Reversibility and Diffusion in Mandelythiamin Decarboxylation. Searching Dynamical Effects in Decarboxylation Reactions

Decarboxylation of mandelylthiamin in aqueous solution is analyzed by means of quantum mechanics/molecular mechanics simulations including solvent effects. The free energy profile for the decarboxylation reaction was traced, assuming equilibrium solvation, while reaction trajectories allowed us to incorporate nonequilibrium effects due to the solvent degrees of freedom as well as to evaluate the rate of the diffusion process in competition with the backward reaction. Our calculations that reproduce the experimental rate constant show that decarboxylation takes place with a non-negligible free energy barrier for the backward reaction and that diffusion of carbon dioxide is very fast compared to the chemical step. According to these findings catalysts would not act by preventing the backward reaction.GV/2012/053. ESTUDIO DEL MECANISMO DE REACCION Y DE LOS MOVIMIENTOS DINAMICOS DE LAS ENZIMAS ADN-METILTRANSFERASAS: CATALISIS Y INHIBICIO

Structural dynamics of calmodulin and troponin C

We present the results of computational simulation studies of the structures of calmodulin (CAM) and troponin C (TNC). Possible differences between the structures of these molecules in the crystal and in solution were suggested by results from some recent experimental studies, which implied that their conformations in solution may be more compacted than the characteristic dumbbell shape observed in the crystal. The molecular dynamics simulations were carried out with the CHARMM system of programs, and the environment was modeled with a distance-dependent dielectric permittivity and discrete water molecules surrounding the proteins at starting positions identified in the crystals of CAM and TNC. Methods of macromolecular structure analysis, including linear distance plots, distance matrices and a matrix representation of hydrogen bonding, were used to analyze the nature, the extent and the source of structural differences between the computed structures of the molecules and their conformations in the crystal. Following the longest simulation, in which intradomain structure was conserved, the crystallographically observed dumbbell structure of the molecule changed due to a kinking or bending in the region of the central tether helix connecting the two Ca2+-binding domains which moved into close proximity. The resulting structure correlates with experimental observations of complexes between CAM and peptides such as melittin and mastoparan. Analysis of the corresponding pair distance distribution functions in comparison to experimental results suggests the dynamic existence of a non-negligible fraction of the compacted structure in aqueous solutions of CAM. In this more nearly globular shape, CAM reveals to the environment two interior pockets that contain a number of hydrophobic residues, in agreement with NMR data suggesting involvement of such residues in the binding of inhibitors and proteins to CA

Aminoacid zwitterions in solution : Geometric, energetic, and vibrational analysis using density functional theory-continuum model calculations

Glycine and alanine aminoacids chemistry in solution is explored using a hybrid three parameters density functional (B3PW91) together with a continuum model. Geometries, energies, and vibrational spectra of glycine and alanine zwitterions are studied at the B3PW91/6-31+G∗∗ level and the results compared with those obtained at the HF and MP2/6-31+G∗∗ levels. Solvents effects are incorporated by means of an ellipsoidal cavity model with a multipolar expansion (up to sixth order) of the solute’s electrostatic potential. Our results confirm the validity of the B3PW91 functional for studying aminoacid chemistry in solution. Taking into account the more favorable scaling behavior of density functional techniques with respect to correlated ab initio methods these studies could be extended to larger [email protected] ; [email protected]

Entalpía de vaporización y Clausius Clapeyron (JLPAG002)

En este problema se hace uso de la la ecuación de Clausius Clapeyron junto el concepto de ciclo termodinámico para calcular diferentes entalpías de transición de fase (fusión, sublimación...

Diagrama de fases L-V. Descripción. (JLPAG003)

Se explica un problema numérico relacionado con los diagramas de fase líquido vapor.Enunciado:• Se mezclan 4 moles de benceno y 6 moles de tolueno a 86,85 ºC y 1 atm. Responder a las siguientes preguntas haciendo uso del diagrama de fases T-x del benceno tolueno a 1 atm.a) Describe los elementos esenciales del diagrama.b) ¿Esta mezcla será líquida, gaseosa, ...? c) ¿A qué temperatura comienza a hervir la disolución?d) ¿Cómo se encontrará la mezcla una vez alcanzado el equilibrio si se calienta hasta 96,85 ºC? ¿Cuál será la composición de cada fase

Calor de disolución y ciclo termodinámico (JLPAG_001)

Haciendo uso del concepto de ciclo termodinámico y de la formula con la que se obtiene el calor integral de disolución, se calcula el calor de disolución en diferentes situaciones

Reversibility and Diffusion in Mandelythiamin Decarboxylation. Searching Dynamical Effects in Decarboxylation Reactions

Decarboxylation of mandelylthiamin in aqueous solution is analyzed by means of quantum mechanics/molecular mechanics simulations including solvent effects. The free energy profile for the decarboxylation reaction was traced, assuming equilibrium solvation, while reaction trajectories allowed us to incorporate nonequilibrium effects due to the solvent degrees of freedom as well as to evaluate the rate of the diffusion process in competition with the backward reaction. Our calculations that reproduce the experimental rate constant show that decarboxylation takes place with a non-negligible free energy barrier for the backward reaction and that diffusion of carbon dioxide is very fast compared to the chemical step. According to these findings catalysts would not act by preventing the backward reaction