New parameterization approaches of the LIE method to improve free energy calculations of PlmII‐Inhibitors complexes

The standard parameterization of the Linear Interaction Energy (LIE) method has been applied with quite good results to reproduce the experimental absolute binding free energies for several protein–ligand systems. However, we found that this parameterization failed to reproduce the experimental binding free energy of Plasmepsin II (PlmII) in complexes with inhibitors belonging to four dissimilar scaffolds. To overcome this fact, we developed three approaches of LIE, which combine systematic approaches to predict the inhibitor‐specific values of α, β, and γ parameters, to gauge their ability to calculate the absolute binding free energies for these PlmII‐Inhibitor complexes. Specifically: (i) we modified the linear relationship between the weighted nonpolar desolvation ratio (WNDR) and the α parameter, by introducing two models of the β parameter determined by the free energy perturbation (FEP) method in the absence of the constant term γ, and (ii) we developed a new parameterization model to investigate the linear correlation between WNDR and the correction term γ. Using these parameterizations, we were able to reproduce the experimental binding free energy from these systems with mean absolute errors lower than 1.5 kcal/mol. © 2010 Wiley Periodicals, Inc. J Comput Chem 2010     

Reactivity of allenoates towards aziridines: synthesis of functionalized methylenepyrrolidines and pyrroles

The reactivity of buta-2,3-dienoates towards aziridines is reported. Typically, allenoates react as the 2π-component in the [3+2] cycloaddition with azomethine ylides generated from aziridines, affording 4-methylenepyrrolidines in a site-, regio- and stereoselective fashion. However, N-cyclohexyl- or N-tert-butyl-2-benzoyl-3-phenylaziridines showed a different reactivity in the reaction with buta-2,3-dienoates. Pyrrole derivatives were obtained as single or major products resulting from a formal [3+2] cycloaddition via C-N bond cleavage of the three-membered ring heterocycle leading to functionalized pyrroles. From the reaction with allenoates bearing bulkier C-4 substituents 4-methylenepyrrolidines were also formed as minor products.     

Measurement of relaxation rates of N(H) and H(alpha) backbone protons in proteins with tailored initial conditions.

Several methods are presented for the selective determination of spin-lattice and spin-spin relaxation rates of backbone protons in labeled proteins. The relaxation rates of amide protons in (15)N labeled proteins can be measured by using two-way selective cross-polarization (SCP). The measurement of H(alpha) relaxation rates can be achieved by combining this method with homonuclear Hartmann-Hahn transfer using doubly selective irradiation. Various schemes for selective or nonselective inversion of the longitudinal proton magnetization lead to different initial recovery rates. The methods have been applied to lysine K6 in (15)N-labeled human ubiquitin and to leucine L5 in (15)N- and (13)C-labeled octapeptide YG*G*F*LRRI (GFL) in which the marked residues are (15)N- and (13)C-labeled.     

Synthesis and characterisation of new pyrazole-phosphinite ligands and their ruthenium(II) arene complexes

The new potentially bidentate pyrazole-phosphinite ligands [(3,5-dimethyl-1H-pyrazol-1-yl)methyl diphenylphosphinite] (L¹) and [2-(3,5-dimethyl-1H-pyrazol-1-yl)ethyl diphenylphosphinite] (L²) were synthesised and characterised. The reaction of L¹ and L² with the dimeric complexes [Ru(η⁶-arene)Cl₂]₂ (arene = p-cymene, benzene) led to the formation of neutral complexes [Ru(η⁶-arene)Cl₂(L)] (L = L¹, L²) where the pyrazole-phosphinite ligand is κ¹-P coordinated to the metal. The subsequent reaction of these complexes with NaBPh₄ or NaBF₄ produced the [Ru(η⁶-p-cymene)Cl(L²)][BPh₄] and [Ru(η⁶-benzene)Cl(L²)][BF₄] compounds which contain the pyrazole-phosphinite ligand κ²-P,N bonded to ruthenium. All the complexes were fully characterised by analytical and spectroscopic methods. The structure of the complex [Ru(η⁶-p-cymene)Cl(L²)][BPh₄] was also determined by a X-ray single crystal diffraction study.     

Sidelobe decline in single-photon 4Pi microscopy by Toraldo rings

We demonstrate theoretically the feasibility of single-photon 4Pi-confocal microscopy. By inserting a pair of properly designed multi-ring phase-only pupil filters in the illumination path of a 4Pi microscope the height of the sidelobes of the point spread function substantially reduced, so that there is no ambiguity in the 3D image. Then, an axial resolution up to four times higher than that of single-photon confocal microscope can be effectively achieved.     

Ambient Moisture Accelerates Hydroamination Reactions of Vinylarenes with Alkali-Metal Amides under Air

A straightforward alkali-metal-mediated hydroamination of styrenes using biorenewable 2-methyltetrahydrofuran as a solvent is reported. Refuting the conventional wisdom of the incompatibility of organolithium reagents with air and moisture, shown here is that the presence of moisture is key in favoring formation of the target phenethylamines over competing olefin polymerization products. The method is also compatible with sodium amides, with the latter showing excellent promise as highly efficient catalysts under inert atmosphere conditions.     

Basic ancillary ligands promote O-O bond formation in iridium-catalyzed water oxidation: a DFT study

The cationic iridium complex [Ir(OH(2))(2)(phpy)(2)](+) (phpy = o-phenylpyridine) is among the most efficient mononuclear catalysts for water oxidation. The postulated active species is the oxo complex [Ir(O)(X)(phpy)(2)](n), with X = OH(2) (n = +1), OH(-) (n = 0) or O(2-) (n = -1), depending on the pH. The reactivity of these species has been studied computationally at the DFT(B3LYP) level. The three [Ir(O)(X)(phpy)(2)](n) complexes have an electrophilic Ir(v)-oxo moiety, which yields an O-O bond by undergoing a nucleophilic attack of water in the critical step of the mechanism. In this step, water transfers one proton to either the Ir(V)-oxo moiety or the ancillary X ligand. Five different reaction pathways associated with this acid/base mechanism have been characterized. The calculations show that the proton is preferably accepted by the X ligand, which plays a key role in the reaction. The higher the basicity of X, the lower the energy barrier associated with O-O bond formation. The anionic species, [Ir(O)(2)(phpy)(2)](-), which has the less electrophilic Ir(V)-oxo moiety but the most basic X ligand, promotes O-O bond formation through the lowest energy barrier, 14.5 kcal mol(-1). The other two active species, [Ir(O)(OH)(phpy)(2)] and [Ir(O)(OH(2))(phpy)(2)](+), which have more electrophilic Ir(V)-oxo moieties but less basic X ligands, involve higher energy barriers, 20.2 kcal mol(-1) and 25.9 kcal mol(-1), respectively. These results are in good agreement with experiments showing important pH effects in similar catalytic systems. The theoretical insight given by the present study can be useful in the design of more efficient water oxidation catalysts. The catalytic activity may increase by using ligand scaffolds bearing internal bases.     

Stereoselective access to fluorinated and non-fluorinated quaternary piperidines: synthesis of pipecolic acid and iminosugar derivatives

The preparation of optically pure quaternary piperidines, both fluorinated and non-fluorinated, has been achieved from a chiral imino lactone derived from (R)-phenylglycinol. In the case of the fluorinated derivatives, the addition of (trifluoromethyl)trimethylsilane (TMSCF(3)) followed by iodoamination and migration of the CF(3) group allowed access to four derivatives of α-(trifluoromethyl)pipecolic acid. A theoretical study of the CF(3)-group rearrangement has been carried out to help establish the reaction mechanism of this uncommon transformation. Moreover, a route to trifluoromethyl-substituted iminosugars was also developed through the diastereoselective dihydroxylation of suitable synthetic intermediates. Conversely, alkylation of the starting substrate and subsequent cross-metathesis and aza-Michael reactions led to α-alkyl derivatives of the target compounds.     

Water oxidation kinetics of nanoporous BiVO4 photoanodes functionalised with nickel/iron oxyhydroxide electrocatalysts

In this work, spectroelectrochemical techniques are employed to analyse the catalytic water oxidation performance of a series of three nickel/iron oxyhydroxide electrocatalysts deposited on FTO and BiVO₄, at neutral pH. Similar electrochemical water oxidation performance is observed for each of the FeOOH, Ni(Fe)OOH and FeOOHNiOOH electrocatalysts studied, which is found to result from a balance between degree of charge accumulation and rate of water oxidation. Once added onto BiVO₄ photoanodes, a large enhancement in the water oxidation photoelectrochemical performance is observed in comparison to the un-modified BiVO₄. To understand the origin of this enhancement, the films were evaluated through time-resolved optical spectroscopic techniques, allowing comparisons between electrochemical and photoelectrochemical water oxidation. For all three catalysts, fast hole transfer from BiVO₄ to the catalyst is observed in the transient absorption data. Using operando photoinduced absorption measurements, we find that water oxidation is driven by oxidised states within the catalyst layer, following hole transfer from BiVO₄. This charge transfer is correlated with a suppression of recombination losses which result in remarkably enhanced water oxidation performance relative to un-modified BiVO₄. Moreover, despite similar electrocatalytic behaviour of all three electrocatalysts, we show that variations in water oxidation performance observed among the BiVO₄/MOOH photoanodes stem from differences in photoelectrochemical and electrochemical charge accumulation in the catalyst layers. Under illumination, the amount of accumulated charge in the catalyst is driven by the injection of photogenerated holes from BiVO₄, which is further affected by the recombination loss at the BiVO₄/MOOH interface, and thus leads to deviations from their behaviour as standalone electrocatalysts.

Elucidating the role of charge accumulation and reaction kinetics in governing the performance of Ni/Fe oxyhydroxides as electrocatalysts and as co-catalysts on BiVO₄ photoanodes water oxidation.     

Combined use of NMR relaxation measurements and hydrodynamic calculations to study protein association. Evidence for tetramers of low molecular weight protein tyrosine phosphatase in solution

We describe a novel method for determining weak association constants of oligomeric protein complexes formed transiently under equilibrium conditions. This type of equilibrium process is recognized as being biologically important, but generally hard to study. Heteronuclear spin relaxation rates measured at multiple protein concentrations are analyzed using relaxation rates predicted from hydrodynamic calculations, yielding equilibrium constants and structural characterization of the protein complexes. The method was used to study the oligomerization equilibrium of bovine low molecular weight protein tyrosine phosphatase. X-ray structures of monomeric and dimeric forms of the protein have been reported previously. Using longitudinal and transverse (15)N relaxation rates measured at four different protein concentrations, we detected the monomer, dimer, and a previously unknown tetramer and measured the dissociation constants of the equilibria involving these species. A comparison of experimental and predicted relaxation rates for individual backbone amide (15)N spins enabled delineation of the tetramerization interface. The results suggest a novel concept for substrate modulation of enzymatic activity based on a "supramolecular proenzyme". The fast and reversible switching of the "supramolecular proenzyme" would have obvious advantages for the regulation of enzymes involved in cell signaling pathways.