Shabaan A. K. Elroby

Experimental and theoretical assignment of the vibrational spectra of triazoles and benzotriazoles. Identification of IR marker bands and electric response properties

The FTIR spectra of a series of 1H- and 2H- 1,2,3- and 1,2,4- triazoles and benzotriazoles were measured in the solid state. Assignments of the observed bands were facilitated by computation of the spectra using the density functional B3LYP method with the 6-311++G** basis set. The theoretical spectra show very good agreement with experiment. Rigorous normal coordinate analyses have been performed, and detailed vibrational assignment has been made on the basis of the calculated potential energy distributions. Several ambiguities and contradictions in the previously reported vibrational assignments have been clarified. “Marker bands” characterize the triazole ring were identified. The effect of substituents, the nature of the characteristic “marker bands” and quenching of intensities of some bands are discussed. Comparison of the topology of the charge density distribution, and the electric response properties of the 1H-, and 2H- isomers of both 1,2,3- and 1,2,4 triazole have been made using the quantum theory of atoms-in-molecules (QTAIM) by calculating the Laplacian of the electron density (∇2ρ(r)). Analysis of the contour plots and relief maps of ∇2ρ(r) reveals that 1,2,3- and 1,2,4-triazoles show completely different topological features for the distribution of the electron density. Thus, while the 1,2,3-isomer is a very polar molecule, the 1,2,4-isomer is much more polarizable. Bonding characteristics show also different features. This would thus underlie the different features of their vibrational spectra. The reported vibrational assignment can be used for further spectroscopic studies of new drugs and biological compounds containing the triazole ring.

Toward the Understanding of the Metabolism of Levodopa I. DFT Investigation of the Equilibrium Geometries, Acid-Base Properties and Levodopa-Water Complexes

Levodopa (LD) is used to increase dopamine level for treating Parkinson’s disease. The major metabolism of LD to produce dopamine is decarboxylation. In order to understand the metabolism of LD; the electronic structure of levodopa was investigated at the Density Functional DFT/B3LYP level of theory using the 6-311+G** basis set, in the gas phase and in solution. LD is not planar, with the amino acid side chain acting as a free rotator around several single bonds. The potential energy surface is broad and flat. Full geometry optimization enabled locating and identifying the global minimum on this Potential energy surface (PES). All possible protonation/deprotonation forms of LD were examined and analyzed. Protonation/deprotonation is local in nature, i.e., is not transmitted through the molecular framework. The isogyric protonation/deprotonation reactions seem to involve two subsequent steps: First, deprotonation, then rearrangement to form H-bonded structures, which is the origin of the extra stability of the deprotonated forms. Natural bond orbital (NBO) analysis of LD and its deprotonated forms reveals detailed information of bonding characteristics and interactions across the molecular framework. The effect of deprotonation on the donor-acceptor interaction across the molecular framework and within the two subsystems has also been examined. Attempts to mimic the complex formation of LD with water have been performed.

A QSAR study for 2-(4-aminophenyl)benzothiazoles: using DFT optimisation of geometry of molecules

Quantitative structure–activity relationships (QSARs) have been established for two sets of antitumour drugs 2-(4-aminophenyl)benzothiazoles (APBT). Constitutional, geometrical, topological, electronic descriptors (computed at the B3LYP/6-31G** level) and some empirical descriptors related to the hypophilicity were computed and analysed. Multiple regression analysis led to a set of equations that reflected the weight of each of the studied descriptors. The most relevant of these descriptors were grouped, and a new multiple regressions analysis was carried out and we arrived at the final QSAR models. A validation set of 11 APBT were selected, and their activities were computed using the proposed QSAR model. The correlation between the predicted and observed activities was excellent. The resulting best models exhibited good q 2 and r 2 values up to 0.867 and 0.954.

Influence of the protonation, deprotonation and transition metal ions on the fluorescence of 8-hydroxyquinoline: a computational study

8-Hydroxyquinoline (8HyQ) and its derivatives are the important constituents in a variety of pharmaceutical compounds. The effect of protonation and deprotonation of 8HyQ on its electronic structure and fluorescence was investigated using B3LYP/6-311G** level of theory. We also investigated the interaction of chemosensor, 8HyQ, with different transition metals (Zn2+, Fe2+, Ni2+ and Co2+) at the same level. Our results revealed that 8HyQ displays an unusual fluorescence intensity–proton transfer relationship with diminished emission in a protonated form but enhanced emission in a deprotonated form. The Zn2+, Fe2+, Ni2+ and Co2+ complexes of 8HyQ, which were investigated at the same level of theory, showed that the order of binding energies was 8HyQ-Ni2+>8HyQ-Zn2+>8HyQ-Co2+>8HyQ-Fe2+. Time-dependent density functional theory calculations indicated that Zn ion enhances the fluorescence of 8HyQ as a consequence of the inhibition of the proton transfer. The results are in good agreement between the predicted properties of transition metal complexes of 8HyQ and previously published experimental and theoretical results. A natural bond orbital analysis was performed to understand the nature of hydrogen-bonding interaction in 8HyQ and also to reveal the inter-relations between electronic structure and other properties.

Theoretical Investigation of the Dispersion Interaction in Argon Dimer and Trimer

The present work attempts to assess and evaluate the performance of some new DFT methods in describing van der Waals (vdW) complexes that are characterized by the dominance of pure dispersion interactions. To achieve this goal, Argon dimers (Ar2) and trimers (Ar3) were investigated. As a reference calculation, the correlation interaction energy have been computed at the CCSD(T) level using the aug-correlated family of basis sets pVXZ (where X=2,3,4). Extrapolation to the CBS limit has been carried out and the behavior of the potential energy function has been analyzed and discussed. Correlation interaction energy has been computed at the MP2 and MP4 levels and compared to those calculated at the CCSD(T) method. Five new correlated DFT functionals, namely M06 and its long rang extension M06L, the B97-2 and its modified version B97-D which was deviseded for the dispersion interaction, and the PBEPBE and its correlated extension PBE0 methods have been used to compute the interaction energy in Ar2 and Ar3. The present work results indicate clearly that M06 and M06L did not only overestimate the equilibrium distance and depth but they also showed fluctuations in the potential energy curve near the minimum and along the dissociative arm. The B97-D and the PBE0 methods are much more reliable. However, these two later methods showed convergence problems when used to treat Ar3+; in addition to being extremely fast when compared to the CCSD(T) method extremely fast as compared to the CCSD(T). These features make them good candidate for investigating large vdW clusters. The BSSE has been estimated, analyzed and discussed. The relative stabilities of the excited states of Ar2 and Ar3 clusters together with those of the ionic species (Ar2+ and Ar3+)have been computed and analyzed.

Understanding the decomposition reaction mechanism of chrysanthemic acid: a computational study

BackgroundChrysanthemic acid (CHA) is a major product from the photodecomposition of pyrethrin which is an important class of pesticide compounds.In the following paper, Hybrid density functional theory (DFT) calculations of the potential energy surface (PES) for three possible channels decomposition of chrysanthemic acid (cis-trans isomerization, rearrangement and fragmentation) have been carried at the B3LYP/6-311+G** level of theory. DFT was employed to optimize the geometry parameters of the reactants, transition states, intermediates and products based on detailed potential energy surfaces (PES).ResultsOur results suggest that all three pathways of CHA are endothermic. DFT calculations revealed that the activation barriers for cis-trans isomerization are low, leading to a thermodynamically favorable process than other two pathways. We also investigated the solvent effect on the PES using the polarizable continuum model (PCM). In addition, time-dependent density functional theory (TDDFT) calculations showed that these reactions occur in the ground state rather than in an excited state.ConclusionThe rearrangement process seems to be more favorable than the decomposition of CHA to carbene formation. The solvent effect calculations indicated no changes in the shape of the PES with three continua (water, ethanol and cyclohexane), although the solvents tend to stabilize all of the species.

Quantum Topology of the Charge Density of Chemical Bonds. QTAIM Analysis of the C-Br and O-Br Bonds☆

Abstract The present study aims to explore the quantum topological features of the electron density and its Laplacian of the understudied molecular bromine species involved in ozone depletion events. The characteristics of the C-Br and O-Br bonds have been analyzed via quantum theory of atoms in molecules (QTAIM) analysis using the wave functions computed at the B3LYP/aug-cc-PVTZ level of theory. Quantum topology analysis reveal that the C-Br and O-Br bonds show depletion of charge density indicating the increased ionic character of these bonds. Contour plots and relief maps have been analyzed for regions of valence shell charge concentrations (VSCC) and depletions (VSCD) in the ground state.

Eclipsed acetaldehyde as a precursor for producing vinyl alcohol.

The MP2 and DFT/B3LYP methods at 6-311++G(d,p) and aug-cc-pdz basis sets have been used to probe the origin of relative stability preference for eclipsed acetaldehyde over its bisected counterpart. A relative energy stability range of 1.02 to 1.20 kcal/mol, in favor of the eclipsed conformer, was found and discussed. An NBO study at these chemistry levels complemented these findings and assigned the eclipsed acetaldehyde preference mainly to the vicinal antiperiplanar hyperconjugative interactions. The tautomeric interconversion between the more stable eclipsed acetaldehyde and vinyl alcohol has been achieved through a four-membered ring transition state (TS). The obtained barrier heights and relative stabilities of eclipsed acetaldehyde and the two conformers of vinyl alchol at these model chemistries have been estimated and discussed.

Theoretical investigation of the photochemical reaction mechanism of cyclopropenone decarbonylation

The gas-phase decomposition mechanism of the photochemical and thermal reaction of cyclopropenone leading to carbon monoxide and acetylene has been investigated theoretically. We employed the B3LYP, MP2, and CASSCF methods with the 6-311 + G** basis set to determine the pathways and the potential energy surface (PES) of this reaction. PES minima were characterized by the absence of any imaginary frequencies and compared with the transition states that contained single imaginary frequencies. The intrinsic reaction coordinate (IRC) method was used to find the minimum energy paths in which reactants and products were connected to the transition states. Activation barrier, thermodynamic, and IRC analyses were performed using the above three methods. Our computations indicated that the decomposition of cyclopropenone proceeds through a stepwise mechanism containing two transition states (TS1 and TS2) and an intermediate. The results show that TS1, the critical transition state, determines the rate of the cyclopropenone decomposition reaction. Therefore, we employed natural bond order (NBO) calculations to probe the structure of the intermediate. The calculations showed that the intermediate has resonance structures containing a carbene and a zwitterion. Our results are in good agreement with previous theoretical and experimental studies.

Theoretical characterization of gas-phase thermolysis products of ethane-1,2-diol, 2-chloroethanol and 2-fluoroethanol

The transition structures and the activation energies for the possible thermal elimination of H2O, HF and HCl from ethane-1,2-diol, 2-fluoroethanol and 2-chloroethanol respectively, were investigated. The relative stabilities and associated barrier heights of syn and anti vinyl alcohol isomers and their acetaldehyde tautomer were estimated. HF, DFT/B3LYP and MP2 methods at 3-21G, 6-31+G(d), 6-311++G(d,p) and aug-cc-pvdz basis sets were applied to identify the stationary points of the studied systems. The optimized geometries and electronic energies of reactants, transition states and products were analyzed. The dependence of these properties upon the theoretical level was discussed. A concerted proton release and a hydroxide or halide ion expulsion mechanism was proposed to account for the thermal rearrangement of reactants to products. A thorough understanding of syn vinyl alcohol preference is provided by performing natural bond orbital (NBO) analysis. The oxygen atom lone pair (LP) and periplanar hyperconjugative effects are responsible for this preference. It was suggested that the LP hyperconjugative interactions with the C=C σ and π antibonds were the most important origin of the structural differences between the two vinyl alcohol isomers.