Biomedical subjects

Rita Kakkar

Publications and source records attributed to Rita Kakkar.

5 recordsLinked to original sources

PubMed2006

First principles density functional study of the adsorption and dissociation of carbonyl compounds on magnesium oxide nanosurfaces.

The adsorption and dissociation of three carbonyl compounds, formaldehyde, acetaldehyde, and acetone, on the magnesium oxide nanosurface, consisting of four stacked (MgO)3 hexagons, is investigated by first principles density functional theory (DFT). In the case of formaldehyde, strongly chemisorbed species, with carboxylate-like structures, are initially formed. These may subsequently undergo heterolytic cleavage of an aldehyde C-H bond to form formate ions involving a surface oxide ion and a hydride ion adsorbed over the magnesium dication [(MgH+)(HCOO-)]. For acetaldehyde, besides this reaction leading to the formation of acetate, the methyl hydrogen of the adsorbed species also tends to attach itself to a surface oxide ion, yielding surface hydroxyl ions and adsorbed [CH2=C(H)OMg]+. These results are in accord with our previous experimental and theoretical results. In particular, the shift of the aldehyde C-H vibration band to higher frequency and the appearance of OH bands in the infrared spectrum are clearly accounted for. For acetone, the mechanism is found to be similar, i.e., a methyl hydrogen shift to yield surface enolate. Again, this is in agreement with experimental studies.

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PubMed2006

A DFT study of the structures of pyruvic acid isomers and their decarboxylation.

Pyruvic acid and its isomers, including the enol tautomers and enantiomeric lactone structures, have been investigated at the B3LYP/6-311 + + G(3df,3pd) level, and it is found that a keto form with trans C(methyl)C(keto)C(acid)O(hydroxyl) and cis C(keto)C(acid)OH, and with one methyl hydrogen in a synperiplanar position with respect to the keto oxygen, is the most stable. This agrees with previous theoretical and experimental determinations. However, no minimum corresponding to protonated pyruvate could be located, although previous semiempirical calculations had found such structures. Decarboxylation by different possible routes was then studied. It was found that the direct formation of acetaldehyde, the most stable of the resulting C2H4O isomers, via a four-center-like transition state is the most feasible, although there is a high activation barrier of 70 kcal mol(-1). In contrast to semiempirical calculations, it is found that no hydroxyethylidene-carbon dioxide complex exists as a product, and no transition state leading to the dissociation to hydroxethylidene could be located.

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PubMed2005

Spectral and theoretical studies of N-p-(ethylbenzene)thiobenzohydroxamic acid metal chelates.

The preparation of N-p-(ethylbenzene)thiobenzohydroxamic acid chelates with several metal ions and their spectral properties are described in this paper. This is followed by a theoretical study of metal complexes of some thiohydroxamic acids, as well as the prepared chelates. The electronic properties of the metal complexes are discussed. The experimental and theoretical electronic spectra are also compared. A possible reason for the smaller pKa values of thiohydroxamic acid complexes than those of the corresponding hydroxamic acids is given.

Chelating Agents↗

PubMed2005

Theoretical study of molecular recognition by Hoechst 33258 derivatives.

The factors responsible for the binding of Hoechst 33258 with DNA residues have been investigated in this work using the AM1 method. First and foremost, it is found that, although all crystal structure determinations indicate a preference for binding at AT rich sites, the hydrogen bond strength is actually greater for complexes with cytosine and guanine. From this, it has been inferred that other factors such as electrostatic, van der Waals interactions and nonbonded contacts with the walls of the minor groove have a strong role to play in the binding process. The hydrogen bond is found to be stronger for complexation with the thymine O2 than with the adenine N3, in line with experimental observations. Combined QM/MM studies on the drug complexed with the Dickerson-Drew dodecamer reveal that binding induces structural changes in both the ligand as well as DNA. Electron donating substituents at the para position in the phenyl ring of Hoechst 33258 lead to stronger binding with DNA. A correlation with the octanol/water partition coefficients points to the importance of hydrophobic and electrostatic interactions.

Adenine↗

PubMed2003

Conformational behavior of some hydroxamic acids.

The conformational preferences of a few hydroxamic acids are investigated by the density functional B3LYP/6-311++G**//B3LYP16-31G* and semiempirical AM1 and PM3 methods in this work. It is found that both semiempirical methods give satisfactory results in comparison with sophisticated DFT and ab initio calculations, except for the activation barriers, which are overestimated. Of the two semiempirical methods, while the PM3 method gives better results for relative stabilities, AM1 geometries are in slightly better agreement with the experiments. The keto forms are found to be most stable and the reaction pathways for the interconversion between the keto and enol forms have been deduced. The effect of solvation on the reaction has also been investigated, as has the effect of methyl substitution at the carbon and nitrogen atoms. All the investigated acids exhibit N-acid behavior.

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