Mechanisms for the deamination reaction of cytosine with H2O/OH(-) and 2H2O/OH(-): a computational study

Mechanisms for the deamination reaction of cytosine with H 2O/OH (-) and 2H 2O/OH (-) to produce uracil were investigated using ab initio calculations. Optimized geometries of reactants, transition states, intermediates, and products were determined at MP2 and B3LYP using the 6-31G(d) basis set and at B3LYP/6-31+G(d) levels of theory. Single point energies were also determined at MP2/G3MP2Large and G3MP2 levels of theory. Thermodynamic properties (Delta E, Delta H, and Delta G), activation energies, enthalpies, and free energies of activation were calculated for each reaction pathway investigated. Intrinsic reaction coordinate (IRC) analysis was performed to characterize the transition states on the potential energy surface. Seven pathways for the deamination reaction were found. All pathways produce an initial tetrahedral intermediate followed by several conformational changes. The final intermediate for all pathways dissociates to product via a 1-3 proton shift. The activation energy for the rate-determining step, the formation of the tetrahedral intermediate for pathway D, the only pathway that can lead to uracil, is 115.3 kJ mol (-1) at the G3MP2 level of theory, in excellent agreement with the experimental value (117 +/- 4 kJ mol (-1)).     

Theoretical study on the hydrolytic deamination reaction mechanism of guanine and (H2O)n

The hydrolytic deamination reaction mechanism of guanine (G) and (H₂O)n (n = 1–4) has been theoretically investigated, including solvent effects at the B3LYP/6-31G (d,p) and MP2/6-311G (d,p) levels. The results show that the hydrolytic deamination reaction of G involves two steps. In the first step, a tetra-coordinated intermediate is generated by a hydrolysis reaction, and then deamination reaction is carried out. In the second step, the final products form via a hydrogen transfer. For the hydrolytic deamination reaction of guanine and 3H₂O or 4H₂O, only two molecules of water participate in the reaction, and other water molecule make the transition state more stable as a catalyst. The study on the potential energy surface shows that the deamination reaction of G and nH₂O does not take place because of a higher barrier for the opening system, which is in agreement with the experimental result.     

Dynamics study of the reaction OH- + C2H2-->C2H- + H2O with crossed beams and density-functional theory calculations

The proton transfer reaction between OH- and C2H2, the sole reactive process observed over the collision energy range from 0.37 to 1.40 eV, has been studied using the crossed beam technique and density-functional theory (DFT) calculations. The center of mass flux distributions of the product C2H- ions at three different energies are highly asymmetric, characteristic of a direct process occurring on a time scale much less than a rotational period of any transient intermediate. The maxima in the flux distributions correspond to product velocities and directions close to those of the precursor acetylene reactants. The reaction quantitatively transforms the entire exothermicity into internal excitation of the products, consistent with an energy release motif in which the proton is transferred early, in a configuration in which the forming bond is extended. This picture is supported by DFT calculations showing that the first electrostatically bound intermediate on the reaction pathway is the productlike C2H- H2O species. Most of the incremental translational energy in the two higher collision energy experiments appears in product translational energy, and provides an example of induced repulsive energy release characteristic of the heavy+light-heavy mass combination.     

Theoretical study of cytosine deamination from the perspective of the reaction force analysis

A theoretical study of two different mechanisms for the spontaneous deamination of cytosine is presented. In the first mechanism, a tetrahedral intermediate results in a two-step mechanism whereas in the second one, it is the result of a concerted step. In this work a link is made between the two pathways through the study of the evolution along the reaction coordinates of chemical concepts such as chemical potential, hardness and electronic populations within the framework of the reaction force analysis. The reaction force profile suggests that the concerted mechanism is composed of two asynchronous events. The observation of the reaction force profile appears as an easy way to identify asynchronous concerted steps and as a privileged tool to study the more or less asynchronous character of chemical reactions.     

Direct ab initio molecular dynamics study on a microsolvated SN2 reaction of OH-(H2O) with CH3Cl

Reaction dynamics for a microsolvated SN2 reaction OH-(H2O)+CH3Cl have been investigated by means of the direct ab initio molecular dynamics method. The relative center-of-mass collision energies were chosen as 10, 15, and 25 kcal/mol. Three reaction channels were found as products. These are (1) a channel leading to complete dissociation (the products are CH3OH+Cl- +H2O: denoted by channel I), (2) a solvation channel (the products are Cl-(H2O)+CH3OH: channel II), and (3) a complex formation channel (the products are CH3OH...H2O+Cl-: channel III). The branching ratios for the three channels were drastically changed as a function of center-of-mass collision energy. The ratio of complete dissociation channel (channel I) increased with increasing collision energy, whereas that of channel III decreased. The solvation channel (channel II) was minor at all collision energies. The selectivity of the reaction channels and the mechanism are discussed on the basis of the theoretical results.     

Theoretical study of the · H reaction with cytosine

We studied three possible reactions of H atom attacking the cytosine, using density functional theory (DFT) calculations. The results indicate that the H atom addition to the N₃ site of cytosine is energetically more favorable than to the C₅ or C₆ site. The reaction of addition to the C₆ site has an energy barrier of ～2.77 kcal/mol, which is ～2 kcal/mol higher than addition to C₅. The energy of C₅ H‐adduct radical is also lower than that of C₆ H‐adduct radical. From the point of view of both energetics and reaction kinetics, the addition of the H atom to the C₅ site is preferred to the addition to the C₆ site. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Computational study on the mechanisms and energetics of trimethylindium reactions with H2O and H2S

The reactions of trimethylindium (TMIn) with H2O and H2S are relevant to the chemical vapor deposition of indium oxide and indium sulfide thin films. The mechanisms and energetics of these reactions in the gas phase have been investigated by density functional theory and ab initio calculations using the CCSD(T)/[6-31G(d,p)+Lanl2dz]//B3LYP/[6-31G(d,p)+Lanl2dz] and CCSD(T)/[6-31G(d,p)+Lanl2dz] //MP2/[6-31G(d,p)+Lanl2dz] methods. The results of both methods are in good agreement for the optimized geometries and relative energies. When TMIn reacts with H2O and H2S, initial molecular complexes [(CH3)3In:OH2 (R1)] and [(CH3)3In:SH2 (R2)] are formed with 12.6 and 3.9 kcal/mol binding energies. Elimination of a CH4 molecule from each complex occurs with a similar energy barrier at TS1 (19.9 kcal/mol) and at TS3 (22.1 kcal/mol), respectively, giving stable intermediates (CH3)2InOH and (CH3)2InSH. The elimination of the second CH4 molecule from these intermediate products, however, has to overcome very high and much different barriers of 66.1 and 53.2 kcal/mol, respectively. In the case of DMIn with H2O and H2S reactions, formation of both InO and InS is exothermic by 3.1 and 30.8 kcal/mol respectively. On the basis of the predicted heats of formation of R1 and R2 at 0 K and -20.1 and 43.6 kcal/mol, the heats of formation of (CH3)2InOH, (CH3)2InSH, CH3InO, CH3InS, InO, and InS are estimated to be -20.6, 31.8, and 29.0 and 48.4, 35.5, and 58.5 kcal/mol, respectively. The values for InO and InS are in good agreement with available experimental data. A similar study on the reactions of (CH3)2In with H2O and H2S has been carried out; in these reactions CH3InOH and CH3InSH were found to be the key intermediate products.     

Calculation of the Gibbs Energy of the Reaction OH-·(H2O)n-1 + H2O = OH-·(H2O)n by the Monte-Carlo Method

The energy, the Gibbs energy of the reaction OH^-·(H₂O) _{n- 1} + H₂O = OH^-·(H₂O) _n are calculated by the Monte-Carlo method with a large canonical ensemble for n = 1, ..., 20. The ion-waternonpair interaction potential was obtained by numerical fitting of calculated Gibbs energy and entropy of (H₂O)_n clusters (n = 1, ..., 5) to experimental ones. A good fit to experiment both of the internal energy and the Gibbs energy can be obtained in terms of a model allowing for nonpair interaction. It is shown that constructing an ion-water interaction potential without allowance for the entropy factor can lead to considerable errors in the Gibbs energy of cluster formation and in the nucleation rate.     

Proton catalyzed hydrolytic deamination of cytosine: a computational study

Two pathways involving proton catalyzed hydrolytic deamination of cytosine (to uracil) are investigated at the PCM-corrected B3LYP/6-311G(d,p) level of theory, in the presence of an additional catalyzing water molecule. It is concluded that the pathway involving initial protonation at nitrogen in position 3 of the ring, followed by water addition at C4 and proton transfer to the amino group, is a likely route to hydrolytic deamination. The rate determining step is the addition of water to the cytosine, with a calculated free energy barrier in aqueous solution of ΔG ^≠=140 kJ/mol. The current mechanism provides a lower barrier to deamination than previous work based on OH ^? catalyzed reactions, and lies closer to the experimental barrier derived from rate constants (E _a = 117  ±  4 kJ/mol).     

Computational study of the reactivity of cytosine derivatives

The aim of the present study is to provide computational insight using dispersion‐corrected density‐functional calculations into the reactivity properties of modified cytosine in the gas phase and in aqueous solution, whereby special emphasis is put on systems that are obtained through demethylation and methylation. Since this field is relatively incipient, our goal is to identify relationships between reactivity and stability for the modified compounds to understand their biological functionalities. Our results show that addition of a methyl, hydroxylmethyl, formyl, or carboxyl group reduces the length of the nearest hydrogen bond between the cytosine–guanine (CG) base pair and increases the length of the longest hydrogen bond of the DNA base pair. © 2017 Wiley Periodicals, Inc.     

Pedagogic Interest of the H2O2, Cu2+, SCN-, OH- Oscillating Reaction

Chemical reactivity is generally taught by considering the chemical properties of the reacting entities (acid-base, oxidation-reduction, complexation, and precipitation) and the values of the corresponding equilibrium thermodynamic constants (K_a, E⁰ K_d, K_s). This approach, however, is not well-suited to the dynamic chemical systems that are often encountered in industrial and environmental chemistry where nonequilibrium conditions prevail. In this respect, oscillating reactions are a good illustration of the limits of equilibrium thermodynamics and show the need for a complementary dynamic nonequilibrium study. We describe here an oscillating reaction that is easy to carry out in an inorganic chemistry practical class as it uses common reactants (H₂O₂, KSCN, CuSO₄, NaOH). This example should enable students to obtain a more realistic grasp of chemical reactivity based on a comprehension of coupled reaction processes, similar to those encountered in population dynamics or in enzymatic regulation.     

The reaction of O(1D) with H2O and the reaction of OH with C3H6

N₂O was photolyzed at 2139 Å to produce O(¹D) atoms in the presence of H₂O and CO. The O(¹D) atoms react with H₂O to produce HO radicals, as measured by CO₂ production from the reaction of OH with CO. The relative importance of the various possible O(¹D )–H₂O reactions is The relative rate constant for O(¹D) removal by H₂O compared to that by N₂O is 2.1, in good agreement with that found earlier in our laboratory. In the presence Of C₃H₆, the OH can be removed by reaction with either CO or C₃H₆: From the CO₂ yield, k₃/k₂ = 75,0 at 100°C and 55.0 at 200°C to within ± 10%. When these values are combined with the value of k₂ = 7.0 × 10^?13exp (–1100/RT) cm³/sec, k₃ = 1.36 × 10^?11 exp (–100/RT) cm³/sec. At 25°C, k₃ extrapolates to 1.1 × 10^?11 cm³/sec.     

Atrazine toxicity reduction following H2O2/TiO2- photocatalyzed reaction and comparison with H2O2- photolytic reaction

An atrazine photodegradation study carried out by a Q-Panel suntest apparatus is reported in this work. H2O2/TiO2 photocatalyzed reaction yield and parameters (time, irradiance, temperature, H2O2 (40%) volume, TiO2 amount) were exactly determined relating to the used atrazine concentration. An experimental kinetic study was performed to establish the reaction order in fixed conditions. Using a biosensor method, 10(-4) M Atrazine solution toxicity and final photocatalytic reaction solution toxicity were quantitatively determined. A consistent toxicity decrease was observed on passing from the analyte to the products of the photocatalytic reaction. An analogous photolytic reaction carried out in absence of TiO2, but in the same experimental conditions of time, irradiance, temperature and H2O2 volume, brings to a toxicity increase.     

Ab initio study of the reaction of CHO+ with H2O and NH3

An MP4(full,SDTQ)/6-311++G(d,p)//MP2(full)/6-311++G(d,p) ab initio study was performed of the reactions of formyl and isoformyl cations with H₂O and NH₃, which play an important role in flame and interstellar chemistries. Two different confluent channels were located leading to CO+H₃O⁺/NH. The first one corresponds to the approach of the neutral molecule to the carbon atom of the cations. The second one leads to the direct proton transfer from the cations to the neutrals. At 900 K the separate products CO+H₃O⁺/NH are the most stable species along the Gibbs energy profiles for the processes. For the reaction with H₂O the reaction channel leading to HC(OH) (protonated formic acid) is disfavored with respect to the two CO+H₃O⁺ channels in agreement with the experimental evidence that H₃O⁺ is the major ion observed in hydrocarbon flames. According to our calculations, NH+H₂O are considerably more stable in Gibbs energy than NH₃+H₃O⁺;NH will predominate in the reaction zone when ammonia is added to CH₄+Ar diffusion flame, as experimentally observed. At 100 K the most stable structures are the intermediate complexes CO…HOH/HNH. Particularly the CO…HOH complex has a lifetime large enough to be detected and, therefore, could play a certain role in interstellar chemistry. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1432–1443, 1999     

The reaction of O(3P) with H2O2

The rate constant for the reaction of O(³P) with H₂O₂ was measured as a function of temperature and the [H₂O₂]₀/[O]₀ ratio. The numerical solution of the appropriate rate equations was used to arrive at a mechanism which adequately describes our results and the rather divergent data in the literature. A recommended expression for the temperature dependence of the absolute rate constant is presented from consideration of the available experimental data.     

A reduced dimensionality quasiclassical and quantum study of the proton transfer reaction H3O(+)+H2O-->H2O+H3O(+)

We report quantum and quasiclassical calculations of proton transfer in the reaction H(3)O(+)+H(2)O in three degrees of freedom, the two OH(+) bond lengths and the OH(+)O angle. The reduced dimensional potential energy surface is obtained from the full dimensional OSS3(p) energy function of H(5)O(2) (+) [L. Ojamae, I. Shavitt, and S. J. Singer, J. Chem. Phys. 109, 5547 (1998)], with an additional long-range correction to reproduce the correct ion-molecule interaction. This surface is used to perform both quasiclassical trajectory and quantum reactive scattering calculations of the zero total angular momentum cumulative reaction probability and cross sections for initial rotational states 0, 1, and 2. Comparison of these quantities are made to assess the importance of quantum effects in this reduced dimensional reaction. Additional quasiclassical cross sections are calculated to obtain the thermal rate constant for the reaction.     

Computational study of the reaction of the methylsulfonyl radical,CH3S(O)2, with NO2

The mechanism of the reaction between the methylsulfonyl radical, CH₃S(O)₂, and NO₂ is examined using density functional theory and ab initio calculations. Two stable association intermediates, CH₃SNO₂ and CH₃S(O)ONO, may be formed through the attack of the nitrogen or the oxygen atom of NO₂ radical to the S atom. Interisomerization and decomposition of these intermediates are investigated using high level energy methods and specifically, CCSD(T), CBS‐QB3, and G3//B3LYP. The computational investigation indicates that the lowest energy reaction pathway leads to the products CH₃S(O)₃ + NO, through the decomposition of the most stable association adduct CH₃S(O)ONO. This result fully supports the relevant assumption of Ray et al. (Ray et al., J. Phys. Chem. 1996, 100, 8895], on which the experimental evaluation of the rate constant was based, namely that CH₃S(O)₃ + NO are the most probable products of the reaction CH₃S(O)₂ + NO₂. © 2014 Wiley Periodicals, Inc.     

Kinetics of Al + H2O reaction: theoretical study

Quantum chemical calculations were carried out to study the reaction of Al atom in the ground electronic state with H(2)O molecule. Examination of the potential energy surface revealed that the Al + H(2)O → AlO + H(2) reaction must be treated as a complex process involving two steps: Al + H(2)O → AlOH + H and AlOH + H → AlO + H(2). Activation barriers for these elementary reaction channels were calculated at B3LYP/6-311+G(3df,2p), CBS-QB3, and G3 levels of theory, and appropriate rate constants were estimated by using a canonical variational theory. Theoretical analysis exhibited that the rate constant for the Al + H(2)O → products reaction measured by McClean et al. must be associated with the Al + H(2)O → AlOH + H reaction path only. The process of direct HAlOH formation was found to be negligible at a pressure smaller than 100 atm.     

Radical-molecule reaction C3H+H2O: a mechanistic study

Despite the importance of the C(3)H radical in both combustion and interstellar space, the reactions of C(3)H toward stable molecules have never been studied. In this paper, we report our detailed mechanistic study on the radical-molecule reaction C(3)H+H(2)O at the Becke's three parameter Lee-Yang-Parr-B3LYP6-311G(d,p) and coupled cluster with single, double, and triple excitations-CCSD(T)6-311G(2d,p) (single-point) levels. It is shown that the C(3)H+H(2)O reaction initially favors formation of the carbene-insertion intermediates HCCCHOH (1a,1b) rather than the direct H- or OH-abstraction process. Subsequently, the isomers (1a,1b) can undergo a direct H- extrusion to form the well-known product propynal HCCCHO (P(5)). Highly competitively, (1a,1b) can take the successive 1,4- and 1,2-H-shift interconversion to isomer H(2)CCCHO(2a,2b) and then to isomer H(2)CCHCO(3a,3b), which can finally take a direct C-C bond cleavage to give product C(2)H(3) and CO (P(1)). The other products are kinetically much less feasible. With the overall entrance barrier 10.6 kcal/mol, the title reaction can be important in postburning processes. Particularly, our calculations suggest that the title reaction may play a role in the formation of the intriguing interstellar molecule, propynal HCCCHO. The calculated results will also be useful for the analogous C(3)H reactions such as with ammonia and alkanes.