Loss Of Hydrogen Atom Research Articles

The vacuum-ultraviolet photoelectron spectra of CH2F2 and CH2Cl2 revisited

The threshold photoelectron spectrum (TPES) of difluoromethane and dichloromethane has been recorded at the Swiss Light Source with a resolution of 2meV or 16cm−1. Electronic and vibronic transitions are simulated and assigned with the help of Franck–Condon (FC) calculations based on coupled cluster electronic structure calculations for the equilibrium geometries and harmonic vibrational frequencies of the neutrals, and of the ground and excited electronic states of the cations. Notwithstanding a high-resolution pulsed-field ionisation study on CH2F2 (Forysinski et al., 2010) in which a number of transitions to the X∼+ state have been recorded with unprecedented accuracy, we report the first complete vibrationally resolved overview of the low-lying electronic states of CH2X2+, X=F or Cl. Hydrogen atom loss from CH2F2+ occurs at low energy, making the ground state rather anharmonic and interpretation of the X∼+ band challenging in the harmonic approximation. By Franck–Condon fits, the adiabatic ionisation energies to the A∼+2B2, C∼+2A2 and D∼+2B2 states have been determined as 14.3±0.1, 15.57±0.01 and 18.0±0.1eV, respectively. The first band in the CH2Cl2 TPES is complex for a different reason, as it is the result of two overlapping ionic states, X∼+2B2 and A∼+2B1, with derived ionisation energies of 11.0±0.2 and 11.317±0.006eV, and dominated by an extended progression in the CCl2 bend (in X∼+) and a short progression in the CCl2 symmetric stretch (in A∼+), respectively. Furthermore, even though Koopmans’ approximation holds for the vertical ionisations, the X∼+ state of CH2Cl2+ is stabilized by geometry relaxation and corresponds to ionisation from the (HOMO−1) orbital. That is, the first two vertical ionisation energies are in the same order as the negative of the orbital energies of the highest occupied orbitals, but the adiabatic ionisation energy corresponding to electron removal from the (HOMO−1) is lower than the adiabatic ionisation energy corresponding to electron removal from the HOMO. The second band in the spectrum could be analysed to identify the vibrational progressions and determine adiabatic ionisation energies of 12.15 and 12.25eV for the B∼+2A1 and C∼+2A2 states. A comparison of the assignment of electronic states with the literature is made difficult by the fact that the B1 and B2 irreducible representations in C2v symmetry depend on the principal plane, i.e. whether the CX2 moiety is in the xz or the yz plane, which is often undefined in older papers.

Combined Crossed Molecular Beam and Ab Initio Investigation of the Reaction of Boron Monoxide (BO; X2Σ+) with 1,3-Butadiene (CH2CHCHCH2; X1Ag) and Its Deuterated Counterparts

The reactions of the boron monoxide ((11)BO; X(2)Σ(+)) radical with 1,3-butadiene (CH2CHCHCH2; X(1)Ag) and its partially deuterated counterparts, 1,3-butadiene-d2 (CH2CDCDCH2; X(1)Ag) and 1,3-butadiene-d4 (CD2CHCHCD2; X(1)Ag), were investigated under single collision conditions exploiting a crossed molecular beams machine. The experimental data were combined with the state-of-the-art ab initio electronic structure calculations and statistical RRKM calculations to investigate the underlying chemical reaction dynamics and reaction mechanisms computationally. Our investigations revealed that the reaction followed indirect scattering dynamics through the formation of (11)BOC4H6 doublet radical intermediates via the barrierless addition of the (11)BO radical to the terminal carbon atom (C1/C4) and/or the central carbon atom (C2/C3) of 1,3-butadiene. The resulting long-lived (11)BOC4H6 intermediate(s) underwent isomerization and/or unimolecular decomposition involving eventually at least two distinct atomic hydrogen loss pathways to 1,3-butadienyl-1-oxoboranes (CH2CHCHCH(11)BO) and 1,3-butadienyl-2-oxoboranes (CH2C ((11)BO)CHCH2) in overall exoergic reactions via tight exit transition states. Utilizing partially deuterated 1,3-butadiene-d2 and -d4, we revealed that the hydrogen loss from the methylene moiety (CH2) dominated with 70 ± 10% compared to an atomic hydrogen loss from the methylidyne group (CH) of only 30 ± 10%; these data agree nicely with the theoretically predicted branching ratio of 80% versus 19%.

Lyman α photolysis of solid nitromethane (CH3NO2) and D3-nitromethane (CD3NO2)--untangling the reaction mechanisms involved in the decomposition of model energetic materials.

Solid nitromethane (CH3NO2) along with its isotopically labelled counterpart D3-nitromethane (CD3NO2) ices were exposed to Lyman α photons to investigate the mechanism involved in the decomposition of energetic materials in the condensed phase. The chemical processes in the ices were monitored online and in situ via infrared spectroscopy complimented by temperature programmed desorption studies utilizing highly sensitive reflectron time-of-flight mass spectrometry coupled with pulsed photoionization (ReTOF-PI) at 10.49 eV. The infrared data revealed the formation of cis-methylnitrite (CH3ONO), formaldehyde (H2CO), water (H2O), carbon monoxide (CO), and carbon dioxide (CO2). Upon sublimation of the irradiated samples, three classes of higher molecular weight products, which are uniquely formed in the condensed phase, were identified via ReTOF-PI: (i) nitroso compounds [nitrosomethane (CH3NO), nitrosoethane (C2H5NO), nitrosopropane (C3H7NO)], (ii) nitrite compounds [methylnitrite (CH3ONO), ethylnitrite (C2H5ONO), propylnitrite (C3H7ONO)], and (iii) higher molecular weight molecules [CH3NONOCH3, CH3NONO2CH3, CH3OCH2NO2, ONCH2CH2NO2]. The mechanistical information obtained in the present study suggest that the decomposition of nitromethane in the condensed phase is more complex compared to the gas phase under collision-free conditions opening up not only hitherto unobserved decomposition pathways of nitromethane (hydrogen atom loss, oxygen atom loss, retro carbene insertion), but also the blocking of several initial decomposition steps due to the 'matrix cage effect'.

Combined Crossed Molecular Beam and ab Initio Investigation of the Multichannel Reaction of Boron Monoxide (BO; X2Σ+) with Propylene (CH3CHCH2; X1A′): Competing Atomic Hydrogen and Methyl Loss Pathways

The reaction dynamics of boron monoxide ((11)BO; X(2)Σ(+)) with propylene (CH(3)CHCH(2); X(1)A') were investigated under single collision conditions at a collision energy of 22.5 ± 1.3 kJ mol(-1). The crossed molecular beam investigation combined with ab initio electronic structure and statistical (RRKM) calculations reveals that the reaction follows indirect scattering dynamics and proceeds via the barrierless addition of boron monoxide radical with its radical center located at the boron atom. This addition takes place to either the terminal carbon atom (C1) and/or the central carbon atom (C2) of propylene reactant forming (11)BOC(3)H(6) intermediate(s). The long-lived (11)BOC(3)H(6) doublet intermediate(s) underwent unimolecular decomposition involving at least three competing reaction mechanisms via an atomic hydrogen loss from the vinyl group, an atomic hydrogen loss from the methyl group, and a methyl group elimination to form cis-/trans-1-propenyl-oxo-borane (CH(3)CHCH(11)BO), 3-propenyl-oxo-borane (CH(2)CHCH(2)(11)BO), and ethenyl-oxo-borane (CH(2)CH(11)BO), respectively. Utilizing partially deuterated propylene (CD(3)CHCH(2) and CH(3)CDCD(2)), we reveal that the loss of a vinyl hydrogen atom is the dominant hydrogen elimination pathway (85 ± 10%) forming cis-/trans-1-propenyl-oxo-borane, compared to the loss of a methyl hydrogen atom (15 ± 10%) leading to 3-propenyl-oxo-borane. The branching ratios for an atomic hydrogen loss from the vinyl group, an atomic hydrogen loss from the methyl group, and a methyl group loss are experimentally derived to be 26 ± 8%:5 ± 3%:69 ± 15%, respectively; these data correlate nicely with the branching ratios calculated via RRKM theory of 19%:5%:75%, respectively.

Directed gas-phase formation of the ethynylsulfidoboron molecule.

As a member of the organo sulfidoboron (RBS) family, the hitherto elusive ethynylsulfidoboron molecule (HCCBS) has been formed via the bimolecular reaction of the boron monosulfide radical (BS) with acetylene (C2H2) under single collision conditions in the gas phase, exploiting the crossed molecular beams technique. The reaction mechanism follows indirect dynamics via a barrierless addition of the boron monosulfide radical with its boron atom to the carbon atom of the acetylene molecule, leading to the trans-HCCHBS intermediate. As predicted by ab initio electronic structure calculations, the initial collision complex either isomerizes to its cis-form or undergoes a hydrogen atom migration to form H2CCBS. The cis-HCCHBS intermediate either isomerizes via hydrogen atom shift from the carbon to the boron atom, leading to the HCCBHS isomer, or decomposes to ethynylsulfidoboron (HCCBS). Both H2CCBS and HCCBHS intermediates were predicted to fragment to ethynylsulfidoboron via atomic hydrogen losses. Statistical (RRKM) calculations report yields to form the ethynylsulfidoboron molecule from cis-HCCHBS, H2CCBS, and HCCBHS to be 21%, 7%, and 72%, respectively, under current experimental conditions. Our findings open up an unconventional path to access the previously obscure class of organo sulfidoboron molecules, which are difficult to access through "classical" formation.

Isomer-Specific Product Detection of Gas-Phase Xylyl Radical Rearrangement and Decomposition Using VUV Synchrotron Photoionization

Xylyl radicals are intermediates in combustion processes since their parent molecules, xylenes, are present as fuel additives. In this study we report on the photoelectron spectra of the three isomeric xylyl radicals and the subsequent decomposition reactions of the o-xylyl radical, generated in a tubular reactor and probed by mass selected threshold photoelectron spectroscopy and VUV synchrotron radiation. Franck-Condon simulations are applied to augment the assignment of elusive species. Below 1000 K, o-xylyl radicals decompose by hydrogen atom loss to form closed-shell o-xylylene, which equilibrates with benzocyclobutene. At higher temperatures relevant to combustion engines, o-xylylene generates styrene in a multistep rearrangement, whereas the p-xylylene isomer is thermally stable, a key point of difference in the combustion of these two isomeric fuels. Another striking result is that all three xylyl isomers can generate p-xylylene upon decomposition. In addition to C8H8 isomers, phenylacetylene and traces of benzocyclobutadiene are observed and identified as further reaction products of o-xylylene, while there is also some preliminary evidence for benzene and benzyne formation. The experimental results reported here are complemented by a comprehensive theoretical C8H8 potential energy surface, which together with the spectroscopic assignments can explain the complex high-temperature chemistry of o-xylyl radicals.

Ion flux dependence of atomic hydrogen loss probabilities on tungsten and carbon surfaces

Concerns over fuel inventory and consequently radiation safety in a fusion device necessitates a better understanding of complex plasma–material interactions. Pulsed induced fluorescence is employed to determine the loss probability of atomic hydrogen on graphite and tungsten in a low-pressure radio-frequency discharge with an applied magnetic field. The interaction between the plasma and sample material surface leads to a two-stage decay in the atomic hydrogen loss rate in the plasma afterglow, from which the loss probability is determined. The loss rates are found to be dependent on the ion flux. An increase in the ion flux from 1.6×1020m−2s−1 to 5.5×1021m−2s−1 leads to an increase in the loss probability by a factor of two for both graphite and tungsten in the near afterglow. The results demonstrate that the plasma operating conditions play an important role in the loss probability of atomic hydrogen at surfaces of fusion-relevant materials.

Radical Additions to Aromatic Residues in Peptides Facilitate Unexpected Side Chain and Backbone Losses

Accurate identification of fragments in tandem mass spectrometry experiments is aided by knowledge of relevant fragmentation mechanisms. Herein, novel radical addition reactions that direct unexpected side-chain dissociations at tryptophan and tyrosine residues are reported. Various mechanisms that can account for the observed dissociation channels are investigated by experiment and theory. The propensity for radical addition at a particular site is found to be primarily under kinetic control, which is largely dictated by molecular structure. In certain peptides, intramolecular radical addition reactions are favored, which leads to the observation of numerous unexpected fragments. In one pathway, radical addition leads to migration of an aromatic side chain to another residue. Alternatively, radical addition followed by hydrogen atom loss leads to cyclization of the peptide and increased observation of internal sequence fragments. Radical addition reactions should be considered when assigning fragmentation spectra obtained from activation of hydrogen deficient peptides.

A crossed molecular beam and ab initio investigation of the exclusive methyl loss pathway in the gas phase reaction of boron monoxide (BO; X2Σ+) with dimethylacetylene (CH3CCCH3; X1A1g)

The crossed molecular beam reaction of boron monoxide ((11)BO; X(2)Σ(+)) with dimethylacetylene (CH3CCCH3; X(1)A(1g)) was investigated at a collision energy of 23.9 ± 1.5 kJ mol(-1). The scattering dynamics were suggested to be indirect (complex forming reaction) and were initiated by the addition of (11)BO(X(2)Σ(+)) with the radical center located at the boron atom to the π electron density at the acetylenic carbon-carbon triple bond without entrance barrier leading to cis-trans(11)BOC4H6 doublet radical intermediates. cis-(11)BOC4H6 underwent cis-trans isomerization followed by unimolecular decomposition via a methyl group (CH3) loss forming 1-propynyl boron monoxide (CH3CC(11)BO) in an overall exoergic reaction (experimental: -91 ± 22 kJ mol(-1); theoretical: -105 ± 9 kJ mol(-1); NIST: -104 ± 12 kJ mol(-1)) via a tight exit transition state; trans-(11)BOC4H6 was found to lose a methyl group instantaneously. Neither atomic nor molecular hydrogen loss pathways were detectable. The experimental finding of an exclusive methyl loss pathway gains full support from our computational study predicting a methyl group versus atomic hydrogen loss branching ratio of 99.99% to 0.01% forming 1-propynyl boron monoxide (CH3CC(11)BO) and 1-methyl-propadienyl boron monoxide (CH3((11)BO)CCCH2), respectively.

Microwave Flash Pyrolysis: C9H8 Interconversions and Dimerisations

The pyrolysis of 2-ethynyltoluene, indene, fluorene, and related compounds has been studied by sealed tube microwave flash pyrolysis (MFP), in concert with modelling of putative mechanistic pathways by density functional theory (DFT) computations. In the MFP technique, samples are admixed with graphite and subjected to intense microwave power (150–300 W) in a quartz reaction tube under a nitrogen atmosphere. The MFP reaction of 2-ethynyltoluene gave mostly indene, the product of a Roger Brown rearrangement (1,2-H shift to a vinylidene) followed by insertion. An additional product was chrysene, the likely result of hydrogen atom loss from indene followed by dimerisation. The intermediacy of dimeric bi-indene structures was supported by pyrolysis of bi-indene and by computational models. Benzo[a]anthracene and benzo[c]phenanthrene are minor products in these reactions. These are shown to arise from pyrolysis of chrysene under the same MFP conditions. MFP reaction of fluorene gave primarily bi-fluorene, bifluorenylidene, and dibenzochrysene, the latter derived from a known Stone–Wales rearrangement.

A Combined Experimental and Theoretical Study on the Gas‐Phase Synthesis of Toluene under Single Collision Conditions

physical-organic chemistry communities. Toluene portrays the simplest representative of an alkyl-substituted benzene molecule with the methyl group enhancing the reactivity toward radical and electrophile aromatic substitution compared to benzene. It is further considered as a crucial building block to form methyl-substituted polycyclic aromatic hydrocarbons (PAHs) such as 1and 2-methylnaphthalene. In combustion flames, the formation of phenylacetylene 2, styrene 3, and biphenyl 4 (Scheme 1) can be rationalized through phenyl addition. Atomic hydrogen is eliminated upon reaction of the phenyl radical with acetylene (C2H2), [14] ethylene (C2H4), [15] and benzene (C6H6). [16] The analogous reaction of the phenyl radical with methane (CH4) does not lead to toluene, but solely to benzene plus a methyl radical (CH3) through hydrogen abstraction. [17] Consequently, the formation routes of toluene in combustion flames and in the interstellar medium have not been unraveled to date. Here, we show that the reaction of the ethynyl radical (CCH; C2H) with isoprene (2-methyl-1,3-butadiene; C5H8) presents a facile, barrierless route to the toluene molecule in a single collision event in the gas phase through the reaction of two acyclic precursor molecules. This reaction is also of interest to the physical-organic chemistry community since it represents a benchmark system to untangle the formation of a methylsubstituted aromatic molecule through radical substitution reactions involving successive isomerizations through cyclization and hydrogen shifts. Reactive scattering signal from the reaction of [D1]ethynyl radical C2D(X S) with isoprene (C5H8; X A’) was monitored at mass-to-charge ratios (m/z) of 93 (C7H7D ), 92 (C7H6D /C7H8 ), and 91 (C7H5D /C7H7 ). The signal atm/ z= 93 originates from the C7H7D product(s) formed through atomic hydrogen loss, whereas ion counts at m/z= 92 could have two contributions: an atomic deuterium loss connected to the formation of C7H8 products or dissociative ionization of C7H7D products in the electron impact ionizer of the detector. The signal at m/z= 91 may depict two contributions from dissociative electron impact ionization of C7H7D and/or C7H6D product molecules. However, all data could be fit with the product mass combinations of 93 amu (C7H7D) plus 1 amu (H). This finding suggests the existence of a [D1]ethynyl (C2D, 26 amu) versus atomic hydrogen replacement channel and the gas-phase synthesis of a molecule with the molecular formula C7H7D (Figure 1). Considering that the [D1]ethynyl reactant does not have a hydrogen atom, the hydrogen atom is emitted from the isoprene molecule. The laboratory angular distribution (Figure 2) extends at least 408 within the scattering plane and peaks close to the center-of-mass angle at 41.1 1.28. These results suggest indirect scattering dynamics through C7H8D complex(es). Scheme 1. Toluene 1, phenylacetylene 2, styrene 3, and biphenyl 4.

A Crossed Molecular Beam and Ab-Initio Investigation of the Reaction of Boron Monoxide (BO; X2Σ+) with Methylacetylene (CH3CCH; X1A1): Competing Atomic Hydrogen and Methyl Loss Pathways

The gas-phase reaction of boron monoxide ((11)BO; X(2)Σ(+)) with methylacetylene (CH3CCH; X(1)A1) was investigated experimentally using crossed molecular beam technique at a collision energy of 22.7 kJ mol(-1) and theoretically using state of the art electronic structure calculation, for the first time. The scattering dynamics were found to be indirect (complex forming reaction) and the reaction proceeded through the barrier-less formation of a van-der-Waals complex ((11)BOC3H4) followed by isomerization via the addition of (11)BO(X(2)Σ(+)) to the C1 and/or C2 carbon atom of methylacetylene through submerged barriers. The resulting (11)BOC3H4 doublet radical intermediates underwent unimolecular decomposition involving three competing reaction mechanisms via two distinct atomic hydrogen losses and a methyl group elimination. Utilizing partially deuterated methylacetylene reactants (CD3CCH; CH3CCD), we revealed that the initial addition of (11)BO(X(2)Σ(+)) to the C1 carbon atom of methylacetylene was followed by hydrogen loss from the acetylenic carbon atom (C1) and from the methyl group (C3) leading to 1-propynyl boron monoxide (CH3CC(11)BO) and propadienyl boron monoxide (CH2CCH(11)BO), respectively. Addition of (11)BO(X(2)Σ(+)) to the C1 of methylacetylene followed by the migration of the boronyl group to the C2 carbon atom and/or an initial addition of (11)BO(X(2)Σ(+)) to the sterically less accessible C2 carbon atom of methylacetylene was followed by loss of a methyl group leading to the ethynyl boron monoxide product (HCC(11)BO) in an overall exoergic reaction (78 ± 23 kJ mol(-1)). The branching ratios of these channels forming CH2CCH(11)BO, CH3CC(11)BO, and HCC(11)BO were derived to be 4 ± 3%, 40 ± 5%, and 56 ± 15%, respectively; these data are in excellent agreement with the calculated branching ratios using statistical RRKM theory yielding 1%, 38%, and 61%, respectively.

A Halomethane Thermochemical Network from iPEPICO Experiments and Quantum Chemical Calculations

Internal energy selected halomethane cations CH(3)Cl(+), CH(2)Cl(2)(+), CHCl(3)(+), CH(3)F(+), CH(2)F(2)(+), CHClF(2)(+), and CBrClF(2)(+) were prepared by vacuum ultraviolet photoionization, and their lowest energy dissociation channel studied using imaging photoelectron photoion coincidence spectroscopy (iPEPICO). This channel involves hydrogen atom loss for CH(3)F(+), CH(2)F(2)(+), and CH(3)Cl(+), chlorine atom loss for CH(2)Cl(2)(+), CHCl(3)(+), and CHClF(2)(+), and bromine atom loss for CBrClF(2)(+). Accurate 0 K appearance energies, in conjunction with ab initio isodesmic and halogen exchange reaction energies, establish a thermochemical network, which is optimized to update and confirm the enthalpies of formation of the sample molecules and their dissociative photoionization products. The ground electronic states of CHCl(3)(+), CHClF(2)(+), and CBrClF(2)(+) do not confirm to the deep well assumption, and the experimental breakdown curve deviates from the deep-well model at low energies. Breakdown curve analysis of such shallow well systems supplies a satisfactorily succinct route to the adiabatic ionization energy of the parent molecule, particularly if the threshold photoelectron spectrum is not resolved and a purely computational route is unfeasible. The ionization energies have been found to be 11.47 ± 0.01 eV, 12.30 ± 0.02 eV, and 11.23 ± 0.03 eV for CHCl(3), CHClF(2), and CBrClF(2), respectively. The updated 0 K enthalpies of formation, Δ(f)H(o)(0K)(g) for the ions CH(2)F(+), CHF(2)(+), CHCl(2)(+), CCl(3)(+), CCl(2)F(+), and CClF(2)(+) have been derived to be 844.4 ± 2.1, 601.6 ± 2.7, 890.3 ± 2.2, 849.8 ± 3.2, 701.2 ± 3.3, and 552.2 ± 3.4 kJ mol(-1), respectively. The Δ(f)H(o)(0K)(g) values for the neutrals CCl(4), CBrClF(2), CClF(3), CCl(2)F(2), and CCl(3)F and have been determined to be -94.0 ± 3.2, -446.6 ± 2.7, -702.1 ± 3.5, -487.8 ± 3.4, and -285.2 ± 3.2 kJ mol(-1), respectively.

A Comparative Study of Homolytic Reactions of Fullerenes with Aldehydes in a Mass Spectrometer under Electron Impact and in Solution under UV Irradiation

C(60) was reacted in the ionization chamber of a mass spectrometer under electron impact (EI) with aldehydes, RCHO (R = Ph, p-FC(6)H(4), F(5)C(6), p-MeOC(6)H(4), α-thienyl, o-HOC(6)H(4), o-BrC(6)H(4), m-BrC(6)H(4) and t-Bu), with the transfer of R• radicals and with Me•-transfer from i-PrCHO and t-BuCHO. Paramagnetic fullerene derivatives were stabilized by the addition of the next R• radical or a hydrogen atom, or hydrogen or bromine atom loss. A detailed study showed that the reaction between C(60) and PhCHO occurred via a homolytic mechanism that matches one reported earlier for the reaction with acetone. This suggests the generality of the mechanism for the reactions of fullerenes with other species in ionization chambers under EI at ca 300°C. All aldehydes, except one, had radicals at the carbonyl group which were different from those in the ketones examined earlier in the reactions. This expanded the variety of radicals which can be transferred to fullerenes during reactions in ionization chambers under EI. Due to this and the hydrogen atom at the CO group of aldehydes, some reactions occurred that were not found for the ketones: the formation of cyclic products C(60)COC(6)H(4) and C(60)OC(6)H(4) for PhCHO, o-BrC(6)H(4)CHO and o-HOC(6)H(4)CHO, respectively, and HC(60)Ph for o- and m-BrC(6)H(4)CHO. The reaction with α- formylthiophen gives the first example of transferring an aromatic heterocyclic radical to C(60) in an ionization chamber under EI. C(70) reacted with PhCHO, p-FC(6)H(4)CHO and i- PrCHO similarly to C(60). The results for the reactions of C(60) with PhCHO and with i- PrCHO were compared with those in solution under UV irradiation. Incomplete but reasonable coincidence was found; in both modes, the addition of Ph•, PhCO• and Me• radicals to C(60) occurred, whereas some other products were formed in solution, and the explanation is given as to why this occurred. This conformity supports the hypothesis based on the results of kindred reactions with ketones and organomercurials: the results of EI-initiated homolytic reactions between fullerenes and other compounds in an ionization chamber can predict the reactivity of the fullerenes toward them in solution.

Perturbing Peptide Cation-Radical Electronic States by Thioxoamide Groups: Formation, Dissociations, and Energetics of Thioxopeptide Cation-Radicals

Thioxodipeptides Gly-thio-Lys (GtK), Ala-thio-Lys (AtK), and Ala-thio-Arg (AtR) in which the amide group has been modified to a thioxoamide were made into dications by electrospray ionization and converted to cation-radicals, (GtK + 2H)(+•), (AtK + 2H)(+•), and (AtR + 2H)(+•), by electron transfer dissociation (ETD) tandem mass spectrometry using fluoranthene anion-radical as an electron donor. The common and dominant dissociation of these cation-radicals was the loss of a hydrogen atom. The dissociation products were characterized by collision-induced dissociation (CID) multistage tandem mass spectrometry up to CID-MS(5). The ground electronic states of several (GtK + 2H)(+•), (AtK + 2H)(+•), and (AtR + 2H)(+•) conformers were explored by extensive ab initio and density functional theory calculations of the potential energy surface. In silico electron transfer to the precursor dications, (GtK + 2H)(2+), (AtK + 2H)(2+), and (AtR + 2H)(2+), formed zwitterionic intermediates containing thioenol anion-radical and ammonium cation groups that were local energy minima on the potential energy surface of the ground electronic state. The zwitterions underwent facile isomerization by N-terminal ammonium proton migration to the thioenol anion-radical group forming aminothioketyl intermediates. Combined potential energy mapping and RRKM calculations of dissociation rate constants identified N-C(α) bond cleavages as the most favorable dissociation pathways, in a stark contrast to the experimental results. This discrepancy is interpreted as being due to the population upon electron transfer of low-lying excited electronic states that promote loss of hydrogen atoms. For (GtK + 2H)(+•), these excited states were characterized by time-dependent density functional theory as A-C states that had large components of Rydberg-like 3s molecular orbitals at the N-terminal and lysine ammonium groups that are conducive to hydrogen atom loss.

Thermochemistry and Bond Dissociation Energies of Ketones

Ketones are a major class of organic chemicals and solvents, which contribute to hydrocarbon sources in the atmosphere, and are important intermediates in the oxidation and combustion of hydrocarbons and biofuels. Their stability, thermochemical properties, and chemical kinetics are important to understanding their reaction paths and their role as intermediates in combustion processes and in atmospheric chemistry. In this study, enthalpies (ΔH°(f 298)), entropies (S°(T)), heat capacities (C(p)°(T)), and internal rotor potentials are reported for 2-butanone, 3-pentanone, 2-pentanone, 3-methyl-2-butanone, and 2-methyl-3-pentanone, and their radicals corresponding to loss of hydrogen atoms. A detailed evaluation of the carbon-hydrogen bond dissociation energies (C-H BDEs) is also performed for the parent ketones for the first time. Standard enthalpies of formation and bond energies are calculated at the B3LYP/6-31G(d,p), B3LYP/6-311G(2d,2p), CBS-QB3, and G3MP2B3 levels of theory using isodesmic reactions to minimize calculation errors. Structures, moments of inertia, vibrational frequencies, and internal rotor potentials are calculated at the B3LYP/6-31G(d,p) density functional level and are used to determine the entropies and heat capacities. The recommended ideal gas-phase ΔH°(f 298), from the average of the CBS-QB3 and G3MP2B3 levels of theory, as well as the calculated values for entropy and heat capacity are shown to compare well with the available experimental data for the parent ketones. Bond energies for primary, secondary, and tertiary radicals are determined; here, we find the C-H BDEs on carbons in the α position to the ketone group decrease significantly with increasing substitution on these α carbons. Group additivity and hydrogen-bond increment values for these ketone radicals are also determined.

Reaction of HO with CO: Tunneling Is Indeed Important.

The potential energy surface and chemical kinetics for the reaction of HO with CO, which is an important process in both combustion and atmospheric chemistry, were computed using high-level ab initio quantum chemistry in conjunction with semiclassical transition state theory under the limiting cases of high and zero pressure. The reaction rate constants calculated from first principles agree extremely well with all available experimental data, which range in temperature over a domain that covers both combustion and terrestrial atmospheric chemistry. The role of quantum tunneling is confirmed to be extremely important, which supports recent work by Continetti and collaborators regarding the loss of hydrogen atoms from vibrationally excited states of HOCO. A sensitivity analysis has been carried out and serves as the basis for a plausible estimate of uncertainty in the calculations.

A Photoactive Antimicrobial Triphenylmethane Derivative

Owing to the ever growing interest for the human health against infectious bacteria, various substances that display antimicrobial activity have been developed. For instance, inorganic silver nanoparticles have been actively investigated as antibacterial agents although the mechanism for the activity is not clearly understood. Recently, photochemically triggerable organic antimicrobial substances have received significant attention since these materials can be formulated with fabrics to produce self-decontaminating clothes. In addition, the irradiation-induced antimicrobial activity is attractive because of the readily available light source (eg. Sun). Among various candidates, benzophenone derivatives have been most actively investigated as photoactive antimicrobial agents owing to the some salient features including facile synthesis and generation of reactive radicals via photosensitization. Thus, benzoquinone with diverse substituents have been prepared and applied to the antimicrobial screening. It has been well known that photoinduced oxidation of certain electron donating group-substituted triphenylmethane derivatives produces brilliantly colored ionic species. Owing to this property, triphenylmethane derivatives have been investigated as precursors of colorants. A mechanistic pathway to the photochemical genartion of an ionic iminium product from a triphenyl methane drivative, 4,4',4''-tris(dimethylaminophenyl) methane (TPM, 1) is presented in Scheme 1. The first step of this process involves excited state single electron transfer (SET) from the triphenylmethane donor to presumably molecular oxygen. The radical cation intermediate 2, produced in this fashion, subsequently undergoes hydrogen atom loss to yield the iminium ion 3. Since the iminium ion 3 is fully conjugated, formation of the ionic moiety can be readily monitored by visible absorption spectroscopy and most often with naked eyes. The generation of reactive ionic/radical species from the photochemical oxidation of TPM is very intriguing since these reactive species might be able to retard the growth of microbes or destroy them. If TPM displays the antimicrobial activity, a new class of photoactive antimicrobial agent can be developed. In order to test the feasibility of TPM as a photoactive antimicrobial agent, a thin (ca. 1 m) polystyrene (PS) film containing TPM was prepared by spin-coating of a chloroform solution containing PS (MW: 280,000, 5 wt%) and TPM (1.5 wt%, based on the weight of PS polymer powder) on a glass substrate. Irradiation of UV light (254 nm, 1 mW/cm) to the film resulted in the gradual increase of the absorption in the visible region, confirming the successful generation of iminium product 3 in the polymer film (Fig. 1). In addition, the colorless transparent TMPcontaining film became pale purple after UV irradiation. We next investigated antimicrobial properties of the TPM containing PS films against Staphylococcus aureus

A VUV Photoionization Study of the Combustion-Relevant Reaction of the Phenyl Radical (C6H5) with Propylene (C3H6) in a High Temperature Chemical Reactor

We studied the reaction of phenyl radicals (C(6)H(5)) with propylene (C(3)H(6)) exploiting a high temperature chemical reactor under combustion-like conditions (300 Torr, 1200-1500 K). The reaction products were probed in a supersonic beam by utilizing tunable vacuum ultraviolet (VUV) radiation from the Advanced Light Source and recording the photoionization efficiency (PIE) curves at mass-to-charge ratios of m/z = 118 (C(9)H(10)(+)) and m/z = 104 (C(8)H(8)(+)). Our results suggest that the methyl and atomic hydrogen losses are the two major reaction pathways with branching ratios of 86 ± 10% and 14 ± 10%. The isomer distributions were probed by fitting the recorded PIE curves with a linear combination of the PIE curves of the individual C(9)H(10) and C(8)H(8) isomers. Styrene (C(6)H(5)C(2)H(3)) was found to be the exclusive product contributing to m/z = 104 (C(8)H(8)(+)), whereas 3-phenylpropene, cis-1-phenylpropene, and 2-phenylpropene with branching ratios of 96 ± 4%, 3 ± 3%, and 1 ± 1% could account for the signal at m/z = 118 (C(9)H(10)(+)). Although searched for carefully, no evidence of the bicyclic indane molecule could be provided. The reaction mechanisms and branching ratios are explained in terms of electronic structure calculations nicely agreeing with a recent crossed molecular beam study on this system.

Variations on a theme – the evolution of hydrocarbon solids

Context. The compositional properties of hydrogenated amorphous carbons are known to evolve in response to the local conditions. Aims. To present a model for low-temperature, amorphous hydrocarbon solids, based on the microphysical properties of random and defected networks of carbon and hydrogen atoms, that can be used to study and predict the evolution of their properties in the interstellar medium. Methods. We adopt an adaptable and prescriptive approach to model these materials, which is based on a random covalent network (RCN) model, extended here to a full compositional derivation (the eRCN model), and a defective graphite (DG) model for the hydrogen poorer materials where the eRCN model is no longer valid. Results. We provide simple expressions that enable the determination of the structural, infrared and spectral properties of amorphous hydrocarbon grains as a function of the hydrogen atomic fraction, XH. Structural annealing, resulting from hydrogen atom loss, results in a transition from H-rich, aliphatic-rich to H-poor, aromatic-rich materials. Conclusions. The model predicts changes in the optical properties of hydrogenated amorphous carbon dust in response to the likely UV photon-driven and/or thermal annealing processes resulting, principally, from the radiation field in the environment. We show how this dust component will evolve, compositionally and structurally in the interstellar medium in response to the local conditions.