Regular induced subgraphs of a random Graph

An old problem of Erd?s, Fajtlowicz, and Staton asks for the order of a largest induced regular subgraph that can be found in every graph on vertices. Motivated by this problem, we consider the order of such a subgraph in a typical graph on vertices, i.e., in a binomial random graph . We prove that with high probability a largest induced regular subgraph of has about vertices. © 2010 Wiley Periodicals, Inc. Random Struct. Alg., 38, 235–250, 2011     

Diamine-catalyzed conjugate addition to acrylate derivatives

Diamines were found to promote catalytic conjugate addition of α-cyano active methine nucleophiles to various acrylate derivatives.     

String kernels and high-quality data set for improved prediction of kinked helices in α-helical membrane proteins

The reasons for distortions from optimal α-helical geometry are widely unknown, but their influences on structural changes of proteins are significant. Hence, their prediction is a crucial problem in structural bioinformatics. For the particular case of kink prediction, we generated a data set of 132 membrane proteins containing 1014 manually labeled helices and examined the environment of kinks. Our sequence analysis confirms the great relevance of proline and reveals disproportionately high occurrences of glycine and serine at kink positions. The structural analysis shows significantly different solvent accessible surface area mean values for kinked and nonkinked helices. More important, we used this data set to validate string kernels for support vector machines as a new kink prediction method. Applying the new predictor, about 80% of all helices could be correctly predicted as kinked or nonkinked even when focusing on small helical fragments. The results exceed recently reported accuracies of alternative approaches and are a consequence of both the method and the data set.     

Raman spectra of long chain hydrocarbons: anharmonic calculations, experiment and implications for imaging of biomembranes

First-principles anharmonic vibrational calculations are carried out for the Raman spectrum of the C-H stretching bands in dodecane, and for the C-D bands in the deuterated molecule. The calculations use the Vibrational Self-Consistent Field (VSCF) algorithm. The results are compared with liquid-state experiments, after smoothing the isolated-molecule sharp-line computed spectra. Very good agreement between the computed and experimental results is found for the two systems. The combined theoretical and experimental results provide insights into the spectrum, elucidating the roles of symmetric and asymmetric CH(3) and CH(2) hydrogenic stretches. This is expected to be very useful for the interpretation of spectra of long-chain hydrocarbons. The results show that anharmonic effects on the spectrum are large. On the other hand, vibrational degeneracy effects seem to be rather modest at the resolution of the experiments. The degeneracy effects may have more pronounced manifestations in higher-resolution experiments. The results show that first-principles anharmonic vibrational calculations for hydrocarbons are feasible, in good agreement with experiment, opening the way for applications to many similar systems. The results may be useful for the analysis of CARS imaging of lipids, for which dodecane is a representative molecule. It is suggested that first-principles vibrational calculations may be useful also for CARS imaging of other systems.     

Derivatization-independent cholesterol analysis in crude lipid extracts by liquid chromatography/mass spectrometry: applications to a rabbit model for atherosclerosis

Direct measurement of various sterols in crude lipid extracts in a single experiment from limited biological samples is challenging. Current mass spectrometry (MS) based approaches usually require chemical derivatization before subjecting to MS analysis. Here, we present a derivatization-independent method for analyzing various sterols, including cholesterol and its congeners, using liquid chromatography and atmospheric pressure chemical ionization mass spectrometry. Based on the specific tandem mass spectrometry pattern of cholesterol, multiple reaction monitoring (MRM) transitions were used to quantify free cholesterol and its fatty acyl esters. Several cholesterol oxidation products could also be measured using the upfront liquid chromatography separation and specific MRM transitions. The method was validated alongside established enzymatic assays in measuring total cholesterol. As a proof of concept, we analyzed plasma sterols in rabbits administrated with a high cholesterol diet (HCD) which is a classical atherosclerotic model. Free cholesterol, cholesterol esters, 7-hydroxycholesterol, and 7-ketocholesterol were elevated in plasma of rabbits on HCD. This method could also serve as an excellent tool for quantitative analysis of other sterols such as ergosterol and sitosterol in other organisms beside mammalian. In Saccharomyces cerevisiae, our results indicated dramatic increases of the ratio of ergosterol esters to free ergosterol in both yeh2Δ and tgl1Δ cells, which are consistent with the function of the respective enzymes.     

Cover Feature: Effects of Microhydration on the Mechanisms of Hydrolysis and Cl− Substitution in Reactions of N2O5 and Seawater (ChemPhysChem 5/2023)

The reaction of N₂O₅ at atmospheric interfaces has recently received considerable attention due to its importance in atmospheric chemistry. N₂O₅ reacts preferentially with Cl⁻ to form ClNO₂/NO₃⁻ (Cl⁻ substitution), but can also react with H₂O to form 2HNO₃ (hydrolysis). In this paper, we explore these competing reactions in a theoretical study of the clusters N₂O₅/Cl⁻/nH₂O (n=2–5), resulting in the identification of three reaction motifs. First, we uncovered an S_N2-type Cl⁻ substitution reaction of N₂O₅ that occurs very quickly due to low barriers to reaction. Second, we found a low-lying pathway to hydrolysis via a ClNO₂ intermediate (two-step hydrolysis). Finally, we found a direct hydrolysis pathway where H₂O attacks N₂O₅ (one-step hydrolysis). We find that Cl⁻ substitution is the fastest reaction in every cluster. Between one-step and two-step hydrolysis, we find that one-step hydrolysis barriers are lower, making two-step hydrolysis (via ClNO₂ intermediate) likely only when concentrations of Cl⁻ are high.