On the influence of secondary structure on the α-C→H bond dissociation energy of proline residues in proteins: a theoretical study

1998 ◽  
Vol 76 (7) ◽  
pp. 1042-1049 ◽  
Author(s):  
D A Block ◽  
D Yu ◽  
D A Armstrong ◽  
A Rauk
Keyword(s):  
Free Radical ◽  
Bond Dissociation Energy ◽  
Dissociation Energy ◽  
Type I ◽  
Structural Constraints ◽  
Type Ii ◽  
Isodesmic Reactions ◽  
Free Radical Damage ◽  
Bond Dissociation ◽  
Dissociation Energies

Ab initio computations (B3LYP/6-31G(D), coupled with isodesmic reactions) were used to predict αC→H bond dissociation energies (BDEs) for proline as a residue in a model peptide, intended to mimic the environment in proteins. The environment was further constrained to mimic common proline positions in turns of different types. The BDEs were found to be very dependent on the structural constraints imposed by the turn type, implying different structure-mediated susceptibilities to free radical damage to proline residues. Unnatural repair of proline (inversion of chirality) was found to be thermodynamically unfavourable. The predicted BDEs for the proline αC→H bond, in kJ mol-1, to an estimated accuracy of ±10 kJ mol-1 are as follows: fully optimized trans rotamer, 368.6; fully optimized cis rotamer, 357.7; ß turn type I, 380.7; ß turn type II, 397.8; ß turn type II', 385.4; ß turn type VIa, 374.0; ß turn type VIb, 355.0. Key words: proline, ß -turns, free radical, bond dissociation energy, molecular structure, oxidative damage.<

The C—Br bond dissociation energy in halogenated bromomethanes

1951 ◽  
Vol 209 (1096) ◽  
pp. 110-131 ◽  
Keyword(s):  
Bond Dissociation Energy ◽  
Dissociation Energy ◽  
Methyl Bromide ◽  
Frequency Factor ◽  
Unimolecular Dissociation ◽  
Bond Dissociation Energies ◽  
Kcal Mole ◽  
Fast Reaction ◽  
Bond Dissociation ◽  
Dissociation Energies

The pyrolyses of methyl bromide and of the halogenated bromomethanes, CH 2 CI. Br, CH 2 Br 2 , CHCl 2 .Br, CHBr 3 , CF 3 Br, CCI 3 . Br and CBr 4 , have been investigated by the ‘toluene-carrier' technique. It has been shown that all these decompositions were initiated by the unimolecular process R Br → R + Br. (1) Since all these decompositions were carried out in the presence of an excess of toluene, the bromine atoms produced in process (1) were readily removed by the fast reaction C 6 H 5 .CH 3 + Br → C 6 H 5 . CH 2 • + HBr. Hence, the rate of the unimolecular process (1) has been measured by the rate of formation of HBr. The C—Br bond dissociation energies were assumed to be equal to the activation energies of the relevant unimolecular dissociation processes. These were calculated by using the expression k ═ 2 x 10 13 exp (- D/RT ). The reason for choosing this particular value of 2 x 10 13 sec. -1 for the frequency factor of these reactions is discussed. The values obtained for the C—Br bond dissociation energies in the investigated bromomethanes are: D (C—Br) D (C—Br) compound (kcal./mole) compound (kcal./mole) CH 3 Br (67.5) CHBr 3 55.5 CH 2 CIBr 61.0 CF 3 Br 64.5 CH 2 Br 2 62.5 CCI 3 Br 49.0 CHCl 2 Br 53.5 CBr 4 49.0 The possible factors responsible for the variation of the C—Br bond dissociation energy in these compounds have been pointed out.

Oxidative damage to the glycyl α-carbon site in proteins: an ab initio study of the C—H bond dissociation energy and the reduction potential of the C-centered radical

1996 ◽  
Vol 74 (6) ◽  
pp. 1192-1199 ◽  
Author(s):  
D.A. Armstrong ◽  
D. Yu ◽  
A. Rauk
Keyword(s):  
Amino Acid ◽  
Ab Initio ◽  
Bond Dissociation Energy ◽  
Dissociation Energy ◽  
Reduction Potential ◽  
Isodesmic Reaction ◽  
Amino Acid Side Chain ◽  
Protein Chain ◽  
Isodesmic Reactions ◽  
Bond Dissociation

The C—H bond dissociation energies (DC—H) of a series of model glycyl proteins were derived from selected isodesmic reactions based on high level ab initio calculations. At 298 K, the recommended values of DC—H, in kJ mol−1 are: NH2CH2CHO, 308; NH2CH2C(O)NH2, 336; HC(O)NHCH2CHO, 331; HC(O)NHCH2C(O)NH2, 350; CH3C(O)NHCH2C(O)NH2, 347; HC(O)NHCH2C(O)NHCH3, 349; and CH3C(O)NHCH2C(O)NHCH3, 346. The average of the last four values, 348 kJ mol−1, is the predicted bond dissociation energy of the α-C—H bond of a glycyl protein. The reduction potential in aqueous medium at 298 K and pH 7 for the process, R• + H+ + e− = RH, where R• = XNHCH•C(O)Y and X and Y represent extension of the protein chain, is E0′ 0.8 V. This result suggests that the α-C—H bond of a glycyl protein is susceptible to attack by RS•, ROO•, tyrosyl, and OH• radicals, whose reduction potentials for the analogous process are higher. The present study has established that the molecule HC(O)NHCHRC(O)NH2 (R = an amino acid side chain) serves as an accurate model for the α-C environment of an amino acid residue in a protein, and that a reliable DC—H value for the α-C—H bond may be obtained from calculations on this model at the B3LYP/6-31G(D) level of theory in conjunction with an isodesmic reaction using neutral glycine as reference. Key words: glycine, peptide, amino acid, bond energy, radicals, ab initio, computation.

The mean bond dissociation energy of the carbonmagnesium bond in bis(2,2-dimethylpropyl)magnesium

2010 ◽  
Vol 102 (2) ◽  
pp. 109-113 ◽  
Author(s):  
O. S. Akkerman ◽  
G. Schat ◽  
E. A. I. M. Evers ◽  
F. Bickelhaupt
Keyword(s):  
Bond Dissociation Energy ◽  
Dissociation Energy ◽  
Bond Dissociation ◽  
The Mean
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