Crystal structure and hydrogen bonding system in cellulose I(alpha) from synchrotron X-ray and neutron fiber diffraction

The crystal and molecular structure, together with the hydrogen-bonding system in cellulose I(alpha), has been determined using atomic-resolution synchrotron and neutron diffraction data recorded from oriented fibrous samples prepared by aligning cellulose microcrystals from the cell wall of the freshwater alga Glaucocystis nostochinearum. The X-ray data were used to determine the C and O atom positions. The resulting structure is a one-chain triclinic unit cell with all glucosyl linkages and hydroxymethyl groups (tg) identical. However, adjacent sugar rings alternate in conformation giving the chain a cellobiosyl repeat. The chains organize in sheets packed in a "parallel-up" fashion. The positions of hydrogen atoms involved in hydrogen-bonding were determined from a Fourier-difference analysis using neutron diffraction data collected from hydrogenated and deuterated samples. The differences between the structure and hydrogen-bonding reported here for cellulose I(alpha) and previously for cellulose I(beta) provide potential explanations for the solid-state conversion of I(alpha) --> I(beta) and for the occurrence of two crystal phases in naturally occurring cellulose.     

Structure and dynamics of a complex of cellulose with EDA: insights into the action of amines on cellulose

The neutron structure of a complex of EDA with cellulose has been determined to reveal the location of hydrogen atoms involved in hydrogen-bonding. EDA disrupts the hydrogen-bonding pattern of naturally occurring cellulose by accepting a strong hydrogen-bond from the O6 hydroxymethyl group as the conformation of this group is rotated from tg to gt. The O3-H·O5 intrachain hydrogen-bond commonly found in cellulose allomorphs is observed to be disordered in the neutron structure, and quantum chemistry and molecular dynamics calculations show that O3 prefers to donate to EDA. The hydrogen-bonding arrangement is highly dynamic with bonds continually being formed and broken thus explaining the difficulty in locating all of the hydrogen atoms in the neutron scattering density maps. Comparison with other polysaccharide-amino complexes supports a common underlying mechanism for amine disruption of cellulose.     

Thermal response in crystalline Ibeta cellulose: a molecular dynamics study

The influence of temperature on structure and properties of the cellulose Ibeta crystal was studied by molecular dynamics simulations with the GROMOS 45a4 force-field. At 300 K, the modeled crystal agreed reasonably with several sets of experimental data, including crystal density, corresponding packing and crystal unit cell dimensions, chain conformation parameters, hydrogen bonds, Young's modulus, and thermal expansion coefficient at room temperature. At high-temperature (500 K), the cellulose chains remained in sheets, despite differences in the fine details compared to the room-temperature structure. The density decreased while the a and b cell parameters expanded by 7.4% and 6%, respectively, and the c parameter (chain axis) slightly contracted by 0.5%. Cell angles alpha and beta divided into two populations. The hydroxymethyl groups mainly adopted the gt orientation, and the hydrogen-bonding pattern thereby changed. One intrachain hydrogen bond, O2'H2'...O6, disappeared and consequently the Young's modulus decreased by 25%. A transition pathway between the low- and high-temperature structures has been proposed, with an initial step being an increased intersheet separation, which allowed every second cellulose chain to rotate around its helix axis by about 30 degrees . Second, all hydroxymethyl groups changed their orientations, from tg to gg (rotated chains) and from tg to gt (non-rotated chains). When temperature was further increased, the rotated chains returned to their original orientation and their hydroxymethyl groups again changed their conformation, from gg to gt. A transition temperature of about 450 K was suggested; however, the transition seems to be more gradual than sudden. The simulated data on temperature-induced changes in crystal unit cell dimensions and the hydrogen-bonding pattern also compared well with experimental results.     

Preparation of large crystals of photoactive yellow protein for neutron diffraction and high resolution crystal structure analysis

The exact positions of all the hydrogen atoms in photoactive yellow protein (PYP) is important for understanding the molecular mechanism of the photoreaction because the protonation/deprotonation of certain amino acid residues and rearrangements in the hydrogen bond network are involved in the conformational changes of PYP. Neutron crystallography is one of the most effective methods to determine the hydrogen positions. However, a large crystal is required for neutron crystallography because a neutron-incident flux is quite limited. In addition, the crystal should be grown from heavy water to reduce the incoherent background from hydrogen. We prepared a large crystal of PYP (dimensions: 1.5 x 0.7 x 0.7 mm3) for neutron crystallography using ammonium sulfate with sodium chloride. The obtained large crystal gave X-ray diffraction spots up to 0.84 angstroms. Although some of the hydrogen atoms could be observed in the high resolution X-ray crystal structure, functionally important hydrogen atoms were impossible to see, indicating the importance of neutron crystallography. Thus, we optimized the crystallization conditions with heavy water and successfully obtained neutron diffraction spots up to 2.1 angstroms with the crystal in D2O.     

Synthesis and X-Ray Crystal Structure of 3-(Pyrazol-4-yl)propargyl Alcohol

The crystal structure of the title compound has been determined by X-ray diffraction. The N and O atoms are involved in chains of hydrogen bonds, running through the whole crystal, which show proton disorder in a 1:1 ratio. This implies an inversion in the sense of the hydrogen bond network and the presence of inversion centers in the structure. Each molecule is engaged in two unconnected chains building sheets of molecules. An analysis of packing modes of NH-pyrazoles containing at least another hydrogen bond donor or acceptor site in the substituents has been performed.     

Solid–solvent molecular interactions observed in crystal structures of β-chitin complexes

Three β-chitin structures [anhydrous, di-hydrate, mono-ethylenediamine (EDA)] recently determined by synchrotron X-ray and neutron fiber diffraction were reviewed from the viewpoint of molecular interactions. Both water and EDA molecules interact with the chitin chains through multiple hydrogen bonds. When water complexes with chitin, the hydrogen bonding pattern rearranges with the replacement of an intrachain chitin hydrogen bond by a stronger hydrogen bond between chitin and water, with an associated reduction in the degrees of freedom; the water oxygen is a much stronger acceptor than the O5 ring atom. The behavior of hydrogen exchange by deuterium supports this interpretation. EDA-molecules change the conformation of hydroxymethyl group from gg to gt, accompanied by changes in hydrogen bonds due to the strong accepting ability of the EDA nitrogen atoms. Some important interactions are in common with experimental crystallographic results of cellulosic crystals and of molecular dynamics studies. These new insights into solid–solvent interactions are valuable in understanding molecular interactions in other polysaccharides-solvents system in solution or on surface.     

Neutron and X-ray investigations on the oxygen bonding in YBa2Cu3O7-x combined with physico-chemical methods

The occupancy of the oxygen lattice positions at different annealing conditions in YBa₂Cu₃O_(7?x) were determined by Rietveld refinements using neutron and X-ray diffraction data. The occupation density for the oxygen positions O1 to O4 were ascertained. The values of the oxygen content of the samples from this method were compared with those measured by thermoanalysis. The O1 and O4 oxygen atoms are exchangeable by thermal treatment. The oxygen in the planes is fixed and can not be removed by thermal treatment up to 935°C. The binding strength of O1 in the lattice is stronger than that of O4 atoms; this is demonstrated by a higher temperature of dissociation of the O1 atoms. The amount of the oxygen taken up is not exactly equal to the oxygen actually in the lattice positions. In the temperature region below 400°C adsorption and chemisorption processes are become dominant.     

Crystal structures of thermoelectric n- and p-type Ba8Ga16Ge30 studied by single crystal, multitemperature, neutron diffraction, conventional X-ray diffraction and resonant synchrotron X-ray diffraction

Comprehensive single-crystal structural investigations of n- and p-type Ba8Ga16Ge30 have been carried out using multitemperature neutron and conventional X-ray diffraction as well as resonant synchrotron X-ray diffraction. The data show that the guest atom positions and dynamics are very similar in the two structures, although the barium atoms are slightly more displaced from the cage centers in the p-type structure than in the n-type structure (Deltad = 0.025 A). For both structures Fourier difference maps calculated from very high-resolution neutron diffraction data (sin theta/lambda > 2 A-1) show that the Ba nuclear density at lowest temperatures (15 K) is distributed in a torus around the crystallographic 6d site with maxima in the 24j positions. At room temperature the maxima have shifted to the 24k position. Analysis of atomic displacement parameters give Einstein temperatures of approximately 60(1) K for both structures. Thus, the fundamental difference in the low temperature thermal conductivity observed for p- and n-type Ba8Ga16Ge30 appear not to be directly related to the guest atom behavior as is commonly assumed in thermoelectric research. The neutron data and the resonant synchrotron X-ray data facilitate refinement of Ga/Ge framework occupancies. The Ga atoms have a clear preference for the 6c site with the preference being somewhat stronger for the n-type structure.     

Neutron crystallographic and molecular dynamics studies of the structure of ammonia-cellulose I: rearrangement of hydrogen bonding during the treatment of cellulose with ammonia

The hydrogen bond arrangement in a complex of cellulose with ammonia has been studied using neutron crystallography in combination with molecular dynamics simulations. The O6 atom of the hydroxymethyl group is donor in a highly occupied hydrogen bond to an ammonia molecule. This rotating ammonia molecule is donor in partially occupied and transient hydrogen bonds to the O2, O3 and O6 atoms of the hydroxyl groups of other chains. The hydrogen atom bound to the O3 atom is disordered but it is almost always involved in some type of hydrogen bonding. It is donated in a hydrogen bond most of the time to the O5 atom on the same chain. However, it also rotates away from this O5 atom to be donated to an ammonia molecule part of the time. On the other hand the hydrogen atom bound to the O2 atom is free from hydrogen bonding most of the time. It is donated in a hydrogen bond to the O6 atom on a neighboring chain only with a relatively small probability. These results provide new insights into how hydrogen bonds are rearranged during the conversion of cellulose I to cellulose III_I by ammonia treatment.     

Neutron and X-ray investigations on the oxygen bonding in YBa2Cu3O7-x combined with physico-chemical methods

The occupancy of the oxygen lattice positions at different annealing conditions in YBa₂Cu₃O_(7–x) were determined by Rietveld refinements using neutron and X-ray diffraction data. The occupation density for the oxygen positions O1 to O4 were ascertained. The values of the oxygen content of the samples from this method were compared with those measured by thermoanalysis. The O1 and O4 oxygen atoms are exchangeable by thermal treatment. The oxygen in the planes is fixed and can not be removed by thermal treatment up to 935°C. The binding strength of O1 in the lattice is stronger than that of O4 atoms; this is demonstrated by a higher temperature of dissociation of the O1 atoms. The amount of the oxygen taken up is not exactly equal to the oxygen actually in the lattice positions. In the temperature region below 400°C adsorption and chemisorption processes are become dominant.     

Crystal structure and high-pressure properties of γ-Mo2N determined by neutron powder diffraction and X-ray diffraction

We prepared samples of cubic γ-MoN_x (x∼0.5) by high-pressure-high-temperature synthesis. N atom site occupancies within the defect rock salt structure were determined from time-of-flight neutron diffraction and powder X-ray diffraction data by Rietveld analysis. The results show that N atoms occupy only octahedral sites within the structure. The semi-metallic compound is a superconductor, with determined by SQUID magnetometry. The compressibility of the material was determined by synchrotron X-ray diffraction measurements at high pressure in the diamond anvil cell. The vibrational density of states was studied by Raman scattering spectroscopy.     

Synthesis and structure of the framework scandium methylphosphonates ScF(H2O)CH3PO3 and NaSc(CH3PO3)2.0.5H2O

Two framework scandium methylphosphonates have been prepared hydrothermally and their structures solved. ScF(H(2)O)CH(3)PO(3) is a non-porous solid built up from -ScF- chains linked by methylphosphonate groups. The ScO(4)F(2) octahedra are completed by a coordinated water molecule. NaSc(CH(3)PO(3))(2).0.5H(2)O was solved ab initio from high-resolution synchrotron X-ray powder diffraction data. It has a fully connected, negatively charged scandium phosphonate framework where ScO(6) octahedra share vertices with PO(3)CH(3) groups. The solid contains charge balancing sodium cations, coordinated by a water molecule, which may be reversibly removed and adsorbed. The structure of the perdeuterated, dehydrated solid has been refined against neutron powder diffraction data collected at 2.5 K, showing the CD(3) groups in a fully staggered orientation with respect to the phosphonate oxygen atoms.     

Neutron powder diffraction studies of sulfuric acid hydrates. I. The structure of sulfuric acid hemitriskaidekahydrate D2SO4.6(1/2)D2O

We report the first neutron diffraction data from D2SO4.6(1/2)D2O. The crystal is monoclinic, space group Cm, with four formula units per unit cell. At 4.2 K the unit cell dimensions are a = 6.253 26(4) A, b = 26.813 62(10) A, c = 5.908 45(2) A, and beta = 112.1939(3) degrees [V = 917.286(6) A3 and rho(deuterated) = 1664.14(2) kg m(-3)]. The deuteron positions refined from the neutron data are in agreement with those established by single crystal x-ray analysis [D. Mootz and A. Merschenz-Quack, Z. Naturforsch. B 42, 1231 (1987)], but not with those found from the ab initio simulation of Hirsch and Ojamae [Acta Crystallogr, Sect. B: Struct. Sci. 60, 179 (2004)]. The crystal consists of SO4(2-), D3O+ ions, and D2O molecules hydrogen bonded to form a layered structure in which sheets of "icelike" D3O+ and D2O are separated by layers of opposing SO4(2-) tetrahedra.     

[Zn2(C7H8O6)2(bipy)2(H2O)2]·4H2O手性配位聚合物的合成与晶体结构

采用溶剂热技术合成了一种新型手性配位聚合物[Zn2(C7H8O6)2(bipy)2(H2O)2]·4H2O(C7H8O6=2,3-氧-异丙叉基-L-酒石酸根, bipy=4,4'-联吡啶), 并通过单晶X射线衍射结构分析、元素分析、热重分析以及红外光谱进行了表征. 结构分析数据表明, 该化合物属单斜晶系, C2空间群, 晶胞参数a=2.02334(14) nm, b=1.13896(4) nm, c=1.01094(6) nm, β=117.366(3)°, V=2.0689(2) nm3. 两个晶体学独立的Zn原子均为八面体构型, 其中Zn1原子赤道配位点被2个酒石酸根中的4个羧酸根氧螯合配位, 2个酒石酸根中剩下的4个羧酸根氧中的2个分别与2个Zn2原子连接形成无限一维链, Zn2原子的另外2个反式赤道配位点被2个水分子氧占据, 同时这两种Zn原子的轴向配位点均被4,4'-联吡啶的氮原子占据, 形成具有矩形格子[0.51165(3) nm×1.13896(5) nm]的二维层状结构, 游离的2个水分子通过氢键作用形成二聚体, 并与酒石酸根中未与Zn配位的羧酸氧连接, 把二维层状结构连接成三维网状的超分子结构.     

A new hydrated ammonium hydroxy­borate, (NH4)2[B10O14(OH)4]·H2O

The structure of a new synthetic compound, di­ammonium tetra­hydroxy­deca­borate monohydrate, has been determined by single‐crystal X‐ray diffraction. It crystallizes in triclinic space group and all atoms occupy general sites. The title compound is composed of [B₁₀O₁₅(OH)₄]⁴⁻ ions as the fundamental building blocks, and these are linked end‐to‐end by sharing two common O atoms, thus producing infinite chains of composition [B₁₀O₁₄(OH)₄]_n^2n–. These chains are linked by hydrogen bonds, thus forming borate sheets. Water mol­ecules and ammonium ions between these sheets connect adjacent sheets via hydrogen bonds.     

Synchrotron X-ray and Neutron Diffraction Studies in Solid-State Chemistry

Neutron diffraction studies, especially with powders, play an important role in structural solid-state chemistry, making possible the precise determination of the location of light atoms, particularly hydrogen, and enabling a distinction to be made between certain neighboring elements in the periodic table that are difficult to distinguish in experiments with X-rays. Neutron diffraction investigations also make a unique contribution in the area of magnetic structure determination. The availability of intense synchrotron X-rays sources, however, is opening up new opportunities to the structural chemist, many of them complementary to the “traditional” strengths of neutron methods. The key features of synchrotron radiation in relation to structural studies are the wavelength tunability, which facilitates the use of resonant diffraction methods, and the high brightness and excellent vertical collimation of the source, which make possible the construction of diffractometers with unparalleled angular and spatial resolution. The following types of experiments are now possible with synchrotron X-ray diffraction: (1) The ab initio determination of structures from powder diffraction data. (2) The differentiation between different oxidation states of an element (valence contrast experiments) based upon the sensitivity of an absorption edge to the valence of the element in question. (3) The differentiation of elements adjacent to each other in the periodic table, which is now feasible with synchrotron X-rays for all elements beyond chromium. (4) Site-selective X-ray absorption spectroscopy. (5) The study of cation occupancies in materials where more than one element occupies a site that is, or may be, partially occupied. (Such problems are important in zeolite chemistry and high-temperature superconductors.) (6) The determination of crystal structures from microcrystals. (7) In situ and rapid, time-resolved diffraction studies. This review examines the roles played by X-ray and neutron diffraction studies in modern solid-state chemistry, and describes some recent examples in which the use of neutron radiation or synchrotron X-rays has been advantageous.     

Ammoniated alkali fullerides (ND(3))(x)NaA(2)C(60): ammonia specific effects and superconductivity

The crystal structure of the superconducting (ND(3))(x)()NaA(2)C(60) (0.7 < or = x < or = 1, A= K, Rb) fullerides (T(c)= 6-15 K) has been studied by synchrotron X-ray and neutron powder diffraction. It is face-centered cubic (fcc) to low temperatures with Na(+)-ND(3) pairs residing in the octahedral interstices. These are disordered over the corners of two "interpenetrating" cubes with the Na(+) ions and the N atoms displaced by approximately 2.0 A and approximately 0.5 A from the center of the site and statically disordered over the corners of the inner and outer cube, respectively. Close contacts between the D atoms of the ND(3) molecules and electron rich 6:6 C-C bonds of neighboring C(60) units provide the signature of weak N-D.pi hydrogen-bonding interactions, which control the intermolecular packing in the crystal and may determine the unusual superconducting properties.     

Structure of AuCN determined from total neutron diffraction

The structure of gold cyanide, AuCN, has been determined at 10 and 300 K using total neutron diffraction. The structure consists of infinite [bond]Au[bond](CN)[bond]Au[bond](CN)[bond] linear chains, hexagonally packed, with the gold atoms in sheets. The Au-C and Au-N bond lengths are found to be identical, with d(Au(-C/N) = 1.9703(5) A at 300 K. This work supersedes a previous study, by others, which used Rietveld analysis of neutron Bragg diffraction in isolation, and found these bonds to have significantly different lengths (Delta d = 0.24 A) at 300 K. The total correlation function, T(r), at 10 and 300 K, has been modeled using information derived from total diffraction. The broadening of inter- and intrachain correlations differs markedly due to random displacements of the chains in the direction of the chain axes. This is a consequence of the relatively weak bonding between the chains. An explanation for the negative thermal expansion in the c-direction, which occurs between 10 and 300 K, is presented.     

Large dielectric susceptibility associated with proton transfer in a supramolecular structure of chloranilic acid and 5,5'-dimethyl-2,2'-bipyridine

A 1:1 adduct of chloranilic acid with 5,5'-dimethyl-2,2'-bipyridine, in which two kinds of molecules are connected by infinite hydrogen bond chains, exhibits a distinct dielectric phase transition when cooled. Below T(c)(=318 K) the hydrogen atoms participating in hydrogen bonding undergo long-range ordering and form an antiferroelectric-like state, taking a single minimum potential in the high-temperature phase (T>T(c)) due to the bifurcate hydrogen bond system. The proton-transfer phenomenon was clearly observed by electron density distribution analysis using a maximum entropy method of synchrotron x-ray diffraction data.     

Hydrothermal synthesis in the system Ni(OH)(2)-NiSO(4): nuclear and magnetic structures and magnetic properties of Ni(3)(OH)(2)(SO(4))(2)(H(2)O)(2)

We present the synthesis, characterization by DT-TGA and IR, single crystal X-ray nuclear structure at 300 K, nuclear and magnetic structure from neutron powder diffraction on a deuterated sample at 1.4 K, and magnetic properties as a function of temperature and magnetic field of Ni(3)(OH)(2)(SO(4))(2)(H(2)O)(2). The structure is formed of chains, parallel to the c-axis, of edge-sharing Ni(1)O(6) octahedra, connected by the corners of Ni(2)O(6) octahedra to form corrugated sheets along the bc-plane. The sheets are connected to one another by the sulfate groups to form the 3D network. The magnetic properties measured by ac and dc magnetization, isothermal magnetization at 2 K, and heat capacity are characterized by a transition from a paramagnet (C = 3.954 emu K/mol and theta = -31 K) to a canted antiferromagnet at T(N) = 29 K with an estimated canting angle of 0.2-0.3 degrees. Deduced from powder neutron diffraction data, the magnetic structure is modeled by alternate pairs of Ni(1) within a chain having their moments pointing along [010] and [010], respectively. The moments of Ni(2) atoms are oppositely oriented with respect to their adjacent pairs. The resulting structure is that of a compensated arrangement of moments within one layer, comprising one ferromagnetic and three antiferromagnetic superexchange pathways between the nickel atoms.