Computational study on the deamination reaction of adenine with OH−/nH2O (n = 0, 1, 2, 3) and 3H2O

2013 ◽  
Vol 91 (7) ◽  
pp. 518-526 ◽  
Author(s):  
Ahmad I. Alrawashdeh ◽  
Mansour H. Almatarneh ◽  
Raymond A. Poirier
Keyword(s):  
Activation Energy ◽  
Water Molecule ◽  
Gas Phase ◽  
Activation Barrier ◽  
Computational Study ◽  
Polarizable Continuum Model ◽  
Intrinsic Reaction Coordinate ◽  
Rate Determining Step ◽  
Additional Water ◽  
Deamination Reaction

Deamination of adenine is one of several forms of premutagenic lesions occurring in DNA. In the present study, mechanisms for the deamination reaction of adenine with OH−/nH2O (n = 0, 1, 2, 3) and 3H2O were investigated. HF/6-31G(d), B3LYP/6-31G(d), MP2/6-31G(d), and B3LYP/6-31+G(d) levels of theory were employed to search for and optimize all geometries. Energies were calculated at the G3MP2B3 and CBS-QB3 levels of theory. The effect of solvent (water) was computed using the polarizable continuum model (PCM). Intrinsic reaction coordinate (IRC) calculations were performed for all transition states. Five pathways were investigated for the deamination reaction of adenine with OH−/nH2O and 3H2O. The first four pathways (A–D) are initiated by deprotonation at the amino group of adenine by OH−, while pathway E is initiated by tautomerization of adenine. For all pathways the next two steps involve formation of a tetrahedral intermediate followed by dissociation to products via a 1,3-proton shift. Deamination with a single OH− has a high activation barrier (190 kJ mol−1 using the G3MP2B3 level) for the rate-determining step. The addition of one water molecule reduces this barrier by 68 kJ mol−1 at the G3MP2B3 level. Adding additional water molecules decreases the overall activation energy of the reaction, but the effect becomes smaller with each additional water molecule. The most plausible mechanism is pathway E, the deamination reaction of adenine with 3H2O, with an overall G3MP2B3 activation energy of 139 and 137 kJ mol−1 for the gas phase and PCM, respectively. This barrier is lower than that for the deamination with OH−/3H2O by 6 and 2 kJ mol−1 for the gas phase and PCM, respectively.

Gas-Phase Clustering of NO+ with H2S and H2O

2007 ◽  
Vol 72 (8) ◽  
pp. 1122-1138 ◽  
Author(s):  
Milan Uhlár ◽  
Ivan Černušák
Keyword(s):  
Hydrogen Bonds ◽  
Water Molecule ◽  
Gas Phase ◽  
Saddle Points ◽  
Solvent Molecule ◽  
Local Minima ◽  
Additional Water ◽  
Three Body ◽  
Rain Formation ◽  
Stable Structures

The complex NO+·H2S, which is assumed to be an intermediate in acid rain formation, exhibits thermodynamic stability of ∆Hº300 = -76 kJ mol-1, or ∆Gº300 = -47 kJ mol-1. Its further transformation via H-transfer is associated with rather high barriers. One of the conceivable routes to lower the energy of the transition state is the action of additional solvent molecule(s) that can mediate proton transfer. We have studied several NO+·H2S structures with one or two additional water molecule(s) and have found stable structures (local minima), intermediates and saddle points for the three-body NO+·H2S·H2O and four-body NO+·H2S·(H2O)2 clusters. The hydrogen bonds network in the four-body cluster plays a crucial role in its conversion to thionitrous acid.

scholarly journals Computational mechanistic study of the unimolecular dissociation of ethyl hydroperoxide and its bimolecular reactions with atmospheric species

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Mansour H. Almatarneh ◽  
Asmaa Alnajajrah ◽  
Mohammednoor Altarawneh ◽  
Yuming Zhao ◽  
Mohammad A. Halim
Keyword(s):  
Activation Energy ◽  
Density Functional ◽  
Computational Study ◽  
Basis Sets ◽  
Mechanistic Study ◽  
Intrinsic Reaction Coordinate ◽  
Unimolecular Dissociation ◽  
Phase Reaction ◽  
Atmospheric Species ◽  
Solvation Models

Abstract A detailed computational study of the atmospheric reaction of the simplest Criegee intermediate CH2OO with methane has been performed using the density functional theory (DFT) method and high-level calculations. Solvation models were utilized to address the effect of water molecules on prominent reaction steps and their associated energies. The structures of all proposed mechanisms were optimized using B3LYP functional with several basis sets: 6-31G(d), 6-31G (2df,p), 6-311++G(3df,3pd) and at M06-2X/6-31G(d) and APFD/6-31G(d) levels of theory. Furthermore, all structures were optimized at the B3LYP/6-311++G(3df,3pd) level of theory. The intrinsic reaction coordinate (IRC) analysis was performed for characterizing the transition states on the potential energy surfaces. Fifteen different mechanistic pathways were studied for the reaction of Criegee intermediate with methane. Both thermodynamic functions (ΔH and ΔG), and activation parameters (activation energies Ea, enthalpies of activation ΔHǂ, and Gibbs energies of activation ΔGǂ) were calculated for all pathways investigated. The individual mechanisms for pathways A1, A2, B1, and B2, comprise two key steps: (i) the formation of ethyl hydroperoxide (EHP) accompanying with the hydrogen transfer from the alkanes to the terminal oxygen atom of CIs, and (ii) a following unimolecular dissociation of EHP. Pathways from C1 → H1 involve the bimolecular reaction of EHP with different atmospheric species. The photochemical reaction of methane with EHP (pathway E1) was found to be the most plausible reaction mechanism, exhibiting an overall activation energy of 7 kJ mol−1, which was estimated in vacuum at the B3LYP/6-311++G(3df,3pd) level of theory. All of the reactions were found to be strongly exothermic, expect the case of the sulfur dioxide-involved pathway that is predicted to be endothermic. The solvent effect plays an important role in the reaction of EHP with ammonia (pathway F1). Compared with the gas phase reaction, the overall activation energy for the solution phase reaction is decreased by 162 and 140 kJ mol−1 according to calculations done with the SMD and PCM solvation models, respectively.

scholarly journals Influence of the number of water molecules on the mechanism of N-sulfinylaniline hydrolysis

2005 ◽  
Vol 83 (9) ◽  
pp. 1588-1596 ◽  
Author(s):  
Elena V Ivanova ◽  
Heidi M Muchall
Keyword(s):  
Water Molecule ◽  
Density Functional ◽  
Weak Interactions ◽  
Activation Barrier ◽  
Water Molecules ◽  
Functional Theory ◽  
High Enthalpy ◽  
Rate Determining Step ◽  
Enthalpy Of Activation ◽  
Hydrolysis Of

The mechanism of the uncatalyzed hydrolysis of N-sulfinylaniline (Ph-N=S=O) has been studied with B3LYP/6-31+G(2d,2p) in the gas phase, with explicit treatment of water molecules. Hydrolysis involves water attack on sulfur, with a close to perpendicular alignment of a water molecule and the NSO plane in both prereaction complexes and transition states for the rate-determining step. Consequently, the distance of the weak S···O interaction, together with the efficiency of protonation of either nitrogen (attack across the N=S bond) or oxygen (attack across the S=O bond) atoms of the NSO group, determines the height of the activation barrier for hydrolysis. While the reaction with one water molecule is characterized by an unreasonably high enthalpy of activation, a cooperative effect from the weak interactions appears with the inclusion of a second water molecule, where both participate in the reaction, and the activation enthalpy drops significantly. The preference for attack across the S=O bond that is found in the reaction with one water molecule switches to a dominance of attack across the N=S bond in the reaction with three water molecules.Key words: N-sulfinylaniline, hydrolysis, mechanism, density functional theory (DFT).

scholarly journals Theoretical Investigation of Glycine Micro-Solvated. Energy and NMR Spin Spin Coupling Constants Calculations

Sci ◽  
2021 ◽  
Vol 3 (4) ◽  
pp. 41
Author(s):  
Maria Cristina Caputo ◽  
Patricio Federico Provasi
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Computational Study ◽  
Water Solution ◽  
Polarizable Continuum Model ◽  
Coupling Constants ◽  
Spin Coupling ◽  
Basis Set ◽  
Spin Coupling Constants ◽  
Spin Spin Coupling

Glycine in its neutral form can exist in the gas phase while its zwitterion form is more stable in water solution, but how many waters are actually necessary to stabilize the zwitterionic structure in the gas phase? Are the intramolecular isotropic spin spin coupling constants sensitive enough to accuse the change in the environment? or the conformer observed? These and related questions have been investigated by a computational study at the level of density functional theory employing the B3LYP functional and the 6-31++G**-J basis set. We found that at least two water molecules explicitly accounted for in the super-molecule structure are necessary to stabilize both conformers of glycine within a water polarizable continuum model. At least half of the SSCCs of both conformers are very stable to changes in the environment and at least four of them differ significantly between Neutral and Zwitterion conformation.

scholarly journals Theoretical Investigation of Glycine Micro-solvated. Energy and NMR Spin Spin Coupling Constants Calculations

2021 ◽  
Author(s):  
Maria Cristina Caputo ◽  
Patricio Federico Provasi
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Computational Study ◽  
Polarizable Continuum Model ◽  
Coupling Constants ◽  
Spin Coupling ◽  
Basis Set ◽  
Spin Coupling Constants ◽  
Spin Spin Coupling ◽  
Polarizable Continuum

Glycine in its neutral form can exist in the gas phase while its zwitterion form is more stable in water solution.But how many waters are actually necessary to stabilize the zwitterionic structure in the gas phase? Are the intramolecular isotropic spin spin coupling constants sensitive enough to accuse the change in the environment? or the conformer observed? These and related questions have been investigated by a computational study at the level of density functional theory employing the B3LYP functional and the 6-31++G**-J basis set. We found that at least two water molecules explicitly accounted in the super-molecule structure are necessary to stabilize both conformers of glycine within a water polarizable continuum model. At least half of the SSCC’s of both conformers are very stable to changes in the environment and at least four of them differ significantly between Neutral and Zwitterion conformation.

Pt-Pd Nanoalloy for the Unprecedented Activation of Carbon-Fluorine Bond at Low Temperature

2019 ◽  
Author(s):  
Raghu Nath Dhital ◽  
keigo nomura ◽  
Yoshinori Sato ◽  
Setsiri Haesuwannakij ◽  
Masahiro Ehara ◽  
...  
Keyword(s):  
Activation Energy ◽  
Low Temperature ◽  
Dft Calculations ◽  
Bond Activation ◽  
Mild Conditions ◽  
Selective Transformation ◽  
Rate Determining Step ◽  
Highly Active ◽  
Harsh Conditions ◽  
Reaction Profile

Carbon-Fluorine (C-F) bonds are considered the most inert organic functionality and their selective transformation under mild conditions remains challenging. Herein, we report a highly active Pt-Pd nanoalloy as a robust catalyst for the transformation of C-F bonds into C-H bonds at low temperature, a reaction that often required harsh conditions. The alloying of Pt with Pd is crucial to activate C-F bond. The reaction profile kinetics revealed that the major source of hydrogen in the defluorinated product is the alcoholic proton of 2-propanol, and the rate-determining step is the reduction of the metal upon transfer of the <i>beta</i>-H from 2-propanol. DFT calculations elucidated that the key step is the selective oxidative addition of the O-H bond of 2-propanol to a Pd center prior to C-F bond activation at a Pt site, which crucially reduces the activation energy of the C-F bond. Therefore, both Pt and Pd work independently but synergistically to promote the overall reaction

Explaining the magnetism of gold

2017 ◽  
Author(s):  
Robson de Farias
Keyword(s):  
Gas Phase ◽  
Computational Study ◽  
Formation Enthalpy ◽  
Gold Atom ◽  
Orbital Energy ◽  
Knudsen Effusion ◽  
Energy Diagram ◽  
Unpaired Electrons ◽  
The Difference ◽  
Good Agreement

<p>In the present work, a computational study is performed in order to clarify the possible magnetic nature of gold. For such purpose, gas phase Au<sub>2</sub> (zero charge) is modelled, in order to calculate its gas phase formation enthalpy. The calculated values were compared with the experimental value obtained by means of Knudsen effusion mass spectrometric studies [5]. Based on the obtained formation enthalpy values for Au<sub>2</sub>, the compound with two unpaired electrons is the most probable one. The calculated ionization energy of modelled Au<sub>2</sub> with two unpaired electrons is 8.94 eV and with zero unpaired electrons, 11.42 eV. The difference (11.42-8.94 = 2.48 eV = 239.29 kJmol<sup>-1</sup>), is in very good agreement with the experimental value of 226.2 ± 0.5 kJmol<sup>-1</sup> to the Au-Au bond<sup>7</sup>. So, as expected, in the specie with none unpaired electrons, the two 6s<sup>1</sup> (one of each gold atom) are paired, forming a chemical bond with bond order 1. On the other hand, in Au<sub>2</sub> with two unpaired electrons, the s-d hybridization prevails, because the relativistic contributions. A molecular orbital energy diagram for gas phase Au<sub>2</sub> is proposed, explaining its paramagnetism (and, by extension, the paramagnetism of gold clusters and nanoparticles).</p>

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.

Gas Cell Infrared and Attenuated Total Reflection Infrared Spectroscopic Studies for Organic–Inorganic Interactions in Adsorption of Fulvic Acid on the Goethite Surface Generating Carbon Dioxide

2021 ◽  
pp. 000370282199121
Author(s):  
Yuki Nakaya ◽  
Satoru Nakashima ◽  
Takahiro Otsuka
Keyword(s):  
Carbon Dioxide ◽  
Activation Energy ◽  
Fulvic Acid ◽  
Spectroscopic Studies ◽  
Reaction Model ◽  
Total Reflection ◽  
Attenuated Total Reflection ◽  
Gas Cell ◽  
Rate Determining Step ◽  
Ir Spectroscopic

The generation of carbon dioxide (CO2) from Nordic fulvic acid (FA) solution in the presence of goethite (α-FeOOH) was observed in FA–goethite interaction experiments at 25–80 ℃. CO2 generation processes observed by gas cell infrared (IR) spectroscopy indicated two steps: the zeroth order slower CO2 generation from FA solution commonly occurring in the heating experiments of the FA in the presence and absence of goethite (activation energy: 16–19 kJ mol–1), and the first order faster CO2 generation from FA solution with goethite (activation energy: 14 kJ mol–1). This CO2 generation from FA is possibly related to redox reactions between FA and goethite. In situ attenuated total reflection infrared (ATR-IR) spectroscopic measurements indicated rapid increases with time in IR bands due to COOH and COO– of FA on the goethite surface. These are considered to be due to adsorption of FA on the goethite surface possibly driven by electrostatic attraction between the positively charged goethite surface and negatively charged deprotonated carboxylates (COO–) in FA. Changes in concentration of the FA adsorbed on the goethite surface were well reproduced by the second order reaction model giving an activation energy around 13 kJ mol–1. This process was faster than the CO2 generation and was not its rate-determining step. The CO2 generation from FA solution with goethite is faster than the experimental thermal decoloration of stable structures of Nordic FA in our previous report possibly due to partial degradations of redox-sensitive labile structures in FA.

Sign in / Sign up

Export Citation Format

Share Document