Soft experimental constraints for soft interactions: a spectroscopic benchmark data set for weak and strong hydrogen bonds

Harmonic and anharmonic vibrational computations for biomolecular building blocks: Benchmarking DFT and basis sets by theoretical and experimental IR spectrum of glycine conformers

Advanced vibrational spectroscopic experiments have reached a level of sophistication that can only be matched by numerical simulations in order to provide an unequivocal analysis, a crucial step to understand the structure-function relationship of biomolecules. While density functional theory (DFT) has become the standard method when targeting medium-size or larger systems, the problem of its reliability and accuracy are well-known and have been abundantly documented. To establish a reliable computational protocol, especially when accuracy is critical, a tailored benchmark is usually required. This is generally done over a short list of known candidates, with the basis set often fixed a priori. In this work, we present a systematic study of the performance of DFT-based hybrid and double-hybrid functionals in the prediction of vibrational energies and infrared intensities at the harmonic level and beyond, considering anharmonic effects through vibrational perturbation theory at the second order. The study is performed for the six-lowest energy glycine conformers, utilizing available "state-of-the-art" accurate theoretical and experimental data as reference. Focusing on the most intense fundamental vibrations in the mid-infrared range of glycine conformers, the role of the basis sets is also investigated considering the balance between computational cost and accuracy. Targeting larger systems, a broad range of hybrid schemes with different computational costs is also tested.

The impact of solvation on the structure and electric field strength in Li+GlyGly complexes

To scrutinise the impact of electric fields on the structure and vibrations of biomolecules in the presence of water, we study the sequential solvation of lithium diglycine up to three water molecules with cryogenic infrared action spectroscopy. Conformer-specific IR-IR spectroscopy and H2O/D2O isotopic substitution experiments provide most of the information required to decipher the structure of the observed conformers. Additional confirmation is provided by scaled harmonic vibrational frequency calculations using MP2 and DFT. The first water molecule is shown to bind to the Li+ ion, which weakens the electric field experienced by the peptide and as a consequence, also the strength of an internal NH⋯NH2 hydrogen bond in the diglycine backbone. The strength of this hydrogen bond decreases approximately linearly with the number of water molecules as a result of the decreasing electric field strength and coincides with an increase in the number of conformers observed in our spectra. The addition of two water molecules is already sufficient to change the preferred conformation of the peptide backbone, allowing for Li+ coordination to the lone pair of the terminal amine group.

Benchmarking the quadrupolar coupling tensor for chlorine to probe weak-bonding interactions

Rotational spectroscopy relies on quantum chemical calculations to interpret observed spectra. Among the most challenging molecules to assign are those with additional angular momenta coupling to the rotation, contributing to the complexity of the spectrum. This benchmark study of computational methods commonly used by rotational spectroscopists targets the nuclear quadrupole coupling constants of chlorine containing molecules and the geometry of its complexes and clusters. For each method, the quality of both structural and electronic parameter predictions is compared with the experimental values. Ab initio methods are found to perform best overall in predicting both the geometry of the complexes and the coupling constants of chlorine with moderate computational cost. This cost can be reduced by combining these methods with density functional theory structure optimization, which still yields adequate predictions. This work constitutes a first step in expanding Bailey's quadrupole coupling data set to encompass molecular clusters. [W. C. Bailey, Calculation of Nuclear Quadrupole Coupling Constants in Gaseous State Molecule, 2019, https://nqcc.wcbailey.net/].

Shape‐Shifting Molecules: Unveiling the Valence Tautomerism Phenomena in Bare Barbaralones

We report a state‐of‐the‐art spectroscopic study of an archetypical barbaralone, conclusively revealing the valence tautomerism phenomena for this bistable molecular system. The two distinct 1‐ and 5‐substituted valence tautomers have been isolated in a supersonic expansion for the first time and successfully characterized by high‐resolution rotational spectroscopy. This work provides irrefutable experimental evidence of the [3,3]‐rearrangement in barbaralones and highlights the use of rotational spectroscopy to analyze shape‐shifting mixtures. Moreover, this observation opens the window toward the characterization of new fluxional systems in the isolation conditions of the gas phase and should serve as a reference point in the general understanding of valence tautomerism.

Rotational Spectrum and Conformational Analysis of Perillartine: Insights into the Structure-Sweetness Relationship

We used high-resolution rotational spectroscopy coupled to a laser ablation source to study the conformational panorama of perillartine, a solid synthetic sweetener. Four conformers were identified under the isolation conditions of the supersonic expansion, showing that all of them present an E configuration of the C=N group with respect to the double bond of the ring. The observed structures were verified against Shallenberger–Acree–Kier’s sweetness theory to shed light on the structure–sweetness relationship for this particular oxime, highlighting a deluge of possibilities to bind the receptor.

Computational optimal transport for molecular spectra: The fully discrete case

The use of computational optimal transport is investigated as a tool for comparing two molecular spectra. Unlike other techniques for comparing molecular spectra in a pattern-recognition framework, transport distances simultaneously encode information about line positions and intensities. In addition, it is shown that transport distances are a useful alternative to Euclidean distances as Euclidean distances are based on line-by-line comparisons, while transport distances reflect broader features of molecular spectra and adequately compare spectra with different resolutions. This paper includes a tutorial on the use of optimal transport and investigates several well-chosen examples to illustrate the utility of computational optimal transport for comparing molecular spectra.

CC-stretched formic acid: isomerisation, dimerisation, and carboxylic acid complexation

The cis-trans-isomerism of the propiolic acid monomer (HC[triple bond, length as m-dash]C-COOH) is examined with linear Raman jet spectroscopy, yielding the first environment-free vibrational band centres of a higher-energy cis-rotamer beyond formic acid (HCOOH) in addition to all fundamentals and a large number of hot and combination/overtone bands of the trans-conformer. Two near-isoenergetic trans-fundamentals of different symmetry (CC[double bond, length as m-dash]O bend and OH torsion) prove to be a sensitive benchmarking target, as their energetic order is susceptible to the choice of electronic structure method, basis set size, and inclusion of vibrational anharmonicity. For the infrared- and Raman-active C[double bond, length as m-dash]O stretching fundamentals of the cyclic (C_2h) trans-propiolic acid dimer, resonance couplings are found that in part extend to the C_s-symmetric heterodimer of trans-propiolic and trans-formic acid. Exploratory vibrational perturbation theory (VPT2) calculations show that all perturbing states involve displacements of the OH moieties located on the doubly hydrogen bonded ring. The comparison of the infrared spectra of the propiolic acid dimer and its heterodimer with formic acid to that of several other carboxylic acid dimers from the literature reveals a notable similarity regarding a non-fundamental dimer band around 1800 cm^-1, which in most cases is so far unassigned. VPT2 calculations and a simple harmonic model suggest an assignment to a combination vibration of the symmetric and antisymmetric OH torsion.

Hydrogen Bonding in Natural and Unnatural Base Pairs-A Local Vibrational Mode Study

In this work hydrogen bonding in a diverse set of 36 unnatural and the three natural Watson Crick base pairs adenine (A)-thymine (T), adenine (A)-uracil (U) and guanine (G)-cytosine (C) was assessed utilizing local vibrational force constants derived from the local mode analysis, originally introduced by Konkoli and Cremer as a unique bond strength measure based on vibrational spectroscopy. The local mode analysis was complemented by the topological analysis of the electronic density and the natural bond orbital analysis. The most interesting findings of our study are that (i) hydrogen bonding in Watson Crick base pairs is not exceptionally strong and (ii) the N-H⋯N is the most favorable hydrogen bond in both unnatural and natural base pairs while O-H⋯N/O bonds are the less favorable in unnatural base pairs and not found at all in natural base pairs. In addition, the important role of non-classical C-H⋯N/O bonds for the stabilization of base pairs was revealed, especially the role of C-H⋯O bonds in Watson Crick base pairs. Hydrogen bonding in Watson Crick base pairs modeled in the DNA via a QM/MM approach showed that the DNA environment increases the strength of the central N-H⋯N bond and the C-H⋯O bonds, and at the same time decreases the strength of the N-H⋯O bond. However, the general trends observed in the gas phase calculations remain unchanged. The new methodology presented and tested in this work provides the bioengineering community with an efficient design tool to assess and predict the type and strength of hydrogen bonding in artificial base pairs.

Quantifying soft degrees of freedom in volatile organic compounds: insight from quantum chemistry and focused single molecule experiments

Sampling of the vast conformational landscape of organic compounds remains a challenging task in computational chemistry, especially when it comes to the characterization of soft-degrees of freedom and relatively small energy barriers between different local minima. Therefore, studying the intrinsic properties of isolated molecules using focused experiments such as high-resolution molecular spectroscopy provides a powerful approach to validate and improve available quantum chemical methods. Here, we report on the most abundant gas-phase structure of ethyl 2-methyl pentanoate under molecular jet conditions, which we used to benchmark several exchange-correlation functionals and ab initio methods at the quantum chemical level. The observed conformer of ethyl 2-methyl pentanoate in the gas-phase is of C1 symmetry and exhibits a large amplitude motion around the C-C bond in proximity to the carbonyl moiety, which, unlike in the case of its structural isomer ethyl 2-ethyl butyrate, is very sensitive to the applied quantum chemical method and basis set. Depending on the applied quantum chemical method, the dihedral angle of the lowest energy conformer is optimized to absolute values of ±20°. This is far above the usual convergence error of the theoretical methods and has a tremendous impact on the rotational constants of this conformer, which complicates the prediction of rotational spectra and the assignment of experimental data. We show that the loss of symmetry in the aliphatic chain bound to the carboxylic moiety of ethyl esters results in a shift of the dihedral angle value due to a flat potential well around the corresponding C-C bond. Our benchmark calculations further indicate the potential relevance of the wB97X-D functional for this ethyl pentanoate and other related ethyl esters.

Understanding benzyl alcohol aggregation by chiral modification: the pairing step

A combination of linear infrared and Raman spectroscopy in supersonic slit jet expansions is used to clarify the conformational preferences in the dimer of the transiently chiral benzyl alcohol (phenylmethanol) under vacuum isolation. By experimentally exploring close analogies with the permanently chiral 1-phenylethanol, which is conformationally locked in the jet through intramolecular chirality induction, and by computational analysis of their conformational energy landscapes, several conclusions are drawn. The lowest energy dimer is confirmed to be cooperatively OHOHπ-bonded and shown to be homochiral. Its heterochiral counterpart is slightly higher in energy and can be spectrally assigned as a minor constituent. A metastable heterochiral OHπ/OHπ structure with weakly coupled hydrogen bonds is efficiently trapped behind a Ci symmetry-enhanced barrier and can be assigned by IR/Raman mutual exclusion. Its homochiral counterpart is kinetically less stable but might be addressed by rotational spectroscopy. Ratings of standard density functionals with a standard basis set in terms of reproducing these experimental chirality synchronization benchmarks are presented.

Stretching force constants as descriptors of energy and geometry of F···HF hydrogen bonds

In this work applicability of proton donor group stretching vibration force constants k_s and intermolecular stretching force constants k_σ for evaluations of hydrogen bond strength and geometry are discussed. For a set of 30 complexes with F···HF hydrogen bonds in a wide range 0.5-48 kcal/mol by means of quantum chemical calculations equilibrium geometries, complexation energies, vibrational frequencies and corresponding force constants were calculated (MP2/aug-cc-pVTZ). It is shown, that properties of a hydrogen bond are more strictly correlated with the values of force constants than with vibrational frequencies. Easy-to-use equations for estimations of hydrogen bond energy ∆E and geometry (r_FH, r_FF) based on k_s and k_σ values are proposed.

Shifting formic acid dimers into perspective: vibrational scrutiny in helium nanodroplets

A metastable dimer of formic acid has been prepared inside superfluid helium nanodroplets and examined using IR spectroscopy and quantum chemical calculations.

Internal Motions and Sulfur Hydrogen Bonding in Methyl 3-Mercaptopropionate

The effect of sulfur hydrogen bonding on the conformational equilibrium of methyl 3-mercaptopropionate was investigated using microwave spectroscopy in a supersonic jet expansion. The two most stable conformers (I and II) were assigned in the rotational spectra, and complex splitting patterns owing to the methyl internal rotation and SH tunneling motion were resolved and analyzed in detail. For both conformers, the experimental torsional barriers for the methyl top are similar and about 5.1 kJ mol^-1, revealing that their geometrical differences do not affect the methyl internal rotation. The experimentally derived rotational and centrifugal distortion constants, along with the methyl internal rotation barriers, are discussed and compared with results from density functional theory and ab initio calculations. Quantum theory of atoms in molecules, noncovalent interactions, and natural bond orbital analyses show that the global minimum geometry (I), which has the thiol hydrogen oriented toward the carbonyl of the ester, is stabilized by an SH···O=C hydrogen bond. The presence of a hydrogen bond is confirmed by the derivation of an accurate experimental geometry that reveals a hydrogen bond distance and S-H-O angle of 2.515(4) Å and 117.4(1)°, respectively. These results are key benchmarks to expand the current knowledge of sulfur hydrogen bonds and the relationship between internal motions and conformational preferences in esters.

The axial/equatorial conformational landscape and intramolecular dispersion: new insights from the rotational spectra of monoterpenoids

Using rotational spectroscopy and quantum chemistry calculations, we show that intramolecular dispersion stabilises the axial conformers of monoterpenoids, and that an accurate account of these interactions is challenging for theoretical methods.