Thermolysis of the CoC bond in adenosylcobalamin (coenzyme B12)—IV. Products, kinetics and CoC bond dissociation energy studies in ethylene glycol
TL;DR: In this article, the full details of product, kinetic and CoC5′ bond dissociation energy studies of the thermolysis of AdoB 12 in ethylene glycol are presented.
About: This article is published in Polyhedron.The article was published on 1988-01-01. It has received 77 citations till now. The article focuses on the topics: Bond-dissociation energy & Homolysis.
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458 citations
TL;DR: The x-ray structure of a substrate-free form of lysine-5,6-aminomutase from Clostridium sticklandii is solved and embodies a locking mechanism to keep the adenosylcobalamin out of the active site and prevent radical generation in the absence of substrate.
Abstract: Lysine 5,6-aminomutase is an adenosylcobalamin and pyridoxal-5′-phosphate-dependent enzyme that catalyzes a 1,2 rearrangement of the terminal amino group of dl-lysine and of l-β-lysine. We have solved the x-ray structure of a substrate-free form of lysine-5,6-aminomutase from Clostridium sticklandii. In this structure, a Rossmann domain covalently binds pyridoxal-5′-phosphate by means of lysine 144 and positions it into the putative active site of a neighboring triosephosphate isomerase barrel domain, while simultaneously positioning the other cofactor, adenosylcobalamin, ≈25 A from the active site. In this mode of pyridoxal-5′-phosphate binding, the cofactor acts as an anchor, tethering the separate polypeptide chain of the Rossmann domain to the triosephosphate isomerase barrel domain. Upon substrate binding and transaldimination of the lysine-144 linkage, the Rossmann domain would be free to rotate and bring adenosylcobalamin, pyridoxal-5′-phosphate, and substrate into proximity. Thus, the structure embodies a locking mechanism to keep the adenosylcobalamin out of the active site and prevent radical generation in the absence of substrate.
135 citations
TL;DR: A systematic analysis of the electronic and structural properties of coenzyme B12 models has been performed to establish the performance of three different functionals including B3LYP, BP86, and revPBE to show differences in axial bonding provided by hybrid and nonhybrid functionals.
Abstract: Computational modeling of the enzymatic activity of B12-dependent enzymes requires a detailed understanding of the factors that influence the strength of the CoC bond and the limits associated with a particular level of theory. To address this issue, a systematic analysis of the electronic and structural properties of coenzyme B12 models has been performed to establish the performance of three different functionals including B3LYP, BP86, and revPBE. In particular the cobalt–carbon bond dissociation energies, axial bond lengths, and selected stretching frequencies have been analyzed in detail. Current analysis shows that widely used B3LYP functional significantly underestimates the strength of the CoC bond while the nonhybrid BP86 functional produces very consistent results in comparison to experimental data. To explain such different performance of these functionals molecular orbital analysis associated with axial bonds has been performed to show differences in axial bonding provided by hybrid and nonhybrid functionals. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 1429–1437, 2006
108 citations
TL;DR: Calculations suggest that CASSCF and CASPT2 may have difficulties with providing a reliable description of the Co-CMe bond breaking in MeCbl, since using adequate active spaces is prohibitively expensive.
Abstract: The Co–CMe bond dissociation in methylcobalamin (MeCbl), modeled by the Im–[CoIIIcorrin]–Me+ system consisting of 58 atoms, is examined using the coupled-cluster (CC), density-functional theory (DFT), complete-active-space self-consistent-field (CASSCF), and CASSCF-based second-order perturbation theory (CASPT2) approaches. The multilevel variant of the local cluster-in-molecule framework, employing the completely renormalized (CR) CC method with singles, doubles, and noniterative triples, termed CR-CC(2,3), to describe higher-order electron correlation effects in the region where the Co–CMe bond breaking takes place, and the canonical CC approach with singles and doubles (CCSD) to capture the remaining correlation effects, abbreviated as CR-CC(2,3)/CCSD, is used to obtain the benchmark potential energy curve characterizing the Co–CMe dissociation in the MeCbl cofactor. The Co–CMe bond dissociation energy (BDE) resulting from the CR-CC(2,3)/CCSD calculations for the Im–[CoIIIcorrin]–Me+ system using the 6...
90 citations
TL;DR: The Occam's Razor conclusion is that at least this adenosylcobalamin-dependent enzyme has not evolved to enhance quantum mechanical tunneling, at least within the present error bars.
Abstract: The literature hypothesis that "the optimization of enzyme catalysis may entail the evolutionary implementation of chemical strategies that increase the probability of quantum-mechanical tunneling" is experimentally tested herein for the first time. The system employed is the key to being able to provide this first experimental test of the "enhanced hydrogen tunneling" hypothesis, one that requires a comparison of the three criteria diagnostic of tunneling (vide infra) for the same, or nearly the same, reaction with and without the enzyme. Specifically, studied herein are the adenosylcobalamin (AdoCbl, also known as coenzyme B(12))-dependent diol dehydratase model reactions of (i). H(D)(*) atom abstraction from ethylene glycol-d(0) and ethylene glycol-d(4) solvent by 5'-deoxyadenosyl radical (Ado(*)) and (ii.) the same H(*) abstraction reactions by the 8-methoxy-5'-deoxyadenosyl radical (8-MeOAdo(*)). The Ado(*) and 8-MeOAdo(*) radicals are generated by Co-C thermolysis of their respective precursors, AdoCbl and 8-MeOAdoCbl. Deuterium kinetic isotope effects (KIEs) of the H(*)(D(*)) abstraction reactions from ethylene glycol have been measured over a temperature range of 80-120 degrees C: KIE = 12.4 +/- 1.1 at 80 degrees C for Ado(*) and KIE = 12.5 +/- 0.9 at 80 degrees C for 8-MeOAdo(*) (values ca. 2-fold that of the predicted maximum primary times secondary ground-state zero-point energy (GS-ZPE) KIE of 6.4 at 80 degrees C). From the temperature dependence of the KIEs, zero-point activation energy differences ([E(D) - E(H)]) of 3.0 +/- 0.3 kcal mol(-)(1) for Ado(*) and 2.1 +/- 0.6 kcal mol(-)(1) for 8-MeOAdo(*) have been obtained, both of which are significantly larger than the nontunneling, zero-point energy only maximum of 1.2 kcal mol(-)(1). Pre-exponential factor ratios (A(H)/A(D)) of 0.16 +/- 0.07 for Ado(*) and 0.5 +/- 0.4 for 8-MeOAdo(*) are observed, both of which are significantly less than the 0.7 minimum for nontunneling behavior. The data provide strong evidence for the expected quantum mechanical tunneling in the Ado(*) and 8-MeOAdo(*)-mediated H(*) abstraction reactions from ethylene glycol. More importantly, a comparison of these enzyme-free tunneling data to the same KIE, (E(D) - E(H)) and A(H)/A(D) data for a closely related, Ado(*)-mediated H(*) abstraction reaction from a primary CH(3)- group in AdoCbl-dependent methylmalonyl-CoA mutase shows the enzymic and enzyme-free data sets are identical within experimental error. The Occam's Razor conclusion is that at least this adenosylcobalamin-dependent enzyme has not evolved to enhance quantum mechanical tunneling, at least within the present error bars. Instead, this B(12)-dependent enzyme simply exploits the identical level of quantum mechanical tunneling that is available in the enzyme-free, solution-based H(*) abstraction reaction. The results also require a similar, if not identical, barrier width and height within experimental error for the H(*) abstraction both within, and outside of, the enzyme.
81 citations
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TL;DR: In this article, a general procedure using EPR spectroscopy has been developed which allows absolute rate constants, k/sub 1/ for unimolecular reactions to be measured in solution over a range of temperature.
Abstract: Organic chemists have, for many years, used competing unimolecular radical reactions as qualitative timing devices to investigate the rates of radical-molecule reactions. The relevant information is obtained simply by product analysis. If unimolecular clock reactions are to be used to determine absolute rate constants for radical-molecule reactions in solution, then, for each class of radical, there is a need for clocks, calibrated for solution work, which cover a range of time scales. For calibration of a clock reaction, a general procedure using EPR spectroscopy has been developed which allows absolute rate constants, k/sub 1/ for unimolecular reactions to be measured in solution over a range of temperature. This yields the Arrhenius parameters, which makes it possible for using clock reactions in studies carried out at temperatures other than those at which k/sub 1/ was measured. The number of clock reactions calibrated by EPR spectroscopy has grown rapidly in recent years. This article illustrates the utility of the approach and presents a few examples taken from the literature.
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TL;DR: In this paper, the 2,2,6,6-tetramethylpiperidine nitrogen oxide series has been synthesized, and a new stable free radicals have been obtained.
153 citations