Topic
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.
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TL;DR: In this paper, the mechanism for the hetero-Diels-Alder reaction of benzaldehyde with Danishefsky's diene catalyzed by various types of achiral and chiral aluminum complexes has been studied from a theoretical point of view using semi-empirical and ab initio calculations.
42 citations
TL;DR: A third generation of inhibitors has been designed that contain an acyclic iminoalcohol to replace the cyclic mimic of the ribooxacarbenium ion at the transition states of PNPs.
Abstract: Transition state analogues of PNP, the Immucillins and DADMe-Immucillins, were designed to match transition state features of bovine and human PNPs, respectively. A third generation of inhibitors has been designed that contain an acyclic iminoalcohol to replace the cyclic mimic of the ribooxacarbenium ion at the transition states of PNPs. The best third generation inhibitor is equivalent to the best inhibitors found in the previous transition state analogues.
42 citations
TL;DR: Thermodynamic properties, activation energies, enthalpies, and free energies of activation were calculated for each reaction pathway investigated, and seven pathways for the deamination reaction were found.
Abstract: Mechanisms for the deamination reaction of cytosine with H2O/OH− and 2H2O/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 (ΔE, ΔH, and ΔG), 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 formati...
42 citations
TL;DR: The results probe the fundamental rate vs. driving force relationships in this MS-CPET reaction at carbon by separately modulating the driving force for the proton and electron transfer components and suggest that the transition states for these reactions are imbalanced.
Abstract: The selective transformation of C-H bonds is a longstanding challenge in modern chemistry. A recent report details C-H oxidation via multiple-site concerted proton-electron transfer (MS-CPET), where the proton and electron in the C-H bond are transferred to separate sites. Reactivity at a specific C-H bond was achieved by appropriate positioning of an internal benzoate base. Here, we extend that report to reactions of a series of molecules with differently substituted fluorenyl-benzoates and varying outer-sphere oxidants. These results probe the fundamental rate versus driving force relationships in this MS-CPET reaction at carbon by separately modulating the driving force for the proton and electron transfer components. The rate constants depend strongly on the pKa of the internal base, but depend much less on the nature of the outer-sphere oxidant. These observations suggest that the transition states for these reactions are imbalanced. Density functional theory (DFT) was used to generate an internal reaction coordinate, which qualitatively reproduced the experimental observation of a transition state imbalance. Thus, in this system, homolytic C-H bond cleavage involves concerted but asynchronous transfer of the H+ and e-. The nature of this transfer has implications for synthetic methodology and biological systems.
42 citations
TL;DR: In this article, rotational level population distributions have been measured for the HCl and DCl products of photo-initiated reaction of Cl atoms with CH3NH2 and CD3ND2 molecules with distributions obtained from reactions of the two partially deuterated isotopomers of methylamine.
Abstract: Nascent rotational level population distributions have been measured for the HCl and DCl products of photo-initiated reaction of Cl atoms with CH3NH2, CD3NH2, CH3ND2 and CD3ND2. The use of the different isotopomers of methylamine enables the dynamics of abstraction of H/D atoms from carbon or nitrogen atoms to be distinguished, and the former channel is found to produce HCl or DCl with greater rotational excitation than the latter channel. Mean HCl rotational energies for the two reactions Cl + CH3ND2 → HCl + CH2ND2 and Cl + CD3NH2 → HCl + CD3NH are, respectively, 501 ± 84 and 122 ± 12 cm−1. Fits of the HCl and DCl rotational distributions for reaction of Cl atoms with the CH3NH2 and CD3ND2 molecules with distributions obtained from reactions of the two partially deuterated isotopomers yield branching ratios for C–H ∶ N–H and C–D ∶ N–D abstraction of 0.48 ∶ 0.52 and 0.58 ∶ 0.42, respectively. Ab initio electronic structure theory calculations of the energetics and geometries of transition states and molecular complexes along the reaction pathways for the two competing channels provide key insights to aid the interpretation of the experimental data. The computed bond angle of the N–H–Cl moiety (142.0°) in the transition state for the CH3NH forming channel deviates more from linearity than the C–H–Cl bond angle (171.1°) in the competing transition state, but leads to lower rotational excitation of the nascent HCl products. This counter-intuitive outcome is explained in terms of dipole–dipole interactions between the HCl and organic radical products as they separate.
42 citations