The application of thermal neutron scattering to the study of the structure and dynamics of condensed matter requires a knowledge of the scattering lengths and the corresponding scattering and absorption cross sections of the elements. Ln some cases, values for the individual isotopes are needed as well. This information is required to obtain an absolute normalization ofthe scatteredneutron distributions, tocalculate unit-cell structure factors in neutron crystallography, and to correct for effects such as absorption, self-shielding, extinction, multiple scattering, incoherent scattering, and detector efficiency.

Neutron scattering lengths and cross sections

This article describes the implementation of real-space refinement in the phenixreal_space_refine program from the PHENIX suite The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available In addition to standard restraints on covalent geometry, phenixreal_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 A or better shows significant improvement of the models and of the fit of these models to the target maps

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Real-space refinement in PHENIX for cryo-EM and crystallography.

https://escholarship.org/content/qt2dj9p3h4/qt2dj9p3h4.pdf?t=pmi3bw

ENDF/B-VIII.0: The 8th Major Release of the Nuclear Reaction Data Library with CIELO-project Cross Sections, New Standards and Thermal Scattering Data

The latest release of the Crystal program for solid-state quantum-mechanical ab initio simulations is presented. The program adopts atom-centered Gaussian-type functions as a basis set, which makes it possible to perform all-electron as well as pseudopotential calculations. Systems of any periodicity can be treated at the same level of accuracy (from 0D molecules, clusters and nanocrystals, to 1D polymers, helices, nanorods, and nanotubes, to 2D monolayers and slab models for surfaces, to actual 3D bulk crystals), without any artificial repetition along nonperiodic directions for 0–2D systems. Density functional theory calculations can be performed with a variety of functionals belonging to several classes: local-density (LDA), generalized-gradient (GGA), meta-GGA, global hybrid, range-separated hybrid, and self-consistent system-specific hybrid. In particular, hybrid functionals can be used at a modest computational cost, comparable to that of pure LDA and GGA formulations, because of the efficient implementation of exact nonlocal Fock exchange. Both translational and point-symmetry features are fully exploited at all steps of the calculation, thus drastically reducing the corresponding computational cost. The various properties computed encompass electronic structure (including magnetic spin-polarized open-shell systems, electron density analysis), geometry (including full or constrained optimization, transition-state search), vibrational properties (frequencies, infrared and Raman intensities, phonon density of states), thermal properties (quasi-harmonic approximation), linear and nonlinear optical properties (static and dynamic [hyper]polarizabilities), strain properties (elasticity, piezoelectricity, photoelasticity), electron transport properties (Boltzmann, transport across nanojunctions), as well as X-ray and inelastic neutron spectra. The program is distributed in serial, parallel, and massively parallel versions. In this paper, the original developments that have been devised and implemented in the last 4 years (since the distribution of the previous public version, Crystal14, occurred in December 2013) are described.

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Quantum-mechanical condensed matter simulations with CRYSTAL

UiO-66 is a highly important prototypical zirconium metal–organic framework (MOF) compound because of its excellent stabilities not typically found in common porous MOFs. In its perfect crystal structure, each Zr metal center is fully coordinated by 12 organic linkers to form a highly connected framework. Using high-resolution neutron power diffraction technique, we found the first direct structural evidence showing that real UiO-66 material contains significant amount of missing-linker defects, an unusual phenomenon for MOFs. The concentration of the missing-linker defects is surprisingly high, ∼10% in our sample, effectively reducing the framework connection from 12 to ∼11. We show that by varying the concentration of the acetic acid modulator and the synthesis time, the linker vacancies can be tuned systematically, leading to dramatically enhanced porosity. We obtained samples with pore volumes ranging from 0.44 to 1.0 cm3/g and Brunauer–Emmett–Teller surface areas ranging from 1000 to 1600 m2/g, the l...

Unusual and Highly Tunable Missing-Linker Defects in Zirconium Metal–Organic Framework UiO-66 and Their Important Effects on Gas Adsorption

An investigation of the plastic phases of polycrystalline specimens of sulphur hexafluoride (SF6) and carbon tetrabromide (CBr4) by neutron elastic scattering and neutron diffraction experiments is reported. A theory of neutron diffraction in plastic crystals, which treats the Bragg scattering and the diffuse scattering from a unified point of view, is developed and applied in the interpretation of the neutron results. The Debye-Scherrer peaks are analysed, both by a cumulant expansion technique and a cubic harmonic analysis, to determine the crystal structures of the plastic phase which are found to be body-centred cubic (space group Im3m) for SF6 and face-centred cubic (space group Fm3m) for CBr4. The bond-orientation distribution function, f(Ω), has maxima in the directions for SF6 and in the directions for CBr4. Since, in both cases, f(Ω) is appreciably different from zero for all orientations, it is apparent that significant thermal reorientation takes place in both these crystals. The tr...

Neutron diffraction study of the plastic phases of polycrystalline SF6 and CBr4

Appendix. Neutron Scattering Lengths and Cross Sections

Fundamental aspects of neutron optics

Introduction General theory of thermal neutron scattering Geometrical optics Rigorous theory of dispersion Kinematical theory of neutron diffraction Dynamical theory of neutron diffraction Neutron interferometry Transport effects in neutron diffraction Appendix A: Lattices Appendix B: Crystals References Subject index

V.F. Sears

Papers

Neutron scattering lengths and cross sections

Neutron diffraction study of the plastic phases of polycrystalline SF6 and CBr4

Appendix. Neutron Scattering Lengths and Cross Sections

Fundamental aspects of neutron optics

Neutron Optics: An Introduction to the Theory of Neutron Optical Phenomena and Their Applications