Molecular dynamics simulations of human [Formula: see text]: the role of modified bases in mRNA recognition

Accuracy in translation of the genetic code into proteins depends upon correct tRNA–mRNA recognition in the context of the ribosome. In human [Formula: see text] three modified bases are present in the anticodon stem–loop—2-methylthio-N6-threonylcarbamoyladenosine at position 37 (ms(2)t(6)A37), 5-methoxycarbonylmethyl-2-thiouridine at position 34 (mcm(5)s(2)U34) and pseudouridine (ψ) at position 39—two of which, ms(2)t(6)A37 and mcm(5)s(2)U34, are required to achieve wild-type binding activity of wild-type human [Formula: see text] [C. Yarian, M. Marszalek, E. Sochacka, A. Malkiewicz, R. Guenther, A. Miskiewicz and P. F. Agris (2000) Biochemistry, 39, 13390–13395]. Molecular dynamics simulations of nine tRNA anticodon stem–loops with different combinations of nonstandard bases were performed. The wild-type simulation exhibited a canonical anticodon stair-stepped conformation. The ms(2)t(6) modification at position 37 is required for maintenance of this structure and reduces solvent accessibility of U36. Ms(2)t(6)A37 generally hydrogen bonds across the loop and may prevent U36 from rotating into solution. A water molecule does coordinate to ψ39 most of the simulation time but weakly, as most of the residence lifetimes are <40 ps

A GLOBAL POTENTIAL ENERGY SURFACE FOR HNO3_3

Author Institution: Institute for Theoretical Chemistry, Department of Chemistry, University of Texas at; Austin, Austin, TX 78712; Cherry L. Emerson Center of Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322A potential energy surface has been fit to the energy and energy gradient for thousands of configurations of HNO$_3$. Prior to explicit inclusion of data for the cis,perp-HOONO conformation, this isomer was predicted to be a local minimum on the fitted surface. The status of cis,perp-HOONO as a minimum was later confirmed through {\it ab initio} frequency calculations. Molecular dynamics simulations were carried out on the fitted surface to investigate the cis/trans isomerization of the HOONO structure

Reaction of a charge-separated ONONO2 species with water in the formation of HONO: an MP2 Molecular Dynamics study.

The reaction of (NO(+))(NO3(-)) with water is modelled in ONONO2·(H2O)4 clusters. Molecular Dynamics simulations using second-order Møller-Plesset perturbation (MP2) theory support the feasibility of the reaction of a charge-separated species to produce HONO and nitric acid

Reaction of a charge-separated ONONO2 species with water in the formation of HONO: an MP2 Molecular Dynamics study.

The reaction of (NO(+))(NO3(-)) with water is modelled in ONONO2·(H2O)4 clusters. Molecular Dynamics simulations using second-order Møller-Plesset perturbation (MP2) theory support the feasibility of the reaction of a charge-separated species to produce HONO and nitric acid

Reactions of Methanesulfonic Acid with Amines and Ammonia as a Source of New Particles in Air.

New particle formation (NPF) from gaseous precursors as a significant source of aerosol needs to be better understood to accurately predict the impacts on visibility, climate change, and human health. While ternary nucleation of sulfuric acid, amines/NH3, and water is recognized as a significant driver for NPF, increasing evidence suggests a contribution from methanesulfonic acid (MSA) and amines under certain conditions. Here we report the formation of particles 2.5-10 nm in diameter from the reactions of MSA with methylamine (MA), dimethylamine (DMA), and NH3 at reaction times of 2.3-7.8 s in a flow reactor and compare these particles with those previously reported to be formed from reaction with trimethylamine (TMA). The effects of water vapor and concentrations of gaseous precursors on the particle number concentration and particle size were studied. The presence of water significantly enhances particle formation and growth. Under similar experimental conditions, particle number concentrations decrease in the order MA ≫ TMA ≈ DMA ≫ NH3, where NH3 is 2-3 orders of magnitude less efficient than DMA. Quantum chemical calculations of likely intermediate clusters were carried out to provide insights into the role of water and the different capacities of amines/NH3 in particle formation. Both gas-phase basicity and hydrogen-bonding capacity of amines/NH3 contribute to the potential for particles to form and grow. Our results indicate that, although amines typically have concentrations 1-3 orders of magnitude lower than that of NH3 in the atmosphere, they still play an important role in driving NPF

Raman spectroscopy of solutions and interfaces containing nitrogen dioxide, water, and 1,4 dioxane: evidence for repulsion of surface water by NO2 gas.

The interaction of water, 1,4 dioxane, and gaseous nitrogen dioxide, has been studied as a function of distance measured through the liquid-vapour interface by Raman spectroscopy with a narrow (&lt;0.1 mm) laser beam directed parallel to the interface. The Raman spectra show that water is present at the surface of a dioxane-water mixture when gaseous NO2 is absent, but is virtually absent from the surface of a dioxane-water mixture when gaseous NO2 is present. This is consistent with recent theoretical calculations that show NO2 to be mildly hydrophobic

Raman spectroscopy of solutions and interfaces containing nitrogen dioxide, water, and 1,4 dioxane: evidence for repulsion of surface water by NO2 gas.

The interaction of water, 1,4 dioxane, and gaseous nitrogen dioxide, has been studied as a function of distance measured through the liquid-vapour interface by Raman spectroscopy with a narrow (&lt;0.1 mm) laser beam directed parallel to the interface. The Raman spectra show that water is present at the surface of a dioxane-water mixture when gaseous NO2 is absent, but is virtually absent from the surface of a dioxane-water mixture when gaseous NO2 is present. This is consistent with recent theoretical calculations that show NO2 to be mildly hydrophobic