Substituent effect on transition structure of Corey-Chaykovsky reaction: A semiempirical study

23-29Effect of various substituents on the conformation of transition structures of Corey-Chaykovsky reaction has been studied by semiempirical quantum mechanical method. It has been observed that steric effect and frontier interaction between substituent π electron and sulphur lone pair play a prominent role in determining the actual conformation of transition states. Based on the energy of the transition states, a probable explanation for showing high stereoselectivity of aromatic reagents involved in the above reaction has also been proposed

Peptidyl transferase activity of tRNA: A quantum chemical study

48-52The mechanism of protein synthesis is still unknown due to inability to detect the so-called enzyme "peptidyl transferase" even after elucidation of high-resolution crystal structure of ribosome. We have recently shown by model building and semi-empirical energy calculations that the tRNA molecule at P-site of ribosome may act as peptidyl transferase (Das et al. (1999) J. Theo. Biol. 200, 193-205). We proposed that the tetrahedral intermediate formed from nucleophylic attack of CO of P-site amino-acylated tRNA by NH2 of A-site amino-acy lated tRNA is converted to a six member ring intermediate by conformational change. This ring intermediate produces a free tRNA and a tRNA covalently linked to a peptide. However, energy of the six-member ring intermediate was calculated to be quite high. We show here that the energy values of all the reactants, intermediates and products are within the expected range when they are calculated using high level ab initio quantum chemical methods

A possible mechanism of peptide bond formation on ribosome without mediation of peptidyl transferase

Ribosome, the ubiquitous organelle, is the site for protein synthesis in all types of cells. The consecutive peptide bonds are formed by the transpeptidation reaction between carboxyl group of peptidyl moiety and the amino group of the aminoacyl moiety. Both the moieties are attached to the appropiate tRNAs positioned on the ribosome at P and A sites, respectively, through codon-anticodon recognition directed by messenger RNA. The reaction seems to proceed by the nucleophillic attack of the amino group of the aminoacyl tRNA at the A site and on the carboxyl of the ester group of the tRNA at P-site of ribosome. The configuration of the carbon atom of the tetrahedral intermediate may be R or S depending on the direction of the nucleophillic attack. After selecting the favorable conformation of this tetrahedral intermediate quantum mechanical calculations have been carried out to determine the energy needed for its formation. A cyclic intermediate where 2'-OH of the ribose sugar of the P-site tRNA is a member of the ring can be formed from the tetrahedral intermediate. This cyclic intermediate produces a free tRNA and a tRNA attached to a planar peptide unit. Analysis of the energetics using semiempirical method for the formation of a cyclic intermediate indicates that the peptide bond formation through the tetrahedral intermediate in S configuration may not need assistance from any outside agent like an enzyme

Effect of electrostatic potential of transition state on the stereoselectivity in ene cyclisation: A theoretical study

45-50Investigation on the transition structure of the ene reaction between propyne and forma ldehyde reveals that negative electrostatic potential is generated around the carbonyl oxygen and acetylenic group. The generated electrostatic potential controls the orientation of the oxygenated substituent present on the forming cyclohexane ring in ene cyclisation. Data from the study of mono substituted transition structures have been used to rationalize the stereoselectivity of an ene cyclisation with poly oxygenated substituents

Changeover from (3,4) ene cyclization to (3,5) mode under the influence of Lewis acid catalyst: A quantum mechanical study

1637-1644Transition structures (TSs) for the Lewis acid catalyzed ene cyclization reaction have been optimized quantum mechanically and the selectivity for the (3,5) ene cyclized product have been compared with that of (3,4) product. Analysis of the result shows that the geometric deformation of the TS produced due to the presence of Lewis acid in the environment plays a significant role in determining the selectivity of (3,5) ene product. This geometric deformation originates from the enlarged dihedral angle around the forming carbon-carbon bond in the Lewis acid catalyzed TS

Theoretical studies on the pyridoxal-5'-phosphate dependent enzyme dopa decarboxylase: Effect of Thr 246 residue on the co-factor-enzyme binding and reaction mechanism

155-164Decarboxylation of amino acid is a key step for biosynthesis of several important cellular metabolites in the biological systems. This process is catalyzed by amino acid decarboxylases and most of them use pyridoxal-5'-phosphate (PLP) as a co-factor. PLP is bound to the active site of the enzyme by various interactions with the neighboring amino acid residues. In the present investigation, density functional theory (DFT) and real-time dynamics studies on both ligand-free and ligand-bound dopa decarboxylases (DDC) have been carried out in order to elucidate the factors responsible for facile decarboxylation and also for proper binding of PLP in the active site of the enzyme. It has been found that in the crystal structure Asp271 interacts with the pyridine nitrogen atom of PLP through H-bonding in both native and substrate-bound DDC. On the contrary, Thr246 is in close proximity to the oxygen of 3-OH of PLP pyridine ring only in the substrate-bound DDC. In the ligand-free enzyme, the distance between the oxygen atom of 3-OH group of PLP pyridine ring and oxygen atom of Thr246 hydroxyl group is not favorable for hydrogen bonding. Thus, present study reveals that hydrogen bonding with O3 of PLP with a hydrogen bond donor residue provided by the enzyme plays an important role in the decarboxylation process

Theoretical Study on the Mechanism of Rearrangement Reactions of Bicyclic Derivatives of Cyclopropane to Monocyclic Derivatives under the Catalysis of Pt-Salt

In this paper, the mechanistic studies on the isomerization of hydroxyl and silyl derivatives of bicyclic cyclopropanes under the catalytic action of Zeise’s salt have been reported. The catalytic activity of both the monomeric and the dimeric forms of Zeise’s salt has been studied by applying the high-level quantum mechanical method. Results from this investigation reveal that the reaction goes favorably under the catalysis of the dimeric form of Zeise’s salt. The calculated activation barrier for the catalytic process using Zeise’s dimer reveals that the rearrangement occurs with an activation barrier of 19–25 kcal mol–1. Depending on the nature of substituents present on the substrate, formation of various products has been explained. This study also includes the heteronuclear counter part of Zeise’s dimer where one of the Pt-metals is replaced by palladium (Pd) and nickel (Ni) successively. The calculated activation barrier using these heteronuclear catalysts is found to be close enough to that calculated for the catalytic pathway using Zeise’s dimer

In-depth experimental and theoretical investigations on Co-SAC catalyzed transfer hydrogenation of azo compounds using methanol and ethanol

Transfer hydrogenation of non-polar bond using methanol or ethanol such hydrogen source is of great challenge, and development of efficient catalyst for performing such challenging reactions always an exciting area to explore. Herein, using Co-SAC various azo bonds were very efficiently hydrogenated to the corresponding amines, including commercially used dyes. A number of kinetics study and Hammett studies were to investigate the plausible mechanism and electronic effects. Further, a detailed DFT-calculation was performed to get a deeper insight about the mechanism