Numerical computation of critical properties and atomic basins from three-dimensional grid electron densities

Claudine Katan ‘s present address : CNRS UMR6082 FOTON, INSA de Rennes, 20 avenue des Buttes de Coësmes, CS 70839, 35708 RENNES cedex 7, FranceInternational audienceInteGriTy is a software package that performs topological analysis following the AIM (atoms in molecules) approach on electron densities given on three-dimensional grids. Tricubic interpolation is used to obtain the density, its gradient and the Hessian matrix at any required position. Critical points and integrated atomic properties have been derived from theoretical densities calculated for the compounds NaCl and TTF-(2,5)Cl(2)BQ (tetrathiafulvalene-2,5-dichlorobenzoquinone), thus covering the different kinds of chemical bonds: ionic, covalent, hydrogen bonds and other intermolecular contacts

Frustrated pretransitional phenomena in aperiodic composites

Citation: Mariette, C., Frantsuzov, I., Wang, B., Guerin, L., Rabiller, P., Hollingsworth, M. D., & Toudic, B. (2016). Frustrated pretransitional phenomena in aperiodic composites. Physical Review B, 94(18), 9. doi:10.1103/PhysRevB.94.184105This paper reports on symmetry breaking in the aperiodic inclusion compound n-octadecane/urea and its isotopomer n-octadecane/urea-d(4). The high-symmetry phase is described by a hexagonal rank-4 superspace group. Pretransitional phenomena in this crystallographic superspace reveal competing short-range-ordering phenomena within the high-symmetry phase. Very high-resolution diffraction data show that critical scattering appears at inequivalent points within the four-dimensional Brillouin zone, although the first phase transition at T-c1 near 158 K implies the condensation at only one of those points. The resulting superspace group remains of dimension 4. Two other phase transitions are reported at T-c2 = 152.8(4) K and T-c3 = 109(4) K in n-octadecane/urea-d(4). The two low-symmetry phases that arise are described by rank-5 superspace groups

Neutron Laue and X-ray diffraction study of a new crystallographic superspace phase in n-nonadecane-urea

International audienceAperiodic composite crystals present long-range order without translational symmetry. These materials may be described as the intersection in three dimensions of a crystal which is periodic in a higher-dimensional space. In such materials, symmetry breaking must be described as structural changes within these crystallographic superspaces. The increase in the number of superspace groups with the increase in the dimension of the superspace allows many more structural solutions. This is illustrated in n-nonadecane-urea, revealing a fifth higher-dimensional phase at low temperature

The creation of modulated monoclinic aperiodic composites in n-alkane/urea compounds

Citation: Mariette, C., Guerin, L., Rabiller, P., Chen, Y. S., Bosak, A., Popov, A., . . . Toudic, B. (2015). The creation of modulated monoclinic aperiodic composites in n-alkane/urea compounds. Zeitschrift Fur Kristallographie, 230(1), 5-11. doi:10.1515/zkri-2014-1773n-Dodecane/urea is a member of the prototype series of n-alkane/urea inclusion compounds. At room temperature, it presents a quasi-one dimensional liquid-like state for the confined guest molecules within the rigid, hexagonal framework of the urea host. At lower temperatures, we report the existence of two other phases. Below T-c=248 K there appears a phase with rank four superspace group P6(1)22(00 gamma), the one typically observed at room temperature in n-alkane/urea compounds with longer guest molecules. A misfit parameter, defined by the ratio gamma=C-h/C-g (C-host/C-guest), is found to be 0.632 +/- 0.005. Below T-c1=123 K, a monoclinic modulated phase is created with a constant shift along c of the guest molecules in adjacent channels. The maximal monoclinic space group for this structure is P12(1)1(alpha 0 gamma). Analogies and differences with n-heptane/urea, which also presents a monoclinic, modulated low-temperature phase, are discussed

Long-range modulation of a composite crystal in a five-dimensional superspace

Citation: Guerin, L., Mariette, C., Rabiller, P., Huard, M., Ravy, S., Fertey, P., . . . Toudic, B. (2015). Long-range modulation of a composite crystal in a five-dimensional superspace. Physical Review B, 91(18), 7. doi:10.1103/PhysRevB.91.184101The intergrowth crystal of n-tetracosane/urea presents a misfit parameter, defined by the ratio gamma = c(h)/c(g) (c(host)/c(guest)), that is very close to a commensurate value (gamma congruent to 1/3). High-resolution diffraction studies presented here reveal an aperiodic misfit parameter of gamma = 0.3369, which is found to be constant at all temperatures studied. A complex sequence of structural phases is reported. The high temperature phase (phase I) exists in the four-dimensional superspace group P6(1)22(00 gamma). At T-c1 = 179(1) K, a ferroelastic phase transition increases the dimension of the crystallographic superspace. This orthorhombic phase (phase II) is characterized by the five-dimensional (5D) superspace group C222(1)(00 gamma)(10 delta) with a modulation vector a(o)* + c(m)* = a(o)* + delta . c(h)*, in which the supplementary misfit parameter is delta = 0.025(1) in host reciprocal units. This corresponds to the appearance of a modulation of very long period (about 440 +/- 16 angstrom). At T-c2 = 163.0(5) K, a 5D to 5D phase transition leads to the crystallographic superspace group P2(1)2(1)2(1)(00 gamma)(00 delta) with a very similar value of delta. This phase transition reveals a significant hysteresis effect

Neutral-ionic phase transition : a thorough ab-initio study of TTF-CA

The prototype compound for the neutral-ionic phase transition, namely TTF-CA, is theoretically investigated by first-principles density functional theory calculations. The study is based on three neutron diffraction structures collected at 40, 90 and 300 K (Le Cointe et al., Phys. Rev. B 51, 3374 (1995)). By means of a topological analysis of the total charge densities, we provide a very precise picture of intra and inter-chain interactions. Moreover, our calculations reveal that the thermal lattice contraction reduces the indirect band gap of this organic semi-conductor in the neutral phase, and nearly closes it in the vicinity of the transition temperature. A possible mechanism of the neutral-ionic phase transition is discussed. The charge transfer from TTF to CA is also derived by using three different technics.Comment: 11 pages, 9 figures, 7 table

Photoactivatable prodrugs of antimelanoma agent Vemurafenib

In this study, we report on novel photoactivatable caged prodrugs of vemurafenib. This kinase inhibitor was the first approved drug for the personalized treatment of BRAF-mutated melanoma and showed impressive results in clinical studies. However, the occurrence of severe side effects and drug resistance illustrates the urgent need for innovative therapeutic approaches. To conquer these limitations, we implemented photoremovable protecting groups into vemurafenib. In general, this caging concept provides spatial and temporal control over the activation of molecules triggered by ultraviolet light. Thus, higher inhibitor concentrations in tumor tissues might be reached with less systemic effects. Our study describes the first development of caged vemurafenib prodrugs useful as pharmacological tools. We investigated their photochemical characteristics and photoactivation. <i>In vitro</i> evaluation proved the intended loss-of-function and the light-dependent recovery of efficacy in kinase and cellular assays. The reported vemurafenib photo prodrugs represent a powerful biological tool for novel pharmacological approaches in cancer research

Role of pulmonary intravascular macrophages in endotoxin-induced lung inflammation and mortality in a rat model

<p>Abstract</p> <p>Background</p> <p>Bile-duct ligated (BDL) rats recruit pulmonary intravascular macrophages (PIMs) and are highly susceptible to endotoxin-induced mortality. The mechanisms of this enhanced susceptibility and mortality in BDL rats, which are used as a model of hepato-pulmonary syndrome, remain unknown. We tested a hypothesis that recruited PIMs promote endotoxin-induced mortality in a rat model.</p> <p>Methods</p> <p>Rats were subjected to BDL to induce PIM recruitment followed by treatment with gadolinium chloride (GC) to deplete PIMs. Normal and BDL rats were treated intravenously with <it>E. coli </it>lipopolysaccharide (LPS) with or without GC pre-treatment followed by collection and analyses of lungs for histopathology, electron microscopy and cytokine quantification.</p> <p>Results</p> <p>BDL rats recruited PIMs without any change in the expression of IL-1β, TNF-α and IL-10. GC caused reduction in PIMs at 48 hours post-treatment (P < 0.05). BDL rats treated intravenously with <it>E. coli </it>LPS died within 3 hours of the challenge while the normal LPS-treated rats were euthanized at 6 hours after the LPS treatment. GC treatment of rats 6 hours or 48 hours before LPS challenge resulted in 80% (1/5) and 100% (0/5) survival, respectively, at 6 hours post-LPS treatment. Lungs from BDL+LPS rats showed large areas of perivascular hemorrhages compared to those pre-treated with GC. Concentrations of IL-1β, TNF-α and IL-10 were increased in lungs of BDL+LPS rats compared to BDL rats treated with GC 48 hours but not 6 hours before LPS (P < 0.05).</p> <p>Conclusion</p> <p>We conclude that PIMs increase susceptibility for LPS-induced lung injury and mortality in this model, which is blocked by a reduction in their numbers or their inactivation.</p

Restoring brain function after stroke - bridging the gap between animals and humans

Stroke is the leading cause of complex adult disability in the world. Recovery from stroke is often incomplete, which leaves many people dependent on others for their care. The improvement of long-term outcomes should, therefore, be a clinical and research priority. As a result of advances in our understanding of the biological mechanisms involved in recovery and repair after stroke, therapeutic opportunities to promote recovery through manipulation of poststroke plasticity have never been greater. This work has almost exclusively been carried out in preclinical animal models of stroke with little translation into human studies. The challenge ahead is to develop a mechanistic understanding of recovery from stroke in humans. Advances in neuroimaging techniques now enable us to reconcile behavioural accounts of recovery with molecular and cellular changes. Consequently, clinical trials can be designed in a stratified manner that takes into account when an intervention should be delivered and who is most likely to benefit. This approach is expected to lead to a substantial change in how restorative therapeutic strategies are delivered in patients after stroke