ToBaD: A method for the estimation of torsion barriers from crystal structure data; conformational analysis of N,N-dimethylaniline and derivatives

A new method for the estimation of torsion barriers and its application to conformational analysis is presented. This method, the ToBaD method (method of the torsion barrier derivative), makes use of crystal structure data. It is based on the assumption that the conformation of a compound in the crystalline phase must be very close to a (local) minimum energy conformation of this compound in the gas phase. The ToBaD method is demonstrated for the rotation of the phenyl-N bond in N,N-dimethylaniline. Two geometries of this compound are handled separately: one in which the nitrogen substituents are in a pyramidal or sp³ geometry, and the other in which the nitrogen atom and its substituents are coplanar (the sp² geometry). It is predicted, by means of the ToBaD method, that for both geometries the conformation in which the nitrogen lone pair or p orbital is perpendicular to the aromatic ring is the lowest energy conformation. © 1994 by John Wiley & Sons, Inc.     

Intrinsic equations for a generalized relaxed elastic line on an oriented surface in the galilean space

In this article, we derive the intrinsic equations for a generalized relaxed elastic line on an oriented surface in the Galilean 3-dimensional space G₃. These equations will give direct and more geometric approach to questions concerning about generalized relaxed elastic lines on an oriented surface in G₃.     

Lentivirus-mediated transgene delivery to the hippocampus reveals sub-field specific differences in expression

Background  

In the adult hippocampus, the granule cell layer of the dentate gyrus is a heterogeneous structure formed by neurons of different ages, morphologies and electrophysiological properties. Retroviral vectors have been extensively used to transduce cells of the granule cell layer and study their inherent properties in an intact brain environment. In addition, lentivirus-based vectors have been used to deliver transgenes to replicative and non-replicative cells as well, such as post mitotic neurons of the CNS. However, only few studies have been dedicated to address the applicability of these widespread used vectors to hippocampal cells in vivo. Therefore, the aim of this study was to extensively characterize the cell types that are effectively transduced in vivo by VSVg-pseudotyped lentivirus-based vectors in the hippocampus dentate gyrus.     

The need for knowledge and reliability in numeric computation: Case study of multivariate Padé approximation

In this paper we review and link the numeric research projects carried out at the Department of Mathematics and Computer Science of the University of Antwerp since 1978. Results have and are being obtained in various areas. A lot of effort has been put in the theoretical investigation of the multivariate Padé approximation problem using different definitions (see Sections 3 and 7). The numerical implementation raises two delicate issues. First, there is the need to see the wood for the trees again: switching from one to many variables greatly increases the number of choices to be made on the way (see Sections 1 and 5). Second, there is the typical problem of breakdown when computing ratios of determinants: the added value of interval arithmetic combined with defect correction turns out to be significant (see Sections 2 and 4). In Section 6 these two problems are thoroughly illustrated and the interested reader is taken by the hand and guided through a typical computation session. On the way some open problems are indicated which motivate us to continue our research mainly in the area of gathering and offering more knowledge about the problem domain on one hand, and improving the arithmetic tools and numerical routines for a reliable computation of the approximants on the other hand.     

Thermal decomposition of barium oxalate hemihydrate BaC2O4·0.5H2O

The thermal behaviour of BaC₂O₄sd0.5H₂O and BaCO₃ in carbon dioxide and nitrogen atmospheres is investigated as part of a study about the thermal decomposition of barium trioxalatoaluminate. For this purpose thermogravimetry, differential thermal analysis, differential scanning calorimetry and high temperature X-ray diffraction were used. An infrared absorption spectrum of BaC₂O₄·0.5H₂O was scanned at room temperature.At increasing temperature, in dry nitrogen, the hydrate water of BaC₂O₄· 0.5H₂O is split off, followed by the oxalate decomposition. A part of the evolved carbon monoxide disproportionates, leaving carbon behind. At higher temperatures the latter reacts with barium carbonate, previously formed. Finally the residual solid barium carbonate decomposes into barium oxide and carbon dioxide.In dry carbon dioxide atmosphere an analogous dehydration occurs, followed by oxalate decomposition. Under these conditions the carbon formation is fully suppressed, and as a consequence no secondary reaction occurs. The barium carbonate decomposition is shifted to much higher temperatures, at a low rate in the solid phase, a strongly accelerated one at the onset of melting, and a moderated one when the melt is saturated with barium carbonate. The two phase transitions of BaCO₃ are detectable in both atmospheres mentioned.     

Virtual screening using protein-ligand docking: avoiding artificial enrichment

This study addresses a number of topical issues around the use of protein-ligand docking in virtual screening. We show that, for the validation of such methods, it is key to use focused libraries (containing compounds with one-dimensional properties, similar to the actives), rather than "random" or "drug-like" libraries to test the actives against. We also show that, to obtain good enrichments, the docking program needs to produce reliable binding modes. We demonstrate how pharmacophores can be used to guide the dockings and improve enrichments, and we compare the performance of three consensus-ranking protocols against ranking based on individual scoring functions. Finally, we show that protein-ligand docking can be an effective aid in the screening for weak, fragment-like binders, which has rapidly become a popular strategy for hit identification. All results presented are based on carefully constructed virtual screening experiments against four targets, using the protein-ligand docking program GOLD.     

Multivariate rational data fitting: general data structure,maximal accuracy and object orientation

Sections 1 and 2 discuss the advantages of an object-oriented implementation combined with higher floating-point arithmetic, of the algorithms available for multivariate data fitting using rational functions. Section 1 will in particular explain what we mean by higher arithmetic. Section 2 will concentrate on the concepts of object orientation. In sections 3 and 4 we shall describe the generality of the data structure that can be dealt with: due to some new results virtually every data set is acceptable right now, with possible coalescence of coordinates or points. In order to solve the multivariate rational interpolation problem the data sets are fed to different algorithms depending on the structure of the interpolation points in then-variate space.This text is a preparatory publication for the development of a scientific expert system for multivariate rational interpolation. The issues addressed are relevant to the implementation of such a system.