The recombination of hydronium and hydroxide ions following water ionization is one of the most fundamental processes determining the pH of water. The neutralization step once the solvated ions are in close proximity is phenomenologically understood to be fast, but the molecular mechanism has not been directly probed by experiments. We elucidate the mechanism of recombination in liquid water with ab initio molecular dynamics simulations, and it emerges as quite different from the conventional view of the Grotthuss mechanism. The neutralization event involves a collective compression of the water-wire bridging the ions, which occurs in approximately 0.5 ps, triggering a concerted triple jump of the protons. This process leaves the neutralized hydroxide in a hypercoordinated state, with the implications that enhanced collective compressions of several water molecules around similarly hypercoordinated states are likely to serve as nucleation events for the autoionization of liquid water.acid-base chemistry | concerted proton transfer | hydronium and hydroxide recombination T he mechanisms of proton transfer and transport through different media has been a subject of great interest in the fields of chemistry and biology (1-6). Several processes involving proton transfer, such as proton conduction through proton wires in proteins, and acid-base neutralization have been receiving elevated attention (7-9). Water is a common solvent for many of these processes. As an ionizable medium with hydrogen bonds that continuously break and reform, water presents a rich environment for sustaining several complex reactions. Perhaps one of the most fundamental studies in this regard is the dissociation of water and the consequent recombination of the ions. This process forms the cornerstone of textbook acid-base chemistry (10). The acid dissociation constant of water (K W ) at room temperature is 1 × 10 −14 , which means that H 2 O rarely autodissociates and the subsequent ionic products quickly recombine. Elucidating the molecular mechanisms of the autodissociation of water and recombination of the ions has far-reaching consequences in enriching our understanding of the anomalous conductivity of protons in different environments.Most of the acid-base neutralization studies are interpreted within the framework of the model proposed by Eigen and de Maeyer (11). This model attributes the rate-limiting step of recombination to the approach of the solvated ionic species by a Grotthuss-like structural diffusion, until a contact distance of about 6 Å (12). At contact distance, the hydronium and hydroxide ions are separated by two water molecules, which form a water wire between the ions as shown in Fig. 1 (11, 12). The Grotthuss mechanism (13) was proposed to explain how the excess proton occurring as H 3 O þ diffuses much faster than expected from its hydrodynamic radius (13). The general consensus on the modern view of the 200-yr-old Grotthuss mechanism (13) is that the excess proton diffuses with a proton transfer from H 3 O þ to the...

Molecular Dynamics (MD) plays a fundamental role in characterizing protein disordered states that are emerging as crucial actors in many biological processes. Here we assess the accuracy of three current force-fields in modeling disordered peptides by combining enhanced-sampling MD simulations with NMR data. These force-fields generate significantly different conformational ensembles, and AMBER03w [ Best and Mittal J. Phys. Chem. B 2010 , 114 , 14916 - 14923 ] provides the best agreement with experiments, which is further improved by adding the ILDN corrections [ Lindorff-Larsen et al. Proteins 2010 , 78 , 1950 - 1958 ].

The SARS-CoV-2 is a type of coronavirus that has caused the pandemic known as the Coronavirus Disease of 2019, or COVID-19. In traditional epidemiological models such as SEIR (Susceptible, Exposed, Infected, Removed), the exposed group E does not infect the susceptible group S . A distinguishing feature of COVID-19 is that, unlike with previous viral diseases, there is a distinct “asymptomatic” group A , which does not show any symptoms, but can nevertheless infect others, at the same rate as infected symptomatic patients. This situation is captured in a model known as SAIR (Susceptible, Asymptomatic, Infected, Removed), introduced in Robinson and Stillianakis (2013). The dynamical behavior of the SAIR model is quite different from that of the SEIR model. In this paper, we use Lyapunov theory to establish the global asymptotic stabililty of the SAIR model, both without and with vital dynamics. Then we develop compartmental SAIR models to cater to the migration of population across geographic regions, and once again establish global asymptotic stability. Next, we go beyond long-term asymptotic analysis and present methods for estimating the parameters in the SAIR model. We apply these estimation methods to data from several countries including India, and demonstrate that the predicted trajectories of the disease closely match actual data. We show that “herd immunity” (defined as the time when the number of infected persons is maximum) can be achieved when the total of infected, symptomatic and asymptomatic persons is as low as 25% of the population. Previous estimates are typically 50% or higher. We also conclude that “lockdown” as a way of greatly reducing inter-personal contact has been very effective in checking the progress of the disease.

In the realm of protein-protein interactions, the assembly process of homooligomers plays a fundamental role because the majority of proteins fall into this category. A comprehensive understanding of this multistep process requires the characterization of the driving molecular interactions and the transient intermediate species. The latter are often short-lived and thus remain elusive to most experimental investigations. Molecular simulations provide a unique tool to shed light onto these complex processes complementing experimental data. Here we combine advanced sampling techniques, such as metadynamics and parallel tempering, to characterize the oligomerization landscape of fibritin foldon domain. This system is an evolutionarily optimized trimerization motif that represents an ideal model for experimental and computational mechanistic studies. Our results are fully consistent with previous experimental nuclear magnetic resonance and kinetic data, but they provide a unique insight into fibritin foldon assembly. In particular, our simulations unveil the role of nonspecific interactions and suggest that an interplay between thermodynamic bias toward native structure and residual conformational disorder may provide a kinetic advantage. molecular dynamics | enhanced sampling | fly-casting mechanism | conformational selection

[1] In the photodissociation of N 2 O, absorption cross sections differ with isotopic substitution, leading to a wavelength-dependent fractionation of the various isotopomers. Several models ranging from shifts by zero-point energy differences to propagation of wave packets on the excited electronic state potential energy surface have been proposed to explain the observed fractionations. We present time-independent fractionation calculations for the isotopomers 447, 448, 456, 546, and 556. Besides largely agreeing with the experimental data, these calculations have the advantage of not being computationally intensive, as well as satisfying the physical facts that the asymmetric stretch and the doubly degenerate bending vibration are the principal Franck-Condon active modes in the photodissociation. The latter is reflected in the actual dissociation and in the high rotational excitation and lack of vibrational excitation of the N 2 product. The calculations are based on a multidimensional reflection principle using an ab initio potential energy surface. The theory for the absorption cross section and isotopomer fractionation accompanying photodissociation is described. The absolute value of the theoretically calculated absorption cross section is very close (90%) to the experimentally observed value. The present computations also provide data for the slope of a threeisotope plot of the fractionation of 447/446 relative to 448/446, using the fractionations at different wavelengths. The resulting slope is compared with a perturbation theoretical expression for direct photodissociation given elsewhere.