omi

This week in Christian history: Georgian king martyred, Baptist denomination founded

Events that occurred this week in Christian history include the martyrdom of a Georgian king, a social reformer claims to have a vision, and the founding of a Baptist denomination.




omi

Kamala Harris promises 'peaceful transfer of power,' talks 'loyalty to Constitution, conscience and God'

Vice President Kamala Harris has conceded the election, promising Americans that there will be a “peaceful transfer of power” and stressing loyalty “to our God,” while also promising to keep fighting.




omi

Workshop 14: Anatomical Historian Alice Dreger

Alice Dreger is a historian of science, anatomy, and medicine, known for her work studying and advocating for people born with atypical sex disorders. She famously resigned from Northwestern University in protest of academic censorship, and gained some infamy on Twitter for live-tweeting her son's sex education class. We had a delightful chat with her about her writing process in advance of the paperback release of her book, Galileo's Middle Finger: Heretics, Activists, and the Search for Justice in Science. Learn more about your ad choices. Visit podcastchoices.com/adchoices




omi

NATO's lost atomic bombs threaten the world

According to international experts, the world has returned to the Cold War, but this time, the state of affairs is even more dramatic than it used to be. Airplanes with nuclear warheads on board are on duty again, like 30 years ago. The danger of such flights lies not only in the possible use of nuclear weapons. Nuclear bombs may go missing, as it had repeatedly happened in the past. Atomic bombs for Spain Several years ago, a Canadian diver, while diving into the sea near the Haida Gwaii archipelago, was horrified to find something that looked like an air nuclear bomb. The diver was right. In 1950, an American B-36 bomber was forced to jettison an atomic bomb into the Pacific Ocean due to a fire on board.




omi

El Departamento de Seguros de Texas anuncia la nueva división de Relaciones Externas y al nuevo Comisionado Adjunto

El Departamento de Seguros de Texas (TDI, por su nombre y siglas en inglés) anunció a Dan Paschal como el Comisionado Adjunto de la recién creada división de Relaciones Externas. Esta división incluirá Comunicaciones (actualmente Asuntos Públicos) y Relaciones Gubernamentales (actualmente Asuntos de la Agencia).




omi

El Departamento de Seguros de Texas recomienda a los residentes costeros a estar preparados para los huracanes

Septiembre se considera la etapa cumbre de la actividad ciclónica, pero es importante recordar que la temporada de huracanes se extiende hasta noviembre.




omi

CIS Summit highlights Russia's role of a strong, dominating power

The summit of the Commonwealth of Independent States (CIS) was a formality, but the issue at hand is the security of the Russian Federation. Moscow needs to change its attitude towards its neighbours before it is too late. The following leaders attended the CIS summit at the personal invitation from Russian President Vladimir Putin: President of Azerbaijan Ilham Aliyev, Prime Minister of Armenia Nikol Pashinyan, President of Belarus Alexander Lukashenko, President of Kyrgyzstan Sadyr Japarov, President of Tajikistan Emomali Rahmon, President of Turkmenistan Serdar Berdimuhamedov, President of Uzbekistan Shavkat Mirziyoyev. Moldovan President Maia Sandu did not attend.




omi

Descartes’ Study Reveals Nearly 90% of Consumers’ Sustainable Home Delivery Choices Are Impacted by Economic Pressure

Descartes Systems Group has released findings from its 2024 Home Delivery Sustainability Report: The Environmentally Conscious Consumer Under Pressure survey, which examined online consumer sentiment of retailers’ sustainability practices around their delivery operations.




omi

Ransomware surge: RansomHub dominates as Lockbit fades, new threats emerge across industries

Check Point Research (CPR) has released a report revealing that ransomware remains the top cyber threat. RansomHub has quickly emerged as the fastest-growing group, operating through Ransomware-as-a-Service (RaaS).




omi

Signs That Your Identity Has Been Compromised (and How To Get Help?)

By Gareth Hunt, freelance writer.

One of the world's most important currencies is information. That information could be about anybody and anything and may be used in a million different ways. With this much personal information people put on the internet, it becomes effortless for cyber criminals to get that information and perpetrate identity thefts.




omi

Ergonomic Solutions: Delivering customer engagement at EuroCIS2024

The retail industry is witnessing an unprecedented level of competition, and traditional marketing strategies are becoming obsolete.

Recognizing the need for enabling innovative digital customer experiences, Ergonomic Solutions will showcase a comprehensive lineup of engaging customer facing solutions to drive personal interaction in retail and hospitality environments at EuroCIS 2024 (Hall 9 A40) in Dusseldorf from 27th – 29th February.




omi

The Ergonomic Solutions Group’s new SpacePole Kiosk – A modular, configurable and customisable platform for a wide range of self-service applications

The Ergonomic Solutions Group, the designer and manufacturer of technology mounting solutions, has launched the SpacePole Kiosk – described as a multifunctional platform with maximum flexibility for a wide range of self-service applications including self-check-in/check-out, self-ordering, endless aisle, product display & advertising, ticketing, click & collect and many more.




omi

More contagious COVID-19 BA.2 omicron to take over the U.S.

Centrers for Disease Control and Prevention suggest that the more contagious subvariant BA.2 of omicron strain now makes up 72% of COVID-19 infections in the U.S. According to the data, the BA.2 is able to displace all other COVID-19 strains and its subvariants. Ali Mokdad, an epidemiologist at the Institute for Health Metrics and Evaluation in Washington state, estimates that the displacement might happen in the next two weeks. According to different sources, the BA.2 is from 30% to 80% more contagious than the BA.1. A top WHO official, Maria Van Kerkhove, describes BA.2 as the most transmissible version of the virus so far. 




omi

Combination Approach Shows Promise for Treating Rare, Aggressive Cancers

UCLA investigators have shown that that combining pembrolizumab, an immunotherapy drug, with standard chemotherapy can improve treatment outcomes for patients with small cell bladder cancer and small cell/neuroendocrine prostate cancer.




omi

Expert Available: Beyonce leads Grammy nominations with 11 nods

Beyonce received 11 Grammy Award nominations, notching more citations than any other artist this year, "Cowboy Carter." ...




omi

Abortion and Women's Future Socioeconomic Attainment

Adolescents in regions with fewer abortion restrictions and those who had an abortion were more likely to have graduated from college, earn higher incomes and have greater financial stability at two time-points over an almost 25-year period. Girls who became teen moms, conversely, were more likely to experience eviction, debt and food insecurity.




omi

Power Broker Myung Tae-kyun Denies Involvement in Election Nomination Scandal

[Politics] :
Myung Tae-kyun, a self-proclaimed political consultant and a key figure in a high-profile scandal involving the president and first lady, was questioned by the prosecution for the second consecutive day on Saturday. The Changwon District Prosecutors' Office grilled Myung for over 12 hours on Saturday ...

[more...]




omi

FM Cho: S. Korea-US Alliance Will Grow Stronger under Incoming Trump Gov’t

[Politics] :
Foreign Minister Cho Tae-yul said he is confident that the South Korea-U.S. alliance will continue to grow stronger under the incoming Donald Trump administration. At a press conference on Tuesday, Cho said President-elect Trump’s foreign policy, which prioritizes U.S. allies’ expanded role and ...

[more...]




omi

Andy Kim Wins in New Jersey, Becoming First Korean American Senator

[International] :
Democratic Rep. Andy Kim was elected to the U.S. Senate on Tuesday, becoming the first Korean American to serve in the Senate.   With elections for the Senate and the House of Representatives taking place the same day as the U.S. presidential election, Kim defeated Curtis Bashaw in the New Jersey senatorial ...

[more...]




omi

Trump Nominates Fox News Host Pete Hegseth as Defense Secretary

[International] :
U.S. President-elect Donald Trump has nominated Pete Hegseth, a Fox News host and veteran of the wars in Iraq and Afghanistan, as the next secretary of defense. In a statement issued Tuesday, Trump called the nominee “tough, smart and a true believer in America First,” adding that with Hegseth at the ...

[more...]




omi

10 Most Dangerous Cities in the World, Based on Homicide Rate

The most dangerous cities in the world are a major concern for residents, visitors, law enforcement and policymakers. While crime exists everywhere, some cities statistically experience consistently high crime levels. We turned to Statista, a global data and business intelligence platform, to find the hard numbers on the murder rate per capita in cities worldwide.




omi

G-Dragon Writes Rrack for Babymonster's Upcoming Album


G-Dragon has helped write a song for Babymonster’s upcoming full-length album which will drop next month. The rookie girl group’s first full-length album “Drip” will drop...

[more...]




omi

No. of Economically Inactive People Increases 245,000 On-Year in August

[Economy] :
The number of economically inactive South Koreans increased by 245-thousand on-year in August. According to Statistics Korea on Wednesday, nearly two-point-57 million people were neither working nor looking for work. Those in their 60s made up 36-point-three percent of the total, while people in their ...

[more...]






omi

Atypical phase transition, twinning and ferroelastic domain structure in bis(ethylenediammonium) tetrabromozincate(II) bromide, [NH3(CH2)2NH3]2[ZnBr4]Br2

A unique phase transition, twinning and ferroelastic domain structure in [NH3(CH2)2NH3]2[ZnBr4]Br2 is found. The new additional domain structure is observed at the phase transition on heating, which is preserved after cooling to room temperature.




omi

Morphological control for hollow rod crystals of a photochromic di­aryl­ethene on spherulites by surface properties of substrates

1,2-Bis(3,5-di­methyl-2-thienyl)perfluoro­cyclo­pentene formed its own spherulites by sublimation onto the hydro­philic surfaces of the (0001) planes of α-quartz and sapphire substrates. The formation of different morphologies of these spherulites was attributed to the surface properties of each substrate. Depending on the morphology of the spherulites, hollow rod crystals with cross sections of different sizes and shapes and branching structures were generated on the surfaces of the spherulites.




omi

Atypical phase transition, twinning and ferroelastic domain structure in bis(ethylenediammonium) tetrabromozincate(II) bromide, [NH3(CH2)2NH3]2[ZnBr4]Br2

Single-crystal growth, differential thermal analysis (DTA), derivative thermogravimetry (DTG), differential scanning calorimetry (DSC), X-ray structural studies and polarized microscopy observations of bis(ethylenediammonium) tetrabromozincate(II) bromide [NH3(CH2)2NH3]2[ZnBr4]Br2 are presented. A reversible phase transition is described. At room temperature, the complex crystallizes in the monoclinic system. In some cases, the single crystals are twinned into two or more large domains of ferroelastic type with domain walls in the (100) crystallographic plane. DTA and DTG measurements show chemical stability of the crystal up to ∼538 K. In the DSC studies, a reversible isostructural phase transition was revealed at ∼526/522 K on heating/cooling run, respectively. Optical observation on the heating run reveals that at the phase transition the plane of twinning (domain wall) does not disappear and additionally the appearance of a new domain structure of ferroelastic type with domain walls in the planes (101), (101), (100) and (001) is observed. The domain structure pattern is preserved after cooling to the room-temperature phase and the symmetry of this phase is unchanged.




omi

Morphological control for hollow rod crystals of a photochromic diarylethene on spherulites by surface properties of substrates

Sublimation methods utilizing the surface properties of substrates can address the challenge of controlling hollow morphologies in rod crystals. Spherulites were formed on the hydrophilic surface of the (0001) planes of α-quartz and sapphire substrates by sublimation of 1,2-bis(3,5-dimethyl-2-thienyl)perfluorocyclopentene (1a). Various types of hollow morphologies, distinguished by the size and shape of their cross sections and by the presence or absence of branching structures, were formed separately on α-quartz and sapphire substrates. Such precise control of the hollow morphologies was attributed to the wettability of each substrate, leading to the formation of spherulites of 1a. In addition, it was indicated that the formation process of the surface morphologies of spherulites was associated with the hollow morphologies of rod crystals of 1a.




omi

Integrating machine learning interatomic potentials with hybrid reverse Monte Carlo structure refinements in RMCProfile

New software capabilities in RMCProfile allow researchers to study the structure of materials by combining machine learning interatomic potentials and reverse Monte Carlo.




omi

Crystal structures of two polymorphs for fac-bromido­tricarbon­yl[4-(4-meth­oxy­phen­yl)-2-(pyridin-2-yl)thia­zole-κ2N,N']rhenium(I)

Crystallization of the title compound from CH2Cl2/n-pentane (1:5 v/v) at room temperature gave two polymorphs, which crystallize in monoclinic (P21/c; α form) and ortho­rhom­bic (Pna21; β form) space groups. The ReI complex mol­ecules in either polymorph adopt a six-coordinate octa­hedral geometry with three facially-oriented carbonyl ligands, one bromido ligand, and two nitro­gen atoms from one chelating ligand ppt-OMe. In the crystal, both polymorph α and β form di-periodic sheet-like architectures supported by multiple hydrogen bonds.




omi

Crystal structure, Hirshfeld surface, DFT and mol­ecular docking studies of 2-{4-[(E)-(4-acetylphen­yl)diazen­yl]phen­yl}-1-(5-bromo­thio­phen-2-yl)ethanone; a bromine⋯oxygen type contact

The title compound is a non-liquid crystal mol­ecule. The mol­ecular crystal is consolidated by C—Br⋯O&z-dbnd;C type contacts running continuously along the [001] direction.




omi

Welcoming two new Co-editors




omi

Integrating machine learning interatomic potentials with hybrid reverse Monte Carlo structure refinements in RMCProfile

Structure refinement with reverse Monte Carlo (RMC) is a powerful tool for interpreting experimental diffraction data. To ensure that the under-constrained RMC algorithm yields reasonable results, the hybrid RMC approach applies interatomic potentials to obtain solutions that are both physically sensible and in agreement with experiment. To expand the range of materials that can be studied with hybrid RMC, we have implemented a new interatomic potential constraint in RMCProfile that grants flexibility to apply potentials supported by the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) molecular dynamics code. This includes machine learning interatomic potentials, which provide a pathway to applying hybrid RMC to materials without currently available interatomic potentials. To this end, we present a methodology to use RMC to train machine learning interatomic potentials for hybrid RMC applications.




omi

Crystal structures of two polymorphs for fac-bromidotricarbonyl[4-(4-methoxyphenyl)-2-(pyridin-2-yl)thiazole-κ2N,N']rhenium(I)

Crystallization of the title compound, fac-[ReBr(ppt-OMe)(CO)3] (ppt-OMe = C15H12N2OS), from CH2Cl2/n-pentane (1:5 v/v) at room temperature gave two polymorphs, which crystallize in monoclinic (P21/c; α form) and orthorhombic (Pna21; β form) space groups. The ReI complex molecules in either polymorph adopt a six-coordinate octahedral geometry with three facially-oriented carbonyl ligands, one bromido ligand, and two nitrogen atoms from one chelating ligand ppt-OMe. In the crystal, both polymorph α and β form di-periodic sheet-like architectures supported by multiple hydrogen bonds. In polymorph α, two types of hydrogen bonds (C—H...O) are found while, in polymorph β, four types of hydrogen bonds (C—H...O and C—H...Br) exist.




omi

The diamond–silicon carbide composite Skeleton® as a promising material for substrates of intense X-ray beam optics

The paper considers the possibility of using the diamond-silicon carbide composite Skeleton® with a technological coating of polycrystalline silicon as a substrate for X-ray mirrors used with powerful synchrotron radiation sources (third+ and fourth generation). Samples were studied after polishing to provide the following surface parameters: root-mean-square flatness ≃ 50 nm, micro-roughness on the frame 2 µm × 2 µm σ ≃ 0.15 nm. The heat capacity, thermal conductivity and coefficient of linear thermal expansion were investigated. For comparison, a monocrystalline silicon sample was studied under the same conditions using the same methods. The value of the coefficient of linear thermal expansion turned out to be higher than that of monocrystalline silicon and amounted to 4.3 × 10−6 K−1, and the values of thermal conductivity (5.0 W cm−1 K−1) and heat capacity (1.2 J K−1 g−1) also exceeded the values for Si. Thermally induced deformations of both Skeleton® and monocrystalline silicon samples under irradiation with a CO2 laser beam have also been experimentally studied. Taking into account the obtained thermophysical constants, the calculation of thermally induced deformation under irradiation with hard (20 keV) X-rays showed almost three times less deformation of the Skeleton® sample than of the monocrystalline silicon sample.




omi

The soft X-ray spectromicroscopy beamline BL08U1A upgrade at SSRF

Beamline BL08U1A is a soft X-ray spectromicroscopy beamline at Shanghai Synchrotron Radiation Facility (SSRF) that exhibits the capabilities of high spatial resolution (30 nm) and high energy resolving power (over 104). As a first-generation beamline of SSRF, owing to its continuous operation over the last ten years, an urgent upgrade of the equipment including the monochromator was deemed necessary. The upgrade work included the overall construction of the monochromator and replacement of the mirrors upstream and downstream of the monochromator. Based on its original skeleton, two elliptically cylinder mirrors were designed to focus the beam horizontally, which can increase the flux density by about three times on the exit slits. Meanwhile, the application of variable-line-space gratings in the monochromator demonstrates the dual functions of dispersing and focusing on the exit slits which can decrease abberations dramatically. After the upgrade of the main components of the beamline, the energy range is 180–2000 eV, the energy resolving power reaches 16333 @ 244 eV and 12730 @ 401 eV, and the photon flux measured in the experimental station is over 2.45 × 109 photons s−1 (E/ΔE = 6440 @ 244 eV).




omi

trans-Di­bromido­tetra­kis­(5-methyl-1H-pyrazole-κN2)manganese(II)

The title compound, trans-di­bromido­tetra­kis­(5-methyl-1H-pyrazole-κN2)manganese(II), [MnBr2(C4H6N2)4] or [Mn(3-MePzH)4Br2] (1) crystallizes in the triclinic Poverline{1} space group with the cell parameters a = 7.6288 (3), b = 8.7530 (4), c = 9.3794 (4) Å and α = 90.707 (4), β = 106.138 (4), γ = 114.285 (5)°, V = 542.62 (5) Å3, T = 120 K. The asymmetric unit contains only half the mol­ecule with the manganese atom is situated on a crystallographic inversion center. The 3-MePzH ligands are present in an AABB type manner with two methyl groups pointing up and the other two down. The supra­molecular architecture is characterized by several inter­molecular C—H⋯N, N—H⋯Br, and C—H⋯π inter­actions. Earlier, a polymorphic structure of [Mn(3-MePzH)4Br2] (2) with a similar geometry and also an AABB arrangement for the pyrazole ligands was described [Reedijk et al. (1971). Inorg. Chem. 10, 2594–2599; a = 8.802 (6), b = 9.695 (5), c = 7.613 (8) Å and α = 105.12 (4), β = 114.98 (4), γ = 92.90 (3)°, V = 558.826 (5) Å3, T = 295 K]. A varying supra­molecular pattern was reported, with the structure of 1 featuring a herringbone type pattern while that of structure 2 shows a pillared network type of arrangement along the a axis. A nickel complex [Ni(3-MePzH)4Br2] isomorphic to 1 and the analogous chloro derivatives of FeII, CoII and CuII are also known.




omi

(SC,RS)-Bromido­(N-{4-methyl-1-[(4-methyl­phenyl)sul­fan­yl]­pentan-2-yl}-N'-(pyridin-2-yl)imidazol-2-yl­idene)palladium(II) bromide

The mol­ecule of the title NCNHCS pincer N-heterocyclic carbene palladium(II) complex, [PdBr(C21H25N3S)]Br, exhibits a slightly distorted square-planar coordination at the palladium(II) atom, with the five-membered chelate ring nearly planar. The six-membered chelate ring adopts an envelope conformation. Upon chelation, the sulfur atom becomes a stereogenic centre with an RS configuration induced by the chiral carbon of the precursor imidazolium salt. There are intra­molecular C—H⋯Br—Pd hydrogen bonds in the structure. The two inter­stitial Br atoms, as the counter-anion of the structure, are both located on crystallographic twofold axes and are connected to the complex cations via C—H⋯·Br hydrogen bonds.




omi

Pinaverium bromide

The structure of pinaverium bromide (systematic name: 4-[(2-bromo-4,5-di­meth­oxy­phen­yl)meth­yl]-4-{2-[2-(6,6-dimethyl-2-bi­cyclo­[3.1.1]hepta­nyl)eth­oxy]eth­yl}morpholin-4-ium bromide; C26H41Br2NO4), was determined at 110 K. It has monoclinic (P21) symmetry. It is of inter­est with respect to its anti-inflammatory properties. The asymmetric unit contains two independent mol­ecules, one of which exhibits disorder of the bi­cyclo terminal group (occupancy factors: 0.78 and 0.22).




omi

Further evaluation of the shape of atomic Hirshfeld surfaces: M⋯H contacts and homoatomic bonds

It is well known that Hirshfeld surfaces provide an easy and straightforward way of analysing inter­molecular inter­actions in the crystal environment. The use of atomic Hirshfeld surfaces has also demonstrated that such surfaces carry information related to chemical bonds which allow a deeper evaluation of the structures. Here we briefly summarize the approach of atomic Hirshfeld surfaces while further evaluating the kind of information that can be retrieved from them. We show that the analysis of the metal-centre Hirshfeld surfaces from structures refined via Hirshfeld Atom Refinement (HAR) allow accurate evaluation of contacts of type M⋯H, and that such contacts can be related to the overall shape of the surfaces. The com­pounds analysed were tetra­aqua­bis­(3-carb­oxy­propionato)metal(II), [M(C4H3O4)2(H2O)4], for metal(II)/M = manganese/Mn, cobalt/Co, nickel/Ni and zinc/Zn. We also evaluate the sensitivity of the surfaces by an investigation of seemingly flat surfaces through analysis of the curvature functions in the direction of C—C bonds. The obtained values not only demonstrate variations in curvature but also show a correlation with the hybridization of the C atoms involved in the bond.




omi

Orientational analysis of atomic pair correlations in nanocrystalline indium oxide thin films

The application of grazing-incidence total X-ray scattering (GITXS) for pair distribution function (PDF) analysis using >50 keV X-rays from synchrotron light sources has created new opportunities for structural characterization of supported thin films with high resolution. Compared with grazing-incidence wide-angle X-ray scattering, which is only useful for highly ordered materials, GITXS/PDFs expand such analysis to largely disordered or nanostructured materials by examining the atomic pair correlations dependent on the direction relative to the surface of the supporting substrate. A characterization of nanocrystalline In2O3-derived thin films is presented here with in-plane-isotropic and out-of-plane-anisotropic orientational ordering of the atomic structure, each synthesized using different techniques. The atomic orientations of such films are known to vary based on the synthetic conditions. Here, an azimuthal orientational analysis of these films using GITXS with a single incident angle is shown to resolve the markedly different orientations of the atomic structures with respect to the planar support and the different degrees of long-range order, and hence, the terminal surface chemistries. It is anticipated that orientational analysis of GITXS/PDF data will offer opportunities to extend structural analyses of thin films by providing a means to qualitatively determine the major atomic orientation within nanocrystalline and, eventually, non-crystalline films.




omi

Transferable Hirshfeld atom model for rapid evaluation of aspherical atomic form factors

Form factors based on aspherical models of atomic electron density have brought great improvement in the accuracies of hydrogen atom parameters derived from X-ray crystal structure refinement. Today, two main groups of such models are available, the banks of transferable atomic densities parametrized using the Hansen–Coppens multipole model which allows for rapid evaluation of atomic form factors and Hirshfeld atom refinement (HAR)-related methods which are usually more accurate but also slower. In this work, a model that combines the ideas utilized in the two approaches is tested. It uses atomic electron densities based on Hirshfeld partitions of electron densities, which are precalculated and stored in a databank. This model was also applied during the refinement of the structures of five small molecules. A comparison of the resulting hydrogen atom parameters with those derived from neutron diffraction data indicates that they are more accurate than those obtained with the Hansen–Coppens based databank, and only slightly less accurate than those obtained with a version of HAR that neglects the crystal environment. The advantage of using HAR becomes more noticeable when the effects of the environment are included. To speed up calculations, atomic densities were represented by multipole expansion with spherical harmonics up to l = 7, which used numerical radial functions (a different approach to that applied in the Hansen–Coppens model). Calculations of atomic form factors for the small protein crambin (at 0.73 Å resolution) took only 68 s using 12 CPU cores.




omi

RCSB Protein Data Bank: supporting research and education worldwide through explorations of experimentally determined and computationally predicted atomic level 3D biostructures

The Protein Data Bank (PDB) was established as the first open-access digital data resource in biology and medicine in 1971 with seven X-ray crystal structures of proteins. Today, the PDB houses >210 000 experimentally determined, atomic level, 3D structures of proteins and nucleic acids as well as their complexes with one another and small molecules (e.g. approved drugs, enzyme cofactors). These data provide insights into fundamental biology, biomedicine, bioenergy and biotechnology. They proved particularly important for understanding the SARS-CoV-2 global pandemic. The US-funded Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) and other members of the Worldwide Protein Data Bank (wwPDB) partnership jointly manage the PDB archive and support >60 000 `data depositors' (structural biologists) around the world. wwPDB ensures the quality and integrity of the data in the ever-expanding PDB archive and supports global open access without limitations on data usage. The RCSB PDB research-focused web portal at https://www.rcsb.org/ (RCSB.org) supports millions of users worldwide, representing a broad range of expertise and interests. In addition to retrieving 3D structure data, PDB `data consumers' access comparative data and external annotations, such as information about disease-causing point mutations and genetic variations. RCSB.org also provides access to >1 000 000 computed structure models (CSMs) generated using artificial intelligence/machine-learning methods. To avoid doubt, the provenance and reliability of experimentally determined PDB structures and CSMs are identified. Related training materials are available to support users in their RCSB.org explorations.




omi

Structural insights into the molecular mechanism of phytoplasma immunodominant membrane protein

Immunodominant membrane protein (IMP) is a prevalent membrane protein in phytoplasma and has been confirmed to be an F-actin-binding protein. However, the intricate molecular mechanisms that govern the function of IMP require further elucidation. In this study, the X-ray crystallographic structure of IMP was determined and insights into its interaction with plant actin are provided. A comparative analysis with other proteins demonstrates that IMP shares structural homology with talin rod domain-containing protein 1 (TLNRD1), which also functions as an F-actin-binding protein. Subsequent molecular-docking studies of IMP and F-actin reveal that they possess complementary surfaces, suggesting a stable interaction. The low potential energy and high confidence score of the IMP–F-actin binding model indicate stable binding. Additionally, by employing immunoprecipitation and mass spectrometry, it was discovered that IMP serves as an interaction partner for the phytoplasmal effector causing phyllody 1 (PHYL1). It was then shown that both IMP and PHYL1 are highly expressed in the S2 stage of peanut witches' broom phytoplasma-infected Catharanthus roseus. The association between IMP and PHYL1 is substantiated through in vivo immunoprecipitation, an in vitro cross-linking assay and molecular-docking analysis. Collectively, these findings expand the current understanding of IMP interactions and enhance the comprehension of the interaction of IMP with plant F-actin. They also unveil a novel interaction pathway that may influence phytoplasma pathogenicity and host plant responses related to PHYL1. This discovery could pave the way for the development of new strategies to overcome phytoplasma-related plant diseases.




omi

Chromic soft crystals based on luminescent platinum(II) complexes

Platinum(II) complexes of square-planar geometry are interesting from a crystal engineering viewpoint because they exhibit strong luminescence based on the self-assembly of molecular units. The luminescence color changes in response to gentle stimuli, such as vapor exposure or weak mechanical forces. Both the molecular and the crystal designs for soft crystals are critical to effectively generate the chromic luminescence phenomenon of Pt(II) complexes. In this topical review, strategies for fabricating chromic luminescent Pt(II) complexes are described from a crystal design perspective, focusing on the structural regulation of Pt(II) complexes that exhibit assembly-induced luminescence via metal–metal interactions and structural control of anionic Pt(II) complexes using cations. The research progress on the evolution of various chromic luminescence properties of Pt(II) complexes, including the studies conducted by our group, are presented here along with the latest research outcomes, and an overview of the frontiers and future potential of this research field is provided.




omi

Structural insight into piezo-solvatochromism of Reichardt's dye

To date, accurate modelling of the solvation process is challenging, often over-simplifying the solvent–solute interactions. The interplay between the molecular arrangement associated with the solvation process and crystal nucleation has been investigated by analysis of the piezo-solvatochromic behaviour of Reichardt's dye, ET(1), in methanol, ethanol and acetone under high pressure. High-pressure single-crystal X-ray diffraction and UV–Vis spectroscopy reveal the impact of solute–solvent interactions on the optical properties of ET(1). The study underscores the intricate relationship between solvent properties, molecular conformation and crystal packing. The connection between liquid and solid phases emphasizes the capabilities of high-pressure methods for expanding the field of crystal engineering. The high-pressure environment allowed the determination of the crystal structures reported here that are built from organic molecules fourfold solvated with ethanol or methanol: ET(1)·4CH3OH and ET(1)·4C2H5OH·H2O. The observed piezo-solvatochromic effects highlight the potential of ET(1) in nonlinear optoelectronics and expand the application of solvatochromic chemical indicators to pressure sensors.




omi

Benchmarking predictive methods for small-angle X-ray scattering from atomic coordinates of proteins using maximum likelihood consensus data

Stimulated by informal conversations at the XVII International Small Angle Scattering (SAS) conference (Traverse City, 2017), an international team of experts undertook a round-robin exercise to produce a large dataset from proteins under standard solution conditions. These data were used to generate consensus SAS profiles for xylose isomerase, urate oxidase, xylanase, lysozyme and ribonuclease A. Here, we apply a new protocol using maximum likelihood with a larger number of the contributed datasets to generate improved consensus profiles. We investigate the fits of these profiles to predicted profiles from atomic coordinates that incorporate different models to account for the contribution to the scattering of water molecules of hydration surrounding proteins in solution. Programs using an implicit, shell-type hydration layer generally optimize fits to experimental data with the aid of two parameters that adjust the volume of the bulk solvent excluded by the protein and the contrast of the hydration layer. For these models, we found the error-weighted residual differences between the model and the experiment generally reflected the subsidiary maxima and minima in the consensus profiles that are determined by the size of the protein plus the hydration layer. By comparison, all-atom solute and solvent molecular dynamics (MD) simulations are without the benefit of adjustable parameters and, nonetheless, they yielded at least equally good fits with residual differences that are less reflective of the structure in the consensus profile. Further, where MD simulations accounted for the precise solvent composition of the experiment, specifically the inclusion of ions, the modelled radius of gyration values were significantly closer to the experiment. The power of adjustable parameters to mask real differences between a model and the structure present in solution is demonstrated by the results for the conformationally dynamic ribonuclease A and calculations with pseudo-experimental data. This study shows that, while methods invoking an implicit hydration layer have the unequivocal advantage of speed, care is needed to understand the influence of the adjustable parameters. All-atom solute and solvent MD simulations are slower but are less susceptible to false positives, and can account for thermal fluctuations in atomic positions, and more accurately represent the water molecules of hydration that contribute to the scattering profile.




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Crystal structures of the isotypic complexes bis­(morpholine)­gold(I) chloride and bis­(morpholine)­gold(I) bromide

The compounds bis­(morpholine-κN)gold(I) chloride, [Au(C4H9NO)2]Cl, 1, and bis­(morpholine-κN)gold(I) bromide, [Au(C4H9NO)2]Br, 2, crystallize isotypically in space group C2/c with Z = 4. The gold atoms, which are axially positioned at the morpholine rings, lie on inversion centres (so that the N—Au—N coordination is exactly linear) and the halide anions on twofold axes. The residues are connected by a classical hydrogen bond N—H⋯halide and by a short gold⋯halide contact to form a layer structure parallel to the bc plane. The morpholine oxygen atom is not involved in classical hydrogen bonding.




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Crystal structure of polymeric bis­(3-amino-1H-pyrazole)­cadmium dibromide

The reaction of cadmium bromide tetra­hydrate with 3-amino­pyrazole (3-apz) in ethano­lic solution leads to tautomerization of the ligand and the formation of crystals of the title compound, catena-poly[[di­bromido­cadmium(II)]-bis­(μ-3-amino-1H-pyrazole)-κ2N3:N2;κ2N2:N3], [CdBr2(C3H5N3)2]n or [CdBr2(3-apz)2]n. Its asymmetric unit consists of a half of a Cd2+ cation, a bromide anion and a 3-apz mol­ecule. The Cd2+ cations are coordinated by two bromide anions and two 3-apz ligands, generating trans-CdN4Br2 octa­hedra, which are linked into chains by pairs of the bridging ligands. In the crystal, the ligand mol­ecules and bromide anions of neighboring chains are linked through inter­chain hydrogen bonds into a two-dimensional network. The inter­molecular contacts were qu­anti­fied using Hirshfeld surface analysis and two-dimensional fingerprint plots, revealing the relative qu­anti­tative contributions of the weak inter­molecular contacts.