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Results for “Prebiotic chemistry”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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12 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Modeling prebiotic chemistries with quantum accuracy at classical costs

Molecular Dynamics (MD) simulations using classical force-fields are commonly employed in numerous scientific investigations. However, many natural processes involve bond breaking and quantum forces. This complexity is compounded by the presence of multiple competing length and timescales. For example, accurately modeling the thermodynamics and dynamics of a chemical reaction requires accounting for the concerted movements of numerous solvent molecules and ions with their own fast or slow timescales. While widely used static Density Functional Theory (DFT) calculations at 0 temperature can be beneficial for such investigations, they do not account for dynamics, and lack precision in describing the molecular environments. They particularly fail at correct, rigorous treatments of finite-temperature fluctuations, and thus generalization to experimentally relevant conditions. In PNAS Benayad et al develop a scalable, generalizable approach for designing Neural Network Potentials (NNPs) that can handle chemical reactivity in solvated systems with quantum accuracy at classical costs. Specifically, they study phosphoester bond formation and rupture, which is fundamentally relevant to the Phosphorus-Oxygen bond formation central to life, and especially for the RNA world hypothesis. The framework developed here has the potential to generalize to different chemical reactions of energy and biological relevance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Creation of an Fe 3 P Schreibersite Density Functional Tight Binding Model for Astrobiological Simulations

The mineral schreibersite, e.g., Fe 3 P, is commonly found in iron-rich meteorites and could have served as an abiotic phosphorus source for prebiotic chemistry. However, atomistic calculations of its degradation chemistry generally require quantum simulation approaches, which can be too computationally cumbersome to study sufficient time and length scales for this process. In this regard, we have created a computationally efficient semiempirical quantum density functional tight binding (DFTB) model for iron and phosphorus-containing materials by adopting an existing semiautomated workflow that represents many-body interactions by linear combinations of Chebyshev polynomials. Here, we have utilized a relatively small training set to optimize a DFTB model that is accurate for schreibersite physical and chemical properties, including its bulk properties, surface energies, and water absorption. We then show that our model shows strong transferability to several iron phosphide solids as well as multiple allotropes of iron metal. Our resulting DFTB parametrization will allow us to interrogate schreibersite aqueous decomposition at longer time and length scales than standard quantum approaches, providing for more detailed investigations of its role in prebiotic chemistry on early Earth.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Dynamics of HCN, HNC, and HNCO Formation in the 193 nm Photodissociation of Formamide

Formamide (NH 2 CHO) is the simplest molecule containing a peptide linkage [-NH-C($=$O)-], and it plays an essential role in the study of prebiotic chemistry. Exposure to UV irradiation allows formamide to decompose and act as a prebiotic feedstock in the formation of nucleobases and other necessary starting materials. The photodissociation mechanism of gaseous formamide at 193 nm is studied using (a) chirped-pulse Fourier transform millimeter-wave spectroscopy in the 260-290 GHz spectral region in a room-temperature flow-tube reactor at 1 mu bar pressure, (b) a combination of electronic structure theory, transition state theory, and quasiclassical trajectories, and (c) the Active Thermochemical Tables. The HCN and HNC photoproducts of hydrogenated (NH 2 CHO) and deuterated (NH 2 CDO and ND 2 CHO) formamide precursors are examined to gain insight into the photodissociation mechanism. Here, the theoretical investigation has characterized the main pathway leading to each of the HCN/HNC isomers from the precursor isotopologues. The theoretical branching ratio [HNC]/[HCN] = 2.1 for nascent photofragments agrees with the experiment. The effect of the postphotolysis HNC ↔ HCN isomerization on the [HNC]/[HCN] ratio is predicted. We report the experimental branching ratio [HNCO]: ([HNC] + [HCN]) = 12 ± 3 and propose that most of HNCO originates from dissociation on the S-1 electronic state of formamide.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Low-temperature formation of pyridine and (iso)quinoline via neutral–neutral reactions

Aromatic molecules represent fundamental building blocks in prebiotic chemistry and are contemplated as vital precursors to DNA and RNA nitrogen bases. However, despite the identification of some 300 molecules in extraterrestrial environments, the pathways to pyridine (C 5 H 5 N), pyridinyl (C 5 H 4 N•), and (iso)quinoline (C 9 H 7 N) – the simplest represen-tative of mono and bicyclic aromatic molecule carrying nitrogen – are elusive. Here, we afford compelling evidence on the gas-phase formation of methylene amidogen (H 2 CN•) and cyanomethyl (H 2 CCN•) radicals via molecular beam studies and electronic structure calcula-tions. The modeling of the chemistries of Taurus Molecular Cloud (TMC-1) and Titan’s atmosphere contemplates a complex chain of reactions synthesizing pyridine, pyridinyl, and (iso)quinoline from H 2 CN• and H 2 CCN• at levels of up to 75%. Furthermore, this study affords unique entry points to precursors of DNA and RNA nitrogen bases in hydrocarbon-rich extraterrestrial environments thus changing the way we think about the origin of prebiotic molecules in our Galaxy.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Selective Adsorption of Thiol-Containing Molecules on Copper Sulfide Surfaces via Molecule–Surface Disulfide Bridges

Recent results in the fields of nanoenhanced agriculture and expanding interest in prebiotic chemistry have placed increased emphasis on understanding the chemically selective interaction of small molecules with the surfaces of metal sulfides. Here, we present an integrated experimental and computational study of the interaction of thiol-containing molecules with copper sulfide (covellite) surfaces in aqueous media. In situ Fourier-transform infrared (FTIR) measurements and ex situ X-ray photoelectron spectroscopy (XPS) measurements show that molecules bearing free thiol groups, including glutathione and cysteine, bind strongly to CuS (covellite) nanoparticles and to CuS (001) single crystals, while control studies show that similar molecules lacking the free thiol group exhibit much less binding. Additional experiments show that these thiol-containing molecules interact transiently with CuO nanoparticle surfaces but are readily removed by rinsing. The FTIR and XPS experiments demonstrate that adsorption of molecular thiols to CuS surfaces occurs in a chemically selective manner. Further experimental studies and density functional calculations show that the preferred mode of binding is through the surface S atoms, forming a Solid–S–S–Molecule disulfide linkage. While the role of disulfide linkages in controlling structure and function of proteins and other biomolecules is widely known, the formation of surface disulfide linkages as a motif for covalent molecular binding at surfaces has not been established previously.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Nonenzymatic RNA copying with a potentially primordial genetic alphabet

Nonenzymatic RNA copying is thought to have been responsible for the replication of genetic information during the origin of life. However, chemical copying with the canonical nucleotides (A, U, G, and C) strongly favors the incorporation of G and C and disfavors the incorporation of A and especially U because of the stronger G:C vs. A:U base pair and the weaker stacking interactions of U. Recent advances in prebiotic chemistry suggest that the 2-thiopyrimidines were precursors to the canonical pyrimidines, raising the possibility that they may have played an important early role in RNA copying chemistry. Furthermore, 2-thiouridine (s 2 U) and inosine (I) form by deamination of 2-thiocytidine (s 2 C) and A, respectively. We used thermodynamic and crystallographic analyses to compare the I:s 2 C and A:s 2 U base pairs. We find that the I:s 2 C base pair is isomorphic and isoenergetic with the A:s 2 U base pair. The I:s 2 C base pair is weaker than a canonical G:C base pair, while the A:s 2 U base pair is stronger than the canonical A:U base pair, so that a genetic alphabet consisting of s 2 U, s 2 C, I, and A generates RNA duplexes with uniform base pairing energies. Consistent with these results, kinetic analysis of nonenzymatic template-directed primer extension reactions reveals that s 2 C and s 2 U substrates bind similarly to I and A in the template, and vice versa. Our work supports the plausibility of a potentially primordial genetic alphabet consisting of s 2 U, s 2 C, I, and A and offers a potential solution to the long-standing problem of biased nucleotide incorporation during nonenzymatic template copying.

Science & Technology - Other Topics↗
DOE OSTI2025

Chemistry of Sugar Formation in the Gas Phase: Following the Activated Aldehyde

Sugars are produced by living organisms, and are required building blocks for life as we know it, which raises the foundational question of how sugars formed in a prebiotic environment. The abiotic formose reaction produces sugars from formaldehyde, but our understanding of its initiation step remains murky, with chemists invoking the concept of an “activated aldehyde” to seed this reaction. Singlet hydroxycarbenes, high-energy isomers of aldehydes, were recently reported to facilitate sugar formation under cold, nonaqueous conditions relevant to interstellar environments. Here, we generate singlet methylhydroxycarbene ( 1 CH 3 –C̈–OH) from the photodissociation of pyruvic acid and experimentally measure its gas-phase reaction with d 4 -acetaldehyde using multiplexed photoionization mass spectrometry. The C 4 H 4 D 4 O 2 isomer d 4 -acetoin is the sole product, which we kinetically link to the reactant CH 3 –C̈–OH, and attribute to a carbonyl-ene formation mechanism. We see no evidence of 3-hydroxybutanal, the C–H insertion product expected in carbene chemistry. Using automated exploration we calculate stationary points on the potential energy surface and report master equation rate coefficients from T = 20–600 K, providing quantitative kinetics of this fast reaction for use in chemical models. The prereactive complex in this reaction is stabilized by both hydrogen bonding and electrophilic carbene C═O interactions. These effects create a short-range dynamical bottleneck for the reaction besides the long- and midrange barrierless bottlenecks. Combined with recent reports of 1 HC̈OH production from methanol photodissociation and pyruvic acid production in cold irradiated ices, this work provides evidence that singlet hydroxycarbene + aldehyde chemistry is a feasible path to prebiotic sugar formation.

aldehydes↗
DOE OSTI2024

Did the exposure of coacervate droplets to rain make them the first stable protocells?

Membraneless coacervate microdroplets have long been proposed as model protocells as they can grow, divide, and concentrate RNA by natural partitioning. However, the rapid exchange of RNA between these compartments, along with their rapid fusion, both within minutes, means that individual droplets would be unable to maintain their separate genetic identities. Hence, Darwinian evolution would not be possible, and the population would be vulnerable to collapse due to the rapid spread of parasitic RNAs. In this study, we show that distilled water, mimicking rain/freshwater, leads to the formation of electrostatic crosslinks on the interface of coacervate droplets that not only suppress droplet fusion indefinitely but also allow the spatiotemporal compartmentalization of RNA on a timescale of days depending on the length and structure of RNA. We suggest that these nonfusing membraneless droplets could potentially act as protocells with the capacity to evolve compartmentalized ribozymes in prebiotic environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Meteor over New York City: Brines in a primitive CM asteroid

The CI (Ivuna-type) carbonaceous material returned from asteroids Ryugu and Bennu contain mobilized sodium from the evaporation or freezing of liquid water into brines, shedding light on the internal structure of ice-rich CI-type worlds and the formation of prebiotic organic compounds. The formation of brines has not been demonstrated in CM (Mighei-type) carbonaceous chondrites, which also supplied organic matter to the early Earth. Here, we announce the fall of a primitive meteorite from a daytime fireball over the New York metropolitan area in July 2024. It is a CM2 breccia that contains unique CM1 clasts rich in water and sodium. The meteorite contains abundant amino acids and other products of organic chemistry in brines that reveal subsurface processes on CM-type asteroid parent bodies.

Geosciences↗
DOE OSTI2025

Abundant ammonia and nitrogen-rich soluble organic matter in samples from asteroid (101955) Bennu

Organic matter in meteorites reveals clues about early Solar System chemistry and the origin of molecules important to life, but terrestrial exposure complicates interpretation. Samples returned from the B-type asteroid Bennu by the Origins, Spectral Interpretation, Resource Identification, and Security–Regolith Explorer mission enabled us to study pristine carbonaceous astromaterial without uncontrolled exposure to Earth’s biosphere. Here we show that Bennu samples are volatile rich, with more carbon, nitrogen and ammonia than samples from asteroid Ryugu and most meteorites. Nitrogen-15 isotopic enrichments indicate that ammonia and other N-containing soluble molecules formed in a cold molecular cloud or the outer protoplanetary disk. We detected amino acids (including 14 of the 20 used in terrestrial biology), amines, formaldehyde, carboxylic acids, polycyclic aromatic hydrocarbons and N-heterocycles (including all five nucleobases found in DNA and RNA), along with ~10,000 N-bearing chemical species. All chiral non-protein amino acids were racemic or nearly so, implying that terrestrial life’s left-handed chirality may not be due to bias in prebiotic molecules delivered by impacts. The relative abundances of amino acids and other soluble organics suggest formation and alteration by low-temperature reactions, possibly in NH 3 -rich fluids. Bennu’s parent asteroid developed in or accreted ices from a reservoir in the outer Solar System where ammonia ice was stable.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

The Photochemistry of Amino Acids Produced on the Polar Cryovolcanic Regions of Titan

The cryovolcanic regions of Titan offer transient opportunities for prebiotic molecules to exist in water–ammonia solutions on the surface of the Saturnian moon. The upcoming NASA’s Dragonfly mission will search for high nitrogen concentrations and amino acids on Titan’s equatorial terrains. Cryovolcanic features, however, are most common on the polar regions. To mitigate the distance, bubble bursting may encapsulate the prebiotic molecules into aerosols, which Titan’s Hadley circulation would subsequently transport to the equator. Here we investigate whether alanine and glycine survive this meridional journey. Despite the unconstrained meridional wind velocities, our results suggest that the amino acids can survive the transport through the mesosphere. Dragonfly may find cryo-volcanogenic amino acids on Titan’s equator. Further, the interaction between the two amino acids increased 10-fold the photodegradation rate of glycine. We justify it based on changes in the environment polarity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Thioesters Support Efficient Protein Biosynthesis by the Ribosome

Thioesters are critical chemical intermediates in numerous extant biochemical reactions and are invoked as key reagents during prebiotic peptide synthesis on an evolving Earth. Here we asked if a thioester could replace the native oxo-ester in acyl-tRNA substrates during protein biosynthesis by the ribosome. We prepared 3'-thio-3'-deoxyadenosine triphosphate in 10 steps from xylose and demonstrated that it is an effective substrate for the Escherichia coli CCA-adding enzyme, which appends 3'-thio-3'-deoxyadenosine to truncated tRNAs ending with 3'-CC. Using a variety of aminoacyl-tRNA synthetases, flexizymes, or a direct thioester exchange reaction, we prepared a suite of 3'-thio-tRNAs acylated with α- and non-α-amino acids. All were recognized and utilized by wild-type E. coli ribosomes during in vitro translation reactions to generate oligopeptides in yields commensurate with native oxo-ester tRNAs. These results indicate that thioester intermediates widely used in Nature can be co-opted to support the incorporation of natural α-amino acids as well as noncanonical monomers by the extant translational machinery for sequence-defined polymer synthesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗