The SN2 reaction between ammonia and formic acid has been studied as a model reaction for peptide bond formation using the semiempirical MNDO and ab initio molecular orbital methods. Two reaction mechanisms have been examined, i.e., a stepwise and a concerted reaction. The stationary points of each reaction including intermediate and transition states have been identified and free energies have been calculated for all geometry optimized reaction species to determine the thermodynamics and kinetics of each reaction. The stepwise mechanism was found to be more favorable than the concerted one by both MNDO and ab initio calculations. However, the ab initio method predicts both mechanisms to be fairly competitive with free energies of activation of about 50 kcal/mol. Despite excellent agreement between both methods in the calculated entropies and thermal energies, the minimum basis set character of MNDO leads to values of free energy of activation much higher than those obtained by the ab initio method. The basis set dependence and effect of correlation of the computed ab initio results and the relative effects of polarization and correlation were also investigated by using a number of basis sets up to 6-31G** and estimates of correlation energy by Moller-Plesset perturbation theory up to fourth order. Correlation energy was found to be a significant factor in the stabilization of transition states.
The development of a flexible intra-and intermolecular empirical potential function is described, which is designed for investigating the geometric structure of large molecular systems. The intramolecular components in the potential consist of harmonic bond stretching and angle bending terms, out-of-plane deformation terms, and torsional terms; intermolecular components include nonbonding, hydrogen bonding, and electrostatic terms. Bond lengths, angles, and torsional angles are predicted to within 2% of experiment, with most cases being within 1%. The suitability of the intermolecular potential was tested by crystal packing calculations; in all cases the results obtained were in excellent agreement with experiment.
Novel transient receptor potential vanilloid 1 (TRPV1) receptor antagonists with various bicyclic heteroaromatic pharmacophores were synthesized, and their in vitro activity in blocking capsaicin activation of TRPV1 was assessed. On the basis of the contribution of these pharmacophores to the in vitro potency, they were ranked in the order of 5-isoquinoline > 8-quinoline = 8-quinazoline > 8-isoquinoline > or = cinnoline approximately phthalazine approximately quinoxaline approximately 5-quinoline. The 5-isoquinoline-containing compound 14a (hTRPV1 IC50 = 4 nM) exhibited 46% oral bioavailability and in vivo activity in animal models of visceral and inflammatory pain. Pharmacokinetic and pharmacological properties of 14a are substantial improvements over the profile of the high-throughput screening hit 1 (hTRPV1 IC50 = 22 nM), which was not efficacious in animal pain models and was not orally bioavailable.
The SN2 reaction between glycine and ammonia molecules with magnesium cation Mg2+ as a catalyst has been studied as a model reaction for Mg(2+)-catalyzed peptide bond formation using the ab initio Hartree-Fock molecular orbital method. As in previous studies of the uncatalyzed and amine-catalyzed reactions between glycine and ammonia, two reaction mechanisms have been examined, i.e., a two-step and a concerted reaction. The stationary points of each reaction including intermediate and transition states have been identified and free energies calculated for all geometry-optimized reaction species to determine the thermodynamics and kinetics of each reaction. Substantial decreases in free energies of activation were found for both reaction mechanisms in the Mg(2+)-catalyzed amide bond formation compared with those in the uncatalyzed and amine-catalyzed amide bond formation. The catalytic effect of the Mg2+ cation is to stabilize both the transition states and intermediate, and it is attributed to the neutralization of the developing negative charge on the electrophile and formation of a conformationally flexible nonplanar five-membered chelate ring structure.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.