Conformers of dehydrogenated glycine isomers

Accurate and reliable thermochemistry by data analysis of complex thermochemical networks using Active Thermochemical Tables: the case of glycine thermochemistry

Active Thermochemical Tables (ATcT) were successfully used to resolve the existing inconsistencies related to the thermochemistry of glycine, based on statistically analyzing and solving a thermochemical network that includes >3350 chemical species interconnected by nearly 35 000 thermochemically-relevant determinations from experiment and high-level theory. The current ATcT results for the 298.15 K enthalpies of formation are -394.70 ± 0.55 kJ mol-1 for gas phase glycine, -528.37 ± 0.20 kJ mol-1 for solid α-glycine, -528.05 ± 0.22 kJ mol-1 for β-glycine, -528.64 ± 0.23 kJ mol-1 for γ-glycine, -514.22 ± 0.20 kJ mol-1 for aqueous undissociated glycine, and -470.09 ± 0.20 kJ mol-1 for fully dissociated aqueous glycine at infinite dilution. In addition, a new set of thermophysical properties of gas phase glycine was obtained from a fully corrected nonrigid rotor anharmonic oscillator (NRRAO) partition function, which includes all conformers. Corresponding sets of thermophysical properties of α-, β-, and γ-glycine are also presented.

Tell Machine Learning Potentials What They Are Needed For: Simulation-Oriented Training Exemplified for Glycine

Machine learning potentials (MLPs) are widely applied as an efficient alternative way to represent potential energy surfaces (PESs) in many chemical simulations. The MLPs are often evaluated with the root-mean-square errors on the test set drawn from the same distribution as the training data. Here, we systematically investigate the relationship between such test errors and the simulation accuracy with MLPs on an example of a full-dimensional, global PES for the glycine amino acid. Our results show that the errors in the test set do not unambiguously reflect the MLP performance in different simulation tasks, such as relative conformer energies, barriers, vibrational levels, and zero-point vibrational energies. We also offer an easily accessible solution for improving the MLP quality in a simulation-oriented manner, yielding the most precise relative conformer energies and barriers. This solution also passed the stringent test by diffusion Monte Carlo simulations.

Coupled Cluster Semiclassical Estimates of Experimental Reaction Rates: The Interconversion of Glycine Conformer VIp to Ip

We apply the full-dimensional Semiclassical Transition State Theory (SCTST) to estimate the rate constant of glycine molecule interconversion between the VIp and Ip conformers. We have reached an electronic structure accuracy up to the explicitly correlated Coupled Cluster method (CCSD(T)-F12b/cc-pVDZ-F12) thanks to our parallel implementation. The reaction has been experimentally investigated in the literature and is known to proceed by quantum mechanical tunneling. The SCTST rates improve over other theoretical methods, and our results align with the experimental measurements, thus confirming the accuracy of the fully coupled anharmonic semiclassical tunneling treatment, providing that the level of electronic structure theory gives a reliable estimate of the reaction barrier height and shape. The comparison with experimental half-life times supports the validity of SCTST for glycine VIp-Ip conformer conversion in the cryogenic temperature range, where this theory is usually not considered applicable due to the onset of the deep tunneling regime.

Effect of Solvation on Glycine Molecules: A Theoretical Study

Ab initio calculations of HF+MP2 and DFT-B3LYP quality have been used in calculating the molecular geometries and properties of neutral and charged molecules of glycine in amino acid as well as zwitterionic forms. A traditional set of molecular descriptors has been enriched by the molecular chemical potential, expressed via the Mulliken electronegativity, and Pearson's chemical hardness. In the global energy minimum, the complete vibrational analysis allowed evaluating the standard Gibbs energy and related thermodynamic quantities.

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

The potential energy surfaces (PESs) of serine and its protonated counterparts are investigated to determine the structures of the minima. A total of 95 neutral serine, 15 N-(amino-) and 46 O-(carbonyl-)protonated serine conformers are found. Their relative energies, geometries and harmonic vibrational frequencies are determined at the MP2/aug-cc-pVDZ level of theory. To obtain highly accurate thermodynamic values, further computations are performed: the ten conformers with the lowest relative energies from each molecule type (neutral, N- and O-protonated) are further optimized using the explicitly correlated CCSD(T)-F12a/cc-pVDZ-F12 method (for neutral serine, harmonic vibrational frequencies were also computed). In addition, auxiliary corrections were determined: basis-set effects up to CCSD(T)-F12b/cc-pVQZ-F12, electron correlation effects up to CCSDT(Q), core correlation and second-order Douglas-Kroll relativistic effects along with zero-point energy contributions. Two important thermodynamic parameters (at 298.15 K), proton affinity (PA)/gas-phase basicity (GB) are calculated considering the two different protonation sites: 218.05 ± 0.2/209.86 ± 0.6 kcal mol^-1 and 205.87 ± 0.2/196.36 ± 0.3 kcal mol^-1 for the amino and carbonyl sites, respectively. The uncertainty of the determined values was approximated based on various sources including auxiliary corrections, basis-set effects, harmonic vibrational frequencies.

Glycine Imine-The Elusive α-Imino Acid Intermediate in the Reductive Amination of Glyoxylic Acid

Simple unhindered aldimines tend to hydrolyze or oligomerize and are therefore spectroscopically not well characterized. Herein we report the formation and spectroscopic characterization of the simplest imino acid, namely glycine imine, by cryogenic matrix isolation IR and UV/Vis spectroscopy. Glycine imine forms after UV irradiation of 2-azidoacetic acid by N₂ extrusion in anti-(E,E)- and anti-(Z,Z)-conformation that can be photochemically interconverted. In matrix isolation pyrolysis experiments with 2-azidoacetic acid, glycine imine cannot be trapped as it further decarboxylates to aminomethylene. In aqueous solution glycine imine is hydrolyzed to hydroxy glycine and hydrated glyoxylic acid. At higher concentrations or in the presence of Fe^II SO₄ as a reducing agent glycine imine undergoes self-reduction by oxidative decarboxylation chemistry. Glycine imine may be seen as one of the key reaction intermediates connecting prebiotic amino acid and sugar formation chemistry.

High-level ab initio mapping of the multiple H-abstraction pathways of the OH + glycine reaction

We perform a systematic search in the transition-state (TS) and product-channel complex (MIN) regions of the multi-channel OH + glycine → H₂O + H₂N-CH-COOH (CH)/HN-CH₂-COOH (NH)/H₂N-CH₂-COO (COOH) reactions. Geometry optimizations reveal {7, 3, 3} CH-TS, {2, 2, 2} CH-MIN, {17, 10, 5} NH-TS, {35, 19, 19} NH-MIN, and {6, 5, 5} COOH-TS conformers at the {MP2/3-21G, MP2/aug-cc-pVDZ, CCSD(T)-F12b/aug-cc-pVDZ} levels of theory as well as 2 additional CH-TSs based on chemical intuition. The benchmark relative energies of the TS, MIN, and product conformers are obtained by considering basis set effects up to aug-cc-pVQZ using the explicitly-correlated CCSD(T)-F12b method, post-(T) correlation up to CCSDT(Q), core correlation, scalar relativistic effects, spin-orbit coupling, and zero-point energy corrections. All the CH [ΔE_e(ΔH₀) = -38.54(-38.61) kcal mol^-1], NH [ΔE_e(ΔH₀) = -16.72(-17.98) kcal mol^-1], and COOH [ΔE_e = -4.98 kcal mol^-1] reactions are exothermic and proceed via shallow, usually negative, classical(adiabatic) barriers of -0.37(-0.95), -1.91(-2.48), and 1.02(-0.57) kcal mol^-1, respectively. In the entrance channel MRCI/aug-cc-pVTZ computations reveal several complexes with reactive(non-reactive) arrangements and binding energies of 1.0, 1.6, 3.3, (5.2 and 5.9) kcal mol^-1, stabilized by CH⋯OH, NH⋯OH, COOH⋯OH, (OH⋯OC and OH⋯N) hydrogen bonds, respectively.

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

A systematic conformational mapping combined with literature data leads to 85 stable neutral cysteine conformers. The implementation of the same mapping process for the protonated counterparts reveals 21 N-(amino-), 64 O-(carbonyl-), and 37 S-(thiol-)protonated cysteine conformers. Their relative energies and harmonic vibrational frequencies are given at the MP2/aug-cc-pVDZ level of theory. Further benchmark ab initio computations are performed for the 10 lowest-lying neutral and protonated amino acid conformers (for each type) such as CCSD(T)-F12a/cc-pVDZ-F12 geometry optimizations (and frequency computations for cysteine) as well as auxiliary correction computations of the basis set effects up to CCSD(T)-F12b/cc-pVQZ-F12, electron correlation effects up to CCSDT(Q), core correlation effects, second-order Douglass-Kroll relativistic effects, and zero-point energy contributions. Boltzmann-averaged 0 (298.15) K proton affinity and [298.15 K gas-phase basicity] values of cysteine are predicted to be 214.96 (216.39) [208.21], 201.83 (203.55) [194.16], and 193.31 (194.74) [186.40] kcal/mol for N-, O-, and S-protonation, respectively, also considering the previously described auxiliary corrections.

The MD17 datasets from the perspective of datasets for gas-phase “small” molecule potentials

There has been great progress in developing methods for machine-learned potential energy surfaces. There have also been important assessments of these methods by comparing so-called learning curves on datasets of electronic energies and forces, notably the MD17 database. The dataset for each molecule in this database generally consists of tens of thousands of energies and forces obtained from DFT direct dynamics at 500 K. We contrast the datasets from this database for three “small” molecules, ethanol, malonaldehyde, and glycine, with datasets we have generated with specific targets for the potential energy surfaces (PESs) in mind: a rigorous calculation of the zero-point energy and wavefunction, the tunneling splitting in malonaldehyde, and, in the case of glycine, a description of all eight low-lying conformers. We found that the MD17 datasets are too limited for these targets. We also examine recent datasets for several PESs that describe small-molecule but complex chemical reactions. Finally, we introduce a new database, “QM-22,” which contains datasets of molecules ranging from 4 to 15 atoms that extend to high energies and a large span of configurations.

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

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 lower-level cost-effective methods such as MP2 and density functional theory with various functionals (SOGGA11-X, M06-2X, PBE0, B3LYP, M06, TPSS).

Benchmark ab initio proton affinity of glycine

A systematic conformational search reveals three N- (amino) and eight O- (carbonyl) protonated glycine conformers with benchmark equilibrium(adiabatic) relative energies in the 0.00-7.51(0.00-7.37) and 25.91-31.61(24.45-30.28) kcal mol-1 ranges, respectively. Benchmark ab initio structures of the glycine conformers and its protonated species are obtained at the CCSD(T)-F12b/aug-cc-pVTZ level of theory and the relative energy computations consider basis-set effects up to aug-cc-pVQZ with CCSD(T)-F12b, electron correlation up to CCSDT(Q), core correlation corrections, scalar relativistic effects, and zero-point energy contributions. The best predictions for Boltzmann-averaged 0(298.15) K proton affinities and [298.15 K gas-phase basicities] of glycine are 211.00(212.43)[204.75] and 186.38(187.64)[180.21] kcal mol-1 for N- and O-protonation, respectively, in excellent agreement with experiments.

Non-energetic, Low-Temperature Formation of Cα-Glycyl Radical, a Potential Interstellar Precursor of Natural Amino Acids

The reaction of H atoms with glycine was investigated at 3.1 K in para-H₂, a quantum-solid host. The reaction was followed by IR spectroscopy, with the spectral analysis aided by quantum chemical computations. Comparison of the experimental IR spectrum with computed anharmonic frequencies and intensities proved that, regardless of the reactant glycine conformation, C_α-glycyl radical is formed in an H-atom-abstraction process with great selectivity. The product of the second H-atom abstraction, iminoacetic acid, was also observed in a smaller amount. The C_α-glycyl radical is sensitive to UV light and decomposes to iminoacetic acid and H atom upon 280 nm radiation. Since the reactive radical center is located on the C_α-atom, it is suggested that natural α-amino acids can be formed from glycine via the C_α-glycyl radical by non-energetic mechanisms in the solid phase of the interstellar medium.

MULTIMODE Calculations of Vibrational Spectroscopy and 1d Interconformer Tunneling Dynamics in Glycine Using a Full-Dimensional Potential Energy Surface

A full-dimensional, permutationally invariant polynomial potential energy surface for glycine recently reported (R. Conte et al., J. Chem. Phys. 2020, 153, 244301) is used with the code MULTIMODE to determine the IR absorption spectra for Conformers I and II using a new separable dipole moment function. The calculated spectra agree well with the experimental ones. The full-dimensional nature of the potential allows us also to examine dynamical results, such as tunneling rates. Remarkably, using a one-dimensional path based on the potential energy surface to estimate the tunneling rate from Conformer VI to Conformer I, good agreement is found with the recent experimental measurement. Finally a brief comparison of our potential energy surface with a recently reported sGDML one is made.