A computational mechanistic study of the deamination reaction of melamine

A detailed computational study of the deamination reaction of melamine by OH^–, n H₂O/OH^–, n H₂O (where n = 1, 2, 3), and protonated melamine with H₂O, has been carried out using density functional theory and ab initio calculations. All structures were optimized at M06/6‐31G(d) level of theory, as well as with the B3LYP functional with each of the basis sets: 6‐31G(d), 6‐31 + G(d), 6‐31G(2df,p), and 6‐311++G(3df,3pd). B3LYP, M06, and ω B97XD calculations with 6‐31 + G(d,p) have also been performed. All structures were optimized at B3LYP/6‐31 + G(d,p) level of theory for deamination simulations in an aqueous medium, using both the polarizable continuum solvation model and the solvation model based on solute electron density. Composite method calculations have been conducted at G4MP2 and CBS‐QB3. Fifteen different mechanistic pathways were explored. Most pathways consisted of two key steps: formation of a tetrahedral intermediate and in the final step, an intermediate that dissociates to products via a 1,3‐proton shift. The lowest overall activation energy, 111 kJ mol^?1 at G4MP2, was obtained for the deamination of melamine with 3H₂O/OH^?.     

Mechanistic study of the deamination reaction of guanine: a computational study

The mechanism for the deamination of guanine with H(2)O, OH(-), H(2)O/OH(-) and for GuaH(+) with H(2)O has been investigated using ab initio calculations. Optimized geometries of the reactants, transition states, intermediates, and products were determined at RHF/6-31G(d), MP2/6-31G(d), B3LYP/6-31G(d), and B3LYP/6-31+G(d) levels of theory. Energies were also determined at G3MP2, G3MP2B3, G4MP2, and CBS-QB3 levels of theory. Intrinsic reaction coordinate (IRC) calculations were performed to characterize the transition states on the potential energy surface. Thermodynamic properties (ΔE, ΔH, and ΔG), activation energies, enthalpies, and Gibbs free energies of activation were also calculated for each reaction investigated. All pathways yield an initial tetrahedral intermediate and an intermediate in the last step that dissociates to products via a 1,3-proton shift. At the G3MP2 level of theory, deamination with OH(-) was found to have an activation energy barrier of 155 kJ mol(-1) compared to 187 kJ mol(-1) for the reaction with H(2)O and 243 kJ mol(-1) for GuaH(+) with H(2)O. The lowest overall activation energy, 144 kJ mol(-1) at the G3MP2 level, was obtained for the deamination of guanine with H(2)O/OH(-). Due to a lack of experimental results for guanine deamination, a comparison is made with those of cytosine, whose deamination reaction parallels that of guanine.     

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).     

A theoretical study on the mechanism and thermodynamics of ozone-water gas phase reaction

Ozone water reaction including a complex was studied at the MP2/6-311++G(d,p) and CCSD/6-311++G(2df,2p)//MP2/6-311++G(d,p) levels of theory. The interaction between water oxygen and central oxygen of ozone produces stable H₂O-O₃ complex with no barrier. With decomposition of this complex through H-abstraction by O₃ and O-abstraction by H₂O, three possible product channels were found. Intrinsic reaction coordinate, topological analyses of atom in molecule, and vibrational frequency calculation have been used to confirm the preferred mechanism. Thermodynamic data at T = 298.15 K and atmospheric pressure have been calculated. The results show that the production of hydrogen peroxide is the main reaction channel with ΔG = ?21.112 kJ mol^-1.     

Theoretical study on the hydrolytic deamination mechanism of adenosine

The hydrolytic deamination mechanism of adenosine to produce inosine was studied using density functional method on two models. One is adenine and the other is adenosine. Optimized geometries of reactants, intermediates, transition states, and products were determined at B3LYP/6-311G(d,p) level. IRC calculations were performed on the transition states to verify whether it is the real transition state that connects the corresponding intermediates. Single point calculations were carried out on the previous optimized geometries obtained during IRC calculations. Four pathways have been determined for the hydrolytic deamination of adenosine. Pathway d is the most favorable pathway. In this pathway a tetra-coordinated intermediate is formed through hydrolysis reaction, then the deamination reaction takes place, which causes the cleavage of C6–N10 bond and the creation of C=O bond. Unlike the deamination of adenine, the attacking side of water molecule has effect on the deamination of adenosine. The energy barriers of adenosine deamination are a little higher than those of adenine deamination. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Water effect on peroxy radical measurement by chemical amplification: Experimental determination and chemical mechanism

The water effect on peroxy radical measurement by chemical amplification was determined experimentally for HO2 and HO2 OH, respectively at room temperature (298±2) K and atmospheric pressure (1×105 Pa). No significant difference in water effect was observed with the type of radicals. A theoretical study of the reaction of HO2·H2O adduct with NO was performed using density functional theory at CCSD(T)/6-311 G(2d, 2p)//B3LYP/6-311 G(2d, 2p) level of theory. It was found that the primary reaction channel for the reaction is HO2·H2O NO→HNO3 H2O (R4a). On the basis of the theoretical study, the rate constant for (R4a) was calculated using Polyrate Version 8.02 program. The fitted Arrenhnius equation for (R4a) is k = 5.49×107 T 1.03exp(?14798/T) between 200 and 2000 K. A chemical model incorporated with (R4a) was used to simulate the water effect. The water effect curve obtained by the model is in accordance with that of the experiment, suggesting that the water effect is probably caused mainly by (R4a).     

A theoretical study of the ground-state potential surface of guanine and its binding with oxygen and water

A molecular orbital geometry optimization study of the potential surface of guanine, guanine? O₂, and guanine? O₂? water reaction products in the ground state has been carried out. The origin of the asymmetric double-well potential surface of guanine suggested earlier on the basis of experimental observations has been explained. The most stable binding of O₂ with guanine (G) is found to occur at the C4C5 double bond of the latter molecule. In the case of G? O₂? water reaction product (HOO? G? OH), the groups ? OOH and ? OH bind at C4 and C8, respectively. The possiblity of a polymeric reaction product of the type R1? (G? O? O? G)n? R2 (R1, R2 = H, OH) has also been suggested. These results are broadly supported by experimental observations. The mechanism of spectral oscillations observed in UV-irradiated guanine solutions has been discussed.     

Theoretical study of hydrogen bonded clusters of water and cyanic acid: Hydrogen bonding in terms of the molecular structure

Ab initio and density functional calculations were used to analyze the interaction between a molecule of cyanic acid (HOCN) and up to 4 molecules of water at the B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) computational levels. The cooperative effect (CE) is increased with the increasing size of the studied clusters. Red shifts of the H–O stretching frequency for complexes involving HOCN as an H-donor were predicted. The strength of the hydrogen bonds in terms of molecular structures could be deduced from a comparison of HOCN–H₂O with HCNO–H₂O, HONC–H₂O and HNCO–H₂O HB clusters. The atom in molecules (AIM) method was used to analyze the cooperative effects on topological parameters.     

Metallo-guanines and metallo-guanosines

Metallo-guanines of the type [M(G)₂·2H₂O] [M = Ni^II, Fe^II, Cu^II and UO₂ ^II; G = anionic guanine], [M(G)₂(GH)· H₂O] (M = Co^II and Mn^II; GH = neutral guanine), [Pd(G)₂]·2H₂O and [Zn(G)Cl]₂ have been isolated and characterised. Anionic guanine functions as a bidentate ligand and links through N(3) and N(9). E.p.r. data indicate that the Cu^II complex has a highly distorted octahedral structure. The magnetic susceptibility data suggest that the Co^II and Ni^II complexes possess pseudooctahedral geometry. Neutral guanines are probably unidentate and coordinate either through N(3) or N(9). The isolated guanosine complexes are of the types: [M(Gs)₂·H₂O] [M = Ni^II and Cu^II, Gs = anionic guanosine] [Pd(Gs)₂]·2H₂O and [UO₂(Gs)₂]. I.r. data indicate that guanosine also functions as a bidentate ligand, but coordinates through N(1) and C₂ — NH₂. The electronic absorption spectra of the complexes indicate that guanine is a stronger ligand than guanosine.     

Potential energy surface and thermochemistry for the direct gas phase reaction of germane and water

Gas phase reaction between germane GeH₄ and water H₂O was investigated at CCSD(T)/[aug-cc-pVTZ-pp for Ge + Lanl2dz for H and O]//MP2/6-31G(d,p) level. Only the hydrogen elimination channels are monitored. Within the energy range of 100 kcal/mol, we located nine equilibrium and six transition states on the potential energy surface (PES) of the Ge–O–H systems. GeH₄ reacts with H₂O exothermically (by 2.37 kcal/mol) without a barrier to form a non-planar complex GeH₄·H₂O which isomerizes to GeH₃OH·H₂ and H₂GeOH₂·H₂ with a barrier of 44.34 kcal/mol and 53.75 kcal/mol respectively. The first step of hydrogen elimination gives two non-planar species, GeH₃OH and H₂GeOH₂ but germinol GeH₃OH is found to be more stable. Further thermal decomposition reactions of GeH₃OH involving hydrogen elimination have been studied extensively using the same method. The final hydrogen elimination step gives HGeOH which can exist in cis and trans forms. As the trans form is more stable, only the trans form is considered on the potential energy surface (PES) of the reaction. The important thermochemical parameters (∆_rE_tot + ZPE), ∆_rH and ∆_rG for the H₂ elimination pathways are predicted accurately.     

Anomerization reaction of bare and microhydrated d‐erythrose via explicitly correlated coupled cluster approach. Two water molecules are optimal

We present a comprehensive benchmark computational study which has explored a complete path of the anomerization reaction of bare d ‐erythrose involving a pair of the low‐energy α‐ and β‐furanose anomers, the former of which was observed spectroscopically (Cabezas et al., Chem. Commun. 2013, 49, 10826). We find that the ring opening of the α‐anomer yields the most stable open‐chain tautomer which step is followed by the rotational interconversion of the open‐chain rotamers and final ring closing to form the β‐anomer. Our results indicate the flatness of the reaction's potential energy surface (PES) corresponding to the rotational interconversion path and its sensitivity to the computational level. By using the explicitly correlated coupled cluster CCSD(T)‐F12/cc‐pVTZ‐F12 energies, we determine the free energy barrier for the α‐furanose ring‐opening (rate‐determining) step as 170.3 kJ/mol. The question of the number of water molecules (n ) needed for optimal stabilization of the erythrose anomerization reaction rate‐determining transition state is addressed by a systematic exploration of the PES of the ring opening in the α‐anomer‐(H₂O)_n and various β‐anomer‐(H₂O)_n (n = 1–3) clusters using density functional and CCSD(T)‐F12 computations. These computations suggest the lowest free energy barrier of the ring opening for doubly hydrated α‐anomer, achieved by a mechanism that involves water‐mediated multiple proton transfer coupled with the furanose C O bond breakage. Among the methods used, the G4 performed best against the CCSD(T)‐F12 reference at estimating the ring‐opening barrier heights for both the hydrated and bare erythrose conformers. Our results for the hydrated species are most relevant to an experimental study of the anomerization reaction of d ‐erythrose to be carried out in microsolvation environment. © 2016 Wiley Periodicals, Inc.     

水助甲酰胺-H2O2氧化乙烯制环氧乙烷反应机理的理论研究

采用MP2方法研究 了甲酰胺-H₂O₂氧化乙烯制取环氧乙烷的反应机理. 优化得到了反应物、过渡态、中间体及产物的几何构型并计算了反应势垒. 研究结果表明: 没有水参与时, 反应需要通过四元环过渡态完成, 反应势垒很高, 在常温下难以进行; 有水参与时, 在水分子的协助下, 反应可以通过六元环过渡态完成, 反应势垒较低, 常温下反应容易进行.     

DFT studies on the mechanism of the reaction of C2H5S with NO2

The mechanisms for the reaction of C₂H₅S with NO₂ are investigated at the QCISD(T)/6‐311++G(d, p)//B3LYP/6‐311++G(d, p) level on both single and triple potential energy surfaces. The geometries, vibrational frequencies and zero‐point energy (ZPE) corrections of all stationary points involved in the title reaction are calculated at the B3LYP/6‐311++G(d, p) level. The results show that the reaction is more predominant on the single potential energy surface, while it is negligible on the triple potential energy surface. Without barrier height in the whole process, the major channel is R → C₂H₅SONO (IM1 and IM2) → P1 (C₂H₅SO+NO). With much heat released in the formation of C₂H₅SNO₂ (IM3) and the transition state involved in the subsequent step more stable than reactants, P4 (CH₃CHS + t‐HONO) is subdominant product energetically. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Influence of π-stacking on the N7 and O6 proton affinity of guanine

The influence of π-stacking interactions between guanine (G) and the side chain of tyrosine (Tyr) on the N7 and O6 proton affinities of guanine and on the capability of these sites to act as hydrogen bond acceptors is analyzed at the B3LYP-D, M05-2X and MP2 levels of theory. With all methods, results from full geometry optimizations indicate that stacking interactions increase the N7 and O6 proton affinities by about 5–6 kcal mol^?1, the increase being slightly larger for N7. Consistently with these results, hydrogen bond distances between guanine and one water molecule decrease in the stacked system. Moreover, interaction energy between H₂O and (G-Tyr) is found to be 2–3 kcal mol^?1 larger than in G···H₂O. This strengthening arises from the additional Tyr–H₂O stabilizing interactions and from a cooperative interplay between stacking and hydrogen bond forces.     

Theoretical study of dihydrogen bonded clusters of water with tetrahydroborate

Ab initio calculations were used to analyze interactions of BH₄ ^? with 1?C4 molecules of H₂O at the MP2/6-311++G(d,p) and B3LYP/6-311++G(d,p) computational levels. The negative cooperativity for dihydrogen bond clusters containing H₂O···H₂O hydrogen bonds is more remarkable. The negative cooperativity is increased with increasing the size and also the number of hydrogen bonds in the cluster. The B?CH stretching frequencies show blue shifts with respect to cluster formation. Also greater blue shift of stretching frequencies where predicted for B?CH bonds which did not contribute in dihydrogen bonding with water molecules. The structures obtained have been analyzed with the Atoms in Molecules (AIM) methodology.     

The reaction between HO and (H2O) n (n?=?1, 3) clusters: reaction mechanisms and tunneling effects

The reaction between the HO radical and (H₂O)n (n?=?1, 3) clusters has been investigated employing high-level quantum mechanical calculations using DFT-BH&HLYP, QCISD, and CCSD(T) theoretical approaches in connection with the 6-311?+?G(2df,2p), aug-cc-pVTZ, and aug-cc-pVQZ basis sets. The rate constants have also been calculated and the tunneling effects have been studied by means of time?Cdependent wavepacket calculations, performed using the Quantum?CReaction Path Hamiltonian method. According to the findings of previously reported theoretical works, the reaction between HO and H₂O begins with the formation of a pre-reactive complex that is formed before the transition state, the formation of a post-reactive complex, and the release of the products. The reaction between HO and (H₂O)₂ also begins with the formation of a pre-reactive complex, which dissociates into H₂O??HO?+?H₂O. The reaction between HO and (H₂O)₃ is much more complex. The hydroxyl radical adds to the water trimer, and then it occurs a geometrical rearrangement in the pre-reactive hydrogen-bonded complex region, before the transition state. The reaction between hydroxyl radical and water trimer is computed to be much faster than the reaction between hydroxyl radical and a single water molecule, and, in both cases, the tunneling effects are very important mainly at low temperatures. A prediction of the atmospheric concentration of the hydrogen-bonded complexes studied in this work is also reported.     

Ab initio calculations on the barrier height for the hydrogen addition to ethylene and formaldehyde. The importance of spin projection

Heats of reaction and barrier heights have been computed for H + CH₂CH₂ → C₂H₅, H + CH₂O → CH₃O, and H + CH₂O → CH₂OH using unrestricted Hartree-Fock and Møller–Plesset perturbation theory up to fourth order (with and without spin annihilation), using single-reference configuration interaction, and using multiconfiguration self-consistent field methods with 3-21G, 6-31G(d), 6-31G(d,p), and 6-311G(d,p) basis sets. The barrier height in all three reactions appears to be relatively insensitive to the basis sets, but the heats of reaction are affected by p-type polarization functions on hydrogen. Computation of the harmonic vibrational frequencies and infrared intensities with two sets of polarization functions on heavy atoms [6-31G(2d)] improves the agreement with experiment. The experimental barrier height for H + C₂H₄ (2.04 ± 0.08 kcal/mol) is overestimated by 7?9 kcal/mol at the MP2, MP3, and MP4 levels. MCSCF and CISD calculations lower the barrier height by approximately 4 kcal/mol relative to the MP4 calculations but are still almost 4 kcal/mol too high compared to experiment. Annihilation of the largest spin contaminant lowers the MP4SDTQ computed barrier height by 8?9 kcal/mol. For the hydrogen addition to formaldehyde, the same trends are observed. The overestimation of the barrier height with Møller-Plesset perdicted barrier heights for H + C₂H₄ → C₂H₅, H + CH₂O → CH₃O, and H + CH₂O → CH₂OH at the MP4SDTQ /6-31G(d) after spin annihilation are respectively 1.8, 4.6, and 10.5 kcal/mol.     

BrO-H2O 及 HOBr-H2O复合物偶合方式的理论研究

在6-311++G(d,p)水平上采用四种方法讨论了两种BrO-H₂O和三种HOBr-H₂O复合物的构型性质。在两种BrO-H₂O复合物中，结合能为11.37–13.92 J/mol的复合物2 （电子态为²A′）最稳定，该复合物是通过BrO中的Br原子和水中的O原子结合的。三种HOBr-H₂O复合物中，复合物3和4的结合能约为16.30–21.32 J/mol，三种复合物的稳定顺序为：复合物3 ≈ 复合物4 > 复合物5。     

Potential energy surface of the reaction of imidazole with peroxynitrite: Density functional theory study

This article presents a theoretical investigation of the reaction mechanism of imidazole nitration by peroxynitrite using density functional theory calculations. Understanding this reaction mechanism will help in elucidating the mechanism of guanine nitration by peroxynitrite, which is one of the assumed chemical pathways for damaging DNA in cells. This work focuses on the analysis of the potential energy surface (PES) for this reaction in the gas phase. Calculations were carried out using Hartree–Fock (HF) and density functional theory (DFT) Hamiltonians with double‐zeta basis sets ranging from 6‐31G(d) to 6‐31++G(d,p), and the triple‐zeta basis set 6‐311G(d). The computational results reveal that the reaction of imidazole with peroxynitrite in gas phase produces the following species: (i) hydroxide ion and 2‐nitroimidazole, (ii) hydrogen superoxide ion and 2‐nitrosoimidazole, and (iii) water and 2‐nitroimidazolide. The rate‐determining step is the formation of a short‐lived intermediate in which the imidazole C₂ carbon is covalently bonded to peroxynitrite nitrogen. Three short‐lived intermediates were found in the reaction path. These intermediates are involved in a proton‐hopping transport from C₂ carbon to the terminal oxygen of the ? O? O moiety of peroxynitrite via the nitroso (ON? ) oxygen. Both HF and DFT calculations (using the Becke3–Lee–Yang–Parr functional) lead to similar reaction paths for proton transport, but the landscape details of the PES for HF and DFT calculations differ. This investigation shows that the reaction of imidazole with peroxynitrite produces essentially the same types of products (nitro‐ and nitroso‐) as observed experimentally in the reaction of guanine with peroxynitrite, which makes the former reaction a good model to study by computation the essential characteristics of the latter reaction. Nevertheless, the computationally determined activation energy for imidazole nitration by peroxynitrite in the gas phase is 84.1 kcal/mol (calculated at the B3LYP/6‐31++G(d,p) level), too large for an enzymatic reaction. Exploratory calculations on imidazole nitration in solution, and on the reaction of 9‐methylguanine with peroxynitrite in the gas phase and solution, show that solvation increases the activation energy for both imidazole and guanine, and that the modest decrease (15 kcal mol^?1) in the activation energy, due to the adjacent six member ring of guanine, is counterbalanced by solvation. These results lead to the speculation that proton tunneling may be at the origin of experimentally observed high reaction rate of guanine nitration by peroxynitrite in solution. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005