Multidimensional De Novo Design Reveals 5‐HT2B Receptor‐Selective Ligands

We report a multi‐objective de novo design study driven by synthetic tractability and aimed at the prioritization of computer‐generated 5‐HT_2B receptor ligands with accurately predicted target‐binding affinities. Relying on quantitative bioactivity models we designed and synthesized structurally novel, selective, nanomolar, and ligand‐efficient 5‐HT_2B modulators with sustained cell‐based effects. Our results suggest that seamless amalgamation of computational activity prediction and molecular design with microfluidics‐assisted synthesis enables the swift generation of small molecules with the desired polypharmacology.     

Solution on the Bethe lattice of a hard core athermal gas with two kinds of particles

Athermal lattice gases of particles with first neighbor exclusion have been studied for a long time as simple models exhibiting a fluid-solid transition. At low concentration the particles occupy randomly both sublattices, but as the concentration is increased one of the sublattices is occupied preferentially. Here, we study a mixed lattice gas with excluded volume interactions only in the grand-canonical formalism with two kinds of particles: small ones, which occupy a single lattice site and large ones, which, when placed on a site, do not allow other particles to occupy its first neighbors also. We solve the model on a Bethe lattice of arbitrary coordination number q. In the parameter space defined by the activities of both particles, at low values of the activity of small particles (z(1)) we find a continuous transition from the fluid to the solid phase as the activity of large particles (z(2)) is increased. At higher values of z(1) the transition becomes discontinuous, both regimes are separated by a tricritical point. The critical line has a negative slope at z(1) = 0 and displays a minimum before reaching the tricritical point, so that a re-entrant behavior is observed for constant values of z(2) in the region of low density of small particles. The isobaric curves of the total density of particles as a function of the density or the activity of small particles show a minimum in the fluid phase.     

Vibrational analysis of excited and ground electronic states of all-trans retinal protonated Schiff-bases

We report on vibrational coherence dynamics in excited and ground electronic states of all-trans retinal protonated Schiff-bases (RPSB), investigated by time-resolved Degenerate Four-Wave-Mixing (DFWM). The results show that wave packet dynamics in the excited state of RPSB consist of only low-frequency (<800 cm(-1)) modes. Such low-frequency wave packet motion is observed over a broad range of detection wavelengths ranging from excited state absorption (～500 nm) to stimulated emission (>600 nm). Our results indicate that low-frequency coherences in the excited state are not activated directly by laser excitation but rather by internal vibrational energy redistribution. This is supported by the observation that similar coherence dynamics are not observed in the electronic ground state. Challenging previous experimental results, we show that the formation of low-frequency coherence dynamics in RPSB does not require significant excess vibrational energy deposition in the excited state vibrational manifolds. Concerning ground state wave packet dynamics, we observe a set of high-frequency (>800 cm(-1)) modes, reflecting mainly single and double bond stretching motion in the retinal polyene-chain. Dephasing of these high-frequency coherences is mode-dependent and partially differs from analogous vibrational dephasing of the all-trans retinal chromophore in a protein environment (bacteriorhodopsin).     

Stabilization of Natural Pigments in Ethanolic Solutions for Food Applications: The Case Study of Chlorella vulgaris

Chlorella vulgaris is a green microalga with a high chlorophyll content, representing a valuable source of green pigments for food applications. As the application of whole biomass can promote an unpleasant fish-like flavor, the use of chlorophyll extract can overcome this drawback. However, chlorophylls tend to easily degrade when out of the chloroplasts, decreasing their potential as a food ingredient. Thus, to study the suitable conditions for isolated chlorophylls preservation, in this work, the influence of temperature (4 to 60 °C), light (dark or 24 h photoperiod), alkaline conditions (with or without aqueous NaOH addition), and modified atmosphere (air or argon atmosphere) on the stability of the color in ethanolic solutions obtained from C. vulgaris were studied. The loss of green color with temperature followed the first-order kinetics, with an activation energy of 74 kJ/mol. Below 28 °C and dark conditions were suitable to preserve isolated chlorophylls. The addition of NaOH and an inert argon-rich atmosphere did not exhibit a statistically positive effect on color preservation. In the case study, cooked cold rice was colored to be used in sushi. The color remained stable for up to 3 days at 4 °C. Therefore, this work showed that C. vulgaris chlorophylls could be preserved in ethanolic solutions at room or lower temperatures when protected from light, allowing them to obtain a suitable natural food ingredient to color foodstuffs.     

New designs for inhibitors of the NF-κB: DNA binding

We present a series of new inhibitors of the association between nuclear factor kappa B (NF-B) and the corresponding B site in DNA. They were designed using the lead compound 15-deoxy-^12,14 -prostaglandin J₂ (PGJ2), which is a natural product with demonstrated inhibitory efficiency for this system. First, the binding mode of PGJ2 to NF-B was unraveled by GOLD docking calculation. Subsequently, substitutions were made to PGJ2 to optimize its association with NF-B. Care was taken not to strongly increase the reactivity of the new compounds, and to keep the overall shape, size and hydrophilicity of the lead compound, which should render them a similar bioavailability. Molecular mechanics calculations were performed to decide on the suitability of the substitutions, and to evaluate the energies of association with NF-B. Density functional theory calculations were performed also to study the overall reactivity of the substituted drugs towards NF-B. Important general conclusions were obtained, concerning the improvement of these natural inhibitors; namely, a set of rational methodologies were deduced to improve the association between the PGJ2 derivatives and NF-B, and their efficiency demonstrated by generating a set of substituted complexes, some of them with a very much increased affinity for NF-B, opening new doors to enlarge the therapeutic capabilities of this class of drugs.     

Fourier-transform infrared spectrum of aspartate hydroxo-aqua nickel (II) complex and DFT-B3LYP/3-21G and 6-311G structural and vibrational calculations

Aspartate hydroxo-aqua nickel (II) complex was synthesized and the structural analysis was carried out through the following methods: determination of the C, N, O and H contents, thermogravimetry and infrared spectrum. Several hypothetic structures were calculated by means of DFT: B3LYP/3-21G and B3LYP/6-311G quantum mechanical method. For [Ni(Asp)(OH)(H(2)O)] we have obtained the minimum of energy and no imaginary frequencies in the calculated infrared spectrum. Moreover, the experimental FT-infrared spectrum shows that the two N-H stretching follow the Bellamy-Williams relation proposed for primary amines. Coordination water bands were also observed in the infrared spectrum. For reasons of accomplishment, the Fourier transforms infrared and Raman spectra of acid aspartic were also discussed.     

Multiplex coherent anti-Stokes Raman microspectroscopy with tailored Stokes spectrum

We combined the ultrabroadband supercontinuum of a photonic crystal fiber with a pulse shaper, resulting in a highly flexible light source for multiplex coherent anti-Stokes Raman microscopy. Implemented as the Stokes pulse, it provides tailored selection of the relevant Raman transitions, resulting in a reduced photon load and partial suppression of the nonresonant background. This experiment exploits the advantages of multiplex excitation with the increased acquisition speed of single-channel detection. The molecule-specific Stokes pulses are demonstrated for chemical mapping of a polymer blend.     

Shaper-assisted full-phase characterization of UV pulses without a spectrometer

A full-phase measurement of low-energy femtosecond UV pulses is presented. The method relies on phase retrieval of measured sonogram traces and is greatly simplified by a two-dimensional shaper-assisted cross correlation setup. As all required pulses are generated by the pulse shaper, the method is free of external references and additional tunable filter setups.