Multi-funnel optimization using Gaussian underestimation

In several applications, underestimation of functions has proven to be a helpful tool for global optimization. In protein–ligand docking problems as well as in protein structure prediction, single convex quadratic underestimators have been used to approximate the location of the global minimum point. While this approach has been successful for basin-shaped functions, it is not suitable for energy functions with more than one distinct local minimum with a large magnitude. Such functions may contain several basin-shaped components and, thus, cannot be underfitted by a single convex underestimator. In this paper, we propose using an underestimator composed of several negative Gaussian functions. Such an underestimator can be computed by solving a nonlinear programming problem, which minimizes the error between the data points and the underestimator in the L ¹ norm. Numerical results for simulated and actual docking energy functions are presented.     

Periodic antiphase boundary spinel-based structures in aluminates,gallates, aluminium oxynitrides and transition aluminas

The crystallographic structures of several transition aluminas possessing a face-centred cubic packing of oxygen anions can be considered as deriving from that of a non-stoichiometric spinel. However, they are not yet known in detail owing to the poor crystallinity of most of the samples studied by X-ray or electron diffraction. Conversely, relatively large crystals have been produced in the case of non-stoichiometric spinels in the alumina-rich (or Ga₂O₃-rich) parts of the Al₂O₃–AlN, Al₂O₃–MgO, Al₂O₃–NiO, Al₂O₃–Li₂O and Ga₂O₃–MgO systems. Detailed studies of their diffraction patterns have shown that all these phases possess periodic antiphase boundary (PAPB) structures based on the spinel structure. In the case of the so-called δ-transition aluminas, various structural models have been previously proposed and in this paper we are focusing on the striking similarities between their diffraction patterns and those of several metastable PAPB aluminate structures. This makes it possible to show that at least three distinct PAPB structures must be taken into account in the case of δ-transition aluminas. APB planes are either {100} or {110} whereas APB vectors are either 1/2??001? or 1/4??110? when referring to the spinel structure. Neighbouring octahedral and tetrahedral incompatible sites are observed in the vicinity of each APB and cation vacancies are shown to occupy these octahedral sites.     

The role of problem representation and feature knowledge in algebraic equation-solving

Domain experts have two major advantages over novices with regard to problem solving: experts more accurately encode deep problem features (feature encoding) and demonstrate better conceptual understanding of critical problem features (feature knowledge). In the current study, we explore the relative contributions of encoding and knowledge of problem features (e.g., negative signs, the equals sign, variables) when beginning algebra students solve simple algebraic equations. Thirty-two students completed problems designed to measure feature encoding, feature knowledge and equation solving. Results indicate that though both feature encoding and feature knowledge were correlated with equation-solving success, only feature knowledge independently predicted success. These results have implications for the design of instruction in algebra, and suggest that helping students to develop feature knowledge within a meaningful conceptual context may improve both encoding and problem-solving performance.     

Adiabatic and nonadiabatic dynamics in the CH3(CD3)+HCl reaction

The scattering dynamics leading to the formation of Cl (2P(3/2)) and Cl* (2P(1/2)) products of the CH(3)+HCl reaction (at a mean collision energy =22.3 kcal mol(-1)) and the Cl (2P(3/2)) products of the CD(3)+HCl reaction (at =19.4 kcal mol(-1)) have been investigated by using photodissociation of CH(3)I and CD(3)I as sources of translationally hot methyl radicals and velocity map imaging of the Cl atom products. Image analysis with a Legendre moment fitting procedure demonstrates that, in all three reactions, the Cl/Cl* products are mostly forward scattered with respect to the HCl in the center-of-mass (c.m.) frame but with a backward scattered component. The distributions of the fraction of the available energy released as translation peak at f(t)=0.31-0.33 for all the reactions, with average values that lie in the range =0.42-0.47. The detailed analysis indicates the importance of collision energy in facilitating the nonadiabatic transitions that lead to Cl* production. The similarities between the c.m.-frame scattering and kinetic energy release distributions for Cl and Cl* channels suggest that the nonadiabatic transitions to a low-lying excited potential energy surface (PES) correlating to Cl* products occur after passage through the transition state region on the ground-state PES. Branching fractions for Cl* are determined to be 0.14+/-0.02 for the CH(3)+HCl reaction and 0.20+/-0.03 for the CD(3)+HCl reaction. The difference cannot be accounted for by changes in collision energy, mass effects, or vibrational excitation of the photolytically generated methyl radical reagents and instead suggests that the low-frequency bending modes of the CD(3)H or CH(4) coproduct are important mediators of the nonadiabatic couplings occurring in this reaction system.     

Substrates and Cyclic Peptide Inhibitors of the Oligonucleotide-Activated Sirtuin 7**

The sirtuins are NAD⁺-dependent lysine deacylases, comprising seven isoforms (SIRT1–7) in humans, which are involved in the regulation of a plethora of biological processes, including gene expression and metabolism. The sirtuins share a common hydrolytic mechanism but display preferences for different ϵ-N-acyllysine substrates. SIRT7 deacetylates targets in nuclei and nucleoli but remains one of the lesser studied of the seven isoforms, in part due to a lack of chemical tools to specifically probe SIRT7 activity. Here we expressed SIRT7 and, using small-angle X-ray scattering, reveal SIRT7 to be a monomeric enzyme with a low degree of globular flexibility in solution. We developed a fluorogenic assay for investigation of the substrate preferences of SIRT7 and to evaluate compounds that modulate its activity. We report several mechanism-based SIRT7 inhibitors as well as de novo cyclic peptide inhibitors selected from mRNA-display library screening that exhibit selectivity for SIRT7 over other sirtuin isoforms, stabilize SIRT7 in cells, and cause an increase in the acetylation of H3 K18.     

Synthesis and structure of iron(iii) diamine-bis(phenolate) complexes

The structures and properties of six new iron(iii) diamine-bis(phenolate) complexes are reported. Reaction of anhydrous FeX(3) salts (where X = Cl or Br) with the diprotonated tripodal tetradentate ligands 2-pyridylamino-N,N-bis(2-methylene-4-methyl-6-tert-butylphenol), H(2)[L(1)], and N,N-dimethyl-N',N'-bis(2-methylene-4-methyl-6-tert-butylphenol)ethylenediamine, H(2)[L(2)], produces the trigonal bipyramidal iron(iii) complexes, [L(1)]FeCl , [L(1)]FeBr , [L(2)]FeCl and [L(2)]FeBr . Reaction of FeX(3) with the related linear tetradentate ligand N,N'-bis(4,6-tert-butyl-2-methylphenol)-N,N'-bismethyl-1,2-diaminoethane, H(2)[L(3)], generates square pyramidal iron(iii) complexes, [L(3)]FeCl and [L(3)]FeBr . Complexes have been characterized using electronic absorption spectroscopy and magnetometry. Single crystal X-ray molecular structures have been determined for complexes 1, 3, 5 and 6.     

Interaction of first row transition metals with α1-3, α1-6 mannotriose and conserved trimannosyl core oligosaccharides: A comparative electrospray ionization study of doubly and singly charged complexes

Electrospray ionization and tandem mass spectrometry were used in the analysis of metalcoordinated oligosaccharides. Four transition metal ions, Cu²⁺, Mn²⁺, Co²⁺, and Zn²⁺, and the alkaline earth metal ion Ca²⁺, were each coordinated to the trimer α1–3, α1–6 mannotriose and the pentamer conserved trimannosyl core (mannotriosyl-chitobiose). Instrumental and concentration ratio optimization studies were carried out to determine the best conditions for producing the [M + Met]²⁺, [M + MetCl]⁺, and [M + Met ? H]⁺ ions (Met = metal dication). These precursors were then subjected to tandem mass spectrometry (MS/MS) analysis and compared. Both the ionic radii and efficacy of ligand coordination were observed as important criteria for producing the precursor ions. Tandem mass spectra for the Cu²⁺- and Zn²⁺-coordinated species did not produce significant structural information about either the trimer or the pentamer. Although tandem mass spectra for the Ca²⁺-, Co²⁺-, and Mn²⁺-coordinated trimer were very similar, those of the pentamer were not. MS/MS of the Co²⁺-coordinated pentamer was the most unique and exhibited very different dissociation pathways.     

Origin of Stability in Branched Alkanes

The potential origins of stability in branched alkanes are investigated, paying close attention to two recent hypotheses: geminal steric repulsion and protobranching. All alkane isomers through C₆H₁₄ along with heptane and octane were investigated at the MPW1B95/6‐311++G(d,p) level. Their geminal steric repulsion, total steric repulsion, and orbital interactions were evaluated by using natural bond orbital analysis. All measures of steric repulsion fail to explain the stability of branched alkanes. The extra stability of branched alkanes and protobranching, in general, is tied to stabilizing geminal σ→σ* delocalization, particularly of the type that involves adjacent C? C bonds and, thus, preferentially stabilizes branched alkanes. This picture is corroborated by valence bond calculations that attribute the effect to additional ionic structures (e.g., CH₃⁺ :CH₂ :CH₃^? and CH₃:^? CH₂: CH₃⁺ for propane) that are not possible without protobranching.     

Three-component Ugi-Smiles couplings of cyclic imines

Cyclic imines react with isocyanides and electron-deficient phenols to afford N-aryl piperidines and pyrrolidines in good yields (Ugi-Smiles couplings of cyclic imines). The starting imines were formed by oxidation with N-chlorosuccinimide followed by a base-induced dehydrochlorination.     

Separation and identification of highly fluorescent compounds derived from trans-resveratrol in the leaves of Vitis vinifera infected by Plasmopara viticola

A method for identification of highly fluorescent compounds in vine leaves infected by Plasmopara viticola was developed using reversed phase liquid chromatography with simultaneous diode array and fluorometric detection. Fluorescent compounds were extracted from leaves with a methanol-water mixture (70:30). Separation by HPLC was performed using a C(18) column and gradient elution with water-acetonitrile mixtures (20-80% of acetonitrile). The main unknown fluorescent compound was identified by line spectral comparison with a standard obtained by UV photoisomerization of trans-resveratrol glucoside, and its structure was confirmed by liquid chromatography-mass spectrometry. Identification and structural elucidation of the fluorescent compound in the leaves of Vitis vinifera allows early detection of Plasmopara viticola invasion.