Deoxyribonucleic acid (DNA) methylation is an epigenetic phenomenon, which adds methyl groups into DNA. This study reveals methylation of a nucleoside antibiotic drug 1-(β-D-ribofuranosyl)-2-pyrimidinone (zebularine or zeb) with respect to its methylated analog, 1-(β-D-ribofuranosyl)-5-methyl-2-pyrimidinone (d5) using density functional theory calculations in valence electronic space. Very simi...

Organic, conjugated donor−acceptor (D−A) systems are essential components of photovoltaic devices. Design and optimization of D−A systems is typically based on trial-and-error experimentation methods that would benefit from fundamental physical insights on structure−function relationships at the molecular level. Here, we implement a nonequilibrium Green’s function methodology at the density fun...

Proteins in the gas phase present an extreme (and unrealistic) challenge for self-consistent-field iteration schemes because their ionized groups are very strong electron donors or acceptors, depending on their formal charge. This means that gas-phase proteins have a very small band gap but that their frontier orbitals are localized compared to "normal" conjugated semiconductors. The frontier o...

Optimized geometries and adsorption energies obtained from non-local density functional calculations are presented for the adsorption of acetylene and ethylene on Ni(lll). Two cluster models, Ni4 and Nil4, are used. The best adsorption modes are #bridging and di-cr for acetylene and ethylene, respectively. In these orientations the overlap between the adsorbate frontier orbitals and the metal c...

The mechanistic understanding and control over transformations of multi-unsaturated hydrocarbons on transition metal surfaces remains one of the major challenges of hydrogenation catalysis. To reveal the microscopic origins of hydrogenation chemoselectivity, we performed a comprehensive theoretical investigation on the reactivity of two α,β-unsaturated carbonyls-isophorone and acrolein-on seven...

We report an electrochemical gating approach with ∼100% efficiency to tune the conductance of single-molecule 4,4'-bipyridine junctions using scanning-tunnelling-microscopy break junction technique. Density functional theory calculation suggests that electrochemical gating aligns molecular frontier orbitals relative to the electrode Fermi-level, switching the molecule from an off resonance stat...

We have carried out a theoretical study on the structure-function relationship for the selective oxidation of lower alkanes (C1-C4). The H abstraction mechanism has been examined over the model catalysts of high-valence d0 transition metal oxides in the tetrahedral coordination. The intrinsic connections among the H abstraction barrier, the strengths of the O-H and the M-O bonds, the ability of...