Kinetics study of the OH + alkene --> H2O + alkenyl reaction class

In this paper we report on the kinetics of hydrogen abstraction for the OH + alkene reaction class, using the reaction class transition state theory (RC-TST) combined with the linear energy relationship (LER) and the barrier height grouping (BHG) approaches. Parameters for the RC-TST were derived from theoretical calculations using a set of 15 reactions representing the hydrogen abstractions from the terminal and nonterminal carbon sites of the double bond of alkene compounds. Both the RC-TST/LER, where only reaction energy is needed at either density functional theory BH&HLYP or semiempirical AM1 levels, and RC-TST/BHG, where no additional information is required, are found to be promising methods for predicting rate constants for a large number of reactions in this reaction class. Detailed error analyses show that, when compared to explicit theoretical calculations, the averaged systematic errors in the calculated rate constants using both the RC-TST/LER and RC-TST/BHG methods are less than 25% in the temperature range 300-3000 K. The estimated rate constants using these approaches are in good agreement with available data in the literature.     

Fast search algorithms for computational protein design

One of the main challenges in computational protein design (CPD) is the huge size of the protein sequence and conformational space that has to be computationally explored. Recently, we showed that state‐of‐the‐art combinatorial optimization technologies based on Cost Function Network (CFN) processing allow speeding up provable rigid backbone protein design methods by several orders of magnitudes. Building up on this, we improved and injected CFN technology into the well‐established CPD package Osprey to allow all Osprey CPD algorithms to benefit from associated speedups. Because Osprey fundamentally relies on the ability of to produce conformations in increasing order of energy, we defined new strategies combining CFN lower bounds, with new side‐chain positioning‐based branching scheme. Beyond the speedups obtained in the new ‐CFN combination, this novel branching scheme enables a much faster enumeration of suboptimal sequences, far beyond what is reachable without it. Together with the immediate and important speedups provided by CFN technology, these developments directly benefit to all the algorithms that previously relied on the DEE/ combination inside Osprey* and make it possible to solve larger CPD problems with provable algorithms. © 2016 Wiley Periodicals, Inc.     

Discrete length-volume inequalities and lower volume bounds in metric spaces

A theorem of W. Derrick ensures that the volume of any Riemannian cube \(([0,1]^n,g)\) is bounded below by the product of the distances between opposite codimension-1 faces. In this paper, we establish a discrete analog of Derrick’s inequality for weighted open covers of the cube \([0,1]^n\), which is motivated by a question about lower volume bounds in metric spaces. Our main theorem generalizes a previous result of the author in Kinneberg (J Differ Geom 100(2):349–388, 2015) which gave a combinatorial version of Derrick’s inequality and was used in the analysis of boundaries of hyperbolic groups. As an application, we answer a question of Y. Burago and V. Zalgaller about length-volume inequalities for pseudometrics on the unit cube.     

Monitoring conformational changes in protein complexes using chemical cross-linking and Fourier transform ion cyclotron resonance mass spectrometry: the effect of calcium binding on the calmodulin-melittin complex

Calmodulin is an EF hand calcium binding protein. Its binding affinities to various protein/peptide targets often depend on the conformational changes induced by the binding of calcium. One such target is melittin, which binds tightly to calmodulin in the presence of calcium, and inhibits its function. Chemical cross-linking combined with Fourier transform ion cyclotron resonance mass spectrometry has been employed to investigate the coordination of calmodulin and melittin in the complex at different concentrations of calcium. This methodology can be used to monitor structural changes of proteins induced by ligand binding, and study the effects these changes have on non- covalent interactions between proteins. Cross-linking results indicate that the binding place of the first melittin in the calcium free calmodulin form is the same as in the calcium loaded calmodulin/melittin complex.     

Contrasting singlet-triplet dynamical behavior of two vibrational levels of the acetylene S1 2(1)3(1)B2 polyad

Surface electron ejection by laser-excited metastables (SEELEM) and LIF spectra of acetylene were simultaneously recorded in the regions of the A1Au-X1Sigmag+ nominal 2(1)3(1)4(2) Ka=1<--00 and 2(1)3(1)6(2) Ka=1<--00 bands near 46,140 cm(-1). The upper states of these two bands are separated by only approximately 100 cm(-1), and the two S1 vibrational levels are known to be strongly mixed by anharmonic and Coriolis interactions. Strikingly different patterns were observed in the SEELEM spectra in the regions of the 2(1)3(1)4(2) and 2(1)3(1)6(2) vibrational levels. Because the equilibrium structure of the T3 electronic state is known to be nonplanar, excitation of nu4 (torsion) and nu6 (antisymmetric in-plane bend) are expected respectively to promote and suppress vibrational overlap between low-lying S1 and T3 vibrational levels. The nearly 50:50 mixed 2(1)3(1)4(2)-2(1)3(1)6(2) character of the S1 vibrational levels rules out this simple Franck-Condon explanation for the different appearance of the SEELEM spectra. A simple model is applied to the SEELEM/LIF spectra to explain the differences between spectral patterns in terms of a T3 doorway-mediated singlet-triplet coupling model.     

Thermoresponsive reversible behavior of multistimuli pluronic-based pentablock copolymer at the air-water interface

Surface behavior of the pH- and thermoresponsive amphiphilic ABCBA pentablock copolymer has been studied with respect to the environmental conditions. We demonstrate that the pentablock copolymer poly((diethylaminoethyl methacrylate)-b-(ethylene oxide)-b-(propylene oxide)-b-(ethylene oxide)-b-(diethylaminoethyl methacrylate)) possesses reversible temperature changes at the air-water interface in a narrow pH range of the water subphase. Significant diversity in the surface morphology of pentablock copolymer monolayers at different pH and temperatures observed were related to the corresponding reorganization of central and terminal blocks. Remarkable reversible variations of the surface pressure observed for the Langmuir monolayers at pH 7.4 in the course of heating and cooling between 27 and 50 degrees C is associated with conformational transformations of terminal blocks crossing the phase line in the vicinity of the lower critical solution temperature point. The observed thermoresponsive surface behavior can be exploited for modeling of the corresponding behavior of pentablock copolymers adsorbed onto various biointerfaces for intracellular delivery for deeper understanding of stimuli-responsive transformations relevant to controlled drug and biomolecules release and retention.     

Formation of protein-metal oxide nanostructures by the sonochemical method: observation of nanofibers and nanoneedles

The sonochemical reaction of iron pentacarbonyl is explored in water and in water with the protein BSA (bovine serum albumen). In water, the reaction is found to produce spherical nanoparticles of magnetite (Fe3O4) with a particle size distribution of <10 to approximately 60 nm. In water with BSA, the reaction produces either nanofibers or nanoneedles, depending on the concentration of BSA. The nanofiber and nanoneedle samples are found to be mixtures of goethite, lepidocrocite, and hematite (alpha-FeOOH, gamma-FeOOH, and alpha-Fe2O3, respectively). The sonochemical reaction of iron pentacarbonyl with BSA in water is thought to proceed through the thermal decomposition mechanism for iron pentacarbonyl with BSA acting as a templating agent.     

Proton NMR assignments for R,S-1,1'-binaphthol (BN) and R,S-1,1'-binaphthyl-2,2'-diyl hydrogen phosphate (BNDHP) interacting with bile salt micelles

We report proton chemical shifts for two model chiral analytes that are commonly used in the study of micellar electrokinetic capillary chromatography (MEKC), R,S-1,1'-binaphthol (1, BN) and R,S-1,1'-binaphthyl-2,2'-diyl hydrogen phosphate (2, BNDHP), in the absence and presence of monomers and micelles of sodium cholate and sodium deoxycholate. The analytes undergo fast exchange in and out of the micelles, which perturbs the analytes' chemical shifts, and which we use to resolve some resonances that are degenerate at both 300 and 600 MHz. Although BN and BNDHP are simple molecules, the proton assignments are only unambiguously established with the aid of the exchange with micelles, an attractive alternative to other methodologies such as the use of paramagnetic shift reagents which may also cause spectral distortions. We rely also upon 2D-NOE spectra of samples in the presence of micelles to perform these assignments. Recently published assignments, which were based upon 2D-COSY spectroscopy, appear to be in error and are corrected here. Finally, we note that these shifts are information-rich reporters on the nature of the interactions of these model analytes with the micelles.     

Lipid-mimicking phosphorus-based glycosidase inactivators as pharmacological chaperones for the treatment of Gaucher's disease

Gaucher''s disease, the most prevalent lysosomal storage disorder, is caused by missense mutation of the GBA gene, ultimately resulting in deficient GCase activity, hence the excessive build-up of cellular glucosylceramide. Among different therapeutic strategies, pharmacological chaperoning of mutant GCase represents an attractive approach that relies on small organic molecules acting as protein stabilizers. Herein, we expand upon a new class of transient GCase inactivators based on a reactive 2-deoxy-2-fluoro-β-d-glucoside tethered to an array of lipid-mimicking phosphorus-based aglycones, which not only improve the selectivity and inactivation efficiency, but also the stability of these compounds in aqueous media. This hypothesis was further validated with kinetic and cellular studies confirming restoration of catalytic activity in Gaucher cells after treatment with these pharmacological chaperones.

Engineered 2-fluoroglucosides containing a phosphorus-based leaving group rapidly form a stable covalent intermediate with GCase, thus stabilising the enzyme during transit to the lysosome, where it is released on a clinically appropriate timescale.     

Structures and Dynamics of Secondary and Tertiary Alkylphosphine Oxides Adsorbed on Silica

The three secondary phosphine oxides [CH₂=CH(CH₂)₄]₂HPO ( 1 ), [CH₂=CH(CH₂)₅]₂HPO ( 2 ), and [CH₂=CH(CH₂)₆]₂HPO ( 3 ), and two diphosphine dioxides, {[CH₂=CH(CH₂)₆]₂PO(CH₂)₇}₂ ( 4 ) and {[CH₂=CH(CH₂)₆]₂PO(CH₂)₄}₂ ( 5 ), incorporating long methylene chains, are described. The single crystal X‐ray structures of 1 , 2 , and 5 have been determined. The phosphine oxides 3 , 4 , and 5 have been adsorbed on silica in submonolayer quantities to give 3 a – 5 a . The ¹H, ¹³C, and ³¹P solid‐state NMR spectra of polycrystalline 3 – 5 have been analyzed and compared with those of 3 a – 5 a . The changes of the solid‐state NMR characteristics upon adsorption and the surface mobilities of the phosphine oxides are discussed.