Determination of azo compounds with N-bromosuccinimide in acetic acid medium

The bromination reaction of azo compounds with N-bromosuccinimide in acetic acid medium has been studied. Some reaction products have been isolated and reaction mechanisms suggested. The reaction study has been applied for the determination of 2-10 mg of azo compounds. The maximum deviation of the results from the theoretical value is generally within +/- 1%.     

Foldamer dynamics expressed via Markov state models. II. State space decomposition

The structural landscape of poly-phenylacetylene (pPA), otherwise known as m-phenylene ethynylene oligomers, has been shown to consist of a very diverse set of conformations, including helices, turns, and knots. Defining a state space decomposition to classify these conformations into easily identifiable states is an important step in understanding the dynamics in relation to Markov state models. We define the state decomposition of pPA oligomers in terms of the sequence of discretized dihedral angles between adjacent phenyl rings along the oligomer backbone. Furthermore, we derive in mathematical detail an approach to further reduce the number of states by grouping symmetrically equivalent states into a single parent state. A more challenging problem requires a formal definition for knotted states in the structural landscape. Assuming that the oligomer chain can only cross the ideal helix path once, we propose a technique to define a knotted state derived from a helical state determined by the position along the helical nucleus where the chain crosses the ideal helix path. Several examples of helical states and knotted states from the pPA 12-mer illustrate the principles outlined in this article.     

Analytical aspects of organic acids

Summary Phenyl acetic acid has been found to be a selective reagent for the estimation of zirconium. The acid gives a white crystalline precipitate which is quantitative between pH values of 3.00 to 5.40. As the composition of the precipitate varies somewhat, direct weighing is not possible and the compound is ignited to the oxide. The ions Be²⁺, Ca²⁺, Sr²⁺, Zn²⁺, Hg²⁺, Pb²⁺, Mg²⁺, Ni²⁺, and Co²⁺ do not interfere, whereas the ions Fe³⁺, UO₂ ²⁺, Cr³⁺, Ba²⁺, Au⁺, Al³⁺, V₂O₄ ²⁺, Ti⁴⁺, Sn²⁺, and Ba²⁺ cause interferences in the estimation.

---

Zusammenfassung Zur gravimetrischen Bestimmung von Zirkonium wird Phenylessigsäure empfohlen. Die weiße, kristalline Fällung ist im pH-Bereich 3,00–5,40 quantitativ. Infolge schwankender Zusammensetzung des Niederschlages ist eine direkte Wägung nicht möglich; er wird daher zum Oxid verglüht. Folgende Ionen stören nicht: Be²⁺, Ca²⁺, Sr²⁺, Zn²⁺, Hg²⁺, Pb²⁺, Mg²⁺, Ni²⁺ und Co²⁺; dagegen verursachen Fe³⁺, UO₂ ²⁺, Cr³⁺, Ba²⁺, Au⁺, Al³⁺, V₂O₄ ²⁺, Ti⁴⁺, Sn²⁺ und Ba²⁺ Störungen bei der Bestim mung.

---

---

Part VI: See Z. analyt. Chem. 175, 29 (1960).     

Direct calculation of the binding free energies of FKBP ligands

Direct calculations of the absolute free energies of binding for eight ligands to FKBP protein were performed using the Fujitsu BioServer massively parallel computer. Using the latest version of the general assisted model building with energy refinement (AMBER) force field for ligand model parameters and the Bennett acceptance ratio for computing free-energy differences, we obtained an excellent linear fit between the calculated and experimental binding free energies. The rms error from a linear fit is 0.4 kcal/mol for eight ligand complexes. In comparison with a previous study of the binding energies of these same eight ligand complexes, these results suggest that the use of improved model parameters can lead to more predictive binding estimates, and that these estimates can be obtained with significantly less computer time than previously thought. These findings make such direct methods more attractive for use in rational drug design.     

Folding probabilities: a novel approach to folding transitions and the two-dimensional Ising-model

The theoretical concept of folding probability, p(fold), has proven to be a useful means to characterize the kinetics of protein folding. Here, we illustrate the practical importance of p(fold) and demonstrate how it can be determined theoretically. We derive a general analytical expression for p(fold) and show how it can be estimated from simulations for systems where the transition rates between the relevant microstates are not known. By analyzing the Ising model we are able to determine the scaling behavior of the numerical error in the p(fold) estimate as function of the number of analyzed Monte Carlo runs. We apply our method to a simple, newly developed protein folding model for the formation of alpha helices. It is demonstrated that our technique highly parallelizes the calculation of p(fold) and that it is orders of magnitude more efficient than conventional approaches.     

ON THE CHROMOPHORE CONFIGURATION OF METARHODOPSIN II

Abstract The nature of the chromophore configuration of metarhodopsin II (meta II) has been a subject of recent controversy. Earlier resonance Raman results from this laboratory had indicated that meta II has an unprotonated Schiff base linkage between the chromophore and apoprotein. It has been argued, on the other hand, that the Raman evidence does not exclude a non-covalently bound retinal chromophore. In this communication we present additional evidence and further arguments in favor of our earlier conclusion regarding the state of the chromophore in meta II.     

Preparation of 4′-Spirocyclobutyl Nucleoside Analogues as Novel and Versatile Adenosine Scaffolds

Despite the large variety of modified nucleosides that have been reported, the preparation of constrained 4′-spirocyclic adenosine analogues has received very little attention. We discovered that the [2+2]-cycloaddition of dichloroketene on readily available 4′-exo-methylene furanose sugars efficiently results in the diastereoselective formation of novel 4′-spirocyclobutanones. The reaction mechanism was investigated via density functional theory (DFT) and found to proceed either via a non-synchronous or stepwise reaction sequence, controlled by the stereochemistry at the 3′-position of the sugar substrate. The obtained dichlorocyclobutanones were converted into nucleoside analogues, providing access to a novel class of chiral 4′-spirocyclobutyl adenosine mimetics in eight steps from commercially available sugars. Assessment of the biological activity of designed 4′-spirocyclic adenosine analogues identified potent inhibitors for protein methyltransferase target PRMT5.     

Evaluation of antioxidant activity and DNA cleavage protection effect of naphthyl hydroxamic acid derivatives through conventional and fluorescence microscopic methods

Antioxidant capacity of N-(1-naphthyl)valerohydroxamic acid (NVHA) and N-(1-naphthyl)phenylacetohydroxamic acid (NPAHA) has been evaluated by a novel approach employing the fluorescence microscopic single molecule observation method. This method allows direct observation of the changes in single DNA molecules. The DNA cleavage protection activity of the compounds was also assessed by the gel electrophoresis method. The applied methods confirmed that both compounds are capable of inhibiting the free radical mediated DNA damage. Free radical scavenging activity was assessed via the 2,2′-diphenyl-1-picrylhydrazyl free radical (DPPH) and lipid peroxidation inhibition methods. The effective concentration causing a 50 % inhibition of the DPPH concentration, EC50, was found to be 371.54 mM for NVHA and 365.95 mM for NPAHA. Its lipid peroxidation inhibition ability was calculated to be 40.91 % at 371.54 mM for NVHA and 41.14 % at 365.95 mM for NPAHA. These results show the antioxidant potential of the naphthyl hydroxamic acids.