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Acceptor Atoms (acceptor + atom)
Selected AbstractsTopological properties of hydrogen bonds and covalent bonds from charge densities obtained by the maximum entropy method (MEM)ACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2009Jeanette Netzel Charge densities have been determined by the Maximum Entropy Method (MEM) from the high-resolution, low-temperature (T, 20,K) X-ray diffraction data of six different crystals of amino acids and peptides. A comparison of dynamic deformation densities of the MEM with static and dynamic deformation densities of multipole models shows that the MEM may lead to a better description of the electron density in hydrogen bonds in cases where the multipole model has been restricted to isotropic displacement parameters and low-order multipoles (lmax = 1) for the H atoms. Topological properties at bond critical points (BCPs) are found to depend systematically on the bond length, but with different functions for covalent C,C, C,N and C,O bonds, and for hydrogen bonds together with covalent C,H and N,H bonds. Similar dependencies are known for AIM properties derived from static multipole densities. The ratio of potential and kinetic energy densities |V(BCP)|/G(BCP) is successfully used for a classification of hydrogen bonds according to their distance d(H...O) between the H atom and the acceptor atom. The classification based on MEM densities coincides with the usual classification of hydrogen bonds as strong, intermediate and weak [Jeffrey (1997). An Introduction to Hydrogen Bonding. Oxford University Press]. MEM and procrystal densities lead to similar values of the densities at the BCPs of hydrogen bonds, but differences are shown to prevail, such that it is found that only the true charge density, represented by MEM densities, the multipole model or some other method can lead to the correct characterization of chemical bonding. Our results do not confirm suggestions in the literature that the promolecule density might be sufficient for a characterization of hydrogen bonds. [source] Synthesis, Solution-State and Solid-State Structural Characterization of Monocationic Nitrido Heterocomplexes [M(N)(DTC)(PNP)]+ (M = 99Tc, Re; DTC = Dithiocarbamate; PNP = Heterodiphosphane)EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 9 2004Cristina Bolzati Abstract Mono-cationic nitrido heterocomplexes of general formula [M(N)(DTC)(PNP)]+ (where M is 99Tc or Re, DTC is the mono-anionic form of a dithiocarbamate ligand, and PNP is a diphosphane ligand with a tertiary amine-containing five-membered spacer) were prepared by ligand-exchange reactions with the labile precursors [M(N)Cl2(PPh3)2] in dichloromethane/alcohol mixtures. The molecular structure of the representative rhenium complex [Re(N)(dedc)(pnp2)][PF6] (1) displays a distorted, square-pyramidal geometry with the dithiocarbamate sulfur and the diphosphane phosphorus atoms spanning the four coordination positions on the equatorial plane. If the additional interactions between the nitrido nitrogen and the weakly bonded transN -diphosphane heteroatom, the molecular geometry can be viewed as pseudo-octahedral. The structure in solution, as established by multinuclear NMR spectroscopy and ESI spectrometry, is monomeric, and identical to that shown in the solid state. Replacement of the phenyl groups on the phosphorous atoms in complexes 1, 2, 5, and 6 with alkyl groups modified neither the course of the reaction nor the composition of the resulting complexes. These results, together with the observation that no symmetrical complexes containing two identical bidentate ligands were produced in these reactions, strongly supports the conclusion that a mixed coordination sphere, composed by a combination of ,-donor and ,-acceptor atoms around the [M,N]2+ group, constitutes a highly stable system. Compounds containing dangling alkyl-substituted groups in the outer sphere (3, 4, 7, and 8) were fully characterized by multinuclear NMR spectroscopy and ESI mass spectrometry. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] Heavy atom motions and tunneling in hydrogen transfer reactions: the importance of the pre-tunneling stateJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 7 2010Hans-Heinrich Limbach Abstract Arrhenius curves of selected hydrogen transfer reactions in organic molecules and enzymes are reviewed with the focus on systems exhibiting temperature-independent kinetic isotope effects. The latter can be rationalized in terms of a ,pre-tunneling state' which is formed from the reactants by heavy atom motions and which represents a suitable molecular configuration for tunneling to occur. Within the Bell,Limbach tunneling model, formation of the pre-tunneling state dominates the Arrhenius curves of the H and the D transfer even at higher temperatures if a large energy Em is required to reach the pre-tunneling state. Tunneling from higher vibrational levels and the over-barrier reaction via the transition state which lead to temperature-dependent kinetic isotope effects dominate the Arrhenius curves only if Em is small compared to the energy of the transition state. Using published data on several hydrogen transfer systems, the type of motions leading to the pre-tunneling state is explored. Among the phenomena which lead to large energies of the pre-tunneling state are (i) cleavage of hydrogen bonds or coordination bonds of the donor or acceptor atoms to molecules or molecular groups in order to allow the formation of the pre-tunneling state, (ii) the occurrence of an energetic intermediate on the reaction pathway within which tunneling takes place, and (iii) major reorganization of a molecular skeleton, requiring the excitation of specific vibrations in order to reach the pre-tunneling state. This model suggests a solution to the puzzle of Kwart's findings of temperature-independent kinetic isotope effects for hydrogen transfer in small organic molecules. Copyright © 2010 John Wiley & Sons, Ltd. [source] Analysis of water solubility data on the basis of HYBOT descriptors.MOLECULAR INFORMATICS, Issue 9-10 2003Part 1. Abstract This work describes the analysis of water-gas phase partitioning data Lw=Cw/Cg for 559 organic chemicals on the basis of physicochemical descriptors calculated by the HYBOT program package. Physicochemical descriptors combined with indicator variables as well as a new approach combining traditional QSAR and molecular similarity are used to take structural features into account. The H-bond acceptor ability of chemicals (i.e. interaction of acceptor atoms with hydrogen atoms of water) is the main factor that influences the partitioning of vapors into water. The simultaneous consideration of H-bond acceptor and donor factors leads to a description of the solubility of vapors with a correlation coefficient of about 0.92. The influence of steric interactions of solutes (characterized by means of molecular polarizability) with water molecules contributes slightly but significantly from the statistics point of view. The use of a set of indicator variables for hydrocarbons and for molecules containing amino, amido, CX3, ether and nitro groups as well as for molecules with ability to form intramolecular hydrogen bonds improves the correlation and helps to take structural features into account. Furthermore, the application of an approach based on the calculation of additional contributions to solubility by considering ,nearest neighbor chemicals' and their difference in physicochemical parameters gives in many cases good results and could be very useful in the analysis of vast data sets. [source] A new amidrazone derivative with antimycobacterial activityACTA CRYSTALLOGRAPHICA SECTION C, Issue 5 2000David C. Billington Of a series of pyridine-2-carboxamidrazone derivatives with activity against mycobacteria, the N1 -[4-(1,1-dimethylpropyl)benzylidene] derivative reported here, C18H22N4, is one of the most active. The predicted E isomer about the C11=N12 double bond is confirmed and intramolecular hydrogen bonding involving both amino H atoms helps to keep the molecule flat. The same donor and acceptor atoms also form intermolecular hydrogen bonds. [source] Two isomorphous cobalt(II) complexes: poly[[diaqua-,-2,5-dicarboxybenzene-1,4-dicarboxylato-,-1,2-di-4-pyridylethene-cobalt(II)] 1,2-di-4-pyridylethene solvate] and the 1,2-di-4-pyridylethane analogueACTA CRYSTALLOGRAPHICA SECTION C, Issue 1 2009Ana María Atria The two isomorphous title structures, formulated as {[Co(C10H4O8)(C12H10N2)(H2O)2]·C12H10N2}n, (I), and {[Co(C10H4O8)(C12H12N2)(H2O)2]·C12H12N2}n, (II), respectively, are reported. They crystallize in the space group P with only one formula unit in the asymmetric unit, so that the organic ligands lie about inversion centres and the Co atom lies on an inversion centre. The Co atoms are octahedrally coordinated by a carboxylate O atom from 2,5-dicarboxybenzene-1,4-dicarboxylate (H2btc), one N atom from 1,2-di-4-pyridylethene (L) in (I) or from 1,2-di-4-pyridylethane (L) in (II), and one coordinated water molecule, plus their inversion-related species. This particular coordination results in a two-dimensional array, with an elemental unit in the shape of a parallelogram having the CoII cations at the corners, linked in one direction by L bridges and in the opposite direction by H2btc groups. The L solvent molecules act as pillars between parallel planes, linking them by strong hydrogen bonds where the H atoms lie midway between the formal donor/acceptor atoms in a `shared' mode. Comparison is made with structures presenting the same structural motif, strongly suggesting that the two-dimensional arrangement reported here might be a very stable robust building block for molecular engineering purposes. [source] | ||||||||||