Search results for "dynamics"
showing 10 items of 9782 documents
Structure and Dynamics of NaCl in Methanol. A Molecular Dynamics Study
1991
Abstract A recently developed flexible three-site model for methanol was employed to perform a Molecular Dynamics simulation of a 0.6 molal NaCl solution. The ion-methanol and ion-ion potential functions were derived from ab initio calculations. The structural properties of the solution are discussed on the basis of radial and angular distribution functions, the orientation of the methanol molecules, and their geometrical arrangement in the solvation shells of the ions. The dynamical properties of the solution - like self-diffusion coefficients, hindered translations, librations, and internal vibrations of the methanol molecules - are calculated from various autocorrelation functions.
On the Importance of Carbohydrate-Aromatic Interactions for the Molecular Recognition of Oligosaccharides by Proteins: NMR Studies of the Structure a…
2005
The specific interaction of a variety of modified hevein domains to chitooligosaccharides has been studied by NMR spectroscopy in order to assess the importance of aromatic-carbohydrate interactions for the molecular recognition of neutral sugars. These mutant AcAMP2-like peptides, which have 4-fluoro-phenylalanine, tryptophan, or 2-naphthylalanine at the key interacting positions, have been prepared by solid-phase synthesis. Their three-dimensional structures, when bound to the chitin-derived trisaccharide, have been deduced by NMR spectroscopy. By using DYANA and restrained molecular dynamics simulations with the AMBER 5.0 force field, the three-dimensional structures of the protein-sugar…
Tritopic phenanthroline and pyridine tail-tied aza-scorpiands
2010
The synthesis of two new tritopic double-scorpiand receptors in which two equivalent 5-(2-aminoethyl)-2,5,8-triaza[9]-(2,6)-pyridinophane moieties have been linked with 2,6-dimethylpyridine (L1) or 2,9-dimethylphenanthroline (L2) units is reported for the first time. Their acid-base behaviour and Zn(2+) coordination chemistry have been studied by pH-metric titrations, molecular dynamic calculations, NMR, UV-Vis and steady-state fluorescence techniques. L1 and L2 behave, respectively, as hexaprotic and heptaprotic bases in the experimental conditions used (298.1 +/- 0.1 K, 0.15 mol dm(-3) NaCl, pH range under study 2.0-11.0). These ligands are able to form mono-, bi- and trinuclear Zn(2+) co…
Thermodynamics of binary mixtures: Volumes, heat capacities, and dilution enthalpies for then-pentanol+2-methyl-2-butanol system
1983
The densities, heat capacities, and dilution enthalpies ofn-pentanol+2-methyl-2-butanol mixtures have been measured, in many cases as a function of temperature, over the complete mole fraction range. Excesses thermodynamic properties, apparent and partial molar heat capacities, volumes and expansibilities were derived. The concentration and temperature dependences of these functions are discussed in terms of the variations of the structure of the system caused by the participation of the two alcohol molecules (with quite different steric hindrance of the alkyl chain around the-OH group) in the dynamic intermolecular association process through hydrogen bonding.
Molecular modeling studies of interactions between styrene–butadiene latex and sodium polyacrylate polymer surface
2010
Abstract The interaction between two important paper coating ingredients, sodium polyacrylate polymer dispersing agent and styrene–butadiene latex binder, was studied using classical force field and quantum chemical methods. The objective was to understand the adsorption of styrene–butadiene latex on the sodium polyacrylate polymer model surfaces at 300 K using molecular dynamics simulations. A quantum mechanical ab initio Hartree–Fock method was also used to obtain detailed information about the above interactions. In addition, the effect of moisture was investigated. Calculations showed that the conformation and orientation of styrene–butadiene latex, the number of carboxylate groups in t…
Impact of surface state on polyethylene glycol conformation confined inside a nanopore.
2021
Solid-state nanopores are a promising platform for characterizing proteins. In order to improve their lifetime and prevent fouling, Polyethylene Glycol (PEG) grafting is one of the most efficient and low-cost solutions. Different models to calculate the PEG thickness do not consider their interaction with the nanopore inner surface nor the effect of confinement. Here, we investigate by molecular dynamic simulation the PEG conformation inside a nanopore in the case of hydrophobic and hydrophilic nanopores. Our results reveal that the nanopore inner surface plays a role in the PEG organization and, thus, in the speed of the salt constituent. The resulting pair interaction between PEG and its …
Networks of Partially Hydrogenatedcis-1,4-Polybutadiene and ‘Rigid Rods’
1996
Networks of 'flexible' and 'rigid' chains were synthesized. As 'flexible' component we have used different partially hydrogenated cis-1,4-polybutadiene. The 'rigid' component was synthesized from bis(1,2,4-triazoline-3,5-dione)s and biscyclohexadienes via repetitive Diels-Alder reaction. A slight excess of bis(1,2, 4-triazoline-3,5-dione)s leads to polymers with 1,2,4-triazoline-3,5-dione end groups, which can easily react with the partially hydrogenated cis-1,4-polybutadiene. The influence of the extent of hydrogenation and the amount of crosslinker on the mechanical and thermal behaviour is described.
Forever Young: Structural Stability of Telomeric Guanine-Quadruplexes in Presence of Oxidative DNA Lesions
2020
AbstractHuman telomeric DNA (h-Telo), in G-quadruplex (G4) conformation, is characterized by a remarkable structural stability that confers it the capacity to resist to oxidative stress producing one or even clustered 8-oxoguanine lesions. We present a combined experimental/computational investigation, by using circular dichroism in aqueous solutions, cellular immunofluorescence assays and molecular dynamics (MD) simulations, that identifies the crucial role of the stability of G4s to oxidative lesions, related also to their biological role as inhibitors of telomerase, an enzyme overexpressed in most cancers associated to oxidative stress.
On The Incompatibility of Dextran and Pullulan in Aqueous Solutions and Its Modeling
2012
Joint aqueous solutions of branched dextran and linear pullulan are investigated with respect to their phase separation. The experiments demonstrate that the polymers are – depending on the molar mass of dextran – incompatible in aqueous solutions despite their chemical similarity. This finding can be modeled on the basis of an approach accounting for chain connectivity and conformational relaxation of the components. According to these calculations, the polymers exhibit a miscibility gap in joint solutions despite the favorable interactions between them. Using information on the subsystems H2O/dextran and H2O/pullulan, the assumption of complete miscibility of the polysaccharides is requir…
Heat capacities of butanol and pentanol in aqueous dodecyltrimethylammonium bromide solutions
1987
Heat capacities of the ternary systems water-dodecyltrimethylammonium bromide (DTAB)-butanol and water-DTAB-pentanol were measured at 25°C. The standard partial molar heat capacities of pentanol in micellar solutions show a maximum at about 0.35 mol-kg−1 DTAB that has been attributed to a micellar structural transition. This maximum tends to vanish by increasing the alcohol concentration and by decreasing the alcohol alkyl chain length; in the case of butanol it was not detected. The behavior of the standard partial molar heat capacities of alcohols in micellar solutions in the region above the cmc and below the structural transition was explained using a previously reported mass-action mod…