Proton Affinity Values Research Articles

Proton affinities of two weakly bidentate molecules: 1,2-dimethoxyethane and methoxyacetone

The proton affinities (PA), of methoxyacetone and 1,2-dimethoxyethane have been determined by the kinetic method, using alkyl ethers and simple ketones having established PA values as their proton bound partners. Both compounds show effects attributed to activation entropies acting against the target molecules’ retaining the proton. The PA values determined in this study were, PA methoxyacetone = 846.5 ± 2 kJ/mol; PA 1,2-dimethoxyethane = 845.5 ± 2 kJ/mol, (which is considerably lower than the previously cited value, 858 kJ/mol). The PA of cyclopentanone was revised to 828 ± 4 kJ/mol from its reference value of 824 kJ/mol. The present work showed that simple ketones and ethers, whose PA values conveniently overlap, cannot indiscriminately be used as reference compounds; care must always be taken in the choice of the proton bound partner (reference) molecule in kinetic method studies.

Structure, Thermochemistry and Reactivity of Protonated Glycolaldehyde

Structures and relative energies of various conformers of the simplest sugar, glycolaldehyde, 1, and its protonated form, [1H]+, were investigated by ab initio molecular orbital calculations. The 298 K heats of formation of the most stable conformers, deduced from the atomization energies at the G2 level, are equal to Δ fH°(1) = −324.8 kJ mol−1 and Δ fH°[1H]+ = 426.0 kJ mol−1. The corresponding proton affinity value is PA(1) = 779.8 kJ mol−1, in perfect agreement with the experimental determination of 783.3 ± 3.8 kJ mol−1 obtained by the kinetic method. A gas-phase basicity value, GB(1), of 745–748 kJ mol−1 is also deduced from theory and experiment. The exclusive dissociation channel of protonated glycolaldehyde, [1H]+, is water loss which leads essentially to the acylium ion [CH3CO]+. The corresponding potential energy profile, investigated at the MP2/6–31G* level, reveals a route via a [CH3CO]+ / water complex after an energy determining step involving a simultaneous 1,2-hydrogen migration and C–O bond elongation. The critical energy of the reaction, evaluated at the G2(MP2,SVP)level, is 170 kJ mol −1 above the most stable conformation of the [1H]+ ion. The 298 K heats of formation of the three most stable [C2H3O]+ ions have been calculated at the G2 level: Δ fH°[CH3CO]+ = 655.0 kJ mol−1, Δ fH°[CH2COH]+ = 833.0 kJ mol−1, Δ fH°[c-CH2CHO]+ = 886.2 kJ mol−1.

The Determination of Proton Affinities of Secondary Alcohols from the Dissociation of Proton-Bound Molecular Trios. A New Application of the Kinetic Method

The kinetic method for determining proton affinity ( PA) values requires that the competing dissociations of proton-bound pairs of bases, AH+Bn, essentially only lead to AH+ and BnH+ ions. The method fails for secondary alcohols because other reactions, involving rearrangement of the AH+Bn ion, are dominant. It was found that proton-bound trios of bases, A2H+Bn, (which incorporate secondary alcohols Bn with a primary alcohol, A) do not suffer from this disadvantage. The proton-bound trios decomposed cleanly, to yield only A2H+ and AH+Bn ions. Application of the kinetic method to these competing reactions allowed the PA values for the secondary alcohols to be determined using the appropriate molecular-pair proton affinity [ MPPA] values. The MPPA is the negative of the enthalpy change, [–Δ H], accompanying the formation of a proton-bound pair from the component alkanols and a proton. These were readily estimated using known binding energies, D[AH+–Bn] and established PA values for n-alkanols. In the present brief study, PA values for isopropanol, cyclobutanol and cyclopentanol were measured to be 796, 792 and 798, all ± 6 kJ mol−1. The results for the cyclic alcohols relate well with the available data from similar compounds, where the C3–C5 rings display lower PA values than their acyclic analogues. This effect is attributed to restricted charge delocalization in the small rings.

Estimation of a Nucleoside Proton Affinity Scale from Dissociations of Hydrogen-Bound Heterodimer Constituted with Amino Acid Partners

Nucleoside proton affinity was determined using Cooks' kinetic method. An ion trap mass spectrometer coupled with an external electrospray source was used to form proton-bound homo- and heterodimers from modified uridines and amino acids at low effective temperature. The experimental proton affinity ( PA) values obtained show the effects of structural changes in nucleosides on PA values (i.e. U < dU and 5IdU < dU < dT). The calculated values are consistent with those reported by tandem sector instruments. In this way, an hypothesis on the interaction site of the heterodimers is proposed: the amino groups are likely to interact with the proton (in the dimer) as expected from its solution behavior.

Proton affinities of saturated aliphatic methyl esters

The kinetic method was used to determine the proton affinities of methyl esters of several saturated fatty acids. Decompositions of the proton-bound dimers of the methyl esters, AHB +, were observed under different conditions with two instruments. The proton affinities (PAs) of the methyl esters increase continually with increasing carbon number in the acid. Equilibrium and initial rate experiments were performed with a Fourier transform ion cyclotron resonance mass spectrometer on the methyl ester of the C 22 saturated acid (methyl behenate). These experiments give values for PA (methyl behenate) that are perhaps slightly lower than those obtained with the kinetic method. The PAs of the methyl esters of the fatty acids could be correlated with the equation: PA (ester) = (40.0 ± 2.5)∗log( n) + (784.7 ± 3.9) kJ/mol or PA (ester) = (864 ± 2) − (479 ± 41)/ n, where n = number of atoms in the molecule. Proton affinities of smaller sets of 1-alkylamines and 1-alkanols can be fit to similar equations.

Interaction of Methanol with Alkali Metal Exchanged Molecular Sieves. 2. Density Functional Study

The structure and stability of various methanol adsorption complexes on alkali metal exchanged zeolites was studied by a density functional method using cluster models of six-rings. In particular, O-bound species coordinated only by the oxygen atom to the metal cation were compared to O,H-bound species coordinated in addition with a hydrogen bond of the methanol proton to a zeolite oxygen center. The coordination bond between the methanol oxygen atom and the metal cation furnishes the main contribution to the interaction of the adsorbate with sodium- or potassium-exchanged zeolites (40−55 kJ/mol), while the hydrogen bond contributes in addition about 15 kJ/mol. The hydrogen bond between the methanol hydroxyl group and a zeolite oxygen center significantly influences the OH stretching frequency in the IR spectra of adsorbed methanol. The calculated red shift of the OH frequency depends strongly on the proton affinity value of the zeolite oxygen center; for a change of the proton affinity by 54 kJ/mol it in...

Protonation of Nucleic Acid Bases. A Comprehensive Post-Hartree−Fock Study of the Energetics and Proton Affinities

The results of an ab initio post-Hartree−Fock study of the protonation of all nucleic acid bases are reported. Rare tautomers of guanine and cytosine, which coexist in the gas phase with the major forms, were also included in the study. The geometries of the local minima and transition states were optimized without symmetry restrictions by the gradient procedure at the HF and MP2 levels of theory and were verified by energy second-derivative calculations. The standard 6-31+G(d,p) basis set was used. The single-point calculations have been performed at the MP4(SDTQ)/6-31+G(d,p)//MP2/6-31+G(d,p) and MP2/6-311++G(d,p)//MP2/6-31+G(d,p) approximations. The relative stabilities of the different protonated forms of all nucleic acid bases have been reported. The values of proton affinities (PA) for each base including contributions of rare tautomers and different protonated forms for guanine and cytosine have been calculated. We have shown that the calculated values of proton affinities are very close to the expe...

Chemical ionization mass spectra of acetals of beta-D-glycopyranosylnitromethanes

O-Isopropylidene and O-benzylidene acetals of common 2, 6-anhydro-1-deoxy-1-nitroalditols (beta-D-glycopyranosylnitromethanes) derived from D-glucose, D-galactose and D-mannose were studied by chemical ionization mass spectrometry (CIMS) using methane, isobutane, ammonia or pyridine as reaction gas. Production of [M+H](+) adduct ions dominates in the case of methane or isobutane possessing proton affinity values PA = 552 or 683 kJ mol(-1), respectively. The collision-induced dissociation time-of-flight product ion spectra of [M+H](+) ions differ characteristically according the stereochemical arrangement of the pyranoid ring. These differences can be helpful when assigning stereochemical arrangements for the pyranoid ring. The dominant process in ammonia (PA = 853 kJ mol(-1)) CIMS for most of the compounds studied is the production of the cluster ions [M+NH(4)](+). The cluster [M+pyridineH](+) ions are observable only for substances possessing the O-benzylidene group (PA of pyridine = 924 kJ mol(-1)). Copyright 2000 John Wiley & Sons, Ltd.

Proton Affinity and Protonation Sites of Aniline. Energetic Behavior and Density Functional Reactivity Indices

High-level theoretical methods based on both density functional and Hartree−Fock and Moller−Plesset theories have been employed in order to give better insight in the longstanding question concerning the protonation site of gaseous aniline. From the thermodynamic point of view, nitrogen and para ring carbon appear to be the preferred protonation sites. Density functional and MP4 computations show that the protonation on para ring carbon atom is the slightly favored process. The orbital Fukui indices analysis does not resolve unequivocally the dilemma of preferred protonation site attributing to para ring carbon and nitrogen atoms the same probability to work as nucleophilic centers. The absolute hardness values of protonated forms of aniline do not follow the maximum hardness principle. Proton affinity values closer to the experimental counterparts are obtained when the G2(MP2), B3LYP, BP, and MP4 levels of theory are used.

The gas phase acid/base properties of 1,3,-dimethyluracil, 1-methyl-2-pyridone, and 1-methyl-4-pyridone: relevance to the mechanism of orotidine-5′-monophosphate decarboxylase

A combination of experimental and theoretical approaches have been used to probe the gas phase acidity and basicity of 1,3-dimethyluracil, 1-methyl-2-pyridone, and 1-methyl-4-pyridone. For the acidity measurements, bracketing experiments were completed in an electrospray/quadrupole ion trap mass spectrometer. The conjugate bases of the title species were formed by collision activated decarboxylation of appropriate carboxylate precursors. The data indicates only a small variation in the acidities (Δ H acid = 369.9–377.0 kcal/mol) with the uracil derivative being ∼7 kcal/mol more acidic than both the pyridones. To determine the basicities of the title compounds, Cooks’ kinetic method was used and a much larger variation (19 kcal/mol) was observed in the proton affinities of the neutral species: 1,3-dimethyluracil, 213.7 ± 3.0 kcal/mol; 1-methyl-2-pyridone, 222.3 ± 2.9 kcal/mol; and 1-methyl-4-pyridone, 233.1 ± 3.0 kcal/mol. Δ H acid and proton affinity values were also computed at the MP2/6-31+G( d, p)//HF/6-31+G( d), and B3LYP/6-31+G( d, p)//HF/6-31+G( d) levels. There is very good agreement between the experimental values and those from both levels of theory.

The proton affinities of amin-alkanes. A test case for the kinetic method

Metastable ion and collision-induced dissociations of proton bound pairs of n-, sec-, and tert-alkyl amines have been studied by tandem mass spectrometry. The logarithms of the product ion ratios were found to be linear functions of the proton affinities (PA) of the amines as expected for the “kinetic method.” However, the assumption that transition state entropies were closely similar for all pairs proved to be unjustified. Revised PA values for benzylamine and 2-phenylethylamine were proposed.

Sites of protonation of N2-substituted N1,N1-dimethyl formamidines from regional reactivity indices

N1,N1-dimethyl-N2-alkyl-formamidines and alkenyl, alkynyl and heteroalkyl derivatives present two potential sites for protonation reactions in the gas phase, namely, the amino (N1) and imino (N2) nitrogen atoms and eventually, a third potential protonation site at the N2 substituents. The protonation sites in polyfunctional molecules may be directly identified by using local reactivity indices. In this work, we present a theoretical analysis to predict protonation sites using the condensed or regional Fukui function formalism associated with a local hard and soft acids and bases (HSAB) principle. Our method correctly assesses the site of protonation in a wide series of N1,N1-dimethyl-N2-formamidines. The imino N2 site is predicted to be the preferred site for protonation, in close agreement with experimental data. Predicted proton affinities evaluated at the preferred (N2) site and obtained from HF/6-31G(d) calculations correlate well with the experimental values. The method is also tested against a short series of nicotinic acid derivatives that present closer values of proton affinity.

Complete basis set, Gaussian, and hybrid density functional theory evaluation of the proton affinities of water and ammonia

Using Dunning’s basis set saturation approach, electronic energies for proton affinities for both ammonia and water were evaluated with hybrid density functional theory methods. It was demonstrated that the zero-point vibrational correction for both of these proton affinities computed at the B3LYP/6-311G(2d,2p) theory level is identical to the values obtained from experimental data and some other theoretical studies. Thus, computed proton affinities for ammonia and water are in excellent agreement with values obtained by G2 and CBSQ ab initio computational studies. The final proton affinity values are 201.8 kcal/mol for ammonia and 162.4 kcal/mol for water. These calculated values are 2–3 kcal/mol below the experimental values for ammonia and water, suggesting that these values might be too high.

Spatial and Electronic Structure of Highly Basic Organic Molecules: Cyclopropeneimines and Some Related Systems

It is shown, by utilizing a reliable model at the MP2 level of theory, that the imino group attached to the cyclopropene moiety exhibits a high proton affinity (PA). The reason behind the appreciable PA is identified as significant aromatization of the three-membered ring spurred by the protonation. Further amplification of the PA can be achieved by NH2 substitutions at the CC endo double bond, since amino groups stimulate aromatization of the cyclopropene fragment. Additionally, they release some of their lone pair electron density thus contributing to a uniform distribution of the positive charge over the entire molecular system. This effect is even more pronounced if the diaminoiminocyclopropene system is substituted by sizable alkyl groups. The aromatic stabilization in the protonated 2,3-diaminocyclopropeneimine, estimated by the corresponding homodesmic reaction, seems to be as high as 59.5 kcal/mol. Very potent organic bases can be obtained by designing polycyclic systems possessing two or more cyclopropene fragments, where the aromatization occurs by the conjugation interaction transmitted through the π-electron network in a typical domino fashion. The highest PA value is found, however, in a calicene-like structure embracing a quinoid six-membered ring and a cyclopropene moiety. Its proton affinity is well above the PA value of the Schwesinger's proton sponge, which is known as the stongest organic base so far. Importance of the iminocyclopropene motif in tayloring of the strong organic superbases is stressed. The role of the intramolecular hydrogen bonding in some specific systems is briefly discussed.

Influence of the Methyl Groups on the Structure, Charge Distribution, and Proton Affinity of the Retinal Schiff Base

The effect of the methyl substitutions at different carbon atoms of the polyene chain of the retinal Schiff base has been studied on the structure, charge distribution, and proton affinity (PA) in a Schiff base model with the same number of conjugated double bonds (six conjugated double bonds including the Schiff base group). The methyl groups were added to the nitrogen atom and/or different carbon atoms along the main chain, and the results were compared to those of the retinal Schiff base. To study the effect of the polarization functions on hydrogen atoms, all of the structures were studied using 6-31G* and 6-31G** basis sets at the Becke3LYP (B3LYP) level of theory. For each optimized model, the PA was then calculated on the basis of the difference of the total energy of the protonated and unprotonated species. The influence of the zero-point energy corrections on the PA values was also examined at the same level of theory. The results show that, for all species, the application of the larger basis se...

Re-evaluated gas phase basicity and proton affinity data from the thermokinetic method

Gas phase basicities (GB) and proton affinities (PA) of molecules are still the subject of active experimental and theoretical investigations. Recently, a formidable compilation of evaluated GB and PA values of ca. 1700 neutrals has appeared (the Hunter and Lias compilation, 1 which will be abreviated HL hereafter), expanding and correcting the previous review established by the same laboratory. 2 Reevaluation of the GB/PA values derived from gas phase equilibrium experiments or from the ‘kinetic method’ has been made in a more or less straightforward manner. 1 For the values obtained by the ‘thermokinetic method’ the corrections have been made by using a bracketing estimate from the original data. The goal of the present note is to examine, in a more elaborate way, the impact of the new standard values on the GB and PA values obtained in the first applications of the thermokinetic method. It may be briefly recalled that the ‘thermokinetic’ method of determination of gas basicity and proton affinity values uses a correlation between the reaction efficiency (RE) and the standard free energy change, DG o , or the standard enthalpy variation, DH o , of a proton transfer process. 3 For a

Computational Estimates of the Gas-Phase Basicity and Proton Affinity of Glutamic Acid

Literature values for the gas-phase basicity (GB) and proton affinity (PA) of glutamic acid range from 216 to 224 kcal/mol (GB) and 218 to 241 kcal/mol (PA). In this paper, a high-level theoretical study aimed at resolving the apparent disagreement among the experimental values is presented. Hartree−Fock, MP2, and DFT calculations with large basis sets were carried out on the neutral and protonated forms of glutamic acid. Nine protonated and 21 neutral conformers were located at the HF/3-21G and B3LYP/6-31+G** levels with full geometry optimization and characterization of stationary points. The energetics were subsequently reevaluated at the MP2(full)/6-311+G(2d,p)//B3LYP/6-31+G** level. Thermodynamic data in the harmonic approximation were obtained at the B3LYP/6-31+G** level. This data was used to estimate the gas-phase distribution of conformers at 298 K. The lowest energy structures of protonated and neutral glutamic acid both exhibit cyclic structures due to the formation of intramolecular hydrogen bonds. The calculated PA and GB are 224.4 and 214.4 kcal/mol, respectively. It is shown that, when certain empirical corrections for the entropy of cyclization are omitted and appropriate adjustments are made to thermodynamic scales, the GB and gas-phase PA values reported here are in excellent agreement with a variety of previous experimental measurements.

Coulomb repulsion in multiply charged ions: a computational study of the effective dielectric constants of organic spacer groups

Using dication and dianion models, effective dielectric constants have been calculated for several organic spacer groups (alkyl, poly-ether, and poly-ketone). Specifically, ab initio calculations at the MP2/6-31+G( d, p)//HF/6−31+G( d) level were used to estimate the Δ H acid and the proton affinity (PA) values of a series of diammonium and dialkoxide ions, respectively. The variation in these values as a function of the distance between charges leads to the effective dielectric constant (ε) of the organic spacer group. For all the spacer groups, effective dielectric constants near unity were obtained indicating that the spacer group does not reduce the Coulomb repulsion in the doubly charged ion (relative to a vacuum). The values obtained in this study are all slightly less than unity (∼0.85) because the definition of the charge separation as the distance between the formal charge centers (N or O) neglects delocalization and overestimates the true charge separation. For similar reasons, ε values slightly less than unity are also appropriate for zwitterionic systems.

Ion-Transport Catalysis: Catalyzed Isomerizations of NNH+ and NNCH3+

High-level ab initio calculations using the G2** and G2(ZPE=MP2) methods have been employed to examine the effect of interaction with a range of neutral molecules (X) on the barrier to the degenerate proton-transport reactions in NNH+ (X = Ar, HF, CO, N2, H2O) and methyl cation-transport reactions in NNCH3+ (X = HF, H2, N2, HCl, H2O). It is found that the barriers to both proton and methyl cation transport are lowered from their values in the isolated ions of 182 and 152 kJ mol-1, respectively, by interaction with species having values of the proton or methyl cation affinity, respectively, lower than that of molecular nitrogen. Interaction with species that have larger values of proton or methyl cation affinities leads to a further lowering of the barrier, but transfer to the neutral molecule X becomes the more energetically favorable process in such cases. It is found that the ideal catalyst for ion transport should have an ion affinity close to but less than that of molecular nitrogen and have a large d...

Determining the proton affinities of nitriles by the kinetic method

The kinetic method was used to determine the proton affinities (PA) of some homologous alkyl nitriles, C1 – C8, and new PA values for five nitriles were derived. Both metastable ion (MI) and collision-induced dissociations (CID) of the proton-bound dimers were studied. The PA values derived depended on whether MI or CID results were used. The effect of different target gases was investigated and was found to be small. Weaknesses in the kinetic method are discussed.