Unravelling strong temperature-dependence of JHD in transition metal hydrides: solvation and non-covalent interactions versus temperature-elastic H-H bonds.

A number of transition metal hydrides reveal intriguing temperature-dependent JHD in their deuterated derivatives and possibly the temperature dependent hydrogen-hydrogen distance (r(H-H)) as well. Previously, theoretical studies rationalized JHD and r(H-H) changes in such compounds through a "temperature-elastic" structure model with a significant population of vibrational states in an anharmonic potential. Based on the first variable temperature neutron diffraction study of a relevant complex, (p-H-POCOP)IrH2, observation of its elusive counterpart with longer r(H-H), crystallized as an adduct with C6F5I, and thorough spectroscopic and computational study, we argue that the model involving isomeric species in solution at least in some cases is more relevant. The existence of such isomers is enabled or enhanced by solvation and weak non-covalent interactions with solvent, such as halogen or dihydrogen bonds. "Non-classical" hydrides with r(H-H) ≈ 1.0-1.6 Å are especially sensitive to the above-mentioned factors.

The spontaneous self-assembly of a molecular water pipe in 3D space.

The self-assembly and self-organization of water molecules are relevant in many fields of research. When water spontaneously reacts with 2,2,6,6-tetra-methyl-piperidine (TMP) to form colourless and crystalline discrete needles, only in the exact ratio of 2:1, it is important to understand the phenomenon. Single-crystal X-ray and neutron diffraction data have unveiled that TMP self-assembles around columns of water molecules, and as such, the resulting adduct may be described as a series of molecular water pipes.

Thermal neutron cross sections of amino acids from average contributions of functional groups.

The experimental thermal neutron cross sections of the 20 proteinogenic amino acids have been measured over the incident-neutron energy range spanning from 1 meV to 10 keV and data have been interpreted using the multi-phonon expansion based on first-principles calculations. The scattering cross section, dominated by the incoherent inelastic contribution from the hydrogen atoms, can be rationalised in terms of the average contributions of different functional groups, thus neglecting their correlation. These results can be used for modelling the total neutron cross sections of complex organic systems like proteins, muscles, or human tissues from a limited number of starting input functions. This simplification is of crucial importance for fine-tuning of transport simulations used in medical applications, including boron neutron capture therapy as well as secondary neutrons-emission induced during proton therapy. Moreover, the parametrized neutron cross sections allow a better treatment of neutron scattering experiments, providing detailed sample self-attenuation corrections for a variety of biological and soft-matter systems.

Nutritional Risk Screening and Body Composition in COVID-19 Patients Hospitalized in an Internal Medicine Ward.

BACKGROUND: Malnutrition in patients hospitalized in internal medicine wards is highly prevalent and represents a prognostic factor of worse outcomes. Previous evidence suggested the prognostic role of the nutritional status in patients affected by the coronavirus disease 2019 (COVID-19). We aim to investigate the nutritional risk in patients with COVID-19 hospitalized in an internal medicine ward and their clinical outcomes using the Nutritional Risk Screening 2002 (NRS-2002) and parameters derived from bioelectrical impedance analysis (BIA). METHODS: Retrospective analysis of patients with COVID-19 aimed at exploring: 1) the prevalence of nutritional risk with NRS-2002 and BIA; 2) the relationship between NRS-2002, BIA parameters and selected outcomes: length of hospital stay (LOS); death and need of intensive care unit (ICU); prolonged LOS; and loss of appetite. RESULTS: Data of 90 patients were analyzed. Patients at nutritional risk were 92% with NRS-2002, with BIA-derived parameters: 88% by phase angle; 86% by body cell mass; 84% by fat-free mass and 84% by fat mass (p-value ≤0.001). In ROC analysis, NRS had the maximum sensitivity in predicting the risk of death and need of ICU and a prolonged hospitalization showing moderate-low specificity; phase angle showed a good predictive power in terms of AUC. NRS-2002 was significantly associated with LOS (ß 12.62, SE 5.79). In a multivariate analysis, blood glucose level and the early warning score are independent predictors of death and need of ICU (OR 2.79, p ≤0.001; 1.59, p-0.029, respectively). CONCLUSION: Present findings confirm the clinical utility of NRS-2002 to assess nutritional risk in patients with COVID-19 at hospital admission and in predicting LOS, and that bioimpedance does not seem to add further predictive value. An early detection of nutritional risk has to be systematically included in the management of COVID-19 patients hospitalized in internal medicine wards.

X-ray diffraction data as a source of the vibrational free-energy contribution in polymorphic systems.

In this contribution we attempt to answer a general question: can X-ray diffraction data combined with theoretical computations be a source of information about the thermodynamic properties of a given system? Newly collected sets of high-quality multi-temperature single-crystal X-ray diffraction data and complementary periodic DFT calculations of vibrational frequencies and normal mode vectors at the Γ point on the yellow and white polymorphs of di-methyl 3,6-di-chloro-2,5-di-hydroxy-terephthalate are combined using two different approaches, aiming to obtain thermodynamic properties for the two compounds. The first approach uses low-frequency normal modes extracted from multi-temperature X-ray diffraction data (normal coordinate analysis), while the other uses DFT-calculated low-frequency normal mode in the refinement of the same data (normal mode refinement). Thermodynamic data from the literature [Yang et al. (1989), Acta Cryst. B45, 312-323] and new periodic ab initio DFT supercell calculations are used as a reference point. Both approaches tested in this work capture the most essential features of the systems: the polymorphs are enantiotropically related, with the yellow form being the thermodynamically stable system at low temperature, and the white form at higher temperatures. However, the inferred phase transition temperature varies between different approaches. Thanks to the application of unconventional methods of X-ray data refinement and analysis, it was additionally found that, in the case of the yellow polymorph, anharmonicity is an important issue. By discussing contributions from low- and high-frequency modes to the vibrational entropy and enthalpy, the importance of high-frequency modes is highlighted. The analysis shows that larger anisotropic displacement parameters are not always related to the polymorph with the higher vibrational entropy contribution.

Autosomal dominant hypocalcemia due to a truncation in the C-tail of the calcium-sensing receptor.

Autosomal Dominant Hypocalcemia (ADH) is an endocrine disorder due to activating mutations of the calcium-sensing receptor (CASR) gene. We report on a young boy who presented low serum calcium with hypercalciuria, hyperphosphatemia and low serum concentration of parathyroid hormone, not accompanied by classic clinical signs of hypocalcemia. Treatment with calcitriol and calcium did not normalize serum calcium and renal calcium excretion. The use of thiazide diuretics slightly reduced calciuria. Despite high calcium excretion, no signs of nephrocalcinosis were detected. The patient had a prolonged Q-T interval at ECG, which did not normalize during treatment. PCR amplification of CASR coding sequence and direct sequencing of PCR products. showed a novel heterozygous deletion of a cytosine (c.2682delC), responsible for a frameshift (p.S895Pfs*44) and a premature stop codon resulting in a truncation of the CaSR's C-tail. Functional studies indicated increased activity of mutant receptor compared to the wild-type.

Poor early growth and high salt intake in Indian infants.

The influence of feeding patterns on the growth of infants and how salt is included in the diet are unknown in the area of West Bengal, India. A cross-sectional study was carried on 517 infants (median age 6.5 months). Negative Z-scores were observed for all anthropometric parameters. About 72.7% of infants aged 0-6 months received exclusive breastfeeding. In the 6-12-month-old group (n = 235), 91.5% had salt added to foods. In a regression model adjusted for age, a low salt diet resulted a significant factor in increasing weight-for-length and BMI for age z-scores, with increments equal to 0.637 SD (p = 0.037) and 0.650 SD (p = 0.036), respectively. In West Bengal infants showing poor growth, breastfeeding was associated with better anthropometric indexes, but early in life salt is added to their diet. Early life low weight coupled with high salt intake may be a risk factor for arterial hypertension in Indian children.

Clinical and molecular heterogeneity in a large series of patients with hypophosphatemic rickets.

CONTEXT: Hypophosphatemic rickets (HR) is a rare disease that includes a group of hereditary and sporadic conditions characterized by renal phosphate loss associated with normal to low vitamin D serum concentration. The most common form is the X-linked hypophosphatemic rickets, with an incidence of 1:20,000. Several mutations have recently been identified in the PHEX, FGF23, DMP1 and ENPP1 genes in patients with HR. Moreover, in vitro and in vivo studies suggested an involvement of MEPE for defective mineralization in HR. OBJECTIVE: The present case series describes the clinical features and the analysis of genes implicated in HR in a cohort of 26 Italian HR patients. SETTING AND DESIGN: All patients were analyzed for the PHEX and FGF23 genes by direct sequencing. When no mutations were detected, Multiplex Ligation-dependent Probe Amplification (MLPA) analysis was performed. The negative patients were screened for the DMP1, MEPE and ENPP1 genes by direct sequencing. RESULTS: Twenty-two patients (84%) harbored mutations in the PHEX gene. In particular, we detected 19 different mutations, 15 of which were novel. One patient presented a novel splice variation in the ENPP1 gene while no alterations were identified in the FGF23, DMP1 and MEPE genes. The genetic study of the families showed that 11 patients (55%) had de novo mutations. Clinical presentation and disease severity did not show an evident correlation between the mutation types. CONCLUSIONS: This report represents the first large familial study performed on Italian patients. It confirms that mutations in PHEX are the most frequent cause of HR. Furthermore, the variety of clinical manifestations identified in our HR patients underlines the extreme clinical and genetic heterogeneity of this disease.

Sclerostin and DKK-1: two important regulators of bone metabolism in HIV-infected youths.

Reduced bone mineral density (BMD) and altered bone metabolism are common findings in HIV-infected patients. Increased bone formation has been described both in HIV-infected adults and children. Wnt ligands promote bone formation by stimulating osteoblast differentiation and their survival. Sclerostin and dickkopf factor 1 (DKK-1), Wnt antagonists, are important negative regulators of bone formation. We studied 86 HIV-infected patients whose ages ranged from 5.7 to 27.9 years. Patients were all on antiretroviral therapy, but seven who were naïve to treatment. Bone alkaline phosphatase (BAP), sclerostin, and DKK-1 were measured in serum by enzyme immunoassay. BMD was measured by dual-energy X-ray absorptiometry at the lumbar spine and in the whole skeleton. Biochemical indexes were also measured in 143 healthy controls (age range 4.5-27.4 years). HIV-infected patients had lower than normal BMD (spine P < 0.005, and whole skeleton P < 0.03). BAP measurements were significantly higher in HIV-infected patients than controls (P ≤ 0.05). Sclerostin and DKK-1 concentrations were markedly lower than in controls (P ≤ 0.0006, and P ≤ 0.03, respectively). The serum concentration of both analytes of patients naïve to antiretroviral treatment was not different from that of treated patients. No correlations were found between sclerostin, DKK-1, and bone mineral measurements. Our data confirm the alteration of bone metabolism pathways in HIV-infected individuals. The lower concentration of Wnt antagonists is consistent with the increased bone formation markers.

Hirshfeld atom refinement.

Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly-l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree-Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints - even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu's), all other structural parameters agree within less than 2 csu's. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Šfor temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å(2) as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements - an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å.

Glycyl-L-alanine: a multi-temperature neutron study.

Neutron diffraction data have been collected at 12, 50, 150 and 295 K for the dipeptide glycyl-L-alanine, C5H10N2O3, in order to obtain accurate positional and anisotropic displacement parameters for the H atoms. The values of these parameters serve as a benchmark for assessing the equivalent parameters obtained from a so-called Hirshfeld-atom refinement of X-ray diffraction data described elsewhere [Capelli et al. (2014). IUCrJ, 1, 361-379]. The flexibility of the glycyl-L-alanine molecule in the solid and the hydrogen-bonding interactions as a function of temperature are also considered.

Areal bone mineral density in pediatric patients with chronic hepatitis B or chronic hepatitis C.

Decreased bone mineral density (BMD) is a known complication of chronic liver disease in adults. Data on bone mass, an important factor for the development of osteoporosis in adult life, in young patients with chronic hepatitis B (HBV) and C virus (HCV) infections are scarce. We measured BMD at the lumbar spine and whole skeleton by dual-energy X-ray absorptiometry in 11 HBV- and 21 HCV-vertically infected untreated youths (3.9-21.1 years). BMD measurements were compared to those of 202 healthy subjects (3.0-21.9 years). The median BMD Z-score of the lumbar spine of HBV-infected patients was -0.3, ranging from -1.6 to 0.6, while the median whole skeleton BMD Z-score was 0.1 (-0.8 to 0.6). HBV-infected patients showed a median Z-score of the lumbar spine of 0.6 (-1.6 to 1.9), and a median whole skeleton BMD Z-score of 0.6, ranging from -1.5 to 1.4. Multivariate analyses have been performed to correct for differences in sex, age, and anthropometric measurements. Lumbar spine BMD values of HBV and HCV-infected patients were not significantly different from those of controls. Similarly, no differences were found between groups in total body BMD measurements. Our data suggest that, unlikely adult patients, untreated young patients with chronic HBV and HCV infection may not have impaired bone mass measurements.

Nature of Si-H interactions in a series of ruthenium silazane complexes using multinuclear solid-state NMR and neutron diffraction.

Three new N-heterocyclic-silazane compounds, 1a-c, were prepared and employed as bidentate ligands to ruthenium, resulting in a series of [Ru(H){(κ-Si,N-(SiMe2-N-heterocycle)}3] complexes (3a-c) featuring the same RuSi3H motif. Detailed structural characterization of the RuSi3H complexes with X-ray diffraction, and in the case of triazabicyclo complex [Ru(H){κ-Si,N-(SiMe2)(C7H12N3)}3] (3a), neutron diffraction, enabled a reliable description of the molecular geometry. The hydride ligand of (3a) is located closer to two of the silicon atoms than it is to the third. Such a geometry differs from that of the previously reported complex [Ru(H){(κ-Si,N-(SiMe2)N(SiMe2H)(C5H4N)}3] (3d), also characterized by neutron diffraction, where the hydride was found to be equidistant from all three silicon atoms. A DFT study revealed that the symmetric and less regular isomers are essentially degenerate. Information on the dynamics and on the Ru···H···Si interactions was gained from multinuclear solid-state ((1)H wPMLG, (29)Si CP MAS, and 2D (1)H-(29)Si dipolar HETCOR experiments) and solution NMR studies. The corresponding intermediate complexes, [Ru{κ-Si,N-(SiMe2-N-heterocycle)}(η(4)-C8H12)(η(3)-C8H11)] (2a-c), involving a single silazane ligand were isolated and characterized by multinuclear NMR and X-ray diffraction. Protonation of the RuSi3H complexes was also studied. Reaction of 3a with NH4PF6 gave rise to [Ru(H)(η(2)-H -SiMe2)κ-N-(C7H12N3){κ-Si,N-(SiMe2)(C7H12N3)}2](+)[PF6](-)(4aPF6) which was isolated and characterized by NMR spectroscopy, X-ray crystallography, and DFT studies. The nature of the Si-H interactions in this silazane series was analyzed in detail.

Step-by-step introduction of silazane moieties at ruthenium: different extents of Ru-H-Si bond activation.

The coordination of pyridine-2-amino(methyl)dimethylsilane ligands to ruthenium has afforded access to a family of novel complexes that display multicenter Ru-H-Si interactions according to the number of incorporated ligands. The new complexes Ru[κ-Si,N-(SiMe2)N(Me)(C5H4N)](η(4)-C8H12)(η(3)-C8H11) (1), Ru2(µ-H)2(H)2[κ-Si,N-(SiMe2)N(Me)(C5H4N)]4 (2), and Ru(H)[κ-Si,N-(SiMe2)N(Me)(C5H4N)]3 (3) were isolated and fully characterized. The complexes exhibit different degrees of Si-H activation: complete Si-H cleavage, secondary interactions between the atoms (SISHA), and η(2)-Si-H coordination. Reversible protonation of 3 leading to the cationic complex [RuH{(η(2)-H-SiMe2)N(Me)κ-N-(C5H4N)}{κ-Si,N-(SiMe2)N(Me)(C5H4N)}2](+)[BAr(F)4](-) (5) was also demonstrated. The coordination modes in these systems were carefully studied with a combination of X-ray and neutron diffraction analysis, DFT geometry optimization, and multinuclear NMR spectroscopy.

Probing highly selective H/D exchange processes with a ruthenium complex through neutron diffraction and multinuclear NMR studies.

Deuterium labeling is a powerful way to gain mechanistic information in biology and chemistry. However, selectivity is hard to control experimentally, and labeled sites can be difficult to assign both in solution and in the solid state. Here we show that very selective high-deuterium contents can be achieved for the polyhydride ruthenium phosphine complex [RuH2(H2)2(PCyp3)2] (1) (PCyp3 = P(C5H9)3). The selectivity of the H/D exchange process is demonstrated by multinuclear NMR and neutron diffraction analyses. It has also been investigated through density functional theory (DFT) calculations. The reactions are performed under mild conditions at room temperature, and the extent of deuterium incorporation, involving selective C-H bond activation within the cyclopentyl rings of the phosphine ligands, can easily be tuned (solvent effects, D2 pressure). It is shown that D2 gas can inhibit the C-H/C-D exchange process.

Dynamics and thermodynamics of crystalline polymorphs: α-glycine, analysis of variable-temperature atomic displacement parameters.

Multitemperature synchrotron diffraction data to 0.5 Å resolution in the temperature range 10-298 K and neutron data at 18 K of the α-glycine polymorph have been collected at the KEK photon factory (PF), SPring-8 and the Institut Laue Langevin (ILL) for the study of molecular motion in the crystal and of the associated thermodynamic functions. Atomic displacement parameters (ADPs) of non-H atoms are obtained from refinements based on nonspherical atomic scattering factors (invariom model) to minimize correlation between parameters describing thermal motion and valence electron density. The ADPs in the temperature range 50-298 K from SPring-8 connect smoothly with those from neutron diffraction at 18 K and 288-323 K. The combined ADPs from both sources covering the temperature range 18-323 K are used for a normal-mode analysis in the molecular mean field approximation. The lattice vibration frequencies from the ADP analysis and the internal vibration frequencies from an ONIOM (B3LYP/6-311+G(2d,p):PM3) calculation together with the Einstein, Debye, and Nernst-Lindemann models of heat capacity are used to calculate Cp, Hvib, and Svib values that are in good agreement with those from calorimetry.

Crystal structure of the insect neuropeptide proctolin.

The crystal structure of the neuropeptide proctolin (Arg-Tyr-Leu-Pro-Thr) is reported revealing the solid-state conformation of its molecules and their association in the crystal.

Molecular motion in crystalline naphthalene: analysis of multi-temperature X-ray and neutron diffraction data.

Single crystals of h8-naphthalene have been examined by both X-ray and neutron diffraction over a range of temperatures from 5 to 295 K. The aim of this case study was to measure the anisotropic displacement parameters (ADPs) of carbons and hydrogens and to interpret them using the model of thermal motion proposed by Bürgi and Capelli (Acta Cryst. 2000, A56, 403). The traditional rigid-body analysis expresses the low-frequency motions in terms of molecular translations and librations only, whereas the Bürgi-Capelli treatment also includes the high-frequency internal modes. We show that a considerable improvement occurs by representing the internal modes by a single second-rank tensor and that a further improvement follows by including a Grüneisen parameter to account for volume thermal expansion. By applying the treatment to multi-temperature diffraction data, there is a considerable reduction in the ratio of number of adjustable parameters/number of independent observations.