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.

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).

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.

Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues

Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.

Volatility Study of Amino Acids by Knudsen Effusion with QCM Mass Loss Detection

This work presents a new Knudsen effusion apparatus employing continuous monitoring of sample deposition using a quartz-crystal microbalance sensor with internal calibration by gravimetric determination of the sample mass loss. The apparatus was tested with anthracene and 1,3,5-triphenylbenzene and subsequently used for the study of sublimation behavior of several proteinogenic amino acids. Their low volatility and thermal instability strongly limit possibilities of studying their sublimation behavior and available literature data. The results presented in this work are unique in their temperature range and low uncertainty required for benchmarking theoretical studies of sublimation behavior of molecular crystals. The possibility of dimerization in the gas phase that would invalidate the effusion experiments is addressed and disproved by theoretical calculations. The enthalpy of sublimation of each amino acid is analyzed based on the contributions in two hypothetical sublimation paths involving the proton transfer in the solid and in the gas phase.

Ideal-gas thermodynamic properties of proteinogenic aliphatic amino acids calculated by R1SM approach

In this work, a R1SM approach was applied for the calculation of ideal-gas thermodynamic properties of five amino acids with aliphatic side chains: glycine, alanine, valine, leucine, and isoleucine. The first step of the calculation was an extensive conformational analysis that located several conformers not reported previously. A new systematic and user-friendly nomenclature of the conformers was introduced, and the stable conformers were clearly assigned with the previously used labeling where possible. Stability and calculated relative energies of the conformers were compared between various levels of theory and with several experimental studies, demonstrating a good performance of the selected B3LYP-D3/6-311+G(2df,p) level of theory. As a second step, the theoretically calculated vibrational frequencies were compared to the previously reported experimental spectra to verify the performance of the applied double-linear scaling factor. Finally, ideal-gas heat capacities, enthalpies, and absolute entropies were calculated, accounting for all stable conformers using the R1SM model. The resulting thermodynamic data are presented for the first time, since they cannot be determined experimentally and their rigorous calculation requires a complex thermodynamic model.

Formic acid dimers in a nitrogen matrix

Formic acid (HCOOH) dimers are studied by infrared spectroscopy in a nitrogen matrix and by ab initio calculations. We benefit from the use of a nitrogen matrix where the lifetime of the higher-energy (cis) conformer is very long (∼11 h vs. 7 min in an argon matrix). As a result, in a nitrogen matrix, a large proportion of the cis conformer can be produced by vibrational excitation of the lower-energy (trans) conformer. Three trans-trans, four trans-cis, and three cis-cis dimers are found in the experiments. The spectroscopic information on most of these dimers is enriched compared to the previous studies in an argon matrix. The cis-cis dimers of ordinary formic acid (without deuteration) are reported here for the first time. Several conformational processes are obtained using selective excitation by infrared light, some of them also for the first time. In particular, we report on the formation of cis-cis dimers upon vibrational excitation of trans-cis dimers. Tunneling decays of several dimers have been detected in the dark. The tunneling decay of cis-cis dimers of formic acid as well as the stabilization of cis units in cis-cis dimers is also observed for the first time.

Influence of Solvent Representation on Nuclear Shielding Calculations of Protonation States of Small Biological Molecules

In this study, we assess the influence of solvation on the accuracy and reliability of isotropic nuclear magnetic shielding calculations for amino acids in comparison to experimental data. We focus particularly on the performance of solvation methods for different protonation states, as biological molecules occur almost exclusively in aqueous solution and are subject to protonation with pH. We identify significant shortcomings of current implicit solvent models and present a hybrid solvation approach that improves agreement with experimental data by taking into account the presence of direct interactions between amino acid protonation state and water molecules.

Isolated neutral peptides

This chapter examines the structural characterisation of isolated neutral amino-acids and peptides. After a presentation of the experimental and theoretical state-of-the-art in the field, a review of the major structures and shaping interactions is presented. Special focus is made on conformationally-resolved studies which enable one to go beyond simple structural characterisation; probing flexibility and excited-state photophysics are given as examples of promising future directions.

Co-adsorption of water and glycine on Cu{110}

In this study, we use density functional theory (DFT) to investigate the surface co-adsorption of glycine with water on Cu{110}. Our results show that, under UHV conditions and for a wide range of temperatures, a pure glycine monolayer is more stable than either mixed gly-water phases or pure water (ice) monolayers, but for a high water pressure half-dissociated water layers can appear on the surface at low and medium temperatures.

Fully anharmonic IR and Raman spectra of medium-size molecular systems: accuracy and interpretation

Computation of full infrared (IR) and Raman spectra (including absolute intensities and transition energies) for medium- and large-sized molecular systems beyond the harmonic approximation is one of the most interesting challenges of contemporary computational chemistry. Contrary to common beliefs, low-order perturbation theory is able to deliver results of high accuracy (actually often better than those issuing from current direct dynamics approaches) provided that anharmonic resonances are properly managed. This perspective sketches the recent developments in our research group toward the development of a robust and user-friendly virtual spectrometer rooted in second-order vibrational perturbation theory (VPT2) and usable also by non-specialists essentially as a black-box procedure. Several examples are explicitly worked out in order to illustrate the features of our computational tool together with the most important ongoing developments.

Accurate structure, thermodynamic and spectroscopic parameters from CC and CC/DFT schemes: the challenge of the conformational equilibrium in glycine

The structures, relative stabilities, and infrared spectra of the six low-energy conformers of glycine have been characterized using a state-of-the-art quantum-mechanical approach allowing the bond distances, conformational enthalpies and vibrational frequencies to be determined well within the chemical accuracy. Transition state structures governing interconversion among the different energy minima have also been characterized. In detail, the gas-phase thermodynamic properties (at 15 K and 410 K) of the glycine conformers considered have been obtained with a 1 kJ mol(-1) accuracy, and it has been shown that the employment of DFT geometries usually reduces such accuracy by at most 0.1 kJ mol(-1). Regarding molecular structures, the use of two different composite schemes allowed us to further confirm the suitability of a rather cost-effective approach and provide geometrical parameters with an overall accuracy better than 0.002 Å for distances and 1 degree for angles. Thanks to a hybrid CC/DFT approach, the infrared spectra of all conformers considered and of several deuterated isotopologues have been reproduced (when experimental data were available) or predicted with an accuracy of 10 cm(-1). Finally, the joint thermodynamic and spectroscopic investigation allowed us to shed some light on the possible observation of elusive conformers. On the whole, the high accuracy of the computational results allows us to draw a fully consistent interpretation of the available experimental data and to obtain a more complete characterization of the potential energy surface of glycine.