Ring Opening of the Cyclopropylcarbinyl Radical and Its N- and O-Substituted Analogues:  A Theoretical Examination of Very Fast Unimolecular Reactions

Smith, David M.; Nicolaides, Athanassios; Golding, c and Bernard T.; Radom, Leo

doi:10.1021/ja980635m

Cited by 101 publications

(144 citation statements)

References 64 publications

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“…Optimization of the structures of the ligands and of the metal (II) complexes was carried out at the DFT/ B3LYP [32][33][34] level of theory using the Lanl2dz basis set [35,36]. All geometric parameters were allowed to relax and the global minimum structure has been identified by calculating the matrix of second derivative and ensures that all its Eigen values are positive.…”

Section: Molecular Modelingmentioning

confidence: 99%

Mixed bivalent transition metal complexes of 1,10-phenanthroline and 2-aminomethylthiophenyl-4-bromosalicylaldehyde Schiff base: Spectroscopic, molecular modeling and biological activities

et al. 2013

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Section: Molecular Modelingmentioning

confidence: 99%

Mixed bivalent transition metal complexes of 1,10-phenanthroline and 2-aminomethylthiophenyl-4-bromosalicylaldehyde Schiff base: Spectroscopic, molecular modeling and biological activities

et al. 2013

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“…The rule for cyclopropyl (exo) ring openings was taken from the well-known literature rate for the cyclopropylcarbinyl radical ring opening [43]. This rule was used for any exocyclopropyl ring opening even though some substituent effects on the rate constant are well-studied [44].…”

Section: Cycloalkyl Radical Ring-opening Rulesmentioning

confidence: 99%

Capturing pressure‐dependence in automated mechanism generation: Reactions through cycloalkyl intermediates

Matheu

Green

Grenda

2002

Int J of Chemical Kinetics

121

180

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Chemical kinetic mechanisms for gas-phase processes (including combustion, pyrolysis, partial oxidation, or the atmospheric oxidation of organics) will often contain hundreds of species and thousands of reactions. The size and complexity of such models, and the need to ensure that important pathways are not left out, have inspired the use of computer tools to generate such large chemical mechanisms automatically. But the models produced by existing computerized mechanism generation codes, as well as a great many large mechanisms generated by hand, do not include pressure-dependence in a general way. This is due to the difficulty of computing the large number of k(T, P) estimates required.Here we present a fast, automated method for computing k(T, P) on-the-fly during automated mechanism generation. It uses as its principal inputs the same high-pressure-limit rate estimation rules and group-additivity thermochemistry estimates employed by existing computerized mechanism-generation codes, and automatically identifies the important chemically activated intermediates and pathways. We demonstrate the usefulness of this approach on a series of pressure-dependent reactions through cycloalkyl radical intermediates, including systems with over 90 isomers and 200 accessible product channels. We test the accuracy of these computer-generated

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“…data]. If a concerted mechanism operates, then the resulting alkylsuccinates should retain the cyclopropane ring, whereas a mechanism via a discrete hex-2-yl radical may lead to a ring opening of the cyclopropyl moiety [Smith et al, 1998]. However, strain HxN1 grew extremely poorly with mixtures of these compounds and n -hexane and no metabolites were detected, possibly indicating toxicity of these cyclopropane derivatives.…”

Section: Stereochemical Evidence For a Concerted Mechanism Of N-alkanmentioning

confidence: 99%

Metabolism of Hydrocarbons in n-Alkane-Utilizing Anaerobic Bacteria

Wilkes

Buckel

Golding³

et al. 2016

Microb Physiol

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The glycyl radical enzyme-catalyzed addition of n-alkanes to fumarate creates a C-C-bond between two concomitantly formed stereogenic carbon centers. The configurations of the two diastereoisomers of the product resulting from n-hexane activation by the n-alkane-utilizing denitrifying bacterium strain HxN1, i.e. (1-methylpentyl)succinate, were assigned as (2S,1′R) and (2R,1′R). Experiments with stereospecifically deuterated n-(2,5-²H₂)hexanes revealed that exclusively the pro-S hydrogen atom is abstracted from C2 of the n-alkane by the enzyme and later transferred back to C3 of the alkylsuccinate formed. These results indicate that the alkylsuccinate-forming reaction proceeds with an inversion of configuration at the carbon atom (C2) of the n-alkane forming the new C-C-bond, and thus stereochemically resembles a S_N2-type reaction. Therefore, the reaction may occur in a concerted manner, which may avoid the highly energetic hex-2-yl radical as an intermediate. The reaction is associated with a significant primary kinetic isotope effect (kH/kD ≥3) for hydrogen, indicating that the homolytic C-H-bond cleavage is involved in the first irreversible step of the reaction mechanism. The (1-methylalkyl)succinate synthases of n-alkane-utilizing anaerobic bacteria apparently have very broad substrate ranges enabling them to activate not only aliphatic but also alkyl-aromatic hydrocarbons. Thus, two denitrifiers and one sulfate reducer were shown to convert the nongrowth substrate toluene to benzylsuccinate and further to the dead-end product benzoyl-CoA. For this purpose, however, the modified β-oxidation pathway known from alkylbenzene-utilizing bacteria was not employed, but rather the pathway used for n-alkane degradation involving CoA ligation, carbon skeleton rearrangement and decarboxylation. Furthermore, various n-alkane- and alkylbenzene-utilizing denitrifiers and sulfate reducers were found to be capable of forming benzyl alcohols from diverse alkylbenzenes, putatively via dehydrogenases. The thermophilic sulfate reducer strain TD3 forms n-alkylsuccinates during growth with n-alkanes or crude oil, which, based on the observed patterns of homologs, do not derive from a terminal activation of n-alkanes.

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Ring Opening of the Cyclopropylcarbinyl Radical and Its N- and O-Substituted Analogues: A Theoretical Examination of Very Fast Unimolecular Reactions

Cited by 101 publications

References 64 publications

Mixed bivalent transition metal complexes of 1,10-phenanthroline and 2-aminomethylthiophenyl-4-bromosalicylaldehyde Schiff base: Spectroscopic, molecular modeling and biological activities

Mixed bivalent transition metal complexes of 1,10-phenanthroline and 2-aminomethylthiophenyl-4-bromosalicylaldehyde Schiff base: Spectroscopic, molecular modeling and biological activities

Capturing pressure‐dependence in automated mechanism generation: Reactions through cycloalkyl intermediates

Metabolism of Hydrocarbons in <b><i>n</i></b>-Alkane-Utilizing Anaerobic Bacteria

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