Bond Dissociation Energies and Radical Stabilization Energies Associated with Substituted Methyl Radicals

Henry, David J.; Parkinson, C. J.; Mayer, Paul M.; Radom, Leo

doi:10.1021/jp010442c

Cited by 265 publications

(312 citation statements)

References 21 publications

Supporting

Mentioning

287

Contrasting

Order By: Relevance

“…A profound performance study of this method has however not yet been done for phosphorus-containing species and hence we compute heats of formation for a set of small organophosphorus molecules for which experimental data is available. The excellent performance of G3(MP2)-RAD for other open-shell species is earlier reported, in particular for carbon- 29,58,59 and nitrogen-centered radicals. 60 Phosphorus-containing additives have been shown to be effective in inhibiting coking rates during thermal cracking processes.…”

Section: Introductionsupporting

confidence: 60%

Bond Dissociation Energies of Organophosphorus Compounds: an Assessment of Contemporary Ab Initio Procedures

et al. 2010

View full text Add to dashboard Cite

Thermodynamic properties of phosphorus-containing compounds were investigated using high-level ab initio computations. An extended set of contemporary density functional theory (DFT) procedures was assessed for their ability to accurately predict bond dissociation energies of a set of phosphoranyl radicals. The results of meta-and double-hybrids as well as more recent methods, in particular M05, M05-2X, M06 and M06-2X, were compared with benchmark G3(MP2)-RAD values. Standard heats of formation, entropies and heat capacities of a set of ten organophosphorus compounds were determined and the low-cost BMK functional was found to provide results consistent with available experimental data. In addition, bond dissociation enthalpies (BDEs) were computed using the BMK, M05-2X and SCS-ROMP2 procedure. The three methods give the same stability trend. The BDEs of the phosphorus(III) molecules were found to be lower than their phosphorus(V) counterparts. Overall the following ordering is found: BDE(P-OPh) < BDE(P-CH 3 ) < BDE(P-Ph) < BDE(P-OCH 3 ).

show abstract

Section: Introductionsupporting

confidence: 60%

Bond Dissociation Energies of Organophosphorus Compounds: an Assessment of Contemporary Ab Initio Procedures

et al. 2010

View full text Add to dashboard Cite

show abstract

“…To our knowledge, the precise value for BDE of C─H bonds in the methyl group of SAM has not been measured or calculated. In general, it is believed that α-heteroatom substituents stabilize methyl radicals through a three-electron interaction between the unpaired electron at the radical center and a lone pair on the heteroatom substituents (27). The magnitude of this mode of stabilization of a methyl radical by an α-sulfonium group, if any, is unclear.…”

Section: Resultsmentioning

confidence: 99%

RNA methylation by Radical SAM enzymes RlmN and Cfr proceeds via methylene transfer and hydride shift

Feng

Fujimori

2011

Proc. Natl. Acad. Sci. U.S.A.

110

View full text Add to dashboard Cite

RlmN and Cfr are Radical SAM enzymes that modify a single adenosine nucleotide-A2503-in 23S ribosomal RNA. This nucleotide is positioned within the peptidyl transferase center of the ribosome, which is a target of numerous antibiotics. An unusual feature of these enzymes is their ability to carry out methylation of amidine carbons of the adenosine substrate. To gain insight into the mechanism of methylation catalyzed by RlmN and Cfr, deuterium labeling experiments were carried out. These experiments demonstrate that the newly introduced methyl group is assembled from an S-adenosyl-L-methionine (SAM)-derived methylene fragment and a hydrogen atom that had migrated from the substrate amidine carbon. Rather than activating the adenosine nucleotide of the substrate by hydrogen atom abstraction from an amidine carbon, the 5′-deoxyadenosyl radical abstracts hydrogen from the second equivalent of SAM to form the SAM-derived radical cation. This species, or its corresponding sulfur ylide, subsequently adds into the substrate, initiating hydride shift and S-adenosylhomocysteine elimination to complete the formation of the methyl group. These findings indicate that rather than acting as methyltransferases, RlmN and Cfr are methyl synthases. Together with the previously described 5′-deoxyadenosyl and 3-amino-3-carboxypropyl radicals, these findings demonstrate that all three carbon atoms attached to the sulfonium center in SAM can serve as precursors to carbon-derived radicals in enzymatic reactions.enzymatic methylation | RNA modification T o evade the action of antibiotics, pathogenic bacteria have evolved specific defense mechanisms, including modification of antibiotic targets (1). The recent identification of cfr, the chloramphenicol-florfenicol resistance gene in clinical isolates of methicillin-resistant Staphylococcus aureus (MRSA), is a particularly severe example of bacterial resistance caused by target modification. The acquisition of this gene renders five important classes of antibiotics ineffective in treating infections (2, 3), including the entirely synthetic oxazolidinone antibiotic linezolid, an important therapeutic option and often the last line of defense in the treatment of infections caused by MRSA (4, 5). The drug resistance enzyme Cfr and its closely related homolog RlmN are enzymes that modify the 23S component of the ribosomal RNA (2, 3, 6, 7). The substrate of both enzymes is a single adenosine nucleotide-A2503-positioned within the catalytically crucial peptidyl transferase center of the ribosome, a common binding site of numerous antibiotics (8-10). RlmN and Cfr modify the substrate adenosine by adding methyl groups to C2 and C8 amidine carbons, respectively (Fig. 1). Commonly, RNA methylation is achieved by addition of substrate nucleophile (either a heteroatom or an enzyme-bound enolate) into the electrophylic methyl group of S-adenosyl-L-methionine (SAM) (11-13). By their reactivity and electronic demands, RlmN and Cfr substrate sites are distinct from other known methylation substrates in ...

show abstract

“…Scheme II indicates that ejection of dioxygen, alone or coupled with the loss of the hydrocarbon radical, gives rise to resonance-stabilized radicals and thus accounts for: (i) the exclusive observation of the radical ion products for conjugated FAME isomers and (ii) a much greater abundance of the m/z 333 product ion for the conjugated than non-conjugated isomers (see Figures 1 and 2). The significant resonance stabilization of the radical ion arising from dissociation of the n7 ozonide (with a conjugated -network that can be represented as a hybrid of up to three allylic resonance forms [39]) also accounts for the absence of an abundant ion arising from the analogous dissociation of an n9 ozonide. Production of carbon-centered radicals in the ozonolysis of alkenes, as illustrated in Scheme II, has some precedent in condensed-phase chemistry where, for example, tert-butyl radicals were detected from the ozonolysis of tert-butyl substituted ethylene accounting for 10% of the reaction flux [40].…”

Section: Characterization Of Oddelectron Product Ionsmentioning

confidence: 99%

Ozone-Induced Dissociation of Conjugated Lipids Reveals Significant Reaction Rate Enhancements and Characteristic Odd-Electron Product Ions

Maccarone

Campbell²,

Mitchell

et al. 2013

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

. Ozone-induced dissociation of conjugated lipids reveals significant reaction rate enhancements and characteristic odd-electron product ions. Journal of the American Society for Mass Spectrometry, 24 (2), 286-296.Ozone-induced dissociation of conjugated lipids reveals significant reaction rate enhancements and characteristic odd-electron product ions AbstractOzone-induced dissociation (OzID) is an alternative ion activation method that relies on the gas phase ionmolecule reaction between a mass-selected target ion and ozone in an ion trap mass spectrometer. Herein, we evaluated the performance of OzID for both the structural elucidation and selective detection of conjugated carbon-carbon double bond motifs within lipids. The relative reactivity trends for [M + X]+ ions (where X = Li, Na, K) formed via electrospray ionization (ESI) of conjugated versus nonconjugated fatty acid methyl esters (FAMEs) were examined using two different OzID-enabled linear ion-trap mass spectrometers. Compared with nonconjugated analogues, FAMEs derived from conjugated linoleic acids were found to react up to 200 times faster and to yield characteristic radical cations. The significantly enhanced reactivity of conjugated isomers means that OzID product ions can be observed without invoking a reaction delay in the experimental sequence (i.e., trapping of ions in the presence of ozone is not required). This possibility has been exploited to undertake neutral-loss scans on a triple quadrupole mass spectrometer targeting characteristic OzID transitions. Such analyses reveal the presence of conjugated double bonds in lipids extracted from selected foodstuffs. Finally, by benchmarking of the absolute ozone concentration inside the ion trap, second order rate constants for the gas phase reactions between unsaturated organic ions and ozone were obtained. These results demonstrate a significant influence of the adducting metal on reaction rate constants in the fashion Li > Na > K. second order rate constants for the gas phase reactions between unsaturated organic ions and ozone were obtained. These results demonstrate a significant influence of the adducting metal on reaction rate constants in the fashion Li > Na > K.3

show abstract

Bond Dissociation Energies and Radical Stabilization Energies Associated with Substituted Methyl Radicals

Cited by 265 publications

References 21 publications

Bond Dissociation Energies of Organophosphorus Compounds: an Assessment of Contemporary Ab Initio Procedures

Bond Dissociation Energies of Organophosphorus Compounds: an Assessment of Contemporary Ab Initio Procedures

RNA methylation by Radical SAM enzymes RlmN and Cfr proceeds via methylene transfer and hydride shift

Ozone-Induced Dissociation of Conjugated Lipids Reveals Significant Reaction Rate Enhancements and Characteristic Odd-Electron Product Ions

Contact Info

Product

Resources

About