A combined ab initio and photoionization mass spectrometric study of polyynes in fuel-rich flames

Polyynic structures in fuel-rich low-pressure flames are observed using VUV photoionization molecular-beam mass spectrometry. High-level ab initio calculations of ionization energies for C2nH2 (n=1-5) and partially hydrogenated CnH4 (n=7-8) polyynes are compared with photoionization efficiency measurements in flames fuelled by allene, propyne, and cyclopentene. C2nH2 (n=1-5) intermediates are unambiguously identified, while HC[triple bond, length as m-dash]C-C[triple bond, length as m-dash]C-CH=C=CH2, HC[triple bond, length as m-dash]C-C[triple bond, length as m-dash]C-C[triple bond, length as m-dash]C-CH=CH2 (vinyltriacetylene) and HC[triple bond, length as m-dash]C-C[triple bond, length as m-dash]C-CH[double bond, length as m-dash]CH-C[triple bond, length as m-dash]CH are likely to contribute to the C7H4 and C8H4 signals. Mole fraction profiles as a function of distance from the burner are presented. C7H4 and C8H4 isomers are likely to be formed by reactions of C2H and C4H radicals but other plausible formation pathways are also discussed. Heats of formation and ionization energies of several combustion intermediates have been determined for the first time.     

Photodissociation of 1,3,5-triazine: an ab initio and RRKM study

The ab initio/Rice-Ramsperger-Kassel-Marcus (RRKM) approach has been applied to investigate the photodissociation mechanism of 1,3,5-triazine at different wavelengths of the absorbed photon. Reaction pathways leading to various decomposition products have been mapped out at the G3(MP2,CC)//B3LYP level, and then the RRKM and microcanonical variational transition state theories have been applied to compute rate constants for individual reaction steps. Relative product yields (branching ratios) for the dissociation products have been calculated using the steady-state approach. The results show that, after being excited by 275, 248, or 193 nm photons, the triazine molecule isomerizes to an opened-ring structure on the first singlet excited-state potential energy surface (PES), which is followed by relaxation into the ground electronic state via internal conversion. On the contrary, excitation by 285 and 295 nm photons cannot initiate the ring-opening reaction on the excited-state PES, and the molecule relaxes into the energized ring isomer in the ground electronic state. The dissociation reaction starting from the ring isomer is calculated to have branching ratios of various reaction channels significantly different from those for the reaction initiating from the opened-ring structure. The existence of two distinct mechanisms of 1,3,5-triazine photodissociation can explain the inconsistency in the translational energy distributions of HCN moieties at different wavelengths observed experimentally.     

Photodissociation of azulene at 193 nm: ab initio and RRKM study

The ab initio/Rice-Ramsperger-Kassel-Marcus (RRKM) approach has been applied to investigate the photodissociation mechanism of azulene at 6.4 eV (the laser wavelength of 193 nm) upon absorption of one UV photon followed by internal conversion into the ground electronic state. Reaction pathways leading to various decomposition products have been mapped out at the G3(MP2,CC)//B3LYP level and then the RRKM and microcanonical variational transition state theories have been applied to compute rate constants for individual reaction steps. Relative product yields (branching ratios) for the dissociation products have been calculated using the steady-state approach. The results show that photoexcited azulene can readily isomerize to naphthalene and the major dissociation channel is elimination of an H-atom from naphthalene. The branching ratio of this channel decreases with an increase of the photon energy. Acetylene elimination is the second probable reaction channel and its branching ratio rises as the photon energy increases. The main C8H6 fragments at 193 nm are phenylacetylene and pentalene and the yield of the latter grows fast with the increasing excitation energy.     

Photodissociation of acetic acid in the gas phase: an ab initio study

Photodissociation of acetic acid in the gas phase was investigated using ab initio molecular orbital methods. The stationary structures on the ground-state potential energy surfaces were mainly optimized at the MP2 level of theory, while those on the excited-state surfaces were determined by complete active space SCF calculations with a correlation-consistent basis set of cc-pVDZ. The reaction pathways leading to different photoproducts are characterized on the basis of the computed potential energy surfaces and surface crossing points. The calculations reproduce the experimental results well and provide additional insight into the mechanism of the ultraviolet photodissociation of acetic acid and related compounds.     

Mass spectrometric fragmentation of the tautomers of 1,3-diketones. A gas chromatographic/mass spectrometric study

The diketo and ketoenol tautomers of aliphatic 1,3-diketones can be easily separated by gas chromatography. The mass spectra of tautomers of pentane-2,4-diones substituted at C(l) and C(3), separated in this way, have been obtained. The fragmentation mechanisms are discussed. The mass spectra of the tautomers are quite different, and the main fragmentation pathways can be easily linked to the structures of the (non-interconverting!) tautomeric molecular ions. Furthermore, isomers differing by the position of the substituent can also be identified by their mass spectra.     

Equilibrium intermetallic particles in the gas phase — A Knudsen cell mass spectrometric study

Using the Knudsen cell effusion technique it is possible to generate a molecular beam containing intermetallic molecules. Mass spectrometric studies were carried out with the systems: cesium/antimony, cesium/antimony/bismuth, cesium/antimony/indium, cesium/antimony/tin and cesium/antimony/bismuth/tin. In all these systems intermetallic particles with extraordinary stoichiometries could be detected. A brief discussion of the appearance energies and the bonding principle of these molecules or clusters are given.     

A gas phase ab initio excited state geometry optimization study of thymine, cytosine and uracil

Molecular geometries of the nucleic acid bases thymine, cytosine and uracil in the ground and the lowest two singlet excited states were optimized using the ab initio approach employing the 4-31G basis set for all the atoms except the amino group of cytosine for which the 6-311+G^* basis set was used. The excited state calculations were performed employing configuration interaction involving singly excited configurations (CIS). Vibrational frequencies were computed in order to examine the nature of the stationary points on the potential energy surfaces obtained by geometry optimization. While the ground state geometries of uracil and thymine (except the methyl group hydrogens) are planar, the corresponding excited state geometries were found to be significantly nonplanar. In the case of cytosine, the amino group is pyramidal and the rest of the molecule is only slightly nonplanar in the ground state, but the excited state geometries are appreciably nonplanar. In particular, consequent to the S₂(n–π^*) excitation of cytosine, the amino group plane is strongly rotated. While thymine is stable in the S₂(π–π^*) excited state, uracil appears to be dissociative in the corresponding excited state.     

Confirmation of the "long-lived" tetra-nitrogen (N4) molecule using neutralization-reionization mass spectrometry and ab initio calculations

Tetra-nitrogen (N(4)), which has been the subject of recent controversy [Cacace, d. Petris, and Troiani, Science 295, 480 (2002); Cacace, Chem. Eur. J. 8, 3839 (2002); Nguyen et al., J. Phys. Chem. A 107, 5452 (2003); Nguyen, Coord. Chem. Rev. 244, 93 (2003)] as well as of great theoretical interest, has been prepared from the N(4) (+) cation and then detected as a reionized gaseous metastable molecule with a lifetime exceeding 0.8 micros in experiments based on neutralization-reionization mass spectrometry. Moreover, we have used the nature of the charge-transfer reaction which occurs between a beam of fast N(4) (+) ions (8 keV translational energy) and various stationary gas targets to identify the vertical neutralization energy of the N(4) (+) ion. The measured value, 10.3+/-0.5, most closely matches that of the lowest energy azidonitrene (4)N(4) (+)C(s)((4)A(')) ion, resulting in the formation of the neutral bound azidonitrene (3)N(4)C(s)((3)A(")). Neutralization of the global minimum (2)N(4) (+)D( infinity h)((2)Sigma(u) (+)) ion leads to a structure 166 kJ mol(-1) above the dissociation products [N(2)((1)Sigma(g) (+))+N(2)((1)Sigma(g) (+))]; moreover, it was not possible to find a minimum on the (1)N(4) neutral potential energy surface for a covalently bonded structure. Ab initio calculations at the G3, QCISD/6-31G(d), and MP2/AUG-cc-pVTZ levels of theory have been used to determine geometries and both vertical neutralization energies of ions (doublet and quartet) and ionization energies of neutrals (singlet and triplet). In addition, we have also described in detail the EI ion source for the Ottawa VG ZAB mass spectrometer [Holmes and Mayer, J. Phys. Chem. A 99, 1366 (1995)] which was modified for high-pressure use, i.e., for the production of dimer and higher number cluster ions.     

Nitramine anion fragmentation: A mass spectrometric and Ab initio study

The fragment ion formation characteristics of the radical anions generated from hexahydro-1,3,5-trinitrotriazine (RDX) and its three nitroso metabolites were studied using GC/MS with negative chemical ionization (NCI) to understand the fragmentation mechanisms responsible for the formation of the most abundant ions observed in their NCI mass spectra. Ab initio and density functional theory calculations were used to calculate relative free energies for different fragment ion structures suggested by the m/z values of the most abundant ions observed in the NCI mass spectra. The NCI mass spectra of the four nitramines are dominated by ions formed by the cleavage of nitrogen-nitrogen and carbon-nitrogen bonds in the atrazine ring. The most abundant anions in the NCI mass spectra of these nitramines have the general formulas C(2)H(4)N(3)O (m/z 86) and C(2)H(4)N(3)O(2) (m/z 102). The analyses of isotope-labeled standards indicate that these two ions are formed by neutral losses that include two exocylic nitrogens and one atrazine ring nitrogen. Our calculations and observations of the nitramine mass spectra suggest that the m/z 86 and m/z 102 ions are formed from either the (M--NO)(-) or (M--NO(2))(-) fragment anions by a single fragmentation reaction producing neutral losses of CH(2)N(2)O or CH(2)N(2)O(2) rather than a set of sequential reactions involving neutral losses of HNO(2) or HNO and HCN.     

On the stability of the hydrogen chloride complexes with ethylene and acetylene. A high resolution gas phase and ab initio study

The temperature dependencies of the intensities of the HCl stretching bands of the hydrogen chloride complexes with acetylene and ethylene have been used to obtain estimates of the dissociation enthalpies of the two complexes. Quantum chemical calculations on the Hartree Fock and DFT/B3LYP levels of theory have been combined with experimental data to give estimates of the intensities of the HCl stretching vibration in the two complexes.     

Electron attachment in ice-HCl clusters: an ab initio study

Experimental work has shown that small amounts of HCl strongly enhance electron capture in ice films. The purpose of the present study was to investigate the effect of adsorbed HCl on the interaction of electrons with small clusters of water. Studies were made with clusters of 6 and 12 water molecules with various geometries both with and without one HCl attached. A number of distinct HCl coordination motifs were examined. All of the neutral structures with HCl exhibited zero thresholds for electron attachment and formed dipole bound anionic states (DBS). The relaxation processes for these "initial DBS" depended on the number of H(2)O (n) and on the number and type of H-bonds to the HCl (x). The initial DBS of systems with only O-H...Cl H-binding underwent dissociative electron attachment (DEA), forming H atoms. Relaxation for systems with ClH...OH(2) bonds was more complex. For the two layer n = 12 systems with x = 2 or 3 the HCl proton moved to the nearest oxygen to form H(3)O(+). Then rearrangement of the proton network occurred, and the Cl(-) became solvated by three HO-H...Cl(-) bonds. The presence of Cl(-) and H(3)O(+) increases the dipole moment and the electron binding energy (EBE) of the network. Further stabilization is achieved by decay into deeper DBS electron traps and/or by reaction of the excess electron with H(3)O(+) to form H(*) atoms. The HCl(H(2)O)(6) clusters with a single Cl-H...OH(2) bond behaved differently. They increased their stability by becoming more linear. This raised the dipole moment and the EBE therefore increased, reducing the total energy. None of these species showed any signs of increasing the number of H-bonds to Cl. The implication of these observations for the interpretation of the results of the experiments with 0.2 monolayer of HCl on 5 monolayer of H(2)O at 20 K, and on the possible role of cosmic ray-induced ionization in polar stratospheric clouds in ozone depletion is discussed.     

The reaction of tricarbon with acetylene: an ab initio/RRKM study of the potential energy surface and product branching ratios

Ab initio calculations of the potential energy surface for the C3(1Sigmag+)+C2H2(1Sigmag+) reaction have been performed at the RCCSD(T)/cc-pVQZ//B3LYP/6-311G(d,p) + ZPE[B3LYP/6-311G(d,p)] level with extrapolation to the complete basis set limit for key intermediates and products. These calculations have been followed by statistical calculations of reaction rate constants and product branching ratios. The results show the reaction to begin with the formation of the 3-(didehydrovinylidene)cyclopropene intermediate i1 or five-member ring isomer i7 with the entrance barriers of 7.6 and 13.8 kcal/mol, respectively. i1 rearranges to the other C5H2 isomers, including ethynylpropadienylidene i2, singlet pentadiynylidene i3, pentatetraenylidene i4, ethynylcyclopropenylidene i5, and four- and five-member ring structures i6, i7, and i8 by ring-closure and ring-opening processes and hydrogen migrations. i2, i3, and i4 lose a hydrogen atom to produce the most stable linear isomer of C5H with the overall reaction endothermicity of approximately 24 kcal/mol. H elimination from i5 leads to the formation of the cyclic C5H isomer, HC2C3, +H, 27 kcal/ mol above C3+C2H2. 1,1-H2 loss from i4 results in the linear pentacarbon C5+H2 products endothermic by 4 kcal/mol. The H elimination pathways occur without exit barriers, whereas the H2 loss from i4 proceeds via a tight transition state 26.4 kcal/mol above the reactants. The characteristic energy threshold for the reaction under single collision conditions is predicted be in the range of approximately 24 kcal/mol. Product branching ratios obtained by solving kinetic equations with individual rate constants calculated using RRKM and VTST theories for collision energies between 25 and 35 kcal/mol show that l-C5H+H are the dominant reaction products, whereas HC2C3+H and l-C5+H2 are minor products with branching ratios not exceeding 2.5% and 0.7%, respectively. The ethynylcyclopropenylidene isomer i5 is calculated to be the most stable C5H2 species, more favorable than triplet pentadiynylidene i3t by approximately 2 kcal/mol.     

The diphosphate monoanion in the gas phase: a joint mass spectrometric and theoretical study

H(3)P(2)O(7) (-) ions were obtained in an electrospray ion source of a Fourier transform ion cyclotron resonance (ESI/FTICR) mass spectrometer from a CH(3)CN/H(2)O (1:1) pyrophosphoric acid solution and in the ionic source of a triple quadrupole (TQ) mass spectrometer from the chemical ionisation (CI) of pyrophosphoric acid introduced by a thermostatically controlled direct insertion probe. The ions were structurally characterised by mass spectrometric techniques and theoretical calculations. Consistent with collisionally activated dissociation (CAD) mass spectrometric results, theoretical calculations identified the linear diphosphate anion (I) as the most stable isomer on the H(3)P(2)O(7) (-) potential energy surface. The joint application of mass spectrometric techniques and theoretical methods provided information on the dissociative processes of diphosphate anions in the gas phase. Finally, this study provides an insight into the structures and stabilities of the [H(3)PO(4).PO(3)](-), [HP(2)O(6).H(2)O](-) and [H(2)PO(4).HPO(3)](-) clusters and allows the stability and structure of the dimetaphosphate anion, HP(2)O(6) (-), to be investigated at the B3LYP6-31+G* and CCSD(T) levels of theory.     

Electrospray ionization ion trap multiple-stage mass spectrometric fragmentation pathways of leucine and isoleucine: an ab initio computational study

We recently demonstrated the possibility to distinguish between leucine and isoleucine in several tryptic peptides by means of consecutive tandem mass steps (Armirotti et al. J. Am. Soc. Mass Spectrom. 2007; 18: 57), exploiting a gas-phase rearrangement of the immonium ion of Ile. In the present paper we explore the tandem mass spectrometric behaviour of the two amino acids. We propose a plausible structure for the diagnostic m/z 69 ion of Ile, that was reported for the first time in 1996 (Hulst and Kientz J. Mass. Spectrom. 1996; 31: 1188), and we explain why its formation is favoured with respect to Leu. Our conclusions are supported by ab initio quantum chemistry calcultations and isotope-labelled standards experiments.     

Bile salt aggregates in the gas phase: an electrospray ionization mass spectrometric study

Helical and ordered structures have previously been identified by X-ray diffraction analysis in crystals and fibers of bile salts, and proposed as models of the micellar aggregates formed by trimeric or dimeric units of dihydroxy and trihydroxy salts, respectively. These models were supported by the results of studies of micellar bile salt solutions performed with different experimental techniques. The study has now been extended to the gas phase by utilizing electrospray ionization mass spectrometry (ESIMS) to investigate the formation and the composition of aggregates stabilized by noncovalent interactions, including polar (ion-ion, ion-dipole, dipole-dipole, hydrogen bonding etc.) and apolar (van der Waals and repulsive) interactions. The positive and negative ESIMS spectra of sodium glycodeoxycholate (NaGDC), taurodeoxycholate (NaTDC), glycocholate (NaGC), and taurocholate (NaTC) aqueous solutions, recorded under different experimental conditions, show in the first place that aggregates analogous to those present in micellar solutions do also exist in the gas phase. Furthermore, consistently with the condensed-phase model, the positive-ion spectra show that the trimers are the most stable oligomers among the aggregates of dihydroxy salts (NaGDC and NaTDC) whilst the dimers are the most stable among the aggregates of trihydroxy salts (NaGC and NaTC). Moreover, the binding energy of the constituent glycocholate salt units in most gaseous oligomers exceeds that of the corresponding taurocholate units. The ESIMS evidence has been confirmed by vapor-pressure measurements performed on NaGC and NaTC crystals and NaGDC and NaTDC fibers, the results of which show that the evaporation enthalpy of glycocholate exceeds that of taurocholate by some 50 kJ mol(-1).     

Equilibrium structure of the carbon dioxide-water complex in the gas phase: an ab initio and density functional study

High-level ab initio (MP2/6-311++G(2d,2p) geometry, Gaussian-2, MP4(SDTQ) and QCISD(T) binding energies) and density-functional (Becke3LYP/6-311++G(2df,2pd)) calculations have been performed on the charge-transfer complex between water and carbon dioxide. The complex appears to have two equivalent non-planar minima of C_s symmetry. Minima are separated by transition states with C₁ symmetry, whereas the totally planar structure with C_2v symmetry is a second-order transition state. All the critical points lie at approximately the same energy (less than 0.05 Kj mol⁻¹ difference). Therefore, the experimentally observable structure should be planar. The best equilibrium intermolecular distance for this complex calculated at the MP2/6-311++G(2d,2p) level is 2.800 Å. Our best estimate of the observable intermolecular distance (corrected for anharmonicity) is 2.84 Å, in agreement with the experimentally derived value of 2.836 Å. Our best estimate of the binding energy at the QCISD(T) level, taking into account the variation of the distance owing to anharmonicity and the use of more sophisticated theoretical treatments, is −12.0 ± 0.2 kJ mol⁻¹. Our best estimate of the barrier to internal rotation, also at the MP2/6-311++G(2d,2p) level, is 4.0 kJ mol⁻¹, outside the error limits of the experimental determination (3.64 ± 0.04 kJ mol⁻¹). Density functional theory at the level employed here gives an equilibrium intermolecular distance that is too large (2.857 Å), a binding energy that is too small (8.1 kJ mol⁻¹), attributable neither to geometry nor to the basis set, and also a barrier to internal rotation that is slightly too small (3.39 kJ mol⁻¹). The overall picture is, however, reasonably good.     

A mass spectrometric and ab initio study of the pathways for dehydration of simple glycine and cysteine-containing peptide [M+H]+ ions

The gas phase fragmentation reactions of the [M+H]⁺ and [M+H?H²O]⁺ ions of glycylglycine, glycylcysteine, N-acetylglycine, N-acetylcysteine, their corresponding methyl esters, as well as several other related model systems have been examined by electrospray ionization (ESI) tandem mass spectrometry (MS ⁿ ) using triple quadrupole and quadrupole ion trap mass spectrometers. Two discrete gas phase fragmentation pathways for the loss of water from glycine-containing peptides, corresponding to retro-Koch and retro-Ritter type reactions were observed. Two pathways were also observed for the loss of water from C-terminal cysteine-containing peptides: a retro-Koch type reaction and an intramolecular nucleophilic attack at the carbonyl of the amide bond by the cysteinyl side chain thiol. Various intermediates involved in these reactions, derived from the [M+H?H²O]⁺ ions of N-formylglycine and N-formylcysteine, were modeled using ab initio calculations at the MP2(FC)/6-31G*//HF/6-31G* level of theory. These calculations indicate that: (i) the retro-Koch reaction product is predicted to be more stable than the product from the retro-Ritter reaction for N-formylglycine, and (ii) the intramolecular nucleophilic attack product is preferred over the retro-Koch and retro-Ritter reaction products for N-formylcysteine. The results from these ab initio calculations are in good agreement with the experimentally determined ion abundances for these processes.     

The structure of trimethoxymethane in the gas phase,an electron diffraction,ab initio and molecular mechanics study

The structure of trimethoxymethane in the gas phase was studied by electron diffraction, ab initio molecular orbital calculations and molecular mechanics. The molecule was found to exist almost exclusively as an asymmetric all-staggered TGG conformer. The electron diffraction structural parameters (r_g distances, r_α angles) as obtained from geometrically consistent r_α-refinements are: r(C-O) central 1.382(6) Å, r(C-O) terminal 1.418(6) Å, r(C-H) 1.112(1) Å, ∠(O-C-O) in the gauche—gauche chain 115.0(1.0)°, in the gauche-anti chains 109.2(0.6)° ∠(C-O-C) 114.3(0.6)°, ∠(O-C-H)_Me 109.9(0.3)°, methyl torsion 68(6)°. The structure is adequately reproduced by molecular mechanics calculations applying Allinger's force field. The structures of methoxymethanes can be explained in terms of the anomeric effect. This is confirmed by ab initio calculations.     

Ab initio and RRKM study of photodissociation of azulene cation

The ab initio/Rice-Ramsperger-Kassel-Marcus (RRKM) approach has been applied to investigate the photodissociation mechanism of the azulene cation at different values of the photon energy. Reaction pathways leading to various decomposition products have been mapped out at the G3(MP2,CC)//B3LYP level and then the RRKM and microcanonical variational transition state theories have been applied to compute rate constants for individual reaction steps. Relative product yields (branching ratios) for the dissociation products have been calculated using the steady-state approach. The results show that a photoexcited azulene cation can readily isomerize to a naphthalene cation. The major dissociation channels are elimination of atomic hydrogen, an H2 molecule, and acetylene. The branching ratio of the H elimination channel decreases with an increase of the photon energy. The branching ratio of the acetylene elimination as well as that of the H2 elimination rise as the photon energy increases. The main C8H6+ fragment at all photon energies considered is a pentalene cation, and its yield decreases slightly with increasing excitation energy, whereas the branching ratios of the other C8H6+ fragments, phenylacetylene and benzocyclobutadiene cations, grow.     

Simple <Emphasis Type="Italic">b</Emphasis> ions have cyclic oxazolone structures. A neutralization-reionization mass spectrometric and computational study of oxazolone radicals

The 2-methyloxazol-5-on-2-yl radical (3) and its deuterium labeled analogs were generated in the gas-phase by femtosecond electron-transfer and studied by neutralization-reionization mass spectrometry and quantum chemical calculations. Radical 3 undergoes fast dissociation by ring opening and elimination of CO and CH(3)CO. Loss of hydrogen is less abundant and involves hydrogen atoms from both the ring and side-chain positions. The experimental results are corroborated by the analysis of the potential energy surface of the ground electronic state in 3 using density functional, perturbational, and coupled-cluster theories up to CCSD(T) and extrapolated to the 6-311 ++ G(3df,2p) basis set. RRKM calculations of radical dissociations gave branching ratios for loss of CO and H that were k(CO)/k(H) > 10 over an 80-300 kJ mol(-1) range of internal energies. The driving force for the dissociations of 3 is provided by large Franck-Condon effects on vertical neutralization and possibly from involvement of excited electronic states. Calculations also provided the adiabatic ionization energy of 3, IE(adiab) = 5.48 eV and vertical recombination energy of cation 3(+), RE(vert) = 4.70 eV. The present results strongly indicate that oxazolone structures can explain fragmentations of b-type peptide ions upon electron capture, contrary to previous speculations.