The proton affinity of proline analogs using the kinetic method with full entropy analysis

109

The proton affinities of the 20 common amino acids have been computed at the G3MP2 level using structures derived from broad conformational searches at a variety of levels including G3MP2. In some cases, the conformational surveys identified more stable species than had been used in previous studies of proton affinities, though the differences in energy are sometimes rather small. The present values are likely the most reliable measure of amino acid proton affinities in the gas phase. An analysis of differences between these values and those obtained experimentally via the kinetic method indicates that the extraction of proton affinities from kinetic method data can potentially lead to large errors linked to the estimation of relative protonation entropies. . As noted by these authors, there is substantial variation in the experimental values reported for these species. The origin of this variability is most likely related to the difficulties of completing thermodynamic measurements in the gas phase on materials with low volatility. As a result, many of the experimental values are from kinetic method measurements and are subject to errors associated with the kinetic method approximation (as well as cumulative errors associated with the development of ladder-type scales). Therefore, in these systems, high-level computational work offers an attractive means of resolving differences in the various experimental measurements.While working on a computational study of the conformational preferences of neutral, gaseous amino acids, we realized that it would be possible to improve on the accuracy of the proton affinities reported by Paizs and coworkers. First, their computational strategy relied on the B3LYP approach to identify global minima and, often, they identified conformations for the neutral amino acids that did not match with those reported in previous computational and experimental studies (apparently in some cases this was the result of the search strategy and in others the computational method). For example, Paizs and coworkers concluded that glycine prefers a structure with an internal hydrogen bond between the carboxylic acid and amine groups. Highlevel ab initio, other B3LYP data [2], and experimental data suggest a structure with a syn carboxyl group and a weak interaction between the amine hydrogens and the carbonyl [3][4][5]. While the energetic impact of this problem is generally minor, we feel it is important to report values based on the most appropriate conformations that can be obtained within a computational method. For the protonated amino acids, this problem is less pronounced because the hydrogen bonding interactions are much stronger; most computational methods identify similar structures as the global minimum. Second, values reported by Paizs and coworkers are at 0 K. We have added a correction for the thermal energy of a proton, which amounts to about 1.5 kcal/mol at 298 K, as well as for the neutral and protonated amino acid. Although these corrections cancel to some extent and while the ge...

Section: Comparison To Experimental Valuesmentioning

confidence: 99%

A reevaluation of computed proton affinities for the common α-amino acids

Gronert

Simpson

Conner

2009

109

“…Researchers using the full entropy analysis method have equated the apparent entropy term either with the entropy difference for dissociation, ⌬⌬S(T), [21][22][23][24], or with the entropy difference for activation, ⌬⌬S ‡ (T) [26]. The assumption ⌬⌬S(T) ϭ ⌬⌬S ‡ (T) is also implicit in implementations of the kinetic method that calibrate against Gibbs energies instead of enthalpies, i.e., ln(I 2 /I 1 ) ϭ Ϫ⌬⌬G/RT eff instead of eq 7.…”

Section: Canonical Formulationmentioning

confidence: 99%

“…Armentrout proposed an improved statistical treatment of extended kinetic method data to obtain enthalpy differences and the apparent entropies with realistic uncertainties [21]. This "full entropy analysis" has been used for measurements of proton affinities and electron affinities [22][23][24][25][26] by the extended kinetic method. In their finite heat bath theory and RRKM theory simulations, Laskin and Futrell [9] found reasonable agreement between the apparent entropy and the thermodynamic entropy difference.…”

mentioning

confidence: 99%

Microcanonical analysis of the kinetic method. The meaning of the “apparent entropy”

Ervin

2002

135

A rigorous analysis of the kinetic method is carried out using Rice-Ramsperger-KasselMarcus (RRKM) theory of microcanonical statistical unimolecular dissociation rates. The model employs a kinetics treatment appropriate for metastable ion dissociation. Protonbound alkoxide dimer anions are used as model systems, with realistic vibrational and rotational parameters calculated by ab initio methods for the cluster ion and transition states leading to the competitive dissociation channels. The numerical simulations show that the kinetic method plots of ln(I 2 /I 1 ) versus ⌬⌬H are nearly linear but can exhibit significant curvature. The apparent entropy obtained in the extended kinetic method is not approximately equal to the thermodynamic entropy difference for dissociation, ⌬⌬S(T), or for activation, ⌬⌬S ‡ (T), either at the effective temperature or at any fixed equilibrium temperature. Instead, the apparent entropy term can be related to the ratio of the microcanonical sum of states of the dissociation transition states for the kinetically selected internal energy of the dissociating ions. (J Am Soc Mass Spectrom 2002, 13, 435-452)

“…For example, the proton affinity of proline, as listed in the NIST compilation [27], is nearly 16 kJ/mol lower than recent redeterminations from our group [20] and from others [18]. Because of these discrepancies, we have avoided using the amino acids as reference bases in our kinetic method experiments.…”

mentioning

confidence: 94%

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

Wind

Papp

Happel

et al. 2005

Self Cite

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 ␤-oxalylaminoalanine (BOAA). The PA of BOAA is found to be 933.1 Ϯ 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/6-311ϩϩG**//B3LYP/6-31ϩG* level. They indicate that the preferred site of protonation is the ␣-nitrogen atom (PA ϭ 935.0 kJ/mol) and that protonated BOAA has a strong hydrogen bond between the hydrogen on the ␣-amino group and one of the carbonyl oxygen atoms on the side chain. (J Am Soc Mass Spectrom 2005, 16, 1151-1161