Although water’s chemical properties are no less important than its exceptional physical properties, its acid–base behavior is relatively poorly understood. In fact, the Grotthus trajectories for ion recombination predicted by density functional theory do not comport well with the almost 100-fold slower diffusive trajectories observed in time-resolved spectroscopy. And, in the reverse reaction, the barrier to autoionization is not well characterized. Here we develop a self-consistent picture of both processes based on the occurrence and role of ultrashort hydrogen bonds. The predicted populations of these special pairs in bulk water are consistent with the high frequency electrodynamics of water and its pressure dependence. The rate-limiting role of the special pairs manifests in autoionization as a two-stage barrier, first to form a contact ion pair and then to separate it by one water molecule. From this configuration, similar frequencies are observed for further separation vs recombination. The requirement of ultrashort hydrogen bonds for proton transfer in autoionization is consistent with the rise in Kw with increasing pressure and points to a role for density fluctuations in autoionization events. In neutralization, the manifestation of the role of special pairs is the prolonged diffusional process observed in time-resolved spectroscopy experiments. The requirement of special pairs as transition states for proton transfer is less obvious for neutralization in isolated water chains than in the bulk liquid only because an unbroken sequence of ultrashort H-bonds is more easily formed in a 1D H-bonded chain than in a 3D H-bonded network.

For a century now, “Lewis dots” have been a mainstay of chemical thinking, teaching and communication. However, chemists have assumed that this semi-classical picture of electrons needs to be abandoned for quantitative work, and the recourse in computational simulations has been to the extremes of first principles treatments of electrons on the one hand and force fields that avoid explicit electrons on the other hand. Given both the successes and limitations of these highly divergent approaches, it seems worth considering whether the Lewis dot picture might be made quantitative after all. Here we review progress to that end, including variations that have been implemented and examples of applications, specifically the acid–base behavior of water, several organic reactions, and electron dynamics in silicon fracture. In each case, the semi-classical approach is highly efficient and generates reasonable and readily interpreted reaction trajectories in turnkey fashion (i.e., without any input about products). Avenues for further progress are also discussed.

The surface charge of water, which is important in a wide range of chemical, biological, material, and environmental contexts, has been a subject of lengthy and heated debate. Recently, it has been shown that the highly efficient LEWIS force field, in which semiclassical, independently mobile valence electron pairs capture the amphiproticity, polarizability and H-bonding of water, provides an excellent description of the solvation and dynamics of hydroxide and hydronium in bulk water. Here we turn our attention to slabs, cylinders, and droplets. In extended simulations with 1000 molecules, we find that hydroxide consistently prefers the surface, hydronium consistently avoids the surface, and the two together form an electrical double layer until neutralization occurs. The behavior of hydroxide can largely be accounted for by the observation that hydroxide moving to the surface loses fewer hydrogen bonds than are gained by the water molecule that it displaces from the surface. At the same time, since the orientation of the hydroxide increases the ratio of dangling hydrogens to dangling lone pairs, the proton activity of the exposed surface may be increased, rather than decreased. Hydroxide also moves more rapidly in the surface than in the bulk, likely because the proton donating propensity of neighboring water molecules is focused on the one hydrogen that is not dangling from the surface.

The past decade has seen the first attempts at quantifying a semiclassical description of electrons in molecules. The challenge in this endeavor is to find potentials for electron interactions that adequately capture quantum effects. As has been the case for density functionals, the challenge is particularly great for the effects that follow from the requirement for wave function antisymmetry. Here we extend our empirical inquiry into effective potentials, from prior work on the monatomic atoms and ions of nonmetals, to diatomic molecules and ions formed by these elements. Newly adjusted and trained for the longer distances relevant to diatomics, pairwise potentials are able to fit the bond orders and magnetic properties of homonuclear species. These potentials are then found to do an excellent job of predicting the magnetism of heteronuclear species. In these molecules the predicted distribution of electrons also correctly reflects increasing ionic character with increasing difference in the electronegativities of the participating atoms. The distinctive features of the current potential are discussed, along with issues calling for further improvements.

We propose a pairwise compensation method for long-range electrostatics, as an alternative to traditional infinite lattice sums. The approach represents the third generation in a series beginning with the shifted potential corresponding to counterions surrounding a cutoff sphere. That simple charge compensation scheme resulted in pairwise potentials that are continuous at the cutoff, but forces that are not. A second-generation approach modified both the potential and the force such that both are continuous at the cutoff. Here, we introduce another layer of softening such that the derivative of the force is also continuous at the cutoff. In strongly ionic liquids, this extension removes structural artifacts associated with the earlier pairwise compensation schemes and provides results that compare well with Ewald sums.

Reactions of short sugars under mild, plausibly prebiotic conditions yield organic microspherules that may have played a role in prebiotic chemistry as primitive reaction vessels. It has been widely thought that nitrogen chemistry, in particular Amadori rearrangement, is central to this process, Here we show that microspherules form in the absence of any nitrogen compounds if the pH is sufficiently low. In particular, while the microspherule formation induced by ammonium acetate (pH 7) is not reproduced by ammonium chloride (pH 5), it is reproduced by oxalic acid and by hydrochloric acid (pH 1). The formation of microspherules in the presence of oxalic acid is similar to that in the presence of ammonium acetate: aqueous reactions of D-erythrose, D-ribose, 2-deoxy-D-ribose and D-fructose in the presence of oxalic acid produce microspherules ranging in size from approximately 1–5 μm after eight weeks incubation at 65°C, while the aldohexoses D-glucose, D-galactose and D-mannose do not. This pattern correlates with the occurrence of furanose forms in these sugars.

Sugar-derived humins and melanoidins figure significantly in food chemistry, agricultural chemistry, biochemistry, and prebiotic chemistry. Despite wide interest and significant experimental attention, the amorphous and insoluble nature of the polymers has made them resistant to conventional structural characterization. Here we make use of solid-state NMR methods, including selective 13C substitution, 1H-dephasing, and double quantum filtration. The spectra, and their interpretation, are simplified by relying exclusively on hydronium for catalysis. The results for polymers derived from ribose, deoxyribose, and fructose indicate diverse pathways to furans, suggest a simple route to pyrroles in the presence of amines, and reveal a heterogeneous network-type polymer in which sugar molecules cross-link the heterocycles.

By exploiting dynamic nuclear polarization (DNP) at 90 K, we observe the first NMR spectrum of the K intermediate in the ion-motive photocycle of bacteriorhodopsin. The intermediate is identified by its reversion to the resting state of the protein in red light and by its thermal decay to the L intermediate. The 15N chemical shift of the Schiff base in K indicates that contact has been lost with its counterion. Under these circumstances, the visible absorption of K is expected to be more red-shifted than is observed and this suggests torsion around single bonds of the retinylidene chromophore. This is in contrast to the development of a strong counterion interaction and double bond torsion in L. Thus, photon energy is stored in electrostatic modes in K and is transferred to torsional modes in L. This transfer is facilitated by the reduction in bond alternation that occurs with the initial loss of the counterion interaction, and is driven by the attraction of the Schiff base to a new counterion. Nevertheless, the process appears to be difficult, as judged by the multiple L substates, with weaker counterion interactions, that are trapped at lower temperatures. The double-bond torsion ultimately developed in the first half of the photocycle is probably responsible for enforcing vectoriality in the pump by causing a decisive switch in the connectivity of the active site once the Schiff base and its counterion are neutralized by proton transfer.

Gas vesicles are gas-filled buoyancy organelles with walls that consist almost exclusively of gas vesicle protein A (GvpA). Intact, collapsed gas vesicles from the cyanobacterium Anabaena flos-aquae were studied by solid-state NMR spectroscopy, and most of the GvpA sequence was assigned. Chemical shift analysis indicates a coil-α-β-β-α-coil peptide backbone, consistent with secondary-structure-prediction algorithms, and complementary information about mobility and solvent exposure yields a picture of the overall topology of the vesicle subunit that is consistent with its role in stabilizing an air-water interface.

For a century now, “Lewis dots” have been a mainstay of chemical thinking, teaching and communication. However, chemists have assumed that this semi-classical picture of electrons needs to be abandoned for quantitative work, and the recourse in computational simulations has been to the extremes of first principles treatments of electrons on the one hand and force fields that avoid explicit electrons on the other hand. Given both the successes and limitations of these highly divergent approaches, it seems worth considering whether the Lewis dot picture might be made quantitative after all. Here we review progress to that end, including variations that have been implemented and examples of applications, specifically the acid–base behavior of water, several organic reactions, and electron dynamics in silicon fracture. In each case, the semi-classical approach is highly efficient and generates reasonable and readily interpreted reaction trajectories in turnkey fashion (i.e., without any input about products). Avenues for further progress are also discussed.

Semi-classical electrons offer access to efficient and intuitive simulations of chemical reactions. As for any treatment of fermions, the greatest difficulty is in accounting for anti-symmetry effects. Semi-classical efforts to-date either reference Slater-determinants from ab initio treatments or adopt a heuristic approach inspired by density functional treatments. Here we revisit the problem with a combined approach. We conclude that semi-classical electrons need to reference a non-conventional wave function and find that (1) contrary to earlier suppositions, contributions from the electrostatic terms in the Hamiltonian are of similar magnitude to those from the kinetic terms and (2) the former point to a need to supplement pair potentials with 3-body potentials. The first result explains features of reported heuristic potentials, and the second provides a firm footing for extending the transferability of potentials across a wider range of elements and bonding scenarios.