Current Organic Chemistry - Volume 14, Issue 2, 2010

Long range electron transfer plays an important role in determining the three-dimensional structures adopted by extended molecular systems such as proteins, nucleic acids, organic-metal complexes, etc. The resulting attraction, which is conceivable as a chemical association of two or more molecules or of different parts of one very large molecule, provides a stabilizing force for the overall donor-acceptor complex. The natur Read More

Recent developments in the dynamics of the elementary electron transfer reactions are reviewed. Attention is mainly focused on discrete state approaches, which combine use of a few experimental data with ab initio calculation of the normal coordinates of vibration of the redox partners. Applications to the early electron transfer in bacterial photosynthetic reaction centers and future perspectives are then discussed.

It has become increasingly apparent that there are a multitude of interactions within the context of proteins where a CH group is situated near an O atom in an arrangement that would lead one to believe that there exists a H-bond between them. Indeed, there are numerous examples in the literature where there is evidence that CH••O H-bonds play important roles in the structure of small molecules and complexes. The com Read More

It has become apparent that molecular modeling is a powerful approach to examining the properties of biomolecular systems like nucleic acids and their noncovalent interactions with other substances. Theoretical studies dealing with the dynamics of such extended molecules are based on the molecular mechanics simulations exhibiting very low computational requirements without sacrificing accuracy. This advantage is balanc Read More

Bioconjugation is a burgeoning field of research. Novel methods for the mild and site-specific derivatization of proteins, DNA, RNA, and carbohydrates have been developed for applications such as ligand discovery, disease diagnosis, and high-throughput screening. These powerful methods owe their existence to the discovery of chemoselective reactions that enable bioconjugation under physiological conditions-a tr Read More

Chemically modified RNA nucleotides have been introduced in the past into various ribozymes in order to understand RNA folding and the mechanism of RNA catalysis. Recently the ribosome, the largest natural ribozyme known to date, has been added to the list of enzymes amenable to synthetic biology. The chemically engineered ribosomes were active in various functional assays including single-turnover peptidyl tra Read More

Hydroxide-catalyzed exchange of the amide hydrogens on the protein backbone provides a highly sensitive monitor of electrostatic interactions at the aqueous interface. Much of the practical utility of these ionizations, relative to the more widely studied sidechain titrations, stems from the brief (∼10 ps) lifetime of the peptide anion intermediate which strongly limits the contribution of conformational reorganization to dielectric s Read More

Atoms-in-molecules (AIM) dual functional analysis is reviewed after brief introduction of AIM. Total electron energy densities (Hb(rc)) are plotted versus Laplacian of electron densities (▽2ρb(rc)) at bond critical points (BCPs). The plots draw a helical stream as a whole. For the better understanding of weak to strong interactions, polar coordinate (R, o) representation is employed for the plot of Hb(rc) versus (ħ2/8m)▽2 Read More

In this article, theoretical and experimental advances in the understanding of electronic processes underlying organic/metal (O/M) interface energetics are reviewed and correlated. The critical outlook comprises several key standpoints: (1) electronic basis of barrier formation at organic/metal interfaces, (2) dependence of organic/metal interface energetics on molecular conformation, (3) organic/ metal interface Read More