Ab Initio Kinetics for Thermal Decomposition of CH(3)N(•)NH(2), cis-CH(3)NHN(•)H, trans-CH(3)NHN(•)H, and C(•)H(2)NNH(2) Radicals

The thermal decomposition of the CH(3)N(?)NH(2), cis-CH(3)NHN(?)H, trans-CH(3)NHN(?)H, and C(?)H(2)NNH(2) radicals, which are the four radical products from the H-abstraction reactions of monomethylhydrazine, were theoretically studied by using ab initio Rice-Ramsperger-Kassel-Marcus (RRKM) transition-state theory and master equation analysis. Various decomposition pathways were identified by using either the QCISD(T)/cc-pV∞Z//CASPT2/aug-cc-pVTZ or the QCISD(T)/cc-pV∞Z//B3LYP/6-311++G(d,p) quantum chemistry methods. The results reveal that the β-scission of NH(2) to form methyleneimine is the predominant channel for the decomposition of the C(?)H(2)NNH(2) radical due to its small energy barrier of 13.8 kcal mol(-1). The high pressure limit rate coefficient for the reaction is fitted by 3.88 × 10(19)T(-1.672) exp(-9665.13/T) s(-1). In addition, the pressure dependent rate coefficients exhibit slight temperature dependence at temperatures of 1000-2500 K. The cis-CH(3)NHN(?)H and trans-CH(3)NHN(?)H radicals are the two distinct spatial isomers with an energy barrier of 26 kcal mol(-1) for their isomerization. The β-scission of CH(3) from the cis-CH(3)NHN(?)H radical to form trans-diazene has an energy barrier of 35.2 kcal mol(-1), and the β-scission of CH(3) from the trans-CH(3)NHN(?)H radical to form cis-diazene has an energy barrier of 39.8 kcal mol(-1). The CH(3)N(?)NH(2) radical undergoes the β-scission of methyl hydrogen and amine hydrogen to form CH(2)═NNH(2), trans-CH(3)N═NH, and cis-CH(3)N═NH products, with the energy barriers of 42.8, 46.0, and 50.2 kcal mol(-1), respectively. The dissociation and isomerization rate coefficients for the reactions were calculated via the E/J resolved RRKM theory and multiple-well master equation analysis at temperatures of 300-2500 K and pressures of 0.01-100 atm. The calculated rate coefficients associated with updated thermochemical property data are essential components in the development of kinetic mechanisms for the pyrolysis and oxidation of MMH and its derivatives.     

Computational study on mechanistic details of the aminoethanol rearrangement catalyzed by the vitamin B12-dependent ethanolamine ammonia lyase: His and Asp/Glu acting simultaneously as catalytic auxiliaries

The rearrangement of aminoethanol catalyzed by ethanolamine ammonia lyase is investigated by computational means employing DFT (B3LYP/6-31G) and ab initio molecular orbital theory (QCISD/cc-pVDZ). The study aims at providing a detailed account on various crucial aspects, in particular a distinction between a direct intramolecular migration of the partially protonated NH(2) group vs elimination of NH(4)(+). Three mechanistic scenarios were explored: (i) According to the calculations, irrespective of the nature of the protonating species, intramolecular migration of the NH(3) group is energetically less demanding than elimination of NH(4)(+). However, all computed activation enthalpies exceed the experimentally derived activation enthalpy (15 kcal/mol) associated with the rate-determining step, i.e., the hydrogen abstraction from the 5'-deoxyadenosine by the product radical. For example, when imidazole is used as a model system for His interacting with the NH(3) group of the substrate, the activation enthalpy for the migration process amounts to 27.4 kcal/mol. If acetic acid is employed to mimic Asp or Glu, the activation enthalpy is somewhat lower, being equal to 24.2 kcal/mol. (ii) For a partial deprotonation of the substrate 2 at the OH group, the rearrangement mechanism consists of the dissociation of an NH(2) radical from C(2) and its association at C(1) atom. For all investigated proton acceptors (i.e., OH(-), HCOO(-), CH(3)COO(-), CH(2)NH, imidazole), the activation enthalpy for the dissociation step also exceeds 15 kcal/mol. Typical data are 20.2 kcal/mol for Ac(-) and 23.8 kcal/mol for imidazole. (iii) However, in a synergistic action of partial protonation of the NH(2) group and partial deprotonation of the OH group by the two conceivable catalytic auxiliaries Asp/Glu and His, the activation enthalpy computed is compatible with the experimental data. For imidazole and acetate as model systems, the activation enthalpy is equal to 13.7 kcal/mol. This synergistic action of the two catalytic groups is expected to take place in a physiologically realistic pH range of 6-9.5, and the present computational findings may help to further characterize the yet unknown structural details of the ethanolamine ammonia lyase's active site.     

Substituent effects on the bond dissociation enthalpies of aromatic amines

Bond dissociation enthalpy differences, Z-X DeltaBDE = BDE(4-YC(6)H(4)Z-X) - BDE(C(6)H(5)Z-X), for Z = CH(2) and O are largely independent of X and are determined mainly by the stabilization/destabilization effect of Y on the 4-YC(6)H(4)Z(*) radicals. The effects of Y are small (< or =2 kcal/mol for all Y) for Z = CH(2), but they are large for Z = O, where good correlations with sigma(p)(+)(Y) yield rho(+) = 6.5 kcal/mol. For Z = NH, two sets of electrochemically measured N-H DeltaBDEs correlate with sigma(p)(+)(Y), yielding rho(+) = 3.9 and 3.0 kcal/mol. However, in contrast to the situation with phenols, these data indicate that the strengthening effect on N-H BDEs of electron-withdrawing (EW) Y's is greater than the weakening effect of electron-donating (ED) Y's. Attempts to measure N-H DeltaBDEs in anilines using two nonelectrochemical techniques were unsuccessful; therefore, we turned to density functional theory. Calculations on 15 4-YC(6)H(4)NH(2) gave N-H DeltaBDEs correlating with sigma(p)(+) (rho(+) = 4.6 kcal/mol) and indicated that EW and ED Y's had comparable strengthening and weakening effects, respectively, on the N-H bonds. To validate theory by connecting it to experiment, the N-H DeltaBDEs of four 4,4'-disubstituted diphenylamines and five 3,7-disubstituted phenothiazines were both calculated and measured by the radical equilibration EPR technique. For all compounds, theory and experiment agreed to better than 1 kcal/mol. Dissection of N-H DeltaBDEs in 4-substituted anilines and O-H DeltaBDEs in 4-substituted phenols into interaction enthalpies between Y and NH(2)/OH (molecule stabilization/destabilization enthalpy, MSE) and NH*/O* (radical stabilization/destabilization enthalpy, RSE) reveals that for both groups of compounds, ED Y's destabilize the molecule and stabilize the radical, while the opposite holds true for EW Y's. However, in the phenols the effects of substituents on the radical are roughly 3 times as great as those in the molecule, whereas in the anilines the two effects are of comparable magnitudes. These differences arise from the stronger ED character of NH(2) vs OH and the weaker EW character of NH* vs O*. The relatively large contributions to N-H BDEs in anilines arising from interactions in the molecules suggested that N-X DeltaBDEs in 4-YC(6)H(4)NH-X would depend on X, in contrast to the lack of effect of X on O-X and CH(2)-X DeltaBDEs in 4-YC(6)H(4)O-X and 4-YC(6)H(4)CH(2)-X. This suggestion was confirmed for X = CH(3), H, OH, and F, for which the calculated NH-X DeltaBDEs yielded rho(+) = 5.0, 4.6, 4.0, and 3.0 kcal/mol, respectively.     

Effect of ring substitution on the S-H bond dissociation enthalpies of thiophenols. An experimental and computational study

There are conflicting reports on the origin of the effect of Y substituents on the S-H bond dissociation enthalpies (BDEs) in 4-Y-substituted thiophenols, 4-YC(6)H(4)S-H. The differences in S-H BDEs, [4-YC(6)H(4)S-H] - [C(6)H(5)S-H], are known as the total (de)stabilization enthalpies, TSEs, where TSE = RSE - MSE, i.e., the radical (de)stabilization enthalpy minus the molecule (de)stabilization enthalpy. The effects of 4-Y substituents on the S-H BDEs in thiophenols and on the S-C BDEs in phenyl thioethers are expected to be almost identical. Some S-C TSEs were therefore derived from the rates of homolyses of a few 4-Y-substituted phenyl benzyl sulfides, 4-YC(6)H(4)S-CH(2)C(6)H(5), in the hydrogen donor solvent 9,10-dihydroanthracene. These TSEs were found to be -3.6 +/- 0.5 (Y = NH(2)), -1.8 +/- 0.5 (CH(3)O), 0 (H), and 0.7 +/- 0.5 (CN) kcal mol(-1). The MSEs of 4-YC(6)H(4)SCH(2)C(6)H(5) have also been derived from the results of combustion calorimetry, Calvet-drop calorimetry, and computational chemistry (B3LYP/6-311+G(d,p)). The MSEs of these thioethers were -0.6 +/- 1.1 (NH(2)), -0.4 +/- 1.1 (CH(3)O), 0 (H), -0.3 +/- 1.3 (CN), and -0.8 +/- 1.5 (COCH(3)) kcal mol(-1). Although all the enthalpic data are rather small, it is concluded that the TSEs in 4-YC(6)H(4)SH are largely governed by the RSEs, a somewhat surprising conclusion in view of the experimental fact that the unpaired electron in C(6)H(5)S(*) is mainly localized on the S. The TSEs, RSEs, and MSEs have also been computed for a much larger series of 4-YC(6)H(4)SH and 4-YC(6)H(4)SCH(3) compounds by using a B3P86 methology and have further confirmed that the S-H/S-CH(3) TSEs are dominated by the RSEs. Good linear correlations were obtained for TSE = rho(+)sigma(p)(+)(Y), with rho(+) (kcal mol(-1)) = 3.5 (S-H) and 3.9 (S-CH(3)). It is also concluded that the SH substituent is a rather strong electron donor with a sigma(p)(+)(SH) of -0.60, and that the literature value of -0.03 is in error. In addition, the SH rotational barriers in 4-YC(6)H(4)SH have been computed and it has been found that for strong electron donating (ED) Ys, such as NH(2), the lowest energy conformer has the S-H bond oriented perpendicular to the aromatic ring plane. In this orientation the SH becomes an electron withdrawing (EW) group. Thus, although the OH group in phenols is always in-plane and ED irrespective of the nature of the 4-Y substituent, in thiophenols the SH switches from being an ED group with EW and weak ED 4-Ys, to being an EW group for strong ED 4-Ys.     

Energetics of C-Cl, C-Br, and C-I bonds in haloacetic acids: enthalpies of formation of XCH2COOH (X=CI, Br, I) compounds and the carboxymethyl radical

The standard molar enthalpies of formation of chloro-, bromo-, and iodoacetic acids in the crystalline state, at 298.15 K, were determined as deltafH(o)m(C2H3O2Cl, cr alpha)=-(509.74+/- 0.49) kJ x mol(-1), deltafH(o)m(C2H3O2Br, cr I)-(466.98 +/- 1.08) kJ x mol(-1), and deltafH(o)m (C2H3O2I, cr)=-(415.44 +/- 1.53) kJ x mol(-1), respectively, by rotating-bomb combustion calorimetry. Vapor pressure versus temperature measurements by the Knudsen effusion method led to deltasubH(o)m(C2H3O2Cl)=(82.19 +/- 0.92) kJ x mol(-1), deltasubH(o)m(C2H3O2Br)=(83.50 +/- 2.95) kJ x mol(-1), and deltasubH(o)m-(C2H3O2I) = (86.47 +/- 1.02) kJ x mol(-1), at 298.15 K. From the obtained deltafH(o)m(cr) and deltasubH(o)m values it was possible to derive deltafH(o)m(C2H3O2Cl, g)=-(427.55 +/- 1.04) kJ x mol(-1), deltafH(o)m (C2H3O2Br, g)=-(383.48 +/- 3.14) kJ x mol(-1), and deltafH(o)m(C2H3O2I, g)=-(328.97 +/- 1.84) kJ x mol(-1). These data, taken with a published value of the enthalpy of formation of acetic acid, and the enthalpy of formation of the carboxymethyl radical, deltafH(o)m(CH2COOH, g)=-(238 +/- 2) kJ x mol(-1), obtained from density functional theory calculations, led to DHo(H-CH2COOH)=(412.8 +/- 3.2) kJ x mol(-1), DHo(Cl-CH2COOH)=(310.9 +/- 2.2) kJ x mol(-1), DHo(Br-CH2COOH)=(257.4 +/- 3.7) kJ x mol(-1), and DHo(I-CH2COOH)=(197.8 +/- 2.7) kJ x mol(-1). A discussion of the C-X bonding energetics in XCH2COOH, CH3X, C2H5X, C2H3X, and C6H5X (X=H, Cl, Br, I) compounds is presented.     

A combined density functional theory and coupled cluster method investigation of the structural properties and stabilities of radical CH(2)CP and its isomers

The doublet potential energy surface of radical system [C(2), H(2), P] is investigated at the UB3LYP/6-311++G(d,p) and UCCSD(T)/6-311++G(2df,2p) (single-point) levels. Eight chainlike and three-membered ring structures are located as energy minima connected by 10 interconversion transition states. At the final UCCSD(T)/6-311++G(2df,2p)//UB3LYP/6-311++G(d,p) level with zero-point vibrational energy correction, species CH(2)CP is found to be thermodynamically the most stable isomer followed by HCCPH, H-cCPC-H, cPCC-H(H), H-cCCP-H, cis-CC(H)PH, trans-CC(H)PH, and CCPH(2) at 11.01, 12.57, 40.07, 43.63, 50.25, 56.82, and 65.36 kcal/mol, respectively. The computed results indicate that the chainlike isomers CH(2)CP and HCCPH and cyclic radical H-cCPC-H possess considerable kinetic stability at extra low pressures and temperatures. Interestingly, radical CCPH(2), whose energy is the highest in all predicted CH(2)CP isomers, can be also regarded as a kinetically stable species with the smallest isomerization barrier of 22.26 kcal/mol at extra low pressures and temperatures. Therefore, considering higher kinetic stability, in addition to the microwave spectroscopy characterized isomer CH(2)CP in previous experiments, the species HCCPH, H-cCPC-H, and CCPH(2) should be considered as excellent candidates for possible experimental observation. Furthermore, the structural nature of stable radical isomers is discussed based on bonding characteristics, single electron spin distribution, and comparison with their analogues.     

Polar group enhanced gas-phase acidities of carboxylic acids: an investigation of intramolecular electrostatic interaction

We studied the effects of polar groups on the gas-phase acidities of carboxylic acids experimentally and computationally. In this connection, the gas-phase acidities (DeltaH(acid), the enthalpy of deprotonation, and DeltaG(acid), the deprotonation free energy) of borane-complexed methylaminoacetic acid ((CH(3))2N(BH(3))CH(2)CO(2)H) and methylthioacetic acid (CH(3)S(BH(3))CH(2)CO(2)H) were measured using the kinetic method in a flowing afterglow-triple quadrupole mass spectrometer. The values of DeltaH(acid) and DeltaG(acid) of (CH(3))2N(BH(3))CH(2)CO(2)H were determined to be 328.8 +/- 1.9 and 322.1 +/- 1.9 kcal/mol, and those of CH(3)S(BH(3))CH(2)CO(2)H were determined to be 325.8 +/- 1.9 and 319.2 +/- 1.9 kcal/mol, respectively. The theoretical enthalpies of deprotonation of (CH(3))2N(BH(3))CH(2)CO(2)H (329.2 kcal/mol) and CH(3)S(BH(3))CH(2)CO(2)H (325.5 kcal/mol) were calculated at the B3LYP/6-31+G(d) level of theory. The calculated enthalpies of deprotonation of N-oxide-acetic acid (CH(3)NOCH(2)CO(2)H, 329.4 kcal/mol) and S-oxide-acetic acid (CH(3)SOCH(2)CO(2)H, 328.6 kcal/mol) are comparable to the experimental results for borane-complexed methylamino- and methylthioacetic acids. The enthalpy of deprotonation of sulfone-acetic acid (CH(3)SO2CH(2)CO(2)H, 326.1 kcal/mol) is about 2 kcal/mol lower than the S-oxide-acetic acid. The calculated enthalpy of deprotonation of sulfoniumacetic acid, (CH(3))2S+CH(2)CO(2)H, is 243.0 kcal/mol. Compared to the corresponding reference molecules, CH(3)NHCH(2)CO(2)H and CH(3)SCH(2)CO(2)H, the dipolar group and the monopolar group substituted carboxylic acids are stronger acids by 11-14 and 97 kcal/mol, respectively. We correlated the changes of the acidity upon a polar group substitution to the electrostatic free energy within the carboxylate anion. The acidity enhancements in polar group substituted carboxylic acids are the results of the favorable electrostatic interactions between the polar group and the developing charge at the carboxyl group.     

Enthalpies of hydrogen-bonds in alpha-helical peptides. An ONIOM DFT/AM1 study

We report the enthalpy differences between alpha-helical and extended beta-strand conformations of acetyl(Ala)nNH2, for n = 8, 10, 12-17, calculated using molecular (MO) orbital theory from complete vibrational analyses of the optimized species. The calculations used the ONIOM method with B3LYP/D95(d.p) as the high and AM1 as the low levels. The incremental change in enthalpy upon addition of one Ala to a growing beta-strand defined using the hypothetical polycondensation reaction, n Ala + CH3COOH + NH3 --> acetyl(Ala)nNH2 + n H2O, reaches its asymptotic limit of -1.4 kcal/mol at n = 10, while that for the alpha-helix continues to increase in magnitude at n = 17. The asymptotic limit of the enthalpic preference of the alpha-helix over beta-strand is estimated to be about 3 kcal/mol, while that for n = 17 is 11.99 kcal/mol or about 0.8 kcal/mol/H-bond, which is similar to measured values for polyalanines of this size in aqueous solution.     

2-Pyridinethiol/2-pyridinethione tautomeric equilibrium. A comparative experimental and computational study

The gas phase and solvent dependent preference of the tautomerization between 2-pyridinethiol (2SH) and 2-pyridinethione (2S) has been assessed using variable temperature Fourier transform infrared (FTIR) experiments, as well as ab initio and density functional theory computations. No spectroscopic evidence (nu(S)(-)(H) stretch) for 2SH was observed in toluene, C(6)D(6), heptane, or methylene chloride solutions. Although, C(s)() 2SH is 2.61 kcal/mol more stable than C(s)() 2S (CCSD(T)/cc-pVTZ//B3LYP/6-311+G(3df,2p)+ZPE), cyclohexane solvent-field relative energies (IPCM-MP2/6-311+G(3df,2p)) favor 2S by 1.96 kcal/mol. This is in accord with the FTIR observations and in quantitative agreement with the -2.6 kcal/mol solution (toluene or C(6)D(6)) calorimetric enthalpy for the 2S/2SH tautomerization favoring the thione. As the intramolecular transition state for the 2S, 2SH tautomerization (2TS) lies 25 (CBS-Q) to 30 kcal/mol (CCSD/cc-pVTZ) higher in energy than either tautomer, tautomerization probably occurs in the hydrogen bonded dimer. The B3LYP/6-311+G(3df,2p) optimized C(2) 2SH dimer is 10.23 kcal/mol + ZPE higher in energy than the C(2)(h)() 2S dimer and is only 2.95 kcal/mol + ZPE lower in energy than the C(2) 2TS dimer transition state. Dimerization equilibrium measurements (FTIR, C(6)D(6)) over the temperature range 22-63 degrees C agree: K(eq)(298) = 165 +/- 40 M(-)(1), DeltaH = -7.0 +/- 0.7 kcal/mol, and DeltaS = -13.4 +/- 3.0 cal/(mol deg). The difference between experimental and B3LYP/6-311+G(3df,2p) [-34.62 cal/(mol deg)] entropy changes is due to solvent effects. The B3LYP/6-311+G(3df,2p) nucleus independent chemical shifts (NICS) are -8.8 and -3.5 ppm 1 A above the 2SH and 2S ring centers, respectively, and the thiol is aromatic. Although the thione is not aromatic, it is stabilized by the thioamide resonance. In solvent, the large 2S dipole, 2-3 times greater than 2SH, favors the thione tautomer and, in conclusion, 2S is thermodynamically more stable than 2SH in solution.     

Retro-[3 + 2]-cycloaddition reactions in the decomposition of five-membered nitrogen-containing heterocycles

Nitrogen-containing heterocycles form the basis for a new generation of high-energy density materials, and they serve as model compounds for nitrogen-containing fuels, such as coal and biomass, and they form the backbone of ionic liquids. A novel retro-[3 + 2]-cycloaddition to a three-membered diene and a two-membered dienophile, analogous to a retro-Diels-Alder reaction, may constitute an important initial reaction step in the thermal decomposition of these heterocyclic compounds. We investigate the kinetics and thermodynamics of these reactions for the heterocycles pyrrole, pyrazole, imidazole, 1,2,3-triazole, 1,2,4-triazole, 1,2,5-triazole, 1,3,4,-triazole, 1H-tetrazole, and 2H-tetrazole, using theoretical computational chemistry. The retro-cycloadditions are shown to form one of the three-membered products: hydrazoic acid (NH=N=N), nitrilimine (NH=N=CH), carbodiimide (NH=C=NH), or ketenimine (NH=C=CH2) plus one of the two-membered products acetylene, hydrogen cyanide, or N2. Accurate enthalpies of formation are calculated for the reaction products using the high-level W1 computational protocol, providing the previously undetermined enthalpy values of 70.09, 88.75, 35.03, and 44.28 kcal mol(-1) for hydrazoic acid, nitrilimine, carbodiimide, and ketenimine, respectively. We apply a variable-order form of the Marcus equation to the dissociation reactions in correlating the enthalpy of reaction with the activation enthalpy. Typical molecular elimination reactions from the heterocycles proceed with an intrinsic activation enthalpy of 36.8 kcal mol(-1) and intrinsic activation free energy of 42.1 kcal mol(-1). However, dissociation reactions resulting in the formation of either NH=C=NH or NH=C=CH2 demonstrate intrinsic barriers ca. 30 kcal mol(-1) higher, as a result of a concerted intramolecular hydrogen shift. Rate constants calculated between 300 and 3000 K indicate that the proposed dissociation reactions should be important in the decomposition of tetrazole and 1,2,3-triazole. This is confirmed by comparison with available experimental data. Decomposition of 1,2,4-triazole to HCN + nitrilimine may also be important at high temperatures. From extrapolation of our Marcus equation relationship, we predict pentazole to decompose to N2 + NHNN with an activation enthalpy of 19.5 kcal mol-1 and a half-life of only 14 s at 298 K.     

Structures, internal rotor potentials, and thermochemical properties for a series of nitrocarbonyls, nitroolefins, corresponding nitrites, and their carbon centered radicals

Structures, enthalpy (Δ(f)H°(298)), entropy (S°(T)), and heat capacity (C(p)(T)) are determined for a series of nitrocarbonyls, nitroolefins, corresponding nitrites, and their carbon centered radicals using the density functional B3LYP and composite CBS-QB3 calculations. Enthalpies of formation (Δ(f)H°(298)) are determined at the B3LYP/6-31G(d,p), B3LYP/6-31+G(2d,2p), and composite CBS-QB3 levels using several work reactions for each species. Entropy (S) and heat capacity (C(p)(T)) values from vibration, translational, and external rotational contributions are calculated using the rigid-rotor-harmonic-oscillator approximation based on the vibration frequencies and structures obtained from the density functional studies. Contribution to Δ(f)H(T), S, and C(p)(T) from the analysis on the internal rotors is included. Recommended values for enthalpies of formation of the most stable conformers of nitroacetone cc(═o)cno2, acetonitrite cc(═o)ono, nitroacetate cc(═o)no2, and acetyl nitrite cc(═o)ono are -51.6 kcal mol(-1), -51.3 kcal mol(-1), -45.4 kcal mol(-1), and -58.2 kcal mol(-1), respectively. The calculated Δ(f)H°(298) for nitroethylene c═cno2 is 7.6 kcal mol(-1) and for vinyl nitrite c═cono is 7.2 kcal mol(-1). We also found an unusual phenomena: an intramolecular transfer reaction (isomerization) with a low barrier (3.6 kcal mol(-1)) in the acetyl nitrite. The NO of the nitrite (R-ONO) in CH(3)C(═O')ONO moves to the C═O' oxygen in a motion of a stretching frequency and then a shift to the carbonyl oxygen (marked as O' for illustration purposes).     

Computational investigation of hydrogen abstraction from 2-aminoethanol by the 1,5-dideoxyribose-5-yl radical: a model study of a reaction occurring in the active site of ethanolamine ammonia lyase

Hydrogen abstraction from 2-aminoethanol by the 5'-deoxyadenosyl radical, which is formed upon Co--C bond homolysis in coenzyme B(12), was investigated by theoretical means with employment of the DFT (B3LYP) and ab initio (MP2) approaches. As a model system for the 5'-deoxyadenosyl moiety the computationally less demanding 1,5-dideoxyribose was employed; two conformers, which differ in ring conformation (C2- and C3-endo), were considered. If hydrogen is abstracted from "free" substrate by the C2-endo conformer of the 1,5-dideoxyribose-5-yl radical, the activation enthalpy is 16.7 kcal mol(-1); with the C3-endo counterpart, the value is 17.3 kcal mol(-1). These energetic requirements are slightly above the activation enthalpy limit (15 kcal mol(-1)) determined experimentally for the rate-determining step of the sequence, that is, hydrogen delivery from 5'-deoxyadenosine to the product radical. The activation enthalpy is lower when the substrate interacts with at least one amino acid from the active site. According to the computations, when a His model system partially protonates the substrate the activation enthalpy is 4.5 kcal mol(-1) for the C3-endo conformer and 5.8 kcal mol(-1) for the C2-endo counterpart. As hydrogen abstraction from the fully as well as the partially protonated substrate is preceded by the formation of quite stable encounter complexes, the actual activation barriers are around 13-15 kcal mol(-1). A synergistic interaction of 2-aminoethanol with two amino acids where His partially protonates the NH(2) group and Asp partially deprotonates the OH group of the substrate results in an activation enthalpy of 12.4 kcal mol(-1) for the C3-endo conformer and 13.2 kcal mol(-1) for the C2-endo counterpart. However, if encounter complexes exist in the active site, the actual activation barriers are much higher (>25 kcal mol(-1)) than that reported for the rate-determining step. These findings together with previous computations suggest that the energetics of the initial hydrogen abstraction decrease with an interaction of the substrate with only a protonating auxiliary, but for the rearrangement of the radical the synergistic effects of two auxiliaries are essential to pull the barrier below the limit of 15 kcal mol(-1).     

Formation of a Criegee intermediate in the low-temperature oxidation of dimethyl sulfoxide

Dimethyl sulfoxide (DMSO) is the major sulfur-containing constituent of the Marine Boundary Layer. It is a significant source of H2SO4 aerosol/particles and methane sulfonic acid via atmospheric oxidation processes, where the mechanism is not established. In this study, several new, low-temperature pathways are revealed in the oxidation of DMSO using CBS-QB3 and G3MP2 multilevel and B3LYP hybrid density functional quantum chemical methods. Unlike analogous hydrocarbon peroxy radicals the chemically activated DMSO peroxy radical, [CH3S(=O)CH2OO*]*, predominantly undergoes simple dissociation to a methylsulfinyl radical CH3S*(=O) and a Criegee intermediate, CH2OO, with the barrier to dissociation 11.3 kcal mol(-1) below the energy of the CH3S(=O)CH2* + O2 reactants. The well depth for addition of O2 to the CH3S(=O)CH2 precursor radical is 29.6 kcal mol(-1) at the CBS-QB3 level of theory. We believe that this reaction may serve an important role in atmospheric photochemical and irradiated biological (oxygen-rich) media where formation of initial radicals is facilitated even at lower temperatures. The Criegee intermediate (carbonyl oxide, peroxymethylene) and sulfinyl radical can further decompose, resulting in additional chain branching. A second reaction channel important for oxidation processes includes formation (via intramolecular H atom transfer) and further decomposition of hydroperoxide methylsulfoxide radical, *CH2S(=O)CH2OOH over a low barrier of activation. The initial H-transfer reaction is similar and common in analogous hydrocarbon radical + O2 reactions; but the subsequent very low (3-6 kcal mol(-1)) barrier (14 kcal mol(-1) below the initial reagents) to beta-scission products is not common in HC systems. The low energy reaction of the hydroperoxide radical is a beta-scission elimination of *CH2S(=O)CH2OOH into the CH2=S=O + CH2O + *OH product set. This beta-scission barrier is low, because of the delocalization of the *CH2 radical center through the -S(=O) group, to the -CH2OOH fragment in the transition state structure. The hydroperoxide methylsulfoxide radical can also decompose via a second reaction channel of intramolecular OH migration, yielding formaldehyde and a sulfur-centered hydroxymethylsulfinyl radical HOCH2S*(=O). The barrier of activation relative to initial reagents is 4.2 kcal mol(-1). Heats of formation for DMSO, DMSO carbon-centered radical and Criegee intermediate are evaluated at 298 K as -35.97 +/- 0.05, 13.0 +/- 0.2 and 25.3 +/- 0.7 kcal mol(-1) respectively using isodesmic reaction analysis. The [CH3S*(=O) + CH2OO] product set is shown to form a van der Waals complex that results in O-atom transfer reaction and the formation of new products CH3SO2* radical and CH2O. Proper orientation of the Criegee intermediate and methylsulfinyl radical, as a pre-stabilized pre-reaction complex, assist the process. The DMSO radical reaction is also compared to that of acetonyl radical.     

Thermodynamic properties (enthalpy, bond energy, entropy, and heat capacity) and internal rotor potentials of vinyl alcohol, methyl vinyl ether, and their corresponding radicals

Vinyl alcohols (enols) have been discovered as important intermediates and products in the oxidation and combustion of hydrocarbons, while methyl vinyl ethers are also thought to occur as important combustion intermediates. Vinyl alcohol has been detected in interstellar media, while poly(vinyl alcohol) and poly(methyl vinyl ether) are common polymers. The thermochemical property data on these vinyl alcohols and methyl vinyl ethers is important for understanding their stability, reaction paths, and kinetics in atmospheric and thermal hydrocarbon-oxygen systems. Enthalpies , entropies , and heat capacities (C(p)()(T)) are determined for CH(2)=CHOH, C(*)H=CHOH, CH(2)=C(*)OH, CH(2)=CHOCH(3), C(*)H=CHOCH(3), CH(2)=C(*)OCH(3), and CH(2)=CHOC(*)H(2). Molecular structures, vibrational frequencies, , and C(p)(T) are calculated at the B3LYP/6-31G(d,p) density functional calculation level. Enthalpies are also determined using the composite CBS-Q, CBS-APNO, and G3 methods using isodesmic work reactions to minimize calculation errors. Potential barriers for internal rotors are calculated at the B3LYP/6-31G(d,p) level and used to determine the hindered internal rotational contributions to entropy and heat capacity. The recommended ideal gas phase values calculated in this study are the following (in kcal mol(-1)): -30.0, -28.9 (syn, anti) for CH(2)=CHOH; -25.6, -23.9 for CH(2)=CHOCH(3); 31.3, 33.5 for C(*)H=CHOH; 27.1 for anti-CH(2)=C(*)OH; 35.6, 39.3 for C(*)H=CHOCH(3); 33.5, 32.2 for CH(2)=C(*)OCH(3); 21.3, 22.0 for CH(2)=CHOC(*)H(2). Bond dissociation energies (BDEs) and group additivity contributions are also determined. The BDEs reveal that the O-H, O-CH(3), C-OH, and C-OCH(3) bonds in vinyl alcohol and methyl vinyl ether are similar in energy to those in the aromatic molecules phenol and methyl phenyl ether, being on average around 3 kcal mol(-1) weaker in the vinyl systems. The keto-enol tautomerization enthalpy for the interconversion of vinyl alcohol to acetaldehyde is determined to be -9.7 kcal mol(-1), while the activation energy for this reaction is calculated as 55.9 kcal mol(-1); this is the simplest keto-enol tautomerization and is thought to be important in the reactions of vinyl alcohol. Formation of the formyl methyl radical (vinoxy radical/vinyloxy radical) from both vinyl alcohol and methyl vinyl ether is also shown to be important, and its reactions are discussed briefly.     

Dissociation of the ground state vinoxy radical and its photolytic precursor chloroacetaldehyde: electronic nonadiabaticity and the suppression of the H+ketene channel

This work is a study of the competition between the two unimolecular reaction channels available to the vinoxy radical (CH(2)CHO), C-H fission to form H+ketene, and isomerization to the acetyl radical (CH(3)CO) followed by C-C fission to form CH(3) + CO. Chloroacetaldehyde (CH(2)ClCHO) was used as a photolytic precursor to the vinoxy radical in its ground state; photodissociation of chloroacetaldehyde at 193 nm produces vinoxy radicals with internal energies spanning the G3//B3LYP calculated barriers to the two available unimolecular reaction channels. The onset of the CH(3) + CO channel, via isomerization to the acetyl radical, was found to occur at an internal energy of 41 +/- 2 kcal/mol, agreeing well with our calculated isomerization barrier of 40.8 kcal/mol. Branching to the H+ketene channel was too small to be detected; we conclude that the branching to the H+ketene channel must be at least a factor of 200 lower than what is predicted by a RRKM analysis based on our electronic structure calculations. This dramatic result may be explained in part by the presence of a conical intersection at planar geometries along the reaction coordinate leading to H+ketene, which results in electronically nonadiabatic recrossing of the transition state.     

Computational study on the mechanisms and energetics of trimethylindium reactions with H2O and H2S

The reactions of trimethylindium (TMIn) with H2O and H2S are relevant to the chemical vapor deposition of indium oxide and indium sulfide thin films. The mechanisms and energetics of these reactions in the gas phase have been investigated by density functional theory and ab initio calculations using the CCSD(T)/[6-31G(d,p)+Lanl2dz]//B3LYP/[6-31G(d,p)+Lanl2dz] and CCSD(T)/[6-31G(d,p)+Lanl2dz] //MP2/[6-31G(d,p)+Lanl2dz] methods. The results of both methods are in good agreement for the optimized geometries and relative energies. When TMIn reacts with H2O and H2S, initial molecular complexes [(CH3)3In:OH2 (R1)] and [(CH3)3In:SH2 (R2)] are formed with 12.6 and 3.9 kcal/mol binding energies. Elimination of a CH4 molecule from each complex occurs with a similar energy barrier at TS1 (19.9 kcal/mol) and at TS3 (22.1 kcal/mol), respectively, giving stable intermediates (CH3)2InOH and (CH3)2InSH. The elimination of the second CH4 molecule from these intermediate products, however, has to overcome very high and much different barriers of 66.1 and 53.2 kcal/mol, respectively. In the case of DMIn with H2O and H2S reactions, formation of both InO and InS is exothermic by 3.1 and 30.8 kcal/mol respectively. On the basis of the predicted heats of formation of R1 and R2 at 0 K and -20.1 and 43.6 kcal/mol, the heats of formation of (CH3)2InOH, (CH3)2InSH, CH3InO, CH3InS, InO, and InS are estimated to be -20.6, 31.8, and 29.0 and 48.4, 35.5, and 58.5 kcal/mol, respectively. The values for InO and InS are in good agreement with available experimental data. A similar study on the reactions of (CH3)2In with H2O and H2S has been carried out; in these reactions CH3InOH and CH3InSH were found to be the key intermediate products.     

Ab initio and direct dynamics studies of the reaction of singlet methylene with acetylene and the lifetime of the cyclopropene complex

The energetics of the (1)CH(2) + C(2)H(2) --> H + C(3)H(3) reaction are accurately calculated using an extrapolated coupled-cluster/complete basis set (CBS) method based on the cc-pVDZ, cc-pVTZ, and cc-pVQZ basis sets. The reaction enthalpy (0 K) is predicted to be -20.33 kcal/mol. This reaction has no classical barrier in either the entrance or exit channel. However, there are several stable intermediates-cyclopropene (c-C(3)H(4)), allene (CH(2)CCH(2)), and propyne (CH(3)CCH)-along the minimum energy path. These intermediates with zero-point energy corrections lie below the reactants by 87.11 (c-C(3)H(4)), 109.69 (CH(2)CCH(2)), and 110.78 kcal/mol (CH(3)CCH). The vibrationally adiabatic ground-state (VAG) barrier height for c-C(3)H(4) isomerization to allene is obtained as 45.2 kcal/mol, and to propyne as 37.2 kcal/mol. In addition, the (1)CH(2) + C(2)H(2) reaction is investigated utilizing the dual-level "scaling all correlation" (SAC) ab initio method of Truhlar et al., i.e., the UCCSD(SAC)/cc-pVDZ theory. Results show that the reaction occurs via long-lived complexes. The lifetime of the cyclopropene intermediate is obtained as 3.2 +/- 0.4 ps. It is found that the intermediate propyne can be formed directly from reactants through the insertion of (1)CH(2) into a C-H bond of C(2)H(2). However, compared to the major mechanism in which the propyne is produced through a ring-opening of the cyclopropene complex, this reaction pathway is much less favorable. Finally, the theoretical thermal rate constant exhibits a negative temperature dependence, which is in excellent agreement with the previous results. The temperature dependence is consistent with the earlier RRKM results but weaker than the experimental observations at high temperatures.     

Observation of cysteine thiolate and -S...H-O intermolecular hydrogen bond

The cysteine anion was produced in the gas phase by electrospray ionization and investigated by photoelectron spectroscopy at low temperature (70 K). The cysteine anion was found to exhibit the thiolate form [-SCH2CH(NH2)CO2H], rather than the expected carboxylate form [HSCH2CH(NH2)CO2-]. This observation was confirmed by two control experiments, that is, methyl cysteine [CH3SCH2CH(NH2)CO2-] and cysteine methyl ester [-SCH2CH(NH2)CO2CH3]. The electron binding energy of [-SCH2CH(NH2)CO2H] was measured to be about 0.7 eV blue-shifted relative to [-SCH2CH(NH2)CO2CH3] due to the formation of an intramolecular -S-...HO2C- hydrogen bond in the cysteine thiolate. Theoretical calculations at the CCSD(T)/6-311++G(2df,p) and B3LYP/6-311++G(2df,p) levels were carried out to estimate the strength of this intramolecular -S-...HO2C- hydrogen bond. Combining experimental measurements and theoretical calculations yielded an estimated value of 16.4 +/- 2.0 kcal/mol for the -S-...HO2C- intramolecular hydrogen-bond strength.     

Chemo- and periselectivity in the addition of [OsO2(CH2)2] to ethylene: a theoretical study

Quantum chemical calculations by using density functional theory at the B3LYP level have been carried out to elucidate the reaction course for the addition of ethylene to [OsO2(CH2)2] (1). The calculations predict that the kinetically most favorable reaction proceeds with an activation barrier of 8.1 kcal mol(-1) via [3+2] addition across the O=Os=CH2 moiety. This reaction is -42.4 kcal mol(-1) exothermic. Alternatively, the [3+2] addition to the H2C=Os=CH2 fragment of 1 leads to the most stable addition product 4 (-72.7 kcal mol(-1)), yet this process has a higher activation barrier (13.0 kcal mol(-1)). The [3+2] addition to the O=Os=O fragment yielding 2 is kinetically (27.5 kcal mol(-1)) and thermodynamically (-7.0 kcal mol(-1)) the least favorable [3+2] reaction. The formal [2+2] addition to the Os=O and Os=CH2 double bonds proceeds by initial rearrangement of 1 to the metallaoxirane 1 a. The rearrangement 1-->1 a and the following [2+2] additions have significantly higher activation barriers (>30 kcal mol(-1)) than the [3+2] reactions. Another isomer of 1 is the dioxoosmacyclopropane 1 b, which is 56.2 kcal mol(-1) lower in energy than 1. The activation barrier for the 1-->1 b isomerization is 15.7 kcal mol(-1). The calculations predict that there are no energetically favorable addition reactions of ethylene with 1 b. The isomeric form 1 c containing a peroxo group is too high in energy to be relevant for the reaction course. The accuracy of the B3LYP results is corroborated by high level post-HF CCSD(T) calculations for a subset of species.     

Arene-cation interactions of positive quadrupole moment aromatics and arene-anion interactions of negative quadrupole moment aromatics

Intermolecular interactions involving aromatic pi-electron density are widely believed to be governed by the aromatic molecular quadrupole moment, Theta(zz). Arene-cation binding is believed to occur primarily with negative Theta(zz) aromatics, and arene-anion binding is believed to occur largely with positive Theta(zz) aromatics. We have performed quantum mechanical computations that show the cation binding of positive Theta(zz) aromatics and the anion binding of negative Theta(zz) aromatics is quite common in the gas phase. The pi-electron density of hexafluorobenzene, the prototypical positive Theta(zz ) aromatic (experimental Theta(zz) = 9.5 +/- 0.5 DA), has a Li+ binding enthalpy of -4.37 kcal/mol at the MP2(full)/6-311G**level of theory. The RHF/6-311G** calculated Theta(zz) value of 1,4-dicyanobenzene is +11.81 DA, yet it has an MP2(full)/6-311G** Li+ binding enthalpy of -12.65 kcal/mol and a Na+ binding enthalpy of -3.72 kcal/mol. The pi-electron density of benzene, the prototypical negative Theta(zz) aromatic (experimental Theta(zz) = -8.7 +/- 0.5 DA), has a F- binding enthalpy of -5.51 kcal/mol. The RHF/6-311G** calculated Theta(zz) of C6H2I4 is -10.45 DA, yet it has an MP2(full)/6-311++G** calculated F- binding enthalpy of -20.13 kcal/mol. Our results show that as the aromatic Theta(zz) value increases the cation binding enthalpy decreases; a plot of cation binding enthalpies versus aromatic Theta(zz) gives a line of best of fit with R2 = 0.778. No such correlation exists between the aromatic Theta(zz) value and the anion binding enthalpy; the line of best fit has R2 = 0.297. These results are discussed in terms of electrostatic and polarizability contributions to the overall binding enthalpies.