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H Atoms (h + atom)
Kinds of H Atoms Selected AbstractsDiffusion versus Desorption: Complex Behavior of H Atoms on an Oxide SurfaceCHEMPHYSCHEM, Issue 2 2008X.-L. Yin Dr. Adsorption of atomic hydrogen on single-crystalline rutile TiO2(110)-(1×1) (see picture) at room temperature leads to ordered H adlayers with (1×1) periodicity and many vacancies. Unexpectedly, almost no recombinative desorption of H2 (or H2O) occurs on heating to above 600 K, because the activation energy of 1.11 eV for H atoms migrating into the bulk is significantly smaller as shown by DFT calculations. [source] Reductive Coupling of Aromatic Aldehydes Promoted by an Aqueous TiCl3/tBuOOH System in Alcoholic CosolventsEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 24 2007Angelo Clerici Abstract The tert -butoxyl radical, generated by the aqueous TiIII/TBHP system, abstracts an H atom from alcoholic cosolvents (EtOH, iPrOH), leading to ,-hydroxyalkyl radicals thatreduce aromatic aldehydes to the corresponding 1,2-diols. The reactivities observed are explained by resonance stabilization of the ,-hydroxybenzyl radicals formed in the electron-transfer (ET) process. Good Hammett-type correlations are obtained. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source] Molecular dynamics study for dissociation phenomena of a gas molecule on a metal surfaceHEAT TRANSFER - ASIAN RESEARCH (FORMERLY HEAT TRANSFER-JAPANESE RESEARCH), Issue 8 2008Takashi Tokumasu Abstract The dissociation phenomena of a gas molecule on a metal surface were analyzed by the molecular dynamics method. A platinum (111) surface and hydrogen were chosen as the metal surface and the gas molecule, respectively. The embedded atom method was used as the interaction between atoms in order to express the dependence of electron density. The parameters were determined so that the results such as the electron density, adsorption energy of an H atom on a Pt(111) surface, and the interaction between H atoms of an H2 molecule obtained by the EAM method were consistent with those obtained by the density functional theory or empirical function. Collisions between a hydrogen molecule and the platinum surface were simulated by the molecular dynamics method, and the dissociation probability was obtained. Using these results, the effect of the motion of the surface atoms or the hydrogen molecule on the dissociation probability was analyzed. © 2008 Wiley Periodicals, Inc. Heat Trans Asian Res; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/htj.20222 [source] H-doped PbTiO3: Structure and electronic propertiesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 6 2007Arvids Stashans Abstract The geometry and electronic properties of the interstitial H atom in the tetragonal PbTiO3 crystal have been studied using an advanced quantum chemical computer code developed for the modeling of crystals. The inserted H atom was found to bind to one of the O atoms and to form the hydroxyl, OH group, with the inter-atomic distance equal to 0.93 Å and 1.00 Å for the hydroxyls containing O atom in the dimerized and nondimerized TiOTi chains, respectively. Atomic displacements in the vicinity of OH complex are calculated and analyzed in relation to the H-produced changes upon the atomic charges in defective region. The role of H impurity on the ferroelectric polarization in the tetragonal PbTiO3 is discussed in terms of the results obtained in our research and those presented in the other studies on this subject. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] Theoretical study of the · H reaction with cytosineINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 1 2007Hongyu Zhang Abstract We studied three possible reactions of H atom attacking the cytosine, using density functional theory (DFT) calculations. The results indicate that the H atom addition to the N3 site of cytosine is energetically more favorable than to the C5 or C6 site. The reaction of addition to the C6 site has an energy barrier of ,2.77 kcal/mol, which is ,2 kcal/mol higher than addition to C5. The energy of C5 H-adduct radical is also lower than that of C6 H-adduct radical. From the point of view of both energetics and reaction kinetics, the addition of the H atom to the C5 site is preferred to the addition to the C6 site. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] Photoionization cross sections with optimized orbital exponents within the complex basis function methodJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2008Masato Morita Abstract We show a new direction to expand the applicability of the complex basis function method for calculating photoionization cross sections through the imaginary part of the frequency-dependent polarizability. Based on the variational stability of the frequency-dependent polarizability, we made nonlinear optimizations of complex orbital exponents in basis functions representing continuum wave functions, and obtained fairly accurate results for H atom with only one or two complex basis functions particularly with dipole velocity gauge. Results were almost independent of whether Slater-type or Gaussian-type orbitals are used, implying the applicability to general many electron problems. The method was also applied to the 1S (1s)2 , 1P (1s)1(kp)1 cross section of He atom and the optimized complex orbital exponents were related to those of H atom through the scaling property. The nonlinear optimizations have converged smoothly and the cross sections were in excellent agreement with experiment throughout wide photon energies, which suggest the effectiveness of the approach for many-electron systems. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Possible molecular hydrogen formation mediated by the radical cations of anthracene and pyreneJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2003Mutsumi Hirama Abstract Hydrogen molecules cannot be formed readily by the association of gaseous hydrogen atoms. Possible H2 formation mediated by the radical cations of typical polycyclic aromatic hydrocarbons (PAHs), anthracene and pyrene, was studied at the B3LYP/6-31G** level of theory. We presumed that H2 is formed by way of two elementary reactions: the addition of an H atom to a PAH molecular cation, and the H abstraction from the resulting monohydro-PAH cation (i.e., arenium ion) by a second H atom to yield H2. The first reaction takes place without any activation energy. The second reaction is also predicted to proceed along almost barrierless pathways, although it is far from being a typical ion,molecule reaction. There is a possibility that these reactions might constitute one of the mechanisms for H2 formation in extremely cold interstellar space. Deuterium enrichment in PAH cations is possibly accompanied by such H2 formation because deuteration lowers the energies of polyatomic PAH cations appreciably. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1378,1382, 2003 [source] Theoretical study of the interaction between a high-valent manganese porphyrin oxyl-(hydroxo)-Mn(IV)-TMPyP and double-stranded DNAJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2003Philippe Arnaud Abstract Cationic porphyrin derivatives such as meso-tetrakis(4- N -methylpyridinium)porphyrin, TMPyP, have been shown to interact with double-stranded DNA. The manganese derivative, Mn(III)-TMPyP, activated by an oxygen donor like potassium monopersulfate, provides an efficient DNA-cleaving system. Previous experimental work1 has shown that DNA cleavage by the Mn(III)-TMPyP/KHSO5 system was due to an oxidative attack, within the minor groove of B-DNA, at the C5, or C1, carbons of deoxyribose units. The aim of this study was to use molecular modeling to elucidate the specificity of the interactions between the transient active species oxyl-Mn(IV)-TMPyP and the DNA target. Geometric parameters, charges, and force field constants consistent with the AMBER 98 force field were calculated by DFT methods. Molecular modeling (mechanics and dynamic simulations) were performed for oxyl-(hydroxo)-Mn(IV)-TMPyP bound in the minor groove of the dodecamer d(5,-TCGTCAAACCGC)-d(5,-GCGGTTTGACGA). Geometry, interactions, and binding energy of the metalloporphyrin located at the A.T triplet region of the dodecamer were analyzed. These studies show no significant structural change of the DNA structure upon ligand binding. Mobility of the metalloporphyrin in the minor groove was restrained by the formation of a hydrogen bond between the hydroxo ligand trans to the metal-oxyl and a DNA phosphate, restricting the access of the oxyl group to the (pro-S) H atom at C5,. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 797,805, 2003 [source] Formation of [b3 , 1 + cat]+ ions from metal-cationized tetrapeptides containing ,-alanine, ,-aminobutyric acid or ,-aminocaproic acid residuesJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 11 2008Sandra M. Osburn Abstract The presence and position of a single ,-alanine (,A), ,-aminobutyric acid (,ABu) or ,-aminocaproic acid (Cap) residue has been shown to have a significant influence on the formation of bn+ and yn+ product ions from a series of model, protonated peptides. In this study, we examined the effect of the same residues on the formation of analogous [b3 , 1 + cat]+ products from metal(Li+, Na+ and Ag+)-cationized peptides. The larger amino acids suppress formation of b3+ from protonated peptides with general sequence AAXG (where X = ,-alanine, ,-aminobutyric acid or ,-aminocaproic acid), presumably because of the prohibitive effect of larger cyclic intermediates in the ,oxazolone' pathway. However, abundant [b3 , 1 + cat]+ products are generated from metal-cationized versions of AAXG. Using a group of deuterium-labeled and exchanged peptides, we found that formation of [b3 , 1 + cat]+ involves transfer of either amide or ,-carbon position H atoms, and the tendency to transfer the atom from the ,-carbon position increases with the size of the amino acid in position X. To account for the transfer of the H atom, a mechanism involving formation of a ketene product as [b3 , 1 + cat]+ is proposed. Copyright © 2008 John Wiley & Sons, Ltd. [source] Intermolecular H-bond in propan-2-ol and its solutions with acetonitrileJOURNAL OF RAMAN SPECTROSCOPY, Issue 12 2007F. H. Tukhvatullin Abstract Formation of propan-2-ol,acetonitrile dimers is manifested in the Raman spectra as an appearance of a band of aggregates in the high-wavenumber side of the CN vibrational band of liquid acetonitrile (,2 cm,1). The intensity of the band of aggregates changes with a change in the concentration of the mixture (1,0.05 mole fraction). For propan-2-ol we carried out nonempirical calculations of a structure of isolated dimer aggregates. The formation of an intramolecular H-bond between the H and the O atom of the \newbox\osprulebox \newdimen\osprulewd \def\osprule#1#2{ \global\setbox\osprulebox=\hbox{#1} \osprulewd=\wd\osprulebox\advance\osprulewd by -8pt \raise0.5pc\hbox{$\matrix{\hskip-1pt\lower6.5pt\hbox{\vrule height #2pt}\lower4.5pt\hbox to \osprulewd{\hrulefill}\lower6.5pt\hbox{\vrule height #2pt}\cr \noalign{\vskip-1pt} \hbox{#1}\cr}$} } $\osprule{{\rm HCO}}{2.5} \hbox{H}$ group of length 2.045 Å is possible in the monomer molecule. The CH3 groups of alcohol are not equivalent. In the dimer formation, intramolecular H-bond in the \newbox\osprulebox \newdimen\osprulewd \def\osprule#1#2{ \global\setbox\osprulebox=\hbox{#1} \osprulewd=\wd\osprulebox\advance\osprulewd by -8pt \raise0.5pc\hbox{$\matrix{\hskip-1pt\lower6.5pt\hbox{\vrule height #2pt}\lower4.5pt\hbox to \osprulewd{\hrulefill}\lower6.5pt\hbox{\vrule height #2pt}\cr \noalign{\vskip-1pt} \hbox{#1}\cr}$} } $\osprule{{\rm HCO}}{2.5} \hbox{H}$ group is preserved. An intermolecular H-bond of length 2.045 Å and energy 15 kJ/mole is formed between the H atom of one molecule and the O atom of another molecule of the OH. The length and energy of the H-bond for the propan-2-ol,acetonitrile dimer formations calculate to 2.27 Å and 12.9 kJ/mole, respectively. The H-bond is formed by ,-electrons of nitrogen. The experimental data and the results of calculations are in good agreement. Copyright © 2007 John Wiley & Sons, Ltd. [source] Deduced catalytic mechanism of d -amino acid amidase from Ochrobactrum anthropi SV3JOURNAL OF SYNCHROTRON RADIATION, Issue 3 2008Seiji Okazaki d -Amino acid amidase (DAA) from Ochrobactrum anthropi SV3 catalyzes d -stereospecific hydrolysis of amino acid amides. DAA has attracted attention as a catalyst for the stereospecific production of d -amino acids, although the mechanism that drives the reaction has not been clear. Previously, the structure of DAA was classified into two types, a substrate-bound state with an ordered , loop, and a ground state with a disordered , loop. Because the binding of the substrate facilitates ordering, this transition was regarded to be induced fit motion. The angles and distances of hydrogen bonds at Tyr149 O,, Ser60 O, and Lys63 N, revealed that Tyr149 O, donates an H atom to a water molecule in the substrate-bound state, and that Tyr149 O, donates an H atom to Ser60 O, or Lys63 N, in the ground state. Taking into consideration the locations of the H atoms of Tyr149 O,, Ser60 O, and Lys63 N,, a catalytic mechanism of DAA activity is presented, wherein a shift of an H atom at Tyr149 O, in the substrate-bound versus the ground state plays a significant role in the reaction. This mechanism explains well why acylation proceeds and deacylation does not proceed in the substrate-bound state. [source] Probing feedback in protogalaxies: multiphase gas in a DLA at z, 2.4MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 1 2008N. Lehner ABSTRACT We investigate the physical processes occurring in the multiphase gas of a damped Ly, absorber (DLA). We base our analysis on a high-quality Keck High-Resolution Echelle Spectrometer (HIRES) spectrum of the QSO J1211+0422 in which a DLA is detected at z, 2.377. There is little contamination of the high-ion (O vi, N v, C iv, Si iv) absorption, allowing us to explore the properties of the highly ionized gas and its connection to other gas phases. The metallicity ([Z/H]=,1.41 ± 0.08), H i column density [], full-width velocity (,vneut, 70 km s,1) and relative abundances ([Si/Fe]=+0.23 ± 0.05 and [N/Si]=,0.88 ± 0.07) of this DLA are not unusual. However, we derive the lowest C ii* cooling rate in a DLA, lc < 10,27.8 erg s,1 per H atom (3,). Using this stringent limit, we show that the neutral gas (confined at |v| < +39 km s,1) must be warm and the star formation rate is <7.1 × 10,3 M, yr,1 kpc,2. Surprisingly, the gas shows strong, complex absorption profiles from highly ionized gas whose kinematics appear connected to each other and the low ions. The total amount of highly and weakly ionized gas is very large with ,1.5. At |v| ,+39 km s,1, the gas is fully and highly ionized []. Based on ionization models, O vi and N v are generally difficult to produce by hard photons, while Si iv and C iv can be photoionized to a large extent. There is, however, no evidence of O vi -bearing gas at T, 106 K associated with this DLA. In contrast, there is some evidence for narrow O vi, N v and C iv components (unexplained by photoionization), implying too low temperatures (T < 105 K) for simple collisional ionization models to produce their observed column densities. Stellar feedback is a possible source for producing the high ions, but we cannot rule out accretion of non-pristine material on to the protogalaxy. [source] Uniaxial stress study of the Cu,H complex in ZnOPHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 12 2006E. V. Lavrov The cover picture of the current issue refers to the article by Lavrov and Weber which was selected as Editor's Choice [1]. The picture shows a microscopic model of the Cu,H complex investigated in the paper. The complex consists of a substitutional Cu atom at the Zn site with an H atom located between nearby O and Cu in the basal plane of the ZnO lattice. The atoms are shown in different colors: yellow for copper, red for hydrogen, cyan for oxygen, and grey for zinc. Hydrogen forms a strong bond with the O atom which gives rise to a local vibrational mode at 3192 cm,1 investigated in the paper under uniaxial stress. The c -axis is parallel to the Cu,O bond pointing to the top of the figure. The authors work at the Institute of Applied Physics/Semiconductor Physics, TU Dresden, Germany. [source] Cover Picture: Plasma Process.PLASMA PROCESSES AND POLYMERS, Issue 9 2005Polym. Cover: Density functional theory was applied to study the thermochemistry of methyl- and methoxymethylsilanes. Predicted bond dissociation energies of methoxymethylsilanes are plotted, and potential reaction pathways of trimethoxymethylsilane and H atom are illustrated with the thermodynamically favored silanol formation highlighted. Further details can be found in the Full Paper by T. B. Casserly and K. K. Gleason* on page 669. [source] Topological 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] Chiral versus racemic building blocks in supramolecular chemistry: malate salts of organic diaminesACTA CRYSTALLOGRAPHICA SECTION B, Issue 3-2 2002Dorcas M. M. Farrell (S)-Malic acid forms a salt with N,N,-dimethylpiperazine, [MeN(CH2CH2)2NMe]H22+·2C4H5O5, (1) (triclinic, P1, Z, = 1), in which the cations link pairs of hydrogen-bonded anion chains to form a molecular ladder. With 4,4,-bipyridyl, (S)-malic acid forms a 1:1 adduct which crystallizes from methanol to yield two polymorphs, (2) (triclinic, P1, Z, = 1) and (3) (monoclinic, C2, Z, = 1), while racemic malic acid with 4,4,-bipyridyl also forms a 1:1 adduct, (4) (monoclinic, P21/c, Z, = 1). In each of (2), (3) and (4) the components are linked by O,H,N and N,H,O into chains of alternating bipyridyl and malate units, which are linked into sheets by O,H,O hydrogen bonds. In each of the 1:1 adducts (5) and (6), formed by, respectively, (S)-malic acid and racemic malic acid with 1,2-bis(4,-pyridyl)ethene, the diamine is disordered over two sets of sites, related by a 180° rotation about the N,N vector. In (5), (C12H10N2)H+·C4H5O5, (triclinic, P1, Z, = 1), the components are again linked by a combination of N,H,O and O,H,O hydrogen bonds into sheets, while in (6) (triclinic, P, Z, = 0.5) there is only partial transfer of the H atom from O to N and the malate component is disordered across a centre of inversion. With 1,4-diazabicyclo[2.2.2]octane, racemic malic acid forms a 1:2 salt, [(C6H12N2)H2]2+·2C4H5O5, (7) (monoclinic, P21/c, Z, = 2), while (S)-malic acid forms a 1:1 adduct, (8) (monoclinic, P21, Z, = 3). There are thus six independent molecular components in each. In (7) the ions are linked by an extensive series of N,H,O and O,H,O hydrogen bonds into a three-dimensional framework, but in (8) there is extensive disorder involving all six components, and no refinement proved to be feasible. [source] X-ray and neutron structure of 1,8-(3,6,9-trioxaundecane-1,11-diyldioxy)-9,10-dihydro-10,10-dimethylanthracene-9-ol (P326); some pitfalls of automatic data collectionACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2001Rex A. Palmer The structure of the crown ether 1,8-(3,6,9-trioxaundecane-1,11-diyldioxy)-9,10-dihydro-10,10-dimethylanthracene-9-ol, C24H30O6·H2O (1), code name P326, the parent compound for a series of derivatives, has been determined by both X-ray diffraction at room temperature and neutron diffraction at very low temperature. The unit cells are very similar at both temperatures and in both cases the crystals exhibit P21 symmetry with Z = 4 (two molecules, A and B, respectively, per asymmetric unit) and pseudosymmetry P21/c. The higher symmetry is broken mainly by the two independent water molecules in the unit cell, some reflections which would be absent in P21/c having strong intensities in both the X-ray and neutron data. In both molecules A and B hydrogen bonds involving the water molecule stabilize the macrocyclic ring structure, one involving the macrocyclic O(9) as a donor. Close contacts between the water and macrocyclic O atoms in each molecule also suggest the presence of two bifurcated hydrogen bonds, involving water HW2 to both O(16) and O(18), and water HW1 to both O(18) and O(20), respectively, with considerable variation in the geometry being present. Both molecules A and B exhibit very close pseudosymmetry across a plane perpendicular to the molecular plane and through atoms C(9) and O(18), and in addition are predominantly planar structures. The X-ray analysis failed to reveal one H atom per water molecule, each being subsequently included after location and refinement in the neutron analysis. [source] Migration of the proton in the strong O,H,O hydrogen bond in urea,phosphoric acid (1/1)ACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2001Chick C. Wilson The structure of urea,phosphoric acid is reported at a large number of temperatures in the range 150,335,K from neutron diffraction data collected using a novel multiple single-crystal data collection method. The work focuses on the behaviour of the H atom involved in the short strong O,H,O hydrogen bond in this material. The position of this atom is shown to vary significantly, by around 0.035 ,Å, as a function of temperature, becoming effectively centred at the highest temperatures studied. This result, only accessible due to the accurate determination of H-atom parameters by neutron diffraction, has implications for the potential governing the hydrogen bond. [source] Green chemistry synthesis: 2-amino-3-[(E)-(2-pyridyl)methylideneamino]but-2-enedinitrile monohydrate and 5-cyano-2-(2-pyridyl)-1-(2-pyridylmethyl)-1H -imidazole-4-carboxamideACTA CRYSTALLOGRAPHICA SECTION C, Issue 9 2010Muhammad Altaf The title compounds, C10H9N5O·H2O (L1·H2O) and C16H12N6O (L2), were synthesized by solvent-free aldol condensation at room temperature. L1, prepared by grinding picolinaldehyde with 2,3-diamino-3-isocyanoacrylonitrile in a 1:1 molar ratio, crystallized as a monohydrate. L2 was prepared by grinding picolinaldehyde with 2,3-diamino-3-isocyanoacrylonitrile in a 2:1 molar ratio. By varying the conditions of crystallization it was possible to obtain two polymorphs, viz. L2-I and L2-II; both crystallized in the monoclinic space group P21/c. They differ in the orientation of one pyridine ring with respect to the plane of the imidazole ring. In L2-I, this ring is oriented towards and above the imidazole ring, while in L2-II it is rotated away from and below the imidazole ring. In all three molecules, there is a short intramolecular N,H...N contact inherent to the planarity of the systems. In L1·H2O, this involves an amino H atom and the C=N N atom, while in L2 it involves an amino H atom and an imidazole N atom. In the crystal structure of L1·H2O, there are N,H...O and O,H...O intermolecular hydrogen bonds which link the molecules to form two-dimensional networks which stack along [001]. These networks are further linked via intermolecular N,H...N(cyano) hydrogen bonds to form an extended three-dimensional network. In the crystal structure of L2-I, symmetry-related molecules are linked via N,H...N hydrogen bonds, leading to the formation of dimers centred about inversion centres. These dimers are further linked via N,H...O hydrogen bonds involving the amide group, also centred about inversion centres, to form a one-dimensional arrangement propagating in [100]. In the crystal structure of L2-II, the presence of intermolecular N,H...O hydrogen bonds involving the amide group results in the formation of dimers centred about inversion centres. These are linked via N,H...N hydrogen bonds involving the second amide H atom and the cyano N atom, to form two-dimensional networks in the bc plane. In L2-I and L2-II, C,H..., and ,,, interactions are also present. [source] Ethyl 3-[1-(5,5-dimethyl-2-oxo-1,3,2-dioxaphosphorin-2-yl)propan-2-ylidene]carbazate: a combined X-ray and density functional theory (DFT) studyACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2010Youssef Arfaoui In the title compound, C11H21N2O5P, one of the two carbazate N atoms is involved in the C=N double bond and the H atom of the second N atom is engaged in an intramolecular hydrogen bond with an O atom from the dimethylphosphorin-2-yl group, which is in an uncommon cis position with respect to the carbamate group. The cohesion of the crystal structure is also reinforced by weak intermolecular hydrogen bonds. Density functional theory (DFT) calculations at the B3LYP/6-311++g(2d,2p) level revealed the lowest energy structure to have a Z configuration at the C=N bond, which is consistent with the configuration found in the X-ray crystal structure, as well as a less stable E counterpart which lies 2.0,kcal,mol,1 higher in potential energy. Correlations between the experimental and computational studies are discussed. [source] N,N,-Diethyl-4-nitrobenzene-1,3-diamine, 2,6-bis(ethylamino)-3-nitrobenzonitrile and bis(4-ethylamino-3-nitrophenyl) sulfoneACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2010Thomas J. Payne N,N,-Diethyl-4-nitrobenzene-1,3-diamine, C10H15N3O2, (I), crystallizes with two independent molecules in the asymmetric unit, both of which are nearly planar. The molecules differ in the conformation of the ethylamine group trans to the nitro group. Both molecules contain intramolecular N,H...O hydrogen bonds between the adjacent amine and nitro groups and are linked into one-dimensional chains by intermolecular N,H...O hydrogen bonds. The chains are organized in layers parallel to (101) with separations of ca 3.4,Å between adjacent sheets. The packing is quite different from what was observed in isomeric 1,3-bis(ethylamino)-2-nitrobenzene. 2,6-Bis(ethylamino)-3-nitrobenzonitrile, C11H14N4O2, (II), differs from (I) only in the presence of the nitrile functionality between the two ethylamine groups. Compound (II) crystallizes with one unique molecule in the asymmetric unit. In contrast with (I), one of the ethylamine groups, which is disordered over two sites with occupancies of 0.75 and 0.25, is positioned so that the methyl group is directed out of the plane of the ring by approximately 85°. This ethylamine group forms an intramolecular N,H...O hydrogen bond with the adjacent nitro group. The packing in (II) is very different from that in (I). Molecules of (II) are linked by both intermolecular amine,nitro N,H...O and amine,nitrile N,H...N hydrogen bonds into a two-dimensional network in the (10) plane. Alternating molecules are approximately orthogonal to one another, indicating that ,,, interactions are not a significant factor in the packing. Bis(4-ethylamino-3-nitrophenyl) sulfone, C16H18N4O6S, (III), contains the same ortho nitro/ethylamine pairing as in (I), with the position para to the nitro group occupied by the sulfone instead of a second ethylamine group. Each 4-ethylamino-3-nitrobenzene moiety is nearly planar and contains the typical intramolecular N,H...O hydrogen bond. Due to the tetrahedral geometry about the S atom, the molecules of (III) adopt an overall V shape. There are no intermolecular amine,nitro hydrogen bonds. Rather, each amine H atom has a long (H...O ca 2.8,Å) interaction with one of the sulfone O atoms. Molecules of (III) are thus linked by amine,sulfone N,H...O hydrogen bonds into zigzag double chains running along [001]. Taken together, these structures demonstrate that small changes in the functionalization of ethylamine,nitroarenes cause significant differences in the intermolecular interactions and packing. [source] Crystallographic characterization of the first reported crystalline form of the potent hallucinogen (R)-2-amino-1-(8-bromobenzo[1,2- b;5,4- b,]difuran-4-yl)propane or `bromodragonfly': the 1:1 anhydrous proton-transfer compound with 3,5-dinitrosalicylic acidACTA CRYSTALLOGRAPHICA SECTION C, Issue 5 2010Graham Smith The 1:1 proton-transfer compound of the potent substituted amphetamine hallucinogen (R)-2-amino-1-(8-bromobenzo[1,2- b;5,4- b,]difuran-4-yl)propane (common trivial name `bromodragonfly') with 3,5-dinitrosalicylic acid, namely 1-(8-bromobenzo[1,2- b;5,4- b,]difuran-4-yl)propan-2-aminium 2-carboxy-4,6-dinitrophenolate, C13H13BrNO2+·C7H3N2O7,, forms hydrogen-bonded cation,anion chain substructures comprising undulating head-to-tail anion chains formed through C(8) carboxyl,nitro O,H...O associations and incorporating the aminium groups of the cations. The intrachain cation,anion hydrogen-bonding associations feature proximal cyclic R33(8) interactions involving both an N+,H...Ophenolate and the carboxyl,nitro O,H...O associations and aromatic ,,, ring interactions [minimum ring centroid separation = 3.566,(2),Å]. A lateral hydrogen-bonding interaction between the third aminium H atom and a carboxyl O-atom acceptor links the chain substructures, giving a two-dimensional sheet structure. This determination represents the first of any form of this compound and is in the (R) absolute configuration. The atypical crystal stability is attributed both to the hydrogen-bonded chain substructures provided by the anions, which accommodate the aminium proton-donor groups of the cations and give crosslinking, and to the presence of the cation,anion aromatic ring ,,, interactions. [source] 2-(Diphenylphosphinoylmethyl)pyrrole,2-(diphenylphosphinomethyl)pyrrole (0.43/0.57) and tetrachlorido(5-diphenylphosphinomethyl-2H -pyrrole-,2N,P)titanium(IV)ACTA CRYSTALLOGRAPHICA SECTION C, Issue 3 2010Lewis M. Broomfield The title phosphine oxide,phosphine, 0.43C17H16NOP·0.57C17H16NP, (I)/(II), was obtained as a 0.861,(6):1.139,(6) cocrystallized mixture. Hydrogen bonding between the two constituents leads to the formation of 2:2 solid-state assemblies. Instead of forming the expected simple N,P -chelated system via loss of the N-bound H atom, reaction of 2-(diphenylphosphinomethyl)pyrrole, (II), with TiCl4 leads to the formation of the title titanium(IV) complex, [TiCl4(C17H16NP)], (IV), containing a rearranged neutral ligand in which the N-bound H atom moves to one of the pyrrole C atoms, giving a partially unsaturated ring. [source] Two solid phases of pyrimidin-1-ium hydrogen chloranilate monohydrate determined at 225 and 120,KACTA CRYSTALLOGRAPHICA SECTION C, Issue 3 2010Kazuma Gotoh The crystal structures of two solid phases of the title compound, C4H5N2+·C6HCl2O4,·H2O, have been determined at 225 and 120,K. In the high-temperature phase, stable above 198,K, the transition temperature of which has been determined by 35Cl nuclear quadrupole resonance and differential thermal analysis measurements, the three components are held together by O,H...O, N...H...O, C,H...O and C,H...Cl hydrogen bonds, forming a centrosymmetric 2+2+2 aggregate. In the N...H...O hydrogen bond formed between the pyrimidin-1-ium cation and the water molecule, the H atom is disordered over two positions, resulting in two states, viz. pyrimidin-1-ium,water and pyrimidine,oxonium. In the low-temperature phase, the title compound crystallizes in the same monoclinic space group and has a similar molecular packing, but the 2+2+2 aggregate loses the centrosymmetry, resulting in a doubling of the unit cell and two crystallographically independent molecules for each component in the asymmetric unit. The H atom in one N...H...O hydrogen bond between the pyrimidin-1-ium cation and the water molecule is disordered, while the H atom in the other hydrogen bond is found to be ordered at the N-atom site with a long N,H distance [1.10,(3),Å]. [source] Hexane-1,6-diaminium chloride [hydrogen bis(chloroacetate)]ACTA CRYSTALLOGRAPHICA SECTION C, Issue 11 2009Agnieszka Paul In the structure of the title compound, C6H18N22+·H(C2H2ClO2)2,·Cl,, the hexane-1,6-diaminium dication is disordered over two sets of positions, with almost equal occupancies. Both alternative positions of the dication are in the fully extended conformation, situated on an inversion centre at (, , ). Two chloroacetic acid moieties, related by another centre of symmetry at (, , ), are connected by a very short symmetrical O...H...O hydrogen bond [O...O = 2.452,(2),Å], with the H atom at the centre of inversion. These two fragments thus effectively form the hydrogen bis(chloroacetate) monoanion, and the overall charge is balanced by an additional chloride anion which resides on a twofold axis. The ions form a layer structure, with alternating layers of dications and anions running along the [101] direction, linked via hydrogen bonds. There are two N,H...O interactions and two N,H...Cl, interactions. [source] Hydrogen-bonded structures of the isomeric compounds of quinoline with 2-chloro-5-nitrobenzoic acid, 3-chloro-2-nitrobenzoic acid, 4-chloro-2-nitrobenzoic acid and 5-chloro-2-nitrobenzoic acidACTA CRYSTALLOGRAPHICA SECTION C, Issue 10 2009Kazuma Gotoh The structures of four isomeric compounds, all C7H4ClNO4·C9H7N, of quinoline with chloro- and nitro-substituted benzoic acid, namely, 2-chloro-5-nitrobenzoic acid,quinoline (1/1), (I), 3-chloro-2-nitrobenzoic acid,quinoline (1/1), (II), 4-chloro-2-nitrobenzoic acid,quinoline (1/1), (III), and 5-chloro-2-nitrobenzoic acid,quinoline (1/1), (IV), have been determined at 185,K. In each compound, a short hydrogen bond is observed between the pyridine N atom and a carboxyl O atom. The N...O distances are 2.6476,(13), 2.5610,(13), 2.5569,(12) and 2.5429,(12),Å for (I), (II), (III) and (IV), respectively. Although in (I) the H atom in the hydrogen bond is located at the O site, in (II), (III) and (IV) the H atom is disordered in the hydrogen bond over two positions with (N site):(O site) occupancies of 0.39,(3):0.61,(3), 0.47,(3):0.53,(3) and 0.65,(3):0.35,(3), respectively. [source] 2-Oxo-2-phenyl- N -[(R)-1-phenylethyl]acetamide and N,N -dimethyl-2-(1-naphthyl)-2-oxoacetamide: possibility of Yang photocyclization in a crystalACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2009Julia B, kowicz The crystal structures of 2-oxo-2-phenyl- N -[(R)-1-phenylethyl]acetamide, C16H15NO2, (I), and N,N -dimethyl-2-(1-naphthyl)-2-oxoacetamide, C14H13NO2, (II), were determined in an attempt to understand the reason for the lack of Yang photocyclization in their respective crystals. In the case of (I), the long distance between the O atom of the carbonyl group and the ,-H atom, and between the C atom of the carbonyl group and the ,-C atom, preclude Yang photocyclization. For (II), the deviation of the ,-H atom from the plane of the carbonyl group and interactions between the naphthalene rings are regarded as possible reasons for the chemical inertia. The two independent molecules of (I) differ in their conformation. N,H...O hydrogen bonds link molecules of (I) into chains extended along the b axis. [source] Conformational isomers of the [(5-methyl-2-pyridinio)aminomethylene]diphosphonate dianion and [(5-methyl-2-pyridyl)aminomethylene]diphosphonate trianion in salts with 4-aminopyridine and ammoniaACTA CRYSTALLOGRAPHICA SECTION C, Issue 6 2009Ewa Matczak-Jon The crystal structures of two salts, products of the reactions between [(5-methyl-2-pyridyl)aminomethylene]bis(phosphonic acid) and 4-aminopyridine or ammonia, namely bis(4-aminopyridinium) hydrogen [(5-methyl-2-pyridinio)aminomethylene]diphosphonate 2.4-hydrate, 2C5H7N2+·C7H10N2O6P22,·2.4H2O, (I), and triammonium hydrogen [(5-methyl-2-pyridyl)aminomethylene]diphosphonate monohydrate, 3NH4+·C7H9N2O6P23,·H2O, (II), have been determined. In (I), the Z configuration of the ring N,C and amino N,H bonds of the bisphosphonate dianion with respect to the Cring,Namino bond is consistent with that of the parent zwitterion. Removing the H atom from the pyridyl N atom results in the opposite E configuration of the bisphosphonate trianion in (II). Compound (I) exhibits a three-dimensional hydrogen-bonded network, in which 4-aminopyridinium cations and water molecules are joined to ribbons composed of anionic dimers linked by O,H...O and N,H...O hydrogen bonds. The supramolecular motif resulting from a combination of these three interactions is a common phenomenon in crystals of all of the Z -isomeric zwitterions of 4- and 5-substituted (2-pyridylaminomethylene)bis(phosphonic acid)s studied to date. In (II), ammonium cations and water molecules are linked to chains of trianions, resulting in the formation of double layers. [source] cis -Dichloridobis{dimethyl[3-(9-phosphabicyclo[3.3.1]non-9-yl)propyl]amine-,P}platinum(II)ACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2009Peter N. Bungu The title compound, [PtCl2(C13H26NP)2], is a rare example of a sterically bulky ligand adopting a cis geometry in a square-planar complex. It crystallizes on a twofold rotation axis which bisects the Pt centre and the P,Pt,P, and Cl,Pt,Cl, angles. The ligand exhibits a random packing disorder in the N,N -dimethylpropylamine substituent, with the two orientations refining to occupancies of 0.404,(15) and 0.596,(15). Weak intermolecular interactions between a Cl and a H atom of the ligand of a neighbouring molecule result in extended chains along the a axis. The effective cone angle for the dimethyl[3-(9-phosphabicyclo[3.3.1]non-9-yl)propyl]amine (Phoban[3.3.1]-C3NMe2) ligand was determined as being in the range 160,181°, depending on the choice of atoms used in the calculations. [source] Unusual hydrate stabilization in the two-dimensional layered structure of quinacrinium bis(2-carboxy-4,5-dichlorobenzoate) tetrahydrate, a proton-transfer compound of the drug quinacrineACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2009Graham Smith The crystal structure of the hydrated proton-transfer compound of the drug quinacrine [rac- N,-(6-chloro-2-methoxyacridin-9-yl)- N,N -diethylpentane-1,4-diamine] with 4,5-dichlorophthalic acid, C23H32ClN3O2+·2C8H3Cl2O4,·4H2O, has been determined at 200,K. The four labile water molecules of solvation in the structure form discrete ...O,H...O,H... hydrogen-bonded chains parallel to the quinacrine side chain, the two N,H groups of which act as hydrogen-bond donors for two of the water acceptor molecules. The other water molecules, as well as the acridinium H atom, also form hydrogen bonds with the two anion species and extend the structure into two-dimensional sheets. Between these sheets there are also weak cation,anion and anion,anion ,,, aromatic ring interactions. This structure represents the third example of a simple quinacrine derivative for which structural data are available but differs from the other two in that it is unstable in the X-ray beam due to efflorescence, probably associated with the destruction of the unusual four-membered water chain structures. [source] | ||||||||||||||||