Unbiased disentanglement of conformational baths with the help of microwave spectroscopy, quantum chemistry and artificial intelligence: the puzzling case of homocysteine

Structures and Rotational Constants of Monocyclic Monoterpenes at DFT Cost by Pisa Composite Schemes and Vibrational Perturbation Theory

The structures and rotational constants of prototypical monocyclic terpenes and terpenoids have been analyzed by a general computational strategy based on recent Pisa composite schemes (PCS) and vibrational perturbation theory at second order (VPT2). Concerning equilibrium geometries, a one-parameter empirical correction is added to bond lengths obtained by the revDSD-PBEP86 double hybrid functional in conjunction with a slightly modified cc-pVTZ-F12 basis set. The same functional and basis set give accurate harmonic frequencies, whereas the cheaper B3LYP hybrid functional in conjunction with a double-ζ basis set is employed to compute the semidiagonal cubic force constants needed to obtain vibrational corrections to the rotational constants in the framework of the VPT2 model. The final results obtained in this way show in most cases average deviations with respect to the experiment close to 0.1%, which correspond to errors around 1 mÅ and 0.1° for bond lengths and valence angles, respectively. The accuracy of the results has produced reliable estimates for species not analyzed yet experimentally. In addition to the intrinsic interest of the studied molecules, this article confirms that high-resolution spectroscopic studies of quite large systems can now be aided by a very accurate yet robust and user-friendly computational tool.

Impact of the Acetyl Group on Cysteine: A Study of N-Acetyl-Cysteine through Rotational Spectroscopy

Herein, we report a spectroscopic study of N-acetyl-L-cysteine, an important antioxidant drug, using Fourier-transform microwave techniques and in isolated conditions. Two conformers are observed, where most stable structure adopts a cis disposition, and the second conformer has a lower abundance and adopts a trans disposition. The rotational constants and the barriers to methyl internal rotation are determined for each conformer, allowing a precise conformation identification. The results show that the cis form adopts an identical structure in the crystal, solution, and gas phases. Additionally, the structures are contrasted against those of cysteine.

Toward Accurate Quantum Chemical Methods for Molecules of Increasing Dimension: The New Family of Pisa Composite Schemes

The new versions of the Pisa composite scheme introduced in the present paper are based on the careful selection of different quantum chemical models for energies, geometries, and vibrational frequencies, with the aim of maximizing the accuracy of the overall description while retaining a reasonable cost for all the steps. In particular, the computation of accurate electronic energies has been further improved introducing more reliable complete basis set extrapolations and estimation of core-valence correlation, together with improved basis sets for third-row atoms. Furthermore, the reduced-cost frozen natural orbital (FNO) model has been introduced and validated for large molecules. Accurate molecular structures can be obtained avoiding complete basis set extrapolation and evaluating core-valence correlation at the MP2 level. Unfortunately, analytical gradients are not available for the FNO version of the model. Therefore, for large molecules, an accurate reduced-cost alternative is offered by evaluation of valence contributions with a double-hybrid functional in conjunction with the same MP2 contribution for core-valence correlation or by means of a one-parameter approximation. The same double-hybrid functional and basis set are employed to evaluate zero-point energies and partition functions. After the validation of the new models for small systems, a panel of molecular bricks of life has been used to analyze their performances for problems of current fundamental or technological interest. The fully black-box implementation of the computational workflow paves the way toward the accurate yet not prohibitively expensive study of medium- to large-sized molecules also by experimentally oriented researchers.

Quantum chemistry meets high-resolution spectroscopy for characterizing the molecular bricks of life in the gas-phase

Computation of accurate geometrical structures and spectroscopic properties of large flexible molecules in the gas-phase is tackled at an affordable cost using a general exploration/exploitation strategy. The most distinctive feature of the approach is the careful selection of different quantum chemical models for energies, geometries and vibrational frequencies with the aim of maximizing the accuracy of the overall description while retaining a reasonable cost for all the steps. In particular, a composite wave-function method is used for energies, whereas a double-hybrid functional (with the addition of core-valence correlation) is employed for geometries and harmonic frequencies and a cheaper hybrid functional for anharmonic contributions. A thorough benchmark based on a wide range of prototypical molecular bricks of life shows that the proposed strategy is close to the accuracy of state-of-the-art composite wave-function methods, and is applicable to much larger systems. A freely available web-utility post-processes the geometries optimized by standard electronic structure codes paving the way toward the accurate yet not prohibitively expensive study of medium- to large-sized molecules by experimentally-oriented researchers.

DFT Meets Wave-Function Composite Methods for Characterizing Cytosine Tautomers in the Gas Phase

A general strategy for the accurate computation of structural and spectroscopic properties of biomolecule building blocks in the gas phase has been further improved and validated with a special reference to tautomeric equilibria. The main improvements concern the use of the cc-pVTZ-F12 basis set in both DFT and CCSD(T)-F12 computations, the inclusion of core-valence correlation in geometry optimizations by double hybrid functionals, and the use of the cc-pVQZ-F12 basis set for complete basis set extrapolation at the MP2-F12 level. The resulting model chemistry is applied to the challenging problem of cytosine tautomers in the gas phase. The results are in remarkable agreement with experiment concerning both rotational and vibrational spectroscopic parameters and permit their unbiased interpretation in terms of structural and thermochemical features. Together with the intrinsic interest of the studied molecule, the accuracy of the results obtained at reasonable cost without any empirical parameter suggests that the proposed composite method can be profitably employed for accurate investigations of other molecular bricks of life.

Accurate Structures and Spectroscopic Parameters of Phenylalanine and Tyrosine in the Gas Phase: A Joint Venture of DFT and Composite Wave-Function Methods

A general strategy for the accurate computation of conformational and spectroscopic properties of flexible molecules in the gas phase is applied to two representative proteinogenic amino acids with aromatic side chains, namely, phenylalanine and tyrosine. The main features of all the most stable conformers predicted by this computational strategy closely match those of the species detected in microwave and infrared experiments. Together with their intrinsic interest, the accuracy of the results obtained with reasonable computer times paves the route for accurate investigations of other flexible bricks of life.

Computational Protocol for the Identification of Candidates for Radioastronomical Detection and Its Application to the C3H3NO Family of Isomers

The C3H3NO family of isomers is relevant in astrochemistry, even though its members are still elusive in the interstellar medium. To identify the best candidate for astronomical detection within this family, we developed a new computational protocol based on the minimum-energy principle. This approach aims to identify the most stable isomer of the family and consists of three steps. The first step is an extensive investigation that characterizes the vast number of compounds having the C3H3NO chemical formula, employing density functional theory for this purpose. The second step is an energy refinement, which is used to select isomers and relies on coupled cluster theory. The last step is a structural improvement with a final energy refinement that provides improved energies and a large set of accurate spectroscopic parameters for all isomers lying within 30 kJ mol−1 above the most stable one. According to this protocol, vinylisocyanate is the most stable isomer, followed by oxazole, which is about 5 kJ mol−1 higher in energy. The other stable species are pyruvonitrile, cyanoacetaldehyde, and cyanovinylalcohol. For all of these species, new computed rotational and vibrational spectroscopic data are reported, which complement those already available in the literature or fill current gaps.

Bringing Machine-Learning Enhanced Quantum Chemistry and Microwave Spectroscopy to Conformational Landscape Exploration: the Paradigmatic Case of 4-Fluoro-Threonine

A combined experimental and theoretical study has been carried out on 4-fluoro-threonine, the only naturally occurring fluorinated amino acid. Fluorination of the methyl group significantly increases the conformational complexity with respect to the parent amino acid threonine. The conformational landscape has been characterized in great detail, with special attention given to the inter-conversion pathways between different conformers. This led to the identification of 13 stable low-energy minima. The equilibrium population of so many conformers produces a very complicated and congested rotational spectrum that could be assigned through a strategy that combines several levels of quantum chemical calculations with the principles of machine learning. Twelve conformers out of 13 could be experimentally characterized. The results obtained from the analysis of the intra-molecular interactions can be exploited to accurately model fluorine-substitution effects in biomolecules.

Benchmark Structures and Conformational Landscapes of Amino Acids in the Gas Phase: A Joint Venture of Machine Learning, Quantum Chemistry, and Rotational Spectroscopy

The accurate characterization of prototypical bricks of life can strongly benefit from the integration of high resolution spectroscopy and quantum mechanical computations. We have selected a number of representative amino acids (glycine, alanine, serine, cysteine, threonine, aspartic acid and asparagine) to validate a new computational setup rooted in quantum-chemical computations of increasing accuracy guided by machine learning tools. Together with low-lying energy minima, the barriers ruling their interconversion are evaluated in order to unravel possible fast relaxation paths. Vibrational and thermal effects are also included in order to estimate relative free energies at the temperature of interest in the experiment. The spectroscopic parameters of all the most stable conformers predicted by this computational strategy, which do not have low-energy relaxation paths available, closely match those of the species detected in microwave experiments. Together with their intrinsic interest, these accurate results represent ideal benchmarks for more approximate methods.

Connections between the accuracy of rotational constants and equilibrium molecular structures

Rotational spectroscopy is the technique of choice for investigating molecular structures in the gas phase. Indeed, rotational constants are strongly connected to the geometry of the molecular system under consideration. Therefore, they are powerful tools for assessing the accuracy that quantum chemical approaches can reach in structural determinations. In this review article, it is shown how it is possible to measure the accuracy of a computed equilibrium geometry based on the comparison of rotational constants. But, it is also addressed what accuracy is required by computations for providing molecular structures and thus rotational constants that are useful to experiment. Quantum chemical methodologies for obtaining the "0.1% accuracy" for rotational constants are reviewed for systems ranging in size from small molecules to small polycyclic aromatic hydrocarbons. This accuracy for systems containing two dozen or so atoms opens the way towards future applications such as the accurate characterization of non-covalent interactions, which play a key role in several biological and technological processes.

Toward Accurate yet Effective Computations of Rotational Spectroscopy Parameters for Biomolecule Building Blocks

The interplay of high-resolution rotational spectroscopy and quantum-chemical computations plays an invaluable role in the investigation of biomolecule building blocks in the gas phase. However, quantum-chemical methods suffer from unfavorable scaling with the dimension of the system under consideration. While a complete characterization of flexible systems requires an elaborate multi-step strategy, in this work, we demonstrate that the accuracy obtained by quantum-chemical composite approaches in the prediction of rotational spectroscopy parameters can be approached by a model based on density functional theory. Glycine and serine are employed to demonstrate that, despite its limited cost, such a model is able to predict rotational constants with an accuracy of 0.3% or better, thus paving the way toward the accurate characterization of larger flexible building blocks of biomolecules.

The eight structures of caffeic acid: a jet-cooled laser ablated rotational study

This work reports a complete conformational analysis of caffeic acid, an exceptionally versatile pharmacophore, using laser ablation chirped-pulse Fourier transform microwave spectroscopy. The whole conformational space consisting of eight distinct species has been fully deciphered based on the trend of the rotational constants supported by theoretical computations. We show how rotational spectroscopy can be confidently used to distinguish between conformers even when the structural differences are minimal, such as those involved in the conformational panorama of caffeic acid. Additionally, the structural information here provided, such as the planarity observed in all the conformers, could help to elucidate the mechanisms underlying the biological and pharmacological activity of hydroxycinnamic acids.

Exploiting the “Lego brick” approach to predict accurate molecular structures of PAHs and PANHs

Polycyclic aromatic hydrocarbons (PAHs) and polycyclic aromatic nitrogen heterocycles (PANHs) are important and ubiquitous species in space. However, their accurate structural and spectroscopic characterization is often missing. To fill this...