High-resolution neutron crystallographic studies of the hydration of the coenzyme cob(II)alamin

Ultrafast X-ray Absorption Spectroscopy Reveals Excited-State Dynamics of B12 Coenzymes Controlled by the Axial Base

Polarized time-resolved X-ray absorption spectroscopy at the Co K-edge is used to probe the excited-state dynamics and photolysis of base-off methylcobalamin and the excited-state structure of base-off adenosylcobalamin. For both molecules, the final excited-state minimum shows evidence for an expansion of the cavity around the Co ion by ca. 0.04 to 0.05 Å. The 5-coordinate base-off cob(II)alamin that is formed following photodissociation has a structure similar to that of the 5-coordinate base-on cob(II)alamin, with a ring expansion of 0.03 to 0.04 Å and a contraction of the lower axial bond length relative to that in the 6-coordinate ground state. These data provide insights into the role of the lower axial ligand in modulating the reactivity of B12 coenzymes.

Efficient data reduction for time-of-flight neutron scattering experiments on single crystals

Event-mode data collection presents remarkable new opportunities for time-of-flight neutron scattering studies of collective excitations, diffuse scattering from short-range atomic and magnetic structures, and neutron crystallography. In these experiments, large volumes of the reciprocal space are surveyed, often using different wavelengths and counting times. These data then have to be added together, with accurate propagation of the counting errors. This paper presents a statistically correct way of adding and histogramming the data for single-crystal time-of-flight neutron scattering measurements. In order to gain a broader community acceptance, particular attention is given to improving the efficiency of calculations.

Controlling inversion disorder in a stoichiometric spinel magnet

While disorder is an inalienable characteristic of real crystalline materials, the capability of controlling various types of disorder often strongly influences our understanding of science and the advancement of technology. Magnetic spinel represents a class of materials with a pyrochlore-structured sublattice to potentially host three-dimensional spin frustration but is strongly influenced by the inversion disorder of two similarly sized cation species. While it remains challenging to experimentally differentiate these two characteristics, here we mitigate the disorder issue at the crystal growth stage. Our independent control of both stoichiometry and inversion disorder clarifies both magnetism and structure in a spinel oxide of interest for seven decades.

In the study of frustrated quantum magnets, it is essential to be able to control the nature and degree of site disorder during the growth process, as many measurement techniques are incapable of distinguishing between site disorder and frustration-induced spin disorder. Pyrochlore-structured spinel oxides can serve as model systems of geometrically frustrated three-dimensional quantum magnets; however, the nature of the magnetism in one well-studied spinel, ZnFe₂O₄, remains unclear. Here, we demonstrate simultaneous control of both stoichiometry and inversion disorder in the growth of ZnFe₂O₄ single crystals, directly yielding a revised understanding of both the collective spin behavior and lattice symmetry. Crystals grown in the stoichiometric limit with minimal site inversion disorder contravene all the previously suggested exotic spin phases in ZnFe₂O₄. Furthermore, the structure is confirmed on the F4¯3m space group with broken inversion symmetry that induces antiferroelectricity. The effective tuning of magnetic behavior by site disorder in the presence of robust antiferroelectricity makes ZnFe₂O₄ of special interest to multiferroic devices.

Study of a position-sensitive scintillator neutron detector prototype based on 6LiF/ZnS scintillator and silicon photomultiplier arrays readout

Due to the shortage of the ³He gas and its rapidly increasing price, scintillator detectors, the advantages of which are high spatial resolution and capability of detection in real time, become widely used in many neutron instruments. In this work, a position-sensitive neutron detector consisting of a ⁶LiF/ZnS scintillation screen and a silicon photomultiplier array linked to a capacitive network to detect the positions of incident neutrons, is constructed and tested. To evaluate the detector performance, a series of neutron beam experiments with the detector prototype were performed in the BL20 at the China Spallation Neutron Source. The spatial resolution was measured, and the energy-selective neutron imaging and Bragg edge measurements of a 316L stainless steel sample were performed. A sub-millimeter spatial resolution could be obtained for the detector prototype under study. The detector with such a high spatial resolution is promising for applications in neutron scattering experimental installations, especially for neutron single-crystal diffractometers.

Direct air capture of CO-2 - topological analysis of the experimental electron density (QTAIM) of the highly insoluble carbonate salt of a 2,6-pyridine-bis(iminoguanidine), (PyBIGH2)(CO3)(H2O)4

Chemical bonding and all intermolecular interactions in the highly insoluble carbonate salt of a 2,6-pyridine-bis(iminoguanidine), (PyBIGH2)(CO3)(H2O)4, recently employed in the direct air capture of CO2 via crystallization, have been analyzed within the framework of the quantum theory of atoms in molecules (QTAIM) based on the experimental electron density derived from X-ray diffraction data obtained at 20 K. Accurate hydrogen positions were included based on an analogous neutron diffraction study at 100 K. Topological features of the covalent bonds demonstrate the presence of multiple bonds of various orders within the PyBIGH2 2+ cation. Strong hydrogen bonds define ribbons comprising carbonate anions and water molecules. These ribbons are linked to stacks of essentially planar dications via hydrogen bonds from the guanidinium moieties and an additional one to the pyridine nitro-gen. The linking hydrogen bonds are approximately perpendicular to the anion-water ribbons. The observation of these putative interactions provided motivation to characterize them by topological analysis of the total electron density. Thus, all hydrogen bonds have been characterized by the properties of their (3,-1) bond critical points. Weaker interactions between the PyBIGH2 2+ cations have similarly been characterized. Integrated atomic charges are also reported. A small amount of cocrystallized hydroxide ion (∼2%) was also detected in both the X-ray and neutron data, and included in the multipole model for the electron-density refinement. The small amount of additional H+ required for charge balance was not detected in either the X-ray or the neutron data. The results are discussed in the context of the unusually low aqueous solubility of (PyBIGH2)(CO3)(H2O)4 and its ability to sequester atmospheric CO2.

Improving the accuracy and resolution of neutron crystallographic data by three-dimensional profile fitting of Bragg peaks in reciprocal space

Neutron crystallography is a powerful technique for directly visualizing the locations of H atoms in biological macromolecules. This information has provided key new insights into enzyme mechanisms, ligand binding and hydration. However, despite the importance of this information, the application of neutron crystallography in biology has been limited by the relatively low flux of available neutron beams and the large incoherent neutron scattering from hydrogen, both of which contribute to weak diffraction data with relatively low signal-to-background ratios. A method has been developed to fit weak data based on three-dimensional profile fitting of Bragg peaks in reciprocal space by an Ikeda-Carpenter function with a bivariate Gaussian. When applied to data collected from three different proteins, three-dimensional profile fitting yields intensities with higher correlation coefficients (CC1/2) at high resolutions, decreased Rfree factors, extended resolutions and improved nuclear density maps. Importantly, additional features are revealed in nuclear density maps that may provide additional scientific information. These results suggest that three-dimensional profile fitting will help to extend the capabilities of neutron macromolecular crystallography.

Real-Time Observation of Order-Disorder Transformation of Organic Cations Induced Phase Transition and Anomalous Photoluminescence in Hybrid Perovskites

A fundamental understanding of the interplay between the microscopic structure and macroscopic optoelectronic properties of organic-inorganic hybrid perovskite materials is essential to design new materials and improve device performance. However, how exactly the organic cations affect the structural phase transition and optoelectronic properties of the materials is not well understood. Here, real-time, in situ temperature-dependent neutron/X-ray diffraction and photoluminescence (PL) measurements reveal a transformation of the organic cation CH₃ NH₃⁺ from order to disorder with increasing temperature in CH₃ NH₃ PbBr₃ perovskites. The molecular-level order-to-disorder transformation of CH₃ NH₃⁺ not only leads to an anomalous increase in PL intensity, but also results in a multidomain to single-domain structural transition. This discovery establishes the important role that organic cation ordering has in dictating structural order and anomalous optoelectronic phenomenon in hybrid perovskites.

Single-Crystal Time-of-Flight Neutron Diffraction and Magic-Angle-Spinning NMR Spectroscopy Resolve the Structure and 1H and 7Li Dynamics of the Uranyl Peroxide Nanocluster U60

Single-crystal time-of-flight neutron diffraction has provided atomic resolution of H atoms of H₂O molecules and hydroxyl groups, as well as Li cations in the uranyl peroxide nanocluster U₆₀. Solid-state magic-angle-spinning nuclear magnetic resonance (MAS NMR) spectroscopy was used to confirm the dynamics of these constituents, revealing the transportation of Li atoms and H₂O through cluster walls. H atoms of hydroxyl units that are located on the cluster surface are involved in the transfer of H₂O and Li cations from inside to outside and vice versa. This exchange occurs as a concerted motion and happens rapidly even in the solid state. As a consequence of its large size and open hexagonal pores, U₆₀ exchanges Li cations more rapidly compared to other uranyl nanoclusters.

SENJU: a new time-of-flight single-crystal neutron diffractometer at J-PARC

SENJU is a new single-crystal time-of-flight neutron diffractometer installed at BL18 at the Materials and Life Science Experimental Facility of the Japan Accelerator Research Complex (J-PARC). The diffractometer was designed for precise crystal and magnetic structure analyses under multiple extreme sample environments such as low temperature, high pressure and high magnetic field, and for diffraction measurements of small single crystals down to 0.1 mm3 in volume. SENJU comprises three choppers, an elliptical shape straight supermirror guide, a vacuum sample chamber and 37 scintillator area detectors. The moderator-to-sample distance is 34.8 m, and the sample-to-detector distance is 800 mm. The wavelength of incident neutrons is 0.4-4.4 Å (first frame). Because short-wavelength neutrons are available and the large solid angle around the sample position is covered by the area detectors, a large reciprocal space can be simultaneously measured. Furthermore, the vacuum sample chamber and collimator have been designed to produce a very low background level. Thus, the measurement of a small single crystal is possible. As sample environment devices, a newly developed cryostat with a two-axis (ω and φ axes) goniometer and some extreme environment devices, e.g. a vertical-field magnet, high-temperature furnace and high-pressure cell, are available. The structure analysis of a sub-millimetre size (0.1 mm3) single organic crystal, taurine, and a magnetic structure analysis of the antiferromagnetic phase of MnF2 have been performed. These results demonstrate that SENJU can be a powerful tool to promote materials science research.

Neutron Nucleic Acid Crystallography

The hydration shells surrounding nucleic acids and hydrogen-bonding networks involving water molecules and nucleic acids are essential interactions for the structural stability and function of nucleic acids. Water molecules in the hydration shells influence various conformations of DNA and RNA by specific hydrogen-bonding networks, which often contribute to the chemical reactivity and molecular recognition of nucleic acids. However, X-ray crystallography could not provide a complete description of structural information with respect to hydrogen bonds. Indeed, X-ray crystallography is a powerful tool for determining the locations of water molecules, i.e., the location of the oxygen atom of H2O; however, it is very difficult to determine the orientation of the water molecules, i.e., the orientation of the two hydrogen atoms of H2O, because X-ray scattering from the hydrogen atom is very small.Neutron crystallography is a specialized tool for determining the positions of hydrogen atoms. Neutrons are not diffracted by electrons, but are diffracted by atomic nuclei; accordingly, neutron scattering lengths of hydrogen and its isotopes are comparable to those of non-hydrogen atoms. Therefore, neutron crystallography can determine both of the locations and orientations of water molecules. This chapter describes the current status of neutron nucleic acid crystallographic research as well as the basic principles of neutron diffraction experiments performed on nucleic acid crystals: materials, crystallization, diffraction experiments, and structure determination.

Free H₂ rotation vs Jahn-Teller constraints in the nonclassical trigonal (TPB)Co-H₂ complex

Proton exchange within the M-H2 moiety of (TPB)Co(H2) (Co-H2; TPB = B(o-C6H4P(i)Pr2)3) by 2-fold rotation about the M-H2 axis is probed through EPR/ENDOR studies and a neutron diffraction crystal structure. This complex is compared with previously studied (SiP(iPr)3)Fe(H2) (Fe-H2) (SiP(iPr)3 = [Si(o-C6H4P(i)Pr2)3]). The g-values for Co-H2 and Fe-H2 show that both have the Jahn-Teller (JT)-active (2)E ground state (idealized C3 symmetry) with doubly degenerate frontier orbitals, (e)(3) = [|mL ± 2>](3) = [x(2) - y(2), xy](3), but with stronger linear vibronic coupling for Co-H2. The observation of (1)H ENDOR signals from the Co-HD complex, (2)H signals from the Co-D2/HD complexes, but no (1)H signals from the Co-H2 complex establishes that H2 undergoes proton exchange at 2 K through rotation around the Co-H2 axis, which introduces a quantum-statistical (Pauli-principle) requirement that the overall nuclear wave function be antisymmetric to exchange of identical protons (I = 1/2; Fermions), symmetric for identical deuterons (I = 1; Bosons). Analysis of the 1-D rotor problem indicates that Co-H2 exhibits rotor-like behavior in solution because the underlying C3 molecular symmetry combined with H2 exchange creates a dominant 6-fold barrier to H2 rotation. Fe-H2 instead shows H2 localization at 2 K because a dominant 2-fold barrier is introduced by strong Fe(3d)→ H2(σ*) π-backbonding that becomes dependent on the H2 orientation through quadratic JT distortion. ENDOR sensitively probes bonding along the L2-M-E axis (E = Si for Fe-H2; E = B for Co-H2). Notably, the isotropic (1)H/(2)H hyperfine coupling to the diatomic of Co-H2 is nearly 4-fold smaller than for Fe-H2.

An improved method for calibrating time-of-flight Laue single-crystal neutron diffractometers

A robust and comprehensive method for determining the orientation matrix of a single-crystal sample using the neutron Laue time-of-flight (TOF) technique is described. The new method enables the measurement of the unit-cell parameters with an uncertainty in the range 0.015-0.06%, depending upon the crystal symmetry and the number of reflections measured. The improved technique also facilitates the location and integration of weak reflections, which are often more difficult to discern amongst the increased background at higher energies. The technique uses a mathematical model of the relative positions of all the detector pixels of the instrument, together with a methodology that establishes a reproducible reference frame and a method for determining the parameters of the instrument detector model. Since all neutron TOF instruments require precise detector calibration for their effective use, it is possible that the method described here may be of use on other instruments where the detector calibration cannot be determined by other means.

Seeing the chemistry in biology with neutron crystallography

New developments in macromolecular neutron crystallography have led to an increasing number of structures published over the last decade. Hydrogen atoms, normally invisible in most X-ray crystal structures, become visible with neutrons. Using X-rays allows one to see structure, while neutrons allow one to reveal the chemistry inherent in these macromolecular structures. A number of surprising and sometimes controversial results have emerged; because it is difficult to see or predict hydrogen atoms in X-ray structures, when they are seen by neutrons they can be in unexpected locations with important chemical and biological consequences. Here we describe examples of chemistry seen with neutrons for the first time in biological macromolecules over the past few years.

Synthesis, structure, and physical properties of Ln(Cu,Al,Ga)(13-x) (Ln = La-Pr, and Eu) and Eu(Cu,Al)(13-x)

Ln(Cu,Al,Ga)(13-x) (Ln = La-Pr, and Eu; x ~ 0.2) were synthesized by a combined Al/Ga flux. Single crystal X-ray and neutron diffraction experiments revealed that these compounds crystallize in the NaZn(13) structure-type (space group Fm3[overline]c) with lattice parameters of a ~ 12 Å, V ~ 1600 Å, and Z ~ 8. Our final neutron models led us to conclude that Cu is occupationally disordered on the 8b Wyckoff site while Cu, Al, and Ga are substitutionally disordered on the 96i Wyckoff site of this well-known structure-type. The magnetic susceptibility data show that Ce(Cu,Al,Ga)(13-x) and Pr(Cu,Al,Ga)(13-x) exhibit paramagnetic behavior down to the lowest temperatures measured while Eu(Cu,Al,Ga)(13-x) displays ferromagnetic behavior below 6 K. Eu(Cu,Al)(13-x) was prepared via arc-melting and orders ferromagnetically below 8 K. The magnetocaloric properties of Eu(Cu,Al,Ga)(13-x) and Eu(Cu,Al)(13-x) were measured and compared. Additionally, an enhanced value of the Sommerfeld coefficient (γ = 356 mJ/mol-K(2)) was determined for Pr(Cu,Al,Ga)(13-x). Herein, we present the synthesis, structural refinement details, and physical properties of Ln(Cu,Al,Ga)(13-x) (Ln = La-Pr, and Eu) and Eu(Cu,Al)(13-x).

Direct observation of hydrogen atom dynamics and interactions by ultrahigh resolution neutron protein crystallography

The 1.1 Å, ultrahigh resolution neutron structure of hydrogen/deuterium (H/D) exchanged crambin is reported. Two hundred ninety-nine out of 315, or 94.9%, of the hydrogen atom positions in the protein have been experimentally derived and resolved through nuclear density maps. A number of unconventional interactions are clearly defined, including a potential O─H…π interaction between a water molecule and the aromatic ring of residue Y44, as well as a number of potential C─H…O hydrogen bonds. Hydrogen bonding networks that are ambiguous in the 0.85 Å ultrahigh resolution X-ray structure can be resolved by accurate orientation of water molecules. Furthermore, the high resolution of the reported structure has allowed for the anisotropic description of 36 deuterium atoms in the protein. The visibility of hydrogen and deuterium atoms in the nuclear density maps is discussed in relation to the resolution of the neutron data.