Non-energetic, Low-Temperature Formation of Cα-Glycyl Radical, a Potential Interstellar Precursor of Natural Amino Acids

Identification of HOC•HC(O)H, HOCH2C•O, and HOCH2CH2O• Intermediates in the Reaction of H + Glycolaldehyde in Solid Para-Hydrogen and Its Implication to the Interstellar Formation of Complex Sugars

Glycolaldehyde [HOCH2C(O)H, GA], the primitive sugar-like molecule detected in the interstellar medium (ISM), is a potential precursor for the synthesis of complex sugars. Despite its importance, the mechanism governing the formation of these higher-order sugars from GA under interstellar circumstances remains elusive. Radical intermediates HOCH2CH2O• (1), HOCH2C•HOH (2), HOCH2C•O (3), HOC•HC(O)H (4), and O•CH2C(O)H (5) derived from GA could be potential precursors for the formation of glyceraldehyde (aldose sugar), dihydroxyacetone (ketose sugar), and ethylene glycol (sugar alcohol) in dark regions of ISM. However, the spectral identification of these intermediates and their roles were little investigated. We conducted reactions involving H atoms and the Cis-cis conformer of GA (Cc-GA) in solid p-H2 at 3.2 K and identified IR spectra of radicals Cc-HOCH2C•O (3) and Cc-HOC•HC(O)H (4) produced from H abstraction as well as closed-shell HOCHCO (6) produced via consecutive H abstraction of GA. In addition, Cc-HOCH2CH2O• (1) and C•H2OH + H2CO (7) were produced through the H addition and the H-induced fragmentation channels, respectively. In darkness, when only H-tunneling reactions occurred, the formation of (3) was major and that of (1) was minor. In contrast, during IR irradiation to produce H atoms with higher energy, the formation of (4) and C•H2OH + H2CO (7) became important. We also successfully converted most Cc-GA to the second-lowest-energy conformer Trans-trans-GA (Tt-GA) by prolonged IR irradiation at 2827 nm to investigate H + Tt-GA; Tt-HOCH2C•O (3'), Tt-HOC•HC(O)H (4'), HOCHCO (6), Tt-HOCH2CH2O• (1'), and C•H2OH + H2CO (7) were observed. We discuss possible routes for the formation of higher-order sugars or related compounds involving (7), (1), (3), and (4), but neither (2), which was proposed previously, nor (5) plays a significant role in H + GA. Such previously unreported rich chemistry in the reaction of H + GA, with four channels of three distinct types, indicates the multiple roles that GA might play in astronomical chemistry.

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.

Investigating H-atom reactions in small PAHs with imperfect aromaticity: A combined experimental and computational study of indene (C9H8) and indane (C9H10)

Polycyclic aromatic hydrocarbons (PAHs) are widely recognized as catalysts for interstellar H2 formation. Extensive exploration into the catalytic potential of various PAHs has encompassed both theoretical investigations and experimental studies. In the present study, we focused on studying the reactivity of an imperfect aromatic molecule, indene (C9H8), and its hydrogenated counterpart, indane (C9H10), as potential catalysts for H2 formation within the interstellar medium. The reactions of these molecules with H atoms at 3.1 K were investigated experimentally using the para-H2 matrix isolation technique. Our experimental results demonstrate that both indene and indane are reactive toward H atoms. Indene can participate in H-atom-abstraction and H-atom-addition reactions, whereas indane primarily undergoes H-atom-abstraction reactions. The H-atom-abstraction reaction of indene results in the formation of the 1-indenyl radical (R1) (C9H7) and H2 molecule. Simultaneously, an H-atom-addition reaction forms the 1,2-dihydro-indene-3-yl radical (R2) (C9H9). Experiments also reveal that the H-atom-abstraction reaction of indane also produces the R2 radical. To the best of our knowledge, this study represents the first reporting of the infrared spectra of R1 and R2 radicals. The experimental results, combined with theoretical findings, suggest that indane and indene may play a role in the catalytic formation of interstellar H2. Furthermore, these results imply a quasi-equilibrium between the investigated molecules and the formed radicals via H-atom-addition and H-atom-abstraction reactions.

Infrared spectroscopy of the α-hydroxyethyl radical isolated in cryogenic solid media

The α-hydroxyethyl radical (CH3·CHOH, 2A) is a key intermediate in ethanol biochemistry, combustion, atmospheric chemistry, radiation chemistry, and astrochemistry. Experimental data on the vibrational spectrum of this radical are crucially important for reliable detection and understanding of the chemical dynamics of this species. This study represents the first detailed experimental report on the infrared absorption bands of the α-hydroxyethyl radical complemented by ab initio computations. The radical was generated in solid para-H2 and Xe matrices via the reactions of hydrogen atoms with matrix-isolated ethanol molecules and radiolysis of isolated ethanol molecules with x rays. The absorption bands with maxima at 3654.6, 3052.1, 1425.7, 1247.9, 1195.6 (1177.4), and 1048.4 cm-1, observed in para-H2 matrices appearing upon the H· atom reaction, were attributed to the OHstr, α-CHstr, CCstr, COstr + CCObend, COstr, and CCstr + CCObend vibrational modes of the CH3·CHOH radical, respectively. The absorption bands with the positions slightly red-shifted from those observed in para-H2 were detected in both the irradiated and post-irradiation annealed Xe matrices containing C2H5OH. The results of the experiments with the isotopically substituted ethanol molecules (CH3CD2OH and CD3CD2OH) and the quantum-chemical computations at the UCCSD(T)/L2a_3 level support the assignment. The photolysis with ultraviolet light (240-300 nm) results in the decay of the α-hydroxyethyl radical, yielding acetaldehyde and its isomer, vinyl alcohol. A comparison of the experimental and theoretical results suggests that the radical adopts the thermodynamically more stable anti-conformation in both matrices.

Ultraviolet Photodissociation of Proteinogenic Amino Acids

The ultraviolet photochemistry of the amino acids glycine, leucine, proline, and serine in their neutral forms was investigated using parahydrogen matrix-isolation spectroscopy. Irradiation by 213 nm light destroys the chirality of all three chiral amino acids as a result of the α-carbonyl C-C bond cleavage and hydrocarboxyl (HOCO) radical production. The temporal behavior of the Fourier-transform infrared spectra revealed that HOCO radicals rapidly reach a steady state, which occurs predominantly due to photodissociation of HOCO into CO + OH or CO₂ + H. In glycine and leucine, the amine radicals generated by the α-carbonyl C-C bond cleavage rapidly undergo hydrogen elimination to yield methanimine and 3-methylbutane-1-imine, respectively. Breaking of the α-carbonyl C-C bond in proline appeared to yield 1-pyrroline, although due to its weak absorption it remains unconfirmed. In serine, additional products were formaldehyde and E/Z ethanimine. The present study shows that the direct production of HOCO previously observed in α-alanine generalizes to other amino acids of varying structure. It also revealed a tendency for amino acid photolysis to form imines rather than amine radicals. HOCO should be useful in the search for amino acids in interstellar space, particularly in combination with simple imine molecules.

Glycine Imine-The Elusive α-Imino Acid Intermediate in the Reductive Amination of Glyoxylic Acid

Simple unhindered aldimines tend to hydrolyze or oligomerize and are therefore spectroscopically not well characterized. Herein we report the formation and spectroscopic characterization of the simplest imino acid, namely glycine imine, by cryogenic matrix isolation IR and UV/Vis spectroscopy. Glycine imine forms after UV irradiation of 2-azidoacetic acid by N₂ extrusion in anti-(E,E)- and anti-(Z,Z)-conformation that can be photochemically interconverted. In matrix isolation pyrolysis experiments with 2-azidoacetic acid, glycine imine cannot be trapped as it further decarboxylates to aminomethylene. In aqueous solution glycine imine is hydrolyzed to hydroxy glycine and hydrated glyoxylic acid. At higher concentrations or in the presence of Fe^II SO₄ as a reducing agent glycine imine undergoes self-reduction by oxidative decarboxylation chemistry. Glycine imine may be seen as one of the key reaction intermediates connecting prebiotic amino acid and sugar formation chemistry.

An air-stable radical with a redox-chameleonic amide

An air-stable (amino)(amido)radical was synthesized by reacting a cyclic (alkyl)(amino)carbene with carbazoyl chloride, followed by one-electron reduction. We show that an adjacent radical center weakens the amide bond. It enables the amino group to act as a strong acceptor under steric contraint, thus enhancing the stabilizing capto-dative effect.

Hydrogen-Atom-Assisted Uphill Isomerization of N-Methylformamide in Darkness

N-Methylformamide, HC(O)NH(CH₃), is the smallest amide detected in the interstellar medium that can exist as cis and trans isomers. We performed reactions of H atoms with trans-NMF in solid para-hydrogen at 3.3 K and found that the cis-NMF isomer, which has higher energy, increased continuously in darkness, demonstrating a previously overlooked and seemingly unlikely isomerization of prebiotic molecules through H-atom tunneling reactions in the absence of light. Infrared spectra of radical intermediates trans-•C(O)NH(CH₃) and trans-HC(O)NH(•CH₂) were identified. Further H addition and H abstraction enhanced the formation of CH₃NCO, HNCO, and CH₂NH in the H-rich experiments. These results indicate that, unlike the dual cycle of H-abstraction and H-addition channels chemically linking formamide and HNCO, the H addition to CH₃NCO produced only cis-radicals that led to cis-NMF. Furthermore, H-atom-induced fragmentation by breaking the C-C bond provides links between NMF and HCNO/CH₂NH. These endothermic isomerization/decomposition reactions become possible through the coupling with H + H → H₂.

Computational studies on the possible formation of glycine via open shell gas-phase chemistry in the interstellar medium

Glycine is the simplest proteinogenic amino acid. It has significant astrobiological implications owing to the ongoing investigation for its detection in the interstellar medium (ISM). Hence, a suitable mechanistic elucidation for its formation in the ISM is of current research interest. In the present work, by employing electronic structure calculations [UCCSD(T) and density functional theory (DFT)], various plausible chemical pathways in the gas phase have been examined for the formation of glycine (whose existence has been indirectly proposed in the ISM) and other simple amino acids (yet to be detected in the ISM) from some simpler molecules present in the ISM. This work suggests that step 1: HO-CO (radical) + CH₂NH → NHCH₂COOH (radical) and step 2a: NHCH₂COOH (radical) + H₂ → glycine + H (radical) have very small barriers of 0.14 kcal mol^-1 and ∼3 kcal mol^-1, respectively (easily surmountable at a temperature of ∼50 K under putative interstellar conditions). Hence this should likely be feasible in interstellar gas-phase chemistry. Therefore, HO-CO (radical), CH₂NH, and H₂ could be the possible precursors for the formation of glycine (subject to the presence of the HO-CO radical). The energetic information related to the interstellar reactions, and how this work takes the putative interstellar conditions into account are presented. This paper also highlights how a reaction found to be unsuitable for interstellar molecular evolution via surface chemistry could nonetheless occur via gas-phase chemistry. Based on our results, this work also recommends detecting three new open-shell molecules, HO-CO radical, NHCH₂COOH radical, and NH₂CHCOOH radical, in the ISM.

A chemical link between methylamine and methylene imine and implications for interstellar glycine formation

Methylamine CH₃NH₂ is considered to be an important precursor of interstellar amino acid because hydrogen abstraction might lead to the aminomethyl radical •CH₂NH₂ that can react with •HOCO to form glycine, but direct evidence of the formation and spectral identification of •CH₂NH₂ remains unreported. We performed the reaction H + CH₃NH₂ in solid p-H₂ at 3.2 K and observed IR spectra of •CH₂NH₂ and CH₂NH upon irradiation and when the matrix was maintained in darkness. Previously unidentified IR spectrum of •CH₂NH₂ clearly indicates that •CH₂NH₂ can be formed from the reaction H + CH₃NH₂ in dark interstellar clouds. The observed dual-cycle mechanism containing two consecutive H-abstraction and two H-addition steps chemically connects CH₃NH₂ and CH₂NH in interstellar media and explains their quasi-equilibrium. Experiments on CD₃NH₂ produced CD₂HNH₂, in addition to •CD₂NH₂ and CD₂NH, confirming the occurrence of H addition to •CD₂NH₂.

Potential Catalytic Role of Small Heterocycles in Interstellar H2 Formation: A Laboratory Astrochemistry Study on Furan and Its Hydrogenated Forms

It is now well-accepted in astrochemistry that the formation of interstellar H₂ is taking place on the surface of interstellar grains. It has also been suggested a long time ago that polyaromatic hydrocarbons (PAHs) can catalyze this process by subsequent H atom addition and H abstraction reactions. Recent quantum chemical computations suggested that small heterocycles can be better catalysts than PAHs. In this study, the reaction of H atoms with furan, 2,3- and 2,5-dihydrofurans, and tetrahydrofuran were studied in solid para-H₂ at 3.1 K. The reactions were followed by Fourier transform infrared (FTIR) spectroscopy. By the analysis of spectra, 2-hydrofuran-3-yl, 3-hydrofuran-2-yl, 2,3,4-trihydrofuran-5-yl, and 2,3,5-trihydrofuran-4-yl radicals were identified among the products. The experiments revealed that all the possible H atom addition and H abstraction cycles connecting furan and tetrahydrofuran proceed effectively in both directions at a low temperature. This indicates the possible important role of small heterocycles in interstellar H₂ formation. Furthermore, it also indicates that, in the case of H atom excess, a quasi-equilibrium exists between the c-C₄H_xO (x = 4-8) species, and the ratios of these species in an astrophysical object are determined by the rate of the different H atom addition and H abstraction reaction steps.

VIZSLA-Versatile Ice Zigzag Sublimation Setup for Laboratory Astrochemistry

In this article, a new multi-functional high-vacuum astrophysical ice setup, VIZSLA (Versatile Ice Zigzag Sublimation Setup for Laboratory Astrochemistry), is introduced. The instrument allows for the investigation of astrophysical processes both in a low-temperature para-H₂ matrix and in astrophysical analog ices. In the para-H₂ matrix, the reaction of astrochemical molecules with H atoms and H⁺ ions can be studied effectively. For the investigation of astrophysical analog ices, the setup is equipped with various irradiation and particle sources: an electron gun for modeling cosmic rays, an H atom beam source, a microwave H atom lamp for generating H Lyman-α radiation, and a tunable (213-2800 nm) laser source. For analysis, an FT-IR (and a UV-visible) spectrometer and a quadrupole mass analyzer are available. The setup has two cryostats, offering novel features for analysis. Upon the so-called temperature-programmed desorption (TPD), the molecules, desorbing from the substrate of the first cryogenic head, can be mixed with Ar and can be deposited onto the substrate of the other cryogenic head. The efficiency of the redeposition was measured to be between 8% and 20% depending on the sample and the redeposition conditions. The well-resolved spectrum of the molecules isolated in an Ar matrix serves a unique opportunity to identify the desorbing products of a processed ice. Some examples are provided to show how the para-H₂ matrix experiments and the TPD-matrix-isolation recondensation experiments can help understand astrophysically important chemical processes at low temperatures. It is also discussed how these experiments can complement the studies carried out by using similar astrophysical ice setups.