C-terminal processing of yeast Spt7 occurs in the absence of functional SAGA complex

Background  

Spt7 is an integral component of the multi-subunit SAGA complex that is required for the expression of ~10% of yeast genes. Two forms of Spt7 have been identified, the second of which is truncated at its C-terminus and found in the SAGA-like (SLIK) complex.     

Protonation of water clusters induced by hydroperoxyl radical surface adsorption

We have investigated the HO(2) adsorption and acid dissociation process on the surface of (H(2)O)(20) and (H(2)O)(21) clusters by using quantum-chemistry calculations. Our results show that the radical forms a stable hydrogen-bond complex on the cluster. The HO(2) acid dissociation is more favorable in the case of the (H(2)O)(21) cluster, for which the inner water molecule plays a crucial role. In fact, acid dissociation of HO(2) is found to occur in two steps. The first step involves H(2) O autoionization in the cluster, and the second one involves the proton transfer from the HO(2) radical to the hydroxide anion. The presence of the HO(2) radicals on the surface of the cluster facilitates water autoionization in the cluster.     

Combined ab initio and classical molecular dynamics simulations of alkyl-lithium aggregates in ethereal solutions

Molecular dynamics simulations of organolithium aggregates in solution are reported for the first time. We use a combined quantum/classical force field (the so-called QM/MM approach) and study ethyl-lithium aggregates in dimethyl ether (DME) solvent. The solutes are described at the Density Functional Theory level while solvent molecules are described using molecular mechanics. NVT Molecular Dynamics simulations at 200 K are carried out in the Born–Oppenheimer approximation. After equilibration, the production phase was run for 80 ps (monomer), 40 ps (dimer) and 26 ps (tetramer). The analysis of the results focuses on Li coordination as a function of aggregate size and we show that the total Li coordination number is always 4. No decoordination has been observed along the simulations. Fluctuations of the structures are predicted to be large in some cases and possible implications on reactivity are discussed.     

Structure of hydrogen tetroxide in gas phase and in aqueous environments: relationship to the hydroperoxyl radical self-reaction

Structural Chemistry - Hydrogen polyoxides are important species in atmospheric chemistry, advanced oxidation processes for wastewater treatment, and biological processes, among other fields....     

A coupled density functional-molecular mechanics Monte Carlo simulation method: The water molecule in liquid water

A theoretical model to investigate chemical processes in solution is described. It is based on the use of a coupled density functional/molecular mechanics Hamiltonian. The most interesting feature of the method is that it allows a detailed study of the solute's electronic distribution and of its fluctuations. We present the results for isothermal-isobaric constant-NPT Monte Carlo simulation of a water molecule in liquid water. The quantum subsystem is described using a double-zeta quality basis set with polarization orbitals and nonlocal exchange-correlation corrections. The classical system is constituted by 128 classical TIP3P or Simple Point Charge (SPC) water molecules. The atom-atom radial distribution functions present a good agreement with the experimental curves. Differences with respect to the classical simulation are discussed. The instantaneous and the averaged polarization of the quantum molecule are also analyzed. © 1996 by John Wiley & Sons, Inc.     

Theoretical Investigation of the Photoexcited NO2+H2O reaction at the Air–Water Interface and Its Atmospheric Implications

The atmospheric role of photochemical processes involving NO₂ beyond its dissociation limit (398 nm) is controversial. Recent experiments have confirmed that excited NO₂^* beyond 420 nm reacts with water according to NO₂^*+H₂O→HONO+OH. However, the estimated kinetic constant for this process in the gas phase is quite small (k≈10⁻¹⁵–3.4×10⁻¹⁴ cm³ molecule⁻¹ s⁻¹) suggesting minor atmospheric implications of the formed radicals. In this work, ab initio molecular dynamics simulations of NO₂ adsorbed at the air–water interface reveal that the OH production rate increases by about 2 orders of magnitude with respect to gas phase, attaining ozone reference values for NO₂ concentrations corresponding to slightly polluted rural areas. This finding substantiates the argument that chemistry on clouds can be an additional source of OH radicals in the troposphere and suggests directions for future laboratory experimental studies.     

An alternative procedure for approximating hyperbolic systems of conservation laws

This work presents an alternative numerical procedure for simulating a class of nonlinear hyperbolic systems, using Glimm's method for advancing in time. The standard procedure to implement this methodology suffers from the disadvantage of requiring a complete solution of the associated Riemann problem—a task, in general, not easily reached. The alternative procedure introduced in this article consists in approximating the solution of the associated Riemann problem by piecewise constant functions always satisfying the jump condition—thus circumventing the difficulty of solving the Riemann problem and giving rise to an approximation easier to implement with lower computational cost. In order to illustrate the good performance of the alternative methodology proposed, two problems are considered—namely the transport of a pollutant in the atmosphere and the dynamics of the filling up of a rigid porous medium, modeled under a mixture theory viewpoint. Comparison with the standard procedure, employing the complete solution of the associated Riemann problem for implementing Glimm's scheme, has shown good agreement.