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Infrared multiple photon dissociation spectra of the proton-bound heterodimers of phenylalanine/glycine (Phe·H + ·Gly) and pentafluorophenylalanine/glycine (F 5 -Phe·H + ·Gly) have been acquired in the 975–1975 cm −1 region. Exhaustive basin hopping molecular dynamics searches and subsequent DFT calculations predict four low energy intermolecular binding motifs. The spectrum of F 5 -Phe·H + ·Gly is assigned predominantly to isomers exhibiting a N H + ⋯O intermolecular interaction between nitrogen-protonated Gly and the carbonyl oxygen atom of F 5 -Phe. In contrast, the spectrum Phe·H + ·Gly is found to consist of a mixture of isomers exhibiting the N H + ⋯O between nitrogen-protonated Gly and the carbonyl oxygen of neutral Phe, and isomers exhibiting a N H + ⋯N interaction between nitrogen-protonated Phe and the neutral Gly moiety. Cation-π effects also seem to influence the cluster geometries, especially in the case of the Phe·H + ·Gly global minimum structure where the phenyl ring orients with the site of protonation so as to maximize charge-quadrupole interactions.

A Hammett plot is a useful tool in physical organic chemistry for determining the effect of substituents on reaction rates and equilibria. In this work, gas phase energetics calculated at the relatively low computational cost B3LYP/6-311++G** level of theory for the ionization of benzoic acids and phenols have been shown to be in excellent agreement with experimental values. These data were used to generate theoretical Hammett plots for the gas phase ionization of substituted phenylacetic acids and phenols, in which good correlation was shown. To determine the effect of solvation on ionization, the calculated energetics for the gas phase ionization of benzoic acids and phenols were compared to experimental solution phase energetics. Resulting ρ values obtained demonstrated the pronounced effect of solvent in damping substituent effects. Overall, a good correlation between experimental solution phase and computational gas phase energetics was shown.

Infrared Multiple Photon Dissociation (IRMPD) Spectroscopy has been used to generate gas phase vibrational spectra for six protonated tetracycline derivatives: chlortetracycline, meclocycline, minocycline, doxycycline, tetracycline, and metacycline. The IRMPD spectrum for protonated chlortetracycline is compared here to theoretical gas phase vibrational spectra obtained from geometry optimization and frequency electronic structure calculations using the B3LYP hybrid density functional method with the 6-311 + G(d,p) basis set. The most energetically favorable protonation sites, tautomer structures, and hydrogen bond orientations were determined. Protonation at the dimethyl amine functional group and an extensive hydrogen bonding network lead to the most energetically favourable structures. Calculated spectra directly resembled the IRMPD spectrum, supporting the conclusion that the probable gas phase structure of protonated chlortetracycline has been determined.

The formation of strong and very strong hydrogen bonds between NFnH3−n (n = 0.2) and F− have been computationally investigated via B3LYP/6-311++G(d,p) geometry optimizations and MP2/6-311++G(d,p) single point energy calculations. The enthalpy of deprotonation of NF2H was found to be 1518.5 kJ mol−1. The hydrogen bond energy in NH3⋯F−, NFH2⋯F− and NF2H⋯F− were calculated to be 67.9, 120.2 and 181.2 kJ mol−1, respectively, and clearly show the effect of fluorination on hydrogen bond strength in amine–fluoride systems. The change in enthalpy and entropy for the clustering of methanol to NF2H⋯F− to form the fluoride bound dimer of methanol and difluoramine has been measured via high pressure mass spectrometry to be 68.3 kJ mol−1 and 90.5 J K−1 mol−1. These values are in excellent agreement with calculated values of 70.9 kJ mol−1 and 88.5 J K−1 mol−1.

The equilibria involved in the formation of the proton-bound dimers of the three simplest amino acid methyl esters (glycine, alanine and valine methyl esters) were characterized by means of pulsed ionization high pressure mass spectrometry (PHPMS) experiments and density functional theory (DFT) calculations. Our results would indicate that, within the temperature range employed in these experiments, the most stable proton-bound dimer conformers are formed in the case of glycine and alanine whereas a more entropically favoured isomer would dominate in the case of valine. Various possible isomers of each of the proton-bound dimer species have been investigated computationally each exhibiting a combination of inter- and intramolecular hydrogen bonding. A system of nomenclature for these various species is proposed. The possibility of structures exhibiting 'salt-bridge’ interactions have also been explored, recognizing that such structures would necessarily result from highly energetic structural rearrangements.

The standard enthalpy and entropy changes (ΔH° and ΔS°) for the formation of solvated SN2 complexes (S)X−(RY) (X, Y = Cl, Br; R = (CH3)2CH; S = CH3OH, CH3CN, (CH3)2CO, CH3CF2H) have been determined by pulsed-ionization high pressure mass spectrometry. Not surprisingly, solvent effects are evident even at this mono-salvation level. Structures of solvated SN2 complexes and transition states for the Cl−(S) + CH3Cl SN2 reaction (S = H2O, H2S, NH3, PH3, SO2) have also been determined at the MP2/6-31+G(d) level of theory. A large variety of solvent dependent structures have been obtained, showing solvent reorganization upon going from the complex to the transition state. Standard binding and activation enthalpies ( Δ H 298 ∘ and Δ H 298 ‡ ) were determined at the MP2/6-311+G(3df,2p)//MP2/6-31+G(d,p) level of theory. For the Cl−(H2O) + CH3Br and Br−(H2O) + CH3Cl reactions, structures and enthalpies were calculated at the MP2/[6-31+G(d)/LanL2DZ(spd)] and MP2/[6-311+G(3df,2p)/LanL2DZ(spdf)]//MP2/[6-31+G(d)/LanL2DZ(spd)] level of theory. For the Cl− + CH3Br and Cl−(H2O) + CH3Br reactions potential energy surface scans were performed at the MP2/[6-31+G(d)/LanL2DZ(spd)] level of theory. Formation of the two possible sets of solvated products, Br−(H2O) + CH3Cl and Br− + (CH3Cl)(H2O) proceeds through two different surfaces. Water transfer to the leaving group can be facilitated by rotation of the Br−(CH3Cl) part in the exit channel Br−(CH3Cl)(H2O) complex. Finally, for the Cl− + CH3Cl reactions in the condensed phase, complexation and activation energies (ΔE(ɛ) and ΔE‡(ɛ)) were determined for a variety of solvents at the MP2/6-31+G(d) level of theory using the isodensity polarized continuum model. A linear correlation between −ΔE(ɛ) and ΔE‡(ɛ) was obtained, and a similar correlation exists for the mono-solvated gas phase SN2 reaction, indicating that mono-solvation already exhibits some features of the condensed phase reaction.

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 thermochemistry of the chloride ion clustering onto dimethyl ether, diethyl ether, and three fluorinated ethers (CH 3 OCF 3 , (CF 2 H) 2 O, and CF 3 OCF 2 H) under thermal equilibrium conditions has been determined using pulsed-ionization high pressure mass spectrometry. The standard enthalpy (Δ H °) and entropy change (Δ S °) values obtained indicate a variety of different types of bonding in these complexes. The mode of binding is mainly determined by the number of fluorine atoms present and by the substitution pattern. In addition ab initio computational methods have been used to obtain more insight into the structures and energetics. Δ H ° 298 value calculated at the MP2/[6-311 ++ G(3 df ,3 pd )/6-311 + G(2 df , p )]//MP2/[6-31 + G( d )/6-31G( d )] level of theory show excellent agreement with the experimentally obtained Δ H ° values.

The use of multiple overlapping gaseous ion–molecule equilibrium measurements to construct thermochemical ladders is reviewed. The types of relative thermochemical data, which may be obtained, are summarized and the types of measurements required to convert the relative equilibrium affinity scales to absolute thermochemical quantities are discussed. The important thermochemical scales produced include proton affinities, gas phase acidities, ionization energies, electron affinities, carbocation stabilities, hydrogen bond energies, Lewis acidities, and metal cation affinities.

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

Fourier transform ion cyclotron resonance experiments have been carried out to probe the nature of the potential energy surface for the reaction of methyl cation (CH3+) with methane (CH4) to give the ethyl cation (C2H5+). Product distributions for reactions of CH3+ and CD3+ with CD4 and CH4, respectively, are found to give a near statistical distribution of ethyl cation products, in good agreement with previous work. When the methyl cation is initially coordinated to HF in the form of a methylfluoronium ion, however, the product distributions are decidedly nonstatistical and are indicative of a reaction which is very nearly thermoneutral. Thermochemical data for relevant species suggest that the reaction is very slightly endothermic. All of the experiments support the intermediacy of a C2H7+ complex in the reactions. Ab initio calculations, in conjunction with all of the experimental data, reveal that there are likely three different stable forms of C2H7+ involved in the potential energy surface for the reaction. One of the forms, a nonclassical C2H5+ coordinated to H2 in a proton bound dimerlike structure, has not previously been considered to play a role in this reaction. The existence of this structure is supported by infrared multiphoton dissociation experiments on C2H7+ previously carried out by Lee and co-workers (J. Am. Chem. Soc. 111 (1989) 5597) and the high pressure mass spectrometric experiments of Hiraoka and Kebarle (J. Am. Chem. Soc. 98 (1976) 6119).

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.

Kinetic and thermodynamic isotope effects on the unimolecular dissociation of proton bound dimers were studied in the gas phase using mass spectrometry techniques. In addition proton transfer reactions were investigated using equilibrium techniques in conjunction with a theoretical study. Normal isotope effects were observed for all of the amine systems studied. The effect of label position, extent of labeling, size and structure of the proton bound dimers have been discussed with respect to (i) the kinetic and thermodynamic isotope effect on the dissociation reaction, (ii) the kinetic energy release on the dissociation reaction, (iii) the thermodynamic isotope effect on the proton exchange reaction between the labeled and unlabeled amines, and (iv) the effective temperatures and the excess energies of the metastable proton bound dimers. Other compound classes (CH3OH, (CH3)2O, CH3CN and (CH3)2CO) were studied and discussed in the same way, though not as thoroughly. All the systems show normal isotope effects, except for the proton bound dimer of CH3CN and CD3CN, which showed an inverse isotope effect.

The spontaneous dissociation of mixed proton bound dimers of nitrile bases has been studied using mass-analyzed ion kinetic energy spectra in a reverse geometry double focusing instrument coupled to a high pressure ion source. A linear correlation was found between the relative ion abundance ratios of the fragments and the ion source temperature. Proton exchange equilibria between the bases were studied using the time resolved capability of the high pressure mass spectrometry system, and relative ΔG°, ΔH°, and ΔS° values were extracted from the van't Hoff plots. The proton affinities (PA) of the nitriles studied were found to be PA(MeCN) = 186.8 kcal/mol, PA(EtCN) = 189.9 kcal/mol, PA (n-PrCN) = 191.0 kcal/mol, and PA(i-PrCN) = 192.2 kcal/mol. The effective temperatures of the metastable protonated nitrile dimers at different ion source temperatures were obtained from a plot of In(I RCN /I ref. ) versus ΔGB (relative gas phase basicity). From a plot of the effective temperature of the protonated metastable nitrile dimers reacting in the second field free region of the mass spectrometer versus the ion source temperature, it was found that the effective temperature decreases with increasing ion source temperature, which can be explained from qualitative considerations of the relevant thermal Boltzmann distributions.

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 slow, low pressure, unimolecular dissociation reactions of the weakly bound cluster ions, [(CH 3 ) 2 CO]·Cl − ,(C 6 H 6 ·Cl − and (CH 3 OCH 3 ) n ·H 3 O + ( n = 2, 3), and their deuterated analogues have been examined by Fourier transform ion cyclotron resonance spectrometry. The unimolecular dissociation rate constant is found to be faster, in all cases, for the deuterium-substituted species; however the magnitude of this increase is ligand and cluster dependent. This observation is attributed to the vibrational frequency shifts of the infrared absorptions of each of the ligand species upon deuteration. The results obtained provide further support for the black-body radiation induced, unimolecular dissociation mechanism for weakly bound cluster ions at low pressure.

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

A Fourier transform ion cyclotron resonance (ICR) spectrometer has been used to determine bond dissociation energies via translation energy controlled collisions between mass-selected ions and a stationary target gas. The ions examined were the proton-bound dimers of diethyl ether, acetone and water, which were generated in a high pressure external ion source. A comparison between bond dissociation energies obtained with this technique and literature values showed that the r.f. excitation of ions in the ICR cell produced ions with a well-defined translation energy. Moreover, the translational energy distribution of the ions was narrow, as indicated by the fact that experimentally obtained threshold curves for dissociation were close to computed curves corrected for Doppler broadening.

The low pressure association reactions for the proton bound dimers of acetonitrile, acetone, dimethyl ether and diethyl ether have been studied using Fourier transform-ion cyclotron resonance spectrometry. Values for the rate constants for the unimolecular decomposition and radiative stabilization reactions of the intermediate proton bound dimer are determined. Trends of molecular size and number of normal modes are examined for unimolecular lifetimes of the association intermediate. No apparent trends are observed to allow the prediction of radiative stabilization lifetimes.

A new external high pressure ion source has been designed, constructed and successfully coupled to a Fourier transform-ion cyclotron resonance (FT-ICR) spectrometer. This instrument incorporates three stages of differential pumping, pulsed electron gun ionization, electrostatic ion optics and novel cylindrical decelerator lens. Theoretical aspects of ion transfer of externally generated ions to the ICR cell are discussed as are the physical characteristics of the decelerator lens. The nine orders of magnitude pressure differential between ion source and ICR cell permit the synthesis of extensively solvated ions whose chemistry can subsequently be examined in detail in the ICR cell. Several Examples of such chemistry are illustrated.

A newly constructed pulsed ionization high-pressure mass spectrometer has been used to examine the methyl cation transfer equilibria between the methylated adducts of acetone and dimethyl ether and the parent compounds. The data indicate that dimethyl ether is a stronger base toward CH+3 than is acetone, a reversal from the proton affinity order. Clustering equilibria of (CH3)2COCH+3 with the acetone and dimethyl ether have also been examined. The thermochemical data obtained show that the adducts are covalently bound species with considerable restriction of internal rotations. New thermochemical data for ΔHof and So for all species observed are reported.