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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.

Gas-phase clusters of protonated methylamine and phenylalanine (Phe) derivatives have been studied using infrared multiple photon dissociation (IRMPD) spectroscopy in combination with electronic structure calculations at the MP2/aug-cc-pVTZ//B3LYP/6-311+G(d,p) level of theory. Experiments were performed on several Phe derivatives including 4-chloro-l-phenylalanine (4Chloro-Phe), 4-nitro-l-phenylalanine (4Nitro-Phe), 3-cyano-l-phenylalanine (3Cyano-Phe), and 3-trifluoromethyl-l-phenylalanine (3CF3-Phe). Through comparisons between experimental IRMPD spectra and stimulated spectra obtained by electronic structure calculations, charge-solvated structures were found to be prevalent in both 4Chloro-Phe and 4Nitro-Phe, whereas 3Cyano-Phe favored zwitterionic structures and 3-CF3-Phe likely have both zwitterionic and charge-solvated structures present.

The binding motifs in the halide adducts with tyrosine ([Tyr + X]−, X = Cl, Br, I) have been investigated and compared with the analogues with 3-nitrotyrosine (nitroTyr), a biomarker of protein nitration, in a solvent-free environment by mass-selected infrared multiple photon dissociation (IRMPD) spectroscopy over two IR frequency ranges, namely 950–1950 and 2800–3700 cm−1. Extensive quantum chemical calculations at B3LYP, B3LYP-D3 and MP2 levels of theory have been performed using the 6-311++G(d,p) basis set to determine the geometry, relative energy and vibrational properties of likely isomers and interpret the measured spectra. A diagnostic carbonyl stretching band at ∼1720 cm−1 from the intact carboxylic group characterizes the IRMPD spectra of both [Tyr + X]− and [nitroTyr + X]−, revealing that the canonical isomers (maintaining intact amino and carboxylic functions) are the prevalent structures. The spectroscopic evidence reveals the presence of multiple non-covalent forms. The halide complexes of tyrosine conform to a mixture of plane and phenol isomers. The contribution of phenol-bound isomers is sensitive to anion size, increasing from chloride to iodide, consistent with the decreasing basicity of the halide, with relative amounts depending on the relative energies of the respective structures. The stability of the most favorable phenol isomer with respect to the reference plane geometry is in fact 1.3, −2.1, −6.8 kJ mol−1, for X = Cl, Br, I, respectively. The change in π-acidity by ring nitration also stabilizes anion–π interactions yielding ring isomers for [nitroTyr + X]−, where the anion is placed above the face of the aromatic ring.

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.

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 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.

A combination of infrared multiple photon dissociation (IRMPD) spectroscopy and density functional theory calculations have been employed to study the structures and mode-specific dissociation pathways of the proton-bound dimer of 3-trifluoromethylphenylalanine (3-CF3-Phe) and trimethylamine (TMA). Three structural motifs are identified: canonical (charge-solvated), zwitterionic (charge-separated), and TMA-bridged. In the 1000-1350 cm(-1) region, similar spectra are observed in the TMA·H(+) and 3-CF3-Phe·H(+) product channels. At wavenumbers above 1350 cm(-1), infrared excitation of charge-solvated structures leads exclusively to production of protonated TMA, while excitation of zwitterionic or TMA-bridged structures results exclusively in production of protonated 3-CF3-Phe. The cluster potential energy landscape is topologically mapped and mechanisms for isomerization and mode-selective dissociation are proposed. In particular, cluster transparency as a result of IR-induced isomerization is implicated in deactivation of some IRMPD channels.

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.

Infrared multiple photon dissociation spectra for the chloride ion solvated by either water, methanol or ethanol have been recorded using an FTICR spectrometer coupled to a free-electron laser, and are presented here along with assignments to the observed bands. The assignments made to the Cl(-)/H(2)O, Cl(-)(CH(3)OH), and Cl(-)(CH(3)CH(2)OH) spectra are based on comparison with the neutral H(2)O, CH(3)OH, and CH(3)CH(2)OH spectra, respectively. This work confirms that a band observed around 1400 cm(-1) in the Cl(-)(H(2)O) spectrum is not due to the Ar tag in Ar predissociation spectra. The carrier of this band is, most likely, the first overtone of the OHCl bend. Based on the position of the overtone in the IRMPD spectrum, 1375 cm(-1), the fundamental must occur very close to 700 cm(-1) and observation of this band should aid theoretical treatments of the spectrum of this complex. B3LYP/6-311++G(2df,2pd) calculations are shown to reproduce the IRMPD spectra of all three solvated chloride species. They also predict that attaching one or two Ar atoms to the Cl(-)(H(2)O) complex results in a shift of no more than a few wavenumbers in the fundamental bands for the bare complex, in agreement with previous experiment. For both alcohol-Cl(-) complexes, the S(N)2 "backside attack" isomers are not observed and Cl(-) is predicted theoretically, and confirmed experimentally, to be bound to the hydroxyl hydrogen. For Cl(-)(CH(3)CH(2)OH), the trans and gauche conformers are similar in energy, with the gauche conformer predicted to be thermodynamically favoured. The experimental infrared spectrum agrees well with that predicted for the gauche conformer but a mixture of gauche and anti conformers cannot be ruled out based on the experimental spectra nor on the computed thermochemistry.

The stationary points on the potential energy surfaces for a number of gas-phase S(N)2 reactions have been determined using a combination of pulsed ionization high-pressure mass spectrometry. MP2/6-311++G**//B3LYP/6-311+G** calculations are shown to provide excellent agreement with the experimentally determined values, providing confidence for the use of this computational method to predict values that are not available experimentally. The binding in the halide/nitrile complexes has been described in the past as either hydrogen bonding or electrostatic bonding. The trends in the binding energies observed here, though, cannot be rationalized in terms of simply hydrogen bonding or ion-dipole bonding but a mixture of the two. The computed structures support the description of binding as a mixture of hydrogen bonding and ion-dipole bonding.

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.

Benzylium versus tropylium ion yields from the fragmentation of ethylbenzene cations at various excitation energies are studied by forming excited ethylbenzene cations by charge transfer from a series of chargetransfer agents and by identifying the benzylium ion by its secondary reaction with neutral ethylbenzene. At lower excitation energies, the tropylium ion yield decreases with increasing energy from values near 16% (at an energy of 230 kJ mol -1 ) to 5% (at an energy of 500 kJ mol -1 ). At higher excitation energies, the tropylium ion yield increases again, which is attributed to secondary isomerization of the vibrationally highly excited benzylium ion arising from the primary fragmentation. It is suggested that this isomerization competes with radiative cooling of the excited benzylium ion. The experimental observations are rationalized in the framework of statistical unimolecular rate theory and electronic structure calculations.

The rate constants for H-D exchange reactions of sodiated polyglycines (GnNa(+), n = 2-8) and polyalanines (AnNa(+), n = 2, 3 and 5) with ND3 have been measured in the cell of an FT-ICR mass spectrometer. All peptides except G2Na(+) are found to undergo three exchange reactions, all of which are consecutive with no sign of multiple exchanges within a single collision event. This information has been used to construct full mechanistic scenarios with the help of detailed quantum chemical calculations of the possible reaction paths for H-D exchange. The first exchange is always located at the C terminus however with different mechanisms depending upon whether the peptide termini can (larger peptides) or cannot (smaller peptides) interact directly without strong energy penalty. The most favourable mechanisms for the second and third exchanges of the N terminus protons, are found to be different from those for the first for all peptide sizes. The peptide distortions that are necessary in order for some of these reactions to occur are made possible by the energy reservoir provided by the favorable interaction of the peptide ion with ND3. Their occurrence and variety preclude any general relationship between H-D exchange kinetics and the most stable ion structures. There is however a break at G7Na(+) in the kinetics trend, with a first exchange rate which is much smaller than for all other peptide sizes. This break can be directly related to a different structural type in which the C terminus is neither free nor close to the N terminus.

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.

Alkyl cation transfer reactions between ethanol and protonated ethanol and ethanol and protonated propionitrile, as well as between n-propanol and protonated n-propanol have been investigated experimentally by low-pressure Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. The two ethyl cation transfer reactions were found to be the dominant reaction channels with association being only a minor reaction pathway. The n-propyl cation transfer reaction was found to compete with the association pathway resulting in an approximately 50:50 mixture of protonated di-n-propyl ether and the proton-bound dimer of n-propanol, depending on temperature and pressure. The enthalpies of activation were determined to be −16.1 ± 0.8, −17.5 ± 0.8, and −15.7 ± 0.9 kJ mol-1 for the ethanol/protonated ethanol, ethanol/protonated propionitrile, and n-propanol/protonated n-propanol alkyl cation transfer reactions, respectively. The entropies of activation were found to be essentially the same, −121 ± 28 J K-1 m...

The reactions of protonated diethyl ether with ethanol and protonated di-n-propyl ether with n-propanol, producing the mixed proton-bound dimers, were studied at low pressures in a FTICR cell. The pressure dependence of the apparent rate constant for proton-bound dimer formation was investigated and yielded unimolecular dissociation rate constants, kb, and photon emission rate constants, kra, for the nascent proton-bound dimers at internal energies equal to the dissociation energies of the dimers. The experimental kra values were found to be 17 ± 3 and 6.3 ± 0.6 s-1, respectively, for the ethanol/diethyl ether and n-propanol/di-n-propyl ether proton-bound dimers. RRKM modeling of the unimolecular dissociation rate constants as a function of the binding energies yielded the 0 K dissociation energies of the proton-bound dimers as 109 ± 1 and 105.1 ± 0.6 kJ mol-1 for the ethanol/diethyl ether and n-propanol/di-n-propyl ether proton-bound dimers, respectively. Using B3LYP/6-311G** thermal energies, the corres...

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.

C–H···X (where X = O or S) intramolecular hydrogen bonding is investigated in three benzyl Meldrum’s acid derivatives using a combination of solution phase NMR spectroscopy, gas phase infrared multiple photon dissociation spectroscopy, and density functional theory calculations. In one compound, an abnormally large C–H···S hydrogen bond energy of 30.4 kJ mol–1 is calculated with a natural bond orbital analysis. Intramolecular C–H···O hydrogen bonding is found to persist in the gas phase. Gibbs energy decomposition pathways are calculated.

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.

Methyl cation transfer reactions between methanol and protonated methanol, protonated acetonitrile, and protonated acetaldehyde have been investigated experimentally by low-pressure FT-ICR mass spectrometry. The temperature dependencies of the rate constants for these reactions were determined in an Arrhenius-type analysis to obtain activation energies, enthalpies, and entropies of activation. The enthalpies of activation were determined to be -16.9 ( 0.6, -16.5 ( 0.6, and -18.4 ( 0.7 kJ mol -1 for the methanol/protonated methanol, methanol/protonated acetonitrile, and methanol/protonated acetaldehyde reactions, respectively. These values agree quite well with ab initio-calculated values. The entropies of activation were found to be quite similar for all three reactions within experimental uncertainty, which is expected due to the similar transitionstate structures for all reactions. Ab initio potential energy surfaces calculated at the MP2/6-311G** level and basis set are reported for the three reactions. For the methanol/protonated acetonitrile and methanol/ protonated acetaldehyde reactions, isomerization of the initially produced proton-bound dimer to a methylbound complex is suggested prior to methyl cation transfer. The barrier for the first isomerization is predicted to be significantly lower than the barrier for methyl cation transfer such that it does not interfere with the experimental determination of the latter.

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.

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.

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

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).

Proton exchange reactions between acetate, n-butanoate, 2-ethylhexanoate, and n-decanoate were studied experimentally by the use of PHPMS and theoretically by the use of ab initio methods. The occurrence of a curvature in some of the van't Hoff plots suggests isomerization of at least one of the participants in the equilibrium. This isomerization is suggested to be an intramolecular solvation of the carboxylate anions via unconventional hydrogen bonding. These interactions are discussed in terms of charge distributions in the unfolded and folded conformers of the carboxylates. Thermochemical values for the intramolecular solvation were deconvoluted from the curved van't Hoff plots by a fitting procedure. The thermochemical data for the intramolecular solvation was used to calculate the conformer composition of the carboxylate anions. Various properties related to the intramolecular solvation of the carboxylate anions are discussed.

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.

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.

A new experimental apparatus is described which permits the determination of binding energetics for metal−ligand complexes. This technique mates laser ablation for the generation of atomic metal ions with the environment of a high-pressure ion source which leads to rapid termolecular stabilization of metal ion-ligand complexes containing one or more ligands. The time resolved capability of the detection system allows equilibrium to be studied quantitatively for binding energies in the range of 5−30 kcal mol-1. Such measurements of the absolute binding energy of formaldehyde to Al+ combined with existing bimolecular Al+ exchange equilibrium data leads to an absolute Al+ affinity scale. For two ligand complexes an extensive ab initio search of the potential energy surfaces shows that the experimentally observed species involving CH3CN and (CH3)2O involve simple ligand complexation with an acute L-Al−L bond angle (L = ligand) rather than hydrogen bonded or inserted structures. In one instance a third ligand ...

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.

Studies of unimolecular dissociation (MIKES) of ions formed in a chemical ionization ion source show that under CI conditions, the reaction of CH3+ with CH3OH or CH3OCH3 leads to the covalent structures (CH3)2OH+ or (CH3)3O+. In contrast a FT-ICR study indicates that these reactions lead either to covalent structures by C−O bond formation and to [CH3+/CH3OH] or [CH3+/CH3OCH3] ion−neutral complexes. Ab initio calculations confirm that such complexes correspond to minima on the potential energy surface. Their geometries correspond to a species in which a hydrogen of the CH3+ cation is weakly bonded to the oxygen of the neutral. The interaction energies are ∼20 kcal/mol.

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 structures of sodiated polyalanine peptides containing 8−12 residues are investigated using infrared multiple photon dissociation (IRMPD) spectroscopy and classical and quantum modeling. Calculations indicate that the α-helical structure is the most stable conformation for the peptides whatever their size. The IRMPD spectra provide evidence for the coexistence of helical and globular shapes for Ala8Na + , and possibly for Ala9Na + . The turning point from globule to helix is thus found at Ala8−9Na + . The N−H and O− H stretching region allows identifying a new spectroscopic pattern typical for α-helical structures of polyalanines. SECTION: Biophysical Chemistry and Biomolecules

Ionic hydrogen-bonding interactions have been found in several clusters formed by 5-fluorocytosine (5-FC). The chloride and trimethylammonium cluster ions, along with the cationic (proton-bound) dimer have been characterized by infrared multiple-photon dissociation (IRMPD) spectroscopy and electronic structure calculations performed at the B2PLYP/aug-cc-pVTZ//B3LYP/6-311+G(d,p) level of theory. IRMPD action spectra, in combination with calculated spectra and relative energetics, indicate that it is most probable that predominantly a single isomer exists in each experiment. For the 5-FC-trimethylammonium cluster specifically, the calculated spectrum of the lowest-energy isomer convincingly matches the experimental spectrum. Interestingly, the cationic dimer of 5-FC was found to have a single energetically relevant isomer (Cationic-IV) involving a tridentate ionic hydrogen-bonding interaction. The three sites of intermolecular ionic hydrogen bonds in this isomer interact very efficiently, leading to a significant calculated binding energy of 180 kJ/mol. The magnitude of the calculated binding energy for this species, in combination with the strong correlation between the simulated and IRMPD spectra, suggests that a tridentate-proton-bound dimer was observed predominantly in the experiments. Comparison of the calculated relative Gibbs free energies (298 K) for this species and several of the other isomers considered also supports the likelihood of the dominant protonated dimer existing as Cationic-IV.

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.

An examination of strong hydrogen bonds found in (ROH)(n)...FHF(-) clusters (n = 1 and 2; R = H, CH(3), C(2)H(5)) is presented. Excellent agreement is observed between thermochemical values obtained from high-pressure mass spectrometric measurements and those predicted from MP2(full)/6-311++G(d,p)//B3LYP/6-311++G(d,p) calculations. Calculated structures are examined, and insight into the geometric nature of the bonding for these systems is obtained. In the case of water binding to FHF(-), it was found that the large entropic advantage of one particular structure, which was not the most enthalpically favored, was significant enough to make it the predominant species within the ion source. In the case of methanol solvation, no evidence of secondary interaction of the methyl group and any other moiety could be found. The structural details revealed from calculations of the ethanol-solvated clusters indicate that secondary interactions between the terminal methyl group and FHF(-) have an impact on the length of the FHF and OHF bonds.

The thermochemical properties associated with the formation of an isomeric distribution of ROHNH(2)CH(2)COO(-) clusters (R=H, CH(3), C(2)H(5)) are measured by using high-pressure mass spectrometry. A comparison of the measured properties with calculated values provides new insights into the thermochemical effects arising from the isomeric nature of this clustering system. When the distribution of isomers is correctly accounted for, the measured values of DeltaH degrees , DeltaS degrees , and DeltaG degrees (298) consistently agree, to a very high degree of accuracy, with those predicted by MP2(full)/6-311++G(d,p)//B3LYP/6-311++G(d,p) calculations.

The protonation sites and structures of a series of protonated amino acids (Gly, Ala, Pro, Phe, Lys and Ser) are investigated by means of infrared multiple-photon dissociation (IRMPD) spectroscopy and electronic-structure calculations. The IRMPD spectra of the protonated species are recorded using the combination of a free-electron laser (FEL) and an electrospray-ion-trap mass spectrometer. The structures of different possible isomers of these protonated species are optimized at the B3LYP/6-311+G(d, p) level of theory and the IR spectra calculated using the same computational method. For every amino acid studied herein, the current results indicate that a proton is bound to the alpha-amino nitrogen, except for lysine, in which the protonation site is the amino nitrogen in the side chain. According to the calculated and experimental IRMPD results, the structures of the protonated amino acids may be assigned unambiguously. For Gly, Ala, and Pro, in each of the most stable isomers the protonated amino group forms an intramolecular hydrogen bond with the adjacent carbonyl oxygen. In the case of Gly, the isomer containing a proton bound to the carbonyl oxygen is theoretically possible. However, it does not exist under the experimental conditions because it has a significantly higher energy (i.e. 26.6 kcal mol(-1)) relative to the most stable isomer. For Ser and Phe, the protonated amino group forms two intramolecular hydrogen bonds with both the adjacent carbonyl oxygen and the side-chain group in each of the most stable isomers. In protonated lysine, the protonated amino group in the side chain forms two hydrogen bonds with the alpha-amino nitrogen and the carbonyl oxygen, which is a cyclic structure. Interestingly, for protonated lysine the zwitterionic structure is a local minimum energy isomer, but the experimental spectrum indicates that it does not exist under the experimental conditions. This is consistent with the fact that the zwitterionic isomer is 9.2 kcal mol(-1) higher in free energy at 298 K than the most stable isomer. The carbonyl stretching vibration in the range of 1760-1800 cm(-1) is especially sensitive to the structural change. In addition, IRMPD mechanisms for the protonated amino acids are also investigated.

Density functional theory computations and pulsed-ionization high-pressure mass spectrometry experiments have been used to explore the potential energy surfaces for gas-phase S(N)2 reactions between halide ions and trifluoromethyl halides, X(-) + CF(3)Y --Y(-) + CF(3)X. Structures of neutrals, ion-molecule complexes, and transition states show the possibility of two mechanisms: back- and front-side attack. From pulsed-ionization high-pressure mass spectrometry, enthalpy and entropy changes for the equilibrium clustering reactions for the formation of Cl(-)(BrCF(3)) (-16.5 +/- 0.2 kcal mol(-1) and -24.5 +/- 1 cal mol(-1) K(-1)), Cl(-)(ICF(3)) (-23.6 +/- 0.2 kcal mol(-1)), and Br(-)(BrCF(3)) (-13.9 +/- 0.2 kcal mol(-1) and -22.2 +/- 1 cal mol(-1) K(-1)) have been determined. These are in good to excellent agreement with computations at the B3LYP/6-311+G(3df)//B3LYP/6-311+G(d) level of theory. It is shown that complex formation takes place by a front-side attack complex, while the lowest energy S(N)2 reaction proceeds through a back-side attack transition state. This latter mechanism involves a potential energy profile which closely resembles a condensed phase S(N)2 reaction energy profile. It is also shown that the Cl(-) + CF(3)Br --Br(-) + CF(3)Cl S(N)2 reaction can be interpreted using Marcus theory, in which case the reaction is described as being initiated by electron transfer. A potential energy surface at the B3LYP/6-311+G(d) level of theory confirms that the F(-) + CF(3)Br --Br(-) + CF(4) S(N)2 reaction proceeds through a Walden inversion transition state.

International audience; Infrared multiphoton dissociation spectra of three homogeneous and two heterogeneous proton-bound dimers were recorded in the gas phase. Comparison of the experimental infrared spectra recorded in the fingerprint region of the proton-bound dimers with spectra predicted by electronic structure calculations shows that all modes which are observed contain motion of the proton oscillating between the two monomers. The O-H-O asymmetric stretch for the homogeneous dimers is shown to occur at around 800 cm-1. As expected, the O-H-O asymmetric stretching modes for the heterogeneous proton-bound dimers are observed to shift to significantly higher energy with respect to those for the homogeneous proton-bound dimers due to the asymmetry of the O-H-O moeity. This shift is shown to be predictable from the difference in proton affinities between the two monomers. Density functional predictions of the infrared spectra based on the harmonic oscillator model are demonstrated to predict the observed spectra of the homogeneous proton-bound dimers with reasonable accuracy. Calculations of the structure and infrared spectrum of protonated diglyme at the B3LYP/6-31+G** level and basis also agree well with an infrared spectrum recorded previously. For both heterogeneous proton-bound dimers, however, the predicted spectra are blue-shifted with respect to experiment.

International audience; The frequency-dependent gas-phase infrared multiple photon dissociation (IRMPD) spectrum for the proton-bound dimer of water is reported. The present spectrum is shown to be only in fair agreement with a spectrum reported in an earlier communication but is in agreement with spectra predicted by theoretical means. Two different possible assignments of the observed infrared bands are provided. The first is based on the harmonic oscillator approximation from density functional theory calculations, and a second is based on a quantum four-dimensional model calculation of anharmonic frequencies and intensities. Both calculated spectra agree fairly well, but the density functional calculation assignments are in better agreement. This is expected despite the anharmonic nature of the asymmetric stretch due to the flat potential energy surface associated with this mode.

The unimolecular isomerization of CH3COCH3+· 1 into its more stable enol counterpart CH3C(OH)CH2+· 2 is known not to occur, as a significant energy barrier separates these ions. However, it is shown in this work that this isomerization can be catalyzed within a 1 : 1 ion-neutral complex. For instance, a Fourier transform ion cyclotron resonance mass spectrometry study shows that one, and only one, molecule of isobutyronitrile catalyzes the isomerization of 1 into 2. The rather low efficiency of the reaction (12%), as well as the strong isotope effect observed when CD3COCD3+· is used as the reactant ion, suggest that the catalyzed isomerization implicates a substantial intermediate energy barrier. This was confirmed by ab initio calculations that allow us to propose an isomerization mechanism in agreement with this experiment. The efficiency of different catalysts was studied. To be efficient, the catalyst must be basic enough to abstract a proton from the methyl group of ionized acetone but not too basic to give back this proton to oxygen. In other words, the proton affinity (PA) of an efficient catalyst must lie, in a first approximation, between the PA of the radical CH3COCH2· at the carbon site (PAC) and its PA at the oxygen site (PAO), which have been determined to be, respectively, 185.5 and 195.0 kcal mol−1. Most of the neutral compounds studied follow this PA rule. The inefficiency of alcohols in the catalytic process, although their PAs lie in the right area, is discussed. Keywords: Catalyzed keto-enol tautomerism; gas-phase proton transport; isomerization kinetics; proton affinity rule; FT-ICR mass spectrometry

International audience; Fourier transform ion cyclotron resonance experiments show that a variety of molecules catalyze the hydrogen transfer which converts ionized acetaldehyde CH3CHO.+ 1 to its vinyl alcohol counterpart CH2CHOH.+ 2. Each of these ions has been characterized by its specific bimolecular reactions with selected reactants. Calculations show that two pathways, for which the rate determining barriers have almost the same energy, are feasible. The first transition state involves a direct catalyzed 1,3-H transfer, while the second involves two successive 1,2-H transfers. A detailed experimental study, using methanol as a catalyst as well as labeled reactants, indicates that only the first pathway operates in the isomerization process. The different steps of these two independent pathways were elucidated. The first begins with the formation of a highly stabilized complex 3, involving a two-center-three-electron interaction between the two oxygen atoms and an interaction between a hydrogen of the methyl group of 1 and the oxygen of methanol. This complex isomerizes into a complex 4, which in turn gives the complex 5, via a transition state located 6.3 kcal mol-1 below the energy of the reactants. This complex 5 corresponds to ionized vinyl alcohol hydrogen bonded to the oxygen of methanol, which dissociates to yield ion 2. The second pathway begins with the interaction between the hydrogen of the CHO group and the oxygen of methanol and gives the complexes 6 and then 7, which correspond to protonated methanol hydrogen bonded to a CH3CO radical. Dissociation of 7 to give protonated methanol is favoured with respect to further isomerization leading to ionized vinyl alcohol. Compared to the unimolecular conversion between energetic ions 1 and 2, which can occur either by a direct 1,3-H transfer or by a double 1,2-H transfer, the reaction of 1 with methanol catalyzes the first pathway while inhibiting the second one. In the case studied, catalysis is perhaps better described as a hydrogen atom transport. (C) 2000 Elsevier Science B.V.