Origin of Terrestrial Bioorganic Homochirality and Symmetry Breaking in the Universe

Xeno Amino Acids: A Look into Biochemistry as We Do Not Know It

Would another origin of life resemble Earth's biochemical use of amino acids? Here, we review current knowledge at three levels: (1) Could other classes of chemical structure serve as building blocks for biopolymer structure and catalysis? Amino acids now seem both readily available to, and a plausible chemical attractor for, life as we do not know it. Amino acids thus remain important and tractable targets for astrobiological research. (2) If amino acids are used, would we expect the same L-alpha-structural subclass used by life? Despite numerous ideas, it is not clear why life favors L-enantiomers. It seems clearer, however, why life on Earth uses the shortest possible (alpha-) amino acid backbone, and why each carries only one side chain. However, assertions that other backbones are physicochemically impossible have relaxed into arguments that they are disadvantageous. (3) Would we expect a similar set of side chains to those within the genetic code? Many plausible alternatives exist. Furthermore, evidence exists for both evolutionary advantage and physicochemical constraint as explanatory factors for those encoded by life. Overall, as focus shifts from amino acids as a chemical class to specific side chains used by post-LUCA biology, the probable role of physicochemical constraint diminishes relative to that of biological evolution. Exciting opportunities now present themselves for laboratory work and computing to explore how changing the amino acid alphabet alters the universe of protein folds. Near-term milestones include: (a) expanding evidence about amino acids as attractors within chemical evolution; (b) extending characterization of other backbones relative to biological proteins; and (c) merging computing and laboratory explorations of structures and functions unlocked by xeno peptides.

Chiral selectivity vs. noise in spontaneous mirror symmetry breaking

Mirror symmetry breaking bifurcations, that occur in nonlinear chemical systems leading to final chiral states with very large enantiomeric excess, can be exploited as an efficient chiral signal selector for even the smallest chiral polarizations. This effect of the chiral polarization requires the system's capacity for overcoming thermal noise, which is manifested as fluctuating reaction rate constants. Therefore, we investigate the chiral selectivity across a range of tiny parity-violating energy differences (PVED) in the presence of inevitable non-equilibrium temperature fluctuations. We use a stochastic differential equation simulation methodology (Ito process) that serves as a valuable tool in open systems for identifying the thresholds at which the chiral force induces chiral selectivity in the presence of non-equilibrium temperature fluctuations. This approach enables us to include and analyze chiral selectivity in the presence of other types of fluctuations, such as perturbations in the rate of fluid flow into and out of the reactor and in the clamped input concentrations. These concepts may be of practical interest (i.e., spontaneous deracemizations) but are also useful for a better understanding of the general principles governing the emergence of biological homochirality.

Fundamental Cause of Bio-Chirality: Space-Time Symmetry—Concept Review

The search for fundamental determinants of bio-molecular chirality is a hot topic in biology, clarifying the meaning of evolution and the enigma of life’s origin. The question of origin may be resolved assuming that non-biological and biological entities obey nature’s universal laws grounded on space-time symmetry (STS) and space-time relativity (SPR). The fabric of STS is our review’s primary subject. This symmetry, encompassing the behavior of elementary particles and galaxy structure, imposes its fundamental laws on all hierarchical levels of the biological world. From the perspective of STS, objects across spatial scales may be classified as chiral or achiral concerning a specific space-related symmetry transformation: mirror reflection. The chiral object is not identical (i.e., not superimposable) to its mirror image. In geometry, distinguish two kinds of chiral objects. The first one does not have any reflective symmetry elements (a point or plane of symmetry) but may have rotational symmetry axes (dissymmetry). The second one does not have any symmetry elements (asymmetry). As the form symmetry deficiency, Chirality is the critical structural feature of natural systems, including sub-atomic particles and living matter. According to the Standard Model (SM) theory and String Theory (StrT), elementary particles associated with the four fundamental forces of nature determine the existence of micro- and galaxy scales of nature. Therefore, the inheritance of molecular symmetry from the symmetry of elementary particles indicates a bi-directional (internal [(micro-scale) and external (galaxy sale)] causal pathway of prevalent bio-chirality. We assume that the laws of the physical world impact the biological matter’s appearance through both extremities of spatial dimensions. The extended network of multi-disciplinary experimental evidence supports this hypothesis. However, many experimental results are derived and interpreted based on the narrow-view prerogative and highly specific terminology. The current review promotes a holistic approach to experimental results in two fast-developing, seemingly unrelated, divergent branches of STS and biological chirality. The generalized view on the origin of prevalent bio-molecular chirality is necessary for understanding the link between a diverse range of biological events. The chain of chirality transfer links ribosomal protein synthesis, cell morphology, and neuronal signaling with the laterality of cognitive functions.

Possible chemical and physical scenarios towards biological homochirality

The single chirality of biological molecules in terrestrial biology raises more questions than certitudes about its origin. The emergence of biological homochirality (BH) and its connection with the appearance of life have elicited a large number of theories related to the generation, amplification and preservation of a chiral bias in molecules of life under prebiotically relevant conditions. However, a global scenario is still lacking. Here, the possibility of inducing a significant chiral bias "from scratch", i.e. in the absence of pre-existing enantiomerically-enriched chemical species, will be considered first. It includes phenomena that are inherent to the nature of matter itself, such as the infinitesimal energy difference between enantiomers as a result of violation of parity in certain fundamental interactions, and physicochemical processes related to interactions between chiral organic molecules and physical fields, polarized particles, polarized spins and chiral surfaces. The spontaneous emergence of chirality in the absence of detectable chiral physical and chemical sources has recently undergone significant advances thanks to the deracemization of conglomerates through Viedma ripening and asymmetric auto-catalysis with the Soai reaction. All these phenomena are commonly discussed as plausible sources of asymmetry under prebiotic conditions and are potentially accountable for the primeval chiral bias in molecules of life. Then, several scenarios will be discussed that are aimed to reflect the different debates about the emergence of BH: extra-terrestrial or terrestrial origin (where?), nature of the mechanisms leading to the propagation and enhancement of the primeval chiral bias (how?) and temporal sequence between chemical homochirality, BH and life emergence (when?). Intense and ongoing theories regarding the emergence of optically pure molecules at different moments of the evolution process towards life, i.e. at the levels of building blocks of Life, of the instructed or functional polymers, or even later at the stage of more elaborated chemical systems, will be critically discussed. The underlying principles and the experimental evidence will be commented for each scenario with particular attention on those leading to the induction and enhancement of enantiomeric excesses in proteinogenic amino acids, natural sugars, and their intermediates or derivatives. The aim of this review is to propose an updated and timely synopsis in order to stimulate new efforts in this interdisciplinary field.

Possibility of chiral recognition by adsorption on enantiomorphous crystals: the impact of crystal surface polarity

The enantioselectivity provided by hippuric acid and phloroglucinol crystals, obtained under Viedma ripening, was studied by the adsorption of menthol enantiomers from solutions and the adsorption of limonene and α-pinene enantiomers from vapors.

Broken symmetry between RNA enantiomers in a crystal lattice

Explaining the origin of the homochirality of biological molecules requires a mechanism of disrupting the natural equilibrium between enantiomers and amplifying the initial imbalance to significant levels. Authors of existing models have sought an explanation in the parity-breaking weak nuclear force, in some selectively acting external factor, or in random fluctuations that subsequently became amplified by an autocatalytic process. We have obtained crystals in which l- and d-enantiomers of short RNA duplexes assemble in an asymmetric manner. These enantiomers make different lattice contacts and have different exposures to water and metal ions present in the crystal. Apparently, asymmetry between enantiomers can arise upon their mutual interactions and then propagate via crystallization. Asymmetric racemic compounds are worth considering as possible factors in symmetry breaking and enantioenrichment that took place in the early biosphere.

"Smart Decomposition" of Cyclic Alanine-Alanine Dipeptide by VUV Radiation: A Seed for the Synthesis of Biologically Relevant Species

A combined experimental and theoretical study shows how the interaction of VUV radiation with cyclo-(alanine-alanine), one of the 2,5-diketopiperazines (DKPs), produces reactive oxazolidinone intermediates. The theoretical simulations reveal that the interaction of these intermediates with other neutral and charged fragments, released in the molecular decomposition, leads either to the reconstruction of the cyclic dipeptide or to the formation of longer linear peptide chains. These results may explain how DKPs could have, on one hand, survived hostile chemical environments and, on the other, provided the seed for amino acid polymerization. Shedding light on the mechanisms of production of such prebiotic building blocks is of paramount importance to understanding the abiotic synthesis of relevant biologically active compounds.

Resonance in Chirogenesis and Photochirogenesis: Colloidal Polymers Meet Chiral Optofluidics

Metastable colloids made of crystalline and/or non-crystalline matters render abilities of photonic resonators susceptible to chiral chemical and circularly polarized light sources. By assuming that μm-size colloids and co-colloids consisting of π- and/or σ-conjugated polymers dispersed into an optofluidic medium are artificial models of open-flow, non-equilibrium coacervates, we showcase experimentally resonance effects in chirogenesis and photochirogenesis, revealed by gigantic boosted chiroptical signals as circular dichroism (CD), optical rotation dispersion, circularly polarized luminescence (CPL), and CPL excitation (CPLE) spectral datasets. The resonance in chirogenesis occurs at very specific refractive indices (RIs) of the surrounding medium. The chirogenesis is susceptible to the nature of the optically active optofluidic medium. Moreover, upon an excitation-wavelength-dependent circularly polarized (CP) light source, a fully controlled absolute photochirogenesis, which includes all chiroptical generation, inversion, erase, switching, and short-/long-lived memories, is possible when the colloidal non-photochromic and photochromic polymers are dispersed in an achiral optofluidic medium with a tuned RI. The hand of the CP light source is not a determining factor for the product chirality. These results are associated with my experience concerning amphiphilic polymerizable colloids, in which, four decades ago, allowed proposing a perspective that colloids are connectable to light, polymers, helix, coacervates, and panspermia hypotheses, nuclear physics, biology, radioisotopes, homochirality question, first life, and cosmology.

Contributions of a modified electrodynamics to the molecular biochirality

In this paper, we investigate the physical basis behind the molecular biochirality from the computation of a parity violation energy difference (PVED) in enantiomers of organic molecules (e.g., amino acids, which occur as levogyrous-type in nature), by considering the influence of fundamental interactions beyond the standard model of elementary particles and interactions. Particularly, we study the role of a 4-D Chern-Simons theory at the origin of this PVED, the Carroll-Field-Jackiw electrodynamics, which violates both Lorentz and parity symmetries. Then, we consider terrestrial and Jovian scenarios where the influence of a modified (effective) magnetic field generated by the planets on the molecules is taken into account in the calculation of PVED. Besides this quantity, we also calculate the relative quantity excess of an enantiomer over the other in a thermal bath. Finally, we compare the obtained results with those ones from other models based on fundamental interactions.

Chiral Dualism as an Instrument of Hierarchical Structure Formation in Molecular Biology

The origin of chiral asymmetry in biology has attracted the attention of the research community throughout the years. In this paper we discuss the role of chirality and chirality sign alternation (L–D–L–D in proteins and D–L–D–L in DNA) in promoting self-organization in biology, starting at the level of single molecules and continuing to the level of supramolecular assemblies. In addition, we also discuss chiral assemblies in solutions of homochiral organic molecules. Sign-alternating chiral hierarchies created by proteins and nucleic acids are suggested to create the structural basis for the existence of selected mechanical degrees of freedom required for conformational dynamics in enzymes and macromolecular machines.

Interactions of Single Particle with Organic Matters: A Facile Bottom-Up Approach to Low Dimensional Nanostructures

A particle induces a pack of chemical reactions in nanospace: chemical reactions confined into extremely small space provide an ultimate technique for the nanofabrication of organic matter with a variety of functions. Since the discovery of particle accelerators, an extremely high energy density can be deposited, even by a single isolated particle with MeV-ordered kinetic energy. However, this was considered to cause severe damages to organic molecules due to its relatively small bond energies, and lack of ability to control the reactions precisely to form the structures while retaining physico-chemical molecular functionalities. Practically, the severely damaged area along a particle trajectory: a core of a particle track has been simply visualized for the detection/dosimetry of an incident particle to the matters, or been removed to lead nanopores and functionalized by refilling/grafting of fresh organic/inorganic materials. The use of intra-track reactions in the so-called “penumbra” or “halo” area of functional organic materials has been realized and provided us with novel and facile protocols to provide low dimensional nano-materials with perfect size controllability in the 21st century. These protocols are now referred to as single particle nanofabrication technique (SPNT) and/or single particle triggered linear polymerization technique (STLiP), paving the way towards a new approach for nanomaterials with desired functionalities from original molecules. Herein, we report on the extremely wide applicability of SPNT/STLiP protocols for the future development of materials for opto-electronic, catalytic, and biological applications among others.