Positions Of Hydrogen Atoms Research Articles

Condensed heterocycles. 46. Crystal structure of 3-mercapto-2-benzo[b]-furylidene-(p-methylphenyl) amine

An x-ray structural examination of 3-mercapto-2-benzo [b] furylidene-(p-methyl-phenyl) amine has been carried out. For the first time, the position of the bridge hydrogen atom in a mercaptoaldimine containing the planar conjugated S=C-C=C-N grouping closed by an intramolecular N-H...S hydrogen bond has been established.

Soft X-ray emission studies of metal-hydrogen bonding states in zirconium-based laves phase hydrides

Parameters of X-ray L emission spectra of all transition metals in the system of Laves phase hydrides ZrVMeH x (Me ≡ Cr, Fe, Co, Cu) have been analysed. The analysis shows unequal participation of valence d states of intermetallic components in metal-hydrogen bonding. Different energy positions of hydrogen atoms in tetrahedral interstitial sites formed by different sets of metal atoms cause splitting of the hydride subband of Zr Lβ 2.15 emission spectra. A correlation between characteristics of Zr Lβ 2.15 emission and hydride thermal stability is found. Valence d states of vanadium take part in metal-hydrogen bonding to a lesser extent than those of zirconium. The d states of chromium, iron, cobalt and copper participate still less in bonding with hydrogen.

Extension of the Anderson-Newns model for hydrogen chemisorption on Ni(100), Ni(111) and W(110)

Extensive calculations of the ground state properties of hydrogen chemisorbed on Ni(100), Ni(111) and W(110) surfaces are presented. The calculations are performed using an extension of the Anderson-Newns model, which includes the core-core repulsion term. The variation of the adatom-metal hopping matrix elements with the hydrogen atom position is considered in the framework of the extended Hückel model. The asymptotic behaviour is well reproduced considering corrections to the adatom Coulomb repulsion U due to the charge image potential. The following properties are discussed: (a) chemisorption energy; (b) preferred site; (c) bond lengths; (d) vibrational frequencies; (e) charge transfer; (f) adatom electron density of states. Comparison with available experimental results shows that our method can give a very good overall picture of H chemisorption on the above mentioned systems. The energy contour plot for a plane parallel to the W(110) surface at the equilibrium distance shows the presence of an elongated region of almost constant energy connecting the trigonal and long bridge sites. This result is in agreement with the experimental findings of Blanchet et al. [Surface Sci. 118 (1982) 496], which have shown that the two sites compete. As a consequence of this picture the calculation predict a parallel vibrational mode, whose frequency turns out to be in good agreement with the experimental value (160 meV) given by Blanchet et al.

The influence of substitutional imperfections on the electronic structure of refractory compounds. SP-element impurities in titanium nitride

Using the SCF MO LCAO (self-consistent MO LCAO method in the Mulliken-Wolfsbergelmholz approximation) cluster method and the Green's function method in the ASA-KKR (Korringa-Kohn-Rostoker method in the atomic spheres) approximation, the effect of substitutional impurities (O, C, B, Be, He) on the electronic structure of titanium nitride has been studied. The distributions of the local electronic states of impurity centers and the location of impurity levels in the total energy spectrum of the crystal have been calculated. A detailed discussion is presented of how the entire system of chemical bonding near a defect and the partial interatomic interactions vary as a function of the nature of the impurity atom. The results obtained are employed to interpret the available X-ray emission spectra of ternary systems, and also in treating problems of the mutual solubility of refractory binary phases and heterogeneous catalysis with their participation. A quantum chemical simulation of possible hydrogen atom positions in the nitride structure has been carried out. Hydrogen has been found to occupy preferentially tetrahedral interstices of the TiN lattice.

Carbon-hydrogen activation mechanisms and regioselectivity in the cyclometalation reactions of bis(pentamethylcyclopentadienyl)thorium dialkyl complexes

This contribution reports on the syntheses, structures and cyclometalation reactions of a series of bis(pentamethylcyclopentadienyl)thorium dialkyl complexes of the type Cp'/sub 2/ThR/sub 2/ (Cp' = eta/sup 5/-C/sub 5/Me/sub 5/). It focuses upon the pathway of C-H ..-->.. C'-H hydrogen atom transfer, hydrogen atom positions in the ground states of Cp'/sub 2/Th(CH/sub 2/CMe/sub 3/)/sub 2/ by single-crystal neutron diffraction, and those structural/electronic factors influencing reaction rate and regioselectivity in both neopentyl and modified neopentyl complexes. While on the surface the present d/sup 0/,f/sup 0/ reaction patterns may appear to exhibit similarities to those of the d/sup 8/ and related systems, it will be seen that there are actually profound mechanistic differences. It will also be seen that Th-C bond enthalpy data are useful in understanding certain of the reaction patterns. 63 references, 7 figures, 7 tables.

Structure of methyl (4'S,16S)-3β-acetoxy-17-oxospiro[5-androstene-16,3'-(4,5-dihydropyrazole)]-4'-carboxylate

C25H34N2Os, M r--442.54, monoclinic, P2~, a = 6 . 4 1 4 ( 1 ) , b=9 .729 (2 ) , c = 1 9 . 1 9 2 ( 3 ) A , f l= 91.09 (1) °, V = 1197.4 (4) A 3, Z = 2, Dx= 1.227 (1) Mg m -a, Mo Ka, 2 = 0.71069 fi,, g = 0.796 mm -~, F(000)=476, T = 293 K, final R = 0-035 for 1150 independent reflections. The configurations at chiral centers 4' and 16 (3')were found to be both S, assuming the S configuration at 13. The bowing of ring A relative to the remainder of the steroid nucleus is 17.03 (2) ° . The rings have the following conformations: A chair; B half chair; C slightly deformed chair; D slightly distorted envelope. Introduetion. In the course of investigations on steroidal lactones having cytostatic properties (Koc6r, Kabat, Wicha & Peczyfiska-Czoch, 1983), the title compound was synthesized by treatment of (E)-3fl,17fl-dihydroxy-5-androsten16-ylidenacetic acid with diazomethane followed by acetylation of the hydroxy group at C(3). The sequence of atoms in the dihydropyrazole ring thus formed was elucidated from the ~H NMR data. However, the configuration at the new chiral centers 16 (3') and 4' could not be established and therefore X-ray structural analysis of the title compound was necessary. Experimental. Crystal (0.25 x 0.36 x 0.67 mm) from methanol. CAD-4D diffractometer (Enraf-Nonius), MoKu radiation. Cell constants refined from 25 reflections (13.3 2tr I. Equivalent reflections averaged automatically by SDP system, Rln t not estimated. Lorentz and polarization, no absorption correction. Space group P2 r Structure solved by direct methods (MUL TAN80; Main et al., 1980). Mean atomic scattering factors taken from International Tables for X-ray Crystallography (1974). Non-H-atom parameters refined anisotropically for one enantio0108-2701/85/111630-03501.50 morph by a full-matrix procedure (XRAY70 system; Stewart, Kundell & Baldwin, 1970) for 1150 observed F's. H-atom positions found from Ap maps, added and refined (damping 0.3) in the last refinement step (B = Beq of adjacent atom + 1A 2, invariant). Final R = 0.035 (wR = 0.033, unit weights) at A/tr < O. 1. Max. and min. electron densities on final Ap map 0.3 and 0 . 2 e A -3, respectively. Programs used for calculations of secondary results were RING (Phrkfinyi, 1979) and PLALIN (Nardelli, Musatti, Domiano & Andreetti, 1978). Computations done on PDP8/I 1, Cyber-73 and MERA-400 computers. Discussion. Table 1 gives the fractional coordinates of non-hydrogen atoms.* The bond lengths and valence angles are given in Table 2. Fig. 1 presents a projection of the steroid molecule oriented at optimal viewing. In the description of the molecular structure of the steroid under investigation the conventions applied by Duax & Norton (1975) are followed. Fig. 2 shows a view of the steroid parallel to the least-squares plane through the atoms C(1) to C(17) (rings B, C and D). The bowing angle of ring A with respect to this plane (A/B-C-D) is 17.03 (2) °. The mean values of C C bond lengths and C C C angles in saturated rings A and C are 1.536 (8)/k and 111.0 (4) °, respectively. For the unsaturated ring B, the mean value for single C C bond lengths is 1.533 (7)/k with the mean angle of 111.6 (4) °. All bond lengths and angles in rings A, B and C are in agreement (within twice the e.s.d.) with the mean values for 13 AS-steroid structures quoted by Duax & Norton (1975) with two exceptions: bonds C(9)-C(11) and C(13)C(14) (ring C) deviate by more than 0.03 A, being longer and shorter, respectively. * Lists of structure factors, hydrogen-atom positions, anisotropic thermal parameters and torsion angles have been deposited with the British Library Lending Division as Supplementary Publication No. SUP 42348 (15 pp.). Copies may be obtained through The Executive Secretary, International Union of Crystallography, 5 Abbey Square, Chester CH 1 2HU, England. © 1985 International Union of Crystallography GLUZIlqSKI, KRAJEWSKI, URBAlqCZYK-LIPKOWSKA, ARGAY A N D P/~RK/~NYI 1631 Ring A of the steroid reported here may be characterized by a chair conformation ~°C 3 (4C 0. The asymmetry parameters are: AC] = 5.6 (6) ° and AC~z ,2 = 3.0 (6) °. Since the deviations of C(3) and C(10) from the least-squares plane of A [defined by C(1), C(2), C(4) and C(5)] are nearly symmetrical [+0.656 (6)/k], an almost ideal chair conformation with mean torsion angle of 54.6 (6) ° may be assumed. The O-acetyl substituent at C(3) is found in the equatorial position. The unsaturated ring B has the half-chair conformation 8H 9. The asymmetry parameter dCSz,6= 0.8 (7) °. The deviations of C(8) and C(9) from the Table 1. Fractional atomic coordinates (× 10 4) with e.s.d. 's in parentheses Origin along b specified by keeping y of O(1) fixed.

Solvent structure in vitamin B12 coenzyme crystals

Both the ordered and disordered solvent networks of vitamin B12 coenzyme crystal hydrate have been generated by Monte Carlo simulation techniques. Several different potential functions have been use to model both water-water and water-solute (i.e., water-coenzyme) interactions. The results have been analysed in terms of the structural properties of the water networks, such as mean water oxygen and hydrogen positions, coordination of each water molecule, and maxima of probability density maps in all four asymmetric units of this crystal. The following results were found: (I) Within each asymmetric unit only one hydrogen bonding network was predicted although there were several hydrogen atom positions for any one solvent molecule (defined as maxima in probability density). (II) Reasonable agreement was obtained between predicted and experimental positions in the ordered solvent region, independent of the potential function used. (III) The positions of the calculated probability density maxima for the disordered channel region were different in different asymmetric units; this led to different simulated hydrogen bond networks which were not always consistent with the experimentally determined alternative (lower occupancy) sites. The results suggest that it is advisable to simulate more than one asymmetric unit if one wishes to look at disorder in the solvent regions. Probability density maps were qualitatively very useful for picturing these disordered regions. However, there were no significant differences between quantitative results predicted using either average atomic positions or maxima of the probability density distributions. Problems in quantifying agreement between experimental and predicted disordered solvent networks are discussed. The potential which included hydrogen atoms explicitly (EMPWI) seemed to give the best overall agreement, mainly because it was successful in predicting the unusually short hydrogen bonds which are found in this crystal.

Synthesis of dinuclear phosphido or arsenido bridged complexes of molydenum via reaction of secondary phosphines or arsines with [Mo(η 5-C 5H 5)(CO) 3] 2: X-ray structures of {[Mo(η 5-C 5H 5)(CO) 2] 2(μ-H)(μ-ER 2)} (E = P, R = t-Bu; or E = As, R = Me)

Reaction of [Mo(η 5-C 5H 5)(CO) 3] 2 with t-Bu 2PH or Me 2AsH yields {[Mo(η 5-C 5H 5(CO) 2] 2(μ-H)(μ-ER 2)}, where E = P, R = t-Bu ( 1) (45%); or E = As, R = Me ( 2) (35%). The X-ray crystal structures of 1 and 2 have been determined. Each complex contains a central planar Mo 2(E)(H) core and the co-ordination geometry about each Mo is best described as a “four-legged stool” in which adjacent H and P (or As) atoms are shared. The positions of the bridging hydrogen atoms are symmetrical to within experimental error.

Neutron diffraction of alpha, beta and gamma cyclodextrins: hydrogen bonding patterns.

Cyclodextrins (CD's) have proved useful as model systems for the study of hydrogen bonding. They are torus-shaped molecules composed of six(alpha), seven(beta) or eight(gamma) (1----4) linked glucoses. Because of their particular geometry, they are able to act as a "host" to form inclusion complexes with "guest" molecules very much like enzymes. Cyclodextrins have been shown to exert catalytic activity on suitable included-substrate molecules; they catalyze the hydrolysis of phenylacetates, of organic pyrophosphates and of penicillin derivatives. They also accelerate aromatic chlorinations and diazo coupling by means of their primary and/or secondary hydroxyl groups, so that the rates of hydrolysis are enhanced by up to a factor of 400. In order to understand the hydrogen bonding in these enzyme models, neutron diffraction data were collected to unambiguously determine the hydrogen atom positions, which could not be done from the x-ray diffraction data. alpha-CD has been shown to have two different structures with well-defined hydrogen bonds, one "tense" and the other "relaxed". An "induced-fit"-like mechanism for alpha-CD complex formation has been proposed. Circular hydrogen bond networks have also been found for alpha-CD due to the energetically favored cooperative effect. beta-CD with a disordered water structure possesses an unusual flip-flop hydrogen bonding system of the type O-H...H-O representing an equilibrium between two states: O-H...O in equilibrium O...H-O. gamma-CD with a disordered water structure similar to beta-CD also possesses the flip-flop hydrogen bond. This study demonstrates that hydrogen bonds are operative in disordered systems and display dynamics even in the solid state.

SOLVENT NETWORKS IN NUCLEOTIDE CRYSTAL HYDRATES

Solvent is known to play a role in stability and transitions of nucleic acid helices. We are using computer simulation techniques to study the structure and energetics of water at nucleic acid interfaces in crystals, which enables a detailed comparison of the predicted solvent molecules to be compared with well characterised experimental data from crystallographic studies. In an effort to improve the predictive power of computer simulation we have been studying the explicit use of both experimentally derived and calculated hydrogen atomic positions on either all solute atoms or on polar solute atoms alone using two different force fields for the solute atoms.

Hydrogen Atom Positions in Kaolinite by Neutron Profile Refinement

AbstractA structure refinement of kaolinite made using the Rietveld neutron profile refinement technique has given non-hydrogen atom positions which were not significantly different from those given by B. B. Zvyagin in 1960. All of the hydrogen atoms have been located; the three inner-surface hydrogen atoms are involved in interlayer hydrogen bonds with lengths of 2.95(4), 2.95(4), and 3.06(4) Å with O-H ... O angles of 168(4)°, 144(4)°, and 146(4)° respectively. The inner hydrogen atom is located in a position consistent with that found earlier in dickite and muscovite which are the only dioctahedral layer silicates studied by neutron diffraction to date. The O-H vector makes an angle of 34° with the (001) plane, away from the octahedral sheet, and the projection of the vector on to (001) is at ~30° to the b axis.

Xanthine oxidase initiated oxidation of model membranes. Effect of position of abstractable hydrogen atoms in the bilayer on the distribution of products

Xanthine oxidase initiated oxidation of model membranes. Effect of position of abstractable hydrogen atoms in the bilayer on the distribution of products

Study of hydrogen positions in Cu(NO3)2.2.5H2O from PMR and DMR

Proton magnetic resonance (PMR) is used to determine the orientation of the proton-proton vectors of the water molecules in Cu(NO3)2.2.5H2O. From a deuteron magnetic resonance (DMR) study of Cu(NO3)2. 2.5D2O the orientations of the electric field gradient tensor at the deuterium sites are found. The NMR data are coupled with the hydrogen bonding scheme in the crystal and the crystal structure to determine the hydrogen atom positions.

The crystal and molecular structures of [Co(NH 3) 6][CuCl 5] as determined from single crystal X-ray and neutron diffraction data

The crystal structure of the title compound was determined at room temperature ( ca. 21°C) using single crystal X-ray and neutron diffraction data. The substance crystallizes in the cubic space group O h 8-Fd3c in a unit cell whose edge is a = 21.992(3)Å. The X-ray data were refined to R(F 0) = 0.026 and R w(F 0) = 0.027, while the neutron data refined to R(F 0) = 0.055. The two sets of coordinates obtained agree remarkably well even for the hydrogen atoms but, since the neutron results are more reliable for the hydrogen atom positions, our discussion is based on these. The Co-N and <N-H > distances are, respectively, 1.968(2)Å and 0.953(5)Å. The most important result, namely the Cu-Cl(axial)Cu-Cl(equat.) ratio, is 0.955; the individual values of these quantities being Cu-Cl(ax) = 2.301 and Cu-Cl(equat.) = 2.409. Thus, the CuCl 5 3− anion is axially compressed by a substantial amount and, in this respect, resembles its octahedral CuF 6 4− relative.

Hydrogen Atoms in Boehmite: A Single Crystal X-Ray Diffraction and Molecular Orbital Study

AbstractThe crystal structure of natural boehmite, AlOOH, from Tveidalen, Langesundsfjorden, Norway, with a = 3.693(1), b = 12.221(2) and c = 2.865(1) Å, was refined from single crystal X-ray diffraction data (MoKα maximum 2θ = 120°) to an Rw value of 0.032 in space groups Amam and A21am. In both cases the proton was found to occupy positions of the type (x, 0.038, 0), where x = 0.104 and 0.396, about 0.75 Å from the donor oxygen atom. This arrangement corresponds to the presence of chains of asymmetric hydrogen bonds with random polarity parallel to the a axis, and indicates that the effective space group is Amam. No significant electron density was observed either at the center (0, 0, 0) or at the position (1/4, y, 0), corresponding to symmetric and bifurcated hydrogen bonds, respectively, between the layers of octahedra.Calculations of the total energy of a representative portion of the boehmite structure as a function of hydroxyl orientation, using semiempirical molecular orbitals of the Hückel type, are in agreement with the observed electron density distribution and suggest a preference for (1) sp3, rather than sp2, hybridization of the donor oxygen atom orbitals, and (2) asymmetric, rather than symmetric hydrogen bonds. Disorder of the hydrogen atom positions within individual hydrogen bond chains is shown to be much less likely than disorder between adjacent fully coherent chains.

Hydrogen Atom Positions in Dickite

Hydrogen Atom Positions in Dickite

Conversion of H 2Os 3(μ 3-NCH 3)(CO) 9 to Os 4(μ 3-NCH 3)(CO) 12; crystal and molecular structure of the two methylnitrene cluster complexes

The complex H 2Os 3(μ 3-NCH 3)(CO) 12 in decalin at 198°C in 35% yield. Crystal data for the former obtained at −158°C are: orthorhombic, space group Pmcn, a 14.113(2), b 6.605(1), c 17.683(4) », Z = 4, D c 3.44 g cm −3. The hydrogen atoms are related by symmetry. The position of the unique hydrogen atom has been refined. It is observed asymmetrically bridging (closer to the unique Os atom) the longer edge of the isosceles triosmium triangle. The hydrogen atoms are out of the trimetal plane away from the triply-bridging nitrogen atom. Crystal data for the tetraosmium complex at 25°C are: monoclinic, space group C2/c a 30.818(9), b 8.463(2), c 16.621(2), », β 108.90(2)°, Z = 8, D c 3.75 g cm −3. The four osmium atoms form a distorted tetrahedral framework capped by the nitrogen atom of the methylnitrene group on the face containing the three longer OsOs separations.

DETERMINATION OF CRYSTAL STRUCTURE OF CHLORO-TENACISS IGENIN

The molecular formula of chloro-tenaciss igenin is C23H33O5Cl. The crystal belongs to monoclinic system. The space group is C22P21. The parameters of unit cell are a=15.782(7)?, 6 = 8.454(4)?, c = 8.074(4)? and β= 101.08(21)°. There are two molecules in an unit cell (Z = 2). Intensity data were collected on a PW-1100 four-circle diffractometer. The total number of independent diffractions amounts to 2097.The structure was solved by direct method (MULTAN 78). The refinement of the structure parameters was acheived by block-matrix least-square method, R=0.075. All the positions of hydrogen atoms were located by the difference Fourier syntheses and two of them, which are in the methyls, present disorder property.The chloro-tenaciss igenin molecule contained the conformation characteristic of tenaciss igenin. B-ring and C-ring, and C-ring and D-ring all exhibit cisforms obviously.

DETERMINATION OF PENTAACETYLSARMENTOSIN CRYSTAL STRUCTURE

Pentaacetylsarmentosin is a derivative of Sarmentosin which is one of effective component of plant Sedum sarmentosum Bunge. The molecular formula is C21H27O12N. Pentaacetylsarmentosin crystals belongs to the orthogonal system, space group D24P212121. The cell dimensions are a = 19.756(3)?, 6 = 17.013(3)?, c = 7.482(1)?; four molecules are contained in a cell (z = 4). Intensity data were collected on a PW-1100 four circle diffractometer.The original MULTAN-78 was not successful in solving the structure, the correct structure solution was obtained by optimal selection method used to improve the index distribution of starting reflection set.Refinement of the structure paramenters was acheived by block-matrix Least-squares (program XTL (1974)), R = 0.051 (sin θ/λ≤ 0.48), R = 0.063 (all observed reflections). All the positions of hydrogen atoms except the methyes were located by the difference syntheses.

Circular hydrogen bonds

CIRCULAR hydrogen bonds present a new, experimentally demonstrated principle showing how hydration water molecules and hydroxyl groups of macromolecules can cooperate to form a network-like pattern. Quantum chemical calculations show that chain-like H-bonds in the crystal lattice1 are energetically favoured above individual ones2,3. This is due to the cooperative effect, which leads to increased H-bonding activity of an OH-group if it is already accepting or donating an H-bond. These linear structures can close up to form circular arrangements comprising four and more OH-groups4–6. Such circles have actually been described for crystal structures of ice7 and of ice clathrates8, but in these cases the water molecules within the circles are related by crystallographic symmetry elements and are therefore not independent of each other. One should expect to find lattice-independent circular H-bonds in crystal structures of large O—H-rich molecules which co-crystallise with water of hydration, conditions which are satisfied by the cyclodextrin family. The smallest member, α-cyclodextrin (α-CD; cyclohexaamylose), consists of six α(1, 4)-linked glucose molecules and contains six primary and 12 secondary hydroxyl groups ((C6H10O5)6, molecular weight 973). From aqueous solution, α-CD crystallises as hexahydrate, α-CD·6H2O, and this complex, with a total of 120 hydroxyl groups (4 × 18 from α-CD and 4 × 12 from the six H2O) in one unit cell has been studied by X-ray and neutron diffraction methods (ref. 9, and Klar, Hingerty and W.S., unpublished). Two other complexes, a second modification of the hexahydrate (K. Lindner and W.S., unpublished) and α-CD·methanol·4H2O (ref. 10) have been investigated by X rays. As refinement in all cases is around R = 4% for data extending to 0.89 A resolution, hydrogen atom positions could be assigned. I discuss here results obtained from the X-ray/neutron study of α-CD·6H2O.