Current Organic Chemistry - Volume 17, Issue 16, 2013

This contribution gives a brief overview of the Dynamic Kinetic Stability (DKS) concept. The concept appears to offer new insights into the central questions of biology – what is life, how it emerged, how would one make it, as well as explaining in basic physicochemical terms the truly remarkable characteristics that life so clearly manifests.

Contemporary theories of the origin of life divide along the same conceptual lines as contemporary accounts of the nature of life, with small molecule theories (e.g., Wachtershauser’s iron pyrite world) corresponding to metabolic theories/definitions of life and genes-first theories (currently dominated by the RNA world) corresponding to evolutionary (e.g., chemical Darwinian) theories/ definitions of life. I discuss some difficulties faced by this general approach: First, it isn’t at all obvious that a successful theory of the origin of life will divide along the same lines as a theory of the nature of life. Second, in both cases there is the worry that signs of life are being mistakenly treated as essential to life. Third, most theories of the origin of life tend to minimize or even side step the transition from nonliving ensembles of molecules to the first proto-organisms. I close with a suggestion for dealing with some of these difficult problems.

Earth’s atmospheric composition at the time of the origin of life is not known, but it has often been suggested that chemical transformation of reactive species in the atmosphere was a significant source of prebiotic organic molecules. Experimental and theoretical studies over the past half century have shown that atmospheric synthesis can yield molecules such as amino acids and nucleobases, but these processes are very sensitive to gas composition and energy source. Abiotic synthesis of organic molecules is more productive in reduced atmospheres, yet the primitive Earth may not have been as reducing as earlier workers assumed, and recent research has reflected this shift in thinking. This work provides a survey of the range of chemical products that can be produced given a set of atmospheric conditions, with a particular focus on recent reports. Intertwined with the discussion of atmospheric synthesis is the consideration of an organic haze layer, which has been suggested as a possible ultraviolet shield on the anoxic early Earth. Since such a haze layer – if formed – would serve as a reservoir for organic molecules, the chemical composition of the aerosol should be closely examined. The results highlighted here show that a variety of products can be formed in mildly reducing or even neutral atmospheres, demonstrating that contributions of atmospheric synthesis to the organic inventory on early Earth should not be discounted. This review intends to bridge current knowledge of the range of possible atmospheric conditions in the prebiotic environment and pathways for synthesis under such conditions by examining the possible products of organic chemistry in the early atmosphere.

Hydrothermal fluids play a major role in the transport and redistribution of inorganic and organic compounds in the Earth’s crust. The unique physico-chemical properties of water at these conditions have demonstrated to facilitate a wide range of novel chemical synthesis and biomass conversion processes, but have also attracted much attention because organic synthesis reactions at elevated temperatures may have contributed towards the origin of life. This short review focuses on the high-temperature stability of aqueous biomolecules. In particular, a review of individual bond breaking reactions in amino acids, nucleosides and nucleotides is presented and corresponding reactions rates and their temperature- and pH-dependence are reported and discussed.

Disequilibrium conditions are central for understanding the origin of life. Taking energetic chemicals at high concentrations to synthesize more complex molecules will not be enough to emulate and understand early molecular evolution. To comprehend the dynamic development of a molecular Darwinian system, the knowledge of energy flows according to the second law of thermodynamics is crucial. We review experiments which explore thermal gradients to trigger Darwinian evolution. On the one hand, laminar thermal convection leads to highly regular temperature oscillations that allow the melting and replication of DNA. In the same setting, molecules move along the thermal gradient, a mechanism termed thermophoresis or Soret effect. If thermophoresis is perpendicular to the convection flow and inside a long chamber, accumulation becomes very efficient and accumulates even short DNA thousand-fold. We showed that replication and accumulation can be implemented in the same micrometer-sized setting. Future experiments will show how replication and accumulation of DNA could give rise to a Darwin process of replication and selection, solely driven by a thermal gradient.

The possible role of Ca2+ as a promoter of the major steps in the evolution of early life is reviewed. The existing biological knowledge about the role of calcium in living systems is summarized and compared with the major bio-evolutionary events that occurred during the first three billion years of Earth’s history. It is proposed that secular changes in Ca2+ concentration in the marine realm during the Precambrian were the crucial driving force behind major innovations in the evolution of early life, such as photosynthesis, eukaryogenesis, multicellularity, origin of metazoans, biocalcification and skeletogenesis.

Several laboratories are pursuing the synthesis of cellular systems from different directions, including those that begin with simple chemicals to those that exploit existing cells. The methods that begin with nonliving components tend to focus on mimicking specific features of life, such as genomic replication, protein synthesis, sensory systems, and compartment formation, growth, and division. Conversely, the more prevalent synthetic biology approaches begin with something that is already alive and seek to impart new behavior on existing cells. Here we discuss advances in building cell-like systems that mimic key features of life with defined components.

Quantum tunnelling is a phenomenon which becomes relevant at the nanoscale and below. It is a paradox from the classical point of view as it enables elementary particles and atoms to permeate an energetic barrier without the need for sufficient energy to overcome it. Tunnelling might seem to be an exotic process only important for special physical effects and applications such as the Tunnel Diode, Scanning Tunnelling Microscopy (electron tunnelling) or Near-field Optical Microscopy operating in photon tunnelling mode. However, this review demonstrates that tunnelling can do far more, being of vital importance for life: physical and chemical processes which are crucial in theories about the origin and evolution of life can be traced directly back to the effects of quantum tunnelling. These processes include the chemical evolution in stellar interiors and within the cold interstellar medium, prebiotic chemistry in the atmosphere and subsurface of planetary bodies, planetary habitability via insolation and geothermal heat as well as the function of biomolecular nanomachines. This review shows that quantum tunnelling has many highly important implications to the field of molecular and biological evolution, prebiotic chemistry and astrobiology.

Photochromic organic dyes can be widely used in materials for optically rewritable data storage, photonic switches, memories, sensors, or actuators. In recent years photochromic materials based on nanoparticles became particularly focused, since they can be dispersed in colloidal aqueous suspensions or incorporated in thin films, avoiding problems of light scattering or shallow light penetration in bulk materials. Spiropyrans, spirooxazines and diarylethenes were by far the most researched photochromes in nanoparticulate systems. Great effort was made to investigate photochromic dyes incorporated into organic nanoparticles via self-assembly strategies, covalent linkage or dispersion of the molecular species in polymers (doping). Nanoparticles composed of solely photochromic dyes were prepared by laser ablation and reprecipitation techniques. Photochromic dyes were microencapsulated by self-assembly, soap free-, emulsion/ microemulsion/miniemulsion or free radical- (co)polymerization. Sol-gel processing from silane precursors to poly(organo)siloxane matrix is a common method to synthesize doped or core-shell photochromic organogels. Colored forms of some photochromes display fluorescence; however, a more effective strategy for fluorescence modulation with photochromic molecules is integrating them, covalently or noncovalently, with a separate fluorophore in the same nanoparticles. These photoresponsive nanoparticles may find applications particularly in biological fields such as cell labelling and bioimaging. The purpose of this review is to summarize the preparation methods of organic nanoparticles containing photochromic dyes and to investigate their typical properties derived from their nanoparticulate character.

Ultrasound irradiation differs from conventional energy sources (such as heat, light, or ionizing radiation) in time, pressure, and energy per molecule. The use of ultrasound waves in organic synthesis has attracted an increasing interest over the last years. Use of ultrasound waves as alternative source of energy is of great interest in the area of green and pharmaceutical chemistry. This review will focus on the uses of ultrasound waves in heterocyclic chemistry, condensation reactions, substitution reactions, oxidation, reduction, addition reactions, photochemical reactions, protection/deprotection reactions, coupling reaction photochemical reactions, polymerization reactions etc