Molecular dynamics simulations,docking and MMGBSA studies of newly designed peptide-conjugated glucosyloxy stilbene derivatives with tumor cell receptors

Molecular Diversity - In this work, for the first time, we designed derivatives of beta-D-glucosyloxy-3-hydroxy-trans-stiblene-2-carboxylic acid (GHS), by conjugating GHS with tumor targeting...     

Effect of External Pressure on the Excitation Energy Transfer from [Cr(ox)3]3− to [Cr(bpy)3]3+ in [Rh1−xCrx(bpy)3][NaM1−yCry(ox)3]ClO4

Resonant excitation energy transfer from [Cr(ox)₃]^3? to [Cr(bpy)₃]³⁺ in the doped 3D oxalate networks [Rh_1?xCr_x(bpy)₃][NaM^III_1?yCr_y(ox)₃]ClO₄ (ox=C₂O₄^?, bpy=2,2′‐bipyridine, M=Al, Rh) is due to two types of interaction, namely super exchange coupling and electric dipole–dipole interaction. The energy transfer probability for both mechanisms is proportional to the spectral overlap of the ²E→⁴A₂ emission of the [Cr(ox)₃]^3? donor and the ⁴A₂→²T₁ absorption of the [Cr(bpy)₃]³⁺ acceptor. The spin‐flip transitions of (pseudo‐)octahedral Cr³⁺ are known to shift to lower energy with increasing pressure. Because the shift rates of the two transitions in question differ, the spectral overlap between the donor emission and the acceptor absorption is a function of applied pressure. For [Rh_1?xCr_x(bpy)₃][NaM_1?yCr_y(ox)₃]ClO₄ the spectral overlap is thus substantially reduced on increasing pressure from 0 to 2.5 GPa. As a result, the energy transfer probability decreases with increasing pressure as evidenced by a decrease in the relative emission intensity from the [Cr(bpy)₃]³⁺ acceptor.     

Novel sulfur-containing rapamycin analogs prepared by precursor-directed biosynthesis

[reaction: see text] Two novel sulfur-containing analogs of the immunosuppressive natural product rapamycin (1) were obtained by feeding cultures of Streptomyces hygroscopicus with l-nipecotic acid (4) and either (S)-1,3-thiazane-4-carboxylic acid (5) or (S)-1,4-thiazane-3-carboxylic acid (6). The structures of the two new compounds, 20-thiarapamycin (2) and 15-deoxo-19-sulfoxylrapamycin (3), were determined by spectroscopic methods.     

Synthesis and Conformational Analysis of 2′-Deoxy-2′-(3-methoxybenzamido)adenosine,a rational-designed inhibitor of trypanosomal glyceraldehyde phosphate dehydrogenase (GAPDH)

A series of 2′-benzamido-2′-deoxyadenosine analogues were synthesized in an effort to find new lead structures for the treatment of sleeping sickness. The 2′-deoxy-2′-(3-methoxybenzamido)adenosine ( 1h ) was proved to be a selective inhibitor of the parasite glyceraldehyde 3-phosphate dehydrogenase which confirms the modeling studies. The solution-state conformation of 2′-(thiophene-2-carboxamido) analogue 1d demonstrates a 2′-endo conformation, an orientation of the thiophene ring under the ribose moiety, and the base part occupying a ‘syn’/‘anti’ equilibrium.     

NMR analysis of surfaces and interfaces in 2-nm CdSe

Solid-state NMR analysis on wurtzite 2-nm hexadecylamine-capped CdSe nanocrystals (CdSe-HDA) provides evidence of discrete nanoparticle reconstruction within the Se sublattice of the nanomaterial. The cadmium and selenium atoms are probed with (1)H-(113)Cd and (1)H-(77)Se cross-polarization magic angle spinning (MAS) experiments, which demonstrate five ordered selenium sites in the nanoparticle that can be assigned to contributions arising from different surface sites and a selenium site one layer down from the surface. Intriguingly, in these materials both HDA and thiophenol are observed to selectively bind to specific sites on the nanoparticle surface. 2D heteronuclear chemical shift correlation (HETCOR) experiments provide evidence for thiophenol selectively binding at surface vacancies. Analysis of the NMR provides a model of a 2-nm CdSe-HDA molecular surface.     

Detecting outlying samples in a parallel factor analysis model

To explore multi-way data, different methods have been proposed. Here, we study the popular PARAFAC (Parallel factor analysis) model, which expresses multi-way data in a more compact way, without ignoring the underlying complex structure. To estimate the score and loading matrices, an alternating least squares procedure is typically used. It is however well known that least squares techniques suffer from outlying observations, making the models useless when outliers are present in the data. In this paper, we present a robust PARAFAC method. Essentially, it searches for an outlier-free subset of the data, on which we can then perform the classical PARAFAC algorithm. An outlier map is constructed to identify outliers. Simulations and examples show the robustness of our approach.     

Isotope-labeling of the fibril binding compound FSB via a Pd-catalyzed double alkoxycarbonylation

We have synthesized two isotopically labeled variants of the β-amyloid binding compound FSB possessing (13)C-labels on the two terminal aryl carboxylic acid moieties. One of these was also fully deuterated on the olefinic spacers. The (13)C-isotope labeling was achieved applying a Pd-catalyzed methoxycarbonylation of the corresponding aryl chlorides with externally (ex situ) generated (13)C-labeled CO. Application of the Shirakawa-Hayashi protocol for the Pd-catalyzed reduction of a dialkyne intermediate using D(2)O allowed for the selective deuterium labeling of the two trans-C,C double bonds of FSB.     

Comparison of thermodynamic stabilities and mechanical properties of CO2, SiO2, and GeO2 polymorphs by first-principles calculations

The recent discovery that molecular CO(2) transforms under compression into carbon four-coordinated, 3-dimensional network solid phases has generated considerable interests on possible new phases in the fourth-main-group elemental oxides. Based on density-functional theory calculations, we have investigated the thermodynamic stability, mechanical properties and electronic structure of proposed guest-free clathrates, quartz and cristobalite phases for CO(2), SiO(2), and GeO(2), and the dry ice phase for CO(2). It was predicted that a GeO(2) clathrate, likely a semiconductor, could be synthesized presumably with some suitable guest molecules. The hypothetical CO(2) guest-free clathrate phase was found hardly to be formed due to the large energy difference with respect to the other polymorphs. This phase is unstable at all pressures, which is also implied by its different electronic structure in comparison with SiO(2) and GeO(2). Finally, the SiO(2) clathrate presents a uniquely high bulk modulus, which is higher than that of quartz and three times of the experimental data, might not be a weak point of ab-initio calculations such as pseudopotentials, correlation functional etc., instead it can be readily understood by the constraint as imposed by the high symmetry. Either temperature or an "exhausted" relaxation (without any symmetry constraint) can remedy this problem.