Combining a polarizable force-field and a coarse-grained polarizable solvent model. II. Accounting for hydrophobic effects

A revised and improved version of our efficient polarizable force-field/coarse grained solvent combined approach (Masella, Borgis, and Cuniasse, J. Comput. Chem. 2008, 29, 1707) is described. The polarizable pseudo-particle solvent model represents the macroscopic solvent polarization by induced dipoles placed on mobile pseudo-particles. In this study, we propose a new formulation of the energy term handling the nonelectrostatic interactions among the pseudo-particles. This term is now able to reproduce the energetic and structural response of liquid water due to the presence of a hydrophobic spherical cavity. Accordingly, the parameters of the energy term handling the nonpolar solute/solvent interactions have been refined to reproduce the free-solvation energy of small solutes, based on a standard thermodynamic integration scheme. The reliability of this new approach has been checked for the properties of solvated methane and of the solvated methane dimer, as well as by performing 10 × 20 ns molecular dynamics (MD) trajectories for three solvated proteins. A long-time stability of the protein structures along the trajectories is observed. Moreover, our method still provides a measure of the protein solvation thermodynamic at the same accuracy as standard Poisson-Boltzman continuum methods. These results show the relevance of our approach and its applicability to massively coupled MD schemes to accurately and intensively explore solvated macromolecule potential energy surfaces.     

Diagrammatic kinetic theory for a lattice model of a liquid. I. Theory

We present a diagrammatic formalism for the time correlation functions of density fluctuations for an excluded volume lattice gas on a simple d-dimensional hypercubic lattice. We consider a multicomponent system in which particles of different species can have different transition rates. Our theoretical approach uses a Hilbert space formalism for the time dependent dynamical variables of a stochastic process that satisfies the detailed balance condition. We construct a Liouville matrix consistent with the dynamics of the model to calculate both the equation of motion for multipoint densities in configuration space and the interactions in the diagrammatic theory. A Boley basis of fluctuation vectors for the Hilbert space is used to develop two formally exact diagrammatic series for the time correlation functions. These theoretical techniques are generalizations of methods previously used for spin systems and atomic liquids, and they are generalizable to more complex lattice models of liquids such as a lattice gas with attractive interactions or polymer models. We use our formalism to construct approximate kinetic theories for the van Hove correlation and self-correlation function. The most simple approximation is the mean field approximation, which is exact for the van Hove correlation function of a one component system but an approximation for the self-correlation function. We use our first diagrammatic series to derive a two site multiple scattering approximation that gives a simple analytic expression for the spatial Fourier transform of the self-correlation function. We employ our second diagrammatic series to derive a simple mode coupling type approximation that provides a system of equations that can be solved for the self-correlation function.     

Model for a three-center decomposition reaction. I. Perfluorodiazirine

A semiempirical approach has been used to evaluate rate parameters for a three-center decomposition reaction from the point of view of transition state theory, with perfluorodiazirine serving as the prototype molecule. Several activated complex models are considered in which the reaction coordinate is chosen as the ? NCN bending mode. The constraints imposed include the principle of concerted bond-order conservation in passing from the initial to the final state, and use is made of empirical bond order–bond length and bond order–force constant relationships. The geometric configuration of the transition state sought is one which conforms with the lowest energy path and is also consistent with the observed entropy of activation. The potential energy of activation is taken as the optimum difference in binding energies (based on the INDO method) between the transition and initial states, and the critical energy is obtained by applying a correction for the zero-point energy difference, derived from normal coordinate analysis. Satisfactory agreement is found in the case of the activated complex model for which the total bond order is conserved and bonds undergoing rupture are assigned a fractional bond order (FBO) of 2/3, derived from the postulate (FBO) = α/β whe re α(=2) is the number of bonds breaking, and β(=3) is the number of bonds undergoing change in the ring opening.     

Statistical mechanical theory for steady state systems. VIII. General theory for a Brownian particle driven by a time- and space-varying force

A Brownian particle subject to a time- and space-varying force is studied with the second entropy theory for nonequilibrium statistical mechanics. A fluctuation expression is obtained for the second entropy of the path, and this is maximized to obtain the most likely path of the particle. Two approaches are used, one based on the velocity correlation function and one based on the position correlation function. The approaches are a perturbation about the free particle result and are exact for weak external forces. They provide a particularly simple way of including memory effects in time-varying driven diffusion. The theories are tested against computer simulation data for a Brownian particle trapped in an oscillating parabolic well. They accurately predict the phase lag and amplitude as a function of drive frequency, and they account quantitatively for the memory effects that are important at high frequencies and that are missing in the simplest Langevin equation.     

The Cyclopropylcarbinyl-Cyclobutyl-Homoallylic Rearrangement. Part III. Evidence for a symmetrical intermediate and for two discrete rearrangement processes

In buffered 70% aqueous dioxane the cyclopropylcarbinyl ( 1 -X), endo-cyclobutyl ( 2 -X) and homoallylic ( 3 -X) derivatives (X = nucleofuge) react to give the same mixture of alcohols 1 -OH and 3 -OH by way of a common intermediate, the symmetrical homoallylic ion 22 . This follows from a study of optically active reactants 1 -X and 3 -X and from the deuterium scrambling pattern in the products from deuteriated 1 -X, endo- 2 -X and 3 -X. The high solvolysis rates of 3 -X indicated π-bond participation in the transition state, while the high rates of 1 -X and endo- 2 -X reflect strong σ-bond participation which is absent in exo- 2 -X. Prolonged heating of 1 -X, endo- 2 -X and 3 -X in formic acid leads to a degenerate rearrangement of the initially formed 3 -formate. As evidenced by deuterium scrambling, carbon atoms 1, 3 and 7 eventually become positionally equivalent in the latter compound.     

Interaction between an ion-penetrable particle and a solid particle. II. Criteria for heterocoagulation

The potential energy of the total interaction between two spherical colloidal particles of different nature is calculated, i. e., of an ion-penetrable particle and an ion-impenetrable solid particle having a constant surface potential or constant surface charge density. The criteria for heterocoagulation are derived. The obtained results suggest a possibility of selective coagulation in the mixed system.     

Diagrammatic kinetic theory for a lattice model of a liquid. II. Comparison of theory and simulation results

We compare the predictions of the mean field, the two site multiple scattering, and the simple mode coupling approximation developed in the previous paper for the dynamics of a tagged particle in an excluded volume lattice gas with the results of computer simulations. The tagged particle has a transition rate of gamma while the background particles have transition rates of alphagamma. We consider the tracer diffusion coefficient and the incoherent intermediate scattering function (IISF) for low, intermediate, and high concentrations of particles and for simple square and cubic lattices. In general, the approximate kinetic theories are more accurate in predicting simulations results at low concentrations, high dimensions, and large alpha. For the tracer diffusion coefficient, the mean field approximation is the least accurate, the two site multiple scattering approximation is more accurate, and the simple mode coupling approximation is the most accurate; all three approximate theories overestimate the simulation results. For the IISF, the mean field approximation is quantitatively accurate in the limit of small concentration and large alpha but in general decays too quickly. The two site multiple scattering approximation is quantitatively accurate at low and intermediate concentrations for large wave vectors; it is always more accurate than the mean field approximation and always decays more quickly than the simulation results. The simple mode coupling approximation is the most accurate of the three approximations in most cases and especially so for small wave vectors, high concentration, and small alpha; unfortunately, its predictions are not quantitatively accurate in these highly nonmean field regimes. We discuss the implications of these results for developing diagrammatic kinetic theories.     

M-DNA: a self-assembling molecular wire for nanoelectronics and biosensing.

M-DNA is a complex between divalent metal ions such as Zn2+ and duplex DNA which forms at pH 8.5. Unlike B-DNA, M-DNA does not bind ethidium so that M-DNA formation can be monitored conveniently by an ethidium fluorescence assay. M-DNA was shown to be a better conductor than B-DNA by fluorometric measurements of electron transport in donor-acceptor labelled duplexes; by direct conductivity measurements of M-DNA bound between gold electrodes and by cyclic voltammetric studies on ferrocene labelled duplexes attached to gold microelectrodes. As is the case with B-DNA, M-DNA can self-assemble into a variety of structures and is anticipated to find widespread use in nanoelectronics and biosensing.     

Porous alumina as a support for catalysts and membranes. Preparation and study

Porous alumina as single tubes and as a multihole structure with controlled properties has been prepared. It is shown that the porous structure of these supports can be controlled without burning out additives but by a variation of the ratio between the main alumina component (α-Al₂O₃) and aluminium hydroxide (binder) in the extrusion masses and thermal treatment conditions. Gas permeability measurements have been used for the characterization of the supports. The properties of the ceramics are shown to satisfy the requirements of membrane supports.     

Alizarin-s,a reagent for thorium. a gravimetric,colorimetric, and spectrophotometric study

The claim of Beck in the use of alizarin-S for separating cerite earths from thorium could not be substantiated. Detailed conditions for estimating from 0.0095 to 6.3 mg of thorium dioxide in 50 ml of solution by the method of Rao and Murthy are described. The absorption characteristics of alizarin-S and its-thorium complex have been studied in their dependance on pH. The thorium complex has been shown by adopting different optical methods to correspond to Th-Al-S (a stoichiometric ratio of 1:1) which is also confirmed from gravimetric analyses. The dissociation coefficient of the complex at pH 2.7 has been computed to be less than 1.10^-8.     

Optimization for a recombinantE. coli fed-batch fermentation

Applied Biochemistry and Biotechnology - The operating strategy that produces the maximum foreign protein expression for a fed-batch process is desired. This is achieved by using a feasible...     

Potential photosensitizers for photodynamic therapy. III. Photophysical properties of a lipophilic chlorin and its zinc and tin chelates.

Photophysical properties of a lipophilic chlorin derivative and its zinc and tin chelates were investigated in chloroform. The quantum yields of the fluorescence phi F, of the S1----T1 intersystem crossing phi T and of singlet oxygen (1 delta g) formation phi delta, as well as the Stern-Volmer constants for the quenching of the S1 states by oxygen and the rate constants of quenching of O2(1 delta g) by the chlorins were measured. In comparison to the metal-free chlorin an increase of phi T and a decrease of phi F have been observed for the metal-containing derivatives, whereas the phi delta values remain constant.     

Regenerated protein fibers. I. Research and development of a novel solvent for silk fibroin

An alcoholic–aqueous solution of LiBr·H₂O is a useful solvent for silk fibroin, if the ratio of alcohol content to water content therein is 1 or more. The mixed solvents consisting of ethanol, water, and LiBr·H₂O showed a higher solubility if they contained a lesser amount of water. They further proved able to easily dissolve more than 20% by weight of silk fibroin. Solvents poorer in water content and richer in LiBr·H₂O showed a higher value of [η]; Huggins' coefficient of said solutions varied within a range 0.5–1.0, the minimum appearing at a water content of about 10% weight. Fibroin molecules remained stable in those solutions. The novel solvents for silk fibroin that have been developed by us are named “MU solvents,” by taking the initials in the names of Matumoto/Uejima. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35 : 1949–1954, 1997     

Renner-Teller vibronic analysis for a tetra-atomic molecule. I. The effective Hamiltonian and matrix elements

The effective vibronic Hamiltonian for a linear tetra-atomic molecule in a Pi state has been investigated. In addition to the usual vibrational and Renner-Teller coupling terms, the bending mode anharmonicity, spin-orbit coupling, and Fermi resonance interactions have been added to the model. Terms in the Hamiltonian up to the fourth order are given explicitly for molecules of C(infinityupsilon) symmetry and simplifications for symmetric D(infinityh) molecules are discussed. The matrix elements for the HCCS free radical have been obtained and are used to analyze the observed ground-state levels of HCCS and DCCS in a companion paper. The Sears resonance vibronic interaction that couples levels with the selection rules DeltaK=+/-1, DeltaSigma=-/+1, and DeltaP=0 has also been studied and the matrix elements derived. The determinable combinations of signs for the major parameters in the model are discussed.