Nasr Yousef M.J. Omar

Enantioselective organocatalytic Diels-Alder reactions: a density functional theory and kinetic isotope effects study.

The mechanism and enantioselectivity of the organocatalytic Diels–Alder reaction were computationally investigated by density functional theory at the B3LYP/6‐31G(d) level of theory. The uncatalyzed Diels–Alder reaction was also studied to explore the effect of the organocatalyst on this reaction in terms of energetics, selectivity, and mechanism. The catalyzed reaction showed improved endo/exo selectivity, and the free energy of activation was significantly lowered in the presence of the catalyst. Both uncatalyzed and catalyzed reactions exhibited concerted asynchronous reaction mechanism with the degree of asynchronicity being more evident in the presence of the catalyst. The Coreys experimentally derived predictive selection rules for the outcome of the organocatalytic Diels–Alder reaction were also theoretically analyzed, and an excellent agreement was found between experiment and theory.

THE ROLE OF INITIATOR tRNAi met IN FIDELITY OF INITIATION OF PROTEIN SYNTHESIS

The proper arrangement of amino acids in a protein determines its proper function, which is vital for the cellular metabolism. This indicates that the process of peptide bond formation requires high fidelity. One of the most important processes for this fidelity is kinetic proofreading. As biochemical experiments suggest that kinetic proofreading plays a major role in ensuring the fidelity of protein synthesis, it is not certain whether or not a misacylated tRNA would be corrected by kinetic proofreading during the peptide bond formation. Using 2-layered ONIOM (QM/MM) computational calculations, we studied the behavior of misacylated tRNAs and compared the results with these for cognate aminoacyl-tRNAs during the process of peptide bond formation to investigate the effect of nonnative amino acids on tRNAs. The difference between the behavior of initiator tRNAi met compared to the one for the elongator tRNAs indicates that only the initiator tRNAi met specifies the amino acid side chain.