MECHANISMS FOR THE DECOMPOSITION OF HYDROXYL-RADICAL-INDUCED CYTOSINE HYDROPEROXIDES: A COMPUTATIONAL STUDY

2013 ◽  
Vol 12 (04) ◽  
pp. 1350027 ◽  
Author(s):  
ZE-QIN CHEN ◽  
YING XUE
Keyword(s):  
Hydroxyl Radical ◽  
Computational Study ◽  
Chemical Properties ◽  
Basis Set ◽  
Stationary Points ◽  
Decomposition Products ◽  
Natural Processes ◽  
Full Optimization ◽  
Explicit Water ◽  
First Time

Hydroxyl-radical-induced damage to cytosine leads to a multitude of base modifications, which contribute to the natural processes of aging, mutagenesis and carcinogenesis. The stable products resulting from the main hydroxyl-radical-induced cytosine hydroperoxide, 5-hydroxy-6-hydroperoxyl-5,6-dihydrocytosine (5-OH-6-OOH-DHC), have been mapped out in the present work for the first time using ab initio calculations. Optimized geometries of all stationary structures in the gas phase were determined at the MP2 and B3LYP using the 6-31G(d) basis set and at the B3LYP/6-311++G(d,p) levels of theory. Energies were also determined at the G3MP2 level of theory. Meanwhile, full optimization of all stationary points were also performed in aqueous solution at the B3LYP/CPCM/6-31G(d) level of theory to evaluate the solvent effect. Three distinct possible pathways, pathways A–C, were evaluated. For pathway C, four channels, channels D–G, were characterized in turn. In each pathway, both the direct and the water-mediated processes were considered. The calculated results clearly manifest that (i) pathway C is kinetically favored over pathways A and B and is the most energetically feasible decomposition process of 5-OH-6-OOH-DHC; (ii) for pathway C, channels D, E and G are energetically feasible mechanisms and 6,7-dihydroxy-[1,3,5]triazepane-2,4-dione, 1-carbamoyl-2-oxo-4,5-dihydroxyimidazolidine, and biuret therefore are predicted to be the kinetically favored decomposition products of 5-OH-6-OOH-DHC; (iii) channel G may be kinetically favored over channels D and E and have the highest possibility to occur; (iv) the thermal decomposition of 5-OH-6-OOH-DHC can be significantly promoted by the presence of one explicit water molecule. Apart from characterizing the experimental products well, the main striking result of the present DFT computational study is the identification of a new theoretical optimum decomposition product, i.e. 6,7-dihydroxy-[1,3,5]triazepane-2,4-dione. The data and insights presented here have elucidated the chemical properties of 5-OH-6-OOH-DHC in free radical reactions and should facilitate to assess their mutagenic features.

Computational study on the reaction of atomic chlorine with 1,2-dibromoethane (CH2BrCH2Br)

2013 ◽  
Vol 91 (11) ◽  
pp. 1123-1129 ◽  
Author(s):  
Ang-yang Yu
Keyword(s):  
Transition State ◽  
Rate Constants ◽  
Transition State Theory ◽  
Computational Study ◽  
Minimum Energy ◽  
State Theory ◽  
Basis Set ◽  
Stationary Points ◽  
Variational Transition State Theory ◽  
Variational Transition State

In this work, the reaction mechanism and kinetics of Cl + CH2BrCH2Br → products are theoretically investigated for the first time. The optimized geometries and frequencies of all of the stationary points and selected points along the minimum-energy path for the three hydrogen abstraction channels and two bromine abstraction channels are calculated at the BH&H-LYP level with the 6-311G** basis set and the energy profiles are further calculated at the CCSD(T) level of theory. The rate constants are evaluated using the conventional transition-state theory, the canonical variational transition-state theory, and the canonical variational transition-state theory with a small-curvature tunneling correction over the temperature range 200–1000 K. The results show that reaction channel 3 is the primary channel and the calculated rate constants are in good agreement with available experimental values. The three-parameter Arrhenius expression for the total rate constants over 200–1000 K is provided.

A Systematic DFT Study of Two Elementary Steps Involving Hydrogen Peroxide and the Hydroxyl Radical in the Fenton Reaction

2018 ◽  
Author(s):  
Danilo Carmona ◽  
David Contreras ◽  
Oscar A. Douglas-Gallardo ◽  
Stefan Vogt-Geisse ◽  
Pablo Jaque ◽  
...  
Keyword(s):  
Hydrogen Peroxide ◽  
Hydroxyl Radical ◽  
Ab Initio ◽  
Fenton Reaction ◽  
Basis Set ◽  
Basis Sets ◽  
Dft Methods ◽  
Elementary Steps ◽  
Oxygen Oxygen ◽  
Complete Basis Set

The Fenton reaction plays a central role in many chemical and biological processes and has various applications as e.g. water remediation. The reaction consists of the iron-catalyzed homolytic cleavage of the oxygen-oxygen bond in the hydrogen peroxide molecule and the reduction of the hydroxyl radical. Here, we study these two elementary steps with high-level ab-initio calculations at the complete basis set limit and address the performance of different DFT methods following a specific classification based on the Jacob´s ladder in combination with various Pople's basis sets. Ab-initio calculations at the complete basis set limit are in agreement to experimental reference data and identified a significant contribution of the electron correlation energy to the bond dissociation energy (BDE) of the oxygen-oxygen bond in hydrogen peroxide and the electron affinity (EA) of the hydroxyl radical. The studied DFT methods were able to reproduce the ab-initio reference values, although no functional was particularly better for both reactions. The inclusion of HF exchange in the DFT functionals lead in most cases to larger deviations, which might be related to the poor description of the two reactions by the HF method. Considering the computational cost, DFT methods provide better BDE and EA values than HF and post--HF methods with an almost MP2 or CCSD level of accuracy. However, no systematic general prediction of the error based on the employed functional could be established and no systematic improvement with increasing the size in the Pople's basis set was found, although for BDE values certain systematic basis set dependence was observed. Moreover, the quality of the hydrogen peroxide, hydroxyl radical and hydroxyl anion structures obtained from these functionals was compared to experimental reference data. In general, bond lengths were well reproduced and the error in the angles were between one and two degrees with some systematic trend with the basis sets. From our results we conclude that DFT methods present a computationally less expensive alternative to describe the two elementary steps of the Fenton reaction. However, choice of approximated functionals and basis sets must be carefully done and the provided benchmark allows a systematic validation of the electronic structure method to be employed

A Comprehensive Computational Study on OCH+-Rg (Rg = He, Ne, Ar, Kr, Xe) Complexes

2003 ◽  
Vol 68 (3) ◽  
pp. 489-508 ◽  
Author(s):  
Yinghong Sheng ◽  
Jerzy Leszczynski
Keyword(s):  
Computational Study ◽  
Relativistic Effects ◽  
Dft Method ◽  
Basis Set ◽  
Rare Gas ◽  
Geometrical Parameters ◽  
Minor Effect ◽  
Dissociation Energies ◽  
Equilibrium Geometries

The equilibrium geometries, harmonic vibrational frenquencies, and the dissociation energies of the OCH+-Rg (Rg = He, Ne, Ar, Kr, and Xe) complexes were calculated at the DFT, MP2, MP4, CCSD, and CCSD(T) levels of theory. In the lighter OCH+-Rg (Rg = He, Ne, Ar) rare gas complexes, the DFT and MP4 methods tend to produce longer Rg-H+ distance than the CCSD(T) level value, and the CCSD-calculated Rg-H+ bond lengths are slightly shorter. DFT method is not reliable to study weak interaction in the OCH+-He and OCH+-Ne complexes. A qualitative result can be obtained for OCH+-Ar complex by using the DFT method; however, a higher-level method using a larger basis set is required for the quantitative predictions. For heavier atom (Kr, Xe)-containing complexes, only the CCSD method predicted longer Rg-H+ distance than that obtained at the CCSD(T) level. The DFT method can be applied to obtain the semiquantitative results. The relativistic effects are expected to have minor effect on the geometrical parameters, the H+-C stretching mode, and the dissociation energy. However, the dissociation energies are sensitive to the quality of the basis set. The nature of interaction between the OCH+ ion and Rg atoms was also analyzed in terms of the interaction energy components.

A vibrational spectroscopic and computational study of the structures of protonated imidacloprid and its fragmentation products in the gas phase

2021 ◽  
Vol 23 (5) ◽  
pp. 3377-3388
Author(s):  
Kelsey J. Menard ◽  
Jonathan Martens ◽  
Travis D. Fridgen
Keyword(s):  
Computational Chemistry ◽  
Gas Phase ◽  
Vibrational Spectroscopy ◽  
Computational Study ◽  
Unimolecular Decomposition ◽  
Decomposition Products

Vibrational spectroscopy and computational chemistry studies were combined with the aim of elucidating the structures of protonated imidacloprid (pIMI), and its unimolecular decomposition products.

scholarly journals The SN2 reaction and its relationship with the Walden inversion, the Finkelstein and Menshutkin reactions together with theoretical calculations for the Finkelstein reaction

2021 ◽  
Author(s):  
Ibon Alkorta ◽  
José Elguero
Keyword(s):  
Linear Models ◽  
Theoretical Calculations ◽  
Computational Method ◽  
Basis Set ◽  
Free Energies ◽  
Nitrogen And Phosphorus ◽  
Atom Pairs ◽  
Leaving Groups ◽  
First Time ◽  
Nitrogen Phosphorus

AbstractThis communication gives an overview of the relationships between four reactions that although related were not always perceived as such: SN2, Walden, Finkelstein, and Menshutkin. Binary interactions (SN2 & Walden, SN2 & Menshutkin, SN2 & Finkelstein, Walden & Menshutkin, Walden & Finkelstein, Menshutkin & Finkelstein) were reported. Carbon, silicon, nitrogen, and phosphorus as central atoms and fluorides, chlorides, bromides, and iodides as lateral atoms were considered. Theoretical calculations provide Gibbs free energies that were analyzed with linear models to obtain the halide contributions. The M06-2x DFT computational method and the 6-311++G(d,p) basis set have been used for all atoms except for iodine where the effective core potential def2-TZVP basis set was used. Concerning the central atom pairs, carbon/silicon vs. nitrogen/phosphorus, we reported here for the first time that the effect of valence expansion was known for Si but not for P. Concerning the lateral halogen atoms, some empirical models including the interaction between F and I as entering and leaving groups explain the Gibbs free energies.

scholarly journals Abandoned agricultural soils from the central part of the Yamal region of Russia: morphology, diversity, and chemical properties

2020 ◽  
Vol 5 (1) ◽  
pp. 94-106
Author(s):  
Evgeny Abakumov ◽  
Evgeniya Morgun ◽  
Alexandr Pechkin ◽  
Vyacheslav Polyakov
Keyword(s):  
Land Use ◽  
Agricultural Soils ◽  
Anthropogenic Impacts ◽  
Chemical Properties ◽  
Organic Carbon Content ◽  
Active Growth ◽  
Natural Processes ◽  
Agrochemical Properties ◽  
Fallow Lands ◽  
Abandoned Lands

AbstractThe post-anthropogenic and soil cover transformations of former agricultural soils on the abandoned lands in the Russian Arctic territory are poorly investigated due to the active growth of the city complexes and increasing area occupied by agricultural lands. That is lead to an increase in the area of the arable lands surrounding the polar urbanized territories. Today, most of that land allocated for agricultural needs has been abandoned or affected by other types of land use. This study aimed to investigate the abandoned lands surrounding some of the settlements in the central part of the Yamal region. The soil diversity, morphology, and chemical and agrochemical properties were investigated with special reference to the specific transformations that occur to fallow lands under permafrost-affected cryogenic-ecosystem conditions. Analysis of data show that these soils are characterized by features relating to both, previous (and existing), anthropogenic impacts and natural processes such as cryogenic mass transfer. The degradation of the arable humus-enriched horizon was not as pronounced as it has been in more humid boreal environments over recent decades. The organic carbon content in topsoil depends on the land use and varied considerably among the soil types. The former arable topsoil horizon has been stable over time in terms of its morphological features and agrochemical state. Despite the high soil acidity levels, thenutrient content in the anthropogenically impacted soils was still high, even though being abandoned for 20 years.

scholarly journals Density Functional Theory and Complete Basis Set Ab Initio Computational Study of Five-, Six-, Seven- and Eight-hydrogen Coordinated Carbon Cations

1999 ◽  
Vol 23 (8) ◽  
pp. 502-503
Author(s):  
Branko S. Jursic
Keyword(s):  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Computational Study ◽  
Basis Set ◽  
Functional Theory ◽  
Complete Basis ◽  
Complete Basis Set ◽  
High Level

High level ab initio and density functional theory studies are performed on highly protonated methane species.

scholarly journals Comparison of ±σ-hole and ±R˙-hole interactions formed by tetrel-containing complexes: a computational study

RSC Advances ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 4011-4021
Author(s):  
Mahmoud A. A. Ibrahim ◽  
Ebtisam M. Z. Telb
Keyword(s):  
Computational Study ◽  
First Time

The characteristics and nature of ±R˙-hole interactions were uncovered for the first time and compared to their ±σ-hole analogs in ˙TF3⋯ and W–T–F3⋯B/R˙/A complexes.

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