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HIV-1 protease is an essential therapeutic target for the design and development of antiviral inhibitors to treat AIDS. We used room temperature neutron crystallography to accurately determine hydrogen atom positions in several protease complexes with clinical drugs, amprenavir and darunavir. Hydrogen bonding interactions were carefully mapped to provide an unprecedented picture of drug binding to the protease target. We demonstrate that hydrogen atom positions within the enzyme catalytic site can be altered by introducing drug resistant mutations and by protonating surface residues that trigger proton transfer reactions between the catalytic Asp residues and the hydroxyl group of darunavir. When protein perdeuteration is not feasible, we validate the use of initial H/D exchange with unfolded protein and partial deuteration in pure D 2 O with hydrogenous glycerol to maximize deuterium incorporation into the protein, with no detrimental effects on the growth of quality crystals suitable for neutron diffraction experiments., (© 2020 Elsevier Inc. All rights reserved.)

HIV-1 protease is an important target for the development of antiviral inhibitors to treat AIDS. A room-temperature joint X-ray/neutron structure of the protease in complex with clinical drug amprenavir has been determined at 2.0 Å resolution. The structure provides direct determination of hydrogen atom positions in the enzyme active site. Analysis of the enzyme-drug interactions suggests that some hydrogen bonds may be weaker than deduced from the non-hydrogen interatomic distances. This information may be valuable for the design of improved protease inhibitors.

The importance of total scattering and its Fourier transform, the pair distribution function, in crystallography was understood soon after it was shown that crystals diffract X-rays. However for the next fifty years or so other techniques based more firmly on the crystal lattice came to the fore and total scattering measurements were largely the domain of those studying liquid and amorphous structure. In the late 1980s it was 'rediscovered' as a way to uncover disorder within crystal structures and since then the combination of improved instrumentation and analysis has led to a resurgence of the total scattering method. This review sets out this journey, highlighting both the early origins and – more importantly – the ways that total scattering and pair distribution functions are routinely used within crystallography today. [ABSTRACT FROM AUTHOR]

The structure of fully hydrated grossular, or katoite, contains an unusual arrangement of four O-H bonds within each O4 tetrahedra. Neutron and X-ray total scattering from a powdered deuterated sample have been measured to investigate the local arrangement of this O4D4 cluster. The O-D bond length determined directly from the pair distribution function is 0.954 Å, although the Rietveld-refined distance between average O and D positions was slightly smaller. Reverse Monte Carlo refinement of supercell models to the total scattering data show that other than the consequences of this correctly determined O-D bond length, there is little to suggest that the O4D4 structure is locally significantly different from that expected based on the average structure determined solely from Bragg diffraction. [ABSTRACT FROM AUTHOR]

The structure of fully hydrated grossular, or katoite, contains an unusual arrangement of four O-H bonds within each O4 tetrahedra. Neutron and X-ray total scattering from a powdered deuterated sample have been measured to investigate the local arrangement of this O4D4 cluster. The O-D bond length determined directly from the pair distribution function is 0.954 Å, although the Rietveld-refined distance between average O and D positions was slightly smaller. Reverse Monte Carlo refinement of supercell models to the total scattering data show that other than the consequences of this correctly determined O-D bond length, there is little to suggest that the O4D4 structure is locally significantly different from that expected based on the average structure determined solely from Bragg diffraction. [ABSTRACT FROM AUTHOR]

The current knowledge and description of guest molecules within clathrate hydrates only accounts for occupancy within regular polyhedral water cages. Experimental measurements and simulations, examining the tert-butylamine+H2+H2O hydrate system, now suggest that H2 can also be incorporated within hydrate crystal structures by occupying interstitial sites, that is, locations other than the interior of regular polyhedral water cages. Specifically, H2 is found within the shared heptagonal faces of the large (43596273) cage and in cavities formed from the disruption of smaller (4454) water cages. The ability of H2 to occupy these interstitial sites and fluctuate position in the crystal lattice demonstrates the dynamic behavior of H2 in solids and reveals new insight into guest-guest and guest-host interactions in clathrate hydrates, with potential implications in increasing overall energy storage properties. [ABSTRACT FROM AUTHOR]

SXD, the single-crystal diffractometer at the ISIS spallation neutron source, uses an array of two-dimensional position-sensitive detectors and the neutron time-of-flight technique to measure diffraction data throughout very large volumes of reciprocal space for each fixed orientation of a single-crystal sample. This paper describes SXD in detail, following major improvements to the instrument. Particular emphasis is placed on the range of science possible, using recent results as examples, and the opportunities for future experiments. [ABSTRACT FROM AUTHOR]

The title complex has been studied using low-temperature X-ray (150 K) and neutron (100 K) diffraction. Molecules of the triazine host form a two-dimensional hexagonal network mediated by trigonally symmetric Cl3 synthons having Cl···Cl interactions of 3.441 (3) Å, a Cl- Cl···Cl angle of 165° and a Cl···Cl-C angle of 105&deg, close to the ideal values of 180 and 90°, respectively. The guest molecules are of an appropriate size to fit the hexagonal networks and interact with the host via C-H···π; (phenyl) and C-Br···π (phenyl) interactions which stabilize the overall structure. Both C-donor bond vectors are directed more closely towards the mid-point (X) of an individual aromatic bond, rather than the ring centroid, with H···X 2.817 (9) Å and C-H···X 174.0 (9)°, and Br···X 3.353 (4) Å and C-Br···X 158.1 (2)°. [ABSTRACT FROM AUTHOR]

Summary: Conversion of aldo to keto sugars by the metalloenzyme D-xylose isomerase (XI) is a multistep reaction that involves hydrogen transfer. We have determined the structure of this enzyme by neutron diffraction in order to locate H atoms (or their isotope D). Two studies are presented, one of XI containing cadmium and cyclic D-glucose (before sugar ring opening has occurred), and the other containing nickel and linear D-glucose (after ring opening has occurred but before isomerization). Previously we reported the neutron structures of ligand-free enzyme and enzyme with bound product. The data show that His54 is doubly protonated on the ring N in all four structures. Lys289 is neutral before ring opening and gains a proton after this; the catalytic metal-bound water is deprotonated to hydroxyl during isomerization and O5 is deprotonated. These results lead to new suggestions as to how changes might take place over the course of the reaction. [Copyright &y& Elsevier]

The N/O anion distributions in the melilite-type phosphor host material Y 2 Si 3 O 3 N 4 and a Ce-doped sample Y 1.5 Ce 0.5 Si 3 O 3 N 4 have been determined from powder neutron diffraction. Both materials have a highly ordered N/O distribution that is not changed significantly by the disorder introduced by Ce doping. This distribution evidences the presence of SiN 3 O and SiN 2 O 2 tetrahedra and although these are not fully long range-ordered, local structural correlations follow simple connectivity rules that lead to an estimated residual molar entropy of R ln3. A broad range of N/O environments is found around 8-coordinate Y(Ce) sites which is expected to broaden their spectroscopic features. SiN 3 O groups in the melilite-type phosphor host material Y 2 Si 3 O 3 N 4 and a Ce-doped sample Y 1.5 Ce 0.5 Si 3 O 3 N 4 have local structural correlations that follow simple connectivity rules and lead to an estimated residual molar entropy of R ln3. Image 1 [ABSTRACT FROM AUTHOR]