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At least 325 records · Page 18

Atomic structure and grain shape evolution of nanodiamond during annealing in oxidizing atmosphere from neutron diffraction and MD simulations

In this work, real space pair-distribution function (PDF) analysis in conjunction with molecular dynamics (MD) simulations was applied to characterize crystal structure, shape and surface structure of diamond nanoparticles annealed in air up to 880 °C. MD simulated models of individual nanodiamond particles of various shapes and sizes were used to calculate theoretical radial distribution functions G(r) for powders with different grain size distributions. The calculated curves, showing distinct differences for the explored parameter space, were compared to the experimental G(r) functions obtained from neutron scattering for annealed detonated nanodiamond samples in a search for a model best describing the actual powders. It was found that as-synthesized nanodiamond grains are terminated by equally abundant (100), (110) and (111) crystallographic faces and their structure does not change upon annealing in air up to 280 °C. The shape and size of grains annealed above 480 °C changes due to surface etching. The etching rate differs between crystals faces and depends on temperature, resulting in the observed differences in grain shape. Below 680 °C the share of the (110) facets gradually increases and at 680 °C the grains become rhombic dodecahedra terminated solely by (110) surfaces. Further increase of the annealing temperature promotes formation of (111) surfaces and at 880 °C the preferred grain shape becomes an octahedron terminated by a variant of (111) surfaces possessing three dangling sp3 bonds per atom. At lower temperatures all grains become smaller and the size distribution moves towards the lower values. Furthermore, as the annealing temperature increases, the smallest grains disappear entirely and the average grain size grows back.

36 MATERIALS SCIENCE↗

Direct observation of symmetrization of hydrogen bond in δ-AlOOH under mantle conditions using neutron diffraction

At ambient pressure, the hydrogen bond in materials such as ice, hydrates, and hydrous minerals that compose the Earth and icy planets generally takes an asymmetric O-H···O confguration. Pressure signifcantly afects this confguration, and it is predicted to become symmetric, such that the hydrogen is centered between the two oxygen atoms at high pressure. Changes of physical properties of minerals relevant to this symmetrization have been found; however, the atomic confguration around this symmetrization has remained elusive so far. Here we observed the pressure response of the hydrogen bonds in the aluminous hydrous minerals δ-AlOOH and δ-AlOOD by means of a neutron difraction experiment. We fnd that the transition from P21nm to Pnnm at 9.0GPa, accompanied by a change in the axial ratios of δ-AlOOH, corresponds to the disorder of hydrogen bond between two equivalent sites across the center of the O···O line. Symmetrization of the hydrogen bond is observed at 18.1GPa, which is considerably higher than the disorder pressure. Moreover, there is a signifcant isotope efect on hydrogen bond geometry and transition pressure. This study indicates that disorder of the hydrogen bond as a precursor of symmetrization may also play an important role in determining the physical properties of minerals such as bulk modulus and seismic wave velocities in the Earth’s mantle.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Neutron diffraction reveals protonation states in pyridoxal‐5′‐phosphate‐free and glycine external aldimine‐bound serine hydroxymethyltransferase

Serine hydroxymethyltransferase (SHMT) is a critical enzyme in the one-carbon (1C) metabolism pathway catalyzing the reversible conversion of L-Ser into Gly and concurrent transfer of 1C unit to tetrahydrofolate (THF) to give 5,10-methylene-THF (5,10-MTHF), which is used in the downstream syntheses of biomolecules critical for cell proliferation. The cellular 1C metabolism is hijacked by many cancer types to support cancer cell proliferation, making SHMT a promising target for the design and development of novel small-molecule antimetabolite chemotherapies. To advance structure-assisted drug design, knowledge of SHMT catalysis is crucial, but can only be fully realized when the atomic details of each reaction step governed by the acid–base catalysis are elucidated by visualizing active site hydrogen atoms. Here, we used room-temperature neutron crystallography to directly determine protonation states in Thermus thermophilus SHMT (TthSHMT), capturing protomer A in the apo form lacking the coenzyme pyridoxal 5′-phosphate (PLP), and protomer B as a ternary complex with PLP–Gly-external aldimine and (6S)-5-methyltetrahydrofolate (5MTHF). We observed protonation of the Schiff base nitrogen in PLP–Gly and neutrality of the catalytic Lys226 side chain in the ternary complex, whereas Lys226 is protonated and positively charged in the apo-active site. Furthermore, we obtained an X-ray structure of TthSHMT in complex with the substrate THF, which binds identically as 5MTHF at the peripheral binding site. In conclusion, the unique structural and functional information provided by neutron crystallography, in combination with X-ray structures, can be employed in the rational design of SHMT inhibitors.

X-ray crystallography↗