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.

Kinetics of the Strongly Correlated CH 3 O + O 2 Reaction: The Importance of Quadruple Excitations in Atmospheric and Combustion Chemistry.

Abstract: Kinetics measurements on radical-radical reactions are often unavailable experimentally, and obtaining quantitative rate constants for such reactions by theoretical methods is challenging because the transition states and the reactants are often strongly correlated. Treating strongly correlated systems by coupled cluster theory limited to single, double, and triple connected excitations is often inadequate. We therefore use a new method, called GMM(P), for extrapolation to the complete configuration interaction limit to go beyond triple excitations and in particular to approximate the CCSDTQ(P)/CBS limit. Here, we present this method and use it to investigate the CH3O + O2 reaction. The contribution of connected quadruple excitations to the barrier height energy is found to be -3.13 kcal/mol, and adding a quasiperturbative calculation of the effect of connected pentuple excitations brings the post-connected-triples contributions to -3.44 kcal/mol, which corresponds to Boltzmann factors that increase calculated rate constants by factors of 1.0 × 103, 3.3 × 102, and 18 at 250, 298, and 600 K, respectively. We present rate constants for temperatures from 250 to 2000 K, and we find that the Arrhenius activation energy increases from 0.58 to 9.68 kcal/mol over this range. We also find reasonably good accuracy for the barrier height with the MN15-L exchange-correlation functional, and we calculate rate constants by a combination of GMM(P) and MN15-L electronic structure calculations and conventional and variational transition state theory, in particular canonical variational theory with small-curvature tunneling. The present findings have broad implications for obtaining quantitative rate constants for complex reaction systems in atmospheric and combustion chemistry.

A new paradigm of DNA synthesis: three-metal-ion catalysis

Abstract: Enzyme catalysis has been studied for over a century. How it actually occurs has not been visualized until recently. By combining in crystallo reaction and X-ray diffraction analysis of reaction intermediates, we have obtained unprecedented atomic details of the DNA synthesis process. Contrary to the established theory that enzyme-substrate complexes and transition states have identical atomic composition and catalysis occurs by the two-metal-ion mechanism, we have discovered that an additional divalent cation has to be captured en route to product formation. Unlike the canonical two metal ions, which are coordinated by DNA polymerases, this third metal ion is free of enzyme coordination. Its location between the α- and β-phosphates of dNTP suggests that the third metal ion may drive the phosphoryltransfer from the leaving group opposite to the 3′-OH nucleophile. Experimental data indicate that binding of the third metal ion may be the rate-limiting step in DNA synthesis and the free energy associated with the metal-ion binding can overcome the activation barrier to the DNA synthesis reaction.

Noncovalent organocatalysis based on hydrogen bonding: elucidation of reaction paths by computational methods.

Abstract: In this article, the functions of hydrogen bonds in organocatalytic reactions are discussed on atomic level by presenting DFT studies of selected examples. Theoretical investigation provides a detailed insight in the mechanism of substrate activation and orientation, and the stabilization of transition states and intermediates by hydrogen bonding (e.g. oxyanion hole). The examples selected comprise stereoselective catalysis by bifunctional thioureas, solvent catalysis by fluorinated alcohols in epoxidation by hydrogen peroxide, and intramolecular cooperative hydrogen bonding in TADDOL-type catalysts.

Negative-ion photodetachment as a probe of bimolecular transition states: the F + H2 reaction

Abstract: The transition-state region of the F + H2, F + D2 and F + HD reactions has been studied by photoelectron spectroscopy of the negative ions FH–2, FD–2 and FDH–. Photodetachment of these anions can access three electronic states of the neutral, but transitions to the ground-state potential-energy surface for the reaction can be observed selectively by adjusting the polarization of the photodetachment laser. Under these conditions, the FH–2 spectrum is similar to the recent simulation by Zhang and Miller which used the T5a potential-energy surface for the F + H2 reaction. The spectra of all three isotopic anions are interpreted by comparison to previous reactive scattering calculations. This comparison strongly suggests that several of the peaks in the photoelectron spectra are due to transitions to scattering resonances.

Sequential clustering reactions of SiD+3 with SiD4 and SiH+3 with SiH4: Another case of arrested growth of hydrogenated silicon particles

Abstract: Sequential clustering reactions of SiD+3 with SiD4 and SiH+3 with SiH4 are observed in the ion cell of a Fourier transform mass spectrometer. Clustering occurs either by addition of SiD2 or SiH2 accompanied by loss of D2 or H2, or by the formation and stabilization of the bimolecular adducts. All of the clustering reactions are highly inefficient and lead to bottleneck structures at small silicon cluster sizes containing two to four silicon atoms. Rates are measured for both the addition and association products for each step of the reaction. Back reaction rates are monitored via silicon‐29 isotope exchange. Ab initio electronic structure calculations of the reaction pathways including intermediates, transition states and products have been performed by Raghavachari and are presented in his companion paper. The overall reaction mechanisms are similar for each reaction step. First an intermediate complex is formed between the ion and neutral which is strongly bound by a bridging deuterium or hydrogen atom....