Accuracy assessment of the linear Poisson–Boltzmann equation and reparametrization of the OBC generalized Born model for nucleic acids and nucleic acid–protein complexes

The generalized Born model in the Onufriev, Bashford, and Case (Onufriev et al., Proteins: Struct Funct Genet 2004, 55, 383) implementation has emerged as one of the best compromises between accuracy and speed of computation. For simulations of nucleic acids, however, a number of issues should be addressed: (1) the generalized Born model is based on a linear model and the linearization of the reference Poisson–Boltmann equation may be questioned for highly charged systems as nucleic acids; (2) although much attention has been given to potentials, solvation forces could be much less sensitive to linearization than the potentials; and (3) the accuracy of the Onufriev–Bashford–Case (OBC) model for nucleic acids depends on fine tuning of parameters. Here, we show that the linearization of the Poisson Boltzmann equation has mild effects on computed forces, and that with optimal choice of the OBC model parameters, solvation forces, essential for molecular dynamics simulations, agree well with those computed using the reference Poisson–Boltzmann model. © 2015 Wiley Periodicals, Inc.     

Probing the metal-to-ligand charge transfer first excited state in (η6-naphthalene)Cr(CO)3 and (η6-phenanthrene)Cr(CO)3 by resonance Raman spectroscopy and density functional theory calculations

The nature of the lowest energy optical transition for the complexes (η(6)-naphthalene)Cr(CO)(3) and (η(6)-phenanthrene)Cr(CO)(3) in the solid state has been investigated by Raman spectroscopy using a range of different excitation wavelengths progressively approaching the resonant condition. Examination of the resonantly enhanced Raman modes confirms that the first absorption is attributed predominantly to a metal-to-arene charge transfer transition for both complexes. A notable difference in the photochemistry of the two complexes was observed. In the case of the phenanthrene complex, population of the lowest energy excited state leads to a photochemical process which resulted in the loss of the arene ligand and formation of Cr(CO)(6).     

Prediction of HPLC retention times in gradient elution from isocratic data application to a set of non-homologous compounds and different stationary phases

Summary Polymethyloctylsiloxane-coated stationary phases have been prepared for liquid chromatography, by thermal reaction. The influence of the reaction conditions on retention and efficiency of test substances with different structures has been discussed. The materials have good stability in both acidic and basic eluents.     

A new approach to the prediction of RP-HPLC retention times in gradient elution from isocratic data

Summary A general chromatographic model has been set up starting from a set of equations based on the concept of the velocity of a solute along the column. The composition of the mobile phase is taken into account solely as a numerical factor entering into suitable equations and totally independent of the chemical-properties of the constituents. A few isocratic experimental runs are necessary as input data, and subsequently a small amount of computational effort is sufficient to make predictions of retention times under gradient elution conditions for solutes of whatever chemical structure. The prediction errors are dependent on the steepness of the linear gradient chosen but are, in any case, acceptably low.     

Structural and chiroptical properties of the two coordination isomers of YbDOTA-type complexes

Studies of the structural, physical, and chemical properties of the lanthanide(III) complexes of DOTA (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) and related ligands are often complicated by the presence of two coordination isomers in solution. Since these coordination isomers are in exchange and cannot be separated, many techniques offer information only on the weighted average of the two isomers. Lanthanide ion complexes formed with the ligands S(RRRR)NO2BnDOTMA and S(SSSS)NO2BnDOTMA preferentially adopt only one of the two common coordination isomers in solution, so the ytterbium complexes of these ligands offer a unique opportunity to study the near-infrared circular dichroism (NIR-CD) characteristics of each coordination geometry in isolation. The spectra acquired support many of the conclusions and assumptions of previous studies and demonstrate that this spectroscopy is particularly sensitive to the distortion of the coordination polyhedron. This will have particularly relevant consequences when studying achiral YbDOTA-like systems forming labile adducts with (chiral) hosts and receptors.     

Positive Solutions of Nonlocal Boundary Value Problems: A Unified Approach

We give a unified approach for studying the existence of multiplepositive solutions of nonlinear differential equations of theform where g, f are non-negativefunctions, subject to various nonlocal boundary conditions.We study these problems via new results for a perturbed integralequation, in the space C[0, 1], of the form where [u], ß[u] are linear functionalsgiven by Stieltjes integrals but are not assumed to be positivefor all positive u. This means we actually cover many more differentialequations than the simple equation written above. Previous resultshave studied positive functionals only, but even for positivefunctionals our methods give improvements on previous work.The well-known m-point boundary value problems are special casesand we obtain sharp conditions on the coefficients, which allowssome of them to have opposite signs. We also use some optimalassumptions on the nonlinear term.