Evidence that alkyl substitution provides little stabilization to radicals: the C-C bond test and the nonbonded interaction contradiction

Although the C-H bond dissociation energies of alkanes have been widely employed as measures of radical stability, it is shown here that the assumptions needed for that conclusion are incompatible with experimental and computational data related to C-C bond dissociation energies. Calculations at the QCISD(T)/6-311+G(d,p) level on model systems show that 1,3 nonbonded interactions in alkanes are repulsive, whereas the conventional radical stabilization analysis of bond dissociation energies requires that they become more attractive with increasing steric bulk. This result puts a severe limit on the role that radical stabilization can play and indicates that another factor must be responsible for the observed variation in the C-H bond dissociation energies of alkanes.     

Multi-structural thermodynamics of C-H bond dissociation in hexane and isohexane yielding seven isomeric hexyl radicals

The C-H bond dissociation processes of n-hexane and isohexane involve 23 and 13 conformational structures, respectively in the parent molecules and 14-45 conformational structures in each of the seven isomeric products that we studied. Here we use the recently developed multi-structural (MS) thermodynamics method and CCSD(T)-F12a/jul-cc-pVTZ//M06-2X/6-311+G(2df,2p) potential energy surfaces to calculate the enthalpy, entropy, and heat capacity of n-hexane, isohexane, and seven of the possible radical products of dissociation of C-H bonds. We compare our calculations with the limited experimental data and with values obtained by group additivity fits used to extend the experimental data. This work shows that using the MS method involving a full set of structural isomers with density functional geometries, scaled density functional frequencies, and coupled cluster single-point energies can predict thermodynamic functions of complex molecules and bond dissociation reactions with chemical accuracy. The method should be useful to obtain thermodynamic data for complex molecules for which such data has not been measured and to obtain thermodynamic data at temperatures outside the temperature range where measurements are available.     

Pathways for C-H bond cleavage of propane σ-complexes on PdO(101)

We used dispersion-corrected density functional theory (DFT-D3) calculations to investigate the initial C-H bond cleavage of propane σ-complexes adsorbed on the PdO(101) surface. The calculations predict that propane molecules adsorbed in η(1) configurations can undergo facile C-H bond cleavage on PdO(101), where the energy barrier for C-H bond activation is lower than that for desorption for each molecular complex. The preferred pathway for propane dissociation on PdO(101) corresponds to cleavage of a primary C-H bond of a so-called staggered p-2η(1) complex which initially coordinates with the surface by forming two H-Pd dative bonds, one at each CH(3) group. Among all of the adsorbed propane complexes, the staggered p-2η(1) complex has the highest binding energy and must overcome the lowest energy barrier for C-H bond scission. Analysis of the atomic charges reveals that propane C-H bond cleavage occurs heterolytically on PdO(101), and suggests that primary C-H bond activation is favored because a more stabilizing charge distribution develops within the 1-propyl transition state structures. Lastly, we conducted kinetic simulations using microkinetic models derived from the DFT-D3 structures, and find that the models reproduce the apparent activation energy for propane dissociation on PdO(101) to within 14% of that determined experimentally. We show that the entropic contributions of the adsorbed transition structures greatly exceed those predicted by the harmonic oscillator model, and that quantitative agreement with the apparent dissociation pre-factor may be obtained by approximating two of the frustrated adsorbate motions as free motions while treating the remaining modes as harmonic vibrations.     

Enthalpy of formation of the cyclopentadienyl radical: photoacoustic calorimetry and ab initio studies

The gas-phase C-H bond dissociation enthalpy (BDE) in 1,3-cyclopentadiene has been determined by time-resolved photoacoustic calorimetry (TR-PAC) as 358 +/- 7 kJ mol(-1). Theoretical results from ab initio complete basis-set approaches, including the composite CBS-Q and CBS-QB3 procedures, and basis-set extrapolated coupled-cluster calculations (CCSD(T)) are reported. The CCSD(T) prediction for the C-H BDE of 1,3-cyclopentadiene (353.3 kJ mol(-1)) is in good agreement with the TR-PAC result. On the basis of the experimental and the theoretical values obtained, we recommend 355 +/- 8 kJ mol(-1) for the C-H BDE of 1,3-cyclopentadiene and 271 +/- 8 kJ mol(-1) for the enthalpy of formation of cyclopentadienyl radical.     

Computational study on the bond dissociation enthalpies in the enolic and ketonic forms of beta-diketones: their influence on metal-ligand bond enthalpies

A computational study on the thermodynamic properties of 13 beta-diketones is presented. The B3LYP//6-311+G(2d,2p)//B3LYP/6-31G(d) theoretical approach was employed to compute the O-H and C-H bond dissociation enthalpies and enthalpy of tautomerization and to estimate standard gas-phase enthalpies of formation for the radicals and for the parent molecules. The gas-phase enthalpies of formation for the neutral molecules are in excellent agreement with available experimental data, supporting the estimates made for the radicals. The latter are very important for the clarification of the thermochemistry of many beta-diketonato metal complexes previously reported in the literature. Importantly, when substituents R = -CHR' are attached to the beta-diketone's scaffold, C-H homolytic bond cleavage is always favored with respect to O-H bond scission.     

Activation of C-H / H-H bonds by rhodium(II) porphyrin bimetalloradicals

Reactivity, kinetic, and thermodynamic studies are reported for reactions of a rhodium(II) bimetalloradical with H(2), and with the methyl C-H bonds for a series of substrates CH(3)R (R = H, CH(3), OH, C(6)H(5)) using a m-xylyl diether tethered diporphyrin ligand. Bimolecular substrate reactions involving the intramolecular use of two metalloradical centers and preorganization of the four-centered transition state (M*...X...Y*...M) result in large rate enhancements as compared to termolecular reactions of monometalloradicals. Activation parameters and deuterium kinetic isotope effects for the substrate reactions are reported. The C-H bond reactions become less thermodynamically favorable as the substrate steric requirements increase, and the activation free energy (DeltaG++) decreases regularly as DeltaG degrees becomes more favorable. An absolute Rh-H bond dissociation enthalpy of 61.1 +/- 0.4 kcal mol(-1) is directly determined, and the derived Rh-CH(2)R BDE values increase regularly with the increase in the C-H BDE.     

Mechanisms of initial propane activation on molybdenum oxides: a density functional theory study

We report the first detailed density functional theory study on the mechanisms of initial propane activation on molybdenum oxides. We consider 6 possible mechanisms of the C-H bond activation on metal oxides, leading to 17 transition states. We predict that hydrogen abstraction by terminal Mo=O is the most feasible reaction pathway. The calculated activation enthalpy and entropy are 32.3 kcal/mol and -28.6 cal/(mol/K), respectively, in reasonably good agreement with the corresponding experimental values (28.0 kcal/mol and -29.1 cal/(mol/K)). We find that activating the methylene C-H bond is 4.7 kcal/mol more favorable than activating the methyl C-H bond. This regioselectivity is correlated with the difference in strength between a methylene C-H bond and a methyl C-H bond. Our calculations suggest that a combined effect from both the methylene and the methyl C-H bond cleavages leads to the experimentally observed overall kinetic isotopic effects from propane to propylene on the MoO(x)/ZrO(2) catalysts.     

Significant effects of phosphorylation on relative stabilities of DNA and RNA sugar radicals: remarkably high susceptibility of h-2' abstraction in RNA

The roles of nucleic acid radicals in DNA and RNA damage cannot be properly understood in the absence of knowledge of the C-H bond strengths depicting the energy cost to generate each of these radicals. However, previous theoretical studies on the relative energies of different nucleic acid radicals are not fully convincing mainly because of the use of oversimplified model compounds. In the present study we chose nucleoside 3',5'-bisphosphates as model compounds for DNA and RNA, in which the effects of both the nucleobase and phosphorylation were taken into consideration. Using the newly developed ONIOM-G3B3 methods, we calculated the gas-phase bond dissociation enthalpies and solution-phase bond dissociation free energies of all the carbohydrate C-H bonds in the model compounds. It was found that the monoanionic phosphate group (OPO3H-) was a better radical stabilization group than the OH group by 1.3 kcal/mol, whereas the neutral phosphate group (OPO3H2) was a significantly worse radical stabilization group than OH by 4.4 kcal/mol. Due to these reasons, the relative thermodynamic susceptibility of H-abstraction from deoxyribonucleotides and ribonucleotides varied considerably depending on the phosphorylation state and the charge carried by the phosphate groups. Strikingly, the bond dissociation free energy of C2'-H in ribonucleotides was dramatically lower than that of all the other C-H bonds by 5-6 kcal/mol regardless of the phosphorylation state and the charge carried by the phosphate group. This explained the previous experimental finding that radiation damage of RNA occurs mainly via H-abstraction at H-2'. A model study suggested that the strength of the hydrogen bonding interaction between the 2'-OH and 3-phosphate groups should dramatically increase from ribonucleoside 3',5'-bisphosphate to its C2' radical. The strengthened hydrogen bonding stabilized the C2' radical, rendering the C2'-H bond of RNA extraordinarily vulnerable to H-abstraction.     

Triradical thermochemistry from collision-induced dissociation threshold energy measurements. The heat of formation of 1,3,5-trimethylenebenzene.

A method for measuring the heats of formation of triradicals using energy-resolved collision-induced dissociation (CID) of chloro-substituted biradical negative ions is described. This method is applied to the determination of the heat of formation of 1,3,5-trimethylenebenzene, which was generated by CID of the 5-chloromethyl-m-xylylene ion. The measured CID threshold energy for chloride loss (0.83 +/- 0.07 eV) is combined with the electron affinity of the 5-chloromethyl-m-xylylene biradical (1.120 +/- 0.059 eV) to give a heat of formation of the triradical of 111.0 +/- 4.1 kcal/mol that agrees with the bond additivity value of 109.3 +/- 2.1 kcal/mol. The measured heat of formation indicates a third C-H bond dissociation energy (BDE) in 1,3,5-trimethylbenzene of 88.2 +/- 5.0 kcal/mol, indistinguishable from the C-H BDE in toluene or the first or second C-H BDEs in m-xylene. The results are in agreement with the predictions made on the basis of simple qualitative and high-level molecular orbital theories that predict negligible interaction between the unpaired electrons in the high-spin triradical.     

Effects of geminal disubstitution on C-H and N-H bond dissociation energies

Composite ab initio methods including G3, CBS-Q, and G3B3 were used to calculate the C-H and N-H bond dissociation energies (BDEs) of a variety of disubstituted methane and ammonia molecules. The calculated BDEs were in excellent agreement with the available experimental data. Using these reliable BDEs we studied the effects of geminal disubstitution on C-H and N-H BDEs. It was found that the effects of the two substituents were not additive. Detailed separation of the substituent effects on BDEs to those associated with the parent molecules and those associated with the radicals was then performed using appropriate isodesmic reactions. It was found the geminal substitution effects on the stabilities of methanes, methyl radicals, amines, and amine radicals were all governed by five basic types of energetic effects, namely, hyperconjugation effect (stabilizing), electrostatic attraction (stabilizing) or repulsion (destabilizing), conjugation saturation effect (destabilizing), captodative effect (stabilizing), and steric effect (destabilizing). The conformations of the species played an essential role in determining whether a particular energetic effect could take place. Because the carbon-centered and nitrogen-centered species often had quite different conformational preferences, the geminal substitution effects on these two classes of species were quite dissimilar to each other.     

Potential reaction initiation points of polycyclic aromatic hydrocarbons

Reaction initiation points of the 16 priority polycyclic aromatic hydrocarbons (PAHs) have been determined by calculating all the different C-H bond dissociation enthalpy (BDE) values. Six density functional theory methods (B3LYP, B3LYP-D3, B97D3, M06-LD3, M06-2X-D3, and ωB97X-D) in combination with 4 basis sets (6-31G(d), 6-31+G(d,p), 6-311++G(d,p), def2-TZVP) have been applied and the most feasible combination has been selected. The BDE values and the corresponding bond lengths have been used to determine potential attack points on the structures. The studied molecules have been categorized structurally as well, within which the position of the hydrogen atoms is considered. Results show that most of the hydrogens are in zig-zag positions, and the BDE and bond length values for the 16 priority PAHs are in a range between 342.0 and 485.6 kJ/mol and 1.0817–1.952 Å, respectively. Most of the initiation points are represented by armchair and peak hydrogens. The lowest and highest BDE and shortest and longest bond length values belong to fluorene and acenaphthylene where the hydrogens were aliphatic and in peak position, respectively.     

Substituent Effects on the C-H Bond Dissociation Energy of Toluene. A Density Functional Study

The bond dissociation energies of the benzylic C-H bond of a series of 16 para-substituted toluene compounds (p-X-C(6)H(4)CH(3)) have been calculated with the density functional method (BLYP/6-31G). The calculated substituent effects correlate well with experimental rates of dimerization of para-substituted alpha,beta,beta-trifluorostyrenes and rearrangement of methylenearylcyclopropanes. Both electron-donating and electron-withdrawing groups reduce the bond dissociation energy (BDE) of the benzylic C-H bond because both groups cause spin delocalization from the benzylic radical center. The calculated spin density variations at the benzylic radical centers correlate well with both the ESR hyperfine coupling constants determined by Arnold et al. and the calculated radical effects of the substituents. The relative radical stabilities are mainly determined by the spin delocalization effect of the substituents, and polar effect of the substituents are not important in the current situation. The ground state effect is also found to influence the C-H BDE.     

Remote substituent effects on homolytic bond dissociation energies

In the study we tried to answer two questions. First, does X-Z homolytic bond dissociation energy (BDE) of Y-C6H4-X-Z obey the Hammett relationship? Second, if it does what factors determine the magnitude and sign of the slope (rho+) of Hammett regression against substituent sigma(p)(+) constants? We collected a large number of X-Z BDEs for over one-thousand Y-C6H4-X-Z systems using the RMP2/6-311++G**//UB3LYP/6-31G* method. We found that remote substituent effects on X-Z BDEs are determined by both the ground effect (i.e. stabilization/destabilization of X-Z by the substituents) and the radical effect (i.e. stabilization/destabilization of X. by the substituents). The ground or radical effect is determined by the electron demand of X-Z or X. in the same way as the deprotonation enthalpy of HOOC-C6H4-X-Z or HOOC-C6H4-X. is affected by X-Z or X. . As a result, rho+ (BDE) for X-Z bond homolysis can be quantitatively predicted by using the change in deprotonation enthalpy from HOOC-C6H4-X-Z to HOOC-C6H4-X. .     

Thermochemistry of acetonyl and related radicals

Density functional and ab initio calculations at CBS-QB3 levels of theory were employed with a series of isodesmic reactions to determine the thermochemistry of the 2-oxopropyl or acetonyl radical (CH(3)COC*H2). In turn, this was used to determine formation enthalpies of 2-oxoethyl or formylmethyl (C*H(2)CHO), 2-oxobutyl (C*H(2)COC(2)H(5)), 1-methyl-2-oxopropyl or methylacetonyl (C*H(CH(3))COCH(3)), 1-methyl-2-oxobutyl (C*H(CH(3))COC(2)H(5)), and 3-oxopentyl (C*H(2)CH2COC(2)H(5)). Our computed standard enthalpy of formation of -34.9 +/- 1.9 kJ mol-1 and a resonance stabilization energy of approximately 22 kJ mol(-1) for acetonyl are in good agreement with recent re-determinations, which have indicated a substantial lowering in the long-established value for DeltaH(f)o (298.15 K). A bond dissociation energy of 401 kJ mol(-1) is suggested for the C-H bond in acetone with consistent values for the others. The calculations support the enthalpy of formation of acetaldehyde obtained from combustion experiments of -166.1 kJ mol(-1) rather than the figure of -170.7 kJ mol(-1) extracted from enthalpies of reduction and, in addition, serve to reduce the uncertainty in DeltaH(f)o the 2-oxoethyl radical to +13 +/- 2 kJ mol(-1).     

Thermodynamics of micellization of beta-sheet forming poly(acrylic acid)-block-poly(l-valine) hybrids

The phase behavior and thermodynamic of micellization of three hybrid poly(acrylic acid)- block-poly( l-valine), namely PAA 40- b-PLVAL 100, PAA 80- b-PLVAL 100, and PAA 80- b-PLVAL 80, were investigated. beta-sheet formation in these polymeric systems resulted in a dominant enthalpic micellization process that exhibited an upper critical solution temperature (UCST). Micelle dissociation at higher temperatures is attributed to the disruption of favorable hydrogen bonds in the micellar core. Separation of hydrogen bond contributions to the micellization thermodynamics through the addition of urea as an external denaturing agent, revealed a shift from a dominant enthalpic contribution of PLVAL segments at low degree of deprotonation (alpha), where significant beta-sheet is formed, to a balanced enthalpy and entropy contributions at high alpha. At high alpha, an enhanced "water cage" hydration of unimers was observed due to the formation of water-PLVAL hydrogen bonds. Hydrophobic forces played an indirect role in enhancing the compactness of the hydrophobic core, which enhanced the strength of hydrogen bonds in the beta-sheet structures.     

Geometric isotope effect of various intermolecular and intramolecular C-H...O hydrogen bonds, using the multicomponent molecular orbital method

The geometric isotope effect (GIE) of sp- (acetylene-water), sp(2)- (ethylene-water), and sp(3)- (methane-water) hybridized intermolecular C-H...O and C-D...O hydrogen bonds has been analyzed at the HF/6-31++G level by using the multicomponent molecular orbital method, which directly takes account of the quantum effect of proton/deuteron. In the acetylene-water case, the elongation of C-H length due to the formation of the hydrogen bond is found to be greater than that of C-D. In contrast to sp-type, the contraction of C-H length in methane-water is smaller than that of C-D. After the formation of hydrogen bonds, the C-H length itself in all complexes is longer than C-D and the H...O distance is shorter than D...O, similar to the GIE of conventional hydrogen bonds. Furthermore, the exponent (alpha) value is decreased with the formation of the hydrogen bond, which indicates the stabilization of intermolecular C-H...O hydrogen bonds as well as conventional hydrogen bonds. In addition, the geometric difference induced by the H/D isotope effect of the intramolecular C-H...O hydrogen bond shows the same tendency as that of intermolecular C-H...O. Our study clearly demonstrates that C-H...O hydrogen bonds can be categorized as typical hydrogen bonds from the viewpoint of GIE, irrespective of the hybridizing state of carbon and inter- or intramolecular hydrogen bond.     

Hydrogen bonding of the nucleobase mimic 2-pyridone to fluorobenzenes: an ab initio investigation

The hydrogen-bonded complexes of the nucleobase mimic 2-pyridone (2PY) with seven different fluorinated benzenes (1-, 1,2-, 1,4-, 1,2,3-, 1,3,5-, 1,2,3,4-, and 1,2,4,5-fluorobenzene) are important model systems for investigating the relative importance of hydrogen bonding versus pi-stacking interactions in DNA. We have shown by supersonic-jet spectroscopy that these dimers are hydrogen bonded and not pi-stacked at low temperature (Leist, R.; Frey, J. A.; Leutwyler, S. J. Phys. Chem. A 2006, 110, 4180). Their geometries and binding energies D(e) were calculated using the resolution of identity (RI) M?ller-Plesset second-order perturbation theory method (RIMP2). The most stable dimers are bound by antiparallel N-H...F-C and C-H...O=C hydrogen bonds. The binding energies are extrapolated to the complete basis set (CBS) limit, , using the aug-cc-pVXZ basis set series. The CBS binding energies range from -D(e,CBS) = 6.4-6.9 kcal/mol and the respective dissociation energies from -D(0,CBS) = 5.9-6.3 kcal/mol. In combination with experiment, the latter represent upper limits to the dissociation energies of the pi-stacked isomers (which are not observed experimentally). The individual C-H...O=C and N-H...F-C contributions to D(e) can be approximately separated. They are nearly equal for 2PY.fluorobenzene; each additional F atom strengthens the C-H...O=C hydrogen bond by approximately 0.5 kcal/mol and weakens the C-F...H-N hydrogen bond by approximately 0.3 kcal/mol. The single H-bond strengths and lengths correlate with the gas-phase acid-base properties of the C-H and C-F groups of the fluorobenzenes.     

Homolytic C-H and N-H bond dissociation energies of strained organic compounds

High-level computations at G3, CBS-Q, and G3B3 levels were conducted, and good-quality C-H and N-H bond dissociation energies (BDEs) were obtained for a variety of saturated and unsaturated strained hydrocarbons and amines for the first time. From detailed NBO analyses, we found that the C-H BDEs of hydrocarbons are determined mainly by the hybridization of the parent compound, the hybridization of the radical, and the extent of spin delocalization of the radical. The ring strain has a significant effect on the C-H BDE because it forces the parent compound and radical to adopt certain undesirable hybridization. A structure-activity relationship equation (i.e., BDE (C-H) = 61.1-227.8 (p(parent)% - 0.75)(2) + 152.9 (p(radical)% - 1.00)(2) + 40.4 spin) was established, and it can predict the C-H BDEs of a variety of saturated and unsaturated strained hydrocarbons fairly well. For the C-H BDEs associated with the bridgehead carbons of the highly rigid strained compounds, we found that the strength of the C-H bond can also be predicted from the H-C-C bond angles of the bridgehead carbon. Finally, we found that N-H BDEs show less dependence on the ring strain than C-H BDEs.