Structure and stability of thioureate anions with water, DFT calculations

Structure and stability of thioureate anion with the water clusters CSNH₂NH⁻-(H₂O)_n = 1–7, are studied, using density functional theory. Molecular structures and the stability of the clusters are discussed based on the calculation results of the stable conformers and their relative energies. All the clusters are stable thermodynamically in gas phase with respect to separate monomers. The clusters are stabilized progressively with an increasing number of water molecules, as indicated by the increasing of the binding energies. The binding energies of CSNH₂NH⁻ and a water molecule are 14.34 and 16.36 kcal/mol for cis CSNH₂NH⁻ and trans CSNH₂NH⁻, respectively. As the reaction in aqueous solution progresses, the CS bond distance increases monotonically, indicating that the CS bond of the thioureate anion unit in the clusters is de-stabilized with an increasing number of water molecules.     

Obtaining thermochemical data by the extended kinetic method

A microcanonical analysis of the extended kinetic method is performed using statistical rate calculations based on orbiting transition state theory. The model systems simulate polydentate bases M which exhibit losses of entropy upon protonation of up to 35 kJ mol(-1) K(-1). It is shown that the correlations using the natural logarithm of the ratio of rate constants vs the proton affinity of the reference bases, at several effective temperatures, lead to correct proton affinity and protonation entropy of the base M of interest. A systematic underestimate of the latter quantity (by 5-15%), mainly due to the use of a linear rather than a polynomial curve fitting procedure, is noted, however. When considering experimental data, more severe underestimates are observed for the protonation entropies of polydentate bases (by 50-90%). The origins of these considerable discrepancies are beyond the limits of the present modeling and remain to be determined.     

A kinetic stability study of MN (MBe,Mg, Ca,Sr, and Ba)

This work describes a structure and kinetic stability study of some complexes with the general formula MN, where M are the alkaline earth metal atoms, Be, Mg, Ca, Sr, and Ba. A complex (A) with two points of attachment to the N₅ ring is the most energetically favored for all metals considered here. Except for Be, structure (B) containing a mono‐coordinated metal atom is a transition state corresponding to the metal atom transfer around the N₅ ring. Pyramidal structure (C) is kinetically unstable with the low isomerization barrier height, ranging from 0.9 to 6.7 kcal/mol. The dissociation barrier heights for the lowest energy isomers (A) are predicted to be 1.2–18.7 kcal/mol (Be to Ba), indicating that kinetic stability increases from lighter to heavier metal atoms. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Study of the inhibition of the corrosion of copper and zinc in HNO3 solution by electrochemical technique and quantum chemical calculations

The corrosion inhibition of copper and zinc in 0.1 M HNO₃ by 1,2,3,4-tetrazole (TTZ) and some of its derivatives has been analysed in a comparative study. Two experimental techniques have been used such as weight-loss and electrochemical polarization measurements. The results obtained reveal that the addition of these compounds reduces preferentially the corrosion of Cu rather than that of Zn. The adsorption of tetrazolic compounds on a copper surface was more favourable than their adsorption on a zinc surface. Moreover the inhibition efficiency calculated for copper was found to attain 95% in the presence of 1-phenyl-5-mercapto-1,2,3,4-tetrazole (PMT) while it remains constant at 1% for all compounds tested using zinc as electrode. Relationship between molecular structure and their inhibition efficiency was elucidated by quantum chemical calculations using the density functional theory (DFT).     

Evaluation of the protonation thermochemistry obtained by the extended kinetic method

An evaluation of the results obtained by the extended kinetic method for a series of representative bases is presented here. Analysis of the original experimental data is conducted using the orthogonal distance regression (ODR) statistical treatment. A comparison with the proton affinities and protonation entropies obtained from variable temperature equilibrium constant measurements demonstrate deviations, which may be ascribed to random and systematic errors. Considerable random errors are associated with the extended kinetic method if the number of reference bases and the range of effective temperatures are too low. It is also confirmed that large systematic errors on proton affinities and protonation entropies are obtained when large protonation entropy is associated with the considered system. It is, however, encouraging to note that the gas phase basicities obtained by the extended kinetic method are generally comparable to that obtained by other methods within a few kJ/mol.     

Configurational analysis of the natural product passifloricin A by quantum mechanical C NMR GIAO chemical shift calculations

Quantum chemical calculations at mPW1PW91 level, with full geometry optimization, using the 6-31g(d) basis set, and GIAO (gauge including atomic orbitals) ¹³C NMR chemical shifts using the 6-31g(d,p) basis set, are here utilized as a support to define the configurational features of the natural product passifloricin A, whose previously proposed relative configuration has been recently shown, by synthetic studies, to be incorrect. This study suggests that the relative stereostructure for passifloricin A corresponds to the δ-lactone of the (5R,7R,9S,11R)-tetrahydroxyhexacos-2-enoic acid.     

A study of vitamin A radical cation generated by chemical and radiolytic oxidation

Electron transfer reaction between vitamin A (1) and tris(p-bromophenyl)aminium hexachloroautimonate (2) in dichloromethane (DCM) has been investigated by means of UV-VIS absorption and ESR spectroscopy. The title radical cation formed in the reaction was characterized by a new absorption band around 600 nm and a singlet unresolved ESR spectrum with g factor of 2.0038-2.0039 and line width of 20 G. Further studies indicated that ESR pattern and parameters of the radical cation generated by 7-irradiation of 1 in CFCl3 matrix at 77 K are consistent with that resulted in the chemical oxidation in DCM at ambient temperature.     

Transition structures and reaction barriers in the styrene–acrylonitrile copolymerization system according to quantum mechanical calculations

The geometries and electronic properties of substrates, transition structures (TS), and product radicals in modeled elementary propagation reactions were studied for the styrene–acrylonitrile monomer system by use of quantum‐mechanical calculations: (DFT/B3‐LYP/6–31G(d), ROMP2/6–311+G(3df,2p)//DFT/B3‐LYP/6–31G(d), and DFT/B3‐LYP/6–311+G(3df,2p)//DFT/B3‐LYP/6–31G(d)) and for some parameters, the high‐level composite method G3 (Gaussian‐3, G3/MP2). Activation enthalpies (ΔH^act) and reaction enthalpies (ΔH_r) for modeled propagation reactions at 298.15 K were evaluated. The enthalpy of activation energy (ΔH^act, kJ/mol) for the investigated elementary reactions rises for the B3‐LYP calculation in the following order: (CH₃A?+S) < (CH₃A?+A) < (CH₃S?+A) < (CH₃S?+S). For three propagation reactions, (CH₃A?+A), (CH₃A?+S), and (CH₃S?+A), correlation between reaction enthalpy and enthalpy of activation suggests weak or negligible polar effects reflecting the Evans–Polanyi relation. However, from the electron affinities and ionization energies values data, it is not excluded that at least for [CH₃A?+S[b]] and [CH₃S?+A[b]] reactions, nucleophilic and electrophilic polar effects, respectively, can also be expected. The dependencies between TS geometries, electronic parameters, and enthalpic effects suggest the presence of a steric factor in all TS, including its exceptionally high contribution to the activation enthalpy for the CH₃S?+S addition. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 1827–1844, 2005     

Carbon‐iodide bond activation by cyclometalated Pt (II) complexes bearing tricyclohexylphosphine ligand: A comparative kinetic study and theoretical elucidation

Cyclometalated Pt (II) complexes [PtMe(C^N)(L)], in which C^N = deprotonated 2,2′‐bipyridine N‐oxide (Obpy), 1 , deprotonated 2‐phenylpyridine (ppy), 2 , deprotonated benzo [h] quinolone (bzq), 3 , and L = tricyclohexylphosphine (PCy₃) were prepared and fully characterized. By treatment of 1–3 with excess MeI, the thermodynamically favored Pt (IV) complexes cis‐[PtMe₂I(C^N)(PCy₃)] (C^N = Obpy, 1a ; ppy, 2a ; and bzq, 3a ) were obtained as the major products in which the incoming methyl and iodine groups adopted cis positions relative to each other. All the complexes were characterized by means of NMR spectroscopy while the absolute configuration of 1a was further determined by X‐ray crystal structure analysis. The reaction of methyl iodide with 1–3 were kinetically explored using UV–vis spectroscopy. On the basis of the kinetic data together with the time‐resolved NMR investigation, it was established that the oxidative addition reaction occurred through the classical S_N2 attack of Pt (II) center on the MeI reagent. Moreover, comparative kinetic studies demonstrated that the electronic and steric nature of either the cyclometalating ligands or the phosphine ligand influence the rate of reaction. Surprisingly, by extending the oxidative addition reaction time, very stable iodine‐bridged Pt (IV)‐Pt (IV) complexes [Pt₂Me₄(C^N)₂(μ‐I)₂] (C^N = Obpy, 1b ; ppy, 2b ; and bzq, 3b ) were obtained and isolated. In order to find a reasonable explanation for the observation, a DFT (density functional theory) computational analysis was undertaken and it was found that the results were consistent with the experimental findings.     

Reinvestigation into the ring‐opening process of monochloroethylene oxide by quantum chemical calculations

Density functional theory (DFT) computation with B3LYP/6‐31++G** has been performed for the ring‐opening process of monochloroethylene oxide. In this study, the energy changes of an isolated monochloroethylene oxide, an O‐protonated one and a Cl‐protonated one, were investigated with respect to the stretching of the C? O bond length. The increased energy in an O‐protonated system is fairly slow compared with that in a neutral system. In an O‐protonated system, rupturing of the C? O bond, in which the carbon atom in the bond binds to the chlorine atom, occurs more easily than another C? O bond rupture. This fact is in agreement with ideas accepted in organic chemistry. Intrinsic reaction coordinate (IRC) calculations were performed for the O‐protonated system, which gave the activation energy of the ring rupture as 3.89 kcal/mol. This also revealed that the production of an aldehyde occurred by a two‐step reaction, that is, the first ring‐opening process and following transfer of the chlorine atom. LMO wave functions were used to analyze the reaction mechanism. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Electronic structure of 1,3-dinitrobenzene radical anion: A multiconfigurational quantum chemical study

The structure of 1,3-dinitrobenzene radical anion in the doublet ground and lowest excited states was studied by ab initio multiconfiguration CASSCF methods. The results of calculations suggest the existence of one symmetrical and two asymmetrical structures of the radical anion. The energies of these structures were estimated. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2645–2647, December, 2005.     

草酰溴一价正离子(BrCO)+2几何构型及反应活性的DFT研究

用密度泛函方法BHandHIYP以6-311 G(d)和6-311 G(2df）为基组对草酰溴的一价正离子(BrCO)2^ 和中性分子(BrCO)2做了构象分析,结果表明,(BrCO)^ 2和(BrCO)2都具有平面反式和交叉式两种构象。交叉式构象存在超共轭现象。此外,对草酰溴离子、中性分子各解离通道初级反应的Gibbs自由能的计算,发现草酰溴离子C-C键解离通道的反应活性总体上大于中性分子,对该反应通道进一步做了反应机理研究,证实了热力学结论。     

A conformational study of hydroxylated isoflavones by vibrational spectroscopy coupled with DFT calculations

The conformational preferences of a series of hydroxylated isoflavones were studied by optical vibrational spectroscopy (FTIR and Raman) coupled with density functional theory (DFT) calculations. Special attention was paid to the effect of the hydroxyl substitution, due to the importance of this group in the biological activity of these systems. The isoflavones investigated – daidzein, genistein and formononetin – were shown to exist in distinct conformations in the solid state, namely regarding the orientation of the hydroxylic groups at C⁷ and within the catechol moiety, that are determinant factors for their conformational behaviour and antioxidant ability. In the light of the most stable conformers obtained for each molecule, a complete assignment of their experimental vibrational spectra was performed.     

Host-guest complexes of the Beer-Can-cryptand: prediction of ion selectivity by quantum chemical calculations XI

Abstract

Based on DFT calculations (B3LYP/LANL2DZp) and the application of model equations, as well as a comparison of M-N-donor length with an unstrained reference ([M(solvent)₆]ⁿ⁺), the selectivity of the alkali and alkaline earth cations (Li⁺ – Cs⁺ and Be²⁺ – Ba²⁺) for the recently synthesized cryptand bis-triazacyclononane tris-pyridyl N₉-azacryptand (Beer-Can) was investigated. The host can bind the alkali cation K⁺ best, followed by the alkaline earth cations Ca²⁺ and Sr²⁺, and by Na⁺ and Ba²⁺. This selectivity pattern is identical to the selectivity of the Lehn-type cryptand [phen.phen.phen], which suggests a similar cavity size. The good flexibility of the Beer-Can is provided by the aza-crown-like top and bottom of the “can,” and the pyridines on the “can-wall.”     

Comprehensive quantum chemical calculations and molecular docking analysis of uracil mustard by first principle

Uracil mustard belongs to the nitrogen mustard family and is primarily used in anticancer drugs. The research that follows, investigates many quantum chemical features such as the computation of global minimum energies with no negative wavenumber values using the Density Functional Theory (DFT) with Becke three functional and 6-311G (d, p)/6–311++G (d, p) basis sets. All the vibrational modes have been calibrated and justified in comparison to their experimental counterparts. Mustard's polarizability and hyperpolarizability components, Natural Bond Analysis (NBO), electronic properties, Fukui function analysis, various global parameters, Quantum Theory of Atoms In Molecule (QTAIM) analysis, ADMET analysis, and docking analysis have all been investigated using the same theory and basis sets, indicating its biochemical significance. The biological activity of the molecule is reported by using PASS software. The Full fitness score and binding affinity parameters are utilized to determine the binding strength with 6cq3 protein. The acidity of the title molecule is calculated in water solvent by polarizable continuum model (PCM) solvent effects (estimated in water). The HOMO, LUMO, and MESP plots are used to explore the nature of binding and surfaces. The Fukui functions are computed using Mulliken atomic charges for neutral atoms, cations, and anions. The Ultraviolet–visible (UV–vis) of the molecule is computed employing the TD-DFT method.     

Establishment and application of a new method for the determination of kinetic parameters by plug-plug kinetic capillary electrophoresis (ppKCE)

A novel plug-plug kinetic capillary electrophoresis method was established, which can be used to si-multaneously determine the kinetic parameters kon and koff in interaction systems. The method is comparatively simple and some restrictions in conventional ppKCE methods can be effectively avoided. The requirements for resolution and detection sensitivity in this method are much lower than those of conventional ppKCE. The successful determination of the kinetic parameters and the binding constant Kb between citalopram and BSA showed availability of this method. The results were confirmed by us-ing the time ratio method. The application field of kinetic capillary electrophoresis can be expanded with this new method.     

A density functional study towards the preferential binding of anions to urea and thiourea

A DFT study predicted the trend towards binding of anions with simple urea/thiourea receptor units, which has been found to be in good agreement with experimentally observed results. Our results provide a trend for the interaction of anions of different shapes with urea/thiourea receptor molecules, which do not always follow the basicity scale of anions.