Search results for "Solvation shell"
showing 10 items of 23 documents
Hydration dependent dynamics in sol-gel encapsulated myoglobin.
2008
In this work we study the effect of hydration on the dynamics of a protein in confined geometry, i.e. encapsulated in a porous silica matrix. Using elastic neutron scattering we investigate the temperature dependence of the mean square displacements of non-exchangeable hydrogen atoms of sol-gel encapsulated met-myoglobin. The study is extended to samples at 0.2, 0.3 and 0.5 g water/g protein fractions and comparison is made with met-myoglobin powders at the same average hydration and with a dry powder sample. Elastic data are analysed using a model of dynamical heterogeneity to take into account deviations of elastic intensity from gaussian behaviour in a large momentum transfer range and r…
Self-consistent continuum solvation (SCCS): the case of charged systems.
2013
The recently developed self-consistent continuum solvation model (SCCS) [O. Andreussi, I. Dabo, and N. Marzari, J. Chem. Phys. 136, 064102 (2012)] is applied here to charged species in aqueous solutions. Describing ions in solution represents a great challenge because of the large electrostatic interactions between the solute and the solvent. The SCCS model is tested over 106 monocharged species, both cations and anions, and we demonstrate its flexibility, notwithstanding its much reduced set of parameters, to describe charged species in solution. Remarkably low mean absolute errors are obtained with values of 2.27 and 5.54 kcal/mol for cations and anions, respectively. These results are co…
Limiting transport properties of lanthanide and actinide ions in pure water
2003
Summary The limiting transport properties, i.e. the limiting ionic conductivity (λ°) and the limiting diffusion coefficient (D°), of lanthanide and actinide ions at 298.15K have been calculated by means of the microscopic version of the Stokes–Einstein law involving (i) the effective charge and the ionic radius of the ions and (ii) the ion micro-viscosity, i.e. the viscosity of the hydrated water molecules in the vicinity of the ion. The latter quantity was derived from the variation of the dynamic properties of the water molecules in the first hydration shell with the surface charge density of common mono-atomic cations of various charges. The obtained results were found to be consistent w…
Multiple points of view of heteronuclear NOE: long range vs short range contacts in pyrrolidinium based ionic liquids in the presence of Li salts.
2015
The nuclear Overhauser enhancement (NOE) is a powerful tool of NMR spectroscopy extensively used to gain structural information in ionic liquids (ILs). A general model for the distance dependence of intermolecular NOE in ILs was recently proposed showing that NOE spots beyond the first solvation shell and accounts for long-range effects. This conclusion prompted for a deep rethinking of the NOE data interpretation in ILs. In this paper we present an extensive and quantitative study of N-propyl-N-methyl pyrrolidinium bis(trifluoromethanesulfonyl)imide (PYR13TFSI), the homologue with bis(fluorosulfonyl)imide (PYR13FSI), and their mixtures with LiTFSI based on 1H-19F and 1H-7LiNOE correlation …
Density functional study of Cu2+-phenylalanine complex under micro-solvation environment
2013
Abstract We present an atomistic study carried out using density functional calculations including structural relaxations and Car–Parrinello Molecular Dynamics (CPMD) simulations, aiming to investigate the structures of phenylalanine-copper (II) ([Phe-Cu] 2+ ) complexes and their micro-solvation processes. The structures of the [Phe-Cu] 2+ complex with up to four water molecules are optimized using the B3LYP/6-311++G** model in gas phase to identify the lowest energy structures at each degree of solvation ( n = 0–4). It is found that the phenylalanine appears to be in the neutral form in isolated and mono-hydrated complexes, but in the zwitterionic form in other hydrated complexes (with n …
Role of Solvent on Nonenzymatic Peptide Bond Formation Mechanisms and Kinetic Isotope Effects
2013
Based on the hypothesis that similar mechanisms are involved in the peptide bond formation in aqueous solution and in the ribosome, the aminolysis of esters in aqueous solution has been the subject of numerous studies as the reference reaction for the catalyzed process. The mechanisms proposed in the literature have been explored in the present paper by hybrid QM/MM molecular dynamics simulations. The free energy profiles have been computed with the QM region of the system described at semiempirical AM1 level and by DFT within the M06-2X functional. According to the results, the formation of adduct zwitterion species is a preliminary step required for all possible mechanisms. Then, from dif…
Elucidation of Carbohydrate Molecular Interaction Mechanism of Recombinant and Native ArtinM
2013
[EN] The quartz crystal microbalance (QCM) technique has been applied for monitoring the biorecognition of ArtinM lectins at low horseradish peroxidase glycoprotein (HRP) concentrations, using a simple kinetic model based on Langmuir isotherm in previous work.(18) The latter approach was consistent with the data at dilute conditions but it fails to explain the small differences existing in the jArtinM and rArtinM due to ligand binding concentration limit. Here we extend this analysis to differentiate sugar-binding event of recombinant (rArtinM) and native (jArtinM) ArtinM lectins beyond dilute conditions. Equivalently, functionalized quartz crystal microbalance with dissipation monitoring (…
Cluster Origin of Solvation Features of C-Nanostructures in Organic Solvents
2016
The existence of fullerenes, Single-Wall Carbon Nanocones (SWNCs), especially Nanohorns (SWNHs), Single-Wall Carbon Nanotube (SWNT) (CNT) (NT), NT-Fullerene Bud (NT-BUD), Nanographene (GR) and GR-Fullerene Bud (GR-BUD) in cluster form is discussed in organic solvents. Theories are developed based on columnlet, bundlet and droplet models describing size-distribution functions. The phenomena present a unified explanation in the columnlet model in which free energy of cluster-involved GR comes from its volume, proportional to number of molecules n in cluster. Columnlet model enables describing distribution function of GR stacks by size. From geometrical considerations, columnlet (GR/GR-BUD), b…
Untersuchung des Solvatationsgleichgewichts im ternären system Tetrachlormethan/Polymethylmethacrylat/Benzol durch kernmagnetische relaxation
1971
Im ternaren System CCl4/Polymethacrylate(PMMA)/Benzol tritt praferentielle Solvatation auf, Benzol ist in der Solvathulle des Polymeren angereichert. Es genugt eine Solvatationsgleichgewichtskonstante, um die praferentielle Solvatation bei variablen Konzentrationsverhaltnissen zu beschreiben. Gemessen wurde die Kernmagnetische Relaxationszeit T1 von Benzol in Abhangigkeit von der Polymerkonzentration. Der Vergleich mit analogen Messungen im System C6D6/PMMA/C6H6 ergibt fur die Solvatationsgleichgewichtskonstante K = (c32 · c10)/(c12 · c30) = 2,5 ± 0,5. Hierbei bedeuten: c10 die CCl4-Konzentrationen im „freien” Losungsmittel, c30 die Benzolkonzentrationen im „freien” Losungsmittel, c12 und c…
NMR relaxation and solvation equilibrium in the ternary system CCl4-polymethylmethacrylate-benzene
2007
In the ternary system CCl4-PMMA-benzene, benzene is preferentially adsorbed in the solvation shell of the polymer. One solvation equilibrium constant allows a satisfactory description of the preferential solvation for a large range of solvent compositions. The nuclear magnetic relaxation time T1 of benzene protons was measured for different values of the polymer concentration. The measurements are compared with analogous measurements in the system C6D6-PMMA-C6H6 where no preferential solvation is to be expected. For the system CCl4-PMMA-benzene the resulting dimensionless solvation equilibrium constant is K = c32c10/c12c30 = 2.5 ± 0.5 where c10 is the CCl4 concentration in the “free” solven…