The Impact of pH on Catalytically Critical Protein Conformational Changes: The Case of the Urease,a Nickel Enzyme

Urease uses a cluster of two Ni^II ions to activate a water molecule for urea hydrolysis. The key to this unsurpassed enzyme is a change in the conformation of a flexible structural motif, the mobile flap, which must be able to move from an open to a closed conformation to stabilize the chelating interaction of urea with the Ni^II cluster. This conformational change brings the imidazole side chain functionality of a critical histidine residue, αHis323, in close proximity to the site that holds the transition state structure of the reaction, facilitating its evolution to the products. Herein, we describe the influence of the solution pH in modulating the conformation of the mobile flap. High-resolution crystal structures of urease inhibited in the presence of N-(n-butyl)phosphoric triamide (NBPTO) at pH 6.5 and pH 7.5 are described and compared to the analogous structure obtained at pH 7.0. The kinetics of urease in the absence and presence of NBPTO are investigated by a calorimetric assay in the pH 6.0–8.0 range. The results indicate that pH modulates the protonation state of αHis323, which was revealed to have pK_a=6.6, and consequently the conformation of the mobile flap. Two additional residues (αAsp224 and αArg339) are shown to be key factors for the conformational change. The role of pH in modulating the catalysis of urea hydrolysis is clarified through the molecular and structural details of the interplay between protein conformation and solution acidity in the paradigmatic case of a metalloenzyme.     

New Type of Columnar Liquid Crystal Superlattice in Double-Taper Ionic Minidendrons

Wedge-shaped molecules, such as dendrons, are among the most important building blocks for directed supramolecular self-assembly. Here we present a new approach aimed at widening the range and complexity of potential mesophases by introducing double-tapered mesogens. Two series of compounds are presented, both alkali metal salts (Li, Na, Cs) of 3,4,5-tris-alkoxybenzoic acid with a second tapered tris-alkoxyaryl group attached at the end of an alkoxy chain. The double-tapered compounds all display an unusual hexagonal columnar phase consisting of one ionic and three non-ionic columns per unit cell. The cation size has an unexpectedly drastic effect on unit cell size. Unlike most columnar phases, the current phases show unusually high dimensional stability on heating, and high stiffness in spite of being 80–85 % aliphatic, attributed to their molecular topology. The described approach may lead to co-assemblies of multifunctional materials, for example, parallel p- and n-semiconducting nanowires or parallel ionic and electronic conductors.     

XANES/EPR Evidence of the Oxidation of Nickel(II) Quinolinylpropioamide and Its Application in Csp3−H Functionalization

An in situ generated oxidation species of nickel quinolinylpropioamide intermediate was produced. Characterization by X-ray absorption near edge structure (XANES) and EPR provides complementary insights into this oxidized nickel species. With aliphatic amides and isocyanides as substrates, a nickel-catalyzed facile synthesis of structurally diverse five-membered lactams could be achieved.     

Functional Organic Semiconductors Based on Bay‐Annulated Indigo (BAI)

The advancement of organic electronics has been continually pushed by the need for stable and high performance acceptor materials. By utilizing inexpensive and stable indigo dye as a starting material, Bay‐Annulated Indigo (BAI) provides a new motif for the development of semiconducting materials. Modular and straightforward synthesis makes BAI an outstanding platform for molecular design, while excellent stability, strong absorption, and high ambipolar mobility render BAI‐based materials excellent candidates for organic electronics. BAI‐based polymers and small molecules have taken advantage of these properties to show promising results in a variety of applications.     

An insight into the potent antioxidant activity of a dithiocarbohydrazone appended cis-dioxidomolybdenum (VI) complexes

In search of antioxidants with enriched potency, the present study focus on the design and synthesis of a dithiocarbohydrazone, H₃TCL derived from thiocarbohydrazide and 3-ethoxysalicylaldehyde and its coordination complexes with molybdenum, viz, [MoO₂(HTCL)D] ( 1 – 2 ) (where D = methanol ( 1 ), DMSO ( 2 )) and [MoO₂(HTCL)D]·DMF (where D = H₂O ( 3 )). The synthesized compounds were characterised by elemental analysis, spectroscopic techniques (FT-IR, UV–vis and ¹H-NMR), conductivity measurements and cyclic voltammetry. Moreover the solid state structures of all the three complexes were established by single crystal X-ray diffraction analysis as mononuclear neutral species in which the molybdenum centre assumes a distorted octahedral geometry. The dithiocarbohydrazone binds to the molybdenum centre through its phenolate oxygen, O(1), azomethine nitrogen, N(1) and thioenolate sulfur, S(1) in a dianionic tridentate mode. The assessment of intermolecular contacts in the crystal arrangement was quantified using Hirshfeld surface analysis. Further the antioxidant potential of the dithiocarbohydrazone, H₃TCL and its molybdenum complexes 1 – 3 were evaluated using 1,1-diphenyl-2-picrylhydrazyl(DPPH), 2,2′-azinobis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS) and total antioxidant assays. The antioxidant activities were then compared with standard antioxidant, L-ascorbic acid. The antioxidant potential of the synthesized compounds were then validated by molecular docking studies. Molecular modelling study was achieved to evaluate the recognition of target compound at the binding pocket of the human antioxidant enzyme, 3MNG. The docking results showed that the complexes selectively bond to the vital amino acids present in the binding pocket of the target enzyme, 3MNG.     

Learning extended tree augmented naive structures

This work proposes an extended version of the well-known tree-augmented naive Bayes (TAN) classifier where the structure learning step is performed without requiring features to be connected to the class. Based on a modification of Edmonds' algorithm, our structure learning procedure explores a superset of the structures that are considered by TAN, yet achieves global optimality of the learning score function in a very efficient way (quadratic in the number of features, the same complexity as learning TANs). We enhance our procedure with a new score function that only takes into account arcs that are relevant to predict the class, as well as an optimization over the equivalent sample size during learning. These ideas may be useful for structure learning of Bayesian networks in general. A range of experiments shows that we obtain models with better prediction accuracy than naive Bayes and TAN, and comparable to the accuracy of the state-of-the-art classifier averaged one-dependence estimator (AODE). We release our implementation of ETAN so that it can be easily installed and run within Weka.     

Selective Benzylic CH-Borylations by Tandem Cobalt Catalysis

Metal-catalyzed C?H activations are environmentally and economically attractive synthetic strategies for the construction of functional molecules as they obviate the need for pre-functionalized substrates and minimize waste generation. Great challenges reside in the control of selectivities, the utilization of unbiased hydrocarbons, and the operation of atom-economical dehydrocoupling mechanisms. An especially mild borylation of benzylic CH bonds was developed with the ligand-free pre-catalyst Co[N(SiMe₃)₂]₂ and the bench-stable and inexpensive borylation reagent B₂pin₂ that produces H₂ as the only by-product. A full set of kinetic, spectroscopic, and preparative mechanistic studies are indicative of a tandem catalysis mechanism of CH-borylation and dehydrocoupling via molecular Co^I catalysts.     

Near-IR absorbing donor–acceptor charge-transfer gallium complex,an example from non-transition metal chemistry

Gallium(III) catecholates with bipyridine ligand [(3,5-Cat)Ga(bipy)2]I and (3,6-Cat)GaI(bipy) (Cat is di-tert-butylcatecholate) were synthesized and characterized by single-crystal X-ray diffraction. The appearance of near-infrared ligand-to-ligand charge transfer for pentacoordinate complex was observed.     

Rapid Discrimination of Crystal Handedness by X-ray Natural Circular Dichroism (XNCD) Mapping

An original method for determining the handedness of individual non-centrosymmetric crystals in a mixture using a tightly-focused, circularly polarized X-ray beam is presented. The X-ray natural circular dichroism (XNCD) spectra recorded at the metal K-edge on selected crystals of [Δ-M(en)₃](NO₃)₂ and [Λ-M(en)₃](NO₃)₂ (M=Co^II, Ni^II) show extrema at the metal pre-edge (7712 eV for Co, 8335 eV for Ni). A mapping of a collection of some 220 crystals was performed at the respective energies by using left and right circular polarizations. The difference in absorption for the two polarizations, being either negative or positive, directly yielded the handedness of the crystal volume probed by the beam. By using this technique, it was found that the addition of l -ascorbic acid during the synthesis of [Co(en)₃](NO₃)₂ resulted in an enantiomeric enrichment of the Λ-isomer of 67±13 %, whereas the Ni analogue was similarly, but conversely, enriched in the Δ-isomer (65±22 %).