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.

Understanding the abundance of the rare sugar ß-D-allose.

The conformational landscape of ß-D-allose, a rare sugar, was investigated using laser ablation in combination with high-resolution rotational spectroscopy. Altogether, three species are identified, exhibiting a counter-clockwise intramolecular hydrogen bond network. The effect of epimerization on the main aldohexose is also studied and, despite the main conformers being very similar, the position of the hydroxyl groups in allose allows the formation of considerably stronger intramolecular hydrogen bonds than in glucose, and this could explain the low abundance of ß-D-allose in Nature.

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.

Rotational spectroscopic study and astronomical search for propiolamide in Sgr B2(N).

CONTEXT: For all the amides detected in the interstellar medium (ISM), the corresponding nitriles or isonitriles have also been detected in the ISM, some of which have relatively high abundances. Among the abundant nitriles for which the corresponding amide has not yet been detected is cyanoacetylene (HCCCN), whose amide counterpart is propiolamide (HCCC(O)NH2). AIMS: With the aim of supporting searches for this amide in the ISM, we provide a complete rotational study of propiolamide from 6 GHz to 440 GHz. METHODS: Time-domain Fourier transform microwave (FTMW) spectroscopy under supersonic expansion conditions between 6 GHz and 18 GHz was used to accurately measure and analyze ground-state rotational transitions with resolved hyperfine structure arising from nuclear quadrupole coupling interactions of the 14N nucleus. We combined this technique with the frequency-domain room-temperature millimeter wave and submillimeter wave spectroscopies from 75 GHz to 440 GHz in order to record and assign the rotational spectra in the ground state and in the low-lying excited vibrational states. We used the ReMoCA spectral line survey performed with the Atacama Large Millimeter/submillimeter Array toward the star-forming region Sgr B2(N) to search for propiolamide. RESULTS: We identified and measured more than 5500 distinct frequency lines of propiolamide in the laboratory. These lines were fitted using an effective semi-rigid rotor Hamiltonian with nuclear quadrupole coupling interactions taken into consideration. We obtained accurate sets of spectroscopic parameters for the ground state and the three low-lying excited vibrational states. We report the nondetection of propiolamide toward the hot cores Sgr B2(N1S) and Sgr B2(N2). We find that propiolamide is at least 50 and 13 times less abundant than acetamide in Sgr B2(N1S) and Sgr B2(N2), respectively, indicating that the abundance difference between both amides is more pronounced by at least a factor of 8 and 2, respectively, than for their corresponding nitriles. CONCLUSIONS: Although propiolamide has yet to be included in astrochemical modeling networks, the observed upper limit to the ratio of propiolamide to acetamide seems consistent with the ratios of related species as determined from past simulations. The comprehensive spectroscopic data presented in this paper will aid future astronomical searches.

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 Conformational Map of the Amino Acid Isovaline.

Four conformers of the non-proteinogenic α-amino acid isovaline, vaporized by laser ablation, are characterized by Fourier-transform microwave techniques in a supersonic expansion. The comparison between the experimental rotational and 14 N nuclear quadrupole coupling constants and the ab initio calculated ones provides conclusive evidence for the identification of the conformers. The most stable species is stabilized by an N-H⋅⋅⋅O =C intramolecular hydrogen bond and a cis-COOH interaction, whereas the higher-energy conformers exhibit an N⋅⋅⋅H-O intramolecular hydrogen bond and trans-COOH, as in other aliphatic amino acids. The spectroscopic data herein reported can be used for the astrophysical purpose in a possible detection of isovaline in space.

Elucidating the multiple structures of pipecolic acid by rotational spectroscopy.

The complex conformational space of the non-proteinogenic cyclic amino acid pipecolic acid has been explored in the gas phase for the first time. Solid pipecolic acid samples were vaporized by laser ablation and expanded in a supersonic jet where the rotational spectral signatures owing to nine different conformers were observed by Fourier transform microwave spectroscopy. All species were identified by comparison of the experimental rotational and nuclear quadrupole coupling constants with those predicted theoretically. Observation of type-III conformers, leading to a difference when compared against the conformational behavior of the analog amino acid proline, has been interpreted by an increment in steric hindrance when increasing the number of carbons present in the ring.

Laboratory rotational spectrum and astronomical search for methoxyacetaldehyde.

CONTEXT: Methoxyacetaldehyde belongs to a group of structural isomers with the general formula C3H6O2, of which methyl acetate and ethyl formate are known interstellar molecules. Rotational data available for methoxyacetaldehyde are limited to 40 GHz, which makes predictions at higher frequencies rather uncertain. AIMS: The aim of this work is to provide accurate experimental frequencies of methoxyacetaldehyde in the millimeter-wave region to support its detection in the interstellar medium. METHODS: The rotational spectrum of methoxyacetaldehyde was recorded at room-temperature from 75 to 120 GHz and from 170 to 310 GHz using the millimeter-wave spectrometer in Valladolid. Additional measurements were also performed at conditions of supersonic expansion from 6 to 18 GHz. The assigned rotational transitions were analyzed using the S -reduced semirigid-rotor Hamiltonian. RESULTS: We newly assigned over 1000 lines for the most stable conformer of methoxyacetaldehyde in its ground state and five lowest excited vibrational states, and precise sets of spectroscopic constants were obtained. We searched for spectral features of methoxyacetaldehyde in the high-mass star-forming regions Orion KL and Sagittarius B2, as well as in the cold dark cloud Barnard 1 (B1-b). No lines belonging to methoxyacetaldehyde were detected above the detection limit of our data. We provide upper limits to the methoxyacetaldehyde colum density in these sources.

The effect of N-methylation on the conformational landscape of alanine: the case of N-methyl-l-alanine.

The non-proteinogenic amino acid N-methyl-l-alanine has been brought into the gas phase using laser ablation techniques and studied by high resolution chirped pulse and molecular-beam Fourier transform microwave spectroscopies coupled to supersonic expansion. Four conformers showing the three types of hydrogen bond interactions I (NHO[double bond, length as m-dash]C), II (OHN) and III (N-HO-H) have been unambiguously identified, based on the comparison of the experimental rotational and 14N nuclear quadrupole constants with the calculated ab initio values. The observation of a type III conformer evidences the role of methyl groups in both sides to impose the steric hindrance, precluding the relaxation from type III to type I conformers and explains the responsibility for the unique conformational landscape observed in the case of NMA.

Millimeter wave spectra of ethyl isocyanate and searches for it in Orion KL and Sgr B2.

CONTEXT: Relatively high abundances of methyl isocyanate (CH3NCO), a methyl derivative of isocyanic acid (HNCO), found in the Orion KL and Sgr B2 molecular clouds suggest that its ethyl derivative, ethyl isocyanate (CH3CH2NCO), may also be present. AIMS: The aim of this work is to provide accurate experimental frequencies of ethyl isocyanate in its ground and excited vibrational states in the millimeter wave region to support searches for it in the interstellar medium. METHODS: The rotational spectrum of ethyl isocyanate was recorded at room temperature from 80 to 340 GHz using the millimeter wave spectrometer in Valladolid. Assigned rotational transitions were analyzed using the S -reduced semirigid-rotor Hamiltonian. RESULTS: More than 1100 distinct frequency lines were analyzed for the ground vibrational state of the cis conformer as well as for three vibrational satellites corresponding to successive excitation of the lowest-energy C-N torsional mode. Newly determined rotational and centrifugal distortion constants were used for searches of spectral features of ethyl isocyanate in Orion KL and Sgr B2 clouds. Upper limits to CH3CH2NCO in these high-mass star-forming regions were obtained.

Rotational spectrum of methoxyamine up to 480 GHz: a laboratory study and astronomical search.

AIMS: Methoxyamine is a potential interstellar amine that has been predicted by gas-grain chemical models for the formation of complex molecules. The aim of this work is to provide direct experimental frequencies of its ground-vibrational state in the millimeter- and submillimeter-wave regions to achieve its detection in the interstellar medium. METHODS: Methoxyamine was chemically liberated from its hydrochloride salt, and its rotational spectrum was recorded at room temperature from 75 to 480 GHz using the millimeter-wave spectrometer in Valladolid. Many observed transitions revealed A-E splitting caused by the internal rotation of the methyl group, which had to be treated with specific internal rotation codes. RESULTS: Over 400 lines were newly assigned for the most stable conformer of methoxyamine, and a precise set of spectroscopic constants was obtained. Spectral features of methoxyamine were then searched for in the Orion KL, Sgr B2, B1-b, and TMC-1 molecular clouds. Upper limits to the column density of methoxyamine were derived.

The last link of the x-aminobutyric acid series: the five conformers of ß-aminobutyric acid.

ß-Aminobutyric acid is a non-proteinogenic amino acid that is known to protect plants against various pathogens. Its structure is midway between α-aminobutyric acid and γ-aminobutyric acid. The structural differences in the position of the amino group in the conformational stabilization of ß-aminobutyric acid have been studied by laser ablation Fourier transform microwave spectroscopy. Five conformers have been detected, and their rotational and quadrupole coupling constants of the 14N nucleus determined. Three of the conformers, including the most stable structure, are stabilized by a non-bifurcated N-HO[double bond, length as m-dash]C intramolecular hydrogen bond. The other two conformers possess a NH-O intramolecular interaction. In this work we highlight that ß-aminobutyric acid shows the conformational peculiarities of α-aminobutyric acid and γ-aminobutyric acid completing the rotational spectroscopic study of the x-aminobutyric acid series.

The role of amino acid side chains in stabilizing dipeptides: the laser ablation Fourier transform microwave spectrum of Ac-Val-NH2.

The steric effects imposed by the isopropyl group of valine in the conformational stabilization of the capped dipeptide N-acetyl-l-valinamide (Ac-Val-NH2) have been studied by laser ablation molecular beam Fourier transform microwave (LA-MB-FTMW) spectroscopy. The rotational and quadrupole coupling constants of the two 14N nuclei determined in this work show that this dipeptide exists as a mixture of C7 and C5 conformers in the supersonic expansion. The conformers are stabilized by a C[double bond, length as m-dash]OH-N intramolecular hydrogen bond closing a seven- or a five-membered ring, respectively. The observation of both conformers is in good agreement with previous results on the related dipeptides containing different residues, confirming that the polarity/non-polarity of the side chains of the amino acid is responsible for the conformational locking/unlocking. The voluminous isopropyl group is not able to prevent the less stable C5 conformer from forming but it destabilizes the C[double bond, length as m-dash]OH-N interaction.

The millimeter wave spectrum of methyl cyanate: a laboratory study and astronomical search in space.

AIMS: The recent discovery of methyl isocyanate (CH3NCO) in Sgr B2(N) and Orion KL makes methyl cyanate (CH3OCN) a potential molecule in the interstellar medium. The aim of this work is to fulfill the first requirement for its unequivocal identification in space, i.e. the availability of transition frequencies with high accuracy. METHODS: The room-temperature rotational spectrum of methyl cyanate was recorded in the millimeter wave domain from 130 to 350 GHz. All rotational transitions revealed A-E splitting owing to methyl internal rotation and were globally analyzed using the ERHAM program. RESULTS: The data set for the ground torsional state of methyl cyanate exceeds 700 transitions within J″ = 10 - 35 and [Formula: see text] and newly derived spectroscopic constants reproduce the spectrum close to the experimental uncertainty. Spectral features of methyl cyanate were then searched for in Orion KL, Sgr B2(N), B1-b, and TMC-1 molecular clouds. Upper limits to the column density of methyl cyanate are provided.