Unveiling the Neutral Forms of Glutamine

Revealing the Structure of 6-Aminopenillanic Acid: The Active Nucleus of Penicillins

6-Aminopenicillanic acid is a penicillanic acid compound and is the active nucleus common to all penicillins. Using laser ablation techniques, we transformed the solid into the gas phase and characterized its conformational panorama by combining supersonic expansions and Fourier transform microwave techniques. Five conformers were determined, adopting different spatial configurations. Among them, the axial and equatorial forms, which are biologically relevant, have been observed. The structural similarity to d-Ala-d-Ala and the detection of both axial and equatorial forms could explain its potential as a penicillin core and its capability as an antibiotic.

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.

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.

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.

Upon DFT-D3 dispersion correction and ECD spectral confirmation, only several conformers can stably coexist for three fungal cycloaspeptides (A, D, G)

Dispersion correction in theoretical determination of cyclopeptide conformations is emphasized. Whether in gas approximation or in solvation simulation, the density functional theory with London dispersion correction (DFT-D3) demonstrates that only 2-3 conformers can stably coexist for cycloaspeptides (A, D, G) at B3LYP-D3 and CAM-B3LYP-D3. Conformational rationality is confirmed by electronic circular dichroism (ECD). Whether for Cotton effect or for excitation energy, TD-B3LYP-D3 has better performances than TD-CAM-B3LYP-D3 because the former can better reproduce the experiment. A molecular orbital analysis is used to interpret ECD, where two energy bands observed in experiment originates from the ππ* transitions other than the σπ* transitions. Long-range correction and solvent effect make H-bonds shorten, and dispersion correction makes them further shorten.

The Nicotinic Agonist Cytisine: The Role of the NH···N Interaction

We report a detailed structural study of cytisine, an alkaloid used to help with smoking cessation, looking forward to unveiling its role as a nicotinic agonist. High-resolution rotational spectroscopy has allowed us to characterize two different conformers exhibiting axial and equatorial arrangements of the piperidinic NH group. Unexpectedly, the axial form has been found as the predominant configuration, in contrast to that observed for related molecules, such as piperidine. This anomalous behavior has been justified in terms of an intramolecular NH···N hydrogen bond. Moreover, this interaction justifies the overstabilization of the axial conformer over the equatorial one and is crucial for the mechanism of action of cytisine over the nicotinic receptor, further rationalizing its behavior as a nicotinic agonist.

Theoretical and experimental study of the infrared and Raman spectra of L-lysine acetylation

Acetylation is a common and extremely important protein modification in biology, referring to the covalent attachment of an acetyl group to the amino group. There are two forms of protein acetylation, which are lysine Nε-acetylation and N-terminal Nα-acetylation, respectively. Protein lysine Nε-acetylation is a globally important post-translational modification which plays a critical regulatory role in almost all aspects of cell metabolism. In addition, whether lysine on the N-terminal of protein can undergo Nα-acetylation is still a controversial viewpoint. Carrying out further molecular study of the role of acetylation is also the one of challenges. In order to investigate the protein acetylation more effectively, it is thus necessary to have a thorough and comprehensive understanding of lysine acetylation. In this work, both Raman and infrared (IR) spectra of L-lysine Nε-Ace-Lys, Nα-Ace-Lys, and NαNε-Ace-Lys were explored through both experimental experiment and theoretical computation based on density function theory (DFT). Vibration assignments and geometry structures of three acetylated lysines were therefore obtained for the first time in this work. The IR or Raman spectra of four molecules are very different from each other, which can be easily distinguished from the characteristic bands at 1500-1700 cm^-1 and 3200-3400 cm^-1 regions. Therefore, this work may provide the guide for probing the protein acetylation by Raman and IR spectroscopy.

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

An integrated experimental-computational strategy for the accurate characterization of the conformational landscape of flexible biomolecule building blocks is proposed. This is based on the combination of rotational spectroscopy with quantum-chemical computations guided by artificial intelligence tools. The first step of the strategy is the conformer search and relative stability evaluation performed by means of an evolutionary algorithm. In this step, last generation semiempirical methods are exploited together with hybrid and double-hybrid density functionals. Next, the barriers ruling the interconversion between the low-lying conformers are evaluated in order to unravel possible fast relaxation paths. The relative stabilities and spectroscopic parameters of the ``surviving' conformers are then refined using state-of-the-art composite schemes. The reliability of the computational procedure is further improved by the inclusion of vibrational and thermal effects. The final step of the strategy is the comparison between experiment and theory without any ad hoc adjustment, which allows an unbiased assignment of the spectroscopic features in terms of different conformers and their spectroscopic parameters. The proposed approach has been tested and validated for homocysteine, a highly flexible non-proteinogenic alpha-amino acid. The synergism of the integrated strategy allowed the characterization of five conformers stabilized by bifurcated N-H-O=C hydrogen bonds, together with an additional conformer involving a more conventional HNH-O hydrogen bond. The stability order estimated from the experimental intensities as well as the number and type of conformers observed in the gas phase are in full agreement with the theoretical predictions. Analogously, a good match has been found for the spectroscopic parameters.

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.

Structural and Energetic Properties of Amino Acids and Peptides Benchmarked by Accurate Theoretical and Experimental Data

Structural, energetic, and spectroscopic data derived in this work aim at the setup of an "experimentally validated" database for amino acids and polypeptides conformers. First, the "cheap" composite scheme (ChS, CCSD(T)/(CBS+CV)^MP2) is tested for evaluation of conformational energies of all eight stable conformers of glycine, by comparing to the more accurate CCSD(T)/CBS+CV computations (Phys. Chem. Chem. Phys. 2013, 15, 10094-10111 and J Mol. Model. 2020, 26, 129). The recently proposed jun-ChS (J. Chem. Theory and Comput. 2020, 16, 988-1006), employing the jun-cc-pVnZ basis set family for CCSD(T) computations and CBS extrapolation, yields conformational energies accurate to 0.2 kJ·mol^-1, at reduced computational cost with respect to aug-ChS employing aug-cc-pVnZ basis sets. The jun-ChS composite scheme is further applied to derive conformational energies for three dipeptide analogues Ac-Gly-NH₂, Ac-Ala-NH₂, and Gly-Gly. Finally, dipeptide conformational energies and semiexperimental equilibrium rotational constants along with the CCSD(T)/(CBS+CV)^MP2 structural parameters (J. Phys. Chem. Lett. 2014, 5, 534-540) stand as the reference for benchmarking of selected density functional methodologies. The double-hybrid functionals B2-PLYP-D3(BJ) and DSD-PBEP86, perform best for structural and energetic characterization of all dipeptide analogues. From hybrid functionals CAM-B3LYP-D3(BJ) and ωB97X-D3(BJ) represent promising methods applicable for larger peptide-based systems for which computations with double-hybrid functionals are not feasible.

An Innovative Approach for the Generation of Species of the Interstellar Medium

The large amount of unstable species in the realm of interstellar chemistry drives an urgent need to develop efficient methods for the in situ generations of molecules that enable their spectroscopic characterizations. Such laboratory experiments are fundamental to decode the molecular universe by matching the interstellar and terrestrial spectra. We propose an approach based on laser ablation of nonvolatile solid organic precursors. The generated chemical species are cooled in a supersonic expansion and probed by high‐resolution microwave spectroscopy. We present a proof of concept through a simultaneous formation of interstellar compounds and the first generation of aminocyanoacetylene using diaminomaleonitrile as a prototypical precursor. With this micro‐laboratory, we open the door to generation of unsuspected species using precursors not typically accessible to traditional techniques such as electric discharge and pyrolysis.

Structural and Vibrational Properties of Amino Acids from Composite Schemes and Double-Hybrid DFT: Hydrogen Bonding in Serine as a Test Case

The structures, relative stabilities, and vibrational wavenumbers of the two most stable conformers of serine, stabilized by the O-H···N, O-H···O═C and N-H···O-H intramolecular hydrogen bonds, have been evaluated by means of state-of-the-art composite schemes based on coupled-cluster (CC) theory. The so-called "cheap" composite approach (CCSD(T)/(CBS+CV)^MP2) allowed determination of accurate equilibrium structures and harmonic vibrational wavenumbers, also pointing out significant corrections beyond the CCSD(T)/cc-pVTZ level. These accurate results stand as a reference for benchmarking selected hybrid and double-hybrid, dispersion-corrected DFT functionals. B2PLYP-D3 and DSDPBEP86 in conjunction with a triple-ζ basis set have been confirmed as effective methodologies for structural and spectroscopic studies of medium-sized flexible biomolecules, also showing intramolecular hydrogen bonding. These best performing double-hybrid functionals have been employed to simulate IR spectra by means of vibrational perturbation theory, also considering hybrid CC/DFT schemes. The best overall agreement with experiment, with mean absolute error of 8 cm^-1, has been obtained by combining CCSD(T)/(CBS+CV)^MP2 harmonic wavenumbers with B2PLYP-D3/maug-cc-pVTZ anharmonic corrections. Finally, a composite scheme entirely based on CCSD(T) calculations (CCSD(T)/CBS+CV) has been employed for energetics, further confirming that serine II is the most stable conformer, also when zero-point vibrational energy corrections are included.

Microwave Spectrum of Two-Top Molecule: 2-Acetyl-3-Methylthiophene

The microwave spectrum of 2-acetyl-3-methylthiophene (2A3MT) was recorded in the frequency range from 2 to 26.5 GHz using a molecular jet Fourier transform microwave spectrometer and could be fully assigned to the anti-conformer of the molecule, while the syn-conformer was not observable. Torsional splittings of all rotational transitions in quintets due to internal rotations of the acetyl methyl and the ring methyl groups were resolved and analyzed, yielding barriers to internal rotation of 306.184(46) cm^-1 and 321.813(64) cm^-1 , respectively. The rotational and centrifugal distortion constants were determined with high accuracy, and the experimental values are compared to those derived from quantum chemical calculations. The experimentally determined inertial defect supports the conclusion that anti-2A3MT is planar, even though a number of MP2 calculations predicted the contrary.

Unveiling Five Naked Structures of Tartaric Acid

The unbiased, naked structures of tartaric acid, one of the most important organic compounds existing in nature and a candidate to be present in the interstellar medium, has been revealed in this work for the first time. Solid samples of its naturally occurring (R,R) enantiomer have been vaporized by laser ablation, expanded in a supersonic jet, and characterized by Fourier transform microwave spectroscopy. In the isolation conditions of the jet, we have discovered up to five different structures stabilized by intramolecular hydrogen-bond networks dominated by O-H⋅⋅⋅O=C and O-H⋅⋅⋅O motifs extended along the entire molecule. These five forms, two with an extended (trans) disposition of the carbon chain and three with a bent (gauche) disposition, can serve as a basis to represent the shape of tartaric acid. This work also reports the first set of spectroscopy data that can be used to detect tartaric acid in the interstellar medium.

Looking for the Elusive Imine Tautomer of Creatinine: Different States of Aggregation Studied by Quantum Chemistry and Molecular Spectroscopy

New spectroscopic experiments and state-of-the-art quantum-chemical computations of creatinine in different aggregation states unequivocally unveiled a significant tuning of tautomeric equilibrium by the environment: from the exclusive presence of the amine tautomer in the solid state and aqueous solution to a mixture of amine and imine tautomers in the gas phase. Quantum-chemical calculations predict the amine species as the most stable tautomer by about 30 kJ mol^-1 in condensed phases. On the contrary, moving to the isolated forms, both Z and E imine isomers become more stable by about 7 kJ mol^-1 . Since the imine isomers and one amine tautomer are separated by significant energy barriers, all of them should be present in the gas phase. This prediction has indeed been confirmed by high-resolution rotational spectroscopy, which provides the first experimental characterization of the elusive imine tautomer. The interpretation of the complicated hyperfine structure of the rotational spectrum, originated by three ¹⁴ N nuclei, makes it possible to use the spectral signatures as a sort of fingerprint for each individual tautomer in the complex sample.

Side-Chain Polarity Modulates the Intrinsic Conformational Landscape of Model Dipeptides

The intrinsic conformational preferences of small peptides may provide additional insight into the thermodynamics and kinetics of protein folding. In this study, we explore the underlying energy landscapes of two model peptides, namely, Ac-Ala-NH₂ and Ac-Ser-NH₂, using geometry-optimization-based tools developed within the context of energy landscape theory. We analyze not only how side-chain polarity influences the structural preferences of the dipeptides, but also other emergent properties of the landscape, including heat capacity profiles, and kinetics of conformational rearrangements. The contrasting topographies of the free energy landscape agree with recent results from Fourier transform microwave spectroscopy experiments, where Ac-Ala-NH₂ was found to exist as a mixture of two conformers, while Ac-Ser-NH₂ remained structurally locked, despite exhibiting an apparently rich conformational landscape.

A rotational study of the AlaAla dipeptide

Herein, we present the first rotational study of the AlaAla dipeptide, brought into the gas phase by laser ablation. Two different structures have been unveiled in the isolated environment of a supersonic expansion by Fourier transform microwave spectroscopy. These structures have been identified through their rotational and 14N quadrupole coupling constants. The flexibility of the -NH2 and -COOH ends allows the formation of strong intramolecular interactions giving rise to five- and seven-membered ring configurations.

Gas-Phase Infrared Spectroscopy of Neutral Peptides: Insights from the Far-IR and THz Domain

Gas-phase, double resonance IR spectroscopy has proven to be an excellent approach to obtain structural information on peptides ranging from single amino acids to large peptides and peptide clusters. In this review, we discuss the state-of-the-art of infrared action spectroscopy of peptides in the far-IR and THz regime. An introduction to the field of far-IR spectroscopy is given, thereby highlighting the opportunities that are provided for gas-phase research on neutral peptides. Current experimental methods, including spectroscopic schemes, have been reviewed. Structural information from the experimental far-IR spectra can be obtained with the help of suitable theoretical approaches such as dynamical DFT techniques and the recently developed Graph Theory. The aim of this review is to underline how the synergy between far-IR spectroscopy and theory can provide an unprecedented picture of the structure of neutral biomolecules in the gas phase. The far-IR signatures of the discussed studies are summarized in a far-IR map, in order to gain insight into the origin of the far-IR localized and delocalized motions present in peptides and where they can be found in the electromagnetic spectrum.