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Allehyani B.H.,King Abdullaziz University | Elroby S.A.,King Abdullaziz University | Elroby S.A.,Benisuief University | Aziz S.G.,King Abdullaziz University | And 2 more authors.
Journal of Biomolecular Structure and Dynamics | Year: 2015

The optimized geometries, harmonic vibrational frequencies, and energies of the structures of monohydrated alloxan were computed at the DFT/ωB97X-D and B3LYP/6-311++G∗∗ level of theory. Results confirm that the monohydrate exists as a dipolar alloxan-water complex which represents a global minimum on the potential energy surface (PES). Trajectory dynamics simulations show that attempt to reorient this monohydrate, to a more favorable orientation for H-bonding, is opposed by an energy barrier of 25.07 kJ/mol. Alloxan seems to prefer acting as proton donor than proton acceptor. A marked stabilization due to the formation of N-H-OH2 bond is observed. The concerted proton donor-acceptor interaction of alloxan with one H2O molecule does not increase the stability of the alloxan-water complex. The proton affinity of the O and N atoms and the deprotonation enthalpy of the NH bond of alloxan are computed at the same level of theory. Results are compared with recent data on uracil, thymine, and cytosine. The intrinsic acidities and basicities of the four pyrimidines were discussed. Results of the present study reveal that alloxan is capable of forming stronger H-bonds and more stable cyclic complex with water; yet it is of much lower basicity than other pyrimidines. © 2014 Taylor and Francis.

Osman O.I.,King Abdulaziz University | Osman O.I.,University of Khartoum | Elroby S.A.,King Abdulaziz University | Elroby S.A.,Benisuief University | And 3 more authors.
International Journal of Molecular Sciences | Year: 2014

MP2, DFT and CCSD methods with 6-311++G** and aug-cc-pvdz basis sets have been used to probe the structural changes and relative energies of -prop-2-ynylideneamine (I), Z-prop-2-ynylideneamine (II), pro-1,2-diene-1-imine (III) and vinyl cyanide (IV). The energy nea-requivalence and provenance of preference of isomers and tautomers were investigated by NBO calculations using HF and B3LYP methodw ith 6-311++G** and aug-cc-pvdz basis sets. All substrates have Cs symmetry. The optimized geometries were found to be mainly theoretical method dependent. All elected levels of theory have computed I/II total energy of isomerization (ΔE) of 1.707 to 3.707 kJ/mol in favour of II at 298.15 K. MP2 and CCSD methods have indicated clearly the preference of II over III; while the B3LYP functional predicted nearly similato tal energies. All tested levels of theory yielded a global II/IV tautomerization total energy (ΔE) of 137.3-148.4 kJ/mol in support of IV at 298.15 K. Thenegative values of ΔS indicated that IV is favoured at low temperature. At high temperature, a reverse tautomerization becomes spontaneous and II is preferred. The existence of II in space was debated throught he interpretation and analysis of the thermodynamic and kinetic studies of this tautomerization reaction and the presence of similar compounds in the Interstellar Medium (ISM). © 2014 by the authors; licensee MDPI, Basel, Switzerland.

Allehyani B.H.,King Abdulaziz University | Elroby S.A.K.,King Abdulaziz University | Elroby S.A.K.,Benisuief University | Aziz S.G.,King Abdulaziz University | And 2 more authors.
Procedia Computer Science | Year: 2014

Detailed DFT computations and classical trajectory dynamics simulations have been carried out to establish the origin of the extra stability of alloxan. The effect of solvent, basis set and DFT methods have been examined. Two non-covalent intermolecular dimers of alloxan, namely the Hbonded and the dipolar dimers have been investigated to establish their relative stability. Quantum theory of atom-in-molecule and NBO analysis has been performed. © The Authors. Published by Elsevier B.V.

Aziz S.G.,King Abdulaziz University | Elroby S.A.K.,King Abdulaziz University | Elroby S.A.K.,Benisuief University | Hilal R.H.,King Abdulaziz University | And 2 more authors.
Computational and Theoretical Chemistry | Year: 2014

The gas phase conformational and nonlinear optical properties of cis-N-phenylbenzohydroxamic acid (cis-NPBHA) keto and enol forms were studied applying traditional hybrid and long-range-corrected Density Functional Theory (DFT) and time-dependent density functional (TD-DFT) methods. The calculated geometrical parameters for the two isomers agreed satisfactorily with literature ones. The keto form was predicted to be more stable than the enol counterpart by 10.70-12.60kcal/mol, and the Gibb's free energies for the conversion: enol ⇌ keto were found to be 11.14kcal/mol (B3LYP/6-311+G**), 12.53kcal/mol (CAM-B3LYP/6-311+G**) and 13.28kcal/mol (ωB97XD/6-311+G**). All the selected functionals have computed larger total hyperpolarizabilities for the enol tautomer compared to those of the keto rival. The traditional hybrid functional yielded higher total hyperpolarizabilities than those of the long-range-corrected ones. The total hyperpolarizabilities were nicely correlated with HOMO-LUMO energy gaps and absorption maxima. The support of these molecular properties by natural bond orbital (NBO) calculations was evaluated and discussed. © 2013 Elsevier B.V.

Elroby S.A.K.,King Abdulaziz University | Elroby S.A.K.,Benisuief University | Makki M.S.I.,King Abdulaziz University | Sobahi T.R.,King Abdulaziz University | And 2 more authors.
International Journal of Molecular Sciences | Year: 2012

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. © 2012 by the authors; licensee MDPI, Basel, Switzerland.

El-Shishtawy R.M.,King Abdulaziz University | El-Shishtawy R.M.,National Research Center of Egypt | Asiri A.M.,King Abdulaziz University | Aziz S.G.,King Abdulaziz University | And 2 more authors.
Journal of Molecular Modeling | Year: 2014

Dye-sensitized solar cells (DSSCs) have drawn great attention as low cost and high performance alternatives to conventional photovoltaic devices. The molecular design presented in this work is based on the use of pyran type dyes as donor based on frontier molecular orbitals (FMO) and theoretical UV-visible spectra in combination with squaraine type dyes as an acceptor. Density functional theory has been used to investigate several derivatives of pyran type dyes for a better dye design based on optimization of absorption, regeneration, and recombination processes in gas phase. The frontier molecular orbital (FMO) of the HOMO and LUMO energy levels plays an important role in the efficiency of DSSCs. These energies contribute to the generation of exciton, charge transfer, dissociation and exciton recombination. The computations of the geometries and electronic structures for the predicted dyes were performed using the B3LYP/6-31+G**level of theory. The FMO energies (EHOMO, ELUMO) of the studied dyes are calculated and analyzed in the terms of the UV- visible absorption spectra, which have been examined using time-dependent density functional theory (TD-DFT) techniques. This study examined absorption properties of pyran based on theoretical UV- visible absorption spectra, with comparisons between TD-DFT using B3LYP, PBE, and TPSSH functionals with 6-31+G (d) and 6-311++G**basis sets. The results provide a valuable guide for the design of donor-acceptor (D-A) dyes with high molar absorptivity and current conversion in DSSCs. The theoretical results indicated 4-(dicyanomethylene)-2-methyl-6-(p-dimethylaminostyryl)-4H-pyran dye (D2-Me) can be effectively used as a donor dye for DSSCs. This dye has a low energy gap by itself and a high energy gap with squaraine acceptor type dye, the design that reduces the recombination and improves the photocurrent generation in solar cell. © Springer-Verlag 2014.

Elroby S.A.K.,King Abdulaziz University | Elroby S.A.K.,Benisuief University | El-Shishtawy R.M.,King Abdulaziz University | Makki M.S.I.,King Abdulaziz University
Molecular Simulation | Year: 2011

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 Zn 2+, 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-Zn 2+>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. © 2011 Taylor & Francis.

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