Conditional and time-dependent radial distribution functions reveal the details of the water structure surrounding the hydronium during the proton mobility process. Using this methodology for classical multistate empirical valence bond (MS-EVB) and ab initio molecular dynamics trajectories, as well as quantal MS-EVB trajectories, we supply statistical proof that proton hops in liquid water occur by a transition from the H3O+[3H2O] Eigen-complex, via the H5O2+ Zundel-complex, to a H3O+[3H2O] centered on a neighboring water molecule. In the "resting period" before a transition, there is a distorted hydronium with one of its water ligands at a shorter distance and another at a longer distance than average. The identity of this "special partner" interchanges rapidly within the three first-shell water ligands. This is coupled to cleavage of an acceptor-type hydrogen bond. Just before the transition, a partner is selected by an additional translation of the H3O+ moiety in its direction, possibly enabled by loosening of donor-type hydrogen bonds on the opposite side. We monitor the transition in real time, showing how the average structure is converted to a distorted H5O2+ cation constituting the transitional complex for proton hopping between water molecules.

Life is that which replicates and evolves, but there is no consensus on how life emerged. We advocate a systems protobiology view, whereby the first replicators were assemblies of spontaneously accreting, heterogeneous and mostly non-canonical amphiphiles. This view is substantiated by rigorous chemical kinetics simulations of the graded autocatalysis replication domain (GARD) model, based on the notion that the replication or reproduction of compositional information predated that of sequence information. GARD reveals the emergence of privileged non-equilibrium assemblies (composomes), which portray catalysis-based homeostatic (concentration-preserving) growth. Such a process, along with occasional assembly fission, embodies cell-like reproduction. GARD pre-RNA evolution is evidenced in the selection of different composomes within a sparse fitness landscape, in response to environmental chemical changes. These observations refute claims that GARD assemblies (or other mutually catalytic networks in the metabolism first scenario) cannot evolve. Composomes represent both a genotype and a selectable phenotype, anteceding present-day biology in which the two are mostly separated. Detailed GARD analyses show attractor-like transitions from random assemblies to self-organized composomes, with negative entropy change, thus establishing composomes as dissipative systems—hallmarks of life. We show a preliminary new version of our model, metabolic GARD (M-GARD), in which lipid covalent modifications are orchestrated by non-enzymatic lipid catalysts, themselves compositionally reproduced. M-GARD fills the gap of the lack of true metabolism in basic GARD, and is rewardingly supported by a published experimental instance of a lipid-based mutually catalytic network. Anticipating near-future far-reaching progress of molecular dynamics, M-GARD is slated to quantitatively depict elaborate protocells, with orchestrated reproduction of both lipid bilayer and lumenal content. Finally, a GARD analysis in a whole-planet context offers the potential for estimating the probability of life's emergence. The invigorated GARD scrutiny presented in this review enhances the validity of autocatalytic sets as a bona fide early evolution scenario and provides essential infrastructure for a paradigm shift towards a systems protobiology view of life's origin.

Proton solvation and proton mobility are both subjects of great interest in chemistry and biology. Here we have studied the hydration shells of H3O+ at temperatures ranging from 260 to 340 K using the multistate empirical valence-bond methodology (MS-EVB2). We have calculated the radial distribution functions for the protonium and its solvation shells. Furthermore, we have determined the Gibbs energy and the enthalpy for hydrogen bonds donated or accepted by the first two solvation shells, in comparison to bulk water. We find systematic bond-energy differences that appear to agree with a recent IR study on proton hydration. Implications of our results to various proton mobility mechanisms are discussed.

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