Computational Exploration of the Chemical Space Surrounding the Molecules of Life

How the transition of disorganized, inanimate matter to organized, living systems took place on our planet and might have occurred on other bodies of our solar system or elsewhere in the universe is one of the fundamental questions studied in the field of astrobiology. The only instance of life known so far is the terrestrial one, and all living organisms on Earth share many of the same biochemical foundations with respect to reproduction and metabolism. These biochemical foundations rely on a small pool of biomolecules, which represent a minute subset of plausible structural analogs, which themselves form only a very small fraction of all possible chemical compounds in chemical space. We believe that one key to understanding the origins of life is to study biomolecules in the context of their surrounding neighborhood in chemical space. Using unique software tools, so-called structure generators, we are able to exhaustively construct well defined subsets of chemical space. These virtual compound libraries are then computationally analyzed with respect to the physico-chemical properties of their constituents. In this talk some basic mathematical models and computational aspects of generating molecular structures are presented, results concerning the amino acid alphabet, nucleotide analogs and the core of intermediary metabolism are summarized, and perspectives of ongoing studies related to astrobiology exploration missions are outlined

Radiolysis of Solid-State Nitrogen Heterocycles Provides Clues to Their Abundance in the Early Solar System

We studied the radiolysis of a wide variety of N-heterocycles, including many of biological importance, and find that the majority are remarkably stable in the solid-state when subjected to large doses of ionizing gamma radiation from a 60Co source. Degradation of N-heterocycles as a function of dose rate and total dose was measured using high performance liquid chromatography with UV detection. Many N-heterocycles show little degradation when γ-irradiated up to a total dose of ~1 MGy, which approximates hundreds of millions of years’ worth of radiation emitted in meteorite parent bodies due to slow radionuclide decay. Extrapolation of these results suggests that these N-heterocyclic compounds would be stable in dry parent bodies over solar system time-scales. We suggest that the abundance of these N-heterocycles as measured presently in carbonaceous meteorites is largely reflective of their abundance at the time aqueous alteration stopped in their parent bodies, and the absence of certain compounds in present-day samples is either due to the formation mechanisms or degradation which occurred during periods of aqueous alteration or thermal metamorphism

Size-Dependent Affinity of Glycine and Its Short Oligomers to Pyrite Surface : A Model for Prebiotic Accumulation of Amino Acid Oligomers on a Mineral Surface

The interaction strength of progressively longer oligomers of glycine, (Gly), di-Gly, tri-Gly, and penta-Gly, with a natural pyrite surface was directly measured using the force mode of an atomic force microscope (AFM). In recent years, selective activation of abiotically formed amino acids on mineral surfaces, especially that of pyrite, has been proposed as an important step in many origins of life scenarios. To investigate such notions, we used AFM-based force measurements to probe possible non-covalent interactions between pyrite and amino acids, starting from the simplest amino acid, Gly. Although Gly itself interacted with the pyrite surface only weakly, progressively larger unbinding forces and binding frequencies were obtained using oligomers from di-Gly to penta-Gly. In addition to an expected increase of the configurational entropy and size-dependent van der Waals force, the increasing number of polar peptide bonds, among others, may be responsible for this observation. The effect of chain length was also investigated by performing similar experiments using L-lysine vs. poly-L-lysine (PLL), and L-glutamic acid vs. poly-L-glutamic acid. The results suggest that longer oligomers/polymers of amino acids can be preferentially adsorbed on pyrite surfaces

The Post-COVID-19 Era: Interdisciplinary Demands of Contagion Surveillance Mass Spectrometry for Future Pandemics

Mass spectrometry (MS) can become a potentially useful instrument type for aerosol, droplet and fomite (ADF) contagion surveillance in pandemic outbreaks, such as the ongoing SARS-CoV-2 pandemic. However, this will require development of detection protocols and purposing of instrumentation for in situ environmental contagion surveillance. These approaches include: (1) enhancing biomarker detection by pattern recognition and machine learning; (2) the need for investigating viral degradation induced by environmental factors; (3) representing viral molecular data with multidimensional data transforms, such as van Krevelen diagrams, that can be repurposed to detect viable viruses in environmental samples; and (4) absorbing engineering attributes for developing contagion surveillance MS from those used for astrobiology and chemical, biological, radiological, nuclear (CBRN) monitoring applications. Widespread deployment of such an MS-based contagion surveillance could help identify hot zones, create containment perimeters around them and assist in preventing the endemic-to-pandemic progression of contagious diseases

Amino Acids Generated from Hydrated Titan Tholins: Comparison with Miller-Urey Electric Discharge Products

Various analogues of Titan haze particles (termed tholins) have been made in the laboratory. In certain geologic environments on Titan, these haze particles may come into contact with aqueous ammonia (NH3) solutions, hydrolyzing them into molecules of astrobiological interest. A Titan tholin analogue hydrolyzed in aqueous NH3 at room temperature for 2.5 years was analyzed for amino acids using highly sensitive ultra-high performance liquid chromatography coupled with fluorescence detection and time-of-flight mass spectrometry (UHPLC-FDToF-MS) analysis after derivatization with a fluorescent tag. We compare here the amino acids produced from this reaction sequence with those generated from room temperature Miller-Urey (MU) type electric discharge reactions. We find that most of the amino acids detected in low temperature MU CH4N2H2O electric discharge reactions are generated in Titan simulation reactions, as well as in previous simulations of Triton chemistry. This argues that many processes provide very similar mixtures of amino acids, and possibly other types of organic compounds, in disparate environments, regardless of the order of hydration. Although it is unknown how life began, it is likely that given reducing conditions, similar materials were available throughout the early Solar System and throughout the universe to facilitate chemical evolution

Comparing the complexity of written and molecular symbolic systems

Symbolic systems (SSs) are uniquely products of living systems, such that symbolism and life may be inextricably intertwined phenomena. Within a given SS, there is a range of symbol complexity over which signaling is functionally optimized. This range exists relative to a complex and potentially infinitely large background of latent, unused symbol space. Understanding how symbol sets sample this latent space is relevant to diverse fields including biochemistry and linguistics.We quantitatively explored the graphic complexity of two biosemiotic systems: genetically encoded amino acids (GEAAs) and written language. Molecular and graphical notions of complexity are highly correlated for GEAAs and written language. Symbol sets are generally neither minimally nor maximally complex relative to their latent spaces, but exist across an objectively definable distribution, with the GEAAs having especially low complexity. The selection pressures guiding these disparate systems are explicable by symbol production and disambiguation efficiency. These selection pressures may be universal, offer a quantifiable metric for comparison, and suggest that all life in the Universe may discover optimal symbol set complexity distributions with respect to their latent spaces. If so, the “complexity” of individual components of SSs may not be as strong a biomarker as symbol set complexity distribution

Prebiotic Synthesis of Methionine and Other Sulfur-Containing Organic Compounds on the Primitive Earth: A Contemporary Reassessment Based on an Unpublished 1958 Stanley Miller Experiment

Original extracts from an unpublished 1958 experiment conducted by the late Stanley L. Miller were recently found and analyzed using modern state-of-the-art analytical methods. The extracts were produced by the action of an electric discharge on a mixture of methane (CH4), hydrogen sulfide (H2S), ammonia (NH3), and carbon dioxide (CO2). Racemic methionine was formed in significant yields, together with other sulfur-bearing organic compounds. The formation of methionine and other compounds from a model prebiotic atmosphere that contained H2S suggests that this type of synthesis is robust under reducing conditions, which may have existed either in the global primitive atmosphere or in localized volcanic environments on the early Earth. The presence of a wide array of sulfur-containing organic compounds produced by the decomposition of methionine and cysteine indicates that in addition to abiotic synthetic processes, degradation of organic compounds on the primordial Earth could have been important in diversifying the inventory of molecules of biochemical significance not readily formed from other abiotic reactions, or derived from extraterrestrial delivery

Catalytic peptide hydrolysis by mineral surface: Implications for prebiotic chemistry

Abstract The abiotic polymerization of amino acids may have been important for the origin of life, as peptides may have been components of the first self-replicating systems. Though amino acid concentrations in the primitive oceans may have been too dilute for significant oligomerization to occur, mineral surface adsorption may have provided a concentration mechanism. As unactivated amino acid polymerization is thermodynamically unfavorable and kinetically slow in aqueous solution, we studied mainly the reverse reaction of polymer degradation to measure the impact of mineral surface catalysis on peptide bonds. Aqueous glycine (G), diglycine (GG), diketopiperazine (DKP), and triglycine (GGG) were reacted with minerals (calcite, hematite, montmorillonite, pyrite, rutile, or amorphous silica) in the presence of 0.05 M, pH 8.1, KHCO 3 buffer and 0.1 M NaCl as background electrolyte in a thermostatted oven at 25, 50 or 70°C. Below 70°C, reaction kinetics were too sluggish to detect catalytic activity over amenable laboratory time-scales. Minerals were not found to have measurable effects on the degradation or elongation of G, GG or DKP at 70°C in solution. At 70°C pyrite was the most catalytic mineral with detectible effects on the degradation of GGG, although several others also displayed catalytic behavior. GGG degraded $1.5-4 times faster in the presence of pyrite than in control reactions, depending on the ratio of solution concentration to mineral surface area. The rate of pyrite catalysis of GGG hydrolysis was found to be saturable, suggesting the presence of discrete catalytic sites on the mineral surface. The mineral-catalyzed degradation of GGG appears to occur via a GGG ? DKP + G mechanism, rather than via GGG ? GG + G, as in solution-phase reactions. These results are compatible with many previous findings and suggest that minerals may have assisted in peptide synthesis in certain geological settings, specifically by speeding the approach to equilibrium in environments where amino acids were already highly concentrated, but that minerals may not significantly alter the expected solution-phase equilibria. Thus the abiotic synthesis of long peptides may have required activating agents, dry heating at higher temperatures, or some form of phase separation

Deep Earth carbon reactions through time and space

The authors acknowledge partial support from the Sloan Foundation grant G-2016-7157.Reactions involving carbon in the deep Earth have limited manifestation on Earth’s surface, yet they have played a critical role in the evolution of our planet. The metal-silicate partitioning reaction promoted carbon capture during Earth’s accretion and may have sequestered substantial carbon in Earth’s core. The freezing reaction involving iron-carbon liquid could have contributed to the growth of Earth’s inner core and the geodynamo. The redox melting/freezing reaction largely controls the movement of carbon in the modern mantle, and reactions between carbonates and silicates in the deep mantle also promote carbon mobility. The ten-year activity of the Deep Carbon Observatory has made important contributions to our knowledge of how these reactions are involved in the cycling of carbon throughout our planet, both past and present, and helped to identify gaps in our understanding that motivate and give direction to future studies.Publisher PDFPeer reviewe

Life-Detection Technologies for the Next Two Decades

Since its inception six decades ago, astrobiology has diversified immensely to encompass several scientific questions including the origin and evolution of Terran life, the organic chemical composition of extraterrestrial objects, and the concept of habitability, among others. The detection of life beyond Earth forms the main goal of astrobiology, and a significant one for space exploration in general. This goal has galvanized and connected with other critical areas of investigation such as the analysis of meteorites and early Earth geological and biological systems, materials gathered by sample-return space missions, laboratory and computer simulations of extraterrestrial and early Earth environmental chemistry, astronomical remote sensing, and in-situ space exploration missions. Lately, scattered efforts are being undertaken towards the R&D of the novel and as-yet-space-unproven life-detection technologies capable of obtaining unambiguous evidence of extraterrestrial life, even if it is significantly different from Terran life. As the suite of space-proven payloads improves in breadth and sensitivity, this is an apt time to examine the progress and future of life-detection technologies.Comment: 6 pages, the white paper was submitted to and cited by the National Academy of Sciences in support of the Astrobiology Science Strategy for the Search for Life in the Univers