Rifaat Hilal

Vibrational analysis of the spectra of furan and thiophene

Abstract Scaled-quantum-mechanical (SQM) force fields were calculated for furan and thiophene, and their isotopomers, at the B3LYP, MP2 and HF levels of theory using the 6-31G** basis set. With the exception of few bands, mainly for the C–H (C–D) stretching mode, an excellent agreement between the calculated and experimental frequencies is obtained. The agreement between the calculated and experimental IR absorption intensities was satisfactory except at the MP2 level where the agreement was poorer than expected. The B3LYP scale factors are better correlated and less divergent than those obtained by the MP2 or the HF force fields. The B3LYP scale factors are also in good agreement with those previously reported.

A theoretical and experimental investigation of the electronic spectra and tautomerization of nucleobases

The electronic structures of all possible tautomers of uracil, thymine, cytosine, adenine and guanine have been carefully examined within the MNDO-MO frame-work. Equilibrium geometries are determined and the relative stabilities are discussed. Allowance for solvent effect on the stabilities is made by assuming a tetrahedral solvent cage with the DNA base occupying its centre. The electronic absorption spectra of the studied DNA bases, in solvents of different polarities are recorded and discussed. Assignments of the observed bands are facilitated using MNDO-CI computations. It is suggested that in solution the DNA bases are in some statistical mixtures of the most stable tautomers, and the Watson-Crick (WC) structure cannot account for the observed spectra alone.

Design of molecular switching and signaling based on proton transfer in 2-hydroxy Schiff bases: a computational study

The present work aims to exploit the possibility of using the tautomerism in 2-hydroxy Schiff bases for molecular switching. The enol imine (E)⇔ enaminone (K) tautomerization in a series of 2-hydroxy Schiff bases have been investigated theoretically at the DFT/B3LYP/6-311G** level of theory. The intramolecular proton transfer processes have been explored, transition structures have been located and characterized. The kinetics and thermodynamics of the proton transfer process, and its time scale have been computed and discussed in the framework of the suitability as molecular switches. Substituent effects have been computed and its effect on the enthalpy changes (∆H*) and activation energies (∆G*) have been analyzed and discussed. Nonspecific solvent effects have also been taken into account by using the polarized continuum model (IPCM) of two different solvent. The tautomerization energies are decreased and hence the endothermic nature of the enol imine ⇔ enaminone tautomerization. The potential energy barriers, on the other hand, are increased due to the relative destabilization of the transition states. The NBO charge populations show that there is a high positive charge on the hydrogen atom during the process in all cases, which confirms that the proton transfer proceeds through a three-center interaction. The proton transfer processes, in all cases studied are kinetically allowed. The low potential energy barrier suggests that interconversion between the two tautomeric forms is spontaneous and the two forms may coexist.

Unconventional hydrogen bonding to organic ions in the gas phase: Stepwise association of hydrogen cyanide with the pyridine and pyrimidine radical cations and protonated pyridine

Equilibrium thermochemical measurements using the ion mobility drift cell technique have been utilized to investigate the binding energies and entropy changes for the stepwise association of HCN molecules with the pyridine and pyrimidine radical cations forming the C5H5N(+·)(HCN)n and C4H4N2 (+·)(HCN)n clusters, respectively, with n = 1-4. For comparison, the binding of 1-4 HCN molecules to the protonated pyridine C5H5NH(+)(HCN)n has also been investigated. The binding energies of HCN to the pyridine and pyrimidine radical cations are nearly equal (11.4 and 12.0 kcal/mol, respectively) but weaker than the HCN binding to the protonated pyridine (14.0 kcal/mol). The pyridine and pyrimidine radical cations form unconventional carbon-based ionic hydrogen bonds with HCN (CH(δ+)⋯NCH). Protonated pyridine forms a stronger ionic hydrogen bond with HCN (NH(+)⋯NCH) which can be extended to a linear chain with the clustering of additional HCN molecules (NH(+)⋯NCH··NCH⋯NCH) leading to a rapid decrease in the bond strength as the length of the chain increases. The lowest energy structures of the pyridine and pyrimidine radical cation clusters containing 3-4 HCN molecules show a strong tendency for the internal solvation of the radical cation by the HCN molecules where bifurcated structures involving multiple hydrogen bonding sites with the ring hydrogen atoms are formed. The unconventional H-bonds (CH(δ+)⋯NCH) formed between the pyridine or the pyrimidine radical cations and HCN molecules (11-12 kcal/mol) are stronger than the similar (CH(δ+)⋯NCH) bonds formed between the benzene radical cation and HCN molecules (9 kcal/mol) indicating that the CH(δ+) centers in the pyridine and pyrimidine radical cations have more effective charges than in the benzene radical cation.

Regioselectivity in the Reactions of Bis- hydrazonoyl Halides with Pyrimidine-2-thiones

Summary. Bis-hydrazonoyl chlorides react regioselectively with pyrimidine-2-thiones, which contain a masked thiourea residue, to give the hitherto unknown annelated 2,3-bis-arylhydrazono-thiazoles and 3,3′-bis-1,2,4-triazoles. Reaction of bis-hydrazonoyl chlorides with 2-methylthio derivatives gave only 3,3′-bis-1,2,4-triazoles.

A comparative quantum chemical study of methyl acetate and S-methyl thioacetate Toward an understanding of the biochemical reactivity of esters of coenzyme A

The electronic structures of methyl acetate and S-methyl thioacetate and the corresponding anions have been investigated using the INDO-MO method. Equilibrium geometries, gas-phase anion proton affinities and barriers to internal rotation have been computed. Analysis of the effect of the d-type functions on sulfur on the static and dynamic properties of the thioester and its anion reveal no role for (p-d) pi conjugative effects. The results of this work indicate that the unique properties of thioester, and hence esters of coenzyme A, may be attributed to the lack of resonance, rather than to a sulfur d-orbital expansion.

How soil organic matter composition controls hexachlorobenzene–soil-interactions: Adsorption isotherms and quantum chemical modeling

Hazardous persistent organic pollutants (POPs) interact in soil with the soil organic matter (SOM) but this interaction is insufficiently understood at the molecular level. We investigated the adsorption of hexachlorobenzene (HCB) on soil samples with systematically modified SOM. These samples included the original soil, the soil modified by adding a hot water extract (HWE) fraction (soil+3 HWE and soil+6 HWE), and the pyrolyzed soil. The SOM contents increased in the order pyrolyzed soil<original soil<soil+3 HWE<soil+6 HWE. For the latter three samples this order was also valid for the HCB adsorption. The pyrolyzed soil adsorbed more HCB than the other samples at low initial concentrations, but at higher concentrations the HCB adsorption became weaker than in the samples with HWE addition. This adsorption combined with the differences in the chemical composition between the soil samples suggested that alkylated aromatic, phenol, and lignin monomer compounds contributed most to the HCB adsorption. To obtain a molecular level understanding, a test set has been developed on the basis of elemental analysis which comprises 32 representative soil constituents. The calculated binding energy for HCB with each representative system shows that HCB binds to SOM stronger than to soil minerals. For SOM, HCB binds to alkylated aromatic, phenols, lignin monomers, and hydrophobic aliphatic compounds stronger than to polar aliphatic compounds confirming the above adsorption isotherms. Moreover, quantitative structure-activity relationship (QSAR) of the binding energy with independent physical properties of the test set systems for the first time indicated that the polarizability, the partial charge on the carbon atoms, and the molar volume are the most important properties controlling HCB-SOM interactions.

Hydration of the pyrimidine radical cation and stepwise solvation of protonated pyrimidine with water, methanol, and acetonitrile.

Equilibrium thermochemical measurements using an ion mobility drift cell technique have been utilized to investigate the binding energies and entropy changes associated with the stepwise hydration of the biologically significant ions pyrimidine radical cation and protonated pyrimidine. The binding energy of the hydrated pyrimidine radical cation is weaker than that of the proton-bound dimer pyrimidineH(+)(H2O) consistent with the formation of a weak carbon-based CH(δ+)··OH2 hydrogen bond (11.9 kcal/mol) and a stronger NH(+)··OH2 hydrogen bond (15.6 kcal/mol), respectively. Other proton-bound dimers such as pyrimidineH(+)(CH3OH) and pyrimidineH(+)(CH3CN) exhibit higher binding energies (18.2 kcal/mol and 22.8 kcal/mol, respectively) due to the higher proton affinities and dipole moments of acetonitrile and methanol as compared to water. The measured collisional cross sections of the proton-bound dimers provide experimental-based support for the DFT calculated structures at the M06-2x/6-311++G (d,p) level. The calculations show that the hydrated pyrimidine radical cation clusters form internally solvated structures in which the water molecules are bonded to the C4N2H4(●+) ion by weak CH(δ+)··OH2 hydrogen bonds. The hydrated protonated pyrimidine clusters form externally solvated structures where the water molecules are bonded to each other and the ion is external to the water cluster. Dissociative proton transfer reactions C4N2H4(●+)(H2O)(n-1) + H2O → C4N2H3(●) + (H2O)(n)H(+) and C4N2H5(+)(H2O)(n-1) + H2O → C4N2H4 + (H2O)(n)H(+) are observed for n ≥ 4 where the reactions become thermoneutral or exothermic. The absence of the dissociative proton transfer reaction within the C4N2H5(+)(CH3CN)n clusters results from the inability of acetonitrile molecules to form extended hydrogen bonding structures such as those formed by water and methanol due to the presence of the methyl groups which block the extension of hydrogen bonding networks.

A Molecular Orbital Treatment of the Electronic Structure and Spectra of Tautomeric Rhodanines

An experimental as well as theoretical investigation of the electronic structure and tautomeric equilibria of 2,4-thiazolidinedione, 4-thiazolidinone-2-thione (rhodanine), 2-thiazolidinone-4-thione (isorhodanine) and 2,4-thiazolidinedithione (thiorhodanine) has been conducted. The origin of the electronic absorption transitions and the effect of replacing oxygen by sulfur atoms on coplanarity have been discussed. The solvent and pH dependence of the electronic spectra of the studied compounds indicate that there should be a statistical distribution of the ground and excited states between all possible tautomeric structures. This has been confirmed via molecular orbital computations. The calculated pK values have been interpreted with a mechanism based on the calculated deprotonation energies. Results of the present investigation concur with the chemistry of the studied compounds and reveal that these compounds are far from complete homocyclization.

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.