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

Abstract

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).

Benchmark Ab Initio Determination of the Conformers, Proton Affinities, and Gas-Phase Basicities of Cysteine

“…The N-protonation hinders the acceptor role of the N atom, while the O protonation blocks the same character of the carbonyl O atom. The cysteine global minimum resembles to the II N 16 and II a 36 structures of the glycine and the alanine with respect to the dihedral angles related to the α and β carbon atoms, and it is also stabilized with a hydrogen bond between the lone electron pair of the N atom and the H atom of the hydroxyl group. There is a much weaker interaction between the H atom of the thiol group and the double bonded oxygen, as their distance is ∼2.7 Å.…”

“…We can explain the relatively high number of the O-protonated conformers by considering the conformational space: in that case we have a new important torsional angle which leads to more stable conformers just like in the case of glycine and alanine. 16 , 36 The occurrence of the conformers upon the three mapping can be seen in Figure 3 . With the initially N-protonated data set (first column), we only got N-protonated structures, 16 of the final 21.…”

“…The N-protonation hinders the acceptor role of the N atom, while the O protonation blocks the same character of the carbonyl O atom. The cysteine global minimum resembles to the II N 16 and II a 36 structures of the glycine and the alanine with respect to the dihedral angles related to the α and β carbon atoms, and it is also stabilized with a hydrogen bond between the lone electron pair The relative energies, enthalpies, free energies, and auxiliary energy corrections of the neutral cysteine can be seen in Table 2. The relative energy order changes at many places at higher level of theory, coupled-cluster order is noted by Roman numerals, while the MP2 order by Arabic numerals.…”

“…After our high-level theoretical studies on glycine and alanine, 16 , 36 here we present an explicitly correlated ab initio investigation on the conformers of the cysteine and its protonated counterparts as well as PA and GB values. From the qualitative side, we map the extended conformational space of the neutral and protonated amino acid; in the latter case, we consider three possible protonation sites.…”

Protonation of serine: conformers, proton affinities and gas-phase basicities at the “gold standard” and beyond

“…Similar to our previous studies on amino acids, 41–44 we would like to add novelties to this theoretical field by the means of possibly revealing new conformers for both the neutral and protonated serine, using a higher level of theory for the conformational mapping. For the protonated serine we are also investigating the protonation at other site(s), in particular the yet neglected carbonyl site.…”