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Whole Molecule (whole + molecule)
Selected AbstractsHighly Symmetrical Tetranuclear Cluster Complexes Supported by p - tert -Butylsulfonylcalix[4]arene as a Cluster-Forming LigandEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 9 2006Takashi Kajiwara Abstract Square-planar tetranuclear clusters [M4(L)(AcO)4(,4 -OH)], (M = MnII, CoII, and NiII) are synthesized using tetra-anionic p - tert -butylsulfonylcalix[4]arene (L4,) as a cluster-forming ligand. Three complexes are crystallographically isostructural, being crystallized in the triclinic crystal system with space group P. The calix[4]arene acts as a tetrakis fac -tridentate ligand through four phenoxo and four sulfonyl oxygen atoms to form square arrangement of four metal ions, which are further bridged by four chelating acetate ions and one hydroxo ion in a ,4 manner to complete the hexacoordination of each metal center. Although the whole molecule of each complex is crystallographically independent, the molecule is highly symmetrical with a pseudo-four-fold axis lying on the ,4 -OH, group. The tetranuclear clusters are stable enough to maintain the core structures even in highly dilute solution (,10 ,M), which was confirmed by mass spectroscopic study, however, bridging acetates were easily exchanged by other carboxylate chelates to form derivatives such as [M4(L)(BzO)4(OH)],. Metal,metal interactions were investigated by means of magnetic susceptibility, and it was revealed that both ferro- and antiferromagnetic interactions occur in the NiII complex depending on the bridging angles of Ni,O,Ni. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source] Modeling the semi-empirical electrotopological index in QSPR studies for aldehydes and ketonesJOURNAL OF CHEMOMETRICS, Issue 5 2009Érica Silva Souza Abstract The semi-empirical electrotopological index, ISET, used for quantitative structure,retention relationship (QSRR) models firstly developed for alkanes and alkenes, was remodeled for organic functions such as ketones and aldehydes. The ISET values for hydrocarbons are calculated through the atomic charge values obtained from a Mulliken population analysis using the semi-empirical AM1 method and their correlation with the SETi values attributed to the different types of carbon atoms according to experimental data. For ketones and aldehydes the interactions between the molecules and the stationary phase are slowly increased relative to the hydrocarbons, due to the charge redistribution that occurs in the presence of heteroatoms. For these polar molecules the increase in the interactions was included in the calculation of the ISET values through the dipole moment of the whole molecule and also through an equivalent local dipole moment related to the net charges of the atoms of the CO and HCO functional groups. Our findings show that the best definition of an equivalent local dipole moment is clearly dependent on the specific features of the charge distribution in the polar region of the molecules (e.g. ketones and aldehydes), which allows them to be distinguished. Thus, the QSRR models for 15 aldehydes and 42 ketones obtained using the remodeled ISET were of good quality as shown by the statistical parameters. The ability of this remodeled index to include charge distribution and structural details opens a new way to study the correlations between the molecular structure and retention indices in gas chromatography. Copyright © 2009 John Wiley & Sons, Ltd. [source] Low- and high-spin iron (II) complexes studied by effective crystal field method combined with molecular mechanicsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2003M. B. Darkhovskii Abstract A computational method targeted to Werner-type complexes is developed on the basis of quantum mechanical effective Hamiltonian crystal field (EHCF) methodology (previously proposed for describing electronic structure of transition metal complexes) combined with the Gillespie,Kepert version of molecular mechanics (MM). It is a special version of the hybrid quantum/MM approach. The MM part is responsible for representing the whole molecule, including ligand atoms and metal ion coordination sphere, but leaving out the effects of the d -shell. The quantum mechanical EHCF part is limited to the metal ion d -shell. The method reproduces with reasonable accuracy geometry and spin states of the Fe(II) complexes with monodentate and polydentate aromatic ligands with nitrogen donor atoms. In this setting a single set of MM parameters set is shown to be sufficient for handling all spin states of the complexes under consideration. © 2003 Wiley Periodicals, Inc. J Comput Chem 14: 1703,1719, 2003 [source] Rotationally disordered phase of 1,3-dibromo-5-iodo-2,4,6-trimethylbenzene at 293 KACTA CRYSTALLOGRAPHICA SECTION C, Issue 10 2009Soumia Ghanemi In the crystal state at room temperature, the molecule of dibromoiodomesitylene (1,3-dibromo-5-iodo-2,4,6-trimethylbenzene), C9H9Br2I, is prone to strong disorder, apparently involving only the three halogen sites (occupied identically by 66.7% Br and 33.3% I). This disorder, of the rotational type according to previously published NMR measurements, corresponds to fast 2,/3 stochastic in-plane reorientations of the whole molecule between three discernable locations. This kind of rotational disorder can be revealed for the first time by diffractometry thanks to the C2v idealized molecular symmetry of the title compound, although it has been indirectly suspected at room temperature in other trihalogenomesitylenes of similar crystal packing but of D3h molecular symmetry. The average endocyclic angles facing the Br/I sites and the methyl groups are 124.14,(6) and 115.85,(2)°, respectively. The angle between the normal to the aromatic ring and the normal to the (100) plane is 4.1°. TLS analysis indicates that only the aromatic ring and the methyl groups behave as a rigid body with respect to the thermal librations. [source] Synthesis and Structural Characterization of 1,4-Di(2-methoxyphenyl)-2,5-piperazinedioneCHINESE JOURNAL OF CHEMISTRY, Issue 5 2007Shu-Sheng Zhang Abstract A new derivative of 2,5-piperazinedione, 1,4-di(2-methoxyphenyl)-2,5-piperazinedione (I), was synthesized by the cyclocondensation reaction of N -2-methoxyphenyl chloroacetamide, and its structure was characterized by elemental analysis, IR, 1H NMR and single crystal X-ray diffraction method. The crystal belongs to monoclinic system, space group P21/c with unit cell dimensions a=0.56934(10) nm, b=1.3880(2) nm, c=1.00329(17) nm, ,=90.376(3)°, V=0.7928(2) nm3, Z=2, Dc=1.367 g·cm,3, ,=0.98 cm,1, R and wR being 0.0606 and 0.1564 respectively for 1549 unique reflections with 1247 observed reflections [I>2,(I)]. The molecule has a crystallographically imposed symmetry center. The three rings in the molecule are each coplanar with their attached groups, excluding methyl H atoms and the H atoms attached to the piperazinedione ring, while the whole molecule is not planar, with dihedral angles of 74.7(1)° between the piperazinedione and each of the two aromatic rings. The crystal structure is stabilized by van der Waals and dipole-dipole forces. [source] Novel B and T cell epitopes of chicken ovomucoid (Gal d 1) induce T cell secretion of IL-6, IL-13, and IFN-,CLINICAL & EXPERIMENTAL ALLERGY, Issue 6 2001E. Holen Background Chicken ovomucoid (OM, Gal d 1) has an important role in the pathogenesis of IgE-mediated allergic reactions to hen's egg white. Objectives The purpose of this study was to clarify the mechanisms of T cell recognition of ovomucoid using intact OM and chemically modified, characterized and homogeneous solid phase synthetic peptides covering the whole molecule. Methods Eighteen overlapping peptides were prepared by solid phase F-moc polyamide peptide synthesis (SPPS), characterized and high-pressure liquid chromatography (HPLC) purified. The peptides, together with intact, denatured and oxidized OM, were used to stimulate patient-derived cell cultures for mapping T cell epitopes. Proliferation responses, T cell phenotype and cytokine secretion using peripheral blood mononuclear cells (PBMC) from eight individuals and T cell lines (TCL) derived from six hen's egg-allergic patients, were examined. In addition, intact, denatured, oxidized and deglycosylated OM, as well as the peptides solely or with their keyhole limpet haemocyanin (KLH) complexes, were tested. For locating IgE and IgG B cell epitopes, seven egg-allergic patient sera and three OM-polyclonal sera were used. Healthy non-allergic individuals were included as controls. Results Seven peptides were recognized by specific IgE, while OM-specific TCL recognized 10 peptides. Six of the OM peptides were commonly recognized both by patient S-IgE and blood-derived TCL. Among those, one novel epitope, peptide OM 61,74, had the ability to bind IgE. Another peptide, OM 101,114, was recognized by IgE and IgG sera, but not by any of the TCLs. In contrast, the peptides OM 41,56, OM 71,84, OM 131,144 and OM 171,186 were exclusively T cell epitopes with no affinity to specific antibodies. Abundant TCL secretion of IFN-,, IL-6, IL-4, IL-13, IL-10 and TNF-, in response to OM stimulation indicates the contribution of Th2 as well as Th1/Th0 CD4+ cell subsets. For allergic patients moderate amounts of IFN-,, IL-13, and high amounts of IL-6, were secreted in response to TCL stimulation by OM peptides. High amounts of IL-6 were secreted in response to all molecular forms of OM (intact-, modified-OM and the peptides 71,84 and 51,64) when TCLs from two non-allergic donors were used. Conclusions One novel B cell epitope (OM 61,74) and 10 T cell epitopes have been identified. The most reactive epitopes of the OM molecule comprise the motifs 1,14 to 71,84, the overlapping peptide-pairs OM 121,134 and OM 131,144 and peptides OM 161,174 and 171,186. Peptides OM 1,14 and 171,186 are the only ones capable of inducing IL-4 secretion. Only one peptide (OM 11,24) induces IL-10 secretion. Those peptides recognized as both T and B cell epitopes or only T cell epitopes, have the potential to induce T cell secretion of moderate to high amounts of IL-13, IFN-, and particularly IL-6. [source] Synthesis and crystal strcucture of two zinc inclusion complexesCRYSTAL RESEARCH AND TECHNOLOGY, Issue 8 2008Min-Le Han Abstract X-ray single crystals of these two inclusion complexes, [Zn(H2O)4L2]·(4-amino-1-naphthalene sulfonate)2 (L = 1,3-bis(4-pyridyl) propane), 1, and [Zn(H2O)(bipy)2]·(4-amino-1-naphthalene sulfonate)(NO3) (bipy = 4,4'-bipyridine), 2 were achieved by the reaction of Zn(NO3)2 and 4-amino-1-naphthalene sulfonate to 1,3-bis(4-pyridyl) propane and 4,4'-bipyridine, respectively. As inclusion complexes, the cationic components of 1 and 2 were formed by two infinite zigzag chains, while, 4-amino-1-naphthalene sulfonate made up the anionic parts of these two complexes. Thus, the whole molecules of these two complexes are neuter. Numous hydrogen bonds could be found in these two inclusion complexes, which help them to form three-dimensional solid-state packing structure architectures. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Structural transformations in organic crystals during photochemical reactionsJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 10 2004Ilona Turowska-Tyrk Abstract In the 1980s and 1990s, x-ray studies of the photochemical reaction course in crystals dealt with the analysis of changes in cell constants or movements of atom groups inside molecules. This review presents the results of crystallographic studies on the monitoring of the behaviour of whole molecules in organic crystals during photochemical reactions. Papers on this subject started to appear only a few years ago. The studies showed quantitatively that reactant and product molecules do not take a fixed position in a crystal during the reaction. The product molecules move smoothly to a position assumed in the pure product crystal and the reactant molecules move from a position occupied in the pure reactant crystal. Moreover, with the reaction progress the adjacent reactant molecules gradually come closer and change their mutual orientation to resemble the product. The analysis of the photoreaction kinetics in crystals is also presented. Copyright © 2004 John Wiley & Sons, Ltd. [source] | ||||||||||