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  • International Union of Crystallography
  • 2020-2022  (1,686)
  • 1950-1954  (1,180)
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  • 1
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    Resolution of a bent‐crystal spectrometer for X‐ray free‐electron laser pulses: diamond versus silicon (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-09-29
    Description: The resolution function of a spectrometer based on a strongly bent single crystal (bending radius of 10 cm or less) is evaluated. It is shown that the resolution is controlled by two parameters: (i) the ratio of the lattice spacing of the chosen reflection to the crystal thickness and (ii) a single parameter comprising crystal thickness, its bending radius, distance to a detector, and anisotropic elastic constants of the chosen crystal. The results allow the optimization of the parameters of bent‐crystal spectrometers for the hard X‐ray free‐electron laser sources.
    Description: The resolution function of a bent‐crystal spectrometer for pulses of an X‐ray free‐electron laser is evaluated. Under appropriate conditions, the energy resolution reaches the ratio of the lattice spacing to the crystal thickness. image
    Keywords: 548 ; X‐ray free‐electron lasers ; X‐ray spectroscopy ; bent crystals ; diamond crystal optics ; femtosecond X‐ray diffraction
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  • 2
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    Separation of the inelastic and elastic scattering in time‐of‐flight mode on the pinhole small‐angle neutron scattering diffractometer KWS‐2 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-09-29
    Description: To study and control the incoherent inelastic background in small‐angle neutron scattering, which makes a significant contribution to the detected scattering from hydrocarbon systems, the KWS‐2 small‐angle neutron scattering diffractometer operated by the Jülich Centre for Neutron Science (JCNS) at Heinz‐Maier Leibnitz Zentrum (MLZ), Garching, Germany, was equipped with a secondary single‐disc chopper that is placed in front of the sample stage. This makes it possible to record in time‐of‐flight mode the scattered neutrons in the high‐Q regime of the instrument (i.e. short incoming wavelengths and detection distances) and to discard the inelastic component from the measured data. Examples of measurements on different materials routinely used as standard samples, sample containers and solvents in the experiments at KWS‐2 are presented. When only the elastic region of the spectrum is used in the data‐reduction procedure, a decrease of up to two times in the incoherent background of the experimentally measured scattering cross section may be obtained. The proof of principle is demonstrated on a solution of bovine serum albumin in D2O.
    Description: A new chopper has been installed at the sample position in front of the sample stage at the KWS‐2 small‐angle neutron‐scattering diffractometer of the Jülich Centre for Neutron Science. The pulsed beam and the time‐of‐flight data acquisition enable the separation of elastic and inelastic scattering from hydrogenous samples.
    Keywords: 548 ; TOF‐SANS ; incoherent neutron scattering ; inelastic neutron scattering ; hydrocarbon systems
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  • 3
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    Czochralski growth of mixed cubic sesquioxide crystals in the ternary system Lu2O3–Sc2O3–Y2O3 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-09-29
    Description: Cubic rare‐earth sesquioxide crystals are strongly demanded host materials for high power lasers, but due to their high melting points investigations on their thermodynamics and the growth of large‐size crystals of high optical quality remain a challenge. Detailed thermal investigations of the ternary system Lu2O3–Sc2O3–Y2O3 revealing a large range of compositions with melting temperatures below 2200°C and a minimum of 2053°C for the composition (Sc0.45Y0.55)2O3 are presented. These reduced temperatures enable for the first time the growth of high optical quality mixed sesquioxide crystals with disordered structure by the conventional Czochralski method from iridium crucibles. An (Er0.07Sc0.50Y0.43)2O3 crystal is successfully grown and characterized with respect to its crystallographic properties as well as its composition, thermal conductivity and optical absorption in the 1 µm range.
    Description: The phase diagram of the ternary system Lu2O3–Sc2O3–Y2O3 is investigated and compositions with melting points below 2200°C are found. This allows for the first successful growth of the mixed cubic sesquioxide crystal (Er0.07Sc0.50Y0.43)2O3 by the Czochralski method from an iridium crucible. image
    Keywords: 548 ; crystal growth ; optical materials ; phase diagrams ; melting points ; rare earth sesquioxides
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  • 4
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    Crystal structures of human coronavirus NL63 main protease at different pH values (2021)
    International Union of Crystallography
    Details
    Publication Date: 2021-09-27
    Description: Human coronavirus NL63 (HCoV-NL63), which belongs to the genus Alphacoronavirus, mainly infects children and the immunocompromized and is responsible for a series of clinical manifestations, including cough, fever, rhinorrhoea, bronchiolitis and croup. HCoV-NL63, which was first isolated from a seven-month-old child in 2004, has led to infections worldwide and accounts for 10% of all respiratory illnesses caused by etiological agents. However, effective antivirals against HCoV-NL63 infection are currently unavailable. The HCoV-NL63 main protease (Mpro), also called 3C-like protease (3CLpro), plays a vital role in mediating viral replication and transcription by catalyzing the cleavage of replicase polyproteins (pp1a and pp1ab) into functional subunits. Moreover, Mpro is highly conserved among all coronaviruses, thus making it a prominent drug target for antiviral therapy. Here, four crystal structures of HCoV-NL63 Mpro in the apo form at different pH values are reported at resolutions of up to 1.78 Å. Comparison with Mpro from other human betacoronaviruses such as SARS-CoV-2 and SARS-CoV reveals common and distinct structural features in different genera and extends knowledge of the diversity, function and evolution of coronaviruses.
    Electronic ISSN: 2053-230X
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Physics
    Published by International Union of Crystallography
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  • 5
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    Spin-resolved charge density and wavefunction refinements using MOLLYNX: a review (2021)
    International Union of Crystallography
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    Publication Date: 2021-09-25
    Description: MOLLYNX is a new crystallographic tool developed to access a more precise description of the spin-dependent electron density of magnetic crystals, taking advantage of the richness of experimental information from high-resolution X-ray diffraction (XRD), unpolarized neutron (UND) and polarized neutron diffraction (PND). This new program is based either on the well known Hansen–Coppens multipolar model (MOLLYNX-mult) or on a new expansion over a set of atomic orbitals (MOLLYNX-orb). The main difference between the two models is the basis of the expansion: in MOLLYNX-mult the expansion is over atom centered real spherical harmonics, in MOLLYNX-orb the expansion is over a set of atomic orbitals with which mono and bicentric contributions are calculated. This new approach of MOLLYNX-orb can also be applied to nonmagnetic crystals. This paper summarizes the theoretical ground of two models and describes the first applications to organic, organometallic and inorganic magnetic materials
    Print ISSN: 2052-5192
    Electronic ISSN: 2052-5206
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by International Union of Crystallography
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  • 6
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    eSPC: an online data-analysis platform for molecular biophysics (2021)
    International Union of Crystallography
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    Publication Date: 2021-09-24
    Description: All biological processes rely on the formation of protein–ligand, protein–peptide and protein–protein complexes. Studying the affinity, kinetics and thermodynamics of binding between these pairs is critical for understanding basic cellular mechanisms. Many different technologies have been designed for probing interactions between biomolecules, each based on measuring different signals (fluorescence, heat, thermophoresis, scattering and interference, among others). Evaluation of the data from binding experiments and their fitting is an essential step towards the quantification of binding affinities. Here, user-friendly online tools to analyze biophysical data from steady-state fluorescence spectroscopy, microscale thermophoresis and differential scanning fluorimetry experiments are presented. The modules of the data-analysis platform (https://spc.embl-hamburg.de/) contain classical thermodynamic models and clear user guidelines for the determination of equilibrium dissociation constants (K d) and thermal unfolding parameters such as melting temperatures (T m).
    Electronic ISSN: 2059-7983
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by International Union of Crystallography
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  • 7
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    Structural and catalytic characterization of Blastochloris viridis and Pseudomonas aeruginosa homospermidine synthases supports the essential role of cation–π interaction (2021)
    International Union of Crystallography
    Details
    Publication Date: 2021-09-24
    Description: Polyamines influence medically relevant processes in the opportunistic pathogen Pseudomonas aeruginosa, including virulence, biofilm formation and susceptibility to antibiotics. Although homospermidine synthase (HSS) is part of the polyamine metabolism in various strains of P. aeruginosa, neither its role nor its structure has been examined so far. The reaction mechanism of the nicotinamide adenine dinucleotide (NAD+)-dependent bacterial HSS has previously been characterized based on crystal structures of Blastochloris viridis HSS (BvHSS). This study presents the crystal structure of P. aeruginosa HSS (PaHSS) in complex with its substrate putrescine. A high structural similarity between PaHSS and BvHSS with conservation of the catalytically relevant residues is demonstrated, qualifying BvHSS as a model for mechanistic studies of PaHSS. Following this strategy, crystal structures of single-residue variants of BvHSS are presented together with activity assays of PaHSS, BvHSS and BvHSS variants. For efficient homospermidine production, acidic residues are required at the entrance to the binding pocket (`ionic slide') and near the active site (`inner amino site') to attract and bind the substrate putrescine via salt bridges. The tryptophan residue at the active site stabilizes cationic reaction components by cation–π interaction, as inferred from the interaction geometry between putrescine and the indole ring plane. Exchange of this tryptophan for other amino acids suggests a distinct catalytic requirement for an aromatic interaction partner with a highly negative electrostatic potential. These findings substantiate the structural and mechanistic knowledge on bacterial HSS, a potential target for antibiotic design.
    Electronic ISSN: 2059-7983
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by International Union of Crystallography
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  • 8
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    Crystal structure, Hirshfeld surface analysis and density functional theory study of 1-nonyl-3-phenylquinoxalin-2-one (2021)
    International Union of Crystallography
    Details
    Publication Date: 2021-09-24
    Description: In the title molecule, C23H28N2O, the phenyl ring is inclined to the quinoxaline ring system at a dihedral angle of 20.40 (9)°. In the crystal, C—H...O interactions between neighbouring molecules form chains along the a-axis direction. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H...H (70.6%), H...C/C...H (15.5%) and H...O/O...H (4.6%) interactions. The optimized structure calculated using density functional theory at the B3LYP/6–311 G(d,p) level is compared with the experimentally determined structure in the solid state. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy gap is 3.8904 eV. Part of the n-nonyl chain attached to one of the nitrogen atoms of the quinoxaline ring system shows disorder and was refined with a double conformation with occupancies of 0.604 (11) and 0.396 (11).
    Electronic ISSN: 2056-9890
    Topics: Chemistry and Pharmacology , Geosciences
    Published by International Union of Crystallography
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  • 9
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    Synthesis, spectroscopic characterization, structural studies, thermal analysis and molecular docking of N-(2-methyl-5-nitrophenyl)-4-(pyridin-2-yl)pyrimidin-2-amine, a precursor for drug design against chronic myeloid leukemia (2021)
    International Union of Crystallography
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    Publication Date: 2021-09-23
    Description: The synthesis, crystal structure and spectroscopic and electronic properties of N-(2-methyl-5-nitrophenyl)-4-(pyridin-2-yl)pyrimidin-2-amine (NPPA), C16H13N5O2, a potential template for drug design against chronic myelogenous leukemia (CML), is reported. The design and construction of the target molecule were carried out starting from the guanidinium nitrate salt (previously synthesized) and the corresponding enaminone. X-ray diffraction analysis and a study of the Hirshfeld surfaces revealed important interactions between the nitro-group O atoms and the H atoms of the pyridine and pyrimidine rings. A crystalline ordering in layers, by the stacking of rings through interactions of the π–π type, was observed and confirmed by a study of the shape-index surfaces and dispersion energy calculations. Quantitative electrostatic potential studies revealed the most positive value of the molecule on regions close to the N—H groups (34.8 kcal mol−1); nevertheless, steric impediments and the planarity of the molecule do not allow the formation of hydrogen bonds from this group. This interaction is however activated when the molecule takes on a new extended conformation in the active pocket of the enzyme kinase (PDB ID 2hyy), interacting with protein residues that are fundamental in the inhibition process of CML. The most negative values of the molecule are seen in regions close to the nitro group (−35.4 and −34.0 kcal mol−1). A molecular docking study revealed an energy affinity of ΔG = −10.3 kcal mol−1 for NPPA which, despite not having a more negative value than the control molecule (Imatinib; ΔG = −12.8 kcal mol−1), shows great potential to be used as a template for new drugs against CML.
    Electronic ISSN: 2053-2296
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by International Union of Crystallography
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  • 10
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    Self-assembling of three rare structurally various homomultinuclear CuII complexes derived from a bis(salamo)-based multioxime ligand (2021)
    International Union of Crystallography
    Details
    Publication Date: 2021-09-23
    Description: A family of rare structurally different homometal multinuclear CuII bis(salamo)-based complexes, [Cu4(L)2(MeOH)2](ClO4)2·2MeOH (1), [Cu4(L)2(EtOH)2](NO3)2·2EtOH (2) and [Cu2(HL)(EtOH)Br2]·CHCl3 (3), has been successfully synthesized by the reactions of cupric salts with a bis(salamo)-based multidentate chelate ligand (H3 L). The salamo-based ligand [R-CH=N—O—(CH2) n —O—N=CH—R] is a new type of salen-based analog. Complexes (1) and (2) are isostructural structures, and crystallize in monoclinic space group P21/n with centrosymmetric spiral structures, where the main structures contain two fully deprotonated ligand (L)3− units, a charged tetranuclear CuII folding center and two coordinated solvent molecules. Complex (3) crystallizes in monoclinic space group Cc and consists of two CuII cations, one incompletely deprotonated ligand (HL)2− unit and one coordinated ethanol molecule, and forms a novel homo-binuclear CuII complex structure due to Br− counter anions. Complexes (1)–(3) have zero-dimensional cluster-based structures and are further assembled into three-dimensional frameworks via intermolecular interactions. Because of the different solvents and counter anions which have a significant influence on the structures of complexes (1)–(3), the interactions were quantitatively evaluated by Hirshfeld surfaces analyses. Complexes (1)–(3) have been characterized by elemental analyses, IR spectra, UV–vis spectra and X-ray crystallography analyses. In addition, fluorescence properties are evaluated and DFT calculations are performed.
    Print ISSN: 2052-5192
    Electronic ISSN: 2052-5206
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by International Union of Crystallography
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