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.     

Gas-phase chemistry of ionized and protonated GeF4: a joint experimental and theoretical study

The gas-phase ion chemistry of GeF(4) and of its mixtures with water, ammonia and hydrocarbons was investigated by ion trap mass spectrometry (ITMS) and ab initio calculations. Under ITMS conditions, the only fragment detected from ionized GeF(4) is GeF(3)(+). This cation is a strong Lewis acid, able to react with H(2)O, NH(3) and the unsaturated C(2)H(2), C(2)H(4) and C(6)H(6) by addition-HF elimination reactions to form F(2)Ge(XH)(+), FGe(XH)(2)(+), Ge(XH)(3)(+) (X = OH or NH(2)), F(2)GeC(2)H(+), F(2)GeC(2)H(3)(+) and F(2)GeC(6)H(5)(+). The structure, stability and thermochemistry of these products and the mechanistic aspects of the exemplary reactions of GeF(3)(+) with H(2)O, NH(3) and C(6)H(6) were investigated by MP2 and coupled cluster calculations. The experimental proton affinity (PA) and gas basicity (GB) of GeF(4) were estimated as 121.5 ± 6.0 and 117.1 ± 6.0 kcal mol(-1), respectively, and GeF(4)H(+) was theoretically characterized as an ion-dipole complex between GeF(3)(+) and HF. Consistently, it reacts with simple inorganic and organic molecules to form GeF(3)(+)-L complexes (L = H(2)O, NH(3), C(2)H(2), C(2)H(4), C(6)H(6), CO(2), SO(2) and GeF(4)). The theoretical investigation of the stability of these ions with respect to GeF(3)(+) and L disclosed nearly linear correlations between their dissociation enthalpies and free energies and the PA and GB of L. Comparing the behavior of GeF(3)(+) with the previously investigated CF(3)(+) and SiF(3)(+) revealed a periodically reversed order of reactivity CF(3)(+) < GeF(3)(+) < SiF(3)(+). This parallels the order of the Lewis acidities of the three cations.     

The structure and dissociation pathways of protonated methanol: An ab initio molecular orbital study

Ab initio molecular orbital calculations with moderately large polarization basis sets and including valence-electron correlation have been used to examine the structure and dissociation mechanisms of protonated methanol [CH₃OH₂]⁺. Stable isomers and transition structures have been characterized using gradient techniques. Protonated methanol is found to be the only stable isomer in the [CH₅O]⁺ potential surface. There is no evidence for a tightly-bound complex, [HOCH₂]⁺…?H₂, analogous to the preferred structure [CH₃]⁺…?H₂ of [CH₅]⁺. Protonated methanol is found to possess a pyramidal arrangement of bonds at the oxygen atom with a barrier to inversion of 8kJ mol^?1. The lowest energy fragmentation pathways are dissociation into methyl cation and water (predicted to require 284 kJ mol^?1 with zero reverse activation energy) and loss of molecular hydrogen (endothermic by 138 kJ mol^?1 but with a reverse activation barrier of 149 kJ mol^?1). The results offer a possible explanation as to why production of [CH₂OH]⁺ from the reaction of methyl cation with water is not observed. Other dissociation processes examined include loss of a hydrogen atom to yield the methylenoxonium radical cation or methanol radical cation (requiring 441 and 490 kJ mol^?1, respectively) and loss of a proton to yield neutral methanol (requiring 784 kJ mol^?1).     

Electronic state of push-pull alkenes: an experimental dynamic NMR and theoretical ab initio MO study

The (1)H and (13)C NMR spectra of a number of push-pull alkenes were recorded and the (13)C chemical shifts calculated employing the GIAO perturbation method. Of the various levels of theory tried, MP2 calculations with a triple-zeta-valence basis set were found to be the most effective for providing reliable results. The effect of the solvent was also considered but only by single-point calculations. Generally, the agreement between the experimental and theoretically calculated (13)C chemical shifts was good with only the carbons of the carbonyl, thiocarbonyl, and cyano groups deviating significantly. The substituents on the different sides of the central C=C partial double bond were classified qualitatively with respect to their donor (S,S < S,N < N,N) and acceptor properties (C identical with N < C=O < C=S) and according to the ring size on the donor side (6 < 7 < 5). The geometries of both the ground (GS) and transition states (TS) of the restricted rotation about the central C=C partial double bond were also calculated at the HF and MP2 levels of theory and the free energy differences compared with the barriers to rotation determined experimentally by dynamic NMR spectroscopy. Structural differences between the various push-pull alkenes were reproduced well, but the barriers to rotation were generally overestimated theoretically. Nevertheless, by correlating the barriers to rotation and the length of the central C=C partial double bonds, the push-pull alkenes could be classified with respect to the amount of hydrogen bonding present, the extent of donor-acceptor interactions (the push-pull effect), and the level of steric hindrance within the molecules. Finally, by means of NBO analysis of a set of model push-pull alkenes (acceptors: -C identical with N, -CH=O, and -CH=S; donors: S, O, and NH), the occupation numbers of the bonding pi orbitals of the central C=C partial double bond were shown to quantitatively describe the acceptor powers of the substituents and the corresponding occupation numbers of the antibonding pi orbital the donor powers of the substituents. Thus, for the first time an estimation of both the acceptor and the donor properties of the substituents attached to the push-pull double bond have been separately quantified. Furthermore, both the balance between strong donor/weak acceptor substituents (and vice versa) and the additional influences on the barriers to rotation (hydrogen bonding and steric hindrance in the GSs and TSs) could be differentiated.     

The structure of the phenol-nitrogen cluster: a joint experimental and ab initio study

The rotationally resolved LIF spectra of four different isotopomers of the phenol--nitrogen cluster have been measured to elucidate the structural parameters of the cluster in ground and electronically excited (S1) state. The fit of the rotational constants has been performed by a genetic algorithm and by an assigned fit to the line frequencies. The results of both methods are compared. The intermolecular structures are fit to the inertial parameters and are compared to the results of ab initio calculations for both states. This fit was performed under the restriction that the geometry of the monomer moieties do not change upon complexation. Of the remaining five intermolecular parameters two dihedral angles were fixed due to the planarity of the complex, which was inferred from the inertial defects of all isotopomers. The distance of the nearest nitrogen atom to the hydrogen atom of the phenolic hydroxy group is found to decrease upon electronic excitation of the chromophore considerably more than predicted from ab initio calculations. This deviation between theory and experiment can be traced back to the absence of electron-electron correlation in the performed complete active space self-consistent field calculations. The shortening of the OH...NN "hydrogen" bond upon electronic excitation is in agreement with the increased dipole moment of phenol in the S1-state.     

Active site structure and mechanism of human glyoxalase I-an ab initio theoretical study.

The structure of the active site of human glyoxalase I and the reaction mechanism of the enzyme-catalyzed conversion of the thiohemiacetal, formed from methylglyoxal and glutathione, to S-D-lactoylglutathione has been investigated by ab initio quantum chemical calculations. To realistically represent the environment of the reaction center, the effective fragment potential methodology has been employed, which allows systems of several hundred atoms to be described quantum mechanically. The methodology and the active site model have been validated by optimizing the structure of a known enzyme-inhibitor complex, which yielded structures in good agreement with the experiment. The same crystal structure has been used to obtain the quantum motif for the investigation of the glyoxalase I reaction. The results of our study confirm that the metal center of the active site zinc complex plays a direct catalytic role by binding the substrate and stabilizing the proposed enediolate reaction intermediate. In addition, our calculations yielded detailed information about the interactions of the substrate, the reaction intermediates, and the product with the active site of the enzyme and about the mechanism of the glyoxalase I reaction. The proton transfers of the reaction proceed via the two highly flexible residues Glu172 and Glu99. Information about the structural and energetic effect of the protein on the first-shell complex has been attained by comparison of the structures optimized in the local protein environment and in a vacuum. The environment of the zinc complex disturbs the Cs symmetry found for the complex in a vacuum, which suggests an explanation for the stereochemical behavior of glyoxalase I.     

A comparative ab initio study of methyl formate, methyl thiolformate and methyl thionoformate

Ab initio SCF-MO calculations have been carried out for HCOOCH₃, HC(=O)SCH₃ and HC(=S)OCH₃. Relative stabilities of s-trans/s-cis conformers are reported and discussed in terms of specific intramolecular interactions. The energy difference between the s-trans and the s-cis form increases in the order methyl thiolformate < methyl thionoformate < methyl formate. The major stabilizing factors of the s-cis forms are the bond dipolar interaction and the mesomeric delocalization through the five member ring involving both the X=C---Y---C (X, Y = O, S) skeleton and the out-of-plane hydrogen atoms. These effects are used to explain the trends mentioned. The non-planarity previously proposed for the thionoester is reinvestigated. Our calculations show that this molecule is planar. Molecular atomic charges, dipole moments and ionisation potentials are determined and compared with available experimental values.     

Gas-phase reactivities of charged platinum dimers with ammonia: A combined experimental/theoretical study

Computational and experimental studies of with ammonia are reported. While ammonia is dehydrogenated with either cluster type, the reaction efficiencies are quite different with  = 0.27 for [K. Koszinowski, D. Schröder, H. Schwarz, J. Phys. Chem. A 107 (2003) 4999.] and  = 0.0033 for . DFT-based relativistic calculations are consistent with this distinct behavior, with maximum energies along the reaction path of −13.3 kcal/mol for the cationic and +1.4 kcal/mol for the anionic clusters relative to the reactants. The recently proposed mechanism for the system [D. Xu. X.-Y. Chen, S.-G. Wang, Int, J. Quant. Chem. 107 (2007) 1985.] needs to be modified to account for the experimental findings.     

Microhydration of protonated glycine: an ab initio family tree

The incremental hydration of the glycine cation is investigated using an ab initio approach fully correcting for basis set superposition errors and explicitly incorporating electron-correlation effects. Structures with zero to four surrounding water molecules have been determined. It is demonstrated that the successive aggregates follow a Darwinian family tree, the most stable complexes systematically belonging to the same branch of the tree. In strong contrast with neutral glycine, the direct hydrogen bonding to the glycine cation is favored over bridging water structures. The agreement between experimental and theoretical hydration enthalpies and Gibbs free energies is impressive, as ab initio estimates almost systematically fit the experimental error bars. For GlyH(+)-(H2O) and GlyH(+)-(H2O)3, we show that two structures are generated by the experimental setup. The present approach also resolves most of the previous theory/experiment discrepancies and provides patterns for the evolution of the vibrational spectra: a decrease of the hydrogen-bond stretching frequency indicating second-shell water molecules. Additionally, the impact of bulk solvent solvation is investigated, as four discrete water molecules still do not fully hydrate the protonated glycine.     

An ab initio MO calculation of the electronic structure and geometry of protonated methanol

Protonated methanol, CH₃ OH₂⁺, has been studied using the LCAO—MO—SCF method with a 7, 3 and 9, 5, 1 Gaussian orbital basis set on the heavy atoms and 4s on hydrogen. It is found that the ground state is non-planar around oxygen, in contrast with previous calculations, with an inversion barrier of 3 kcal mol^?1. The changes in electron distribution in the reacting systemCH₃⁺ + H₂O → CF₃OH₂⁺is also examined.     

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.     

Gas-phase reaction: alkyl cation transfer in the dissociation of protonated pyridyl carbamates in mass spectrometry

In the mass spectrometry of pyridyl carbamates, alkyl cation transfer is one of the major fragmentation reactions of the protonated molecules. Literature results and theoretical calculations indicate that the pyridine nitrogen is the most favorable site for protonation in these structures. Substituent and comparison experiments run to elucidate the fragmentation patterns reveal that the proton is localized at the pyridine nitrogen and the reaction center is charge-remote when the alkyl cation transfer occurs. The mechanism involving configuration inversion via an ion-neutral complex is favorable in energy for the alkyl cation transfer in these structures.     

Gas-phase vibrational spectroscopy and ab initio study of organophosphorus compounds: discrimination between species and conformers

Gas phase vibrational spectra of dimethyl methylphosphonate (DMMP), trimethyl phosphate (TMP), and triethyl phosphate (TEP) have been measured using FTIR spectroscopy. For DMMP, TMP, and TEP, most of the infrared active vibrational modes have been observed in the 50-5000 cm (-1) spectral range, allowing an unambiguous discrimination between the three molecules. The vibrational analysis of the spectra was performed by comparing with MP2 and B3LYP harmonic and anharmonic force field ab initio calculations. The extension to anharmonic calculations provides the best agreement for the mid-infrared and the near-infrared spectra, but they do not improve the harmonic frequency predictions in the far-infrared domain. This part of the vibrational spectra associated with collective and nonlocalized vibrational modes presents the largest frequency differences between the two lowest energy conformers of DMMP and TMP. These two conformers were taken into account in the vibrational assignment of the spectra. Their experimental evidence was obtained by deconvoluting vibrational bands in the mid-infrared and in the far-infrared regions, respectively. For TEP, the conformational landscape appears very complicated at ambient temperature, and a further analysis at low temperature is required to explain the vibrational features of each conformer.     

The structure of potassium hydrogentartrate: A combined X-ray,semiempirical, and ab initio study

Single crystals of potassium hydrogentartrate, (2R,2R)-KO₂C(CHOH)₂CO₂H, were taken from a three-year-old wine bottle. The structure was determined by low-temperature single-crystal X-ray diffraction analysis using a Siemens SMART diffractometer. (2R,2R)-KO₂C(CHOH)₂CO₂H crystallizes in the orthorhombic space group P2₁2₁2₁ with Z = 4 and unit cell dimensions a = 7.6065(5), b = 7.7599(5), and c = 10.6054(7) Å. The structure of an isolatedhydrogentartrate anion, (2R,2R)-[O₂C(CHOH)₂-CO₂H]⁻, was calculated at the semiempirical AM1 and PM3 levels of theory with a VSTO-3G* basis set and in addition ab initio at the self-consistent level of theory using a standard 6-31G(d, p) basis set (Non-SI units employed: kcal ≈ 4.184 kJ, Å = 10⁻¹⁰ m).© 1998 John Wiley & Sons, Inc. Heteroatom Chem 9:307–310, 1998     

An ab initio theoretical study of the stereoisomers of tetrahydrocannabinols

An extensive theoretical study of the stereoisomers of tetrahydrocannabinols has been performed at the ab initio HF/6-31G^* and B3LYP/6-31G^* levels. Effects of solvation were calculated with the Onsager model (with full geometry optimization), SCRF with Tomasi's PCM, and isodensity polarization continuum models. Single-point MP2//HF/6-31G^* calculations were carried out. Frequency calculations for all the isomers at the HF/6-31G^* level and for two natural isomers ¹-THC-RR and ⁶-THC-RR at the B3LYP/6-31G^* level were performed. Our results support the findings of the previous AM1 studies that the orientation of the carbocyclic ring and its C1 substituent with respect to the phenyl group hydroxyl oxygen play the major role in the activity. The calculated values of the LUMO energy (lowest unoccupied molecular orbital) and the hardness of the stereoisomers show that for the trans isomers it is easier to remove one electron from its HOMO (highest occupied molecular orbital) to the LUMO and easier to accept an electron from the receptor binding site than for the cis isomers. Combining geometric features (the orientation of the carbocyclic ring and its C1 substituent with respect to the phenyl group hydroxyl oxygen) with electronic features (LUMO and hardness), we explain the activity differences among the stereoisomers.     

Interaction energy anisotropy of the pyrrole dimer: ab initio theoretical study

The van der Waals pyrrole dimer is studied using supermolecular and perturbation ab initio treatment with inclusion of correlation energy. The influence of selected geometry variations on the interaction energy components is investigated. Our calculations verified the minimum on the potential energy surface deduced from microwave spectra. Its stability is possibly related not to the extremal values of the selected interaction energy contributions but its physical origin is connected with the delicate equilibrium between the repulsive and attractive forces. Any structure variation connected with the extremal attraction energy is more than compensated for by the repulsion energy. Received: 11 June 1998 / Accepted: 6 October 1998 / Published online: 1 February 1999     

A combined ab initio and semi-empirical study on the theoretical vibrational spectra and physical properties of polypyrrole

This study concentrates on the important conducting polymer, polypyrrole. Detailed atomistic molecular models have been developed with the help of ab initio and semi-empirical quantum mechanical calculations.The vibrational spectra of isolated pyrrole monomers and oligomers from n=1 and 2, where n is the number of structural repeat units used, have been computed using the ab initio 3-21G basis set. The results obtained are compared with data for the case of oligomers with n=2–5 for both neutral benzenoid and quinonoid oligopyrroles, from semi-empirical predictions obtained by AM1 and PM3. The trends in the computed harmonic force fields, vibrational frequencies and intensities are monitored as a function of the chain length. The data are analysed in conjunction with the trends in computed equilibrium geometries.Also the examination of the heat of formation of these two degenerate forms (quinonoid and benzenoid) has been conducted with respect to increases in the number of rings and the change of methods from AM1 to PM3.     

Gas-phase spectroscopy of protonated 3-OH kynurenine and argpyrimidine. comparison of experimental results to theoretical modeling

The aging process of the human lens is associated with accumulation of chromophores and fluorophores that impair visual function. In the present study, we examined the photodissociation of 3-OH-kynurenine and argpyrimidine. Furthermore, absorption spectra obtained in gas phase using an electrostatic ion storage ring were studied as gas phase absorption have been shown to be more similar to the in vivo condition than absorption spectra obtained in the liquid phase. Experimental results were compared to theoretical modeling using the multistate, multireference perturbation theory approach combined with advanced molecular modeling tools to account for the solvent effects and to provide direct support for band assignments. Absorption maxima were determined both experimentally and theoretically and significant differences between the two chromophores were found. In particular, 3-OH-kynurenine demonstrated a blue-shift of more than 130 nm in the aqueous phase compared to the gas-phase due to the existence of different 3-OH-kynurenine conformers, which are stable under different conditions and originate from the interplay between intra- and intermolecular interactions. Photodissociation of argpyrimidine and 3-OH-kynurenine was observed in vacuum thus confirming the results previously obtained in liquid phase demonstrating that the photodestruction takes place in both media.     

Electronic structure of NH+: An ab initio study

We report ab initio self‐consistent field MRSD‐CI electronic structure calculations of the NH⁺ cation. A basis set of DZ + POL quality augmented with Rydberg and bond functions was employed together with an extensive treatment of electron correlation. More than 50 electronic states of NH⁺ are reported, including doublets, quartets, and sextets. Leading configurations, vertical ionization energies of NH, vertical excitation energies of NH⁺, and potential energy curves are reported. Spectroscopic properties calculated for the known bound electronic states of NH⁺ are found in good agreement with experiment. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005