Proton Affinity Values Research Articles

Gas-Phase Protonation Thermochemistry of Adenosine

The goal of this work was to obtain a detailed insight on the gas-phase protonation energetic of adenosine using both mass spectrometric experiments and quantum chemical calculations. The experimental approach used the extended kinetic method with nanoelectrospray ionization and collision-induced dissociation tandem mass spectrometry. This method provides experimental values for proton affinity, PA(adenosine) = 979 +/- 1 kJ.mol (-1), and for the "protonation entropy", Delta p S degrees (adenosine) = S degrees (adenosineH +) - S degrees (adenosine) = -5 +/- 5 J.mol (-1).K (-1). The corresponding gas-phase basicity is consequently equal to: GB(adenosine) = 945 +/- 2 kJ.mol (-1) at 298K. Theoretical calculations conducted at the B3LYP/6-311+G(3df,2p)//B3LYP/6-31+G(d,p) level, including 298 K enthalpy correction, predict a proton affinity value of 974 kJ.mol (-1) after consideration of isodesmic proton transfer reactions with pyridine as the reference base. Moreover, computations clearly showed that N3 is the most favorable protonation site for adenosine, due to a strong internal hydrogen bond involving the hydroxyl group at the 2' position of the ribose sugar moiety, unlike observations for adenine and 2'-deoxyadenosine, where protonation occurs on N1. The existence of negligible protonation entropy is confirmed by calculations (theoretical Delta p S degrees (adenosine) approximately -2/-3 J.mol (-1).K (-1)) including conformational analysis and entropy of hindered rotations. Thus, the calculated protonation thermochemical properties are in good agreement with our experimental measurements. It may be noted that the new PA value is approximately 10 kJ.mol (-1) lower than the one reported in the National Institute of Standards and Technology (NIST) database, thus pointing to a correction of the tabulated protonation thermochemistry of adenosine.

Methyl Cation Affinities of Commonly Used Organocatalysts

Methyl cation affinities (MCAs) and proton affinities (PAs) of a variety of N- and P-based organocatalysts have been calculated at the MP2(FC)/6-31+G(2d,p)//B98/6-31G(d) level of theory. Correlations between MCA and PA values have been used to identify factors leading to the potentially poor predictive value of PA data for organocatalytic activity. One of the relevant factors concerns steric effects between organocatalysts and the reactant electrophiles, which are not well-modeled by reaction with a proton. A second important factor concerns systematic differences in bond strengths between second- and third-row elements. This latter point makes MCA values much better descriptors of the catalytic activity of phosphanes than PA or pKa data.

Gas-Phase Protonation Thermochemistry of Arginine

The gas-phase basicity (GB), proton affinity (PA), and protonation entropy (DeltapS degrees (M)=S degrees (MH+)-S degrees (M)) of arginine (Arg) have been experimentally determined by the extended kinetic method using an electrospray ionization quadrupole time-of-flight (ESI-Q-TOF) mass spectrometer. This method provides GB(Arg)=1004.3+/-2.2 (4.9) kJ.mol(-1) (indicated errors are standard deviations, and in parentheses, 95% confidence limits are given). Consideration of previous experimental data using a fast atom bombardment ionization tandem sector mass spectrometer slightly modifies these estimates since GB(Arg)=1005.9+/-3.1 (6.6) kJ.mol(-1). Lower limits of the proton affinity, PA(Arg)=1046+/-4 (7) kJ.mol(-1), and of the "protonation entropy", DeltapS degrees (Arg)=S degrees (ArgH+)-S degrees (Arg)=-27+/-7 (15) J.mol(-1).K(-1), are also provided by the experiments. Theoretical calculations conducted at the B3LYP/6-311+G(3df,2p)//B3LYP/6-31+G(d,p) level, including 298 K enthalpy correction, predict a proton affinity value of ca. 1053 kJ.mol-1 after consideration of isodesmic proton-transfer reactions with guanidine as the reference base. Computations including explicit treatment of hindered rotations and mixing of conformers confirm that a noticeable entropy loss does occur upon protonation, which leads to a theoretical DeltapS degrees (Arg) term of ca. -45 J.mol(-1).K(-1). The following evaluated thermochemical parameter values are proposed: GB(Arg)=1005+/-3 kJ.mol(-1); PA(Arg)=1051+/-5 kJ.mol(-1), and DeltapS degrees (Arg)=-45+/-12 J.mol(-1).K(-1).

Quantum-Chemical Calculations of the Affinity of Neutral Molecules for Protons

Quantum-chemical calculations (B3LYP/6-31++G(d,p)) of proton affinities were performed for molecules of various structures in the gas phase. The errors in calculation results were estimated. The data on the proton affinity of several molecules for which experimental proton affinity values are unavailable were obtained. The hypothesis according to which the structure of heteroassociates in the HF-aprotic organic solvent systems depended on the proton affinity of solvent molecules was substantiated.

Probing Lead(II) Bonding Environments in 4-Substituted Pyridine Adducts of (2,6-Me2C6H3S)2Pb: An X-ray Structural and Solid-State 207Pb NMR Study

The effect of subtle changes in the sigma-electron donor ability of 4-substituted pyridine ligands on the lead(II) coordination environment of (2,6-Me(2)C(6)H(3)S)(2)Pb (1) adducts has been examined. The reaction of 1 with a series of 4-substituted pyridines in toluene or dichloromethane results in the formation of 1:1 complexes [(2,6-Me(2)C(6)H(3)S)(2)Pb(pyCOH)](2) (3), [(2,6-Me(2)C(6)H(3)S)(2)Pb(pyOMe)](2) (4), and (2,6-Me(2)C(6)H(3)S)(2)Pb(pyNMe(2)) (5) (pyCOH = 4-pyridinecarboxaldehyde; pyOMe = 4-methoxypyridine; pyNMe2 = 4-dimethylaminopyridine), all of which have been structurally characterized by X-ray crystallography. The structures of 3 and 4 are dimeric and have psi-trigonal bipyramidal S(3)N bonding environments, with the 4-substituted pyridine nitrogen and bridging sulfur atoms in axial positions and two thiolate sulfur atoms in equatorial sites. Conversely, compound 5 is monomeric and exhibits a psi-trigonal pyramidal S(2)N bonding environment at lead(II). The observed structures may be rationalized in terms of a simple valence bond model and the sigma-electron donor ability of the 4-pyridine ligands as derived from the analysis of proton affinity values. Solid-state (207)Pb NMR experiments are applied in combination with density functional theory (DFT) calculations to provide further insight into the nature of bonding in 4, 5, and (2,6-Me(2)C(6)H(3)S)(2)Pb(py)(2) (2). The lead chemical shielding (CS) tensor parameters of 2, 4, and 5 reveal some of the largest chemical shielding anisotropies (CSA) observed in lead coordination complexes to date. DFT calculations using the Amsterdam Density Functional (ADF) program, which take into account relativistic effects using the zeroth-order regular approximation (ZORA), yield lead CS tensor components and orientations. Paramagnetic contributions to the lead CS tensor from individual pairs of occupied and virtual molecular orbitals (MOs) are examined to gain insight into the origin of the large CSA. The CS tensor is primarily influenced by mixing of the occupied MOs localized on the sulfur and lead atoms with virtual MOs largely comprised of lead 6p orbitals.

Computational study on IM-5 zeolite: What is its preferential location of Al and proton siting?

The topological structure of IM-5 zeolite has remained a mystery for nearly 10 years. Stimulated by the recently structural solution of IM-5, we firstly report the computational study on the Al locations, acid sites and acid strength, which are important to understand the catalytic mechanism of IM-5. At the B3LYP/6-31+G(d,p) level, the 8T models were applied. The substitutions of Si by Al atom at 24 inequivalent tetrahedral crystallographic sites and the corresponding H proton localizations were examined by calculating the Al, H substitution energies, proton affinities, the atomic charges on proton and hydroxyl stretching vibrational frequencies. Based on the calculated results it was predicted that the most favorable sites for Al atom substitution in IM-5 were T4, T5, T14, T15 and T19 sites, whereas the least favorable sites were T1, T3, T8, T11, and T16 sites. There are about 40 preferable Al, H locations with relatively high acidity, including the nine strongest acid sites Al19H43 > Al14H18 > Al5H13 > Al4H8 > Al10H26, Al15H26, Al15H37, Al22H45 and Al24H47. The last five sites have equivalent proton affinity values. The numerous Al, H-sites with high acidity may be responsible for the high catalytic ability of IM-5. The calculated results should be helpful for understanding the chemistry of IM-5, the most complicated zeolite material known up to now.

Nucleophilicity of Indole Derivatives: Activating and Deactivating Effects Based on Proton Affinities and Electron Density Properties

Activating and deactivating abilities of several substituents (-CH3, -F, -NH2, -NO2) in indole have been theoretically studied using a series of electron density based reactivity indices. Calculations have been performed at the B3LYP/6-311++G(2d,2p) level. An energetic criterion based on the proton affinities (PAs) has been employed to check the validity of these reactivity indices. Relative PAs reflect the ortho and para orientation ability of -CH3, -F, and -NH2 groups, whereas the large deactivating effect of -NO2 is mainly observed at these positions. Also, substitutions in carbons 2 and 6 (IUPAC nomenclature) activate/deactivate carbons 6 and 2, respectively. Inductive effects are also reflected on the values of the relative PAs. The -CH3 group is shown to have inductive electron-withdrawing character instead of electron-releasing with its activating ability being due to a small mesomeric electron-releasing character. pi atomic electron populations and the zz component of the atomic quadrupole electric tensor qualitatively explain the order of PAs. Fukui indices approximately predict the results obtained by the previous properties, whereas no correlation is found between the values of the (triangle down)2rho(r) at the secondary charge concentrations and the PA scale.

Electron-impact ionization of benzoic acid, nicotinic acid and their n-butyl esters: An approach to regioselective proton affinities derived from ionization and appearance energy data

Electron-impact ionization mass spectra, the decay of metastable ions, ionization and appearance energies and bond energies, as dissociation energies, are reported for the title compounds. An ionization energy of 9.47 eV was obtained for benzoic acid, 9.43 eV for benzoic acid n-butyl ester, 9.61 eV for nicotinic acid and 9.97 eV for nicotinic acid n-butyl ester. Molecular ions of both butyl esters show two common main fragmentation pathways: the first process is a McLafferty rearrangement, characterized by the transfer of one H-atom from the aliphatic ester chain, which leads to the ions of either the organic acid or 1-butene. From their appearance energies and known thermodynamic data, gas-phase formation enthalpies ( Δ H f 0 ) of the parent n-butyl esters are calculated. Values of Δ H f 0 = ( − 4.29 ± 0.3 ) eV for benzoic acid n-butyl ester and Δ H f 0 = ( − 3.66 ± 0.3 ) eV for nicotinic acid n-butyl ester were obtained. The second process is characterized by the transfer of two H-atoms from the ester chain leading to a protonated form of the corresponding organic acids and C 4H 7 radicals. Good evidence is provided for the formation of methylallyl radicals. Appearance energies are used to calculate a proton affinity (PA) for benzoic acid. The obtained value of PA = (8.73 ± 0.3) eV, corresponding to a protonation of the carbonyl group, is in close corroboration with published data (PA = 8.51 eV). Activation energies for the intermediate H-transfers were found to be insignificant. This methodic gateway is applied to the system of nicotinic acid and its butyl ester. Adopting the formation of a methylallyl radical, the obtained proton affinity of nicotinic acid, PA = 8.58 eV, is very near to the published data of benzoic acid. An alternative fragmentation mechanism leading to a value of PA ≈ 9.5 eV (typical for a protonation of the pyridine-nitrogen) is very unlikely. It is concluded that this transfer of two H-atoms from the ester chain is controlled by a charge switching between the carboxylic oxygen atoms which leads to a regiospecific protonation site, in this case to the protonated carbonyl group. This is conform with a B3LYP DFT calculation with a corresponding proton affinity of PA = 8.29 eV.

Ab initio and density functional theory calculations of proton affinities for volatile organic compounds

The Hatree-Fock method with 6-311G** split-valence molecular orbitals basis sets and the density function theory-B3LYP have been applied to geometrical optimizations and calculations of total electronic, zero point vibrational energies and proton affinities at 298 K for volatile organic compounds. Calculated values of proton affinities are compared with experimental data.

Protonated Heme

The ions formally corresponding to protonated heme [Fe(II)-hemeH](+) have been obtained by collision-induced dissociation from the electrospray ionization of microperoxidase (MP11) and their gas-phase chemistry has been studied by FTICR mass spectrometry. H/D-exchange reactions, used as a tool to gain information on the protonation sites in polyfunctional molecules, show that labile hydrogens pertain to the propionyl substituents at the periphery of the protoporphyrin IX. Several conceivable isomers for protonated heme have been evaluated by density functional theory. The most stable among the species investigated is the one corresponding to protonation at the beta carbon atom of a vinyl group, yielding a proton affinity (PA) value for [Fe(II)-heme] of 1220 kJ mol(-1). This high PA is consistent with the inertness of the hydrogen atoms at the protonation site towards H/D exchange with ND(3) and CD(3)CO(2)D. Peculiar features of this [Fe(II)-hemeH](+) isomer emerge by analysis of its electronic structure, showing that the vinyl group undergoing formal protonation has gained significant radical character due to electron transfer from the metal center. As a consequence, the iron atom acquires partial iron(III) character and none of the two formal descriptions [Fe(II)-hemeH(+)] and [Fe(III)-hemeH(.)](+) alone may adequately illustrate the protonated heme ion. In agreement with this description, the reactivity of protonated heme presents dual facets, resembling iron(III) in some aspects and iron(II) in others. On the one hand, protonated heme behaves like [Fe(III)-heme](+) ions in H/D-exchange reactions. On the other, it shows markedly decreased reactivity towards the addition of ligands with the notable exception of NO, in line with the high affinity shown by iron(II) complexes towards this molecule, NO, of key biological role.

Theoretical Investigation of the Proton Affinity and Gas-Phase Basicity of Neutral x,y-Dihydroxybenzoic Acid and its Derivatives

Proton affinities ( PA), gas-phase basicities ( GB) and acidities ( GA), which are some of the important physical properties of a matrix in matrix-assisted laser desorption ionization mass spectrometry, have been calculated using density functional theory (DFT) for a number of dihydroxybenzoic (DHB) acid isomers and derivatives. The theoretical PA and gas-phase basicity ( GB) values for the neutral x,y-DHB acids, ionic radicals, Na+ and K+ salts as well as oxygen- and hydrogen-bridged dimers of x,y-DHB have been calculated. Analysis of the computational data indicates that there are lower PA/ GB values for the anionic dimers compared to the PA/ GB values for the electrically neutral oxygen-bridged dimers. The PA/ GB values for the neutral and radical cations are larger than the neutral monomers and the PA/ GB values for the radical anions are slightly lower than the anionic class of isomers. The PA/ GB values for the salts (x, y-DHB−Na/K+) are significantly higher (100–150 kJ mol−1) than the neutral x,y-DHB acids. The above theoretical results are in agreement with experimental values obtained by Fourier transorm ion cyclotron resonance mass spectrometry employing a thermokinetic method. Correlation of experimentally and theoretically predicted values suggests that this theoretical calculation method could be used to derive information on different matrices.

Proton affinities of simple organic compounds

The Restricted Hatree-Fock method with 6-311G** split-valence molecular orbitals basis sets has been applied to geometrical optimizations and calculations of total electronic, zero point vibrational energies and proton affinities at 298 K for small neutral and protonated alkanes, alcohols, acetic acid, methyl and ethyl acetate, acetone, and acetaldehyde. Calculated values of proton affinities are compared with experimental data.

Comprehensive theoretical study towards the accurate proton affinity values of naturally occurring amino acids

AbstractSystematic quantum chemical studies of Hartree–Fock (HF) and second‐order Møller–Plesset (MP2) methods, and B3LYP functional, with a range of basis sets were employed to evaluate proton affinity values of all naturally occurring amino acids. The B3LYP and MP2 in conjunction with 6‐311+G(d,p) basis set provide the proton affinity values that are in very good agreement with the experimental results, with an average deviation of ∼1 kcal/mol. The number and the relative strength of intramolecular hydrogen bonding play a key role in the proton affinities of amino acids. The computational exploration of the conformers reveals that the global minima conformations of the neutral and protonated amino acids are different in eight cases. The present study reveals that B3LYP/6‐311+G(d,p) is a very good choice of technique to evaluate the proton affinities of amino acids and the compounds derived from them reliably and economically. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006

Multilevel and Density Functional Electronic Structure Calculations of Proton Affinities and Gas-Phase Basicities Involved in Biological Phosphoryl Transfer

Five multilevel model chemistries (CBS-QB3, G3B3, G3MP2B3, MCG3/3, and MC-QCISD/3) and seven hybrid density functional methods (PBE0, B1B95, B3LYP, MPW1KCIS, PBE1KCIS, and MPW1B95) have been applied to the calculation of gas-phase basicity and proton affinity values for a series of 17 molecules relevant to the study of biological phosphoryl transfer. In addition, W1 calculations were performed on a subset of molecules. The accuracy of the methods was assessed and the nature of systematic errors was explored, leading to the introduction of a set of effective bond enthalpy and entropy correction terms. The multicoefficient correlation methods (MCG3/3 and MC-QCISD), with inclusion of specific zero-point scale factors, slightly outperform the other multilevel methods tested (CBS-QB3, G3B3, and G3MP2B3), with significantly less computational cost, and in the case of MC-QCISD, slightly less severe scaling. Four density functional methods, PBE1KCIS, MPW1B95, PBE0, and B1B95 perform nearly as well as the multilevel methods. These results provide an important set of benchmarks relevant to biological phosphoryl transfer reactions.

Theoretical proton affinities of α1 adrenoceptor ligands

A systematic study has been performed of the proton affinity of a large family of agonists and antagonists of the α1-adrenoceptor at the B3LYP/6-31G* level of theory. After a conformational search, all the N atoms were considered as protonation sites and protonation energy values were determined. The inclusion of solvation by means of the Onsager model yielded stabilization in the proton affinity values obtained. In addition, a good correlation was found between the proton affinity values corresponding to the first protonation in gas phase of some of the compounds and their corresponding experimental affinity constants K i for the α1A adrenergic receptor.

Improved proton affinity measurements for proline and modified prolines using triple quadrupole and ion trap mass spectrometers

Proton affinity (PA) of compounds such as proline, cis-3-methylproline, cis-3-ethylproline, cis-3-isopropylproline and cis-3-isopentanylproline was determined by kinetic method with amines as the reference bases. The effective temperatures determined using ion trap and triple quadrupole mass spectrometers were found to be significantly different. In the case of the triple quadrupole instruments, the effective temperature depends significantly on the collision energy. The influence of the apparent basicity (GBapp) on the effective temperature may be used to estimate the difference in protonation entropy (DeltaDeltaS degrees) between the sample and reference compounds. In case of the ion trap mass spectrometer, the variation of the effective temperature as a function of the excitation amplitude is small, so it is difficult to account for the contribution of the entropy effects to the proton affinity value. A better estimation of the PA and DeltaDeltaS degrees values for the investigated molecules is obtained by combining the GBapp and Teff data pairs that are obtained from both the mass spectrometers.

Proton affinity of diastereoisomers of modified prolines using the kinetic method and density functional theory calculations: role of the cis/trans substituent on the endo/exo ring conformation

The proton affinity (PA) of cis/trans-3-prolinoleucines and cis/trans-3-prolinoglutamic acids have been studied by the kinetic method and density functional theory (DFT) calculations. Several conformations of the neutral and the protonated modified prolines, in particular the endo and exo ring conformations, were analyzed with respect to their contribution to the PA values. When the substituent is an alkyl, both the diastereoisomers have the same PA value. However, the PA values for the diastereoisomers are different when the substituted chain contains functional groups (e.g. a carboxyl group). This variation in PA values could be attributed to the existence of intramolecular hydrogen bonds.

Polyglycine Conformational Analysis: Calculated vs Experimental Gas-Phase Basicities and Proton Affinities

Structures of neutral and protonated polyglycines (Gly(n) and Gly(n)H(+) with n = 1-6) in the vicinity of global energy minima were calculated using the density functional theory at the B3LYP/6-311++G** (A) and B3LYP/6-31+G** (B) levels. Ninety-three structures were chosen for conformation and protonation studies. Geometries of the peptides are found to vary from open chains to multiple rings. Intramolecular hydrogen bonding is deduced to be the driving force for conformational stability. The preferred protonation sites are shown to be the terminal nitrogen atom and its adjacent amide oxygen atom. Structural series are developed according to geometrical form, hydrogen bonding, and protonation site. Physical factors that influence the relative electronic and thermodynamic stabilities of different structural series are examined. To obtain ab initio values of highest quality for gas-phase basicity (GB) and proton affinity (PA), electronic energies for n = 1-6 and thermal corrections to Gibbs free energy and enthalpy for n = 1-3 were calculated at level A, supplemented by thermal corrections for n = 4-6 at level B. Calculated GB and PA values are compared with mass spectral results obtained by the kinetic method (KM) and reaction bracketing (RB). The KM results and the ab initio values derived from structurally compatible pairs of lowest free energies are generally in good agreement, but the RB results for GB are lower by 2-8 kcal/mol for n = 2-6. Several reaction pathways are proposed to elucidate the experimental results. On the basis of theoretical structures consistent with the measurements, it is concluded that KM mostly samples the neutral and protonated structures of highest populations at thermal equilibrium, whereas RB targets those with sterically most accessible sites for protonation and deprotonation.

A theoretical study of uracil and its tautomers in their lowest-lying triplet state

The potential-energy surface of the lowest-lying triplet uracil tautomerization is comprised of the 13 possible tautomeric forms including uracil itself. Their structures are determined at the B3LYP/6 - 31 + G(d,p) level. Some characteristics of the tautomeric geometries are described. The intra-molecular proton transfer reaction mechanism and the variation of thermodynamic properties show that reaction enthalpy is the determining factor for the occurrences and populations of the stable tautomers. The relative stability ordering of all the triplet uracil tautomers is established. The proton affinities (PAs) and the deprotonation enthalpies (DPEs) of the atoms or bonds involved in the tautomerization process are calculated at both B3LYP and MP2 methods. The PA and DPEs values sensitively depend on the tautomeric form. The N1 site has a greater PA value than other sites and the PA of O4 is greater than that at the N2 site in the same tautomer. The DPE of OH is larger than that of NH in the keto-enol tautomers and the DPE of O4H4 larger than that of O2H2. These results provide a rationale for the fact that the dioxo form of uracil is the most stable one among the tautomers. The relative energies of the uracil tautomers are then rationalized in terms of a second-order polynomial of the difference between their mean PAs and DPEs.

Resonance stabilization and gas phase protonation in phosphorus ylides: probing through MO and DFT computations

Protonation energy (PE) calculations at the MP2/6-31G* level of theory on a set of resonance stabilized model ylides reveal that, resonance effect make these ylides multi-site basic. In some cases the ylidic carbon is not the most favored site of protonation and points out to the stability of P +–C − bond. B3LYP/6-31G* calculations yield closely related PE values, indicating its validity. The protonation energy of these ylides are intermediate to those of proton sponges and super bases. PM3 calculations were used to calculate proton affinity (PA) values for a set of the most common triphenylphosphine family of ylides. The PA values of the model ylides at PM3 level bear close resemblances to those calculated at the MP2/6-31G* and B3LYP/6-31G* levels of theory, indicating the inconsiderable contribution of zero point vibration energy (ZPVE) to the PA of these ylides. The proton affinity of the metallated ylide, Ph 3PCHLi is computed to be 287.6 kcal/mol and becomes the metal-ylide upon protonation. Introduction of nine NMe 2 groups on the three P-phenyl groups of Ph 3P CH 2 increases the PA to 301.6 kcal/mol.