Computational Modeling of the Interaction of Silver Clusters with Carbohydrates.

Silver nanoparticles are recognized for their numerous physical, biological, and pharmaceutical applications. In the present study, the interaction of silver clusters with monosaccharide molecules is examined to identify which molecule works better as a reducing agent in the application of a green synthesis approach. Geometry optimization of clusters containing one, three, and five silver atoms is performed along with the optimization of α-d-glucose, α-d-ribose, d-erythrose, and glyceraldehyde using density functional theory. Optimized geometries allow identifying the interaction formed in the silver cluster and monosaccharide complexes. An electron localization function analysis is performed to further analyze the interaction found and explain the reduction process in the formation of silver nanoparticles. The overall results indicate that glyceraldehyde presents the best characteristics to serve as the most efficient reducing agent.

Molecular modeling of four Dermaseptin-related peptides of the gliding tree frog Agalychnis spurrelli.

In this research, we present a preliminary computational study of four Dermaseptin-related peptides from the skin exudate of the gliding tree frog Agalychnis spurrelli. Experimentally, the amino acid sequence of these peptides was elucidated through molecular cloning and tandem mass spectrometry and synthetic peptides were assayed against E. coli, S. aureus, and C. albicans to determine their antimicrobial properties. With the sequences on hand, a computational study of the structures was carried out, obtaining their physicochemical properties, secondary structure, and their similarity to other known peptides. A molecular docking study of these peptides was also performed against cell membrane and several enzymes are known to be vital for the organisms. Results showed that Dermaseptin-related peptides are α-helical cationic peptides with an isoelectric point above 9.70 and a positive charge of physiological pH. Introducing theses peptides in a database, it was determined that their identity compared with known peptides range from 36 to 82% meaning these four Dermaseptins are novel peptides. This preliminary study of molecular docking suggests the mechanism of action of this peptide is not given by the inhibition of essential enzymatic pathways, but by cell lysis. Graphical abstract.

On the Reaction Mechanism of the 3,4-Dimethoxybenzaldehyde Formation from 1-(3',4'-Dimethoxyphenyl)Propene.

Lignin peroxidase (LiP) is an important enzyme for degrading aromatic hydrocarbons not only in nature but also in industry. In the presence of H2O2, this enzyme can easily decompose lignin and analogue compounds under mild conditions. In this reaction mechanism, LiP catalyzes the C-C cleavage of a propenyl side chain, being able to produce veratraldehyde (VAD) from 1-(3',4'-dimethoxyphenyl) propene (DMPP). One of the few and complete proposed mechanisms includes several non-enzymatic reactions. In this study, we performed a computational study to gain insight about the non-enzymatic steps involved in the reaction mechanism of VAD formation from DMPP using LiP as a catalyst. A kinetic characterization of the reaction using the reaction force and the reaction force constant concepts within the density functional theory (DFT) framework is proposed. All theoretical calculations for the reaction pathway were performed using the Minnesota Global Hybrid functional M06-2X and a 6-31++G(d,p) basis set. The complete reaction comprises seven steps (five steps not including LiP as a catalyst), which include radical species formation, bond transformation, water and oxygen addition, atom reordering, and deacetylation. The overall mechanism is an endothermic process with mixed activation energies depending on the four transition states. These results are the first attempt to fully understand the catalytic role of LiP in the degradation of lignin and its aromatic derivative compounds in terms of the electronic structure methods and future hybrid calculation approaches that we have recently been performing.