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Biomedical subjects

U Deva Priyakumar

Publications and source records attributed to U Deva Priyakumar.

6 recordsLinked to original sources
PubMed2006

NMR imino proton exchange experiments on duplex DNA primarily monitor the opening of purine bases.

Molecular dynamics simulations were performed to investigate GC and AT base opening events in DNA. Calculated equilibrium constants between the base open (or flipped) and closed states were shown to be in good agreement with experimental data from NMR imino proton exchange experiments. Analysis of the computed results indicates that the equilbrium constants are dominated by the opening of the A and G bases in the AT and GC base pairs, respectively. Thus, the present results predict that NMR imino proton exchange experiments of base opening are primarily monitoring the opening of purine bases.

Adenine↗
PubMed2005

Conformational determinants of tandem GU mismatches in RNA: insights from molecular dynamics simulations and quantum mechanical calculations.

Structure and energetic properties of base pair mismatches in duplex RNA have been the focus of numerous investigations due to their role in many important biological functions. Such efforts have contributed to the development of models for secondary structure prediction of RNA, including the nearest-neighbor model. In RNA duplexes containing GU mismatches, 5'-GU-3' tandem mismatches have a different thermodynamic stability than 5'-UG-3' mismatches. In addition, 5'-GU-3' mismatches in some sequence contexts do not follow the nearest-neighbor model for stability. To characterize the underlying atomic forces that determine the structural and thermodynamic properties of GU tandem mismatches, molecular dynamics (MD) simulations were performed on a series of 5'-GU-3' and 5'-UG-3' duplexes in different sequence contexts. Overall, the MD-derived structural models agree well with experimental data, including local deviations in base step helicoidal parameters in the region of the GU mismatches and the model where duplex stability is associated with the pattern of GU hydrogen bonding. Further analysis of the simulations, validated by data from quantum mechanical calculations, suggests that the experimentally observed differences in thermodynamic stability are dominated by GG interstrand followed by GU intrastrand base stacking interactions that dictate the one versus two hydrogen bonding scenarios for the GU pairs. In addition, the inability of 5'-GU-3' mismatches in different sequence contexts to all fit into the nearest-neighbor model is indicated to be associated with interactions of the central four base pairs with the surrounding base pairs. The results emphasize the role of GG and GU stacking interactions on the structure and thermodynamics of GU mismatches in RNA.

Base Pair Mismatch↗
PubMed2003

Silaaromaticity in polycyclic systems: a computational study.

Density functional theory (B3LYP) calculations were performed to examine the effect of Si substitution on the aromaticity of some polycyclic hydrocarbons using geometric criterion (HOMA), isodesmic isomerization reactions, homodesmotic equations, NICS values, chemical hardness, and out-of-plane distortive tendencies. The HOMA values are lower and the NICS values are higher in the Si-substituted rings compared to those in the hydrocarbon counterpart, whereas the homodesmotic equations predict little loss of aromaticity upon Si replacement in polycylic systems. The chemical hardness values decrease and the out-of-plane distortive tendency increases upon silicon substitution. The relative energies of the positional isomers and the causative factors are analyzed. The high reactivity of some silaaromatics toward dimerization is explained based on local softness indices.

Journal Article↗
PubMed2002

A theoretical study of the structures, energetics, stabilities, reactivities, and out-of-plane distortive tendencies of skeletally substituted benzenes (CH)(5)XH and (CH)(4)(XH)(2) (X = B(-), N(+), Al(-), Si, P(+), Ga(-), Ge, and As(+)).

Ab initio molecular orbital theory at Hartree-Fock (HF), post-Hartree-Fock (MP2 and CCSD(T)), and the hybrid density functional theory (B3LYP) calculations were done on the mono-(CH)(5)XH and diskeletally substituted (CH)(4)(XH)(2) benzenes (X = B(-), N(+), Al(-), Si, P(+), Ga(-), Ge, and As(+)). The computed relative energies of the disubstituted isomers show interesting trends. While the ortho-isomer is the most stable for X = Ga(-), Ge, and As(+), meta was found to be the most stable for X = B(-), N(+), Al(-) and Si, and para was found to be the most stable for X = P(+). Various intricate factors that govern the relative stabilities, such as the sum of bond strengths in the twin Kekule forms, rule of topological charge stabilization (TCS), and electrostatic repulsion were critically examined. The sum of bond strengths in the twin Kekule forms was proved to be quite a successful measure in predicting the relative stability orders between ortho- and meta-/para-isomers. The rule of TCS breaks down especially in the presence of overwhelming factors such as the differences in the cumulative bond strengths of the two positional isomers; however, the stability ordering between the para- and meta-isomers is successfully predicted in most cases. The tendency for ring puckering increases a great deal especially when the substituents are from 3rd or 4th row. Extension of the popular inverse relationship between the thermodynamic stability and reactivity was found to be inapplicable for this class of compounds. The computed singlet-triplet energy differences and the chemical hardness (eta) values indicate that the skeletal substitution weakens the pi-strength of the benzenoid system and increases their reactivity.

Journal Article↗