Extending the novel |ρ|-based phasing algorithm to the solution of anomalous scattering substructures from SAD data of protein crystals.

Owing to the importance of the single-wavelength anomalous diffraction (SAD) technique, the recently developed |ρ|-based phasing algorithm (SM,|ρ|) incorporating the inner-pixel preservation (ipp) procedure [Rius & Torrelles (2021). Acta Cryst A77, 339-347] has been adapted to the determination of anomalous scattering substructures and its applicability tested on a series of 12 representative experimental data sets, mostly retrieved from the Protein Data Bank. To give an idea of the suitability of the data sets, the main indicators measuring their quality are also given. The dominant anomalous scatterers are either SeMet or S atoms, or metals/clusters incorporated by soaking. The resulting SAD-adapted algorithm solves the substructures of the test protein crystals quite efficiently.

Clinical Debriefing in Cardiology Teams: A National Survey in Spain.

BACKGROUND: Clinical debriefing (CD) improves patient safety and builds team resilience. PURPOSE: We describe the current use of CD by multiprofessional Spanish cardiology team members. METHODS: A self-administered survey exploring 31 items was disseminated online in October 2020. A comparison was made between respondents that who experience in CD with inexperienced respondents. Inferential analysis was done using Pearson's χ 2 test. RESULTS: Out of 167 valid responses, 45.5% had been completed by cardiology nurses. One-third of the respondents had experience in CD. Most common situations preceding CD were those with negative outcomes (81.8%). Time constraint was the most commonly reported barrier (76.3%); however, it was significantly less than the expectation of inexperienced respondents (92%, P < .01). Overall, only 28.2% reported self-confidence in their skills to lead a CD. CONCLUSIONS: There is a necessity in Spanish cardiology teams to receive training in CD and embed it in their daily practice.

A new density-modification procedure extending the application of the recent |ρ|-based phasing algorithm to larger crystal structures.

The incorporation of the new peakness-enhancing fast Fourier transform compatible ipp procedure (ipp = inner-pixel preservation) into the recently published SM algorithm based on |ρ| [Rius (2020). Acta Cryst A76, 489-493] improves its phasing efficiency for larger crystal structures with atomic resolution data. Its effectiveness is clearly demonstrated via a collection of test crystal structures (taken from the Protein Data Bank) either starting from random phase values or by using the randomly shifted modulus function (a Patterson-type synthesis) as initial ρ estimate. It has been found that in the presence of medium scatterers (e.g. S or Cl atoms) crystal structures with 1500 × c atoms in the unit cell (c = number of centerings) can be routinely solved. In the presence of strong scatterers like Fe, Cu or Zn atoms this number increases to around 5000 × c atoms. The implementation of this strengthened SM algorithm is simple, since it only includes a few easy-to-adjust parameters.

Long-term effects of coronavirus disease 2019 on the cardiovascular system, CV COVID registry: A structured summary of a study protocol.

BACKGROUND: Patients presenting with the coronavirus-2019 disease (COVID-19) may have a high risk of cardiovascular adverse events, including death from cardiovascular causes. The long-term cardiovascular outcomes of these patients are entirely unknown. We aim to perform a registry of patients who have undergone a diagnostic nasopharyngeal swab for SARS-CoV-2 and to determine their long-term cardiovascular outcomes. STUDY AND DESIGN: This is a multicenter, observational, retrospective registry to be conducted at 17 centers in Spain and Italy (ClinicalTrials.gov number: NCT04359927). Consecutive patients older than 18 years, who underwent a real-time reverse transcriptase-polymerase chain reaction (RT-PCR) for SARS-CoV2 in the participating institutions, will be included since March 2020, to August 2020. Patients will be classified into two groups, according to the results of the RT-PCR: COVID-19 positive or negative. The primary outcome will be cardiovascular mortality at 1 year. The secondary outcomes will be acute myocardial infarction, stroke, heart failure hospitalization, pulmonary embolism, and serious cardiac arrhythmias, at 1 year. Outcomes will be compared between the two groups. Events will be adjudicated by an independent clinical event committee. CONCLUSION: The results of this registry will contribute to a better understanding of the long-term cardiovascular implications of the COVID19.

Impact of simulation-based teamwork training on COVID-19 distress in healthcare professionals.

CONTEXT: Non-technical skills such as leadership, communication, or situation awareness should lead to effective teamwork in a crisis. This study aimed to analyse the role of these skills in the emotional response of health professionals to the COVID-19 pandemic. METHODS: Before the COVID-19 outbreak, 48 doctors and 48 nurses participated in a simulation-based teamwork training program based on teaching non-technical skills through simulation. In May 2020, this group of professionals from a COVID-19 referral hospital was invited to participate in a survey exploring stress, anxiety, and depression, using the PSS-14 (Perceived Stress Scale) and the HADS (Hospital Anxiety and Depression Scale) measures. A control group that did not receive the training was included. We conducted a logistic regression to assess whether having attended a simulation-based teamwork training program modified the probability of presenting psychological distress (PSS-14 > 18 or HADS> 12). RESULTS: A total of 141 healthcare professionals were included, 77 in the intervention group and 64 in the control group. Based on the PSS-14, 70.1% of the intervention group and 75% of the control group (p = 0.342) had symptoms of stress. Having contact with COVID-19 patients [OR 4.16(1.64-10.52)]; having minors in charge [OR 2.75 (1.15-6.53)]; working as a doctor [0.39(0.16-0.95)], and being a woman [OR 2.94(1.09-7.91)] were related with PSS14 symptoms. Based on the HADS, 54.6% of the intervention group and 42.2% of the control group (p = 0.346) had symptoms of anxiety or depression. Having contact with COVID-19 patients [OR 2.17(1.05-4.48)] and having minors in charge [OR 2.14(1.06-4.32)] were related to HADS symptoms. Healthcare professionals who attended COVID-19 patients showed higher levels of anxiety and depression [OR 2.56(1.03-6.36) (p = 0.043)]. CONCLUSION: Healthcare professionals trained in non-technical skills through simulation tended towards higher levels of anxiety and depression and fewer levels of stress, during the COVID-19 pandemic.

Novel phasing method using the origin-free modulus sum function expressed in terms of the absolute electron density.

The origin-free modulus sum function SM refines the set Φ of phases of the structure factors by maximizing the coincidence between the experimental origin-free modulus function and the calculated one in terms of the ρ(Φ)2 density function [Rius, J. (1993). Acta Cryst. A49, 406-409]. Maximization is normally achieved through the recursive application of a Fourier-based algorithm. The purpose of the present study is: (i) to show that ρ(Φ)2 can be replaced by |ρ(Φ)| in SM; (ii) to illustrate the viability of the corresponding phasing algorithm with experimental data.

Ag2Cu3Cr2O8(OH)4: a new bidimensional silver-copper mixed-oxyhydroxide with in-plane ferromagnetic coupling.

Ag2Cu3Cr2O8(OH)4, a new Ag-Cu-Cr-O layered mixed oxide, prepared by soft hydrothermal heterogeneous reactions, is reported. The new phase is an oxyhydroxide and presents a structure with alternating brucite-like Cu-O and Ag-O layers connected by individual chromate groups. The crystallographic structure has been solved and refined from high resolution powder X-ray diffraction data and is supported by density functional theory calculations, yielding a triclinic, space group P1[combining macron], a = 5.3329(1) Å, b = 5.3871(1) Å, c = 10.0735(1) Å, α = 80.476(1)°, ß = 87.020(1)°, γ = 62.383(1)°. Bond valence sums suggest the formulation of Ag+2Cu2+3Cr6+2O8(OH)4, an electronic state fully supported by X-ray photoelectron spectroscopy (XPS) and Cr K-edge X-ray absorption near edge structure (XANES) measurements. Ag2Cu3Cr2O8(OH)4 exhibits bidimensional Cu-O-Cu ferromagnetic correlations that are apparent at much higher temperatures than in other similar Cu-O layered structures, without coupling between Cu-O layers, which represents a unique case in the recent family of silver copper oxides. The role of Ag inducing bidimensionality in copper oxides is therefore expanded further with the presence of chromate anions. Ab initio calculations using density functional theory show that the electronic states involved originate mainly from Cu and OH orbitals, with minor contributions from Cr and the O atoms linking the Cr tetrahedra to the brucitic Cu-O layer, and almost no contribution from Ag. Further modeling of the in-plane magnetic interactions between Cu atoms suggests that the coupled magnetized stripes are responsible for the observed behavior. The results are discussed in relation with previous Ag-Cu mixed oxide phases where metallic behavior or ferro-antiferro transitions had been observed. The structure of this new Ag-Cu-O phase as compared with previous silver copper oxides supports the conclusion that the Ag-Cu layered ordering is favored under oxidizing conditions.

Application of synchrotron through-the-substrate microdiffraction to crystals in polished thin sections.

The synchrotron through-the-substrate X-ray microdiffraction technique (tts-µXRD) is extended to the structural study of microvolumes of crystals embedded in polished thin sections of compact materials [Rius, Labrador, Crespi, Frontera, Vallcorba & Melgarejo (2011 ▸). J.Synchrotron Rad. 18, 891-898]. The resulting tts-µXRD procedure includes some basic steps: (i) collection of a limited number of consecutive two-dimensional patterns (frames) for each randomly oriented crystal microvolume; (ii) refinement of the metric from the one-dimensional diffraction pattern which results from circularly averaging the sum of collected frames; (iii) determination of the reciprocal lattice orientation of each randomly oriented crystal microvolume which allows assigning the hkl indices to the spots and, consequently, merging the intensities of the different frames into a single-crystal data set (frame merging); and (iv) merging of the individual crystal data sets (multicrystal merging) to produce an extended data set suitable for structure refinement/solution. Its viability for crystal structure solution by Patterson function direct methods (δ recycling) and for accurate single-crystal least-squares refinements is demonstrated with some representative examples from petrology in which different glass substrate thicknesses have been employed. The section of the crystal microvolume must be at least of the same order of magnitude as the focus of the beam (15 × 15 µm in the provided examples). Thanks to its versatility and experimental simplicity, this method-ology should be useful for disciplines as disparate as petrology, materials science and cultural heritage.

Application of Patterson-function direct methods to materials characterization.

The aim of this article is a general description of the so-called Patterson-function direct methods (PFDM), from their origin to their present state. It covers a 20-year period of methodological contributions to crystal structure solution, most of them published in Acta Crystallographica Section A. The common feature of these variants of direct methods is the introduction of the experimental intensities in the form of the Fourier coefficients of origin-free Patterson-type functions, which allows the active use of both strong and weak reflections. The different optimization algorithms are discussed and their performances compared. This review focuses not only on those PFDM applications related to powder diffraction data but also on some recent results obtained with electron diffraction tomography data.

Anion-π and halide-halide nonbonding interactions in a new ionic liquid based on imidazolium cation with three-dimensional magnetic ordering in the solid state.

We present the first magnetic phase of an ionic liquid with anion-π interactions, which displays a three-dimensional (3D) magnetic ordering below the Néel temperature, TN = 7.7 K. In this material, called Dimim[FeBr4], an exhaustive and systematic study involving structural and physical characterization (synchrotron X-ray, neutron powder diffraction, direct current and alternating current magnetic susceptibility, magnetization, heat capacity, Raman and Mössbauer measurements) as well as first-principles analysis (density functional theory (DFT) simulation) was performed. The crystal structure, solved by Patterson-function direct methods, reveals a monoclinic phase (P21 symmetry) at room temperature with a = 6.745(3) Å, b = 14.364(3) Å, c = 6.759(3) Å, and ß = 90.80(2)°. Its framework, projected along the b direction, is characterized by layers of cations [Dimim](+) and anions [FeBr4](-) that change the orientation from layer to layer, with Fe···Fe distances larger than 6.7 Å. Magnetization measurements show the presence of 3D antiferromagnetic ordering below TN with the existence of a noticeable magneto-crystalline anisotropy. From low-temperature neutron diffraction data, it can be observed that the existence of antiferromagnetic order is originated by the antiparallel ordering of ferromagnetic layers of [FeBr4](-) metal complex along the b direction. The magnetic unit cell is the same as the chemical one, and the magnetic moments are aligned along the c direction. The DFT calculations reflect the fact that the spin density of the iron ions spreads over the bromine atoms. In addition, the projected density of states (PDOS) of the imidazolium with the bromines of a [FeBr4](-) metal complex confirms the existence of the anion-π interaction. Magneto-structural correlations give no evidence for direct iron-iron interactions, corroborating that the 3D magnetic ordering takes place via superexchange coupling, the Fe-Br···Br-Fe interplane interaction being defined as the main exchange pathway.

Charge transfer states in stable neutral and oxidized radical adducts from carbazole derivatives.

In this paper we report the spectral properties of the stable radical adducts 1(•)-3(•), which are formed by an electron donor moiety, the carbazole ring, and an electron acceptor moiety, the polychlorotriphenylmethyl radical. The molecular structure of radical adduct 1(•) in the crystalline state shows a torsion angle of approximately 90° between the phenyl and the carbazole rings due to steric interactions. They exhibit a charge transfer band in the visible range of the electronic spectrum. All of them are chemically oxidized with copper(II) perchlorate to the respective cation species, which show a strong charge transfer band into the near-infrared region of the spectrum. Radical adducts 1(•)-3(•) and the corresponding stable oxidized species 1(+)-3(+) are real organic mixed-valence compounds due to the open-shell nature of their electronic structure. Charge transfer bands of the cation species are stronger and are bathochromically shifted with respect to those of the neutral species due to the greater acceptor ability of the positively charged central carbon atom of the triphenylmethyl moiety. The cationic species 1(+)-3(+) are diamagnetic, as shown by the absence of a signal in the EPR spectrum in acetonitrile solution at room temperature, but they show an intense and unique band in frozen solutions (183 K).

A magnetic ionic liquid based on tetrachloroferrate exhibits three-dimensional magnetic ordering: a combined experimental and theoretical study of the magnetic interaction mechanism.

A new magnetic ionic liquid (MIL) with 3D antiferromagnetic ordering has been synthetized and characterized. The information obtained from magnetic characterization was supplemented by analysis of DFT calculations and the magneto-structural correlations. The result gives no evidence for direct iron-iron interactions, corroborating that the 3D magnetic ordering in MILs takes place via super-exchange coupling containing two diamagnetic atoms intermediaries.

Application of δ recycling to electron automated diffraction tomography data from inorganic crystalline nanovolumes.

δ Recycling is a simple procedure for directly extracting phase information from Patterson-type functions [Rius (2012). Acta Cryst. A68, 399-400]. This new phasing method has a clear theoretical basis and was developed with ideal single-crystal X-ray diffraction data. On the other hand, introduction of the automated diffraction tomography (ADT) technique has represented a significant advance in electron diffraction data collection [Kolb et al. (2007). Ultramicroscopy, 107, 507-513]. When combined with precession electron diffraction, it delivers quasi-kinematical intensity data even for complex inorganic compounds, so that single-crystal diffraction data of nanometric volumes are now available for structure determination by direct methods. To check the tolerance of δ recycling to missing data-collection corrections and to deviations from kinematical behaviour of ADT intensities, δ recycling has been applied to differently shaped nanocrystals of various inorganic materials. The results confirm that it can phase ADT data very efficiently. In some cases even more complete structure models than those derived from conventional direct methods and least-squares refinement have been found. During this study it has been demonstrated that the Wilson-plot scaling procedure is largely insensitive to sample thickness variations and missing absorption corrections affecting electron ADT intensities.

High proton conductivity in a flexible, cross-linked, ultramicroporous magnesium tetraphosphonate hybrid framework.

Multifunctional materials, especially those combining two or more properties of interest, are attracting immense attention due to their potential applications. MOFs, metal organic frameworks, can be regarded as multifunctional materials if they show another useful property in addition to the adsorption behavior. Here, we report a new multifunctional light hybrid, MgH(6)ODTMP·2H(2)O(DMF)(0.5) (1), which has been synthesized using the tetraphosphonic acid H(8)ODTMP, octamethylenediamine-N,N,N',N'-tetrakis(methylenephosphonic acid), by high-throughput methodology. Its crystal structure, solved by Patterson-function direct methods from synchrotron powder X-ray diffraction, was characterized by a 3D pillared open framework containing cross-linked 1D channels filled with water and DMF. Upon H(2)O and DMF removal and subsequent rehydration, MgH(6)ODTMP·2H(2)O (2) and MgH(6)ODTMP·6H(2)O (3) can be formed. These processes take place through crystalline-quasi-amorphous-crystalline transformations, during which the integrity of the framework is maintained. A water adsorption study, at constant temperature, showed that this magnesium tetraphosphonate hybrid reversibly equilibrates its lattice water content as a function of the water partial pressure. Combination of the structural study and gas adsorption characterization (N(2), CO(2), and CH(4)) indicates an ultramicroporous framework. High-pressure CO(2) adsorption data are also reported. Finally, impedance data indicates that 3 has high proton conductivity σ = 1.6 × 10(-3) S cm(-1) at T = 292 K at ~100% relative humidity with an activation energy of 0.31 eV.

A new partially deprotonated mixed-valence manganese(II,III) hydroxide-arsenate with electronic conductivity: magnetic properties of high- and room-temperature sarkinite.

A new three-dimensional hydroxide-arsenate compound called compound 2 has been synthesized by heating (in air) of the sarkinite phase, Mn(2)(OH)AsO(4) (compound 1), with temperature and time control. The crystal structure of this high-temperature compound has been solved by Patterson-function direct methods. A relevant feature of this new material is that it is actually the first member of the adamite-type family with mixed-valence manganese(II,III) and electronic conductivity. Crystal data: a = 6.7367(5) Å, b = 7.5220(6) Å, c = 9.8117(6) Å, α = 92.410(4)°, ß = 109.840(4)°, γ = 115.946(4)°, P1̅. The unit cell content derived from Rietveld refinement is Mn(8)(O(4)H(x))(AsO(4))(4). Its framework, projected along [111], is characterized by rings of eight Mn atoms with the OH(-)/O(2-) inside the rings. These rings form an almost perfect hexagonal arrangement with the AsO(4) groups placed in between. Bond-valence analysis indicates both partial deprotonation (x ≅ 3) and the presence of Mn in two different oxidation states (II and III), which is consistent with the electronic conductivity above 300 °C from electrochemical measurements. The electron paramagnetic resonance spectra of compound 1 and of its high-temperature form compound 2 show the presence of antiferromagnetic interactions with stronger magnetic coupling for the high-temperature phase. Magnetization measurements of room-temperature compound 1 show a complex magnetic behavior, with a three-dimensional antiferromagnetic ordering and magnetic anomalies at low temperatures, whereas for compound 2, an ordered state is not reached. Magnetostructural correlations indicate that superexchange interactions via oxygen are present in both compounds. The values of the magnetic exchange pathways [Mn-O-Mn] are characteristic of antiferromagnetic couplings. Notwithstanding, the existence of competition between different magnetic interactions through superexchange pathways can cause the complex magnetic behavior of compound 1. The loss of three-dimensional magnetic ordering by heating of compound 1 could well be based on the presence of Mn(3+) ions (d(4)) in compound 2.

Patterson function and δ recycling: derivation of the phasing equations.

Two phasing equations based on the Fourier syntheses δ(P) = T(-1)[(E(2) - )exp(iφ)] and δ(M) = T(-1)[(E - )exp(iφ)] were recently described [Rius (2012). Acta Cryst. A 68, 77-81] (E is the quasi-normalized structure factor and is the average over all reflections). These equations were found by comparison with the direct methods origin-free modulus sum function and constitute the core of the `δ recycling' phasing procedure. The derivation of these phasing equations from the minimization of a residual (R(P)) between two differently calculated density functions (one of them including the positivity constraint) is shown.

Direct phasing from Patterson syntheses by δ recycling.

The direct methods origin-free modulus sum function [Rius (1993). Acta Cryst. A49, 406-409] includes in its definition the structure factor G(Φ) of the squared crystal structure expressed in terms of Φ, the set of φ phases of the normalized structure factors E's of the crystal structure of unit-cell volume V. Here the simpler sum function variant S'(P) = ∑(H)E(-H)∫(V)δ(P,Δ)(Φ)exp(i2πHr)dV extended over all H reflections is introduced which involves no G's and in which the δ(P,Δ) function corresponds to δ(P) = FT(-1){(E(2)(H) - )exp[iφ(H)(Φ)]} (where FT = Fourier transform) with all values smaller than Δ = 2.5σ(P) equated to zero (σ(2)(P) is the variance of δ(P) calculable from the experimental intensities). The new phase estimates are obtained by Fourier transforming δ(P,Δ). This iterative phasing method (δ recycling) only requires calculation of Fourier transforms at two stages. Since δ(M) ≃ δ(P)/2, similar arguments are valid for δ(M) = FT(-1)[(E(H) - )exp(iφ(H))] from which the corresponding S'(M) phasing function follows.

(Z)-3-Methyl-N-(7-nitroacridin-3-yl)-2,3-dihydro-1,3-benzothiazol-2-imine from laboratory powder diffraction data.

The title compound, C(21)H(14)N(4)O(2)S, belongs to a family of molecules possessing nonlinear optical properties in solution. Its structure has been solved from laboratory X-ray powder diffraction data using a new direct-space structure solution method, where the atomic coordinates are directly used as parameters and the molecular geometry is described by restraints. The molecular packing is controlled by two systems of π-π interactions and one weak edge-to-face interaction.

Capabilities of through-the-substrate microdiffraction: application of Patterson-function direct methods to synchrotron data from polished thin sections.

Some theoretical and practical aspects of the application of transmission microdiffraction (µXRD) to thin sections (≤30 µm thickness) of samples fixed or deposited on substrates are discussed. The principal characteristic of this technique is that the analysed micro-sized region of the thin section is illuminated through the substrate (tts-µXRD). Fields that can benefit from this are mineralogy, petrology and materials sciences since they often require in situ lateral studies to follow the evolution of crystalline phases or to determine new crystal structures in the case of phase transitions. The capability of tts-µXRD for performing structural studies with synchrotron radiation is shown by two examples. The first example is a test case in which tts-µXRD intensity data of pure aerinite are processed using Patterson-function direct methods to directly solve the crystal structure. In the second example, tts-µXRD is used to study the transformation of laumonite into a new aluminosilicate for which a crystal structure model is proposed.