Study of the cap structure of (3,3), (4,4) and (5,5)-SWCNTs: application of the sphere-in-contact model

We have applied the sphere-in-contact model supported by hybrid Density Functional Theory (DFT) calculations to elucidate the cap geometry of the sub-nanometer in dimension (3,3), (4,4) and (5,5) single-wall carbon-nanotubes (SWCNTs). Our approach predicts certain cap-geometries that do not comprise of the commonly known for their stability combination of pentagonal and hexagonal carbon rings but also tetragonal, trigonal and all-pentagonal structures. Based on hybrid-DFT calcula-tions carbon atoms in these new cap geometries have similar stability to carbon found in other fullerene-like capped zig-zag and arm-chair nanotubes (i.e., (5,5), (6,6), (9,0) and (10,0)) that are known to be stable and synthetically accessible. We find that the cap structure of the (3,3)-CNTs is a pointy carbon geometry comprised of six pentagonal rings with a single carbon atom at the tip apex. In this tip geome-try the carbon atom at the tip apex does not have the usual sp2 or sp3 geometry but an unusual trigonal pyramidal configuration. DFT calculations of the molecular orbitals and density-of-states of the tip show that this tip structure apart from being stable can be used in scanning probe microscopies such as STM for very high resolution imaging

Computational inhibition studies of the human proteasome by argyrin-based analogues with subunit specificity

A computational procedure was developed to study the subunit-specific interactions of the proteasome inhibitors argyrin A and F, with the aim of indentifying the determinants of subunit selectivity. Three-dimensional models of humanized proteasome active sites β1, β2 and β5 were developed and subsequently used in molecular docking simulations with the argyrin analogues. The subunit selectivity exhibited by each analogue could be explained based on the site-specific interactions and a probability-based specificity parameter derived in this study. A rational approach that involved maximizing site-specific interactions was followed to guide the design of new argyrin analogues as specific inhibitors of the caspase-like (β1 site) activity

An experimental FTIR-ATR and computational study of H-bonding in ethanol/water mixtures

Ethanol/water mixtures have served as a model to study the hydrophobic effect and the formation of clathrate and other cage like water formations around the hydrophobic end of ethanol. We have studied the evolution of FTIR-ATR spectra of ethanol/water mixtures as a function of the content of water in the mixture. The experimental spectra show redshift of primarily the H-O-H bending vibration, which is 18.9 cm−1 in total width. It also shows a blueshift of 9.0 cm−1 of the asymmetric stretching vibration of C-H groups of β-CH3. These infrared spectral shifts are consistent with the formation of a cyclic H-bonded network between ethanol and H-bonded water molecules. This hypothesis has been supported by full optimizations of high-level B3LYP/aug-cc-pVQZ calculations in implicit and explicit water and ethanol solvents as well as MMFF94s simulations of ethanol in explicit water clusters with up to 30 water molecules

Receptor-attached amphiphilic terpolymer for selective drug recognition in aqueous solutions

In the present work, a combination of binding studies and molecular docking were employed to demonstrate drug encapsulation and host–guest chemistry in self-assembled micelles consisting of amphiphilic terpolymers. The terpolymer is composed of poly(3-sulfopropyl methacrylate), as the hydrophilic component, poly(n-dodecyl acrylate), as the hydrophobic component and poly(barbiturate receptor), as the component for drug recognition. The combined approach was tested on four model compounds from the family of barbiturates, phenobarbital, mephobarbital, secobarbital, and thiopental, chosen based on their differential hydrogen bonding capabilities. Drug encapsulation and hydrogen-bonding based recognition within the micellar core of the receptor–terpolymer was demonstrated by micellar electrokinetic chromatography. The resulting trends in the binding affinity of the barbiturates to the receptor–terpolymer, were correlated to the trends obtained from computational docking simulations. This receptor-modified polymeric micelle is intended to serve as a model for the design of novel, versatile, and highly selective molecular scaffolds that will provide suitable environment for host–guest chemistry and act as simplified mimics to more complex biological systems

Artificial receptor-attached amphiphilic copolymer for barbiturate binding in aqueous media

A water-soluble self-associating amphiphilic copolymer was employed to provide a microenvironment for the solvation of a hydrogen-bonding barbiturate artificial receptor, to facilitate molecular recognition in water. The receptor-attached amphiphilic polymer (RP) was synthesized through random copolymerization of 3% (mol) barbiturate receptor-monomer, 70% (mol) 3-sulfopropyl methacrylate, and 27% (mol) n-dodecyl acrylate. Difference UV spectra of pH 6.5 aqueous solutions of phenobarbital and receptor-polymer (RP) gave peaks and valleys at 272 and 301 nm respectively, consistent with binding characteristics of monomeric barbiturate receptors in chloroform. Specific association between phenobarbital and the receptor-polymer was further indicated based on investigations of a receptor-free control polymer (CP) of similar polar/nonpolar monomer ratio. Micellar electrokinetic chromatography was applied for studying polymer-phenobarbital association, by capillary electrophoresis

Analysis of binding parameters of HIV-1 integrase inhibitors: correlates of drug inhibition and resistance

This study undertook an exploratory data analysis of the binding parameters of HIV-1 integrase inhibitors. The study group involved inhibitors in preclinical development from the diketo acid, pyrroloquinoline and naphthyridine carboxamide families and the most advanced inhibitors Raltegravir and Elvitegravir. Distinct differences were observed in the energetics of binding between the studied classes of inhibitors that also correlated with drug resistant patterns. Quantitative-property–activity-relationships correlated experimental IC50 values to the binding energy and the logarithm of the partition coefficient between n-octanol and water (clog P). The approach followed here serves as an improved basis for the development of ‘second generation’ integrase inhibitors

Implications of HIV-1 M group polymorphisms on intergase inhibitor efficacy and resistance: genetic and structural in-silico analyses

The extensive polymorphisms among HIV-1 subtypes have been implicated in drug resistance development. Integrase inhibitors represent the latest addition to the treatment of HIV-1, and their efficacy and resistance patterns among M group strains are currently under investigation. This study analyzed the intersubtype variation within 108 integrase sequences from seven subtypes. The residues associated with catalytic activity and primary resistance to raltegravir were highly conserved among all strains. Variations were observed in residues associated with secondary resistance. Molecular modeling studies indicated a two-way binding mode of raltegravir that explains the resistance pathways and the implication of nonconservative mutations in integrase−raltegravir interactions