Enhancing the accuracy of virtual screening: molecular dynamics with quantum-refined force fields

Summary A methodology aimed at improving the accuracy of current docking–scoring procedures is proposed, and validated through detailed tests of its performance in predicting the activity of HIV-1 protease inhibitors. This methodology is based on molecular dynamics simulations using a force field whose effective charges are refined by means of a novel procedure that relies on quantum-mechanical calculations and preserves the internal consistency of the parameterization scheme.     

Surface reactions kinetics between nanocrystalline magnetite and uranyl

Magnetite is the most important end member of iron corrosion products under reducing environment, which is the condition expected in a deep geological high level radioactive waste disposal. Nanocrystalline magnetite was synthesized in the laboratory and its physicochemical properties were analyzed in detail. The kinetics of the adsorption of U(VI) and the kinetics of the actinide reduction to a lower oxidation state, in presence of the oxide, were studied by means of batch sorption techniques and X-ray photoelectron spectroscopy (XPS) analysis. The results showed that the uranium sorption and reduction processes on the magnetite surface have very fast kinetics (hours), the reduction process being triggered by sorption. XPS measurements showed that the speciation of uranium at the surface does not show significant changes with time (from 1 day to 3 months), as well as the quantity of uranium detected at the surface. The surface speciation depended on the initial pH of the contact solution. Considering that the Eh of equilibrium between magnetite and the solution, under our experimental conditions, is slightly positive (50-100 mV), the uranium reduction would also be thermodynamically possible within the liquid phase. However, the kinetics of reduction in the liquid occur at a much slower rate which, in turn, has to depend on the attainment of the magnetite/solution equilibrium. The decrease of uranium in solution, observed after the uranyl adsorption stage, and particularly at acidic pH, is most probably due to the precipitation of U(IV) formed in the solution.     

Metal ion catalysis in the beta-elimination reactions of N-[2-(4-pyridyl)ethyl]quinuclidinium and N-[2-(2-pyridyl)ethyl]quinuclidinium in aqueous solution

Catalysis of the beta-elimination reaction of N-[2-(4-pyridyl)ethyl]quinuclidinium (1) and N-[2-(2-pyridyl)ethyl]quinuclidinium (2) by Zn(2+) and Cd(2+) in OH(-)/H(2)O (pH = 5.20-6.35, 50 degrees C, and mu = 1 M KCl) has been studied. In the presence of Zn(2+), the elimination reactions of both isomers occur from the Zn(2+)-complexed substrates (C). The equilibrium constants for the dissociation of the Zn(2+)-complexes are as follows: K(d) = 0.012 +/- 0.003 M (isomer 1) and K(d) = 0.065 +/- 0.020 M (isomer 2). The value of k(C)(H2O) for isomer 1 is 4.81 x 10(-6) s(-1). For isomer 2 both the rate constants for the "water" and OH(-)-induced reaction of the Zn(2+)-complexed substrate could be measured, despite the low concentration of OH(-) in the investigated reaction mixture [k(C)H2O)= 1.97 x 10(-6) s(-1) and k(C)(OH-)= 21.9 M(-1) s(-1), respectively]. The measured metal activating factor (MetAF), i.e., the reactivity ratio between the complexed and the uncomplexed substrate, is 8.1 x 10(4) for the OH(-)-induced elimination of 2. This high MetAF can be compared with the corresponding proton activating factor (Alunni, S.; Conti, A.; Palmizio Errico, R. J. Chem. Soc., Perkin Trans. 2 2000, 453), PAF = 1.5 x 10(6) and is in agreement with an E1cb irreversible mechanism (A(xh)D(E)* + D(N)) (Guthrie, R. D.; Jencks, W. P. Acc. Chem. Res. 1989, 22, 343). A value of k(C)(H2O)>or= 23 x 10(-7) s(-1) is estimated for the Cd(2+)-complexed isomer 2, while catalysis by Cd(2+) has not been observed for isomer 1.     

Ferrocene and Porphyrin Monolayers on Si(100) Surfaces: Preparation and Effect of Linker Length on Electron Transfer

The missing link : Ferrocene and porphyrin monolayers are tethered on silicon surfaces with short (see picture, left) or long (right) linkers. Electron transfer to the silicon substrate is faster for monolayers with a short linker.

     

Bounds and monotonicity for the generalized Robin problem

We consider the principal eigenvalue λ ₁^Ω(α) corresponding to Δu = λ (α) u in W, \frac?u?v = au \Omega, \frac{\partial u}{\partial v} = \alpha u on ∂Ω, with α a fixed real, and W ì Rⁿ\Omega \subset {\mathcal{R}}^n a C ^0,1 bounded domain. If α > 0 and small, we derive bounds for λ ₁^Ω(α) in terms of a Stekloff-type eigenvalue; while for α > 0 large we study the behavior of its growth in terms of maximum curvature. We analyze how domain monotonicity of the principal eigenvalue depends on the geometry of the domain, and prove that domains which exhibit domain monotonicity for every α are calibrable. We conjecture that a domain has the domain monotonicity property for some α if and only if it is calibrable.     

Photo-induced pyridine substitution in cis-[Ru(bpy)(2)(py)(2)]Cl(2): a snapshot by time-resolved X-ray solution scattering

Determination of transient structures in light-induced processes is a challenging goal for time-resolved techniques. Such techniques are becoming successful in detecting ultrafast structural changes in molecules and do not require the presence of probe-like groups. Here, we demonstrate that TR-WAXS (Time-Resolved Wide Angle X-ray Scattering) can be successfully employed to study the photochemistry of cis-[Ru(bpy)(2)(py)(2)]Cl(2), a mononuclear ruthenium complex of interest in the field of photoactivatable anticancer agents. TR-WAXS is able to detect the release of a pyridine ligand and the coordination of a solvent molecule on a faster timescale than 800 ns of laser excitation. The direct measurement of the photodissociation of pyridine is a major advance in the field of time-resolved techniques allowing detection, for the first time, of the release of a multiatomic ligand formed by low Z atoms. These data demonstrate that TR-WAXS is a powerful technique for studying rapid ligand substitution processes involving photoactive metal complexes of biological interest.