1,2-Dibenzoylhydrazine as a Multi-Inhibitor Compound: A Morphological and Docking Study.

In the framework of the multitarget inhibitor study, we report an in silico analysis of 1,2-dibenzoylhydrazine (DBH) with respect to three essential receptors such as the ecdysone receptor (EcR), urease, and HIV-integrase. Starting from a crystallographic structural study of accidentally harvested crystals of this compound, we performed docking studies to evaluate the inhibitory capacity of DBH toward three selected targets. A crystal morphology prediction was then performed. The results of our molecular modeling calculations indicate that DBH is an excellent candidate as a ligand to inhibit the activity of EcR receptors and urease. Docking studies also revealed the activity of DBH on the HIV integrase receptor, providing an excellent starting point for developing novel inhibitors using this molecule as a starting lead compound.

A Pseudouridine Isoxazolidinyl Nucleoside Analogue Structural Analysis: A Morphological Approach.

An in silico study has been conducted upon (3'RS,5'SR)-5-[2'-benzyl-5'-hydroxymethyl-1',2'-isoxazolidin-3'-yl]uracil through a molecular dynamics/docking approach that highlights its potential inhibitory activity upon the wild-type pseudouridine 5'-monophosphate glycosidase. The crystal structure of this compound has been solved by means of X-ray single crystal diffraction and the data inferred were used to predict its crystal morphology. These data were compared with optical microscopy images and confirmed the validity of the computed models. This robust approach, already used for several other different compounds, provides a fast and reliable tool to standardize a crystallization method in order to get similar and good quality crystals. As different crystal shapes could be associated with different polymorphic forms, this method could be considered a fast and cheap screening to choose among different and coexistent polymorphic forms. Furthermore, a match with the original crystal structure of pseudouridine 5'-monophosphate is provided.

Probing nonlinear optical coefficients in self-assembled peptide nanotubes.

Self-assembled l,l-diphenylalanine (FF) peptide micro/nanotubes represent a class of biomimetic materials with a non-centrosymmetric crystal structure and strong piezoelectricity. The peptide nanotubes synthesized by a liquid phase method yield tube lengths in the hundreds of micron range, inner diameters in the few hundred nanometer range, and outer diameters in the 5-15 µm range. Second harmonic generation (SHG) polarimetry from individual self-assembled FF nanotubes is used to obtain the nonlinear (NLO) optical coefficients as a function of the tube diameter and thermal treatment. The ratio of the shear to the longitudinal component (d15/d33) of the NLO coefficient increases with the diameter of the tubes. One of the transverse components of the nonlinear coefficient is found to be negative, and its magnitude with respect to the longitudinal component increases with the tube diameter. Thermal treatment of individual FF tubes has a similar effect upon increasing the diameter of the tubes in SHG polarimetry. Concurrent Raman scattering measurements from individual FF tubes show a distinct change in the low frequency (100 cm-1) region with the diameter of the tubes reflecting subtle effects of water.

Modulating Polymer Ultrathin Film Crystalline Fraction and Orientation with Nanoscale Curvature.

We investigated the effect of nanoscale curvature on the structure of thermally equilibrated poly-3-hexylthiophene (P3HT) ultrathin films. The curvature-induced effects were investigated with synchrotron grazing incidence X-ray diffraction (GIXRD) and atomic force microscopy (AFM). Our results demonstrate that nanoscale curvature reduces the polymer crystalline fraction and the crystal length. The first effect is strongest for the lowest curvature and results in a decrease in the out-of-plane thickness of the polymer crystals. On the other hand, the crystal in-plane length decreases with the increase in substrate curvature. Finally, the semi-quantitative analysis of crystal anisotropy shows a marked dependence on the substrate curvature characterized by a minimum at curvatures between 0.00851 nm-1 and 0.0140 nm-1. The results are discussed in terms of a curvature-dependent polymer fraction, which fills the interstices between neighboring particles and cannot crystallize due to extreme space confinement. This fraction, whose thickness is highest at the lowest curvatures, inhibits the crystal nucleation and the out-of-plane crystal growth. Moreover, because of the adhesion to the curved portion of the substrates, crystals adopt a random orientation. By increasing the substrate curvature, the amorphous fraction is reduced, leading to polymer films with higher crystallinity. Finally, when the thickness of the film exceeds the particle diameter, the curvature no longer affects the crystal orientation, which, similarly to the flat case, is predominantly edge on.

Interfacial free energy driven nanophase separation in poly(3-hexylthiophene)/[6,6]-phenyl-C61-butyric acid methyl ester thin films.

The nanostructure of thermally annealed thin films of poly(3-hexylthiophene) (P3HT) and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) blends on hydrophobic and hydrophilic substrates was studied to unravel the relationship between the substrate properties and the phase structure of polymer blends in confined geometry. Indeed, the nature of the employed substrates was found to affect the extent of phase separation, the PCBM aggregation state and the texture of the whole system. In particular, annealing below the melting temperature of the polymer yielded the formation of PCBM nanometric crystallites on the hydrophobic substrates, while mostly amorphous microscopic aggregates were formed on the hydrophilic ones. Moreover, while an enhanced in-plane orientation of P3HT lamellae was promoted on hydrophobic substrates, a markedly tilted geometry was produced on the hydrophilic ones. The observed effects were interpreted in terms of a simple model connecting the interface free energy for the blend films to the different polymer chain mobility and diffusion velocity of PCBM molecules on the different substrates.

α-d-Tagatopyran-ose.

The title compound, C(6)H(12)O(6), also known as d-Tagatose, occurs in its furanose and pyranose forms in solution, but only the α-pyran-ose form crystallizes out. In the crystal, the molecules form hydrogen bonded chains propagating in [100] linked by O-H⋯O interactions. Further O-H⋯O bonds cross-link the chains.

Molecular modeling studies of pseudouridine isoxazolidinyl nucleoside analogues as potential inhibitors of the pseudouridine 5'-monophosphate glycosidase.

In this paper, we investigated the hypothesis that pseudouridine isoxazolidinyl nucleoside analogues could act as potential inhibitors of the pseudouridine 5'-monophosphate glycosidase. This purpose was pursued using molecular modeling and in silico ADME-Tox profiling. From these studies emerged that the isoxazolidinyl derivative 1 5'-monophosphate can be effectively accommodated within the active site of the enzyme with a ligand efficiency higher than that of the natural substrate. In this context, the poor nucleofugality of the N-protonated isoxazolidine prevents or slows down, the first mechanistic step proposed for the degradation of the pseudouridine 5'-monophosphate glycosidase, leading to the enzyme inhibition. Finally, the results of the physicochemical and ADME-Tox informative analysis pointed out that compound 1 is weakly bounded to plasma protein, only moderately permeate the blood-brain barrier, and is non-carcinogen in rat and mouse. To the best of our knowledge, this is the first paper that introduces the possibility of inhibition of pseudouridine 5'-monophosphate glycosidase by a molecule that competing with the natural substrate hinders the glycosidic C-C bond cleavage.

(+)-Methyl (1R,2S)-2-{[4-(4-Chlorophenyl)-4-hydroxypiperidin-1-yl]methyl}-1-phenylcyclopropanecarboxylate [(+)-MR200] Derivatives as Potent and Selective Sigma Receptor Ligands: Stereochemistry and Pharmacological Properties.

Methoxycarbonyl-1-phenyl-2-cyclopropylmethyl based derivatives cis-(+)-1a [cis-(+)-MR200], cis-(-)-1a [cis-(-)-MR201], and trans-(±)-1a [trans-(±)-MR204], have been identified as new potent sigma (σ) receptor ligands. In the present paper, novel enantiomerically pure analogues were synthesized and optimized for their σ receptor affinity and selectivity. Docking studies rationalized the results obtained in the radioligand binding assay. Absolute stereochemistry was unequivocally established by X-ray analysis of precursor trans-(+)-5a as camphorsulfonyl derivative 9. The most promising compound, trans-(+)-1d, showed remarkable selectivity over a panel of more than 15 receptors as well as good chemical and enzymatic stability in human plasma. An in vivo evaluation evidenced that trans-(+)-1d, in contrast to trans-(-)-1d, cis-(+)-1d, or cis-(-)-1d, which behave as σ1 antagonists, exhibited a σ1 agonist profile. These data clearly demonstrated that compound trans-(+)-1d, due to its σ1 agonist activity and favorable receptor selectivity and stability, provided an useful tool for the study of σ1 receptors.

X-Ray crystallographic and computational study on uranyl-salophen complexes bearing nitro groups.

In the solid state, salophen-UO2 complexes bearing one, two, or three NO2 groups lack the pronounced ligand curvature that represents a structural hallmark for this class of compounds. A detailed structural study based on single-crystal X-ray crystallography and computational methods, comprising molecular dynamics, gas-phase Hartree Fock, and DFT calculations, was carried out to investigate the coordination properties of the uranyl cation.

Structure and aggregation properties of a Schiff-base zinc(II) complex derived from cis-1,2-diaminocyclohexane.

This contribution explores the effect of the bridging diamine upon the aggregation properties of a Zn(II) Schiff-base complex, , both in the solid state and in solution. The X-ray structure of , resulting from the harvest of good quality crystals using chloroform and diethyl ether as solvents, shows the presence of a densely packed dimer in the solid state which pentacoordinates two Zn atoms involved in a µ-phenoxo bridge. Detailed studies in solution, through (1)H NMR, DOSY NMR, and optical spectroscopic investigations, indicate the typical aggregation/deaggregation behaviour on switching from non-coordinating to coordinating solvents, in relation to the Lewis acidic character of such Zn(II) complexes. Thus, while in DMSO-d6 both (1)H NMR and DOSY studies suggest the existence of monomeric species, in chloroform solution experimental data support the existence of aggregates. However, unlike our previous studies, (1)H NMR data in chloroform solution indicate the existence of an asymmetric dimer, as observed in the X-ray crystal structure. This further evidences a very rigid backbone of the dimeric aggregate and can be related to the defined stereochemistry of the chelate cis-1,2-diaminocyclohexane bridge.

Eustachian Valve Endocarditis in an Elderly Woman.

We describe the transesophageal echocardiographic findings in Eustachian valve endocarditis for a 73-year-old woman with a previous history of mitral valve disease. After a 4-week treatment with antibiotics, follow-up echocardiographic examination showed a smaller vegetation.

A top-down approach to crystal engineering of a racemic Δ2-isoxazoline.

The crystal structure of racemic dimethyl (4RS,5RS)-3-(4-nitrophenyl)-4,5-dihydroisoxazole-4,5-dicarboxylate, C13H12N2O7, has been determined by single-crystal X-ray diffraction. By analysing the degree of growth of the morphologically important crystal faces, a ranking of the most relevant non-covalent interactions determining the crystal structure can be inferred. The morphological information is considered with an approach opposite to the conventional one: instead of searching inside the structure for the potential key interactions and using them to calculate the crystal habit, the observed crystal morphology is used to define the preferential lines of growth of the crystal, and then this information is interpreted by means of density functional theory (DFT) calculations. Comparison with the X-ray structure confirms the validity of the strategy, thus suggesting this top-down approach to be a useful tool for crystal engineering.

Crystal morphologies and polymorphs in tolbutamide microcrystalline powder.

The growing interest of pharmaceutical companies toward the crystal morphology prediction of active pharmaceutical ingredients is a consequence of the dramatic effect of the crystal habit on the tableting behavior of drugs. In order to help the optimization of the industrial process, molecular mechanics calculations together with X-ray diffraction analysis and optical microscopy (OM) were used to shed light over the structural properties of N-(butylcarbamoyl)-4-methylbenzenesulfonamide-commercially known as tolbutamide-a drug used in the management of type II diabetes, especially in elderly diabetics because of its rapid metabolism. As there are several known polymorphs of this molecule, we first defined, by means of a quantitative phase analysis, performed by X-ray powder diffraction, which and how much each of the five crystallographic structures present in the Cambridge Crystallographic Database represent the commercial crystalline powder. The structures of the resulting candidates were first analyzed by means of molecular mechanics, and the crystal morphologies of the compounds were therefore predicted and compared with the ones observed by means of OM. Analogies and differences among the different morphologies, together with the potential role of crystallization solvents, were commented in the attempt to bridge the gap between the molecular structure-that is, the atomic point of view-and the crystal habit.

Potassium caffeate/caffeic acid co-crystal: the rat race between the catecholic and carboxylic moieties in an atypical co-crystal.

The vast literature concerning caffeic acid and its derivatives lacks any reference to the solid state structures of its inorganic salts as these crystals are quite difficult grow. Most of the already published works deal with computational studies of these compounds as well as investigations of their behaviour in solution. Having obtained good quality potassium caffeate/caffeic acid co-crystals, we solved their structure and used a robust approach, already applied to caffeic acid alone, to compare the X-ray structure with the one inferred by Molecular Dynamics (MD), focusing our attention on the structure-property relationships. The reliability of this method is confirmed by the overall agreement extended up to the anisotropic displacement parameters calculated, on one hand, by means of MD and the ones gathered, on the other hand, by X-ray measurements. Moreover, the lack of experimental evidence of an enthalpically favored polymorph, arising from the MD calculations, were explained on the basis of the Shannon's entropy.

An integrated X-ray and molecular dynamics study of uranyl-salen structures and properties.

Uranium complexes of bis(p-tert-butyl-salicylidene)-1,2-diphenylethylenediamine (1) and bis(salicylidene)-1,2-diphenylethylenediamine (2) have been synthesized and investigated by X-ray single crystal diffraction and MD calculations in Periodic Boundary Conditions. Both compounds form crystals which are densely packed and do not provide voids accessible to solvent molecules. The configurations adopted by 1 and 2 are determined by well defined T-shaped and π-stacking non covalent interactions between phenyl groups of adjacent molecules as well as by a network of hydrogen bonds. These interactions and the relative arrangements of the molecules, explain the packing in the crystal structures. Each uranyl moiety shows a penta-coordination in the equatorial plane perpendicular to the trans oxygens giving rise, in both compounds, to a bypiramidal geometry. As usual for this class of compounds, the 5th position is characterized by the presence of the coordinated solvent. The in silico simulations confirm this hypothesis in very fine details. Moreover, in 1, even the partial occupancy of the solvent molecule determined from the crystal structure refinement, was shown to be due to a constrained freedom of motion of the solvent molecule that can be reproduced by molecular dynamics. This suggests that the reported disorder is not due to a poor quality of the harvested crystals but to a structural feature. In further agreement with the above mentioned results, DFT calculations demonstrated that the molecular orbital configuration and energies suit the described properties of complexes 1 and 2 suggesting a potential enantioselective activity as already shown by molecules belonging to this class of compounds.

How molecular interactions affect crystal morphology: the case of haloperidol.

The tableting behaviour of drugs can be dramatically affected by changes in the crystal habit of the drug molecule. Pharmaceutical companies are therefore interested in the morphology prediction as a possible tool to optimise the industrial process. Molecular mechanics calculations embedded in dedicated software together with X-ray diffraction analysis were used to enlighten the structural properties of 4-[4-(4-chlorophenyl)-4-hydroxypiperidin-1-yl]-1-(4-fluorophenyl)butan-1-one-whose commercial name is haloperidol--an antipsychotic drug that contributed to the progress and revolution of psychiatric care. We defined, by means of X-ray powder diffraction, which--or how much--of the two crystallographic structures present in the Cambridge Crystallographic Database represents the commercial crystalline powder. Once the correct structure was selected, the whole structural analysis was carried out as a comparison with the already deposited structures. The available single crystal structure was used to model the X-ray powder diffraction pattern. The "real" structure was then optimised by means of molecular mechanics and the crystal morphology of the compounds was predicted with different computational methods. Analogies and differences among the different morphologies, together with the potential role of several solvents were used to try to bridge the gap between the molecular structure--that is, the atomic point of view--and the crystal habit.

Part I: A comparative study of bismuth-modified screen-printed electrodes for lead detection.

Lead determination was carried out in the frame of the European Union project Biocop (www.biocop.org) using a bismuth-modified screen-printed electrode (Bi-SPE) and the stripping analysis technique. In order to choose a sensitive Bi-SPE for lead detection, an analytical comparative study of electrodes modified by Bi using "in situ", "ex situ" and "bulk" procedures was carried out. On the basis of the results obtained, we confirmed that the "in situ" procedure resulted in better analytical performances with respect to not only "ex situ" but also to "Bi(2)O(3) bulk" modified electrodes, allowing for a linear range of lead ion concentration from 0.5 to 100 µg L(-1) and a detection limit of 0.15 µg L(-1). We demonstrated that, before the Bi film deposition, an oxidative electrochemical pre-treatment of the working electrode could be useful because it eliminates traces of lead in the graphite-ink, as shown with stripping measurements. It also improves the electrochemical performance of the electrodes as demonstrated with Electrochemical Impedance Spectroscopy (EIS) measurements. The influence of different analytical parameters, such as the electrolyte solution composition (acetate buffer, chloridric acid, nitric acid, perchloric acid) and the ionic strength was investigated in order to evaluate how to treat the sample before the analysis. The morphology of prepared "in situ" Bi-SPEs was also characterized by Atomic Force Microscopy (AFM). Finally, the Bi-SPEs were used to determine the concentration of lead ions in tap and commercial water samples obtaining satisfactory values of the recovery percentage (81% and 98%).

Bile salt aggregates in the gas phase: an electrospray ionization mass spectrometric study.

Helical and ordered structures have previously been identified by X-ray diffraction analysis in crystals and fibers of bile salts, and proposed as models of the micellar aggregates formed by trimeric or dimeric units of dihydroxy and trihydroxy salts, respectively. These models were supported by the results of studies of micellar bile salt solutions performed with different experimental techniques. The study has now been extended to the gas phase by utilizing electrospray ionization mass spectrometry (ESIMS) to investigate the formation and the composition of aggregates stabilized by noncovalent interactions, including polar (ion-ion, ion-dipole, dipole-dipole, hydrogen bonding etc.) and apolar (van der Waals and repulsive) interactions. The positive and negative ESIMS spectra of sodium glycodeoxycholate (NaGDC), taurodeoxycholate (NaTDC), glycocholate (NaGC), and taurocholate (NaTC) aqueous solutions, recorded under different experimental conditions, show in the first place that aggregates analogous to those present in micellar solutions do also exist in the gas phase. Furthermore, consistently with the condensed-phase model, the positive-ion spectra show that the trimers are the most stable oligomers among the aggregates of dihydroxy salts (NaGDC and NaTDC) whilst the dimers are the most stable among the aggregates of trihydroxy salts (NaGC and NaTC). Moreover, the binding energy of the constituent glycocholate salt units in most gaseous oligomers exceeds that of the corresponding taurocholate units. The ESIMS evidence has been confirmed by vapor-pressure measurements performed on NaGC and NaTC crystals and NaGDC and NaTDC fibers, the results of which show that the evaporation enthalpy of glycocholate exceeds that of taurocholate by some 50 kJ mol(-1).

Molecular dynamics (MD) simulations and large-angle X-ray scattering (LAXS) studies of the solid-state structure and assembly of isotactic (R)-poly(2,2'-dioxy-1,1'-binaphthyl-)phosphazene in the bulk state and in the cast film.

The intrachain conformation, molecular structure and interchain assembly of isotactic (R)-poly(2,2'-dioxy-1,1'-binaphthyl)phosphazene (P-DBNP) both in the bulk state (I) and in the cast film (II) were studied by molecular dynamics (MD) simulations of models, as implemented by a bias potential for the analysis of the radial distribution function (RDF) obtained from large-angle X-ray scattering (LAXS) data. The microscopic structure and order extension of the polymer changed from I to II, as qualitatively shown in the shapes of their experimentally measured RDF curves. With the use of a bias potential, the MD simulations provided a much more accurate analysis of the models, as seen in the reproduction of the RDFs. The chiral P-DBNP chain was found to be consistent with helix conformations in both the I and the II samples. The predominant interchain clustering motif was best reproduced with a seven-chain model. In the case of I, the maximum chain length was 18 monomeric -R(2)NP- units, while in the case of the cast film II the chain was more elongated, up to distances of approximately 100 A, equivalent to over 48 monomeric -R(2)NP- units. The seven-chain assembly was accounted for in terms of nonbonded interactions favouring the minimum voids area between the seven tubular structures of the material. The results validate our earlier finding that MD analysis with implementation of a biasing potential for the RDFs can provide quantitative information on the structural and conformational features of amorphous solids. The combined theoretical and experimental approach was found to be a useful tool to detect, locate and evaluate the intra- and intermolecular modifications of materials subsequent to their phase transformation and, as in the present case, changes in their microscopic structures or preparation methods.