Importance of Molecular Simulation for Studying Structural Properties

Abstract The importance of molecular simulation is due to its application in different subjects as such as drug design, computational biology and materials science for studying molecular systems ranging from small chemical systems to large biological molecules and material assemblies. Some properties of molecular simulation are, quantitative structure-activity relationships (QSARs) which establish a quantitative relationship between chemical structures and their properties (structural and physicochemical), and this contributes to assisting and guiding the design and the selection of potent and safe drug candidates. The molecular electrostatic potential (MESP) is the potential energy of a proton at a particular location near a molecule, which correlates with dipole moment, electronegativity, and partial charges. MESP are valuable in computer-aided-drug-design because they help in optimization of electrostatic interactions between the protein and the ligand. These surfaces can be used to compare different inhibitors with substrates or transitions states of the reaction. FTIR technique is applied to obtain different functional groups present in the molecule or reaction. Besides, we can realize several studies as for example, kinetics, absorption and others

Structural analysis of adsorption processes of 5FU and imiquimodon hydrogels using AMBER/PM3 hybrid model

AMBER/PM3 hybrid model allowed determining the structural properties of 5FU and imiquimod individually and after the adsorption of chitosan hydrogels crosslinked with genipin, respectively. It was observed that the Gibbs free energy (ΔG) decreases with the adsorption, but indicates thermodynamic stability and spontaneity in both processes; ΔG was verified by the increase in the dipole moments. On the one hand, the partition coefficient established the hydrophilic character with respect to the water present in the hydrogel, which increases with the adsorption. The FTIR showed that there were displacements in the signals, however, the hydrogen bond bands attributed to the formation of new bonds to perform the adsorption of the drugs were observed. The adsorption was verified by the MESP and the surface analysis, where the distribution of nucleophilic and electrophilic zone was observed.O modelo hibrido AMBER/PM3 permitiu determinar as propriedades estruturadas do 5FU e imiquimod individualmente e depois da adsorção em hidrogeles de quitosano entrecruzados com genipina, respectivamente. Observou-se que o poder livre de Gibbs (ΔG) diminui com a adsorção, sem embargo, em ambos os processos se encontró estabilidade termodinâmica e espontaneidad; ΔG foi verificado através do aumento nos momentos de dipolares. Por outro lado, o coeficiente de divisão estabeleceu o carácter hidrofílico em relação à água presente no hidrogel, o qual aumenta com a adsorção. El FTIR evidenció que existem deslocamentos em las señales. Se observe as bandas de puente de hidrógeno, atribuições à formação de enlaces, para realizar a adsorção dos fármacos. A adsorção foi verificada através do MESP e os análises de superfície, em donde se apreciou a distribuição de zonas nucleofílicas e eletrofílicas.El modelo hibrido AMBER/PM3permitió determinar las propiedades estructurales del 5FU e imiquimod individualmente y después de la adsorción en hidrogeles de quitosano entrecruzados con genipina, respectivamente. Se observó que la energía libre de Gibbs (ΔG) disminuye con la adsorción, sin embargo, en ambos procesos se encontró estabilidad termodinámica y espontaneidad; ΔG fue verificado mediante el incremento en los momentos dipolares. Por otro lado, el coeficiente de partición estableció el carácter hidrofìlico con respecto al agua presente en el hidrogel, el cual aumenta con la adsorción. El FTIR evidenció que existen desplazamientos en las señales. Se observaron las bandas de puente de hidrógeno, atribuidas a la formación de enlaces, para realizar la adsorción de los fármacos. La adsorción fue verificada mediante los MESP y los análisis de superficie, en donde se apreció la distribución de zonas nucleofílicas y electrofílicas