Peptide cation-radicals. A computational study of the competition between peptide N-Calpha bond cleavage and loss of the side chain in the [GlyPhe-NH2 + 2H]+. cation-radical

Cation‐radicals and dications corresponding to hydrogen atom adducts to N‐terminus‐protonated N_α‐glycylphenylalanine amide (Gly‐Phe‐NH₂) are studied by combined density functional theory and Møller‐Plesset perturbational computations (B3‐MP2) as models for electron‐capture dissociation of peptide bonds and elimination of side‐chain groups in gas‐phase peptide ions. Several structures are identified as local energy minima including isomeric aminoketyl cation‐radicals, and hydrogen‐bonded ion‐radicals, and ylid‐cation‐radical complexes. The hydrogen‐bonded complexes are substantially more stable than the classical aminoketyl structures. Dissociations of the peptide N? C_α bonds in aminoketyl cation‐radicals are 18–47 kJ mol^?1 exothermic and require low activation energies to produce ion‐radical complexes as stable intermediates. Loss of the side‐chain benzyl group is calculated to be 44 kJ mol^?1 endothermic and requires 68 kJ mol^?1 activation energy. Rice‐Ramsperger‐Kassel‐Marcus (RRKM) and transition‐state theory (TST) calculations of unimolecular rate constants predict fast preferential N? C_α bond cleavage resulting in isomerization to ion‐molecule complexes, while dissociation of the C_α? CH₂C₆H₅ bond is much slower. Because of the very low activation energies, the peptide bond dissociations are predicted to be fast in peptide cation‐radicals that have thermal (298 K) energies and thus behave ergodically. Copyright © 2003 John Wiley & Sons, Ltd.     

Addition of hot hydrogen atoms to 1-butene in the gas phase and dissociation of excited butyl radicals

The reaction of hot hydrogen atoms originating from 253.7- and 228.8-nm photolyses of hydrogen sulfide with 1-butene was investigated. Of the hydrogen atoms undergoing addition a substantial part undergoes it in a first collision (37 and 48% at 253.7 and 228.8 nm, respectively) yielding highly excited butyl radicals. The ratio of nonterminal to terminal addition is 0.5 and practically does not depend on the energy of the hydrogen atoms over the range of 15–33 kcal/mol. Comparing the results of 229- and 254-nm photolyses of hydrogen sulfide with those of 313- and 334-nm photolyses of hydrogen iodide with the use of the decomposition rate constants of n-butyl radicals calculated by the RRKM methods, the conclusion is reached that the hydrogen atom from H₂S photodissociation has 90–95% of the available energy.     

Quantum mechanical investigation of effects in formation of carbonyl and thiocarbonyl cations. Part I. Fragmentation reactions of 1,2-hemithiodione radical cations

In order to study decomposition reactions of ionic oxygen and sulphur-containing compounds, such as hemithiodione radical cations, a quantum chemical investigation of the formation of formyl, thioformyl, acyl and thioacyl cations and radicals was performed. Calculations were carried out mainly at the 6–31G^* level involving complete geometry optimizations. In the ionization of aldehydes and thioaldehydes, no important energy differences were found between the oxygen and sulphur analogues studied. A stepwise generation of formyl and thioformyl cations from formaldehyde and thioformaldehyde, by hydrogen atom abstraction followed by expulsion of unpaired electrons from the resulting radicals, showed the radicalization of formaldehyde to be only 12.6 kJ mol^?1 more favoured than that of thioformaldehyde. The electron expulsion from formyl radical was 23.8 kJ mol^?1 more favoured than that from thioformyl radical. Substitution of hydrogens of formyl and thioformyl groups by methyls lowered the total formation energies of carbonyl and thiocarbonyl cations 119.2 and 96.2 kJ mol^?1. The formation energy difference between acyl and thioacyl cations was also very small.     

Reaction of energetic hydrogen atoms with 1-chloropropane

The reaction of photochemically generated energetic hydrogen atoms with 1-chloropropane, reaction (1), has been examined for translational energies of H* in the range 40 to 110 kJ mol^?1. Integral probabilities for reaction (1) have been determined, and the phenomenological threshold energy is 47 ± 10 kJ mol^?1. The moderating effect of CO₂ on reaction (1) for hydrogen atoms of initial energy 108 kJ mol^?1 has also been studied. © 1993 John Wiley & Sons, Inc.     

The mechanism of the retro-Diels-Alder reaction in 4-vinylcyclohexene cation radical

Butadiene cation radicals are produced symmetrically from the ring and side-chain of the vinylcyclohexene cation radical near the onset of the fragmentation. The appearance energies of C₄H₆^+? and C₄H₂D₄^+? from (3,3,6,6-D₄)vinylcyclohex ene were measured as 11.07 ± 0.05 and 11.06 ± 0.06 eV, respectively. This sets the barrier to retro-Diels-Alder decomposition at 1140 kJ mol^?1 above the energy of 1 and 44 kJ mol^?1 above the thermochemical threshold corresponding to C₄H₆^+? + C₄H₆. Topological molecular orbital calculations indicate that this lowest-energy path involves a sequential rupture of the C₃C₄ and C₅C₆ bonds, with a calculated barrier of 211 kJ mol^?1. The second, two-step reaction channel proceeds by subsequent fission of the C₅C₆ and C₃C₄ bonds with a barrier of 299 kJ mol^?1. This channel is found experimentally as a break on the ionization efficiency curve at 12.1 eV. Both the supra-supra and the supra-antara pericyclic reactions go through energy maxima and are therefore forbidden. The supra-supra process is the most favorable route for decomposition from the first excited state, the activation energy being 333 kJ mol^?1. The preference for the two-step mechanism is due to hyperconjugative stabilization of intermediate molecular configurations.     

Mass spectrometric study on 2-amino-as-triazino[6,5-c]quinoline and some of its derivatives

Electron impact induced fragmentations of 2-amino-as-triazino[6,5-c]quinoline and its 2-methylamino, 2-dimethylamino and 2-benzylamino analogues have been investigated. The main primary decomposition route of both the singly and the doubly charged molecular ions is the N₂ loss. For the singly charged ions the critical energy of this reaction is 110±10 kJ mol^?1 and the kinetic energy release is 61±4 kJ mol^?1. For the doubly charged ions these values are 90±10 kJ mol^?1 and 5±2 kJ mol^?1, respectively, indicating a significantly different reaction profile. The further fragmentation of [M? N₂]⁺˙ ions consists of radical eliminations from the 2-amino group with cleavages of the α- and β-bonds. Here a significant substituent effect is eliminations found suggesting an intramolecular cyclization reaction with a substituent migration. D and ¹⁵N labelling experiments have shown a minor extent of randomization of the labelled atoms and the occurrence of other hidden skeletal rearrangements during the fragmentation.     

Rate constants for the addition of the 2-hydroxy-2-propyl radical to alkenes in solution

Absolute rate constants for the addition of the 2-hydroxy-2-propyl radical to 18 substituted alkenes (CH₂ = CXY) were determined at (296 ± 1) K in 2-propanol by time-resolved electronspin-resonance spectroscopy. With alkene substitution the rate constants vary by more than 6 orders of magnitude. For 3,3-dimethyl-but-1-ene the temperature dependence is given by log k/M^?1 · s^?1 = 6.4 minus;; 19.1/Θ where Θ = 2.303 RT in kJ/mol^?1. As shown by a good correlation with the alkene electron affinities, log k₂₉₆/M^?1 · s^?1 = 6.46 + 1.71 · EA/eV (r = 0.930), 2-hydroxy-2-propyl is a very nucleophilic radical, and its addition rates are highly governed by polar effects. © 1993 John Wiley & Sons, Inc.     

Rotation about the C?N bond in 2-aza-1,3-butadiene and the N?N bond in 2,3-diaza-1,3 butadiene: A molecular orbital study

The geometry and energy of 2-aza-1,3-butadiene and 2,3-diaza-1,3-butadiene have been calculated using the 6-31G* basis set as a function of the CNCC and CNNC dihedral angles, respectively. With the 2-aza derivative potential minima are located at 0° (trans) and at about 130° for a gauche structure approximately 9.5 kJ mol^?1 less stable than the trans. Potential maxima are at about 75° giving a gauche barrier height of approximately 19 kJ mol^?1 relative to the trans structure, and at 180° (cis) giving a barrier height of approximately 14.5 kJ mol^?1 relative to the 130° gauche structure. With the 2,3-diaza derivative the gauche barrier has disappeared and there are a series of gauche structures in the region 70°–100° of almost equal energy 12.5-15 kJ mol^?1 less stable than the trans. In addition the cis barrier is much greater, nearly 70 kJ mol^?1 relative to the trans structure. Inclusion of electron correlation, accounting for about 50% of the correlation energy, produces no significant changes in the shape of the potential energy curves. There are systematic and progressive changes in almost all the geometrical parameters as the ?CH? groups in butadiene are replaced by ?N? . The outward tilt and compression within the methylene groups show adverse steric interactions to be operative in the cis structures. The values of V_nn indicate that gauche structures of both the 2-aza and the 2,3-diaza derivatives near the cis structure are more compact (as with butadiene), and gauche structures of the 2-aza derivative near the trans structure are less compact (as with butadiene). Originating in the changes in bond lengths and bond angles, rotation-independent nuclear–nuclear interactions again play an important role.     

A theoretical study on the effect of intercalating sulfur atom and doping boron atom on the adsorption of hydrogen molecule on (10,0) single-walled carbon nanotubes

Adsorption of molecular hydrogen on single-walled carbon nanotube (SWCNT), sulfur-intercalated SWCNT (S-SWCNT), and boron-doped SWCNT (BSWCNT), have been studied by means of density functional theory (DFT). Two methods KMLYP and local density approximation (LDA) were used to calculate the binding energies. The most stable configuration of H₂ on the surface of pristine SWCNT was found to be on the top of a hexagonal at a distance of 3.54 Å in good agreement with the value of 3.44 Å reported by Han and Lee (Carbon, 2004, 42, 2169). KMLYP binding energies for the most stable configurations in cases of pristine SWCNT, S-SWCNT, and BSWCNT were found to be ?2.2 kJ mol^?1, ?3.5 kJ mol^?1, and ?3.5 kJ mol^?1, respectively, while LDA binding energies were found to be ?8.8 kJ mol^?1, ?9.7 kJ mol^?1, and ?4.1 kJ mol^?1, respectively. Increasing the polarizability of hydrogen molecule due to the presence of sulfur in sulfur intercalated SWCNT caused changes in the character of its bonding to sulfur atom and affected the binding energy. In H₂-BSWCNT system, stronger charge transfer caused stronger interaction between H₂ and BSWCNT to result a higher binding energy relative to the binding energy for H₂-SWCNT.     

The influence of reagents solvation on enthalpy change of glycine-ion protonation and silver(I) glycine-ion complexation in aqueous-dimethylsulfoxide solutions

The thermal decomposition process and non-isothermal decomposition kinetic of glyphosate were studied by the Differential thermal analysis (DTA) and Thermogravimetric analysis (TGA). The results showed that the thermal decomposition temperature of glyphosate was above 198?°C. And the decomposition process was divided into three stages: The zero stage is the decomposition of impurities, and the mass loss in the first and second stage may be methylene and carbonyl, respectively. The mechanism function and kinetic parameters of non-isothermal decomposition of glyphosate were obtained from the analysis of DTA?CTG curves by the methods of Kissinger, Flynn?CWall?COzawa, Distributed activation energy model, Doyle and ?atava-?esták, respectively. In the first stage, the kinetic equation of glyphosate decomposition obtained showed that the decomposition reaction is a Valensi equation of which is two-dimensional diffusion, 2D. Its activation energy and pre-exponential factor were obtained to be 201.10?kJ?mol^?1 and 1.15?×?10¹⁹?s^?1, respectively. In the second stage, the kinetic equation of glyphosate decomposition obtained showed that the decomposition reaction is a Avrami?CErofeev equation of which is nucleation and growth, and whose reaction order (n) is 4. Its activation energy and pre-exponential factor were obtained to be 251.11?kJ?mol^?1 and 1.48?×?10²¹?s^?1, respectively. Moreover, the results of thermodynamical analysis showed that enthalpy change of ??H ^??, entropy change of ??S ^?? and the change of Gibbs free energy of ??G ^?? were, respectively, 196.80?kJ?mol^?1,107.03?J?mol^?1?K^?1, and 141.77?kJ?mol^?1 in the first stage of the process of thermal decomposition; and 246.26?kJ?mol^?1,146.43?J?mol^?1?K^?1, and 160.82?kJ?mol^?1 in the second stage.     

Theoretical study of the structure and unimolecular decomposition pathways of ethyloxonium, [CH3CH2OH2]+

Ab initio molecular orbital calculations with split-valence plus polarization basis sets and incorporating valence-electron correlation have been performed to determine the equilibrium structure of ethyloxonium ([CH₃CH₂OH₂]⁺) and examine its modes of unimolecular dissociation. An asymmetric structure (1) is predicted to be the most stable form of ethyloxonium, but a second conformational isomer of C_s symmetry lies only 1.4 kJ mol^?1 higher in energy than 1. Four unimolecular decomposition pathways for 1 have been examined involving loss of H₂, CH₄, H₂O or C₂H₄. The most stable fragmentation products, lying 65 kJ mol^?1 above 1, are associated with the H₂ elimination reaction. However, large barriers of 257 and 223 kJ mol^?1 have to be surmounted for H₂ and CH₄ loss, respectively. On the other hand, elimination of either C₂H₄ or H₂O from ethyloxonium can proceed without a barrier to the reverse associations and, with total endothermicities of 130 and 160 kJ mol^?1, respectively, these reactions are expected to dominate at lower energies. A second important equilibrium structure on the surface is a hydrogen-bridged complex, lying 53 kJ mol^?1 above 1. This complex is involved in the C₂H₄ elimination reaction, acts as an intermediate in the proton-transfer reaction connecting [C₂H₅]⁺ +H₂O and C₂H₄ + [H₃O]⁺ and plays an important role in the isotopic scrambling that has been observed experimentally in the elimination of either H₂O or C₂H₄ from ethyloxonium. The proton affinity of ethanol was calculated as 799 kJ mol^?1, in close agreement with the experimental value of 794 kJ mol^?1.     

Activation energy of thermal decomposition of LaC2O4Br

The activation energy of the thermal decomposition of finely ground LaC₂O₄Br was determined according to the method of Ozawa asE _a=203.83 kJ mol^?1. As compared to the value for the parent oxalate La₂(C₂O₄)₃ E _a=130 kJ/mol), this value is higher by about 70 kJ/mol, which is consistent with the increased interaction between the metal and oxalate ions. The substitution of Br by Cl does not affect the decomposition kinetics profoundly.     

Rate constants and transition‐state geometry of reactions of alkyl,alkoxyl, and peroxyl radicals with thiols

Enthalpy, activation energy, and rate constant of 9 alkyl, 3 acyl, 3 alkoxyl, and 9 peroxyl radicals with alkanethiols, benzenethiol, and L ‐cysteine are calculated. The intersection parabolas model is used for activation energy calculations. Depending on the structure of attacking radical, the activation energy of reactions with alkylthiols varies from 3 to 43 kJ mol^?1 for alkyl radicals, from 7 to 9 kJ mol^?1 for alkoxyl, and from 18 to 35 kJ mol^?1 for peroxyl radicals. The influence of adjacent π‐bonds on activation energy is estimated. The polar effect is found in reactions of hydroxyalkyl and acyl radicals with alkylthiols. The steric effect is observed in reactions of alkyl radicals with tert‐alkylthiols. All these factors are characterized via increments of activation energy. Quantum chemical calculations of activation energy and geometry of transition state were performed for model reactions: C^?H₃ + CH₃SH, CH₃O^? + CH₃SH, and HO₂^? + CH₃SH with using density functional theory and Gaussian‐98. © 2008 Wiley Periodicals, Inc. Int J Chem Kinet 41: 284–293, 2009     

High temperature collisional energy transfer in highly vibrationally excited molecules: Isotope effects in tert-butyl chloride systems

The average downward collisional energy transfer (<ΔE_down>) is obtained for highly vibrationally excited tert-butyl chloride, both undeuterated and per-deuterated, with Kr, N₂, CO₂, and C₂H₄ bath gases, at ca. 760 K. Data are obtained using the technique of pressure-dependent very low-pressure pyrolysis. Reactant internal energies to which the data are sensitive are in the range 200–250 kJ mol^?1. For C₄H₉Cl, the <ΔE_down> values (cm^?1) are 255 (Kr), 265 (N₂), 440 (CO₂), and 585 (C₂H₄), and for C₄D₉Cl, 245 (N₂), 370 (CO₂), and 540 (C₂H₄). The uncertainties in these values are ca. 20% (40% for Kr); the uncertainties in the deuteration ratios are 10–15%. The value for Kr is in agreement with theoretical predictions of a biased random walk model for internal energy change in monatomic/substrate collisions. The effect of deuteration of <ΔE_down> is also in accord with that predicted by a modification of the theory. Extrapolated highpressure rate coefficients for the thermal decomposition of reactant are 10^13.6 exp(-187 kJ mol^?1/RT) s^?1 (C₄H₉Cl) and 10^14.2 exp(?196 kJ mol^?1/RT) s^?1 (C₄D₉Cl), in accord with other studies and the expected isotope effect.     

An extended mechanism for chemical activation systems

The classical mechanism of chemically activated unimolecular reactions is extended to interpret experimental results in systems olefin/hydrogen atoms. In the case of a large excess of the latter, one has to take into consideration a second chemical activation of the primarily formed radicals by their recombination with H-atoms to yield chemically activated alkane molecules. The radicals as well as the alkane molecules may decompose, and a method based on the coupling of two steady-state master equations is developed to evaluate the contribution of either of the two reaction paths to the ratio decomposition to stabilization. The treatment proposed is demonstrated for the example cis but-2-ene/excess of thermal hydrogen atoms in the presence of molecular hydrogen as a bath gas at 298 K. It turns out that the step via activated butane is not negligible under these conditions.     

The methylamine radical cation [CH3NH2]+˙ and its stable isomer the methylenammonium radical cation [CH2NH3]+˙

The potential energy surface for the [CH₅N]^+˙ system has been investigated using ab initio molecular orbital calculations with large, polarization basis sets and incorporating valence-electron correlation. Two [CH₅N]^+˙ isomers can be distinguished: the well known methylamine radical cation, [CH₃NH₂]^+˙, and the less familiar methylenammonium radical cation, [CH₂NH₃]^+˙. The latter is calculated to lie 8 kJ mol^?1 lower in energy. A substantial barrier (176 kJ mol^?1) is predicted for rearrangement of [CH₂NH₃]^+˙ to [CH₃NH₂]^+˙. In addition, a large barrier (202 kJ mol^?1) is found for loss of a hydrogen radical from [CH₂NH₃]^+˙ via direct N—H bond cleavage to give the aminomethyl cation [CH₂NH₂]⁺. These results are consistent with the existence of the methylenammonium ion [CH₂NH₃]^+˙ as a stable observable species. The barrier to loss of a hydrogen radical from [CH₃NH₂]^+˙ is calculated to be 140 kJ mol^?1.     

Kinetics of the thermal unimolecular decomposition of hex-1-ene-3-yne. Heat of formation and resonance stabilization energy of the 3-ethenylpropargyl radical

The thermal unimolecular decomposition of hex-1-ene-3-yne (HEY) has been investigated over the temperature range 949–1230 K using the technique of very low-pressure pyrolysis (VLPP). One reaction pathway is the expected C₅? C₆ bond fission to form the resonance-stabilized 3-ethenylpropargyl radical. There is a concurrent process producing molecular hydrogen which probably occurs via the intermediate formation of hexatrienes and cyclohexa-1,3-diene. RRKM calculations yield the extrapolated high-pressure rate parameters at 1100 K given by the expressions 10^16.0±0.3 exp(?300.4 ± 12.6 kJ mol^?1/RT) s^?1 for bond fission and 10^13.2+0.4 exp(?247.7 ± 8.4 kJ mol^?1/RT) for the overall formation of hydrogen. The A factors were assigned from the results of previous studies of related alkynes, alkenes, and alkadienes. The activation energy for the bond fission reaction leads to ΔH [H₂CCHCC?H₂] = 391.9, DH [H₂CCHCCCH₂? H] = 363.3, and a resonance stabilization energy of 56.9 ± 14.0 kJ mol^?1 for the 3-ethenylpropargyl radical, based on a value of 420.2 kJ mol^?1 for the primary C? H bond dissociation energy in alkanes. Comparison with the revised value of 46.6 kJ mol^?1 for the resonance energy of the unsubstituted propargyl radical indicates that the ethenyl substituent (CH₂?CH) on the terminal carbon atom has only a small effect on the propargyl resonance energy. © John Wiley & Sons, Inc.     

Evaluation of the individual hydrogen bonding energies in N-methylacetamide chains

The individual hydrogen bonding energies in N-methylacetamide chains were evaluated at the MP2/6-31+G** level including BSSE correction and at the B3LYP/6-311++G(3df,2pd) level including BSSE and van der Waals correction. The calculation results indicate that compared with MP2 results, B3LYP calculations without van der Waals correction underestimate the individual hydrogen bonding energies about 5.4 kJ mol^?1 for both the terminal and central hydrogen bonds, whereas B3LYP calculations with van der Waals correction produce almost the same individual hydrogen bonding energies as MP2 does for those terminal hydrogen bonds, but still underestimate the individual hydrogen bonding energies about 2.5 kJ mol^?1 for the hydrogen bonds near the center. Our calculation results show that the individual hydrogen bonding energy becomes more negative (more attractive) as the chain becomes longer and that the hydrogen bonds close to the interior of the chain are stronger than those near the ends. The weakest individual hydrogen bonding energy is about ?29.0 kJ mol^?1 found in the dimer, whereas with the growth of the N-methylacetamide chain the individual hydrogen bonding energy was estimated to be as large as ?62.5 kJ mol^?1 found in the N-methylacetamide decamer, showing that there is a significant hydrogen bond cooperative effect in N-methylacetamide chains. The natural bond orbital analysis indicates that a stronger hydrogen bond corresponds to a larger positive charge for the H atom and a larger negative charge for the O atom in the N-H?O=C bond, corresponds to a stronger second-order stabilization energy between the oxygen lone pair and the N-H antibonding orbital, and corresponds to more charge transfer between the hydrogen bonded donor and acceptor molecules.     

Kinetics and mechanism of the reaction of Cl atoms with CH2 CO (Ketene)

The kinetics and mechanism of the gas-phase reaction of Cl atoms with CH₂CO have been studied with a FTIR spectrometer/smog chamber apparatus. Using relative rate methods the rate of reaction of Cl atoms with ketene was found to be independent of total pressure over the range 1–700 torr of air diluent with a rate constant of (2.7 ± 0.5) × 10⁻¹⁰ cm³ molecule⁻¹ s⁻¹ at 295 K. The reaction proceeds via an addition mechanism to give a chloroacetyl radical (CH₂ClCO) which has a high degree of internal excitation and undergoes rapid unimolecular decomposition to give a CH₂Cl radical and CO. Chloroacetyl radicals were also produced by the reaction of Cl atoms with CH₂ClCHO; no decomposition was observed in this case. The rates of addition reactions are usually pressure dependent with the rate increasing with pressure reflecting increased collisional stabilization of the adduct. The absence of such behavior in the reaction of Cl atoms with CH₂CO combined with the fact that the reaction rate is close to the gas kinetic limit is attributed to preferential decomposition of excited CH₂ClCO radicals to CH₂Cl radicals and CO as products as opposed to decomposition to reform the reactants. As part of this work ab initio quantum mechanical calculations (MP2/6-31G(d,p)) were used to derive Δ_fH₂₉₈(CH₂ClCO) = −(5.4 ± 4.0) kcal mol⁻¹. © 1996 John Wiley & Sons, Inc.     

Kinetics and modelling of heptane steam-cracking

The kinetics and product distribution during the cracking of heptane in the presence of steam were investigated. The experiments were performed in a flow reactor under atmospheric pressure in a temperature range of 680–760°C with a mass ratio of steam to heptane of 3: 1. The overall decomposition of heptane is represented by a first-order reaction with activation energy of 249.1 kJ mol^?1 and a frequency factor of 3.13 × 10¹³ s^?1. The reaction products were analysed using gas chromatography, the main product being ethylene. The molecular reaction scheme, which consists of a primary reaction and 24 secondary reactions between primary products, was used for modelling the experimental product yields. The yields of ethylene and hydrogen were in good agreement; however the experimental yields of propylene were higher than the predicted yields.