DNA Nucleobase Synthesis at Titan Atmosphere Analog by Soft X-rays

Astrochemical Pathways to Complex Organic and Prebiotic Molecules: Experimental Perspectives for In Situ Solid-State Studies

A deep understanding of the origin of life requires the physical, chemical, and biological study of prebiotic systems and the comprehension of the mechanisms underlying their evolutionary steps. In this context, great attention is paid to the class of interstellar molecules known as "Complex Organic Molecules" (COMs), considered as possible precursors of prebiotic species. Although COMs have already been detected in different astrophysical environments (such as interstellar clouds, protostars, and protoplanetary disks) and in comets, the physical-chemical mechanisms underlying their formation are not yet fully understood. In this framework, a unique contribution comes from laboratory experiments specifically designed to mimic the conditions found in space. We present a review of experimental studies on the formation and evolution of COMs in the solid state, i.e., within ices of astrophysical interest, devoting special attention to the in situ detection and analysis techniques commonly used in laboratory astrochemistry. We discuss their main strengths and weaknesses and provide a perspective view on novel techniques, which may help in overcoming the current experimental challenges.

Photolysis of CH3CN Ices by Soft X-rays: Implications for the Chemistry of Astrophysical Ices at the Surroundings of X-ray Sources

In this work, broad-band soft X-ray (6-2000 eV) was employed to irradiate frozen acetonitrile CH₃CN, at the temperature 13 K, with different photon fluences up to 1.5 × 10¹⁸ photons cm^-2. Here, acetonitrile is considered as a representative complex organic molecule (COM) present in astrophysical water-rich ices. The experiments were conduced at the Brazilian synchrotron facility (LNLS/CNPEM) employing infrared spectroscopy (FTIR) to monitor chemical changes induced by radiation. The effective destruction cross section of acetonitrile and effective formation cross section for daughter species formed inside the ice were obtained. The identified radiation products were HCN, CH₄, H₂CCNH, and CH₃NC showing that fragmentation and rearrangement contribute to acetonitrile destruction. Chemical equilibrium and molecular abundances at this stage were determined, which also includes the abundance estimates of unknown molecules, produced but not directly detected, in the ice. The chemical equilibrium was reached at fluence around 1.5 × 10¹⁸ photons cm^-2. Time scales for ices, at hypothetical snow line distances, to reach chemical equilibrium around compact objects, young stellar objects, and O/B stars and inside solar system were given. Among the obtained results are the time scales for reaching chemical equilibrium around different astronomical strong X-ray emitters, e.g., 14 days (for the Sun at 5 AU), 41 and 82 days (for O/B stars at 5 AU), 10⁹-10¹¹ years (for white dwarfs at 1 LY), 450 years (for Crab pulsar at 2.25 LY), around 10⁷ years (for Vela pulsar at 2.25 LY), and 7.5 × 10⁶ years (for Sagittarius A* at 3 LY).

On an EUV Atmospheric Simulation Chamber to Study the Photochemical Processes of Titan's Atmosphere

The in situ exploration of Titan’s atmosphere requires the development of laboratory experiments to understand the molecular growth pathways initiated by photochemistry in the upper layers of the atmosphere. Key species and dominant reaction pathways are used to feed chemical network models that reproduce the chemical and physical processes of this complex environment. Energetic UV photons initiate highly efficient chemistry by forming reactive species in the ionospheres of the satellite. We present here a laboratory experiment based on a new closed and removable photoreactor coupled here to an Extreme Ultraviolet (EUV) irradiation beam produced by the high-order harmonic generation of a femtosecond laser. This type of EUV stable source allow long-term irradiation experiments in which a plethora of individual reactions can take place. In order to demonstrate the validity of our approach, we irradiated for 7 hours at 89.2 nm, a gas mixture based on N₂/CH₄ (5%). Using only one wavelength, products of the reaction reveal an efficient photochemistry with the formation of large hydrocarbons but especially organic compounds rich in nitrogen similar to Titan. Among these nitrogen compounds, new species had never before been identified in the mass spectra obtained in situ in Titan’s atmosphere. Their production in this experiment, on the opposite, corroborates previous experimental measurements in the literature on the chemical composition of aerosol analogues produced in the laboratory. Diazo-compounds such as dimethyldiazene (C₂H₆N₂), have been observed and are consistent with the large nitrogen incorporation observed by the aerosols collector pyrolysis instrument of the Huygens probe. This work represents an important step forward in the use of a closed cell chamber irradiated by the innovative EUV source for the generation of photochemical analogues of Titan aerosols. This approach allows to better constrain and understand the growth pathways of nitrogen incorporation into organic aerosols in Titan’s atmosphere.

Photochemistry and desorption induced by X-rays in water rich astrophysical ice analogs: implications for the moon Enceladus and other frozen space environments

Soft X-rays are an important agent for chemical processing in the Solar System and in the interstellar medium. The photolysis and photodesorption processes of H2O-rich ices triggered by soft X-rays was, experimentally, addressed in this paper. The experiments were performed at the Brazilian synchrotron facility LNLS/CNPEN employing broadband radiation (from 6 to 2000 eV; mainly soft X-rays and a small fraction of VUV) in solid samples at temperatures of 20 and 80 K. The icy samples were monitored by infrared spectroscopy. We determined the effective destruction cross section (in the order 10-18 cm2) as well as the formation cross section for the new species produced after the irradiation. Among them, we list OCN-, CO, CO3, CH3OH, H2O2, HCOO-, NH4 +, HCONH2 and CH3HCO, mostly formed in the experiment at 80 K. The chemical equilibrium stage was characterized and molecular abundances were quantified. In addition, we discuss a methodology to estimate the amount of unknown species in the ice produced by photolysis. The samples reach chemical equilibrium at fluences around 2-3 × 1018 cm-2. Timescales for reaching chemical equilibrium in space environments illuminated by X-rays were given, as well as the desorption yields induced by X-rays. The astrophysical implication on the surface chemistry and desorption processes at the moon Enceladus are provided.

Gas-Phase Reactions of Deprotonated Nucleobases with H, N, and O Atoms

Complex organic molecules, the hallmark of terrestrial life, are increasingly detected in exotic environments throughout the universe. Our studies probe the ion chemistry of these biomolecules. We report gas-phase reaction rate constants for five deprotonated nucleobases (adenine, cytosine, guanine, thymine, and uracil) reacting with the atomic species H, N, and O. Hydrogen atoms react at moderate rates via associative electron detachment. Oxygen atom reactions occur more rapidly, generating complex product distributions; reaction pathways include associative electron detachment, substitution of the hydrogen atom by an oxygen atom, and generation of OCN^-. Nitrogen atoms do not react with the nucleobase anions. The reaction thermodynamics were investigated computationally, and reported product channels are exothermic. Many of the proposed products have been observed in various astrochemical environments. These reactions provide insight into chemical processes that may occur at the boundaries between diffuse and dense interstellar clouds and in complex extraterrestrial ionospheres.

Nucleic acid bases in Titan tholins and possible genetic systems in the Titan liquidosphere

Titan is the largest moon of Saturn and possesses a dense atmosphere composed of nitrogen and methane. Various types of organic compounds (hydrocarbons, nitriles, etc.) have been found on Titan, which were generated by reactions taking place in its atmosphere. These reactions are considered to provide crucial evidence for chemical reactions which may have occurred in the atmosphere of primitive Earth. Cassini discovered several lakes of liquid methane and ethane on Titan's surface; in addition, the presence of ammonia water in its sub-surface was implied. In order to simulate the chemical reactions in Titan's atmosphere, gas mixtures of nitrogen and methane have been exposed to plasma discharges to synthesize complex organic matters. In this study, we focused on the formation of nucleic acid bases and related compounds recovered from synthesized Titan tholins. The five nucleic acid bases that terrestrial life uses (adenine, cytosine, thymine, guanine, and uracil) have already been reported to be present in synthesized Titan tholins. Purines and pyrimidines, including the five aforementioned nucleic acid bases, were extracted from synthesized Titan tholins and analyzed by HPLC and LC/MS. As a result, the pyrimidine bases of isocytosine and 2, 4-diaminopyrimidine were detected together with the terrestrial nucleic acid bases of adenine, uracil, and cytosine. The results obtained in conjunction with those from previous studies show that some nucleic acid bases and related pyrimidine bases are found in synthesized Titan tholins, suggesting that chemical evolutions toward xenogenetic systems could occur in Titan's environment.

SO3 formation from the X-ray photolysis of SO2 astrophysical ice analogues: FTIR spectroscopy and thermodynamic investigations

In this combined experimental-theoretical work we focus on the physical and chemical changes induced by soft X-rays on sulfur dioxide (SO₂) ice at a very low temperature, in an attempt to clarify and quantify its survival and chemical changes in some astrophysical environments. SO₂ is an important constituent of some Jupiter moons and has also been observed in ices around protostars. The measurements were performed at the Brazilian Synchrotron Light Source (LNLS/CNPEM), in Campinas, Brazil. The SO₂ ice sample (12 K) was exposed to a broadband beam of mainly soft X-rays (6-2000 eV) and in situ analyses were performed by IR spectroscopy. The X-ray photodesorption yield (upper limit) was around 0.25 molecules per photon. The values determined for the effective destruction (SO₂) and formation (SO₃) cross sections were 2.5 × 10^-18 cm² and 2.1 × 10^-18 cm², respectively. The chemical equilibrium (88% of SO₂ and 12% of SO₃) was reached after the fluence of 1.6 × 10¹⁸ photons cm^-2. The SO₃ formation channels were studied at the second-order Møller-Plesset perturbation theory (MP2) level, which showed the three most favorable reaction routes (ΔH < -79 kcal mol^-1) in simulated SO₂ ice: (i) SO + O₂ → SO₃, (ii) SO₂ + O → SO₃, and (iii) SO₂ + O⁺ → SO₃⁺ + e^- → SO₃. The amorphous solid environment effect decreases the reactivity of intermediate species towards SO₃ formation, and ionic species are even more affected. The experimentally determined effective cross sections and theoretical reaction channels identified in this work allow us to better understand the chemical evolution of certain sulfur-rich astrophysical environments.

Radiolysis of N2-rich astrophysical ice by swift oxygen ions: implication for space weathering of outer solar system bodies

In order to investigate the role of medium mass cosmic rays and energetic solar particles in the processing of N₂-rich ice on frozen moons and cold objects in the outer solar system, the bombardment of an N₂ : H₂O : NH₃ : CO₂ (98.2 : 1.5 : 0.2 : 0.1) ice mixture at 16 K employing 15.7 MeV ¹⁶O⁵⁺ was performed. The changes in the ice chemistry were monitored and quantified by Fourier transformed infrared spectroscopy (FTIR). The results indicate the formation of azide radicals (N₃), and nitrogen oxides, such as NO, NO₂, and N₂O, as well as the production of CO, HNCO, and OCN^-. The effective formation and destruction cross-sections are roughly on the order of 10^-12 cm² and 10^-13 cm², respectively. From laboratory molecular analyses, we estimated the destruction yields for the parent species and the formation yields for the daughter species. For N₂, this value was 9.8 × 10⁵ molecules per impact of ions, and for the most abundant new species (N₃), it was 1.1 × 10⁵ molecules per impact of ions. From these yields, an estimation of how many species are destroyed or formed in a given timescale (10⁸ years) in icy bodies in the outer solar system was calculated. This work reinforces the idea that such physicochemical processes triggered by cosmic rays, solar wind, and magnetospheric particles (medium-mass ions) in nitrogen-rich ices may play an important role in the formation of molecules (including pre-biotic species precursors such as amino acids and other "CHON" molecules) in very cold astrophysical environments, such as those in the outer region of the solar system (e.g. Titan, Triton, Pluto, and other KBOs).

Unified reaction pathways for the prebiotic formation of RNA and DNA nucleobases

The reaction pathways for the prebiotic formation of nucleobases are complex and lead to the formation of a mixture of products.

Determination of optical constants n and k of thin films from absorbance data using Kramers-Kronig relationship

We present a code, called NKABS, to determine optical constants (complex refractive index) of thin films directly from the absorbance data in the infrared. The code is written in the Python language, which is more accurate and faster than previous methods in the literature. For solving the Kramers-Kronig relationship, we used the Maclaurin's methodology. Unlike other codes, which found convergence in 30-40 iterations, the NKABS reach the convergence in just 4 or 5 iterations. Additionally, to evaluate the error, this code calculates the MAPE (Mean Absolute Percentage Error) and the chi-square χ(2). The typical MAPE error obtained using NKABS is less than 1×10(-3)%. To illustrate the functionality of this code, we calculate the optical constants in the infrared spectral region of 28 different samples of astrophysical interest at different temperatures (10-300K), which simulates molecules in space environments, mostly the ones called astrophysical ices. The samples were obtained from the condensation of pure gases (e.g. CO, CO2, NH3, SO2), from the sublimation in vacuum of pure liquids (e.g. water, acetone, acetonitrile, acetic acid, formic acid, ethanol and methanol) and from mixtures of different species (e.g. H2O:CO2, H2O:CO:NH3, H2O:CO2:NH3:CH4). Additionally films of solid biomolecules samples of astrochemistry/astrobiology interest (e.g. glycine, adenine) were probed. The code and the data-base obtained here are available on-line. The NKABS can also be employed to calculate refractive index of processed samples (by heating or radiation). Such data and the refractive index of virgin samples are required as input in several astrophysical models that calculate the radiative transfer in dusty astrophysical environments such as protoplanetary disks and circumstellar environments as well as dense molecular clouds.

VUV photochemistry simulation of planetary upper atmosphere using synchrotron radiation

The coupling of a gas reactor, named APSIS, with a vacuum-ultraviolet (VUV) beamline at the SOLEIL synchrotron radiation facility, for a photochemistry study of gas mixtures, is reported. The reactor may be irradiated windowless with gas pressures up to hundreds of millibar, and thus allows the effect of energetic photons below 100 nm wavelength to be studied on possibly dense media. This set-up is perfectly suited to atmospheric photochemistry investigations, as illustrated by a preliminary report of a simulation of the upper atmospheric photochemistry of Titan, the largest satellite of Saturn. Titan's atmosphere is mainly composed of molecular nitrogen and methane. Solar VUV irradiation with wavelengths no longer than 100 nm on the top of the atmosphere enables the dissociation and ionization of nitrogen, involving a nitrogen chemistry specific to nitrogen-rich upper atmospheres.

Mechanisms of prebiotic adenine synthesis from HCN by oligomerization in the gas phase

We explored the potential energy surfaces for adenine synthesis by oligomerizations of HCN or HNC from CBS-QB3 calculations. The pathways have been obtained for the formation of the covalently bound HCN dimer, trimer, tetramer, and pentamer (adenine) by sequential additions of HCN or HNC. The activation energies of the individual oligomerization stages are a few hundred kilojoules per mole, which prevent efficient adenine synthesis in interstellar space or in the atmosphere of Titan. On the other hand, when the oligomerizations start from HCNH(+), the activation energies of sequential HCN or HNC additions are significantly reduced. Kinetic analyses results suggest that adenine synthesis by proton-catalyzed oligomerizations cannot occur efficiently in interstellar space or in the atmosphere of Titan, even though some oligomerization stages can occur under the latter condition.

An RF-powered micro-reactor for the detection of astrobiological target molecules on planetary bodies

We describe a sample-processing micro-reactor that utilizes 60 GHz RF radiation with approximately 730 mW of output power. The instrument design and performance characterization are described and then illustrated with modeling and experimental studies. The micro-reactor's efficiency on affecting hydrolysis of chemical bonds similar to those within large complex molecules was demonstrated: a disaccharide-sucrose-was hydrolyzed completely under micro-reactor conditions. The products of the micro-reactor-facilitated hydrolysis were analyzed using mass spectroscopy and proton nuclear magnetic resonance analytical techniques.

Theoretical-experimental study of formic acid photofragmentation in the valence region

Photoionization and photofragmentation studies of formic acid (HCOOH) are performed for the valence shell electron ionization process. The total and partial ion yield of gaseous HCOOH were collected as a function of photon energy in the ultraviolet region, between 11.12 and 19.57 eV. Measurements of the total and partial ion yield of gaseous formic acid molecule are performed with a time-of-flight mass spectrometer at the Synchrotron Light Brazilian Laboratory. Density functional theory and time dependent density functional theory are employed to calculate the ground and excited electronic state energies of neutral and ionic formic acid as well as their fragments and normal vibration modes. The ionization potential energies, the stability of electronic excited states of HCOOH(+), and the energies of opening fragmentation channels are estimated from theoretical-experimental analysis. Additionally, the main formic acid photofragmentation pathways by exposition of photons within that energy range are determined experimentally. These produced ions primarily have the following mass/charge ratios: 46 (HCOOH(+)), 45 (COOH(+)), 29 (HCO(+)), and 18 (H(2)O(+)).

Prebiotic chemistry in eutectic solutions at the water-ice matrix

A crystalline ice matrix at subzero temperatures can maintain a liquid phase where organic solutes and salts concentrate to form eutectic solutions. This concentration effect converts the confined reactant solutions in the ice matrix, sometimes making condensation and polymerisation reactions occur more favourably. These reactions occur at significantly high rates from a prebiotic chemistry standpoint, and the labile products can be protected from degradation. The experimental study of the synthesis of nitrogen heterocycles at the ice-water system showed the efficiency of this scenario and could explain the origin of nucleobases in the inner Solar System bodies, including meteorites and extra-terrestrial ices, and on the early Earth. The same conditions can also favour the condensation of monomers to form ribonucleic acid and peptides. Together with the synthesis of these monomers, the ice world (i.e., the chemical evolution in the range between the freezing point of water and the limit of stability of liquid brines, 273 to 210 K) is an under-explored experimental model in prebiotic chemistry.

Formation routes of interstellar glycine involving carboxylic acids: possible favoritism between gas and solid phase

Despite the extensive search for glycine (NH₂CH₂COOH) and other amino acids in molecular clouds associated with star-forming regions, only upper limits have been derived from radio observations. Nevertheless, two of glycine's precursors, formic acid and acetic acid, have been abundantly detected. Although both precursors may lead to glycine formation, the efficiency of reaction depends on their abundance and survival in the presence of a radiation field. These facts could promote some favoritism in the reaction pathways in the gas phase and solid phase (ice). Glycine and these two simplest carboxylic acids are found in many meteorites. Recently, glycine was also observed in cometary samples returned by the Stardust space probe. The goal of this work was to perform theoretical calculations for several interstellar reactions involving the simplest carboxylic acids as well as the carboxyl radical (COOH) in both gas and solid (ice) phase to understand which reactions could be the most favorable to produce glycine in interstellar regions fully illuminated by soft X-rays and UV, such as star-forming regions. The calculations were performed at four different levels for the gas phase (B3LYP/6-31G*, B3LYP/6-31++G**, MP2/6-31G*, and MP2/6-31++G**) and at MP2/6-31++G** level for the solid phase (ice). The current two-body reactions (thermochemical calculation) were combined with previous experimental data on the photodissociation of carboxylic acids to promote possible favoritism for glycine formation in the scenario involving formic and acetic acid in both gas and solid phase. Given that formic acid is destroyed more in the gas phase by soft X-rays than acetic acid is, we suggest that in the gas phase the most favorable reactions are acetic acid with NH or NH₂OH. Another possible reaction involves NH₂CH₂ and COOH, one of the most-produced radicals from the photodissociation of acetic acid. In the solid phase, we suggest that the reactions of formic acid with NH₂CH or NH₂CH₂OH are the most favorable from the thermochemical point of view.