hERG stereoselective modulation by mexiletine-derived ureas: Molecular docking study, synthesis, and biological evaluation.

Long QT syndrome (LQTS) is a disorder of cardiac electrophysiology resulting in life-threatening arrhythmias; nowadays, only a few drugs are available for the management of LQTS. Focusing our attention on LQT2, one of the most common subtypes of LQTS caused by mutations in the human ether-à-go-go-related gene (hERG), in the present work, the stereoselectivity of the recently discovered mexiletine-derived urea 8 was investigated on the hERG potassium channel. According to preliminary in silico predictions, in vitro studies revealed a stereoselective behavior, with the meso form showing the greatest hERG opening activity. In addition, functional studies on guinea pig isolated left atria, aorta, and ileum demonstrated that 8 does not present any cardiac or intestinal liability in our ex vivo studies. Due to its overall profile, (R,S)-8 paves the way for the design and development of a new series of compounds potentially useful in the treatment of both congenital and drug-induced forms of LQTS.

Stable CsPbBr3 Nanoclusters Feature a Disk-like Shape and a Distorted Orthorhombic Structure.

CsPbBr3 nanoclusters have been synthesized by several groups and mostly employed as single-source precursors for the synthesis of anisotropic perovskite nanostructures or perovskite-based heterostructures. Yet, a detailed characterization of such clusters is still lacking due to their high instability. In this work, we were able to stabilize CsPbBr3 nanoclusters by carefully selecting ad hoc ligands (benzoic acid together with oleylamine) to passivate their surface. The clusters have a narrow absorption peak at 400 nm, a band-edge emission peaked at 410 nm at room temperature, and their composition is identified as CsPbBr2.3. Synchrotron X-ray pair distribution function measurements indicate that the clusters exhibit a disk-like shape with a thickness smaller than 2 nm and a diameter of 13 nm, and their crystal structure is a highly distorted orthorhombic CsPbBr3. Based on small- and wide-angle X-ray scattering analyses, the clusters tend to form a two-dimensional (2D) hexagonal packing with a short-range order and a lamellar packing with a long-range order.

Colloidal Bismuth Chalcohalide Nanocrystals.

Here we present a colloidal approach to synthesize bismuth chalcohalide nanocrystals (BiEX NCs, in which E=S, Se and X=Cl, Br, I). Our method yields orthorhombic elongated BiEX NCs, with BiSCl crystallizing in a previously unknown polymorph. The BiEX NCs display a composition-dependent band gap spanning the visible spectral range and absorption coefficients exceeding 105  cm-1 . The BiEX NCs show chemical stability at standard laboratory conditions and form colloidal inks in different solvents. These features enable the solution processing of the NCs into robust solid films yielding stable photoelectrochemical current densities under solar-simulated irradiation. Overall, our versatile synthetic protocol may prove valuable in accessing colloidal metal chalcohalide nanomaterials at large and contributes to establish metal chalcohalides as a promising complement to metal chalcogenides and halides for applied nanotechnology.

Structural Insights into the Vapochromic Behavior of Pt- and Pd-Based Compounds.

Anionic complexes having vapochromic behavior are investigated: [K(H2O)][M(ppy)(CN)2], [K(H2O)][M(bzq)(CN)2], and [Li(H2O)n][Pt(bzq)(CN)2], where ppy = 2-phenylpyridinate, bzq = 7,8-benzoquinolate, and M = Pt(II) or Pd(II). These hydrated potassium/lithium salts exhibit a change in color upon being heated to 380 K, and they transform back into the original color upon absorption of water molecules from the environment. The challenging characterization of their structure in the vapochromic transition has been carried out by combining several experimental techniques, despite the availability of partially ordered and/or impure crystalline material. Room-temperature single-crystal and powder X-ray diffraction investigation revealed that [K(H2O)][Pt(ppy)(CN)2] crystallizes in the Pbca space group and is isostructural to [K(H2O)][Pd(ppy)(CN)2]. Variable-temperature powder X-ray diffraction allowed the color transition to be related to changes in the diffraction pattern and the decrease in sample crystallinity. Water loss, monitored by thermogravimetric analysis, occurs in two stages, well separated for potassium Pt compounds and strongly overlapped for potassium Pd compounds. The local structure of potassium compounds was monitored by in situ pair distribution function (PDF) measurements, which highlighted changes in the intermolecular distances due to a rearrangement of the crystal packing upon vapochromic transition. A reaction coordinate describing the structural changes was extracted for each compound by multivariate analysis applied to PDF data. It contributed to the study of the kinetics of the structural changes related to the vapochromic transition, revealing its dependence on the transition metal ion. Instead, the ligand influences the critical temperature, higher for ppy than for bzq, and the inclination of the molecular planes with respect to the unit cell planes, higher for bzq than for ppy. The first stage of water loss triggers a unit cell contraction, determined by the increase in the b axis length and the decrease in the a (for ppy) or c (for bzq) axis lengths. Consequent interplane distance variations and in-plane roto-translations weaken the π-stacking of the room-temperature structure and modify the distances and angles of Pt(II)/Pd(II) chains. The curve describing the intermolecular Pt(II)/Pd(II) distances as a function of temperature, validated by X-ray absorption spectroscopy, was found to reproduce the coordinate reaction determined by the model-free analysis.

Mechanistic and Structural Basis for Inhibition of Copper Trafficking by Platinum Anticancer Drugs.

Copper (Cu) is required for maturation of cuproenzymes, cell proliferation, and angiogenesis, and its transport entails highly specific protein-protein interactions. In humans, the Cu chaperone Atox1 mediates Cu(I) delivery to P-type ATPases Atp7a and Atp7b (the Menkes and Wilson disease proteins, respectively), which are responsible for Cu release to the secretory pathway and excess Cu efflux. Cu(I) handover is believed to occur through the formation of three-coordinate intermediates where the metal ion is simultaneously linked to Atox1 and to a soluble domain of Cu-ATPases, both sharing a CxxC dithiol motif. The ultrahigh thermodynamic stability of chelating S-donor ligands secures the redox-active and potentially toxic Cu(I) ion, while their kinetic lability allows facile metal transfer. The same CxxC motifs can interact with and mediate the biological response to antitumor platinum drugs, which are among the most used chemotherapeutics. We show that cisplatin and an oxaliplatin analogue can specifically bind to the heterodimeric complex Atox1-Cu(I)-Mnk1 (Mnk1 is the first soluble domain of Atp7a), thus leading to a kinetically stable adduct that has been structurally characterized by solution NMR and X-ray crystallography. Of the two possible binding configurations of the Cu(I) ion in the cage made by the CxxC motifs of the two proteins, one (bidentate Atox1 and monodentate Mnk1) is less stable and more reactive toward cis-Pt(II) compounds, as shown by using mutated proteins. A Cu(I) ion can be retained at the Pt(II) coordination site but can be released to glutathione (a physiological thiol) or to other complexing agents. The Pt(II)-supported heterodimeric complex does not form if Zn(II) is used in place of Cu(I) and transplatin instead of cisplatin. The results indicate that Pt(II) drugs can specifically affect Cu(I) homeostasis by interfering with the rapid exchange of Cu(I) between Atox1 and Cu-ATPases with consequences on cancer cell viability and migration.

New Hints on the Maya Blue Formation Process by PCA-Assisted In Situ XRPD/PDF and Optical Spectroscopy.

The exact recipe to prepare the ancient Maya Blue (MB), an incredibly resistant and brilliant pigment prepared from indigo (dye) and Palygorskite (clay), is lost to the ages. To unravel the key features of the MB formation process, several inorganic-dye couples were heated to 200 °C and cooled to RT, to investigate their reactivity and the diffusion and degree of sequestration of the dye into the inorganic host. In situ XRPD/PDF and fiber optic reflectance spectroscopy (FORS) data, along with TGA, provided a comprehensive overview on MB formation mechanism. XRPD/PDF gave information on long/short range behaviors of water desorption/adsorption and indigo sequestration, while TGA and in situ FORS gave information on mass and optical changes within temperature. Ex situ dye removal was used to understand the sample stability after the thermal treatment. A statistical approach based on principal component analysis was exploited to efficiently and jointly analyze the ≈3000 collected patterns. MB formation starts below 110 °C with disordered distribution of indigo within the channels, reaching maximum reaction speed and higher ordering at 150 °C. Above 175 °C, color changes and a stronger sequestration of indigo into framework channels are observed, whereas the affinity for water is dramatically reduced. The origin of different colors, hues, and stability in historical MB samples can then be explained in terms of different thermal histories of the starting mechanical indigo/palygorskite mixtures.

Oxidation of Human Copper Chaperone Atox1 and Disulfide Bond Cleavage by Cisplatin and Glutathione.

Cancer cells cope with high oxidative stress levels, characterized by a shift toward the oxidized form (GSSG) of glutathione (GSH) in the redox couple GSSG/2GSH. Under these conditions, the cytosolic copper chaperone Atox1, which delivers Cu(I) to the secretory pathway, gets oxidized, i.e., a disulfide bond is formed between the cysteine residues of the Cu(I)-binding CxxC motif. Switching to the covalently-linked form, sulfur atoms are not able to bind the Cu(I) ion and Atox1 cannot play an antioxidant role. Atox1 has also been implicated in the resistance to platinum chemotherapy. In the presence of excess GSH, the anticancer drug cisplatin binds to Cu(I)-Atox1 but not to the reduced apoprotein. With the aim to investigate the interaction of cisplatin with the disulfide form of the protein, we performed a structural characterization in solution and in the solid state of oxidized human Atox1 and explored its ability to bind cisplatin under conditions mimicking an oxidizing environment. Cisplatin targets a methionine residue of oxidized Atox1; however, in the presence of GSH as reducing agent, the drug binds irreversibly to the protein with ammine ligands trans to Cys12 and Cys15. The results are discussed with reference to the available literature data and a mechanism is proposed connecting platinum drug processing to redox and copper homeostasis.

Principal component analysis for automatic extraction of solid-state kinetics from combined in situ experiments.

Solid-state reactivity is often studied by in situ experiments with a multi-technique approach, where complementarity of different probes is exploited. In situ data are usually analysed using a complex protocol: first the reaction model most suited to describe the specific solid-state reaction is chosen, second the reaction coordinate is obtained from the data, the order of reaction is then calculated by applying a specific kinetic equation, and finally kinetic parameters are obtained with an Arrhenius plot. The approach is both time consuming and subject to errors due to the arbitrariness of extraction of the reaction coordinate, typically from individual peak intensity variations during the reaction. In addition, application of the different kinetic equations to obtain the best fitting one is tedious and no general method to select the best model with an unbiased approach is available. Here we propose a new procedure based on principal component analysis to get kinetic information from in situ data, which simplifies and speeds up the process of kinetic parameter calculation from a three- to a two- or even a one-step form, reaching a high degree of automation and the ability to manage the huge amount of data produced by in situ multi-technique experiments. The new approach treats data as a whole, without biases introduced by manual methods of obtaining the reaction coordinate by peak intensity evaluation from individual patterns typical of the traditional approach. The procedure is described in its theoretical framework and applied to the formation of a molecular complex, monitored by in situ X-ray powder diffraction and Raman measurements.

Improved multivariate analysis for fast and selective monitoring of structural dynamics by in situ X-ray powder diffraction.

The development of two solid-state reactions, Xe absorption into MFI and molecular complex formation, where samples are affected by changes of crystal lattice due to temperature or pressure variation was structurally monitored through in situ or in operando X-ray powder diffraction experiments. Consequent variations of the peak positions prevent collective analysis of measured patterns, aiming at investigating structural changes occurring within the crystal cell. Moreover, an intrinsic and variable error in peak position is unavoidable when using the Bragg-Brentano geometry and, in some cases (sticky, bulky, aggregate samples) the sample mounting can increase the error within a dataset. Here we present a general multivariate analysis method to process in a fast and automatic way in situ XRPD data collected on charge transfer complexes and porous materials, with the capacity of disentangling peak shifts from intensity and shape variations in diffraction signals, thus allowing an efficient separation of the contribution of crystal lattice changes from structural changes. The peak shift correction allowed an improved PCA analysis that turned out to be more sensible than the traditional single pattern Rietveld analysis. The developed algorithms allowed, with respect to the traditional approach, the location of two new Xe positions into MFI with a better interpretation of the experimental data, while a much faster and more efficient recovery of the reaction coordinate was achieved in the molecular complex formation reaction.

Static and Dynamical Structural Investigations of Metal-Oxide Nanocrystals by Powder X-ray Diffraction: Colloidal Tungsten Oxide as a Case Study.

We have developed a general X-ray powder diffraction (XPD) methodology for the simultaneous structural and compositional characterization of inorganic nanomaterials. The approach is validated on colloidal tungsten oxide nanocrystals (WO3-x NCs), as a model polymorphic nanoscale material system. Rod-shaped WO3-x NCs with different crystal structure and stoichiometry are comparatively investigated under an inert atmosphere and after prolonged air exposure. An initial structural model for the as-synthesized NCs is preliminarily identified by means of Rietveld analysis against several reference crystal phases, followed by atomic pair distribution function (PDF) refinement of the best-matching candidates (static analysis). Subtle stoichiometry deviations from the corresponding bulk standards are revealed. NCs exposed to air at room temperature are monitored by XPD measurements at scheduled time intervals. The static PDF analysis is complemented with an investigation into the evolution of the WO3-x NC structure, performed by applying the modulation enhanced diffraction technique to the whole time series of XPD profiles (dynamical analysis). Prolonged contact with ambient air is found to cause an appreciable increase in the static disorder of the O atoms in the WO3-x NC lattice, rather than a variation in stoichiometry. The time behavior of such structural change is identified on the basis of multivariate analysis.

Oxaliplatin Binding to Human Copper Chaperone Atox1 and Protein Dimerization.

Copper trafficking proteins have been implicated in the cellular response to platinum anticancer drugs. We investigated the reaction of the chaperone Atox1 with an activated form of oxaliplatin, the third platinum drug to reach worldwide approval. Unlike cisplatin, which contains monodentate ammines, oxaliplatin contains chelated 1,2-diaminocyclohexane (DACH), which is more resistant to displacement by nucleophiles. In solution, one or two {Pt(DACH)(2+)} moieties bind to the conserved CXXC metal-binding motif of Atox1; in the latter case the two sulfur atoms likely bridging the two platinum units. At longer reaction times, a dimeric species is formed whose composition, Atox12·Pt(2+)2, indicates complete loss of the diamine ligands. Such a dimerization process is accompanied by partial unfolding of the protein. Crystallization experiments aiming at the characterization of the monomeric species have afforded, instead, a dimeric species resembling that already obtained by Boal and Rosenzweig in a similar reaction performed with cisplatin. However, while in the latter case there was only one Pt-binding site (0.4 occupancy) made of four sulfur atoms of the CXXC motifs of the two Atox1 chains in a tetrahedral arrangement, we found, in addition, a secondary Pt-binding site involving Cys41 of the B chain (0.25 occupancy). Moreover, both platinum atoms have lost their diamines. Thus, there appears to be little relationship between what is observed in solution and what is formed in the solid state. Since full occupancy of the tetrahedral cavity is a common feature of all Atox1 dimeric structures obtained with other metal ions (Cu(+), Cd(2+), and Hg(2+)), we propose that in the case of platinum, where the occupancy is only 0.4, the remaining cavities are occupied by Cu(+) ions. Experimental evidence is reported in support of the latter hypothesis. Our proposal represents a meeting point between the initial proposal of Boal and Rosenzweig (0.4 Pt occupancy) and the reinterpretation of the original crystallographic data put forward by Shabalin et al. (1 Cu occupancy), and could apply to other cases.

Chemical selectivity in structure determination by the time dependent analysis of in situ XRPD data: a clear view of Xe thermal behavior inside a MFI zeolite.

X-ray diffraction methods in general provide a representation of the average structure, thus allowing only limited chemical selectivity. As recently shown [D. Chernyshov, et al., Acta Crystallogr., Sect. A: Found. Crystallogr., 2011, 67, 327], some structural information on a subset of atoms can be obtained using the modulation enhanced diffraction (MED), thus providing a new tool that is able to enhance selectivity in diffraction. MED uses a periodic stimulus supplied in situ on a crystal while diffraction data are collected continuously during one or more stimulation periods. Such large data sets can then be treated by different methods. Herein, we present and compare phase sensitive detection (PSD) and principal component analysis (PCA) for in situ X-ray powder diffraction (XRPD) data treatment. The application of PCA to MED data is described for the first time in the present paper. Simulated and experimental MED powder data were produced using an MFI zeolite as a static spectator in which Xe, acting as the active species, is adsorbed and desorbed in a periodic manner. By demodulating the simulated and experimental data, MED allowed the powder diffraction pattern of the responding scattering density to be obtained and enabled the selective extraction of crystallographic information on Xe by solving the crystal structure of the active species independently of the static zeolite framework. The "real world" experiments indicated that the PSD-MED approach has some limitations related to the degree of fulfilment of some theoretical assumptions. When applied to in situ XRPD data, PCA, despite being based on blind statistical analysis, gave results similar to those obtained by PSD (based on Fourier analysis) for simulated data. Moreover, PCA is complementary to PSD thanks to its capability of gathering information on the Xe substructure even in the presence of a non-periodic stimulus, i.e. using the most simple stimulus shape as a single temperature ramp. In particular, PC1 results are able to perfectly reproduce the corresponding 1Ω signal from a traditional PSD analysis. Moreover PCA can be applied directly to raw non periodic XRPD data, opening the possibility of using it during an "in situ" experiment. PCA can thus be envisaged as a very useful, fast and efficient tool to improve data collection and maximize data quality. To date, however, PSD remains superior for substructure solution from the analysis of 2Ω demodulated data.

Protein phasing at non-atomic resolution by combining Patterson and VLD techniques.

Phasing proteins at non-atomic resolution is still a challenge for any ab initio method. A variety of algorithms [Patterson deconvolution, superposition techniques, a cross-correlation function (C map), the VLD (vive la difference) approach, the FF function, a nonlinear iterative peak-clipping algorithm (SNIP) for defining the background of a map and the free lunch extrapolation method] have been combined to overcome the lack of experimental information at non-atomic resolution. The method has been applied to a large number of protein diffraction data sets with resolutions varying from atomic to 2.1 Å, with the condition that S or heavier atoms are present in the protein structure. The applications include the use of ARP/wARP to check the quality of the final electron-density maps in an objective way. The results show that resolution is still the maximum obstacle to protein phasing, but also suggest that the solution of protein structures at 2.1 Šresolution is a feasible, even if still an exceptional, task for the combined set of algorithms implemented in the phasing program. The approach described here is more efficient than the previously described procedures: e.g. the combined use of the algorithms mentioned above is frequently able to provide phases of sufficiently high quality to allow automatic model building. The method is implemented in the current version of SIR2014.

Structural insights into the C-terminus of the histone-lysine N-methyltransferase NSD3 by small-angle X-ray scattering.

NSD3 is a member of six H3K36-specific histone lysine methyltransferases in metazoans. Its overexpression or mutation is implicated in developmental defects and oncogenesis. Aside from the well-characterized catalytic SET domain, NSD3 has multiple clinically relevant potential chromatin-binding motifs, such as the proline-tryptophan-tryptophan-proline (PWWP), the plant homeodomain (PHD), and the adjacent Cys-His-rich domain located at the C-terminus. The crystal structure of the individual domains is available, and this structural knowledge has allowed the designing of potential inhibitors, but the intrinsic flexibility of larger constructs has hindered the characterization of mutual domain conformations. Here, we report the first structural characterization of the NSD3 C-terminal region comprising the PWWP2, SET, and PHD4 domains, which has been achieved at a low resolution in solution by small-angle X-ray scattering (SAXS) data on two multiple-domain NSD3 constructs complemented with size-exclusion chromatography and advanced computational modeling. Structural models predicted by machine learning have been validated in direct space, by comparison with the SAXS-derived molecular envelope, and in reciprocal space, by reproducing the experimental SAXS profile. Selected models have been refined by SAXS-restrained molecular dynamics. This study shows how SAXS data can be used with advanced computational modeling techniques to achieve a detailed structural characterization and sheds light on how NSD3 domains are interconnected in the C-terminus.

Resolving a structural issue in cerium-nickel-based oxide: a single compound or a two-phase system?

CeNiO3 has been reported in the literature in the last few years as a novel LnNiO3 compound with promising applications in different catalytic fields, but its structure has not been correctly reported so far. In this research, CeNiO3 (RB1), CeO2 and NiO have been synthesized in a nanocrystalline form using a modified citrate aqueous sol-gel route. A direct comparison between the equimolar physical mixture (n(CeO2) : n(NiO) = 1 : 1) and compound RB1 was made. Their structural differences were investigated by laboratory powder X-ray diffraction (PXRD), selected area electron diffraction (SAED), transmission electron microscopy (TEM) with an energy-dispersive X-ray spectroscopy (EDS) detector, and Raman spectroscopy. The surface of the compounds was analyzed by X-ray photoelectron spectroscopy (XPS), while the thermal behaviour was explored by thermogravimetric analysis (TGA). Their magnetic properties were also investigated with the aim of exploring the differences between these two compounds. There were clear differences between the physical mixture of CeO2 + NiO and RB1 presented by all of these employed methods. Synchrotron methods, such as atomic pair distribution function analysis (PDF), X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS), were used to explore the structure of RB1 in more detail. Three different models for the structural solution of RB1 were proposed. One structural solution proposes that RB1 is a single-phase pyrochlore compound (Ce2Ni2O7) while the other two solutions suggest that RB1 is a two-phase system of either CeO2 + NiO or Ce1-xNixO2 and NiO.

A molecular dynamics simulation-based interpretation of nuclear magnetic resonance multidimensional heteronuclear spectra of α-synuclein·dopamine adducts.

Multidimensional heteronuclear nuclear magnetic resonance (NMR) spectroscopy provides valuable structural information about adducts between naturally unfolded proteins and their ligands. These are often highly pharmacologically relevant. Unfortunately, the determination of the contributions to observed chemical shifts changes upon ligand binding is complicated. Here we present a tool that uses molecular dynamics (MD) trajectories to help interpret two-dimensional (2D) NMR data. We apply this tool to the naturally unfolded protein human α-synuclein interacting with dopamine, an inhibitor of fibril formation, and with its oxidation products in water solutions. By coupling 2D NMR experiments with MD simulations of the adducts in explicit water, the tool confirms with experimental data that the ligands bind preferentially to (125)YEMPS(129) residues in the C-terminal region and to a few residues of the so-called NAC region consistently. It also suggests that the ligands might cause conformational rearrangements of distal residues located at the N-terminus. Hence, the performed analysis provides a rationale for the observed changes in chemical shifts in terms of direct contacts with the ligand and conformational changes in the protein.

Insights into the polymorphism of glycine: membrane crystallization in an electric field.

In this work we studied glycine crystallization with two main objectives: (i) to get improved control of crystal growth and polymorphic selectivity of organic molecules; (ii) to achieve additional insights into the nucleation mechanisms of glycine polymorphs. To reach these goals, membrane crystallization technology, a tool which allows improved control of supersaturation in solution crystallization, was used under different operating conditions: the variable solvent removal rate, acidic and almost neutral pH, the presence of a pulsed electric field. The traditional explanation for the crystallization of α and γ glycine polymorphs from aqueous solution is based on the general cyclic dimer hypothesis and the self-poisoning mechanism. In contrast with both the conventional theories, experimental results suggest that the relative nucleation rates with respect to the relative growth kinetics of the two forms under the different conditions play a dominant role in determining the polymorphic outcome. Our results instead support a molecular nucleation route where open chain dimers can behave as building units for both γ- and α-glycines in the rate determining structuring step of the two-step nucleation mechanism.

Cobalt binding in the photosynthetic bacterium R. sphaeroides by X-ray absorption spectroscopy.

Cobalt is an important oligoelement required for bacteria; if present in high concentration, exhibits toxic effects that, depending on the microorganism under investigation, may even result in growth inhibition. The photosynthetic bacterium Rhodobacter (R.) sphaeroides tolerates high cobalt concentration and bioaccumulates Co(2+) ion, mostly on the cellular surface. Very little is known on the chemical fate of the bioaccumulated cobalt, thus an X-ray absorption spectroscopy investigation was conducted on R. sphaeroides cells to gain structural insights into the Co(2+) binding to cellular components. X-ray absorption near-edge spectroscopy and extended X-ray absorption fine structure measurements were performed on R. sphaeroides samples containing whole cells and cell-free fractions obtained from cultures exposed to 5 mM Co(2+). An octahedral coordination geometry was found for the cobalt ion, with six oxygen-ligand atoms in the first shell. In the soluble portion of the cell, cobalt was found bound to carboxylate groups, while a mixed pattern containing equivalent amount of two sulfur and two carbon atoms was found in the cell envelope fraction, suggesting the presence of carboxylate and sulfonate metal-binding functional groups, the latter arising from sulfolipids of the cell envelope.

Towards the extraction of the crystal cell parameters from pair distribution function profiles.

The approach based on atomic pair distribution function (PDF) has revolutionized structural investigations by X-ray/electron diffraction of nano or quasi-amorphous materials, opening up the possibility of exploring short-range order. However, the ab initio crystal structural solution by the PDF is far from being achieved due to the difficulty in determining the crystallographic properties of the unit cell. A method for estimating the crystal cell parameters directly from a PDF profile is presented, which is composed of two steps: first, the type of crystal cell is inferred using machine-learning approaches applied to the PDF profile; second, the crystal cell parameters are extracted by means of multivariate analysis combined with vector superposition techniques. The procedure has been validated on a large number of PDF profiles calculated from known crystal structures and on a small number of measured PDF profiles. The lattice determination step has been benchmarked by a comprehensive exploration of different classifiers and different input data. The highest performance is obtained using the k-nearest neighbours classifier applied to whole PDF profiles. Descriptors calculated from the PDF profiles by recurrence quantitative analysis produce results that can be interpreted in terms of PDF properties, and the significance of each descriptor in determining the prediction is evaluated. The cell parameter extraction step depends on the cell metric rather than its type. Monometric, dimetric and trimetric cells have top-1 estimates that are correct 40, 20 and 5% of the time, respectively. Promising results were obtained when analysing real nanocrystals, where unit cells close to the true ones are found within the top-1 ranked solution in the case of monometric cells and within the top-6 ranked solutions in the case of dimetric cells, even in the presence of a crystalline impurity with a weight fraction up to 40%.

Unveiling the Influence of Hydrated Deep Eutectic Solvents on the Dynamics of Water-Soluble Proteins.

Deep eutectic solvents (DESs) are mixtures of two or more pure compounds (e.g., Lewis or Brønsted acids and bases, anionic and/or cationic species) in a well-defined stoichiometric proportion, with a melting point lower to that of an ideal liquid mixture. These neoteric solvents are highly tunable through varying the structure or relative ratio of parent components and have been evaluated as solvents able to improve biomolecules' performance, specifically their stability and biocatalytic properties. Inspired by a recent crystallographic study, we have explored through molecular dynamics (MD) simulations the dynamic properties of two different proteins (hen egg-white lysozyme and the human VH antibody fragment HEL4) in a (20% w/w) hydrated solution of choline chloride-glycerol (1:2). We have developed proper force fields to account for DES, protein, and DES-protein interactions, which have been calibrated using pair distribution function measurements of pure DES solutions. MD results show that the presence of DES quenches the protein motion, increasing the rigidity of the overall protein structure. Specific interactions among DES components and protein residues, such as those between choline ions and two Tryptophan residues of lysozyme, may amplify the protein-DES interactions and lead to protein crystallization in the presence of hydrated DES. These findings open new horizons to improve or achieve control on protein properties by a proper choice of hydrated DESs used as solvents.