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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.

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.

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.

Mass spectrometry-based methods have been employed in order to study the reactions of non- (h6/h6), half (d6/h6), and fully (d6/d6) deuterium labeled protonated dimers of acetone in the gas phase. Neither kinetic nor thermodynamic isotope effects were found. From MIKES experiments (both spontaneous and collision-induced dissociations), it was found that the relative ion yield (m/z 65 vsm/z 59) from the dissociation reaction of half deuterium labeled (d6/h6) protonated dimer of acetone is dependent on the internal energy. A relative ion yield (m/z 65 vsm/z 59) close to unity is observed for cold, nonactivated, metastable ions, whereas the ion yield is observed to increase (favoring m/z 65) when the pressure of the collision gas is increased. This is in striking contrast to what would be expected if a kinetic isotope effect were present. A combined study of the kinetics and the thermodynamics of the association reaction between acetone and protonated acetone implicates the presence of at least two isomeric adducts. We have employed G3(MP2) theory to map the potential energy surface leading from the reactants, acetone and protonated acetone, to the various isomeric adducts. The proton-bound dimer of acetone was found to be the lowest-energy isomer, and protonated diacetone alcohol the next lowest-energy isomer. Protonated diacetone alcohol, even though it is an isomer hidden behind many barriers, can possibly account for the observed relative ion yield and its dependence on the mode of activation. Copyright © 2005 John Wiley & Sons, Ltd.

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.

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.

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.

As a result of an extensive delocalization of charge and a unique covalent structure, the CH3OCH2+ cation has, in effect, the character of an ambident electrophile. This cation can, on the one hand, be considered to be a classical electrophile. On the other hand, it may be considered to be a facile methyl cation donor. The former character predominates when this cation reacts with alcohols, as is shown in this work. In both the chemical ionization (CI) source of a conventional mass spectrometer and also via low-pressure bimolecular reactions in a Fourier transform ion cyclotron resonance (ICR) cell, the dominant reaction between alkoxymethyl cations and alcohols is the very exothermic formation of a C—O bond to give a covalent adduct having the structure of a protonated dialkoxymethane. A 1,3-hydrogen transfer is observed for the covalent adducts. In the case of those generated in the ICR cell this process is a slow unimolecular reaction. However, the rapid 1,3-hydrogen transfer observed in the CI source is a bimolecular reaction catalysed by a second molecule of alcohol. This is a new example of catalysed isomerization in the gas phase. In competition with the 1,3-hydrogen transfer, the covalent adducts may either undergo simple bond cleavage or may isomerize to proton-bound dimer adducts of ether and aldehyde (or ketone) via a hydride transfer mechanism. This mechanism either may involve an electrostatic complex intermediate or may be an asynchronous concerted process. Since the proton affinities of the ethers involved in these proton-bound dimer intermediates are greater than those of the aldehydes derived from primary alcohols, such dimers dissociate to yield protonated ether and aldehyde. Conversely, those dimers resulting from secondary alcohols involve ketones whose proton affinities are greater than those of the partner ethers and these dimers dissociate to yield protonated ketone and ether. In summary, the reactions of CH3OCH2+ with alcohols occur via several successive and specific steps. © 1997 by John Wiley & Sons, Ltd.

Infrared multiple photon dissociation (IRMPD) spectroscopy experiments and quantum chemical calculations have been used to explore the possible structures of protonated azidothymidine and the corresponding protonated dimer. Many interesting differences between the protonated and neutral forms of azidothymidine were found, particularly associated with keto-enol tautomerization. Comparison of computational vibrational and the experimental IMRPD spectra show good agreement and give confidence that the dominant protonated species has been identified. The protonated dimer of azidothymidine exhibits three intramolecular hydrogen bonds. The IRMPD spectrum of the protonated dimer is consistent with the spectrum of the most stable computational structure. This work brings to light interesting keto-enol tautomerization and exocyclic hydrogen bonding involving azidothymidine and its protonated dimer. The fact that one dominant protonated species is observed in the gas phase, despite both the keto and enol structures being similar in energy, is proposed to be the direct result of the electrospray ionization process in which the dominant protonated dimer structure dissociates in the most energetically favorable way.

Protonated ferulic acid and its principle fragment ion have been characterized using infrared multiple photon dissociation spectroscopy and electronic structure calculations at the B3LYP/6-311 + G(d,p) level of theory. Due to its extensively conjugated structure, protonated ferulic acid is observed to yield three stable fragment ions in IRMPD experiments. It is proposed that two parallel fragmentation pathways of protonated ferulic acid are being observed. The first pathway involves proton transfer, resulting in the loss of water and subsequently carbon monoxide, producing fragment ions m/z 177 and 149, respectively. Optimization of m/z 177 yields a species containing an acylium group, which is supported by a diagnostic peak in the IRMPD spectrum at 2168 cm(-1). The second pathway involves an alternate proton transfer leading to loss of methanol and rearrangement to a five-membered ring.

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

The metastable dissociation of the methoxymethyl cation and a number of its deuterium and 13C variants was examined using a reverse-geometry double-focusing mass spectrometer. The loss of methane from the methoxymethyl cation clearly showed a composite peak shape which, when deconvoluted, revealed a bimodal kinetic energy release distribution in the resulting formyl cations. Labelling experiments revealed that the two carbon atoms and all hydrogens become equivalent on the time-scale of the unimolecular dissociation lifetime of the decomposing ion. A small deuterium isotope effect was found which can be rationalized on the basis of zero point energy effects. The bimodal kinetic energy release distribution was shown, with the aid of a four-sector instrument, to be due to the production of both formyl cation (with a large kinetic energy release) and isoformyl cation (with a much smaller kinetic energy release). The methoxymethyl cation was also prepared with a precisely defined amount of internal energy in a Fourier transform ion cyclotron resonance (FTICR) spectrometer by the reaction of methyl cation with formaldehyde. Experiments with 13C and deuterium labelling revealed that the dissociation to formyl cation of the methoxymethyl cations formed in the low-pressure FTICR cell by reaction of methyl cation with formaldehyde is accompanied by complete scrambling of the carbons and incomplete scrambling of the hydrogens. Ab initio calculations were carried out which identified and characterized each of the stable minima and transition states for the appropriate reactions. The calculations were fully consistent with the mechanism deduced on the basis of the experimental data.

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.

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.

The structure of the proton-bound lysine dimer has been investigated by infrared multiple photon dissociation (IRMPD) spectroscopy and electronic structure calculations. The structures of different possible isomers of the proton-bound lysine dimer have been optimized at the B3LYP/6-31 + G(d) level of theory and IR spectra calculated using the same computational method. Based on relative Gibbs free energies (298 K) calculated at the MP2/aug-cc-pVTZ//B3LYP/6-31 + G(d) level of theory, LL-CS01, and followed closely (1.1 kJ mol(-1)) by LL-CS02 are the most stable non-zwitterionic isomers. At the MP2/aug-cc-pVTZ//6-31 + G(d) and MP2/aug-cc-pVTZ//6-31 + (d,p) levels of theory, isomer LL-CS02 is favored by 3.0 and 2.3 kJ mol(-1), respectively. The relative Gibbs free energies calculated by the aforementioned levels of theory for LL-CS01 and LL-CS02 are very close and strongly suggest that diagnostic vibrational signatures found in the IRMPD spectrum of the proton-bound dimer of lysine can be attributed to the existence of both isomers. LL-ZW01 is the most stable zwitterionic isomer, in which the zwitterionic structure of the neutral lysine is well stabilized by the protonated lysine moiety via a very strong intermolecular hydrogen bond. At the MP2/aug-cc-pVTZ//B3LYP/6-31 + G(d), MP2/aug-cc-pVTZ//6-31 + G(d) and MP2/aug-cc-pVTZ//6-31 + G(d,p) levels of theory, the most stable zwitterionic isomer (LL-ZW01) is less favored than LL-CS01 by 7.3, 4.1 and 2.3 kJ mol(-1), respectively. The experimental IRMPD spectrum also confirms that the proton-bound dimer of lysine largely exists as charge-solvated isomers. Investigation of zwitterionic and charge-solvated species of amino acids in the gas phase will aid in a further understanding of structure, property, and function of biological molecules.

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

Both Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and high-pressure mass spectrometry (HPMS) are very powerful tools in the field of gas phase ion chemistry. Many experimental method developments based on FTICR-MS and HPMS are summarized, including the coupling of a high-pressure external ion source to a FTICR mass spectrometer, blackbody infrared radiative dissociation (BIRD), coupling laser desorption ionization with HPMS, infrared multiple photon dissociation (IRMPD), radiative association and bimolecular routes to gas phase cluster ion formation. An abundance of thermochemical data, such as proton affinities, gas phase acidities, methyl cation affinities and metal cation affinities, have been obtained. Some of these data are the basis of the standard data listed in the NIST thermochemical databases. Ion–molecule interactions, energetics, reactivities, and structures of molecules have been extensively investigated using the methods developed based on HPMS and FTICR mass spectrometric techniques. © 2009 Wiley Periodicals, Inc., Mass Spec Rev 28:546–585, 2009

Zwitterionic structures exist extensively in biological systems and the electric field resulting from zwitterion formation is the driving force for determination of the properties, function and activity of biological molecules, such as amino acids, peptides and proteins. It is of considerable interest and import to investigate the stabilization of zwitterionic structures in the gas phase. Infrared multiple photon dissociation (IRMPD) spectroscopy is a very powerful and sensitive technique, which may elucidate clearly the structures of both ions and ionic clusters in the gas phase, since it provides IR vibrational fingerprint information. The structures of the clusters of glycine and ammonium ion and of the betaine proton-bound homodimer have been investigated using IRMPD spectroscopy, in combination with electronic structure calculations. The experimental and calculated results indicate that zwitterionic structure of glycine may be effectively stabilized by an ammonium ion. This is the smallest zwitterionic structure of an amino acid to be demonstrated in the gas phase. On the basis of the experimental IRMPD and calculated results, it is very clear that a zwitterionic structure exists in the proton-bound betaine dimer. The proton is bound to one of the carboxylate oxygens of betaine, rather than being equally shared. Investigations of zwitterionic structures in the isolated state are essential for an understanding of the intrinsic characteristics of zwitterions and salt bridge interactions in biological systems.

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.

Protonation sites in biological molecules are very important because they directly determine their structures, properties, and functions. The protonation sites and structures of the tripeptides of Gly and Ala have been investigated using infrared multiple photon dissociation (IRMPD) spectroscopy in combination with theoretical calculations. The experimental and calculated results indicate that two isomers coexist under the experimental conditions. Different protonation sites result in the different structures. If the excess proton is bound to the amino group, a cyclic structure is formed, in which the N-terminus and carbonyl oxygen of the C-terminus are linked by a strong hydrogen bond. In contrast, if the excess proton is bound to the amide carbonyl oxygen, a linear structure is formed in which a very strong hydrogen bond is formed, linking the two amide carbonyls. For the first time, IR spectroscopic evidence confirms that an amide oxygen may serve as the protonation site for peptides.

International audience; In the gas phase, the CH2CHOH.+ enol radical cation 1 as well as its higher homologues CH3CHCHOH.+ 2 and (CH3)2CCHOH.+ 3, undergo exactly the same sequence of reactions with tert-butanol, leading to the losses of isobutene, water and water plus alkene. Fourier transform ion cyclotron resonance (FT-ICR) experiments using labeled reactants as well as ab initio calculations show that independent pathways can be proposed to explain the observed reactivity. For ion 1, taken as the simplest model, the first step of the reaction is formation of a proton bound complex which gives, by a simple exothermic proton transfer, the ter-body intermediate [CH2CHO., H2O, C(CH3)3+]. This complex, which was shown to possess a significant lifetime, is the key intermediate which undergoes three reactions. First, it can collapse to yield tert-butylvinyl ether with elimination of water. Second, by a regiospecific proton transfer, this complex can isomerize into three different ter-body complexes formed of water, isobutene and ionized enol. Within one of these complexes, which does not interconvert with the others, elimination of isobutene leads to the formation of a solvated enol ion. Within the others, a cycloaddition-cycloreversion process can proceed to yield the ionized enol 3 (loss of water and ethylene channel).

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.

Infrared multiple photon dissociation (IRMPD) spectroscopy is a very powerful technique to characterize the structures of ions and ionic clusters. The structures of Gly and Pro proton-bound homodimers have been investigated using this method in combination with theoretical calculations. For the protonated Gly dimer, a new most stable isomer, GG-CS01, has been experimentally confirmed to be the dominant species. Direct IR spectroscopic evidence indicates that zwitterionic proline exists in the protonated proline dimer in the gas phase. This zwitterionic isomer (PP-ZW01) is the dominant species, and the most stable nonzwitterionic isomer (PP-CS01) also coexists under the experimental conditions.

A compact, field-free high pressure ion source designed to replace, with minimum disruption, the electron impact/chemical ionization ion source of a VG Analytical ZAB-2FQ hybrid BEqQ mass spectrometer is described. This ion source may be operated at temperatures from ∼ 40 to 250 °C and at pressures up to 4–5 torr, and, thus, is capable of producing proton-bound cluster ions up to hexamers in good yields. Examples of high energy collision-induced dissociation, low energy collision-induced dissociation, and neutralization-reionization studies of proton-bound cluster ions produced in this source are presented.

Fourier transform ion cyclotron resonance mass spectrometry has been used to measure the reaction rates for ions derived from methylamine with dimethylamine or trimethylamine. The use of the selective ion ejection technique greatly simplifies the elucidation of the ion-molecule reaction channels. The rate constants for proton transfer from protonated metwlamine, CH3NH 3 + (m/z 32), to dimethylamine and trimethylamine are 16.1 ± 1.6 × 10−10 and 9.3 ± 0.9 × 10−10 cm3 molec−1s−1, respectively. The rate constants for charge transfer from methylamine molecular ion, CH3NH 2 + (m/z 31), to dimethylamine and trimethylamine are 9.3 ± 1.8 x 10−10 and 15.0 ± 5 × 10−10 cm3molec−1s−1, respectively.

The results of both mass-analysed ion kinetic energy spectroscopy and Fourier transform ion cyclotron resonance experiments involving reactions of the methoxymethyl cation CH3OCH2+ with a variety of aldehydes and ketones are reported. With ketones, the reaction yields a covalent complex whose dissociation either gives back the CH3OCH2+ cation or leads to a methyl cation transfer to the ketone. Except for CH2O, a third pathway is open with aldehydes. A hydride transfer to CH3OCH2+ yields a RCO+ acylium product ion. The branching ratio of these three pathways strongly depends on the structure of the aldehyde. Ab initio calculations confirm that the results can be explained by the interconversion of covalent structures and electrostatic complexes on the potential energy surface.

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.

Gas-phase ion–molecule reactions of a variety of fluorosilyl carbanions with compounds containing double bonds to oxygen, XO, have been examined using pulsed ion cyclotron resonance spectroscopy. The predominant reaction channel observed for species not containing acidic hydrogens is a Wittig-like process involving SiO bond formation and elimination of XCH2 species. The gas-phase acidity of F3Si(CH3) has been determined and those of F2Si(CH3)2 and FSi(CH3)3 have been estimated. From the fluoride transfer reactions of F3SiCH2− the fluoride affinity of F2SiCH2 has been estimated and limits on the π bond strength in this silaethene obtained. Potential analytical applications of the Wittig reactivity have been discussed.