Efficient multipole expansion: Choice of order and density partitioning techniques

Two approaches to improve the convergence of the multipole series were considered: 1) an increase in the order of the expansion; 2) decomposition of the molecular charge density into smaller distributions. New decompositions of the molecular electronic density and a computational procedure to generate high-order moments are presented. The accuracy and timing of test calculations on the H₂O ... H₂O system are given and suggestions are made for optimizing the choice of an expansion for more general systems.We express our appreciation to the National Institutes of Health which supported this work under Grant 1 R01 GM 20436-02.     

Use of circular variance to quantify the deviation of a macromolecule from the spherical shape

It is shown that the extent of deviation of a molecular shape from spherical can be characterized by comparing the distribution of the circular variances, a measure originally proposed to quantify angular spread, of the vectors from each atom to the rest of the molecule to the circular variance of a collection of atoms filling the unit sphere. Different measures for quantifying the difference between distribution are proposed and compared.     

Analytical selenoamino acid studies by chromatography with interfaced atomic mass spectrometry and atomic emission spectral detection

Consumption of selenium enriched plants or yeast-based nutritional supplements has been reported to provide anticarcinogenic benefits which are selenium compound dependent. Separation and identification of these selenium compounds is critical to understand the activity. Plants and yeast convert inorganic selenium in the soil or growth media into organoselenium compounds, probably following a route similar to the sulfur assimilatory pathway. Non-volatile selenium compounds produced include selenoamino acids, some of which have shown anticarcinogenic activity. Volatile compounds produced by chemical reaction of involatile precursors have also been found. An ion pair chromatographic method with ICP-MS detection for the separation of selenoamino acid standards potentially present in real samples is given. The method allows separation of selenoamino acids including such analytes as the cis-trans isomers of Se-1-propenyl-dl-selenocysteine. The method also provides the capability of determining the presence of selenoxides and possibly selenones, and tracking of other functionalities and reactions by selective derivatization. Alternatively, selenoamino acids are treated with ethylchloroformate to produce stable volatile derivatives which are amenable to GC separation with element specific atomic emission detection (GC-AED). Results of total selenium determination and speciation of selenium enriched yeast-based nutritional supplements, selenium enriched allium vegetables and bioremediation samples are presented.     

Determination of selenocysteine and selenomethionine in edible animal tissues by 2D size-exclusion reversed-phase HPLC-ICP MS following carbamidomethylation and proteolytic extraction

A method was developed for the simultaneous determination of selenomethionine (SeMet) and selenocysteine (SeCys) in meat (chicken and lamb muscles) and different offal tissues (heart, liver, kidney). The analytical procedure was based on the protein extraction with urea under reducing conditions (dithiothreitol), derivatization of SeCys and SeMet by carbamidomethylation with iodoacetamide (IAM) followed by quantitative proteolysis. The mixture of the derivatized Se-amino acids was purified by size-exclusion liquid chromatography (LC) and analysed by ion-paring reversed-phase HPLC–inductively coupled plasma mass spectroscopy (ICP MS). The quantification of SeCys and SeMet was carried out by the method of standard additions. ⁷⁷SeMet was used to control the SeMet derivatization efficiency and recovery. The method was validated by the determination of the Se mass balance. The Se-amino acids accounted for 91 ± 8% of the total selenium (mean of 95 samples of seven tissues analysed over a period of 18 months). The method was applied to the discrimination of the contribution of selenoproteins (containing SeCys) and other Se-containing proteins (containing SeMet) in tissues of animals during supplementation studies (dose–effect and tolerance).     

Standardless identification of selenocystathionine and its gamma-glutamyl derivatives in monkeypot nuts by 3D liquid chromatography with ICP-MS detection followed by nanoHPLC-Q-TOF-MS/MS

A three-step chromatographic procedure using orthogonal separation mechanisms (size-exclusion, cation-exchange and ion-pairing reversed phase) was developed to purify three low molecular weight selenospecies, including the major compound, from the aqueous extract of monkeypot (Lecythis minor) nuts. The following reversed-phase nanoHPLC-electrospray Q-TOF-MS/MS allowed the formal standardless identification of selenocystathionine and two isoforms of gamma-glutamyl-selenocystathionine. This is the first MS and MS/MS-based formal evidence of the presence of these compounds in a biological sample.     

DFTB+, a sparse matrix-based implementation of the DFTB method

A new Fortran 95 implementation of the DFTB (density functional-based tight binding) method has been developed, where the sparsity of the DFTB system of equations has been exploited. Conventional dense algebra is used only to evaluate the eigenproblems of the system and long-range Coulombic terms, but drop-in O(N) or O(N2) modules are planned to replace the small code sections that these entail. The developed sparse storage structure is discussed in detail, and a short overview of other features of the new code is given.     

TRAJELIX: A Computational Tool for the Geometric Characterization of Protein Helices During Molecular Dynamics Simulations

Summary We have developed a computer program with the necessary mathematical formalism for the geometric characterization of distorted conformations of alpha-helices proteins, such as those that can potentially be sampled during typical molecular dynamics simulations. This formalism has been incorporated into TRAJELIX, a new module within the SIMULAID framework (http://inka.mssm.edu/~mezei/simulaid/) that is capable of monitoring distortions of alpha-helices in terms of their displacement, global and local tilting, rotation around their axes, compression/extension, winding/unwinding, and bending. Accurate evaluation of these global and local structural properties of the helix can help study possible intramolecular and intermolecular changes in the helix packing of alpha-helical membrane proteins, as shown here in an application to the interacting helical domains of rhodopsin dimers. Quantification of the dynamic structural behavior of alpha-helical membrane proteins is critical for our understanding of signal transduction, and may enable structure-based design of more specific and efficient drugs.     

Dielectric response enhancement in the current carrying CDW state

The dc electric field dependence of the low frequency dielectric constant was investigated in the linear chain compound orthorhombic TaS₃. While the dielectric constant is barely effected by an applied dc field below the threshold field of the nonlinear conduction, in the current carrying state a large enhancement is observed. Inductive response at the narrow band noise frequency was also detected.