Refinement of two different crystal structures simultaneously from a multiple-crystal sample: neutron study of 3-deazauracil and lead hydrogen arsenate at 100 K

The structures of 3-deazauracil and lead hydrogen arsenate have been studied by neutron single crystal diffraction at 100 K, using a sample containing one crystal of each material. The experiment on the composite sample was entirely routine, using recently developed multiple-crystal techniques. The structures themselves represent the best low temperature neutron determinations on each of these materials and are discussed.     

Low-Barrier Hydrogen Bonds in Negative Thermal Expansion Material H3[Co(CN)6]

The covalent nature of the low-barrier N−H−N hydrogen bonds in the negative thermal expansion material H₃[Co(CN)₆] has been established by using a combination of X-ray and neutron diffraction electron density analysis and theoretical calculations. This finding explains why negative thermal expansion can occur in a material not commonly considered to be built from rigid linkers. The pertinent hydrogen atom is located symmetrically between two nitrogen atoms in a double-well potential with hydrogen above the barrier for proton transfer, thus forming a low-barrier hydrogen bond. Hydrogen is covalently bonded to the two nitrogen atoms, which is the first experimentally confirmed covalent hydrogen bond in a network structure. Source function calculations established that the present N−H−N hydrogen bond follows the trends observed for negatively charge-assisted hydrogen bonds and low-barrier hydrogen bonds previously established for O−H−O hydrogen bonds. The bonding between the cobalt and cyanide ligands was found to be a typical donor–acceptor bond involving a high-field ligand and a transition metal in a low-spin configuration.     

Neutron elastic scattering studies of biological molecules and complexes

Neutron diffraction can provide very precise stereochemical information about hydrogen bonds and other features involving hydrogen atoms in crystals. This is because, unlike for x rays, the hydrogen atom has a significant scattering amplitude for neutrons relative to other atoms. High-precision studies of a class of molecules, like those on α-amino acids carried out at Brookhaven and Trombay, can provide important information on systematics of the structure, conformation, and hydrogen bonding parameters. Some attempts have also been made to extend these single-crystal studies to some proteins like myoglobin, lysozyme, and trypsin. The large anomalous scattering amplitudes for some stable isotopes like ¹¹³Cd and ¹⁴⁹Sm and the easy variability of neutron wavelength also provides, in principle, a method for solving the phase problem without crystallizing too many heavy atom derivatives. The combination of neutron and x-ray diffraction data, now being used to study charge density distributions in organic molecules and hydrogen bonds, may be extended in the future to larger molecules of biological importance. The small-angle scattering of neutrons is also a powerful technique for studying large biological particles in solution at low resolution to obtain information about sizes, shapes and distribution of constituents.     

Protonation Equilibrium in the Active Site of the Photoactive Yellow Protein

The role and existence of low-barrier hydrogen bonds (LBHBs) in enzymatic and protein activity has been largely debated. An interesting case is that of the photoactive yellow protein (PYP). In this protein, two short HBs adjacent to the chromophore, p-coumaric acid (pCA), have been identified by X-ray and neutron diffraction experiments. However, there is a lack of agreement on the chemical nature of these H-bond interactions. Additionally, no consensus has been reached on the presence of LBHBs in the active site of the protein, despite various experimental and theoretical studies having been carried out to investigate this issue. In this work, we perform a computational study that combines classical and density functional theory (DFT)-based quantum mechanical/molecular mechanical (QM/MM) simulations to shed light onto this controversy. Furthermore, we aim to deepen our understanding of the chemical nature and dynamics of the protons involved in the two short hydrogen bonds that, in the dark state of PYP, connect pCA with the two binding pocket residues (E46 and Y42). Our results support the existence of a strong LBHB between pCA and E46, with the H fully delocalized and shared between both the carboxylic oxygen of E46 and the phenolic oxygen of pCA. Additionally, our findings suggest that the pCA interaction with Y42 can be suitably described as a typical short ionic H-bond of moderate strength that is fully localized on the phenolic oxygen of Y42.     

Lattice vibration spectra Part XCI. Single-crystal Raman and single-crystal neutron diffraction studies on partially deuterated Ca(IO3)2·6H2O; assignment of hydrogen bonds

The crystal structure of Ca(IO₃)₂·6H₂O (Fdd2, Z = 8, a = 1485.9(1) pm, b = 2301.8(2) pm, and c = 639.44(5) pm, R_W = 4.7%) has been refined by single-crystal neutron diffraction studies on the basis of 1150 reflections using the Becker and Coppens formalism for refinement of the extinction parameters. The X-ray structure reported in the literature has been confirmed and the positions of the six crystallographically different hydrogen atoms have been established for the first time. The HO distances of the hydrogen bonds formed are 167.8, 177.8, 180.2, 191.8, 194.8, and 198.0 pm, which correspond to the six uncoupled OD stretching modes (2307, 2378, 2409, 2488, 2516, and 2526 cm⁻¹, 90 K) in the infrared and Raman spectra of isotopically dilute samples. For assignment of the observed bands to the hydrogen positions of the structure we performed single-crystal Raman studies on partially deuterated samples, as proposed in 1984. The limits of this procedure and those of other methods for assigning water bands and the relationship of the strengths of the hydrogen bonds with spectroscopic and structural data, including bond valences and I---OH bond angles, are discussed.     

A new material for hydrogen storage; ScAl0.8Mg0.2

A novel aluminium rich alloy for hydrogen storage has been discovered, ScAl_0.8Mg_0.2, which has very promising properties regarding hydrogen storage capacity, kinetics and stability towards air oxidation in comparison to hydrogen absorption in state-of-the-art intermetallic compounds. The absorption of hydrogen was found to be very fast, even without adding any catalyst, and reversible. The discovered alloy crystallizes in a CsCl-type structure, but decomposes to ScH₂ and Al(Mg) during hydrogen absorption. Detailed analysis of the hydrogen absorption in ScAl_0.8Mg_0.2 has been performed using in situ synchrotron radiation powder X-ray diffraction, neutron powder diffraction and quantum mechanical calculations. The results from theory and experiments are in good agreement with each other.     

The structure of water in p-sulfonatocalix[4]arene

Tetrasodium p-sulfonatocalix[4]arene exists as a hydrate with approximately 14 water molecules and has three polymorphic modifications, all of which contain a water molecule in the molecular cavity that is engaged in OH···π interactions. Single-crystal neutron structures are reported for two of these three forms and reveal a "compressed" water molecule with short OH bonds. Partial atomic charges and hardness analysis (PACHA) calculations based on the neutron coordinates give an OH···π interaction energy of 6.9-7.5 kJ mol(-1). The PACHA analysis also reveals the dominance of the charge-assisted hydrogen bonds from the Na(+)-coordinated water molecules. The instability of the crystal towards dehydration can be traced to an uncoordinated lattice water site. The remarkable calixarene-Na(+)-hydrate motif is conserved almost unchanged across all three polymorphs. A single-crystal neutron structure is also reported for pentasodium p-sulfonatocalix[4]arene·12H(2)O, which exhibits an intracavity water molecule that is engaged in both OH···π and OH···O hydrogen bonding. The shorter covalent bond to the hydrogen atom that forms the interaction with the aromatic ring is again apparent.     

A supramolecular assembly containing an unusually short n‐h…n hydrogen bond ‐ an x‐ray and neutron diffraction study

A supramolecular assembly formed between phthalimide and 2‐guanidinobenzimidazole, containing a short 2.692(4)AR N‐H…N hydrogen bond, is reported. The crystal structure of this species was determined by both X‐ray and neutron diffraction. The diffraction data reveal that the proton involved in the short hydrogen bond has been transferred from the phthalimide to the guanidinobenzimidazole to form an ion pair. There is also an interesting stacking interaction between the atoms involved in the short hydrogen bond and the π system of a phthalimide molecule that is approximately 3.3 Å away. The structure is compared with the structure of a similar assembly formed between 4‐nitrophthalimide and 2‐guanidinobenzimidazole.     

Investigation of Steric Influences on Hydrogen‐Bonding Motifs in Cyclic Ureas by Using X‐Ray,Neutron, and Computational Methods

A series of urea‐derived heterocycles, 5N‐substituted hexahydro‐1,3,5‐triazin‐2‐ones, has been prepared and their structures have been determined for the first time. This family of compounds only differ in their substituent at the 5‐position (which is derived from the corresponding primary amine), that is, methyl ( 1 ), ethyl ( 2 ), isopropyl ( 3 ), tert‐butyl ( 4 ), benzyl ( 5 ), N,N‐(diethyl)ethylamine ( 6 ), and 2‐hydroxyethyl ( 7 ). The common heterocyclic core of these molecules is a cyclic urea, which has the potential to form a hydrogen‐bonding tape motif that consists of self‐associative (8) dimers. The results from X‐ray crystallography and, where possible, Laue neutron crystallography show that the hydrogen‐bonding motifs that are observed and the planarity of the hydrogen bonds appear to depend on the steric hindrance at the α‐carbon atom of the N substituent. With the less‐hindered substituents, methyl and ethyl, the anticipated tape motif is observed. When additional methyl groups are added onto the α‐carbon atom, as in the isopropyl and tert‐butyl derivatives, a different 2D hydrogen‐bonding motif is observed. Despite the bulkiness of the substituents, the benzyl and N,N‐(diethyl)ethylamine derivatives have methylene units at the α‐carbon atom and, therefore, display the tape motif. The introduction of a competing hydrogen‐bond donor/acceptor in the 2‐hydroxyethyl derivative disrupts the tape motif, with a hydroxy group interrupting the N? H???O?C interactions. The geometry around the hydrogen‐bearing nitrogen atoms, whether planar or non‐planar, has been confirmed for compounds 2 and 5 by using Laue neutron diffraction and rationalized by using computational methods, thus demonstrating that distortion of O‐C‐N‐H torsion angles occurs to maintain almost‐linear hydrogen‐bonding interactions.     

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.     

Synthesis and Crystal Structure of SnPd3D0.138(7) by Neutron Powder Diffraction

Palladium-rich intermetallic compounds have attracted attention for their use in heterogeneous catalysis and their interesting hydrogenation properties. SnPd₃ was synthesized from the elements using selenium as a mineralizing agent. The stoichiometric composition was confirmed by energy-dispersive X-ray spectra (Sn_0.98(5)Pd_3.02(5)). X-ray diffraction showed an ordered AuCu₃ type structure [Pm3 m, a = 397.799(1) pm]. SnPd₃ takes up hydrogen at 703 K under 5.0 MPa, resulting in a volume expansion of 0.4 %. The crystal structure was determined from neutron powder diffraction data of the deuteride. SnPd₃D_0.138(7) belongs to the cubic anti-perovskite type [Pm3 m, a = 398.338(11) pm]. Deuterium occupies [Pd₆] octahedral sites [d(Pd–D) = 199.169(6) pm] in a statistical manner.     

Synchrotron and neutron techniques in biological crystallography

Synchrotron radiation (SR) techniques are continuously pushing the frontiers of wavelength range usage, smaller crystal sample size, larger protein molecular weight and complexity, as well as better diffraction resolution. The new research specialism of probing functional states directly in crystals, via time-resolved Laue and freeze trapping structural studies, has been developed, with a range of examples, based on research stretching over some 20 years. Overall, SR X-ray biological crystallography is complemented by neutron protein crystallographic studies aimed at cases where much more complete hydrogen details are needed involving synergistic developments between SR and neutron Laue methods. A big new potential exists in harnessing genome databases for targeting of new proteins for structural study. Structural examples in this tutorial review illustrate new chemistry learnt from biological macromolecules.     

Experimental Electron Densities and Chemical Bonding

Some recent results of charge density analysis by X-ray and neutron diffraction are discussed. Problems that have been studied in a number of laboratories include the nature of single, double, and triple bonds, lone-pair hybridization, bonding in some metals, alloys, and organometallic compounds, and the derivation of physical properties from X-ray diffraction densities. At the present stage of development of methods studies of series of related compounds are feasible and expected to find widespread application.     

Host Perturbation in a β‐Hydroquinone Clathrate Studied by Combined X‐ray/Neutron Charge‐Density Analysis: Implications for Molecular Inclusion in Supramolecular Entities

X‐ray/neutron (X/N) diffraction data measured at very low temperature (15 K) in conjunction with ab initio theoretical calculations were used to model the crystal charge density (CD) of the host–guest complex of hydroquinone (HQ) and acetonitrile. Due to pseudosymmetry, information about the ordering of the acetonitrile molecules within the HQ cavities is present only in almost extinct, very weak diffraction data, which cannot be measured with sufficient accuracy even by using the brightest X‐ray and neutron sources available, and the CD model of the guest molecule was ultimately based on theoretical calculations. On the other hand, the CD of the HQ host structure is well determined by the experimental data. The neutron diffraction data provide hydrogen anisotropic thermal parameters and positions, which are important to obtain a reliable CD for this light‐atom‐only crystal. Atomic displacement parameters obtained independently from the X‐ray and neutron diffraction data show excellent agreement with a |ΔU| value of 0.00058 Ų indicating outstanding data quality. The CD and especially the derived electrostatic properties clearly reveal increased polarization of the HQ molecules in the host–guest complex compared with the HQ molecules in the empty HQ apohost crystal structure. It was found that the origin of the increased polarization is inclusion of the acetonitrile molecule, whereas the change in geometry of the HQ host structure following inclusion of the guest has very little effect on the electrostatic potential. The fact that guest inclusion has a profound effect on the electrostatic potential suggests that nonpolarizable force fields may be unsuitable for molecular dynamics simulations of host–guest interaction (e.g., in protein–drug complexes), at least for polar molecules.     

Dynamics of water studied by coherent and incoherent inelastic neutron scattering

This paper reviews the more recent results obtained on the dynamics of water by neutron scattering and shows that some information can be obtained by this technique at the microscopic level of the hydrogen bond. It also accounts for some very recent results obtained with the hydrated protein C-phycocyanin.

Incoherent quasi-elastic and inelastic neutron scattering by water has been performed in a temperature range extending to the supercooled state. The analysis of the quasi-elastic spectrum separates two main components and gives two characteristic times, one of them being related to the hydrogen-bond lifetime. The inelastic spectra extend until 600 meV, i.e. covering the intramolecular vibration region, showing for the first time the stretching band.

Collective excitations propagating at 3310 m s⁻¹ have been observed by coherent inelastic neutron scattering. This result was predicted by previous computer molecular dynamics simulations of water. The data are interpreted as a manifestation of short wavelength collective modes propagating within patches of highly bonded water molecules, and distinct from the ordinary sound wave.     

Pressure-Dependent Structure of Methanol–Water Mixtures up to 1.2 GPa: Neutron Diffraction Experiments and Molecular Dynamics Simulations

Total scattering structure factors of per-deuterated methanol and heavy water, CD₃OD and D₂O, have been determined across the entire composition range as a function of pressure up to 1.2 GPa, by neutron diffraction. The largest variations due to increasing pressure were observed below a scattering variable value of 5 Å⁻¹, mostly as shifts in terms of the positions of the first and second maxima. Molecular dynamics computer simulations, using combinations of all-atom potentials for methanol and various water force fields, were conducted at the experimental pressures with the aim of interpreting neutron diffraction results. The peak-position shifts mentioned above could be qualitatively reproduced by simulations, although in terms of peak intensities, the accord between neutron diffraction and molecular dynamics was much less satisfactory. However, bearing in mind that increasing pressure must have a profound effect on repulsive forces between neighboring molecules, the agreement between experiment and computer simulation can certainly be termed as satisfactory. In order to reveal the influence of changing pressure on local intermolecular structure in these “simplest of complex” hydrogen-bonded liquid mixtures, simulated structures were analyzed in terms of hydrogen bond-related partial radial distribution functions and size distributions of hydrogen-bonded cyclic entities. Distinct differences between pressure-dependent structures of water-rich and methanol-rich composition regions were revealed.