Proton Affinities of Simple Amines; Entropies and Enthalpies of Activation and Their Effect on the Kinetic Method for Evaluating Proton Affinities

Mechanistic understanding of catalysis by combining mass spectrometry and computation

The combination of mass spectrometry and computational chemistry has been proven to be powerful for exploring reaction mechanisms. The former provides information of reaction intermediates, while the latter gives detailed reaction energy profiles.

Metal ion hydrocarbon bidentate bonding in alkyl acetates, methyl alkanoates, alcohols and 1-alkenes: a comparative study

The relative affinity of the monovalent metal ions Li⁺, Na⁺, Cu⁺ and Ag⁺ towards a series of aliphatic alkyl acetates and some selected 1-alkenes (P) was examined using the kinetic method. A detailed analysis of the dissociation characteristics of a series of mixed metal-bound dimer ions of the type P₁-M⁺-P₂ and the evaluated proton affinities (PAs) of the monomers shows that the affinity of the cation towards long-chain alkyl acetates and alkenes (having a chain length ≤ C₄) is markedly enhanced. In line with recent studies of nitriles, alcohols and methyl alkanoates, this is attributed to a bidentate interaction of the metal ion with the functional group or double bond and the aliphatic chain. In particular, the longer chain alkyl acetates, methyl alkanoates and alcohols show a remarkably similar behaviour with respect to silver ion hydrocarbon bonding. The Ag⁺ adducts of the alkyl acetates dissociate by loss of CH₃COOH. This reaction becomes more pronounced at longer chain lengths, which points to metal ion bidentate formation in [Ag⁺···1-alkene] product ions having a long hydrocarbon chain. In the same vein, the heterodimers [1- hexene···Ag⁺···1-heptene] and [1- heptene···Ag⁺···1-octene] dissociate primarily into [Ag⁺···1-heptene] and [Ag⁺···1-octene] ions, respectively. Hydrocarbon bidentate formation in [Ag⁺···1-octene] also reveals itself by the reluctance of this ion to react with water in an ion trap, as opposed to [Ag⁺···1-hexene] which readily undergoes hydration.

Interaction of metal cations with functionalised hydrocarbons in the gas phase: further experimental evidence for solvation of metal ions by the hydrocarbon chain

Relative affinity measurements of monovalent metal ions (= Li(+), Cu(+) and Ag(+)) towards aliphatic amines, alcohols and methyl alkanoates (P) have been performed using the kinetic method on the dissociation of metal bound dimer ions of the type P(1)-M(+)-P(2). It was found that the cations' affinity towards long chain (≥C(4) chain length) n- and s-alkylamines, n-alkanols and methyl n- alkanoates was unexpectedly enhanced. This is attributed to a bidentate interaction of the metal ion with the amine, alcohol or ester functional group and the aliphatic chain, paralleling earlier observations on metal bound nitriles. Methyl substitution at the functional group (s-alkylamines compared with n-alkylamines) serves to strengthen only the N•••M(+) bond, and this can be rationalized by the larger proton affinities of s-alkylamines compared to n-alkylamines. This substitution, however, has no effect on the metal ion-hydrocarbon bond. In contrast, methyl substitution remote from the functional group, as in iso-pentylamine, does lead to strengthening of the metal ion-hydrocarbon bond. The cuprous ion affinity of hexadecylamine, C(16)H(33)NH(2) was found to be as large as that for ethylenediamine (352 kJ mol(-1)), known to be a strong copper binding agent. It is argued that such a metal ion-hydrocarbon interaction does not occur in the metal bound dimers.

Interaction of metal cations with alkylnitriles in the gas phase: solvation of metal ions by the hydrocarbon chain

Relative affinity measurements of monovalent metal ions (M = Li(+), Na(+), Cu(+)and Ag(+)) toward aliphatic nitriles have been performed using the kinetic method by dissociation of metal bound dimer ions of the type R1C≡N-M(+)-N≡CR(2). It is found, particularly for Cu(+) and Ag(+), that the affinity towards nitriles having long chains (>C(6)) is markedly enhanced. This is attributed to a bidentate interaction of the metal ion with the nitrile moiety and the aliphatic chain. Theoretical calculations on the copper complexes show that these bidentate structures enjoy about 30% greater copper ion affinities compared to their linear counterparts. Such aliphatic interactions also play a major role in the dissociation chemistry of copper bound tetramers of the kind (RC≡N)(4)Cu(2+∙) where the long aliphatic chain R curls around the copper ion to facilitate electron transfer or a redox reaction to produce (RC≡N)(2)Cu(+) + RC≡N(+∙) + RC≡N.

Gas-phase basicities of polyfunctional molecules. Part 2: Saturated basic sites

The present article is the second part of a general overview of the gas-phase protonation thermochemistry of polyfunctional molecules. The first part of the review (Mass Spectrom. Rev., 2007, 26:775-835) was devoted to the description of the physico-chemical concepts and of the methods of determination, both experimental and theoretical, of gas-phase basicity. Several clues concerning the structural and energetic aspects of the protonation of isolated species have been emphasized. In the present article, specific examples are examined. The field of investigation is limited to molecules containing a "saturated" basic site, that is, nitrogen or oxygen atoms engaged in simple σ bonds with their neighboring. Aliphatic, cyclic and aromatic poly-amines, amino alcohols, alcohols, ethers, and hydroxyl-ethers, are successively presented.

Can cluster structure affect kinetic method measurements? The curious case of glutamic acid's gas-phase acidity

The gas-phase acidities of aspartic, glutamic, and 2-aminoadipic acid have been determined by the kinetic method in a triple-quadrupole instrument. Although aspartic acid behaves in the conventional way and gives a DeltaH(acid) value of 1340 kJ mol(-1), glutamic and 2-aminoadipic acids give kinetic method plots with two distinct slopes. This leads to DeltaH(acid) values of 1350 and 1366 kJ mol(-1) for glutamic acid, and 1355 and 1369 kJ mol(-1) for 2-aminoadipic acid. The value for aspartic acid and the low collision energy value for glutamic acid are consistent with recent measurements by Poutsma and co-workers in a quadrupole ion trap. The experiments are supported by calculations at the G3(MP2) and OLYP/aug-cc-pVTZ levels. Computational studies of model clusters of the amino acids with trifluoroacetate suggest there are distinct preferences. Glutamic and 2-aminoadipic acid prefer clusters where the amino acid adopts a zwitterion-like structure whereas aspartic acid prefers to adopt a conventional (canonic) structure in its clusters. This result along with the computed stabilities of zwitterion-like conformations of the deprotonated amino acids leads to the following explanation for the presence of two slopes in the kinetic method plots. At low collision energies, the deprotonated amino acid dissociates from the cluster, with rearrangement if necessary, to give its preferred conformation, but at high collision energies, the deprotonated amino acid directly dissociates in the conformation preferred in the cluster. For glutamic and 2-aminoadipic acids, this is a zwitterion-like structure that is about 20 kJ mol(-1) less stable than the global minimum.

Gas-phase basicities of polyfunctional molecules. Part 1: Theory and methods

The experimental and theoretical methods of determination of gas-phase basicities, proton affinities and protonation entropies are presented in a tutorial form. Particularities and limitations of these methods when applied to polyfunctional molecules are emphasized. Structural effects during the protonation process in the gas-phase and their consequences on the corresponding thermochemistry are reviewed and classified. The role of the nature of the basic site (protonation on non-bonded electron pairs or on pi-electron systems) and of substituent effects (electrostatic and resonance) are first examined. Then, linear correlations observed between gas-phase basicities and ionization energies or substituent constants are recalled. Hydrogen bonding plays a special part in proton transfer reactions and in the protonation characteristics of polyfunctional molecules. A survey of the main properties of intermolecular and intramolecular hydrogen bonding in both neutral and protonated species is proposed. Consequences on the protonation thermochemistry, particularly of polyfunctional molecules are discussed. Finally, chemical reactions which may potentially occur inside protonated clusters during the measurement of gas-phase basicities or inside a protonated polyfunctional molecule is examined. Examples of bond dissociations with hydride or alkyl migrations, proton transport catalysis, tautomerization, cyclization, ring opening and nucleophilic substitution are presented to illustrate the potentially complex chemistry that may accompany the protonation of polyfunctional molecules.

The sodium ion affinities of simple di-, tri-, and tetrapeptides

The sodium ion affinities (binding energies) of nineteen peptides containing 2-4 residues have been determined by experimental and computational approaches. Na(+)-bound heterodimers with amino acid and peptide ligands (Pep(1), Pep(2)) were produced by electrospray ionization. The dissociations of these Pep(1)-Na(+)-Pep(2) ions to Pep(1)-Na(+) and Pep(2)-Na(+) were examined by collisionally activated dissociation to construct a ladder of relative affinities via the kinetic method. The accuracy of this ladder was subsequently ascertained by experiments using several excitation energies for four peptide pairs. The relative scale was converted to absolute affinities by anchoring the relative values to the known Na(+) affinity of GlyGly. The Na(+) affinities of AlaAla, HisGly, GlyHis, GlyGlyGly, AlaAlaAla, GlyGlyGlyGly, and AlaAlaAlaAla were also calculated at the MP2(full)/6-311 + G(2d,2p) level of ab initio theory using geometries that were optimized at the MP2(full)/6-31G(d) level for AlaAla or HF/6-31G(d) level for the other peptides; the resulting values agree well with experimental Na(+) affinities. Increasing the peptide size is found to dramatically augment the Na(+) binding energy. The calculations show that in nearly all cases, all available carbonyl oxygens are sodium binding sites in the most stable structures. Whenever side chains are available, as in HisGly and GlyHis, specific additional binding sites are provided to the cation. Oligoglycines and oligoalanines have similar binding modes for the di- and tripeptides, but differ significantly for the tetrapeptides: while the lowest energy structure of GlyGlyGlyGly-Na(+) has the peptide folded around the ion with all four carbonyl oxygens in close contact with Na(+), that of AlaAlaAlaAla-Na(+) involves a pseudo-cyclic peptide in which the C and N termini interact via hydrogen bonding, while Na(+) sits on top of the oxygens of three nearly parallel C=O bonds.

Proton Affinity of Canavanine and Canaline, Oxyanalogues of Arginine and Ornithine, from the Extended Kinetic Method

The absolute proton affinities of the nonprotein amino acids canavanine and canaline have been determined using the extended kinetic method in an electrospray ionization quadrupole ion trap instrument. Canavanine results from the substitution of an oxygen atom for the delta-CH2 group in the side chain of the protein amino acid arginine, whereas canaline results from a similar substitution at the delta-CH2 group in the side chain of ornithine. Absolute proton affinities of 1001+/-9 and 950+/-7 kJ/mol are obtained for canavanine and canaline, respectively. For canaline, this proton affinity is in excellent agreement with theoretical predictions obtained using the hybrid density functional theory method B3LYP/6-311++G**//B3LYP/6-31+G*. For canavanine, theory predicts a somewhat larger proton affinity of 1015 kJ/mol. Oxygen atom substitution in these nonprotein amino acids results in a decrease in their proton affinities of 40-50 kJ/mol compared to arginine and ornithine.

Evaluation of the protonation thermochemistry obtained by the extended kinetic method

An evaluation of the results obtained by the extended kinetic method for a series of representative bases is presented here. Analysis of the original experimental data is conducted using the orthogonal distance regression (ODR) statistical treatment. A comparison with the proton affinities and protonation entropies obtained from variable temperature equilibrium constant measurements demonstrate deviations, which may be ascribed to random and systematic errors. Considerable random errors are associated with the extended kinetic method if the number of reference bases and the range of effective temperatures are too low. It is also confirmed that large systematic errors on proton affinities and protonation entropies are obtained when large protonation entropy is associated with the considered system. It is, however, encouraging to note that the gas phase basicities obtained by the extended kinetic method are generally comparable to that obtained by other methods within a few kJ/mol.

Proton affinity of beta-oxalylaminoalanine (BOAA): incorporation of direct entropy correction into the single-reference kinetic method

A new version of the single-reference-extended kinetic method is presented in which direct entropy correction is incorporated. Results of calibration experiments with the monodentate base pyridine and the bidentate base ethylenediamine are presented for which the method provides proton affinities in excellent agreement with published values and reasonable predictions for the protonation entropies. The method is then used to determine the proton affinity and protonation entropy of the non-protein amino acid beta-oxalylaminoalanine (BOAA). The PA of BOAA is found to be 933.1 +/- 7.8 kJ/mol and a prediction for the protonation entropy of -39 J mol(-1) K(-1) is also obtained, indicating a significant degree of intramolecular hydrogen bonding in the protonated form. These results are supported by hybrid density functional theory calculations at the B3LYP/6-311++G**//B3LYP/6-31+G* level. They indicate that the preferred site of protonation is the alpha-nitrogen atom (PA = 935.0 kJ/mol) and that protonated BOAA has a strong hydrogen bond between the hydrogen on the alpha-amino group and one of the carbonyl oxygen atoms on the side chain.

Water dimer proton affinity from the kinetic method: dissociation energy of the water dimer

The proton affinity of water dimer was measured, using the kinetic method with nitrile reference bases, to be 808 +/- 6 kJ mol(-1). The difference between the measured value and the proton affinity of a single water molecule (690 +/- 4 kJ mol(-1)) reflects the difference in solvation energy for two neutral water molecules (the hydrogen bond energy of water dimer), and the energy for solvation of hydronium cation and water. Using the measured proton affinity of the dimer along with ancillary data yields an experimental value of the hydrogen bond energy of neutral water dimer, 18 +/- 9 kJ mol(-1), in good agreement with previous experimental and theoretical values. The proton affinity of the dimer measured by using alcohol references is ca 100 kJ mol(-1) too low, likely because the structure of the protonated cluster is not well-suited for kinetic method measurements. These results highlight the importance of choosing reference bases that form cluster ions consisting of a proton bound complex between the water dimer and the reference base.

Protonation thermochemistry of alpha-aminoacids bearing a basic residue

The proton affinity, PA, and protonation entropy, Delta(p)S degree, of glycine (Gly), 1, aspartic acid (Asp), 2, asparagine (Asn), 3, histidine (His), 4, lysine (Lys), 5, glutamic acid (Glu), 6, and glutamine (Gln), 7, have been reinvestigated by the extended kinetic method, using the "isothermal point" method and the orthogonal distance regression, ODR, technique. The proton affinity values of a-aminoacids bearing a basic residue (PA = 926.8; 965.2; 996.0; 993.9; 981.8 and 988.1 kJ.mol(-1) for 2-7, respectively) show significant deviation from the tabulated values. As expected from the effect of a strong intramolecular hydrogen bond in the protonated forms of these peculiar aminoacids, negative protonation entropies are detected (Delta(p)S degree = 36; 43; 37; 29; 95 and 55 J mol(-1) K(-1) for for 27 respectively).

Entropy evaluation using the kinetic method: is it feasible?

The kinetic method is one of the most widely used experimental techniques for the measurement of thermochemical parameters by mass spectrometry. Recently it has been realized that it can also be used to determine reaction entropies, but the validity of this approach has not been established. This Perspective evaluates kinetic method plots in cases where there is a significant entropy difference between the competing fragmentation channels (i.e. between sample and reference compounds in the dissociating cluster ion). The concept underlying this study is to calculate mass spectra theoretically, based on known thermochemical parameters and as a function of experimental conditions. This can be done accurately using the RRKM-based MassKinetics software. The resulting mass spectra are then interpreted by the kinetic method, yielding DeltaH and DeltaS values. These values are, in turn, compared with the true values used to generate the calculated mass spectra. The results show that the reaction entropy difference between sample and reference has a very large influence on kinetic method plots. This should always be considered when studying energy-dependent mass spectra (using metastable ions or low- or high-energy collision-induced dissociation (CID)), even if only DeltaH is to be determined. Kinetic method plots are not strictly linear and this becomes a serious issue in the case of small molecules showing a large entropy effect. In such cases, results obtained at a low degree of excitation are more accurate. Energy and entropy effects can be evaluated in a relatively straightforward manner: first, the apparent Gibbs energy (DeltaG(app)) and effective temperature (T(eff)) are determined from kinetic method plots (intercept and slope, respectively), obtained from experiments using various degrees of excitation. Second, the resulting DeltaG(app) is plotted against T(eff), the slope yielding DeltaS while the intercept (extrapolation to zero temperature) yields DeltaH. This data evaluation yields more accurate results than alternative methods used in the literature. The resulting DeltaH values are fairly accurate, with errors, in most cases, <4 kJ mol(-1). On the other hand, DeltaS is systematically underestimated by 20-40%. Empirically scaling DeltaS values determined by the kinetic method by 1.35 results in a DeltaS value within 20% (or 10 J mol(-1) K(-1)) of the theoretical value.