Transition state

About: Transition state is a research topic. Over the lifetime, 4978 publications have been published within this topic receiving 117965 citations. The topic is also known as: transition state of elementary reaction.

Formation of 8‐nitroguanine and 8‐oxoguanine due to reactions of peroxynitrite with guanine

Abstract: Reactions of peroxynitrite with guanine were investigated using density functional theory (B3LYP) employing 6-31G** and AUG-cc-pVDZ basis sets. Single point energy calculations were performed at the MP2/AUG-cc-pVDZ level. Genuineness of the calculated transition states (TS) was tested by visually examining the vibrational modes corresponding to the imaginary vibrational frequencies and applying the criterion that the TS properly connected the reactant and product complexes (PC). Genuineness of all the calculated TS was further ensured by intrinsic reaction coordinate (IRC) calculations. Effects of aqueous media were investigated by solvating all the species involved in the reactions using the polarizable continuum model (PCM). The calculations reveal that the most stable nitro-product complex involving the anion of 8-nitroguanine and a water molecule i.e. 8NO(2)G(-) + H(2)O can be formed according to one reaction mechanism while there are two possible reaction mechanisms for the formation of the oxo-product complex involving 8-oxoguanine and anion of the NO(2) group i.e. 8OG + NO(2)(-). The calculated relative stabilities of the PC, barrier energies of the reactions and the corresponding enthalpy changes suggest that formation of the complex 8OG + NO(2)(-) would be somewhat preferred over that of the complex 8NO(2)G(-) + H(2)O. The possible biological implications of this result are discussed.

Hydroxyl Radical Reactions with Adenine: Reactant Complexes, Transition States, and Product Complexes

Abstract: In order to address problems such as aging, cell death, and cancer, it is important to understand the mechanisms behind reactions causing DNA damage. One specific reaction implicated in DNA oxidative damage is hydroxyl free-radical attack on adenine (A) and other nucleic acid bases. The adenine reaction has been studied experimentally, but there are few theoretical results. In the present study, adenine dehydrogenation at various sites, and the potential-energy surfaces for these reactions, are investigated theoretically. Four reactant complexes [A⋅⋅⋅OH]. have been found, with binding energies relative to A+OH. of 32.8, 11.4, 10.7, and 10.1 kcal mol−1. These four reactant complexes lead to six transition states, which in turn lie +4.3, −5.4, (−3.7 and +0.8), and (−2.3 and +0.8) kcal mol−1 below A+OH., respectively. Thus the lowest lying [A⋅⋅⋅OH]. complex faces the highest local barrier to formation of the product (AH).+H2O. Between the transition states and the products lie six product complexes. Adopting the same order as the reactant complexes, the product complexes [(AH)⋅⋅⋅H2O]. lie at −10.9, −22.4, (−24.2 and −18.7), and (−20.5 and −17.5) kcal mol−1, respectively, again relative to separated A+OH.. All six A+OH. → (AH).+H2O pathways are exothermic, by −0.3, −14.7, (−17.4 and −7.8), and (−13.7 and −7.8) kcal mol−1, respectively. The transition state for dehydrogenation at N6 lies at the lowest energy (−5.4 kcal mol−1 relative to A+OH.), and thus reaction is likely to occur at this site. This theoretical prediction dovetails with the observed high reactivity of OH radicals with the NH2 group of aromatic amines. However, the high barrier (37.1 kcal mol−1) for reaction at the C8 site makes C8 dehydrogenation unlikely. This last result is consistent with experimental observation of the imidazole ring opening upon OH radical addition to C8. In addition, TD-DFT computed electronic transitions of the N6 product around 420 nm confirm that this is the most likely site for hydrogen abstraction by hydroxyl radical.

Shape Complementarity, Binding-Site Dynamics, and Transition State Stabilization: A Theoretical Study of Diels–Alder Catalysis by Antibody 1E9

Abstract: Antibody 1E9 is a protein catalyst for the Diels–Alder reaction between tetrachlorothiophene dioxide and N-ethylmaleimide. Quantum mechanical calculations have been employed to study the 1E9-catalyzed Diels–Alder reaction in the gas phase. The transition states and intermediates were all determined at the B3LYP/6-31G*//HF/6-31G* level. The cycloaddition step is predicted to be rate-determining, and the endo reaction pathway is strongly favored. Binding of the reactants and the transition states to antibody 1E9 was investigated by docking and molecular dynamics simulations. The linear interaction energy (LIE) method was adopted to estimate the free energy barrier of the 1E9-catalyzed Diels–Alder reaction. The catalytic efficiency of antibody 1E9 is achieved by enthalpic stabilization of the transition state, near-perfect shape complementarity of the hydrophobic binding site for the transition state, and a strategically placed hydrogen-bonding interaction.

A systematic computational study of the reactions of HO2 with RO2: the HO2 + CH2ClO2, CHCl2O2, and CCl3O2 reactions.

Abstract: Potential energy surfaces for the reactions of HO(2) with CH(2)ClO(2), CHCl(2)O(2), and CCl(3)O(2) have been calculated using coupled cluster theory and density functional theory (B3LYP). It is revealed that all the reactions take place on both singlet and triplet surfaces. Potential wells exist in the entrance channels for both surfaces. The reaction mechanism on the triplet surface is simple, including hydrogen abstraction and S(N)2-type displacement. The reaction mechanism on the singlet surface is more complicated. Interestingly, the corresponding transition states prefer to be 4-, 5-, or 7-member-ring structures. For the HO(2) + CH(2)ClO(2) reaction, there are two major product channels, viz., the formation of CH(2)ClOOH + O(2) via hydrogen abstraction on the triplet surface and the formation of CHClO + OH + HO(2) via a 5-member-ring transition state. Meanwhile, two O(3)-forming channels, namely, CH(2)O + HCl + O(3) and CH(2)ClOH + O(3) might be competitive at elevated temperatures. The HO(2) + CHCl(2)O(2) reaction has a mechanism similar to that of the HO(2) + CH(2)ClO(2) reaction. For the HO(2) + CCl(3)O(2) reaction, the formation of CCl(3)O(2)H + O(2) is the dominant channel. The Cl-substitution effect on the geometries, barriers, and heats of reaction is discussed. In addition, the unimolecular decomposition of the excited ROOH (e.g., CH(2)ClOOH, CHCl(2)OOH, and CCl(3)OOH) molecules has been investigated. The implication of the present mechanisms in atmospheric chemistry is discussed in comparison with the experimental measurements.

Quantum mechanical modelling of alkene hydroformylation as catalyzed by xantphos-Rh complexes

Abstract: Fundamental issues concerning the hydroformylation of 1-alkenes as catalyzed by Rh complexes ligated with the xantphos diphosphine ligand are explored using ONIOM calculations. In this study xantphos serves as a prototype of the large bite-angle ligands that are associated with high regioselectivity and rates in catalytic hydroformylation. Computations have been used to explore the thermodynamics of 56 unique isomers (e.g., cis vs. trans isomers of square planar complexes, diequatorial vs. axial-equatorial five-coordinate complexes) and conformers for intermediates along the reaction pathway. More than 20 transition states relevant to the catalyst mechanism have been determined. In terms of realistically modelling experiment, the computational results are mixed. In agreement with experiment, the computations yield a mixture of diequatorial and axial-equatorial isomers of HRh(xantphos)(CO)2 as the catalyst resting state. Dissociation of CO from these complexes is computed to be barrierless leading to a computed free energy for exchange of CO ligands around 15 kcal mol−1, somewhat lower than the value of ca. 20 kcal mol−1 derived from experimental data. The computed ratios of rates of propene insertion to form n-propyl and i-propyl Rh-alkyl (42 ∶ 1) is in good agreement with experimental ratios of n-nonanal to i-nonanal (52 ∶ 1) for 1-octene hydroformylation. Nonetheless, the computations dramatically overestimate the overall activation free energies for catalytic hydroformylation. Thus, at this stage computations do not provide useful insight into the the kinetics of hydroformylation and detailed mechanistic issues. It appears that much of this discrepancy between computed and experimental activation energies originates from the underestimation of propene bonding energies.