AbInitio SCF MO calculations on the reaction of hydroxyl radical with cytosine

1986 ◽  
Vol 64 (5) ◽  
pp. 914-919 ◽  
Author(s):  
Beverley G. Eatock ◽  
William L. Waltz ◽  
Paul G. Mezey
Keyword(s):  
Hydroxyl Radical ◽  
Radiation Damage ◽  
Gas Phase ◽  
Solvent Effects ◽  
Oh Radical ◽  
Mo Calculations ◽  
Relative Stabilities ◽  
Ring Atom ◽  
Living Tissues ◽  
Abinitio Calculations

Abinitio calculations have been carried out on the relative stabilities of various possible products of the reaction between cytosine and the OH radical. These products are of importance in modelling radiation damage to living tissues. The preferred theoretical gas-phase addition site is the C6 ring atom according to these calculations. The analysis of a series of possible contributions to solvent effects strongly suggests the predominance of intermolecular H bonds in stabilizing the experimentally observed C5 adduct.

Abinitio SCF MO calculations on the reactions of OH radical with pyridine and pyridinium ion

1982 ◽  
Vol 60 (7) ◽  
pp. 813-819 ◽  
Author(s):  
M. C. Anthony ◽  
W. L. Waltz ◽  
P. G. Mezey
Keyword(s):  
Hydroxyl Radical ◽  
Experimental Information ◽  
Electron Delocalization ◽  
Oh Radical ◽  
Reaction Paths ◽  
Mo Calculations ◽  
Relative Stabilities ◽  
Electrophilic Character ◽  
Determining Factor ◽  
Pyridinium Ion

Relative energies of various products formed in the reaction of pyridine and pyridinium ion with the hydroxyl radical are calculated using non-empirical SCF MO techniques. The favourable electron delocalization in the meta-products, rather than the electrophilic character of the OH radical is the determining factor of relative stabilities. Calculated energy barriers along approximate reaction paths correlate with the available experimental information.

2-Deoxyribose Radicals in the Gas Phase and Aqueous Solution. Transient Intermediates of Hydrogen Atom Abstraction from 2-Deoxyribofuranose

2005 ◽  
Vol 70 (11) ◽  
pp. 1769-1786 ◽  
Author(s):  
Luc A. Vannier ◽  
Chunxiang Yao ◽  
František Tureček
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Atom ◽  
Gas Phase ◽  
Computational Study ◽  
Hydrogen Atom Abstraction ◽  
Oh Radical ◽  
Free Energies ◽  
Intramolecular Hydrogen ◽  
Solvation Free Energies ◽  
Transient Intermediates

A computational study at correlated levels of theory is reported to address the structures and energetics of transient radicals produced by hydrogen atom abstraction from C-1, C-2, C-3, C-4, C-5, O-1, O-3, and O-5 positions in 2-deoxyribofuranose in the gas phase and in aqueous solution. In general, the carbon-centered radicals are found to be thermodynamically and kinetically more stable than the oxygen-centered ones. The most stable gas-phase radical, 2-deoxyribofuranos-5-yl (5), is produced by H-atom abstraction from C-5 and stabilized by an intramolecular hydrogen bond between the O-5 hydroxy group and O-1. The order of radical stabilities is altered in aqueous solution due to different solvation free energies. These prefer conformers that lack intramolecular hydrogen bonds and expose O-H bonds to the solvent. Carbon-centered deoxyribose radicals can undergo competitive dissociations by loss of H atoms, OH radical, or by ring cleavages that all require threshold dissociation or transition state energies >100 kJ mol-1. This points to largely non-specific dissociations of 2-deoxyribose radicals when produced by exothermic hydrogen atom abstraction from the saccharide molecule. Oxygen-centered 2-deoxyribose radicals show only marginal thermodynamic and kinetic stability and are expected to readily fragment upon formation.

Solvent and temperature effects on the tautomerization of a carbonitrile molecule: A conductor-like polarizable continuum model (CPCM) study

2021 ◽  
Vol 20 (1) ◽  
pp. 59-68
Author(s):  
Zohreh Khanjari ◽  
Bita Mohtat ◽  
Reza Ghiasi ◽  
Hoorieh Djahaniani ◽  
Farahnaz Kargar Behbahani
Keyword(s):  
Gas Phase ◽  
Solvent Effects ◽  
Continuum Model ◽  
Solvent Polarity ◽  
Polarizable Continuum Model ◽  
Dielectric Constants ◽  
Frontier Orbitals ◽  
Reaction Field ◽  
Polarizable Continuum ◽  
Homo Lumo

This research examined the effects of solvent polarity and temperature on the tautomerization of a carbonitrile molecule at CAM-B3LYP/6-311G (d,p) level of theory. The selected solvents were n-hexane, diethyl ether, pyridine, ethanol, methanol, and water. The solvent effects were examined by the self-consistent reaction field theory (SCRF) based on conductor-like polarizable continuum model (CPCM). The solvent effects were explored on the energy barrier, frontier orbitals energies, and HOMO-LUMO gap. Dependencies of thermodynamic parameters (ΔG and ΔH) on the dielectric constants of solvents were also tested. Specifically, the temperature dependencies of the thermodynamics parameters were studied within 100–1000 K range. The rate constant of the tautomerism reaction was computed from 300 to 1200 K, in the gas phase.

scholarly journals Volatility of secondary organic aerosol during OH radical induced ageing

2011 ◽  
Vol 11 (21) ◽  
pp. 11055-11067 ◽  
Author(s):  
K. Salo ◽  
M. Hallquist ◽  
Å. M. Jonsson ◽  
H. Saathoff ◽  
K.-H. Naumann ◽  
...  
Keyword(s):  
Gas Phase ◽  
Organic Aerosol ◽  
Oh Radical ◽  
High Concentration ◽  
Volatile Material ◽  
Phase Oxidation ◽  
Gas Phase Oxidation ◽  
Institute Of Technology ◽  
Set Up ◽  
Pinic Acid

Abstract. The aim of this study was to investigate oxidation of SOA formed from ozonolysis of α-pinene and limonene by hydroxyl radicals. This paper focuses on changes of particle volatility, using a Volatility Tandem DMA (VTDMA) set-up, in order to explain and elucidate the mechanism behind atmospheric ageing of the organic aerosol. The experiments were conducted at the AIDA chamber facility of Karlsruhe Institute of Technology (KIT) in Karlsruhe and at the SAPHIR chamber of Forchungzentrum Jülich (FZJ) in Jülich. A fresh SOA was produced from ozonolysis of α-pinene or limonene and then aged by enhanced OH exposure. As an OH radical source in the AIDA-chamber the ozonolysis of tetramethylethylene (TME) was used while in the SAPHIR-chamber the OH was produced by natural light photochemistry. A general feature is that SOA produced from ozonolysis of α-pinene and limonene initially was rather volatile and becomes less volatile with time in the ozonolysis part of the experiment. Inducing OH chemistry or adding a new portion of precursors made the SOA more volatile due to addition of new semi-volatile material to the aged aerosol. The effect of OH chemistry was less pronounced in high concentration and low temperature experiments when lower relative amounts of semi-volatile material were available in the gas phase. Conclusions drawn from the changes in volatility were confirmed by comparison with the measured and modelled chemical composition of the aerosol phase. Three quantified products from the α-pinene oxidation; pinonic acid, pinic acid and methylbutanetricarboxylic acid (MBTCA) were used to probe the processes influencing aerosol volatility. A major conclusion from the work is that the OH induced ageing can be attributed to gas phase oxidation of products produced in the primary SOA formation process and that there was no indication on significant bulk or surface reactions. The presented results, thus, strongly emphasise the importance of gas phase oxidation of semi- or intermediate-volatile organic compounds (SVOC and IVOC) for atmospheric aerosol ageing.

Rapid Evaluation of Suitable Substrates with High Affinity to Artificial Caffeine Receptors by MS Based Techniques

2005 ◽  
Vol 60 (10) ◽  
pp. 1077-1082 ◽  
Author(s):  
Daniela Mirk ◽  
Heinrich Luftmann ◽  
Siegfried R. Waldvogel
Keyword(s):  
Mass Spectrometry ◽  
Gas Phase ◽  
Collision Induced Dissociation ◽  
Rapid Evaluation ◽  
Tandem Mass ◽  
Binding Affinities ◽  
Electrospray Tandem Mass Spectrometry ◽  
Relative Stabilities ◽  
Receptor Complexes ◽  
High Affinity

A modification of our triphenylene ketal based receptor facilitates electrospray tandem mass spectrometry investigations. Binding affinities of eleven potential substrates, e.g. caffeine and other xanthine alkaloids, are probed in the gas phase with collision induced dissociation. The relative stabilities of the substrate-receptor complexes are rapidly determined and the findings are correlated with the corresponding results in solution.

scholarly journals Role of (H2O)n (n = 1–2) in the Gas-Phase Reaction of Ethanol with Hydroxyl Radical: Mechanism, Kinetics, and Products

ACS Omega ◽  
2019 ◽  
Vol 4 (3) ◽  
pp. 5805-5817 ◽  
Author(s):  
Li Xu ◽  
Narcisse T. Tsona ◽  
Shanshan Tang ◽  
Junyao Li ◽  
Lin Du
Keyword(s):  
Hydroxyl Radical ◽  
Gas Phase ◽  
Radical Mechanism ◽  
Phase Reaction ◽  
Gas Phase Reaction

scholarly journals Modeling nitrous acid and its impact on ozone and hydroxyl radical during the Texas Air Quality Study 2006

2012 ◽  
Vol 12 (2) ◽  
pp. 5851-5880 ◽  
Author(s):  
B. H. Czader ◽  
B. Rappenglück ◽  
P. Percell ◽  
D. W. Byun ◽  
F. Ngan ◽  
...  
Keyword(s):  
Air Quality ◽  
Hydroxyl Radical ◽  
Gas Phase ◽  
Nitrous Acid ◽  
Organic Materials ◽  
Optical Absorption Spectroscopy ◽  
Ozone Formation ◽  
Mixing Ratios ◽  
Quality Study ◽  
Mist Chamber

Abstract. Nitrous acid (HONO) mixing ratios for the Houston metropolitan area were simulated with the Community Multiscale Air Quality (CMAQ) model for an episode during the Texas Air Quality Study (TexAQS) II in August/September 2006 and compared to in-situ MC/IC (mist-chamber/ion chromatograph) and long path DOAS (Differential Optical Absorption Spectroscopy) measurements at three different altitudes. Several HONO sources were accounted for in simulations, such as gas phase formation, direct emissions, nitrogen dioxide (NO2*) hydrolysis, photo-induced formation from excited NO2* and photo-induced conversion of NO2 into HONO on surfaces covered with organic materials. Compared to the gas-phase HONO formation there was about a tenfold increase in HONO mixing ratios when additional HONO sources were taken into account, which improved the correlation between modeled and measured values. Concentrations of HONO simulated with only gas phase chemistry did not change with altitude, while measured HONO concentrations decrease with height. A trend of decreasing HONO concentration with altitude was well captured with CMAQ predicted concentrations when heterogeneous chemistry and photolytic sources of HONO were taken into account. Heterogeneous HONO production mainly accelerated morning ozone formation, albeit slightly. Also HONO formation from excited NO2 only slightly affected HONO and ozone (O3) concentrations. Photo-induced conversion of NO2 into HONO on surfaces covered with organic materials turned out to be a strong source of daytime HONO. Since HONO immediately photo-dissociates during daytime its ambient mixing ratios were only marginally altered (up to 0.5 ppbv), but significant increase in the hydroxyl radical (OH) and ozone concentration was obtained. In contrast to heterogeneous HONO formation that mainly accelerated morning ozone formation, inclusion of photo-induced surface chemistry influenced ozone throughout the day.

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