Protonation Thermochemistry of α-Amino Acids Bearing a Basic Residue

Bouchoux, Guy; Buisson, David‐Alexandre; Colas, Cyril; Sablier, Michel

doi:10.1255/ejms.687

Cited by 39 publications

(80 citation statements)

References 42 publications

(83 reference statements)

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“…Tabet [42] did not include entropy corrections and found that glutamine's PA was about 3 kcal/mol above asparagine, but 6.4 kcal/mol below the computed value. Bouchoux [44] found a 5.5 kcal/mol difference in proton affinities, but their values for asparagine and glutamine are 7.1 and 3.6 kcal/mol over the computed values. In addition, their entropy corrections are similar for the two amino acids.…”

Section: Comparison To Experimental Valuesmentioning

confidence: 80%

“…As a result, the computational value for histidine, 233.9 kcal/mol, has a high probability of being reasonably accurate. The experimental values vary from 229.2 (Tabet) [42] to 238.1 (Bouchoux) [44]. The first value can be discounted because entropy corrections were not made, but the second is quite high.…”

Section: Comparison To Experimental Valuesmentioning

confidence: 99%

“…In Table 3, the computed PA values from the present study are reported along with those from Harrison [41], Tabet [42], Bouchoux [34,[43][44][45], and the NIST website [9]. For Harrison's scale, we have adopted his values that included an estimated entropy correction for cases where protonation was expected to lead to cyclization of the cation (values listed parenthetically in his paper).…”

Section: Comparison To Experimental Valuesmentioning

confidence: 99%

“…The inability to adequately correct for entropy effects in the formation of these cations is a likely source of error for them (all experimental measures directly probe the free-energy of protonation so assumptions tend to be made in the extraction of the enthalpy of protonation from these data). The most recent data from Tabet [42] and Bouchoux [43,44] employ the Cooks kinetic method [46,47], and in Bouchoux's case, make explicit corrections for entropy changes based on the energy dependence of the dissociation processes used in the kinetic method.…”

Section: Comparison To Experimental Valuesmentioning

confidence: 99%

“…This is also reflected in the fact that our glutamic acid structure and Paizs's have very different hydrogen bonding patterns, yet similar stabilities. However, Bouchoux [44] finds that glutamic acid's PA is 13 kcal/mol greater than that of aspartic acid, driven mainly by a very large entropy correction for glutamic acid (almost twice as large as lysine and glutamine). Again, it is difficult to reconcile this PA value for glutamic acid with the computed one, and the reason for the discrepancy mainly rests with the experimental entropy correction.…”

Section: Comparison To Experimental Valuesmentioning

confidence: 99%

See 4 more Smart Citations

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

Gronert

Simpson

Conner

2009

J. Am. Soc. Mass Spectrom.

109

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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...

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Section: Comparison To Experimental Valuesmentioning

confidence: 80%

Section: Comparison To Experimental Valuesmentioning

confidence: 99%

Section: Comparison To Experimental Valuesmentioning

confidence: 99%

Section: Comparison To Experimental Valuesmentioning

confidence: 99%

Section: Comparison To Experimental Valuesmentioning

confidence: 99%

See 3 more Smart Citations

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

Gronert

Simpson

Conner

2009

J. Am. Soc. Mass Spectrom.

109

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Why Are Selenouracils as Basic as but Stronger Acids than Uracil in the Gas Phase?

2008

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The gas-phase basicity and acidity of 2-selenouracil (2SU), 4-selenouracil (4SU), and 2,4-diselenouracil (24SU) have been calculated at the B3LYP/6-311+G(3df,2p) level of theory. Our results showed that all these compounds behave as bases of moderate strength in the gas phase. As was found for uracil and for the thiouracil analogues, the most basic site is the heteroatom at position 4, and only for 2SU is there a certain ambiguity in assigning the basic site. More importantly, with the only exception of 2SU, selenouracils are as basic as or slightly less basic than uracil, because the replacement of the oxygen atom at position 2 by a selenium atom leads to an increase of the electron delocalization inside the six-membered ring, which decreases the intrinsic basicity of the heteroatom at position 4. As already reported for uracil and thiouracils, for selenouracils N1 is the most acidic site. However, selenouracils are predicted to be stronger acids than uracil. This acidity enhancement is essentially due to a specific stabilization of the anion when O is replaced by Se. Two factors are responsible for this stabilization: a significant aromatization of the ring upon deprotonation and a better dispersion of the excess electron density when the system contains third-row atoms.

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Benchmark ab initio proton affinity and gas‐phase basicity of α‐alanine based on coupled‐cluster theory and statistical mechanics

Dékány

Czakó

2021

J Comput Chem

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We determine the proton affinity (PA) and gas-phase basicity (GB) of amino acid α-alanine at a chemically accurate level by performing explicitly-correlated CCSD(T)-F12b/aug-cc-pVDZ geometry optimizations and normal mode vibrational frequency calculations as well as CCSD(T)-F12b/aug-cc-pVTZ energy computations at the possible neutral and protonated geometries. Temperature effects at 298.15 K considering translational, rotational, and vibrational enthalpy and entropy corrections are obtained via standard statistical mechanics utilizing the molecular geometries and the harmonic vibrational energy levels. Both the amino nitrogen (N) and the carbonyl oxygen (O) atoms are proven to be potential protonation sites and a systematic conformational search reveals 3 N-and 9 O-protonated conformers in the 0.00-7.88 and 25.43-30.43 kcal/mol energy ranges at 0 K, respectively. The final computed PA and GB values at (0)298.15 K in case of N-protonation are (214.47)216.80 and 207.07 kcal/mol, respectively, whereas the corresponding values for O-protonation are (189.04)190.63 and 182.31 kcal/mol. The results of the benchmark high-level coupled-cluster computations are utilized to assess the accuracy of several lowerlevel cost-effective methods such as MP2 and density functional theory with various functionals (SOGGA11-X, M06-2X, PBE0, B3LYP, M06, TPSS).

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Protonation Thermochemistry of α-Amino Acids Bearing a Basic Residue

Cited by 39 publications

References 42 publications

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

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

Why Are Selenouracils as Basic as but Stronger Acids than Uracil in the Gas Phase?

Benchmark ab initio proton affinity and gas‐phase basicity of α‐alanine based on coupled‐cluster theory and statistical mechanics

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