Biomedical subjects

Christian Van Alsenoy

Publications and source records attributed to Christian Van Alsenoy.

12 recordsLinked to original sources

PubMed2006

Hartree-Fock energy partitioning in terms of Hirshfeld atoms.

A Hirshfeld decomposition scheme of the Hartree-Fock total molecular energy into atomic energies is presented. The calculations are performed by direct numerical integration and the results are compared for a set of 28 molecules containing different kinds of atoms. The calculated atomic energies show a strong dependency on changes of atomic electron population and hybridization. Linear correlations are found between the energy and the population for H, these being related to the electronegativity of this atom and to the external potential created by the remaining atoms. The proposed energy partitioning scheme appears to be useful for studies such as proton acidity, the anomeric effect and group transferability, and allows atomic virial ratios to be obtained. Finally, the atomic potential energies are found to mimic trends based on exact expressions as well as trends displayed by molecular quantities, thus lending credibility to the partitioning scheme used.

Journal Article↗

PubMed2006

Study of molecular quantum similarity of enantiomers of amino acids.

Molecular quantum similarity is evaluated for enantiomers in the case of molecules showing conformational flexibility, using our earlier proposed Boltzmann weighted similarity index. The conformers of the enantiomers of the amino acids alanine, asparagine, cysteine, leucine, serine, and valine were examined. Next to studying global indices, the evaluation of local similarity is carried out using our earlier proposed local similarity index based on the Hirshfeld partitioning, to further illustrate Mezey's holographic electron density theorem in chiral systems and to quantify dissimilarity of enantiomers.

Amino Acids↗

PubMed2006

5,6,7,8-Tetrafluoro-3lambda4delta2,1,2,4-benzothiaselenadiazine, 5,6,7,8-tetrafluoro-1,3lambda4delta2,2,4-benzodithiadiazine, and their hydrocarbon analogues: molecular and crystal structures.

5,6,7,8-Tetrafluoro-3lambda4delta2,1,2,4-benzothiaselenadiazine (1) is prepared by the intramolecular nucleophilic cyclization of C6F5SeN=S=NSiMe3 (2) mediated by CsF. According to an X-ray diffraction analysis, the heterocycle of 1 is bent along the Se(1)...N4 line by 6.0(2) degrees in the crystal. Despite the obvious similarities between 1 and its 1,3-dithia analogue (7) with respect to molecular composition and shape, the crystal packing of 1 is substantially different from that of 7. An interesting consequence of this is the inclusion of atmospheric N2 in the crystal lattice of the selenium derivative 1. The molecular structure and bonding of 1 have been investigated using quantum-chemical calculations at the DFT/B3LYP/6-311+G level of theory, and the results have been compared to those of 5,6,7,8-tetrafluoro-1,3lambda4delta2,2,4-benzodithiadiazine (7) and their hydrocarbon analogues (5 and 8).

Journal Article↗

PubMed2006

E2(CN)2 (E = S, Se) and related compounds.

A synthetic, spectroscopic, and theoretical study of Ex(CN)2 (E = S, Se; x = 1-3) is described. The X-ray structures of Se2(CN)2 and Se3(CN)2 have been determined. Se2(CN)2 crystallizes in a chiral space group with the CN groups approximately gauche.

Journal Article↗

PubMed2005

Joint QTAIM and Hirshfeld study of the sigma and pi charge distribution and electron delocalization in carbonyl compounds: a comparative study with the resonance model.

Atomic charges and delocalization indexes (DIs) for a series of carbonyl compounds comprising dimethyl ketone, acetaldehyde, acetic acid, methyl acetate, acetamide, methyl vinyl ketone, divinyl ketone, and benzoic acid were studied using two different atomic partitionings: the QTAIM and the Hirshfeld (stockholder) scheme. The resonance model, traditionally employed to explain the reactivity of these compounds, is not in line with the total atomic charges and DIs calculated by both methodologies. However, the resonance model is supported to some extent by the pi charges and pi DIs calculated by both schemes, but the calculated values indicate that the pi population delocalizes only to a small degree. Although the absolute values of QTAIM and stockholder atomic charges are significantly different, the pi charges and the values of the DIs show similar trends for all the atoms and molecules of this study; this is especially the case for the pi DIs. A study of the electron density on the level of a single MO performed for CO, H2CO, F2CO, and H2CS reveals that the differences in the atomic sigma charges computed with both partitionings can be traced back to their different treatment of interatomic regions.

Journal Article↗

PubMed2005

Topological study of intramolecular hydrogen bonding in beta-hydroxyethylperoxy radical and beta-hydroxyethoxy radical along its dissociation pathway.

The presence of intramolecular hydrogen bond (IHB) in beta-hydroxyethylperoxy and beta-hydroxyethoxy radicals was investigated using the QTAIM topological study on UB3LYP/6-311++G(2d,2p) charge densities. Only one of the two conformers of beta-hydroxyethylperoxy radical which were previously considered to present IHB displays a bond critical point (BCP) associated to an IHB. Furthermore, the atomic energies and electron populations indicate no evidence of IHB in the second conformer. Nevertheless, very small differences in molecular energies were obtained using several one-step and multi-step methods (G3, G3B3) between both conformers. No BCP is found between the hydroxyl hydrogen and the oxygen in the most stable conformer or in the transition state for the dissociation path of beta-hydroxyethoxy radical. However, a BCP is formed in the last steps of this path, thereby yielding H-bonded products.

Ethylene Glycols↗

PubMed2005

Does a stabilising interaction favouring the Z,Z configuration of -S-N=S=N-S- systems exist?

The existence of the orbital interaction presented in the literature as being the cause for the stabilisation of the Z,Z configuration of Ph-S-N=S=N-S-Ph (1) and its derivatives in the crystal phase, has been investigated. The results of theoretical calculations at the DFT/B3LYP/6-311+G* level of theory suggest that such a stabilising interaction might not exist or be extremely weak and that packing forces must be the main cause of the observed Z,Z configuration in the solid. To reach this conclusion structural and energetic parameters were combined to study the bonding in these -S-N=S=N-S- systems. For the analogous Ph-Se-N=S=N-Se-Ph (2) in particular the isomeric equilibrium in solution found in the variable-temperature 77Se NMR spectrum indicates that, in the gas phase or in solution, the observed Z,Z configuration is not stabilised to a greater extent than the Z,E configuration.

Journal Article↗

PubMed2005

Multidimensional description of the aromaticity in planar five-membered NSNS ring systems.

The effect of the ring-closing fragment on the aromaticity of planar five-membered rings containing an NSNS fragment is investigated systematically. The influence of changing the group or period number of the ring-closing atom is studied as well as the effect of a substituent on this ring-closing element. Two sets of four five-membered ring systems were investigated. To reach a multidimensional description of the aromaticity, a robust set of geometrical, magnetic and energetic aromaticity criteria were combined. pi-Electron populations based on the stockholder scheme were calculated and lead to a quantity that correlates to the other aromaticity criteria. A third set of molecules was introduced to verify the conclusions.

Journal Article↗

PubMed2003

Molecular and crystal properties of E-1,2-bis(3-methoxy-2-thienyl)ethene: static disorder in the crystal.

The crystal structure of E-1,2-bis(3-methoxy-2-thienyl)ethene (C12H12O2S2) has been determined at five different temperatures, i.e. room temperature (293), 223, 173, 123 and 93 K. The solid-state work is complemented by the results of theoretical calculations of energies, geometries, difference electron densities and atomic charges of the free molecule. Analysis revealed static disorder caused by a higher energy conformer of the title compound, probably contaminating the crystal during its growth. The results support the contention that the electrical properties are mainly governed by the carbon backbone.

Journal Article↗

PubMed2003

Ab initio study of the binding of Trichostatin A (TSA) in the active site of histone deacetylase like protein (HDLP).

Histone deacetylase (HDAC) inhibitors have recently attracted considerable interest because of their therapeutic potential for the treatment of cell proliferative diseases. An X-ray structure of a very potent inhibitor, Trichostatin A (TSA), bound to HDLP (an HDAC analogue isolated from Aquifex aeolicus), is available. From this structure, an active site model (322 atoms), relevant for the binding of TSA and structural analogues, has been derived, and TSA has been minimized in this active site at HF 3-21G* level. The resulting conformation is in excellent accordance with the X-ray structure, and indicates a deprotonation of the hydroxamic acid in TSA by His 131. Also, a water molecule was minimized in the active site. In addition to a similar deprotonation, in accordance with a possible catalytic mechanism of HDAC as proposed by Finnin et al. (M. S. Finnin, J. R. Donigian, A. Cohen, V. M. Richon, R. A. Rifkind and P. A. Marks, Nature, 1999, 401, 188-193), a displacement of the resulting OH- ion in the active site was observed. Based on these results, the difference in energy of binding between TSA and water was calculated. The resulting value is realistic in respect to experimental binding affinities. Furthermore, the mechanism of action of the His 131-Asp 166 charge relay system was investigated. Although the Asp residue in this motif is known to substantially increase the basicity of the His residue, no proton transfer from His 131 to Asp 166 was observed on binding of TSA or water. However, in the empty protonated active site, this proton transfer does occur.

Bacterial Proteins↗

PubMed2003

The vibrational spectra of E-1,2-bis(3-methoxy-2-thienyl)ethene in the crystalline phase.

Density functional theoretical (DFT) calculations using the 6-311+G* basis set were carried out to study the vibrational spectrum of E-1,2-bis(3-methoxy-2-thienyl)ethene in the solid state. Based on the calculated frequencies, infrared intensities and potential energy distributions (PED), the experimental IR and Raman spectra of the solid phase were assigned.

Chemistry Techniques, Analytical↗

PubMedDate not supplied

Quality of approximate electron densities and internal consistency of molecular alignment algorithms in molecular quantum similarity.

The calculation of molecular quantum similarity measures using the molecular electron density requires the electron density and molecular alignment between two molecules. To obtain meaningful quantum similarity matrices, the electron density should be calculated efficiently and accurately and the alignment should be internally consistent. The internal consistency of the alignment for a series of molecules is investigated through distance geometry concepts. The calculation of the quantum similarity matrix requires the calculation of a quadratic number of similarity integrals, and a scheme to obtain these efficiently is developed. Both the alignment procedure and the ASA method for approximate molecular electron densities are tested for a set of steroid molecules.

Journal Article↗