Atomistic simulations in prebiotic chemistry – a dialog between experiment and theory
Sorbonne University, Pierre et Marie Curie Campus 4 Place Jussieu, 75005 Paris France
The origin of life is among the greatest open problems in science—How is it that life can emerge from non-living matter? An answer is critical for understanding our own origins, for identifying the most promising targets in the search for life in other worlds, and for synthesizing new life in the lab. The beginnings of life on our planet date back approximately 4 billion years. During this time period in Earth’s history, a process of prebiotic chemical evolution was sparked, which gave rise to the emergence of simple biologically active molecules from an inanimate matter.
During the second part of the 19th century, the emergence of Darwin’s evolutionary theory fostered scientific efforts to understand life’s origins on our planet. In 1924, A. I. Oparin, a Soviet biologist, published his primordial soup theory proposing that life originated from simple nonliving organic compounds through gradual chemical evolution. Haldane introduced a similar concept for abiogenesis and their contribution is nowadays known as the Oparin-Haldane Hypothesis. In 1953, Miller and Urey reported (Miller & Urey 1) the surprising results they have achieved by the application of an electric discharge on a mixture of the gases composed of CH4, NH3, H2O, and H2 that simulated what was considered at the time as a model atmosphere for the primordial Earth. The result of this experiment was a substantial yield of a mixture of aminoacids (Lazcano 2). Similarly, Orò demonstrated the spontaneous formation of nucleic acids bases from aqueous hydrogen cyanide subjected to heating (Oro 3). Since then, a number of different hypotheses have been formulated in order to explain the synthesis of the building blocks of the first biological materials from small inorganic and organic precursors as well as how these building blocks could self-assemble to form functional biomolecules. In the last 60 years various prebiotic scenarios have been suggested differing in the type of energy used for the synthesis: e.g. UV irradiation both in extra-terrestrial and terrestrial environments (Munoz 4), hydrothermal energy from deep sea vents (Amend 5), shock waves from meteorite impact (Martins 6), redox energy in the “iron-sulphur world” hypothesis (Huber 7), radioactive emission from uranium accumulation (Parnel 8), mineral geochemistry (Lambert 9) and, of course, electric discharges originated by lightning, which motivated the Miller-Urey experiment. The last couple of years witnessed an unprecedented development in the research of the origin of the first genetic materials. Two main concurrent scenarios have been formulated for the prebiotic synthesis of nucleotides (Saladino 10, Sutherland 11). Moreover, recent experimental papers point to formamide as a prebiotic hub (Ferus 12, Saladino 13). Self-organization of nucleotide precursors leading to RNA-like molecules has also been addressed recently (Maurel 14, Di Mauro&Sponer 15).
Theory and modeling have generally provided considerable insight (Barone 16, Koch 17, Wang 18, Woon 19) into prebiotic chemistry, as developments in computational chemistry methodologies have opened the door to in silico modeling of more and more complex systems. Ab initio molecular dynamics (AIMD) is one of such computational methods, which incorporates quantum chemical calculations and molecular dynamics allowing for the simulation of chemical reactivity at finite temperature and pressure. Significant new insight has been obtained through AIMD studies on the mechanisms and barriers for the synthesis of simple organic molecules on substrates such as ice (Rimola 20) or minerals (Wang 21, Jeilani 22), the simulation of the effect of the pressure/temperature shock waves induced by the impact of bolides in the early Earth (Goldman 23), the recent first in silico Miller-Urey experiment (Saitta&Saija 24), the simulation of peptide synthesis and oligomerization at hydrothermal conditions (Schreiner 25, Pietrucci 38), or the determination of chemical paths leading to the formation of sugars (Cassone 26, Civis 27), nucleosides (Saladino 28, Ferus 41), and nucleotides (Sponer 29, Perez-Villa 39). Photochemistry of life’s origin has been addressed in several theoretical works (Barbatti 30, Szabla 31). Classical MD calculations have been used to unravel how the first RNA molecules could acquire their catalytic function that made possible evolution of the species on the Earth (Stadlbauer 32). A review on "Prebiotic Chemistry and the Origins of Life Research with atomistic computer simulations" by two of the proponents has just been accepted in "Physics of Life: reviews" (Perez-Villa 40).
A newly emerging direction of the modern origin of life research focusses on the non-equilibrium aspects of prebiotic chemistry. Pioneering studies of the Braun group have shown that length-selective accumulation of oligonucleotides can be achieved via thermophoresis in thermal traps, hinting at the fact that accumulation of biopolymers on the early Earth was not necessarily dictated by the rules of equilibrium thermodynamics (Mast 33). Another study has used theoretical tools to demonstrate that formamide, a molecule generally considered to be a highly relevant prebiotic feedstock molecule, could accumulate on the early Earth in the pores of rocks due to thermophoresis and convection (Niether 34). Non-equilibrium chemistry forms the basis of a recently formulated formamide-based origin model, in which the stepwise decrease of the temperature of the environment drives those complex chemical transformations that could lead to the emergence of more and more complex molecules from the prebiotic pool (Sponer 35). The importance of non-equilibrium chemistry in the evolution of droplet protocells (Parrilla-Gutierrez 36) or in the bistable behavior of non-enzymatic self-replication networks (Wagner 37) has been demonstrated by recent studies.
However, if the potential benefit of computer simulations in the study of atomic processes at conditions hard or even impossible to reach experimentally is clear, huge challenges remain to be tackled because of the chemical complexity of the systems and the many different time and length scales involved, as well as due to the many possible scenarios.
Judit Sponer (Institute of Biophysics, Brno) - Organiser
Fabio Pietrucci (Sorbonne Université) - Organiser
A. Marco Saitta (IMPMC - Université Pierre et Marie Curie (UPMC) - Paris) - Organiser
Rodolphe Vuilleumier (Sorbonne Université - ENS-PSL) - Organiser
Franz Saija (National Research Council) - Organiser