Search results for "solvents"
showing 10 items of 291 documents
Effects of static and dynamic perturbations on isotropic hyperfine coupling constants in some quinone radicals.
2004
The effects of solvent dielectric response on the isotropic hyperfine coupling constants of the 1,4-benzoquinone, 1,4-naphthoquinone and 9,10-anthraquinone anions and 1,4-naphthalenediol cation radicals were studied by electron spin resonance (ESR) spectroscopy and by the theoretical density functional method within the polarizable continuum model. Experimental results demonstrate that the isotropic hyperfine coupling constants can be obtained with high accuracy and that the effects of solvent impurities can be minimized by careful sample preparation. The results obtained correlate well with theoretical predictions from density functional theory calculations. For 1,4-naphthalenediol both th…
Factors Governing the Chemical Stability and NMR Parameters of Uracil Tautomers and Its 5-Halogen Derivatives
2020
We report on the density functional theory (DFT) modelling of structural, energetic and NMR parameters of uracil and its derivatives (5-halogenouracil (5XU), X = F, Cl, Br and I) in vacuum and in water using the polarizable continuum model (PCM) and the solvent model density (SMD) approach. On the basis of the obtained results, we conclude that the intramolecular electrostatic interactions are the main factors governing the stability of the six tautomeric forms of uracil and 5XU. Two indices of aromaticity, the harmonic oscillator model of aromaticity (HOMA), satisfying the geometric criterion, and the nuclear independent chemical shift (NICS), were applied to evaluate the aromaticity of ur…
Synthesis, characterisation and crystal structures of Schiff bases from the reaction of 4,6-O-ethylidene-β-D-glucopyranosylamine with substituted sal…
2001
Multiple chemical modifications were carried out on D-glucose to result in the corresponding Schiff bases. Such modifications performed on D-glucose not only helped in increasing the solubility of the products in nonaqueous solvents, but also restricted the anomerisation of the saccharide moiety in solution. NMR study of the products revealed the presence of the β-anomeric form of the saccharide moiety in Me2SO solution. All the compounds were characterised by analytical and spectral methods. The literature is devoid of any crystal structures of saccharide–Schiff base combinations of the type reported in this paper. The crystal structures of these molecules exhibited a tridentate, ONO bindi…
Structural studies of five novel bile acid-4-aminopyridine conjugates
2012
Abstract Synthesis and solid-state structural characterization of five bile acid amides of 4-aminopyridine (4-AP) are reported. Systematic crystallization experiments revealed a number of structural modifications and/or solvate/hydrate systems for these conjugates. Particularly, cholic acid conjugate exhibited five distinct structure modifications, including one anhydrous form, mono- and dihydrates, as well as ethanol and 2-butanol solvates. The obtained crystal forms were examined extensively with various analytical methods, including solid-state NMR, Raman, and IR spectroscopies, powder and single crystal X-ray diffraction methods, thermogravimetry, and differential scanning calorimetry. …
Cationic Nanohydrogel Particles as Potential siRNA Carriers for Cellular Delivery
2012
Oligonucleotides such as short, double-stranded RNA (siRNA) or plasmid DNA (pDNA) promise high potential in gene therapy. For pharmaceutical application, however, adequate drug carriers are required. Among various concepts progressing in the market or final development, nanosized hydrogel particles may serve as novel transport media especially for siRNA. In this work, a new concept of synthesizing polymeric cationic nanohydrogels was developed, which offers a promising strategy to complex and transport siRNA into cells. For this purpose, amphiphilic reactive ester block copolymers were synthesized by RAFT polymerization of pentafluorophenyl methacrylate as reactive ester monomer together wi…
Atomic Mean-Square Displacements in Proteins by Molecular Dynamics: A Case for Analysis of Variance
2004
AbstractInformation on protein internal motions is usually obtained through the analysis of atomic mean-square displacements, which are a measure of variability of the atomic positions distribution functions. We report a statistical approach to analyze molecular dynamics data on these displacements that is based on probability distribution functions. Using a technique inspired by the analysis of variance, we compute unbiased, reliable mean-square displacements of the atoms and analyze them statistically. We applied this procedure to characterize protein thermostability by comparing the results for a thermophilic enzyme and a mesophilic homolog. In agreement with previous experimental observ…
Solid-state NMR and computational investigation of solvent molecule arrangement and dynamics in isostructural solvates of droperidol.
2015
(13)C, (15)N and (2)H solid-state NMR spectroscopy have been used to rationalize arrangement and dynamics of solvent molecules in a set of isostructural solvates of droperidol. The solvent molecules are determined to be dynamically disordered in the methanol and ethanol solvates, while they are ordered in the acetonitrile and nitromethane solvates. (2)H NMR spectra of deuterium-labelled samples allowed the characterization of the solvent molecule dynamics in the alcohol solvates and the non-stoichiometric hydrate. The likely motion of the alcohol molecules is rapid libration within a site, plus occasional exchange into an equivalent site related by the inversion symmetry, while the water mo…
The hairpin extension controls solvent access to the chromophore binding pocket in a bacterial phytochrome: a UV-vis absorption spectroscopy study.
2021
AbstractSolvent access to the protein interior plays an important role in the function of many proteins. Phytochromes contain a specific structural feature, a hairpin extension that appears to relay structural information from the chromophore to the rest of the protein. The extension interacts with amino acids near the chromophore, and hence shields the chromophore from the surrounding solvent. We envision that the detachment of the extension from the protein surface allows solvent exchange reactions in the vicinity of the chromophore. This can facilitate for example, proton transfer processes between solvent and the protein interior. To test this hypothesis, the kinetics of the protonation…
Unveiling the Lewis Acid Catalyzed Diels–Alder Reactions Through the Molecular Electron Density Theory
2020
The effects of metal-based Lewis acid (LA) catalysts on the reaction rate and regioselectivity in polar Diels&ndash
Atomic structure of the major capsid protein of rotavirus: implications for the architecture of the virion
2001
The structural protein VP6 of rotavirus, an important pathogen responsible for severe gastroenteritis in children, forms the middle layer in the triple-layered viral capsid. Here we present the crystal structure of VP6 determined to 2 A resolution and describe its interactions with other capsid proteins by fitting the atomic model into electron cryomicroscopic reconstructions of viral particles. VP6, which forms a tight trimer, has two distinct domains: a distal beta-barrel domain and a proximal alpha-helical domain, which interact with the outer and inner layer of the virion, respectively. The overall fold is similar to that of protein VP7 from bluetongue virus, with the subunits wrapping …