Mechanochemical Prebiotic Peptide Bond Formation*

Prebiotic Formation of Peptides Through Bubbling and Arc Plasma

The abiotic synthesis of peptides, widely regarded as one of the key chemical reactions on the prebiotic Earth, is thermodynamically constrained in solution. Herein, a simulation of the lightning phenomenon on the sea surface using bubble bursting and arc plasma under ambient conditions enables dipeptide formation of six amino acids with conversion ratios ranging from 2.6 % to 25.5 %. Additionally, we observed the formation of biologically active tripeptides and investigated the stereoselectivity of the dipeptide formation reaction. By utilizing a mixture of 20 amino acids in the reaction, 102 possible dipeptides were generated. These results establish experimental constructions to mimic achievable prebiotic conditions and provide a credible pathway for endogenous biopolymer synthesis on prebiotic Earth.

Base-pairing of uracil and 2,6-diaminopurine: from cocrystals to photoreactivity

We show that the non-canonical nucleobase 2,6-diaminopurine (D) spontaneously base pairs with uracil (U) in water and the solid state without the need to be attached to the ribose-phosphate backbone. Depending on the reaction conditions, D and U assemble in thermodynamically stable hydrated and anhydrated D-U base-paired cocrystals. Under UV irradiation, an aqueous solution of D-U base-pair undergoes photochemical degradation, while a pure aqueous solution of U does not. Our simulations suggest that D may trigger the U photodimerization and show that complementary base-pairing modifies the photochemical properties of nucleobases, which might have implications for prebiotic chemistry.

Shock-Induced Degradation of Guanosine and Uridine Promoted by Nickel and Carbonate: Potential Applications

Experimental studies of the degradation of two ribonucleosides (guanosine and uridine) were carried out by making use of mechanochemistry. Mechanochemical experiments reveal the decomposition of guanosine and uridine, promoted by nickel(II) and carbonate ions, into guanine and uracil, respectively. These nucleobases were identified by HPLC and 1H NMR spectroscopy (this applied only to uracil). Additionally, density-functional theory (DFT) methodologies were used to probe the energetic viability of several degradation pathways, including in the presence of the abovementioned ions. Three mechanisms were analysed via ribose ring-opening: dry, single-molecule water-assisted, and metal-assisted, wherein the last two mechanisms confirmed the mechanochemical degradation of both ribonucleosides into respective nucleobase moieties. These results can contribute to an astrobiological interpretation of the extraterrestrial sample's contents.

Ball milling synthesis of S-quinolyl xanthates via coupling of haloquinolines with potassium O-alkyl xanthates

An environmentally benign protocol that provides various S-quinolyl xanthates via a ball milling enabled cross coupling reaction of haloquinolines and readily available potassium O-alkyl xanthates is first reported. The reaction proceeded well under mild, transition metal- and solvent-free conditions, making it an attractive method for the introduction of xanthates into the quinoline scaffold.

Supramolecular intermediates in thermo-mechanochemical direct amidations

We present a solvent-free thermo-mechanochemical approach for the direct coupling of carboxylic acids and amines, which avoids activators and additives. Detailed analysis of the reactions by ex situ and in situ monitoring methods led to the observation, isolation, and characterisation of multicomponent crystalline intermediates that precede the formation of amides. We applied our methodology for the quantitative synthesis of the active pharmaceutical ingredient moclobemide.

Tensorial stress-plastic strain fields in α - ω Zr mixture, transformation kinetics, and friction in diamond-anvil cell

Various phenomena (phase transformations (PTs), chemical reactions, microstructure evolution, strength, and friction) under high pressures in diamond-anvil cell are strongly affected by fields of stress and plastic strain tensors. However, they could not be measured. Here, we suggest coupled experimental-analytical-computational approaches utilizing synchrotron X-ray diffraction, to solve an inverse problem and find fields of all components of stress and plastic strain tensors and friction rules before, during, and after α-ω PT in strongly plastically predeformed Zr. Results are in good correspondence with each other and experiments. Due to advanced characterization, the minimum pressure for the strain-induced α-ω PT is changed from 1.36 to 2.7 GPa. It is independent of the plastic strain before PT and compression-shear path. The theoretically predicted plastic strain-controlled kinetic equation is verified and quantified. Obtained results open opportunities for developing quantitative high-pressure/stress science, including mechanochemistry, synthesis of new nanostructured materials, geophysics, astrogeology, and tribology.

Mechanochemical Mediated Coexistence of B←N Coordination and Hydrogen Bonding

Mechanochemistry afforded a photoactive cocrystal via coexisting (B)O-H⋅⋅⋅N hydrogen bonds and B←N coordination. Specifically, solvent-free mechanochemical ball mill grinding and liquid-assisted grinding of a boronic acid and an alkene resulted in mixtures of hydrogen-bonded and coordinated complexes akin to mixtures of noncovalent complexes that can be obtained in solution in equilibria processes. The alkenes of the hydrogen-bonded assembly undergo an intermolecular [2+2] photodimerization in quantitative conversion, effectively reporting the outcome of the self-assembly processes. Our results suggest that interplay involving noncovalent bonds subjected to mechanochemical conditions can lead to functional solids where, in the current case, the structure composed of the weaker hydrogen bonding interactions predominates.

Linnaeite Mineral for NIR Light-Triggered Disruption of Alzheimer's Pore-Forming Aβ Oligomers

Minerals in the Earth's crust have contributed to the natural functioning of ecosystems via biogeochemical interactions. Linnaeite is a cobalt sulfide mineral with a cubic spinel structure that promotes charge transfer reactions with its surroundings. Here we report the hidden feature of linnaeite mineral to dissociate Alzheimer's β-amyloid (Aβ) oligomers under near-infrared (NIR) light irradiation. Alzheimer's disease (AD) is a neurodegenerative disorder caused by the abnormal accumulation of self-assembled Aβ peptides in the elderly brain. The β-sheet structured pore-forming Aβ oligomer (βPFO) is the most neurotoxic species exacerbating the symptoms of AD. However, a therapeutic agent that is capable of inactivating βPFO has not yet been developed. Our microscopic and spectroscopic analysis results have revealed that NIR-excited linnaeite mineral can modulate the structure of βPFO by inducing oxidative modifications. We have verified that linnaeite mineral is biocompatible with and has a mitigating effect on the neurotoxicity of βPFO. This study suggests that minerals in nature have potential as drugs to reduce AD pathology.

Advancing mechanochemical synthesis by combining milling with different energy sources

Owing to its efficiency and unique reactivity, mechanochemical processing of bulk solids has developed into a powerful tool for the synthesis and transformation of various classes of materials. Nevertheless, mechanochemistry is primarily based on simple techniques, such as milling in comminution devices. Recently, mechanochemical reactivity has started being combined with other energy sources commonly used in solution-based chemistry. Milling under controlled temperature, light irradiation, sound agitation or electrical impulses in newly developed experimental setups has led to reactions not achievable by conventional mechanochemical processing. This Perspective describes these unique reactivities and the advances in equipment tailored to synthetic mechanochemistry. These techniques - thermo-mechanochemistry, sono-mechanochemistry, electro-mechanochemistry and photo-mechanochemistry - represent a notable advance in modern mechanochemistry and herald a new level of solid-state reactivity: mechanochemistry 2.0.

A Physicochemical Consideration of Prebiotic Microenvironments for Self-Assembly and Prebiotic Chemistry

The origin of life on Earth required myriads of chemical and physical processes. These include the formation of the planet and its geological structures, the formation of the first primitive chemicals, reaction, and assembly of these primitive chemicals to form more complex or functional products and assemblies, and finally the formation of the first cells (or protocells) on early Earth, which eventually evolved into modern cells. Each of these processes presumably occurred within specific prebiotic reaction environments, which could have been diverse in physical and chemical properties. While there are resources that describe prebiotically plausible environments or nutrient availability, here, we attempt to aggregate the literature for the various physicochemical properties of different prebiotic reaction microenvironments on early Earth. We introduce a handful of properties that can be quantified through physical or chemical techniques. The values for these physicochemical properties, if they are known, are then presented for each reaction environment, giving the reader a sense of the environmental variability of such properties. Such a resource may be useful for prebiotic chemists to understand the range of conditions in each reaction environment, or to select the medium most applicable for their targeted reaction of interest for exploratory studies.

Mechanochemistry: New Tools to Navigate the Uncharted Territory of "Impossible" Reactions

Mechanochemical transformations have made chemists enter unknown territories, forcing a different chemistry perspective. While questioning or revisiting familiar concepts belonging to solution chemistry, mechanochemistry has broken new ground, especially in the panorama of organic synthesis. Not only does it foster new "thinking outside the box", but it also has opened new reaction paths, allowing to overcome the weaknesses of traditional chemistry exactly where the use of well-established solution-based methodologies rules out progress. In this Review, the reader is introduced to an intriguing research subject not yet fully explored and waiting for improved understanding. Indeed, the study is mainly focused on organic transformations that, although impossible in solution, become possible under mechanochemical processing conditions, simultaneously entailing innovation and expanding the chemical space.

R-Group stabilization in methylated formamides observed by resonant inelastic X-ray scattering

The inherent stability of methylated formamides is traced to a stabilization of the deep-lying σ-framework by resonant inelastic X-ray scattering at the nitrogen K-edge. Charge transfer from the amide nitrogen to the methyl groups underlie this stabilization mechanism that leaves the aldehyde group essentially unaltered and explains the stability of secondary and tertiary amides.

Nanostructured silicate catalysts for environmentally benign Strecker-type reactions: status quo and quo vadis

Chemical processes are usually catalytic transformations. The use of catalytic reagents can reduce the reaction temperature, decrease reagent-based waste, and enhance the selectivity of a reaction potentially avoiding unwanted side reactions leading to green technology. Chemical processes are also frequently based on multicomponent reactions (MCRs) that possess evident improvements over multistep processes. Both MCRs and catalysis tools are the most valuable principles of green chemistry. Among diverse MCRs, the three-component Strecker reaction (S-3-CR) is a particular transformation conducive to the formation of valuable bifunctional building blocks (α-amino nitriles) in organic synthesis, medicinal chemistry, drug research, and organic materials science. To be a practical synthetic tool, the S-3-CR must be achieved using alternative energy input systems, safe reaction media, and effective catalysts. These latter reagents are now deeply associated with nanoscience and nanocatalysis. Continuously developed, nanostructured silicate catalysts symbolize green pathways in our quest to attain sustainability. Studying and developing nanocatalyzed S-3-CR condensations as an important model will be suitable for achieving the current green mission. This critical review aims to highlight the advances in the development of nanostructured catalysts for technologically important Strecker-type reactions and to analyze this progress from the viewpoint of green and sustainable chemistry.

Towards Predicting the Sequential Appearance of Zeolitic Imidazolate Frameworks Synthesized by Mechanochemistry

We use computational materials methods to study the sequential appearance of zinc-based zeolitic imidazolate frameworks (ZIFs) generated in the mechanochemical conversion process. We consider nine ZIF topologies, namely RHO, ANA, QTZ, SOD, KAT, DIA, NEB, CAG and GIS, combined with the two ligands 2-methylimidazolate and 2-ethylimidazolate. Of the 18 combinations obtained, only six (three for each ligand) were actually observed during the mechanosynthesis process. Energy and porosity calculations based on density functional theory, in combination with the Ostwald rule of stages, were found to be insufficient to distinguish the experimentally observed ZIFs. We then show, using classical molecular dynamics, that only ZIFs withstanding quasi-hydrostatic pressure P ≥ 0.3 GPa without being destroyed were observed in the laboratory. This finding, along with the requirement that successive ZIFs be generated with decreasing porosity and/or energy, provides heuristic rules for predicting the sequences of mechanically generated ZIFs for the two ligands considered.

Chirality in Organic and Mineral Systems: A Review of Reactivity and Alteration Processes Relevant to Prebiotic Chemistry and Life Detection Missions

Chirality is a central feature in the evolution of biological systems, but the reason for biology’s strong preference for specific chiralities of amino acids, sugars, and other molecules remains a controversial and unanswered question in origins of life research. Biological polymers tend toward homochiral systems, which favor the incorporation of a single enantiomer (molecules with a specific chiral configuration) over the other. There have been numerous investigations into the processes that preferentially enrich one enantiomer to understand the evolution of an early, racemic, prebiotic organic world. Chirality can also be a property of minerals; their interaction with chiral organics is important for assessing how post-depositional alteration processes could affect the stereochemical configuration of simple and complex organic molecules. In this paper, we review the properties of organic compounds and minerals as well as the physical, chemical, and geological processes that affect organic and mineral chirality during the preservation and detection of organic compounds. We provide perspectives and discussions on the reactions and analytical techniques that can be performed in the laboratory, and comment on the state of knowledge of flight-capable technologies in current and future planetary missions, with a focus on organics analysis and life detection.

Mechanochemically-Assisted Synthesis of Polyimides

Polyimides were obtained in 99 % yield in under 1 h through the "beat and heat" approach, involving solvent-free vibrational ball milling and a thermal treatment step. The influence of a plethora of additives was explored, such as Lewis acids, Lewis bases, and dehydrating agents, and the mechanochemical reaction was identified to run via a polyamic acid intermediate. The protocol was adopted to a range of substrates inaccessible through solution-based processes, including perylene tetracarboxylic acid dianhydride and melamine. Furthermore, quantum chemical calculations were conducted to identify the water removal as the crucial step in the reaction mechanism. The presented method is substantially faster and more versatile than the solution-based process.

Zirconium oxo clusters as discrete molecular catalysts for the direct amide bond formation

A discrete dodecanuclear Zr oxo cluster catalyzed the direct formation of amide bonds without the need of water scavenging or dry reactions conditions showcasing the potential of these molecular clusters to become a new class of efficient catalysts.

From amino acid mixtures to peptides in liquid sulphur dioxide on early Earth

The formation of peptide bonds is one of the most important biochemical reaction steps. Without the development of structurally and catalytically active polymers, there would be no life on our planet. However, the formation of large, complex oligomer systems is prevented by the high thermodynamic barrier of peptide condensation in aqueous solution. Liquid sulphur dioxide proves to be a superior alternative for copper-catalyzed peptide condensations. Compared to water, amino acids are activated in sulphur dioxide, leading to the incorporation of all 20 proteinogenic amino acids into proteins. Strikingly, even extremely low initial reactant concentrations of only 50 mM are sufficient for extensive peptide formation, yielding up to 2.9% of dialanine in 7 days. The reactions carried out at room temperature and the successful use of the Hadean mineral covellite (CuS) as a catalyst, suggest a volcanic environment for the formation of the peptide world on early Earth.

Peptide bond formation is one of the key biochemical reactions needed for the formation of life, but is thermodynamically unfavoured in water. Here, the authors report on the possibility of complex oligomer formation in liquid sulphur dioxide which may have existed on early Earth at the emergence of life.

Direct Amidation of Esters by Ball Milling*

The direct mechanochemical amidation of esters by ball milling is described. The operationally simple procedure requires an ester, an amine, and substoichiometric KOtBu and was used to prepare a large and diverse library of 78 amide structures with modest to excellent efficiency. Heteroaromatic and heterocyclic components are specifically shown to be amenable to this mechanochemical protocol. This direct synthesis platform has been applied to the synthesis of active pharmaceutical ingredients (APIs) and agrochemicals as well as the gram-scale synthesis of an active pharmaceutical, all in the absence of a reaction solvent.