Ribose Accumulation in Borate-Rich Prebiotic Environments.

The phosphorylation of nucleosides and their polymerization are crucial issues concerning the origin of life. The question of how these plausible chemical processes took place in the prebiotic Earth is still perplexing, despite several studies that have attempted to explain these prebiotic processes. The purpose of this article is to review these chemical reactions with respect to chemical evolution in the primeval Earth. Meanwhile, from our perspective, the chiral properties and selection of biomolecules should be considered in the prebiotic chemical origin of life, which may contribute to further research in this field to some extent.

Toward abiotic sugar synthesis from CO2 electrolysis

Complex reaction mixtures, like those postulated on early Earth, present an analytical challenge because of the number of components, their similarity, and vastly different concentrations. Interpreting the reaction networks is typically based on simplified or partial data, limiting our insight. We present a new approach based on online monitoring of reaction mixtures formed by the formose reaction by ion-mobility-separation mass-spectrometry. Monitoring the reaction mixtures led to large data sets that we analyzed by non-negative matrix factorization, thereby identifying ion-signal groups capturing the time evolution of the network. The groups comprised ≈300 major ion signals corresponding to sugar-calcium complexes formed during the formose reaction. Multivariate analysis of the kinetic profiles of these complexes provided an overview of the interconnected kinetic processes in the solution, highlighting different pathways for sugar growth and the effects of different initiators on the initial kinetics. Reconstructing the network's topology further, we revealed so far unnoticed fast retro-aldol reaction of ketoses, which significantly affects the initial reaction dynamics. We also detected the onset of sugar-backbone branching for C6 sugars and cyclization reactions starting for C5 sugars. This top-down analytical approach opens a new way to analyze complex dynamic mixtures online with unprecedented coverage and time resolution.

ConspectusCentral to the quest of understanding the emergence of life isto uncover the role of metals, particularly iron, in shaping prebioticchemistry. Iron, as the most abundant of the accessible transitionmetals on the prebiotic Earth, played a pivotal role in early biochemicalprocesses and continues to be indispensable to modern biology. Here,we discuss our recent contributions to probing the plausibility ofprebiotic complexes with iron, including heme and iron–sulfurclusters, in mediating chemistry beneficial to a protocell. Laboratoryexperiments and spectroscopic findings suggest plausible pathways,often facilitated by UV light, for the synthesis of heme and iron–sulfurclusters. Once formed, heme displays catalytic, peroxidase-like activitywhen complexed with amphiphiles. This activity could have been beneficialin two ways. First, heme could have catalytically removed a molecule(H2O2) that could have had degradative effectson a protocell. Second, heme could have helped in the synthesis ofthe building blocks of life by coupling the reduction of H2O2 with the oxidation of organic substrates. The necessityof amphiphiles to avoid the formation of inactive complexes of hemeis telling, as the modern-day electron transport chain possesses hemeembedded within a lipid membrane. Conversely, prebiotic iron–sulfurpeptides have yet to be reported to partition into lipid membranes,nor have simple iron–sulfur peptides been found to be capableof participating in the synthesis of organic molecules. Instead, iron–sulfurpeptides span a wide range of reduction potentials complementary tothe reduction potentials of hemes. The reduction potential of iron–sulfurpeptides can be tuned by the type of iron–sulfur cluster formed,e.g., [2Fe-2S] versus [4Fe-4S], or by the substitution of ligandsto the metal center. Since iron–sulfur clusters easily formupon stochastic encounters between iron ions, hydrosulfide, and smallorganic molecules possessing a thiolate, including peptides, the likelihoodof soluble iron–sulfur clusters seems to be high. What remainschallenging to determine is if iron–sulfur peptides participatedin early prebiotic chemistry or were recruited later when protocellularmembranes evolved that were compatible with the exploitation of electrontransfer for the storage of energy as a proton gradient. This problemmirrors in some ways the difficulty in deciphering the origins ofmetabolism as a whole. Chemistry that resembles some facets of extantmetabolism must have transpired on the prebiotic Earth, but thereare few clues as to how and when such chemistry was harnessed to supporta (proto)cell. Ultimately, unraveling the roles of hemes and iron–sulfurclusters in prebiotic chemistry promises to deepen our understandingof the origins of life on Earth and aids the search for life elsewherein the universe.

Proteins function by sampling conformational sub-states within a given fold. How this configurational flexibility and the associated protein dynamics affect the rates of chemical reactions are open questions. The difficulty in exploring this issue arises in part from the need to identify the relevant nuclear modes affecting the reaction rate for each characteristic time-scale of the reaction. Proteins as reaction media display a hierarchy of such nuclear modes, of increasingly collective character, that produce both a broad spectrum of static fluctuations and a broad spectrum of relaxation times. In order to understand the effect of protein dynamics on reaction rates, we have chosen to study a sub-nanosecond electron transfer reaction between the bacteriopheophytin and primary quinone cofactors of the photosynthetic bacterial reaction center. We show that dynamics affects the activation barrier of the reaction through a dynamical restriction of the configurational space sampled by the protein–water solvent on the reaction time-scale. The modes which become dynamically arrested on the reaction time-scale of hundreds of picoseconds are related to elastic motions of the protein that are strongly coupled to the hydration layer of water. Several mechanistic consequences for protein electron transfer emerge from this picture. Importantly, energy parameters used to define the activation barrier of electron transfer reactions lose their direct connection to equilibrium thermodynamics and become dependent in a very direct way on the relative magnitudes of the reaction and nuclear reorganization time-scales. As a result, the energetics of protein electron transfer need to be defined on each specific reaction time-scale. This perspective offers a mechanism to optimize protein electron transfer by tuning the reaction rate to the relaxation spectrum of the reaction coordinate.

In the presence of formamide, crystal phosphate minerals may act as phosphate donors to nucleosides, yielding both 5'- and, to a lesser extent, 3'-phosphorylated forms. With the mineral Libethenite the formation of 5'-AMP can be as high as 6% of the adenosine input and last for at least 10(3) h. At high concentrations, soluble non-mineral phosphate donors (KH(2)PO(4) or 5'-CMP) afford 2'- and 2':3'-cyclic AMP in addition to 5'-and 3'-AMP. The phosphate minerals analyzed were Herderite Ca[BePO(4)F], Hureaulite Mn(2+)(5)(PO(3)(OH)(2)(PO(4))(2)(H(2)O)(4), Libethenite Cu(2+)(2)(PO(4))(OH), Pyromorphite Pb(5)(PO(4))(3)Cl, Turquoise Cu(2+)Al(6)(PO(4))(4)(OH)(8)(H(2)O)(4), Fluorapatite Ca(5)(PO(4))(3)F, Hydroxylapatite Ca(5)(PO(4))(3)OH, Vivianite Fe(2+)(3)(PO(4))(2)(H(2)O)(8), Cornetite Cu(2+)(3)(PO(4))(OH)(3), Pseudomalachite Cu(2+)(5)(PO(4))(2)(OH)(4), Reichenbachite Cu(2+)(5)(PO(4))(2)(OH)(4), and Ludjibaite Cu(2+)(5)(PO(4))(2)(OH)(4)). Based on their behavior in the formamide-driven nucleoside phosphorylation reaction, these minerals can be characterized as: 1) inactive, 2) low level phosphorylating agents, or 3) active phosphorylating agents. Instances were detected (Libethenite and Hydroxylapatite) in which phosphorylation occurs on the mineral surface, followed by release of the phosphorylated compounds. Libethenite and Cornetite markedly protect the beta-glycosidic bond. Thus, activated nucleic monomers can form in a liquid non-aqueous environment in conditions compatible with the thermodynamics of polymerization, providing a solution to the standard-state Gibbs free energy change (DeltaG degrees ') problem, the major obstacle for polymerizations in the liquid phase in plausible prebiotic scenarios.

The proposition that comet dust provided the necessary ingredients for prebiotic chemical evolution on the earth is supported in five ways: (1) comet dust contains prebiotic organics; (2) comet dust is chiral; (3) comet dust could have been brought “safely” to the earth’s surface as a consequence of its fluffy character and of fragmentation processes occurring in the earth’s vicinity; (4) the morphological as well as chemical structure of comet dust particles of 3–5 µm provide the thermodynamic basis for directed chemical organization; (5) each 3 km size comet deposited 1025 such seeds of comet dust on the prebiotic earth.

The process of delineating the origins of the chemistry of life starts with the consideration of the molecules that might have existed on prebiotic earth and extends to the discussion of potential mechanisms for assembly of these molecules into informational polymers capable of self-replication and transmittance of genetic information. At some point along this pathway, the property of single chirality emerges as the hallmark of the amino acids and sugars present in biological molecules. In the 20th century, researchers developed abstract mathematical theses for the origin of biomolecular homochirality from a presumably racemic collection of prebiotic molecules. Before the end of that century, experimental findings corroborated a number of basic features of these theoretical models, but these studies involved chemical systems without direct prebiotic relevance. Currently researchers are examining prebiotically plausible conditions that couple chemical and physical processes leading to single chirality of sugars and amino acids with subsequent chemical reactions that enhance molecular complexity. While these studies have been conducted for the most part in the context of the RNA World hypothesis, the experimental findings remain relevant to a "metabolism first" model for the origin of life. To many chemists interested in chembiogenesis, the synthesis of activated pyrimidine ribonucleotides under potentially prebiotic conditions by Sutherland's group provided a landmark demonstration of what Eschenmoser has described as "an intrinsic structural propinquity" between certain elementary chemical structures and modern biological molecules. Even while some synthetic issues for plausible prebiotic construction of RNA remain unsolved, our work has focused on coupling these synthetic advances with concepts for the evolution of biomlolecular homochirality. Drawing on our own findings as well as those from others, we present an intriguing "chicken or egg" scenario for the emergence of single chirality of sugars and amino acids. Our work incorporates both chemical and physical phenomena that allow for the amplification of a small initial imbalance of either sugars by amino acids or amino acid by sugars, suggesting that an enantioenriched chiral pool of one type of molecule could lead to a similarly enantioenriched pool of the other.

Ferrihydrite is widespread in clays, soils, and living organisms and was found on Mars. This iron-mineral could be found on the prebiotic Earth, which also contained simple monomeric amino acids. For prebiotic chemistry, it is important to understand how amino acids have an effect on the process of iron oxide formations. There are three important results in this work: (a) preconcentration of cysteine and aspartic acid, (b) formation of cystine and probably the cysteine peptide occurred during ferrihydrite syntheses, and (c) amino acids have an effect on iron oxide synthesis. For samples containing aspartic acid and cysteine, their presence on the surface or mineral structure can be confirmed by FT-IR spectra. Surface charge analysis showed a relatively high decrease for samples synthesized with cysteine. Scanning electron microscopy did not show marked morphological differences among the samples, except for the seawater sample containing cysteine, which had a lamina-shaped morphology surrounded by circular iron particles, indicating the possible formation of a cysteine structure involving iron oxide particles. The thermogravimetric analysis of the samples indicates that the presence of salts and amino acids in the synthesis of ferrihydrite has an effect on the thermal behavior of the iron oxide/amino acids and modifying the water-loss temperature. The heating of the cysteine samples, synthesized in distilled water and artificial seawater, showed several peaks of degradation of cysteine. In addition, heating of the aspartic acid samples produced the polymerization of this amino acid and peaks of degradation of it. FTIR spectra and XRD patterns did not indicate the precipitation of methionine, 2-aminoisobutyric acid, lysine, or glycine with the iron oxide formations. However, the heating of the glycine, methionine and lysine samples, synthesized in artificial seawater, showed peaks that could be attributed to the degradation of them. Then this could be an indication that these amino acids precipitate with the minerals during the syntheses. Also, the dissolution of these amino acids in artificial seawater prevents the formation of ferrihydrite.

In Chapter 11 we discussed the impact of the turbulence on the gas-phase chemistry with particular application to gaseous fuels. We also examined the problems in obtaining time-mean reaction rates for chemical reactions in the homogeneous phase. We limited our discussion to turbulent diffusion flames and noted three types of turbulence—chemistry interactions. The majority of Chapter 11 focused on Type B flames when the reaction time scale was much less than the turbulent time scale and thus the turbulence mixing process controlled the chemical reactions. All of Chapter 11 focused on gaseous fuels. An appropriate mixture fraction or conserved scalar was defined; the statistics of the turbulence were characterized by an appropriate probability density function; and the mean chemical properties were obtained by convolution over this PDF of either chemical equilibrium properties or experimental data.

A fractal-based approach to evaluate the effect of microstructure on the permeability of two-dimensional porous media

Narrow escape in composite domains forming heterogeneous networks

Obtaining efficient and robust solutions to real reacting flow problems is a challenging task in numerical simulation due to severe nonlinearities in the conservation equations and the wide range of time scales of chemical reactions. However, there are many important industrial applications for such simulations, e.g., premixed and non-premixed combustion, catalytic combustion, or materials processing. A finite volume method on unstructured, non-staggered grids is presented for the solution of two-dimensional low Mach number reacting flows. The conservation law form of the flow equations are discretized in terms of primitive variables. An artificial compressibility method is employed so that low Mach number flows can be solved economically. The equations are marched in time using an implicit extrapolation method. Numerical results are obtained for three different applications: A reaction-diffusion controlled flow in the process chamber of a chemical downstream etch system, the simulation of a premixed ozone flame, and a methane diffusion flame.

Conservative multi-implicit spectral deferred correction methods for reacting gas dynamics

Hydrogels are characterized by substantial volume changes in response to external stimuli, making them promising candidates for developing smart materials with enhanced adaptability and responsiveness. By integrating chemical reactions, hydrogels acquire dynamic and tunable responsiveness to external stimuli through chemo‐mechanical coupling, expanding their potential in emerging applications. However, capturing their transient behavior remains challenging due to the complex interplay of chemical reactions, solvent transport, and polymer network deformation. Classical theories capture equilibrium swelling but fail to describe time‐dependent phenomena. To address this, a time‐dependent continuum model is developed that explicitly couples these processes. Volume phase transition in hydrogels with homogeneous chemical reactions is investigated, then the effects of reaction kinetics on these transitions are analyzed. The coupling of these mechanisms is further explored through a study of transient mechanical instabilities. To illustrate the impact of distinct reaction and diffusion timescales, a photo‐active gripper is studied for robotic applications. Finally, a photo‐active microswimmer that exhibits non‐reciprocal motion is proposed to highlight the solvent diffusion for locomotion at the micro‐ and nano‐ scales. The work establishes that transient dynamics of chemo‐mechanical hydrogels generate functions not accessible by steady state models and provides a predictive platform for designing adaptive materials in emerging applications.