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Density functional theory calculations are used to study the thermodynamics and kinetics for the glycosidic bond cleavage in deoxyuridine. The results have shown that the nature of the nucleophile plays a major role in reducing the barrier to glycosidic bond cleavage than the nature of the small molecule bound.

Density functional theory is used to study the effects of the environment on the enhancement in natural and damaged DNA nucleobase acidities because of multiple hydrogen-bonding interactions. The results have indicated that hydrogen-bonding interactions have played a vital role in many biological processes by changing the physical and chemical properties of the nucleobases.

The density functional theory is employed to study and explain the various effects of the hydrogen-bonding and stacking interactions with amino acids on the acidity of uracil, which depends on the nature of amino acid and binding orientation. The results show that such interactions decrease the gas-phase acidity of uracil, which also varies with the nature of the molecule bound, as well as the binding orientations and strengths.

The characterization of the gas-phase stacking interactions between four aromatic amino acid residues (histidine, phenylalanine, tyrosine, and tryptophan) and adenine or 3-methyladeninde due to the proposed utilization of these interactions by enzymes that repair DNA alkylation damage is presented. The results suggest that alkylation likely plays a more important role in substrate identification and removal than the nature of the aromatic amino acid that interacts with the substrate via stacking interactions.

The study investigates the effects of hydrogen bonds on the properties of cytosine. The results shows that the effects of hydrogen bonds on the (N1) acidity is similar for corresponding binding sites in all pyrimidines, but differ more significantly when the hydrogen bonding pattern changes.

The density functional theory used to examine a hypothetical five-step catalytic cycle for Bronsted-mediated fission of an all-trans n-alkane is discussed. The predicted intermediates varied with catalyst acidity.

The geometry and relative energies of torsional conformers of centrally protonated C[sub 4]H[sub 11][sup +] were studied with ab initio methods, to (a) obtain the most accurate geometry of the three-center–two-electron CHC bond to date, (b) evaluate the performance of lower levels of approximation upon this challenging structure, and (c) gain an understanding of the torsional dynamics of C[sub 4]H[sub 11][sup +]. Twenty-nine combined levels of theory were used to optimize the geometry of the C[sub 2]-symmetry minimum for trans-C[sub 4]H[sub 11][sup +], and the most accurate one [CCSD(T)/cc-pVTZ] gave the following CHC bond geometry: θ[sub CHC]=122.4°, R[sub CC]=2.177 Å, R[sub CH]=1.2424 Å. Molecular-orbital-based methods generally perform better than density functional methods for describing the three-center–two-electron bond. A smaller subset of levels of theory was used to optimize other torsional conformers of centrally protonated C[sub 4]H[sub 11][sup +], varying the CCCC dihedral (trans, gauche, cis) and the dihedral for the bridging proton (various eclipsed and staggered positions). The results show that all conformers lie within a 4 kJ mol[sup -1] range, with the lowest-energy conformer being either trans or gauche with a staggered dihedral for the bridging proton. The effect of core-valence correlation was also investigated. Finally, the potential energy surface as a function of the CCCC and bridging-proton dihedral angles was qualitatively estimated and drawn, based on our computed data, to aid in understanding the fluxional character of C[sub 4]H[sub 11][sup +]. © 2003 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Complexes between ammonia, water, or hydrogen fluoride and adenine, guanine, or their 8-oxo derivatives are investigated using density functional theory. This provides a greater fundamental understanding of hydrogen-bonding interactions involving the natural purines, as well as those generated through oxidative DNA damage, which may aid the understanding of important biological processes.

A study is conducted to examine the cracking of an all-trans n-alkane, via idealized Lewis acid and Bronsted acid catalysis using density functional theory. However, results of exploratory optimizations of various intermediates with Al2Cl7(super -) as the catalyst are presented to provide the first step for future modeling studies in the ionic liquid system.

The study uses density functional theory to investigate the effects of hydrogen bonding on the acidity of C5- and C6-substituted uracil derivatives . The magnitude of the effect of hydrogen bonding on the acidity of uracil derivatives is not dependent on the nature or position of the substituent.

Cracking of an all-trans n-alkane, via idealized Lewis acid and Bronsted acid catalysis, was examined using density functional theory. Optimized geometries and transitions states were determined for catalyst-reactant complexes, using AlCl3 and HCl.AlCl3 as the Lewis and Bronsted acids. For the Lewis acid cycle, hydride-transfer steps are seen to have large barriers in both forward and reverse directions, and an unstable physisorbed carbenium ion (lying 20 kcal mol(-1) above the chemisorbed intermediate) is the launching point for the beta-scission that leads to products. For the Bronsted acid cycle, proton-transfer steps have smaller barriers in both forward and reverse directions, and a semistable physisorbed alkanium ion is the launching point for the alkanium alpha-scission that leads to products. In the idealized Lewis cycle, formation of HCl units (and hence Bronsted acids) was found to be a common side reaction. A recent ionic-liquid catalysis study is mentioned as motivation, although our study is not a computational modeling study; we are more interested in the fundamental differences between Brosnted and Lewis mechanisms rather than merely mimicking a particular system. However, results of exploratory optimizations of various intermediates with Al2Cl7- as the catalyst are presented to provide the first step for future modeling studies on the ionic liquid system.