Phosphorylation reaction in cAPK protein kinase-free energy quantum mechanical/molecular mechanics simulations

We present results of a theoretical analysis of the phosphorylation reaction in cAMP-dependent protein kinase using a combined quantum mechanical and molecular mechanics (QM/MM) approach. Detailed analysis of the reaction pathway is provided using a novel QM/MM implementation of the nudged elastic band method, finite temperature fluctuations of the protein environment are taken into account using free energy calculations, and an analysis of hydrogen bond interactions is performed on the basis of calculated frequency shifts. The late transfer of the substrate proton to the conserved aspartate (D166), the activation free energy of 15 kcal/mol, and the slight exothermic (-3 kcal/mol) character of the reaction are all consistent with the experimental data. The near attack conformation of D166 in the reactant state is maintained by interactions with threonine-201, asparagine-177, and most notably by a conserved water molecule serving as a strong structural link between the primary metal ion and the D166. The secondary Mg ion acts as a Lewis acid, attacking the beta-gamma bridging oxygen of ATP. This interaction, along with a strong hydrogen bond between the D166 and the substrate, contributes to the stabilization of the transition state. Lys-168 maintains a hydrogen bond to a transferring phosphoryl group throughout a reaction process. This interaction increases in the product state and contributes to its stabilization.     

Development of a Mild and Versatile Directed Cycloaddition Approach to Pyridines

The aza‐Diels–Alder cycloaddition of 1,2,4‐triazines with alkynes offers a rapid and convenient method for the synthesis of highly substituted pyridines, but often requires harsh conditions and long reaction times. The present study offers a solution to these limitations by use of a temporary tether established by a Lewis acid–base complexation of in situ generated alkynylboranes and triazines bearing a Lewis basic donor. The cycloaddition reactions take place within 20 min at 40 °C and provide direct access to a broad range of pyridines with complete and predictable regiocontrol. The carbon?boron bond can be further functionalised by cross‐coupling allowing further functionality to be introduced after cycloaddition.     

Magnetically Aligned Supramolecular Hydrogels

The magnetic‐field‐induced alignment of the fibrillar structures present in an aqueous solution of a dipeptide gelator, and the subsequent retention of this alignment upon transformation to a hydrogel upon the addition of CaCl₂ or upon a reduction in solution pH is reported. Utilising the switchable nature of the magnetic field coupled with the slow diffusion of CaCl₂, it is possible to precisely control the extent of anisotropy across a hydrogel, something that is generally very difficult to do using alternative methods. The approach is readily extended to other compounds that form viscous solutions at high pH. It is expected that this work will greatly expand the utility of such low‐molecular‐weight gelators (LMWG) in areas where alignment is key.     

First measurement of the double spin asymmetry in (-->)e(-->)p-->e(prime)pi(+)n in the resonance region

The double spin asymmetry in the (-->)e(-->)p --> e(prime)pi(+)n reaction has been measured for the first time in the resonance region for four-momentum transfer Q2 = 0.35-1.5 GeV(2). Data were taken at Jefferson Lab with the CLAS detector using a 2.6 GeV polarized electron beam incident on a polarized solid NH3 target. Comparison with predictions of phenomenological models shows strong sensitivity to resonance contributions. Helicity-1/2 transitions are found to be dominant in the second and third resonance regions. The measured asymmetry is consistent with a faster rise with Q(2) of the helicity asymmetry A1 for the F(15)(1680) resonance than expected from the analysis of the unpolarized data.     

Q2 Dependence of quadrupole strength in the gamma*p --> Delta(+)(1232) --> p pi(0) transition

Models of baryon structure predict a small quadrupole deformation of the nucleon due to residual tensor forces between quarks or distortions from the pion cloud. Sensitivity to quark versus pion degrees of freedom occurs through the Q2 dependence of the magnetic (M1+), electric (E1+), and scalar (S1+) multipoles in the gamma*p-->Delta(+)-->p pi(0) transition. We report new experimental values for the ratios E(1+)/M(1+) and S(1+)/M(1+) over the range Q2 = 0.4-1.8 GeV2, extracted from precision p(e,e(')p)pi(0) data using a truncated multipole expansion. Results are best described by recent unitary models in which the pion cloud plays a dominant role.     

Low-molecular-weight organoiodine and organobromine compounds released by polar macroalgae--the influence of abiotic factors

The influence of temperature, light, salinity and nutrient availability on the release of volatile halogenated hydrocarbons was investigated in the Antarctic red macroalgal species Gymnogongrus antarcticus Skottsberg. Compared to standard culture condition, an increase in the release rates of iodocompounds was generally found for the exposure of the alga to altered environmental conditions. Macroalgae exhibited higher release rates after adaptation for two months to the changed factors, than after short-term exposure. Monitoring the release rates during a 24 h incubation period (8.25 h light, 15.75 h darkness) showed that changes between light and dark periods had no influence on the release of volatile halocarbons. Compounds like bromoform and 1-iodobutane exhibited constant release rates during the 24 h period. The formation mechanisms and biological role of volatile organohalogens are discussed. Although marine macroalgae are not considered to be the major source of biogenically-produced volatile organohalogens, they contribute significantly to the bromine and iodine cycles in the environment. Under possible environmental changes like global warming and uncontrolled entrophication of the oceans their significance may be increase.     

Possible effects of a cosmological constant on black hole evolution

We explore possible effects of vacuum energy on the evolution of black holes. If the universe contains a cosmological constant, and if black holes can absorb energy from the vacuum, then black hole evaporation could be greatly suppressed. For the magnitude of the cosmological constant suggested by current observations, black holes larger than 4×10²⁴ g would accrete energy rather than evaporate. In this scenario, all stellar and supermassive black holes would grow with time until they reach a maximum mass scale of 6×10⁵⁵ g, comparable to the mass contained within the present day cosmological horizon.     

Surface- and microanalysis as a tool for studying the corrosion of aluminium

Corrosion phenomena of Al-1 % Si bond wires, observed after life testing of certain transistors, are studied. The following information is derived from laboratory simulation tests: the kinetics of the corrosion process, information about the corrosion mechanism and critical parameters, especially the influence of the environmental gas and Si content and finally the identification of the corrosion products and their comparison with those found for the transistor. It is demonstrated, using a combination of several surface analytical techniques, that the A1 pitting corrosion is induced and enhanced by the presence of water as a transport medium and surface electrolyte in an oxygen-rich atmosphere, with chloride ions as a stimulating and activating species. The effect of 1 % Si in the wire consists in acceleration of the corrosion rate, and is probably due to grain boundary effects. All critical corrosion parameters could be traced in the transistor system by electron microscopy, laser microprobe mass analysis and residual gas (and moisture) analysis by mass spectrometry.     

A CNDO/2 study of σ- and π- relaxation energies and core electron binding energy shifts in some simple molecules

A relaxation potential model has been used to study relaxation energies and shifts in core electron binding energies for some substituted alkenes and carbonyl compounds in terms of σ- and π-contributions.The conclusions from this study may be summarized as follows:(A) For the series R₁R₂C^*CH₂ and R₁R₂C^*O: (i) The total shifts vary in a regular manner, similar to the shifts in saturated systems; (ii) The variation in σ-relaxation energies is greater than the variation in π-relaxation energies.(B) For the series R₁R₂CCH₂ and R₁R₂CO: (i) There is little variation in the σ-relaxation energies; (ii) The π-relaxation energies show moderately large variations and the higher values are associated with unsaturated substituents which can donate π-electrons to the core-ionized atom via the conjugated π-system; (iii) The π-relaxation energies in the fluorinated systems are similar to those in the unsubstituted molecules; and (iv) The large -ve π-shift in the fluorinated systems results from a ground state build up of electron density at the site of core ionization.