A density functional theory study of a series of symmetric dibenzylideneacetone analogues as potential chemical UV-filters.

The aim of this research was to provide valuable insights on symmetrical α,β-unsaturated ketones as potential chemical ultraviolet (UV) filters from experimental data and theoretical aspects. Towards this end, density functional theory (DFT/B3LYP) calculations on a series of symmetrical α,β-unsaturated ketones, ()-1,5-bis[4-(R)phenyl]penta-1,4-diene-3-one (R = methylthio, ; R = dimethylamino, ; R = ethyl, ), were performed to determine the effect of different electron-donating substituents on their stability when exposed to solar UV radiation. Their molecular structures, and UV-visible, infrared (IR) and NMR (H and C) spectra were theoretically obtained from their optimized geometries with the B3LYP/6-311++ G (d, p) basis set and were compared with the experimental results.

Theoretical insights and implications of pH-dependent drug delivery systems using silica and carbon nanotube.

In this paper we have studied the density functional theory of four drugs ibuprofen, alendronate, Sulfasalazine and paracetamol with quartz, propylamine, trimethylamine functionalized quartz and carboxyl modified carbon nanotube. The attractive and repulsive interaction energies between drugs and quartz is obtained at various pH values. The attractive and repulsive energies are well correlated with experimental drug loading and releasing behavior by mesoporous silica nanoparticles.

A coarse-grained molecular dynamics investigation on spontaneous binding of Aβ fibrils with cholesterol-mixed DPPC bilayers.

Alzheimer's disease is the most common form of dementia. Its aetiology is characterized by the misfolding and aggregation of amyloid-β (Aβ) peptides into β-sheet-rich Aβ oligomers/fibrils. Although multiple experimental studies have suggested that Aβ oligomers/fibrils interact with the cell membranes and perturb their structures and dynamics, the molecular mechanism of this interaction is still not fully understood.

Acidity constant and DFT-based modelling of pH-responsive alendronate loading and releasing on propylamine-modified silica surface.

A computational methodology that couples the acidity (Ka) and density functional theory (DFT) calculations has been developed to explain the pH-dependent drug loading on and releasing from mesoporous silica nanoparticles. The model has been validated by investigating the pH-dependent loading and releasing of a bisphosphonate drug molecule, alendronate, on a propylamine-modified quartz surface (101), a model for functionalized mesoporous silica nanoparticles. The pH-dependent interacting molecular species are the neutral and anionic forms of the drug molecule, silanol group of quartz surface and the functional group in the case of functionalized quartz surface.

Exploiting Covalent, H-Bonding, and π-π Interactions to Design Antibacterial PDMS Interfaces That Load and Release Salicylic Acid.

Smart antimicrobial surfaces are a powerful tool to prevent bacterial colonization at surfaces. In this work, we report a successful strategy for the functionalization of polydimethylsiloxane (PDMS) surfaces, widely used in medical devices, with salicylic acid (SA), a biocide approved for use in humans. Antimicrobial PDMS surfaces were fabricated via a rational design in which bifunctional silane linker molecules were covalently grafted onto the PDMS via one end, while soft intermolecular interactions with SA were generated at the other end to enable reversible load and release of the biocide.

Structure and Function of Alzheimer's Amyloid βeta Proteins from Monomer to Fibrils: A Mini Review.

Alzheimer's disease is the most common form of dementia, that affects millions of people worldwide. According to the widely accepted amyloid cascade hypothesis, misfolding and aggregation of Aβ peptides is the principal cause of Alzheimer's disease. In the present mini-review, we have discussed the different structures of Aβ protein from monomer to fibrils and their arrangement in different symmetries.

Unraveling the mechanism of l-gulonate-3-dehydrogenase inhibition by ascorbic acid: Insights from molecular modeling.

l-Gulonate dehydrogenase (GuDH) is a crucial enzyme in the non-phosphorylated sugar metabolism or glucuronate-xylulose (GX) pathway. Some naturally occurring compounds inhibit GuDH. Ascorbic acid is one of such inhibitors for GuDH.

ReaxFF Molecular Dynamics Simulation for the Graphitization of Amorphous Carbon: A Parametric Study.

A parametric study of ReaxFF for molecular dynamics simulation of graphitization of amorphous carbon was conducted. The responses to different initial amorphous carbon configurations, simulation time steps, simulated temperatures, and ReaxFF parameter sets were investigated. The results showed that a time step shorter than 0.

Binding of 12-Crown-4 with Alzheimer's Aβ40 and Aβ42 Monomers and Its Effect on Their Conformation: Insight from Molecular Dynamics Simulations.

Alzheimer's disease is the most common form of dementia and is considered to be caused by the conformational change of Aβ monomers, from their native monomeric states, to form Aβ oligomers/aggregates in the brain. Turn formation in Aβ monomer has been suggested to be the nucleation step for Aβ misfolding. In the present work, we have performed a series of all-atom molecular dynamics simulations, a total time of 11.

12-Crown-4 Ether Disrupts the Patient Brain-Derived Amyloid-β-Fibril Trimer: Insight from All-Atom Molecular Dynamics Simulations.

Recent experimental data elucidated that 12-crown-4 ether molecule can disrupt Aβ40 fibrils but the mechanism of disruption remains elusive. We have performed a series of all-atom molecular dynamics simulations to study the molecular mechanism of Aβ40 fibril disruption by 12-crown-4. In the present study we have used the Aβ40 fibril trimer as it is the smallest unit that maintains a stable U-shaped structure, and serves as the nucleus to form larger fibrils.

Synthesis, characterization, antiproliferative and molecular docking study of new half sandwich Ir(III), Rh(III) and Ru(II) complexes.

The new carbazole N,N' ligand containing [(η(5)-C5Me5)MCl(L)]PF6, (M=Ir (1) and Rh (2)) and [(η(6)-C6H6)RuCl(L)]PF6 (3) (C5Me5=pentamethylcyclopentadienyl, L=9-ethyl-N-(pyridine-2-yl methylene)-9H-carbazole-3-amine) complexes has been synthesized and characterized by (1)H NMR, (13)C NMR, 2D NMR, melting point analysis, electronic absorption, infrared spectroscopy, HR-Mass spectroscopy and elemental analyses. The crystal structure of the [(η(5)-C5Me5)RhCl(L)]PF6 has been confirmed by single crystal XRD. The anticancer study of the synthesized complexes 1-3 clearly showed a potent inhibitor of human breast cancer cells (MCF-7) under in vitro conditions.

Molecular dynamics simulation and conformational analysis of some catalytically active peptides.

The design of stable and inexpensive artificial enzymes with potent catalytic activity is a growing field in peptide science. The first step in this design process is to understand the key factors that can affect the conformational preference of an enzyme and correlate them with its catalytic activity. In this work, molecular dynamics simulations in explicit water of two catalytically active peptides (peptide 1: Fmoc-Phe1-Phe2-His-CONH2; peptide 2: Fmoc-Phe1-Phe2-Arg-CONH2) were performed at temperatures of 300, 400, and 500 K.

A critical survey of average distances between catalytic carboxyl groups in glycoside hydrolases.

Published X-ray crystallographic structures for glycoside hydrolases (GHs) from 39 different families are surveyed according to some rigorous selection criteria, and the distances separating 208 pairs of catalytic carboxyl groups (20 α-retaining, 87 β-retaining, 38 α-inverting, and 63 β-inverting) are analyzed. First, the average of all four inter-carboxyl O…O distances for each pair is determined; second, the mean of all the pair-averages within each GH family is determined; third, means are determined for groups of GH families. No significant differences are found for free structures compared with those complexed with a ligand in the active site of the enzyme, nor for α-GHs as compared with β-GHs.

Adsorption of arginine-glycine-aspartate tripeptide onto negatively charged rutile (110) mediated by cations: the effect of surface hydroxylation.

Classical molecular dynamics (MD) simulations were employed to investigate the adsorption behaviors of arginine-glycine-aspartate (RGD) tripeptide onto the negatively charged hydroxylated/nonhydroxylated rutile (110) surfaces, mediated by biologically important cations (Na+ or Ca2+). The simulation results indicate that the inherent nature of the cation determines its binding strength, thereby regulating the adsorption geometry of the peptide. The sparse hydroxyl groups on the nonhydroxylated rutile diminish the probability of H-bond formation between RGD and the surface, resulting in an early desorption of the peptide even with a mediating Na+ ion.

Modeling the interaction between integrin-binding peptide (RGD) and rutile surface: the effect of cation mediation on Asp adsorption.

The binding of a negatively charged residue, aspartic acid (Asp) in tripeptide arginine-glycine-aspartic acid, onto a negatively charged hydroxylated rutile (110) surface in aqueous solution, containing divalent (Mg(2+), Ca(2+), or Sr(2+)) or monovalent (Na(+), K(+), or Rb(+)) cations, was studied by molecular dynamics (MD) simulations. The results indicate that ionic radii and charges will significantly affect the hydration, adsorption geometry, and distance of cations from the rutile surface, thereby regulating the Asp/rutile binding mode. The adsorption strength of monovalent cations on the rutile surface in the order Na(+) > K(+) > Rb(+) shows a "reverse" lyotropic trend, while the divalent cations on the same surface exhibit a "regular" lyotropic behavior with decreasing crystallographic radii (the adsorption strength of divalent cations: Sr(2+) > Ca(2+) > Mg(2+)).

Interplay of sequence, conformation, and binding at the Peptide-titania interface as mediated by water.

The initial stages of the adsorption of a hexapeptide at the aqueous titania interface are modeled using atomistic molecular dynamics simulations. This hexapeptide has been identified by experiment [Sano, K. I.