Molecular modeling of diphenylalanine peptide nanotubes (FF PNT) is performed using PM3 method in HyperChem. The study focuses on the polar properties of FF PNT structures having different chiralities (L, D) and conformations (alpha-helix, beta-sheet). The results show that the optimized structures for L-PNT possess higher polarization in both conformations (0.023 C/m(2) - alpha, 0.04 C/m(2) - beta) compared with D-PNT (0.016 C/m(2) - alpha, 0.014 C/m(2) - beta). The water structures inside PNT are investigated, too. The hexagonal ice/water structures used for these models are analyzed in respect to the XRD data recently obtained.

The electron and electrostatic properties of piroxicam (PX) were derived from high resolution X-ray diffraction experiments carried out at 100 K.

A new target in AIDS therapy development is HIV-1 integrase (IN). It was proven that HIV-1 IN required divalent metal cations to achieve phosphodiester bond cleavage of DNA. Accordingly, all newly investigated potent IN inhibitors contain chemical fragments possessing a high ability to chelate metal cations. One of the promising leads in the polyhydroxylated styrylquinolines (SQLs) series is (E)-8-hydroxy-2-[2-(4,5-dihydroxy-3-methoxyphenyl)-ethenyl]-7-quinoline carboxylic acid (1). The present study focuses on the quinoline-based progenitor (2), which is actually the most probable chelating part of SQLs. Conventional and synchrotron low-temperature X-ray crystallographic studies were used to investigate the chelating power of progenitor 2. Mg2+ and Cu2+ cations were selected for this purpose, and three types of metal complexes of 2 were obtained: Mg(II) complex (4), Cu(II) complex (5) and mixed Mg(II)-Cu(II) complexes (6 and 7). The analysis of the crystal structure of complex 4 indicates that two tridentate ligands coordinate two Mg2+ cations, both in octahedral geometry. The Mg-Mg distance was found equal to 3.221(1) A, in agreement with the metal-metal distance of 3.9 A encountered in the crystal structure of Escherichia coli DNA polymerase I. In 5, the complex is formed by two bidentate ligands coordinating one copper ion in tetrahedral geometry. Both mixed Mg(II)-Cu(II) complexes, 6 and 7 exhibit an original arrangement of four ligands linked to a central heterometallic cluster consisting of three octahedrally coordinated magnesium ions and one tetrahedrally coordinated copper ion. Quantum mechanics calculations were also carried out in order to display the electrostatic potential generated by the dianionic ligand 2 and complex 4 and to quantify the binding energy (BE) during the formation of the magnesium complex of progenitor 2. A comparison of the binding energies of two hypothetical monometallic Mg(II) complexes with that found in the bimetallic magnesium complex 4 was made.

Piperidine and 1,1,1-3,3,3 hexafluoro-2-propanol (HFIP) have been co-crystallized and X-ray crystal structure has been explored. Single-crystal X-ray analysis displays the existence of hydrogen bonding aggregates through dimers 1 of the complex (one piperidine/two HFIP) where the heteroatoms form a six-center ring. In this cluster 1, each heteroatom (N, O) is multiple H-bond donor and acceptor. Surprisingly the strongest H-bond of the network is where HFIP acts as an acceptor from the amine. In this complex HFIP adopts a conformation different from that of HFIP aggregates. The supramolecular architecture is also based on discrimination between polar and hydrophobic parts that allows the alignment of molecules and the formation of parallel channels. NMR experiments show that strong interactions between piperidine and HFIP are maintained in solution.

Organoclays were prepared from two tunisian purified Na-bentonites using benzyltetradecyldimethylammonium chloride (C14) and benzyldodecyldimethylammonium chloride (C12). The added quantities of organic salts, expressed as a function of the clay's cationic exchange capacity (CEC), have been varied from 0.3 to 4 CEC. Two different methods were investigated in order to determine the influence of the preparation method on the adsorption properties: on one hand, dry powder clay (method I) and, on the other hand, aqueous clay suspensions (method II) were mixed with the organic salt solutions. The adsorption of organic cations on clays was studied by adsorption isotherms, FTIR spectroscopy and X-ray diffraction. It appears that more salts are adsorbed in the clay interlayer space when using method II. The arrangement of salts within clay is rather complicated. It depends on clay composition, nature of tensioactive molecules, CEC of the clay, and preparation method. According to these parameters, the inserted surfactants can be arranged in monolayer, paraffin, or admicelles structures.

24 European Crystallographic Meeting, ECM24, Marrakech, 2007 Page s163 Acta Cryst. (2007). A63, s163 MS14 P05 Atomic Surface Modeling and AIM Charges Nouzha Bouhmaida, Nour Eddine Ghermani, Paul Louis George, Patrick Laug and Pascal J. Frey. Laboratoire des Sciences des Materiaux, LSM, Universite Cadi Ayyad, Faculte des Sciences Semlalia, Boulevard Prince Moulay Abdallah, BP 2390, 40000 Marrakech, Morocco. Laboratoire de Physique Pharmaceutique, UMR CNRS 8612, Universite Paris-Sud 11, Faculte de Pharmacie, 5 rue Jean-Baptiste Clement, 92296 Châtenay-Malabry, France. Projet Gamma, INRIA, Domaine de Voluceau–Rocquencourt BP 105, 78153 Le Chesnay cedex, France. Laboratoire Jacques Lions, Universite Pierre et Marie Curie, 175 rue du Chevaleret, 75013 Paris, France. E-mail : nouzha@ucam.ac.ma

A new discrete supramolecular pseudo-helicate has been obtained from a saturated heterotopic methylbipyrazyl–methylbipyridyl ligand strand and NiCl2. The X-ray structure of the dinuclear complex shows the 2-oxapropylene bridge oxygen atoms are engaged in coordination to the octahedral metal centre and a selective ligand inter-strand orientation is promoted in the complex. The crystal packing shows a perfect regular linear arrangement of the asymmetric units giving a packing of interacting molecules having well-defined rectangular and polygonal open channels. Although a paramagnetic behaviour is observed above 10 K, below this temperature a significant deviation of this behaviour suggests the presence of an NiII–NiII magnetic coupling. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)

In our course of obtaining new organic-inorganic complexes built up of flexible dicarboxylate ligands, we have noticed the peculiar behavior of the ligands derived from glutaric acid. Linked to rareearth or alkaline-earth metals, they lead to a wide variety of structural types : catena polynuclear complex [1], uncommon cage feature [2], isolated polyhedra [3] involving completely or partially deprotonated unities. The new strontium biglutarate has been obtained on single crystal form via silica medium synthetic route. It is different from barium biglutarate in that it completes its coordination sphere by two coordinated water molecules, and crystalizes in space group P . The metal is nine coordinated forming infinite chains of one-antiprism SrO7(H2O)2 within which te distance between two neighbouring Sr ions are 4.272(6)Å. These chains are cross-linked, leading to a layered structure.

In our course of obtaining new organic-inorganic complexes built up of flexible dicarboxylate ligands, we have noticed the peculiar behavior of the ligands derived from glutaric acid.Linked to rareearth or alkaline-earth metals, they lead to a wide variety of structural types : catena polynuclear complex [1], uncommon cage feature [2], isolated polyhedra [3] involving completely or partially deprotonated unities.The new strontium biglutarate has been obtained on single crystal form via silica medium synthetic route.It is different from barium biglutarate in that it completes its coordination sphere by two coordinated water molecules, and crystalizes in space group P .The metal is nine coordinated forming infinite chains of one-antiprism SrO 7 (H 2 O) 2 within which te distance between two neighbouring Sr 2+ ions are 4.272(6)Å.These chains are cross-linked, leading to a layered structure.

The aim of this study is to probe the crystal density (Dc) description in terms of pertinent molecular characteristics and properties. In this purpose, the electrostatic potential was derived from available experimental electron density multipole parameters of molecular compounds with different Dc magnitudes. The surface electrostatic potential has been analyzed through the positive and negative statistical variances. The surface of the molecule is here corresponding to particular isodensity values according to Bader’s topological theory. Following the successful Politzer’s method based on quantum mechanics calculations to empirically describe macroscopic properties, the crystal density was regressed on the molecular density and the surface electrostatic potential variance. This latter appears to be a poor statistical descriptor of the crystal density when the experimentally derived electrostatic potential is used and it does not significantly improve the fit of Dc to molecular density alone. Compared to Politzer’s approach based on gas phase isolated molecules, the experimental electrostatic potential is biased by the interactions in the crystal lattice. As an alternative to other sophisticated methods, the promolecule isodensity surface offers a quite useful and straightforward way to define the molecular volumes. The reported description of the crystal density for a set of 50 molecules using the promolecule approach yields satisfactory results.

Four novel his (heterocyclic) sequences, which incorporate a 2,2'-bipyridine system with the 2,2'-bithiazole, 4,4'-bithiazole, 2,2'-bipyrazine or 4,4'-bipyrimidine units, have been synthesized. In the presence of stoichiometric amounts of Cu-I, Ag-I or Zn-II cations, fully oriented discrete head-to-head (H-H) or head-to-tail (H-T) species have been observed by NMR and X-ray crystallography. The orientation of the ligands in the Ag-I, Cu-I or Zn-II dinuclear complexes during the self-assembly process appears to be under the control of electronic factors relating to the electronic configuration of the different his (heterocyclic) sequences. ((C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004).

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

1. High resolution X-ray diffraction data Collecte at 100K on a Smart CCD diffractometer 2. Data refinement by the Hansen-Coppens (2) multipole model 3. Characterization of the chemical bonds and the electrophilic/nucleophilic characters of the two precursors: electron density topological properties and the electrostatic potential 4. Comparaison between the experimental results and the ab initio quantum mechanic calculations for (2) and (3) isolated molecules 5. Theorical calculations for (1) molecule Styrylquinoline derivatives are potent inhibitors of the HIV-1 virus integrase activity (1). The biologically tested molecules contain one aromatic part connected to the quinoline group through different chemical spacers. The most promising molecule in the inhibition of the HIV-1 integrase is the (E)-8-hydroxy-2[2-(4,5-dihydroxy-3-methoxyphenyl)-ethenyl]-7-quinolinecarboxylic acid (1) where the spacer is a C=C double bond. The crystallization of this molecule is particularly difficult giving rise to very small needle-shape crystals which are instable in time. In order to recover the molecular property, we have synthesized and crystallized the two precursors of this molecule: the 3', 4', 5'-methoxy-dihydroxy benzaldehyde aromatic part (2) and the 8-hydroxy-7-quinolinic acid (3).

In this paper new aspects on the self-assembly processes of didentate coordinating ligands leading to a double-stranded helicate are described. It was reported, that directionality in the self-recognition of Cu, ions could be driven by factors relating to the electronic configuration of heterocycles in carefully designed heterotopic ligands. If the sequential bipyrazine-bipyridine ligand strand 4 reacts with 1 equiv. of Cu-I the dimetallic complex [Cu-2(L4)(2)][PF6](2) is formed in a cooperative process. In this coordination compound the two strands are oriented in opposite directions (HT) as illustrated by the X-ray structure of [Cu-2(L4)(2)][PF6](2).

The present study focuses on the electric field features and related physical properties which can be derived from the topology of the experimental electrostatic potential. These properties were retrieved from the electron density multipole refinement of high-resolution x-ray data collected on a racemic crystal of ibuprofen drug. The electric field lines are depicted around the molecule revealing gradient vector zero flux atomic basins and critical points (CP’s) having a different significance than that brought out by the topology of the electron density. This method emphasizes a partioning of the molecular system mainly governed by the nuclear–electron interaction. The concept of Slater’s nuclear screening is here explored from the inspection of the gradient field zero flux surface separating the atoms in the molecule. Moreover, empirical parameters like covalent or atomic bond radii are accurately estimated from CP–atom distances in the molecular heteroatomic bonds. The local minima of the electrostatic potential are searched around the ibuprofen molecule in order to locate the binding sites for further molecular interactions with biological targets or with excipients in pharmaceutical preparations. Ibuprofen dipole moment is also estimated by a method based upon the fit to the experimental electrostatic potential values generated around the molecule.

Charge distribution plays a dominant role in conformational studies on molecules or solids.Conformational analysis relies on the minimization of empirical potential energy functions which imply a large number of parameters.A major part of conformational energy is of coulombic origin, and thus totally controlled by the charge density.Since the calculation of this density is computationally very expensive for large systems, most programs use a 'naive' approach, simulating the density by a set of point charges and dipoles adjusted from quantum calculations on small molecules, and therefore transferable within a large set of molecule environment : this often constitutes a poor approximation to the problem, leading to biased results concerning the effective conformation of the system.A simple method is introduced to predict the electron density in large molecules.A molecule is decomposed into subsystems, the density of which can be considered as additive with a controlled accuracy.This method is based on the Hirshfeld's partitioning scheme, which is very general and independent on any basis set.For a complex molecule we predict a model density built upon fragments that are transferred from simpler systems.The method is compared with Mezey's approach.A significant difference arises when transferability is considered and our approach is not sensitive to basis set problems.Conformational energies of the complex system are then predicted from the model density, using a density functional scheme, and are compared with ab-initio results.The prediction of the variations of coulombic and kinetic energies requires a very high numerical accuracy (relative accuracy better than 10 -7 !).The errors introduced by the computational calculations should thus be smaller than this threshold, which constitute a sensitive problem : for several years, many research teams have been working on improving the numerical convergence.When estimating energy changes associated with a variation of conformation, it turns out that the hypothesis of total transferability is too crude.The density of a fragment is not totally transferable between different conformations.The non-transferable part is very weak compared with the density itself, and would hardly be detected by X Ray diffraction experiments, however it has been shown that this non-transferable contribution to the density plays a dominant role in the energies variations.For polypeptides, we have found no general way to modelise the deviation of the predicted density with respect to relevant structural parameters.Nevertheless, it appears that the non-transferable density of a given fragment in a molecule can be transferred from a smaller molecule with a similar environment, in the same conformation.Let's assume a torsion around a given bond.Non transferability affects only the neighbors of that bond.The correction of the density can be estimated from a simple analog involving this bond and its immediate environment.The first model of additive fragment densities for a large system is significantly improved by introducing the non-transferable contributions calculated from smaller molecules.While using the corrected density, the predicted variations of energies now agree with ab-initio calculations with a satisfying accuracy.One can thus predict the conformational energy of a large system by using this reliable model of corrected densities, at a reasonable computational cost.s2.m2.

Volkonskoite is unique mineral from smectite group containing dominant chromium in the octahedral position.Volkonskoites are differ not only in their chromium content but also in their basic structure, the species status of the mineral has been unclear.To resolve this uncertainty we examined about 15 samples of volkonskoites from permian deposits (West Ural) by several mineralogycal techniques.Chemical analysis shows great variations in chromium content (17-30 wt.%) in volkonskoites.Calculated strutural formulas show that mineral with 17-20 wt.% of Cr 2 O 3 is dioctahedral smectite and volkonskoite with high chromium content is tridioctahedral one.But IR and X-ray characteristics indicate dioctahedral type of struture of all the volkonskoites.X-ray powder diffraction patterns of all samples have broad lines corresponding to minerals of the smectite group, and X-ray patterns of species with high chromium content indicate the presence of several smectites with different d 001 value.SEM investigations indicate the presence of different microstructures in volkonskoites: globular, acicular, tabular.The green and black varieties of volkonskoite has some differences in microstructures, IR-spectra and thermoanalytical characteristics.SEM examinations suggest to exist a continious solid solution series between volkonskoite and nontronite with Cr-Fe substitution in the octahedral position.