We optimize force fields for H3O(+) and OH(-) that reproduce the experimental solvation free energies and the activities of H3O(+) Cl(-) and Na(+) OH(-) solutions up to concentrations of 1.5 mol/l. The force fields are optimized with respect to the partial charge on the hydrogen atoms and the Lennard-Jones parameters of the oxygen atoms. Remarkably, the partial charge on the hydrogen atom of th...

As a basic tool of modern biology, sequence alignment can provide us useful information in fold, function, and active site of protein. For many cases, the increased quality of sequence alignment means a better performance. The motivation of present work is to increase ability of the existing scoring scheme/algorithm by considering residue-residue correlations better. Based on a coarse-grained a...

The elastic response of single plasmid and lambda phage DNA molecules was probed using optical tweezers at concentrations of trivalent cations that provoked DNA condensation in bulk. For uncondensed plasmids, the persistence length, P, decreased with increasing spermidine concentration before reaching a limiting value 40 nm. When condensed plasmids were stretched, two types of behavior were obs...

Thermal intramolecular electron transfer from the ferrocene (Fc) to naphthoquinone (NQ) moiety occurs efficiently by the addition of metal triflates (M(n)()(+): Sc(OTf)(3), Y(OTf)(3), Eu(OTf)(3)) to an acetonitrile solution of a ferrocene-naphthoquinone (Fc-NQ) linked dyad with a flexible methylene and an amide spacer, although no electron transfer takes place in the absence of M(n)()(+). The r...

Allyl N-tosyloxycarbamates are found to be catalytically transformed into β-brominated oxazolidinones with FeBr(2)/n-Bu(4)NBr in t-BuOH.

The di-heme protein Pseudomonas stutzeri cytochrome c(4) (cyt c(4)) has emerged as a useful model for studying long-range protein electron transfer (ET). Recent experimental observations have shown a dramatically different pattern of intramolecular ET between the two heme groups in different local environments. Intramolecular ET in homogeneous solution is too slow (>10 s) to be detected but fas...

the nmr spectra of azo dyes, 5-arylazobarbituric (5a-g), 5-arylazo-1,3-dimethylbarbituric(6a-g) and 5-arylazothiobarbituric acids (7a-g) were studied in dmso-d6 in differentconcentrations. an intramolecular hydrogen bond was observed and indicating that thehydrazone forms is mostly predominant. the peak of the hydrazone proton was severelybroadened and its chemical shift appeared at down field ...

We have combined high-resolution atomic force microscopy (AFM) imaging and force spectroscopy to gain insight into the interaction forces between the individual protomers of the hexagonally packed intermediate (HPI) layer of Deinococcus radiodurans. After imaging the HPI layer, the AFM stylus was attached to individual protomers by enforced stylus-sample contact to allow force spectroscopy expe...

In this contribution we introduce the technical concept and implementation details concerning the front end of our force-field optimization workflow package for intramolecular degrees of freedom, called Wolf2Pack. The package's design follows our belief that parameter optimization should be a user-driven, but program guided, workflow with specific modular tasks that reduce human errors and save...