From Rational Design of Drug Crystals to Understanding of Nucleic Acid Structures: Lamivudine Duplex

A DNA-like duplex of nucleosides is probable to exist even without the 5`-phosphate groups needed to assemble the chain backbone. However, double-stranded helical structures of nucleosides are unknown. Here, we report a duplex of nucleoside analogs that is spontaneously assembled due to stacking of the neutral and protonated molecules of lamivudine, a nucleoside reverse transcriptase inhibitor (NTRI) widely used in anti-HIV drug combinatory medication. The left-handed lamivudine duplex has features similar to those of i-motif DNA, as the face-to-face base stacking and the helix rise per base pair. Furthermore, the protonation pattern on alternate bases expected for it DNA-like duplex stabilized by pairing of neutral and protonated cytosine fragments was observed for the first time in the lamivudine double-stranded helix. This structure demonstrates that hydrogen bonds can substitute for covalent phosphodiester linkage in the stabilization of the duplex backbone. This interesting example of spontaneous molecular self-organization indicates that the 5`-phosphate group could not be a requirement for duplex assembly.

Conformational Polymorphism in Racemic Crystals of the Diuretic Drug Chlortalidone

Chlortalidone (HIGROTON) is a diuretic drug widely used in antihypertensive therapy. Thus far, only two solid-state polymorphs of chlortalidone have been reported. We elucidated the structure of chlortalidone form I and a new polymorph. This new phase, namely, chlortalidone form III, was also entirely characterized. It was possible to conclude that it is a conformer with a different orientation of the chlorobenzenesulfonamide moiety. Compared to form I, it has a rotation of about 90 degrees on the axis of the C-C bond bridging the substituted phenyl and isoindolinyl rings. This conformational feature is related to the crystal packing patterns of the chlortalidone forms. Furthermore, certain intermolecular hydrogen bonds are present in both polymorphs, giving rise to ribbons with chlortalidone enantiomers alternately placed into them. The chlortalidone form I and form III crystallize in the triclinic space group P (1) over bar as racemic mixtures. Additional conformational details also differentiate the chlortalidone conformers. Slight twists on the isoindolinyl and sulfamyl groups exist. Considering all structural relationships, the fingerprint plots derived from the Hirshfeld surfaces exhibited the characteristics of the chlortalidone form I and form III crystal structures.

Triple Structural Transition below Room Temperature in the Antifilarial Drug Diethylcarbamazine Citrate

A very unusual triple structural transition pattern below room temperature was observed for the antifilarial drug diethylcarbamazine citrate. Besides the first thermal, crystallographic, and vibrational investigations of this first-line drug used in clinical treatment for lymphatic filariasis, a noteworthy behavior with three structural transformations as a function of temperature was demonstrated by differential scanning calorimetry, Raman spectroscopy, and single-crystal X-ray diffractometry. Our X-ray data on single crystals allow for a complete featuring and understanding of all transitions, since the four structures associated with the three solid-solid phase transformations were accurately determined. Two of three structural transitions show an order-disorder mechanism and temperature hysteresis with exothermic peaks at 224 K (T(1)`) and 213 K (T(2)`) upon cooling and endothermic ones at 248 K (T(1)) and 226 K (T(2)) upon heating. The other transition occurs at 108 K (T(3)) and it is temperature-rate sensitive. Molecular displacements onto the (010) plane and conformational changes of the diethylcarbamazine backbone as a consequence of the C-H center dot center dot center dot N hydrogen bonding formation/cleavage between drug molecules explain the mechanism of the transitions at T(1)`/T(2). However, such changes are observed only on alternate columns of the drug intercalated by citrate chains, which leads to a doubling of the lattice period along the a axis of the 235 K structure with respect to the 150 and 293 K structures. At T(2)`/T(1), these structural alterations occur in all columns of the drug. At T(3), there is a rotation on the axis of the N-C bond between the carbamoyl moiety and an ethyl group of one crystallographically independent diethylcarbamazine molecule besides molecular shifts and other conformational alterations. The impact of this study is based on the fascinating finding in which the versatile capability of structural adaptation dependent on the thermal history was observed for a relatively simple organic salt, diethylcarbamazine citrate.

Solvothermal Preparation of Drug Crystals: Didanosine

For the first time, crystals of suitable size for X-ray diffractometry structure determination (Dian important anti-HI V drug were prepared under solvothermal conditions. In this study, the crystal structure of didanosine (2`,3`-dideoxyinosine, ddI) in the form of a hydrate was determined using single-crystal X-ray diffractometry. Powder X-ray diffraction analysis revealed that the solid-state phase of the drug incorporated into pharmaceutical solid dosage forms is isostructural to the solvothermally prepared ddI material, even though they do not exhibit an identical chemical composition due to different water fractions occupying hydrophobic channels formed within the crystal lattice. Two ddI conformers are present in the structure, in agreement with a previous structure elucidation attempt. Concerning the keto enol equilibrium of ddI, our crystal data and vibrational characterizations by Fourier transform infrared (FTIR) and FT-Raman spectroscopy techniques were conclusive to state that both conformers exist in the keto form, contrary to solid-state NMR spectroscopic assignments that suggested ddI molecules occur as enol tautomers. In addition, characterizations by thermal (differential scanning calorimetry) and spectroscopic techniques allowed us to understand the structural similarities and the differences related to the hydration pattern of the nonstoichiometric hydrates.

Adhesion as a tool for in-built nanotechnology design in cementitious materials

Confined water, such as those molecules in nanolayers of 2-3 nm in length, plays an important role in the adhesion of hydrophilic materials, mainly in cementitious ones. In this study, the effects of water containing kosmotropic substances on adhesion, known for their ability of enhancing the hydrogen bond (H-bond) network of confined water, were evaluated using mechanical strength tests. Indeed, to link adhesion provided by water confined in nanolayers to a macro-response of the cementitious samples, such as the bending strength, requires the evaluation of local water H-bond network configuration in the presence of kosmotropes, considering their influences on the extent and the strength of H-bonds. Among the kosmotropes, trimethylamine and sucrose provided a 50% increase in bending strength compared to the reference samples, the latter just using water as an adhesive, whereas trehalose was responsible for reducing the bending strength to a value close to the samples without any adhesive. The results attained opened up perspectives regarding exploring the confined water behavior which naturally occurs throughout the hydration process in cement-based materials.

Mechanochemical synthesis of niobium pentoxide nanoparticles

Acicular α-FeOOH particles are formed through aging of ferric oxyhydroxide colloidal solution formed by the neutralization of FeCl₃ aqueous solution by NaOH. The effect of foreign ion addition to the colloidal solution on the formation and morphology of α-FeOOH particles has been investigated. The magnetic properties of Fe₃O₄ particles made from the obtained particles have also been investigated. The rate constant of the formation of α-FeOOH remarkably decreased, but the crystallite size of α-FeOOH particles increased with increasing the quantity of phosphate ion added even with small amounts. These results have been explained as follows: the phosphate ions are selectively adsorbed on the (a) plane of α-FeOOH, cover the (a) plane, and block the crystal growth of the (a) plane of the α-FeOOH. The quantities of the phosphate ion adsorbed on the b and c planes are relatively small. The complex ion of Fe(OH)₄^- is preferentially deposited on both (b) and (c) planes, and the crystal growth of (b) and (c) planes is greatly accelerated. The relationship between the morphology of the formed α-FeOOH particles and the quantity of phosphate ion added has been investigated. The asterisk type particles: α-FeOOH particles heterogeneously junctioned to α-Fe₂O₃ particles, were formed when a small amount of phosphate was added to the mother liquid. The α-FeOOH crystal epitaxially grew on the junction interface with the α-Fe₂O₃ crystal. In the case of the aging at the temperature as high as 80°C, the cross type junctioned particles were stably formed at pH below 12.0. The Fe₃O₄ particles with screw-like unique three-dimensional morphology were produced from the heterogeneously junctioned particles.

Plastic deformation in a partially crystallized Zr-based BMG under Vickers indenter

Vickers indentations were carried out on an anneal-introduced partially crystallized Zr₄₁Ti₁₄Cu_12.5 Ni₁₀Be_22.5 bulk metallic glass (BMG), and the evolution of the shear bands in this samplewas investigated and compared to the as-cast, aswell as the structurally relaxed counterparts. The results indicate that the plastic deformation in the partially crystallized BMG was accommodated by the semi-circular (primary) and radial (secondary) shear bands. A full crack or flake that was produced due to the spring back during the load removal was observed. The shear band density in the annealed alloy which was dispersed with crystalliteswas significantly lower than that of the as-cast alloy. The difference of the shear band features among the three kinds of alloy status, i.e., partially crystallized, structurally relaxed and as-cast alloys was discussed in terms of the free volume in the BMGs and the characteristics of nano-composites. It has been demonstrated that the plasticity for the three statuses of alloys queues in the descending order as the as-cast, annealed with partial crystallization, and annealed without crystallization.

New insight into non-isothermal crystallization of PVA-graphene composites

The melt crystallization of poly(vinyl alcohol) (PVA) and PVA composites has been a controversial subject due to inconclusive evidence and different opinions for its decomposition during crystallization. Using graphene as a model, the melt crystallization of PVA and PVA-graphene composites occurring during single-cycle and multiple-cycle non-isothermal annealing processes was systematically analyzed using different characterization techniques. The results obtained using single-cycle non-isothermal annealing indicated that the entire crystallization process took place through two main stages. The graphene in the PVA matrix regulates the nucleation and crystal growth manner of the PVA, yet resulting in retardation of the entire crystallization. The FTIR and Raman spectroscopic results particularly demonstrated that the annealing process not only improved the crystallinity but also led to clear decomposition in PVA and PVA-graphene composites, such as the elimination of hydroxyl groups and the production of C=C double bonds. The newly produced C=C double bonds were found to be responsible for the retardation of PVA macromolecule crystallization and the breaking of hydrogen bonds among the hydroxyl groups in the PVA chains. In addition, the morphological observation and multi-cycle non-isothermal crystallization further confirmed the existence of decomposition based on the surface damage as well as decreased crystallization enthalpy and crystallization peak temperature. Therefore, the non-isothermal crystallizations of the pure PVA and the PVA-graphene composites were in fact the combination of non-isothermal crystallization and non-isothermal degradation processes.

Testing the transferability of a coarse-grained model to intrinsically disordered proteins

The intermediate-resolution coarse-grained protein model PLUM [T. Bereau and M. Deserno, J. Chem. Phys., 2009, 130, 235106] is used to simulate small systems of intrinsically disordered proteins involved in biomineralisation. With minor adjustments to reduce bias toward stable secondary structure, the model generates conformational ensembles conforming to structural predictions from atomistic simulation. Without additional structural information as input, the model distinguishes regions of the chain by predicted degree of disorder, manifestation of structure, and involvement in chain dimerisation. The model is also able to distinguish dimerisation behaviour between one intrinsically disordered peptide and a closely related mutant. We contrast this against the poor ability of PLUM to model the S1 quartz-binding peptide.

Direct Observation of Tetragonal Distortion in Epitaxial Structures through Secondary Peak Split in a Synchrotron Radiation Renninger Scan

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Nucleation kinetics of crystalline phases from a kaolinitic body used in the processing of red ceramics

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Understanding the Crystallization Mechanism of a Wollastonite Base Glass Using Isoconversional, IKP Methods and Master Plots

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Columnar microstructure of nanocrystalline Ga1-xMnxN films deposited by reactive sputtering

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)