Diamond Light Source

Three-dimensional (3D) topological Dirac semimetals (TDSs) represent an unusual state of quantum matter that can be viewed as "3D graphene." In contrast to 2D Dirac fermions in graphene or on the surface of 3D topological insulators, TDSs possess 3D Dirac fermions in the bulk. By investigating the electronic structure of Na3Bi with angle-resolved photoemission spectroscopy, we detected 3D Dirac fermions with linear dispersions along all momentum directions. Furthermore, we demonstrated the robustness of 3D Dirac fermions in Na3Bi against in situ surface doping. Our results establish Na3Bi as a model system for 3D TDSs, which can serve as an ideal platform for the systematic study of quantum phase transitions between rich topological quantum states.

This paper describes the mathematical basis for olex2.refine, the new refinement engine which is integrated within the Olex2 program. Precise and clear equations are provided for every computation performed by this engine, including structure factors and their derivatives, constraints, restraints and twinning; a general overview is also given of the different components of the engine and their relation to each other. A framework for adding multiple general constraints with dependencies on common physical parameters is described. Several new restraints on atomic displacement parameters are also presented.

An expert system for macromolecular crystallography data reduction is presented, which builds on existing software to automate the complete data reduction process from images to merged structure factor amplitudes. This can automatically identify multi-wedge, multi-pass and multiwavelength data sets and includes explicit procedures to test for crystallographic special cases. With the push towards high-thoughput crystallography at synchrotron beamlines and automation of structure solution, the ability to reduce data with no user input fills an important gap in the pipeline.

Antiferromagnets are hard to control by external magnetic fields because of the alternating directions of magnetic moments on individual atoms and the resulting zero net magnetization. However, relativistic quantum mechanics allows for generating current-induced internal fields whose sign alternates with the periodicity of the antiferromagnetic lattice. Using these fields, which couple strongly to the antiferromagnetic order, we demonstrate room-temperature electrical switching between stable configurations in antiferromagnetic CuMnAs thin-film devices by applied current with magnitudes of order 10(6) ampere per square centimeter. Electrical writing is combined in our solid-state memory with electrical readout and the stored magnetic state is insensitive to and produces no external magnetic field perturbations, which illustrates the unique merits of antiferromagnets for spintronics.

The DIALS project is a collaboration between Diamond Light Source, Lawrence Berkeley National Laboratory and CCP4 to develop a new software suite for the analysis of crystallographic X-ray diffraction data, initially encompassing spot finding, indexing, refinement and integration. The design, core algorithms and structure of the software are introduced, alongside results from the analysis of data from biological and chemical crystallography experiments.

The race to produce vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began when the first sequence was published, and this forms the basis for vaccines currently deployed globally. Independent lineages of SARS-CoV-2 have recently been reported: UK, B.1.1.7; South Africa, B.1.351; and Brazil, P.1. These variants have multiple changes in the immunodominant spike protein that facilitates viral cell entry via the angiotensin-converting enzyme-2 (ACE2) receptor. Mutations in the receptor recognition site on the spike are of great concern for their potential for immune escape. Here, we describe a structure-function analysis of B.1.351 using a large cohort of convalescent and vaccinee serum samples. The receptor-binding domain mutations provide tighter ACE2 binding and widespread escape from monoclonal antibody neutralization largely driven by E484K, although K417N and N501Y act together against some important antibody classes. In a number of cases, it would appear that convalescent and some vaccine serum offers limited protection against this variant.

The tolerance factor is a widely used predictor of perovskite stability. The recent interest in hybrid perovskites for use as solar cell absorbers has lead to application of the tolerance factor to these materials as a way to explain and predict structure. Here we critically assess the suitability of the tolerance factor for halide perovskites. We show that the tolerance factor fails to accurately predict the stability of the 32 known inorganic iodide perovskites, and propose an alternative method. We introduce a revised set of ionic radii for cations that is anion dependent, this revision is necessary due to increased covalency in metal-halide bonds for heavier halides compared with the metal-oxide and fluoride bonds used to calculate Shannon radii. We also employ a 2D structural map to account for the size requirements of the halide anions. Together these measures yield a simple system which may assist in the search for new hybrid and inorganic perovskites.

201-F6, was shown to exhibit the rare ability to grow on PET as a major carbon and energy source. Central to its PET biodegradation capability is a secreted PETase (PET-digesting enzyme). Here, we present a 0.92 Å resolution X-ray crystal structure of PETase, which reveals features common to both cutinases and lipases. PETase retains the ancestral α/β-hydrolase fold but exhibits a more open active-site cleft than homologous cutinases. By narrowing the binding cleft via mutation of two active-site residues to conserved amino acids in cutinases, we surprisingly observe improved PET degradation, suggesting that PETase is not fully optimized for crystalline PET degradation, despite presumably evolving in a PET-rich environment. Additionally, we show that PETase degrades another semiaromatic polyester, polyethylene-2,5-furandicarboxylate (PEF), which is an emerging, bioderived PET replacement with improved barrier properties. In contrast, PETase does not degrade aliphatic polyesters, suggesting that it is generally an aromatic polyesterase. These findings suggest that additional protein engineering to increase PETase performance is realistic and highlight the need for further developments of structure/activity relationships for biodegradation of synthetic polyesters.

November 2021, the sequence of a new SARS-CoV-2 viral isolate Omicron-B.1.1.529 was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titers of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic Alpha, Beta, Gamma, or Delta are substantially reduced, or the sera failed to neutralize. Titers against Omicron are boosted by third vaccine doses and are high in both vaccinated individuals and those infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of the large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses and uses mutations that confer tight binding to ACE2 to unleash evolution driven by immune escape. This leads to a large number of mutations in the ACE2 binding site and rebalances receptor affinity to that of earlier pandemic viruses.

Magnetic Weyl semimetals Weyl semimetals (WSMs)—materials that host exotic quasiparticles called Weyl fermions—must break either spatial inversion or time-reversal symmetry. A number of WSMs that break inversion symmetry have been identified, but showing unambiguously that a material is a time-reversal-breaking WSM is tricky. Three groups now provide spectroscopic evidence for this latter state in magnetic materials (see the Perspective by da Silva Neto). Belopolski et al. probed the material Co 2 MnGa using angle-resolved photoemission spectroscopy, revealing exotic drumhead surface states. Using the same technique, Liu et al. studied the material Co 3 Sn 2 S 2 , which was complemented by the scanning tunneling spectroscopy measurements of Morali et al. These magnetic WSM states provide an ideal setting for exotic transport effects. Science , this issue p. 1278 , p. 1282 , p. 1286 ; see also p. 1248

The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.

Abstract We report a novel microwave plasma enhanced chemical vapor deposition strategy for the efficient synthesis of multilayer graphene nanoflake films (MGNFs) on Si substrates. The constituent graphene nanoflakes have a highly graphitized knife‐edge structure with a 2–3 nm thick sharp edge and show a preferred vertical orientation with respect to the Si substrate as established by near‐edge X‐ray absorption fine structure spectroscopy. The growth rate is approximately 1.6 µm min −1 , which is 10 times faster than the previously reported best value. The MGNFs are shown to demonstrate fast electron‐transfer (ET) kinetics for the Fe(CN) 6 3−/4− redox system and excellent electrocatalytic activity for simultaneously determining dopamine (DA), ascorbic acid (AA) and uric acid (UA). Their biosensing DA performance in the presence of common interfering agents AA and UA is superior to other bare solid‐state electrodes and is comparable only to that of edge plane pyrolytic graphite. Our work here, establishes that the abundance of graphitic edge planes/defects are essentially responsible for the fast ET kinetics, active electrocatalytic and biosensing properties. This novel edge‐plane‐based electrochemical platform with the high surface area and electrocatalytic activity offers great promise for creating a revolutionary new class of nanostructured electrodes for biosensing, biofuel cells and energy‐conversion applications.

Abstract The laser–matter interaction and solidification phenomena associated with laser additive manufacturing (LAM) remain unclear, slowing its process development and optimisation. Here, through in situ and operando high-speed synchrotron X-ray imaging, we reveal the underlying physical phenomena during the deposition of the first and second layer melt tracks. We show that the laser-induced gas/vapour jet promotes the formation of melt tracks and denuded zones via spattering (at a velocity of 1 m s −1 ). We also uncover mechanisms of pore migration by Marangoni-driven flow (recirculating at a velocity of 0.4 m s −1 ), pore dissolution and dispersion by laser re-melting. We develop a mechanism map for predicting the evolution of melt features, changes in melt track morphology from a continuous hemi-cylindrical track to disconnected beads with decreasing linear energy density and improved molten pool wetting with increasing laser power. Our results clarify aspects of the physics behind LAM, which are critical for its development.

The Omicron lineage of SARS-CoV-2, which was first described in November 2021, spread rapidly to become globally dominant and has split into a number of sublineages. BA.1 dominated the initial wave but has been replaced by BA.2 in many countries. Recent sequencing from South Africa's Gauteng region uncovered two new sublineages, BA.4 and BA.5, which are taking over locally, driving a new wave. BA.4 and BA.5 contain identical spike sequences, and although closely related to BA.2, they contain further mutations in the receptor-binding domain of their spikes. Here, we study the neutralization of BA.4/5 using a range of vaccine and naturally immune serum and panels of monoclonal antibodies. BA.4/5 shows reduced neutralization by the serum from individuals vaccinated with triple doses of AstraZeneca or Pfizer vaccine compared with BA.1 and BA.2. Furthermore, using the serum from BA.1 vaccine breakthrough infections, there are, likewise, significant reductions in the neutralization of BA.4/5, raising the possibility of repeat Omicron infections.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has undergone progressive change, with variants conferring advantage rapidly becoming dominant lineages, e.g., B.1.617. With apparent increased transmissibility, variant B.1.617.2 has contributed to the current wave of infection ravaging the Indian subcontinent and has been designated a variant of concern in the United Kingdom. Here we study the ability of monoclonal antibodies and convalescent and vaccine sera to neutralize B.1.617.1 and B.1.617.2, complement this with structural analyses of Fab/receptor binding domain (RBD) complexes, and map the antigenic space of current variants. Neutralization of both viruses is reduced compared with ancestral Wuhan-related strains, but there is no evidence of widespread antibody escape as seen with B.1.351. However, B.1.351 and P.1 sera showed markedly more reduction in neutralization of B.1.617.2, suggesting that individuals infected previously by these variants may be more susceptible to reinfection by B.1.617.2. This observation provides important new insights for immunization policy with future variant vaccines in non-immune populations.

Terminating the SARS-CoV-2 pandemic relies upon pan-global vaccination. Current vaccines elicit neutralizing antibody responses to the virus spike derived from early isolates. However, new strains have emerged with multiple mutations, including P.1 from Brazil, B.1.351 from South Africa, and B.1.1.7 from the UK (12, 10, and 9 changes in the spike, respectively). All have mutations in the ACE2 binding site, with P.1 and B.1.351 having a virtually identical triplet (E484K, K417N/T, and N501Y), which we show confer similar increased affinity for ACE2. We show that, surprisingly, P.1 is significantly less resistant to naturally acquired or vaccine-induced antibody responses than B.1.351, suggesting that changes outside the receptor-binding domain (RBD) impact neutralization. Monoclonal antibody (mAb) 222 neutralizes all three variants despite interacting with two of the ACE2-binding site mutations. We explain this through structural analysis and use the 222 light chain to largely restore neutralization potency to a major class of public antibodies.

Hybrid halide perovskites such as methylammonium lead iodide (CH3NH3PbI3) exhibit unusually low free-carrier concentrations despite being processed at low-temperatures from solution. We demonstrate, through quantum mechanical calculations, that an origin of this phenomenon is a prevalence of ionic over electronic disorder in stoichiometric materials. Schottky defect formation provides a mechanism to self-regulate the concentration of charge carriers through ionic compensation of charged point defects. The equilibrium charged vacancy concentration is predicted to exceed 0.4% at room temperature. This behavior, which goes against established defect conventions for inorganic semiconductors, has implications for photovoltaic performance.

xia2 is an expert system for the automated reduction of macromolecular crystallography (MX) data employing well trusted existing software. The system can process a full MX data set consisting of one or more sequences of images at one or more wavelengths from images to structure-factor amplitudes with no user input. To achieve this many decisions are made, the rationale for which is described here. In addition, it is critical to support the testing of hypotheses and to allow feedback of results from later stages in the analysis to earlier points where decisions were made: the flexible framework employed by xia2 to support this feedback is summarized here. While the decision-making protocols described here were developed for xia2, they are equally applicable to interactive data reduction.

Vacancy-ordered double perovskites of the general formula A2BX6 are a family of perovskite derivatives composed of a face-centered lattice of nearly isolated [BX6] units with A-site cations occupying the cuboctahedral voids. Despite the presence of isolated octahedral units, the close-packed iodide lattice provides significant electronic dispersion, such that Cs2SnI6 has recently been explored for applications in photovoltaic devices. To elucidate the structure-property relationships of these materials, we have synthesized solid-solution Cs2Sn1-xTexI6. However, even though tellurium substitution increases electronic dispersion via closer I-I contact distances, the substitution experimentally yields insulating behavior from a significant decrease in carrier concentration and mobility. Density functional calculations of native defects in Cs2SnI6 reveal that iodine vacancies exhibit a low enthalpy of formation, and that the defect energy level is a shallow donor to the conduction band rendering the material tolerant to these defect states. The increased covalency of Te-I bonding renders the formation of iodine vacancy states unfavorable and is responsible for the reduction in conductivity upon Te substitution. Additionally, Cs2TeI6 is intolerant to the formation of these defects, because the defect level occurs deep within the band gap and thus localizes potential mobile charge carriers. In these vacancy-ordered double perovskites, the close-packed lattice of iodine provides significant electronic dispersion, while the interaction of the B- and X-site ions dictates the properties as they pertain to electronic structure and defect tolerance. This simplified perspective based on extensive experimental and theoretical analysis provides a platform from which to understand structure-property relationships in functional perovskite halides.

The CCP4 (Collaborative Computational Project, Number 4) software suite for macromolecular structure determination by X-ray crystallography groups brings together many programs and libraries that, by means of well established conventions, interoperate effectively without adhering to strict design guidelines. Because of this inherent flexibility, users are often presented with diverse, even divergent, choices for solving every type of problem. Recently, CCP4 introduced CCP4i2, a modern graphical interface designed to help structural biologists to navigate the process of structure determination, with an emphasis on pipelining and the streamlined presentation of results. In addition, CCP4i2 provides a framework for writing structure-solution scripts that can be built up incrementally to create increasingly automatic procedures.