H-atom Positions Research Articles

(R,R)-Disynephrine ether bis(hydrogen sulfate)

The asymmetric unit of the title compound [systematic name: (R,R)-2,4-bis­(4-hydroxy­phen­yl)-N,N′-dimethyl-3-oxapentane-1,5-diammonium bis­(hydrogen sulfate)], C18H26N2O3 2+·2HSO4 −, contains one half-cation and one hydrogen sulfate anion. The cation has crystallographically imposed twofold symmetry with the rotation axis passing through the central ether O atom. Hydrogen bonds between the hydr­oxy group and amine H atoms of the cation to two hydrogen sulfate anions link the three ions in a ring motif. A three-dimensional network is accomplished by additional O—H⋯O hydrogen bonds between the anions and by N—H⋯O hydrogen bonds between the cations. Disorder with equally occupied sites affects the H-atom position in the anion.

Redetermination of bis(O,O′-diethyl dithiophosphato-κ2S,S′)nickel(II)

The centrosymmetric title complex, [Ni{S2P(OC2H5)2}2], has been redetermined using area-detector data. The central Ni(S2P)2 core is essentially planar and confirms the early results of McConnell & Kastalsky [Acta Cryst. (1967), 22, 853–859] based on multiple film technique data. In the title structure, the standard uncertainty values are approximately seven times lower and all H-atom positions are calculated. A pair of short symmetry-related H⋯H contacts with distances of 2.33 Å is observed in the crystal structure.

H-Atom Position as Pattern-Determining Factor in Arenethiol Films

The evolution of a low coverage of benzenethiol molecules on Cu(111) during annealing shows the prevalence of S...H hydrogen bonds involving hydrogen atoms in the ortho position. The row and pattern formation of (methylated) anthracenethiols indicates intermolecular interactions in which hydrogen atoms at the terminal position of the aromatic moiety dominate. In combination, this leads to the notion that pattern formation in classes of arenethiol molecules is each governed by optimization of the intermolecular interactions of the hydrogen atom at one particular position on the arene. This may provide a general guiding principle for the design of arenethiol films.

Redetermination ofcyclo-trimethylenetrinitramine

The redetermined structure of 1,3,5-trinitro-1,3,5-triaza­cyclo­hexane, C3H6N6O6, at 90 (2) K has ortho­rhom­bic (Pbca) symmetry. It is of inter­est with respect to energetic compounds. The structure was originally investigated through X-ray diffraction by Hultgren [(1936). J. Chem. Phys. 4, 84]. Later X-ray investigations were completed by McCrone [(1950). Anal. Chem. 22, 954–955] and Harris, Reed & Gluyas [(1959). AFOSR-TR-59-165 Ohio State University Research Foundation, Columbus, Ohio, USA]. A single-crystal neutron diffraction study was performed by Choi & Prince [(1972). Acta Cryst. B28, 2857–2862] to ascertain the H-atom positions, which had not been defined by the earlier X-ray diffraction studies. All previous studies were performed at or near room temperature. The structure provided is the α polymorph of the title compound. The ring atoms are arranged in the chair conformation with two nitro groups occupying pseudo-equatorial positions and the remaining nitro group is axial. The crystal packing is stabilized by close intramolecular interactions from one H atom in each methylene group to O atoms of adjacent nitro groups, ranging from 2.251 to 2.593 Å.

Structure and energy in organic crystals with two molecules in the asymmetric unit: causality or chance?

The structures of 5547 organic crystals with two molecules in the asymmetric unit (Z′ = 2) are collected from the Cambridge Structural Database, and compared with a sample of 45182 crystal structures with one molecule in the asymmetric unit (Z′ = 1). A new method for standardizing H-atom positions is described. Approximate symmetry in Z′ = 2 crystals is analyzed using real-space information only. Lattice energies are calculated by the PIXEL method and partitioned into contributions from the two different sites in Z′ = 2 crystals and into molecule–molecule contributions, with special attention paid to the most energetic molecular pair. There are no obvious differences between the Z′ = 1 and Z′ = 2 sets in chemical composition, except for a slightly smaller average size of Z′ = 2 molecules. The frequency of space groupsP1, P21 and P increases in Z′ = 2 crystals, while the frequency of space groupsP21/c and P212121 decreases. 83% of the Z′ = 2 crystals show some form of pseudosymmetry with a tolerance of 0.5 Å atom−1. The most energetic pair is on average more tightly bound in Z′ = 2 crystals than in Z′ = 1 crystals, and in Z′ = 2 crystals the asymmetric pair ranks first in the list of molecule–molecule energies in 55–60% of the cases. However, even in crystals where the asymmetric pair is the most energetic, its contribution to the total lattice energy can be as high as 70% or as low as 10%: in many cases, the asymmetry is between weakly interacting molecules. Structural molecular features leading to Z′ = 2 crystals are tentatively analyzed. On the whole, there appears to be a continuum of situations from asymmetric pairs formed between clearly different molecules that pack in clearly different environments (hinting at causality of Z′ = 2) and pairs formed by nearly identical molecules packing in nearly identical environments (hinting at casual, local conditions), but even in the latter case, there is no proof that a fully symmetric structure would be more stable.

Neutron protein crystallography: beyond the folding structure of biological macromolecules

Neutron diffraction provides an experimental method of directly locating H atoms in proteins, a technique complementary to ultra-high-resolution X-ray diffraction. Three different types of neutron diffractometers for biological macromolecules have been constructed in Japan, France and the USA, and they have been used to determine the crystal structures of proteins up to resolution limits of 1.5-2.5 A. Results relating to H-atom positions and hydration patterns in proteins have been obtained from these studies. Examples include the geometrical details of hydrogen bonds, the role of H atoms in enzymatic activity, CH3 configuration, H/D exchange in proteins and oligonucleotides, and the dynamical behavior of hydration structures, all of which have been extracted from these structural results and reviewed. Other techniques, such as the growth of large single crystals and a database of hydrogen and hydration in proteins, are described.

Compressed hydrogen-bond effects in the pressure-frozen chloroacetic acid

The competing effects of squeezed OH...O bonds, destabilizing the H-atom position, and of displaced hydrogen donor and acceptor groups, favouring the ordered H-atom sites, have been tuned by pressure in the pressure-frozen dichloroacetic acid. Its structure has been determined at 0.1, 0.7, 0.9 and 1.4 GPa: in this pressure range the crystals are stable in the monoclinic space group P2(1)/n. The molecules are O-H...O hydrogen bonded into dimers, which in turn interact via a unique pattern of halogen...halogen contacts. Between 0.1 and 1.4 GPa the OH...O bond is squeezed from 2.674 (13) to 2.632 (9) A. Within the pressure range investigated the hydrogen bonds are squeezed and the shear displacement of the molecules compensate, and the H atoms remain ordered.

Reinvestigation of bis(2,2′-bipyridine)(nitrato-κ2O,O′)cobalt(III) hydroxide nitrate tetrahydrate

Single crystals of the title compound, [Co(NO3)(C10H8N2)2](OH)(NO3)·4H2O, were obtained from a Co2+–2,2′-bipyridine–CrO42− mixture as the second crystalline product. The present single-crystal study confirms a previous refinement [Reimann, Zocchi, Mighell & Santoro (1971). Acta Cryst. B27, 2211–2218], and also includes all H-atom positions, which were identified from a difference map. The structure displays an O—H⋯O hydrogen-bonding network between the non-coordinated nitrate group, the hydroxide anion and the water mol­ecules, forming a framework around the distorted octahedral Co complex. A twofold rotation axis passes through Co and the nitrato ligand.

Putrescinium dichloride: a redetermination at 100 K

The crystal structure of the title compound, C4H14N22+·2Cl−, has been redetermined at 100 (1) K. In the room-temperature structure [Chandrasekhar & Pattabhi (1980). Acta Cryst. B36, 2486–2488], the H atoms were located but their parameters were not refined. Since the hydrogen bonds in this structure are extensive, the H-atom positions are of primary importance. The dication lies on a centre of symmetry and the N atoms are slightly displaced [0.019 (4) A] from the plane of the four C atoms. N—H⋯Cl and C—H⋯Cl hydrogen bonds form a three-dimensional network.

(11SR,13RS)-12-Oxa-9-azatetracyclo[7.4.1.02,7.011,13]tetradeca-2(7),3,5-trien-8-one

The title compound, C13H13NO2, was prepared by the epoxidation of its racemic precursor. Its structure was determined in order to establish which of two diastereomers would be favored in that reaction and in other reactions of inter­est. The presence of inter­molecular C—H⋯O inter­actions was considered probable, although H-atom positions were not refined. These inter­actions link the mol­ecules into a two-dimensional network.

Sodium tungstate dihydrate: a redetermination

There have been two previous structure determinations of the title compound, Na2WO4·2H2O: in 1969 [Mitra & Verma (1969). Indian J. Chem. 7, 598–602] and in 1974 [Okada et al. (1974a). Bull. Tokyo Inst. Technol. 120, 7–11]. However, both structures are incorrect according to their entries in the Inorganic Crystal Structure Database [(2007), URL: http://www.fiz-karlsruhe.de/ecid/Internet/en/DB/icsd/index.html]. Despite the high absorption coefficient, the H-atom positions could be observed and refined in the present study. Owing to the accurate analytical absorption correction, all non-H atoms could be refined satisfactorily with anisotropic displacement parameters. There are hydrogen-bonding inter­actions between all H atoms and the O atoms of the tungstate dianion.

Reinvestigation of eakerite, Ca2SnAl2Si6O18(OH)2·2H2O: H-atom positions by single-crystal X-ray diffraction and correlation with Raman spectroscopic data

The crystal structure of natural eakerite [Kossiakoff & Leavens (1976). Am. Mineral. 61, 956–962] has been reinvestigated, the H-atom positions determined and the hydrogen-bonding scheme elucidated. The O⋯O separations of the O—H⋯O hydrogen bonds correlate well with the frequencies of the three corresponding Raman peaks according to Libowtzky's regression curve. The Sn atom has site symmetry \overline{1}.

Invariom-model refinement ofL-valinol

The structure of L-valinol [(S)-(+)-2-amino-3-methylbutan-1-ol or hydroxylated L-valine], C5H13NO, has been determined at 100 K by single-crystal X-ray diffraction. The independent atom model geometry, Flack parameter and figures of merit are compared with results from an invariom structure refinement. The latter provides H-atom positions free of independent atom model bias and therefore yields a more accurate hydrogen-bond pattern, and the geometry from invariom refinement shows an improved agreement with results from a quantum chemical geometry optimization.

Accurate molecular structures and hydrogen bonding in two polymorphs of ortho-acetamidobenzamide by single-crystal neutron diffraction

The structures of both known forms of the polymorphic material ortho-acetamidobenzamide, C(9)H(10)N(2)O(2), have been determined by low-temperature neutron single-crystal diffraction. Neutron diffraction allows the full description of the H-atom positions in this molecular material, which is vital in benchmarking related crystal-structure predictions. Significant conformational differences are indicated by a number of the torsion angles involving H atoms when compared with previous X-ray studies. A comprehensive description of the hydrogen-bonding scheme in both polymorphs is given.

Trophic transfer and biotransformation of polychlorinated biphenyls in zebra mussel, round goby, and smallmouth bass in Lake Erie, USA

Trophic transfer of polychlorinated biphenyl (PCB) congeners in zebra mussels (Dreissena polymorpha), round gobies (Neogobius melanstomus), and smallmouth bass (Micropterus dolomieu) were assessed in four sites along the south shore of the west and central basin of Lake Erie (all sites were in OH, USA). Total PCB levels in smallmouth bass (1,091-1,520 ng/g wet weight) and round gobies (118-256 ng/g wet weight) were similar among sites despite a west-to-east decrease in total PCB concentrations in zebra mussels (29-97 ng/g wet weight). At all sites, PCB body burden increased three- to fivefold at each successive trophic level, suggesting biomagnification in this nonnative food chain. Whereas fish species were dominated by the hexachlorine homologue, zebra mussels were dominated by penta- and hexachlorine homologues; the average degree of chlorination of PCBs was 56.1% for zebra mussels, 60.4% for round goby, and 59.9% for smallmouth bass bodies. Predictive structure-activity relationships based on chemical characteristics, such as the octanol-water partition coefficient (log K(ow)), had little predictive power on bioaccumulation and biotransformation of PCB congeners because of nonlinearity, threshold relationships, and species-specific differences. Calculated trophic transfer for the smallmouth bass-round goby linkage was higher than for the round goby-zebra mussel linkage. Only when PCB congeners were grouped by chemical structure first (vicinal [adjacent] H-atom position in the phenyl ring) were linear relationships achieved. It appeared that the chemical group to which each congener belonged influenced biotransformation more than species-specific (round gobies vs smallmouth bass) differences. Biotic changes at midtrophic levels, such as exotic species invasions, may have an increasingly important role in determining pollutant cycling and hence pollutant residues in top predators.

Redetermination of CaB8O11(OH)4at low temperature

The structure of CaB8O11(OH)4 (calcium octa­borate tetra­hydroxide) [Zayakina & Brovkin (1978). Kristallografiya, 23, 1167–1170] has been redetermined at 120 (2) K with improved precision. The O—H⋯O hydrogen-bonding arrangement has been established, based on freely refined H-atom positions.

Powder diffraction crystal structure analysis using derivative difference minimization: example of the potassium salt of 1-(tetrazol-5-yl)-2-nitroguanidine

The crystal structure of the potassium salt of 1-(tetrazol-5-yl)-2-nitroguanidine [K(C2H3N8O2)] was solved and refined from X-ray powder diffraction data by applying the derivative difference minimization (DDM) method. The compound is of interest as an energetic substance. The structure model was found from a Patterson search. The reflection intensities for the Patterson synthesis were derived from the powder profile by applying a newly developed DDM-based profile decomposition procedure. The use of the DDM method allowed successful location and unconstrained refinement of all the atomic positions, including those of three independent H atoms. The advantages of DDM in terms of the precision and reproducibility of the structural parameters are discussed in comparison to Rietveld refinement results. The failure to refine the H-atom positions by the Rietveld method was attributed to systematic errors associated with the background modelling, which are avoided by DDM.

Production and X-ray crystallographic analysis of fully deuterated cytochrome P450cam

Neutron protein crystallography allows H-atom positions to be located in biological structures at the relatively modest resolution of 1.5-2.0 A. A difficulty of this technique arises from the incoherent scattering from hydrogen, which considerably reduces the signal-to-noise ratio of the data. This can be overcome by preparing fully deuterated samples. Efficient protocols for routine and low-cost production of in vivo deuterium-enriched proteins have been developed. Here, the overexpression and crystallization of highly (>99%) deuterium-enriched cytochrome P450cam for neutron analysis is reported. Cytochrome P450cam from Pseudomonas putida catalyses the hydroxylation of camphor from haem-bound molecular O(2) via a mechanism that is thought to involve a proton-shuttle pathway to the active site. Since H atoms cannot be visualized in available X-ray structures, neutron diffraction is being used to determine the protonation states and water structure at the active site of the enzyme. Analysis of both hydrogenated and perdeuterated P450cam showed no significant changes between the X-ray structures determined at 1.4 and 1.7 A, respectively. This work demonstrates that the fully deuterated protein is highly isomorphous with the native (hydrogenated) protein and is appropriate for neutron protein crystallographic analysis.

Structure determination of forms I and II of phenobarbital from X-ray powder diffraction

From pure powders of forms I and II of phenobarbital, X-ray diffraction patterns were recorded at room temperature. The starting crystal structural models were found by a Monte-Carlo simulated annealing method. The structures of the two forms were obtained through Rietveld refinements. Soft restraints were applied on bond lengths and bond angles, all H-atom positions were calculated. The cell of form I is monoclinic with the space group P2(1)/n, Z=12, Z'=3. Form II has a triclinic cell, with the space group P1 , Z=6, Z'=3. For both forms, the crystal cohesion is achieved by networks of N-H...O hydrogen bonds along [101]. The broadening of the Bragg peak profiles is interpreted in terms of isotropic strain effects and anisotropic size effects.

An investigation of H-atom positions in sulfuric acid crystal structures.

Hydrogen conformations in crystalline H2SO4.8H2O and H2SO4.6.5H2O have been studied using a system developed by Hirsch [(2003), Z. Anorg. Allg. Chem. 629, 666-672]. New H-atom coordinates, as estimated from DFT calculations, are given for these structures.