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High-pressure mass spectrometric equilibrium experiments and electronic structure calculations have been carried out to investigate the energetics of the interactions of chloride ion with a series of normal alkanes and cycloalkanes in the gas phase. The structures of the complexes obtained from the electronic structure calculations provide considerable insight into the nature of the interaction between the negatively charged ion and the alkanes, which has the character of a purely ion-induced dipole interaction. The structural information also shows how the charged species affect the confirmation of the normal alkanes.

The gas-phase ion-molecule reactions of 1,1,3,3-tetrafluorodimethyl ether and water have been examined using Fourier transform ion cyclotron resonance mass spectrometry, infrared multiphoton dissociation (IRMPD) spectroscopy, and ab initio molecular orbital calculations. This reaction sequence leads to the efficient bimolecular production of the proton-bound dimer of water (H5O2+). Evidence for the dominant mechanistic pathway involving the reaction of CF2H-O=CHF+, an ion of m/z 99, with water is presented. The primary channel occurs via nucleophilic attack of water on the ion of m/z 99 (CF2H-O=CHF+), to lose formyl fluoride and yield-protonated difluoromethanol (m/z 69). Association of a second water molecule with protonated difluoromethanol generates a reactive intermediate that decomposes via a 1,4-elimination to release hydrogen fluoride and yield the proton-bound dimer of water and formyl fluoride (m/z 67). Last, the elimination of formyl fluoride occurs by the association of a third water molecule to produce H5O2+ (m/z 37). The most probable isomeric forms of the ions with m/z 99 and 69 were found using IRMPD spectroscopy and electronic structure theory calculations. Thermochemical information for reactant, transition state, and product species was obtained using MP2(full)/6-311+G**//6-31G* level of theory.

The thermochemistry of gas-phase ion molecule interactions and the structures of various clusters between protonated glycine (GlyH+), glycine, and ammonia have been studied by high pressure mass spectrometry (HP-MS) and ab initio calculations. For the association reactions of GlyH+ with NH3, Gly(NH3)H+ with NH3, and (Gly)2H+ with NH3, the enthalpy changes experimentally determined are –23.2, –18.3, and –19.1 kcal mol–1 (1 cal = 4.184 J), respectively. For all clusters investigated, the measured binding enthalpies are in excellent agreement with those obtained from ab initio calculations at the B3LYP/6-311+G(d,p) level of theory. Different isomers of each of these clusters have been obtained and the corresponding binding energies have been computed. The potential energy surface for isomerization of the clusters of protonated glycine with ammonia has also been computed at the same level. For this cluster, the three most stable isomers all involve a proton transfer from protonated glycine to ammonia. According to the calculated potential energy surface, the barrier between GN4, the least stable isomer, and the most stable isomer (GN1) is 11.5 kcal mol–1 at 298 K. Thus, this isomerization will be facile given the exothermicity of the association reaction. Therefore, a statistical distribution of isomers will be present under thermal equilibrium conditions. Single point energy calculations at the MP2(full)/6-311++G(2d,2p)//B3LYP/6-311+G(d,p) level of theory reveal that the isomer GN2 in which glycine has a zwitterionic structure has the same energy as the most stable non-zwitterionic isomer GN1. NH4+ evidently may stabilize the zwitterionic structure of glycine. In contrast, N2H7+ and GlyH+ are not as effective in stabilizing the zwitterionic structure of glycine. This likely results from the more localized charge in NH4+ giving rise to stronger hydrogen bonds with the carboxylate moiety of zwitterionic glycine. This conjecture is supported by the computational results.Key words: high pressure mass spectrometry, glycine, gas-phase ion thermochemistry, ab initio calculations, cluster structure.

The thermochemistry of chloride ion clustering onto acetone and four fluorinated acetones (CH3C(O)CH2F, CF3C(O)CH3, CF3C(O)CF2H, and CF3C(O)CF3) under thermal equilibrium conditions has been determined by pulsed-ionization high pressure mass spectrometry (PHPMS). The standard enthalpy (ΔH°) and entropy (ΔS°) changes obtained indicate a variety of different types of bonding in these complexes. Ab initio computational methods have been used to obtain more insight into the structures and energetics. Surprisingly, in the Cl−(CF3C(O)CF2H) complex the chloride ion is not linearly hydrogen bonded, despite the presence of a very acidic CF2H bond. Instead, coordination with the carbonyl group carbon atom seems to be more pronounced, as found for the Cl−(CF3C(O)CF3) complex. For the Cl−(CF3C(O)CF3) clustering equilibrium a ΔS° value of −37.6 cal mol−1 K−1 has been measured, indicating that one or both CF3 group rotations will be hindered upon complex formation. Excellent agreement between ΔH°298 values calculated at the MP2/[6-311++G(3df,3pd)/6-311+G(2df,p)]//MP2/[6-31+G(d)/6-31G(d)] level of theory and experimental ΔH° values has been obtained. In addition, ΔacidH°298 values for a set of small to medium sized organic and inorganic acids, and the fluorinated acetones have been determined at the G3 and G3(MP2) levels of theory. Good to excellent agreement was obtained compared to experimental data, indicating that these composite methods perform well for the determination of reliable ΔacidH°298 results for medium sized molecules containing up to eight second row atoms. No linear correlation between clustering ΔH°298 and ΔacidH°298 values was found, indicating that most likely ion–dipole and ion-induced dipole interactions are determining the observed thermochemical trends. Finally, gas phase FT-IR spectra of CH3C(O)CH2F, CF3C(O)CH3, CF3C(O)CF2H, and CF3C(O)CF3 have been obtained, and the normal mode vibrational frequencies compared to results from calculations at the HF/6-31G(d) level of theory, scaled by 0.8953, and the B3LYP/6-311++G(3d,3p) level of theory. For the Cl−(CF3C(O)CF3) complex some large shifts in frequencies and IR absorption intensities are observed relative to CF3C(O)CF3, especially for the CO stretch.

The enthalpy and entropy changes for the formation of the 1:1 complexes of methanol with various gaseous protonated amino acids have been measured using pulsed-ionization high-pressure mass spectrometry. The enthalpy changes for formation of the clusters Gly(MeOH)H(+), Ala(MeOH)H(+), Val(MeOH)H(+), Leu(MeOH)H(+), Ile(MeOH)H(+), and Pro(MeOH)H(+) have been determined to be -92.0, -83.3, -82.4, -79.5, -78.7, and -73.6 kJ mol(-1), respectively. These values agree very well with the energetic values computed at the MP2(full)/6-311++G(2d,2p)//B3LYP/6-311+G(d,p) level of theory for the lowest energy adducts in each system. Both experimental observations and computational determinations of the potential energy surface for the glycine system suggest that a mixture of low-lying isomers may be present for each of the cluster systems examined. The primary structural motif for these clusters is the coordination of the methanol molecule to the ammonium group of the protonated amino acid via a strong ionic hydrogen bond. For the amino acids studied here, computational results reveal that one methanol molecule does not sufficiently stabilize any zwitterionic structure such that no appreciable extent of proton transfer from the amino acid to methanol was observed.

The temperature dependence of the low-pressure association reaction of dimethyl ether with protonated dimethyl ether has been investigated using Fourier transform ion cyclotron resonance mass spectrometry. The unimolecular dissociation of nascent proton-bound dimers is complicated by two factors: (1) the presence of another unimolecular dissociation route producing trimethyloxonium cation and methanol through a highenergy isomer of the proton-bound dimer and (2) the presence of at least two high-energy isomers of the proton-bound dimer en route to dissociation of the nascent proton-bound dimer. RRKM modeling of the experimental temperature dependence of the unimolecular dissociation of nascent proton-bound dimers strongly suggests that dissociation of the nascent proton-bound dimer proceeds through a high-energy isomer. The possible existence of such species is also shown by ab initio calculations. The original mechanism for the ion/molecule reaction and analysis of radiative association kinetics used in the past was found to be too simple for accurate modeling of the reaction between protonated dimethyl ether and dimethyl ether. A slightly more complicated mechanism is proposed which more accurately accounts for the temperature dependence of the unimolecular dissociation to re-form reactants. As well, three isotopomeric variants of the protonated dimethyl ether/dimethyl ether reaction were examined experimentally and theoretically.

Fourier transform ion cyclotron resonance (FT-ICR) ligand exchange equilibrium experiments have been used to establish a relative scale of sodium binding free energies of about fifty organic molecules. Ab initio calculations yield accurate enthalpies and entropies of complexation for a new set of 30 molecules. These calculations establish an absolute basis for the relative experimental free energy scale. In addition, they provide structural information for the complexes which permits considerable insight into the nature of sodium ion binding. We found that when the binding site is a first row atom, the sodium ion aligns with the molecular dipole axis in order to maximize charge-dipole electrostatic interactions. Strong deviations from this behavior occur when the ion is attached to a heavier atom such as sulfur, chlorine or bromine. For flexible molecules such as the isomers of butyl chloride, there are several isomers of low energy, and differences exist between the enthalpy and free energy orders of stability. Finally, sodium ion affinities have been obtained for several aromatic molecules which lend support to the importance of charge-quadrupole interactions in such cation-π complexes.

The gas-phase clustering equilibria of halide ions to a homologous series of alcohol molecules, X- + HOR ⇌ X-(HOR) (X = F, Cl, Br, I; R = CH3, CH3CH2, (CH3)2CH, (CH3)3C), have been investigated using ab initio (MP2(full)) and density functional theory (B3LYP) computational methods. For both methods, extended basis sets, including diffuse and polarization functions for all atoms and anions, except I-, were used. For I- three different effective core potentials (ECP) were used to test their suitability for these systems. Comparing the Δ and Δ values obtained with various experimental data indicates that the MP2 and MP2//B3LYP methods perform best. Structural and spectroscopic features, as well as charge distributions, show interesting trends for the various X-(HOR) complexes, and the intrinsic contributions of the halide ions and the alcohol molecules to these trends are discussed. Finally, two-dimensional potential energy surface scans were performed for the X-(HOCH3) complexes at the MP2/6-311++G(d,p) lev...

Fourier transform ion cyclotron resonance (FTICR) measurements of solvent exchange equilibria, where the solvents differ only by a single deuterium substitution at the labile hydroxylic site, have been used to study the deuterium isotope effect on ion–molecule hydrogen-bonding interactions. The systems studied include chloride ion, fluoride ion, and alkoxide ions solvated by up to three molecules of alcohol: (ROH)n · Cl−, (ROH)n · F−, and (ROH)n · RO−. Differences in the measured isotope effects are explained on the basis of the differing hydrogen bond strengths in the adducts and by the ability of the chloride ion to partake in multiple site interactions. Keywords: Kinetic isotope effect; Hydrogen bonding; Fourier transform ion cyclotron resonance (FTICR); Ion–molecule reactions

The gas phase equilibrium clustering reactions X−(ROH)n + ROH ⇌ X−(ROH)n+1 (X = F, Cl, Br, I; R = CH3, CH3CH2, (CH3)2CH, (CH3)3C; n = 0, 1, 2) have been investigated by using pulsed-ionization high pressure mass spectrometry (PHPMS). From the corresponding van’t Hoff plots the standard enthalpies (ΔHn,n+1O) and entropies (ΔSn,n+1O) were obtained, which are discussed in terms of the radii of the halides, the geometry of the alcohol molecules, the number of alcohol molecules, and molecular properties such as polarizability and gas phase acidity. The observed enthalpy trends can be explained on the basis of ion-dipole, ion-induced dipole, and dipole-dipole interactions within the clusters. The observed entropy trends are qualitatively discussed in terms of hindered rotations and low frequency intermolecular vibrations. In general, where available, there is good agreement between the present data and literature values obtained by various experimental techniques. In addition to the experiments, both density functional theory (DFT) calculations at the B3LYP/6–311+G(d,p) level of theory and G2 level calculations have been performed on a number of selected systems to test these methods for obtaining energetic data and to gain more insight into the structures of the investigated clusters.

Fourier Transform Ion Cyclotron Resonance (FT-ICR) and High Pressure Mass Spectrometric (HPMS) measurements of the deuterium isotope effect and kinetics of adduct ion formation have been used to probe the nature of the potential describing the motion of the hydrogen in gas phase ion-molecule hydrogen-bonding interactions. Hydrogen-bonding systems reported in this paper are alkoxide ion and chloride ion solvated by one molecule of alcohol, ROH●OR- and ROH●Cl-. Significant differences in the isotope effects were observed for the two systems. These differences are explained on the basis of the differing hydrogen bond strengths of the adduct ions, and the ability of the chloride ion to partake in multiple site, or chelate, interactions. In addition, HPMS studies of the kinetics of the reaction of CH3O− with CH3OH reveal that a double minimum potential energy surface may be appropriate for describing the adduct ion formation. These experimental studies have been supplemented by ab initio calculations to determine adduct ion structures as well as to permit statistical thermodynamic calculations of the isotope effect.

The proton affinity (PA) of a molecule in the gas phase is an expression of its fundamental basicity and is a possible factor controlling the course of many ion−molecule reactions. The formation of an intramolecular hydrogen bond increases the PA value over that of similarly sized monofunctional molecules and the values of ΔS° are an indication of an intramolecular cyclization which occurs via hydrogen bonding in protonated bifunctional molecules. The first step in exploring these thermochemical properties has been the examination of the experimental proton-transfer equilibria using both ion cyclotron resonance (ICR) and high-pressure mass spectrometric (HPMS) studies. Parallel ab initio molecular orbital (MO) calculations on the protonated species show that the cyclized structures are the most stable species, in agreement with the experimental PA and entropy observations.

The gas-phase reactivity of W+ with hydrocarbons containing up to six carbon atoms has been studied by Fourier-transform ion cyclotron resonance mass spectrometry. W+ is found to be one of the most reactive bare metal cations studied to date with all hydrocarbons except acetylene being activated at thermal energies. The observed reactivity is dominated by dehydrogenation, which is often multiple. Thus, reaction with propene leads to loss of two dihydrogen molecules (yielding WC3H2) and reaction with n-hexane leads to loss of 4 H2 (yielding WC6H6). In all cases, the product ions are themselves reactive with the same neutral species, leading to reaction sequences of various lengths. Isotope labeling, collisioninduced dissociation, and ligand exchange experiments have been extensively carried out in order to try to establish the structure of some of the intermediate and final product ions. It turned out that deriving structures from such experiments is much more difficult than for first-row transition metal ions. This is due to the higher reactivity and metal-ligand binding energies of tungsten.

The gas-phase reactions of the bare tungsten cation W+ with silane have been investigated using Fourier-Transform Ion Cyclotron Resonance mass spectrometry. Dehydrogenation of a first molecule leads to the formation of WSiH2+. This ion is itself reactive with a second silane molecule, this time through elimination of 2H2, to form WSi2H2+. A similar reaction follows, yielding WSi3H2+ as the next product ion, which itself leads to both WSi4H4+ and WSi4H2+. This seems to initiate two parallel reaction sequences, yielding WSi10H6+ as the major final product, together with a minor amount of WSi10H4+. CID experiments on the products of the first three reactions were carried out to aid in their structural elucidation. Ab initio calculations at the CASSCF level have been performed in order to derive optimum structures for the first two product ions WSiH2+ and WSi2H2+, and for the non-observed intermediate WSi2H4+. The results show that structural isomerism exists for these three ions, due to the versatile bonding...

Pulsed ionization High-Pressure Mass Spectrometry (PHPMS) has been used to investigate the thermochemistry of the association reactions of t-C4H9+ with various neutral molecules in the gas phase. The behavior of the logarithm of the association equilibrium constant as a function of inverse reaction temperature (a van't Hoff plot) has been examined over a broad temperature range to yield accurate thermochemical data for the enthalpy and entropy of association. All of the systems investigated show either a pronounced break or a subtle curvature in the van't Hoff plot. This behavior is consistent with two coexisting isomeric forms of the association adduct, viz, (i) a low-temperature, covalently bound isomer characterized by larger −ΔH° and −ΔS° values and (ii) a high-temperature, electrostatically bound isomer of lower −ΔH° and −ΔS° values. Experimental thermochemical data for the association reactions are reported. From the low-temperature data, proton affinities (PA) of t-C4H9OCH3 (205.1 kcal/mol) and t-C...

The association reactions of methylated acetone with acetone and dimethyl ether were studied over an extended temperature range (30–250°C) by high-pressure mass spectrometry. In addition, the association reactions of various deuterium-substituted analogues of both the reactant ion and neutral molecules were investigated. Two distinct isomeric forms are apparent from the examination of the behaviour of the association equilibrium constant as a function of reaction temperature: (i) a low-temperature, covalently bound isomer characterized by larger −ΔH° and −ΔS° values and significant equilibrium isotope effects on the entropy of association; and (ii) a high-temperature, electrostatically bound isomer of lower −ΔH° and −ΔS° values and with insignificant equilibrium isotope effects. The equilibrium isotope effects and larger −ΔS° values are more pronounced for the methylated acetone–dimethyl ether adduct than for the less sterically congested methylated acetone-acetone adduct. Molecular models of the low-temperature isomers show severe restriction or complete loss of internal rotations and is the origin of the observed equilibrium isotope effects. No such phenomenon is expected or observed in the more loosely bound high-temperature, electrostatic isomers. Potential energy surfaces for the transfer of methylcation from methylated acetone to a second acetone molecule and to dimethyl ether are proposed.

Hydrogen/deuterium exchange reactions involving protonated triglycine and deuterated ammonia (ND(3)) have been examined in the gas phase using a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Ab initio and density functional theory (DFT) calculations have been carried out to model the exchanges and to obtain energetics and vibrational frequencies for molecules involved in the proposed exchange mechanisms. Structural optimization and frequency calculations have been performed at the B3LYP level of theory with the 6-311+G(d,p) basis set. Transition states have been calculated at the same level of theory and basis set as above using the QST2 and QST3 methods. Single-point energy calculations have been performed at the MP2/6-311+G(d,p) level. Six labile sites of protonated triglycine were found to undergo H/D exchange. Of these six labile hydrogens, two are amide, three are ammonium, and one is carboxyl. Detailed mechanisms for each of these transfers are proposed. Qualitative onium ion and tautomer mechanisms for the exchanges of ammonium and amide hydrogens, respectively, using semiempirical calculations were suggested in previous studies by Beauchamp et al. As shown by the current ab initio and DFT calculations completed during this study, the mechanisms proposed in that study are notionally correct; however, the tautomer mechanisms are shown here to be the result of the fact that a second stable isomer of protonated triglycine exists in which the amide1 carbonyl oxygen is protonated. The exchange of the carboxyl hydrogen is found to proceed via a transition state resembling an ammonium ion interacting with a carboxylate moiety via two hydrogen bonds. The current work thus provides significant mechanistic and structural detail for a considerably more in-depth understanding of the processes involved in gas phase H/D exchange of peptides.

The tert -butyl cation ( t Bu + ) is widely used as a chemical ionization reagent ion, for which it is often assumed that simple proton transfer to neutral substrates is the dominant reaction. Mass-analyzed ion kinetic energy (MIKE) spectrometry and the collisionally activated decomposition (CAD) of ions corresponding to the adducts R′O(H)R + formed from mixtures of ROH and R′OH (R = t Bu, R′ = t Bu or 1-methylcyclopentyl, and their deuterated analogues) show a much more complicated pattern of reactivity, which is mirrored in the bimolecular reactions of t Bu + with R′OH in the Fourier transform ion cyclotron resonance (FT-ICR) technique. Production of R′ + in the CAD and FT-ICR experiments is accompanied by isotopic exchange between the alkyl groups, which implicates ion-neutral complexes as accessible intermediates in addition to the covalent adduct ions. A unified pathway for MIKE spectrometry, CAD, and FT-ICR regimes is presented, involving terbody complexes of the form [cation water alkene] as well as two-body complexes of the form [cation alcohol].

Fourier transform ion cyclotron resonance measurements of the deuterium isotope effect have been used to probe the nature of the potential describing the motion of the hydrogen in gas phase ion/molecule hydrogen bond interactions. The hydrogen bonding system studied is fluoride ion solvated by one molecule of aliphatic alcohol, ROH · F−. No variation of the isotope effect with alcohol acidity was observed for unsubstituted aliphatic alcohols. Arguments are presented which imply that the internal rotation of the neutral alcohols plays an important role in the determination of the overall isotope effect, as well as the more commonly considered zero-point energy effects.

The measurement of rate constants for ion/molecule reactions in systems where a continuous ejection of secondary ions interfering in reverse processes is performed requires the use of absolute intensities of primary and secondary ions in the kinetics determination. A general kinetic formalism allows the calculation of the rate constants in the presence of unknown concentrations of impurities, provided that their ion products formed in reaction with the primary ion are well established. The use of this kinetic formalism to study ion/molecule reactions of protonated methyl chloride, CH 4 Cl + , with neutral methyl chloride gave the following rate constants values

The formation of C6H7+ species in ion/molecule reactions in gaseous vinyl chloride was studied in a high pressure photoionization mass spectrometer and in a Fourier transform ion cyclotron resonance (FT-ICR) spectrometer. Collision-induced dissociation (CID) mass spectra of C4H5Cl+, C4H6Cl+, and C6H7+ species suggest a "butadiene-like" structure for the two former ions, and a non-benzenium structure for the last species. The C6H7+ ions are formed in a two-step mechanism involving C4H5+ as intermediate ions. These processes are in competition with condensation reactions leading to the formation of C6H7–9Cl+ species. Key words: ion–molecule reactions, gaseous vinyl chloride, collision-induced dissociation.

Ionic hydrogen bond (IHB) interactions, resulting from the association of ammonia and the two protonated methylxanthine derivatives, caffeine and theophylline, have been characterized using infrared multiphoton dissociation (IRMPD) spectroscopy and electronic structure calculations at the MP2/aug-cc-pVTZ//B3LYP/6-311+G(d,p) level of theory. The proton-bound dimer (PBD) of caffeine and ammonia exhibits a low binding energy and was found to be elusive under the experimental conditions due, most probably, to collision-induced dissociation of the complex with helium buffer gas before IRMPD irradiation. The IRMPD spectrum of a PBD of theophylline and ammonia was obtained and revealed bidentate IHB formation within the complex, which greatly increased the binding energy relative to the most stable isomer of the PBD of caffeine and ammonia. The IRMPD spectra of the protonated forms of caffeine and theophylline have also been obtained. The spectrum of protonated caffeine showed dominant protonation at the N(9) site, whereas the spectrum of protonated theophylline showed a mixture of two isomers. The first protonated isomer of theophylline exhibits protonation at the N(9) site and the second isomer demonstrated protonation at the C(6) carbonyl oxygen. The protonated carbonyl isomer of theophylline cannot be produced as a result of direct protonation and is thus suggested to be a consequence of proton-transport catalysis (PTC) initiated by the electrostatic interaction between water and N(9) protonated theophylline. Calculated anharmonic spectra have been simulated at the B3LYP/6-311+G(d,p) level of theory. It is shown that calculated anharmonic frequencies significantly outperform calculated harmonic frequencies in providing simulated IRMPD spectra in all cases.

Interaction with polar neutral molecules can cause α-distonic radical cations and conventional molecular ions to interconvert in the gas phase, in spite of substantial energy barriers for the unassisted isomerization; the interconversion is particularly facile when the proton affinity of the neutral molecule is close to that of the deprotonated radical cation.

Measurement of the gas phase ion equilibria between ions M and solvent molecules Sl provide binding energies of the complexes M±(S1)n(for n= 1 to ∼6). Comparison of these data with single ion energies of solvation shows that differences in ion solvation in solution are reflected in the binding energies of ion-molecule complexes in the gas phase. The weaker solvation of negative ions (relative to positive ions) observed in liquid aprotic solvents is reflected in the binding energies of negative ion aprotic molecule complexes, a weaker binding being found for the first and subsequent few aprotic molecules. An analysis of the bonding in Cl–(CH3CN) and K+(CH3CN) shows that the weaker bonding to Cl– is due to the very diffuse distribution of the positive pole of the dipole in acetonitrile. In effect the dipole can not come close to the negative ion. Analysis shows a similar picture also for acetone. Experimental results for the bonding between Cl–HR are given for a variety of compounds HR. These show that for RH = protic compounds, like oxygen acids, the hydrogen bond in Cl–HR increases with the acidity of HR. For aprotic compounds, i.e., carbon acids, no relationship between the bond in the complex and the acidity of HR is found. An examination of the solvation of substituted phenoxide ions by protic and aprotic solvents shows that solvation by protic solvents is adversely affected by charge dispersal in the ion, while aprotic solvents are much less sensitive to charge dispersal. The reasons for this important difference in behaviour are examined.