Tyrosine nitration of human ERK1 introduces an intra-hydrogen bond by molecular dynamics simulations

Structural Chemistry - ERK1 is an important kinase in Ras–Raf–MEK signaling. We have recently demonstrated by mass spectrometry that Tyr210 of ERK1 can be nitrated, and the nitration...     

Inverse Monte Carlo renormalization group transformations for critical phenomena

We introduce a computationally stable inverse Monte Carlo renormalization group transformation method that provides a number of advantages for the calculation of critical properties. We are able to simulate the fixed point of a renormalization group for arbitrarily large lattices without critical slowing down. The log-log scaling plots obtained with this method show remarkable linearity, leading to accurate estimates for critical exponents. We illustrate this method with calculations in two- and three-dimensional Ising models for a variety of renormalization group transformations.     

Correlation and prediction of solute transfer to chloroalkanes from both water and the gas phase

Data have been compiled from the published literature on the partition coefficients of solutes and vapors into chloroform, carbon tetrachloride, dichloromethane and 1-chlorobutane from both water and from the gas phase. The logarithms of the water-to-chloroalkane (log P) and gas-to-chloroalkane partition coefficients (log K) are correlated with the Abraham solvation parameter model. The derived correlations describe the observed log P and log K values within standard deviations of about 0.13–0.20 log units. For chloroform and carbon tetrachloride, the derived correlations were validated using training set and test set analyses.     

A model for the vertical sound speed and absorption profiles in Titan's atmosphere based on Cassini-Huygens data

Measurements of thermodynamic quantities in Titan's atmosphere during the descent of Huygens in 2005 are used to predict the vertical profiles for the speed and intrinsic attenuation (or absorption) of sound. The calculations are done using one author's previous model modified to accommodate non-ideal equations of state. The vertical temperature profile places the tropopause about 40 km above the surface. In the model, a binary nitrogen-methane composition is assumed for Titan's atmosphere, quantified by the methane fraction measured by the gas chromatograph/mass spectrometer (GCMS) onboard Huygens. To more accurately constrain the acoustic wave number, the variation of thermophysical properties (specific heats, viscosity, and thermal conductivity) with altitude is included via data extracted from the NIST Chemistry WebBook [URL webbook.nist.gov, National Institute of Standards and Technology Chemistry WebBook (Last accessed 10/20/2011)]. The predicted speed of sound profile fits well inside the spread of the data recorded by Huygens' active acoustic sensor. In the N(2)-dominated atmosphere, the sound waves have negligible relaxational dispersion and mostly classical (thermo-viscous) absorption. The cold and dense environment of Titan can sustain acoustic waves over large distances with relatively small transmission losses, as evidenced by the small absorption. A ray-tracing program is used to assess the bounds imposed by the zonal wind-measured by the Doppler Wind Experiment on Huygens-on long-range propagation.     

Allylation and oxidation reactions promoted by cobalt(II) complexes

Two examples of radical reactions involving cobalt complexes are described. The first one concerns the reactions of allylcobaloximes with 2-bromo 2-phenylacetonitriles leading to the corresponding monoallyl derivatives. It is shown that both the rate and regioselectivity of the reactions are affected by the nature of the substituents on the phenyl group: electron-withdrawing groups give higher rates and highly regiospecific reactions. The second type of radical reaction which finds useful synthetic applications is the oxidation of phenols by 02 catalyzed by Schiff base cobalt complexes. By choosing carefully the catalyst and the solvent, these oxidations can be highly selective, quinones being the major oxidation products in most cases.     

Asymmetric Synthesis of Phosphinous Tungsten Complexes

Abstract

The asymmetric synthesis of phosphinous compounds from diheterophosphacycloal kane-1,3,2 was investigated in a transition metal complex series. Complexes 1 and 2 were prepared from diaminophosphine, (?)-ephedrine and W (CO)₅ THP (1: δ³¹ P=+147,6 ppm; J_PW=313 Hz M^.+=595;2 δ³ p=+156 ppm J_PW=304 Hz M^.+=533; 90%dp) in two steps. Methyl lithium reacted with 1 to give stereospecific 3 (83%Yield) by P-O linkage (3 δ³¹ P=+64 ppm; J_PW =261 Hz; M^.+ ? 28=583). The aminophosphine complex 3 was stereochemically stable and was used for studies of synthetic applications. HCL gas reacted with 3 in CH₂Cl₂ to give the non optically active chlorophosphine complex 4 (δ³¹ P=+103,6 ppm; J_PW=290 Hz; M^.+ =482). This compound immediately gave salt 6 (δ³¹ P=+66,7 ppm; J_PW =240 Hz) by reaction with (?)-menthol and triethylamine. The acid methanolysis of 3 gave a mixture of 5 and 6 and the unchanged (?)-ephedrine salt [5:30% yield; δ³¹ P=+114 ppm; J_pw=280 Hz; [α]_D=+1,2° (CH₂Cl₂); M^.+=478; 6 : 60% yield; δ³¹p=+102,9 ppm; J_PW=264 Hz; [α]_D =+16,9° (CH₂Cl₂); M^.+=464]. Compound 6 was thus obtained with a 80% yield and a specific rotation of + 20,2° (CH₂Cl₂) in isopropanol/H₂SO₄ 5M medium. The enantiomeric excess of 6 was determined by RMN³¹P. Acid hydrolysis of 3 or the reaction with CH₃SO₃H, gave phosphinous acid complex 6 with an optical rotation of + 4,8° or ?1,8° respectively. These results provide precious informations about the stereochemistry and reactivity of the P-N linkage in this aminophosphine transition metal series, which differs notably from that of the corresponding (PO) N bond.     

Bootstrap Algebraic Multigrid: Status Report,Open Problems,and Outlook

This paper provides an overview of the main ideas driving the bootstrap algebraic multigrid methodology, including compatible relaxation and algebraic distances for defining effective coarsening strategies, the least squares method for computing accurate prolongation operators and the bootstrap cycles for computing the test vectors that are used in the least squares process. We review some recent research in the development, analysis and application of bootstrap algebraic multigrid and point to open problems in these areas. Results from our previous research as well as some new results for some model diffusion problems with highly oscillatory diffusion coefficient are presented to illustrate the basic components of the BAMG algorithm.     

Geometry of intensive scalar dissipation events in turbulence

The maxima of the scalar dissipation rate in turbulence appear in the form of sheets and correspond to the potentially most intensive scalar mixing events. Their cross section extension determines a locally varying diffusion scale of the mixing process and extends the classical Batchelor picture of one mean diffusion scale. The distribution of the local diffusion scales is analyzed for different Reynolds and Schmidt numbers with a fast multiscale technique applied to very high-resolution simulation data. The scales always take values across the whole Batchelor range and beyond. Furthermore, their distribution is traced back to the distribution of the contractive short-time Lyapunov exponent of the flow.     

Renormalization Multigrid (RMG): Statistically Optimal Renormalization Group Flow and Coarse-to-Fine Monte Carlo Acceleration

New renormalization-group algorithms are developed with adaptive representations of the renormalized system which automatically express only significant interactions. As the amount of statistics grows, more interactions enter, thereby systematically reducing the truncation error. This allows statistically optimal calculation of thermodynamic limits, in the sense that it achieves accuracy in just O(^–2) random number generations. There are practically no finite-size effects and the renormalization transformation can be repeated arbitrarily many times. Consequently, the desired fixed point is obtained and the correlation-length critical exponent is extracted. In addition, we introduce a new multiscale coarse-to-fine acceleration method, based on a multigrid-like approach. This general (non-cluster) algorithm generates independent equilibrium configurations without slow down. A particularly simple version of it can be used at criticality. The methods are of great generality; here they are demonstrated on the 2D Ising model.