Search results for "Names"

Amino acid chemistry in solution: structural properties and vibrational dynamics of serine using density functional theory and a continuum solvent mo…

2004

A structural and vibrational study of amino acid serine in aqueous solution has been carried out using Fourier transform spectroscopies and quantum mechanical calculations. FT-IR and FT-Raman spectra of serine in H2O and D2O solutions were recorded and a general assignment of the observed bands was proposed on the basis of a zwitterionic structure for serine. Main criteria were the observed wavenumber shifts upon deuteration and previous assignments for other amino acids. A quadratic force field was computed using ab initio methodology at the 6-31+G** level and the hybrid functional B3LYP. The solvent effect was simulated by placing the serine molecule into an ellipsoidal cavity surrounded …

Influence of Dynamics on The Analysis of Solid-State NMR Data From Membrane-bound Peptides

2009

By isotope labeling of membrane-bound peptides, typically with 2H, 19F, or 15N, solid-state NMR experiments can yield data from which the orientation of peptides in a native membrane environment can be determined. Such an orientation is defined by a tilt angle and an azimuthal rotation angle.Here we show that to obtain correct values of the orientation angles, it is important to include dynamics in the analysis of the NMR data. Nevertheless the effects of dynamics are different depending on the type of isotope labeling and NMR experiment considered.To analyze the influence of dynamics in detail, we generated virtual NMR observables using a model peptide undergoing explicit Gaussian fluctuat…

Difficulties of density functional theory in predicting the torsional potential of 2,2?-bithiophene

1998

The internal rotation of 2,2′-bithiophene was investigated within the density functional theory (DFT) approach. Fully optimized DFT torsional potentials are compared with Moller–Plesset (MP2) results which predict a fourfold potential with s-cis- and s-trans-gauche minima. DFT calculations fail in describing the energetics of the internal rotation because they favor planar vs. perpendicular conformers. Gradient-corrected functionals provide torsional potentials where the gauche minima have almost vanished and the s-ciss-trans interconversion barriers are twice as high as the barriers obtained at the MP2 level. The use of local functionals augments the shortcomings of the DFT approach. The g…

1982

The molecular weight distribution (MWD) of a high polymer is calculated from a weakly perturbed Zimm-plot of the classical light scattering on dilute solutions of Gaussian polymer coils (theta state). A typical Zimm-plot is simulated corresponding to the measurements of high accuracy as would be obtained by using the laser photometer described by Hack and Meyerhoff. The accuracy as published by these authors for small dissymmetries is used. Two numerical methods for calculating the MWD are briefly described and tested, both using an empirical formula for the Laplace image of the calculated MWD.

Polyelectrolyte Molecule in an Elongational Flow

1995

The theory describing the stretching of a weakly charged polyelectrolyte molecule by elongational shear flow is developed. It is shown that for a polyelectrolyte immersed in a salt-added solution two critical values of shear flow gradient exist: the lower critical point corresponds to the chain stretching on the scale of superblobs of size equal to the Debye screening length and the upper critical point corresponds to the complete stretching of the chain on the scale of monomer units.

Iterative integral equation methods for structural coarse-graining

2021

In this paper, new Newton and Gauss-Newton methods for iterative coarse-graining based on integral equation theory are evaluated and extended. In these methods, the potential update is calculated from the current and target radial distribution function, similar to iterative Boltzmann inversion, but gives a potential update of quality comparable with inverse Monte Carlo. This works well for the coarse-graining of molecules to single beads, which we demonstrate for water. We also extend the methods to systems that include coarse-grained bonded interactions and examine their convergence behavior. Finally, using the Gauss-Newton method with constraints, we derive a model for single bead methano…

Statics and dynamics of dense polymer systems studied by monte carlo simulation

1995

Monte Carlo simulations of coarse–grained models of macromolecules offer a unique tool to study the interplay between coil conformations, thermodynamic properties, and chain configurational relaxation and diffusion. Two examples are discussed where the chain conformation strongly differs from a gaussian coil: (i) collapsed chains in a bad solvent, where anomalous diffusion occurs in the Rouse limit and the relaxation time increases at least with the third power of chain length. (ii) Expulsion of a chain from a semidilute polymer brush. The initially stretched chain contracts to a gaussian coil and the center of mass moves outward with constant velocity until it reaches the region of the “la…

Estimation of individual Gibbs energies of cation transfer employing the insertion electrochemistry of solid Prussian blue

2011

Abstract A novel method to determine the Gibbs energy of cation transfer between two miscible solvents is described. This method uses electrochemical data for the reversible cation-assisted solid-state reduction of Prussian blue using ferrocene as internal potential standard. Voltammetric data can be used for a direct measurement of the Gibbs energy of ion transfer from one solvent to another using midpeak potentials in solutions of suitable salts in each one of the solvents separately or mixtures of the solvents. Excess Gibbs energies of solvation in solvent mixtures can also be directly estimated. Gibbs energies of cation transfer of Li+, Na+ and K+ ions from water to MeOH, MeCN and DMSO …

Periodic orbits of single neuron models with internal decay rate 0 < β ≤ 1

2013

In this paper we consider a discrete dynamical system x n+1=βx n – g(x n ), n=0,1,..., arising as a discrete-time network of a single neuron, where 0 &lt; β ≤ 1 is an internal decay rate, g is a signal function. A great deal of work has been done when the signal function is a sigmoid function. However, a signal function of McCulloch-Pitts nonlinearity described with a piecewise constant function is also useful in the modelling of neural networks. We investigate a more complicated step signal function (function that is similar to the sigmoid function) and we will prove some results about the periodicity of solutions of the considered difference equation. These results show the complexity of …

Bond-extended stochastic and nonstochastic bilinear indices. I. QSPR/QSAR applications to the description of properties/activities of small-medium si…

2010

Bond-extended stochastic and nonstochastic bilinear indices are introduced in this article as novel bond-level molecular descriptors (MDs). These novel totals (whole-molecule) MDs are based on bilinear maps (forms) similar to use defined in linear algebra. The proposed nonstochastic indices try to match molecular structure provided by the molecular topology by using the kth Edge(Bond)-Adjacency Matrix (Ek, designed here as a nonstochastic E matrix). The stochastic parameters are computed by using the kth stochastic edge-adjacency matrix, ESk, as matrix operators of bilinear transformations. This new edge (bond)-adjacency relationship can be obtained directly from Ek and can be considered li…