Methanol on the rocks: green rust transformation promotes the oxidation of methane.

Shared coordination geometries between metal ions within reactive minerals and enzymatic metal cofactors hints at mechanistic and possibly evolutionary homology between particular abiotic chemical mineralogies and biological metabolism. The octahedral coordination of reactive Fe2+/3+ minerals such as green rusts, endemic to anoxic sediments and the early Earth's oceans, mirrors the di-iron reaction centre of soluble methane monooxygenase (sMMO), responsible for methane oxidation in methanotrophy. We show that methane oxidation occurs in tandem with the oxidation of green rust to lepidocrocite and magnetite, mimicking radical-mediated methane oxidation found in sMMO to yield not only methanol but also halogenated hydrocarbons in the presence of seawater. This naturally occurring geochemical pathway for CH4 oxidation elucidates a previously unidentified carbon cycling mechanism in modern and ancient environments and reveals clues into mineral-mediated reactions in the synthesis of organic compounds necessary for the emergence of life.

Network Analysis Reveals Spatial Clustering and Annotation of Complex Chemical Spaces: Application to Astrochemistry.

How are molecules linked to each other in complex systems? In a proof-of-concept study, we have developed the method mol2net (https://zenodo.org/record/7025094) to generate and analyze the molecular network of complex astrochemical data (from high-resolution Orbitrap MS1 analysis of H2O:CH3OH:NH3 interstellar ice analogs) in a data-driven and unsupervised manner, without any prior knowledge about chemical reactions. The molecular network is clustered according to the initial NH3 content and unlocked HCN, NH3, and H2O as spatially resolved key transformations. In comparison with the PubChem database, four subsets were annotated: (i) saturated C-backbone molecules without N, (ii) saturated N-backbone molecules, (iii) unsaturated C-backbone molecules without N, and (iv) unsaturated N-backbone molecules. These findings were validated with previous results (e.g., identifying the two major graph components as previously described N-poor and N-rich molecular groups) but with additional information about subclustering, key transformations, and molecular structures, and thus, the structural characterization of large complex organic molecules in interstellar ice analogs has been significantly refined.

Visualization and identification of single meteoritic organic molecules by atomic force microscopy.

Using high-resolution atomic force microscopy (AFM) with CO-functionalized tips, we atomically resolved individual molecules from Murchison meteorite samples. We analyzed powdered Murchison meteorite material directly, as well as processed extracts that we prepared to facilitate characterization by AFM. From the untreated Murchison sample, we resolved very few molecules, as the sample contained mostly small molecules that could not be identified by AFM. By contrast, using a procedure based on several trituration and extraction steps with organic solvents, we isolated a fraction enriched in larger organic compounds. The treatment increased the fraction of molecules that could be resolved by AFM, allowing us to identify organic constituents and molecular moieties, such as polycyclic aromatic hydrocarbons and aliphatic chains. The AFM measurements are complemented by high-resolution mass spectrometry analysis of Murchison fractions. We provide a proof of principle that AFM can be used to image and identify individual organic molecules from meteorites and propose a method for extracting and preparing meteorite samples for their investigation by AFM. We discuss the challenges and prospects of this approach to study extraterrestrial samples based on single-molecule identification.

Integrative analytical workflow to enhance comprehensive analysis of organic molecules in extraterrestrial objects.

Molecular identification is a fundamental issue in astrobiology to investigate the routes of emergence of life on our planet involving in particular a potential seeding of extraterrestrial organic matter on the primitive Earth. However, this project encompasses major difficulties due to the low concentration of molecules present in bodies of the Solar System. This work proposes an integrative analytical workflow, no longer based on GC-MS instruments, to enhance comprehensive analysis of organic markers in these objects. Our strategy combines UPLC-HRMS and UPLC-MRM MS methods to bring both a broad molecular mapping and detailed data on indigenous compounds present in any extraterrestrial objects or laboratory analogs. Applied on water extracts from fresh meteorites, our workflow highlights a wide range of free molecules in the non-treated extracts and reveals the wide diversity of amino acid and nucleobase isomers that could lead to misinterpretation as far as the molecular composition of meteorite extracts cannot be anticipated. This strategy, never explored so far, would provide new clues for studying the organic matter in space and should offer new perspectives on its evolution and reactivity.

Identify low mass volatile organic compounds from cometary ice analogs using gas chromatography coupled to an Orbitrap mass spectrometer associated to electron and chemical ionizations.

Analysis of organic matter extracted from meteorites showed that solar system objects present an important molecular diversity. To improve our understanding of such organic matter, new analytical technologies must be developed. The present study displays the first experiments using a GC-FT-Orbitrap-MS to decipher the molecular diversity observed in experiments simulating the evolution of cometary ices. The proposed analytical strategy focuses on the analysis of 110 volatile organic compounds (VOC) with mainly 1 to 6 carbon atoms generated in such cometary ice analogs. Electron ionization (EI) and chemical ionization (CI) modes with methane (CH4) or ammonia (NH3) were optimized and compared. Those developments maximized the intensity of molecular, protonated or deprotonated ions, and improved high-resolution molecular formula unambiguous identification: EI mode is too energetic to provides there detection, while it is not the case in CI mode. Particularly, NH3 as a reagent gas improves amine identification in positive mode (PCI), and esters, alcohols, carbonyls, amides, carboxylic acids and nitriles in negative mode (NCI). The combination of both EI and CI mass spectrum analysis improves molecular identification, thanks to the detection of molecular, deprotonated or protonated ion of highest intensity and fragment formula assignments. The EI and NCI NH3 combination allows formula assignments up to 94% of our database with limit of detection up to 7 ppm. This procedure has been validated for untargeted GC-FT-Orbitrap-MS analysis of VOC coming from the processing of cometary ice analogs.

A Novel Proteomics-Based Strategy for the Investigation of Peptide Sequences in Extraterrestrial Samples.

Method development is one of the objectives of the astrophysical community for characterizing the organic matter in objects of the solar system. In this context, we report on the development of an enzyme-catalyzed stereoselective hydrolysis, inspired by the proteomics discipline, which has enabled the indirect detection of peptide sequences in extraterrestrial samples. A proof of concept has been performed on a Murchison extract. We show that our approach can successfully highlight l- and d-amino acids involved in peptide bonds. While we show that some d-amino acids must have been involved in peptide bonds, we cannot at this stage conclude on the indigenous or exogenous nature of these biopolymers. However, our strategy constitutes the first step toward direct UPLC-MS evidence of peptide sequences in extraterrestrial samples. It should thus contribute to deepening knowledge on the molecules available in the solar system, hence providing new clues about their chemical history, especially on Earth.

On the conditions for mimicking natural selection in chemical systems.

The emergence of natural selection, requiring that reproducing entities present variations that may be inherited and passed on, was arguably the most important breakthrough in the self-organization of life. In this Perspective, the assumptions governing biological reproduction are confronted with physico-chemical principles that control the evolution of material systems. In biology, the reproduction of living organisms is never considered to be reversible, whereas microscopic reversibility is an essential principle in the physical description of matter. Here, we show that this discrepancy places constraints on the possibility of finding kinetic processes in the chemical world that are equivalent to natural selection in the biological one. Chemical replicators can behave in a similar fashion to living entities, provided that the reproduction cycle proceeds in a unidirectional way. For this to be the case, kinetic barriers must hinder the reverse process. The system must, thus, be held far from equilibrium and fed with a non-degraded (low-entropy) form of energy. The ensuing constraints must be factored in when proposing scenarios that account for the origin of life at the molecular level.

Sensitivity and resolution optimization in gas chromatography coupled to mass spectrometry analyses of volatile organic compounds present in vacuum environment.

The gaseous phase analyses of volatile organic compounds (VOCs) are an important challenge especially when these organics are formed in high vacuum environments (10-8 mbar) reproducing the environment of astrophysical ices formation and processing. Several analytical techniques have been developed to identify the molecular diversity formed from the processing of these ices. Among them, the coupling of a GC-MS to the vacuum chamber where ices are processed highlighted the interesting chemical diversity of such processed ices. These analyses were possible due to the development of a specific system, the VAHIIA interface that enables the preconcentration of VOCs at low pressure (10-8 mbar) and their transfer at higher pressure to the injection unit of a GC for their subsequent analyses. This system showed sufficient repeatability (13%) and low detection limits (nmol) for simple ices [1], but presents limits when ice mixtures are complex (such as multi-component ices including water, methanol and ammonia). In this contribution, we present the optimization of our previous VAHIIA system by implementing a cryofocusing system in the GC oven and by improving the recovery yield of VOCs from the vacuum chamber to the VAHIIA interface. The cryofocusing provides an improvement of efficiencies leading to higher resolution and signal to noise ratio, while the addition of argon in the vacuum chamber during the VOC recovery allows increasing the amount of molecules recovered by a factor of ∼200. The coupling of both approaches provides an increase of sensitivity of a factor ∼400. At the end, experiments on astrophysical ices are shown demonstrating the interest of such optimizations for VOC analyses.

Data-Driven UPLC-Orbitrap MS Analysis in Astrochemistry.

Meteorites have been found to be rich and highly diverse in organic compounds. Next to previous direct infusion high resolution mass spectrometry experiments (DI-HR-MS), we present here data-driven strategies to evaluate UPLC-Orbitrap MS analyses. This allows a comprehensive mining of structural isomers extending the level of information on the molecular diversity in astrochemical materials. As a proof-of-concept study, Murchison and Allende meteorites were analyzed. Both, global organic fingerprint and specific isomer analyses are discussed. Up to 31 different isomers per molecular composition are present in Murchison suggesting the presence of ≈440,000 different compounds detected therein. By means of this time-resolving high resolution mass spectrometric method, we go one step further toward the characterization of chemical structures within complex extraterrestrial mixtures, enabling a better understanding of organic chemical evolution, from interstellar ices toward small bodies in the Solar System.

Development of liquid chromatography high resolution mass spectrometry strategies for the screening of complex organic matter: Application to astrophysical simulated materials.

The present work aims at developing two LC-HRMS setups for the screening of organic matter in astrophysical samples. Their analytical development has been demonstrated on a 100-µg residue coming from the photo-thermo chemical processing of a cometary ice analog produced in laboratory. The first 1D-LC-HRMS setup combines a serially coupled columns configuration with HRMS detection. It has allowed to discriminate among different chemical families (amino acids, sugars, nucleobases and oligopeptides) in only one chromatographic run without neither a priori acid hydrolysis nor chemical derivatisation. The second setup is a dual-LC configuration which connects a series of trapping columns with analytical reverse-phase columns. By coupling on-line these two distinct LC units with a HRMS detection, high mass compounds (350

The Prebiotic C-Terminal Elongation of Peptides Can Be Initiated by N-Carbamoyl Amino Acids.

The formation of peptides upon 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC)-promoted activation of N-carbamoylamino acids (CAA), was considered in the scope of our recent works on carbodiimide promoted C-terminus elongation of peptides in a prebiotic context. Thus EDC promoted activation of CAA derivatives of Tyr(Me) or Ala in dilute aqueous medium pH 5.5-6.5 in the presence of excess of AA, resulted in peptide formation by C-terminus activation/elongation. Kinetic results similar to those of EDC-mediated activation of N-acyl-AA lead us to postulate the formation of a 2-amino-5(4H)-oxazolone intermediate by cyclization of the activated CAA, in spite of the absence of epimerization occurred at CAA residues. Thus, in a prebiotic context, CAA may have played a similar role as N-acyl-AA in the initiation of C-terminus peptide elongation.

Development and optimization of an analytical system for volatile organic compound analysis coming from the heating of interstellar/cometary ice analogues.

This contribution presents an original analytical system for studying volatile organic compounds (VOC) coming from the heating and/or irradiation of interstellar/cometary ice analogues (VAHIIA system) through laboratory experiments. The VAHIIA system brings solutions to three analytical constraints regarding chromatography analysis: the low desorption kinetics of VOC (many hours) in the vacuum chamber during laboratory experiments, the low pressure under which they sublime (10(-9) mbar), and the presence of water in ice analogues. The VAHIIA system which we developed, calibrated, and optimized is composed of two units. The first is a preconcentration unit providing the VOC recovery. This unit is based on a cryogenic trapping which allows VOC preconcentration and provides an adequate pressure allowing their subsequent transfer to an injection unit. The latter is a gaseous injection unit allowing the direct injection into the GC-MS of the VOC previously transferred from the preconcentration unit. The feasibility of the online transfer through this interface is demonstrated. Nanomoles of VOC can be detected with the VAHIIA system, and the variability in replicate measurements is lower than 13%. The advantages of the GC-MS in comparison to infrared spectroscopy are pointed out, the GC-MS allowing an unambiguous identification of compounds coming from complex mixtures. Beyond the application to astrophysical subjects, these analytical developments can be used for all systems requiring vacuum/cryogenic environments.

Diastereoselectivity in prebiotically relevant 5(4H)-oxazolone-mediated peptide couplings.

A stereochemical study of a potentially prebiotic peptide-forming reaction was carried out as the first part of a systems chemistry investigation of potential paths for symmetry breaking. Substantial diastereomeric excesses result from a fast epimerization of the 5(4H)-oxazolone intermediate in aqueous solution.

Formation of hydroxyacetonitrile (HOCH2CN) and polyoxymethylene (POM)-derivatives in comets from formaldehyde (CH2O) and hydrogen cyanide (HCN) activated by water.

Studying chemical reactivity is an important way to improve our understanding of the origin of organic matter in astrophysical environments such as molecular clouds, protoplanetary disks, and possibly, as a final destination, in our solar system bodies such as in comets. Laboratory simulations on the reactivity of ice analogs can provide important insights into this complex reactivity. Here, the role of water as a catalytic agent is investigated under the conditions of simulated interstellar and cometary grains in the formation of complex organic molecules: the hydroxyacetonitrile (HOCH2CN) and formaldehyde polymers (polyoxymethylene POM). Using infrared spectroscopy and mass spectrometry, we show that HCN reacts with CH2O only in the presence of H2O, whereas in the absence of H2O, HCN is not sufficiently reactive to promote this reaction. Furthermore, depending on the dilution of CH2O and HCN in the water matrix, 1-cyanopolyoxymethylene polymers can also be formed (H-(O-CH2)n-CN, POM-CN), as confirmed by mass spectrometry using the HC(15)N isotopologue. Moreover, quantum chemical calculations allowed us to suggest mechanistic proposals for these reactions, the first step being the activation of HCN by water forming H3O(+) and CN(-), which subsequently condense on a neighbouring CH2O promoting the formation of (-)OCH2CN. Once (-)OCH2CN is formed, it can either recover a proton by reacting with H3O(+) or condense on CH2O molecules leading to POM-CN structures. Implications of this work for the forthcoming Rosetta mission are also addressed.

2-Oxo-2H-chromen-4-yl propionate.

In the title compound, C12H10O4, the atoms of the 2-oxo-2H-chromene ring system and the non-H atoms of the 4-substituent all lie on a crystallographic mirror plane. The mol-ecular structure exhibits an intra-molecular C-H⋯O hydrogen bond, which generates an S(6) ring. In the crystal, mol-ecules form R 3 (2)(12) trimeric units via C-H⋯O inter-actions which propagate into layers parallel to the ac plane. These layers are linked by weak C-H⋯O inter-actions along the [010] direction, generating a three-dimensional network.

5(4H)-oxazolones as intermediates in the carbodiimide- and cyanamide-promoted peptide activations in aqueous solution.

The early days: although considered a species to be avoided in peptide chemistry, the intermediacy of 5(4H)-oxazolones is demonstrated to be essential for the formation of peptides through cyanamide and carbodiimide activation in aqueous solution.

The mechanism of hexamethylenetetramine (HMT) formation in the solid state at low temperature.

There is convincing evidence that the formation of complex organic molecules occurred in a variety of environments. One possible scenario highlights the universe as a giant reactor for the synthesis of organic complex molecules, which is confirmed by numerous identifications of interstellar molecules. Among them, precursors of biomolecules are of particular significance due to their exobiological implications, and some current targets concern their search in the interstellar medium as well as understanding the mechanisms of their formation. Hexamethylenetetramine (HMT, C(6)H(12)N(4)) is one of these complex organic molecules and is of prime interest since its acid hydrolysis seems to form amino acids. In the present work, the mechanism for HMT formation at low temperature and pressure (i.e. resembling interstellar conditions) has been determined by combining experimental techniques and DFT calculations. Fourier transform infra-red spectroscopy and mass spectrometry techniques have been used to follow experimentally the formation of HMT as well as its precursors from thermal reaction of NH(3):H(2)CO:HCOOH and CH(2)NH:HCOOH ice mixtures, from 20 K to 330 K. DFT calculations have been used to compute the mechanistic steps through which HMT can be formed starting from the experimental reactants observed in solid phase. The fruitful interplay between theory and experiment has allowed establishing that the mechanism in the solid state at low temperature is different from the one proposed in liquid phase, in which a new intermediate (1,3,5-triazinane, C(3)H(9)N(3)) has been identified. In the meantime, aminomethanol has been unambiguously confirmed as the first intermediate whereas the hypothesis of methylenimine as the second is further strengthened.

Pathways for the formation and evolution of peptides in prebiotic environments.

α-Amino acids are easily accessible through abiotic processes and were likely present before the emergence of life. However, the role they could have played in the process remains uncertain. Chemical pathways that could have brought about features of self-organization in a peptide world are considered in this review and discussed in relation with their possible contribution to the origin of life. An overall scheme is proposed with an emphasis on possibilities that may have led to dynamically stable far from equilibrium states. This analysis defines new lines of investigation towards a better understanding of the contribution of the systems chemistry of amino acids and peptides to the emergence of life.

Activation of carboxyl group with cyanate: peptide bond formation from dicarboxylic acids.

The reaction of cyanate with C-terminal carboxyl groups of peptides in aqueous solution was considered as a potential pathway for the abiotic formation of peptide bonds under the condition of the primitive Earth. The catalytic effect of dicarboxylic acids on cyanate hydrolysis was definitely attributed to intramolecular nucleophilic catalysis by the observation of the 1H-NMR signal of succinic anhydride when reacting succinic acid with KOCN in aqueous solution (pH 2.2-5.5). The formation of amide bonds was noticed when adding amino acids or amino acid derivatives into the solution. The reaction of N-acyl aspartic acid derivatives was observed to proceed similarly and the scope of the cyanate-promoted reaction was analyzed from the standpoint of prebiotic peptide formation. The role of cyanate in activating peptide C-terminus constitutes a proof of principle that intramolecular reactions of adducts of peptides C-terminal carboxyl groups with activating agents represent a pathway for peptide activation in aqueous solution, the relevance of which is discussed in connexion with the issue of the emergence of homochirality.