Carbonate radical anion — Thermochemistry

High level ab initio calculations along with isodesmic reactions have been used to derive a set of self-consistent free energies of formation for carbonate and nitrate species in the gas phase and in aqueous solution. The results show that HCO3· is a strong acid, pKa = –4.1, and that E°(CO3·–/CO32) = 1.23 ± 0.15 V.Key words: carbonate radical anion, theoretical, thermochemistry, acidity, reduction potentials.

Glutathione radical: Intramolecular H abstraction by the thiyl radical

Ab initio computations (B3LYP/6-31G(D)) were used to predict transition structures and energies of activation for intramolecular H atom transfer to a thiyl radical (RS.) from the α-C—H bonds of glutathione (1) and from the model compounds, N-formylcysteinylglycine (2) and N-(2-thioethanyl)-γ-glutamine (3). For each compound, transition structures were located by in vacuo calculations on the neutral non-zwitterionic system. Thermodynamic functions derived at the same level and single point calculations at the B3LYP/6-311+G(3df,2p) level, were used to derive free energies of activation (ΔG[Formula: see text]) and reaction (ΔG°). For abstraction of the α-C—H (Gly) by the thiyl radical in the gas phase, ΔG[Formula: see text] = 134 kJ mol–1 if the amide link to Gly is in the more stable (Z)-configuration, and ΔG[Formula: see text] = 52 kJ mol–1 if it is in the less stable (E)-configuration. The isomerization of the amide group requires about 95 kJ mol–1. Previous studies had indicated that for intramolecular reaction of the thiyl radical at α-C—H (Cys), ΔG[Formula: see text] = 110 kJ mol–1. The lowest energy pathway for intramolecular H-transfer to the thiyl radical is from α-C—H (Gln), ΔG[Formula: see text] = 37–42 kJ mol–1, and corresponds rather well with experimental results in solution (ΔG[Formula: see text] = 43 kJ mol–1). The calculated free energy change for the equilibrium between thiyl and α-C forms of the glutathione radical is ΔG° = –54 kJ mol–1. The value estimated from experimental data is ΔG° = –37 kJ mol–1. The agreement between the energies from theory in the gas phase and experiment in solution suggests that the free energies of solvation of reactant thiyl radical, transition structures for H abstraction, and the product α-C-centred radical, are very similar. The effects of solution were estimated by two continuum models (SCIPCM and COSMO). The SCIPCM model yields results very similar to the gas phase, predicting a modest lowering of the activation free energy. The results from the COSMO method were inconclusive as to whether a rate enhancement or decrease could be expected.Key words: glutathione, thiyl radical, α-C-radical, hydrogen transfer.

Cheletropic decomposition of cyclic nitrosoamines revisited: the nature of the transition states and a critical role of the ring strain

The cheletropic decompositions of 1-nitrosoaziridine (1), 1-nitroso-Delta(3)-pyrroline (2), 7-nitroso-7-azabicyclo[2.2. 1]hepta-2,5-diene (3), and 6-nitroso-6-azabicyclo[2.1.1]hexa-4-ene (4) have been studied theoretically using high level ab initio computations. Activation parameters of the decomposition of nitrosoaziridine 1 were obtained experimentally in heptane (DeltaH()(298) = 18.6 kcal mol(-)(1), DeltaS()(298) = -7.6 cal mol(-)(1) K(-)(1)) and methanol (20.3 kcal mol(-)(1), 0.3 cal mol(-)(1) K(-)(1)). Among employed theoretical methods (B3LYP, MP2, CCD, CCSD(T)//CCD), the B3LYP method in conjunction with 6-31+G, 6-311+G, and 6-311++G(3df,2pd) basis sets gives the best agreement with experimental data. It was found that typical N-nitrosoheterocycles 2-4 which have high N-N bond rotation barriers (>16 kcal mol(-)(1)) extrude nitrous oxide via a highly asynchronous transition state with a planar ring nitrogen atom. Nitrosoaziridine 1, with a low rotation barrier (<9 kcal mol(-)(1)) represents a special case. This compound can eliminate N(2)O via a low energy linear synperiplanar transition state (DeltaH()(298) = 20.6 kcal mol(-)(1), DeltaS()(298) = 2.5 cal mol(-)(1) K(-)(1)). Two higher energy transition states are also available. The B3LYP activation barriers of the cheletropic fragmentation of nitrosoheterocycles 2-4 decrease in the series: 2 (58 kcal mol(-)(1)) >> 3 (18 kcal mol(-)(1)) > 4 (12) kcal mol(-)(1). The relative strain energies increase in the same order: 2 (0 kcal mol(-)(1)) << 3 (39 kcal mol(-)(1)) < 4 (52 kcal mol(-)(1)). Comparison of the relative energies of 2-4 and their transition states on a common scale where the energy of nitrosopyrroline 2 is assumed as reference indicates that the thermal stability of the cyclic nitrosoamines toward cheletropic decomposition is almost entirely determined by the ring strain.

Effects of structure on alpha C-H bond enthalpies of amino acid residues: relevance to H transfers in enzyme mechanisms and in protein oxidation

The bond dissociation enthalpies (BDE) of all of the amino acid residues, modeled by HC(O)NHCH(R)C(O)NH(2) (PH(res)), were determined at the B3LYP/6-31G//B3LYP/6-31G level, coupled with isodesmic reactions. The results for neutral side chains with phi, psi angles approximately 180 degrees, approximately 180 degrees in ascending order, to an expected accuracy of +/-10 kJ mol(-)(1), are Asn 326; cystine 330; Asp 332; Gln 334; Trp 337; Arg 340; Lys 340; Met 343; His 344; Phe 344; Tyr 344; Leu 344; Ala 345; Cys 346; Ser 349; Gly 350; Ile 351; Val 352; Glu 354; Thr 357; Pro-cis 358; Pro-trans 369. BDEs calculated at the ROMP2/6-31G//B3LYP/6-31G level exhibit the same trends but are approximately 7 kJ mol(-)(1) higher. All BDEs are smaller than those of typical secondary or tertiary C-H bonds due to the phenomenon of captodative stabilization. The stabilization is reduced by changes in the phi,psi angles. As a result the BDEs increase by about 10 kJ mol(-)(1) in beta-sheet and 40 kJ mol(-)(1) in alpha-helical environments, respectively. In effect the alpha C-H BDEs can be "tuned" from about 345 to 400 kJ mol(-)(1) by adjusting the local environment. Some very significant effects of this are seen in the current literature on H-transfer processes in enzyme mechanisms and in oxidative damage to proteins. These observations are discussed in terms of the findings of the present study.

Structure reassignment of the major isomer from the Diels-Alder reaction of acryloyl chloride and 4,5,6,6a-tetrahydropentalene

After hydrogenation and hydrolysis, the two adducts formed from the Diels-Alder reaction of acryloyl chloride and 4,5,6,6a-tetrahydropentalene were originally assigned 7-exo- and 7-endo-carboxylic acid structures 3 and 4. Based on unexpected results in using these acids as starting materials for a superacid carbocation study, a reinvestigation of these structural assignments was carried out. From an extensive series of 2D NMR experiments, we conclude that 4 is correctly assigned, but that the other isomer is the 9-endo carboxylic acid 8. The formation of these two isomers (out of eight possible modes of addition) can be rationalized. Finally, an X-ray study of 8 was carried out as a final proof of structure.Key words: Diels-Alder reaction, facial selectivity, regioselectivity, X-ray structure, MO calculation.

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

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.<

Skeletal vibrational circular dichroism of a series of bicyclic dilactones: the fingerprint region?

The vibrational circular dichroism (VCD) spectra of 2,5-dioxabicyclo[2.2.1]heptane-3,6-dione 1 (R = H) and the 1,4-dialkyl derivatives, 1 (R = Me) and 1 (R = t-Bu), were calculated by the ab initio magnetic field perturbation (MFP) procedure with a B3LYP/6-31G* force field, and the VCD spectra of the dimethyl and di-t-butyl derivatives were measured in the region 800-1500 cm-1. While the absolute configurations of 1 (R = Me) and 1 (R = t-Bu) could be assigned unambiguously by comparison of the experimental and predicted spectra, there is little obvious correspondence between the spectra of the series of compounds. The VCD spectra are analysed on the basis of operation of a coupled oscillator mechanism involving motions of the polar bonds. In the case of the parent dihydro system, bridgehead C-H bond motions appear to dominate contributions to the VCD of vibrational transitions into which they are mixed.Key words: vibrational circular dichroism (VCD), 2,5-dioxabicyclo[2.2.1]heptane-3,6-dione, dilactones, optical activity.

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

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.

Stereochemistry and chiroptical properties of 1,3-dialkylaziridinones (α-lactams). Chiral rules for the nonplanar amide chromophore

Structural features, configurational stability, and chiroptical properties of the nonplanar amide group in α-lactams were investigated by means of ab initio (6-31 + G*) molecular orbital calculations on (1R)-aziridinone 1, (1R)-1-methylaziridinone 2, (1R,3R)-3-methylaziridinone 3, (1R,3R)-1,3-dimethylaziridinone 4a, its cis diastereomer (1S,3R)-1,3-dimethylaziridinone 4b, and (1R,3R)-3-tert-butyl-1-methylaziridinone 5, and by experimental CD spectra of 1-tert-butyl- and 1-(1′-adamantyl)-substituted 3(R)-3-tert-butylaziridinones 6 and 7. The nitrogen inversion barriers of 4a and 4b are 2.8 and 1.6 kcal mol−1, respectively. The lowest excited singlet state of all of the aziridinones is a valence state (the nO–πCO* transition); the second is a Rydberg state (the nN–3s transition). The signs of the first and second Cotton effects in the CD spectra of the compounds 6 and 7 coincide with the calculated ones for 1 and 2 and the trans isomers 3, 4a, and 5. According to the calculated and experimental data for aziridinones 1–7 as well as to the well-known data for other nonplanar amides, the sign of the first Cotton effects is determined by the intrinsic chirality of the nonplanar amide chromophore and obeys a spiral rule. For cases where the chromophore has the conformation around the N—C(O) bond, which is close to the antiperiplanar, a reverse octant rule is proposed.

Mechanistic consequences of charge transfer systems in serine proteases and angiotensin: semiempirical computations

Structures and relative energies for the triads of interacting groups in the serine charge relay system of serine proteases and the proposed tyrosine charge relay system of angiotensin II, respectively, were computed according to the standard MNDOC procedure. The most stable configuration obtained for both systems was one in which the histidine residue was negatively charged. These findings indicate that the histidine ring and not the serine hydroxyl group at the active site of serine proteases would be the nucleophilic center which is acylated by substrate. Similarly, the extreme nucleophilicity of the imidazole anion produced by the proposed triad of interacting groups in angiotensin could provoke the formation of a transient covalent bond (acyl intermediate) between receptor and peptide in the receptor activation mechanism.

Nonempirical s.c.f. calculations on sulfur atom, hydrogen sulfide, and dihydrogen sulfoxide

This paper reports the first attempt to use Gaussian basis sets in nonempirical self-consistent field (s.c.f.) calculations on sulfur-containing chemical systems. Exponents for Gaussian-type functions (G.t.f.) on S atom are given for the minimal basis set. The optimization procedure is described and the optimized exponents utilized on calculations on S atom, H2S, and the hypothetical dihydrogen sulfoxide (H2SO). Calculations by the minimal basis set of (G.t.f.), using these exponents, gave a value for the HSH angle of H2S that agrees well with the experimentally determined value. Calculations of H2SO support a "multiple bond" picture of the S—O bond.