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Models of the active site in [NiFe]hydrogenase enzymes have proven challenging to prepare. We isolated a paramagnetic dinuclear nickel-ruthenium complex with a bridging hydrido ligand from the heterolytic cleavage of H2 by a dinuclear NiRu aqua complex in water under ambient conditions (20°C and 1 atmosphere pressure). The structure of the hexacoordinate Ni(μ-H)Ru complex was unequivocally determined by neutron diffraction analysis, and it comes closest to an effective analog for the core structure of the proposed active form of the enzyme. [ABSTRACT FROM AUTHOR]

In this study, we investigated reversible intermolecular proton shifting (IPS) coupled with spin transition (ST) in a novel Fe II complex. The host Fe II complex and the guest carboxylic acid anion were connected by intermolecular hydrogen bonds (IHBs). We extended the intramolecular proton transfer coupled ST phenomenon to the intermolecular system. The dynamic phenomenon was confirmed by variable-temperature single-crystal X-ray diffraction, neutron crystallography, and infrared spectroscopy. The mechanism of IPS was further validated using density functional theory calculations. The discovery of IPS-coupled ST in crystalline molecular materials provides good insights into fundamental processes and promotes the design of novel multifunctional materials with tunable properties for various applications, such as optoelectronics, information storage, and molecular devices., (© 2024 Wiley-VCH GmbH.)

X-ray diffraction, neutron diffraction, and theoretical calculations were used to investigate the relationship between the optical properties and degree of protonation in acid-base complexes. We prepared five acid-base complexes by using a pyridine-modified pyrrolopyrrole derivative and salicylic acid. Two of the prepared acid-base complexes were polymorphs of guest-free crystals with green emission; the other three were guest-inclusion crystals with yellow emission containing CH 2 Cl 2 , CH 2 Br 2 , or C 2 H 4 Cl 2 . The presence or absence of guests caused the emission to change color, altering the hydrogen bond strength between the acid-base complexes. Accurate N⋅⋅⋅H distances between the pyridyl moiety and the carboxy group over the temperature range 123 to 273 K were 1.40 Å for the guest-free crystals and 1.25 Å for the guest-inclusion crystals. Our findings contribute to a better understanding of the complex relationship between photofunction and proton dynamics in acid-base complexes., (© 2021 Wiley-VCH GmbH.)

The two-dimensional quadratic lattice magnet, bis(glycolato)cobalt(ii) ([Co(HOCH2CO2)2]), showed antiferromagnetic ordering at 15.0 K and an abrupt increase in magnetisation at H = 22 600 Oe and 2 K, thereby acting as a metamagnet. Heat capacity measurements revealed that the associated entropy change ΔS around the transition temperature was evaluated to be 6.20 J K-1 mol-1 and that the Co(ii) ion had the total angular momentum of J = 1/2 at low temperatures. Neutron diffraction studies suggested that the magnetic moment vectors of the Co(ii) ions had an amplitude of 3.59μB and were not aligned in a fully antiparallel fashion to those of their neighbours, which caused canting between the magnetic moment vectors in the sheet. The canting angle was determined to be 7.1°. Canting induced net magnetisation in the sheet, but this magnetisation was cancelled between sheets. The magnetisations in the sheets were oriented parallel to the magnetic field at the critical magnetic field.

A newly synthesized one-dimensional (1D) hydrogen-bonded (H-bonded) rhodium(II)-η(5)-semiquinone complex, [Cp*Rh(η(5)-p-HSQ-Me4)]PF6 ([1]PF6; Cp* = 1,2,3,4,5-pentamethylcyclopentadienyl; HSQ = semiquinone) exhibits a paraelectric-antiferroelectric second-order phase transition at 237.1 K. Neutron and X-ray crystal structure analyses reveal that the H-bonded proton is disordered over two sites in the room-temperature (RT) phase. The phase transition would arise from this proton disorder together with rotation or libration of the Cp* ring and PF6(-) ion. The relative permittivity εb' along the H-bonded chains reaches relatively high values (ca., 130) in the RT phase. The temperature dependence of (13)C CP/MAS NMR spectra demonstrates that the proton is dynamically disordered in the RT phase and that the proton exchange has already occurred in the low-temperature (LT) phase. Rate constants for the proton exchange are estimated to be 10(-4)-10(-6) s in the temperature range of 240-270 K. DFT calculations predict that the protonation/deprotonation of [1](+) leads to interesting hapticity changes of the semiquinone ligand accompanied by reduction/oxidation by the π-bonded rhodium fragment, producing the stable η(6)-hydroquinone complex, [Cp*Rh(3+)(η(6)-p-H2Q-Me4)](2+) ([2](2+)), and η(4)-benzoquinone complex, [Cp*Rh(+)(η(4)-p-BQ-Me4)] ([3]), respectively. Possible mechanisms leading to the dielectric response are discussed on the basis of the migration of the protonic solitons comprising of [2](2+) and [3], which would be generated in the H-bonded chain., (© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Ibaraki Prefectural Government together with Ibaraki University and Japan Atomic Energy Agency (JAEA) has almost finished constructing a time-of-flight (TOF) neutron diffractometer for biological macromolecules for industrial use at J-PARC, IBARAKI Biological Crystal Diffractometer (iBIX). Since 2009, Ibaraki University has been asked to operate this machine in order for users to do experiments by Ibaraki Prefecture. The diffractometer is designed to cover sample crystals which have their cell edges up to around 150 A. It is expected to measure more than 100 samples per year if they have 2 mm(3) in crystal volume, and to measure even around 0.1 mm(3) in crystal volume of biological samples. The efficiency of iBIX is also expected about 100 times larger than those of the present high performance diffractometers at JRR-3 in JAEA when 1MW power realizes in J-PARC. Since December 2008, iBIX has been open to users and several proteins and organic compounds were tested under 20 kW proton power of J-PARC. It was found that one of their proteins was diffracted up to 1.4 A in d-spacing, which was nearly comparable resolution to that of BIX-3 in JRR-3 when used the same crystal as at iBIX for reasonable exposure time. In May 2009, 14 detector units were set up. By the end of fiscal year 2009, the basic part of data reduction software will be finished and an equipment blowing low temperature gas to the sample will be installed with the cooperation of JAEA.

HIV-1 protease is a dimeric aspartic protease that plays an essential role in viral replication. To further understand the catalytic mechanism and inhibitor recognition of HIV-1 protease, we need to determine the locations of key hydrogen atoms in the catalytic aspartates Asp-25 and Asp-125. The structure of HIV-1 protease in complex with transition-state analog KNI-272 was determined by combined neutron crystallography at 1.9-A resolution and X-ray crystallography at 1.4-A resolution. The resulting structural data show that the catalytic residue Asp-25 is protonated and that Asp-125 (the catalytic residue from the corresponding diad-related molecule) is deprotonated. The proton on Asp-25 makes a hydrogen bond with the carbonyl group of the allophenylnorstatine (Apns) group in KNI-272. The deprotonated Asp-125 bonds to the hydroxyl proton of Apns. The results provide direct experimental evidence for proposed aspects of the catalytic mechanism of HIV-1 protease and can therefore contribute substantially to the development of specific inhibitors for therapeutic application.

Two chiral tetraphenylenes, 2,15-dideuteriotetraphenylene (7) and 2,7-dimethyltetraphenylene (15) were synthesized and resolved to address the tetraphenylene inversion barrier problem. Neutron diffraction investigation of enantiopure 7 showed that the molecule retained its chirality integrity during its synthesis from enantiopure precursors and therefore rules out the possibility of the tetraphenylene framework possessing a low-energy barrier to inversion. Thermal study on 15 and tetraphenylene 1 further revealed that their inversion barriers were not overcome up to 600 degrees C, at which temperature these compounds underwent skeletal contraction into triphenylene with activation energies of 62.8 and 58.2 kcal/mol, respectively. This result is supported by computational studies which yielded an inversion barrier of 135 kcal/mol for tetraphenylene as a consequence of the peri-hydrogen repulsions at its planar conformation.

Models of the active site in [NiFe]hydrogenase enzymes have proven challenging to prepare. We isolated a paramagnetic dinuclear nickel-ruthenium complex with a bridging hydrido ligand from the heterolytic cleavage of H2 by a dinuclear NiRu aqua complex in water under ambient conditions (20 degrees C and 1 atmosphere pressure). The structure of the hexacoordinate Ni(mu-H)Ru complex was unequivocally determined by neutron diffraction analysis, and it comes closest to an effective analog for the core structure of the proposed active form of the enzyme.

Since N,N-dibenzyl-1-cyclohexenecarbothioamide is photo-isomerized to the optically active beta-thiolactam with the retention of the single-crystal form, the mechanism of chirality induction was identified by X-ray crystal structure analyses during the process of the reaction [Hosoya et al. (2002). Bull. Chem. Soc. Jpn, 75, 2147-2151]. In order to clarify the mechanism of hydrogen transfer in the reaction, the H atoms of the benzyl groups were replaced with deuterium atoms. The crystal structure after photoisomerization was analyzed by neutron diffraction. One of four deuterium atoms of the two benzyl groups is transferred to the C atom of the cyclohexene ring. The absolute configuration of the -C*HD- group (chiral methylene) in the photoproduct beta-thiolactam revealed that the deuterium atom occupies the equatorial position. This suggests that the deuterium atom is not transferred from the benzyl group of a neighbouring molecule, but from one of the benzyl groups within the molecule.

It has long been suspected that the structure and function of a DNA duplex can be strongly dependent on its degree of hydration. By neutron diffraction experiments, we have succeeded in determining most of the hydrogen (H) and deuterium (D) atomic positions in the decameric d(CCATTAATGG)2 duplex. Moreover, the D positions in 27 D2O molecules have been determined. In particular, the complex water network in the minor groove has been observed in detail. By a combined structural analysis using 2.0 A resolution X-ray and 3.0 A resolution neutron data, it is clear that the spine of hydration is built up, not only by a simple hexagonal hydration pattern (as reported in earlier X-ray studies), but also by many other water bridges hydrogen-bonded to the DNA strands. The complexity of the hydration pattern in the minor groove is derived from an extraordinary variety of orientations displayed by the water molecules.

An adamantanoid (H2O)10 cluster is formed within the hydrophobic cavity of a self-assembled coordination cage. This cluster is termed "molecular ice" because it is the smallest unit of naturally occurring Ic-type ice. X-ray structural analysis, coupled with neutron diffraction study, reveals that the molecular ice is formed not by a simple space-filling effect but by efficient molecular recognition within the cage via H2O:...pi interaction.

When the crystal of [(R)-1,2-bis(ethoxycarbonyl)ethyl](pyridine)bis(dimethylglyoximato)cobalt(III) was exposed to a xenon lamp, the chiral 1,2-bis(ethoxycarbonyl)ethyl group was partly inverted to the opposite configuration and finally the racemic group was produced with retention of the single crystal form. To make clear the mechanism, the hydrogen atom bonded to the chiral carbon of the chiral group was exchanged with the deuterium atom and the crystal was exposed to the xenon lamp for 3 days. The crystal after irradiation was analyzed by neutron diffraction. About 33% of the (R)-isomers were inverted to the (S) isomers in a crystal. The deuterium atom in the (S)-isomer was bonded to the same chiral carbon atom. This result clearly indicates that the inversion proceeds in the three steps; (i) the Co-C bond was homolytically cleaved by photoirradiation and the 1,2-bis(ethoxycarbonyl)ethyl radical and Co(II) were produced, (ii) the radical rotated by 180 degrees directing the C-D bond to the cobalt atom and the opposite plane of the radical faced to the cobalt atom, and (iii) the radical made a bond with Co(II). Because the peripheral atoms of the long radical occupy approximately the same positions in the process of the radical rotation, the crystal was not decomposed. The above rotation is a good example of hula-twist rotation in the process of photoisomerization of polyenes such as rhodopsin.