Fragmentation mechanisms of protonated benzylamines. Electrospray ionisation-tandem mass spectrometry study and ab initio molecular orbital calculations

Our research into neurotransmitters in a biological fluid presented an opportunity to investigate the fragmentations under low collision energy characterising benzyl-amines protonated under electrospray ionisation (ESI) conditions in a triple quadrupole mass spectrometer. In this work we present the breakdown graphs of protonated 3,4-dihydroxybenzylamine, DHBAH(+), and 3-methoxy, 4-hydroxybenzylamine, HMBAH(+), at various source temperatures and various pressures in the collision cell, the collision energy varying from 0 to 46 eV in the laboratory frame. Both parent ions eliminate first NH(3) at very low collision energy. The fragmentations of [MH - NH(3)](+) occur at high collision energy and are quite different for DHBAH(+) and HMBAH(+): formation of [MH - NH(3) - H(2)O - CO](+) for the former; formation of the radical cation [MH - NH(3) - CH(3)](+.) for the latter. These fragmentations are interpreted by means of ab initio calculations up to the B3LYP/6-311+G(2d,2p) level of theory. The successive losses of H(2)O and CO involve first the rearrangement in two steps of benzylic ions formed by loss of NH(3) into tropylium ions. The transition states associated with this rearrangement are very high in energy (about 400 kJ mol(-1) above MH(+)) explaining (i). the absence of an ion corresponding to [DHBAH - NH(3) - H(2)O](+). The determining steps associated with the losses of H(2)O and with H(2)O + CO are located lower in energy than the transition states associated with the isomerisation of benzylic ions into tropylium ions; explaining (ii). the formation of the radical cation [MH - NH(3) - CH(3)](+.). The homolytic cleavage of CH(3)-O requires less energy than does the rearrangement.     

Positive ion chemistry of SiH4/GeF4 gaseous mixtures studied by ion trap mass spectrometry and ab initio calculations

The positive ion chemistry occurring in SiH(4)/GeF(4) gaseous mixtures was investigated by ion trap mass spectrometry and ab initio theoretical calculations. The GeF(3)(+) cation, the only fragment obtained from ionized GeF(4), was unreactive towards SiH(4). All the primary ions SiH(n)(+) (n = 0-3) react instead with GeF(4) so to form SiF(+) or SiH(2)F(+). The latter species reacts in turn with SiH(4) and GeF(4) so to form SiH(3)(+) and SiHF(2)(+), respectively. The potential energy profiles conceivably involved in these reactions were investigated by ab initio calculations performed at the MP2 and coupled cluster (CCSD(T)) level of theory.     

AB initio calculations and matrix ftir studies of the sulfur trioxide radical anion

The structures and vibrational frequencies of SO⁻₃ (C_3v) and SO⁻₂ (C_2v) have been calculated at the UHF SCF/3-21 + G¹ level. By cocondensation of Cs atoms and SO₃ in an Ar matrix the FTIR spectrum of Cs₄SO₃ has been measured. The molecule is proposed to have C_s symmetry with SO₃ binding to Cs in a bidentate fashion.     

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.     

Structure and dissociation characteristics of metal chloride anion clusters containing redox-active metal ions studied by laser desorption and electrospray ionization mass spectrometry and ab initio calculations

Copper chloride anion clusters with both copper oxidation states can be made by laser desorption of CuCl(2) crystals. We have used this method to study the dissociation characteristics of such cluster ions. The stability and the structure of the observed complexes were probed by ab initio calculations. These calculations show that many of these complexes are bridged structures. Thus, for the Cu(2)Cl(4) dimer anion, formally [ClCu-Cl-CuCl(2)](-) , with putative mixed copper oxidation states, the two copper ions become equivalent through bridging. Such bridging does not occur when redox inactive metal ions are present as in [ClCu-Cl-CaCl(2)](-) . By observing the dissociation characteristics of a variety of metal chloride cluster anions produced from binary mixtures, the following Cl(-) affinity order is obtained: FeCl(3) > CuCl > CaCl(2) > FeCl(2) > AgCl ≈ CuCl(2) ≈ ZnCl(2) > LiCl. Ab initio calculations on the Cl(-) affinity of selected chlorides confirm this order as do Cl(-) affinity estimates from the experimentally known vertical electron detachment energies of the superhalogens CaCl(3)(-) and LiCl(2)(-) . An equimolar mixture of CuCl(2) and FeCl(3) produces an intense cluster ion, which, from (65)Cu labeling experiments, is best described as FeCl(4)(-)···Cu(+)···(-)Cl(4) Fe, a Cu(+) bound superhalogen FeCl(4)(-) dimer. The Cu(+) ion can be replaced by the redox inactive alkali cations and by Ag(+) but these metal ion bound FeCl(4)(-) dimers show an entirely different fragmentation behavior which is attributed to the absence of bridging. Electrospray ionization (ESI) of CuCl(2) produces an extended series of (CuCl(2))(n) Cl(-) anions (n = 1-11) and so in ESI very limited reduction of Cu(2+) takes place. The (CuCl(2))(n) Cl(-) anions show an abundant dissociation via loss of neutral Cu(2)Cl(4) which according to our ab initio calculations is 9 kcal/mol more stable than two CuCl(2).     

Infrared spectra and ab initio calculations for the F- -(CH4)n (n = 1-8) anion clusters

Infrared spectra of mass-selected F- -(CH4)n (n = 1-8) clusters are recorded in the CH stretching region (2500-3100 cm-1). Spectra for the n = 1-3 clusters are interpreted with the aid of ab initio calculations at the MP2/6-311++G(2df 2p) level, which suggest that the CH4 ligands bind to F- by equivalent, linear hydrogen bonds. Anharmonic frequencies for CH4 and F--CH4 are determined using the vibrational self-consistent field method with second-order perturbation theory correction. The n = 1 complex is predicted to have a C3v structure with a single CH group hydrogen bonded to F-. Its spectrum exhibits a parallel band associated with a stretching vibration of the hydrogen-bonded CH group that is red-shifted by 380 cm-1 from the nu1 band of free CH4 and a perpendicular band associated with the asymmetric stretching motion of the nonbonded CH groups, slightly red-shifted from the nu3 band of free CH4. As n increases, additional vibrational bands appear as a result of Fermi resonances between the hydrogen-bonded CH stretching vibrational mode and the 2nu4 overtone and nu2+nu4 combination levels of the methane solvent molecules. For clusters with n < or = 8, it appears that the CH4 molecules are accommodated in the first solvation shell, each being attached to the F- anion by equivalent hydrogen bonds.     

Pyrrolidinium-based ionic liquids. 1-Butyl-1-methyl pyrrolidinium dicyanoamide: thermochemical measurement, mass spectrometry, and ab initio calculations

The standard molar enthalpy of formation of the ionic liquid 1-butyl-1-methylpyrrolidinium dicyanamide has been determined at 298 K by means of combustion calorimetry, while the enthalpy of vaporization and the mass spectrum of the vapor (ion pairs) have been determined by temperature-programmed desorption and line of sight mass spectrometry. Ab initio calculations for 1-butyl-1-methylpyrrolidinium dicyanamide have been performed using the G3MP2 and CBS-QB3 theory, and the results from homodesmic reactions are in excellent agreement with the experiments.     

Infrared spectra and ab initio calculations for the Cl--(CH4)n (n = 1-10) anion clusters

In an effort to elucidate their structures, mass-selected Cl--(CH4)n (n = 1-10) clusters are probed using infrared spectroscopy in the CH stretch region (2800-3100 cm(-1)). Accompanying ab initio calculations at the MP2/6-311++G(2df,2p) level for the n = 1-3 clusters suggest that methane molecules prefer to attach to the chloride anion by single linear H-bonds and sit adjacent to one another. These conclusions are supported by the agreement between experimental and calculated vibrational band frequencies and intensities. Infrared spectra in the CH stretch region for Cl--(CH4)n clusters containing up to ten CH4 ligands are remarkably simple, each being dominated by a single narrow peak associated with stretching motion of hydrogen-bonded CH groups. The observations are consistent with cluster structures in which at least ten equivalent methane molecules can be accommodated in the first solvation shell about a chloride anion.     

Microscopic solvation of NaBO2 in water: anion photoelectron spectroscopy and ab initio calculations

We investigated the microscopic solvation of NaBO(2) in water by conducting photoelectron spectroscopy and ab initio studies on NaBO(2)(-)(H(2)O)(n) (n = 0-4) clusters. The vertical detachment energy (VDE) of NaBO(2)(-) is estimated to be 1.00 ± 0.08 eV. The photoelectron spectra of NaBO(2)(-)(H(2)O)(1) and NaBO(2)(-)(H(2)O)(2) are similar to that of bare NaBO(2)(-), except that their VDEs shift to higher electron binding energies (EBE). For the spectra of NaBO(2)(-)(H(2)O)(3) and NaBO(2)(-)(H(2)O)(4), a low EBE feature appears dramatically in addition to the features observed in the spectra of NaBO(2)(-)(H(2)O)(0-2). Our study shows that the water molecules mainly interact with the BO(2)(-) unit in NaBO(2)(-)(H(2)O)(1) and NaBO(2)(-)(H(2)O)(2) clusters to form Na-BO(2)(-)(H(2)O)(n) type structures, while in NaBO(2)(-)(H(2)O)(3) and NaBO(2)(-)(H(2)O)(4) clusters, the water molecules can interact strongly with the Na atom, therefore, the Na-BO(2)(-)(H(2)O)(n) and Na(H(2)O)(n)···BO(2)(-) types of structures coexist. That can be seen as an initial step of the transition from a contact ion pair (CIP) structure to a solvent-separated ion pair (SSIP) structure for the dissolution of NaBO(2).     

ESR study and ab initio calculations of some methylbenzoates derivatives.

The preferred twisted conformation in orthomethylbenzoic acids is analyzed by means of an ab initio calculation. However, the esr data indicate a planar structure in the orthomethylbenzoates. The increase of the conjugation in the ester radical anions is also analyzed by OS-SCF ab initio calculations using an STO 3G basis set.     

Systematic ab initio calculations on the energetics and stability of covalent O4

Ab initio calculations with highly correlated methods together with extensive basis sets have been used to obtain the most accurate heat of formation and stability with respect to dissociation (into molecular oxygen) for the chemically bound tetraoxygen molecule. Our calculations show that the heat of formation is significantly smaller and that the barrier to dissociation is larger than previously assumed. In particular, we have shown that the previous theoretical estimate for the heat of formation of tetraoxygen was in error by a significant amount (18%-24%) owing to lack of accuracy in the theoretical method then used. Our best estimates places that value in the range 93-95 kcal/mol and this should be taken into consideration when discussing the possible relevance of tetraoxygen in a variety of experiments, as well as in the fundamental atmospheric chemical processes where oxygen species participate.     

Chemical bonding in Si5(2-) and NaSi5(-) via photoelectron spectroscopy and ab initio calculations

Photoelectron spectroscopy and ab initio calculations are used to investigate the electronic structure and chemical bonding of Si5(-) and Si5(2-) in NaSi5(-). Photoelectron spectra of Si5(-) and NaSi5(-) are obtained at several photon energies and are compared with theoretical calculations at four different levels of theory, TD-B3LYP, R(U)OVGF, UCCSD(T), and EOM-CCSD(T), all with 6-311+G(2df) basis sets. Excellent agreement is observed between experiment and theory, confirming the obtained ground-state structures for Si5(-) and Si5(2-), which are both found to be trigonal bipyramid with D3h symmetry at several levels of theory. Chemical bonding in Si5, Si5(-), and Si5(2-) is analyzed using NPA, molecular orbitals, ELF, and NICS indices. The bonding in Si5(2-) is compared with that in the isoelectronic and isostructural B5H5(2-) species, but they are found to differ due to the involvement of electron densities, which are supposed to be lone pairs in the skeletal bonding in Si5(2-).     

Excited states and photochemistry of saturated molecules. ab initio calculations on methane

STO 4G calculations are carried out on methane in both tetrahedral and Jahn—Teller distorted C_2v and C_3v symmetries. Large increases in CH bond lengths are predicted in all states, and the ^IB₁ state in C_2v symmetry is predicted to dissociate to ^IB₁ methylene and ¹A₁ H₂ width no energy barrier. THe results are compared with earlier INDO calculations, and the latter are found to qualitatively consistent with the ab initio results.     

Quantum chemical mass spectrometry: ab initio prediction of electron ionization mass spectra and identification of new fragmentation pathways

The electron ionization mass spectra of four organic compounds are predicted based on the results of quantum chemical calculations at the DFT/B3LYP/6‐311 + G* level of theory. This prediction is performed ‘ab initio’, i.e. without any prior knowledge of the thermodynamics or kinetics of the reactions under consideration. Using a set of rules determining which routes will be followed, the fragmentation of the molecules' bonds and the complete resulting fragmentation pathways are studied. The most likely fragmentation pathways are identified based on calculated reaction energies ΔE when bond cleavage is considered and on activation energies ΔE^? when rearrangements are taken into account; the final intensities of the peaks in the spectrum are estimated from these values. The main features observed in the experimental mass spectra are correctly predicted, as well as a number of minor peaks. In addition, the results of the calculations allow us to propose fragmentation pathways new to empirical mass spectrometry, which have been experimentally verified using tandem mass spectrometry measurements. Copyright © 2016 John Wiley & Sons, Ltd.     

Investigation of possible structures of silicon nanotubes via density-functional tight-binding molecular dynamics simulations and ab initio calculations

We show, computationally, that single-walled silicon nanotubes (SiNTs) can adopt a number of distorted tubular structures, representing respective local energy minima, depending on the theory used and the initial models adopted. In particular, "gearlike" structures containing alternating sp(3)-like and sp(2)-like silicon local configurations have been found to be the dominant structural form for SiNTs via density-functional tight-binding molecular dynamics simulations (followed by geometrical optimization using Hartree-Fock or density function theory) at moderate temperatures (below 100 K). The gearlike structures of SiNTs deviate considerably from, and are energetically more stable than, the smooth-walled tubes (the silicon analogues of single-walled carbon nanotubes). They are, however, energetically less favorable than the "string-bean-like" SiNT structures previously derived from semiempirical molecular orbital calculations. The energetics and the structures of gearlike SiNTs are shown to depend primarily on the diameter of the tube, irrespective of the type (zigzag, armchair, or chiral). In contrast, the energy gap is very sensitive to both the diameter and the type of the nanotube.     

Accurate ab initio structure, dissociation energy, and vibrational spectroscopy of the F(-)-CH4 anion complex

Accurate equilibrium structure, dissociation energy, global potential energy surface (PES), dipole moment surface (DMS), and the infrared vibrational spectrum in the 0-3000 cm(-1) range of the F(-)-CH4 anion complex have been obtained. The equilibrium electronic structure calculations employed second-order M?ller-Plesset perturbation theory (MP2) and coupled-cluster (CC) method up to single, double, triple, and perturbative quadruple excitations using the aug-cc-p(C)VXZ [X = 2(D), 3(T), 4(Q), and 5] correlation-consistent basis sets. The best equilibrium geometry has been obtained at the all-electron CCSD(T)/aug-cc-pCVQZ level of theory. The dissociation energy has been determined based on basis set extrapolation techniques within the focal-point analysis (FPA) approach considering (a) electron correlation beyond the all-electron CCSD(T) level, (b) relativistic effects, (c) diagonal Born-Oppenheimer corrections (DBOC), and (d) variationally computed zero-point vibrational energies. The final D(e) and D0 values are 2398 +/- 12 and 2280 +/- 20 cm(-1), respectively. The global PES and DMS have been computed at the frozen-core CCSD(T)/aug-cc-pVTZ and MP2/aug-cc-pVTZ levels of theory, respectively. Variational vibrational calculations have been performed for CH4 and F(-)-CH4 employing the vibrational configuration interaction (VCI) method as implemented in Multimode.     

Peculiarities of atomic interaction in organic molecules of 3- and 4-coordinated phosphorus using ab initio calculations and Cl NQR

The results of ab initio calculations at the MP2/6-31G(d) level of molecules of the series ClPXX′ (X, X′=C₂H₅, N(CH₃)₂, OCH₃) and ClP(M)XX′ (M=O, S; X=CH₃, ?CH₃; X′=C₂H₅, OCH₃) with total optimization of their geometry were presented. They were compared with the obtained earlier results of such calculations at the RHF/6-31G(d) level and with experimental ³⁵Cl nuclear quadrupole resonance (NQR) spectra for these compounds. MP2/6-31G(d) calculations confirm non-inductive influence of heteroatoms on the geminal Cl atom in the non-linear three-atomic Cl–P–M groups. They agree to the conclusion that the abnormal correlation of the ³⁵Cl NQR frequencies for the compounds studied at different X, X′ and M is caused, in general, by the P–Cl bond polarization under the action of the geminal atom partial charges directly through the field. The satisfactory conformity between the experimental ³⁵Cl NQR frequencies and those estimated from 3p-components of the Cl atom valence p-orbitals calculated at the MP2/6-31G(d) level was obtained.     

Molecular structures and vibrational frequencies of 2-, 3- and 4-pyridine carboxaldehydes by ab initio Hartree-Fock and density functional theory calculations

The optimised molecular structures, vibrational frequencies and corresponding vibrational assignments of the cis and trans conformers of 2-, 3- and 4-pyridine carboxaldehydes have been calculated using ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods with 6-311++G(d, p) basis set. The calculations were adapted to the C(S) symmetries of all the molecules. The mean vibrational deviations between the vibrational frequency values of the two conformers of all the compounds have been seen to increase while the relative energies increase and it was concluded the more different the molecular structure of the two conformers is the higher the relative energy is between them, and thus a bigger mean vibrational deviation.     

Vibrational spectroscopic studies and ab initio calculations of 5-methyl-2-(p-fluorophenyl)benzoxazole

FT-Raman and FT-IR spectra of 5-methyl-2-(p-fluorophenyl)benzoxazole were recorded and analysed. The vibrational frequencies of the compound have been computed using the Hartree-Fock/6-31G* basis and compared with the experimental values.