20 research outputs found
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
Raman spectroscopy of solutions and interfaces containing nitrogen dioxide, water, and 1,4 dioxane: Evidence for repulsion of surface water by NO 2
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Theoretical thermochemistry and spectroscopy of weakly bound molecules
textThe weakly bound association products of atmospherically relevant radical species (O₂, OH, NO₂, HO₂ and NO) have been studied theoretically using quantum-chemical methods. The thermodynamic stabilities, which are crucial to determining the probability of formation in Earth's atmosphere, were calculated for the hydrotrioxy radical (HOOO) and peroxynitrous acid (HOONO, an isomer of nitric acid) relative to the radical dissociation products. In the case of HOONO, the experimentally determined values were confirmed. For HOOO, the predicted stability was significantly lower than the experimentally determined value; a conclusion that was supported by later experimental work and indicates that HOOO will not form in significant quantities in Earth's atmosphere. The fundamental and multi-quantum vibrational transitions were also predicted for both the HOONO and HOOO systems. The theoretical work on the HOONO system aided the assignment of experimental spectra and was used to correct equilibrium rotational constants. The HOOO system presented a challenge for the methods used here and work to apply other approaches in describing the vibrational modes is ongoing. Second-order vibrational perturbation theory, combined with a correlated quantum-chemical method and a moderately sized basis set, provides a method for accurately predicting fundamental and low-order multi-quantum transition energies and intensities for many systems (HOOO being an exception). Here coupled cluster theory, at a level which treats one- and two-electron correlation with a correction for three-electron correlation, and atomic natural orbitals basis sets were used in the vibrational calculations. To predict the dissociation energies of weakly bound species with the precision required (due to the small energy differences involved), high-order correlation contributions (a full treatment of three-electron correlation and a correction for four-electron correlation) are included, as is extrapolation to the basis set limit. Other contributions, such as that for the zero-point energy, were also considered. For the HOOO system, one-dimensional potential curves along the dissociation and torsional coordinates were constructed with standard single-reference and equation-of-motion coupled-cluster methods. The latter is better able to describe the nature of a system in the bond-breaking region and the complex electronic structure of a species formed from two radical fragments, one doubly degenerate in the ground state: X²[Pi] OH and X³[Sigma] O₂. A possible barrier to dissociation and the torsional potential for HOOO were investigated.Chemistry and Biochemistr
Reaction of a charge-separated ONONO 2 species with water in the formation of HONO: an MP2 Molecular Dynamics study
A GLOBAL POTENTIAL ENERGY SURFACE FOR HNO
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. 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
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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
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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
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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
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Reactions of Methanesulfonic Acid with Amines and Ammonia as a Source of New Particles in Air
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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 (<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