V, Vennila M, Jayamoorthy K. Potential fluorescent chemosensor based on L-tryptophan derivative: DFT based ESIPT process. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 95:446-451. [PMID: 22580140 DOI: 10.1016/j.saa.2012.04.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 03/12/2012] [Accepted: 04/03/2012] [Indexed: 05/31/2023]
Abstract
The spectroscopic properties of (E)-2-(2-hydroxybenzylideneamino)-3-(1H-indol-3-yl) propanoic acid (HBDIPPA) has been studied in a series of different solvents. An excited state intramolecular proton transfer (ESIPT) process in hydroxy Schiff base has been studied using emission spectroscopy. DFT calculations on energy, HOMO-LUMO energies, MEP, dipole moment, charge distribution of the Schiff base derivative have been performed and discussed. The energy barrier for the interconversion of two rotamers is too high in the excited state than the ground state is shown by PES calculation. Positive values of laplacian ▿(2)ρ((rc)) (2.81) and electron density ρ((rc)) (0.22) are indicative of hydrogen bonds interactions. Absorption as well as fluorescence wavenumbers are correlated with Marcus and Reichardt-Dimroth solvent functions and also with Taft and Catalan solvent parameters. Schiff base HBDIPPA can be used as a new fluorescent sensor.
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Affiliation(s)
- Jayaraman Jayabharathi
- Department of Chemistry, Annamalai University, Annamalainagar, Tamilnadu 608 002, India.
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248
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Galabov B, Ilieva S, Koleva G, Allen WD, Schaefer III HF, von R. Schleyer P. Structure-reactivity relationships for aromatic molecules: electrostatic potentials at nuclei and electrophile affinity indices. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1112] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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249
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de Abreu L, López-Castillo A. Theoretical characterization of the BN and BP coronenes by IR, Raman, and UV-VIS spectra. J Chem Phys 2012; 137:044309. [PMID: 22852620 DOI: 10.1063/1.4737519] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Leandro de Abreu
- Departamento de Química, UFSCar, São Carlos, SP 13560-970, Brazil
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250
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Heptachlorepoxides: theoretical versus experimental study of the embedded samples in the matrixes of organic crystals. J INCL PHENOM MACRO 2012. [DOI: 10.1007/s10847-012-0213-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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