Competing Reaction Mechanisms of Peptide Bond Formation in Water Revealed by Deep Potential Molecular Dynamics and Path Sampling.

The formation of an amide bond is an essential step in the synthesis of materials and drugs, and in the assembly of amino acids to form peptides. The mechanism of this reaction has been studied extensively, in particular to understand how it can be catalyzed, but a representation capable of explaining all the experimental data is still lacking. Numerical simulation should provide the necessary molecular description, but the solvent involvement poses a number of challenges. Here, we combine the efficiency and accuracy of neural network potential-based reactive molecular dynamics with the extensive and unbiased exploration of reaction pathways provided by transition path sampling. Using microsecond-scale simulations at the density functional theory level, we show that this method reveals the presence of two competing distinct mechanisms for peptide bond formation between alanine esters in aqueous solution. We describe how both reaction pathways, via a general base catalysis mechanism and via direct cleavage of the tetrahedral intermediate respectively, change with pH. This result contrasts with the conventional mechanism involving a single pathway in which only the barrier heights are affected by pH. We show that this new proposal involving two competing mechanisms is consistent with the experimental data, and we discuss the implications for peptide bond formation under prebiotic conditions and in the ribosome. Our work shows that integrating deep potential molecular dynamics with path sampling provides a powerful approach for exploring complex chemical mechanisms.

Molecular Origin of Distinct Hydration Dynamics in Double Helical DNA and RNA Sequences.

Water molecules are essential to determine the structure of nucleic acids and mediate their interactions with other biomolecules. Here, we characterize the hydration dynamics of analogous DNA and RNA double helices with unprecedented resolution and elucidate the molecular origin of their differences: first, the localization of the slowest hydration water molecules─in the minor groove in DNA, next to phosphates in RNA─and second, the markedly distinct hydration dynamics of the two phosphate oxygen atoms OR and OS in RNA. Using our Extended Jump Model for water reorientation, we assess the relative importance of previously proposed factors, including the local topography, water bridges, and the presence of ions. We show that the slow hydration dynamics at RNA OR sites is not due to bridging water molecules but is caused by both the larger excluded volume and the stronger initial H-bond next to OR, due to the different phosphate orientations in A-form double helical RNA.

Activation and friction in enzymatic loop opening and closing dynamics.

Protein loop dynamics have recently been recognized as central to enzymatic activity, specificity and stability. However, the factors controlling loop opening and closing kinetics have remained elusive. Here, we combine molecular dynamics simulations with string-method determination of complex reaction coordinates to elucidate the molecular mechanism and rate-limiting step for WPD-loop dynamics in the PTP1B enzyme. While protein conformational dynamics is often represented as diffusive motion hindered by solvent viscosity and internal friction, we demonstrate that loop opening and closing is activated. It is governed by torsional rearrangement around a single loop peptide group and by significant friction caused by backbone adjustments, which can dynamically trap the loop. Considering both torsional barrier and time-dependent friction, our calculated rate constants exhibit very good agreement with experimental measurements, reproducing the change in loop opening kinetics between proteins. Furthermore, we demonstrate the applicability of our results to other enzymatic loops, including the M20 DHFR loop, thereby offering prospects for loop engineering potentially leading to enhanced designs.

Neural Network-Based Sum-Frequency Generation Spectra of Pure and Acidified Water Interfaces with Air.

The affinity of hydronium ions (H3O+) for the air-water interface is a crucial question in environmental chemistry. While sum-frequency generation (SFG) spectroscopy has been instrumental in indicating the preference of H3O+ for the interface, key questions persist regarding the molecular origin of the SFG spectral changes in acidified water. Here we combine nanosecond long neural network (NN) reactive simulations of pure and acidified water slabs with NN predictions of molecular dipoles and polarizabilities to calculate SFG spectra of long reactive trajectories including proton transfer events. Our simulations show that H3O+ ions cause two distinct changes in phase-resolved SFG spectra: first, a low-frequency tail due to the vibrations of H3O+ and its first hydration shell, analogous to the bulk proton continuum, and second, an enhanced hydrogen-bonded band due to the ion-induced static field polarizing molecules in deeper layers. Our calculations confirm that changes in the SFG spectra of acidic solutions are caused by hydronium ions preferentially residing at the interface.

A structure-dynamics relationship enables prediction of the water hydrogen bond exchange activation energy from experimental data.

It has long been understood that the structural features of water are determined by hydrogen bonding (H-bonding) and that the exchange of, or "jumps" between, H-bond partners underlies many of the dynamical processes in water. Despite the importance of H-bond exchanges there is, as yet, no direct method for experimentally measuring the timescale of the process or its associated activation energy. Here, we identify and exploit relationships between water's structural and dynamical properties that provide an indirect route for determining the H-bond exchange activation energy from experimental data. Specifically, we show that the enthalpy and entropy determining the radial distribution function in liquid water are linearly correlated with the activation energies for H-bond jumps, OH reorientation, and diffusion. Using temperature-dependent measurements of the radial distribution function from the literature, we demonstrate how these correlations allow us to infer the value of the jump activation energy, Ea,0, from experimental results. This analysis gives Ea,0 = 3.43 kcal mol-1, which is in good agreement with that predicted by the TIP4P/2005 water model. We also illustrate other approaches for estimating this activation energy consistent with these estimates.

Water dynamics and sum-frequency generation spectra at electrode/aqueous electrolyte interfaces.

The dynamics of water at interfaces between an electrode and an electrolyte is essential for the transport of redox species and for the kinetics of charge transfer reactions next to the electrode. However, while the effects of electrode potential and ion concentration on the electric double layer structure have been extensively studied, a comparable understanding of dynamical aspects is missing. Interfacial water dynamics presents challenges since it is expected to result from the complex combination of water-water, water-electrode and water-ion interactions. Here we perform molecular dynamics simulations of aqueous NaCl solutions at the interface with graphene electrodes, and examine the impact of both ion concentration and electrode potential on interfacial water reorientational dynamics. We show that for all salt concentrations water dynamics exhibits strongly asymmetric behavior: it slows down at increasingly positively charged electrodes but it accelerates at increasingly negatively charged electrodes. At negative potentials water dynamics is determined mostly by the electrode potential value, but in contrast at positive potentials it is governed both by ion-water and electrode-water interactions. We show how these strikingly different behaviors are determined by the interfacial hydrogen-bond network structure and by the ions' surface affinity. Finally, we indicate how the structural rearrangements impacting water dynamics can be probed via vibrational sum-frequency generation spectroscopy.

How the Acidity of Water Droplets and Films Is Controlled by the Air-Water Interface.

Acidity is a key determinant of chemical reactivity in atmospheric aqueous aerosols and water microdroplets used for catalysis. However, many fundamental questions about these systems have remained elusive, including how their acidity differs from that of bulk solutions, the degree of heterogeneity between their core and surface, and how the acid-base properties are affected by their size. Here, we perform hybrid density functional theory (DFT)-quality neural network-based molecular simulations with explicit nuclear quantum effects and combine them with an analytic model to describe the pH and self-ion concentrations of droplets and films for sizes ranging from nm to µm. We determine how the acidity of water droplets and thin films is controlled by the properties of the air-water interface and by their surface-to-volume ratio. We show that while the pH is uniform in each system, hydronium and hydroxide ions exhibit concentration gradients that span the two outermost molecular layers, enriching the interface with hydronium cations and depleting it with hydroxide anions. Acidity depends strongly on the surface-to-volume ratio for system sizes below a few tens of nanometers, where the core becomes enriched in hydroxide ions and the pH increases as a result of hydronium stabilization at the interface. These results obtained for pure water systems have important implications for our understanding of chemical reactivity in atmospheric aerosols and for catalysis in aqueous microdroplets.

Dielectric response of confined water films from a classical density functional theory perspective.

We re-examine the problem of the dielectric response of highly polar liquids such as water in confinement between two walls using simple two-variable density functional theory involving number and polarisation densities. In the longitudinal polarisation case where a perturbing field is applied perpendicularly to the walls, we show that the notion of the local dielectric constant, although ill-defined at a microscopic level, makes sense when coarse-graining over the typical size of a particle is introduced. The approach makes it possible to study the effective dielectric response of thin liquid films of various thicknesses in connection with the recent experiments of Fumagalli et al., [Science, 2018, 360, 1339-1342], and to discuss the notion of the interfacial dielectric constant. We argue that the observed properties as a function of slab dimensions, in particular the very low dielectric constants of the order of 2-3 measured for thin slabs of ∼1 nm thickness do not highlight any special properties of water but can be recovered for a generic polar solvent having similar particle size and the same high dielectric constant. Regarding the transverse polarisation case where the perturbing field is parallel to the walls, the associated effective dielectric constant as a function of slab dimensions reaches bulk-like values at much shorter widths than in the longitudinal case. In both cases, we find an oscillatory behaviour for slab thicknesses in the one nanometer range due to packing effects.

Explicit Models of Motion to Understand Protein Side-Chain Dynamics.

Nuclear magnetic relaxation is widely used to probe protein dynamics. For decades, most analyses of relaxation in proteins have relied successfully on the model-free approach, forgoing mechanistic descriptions of motion. Model-free types of correlation functions cannot describe a large carbon-13 relaxation dataset in protein side chains. Here, we use molecular dynamics simulations to design explicit models of motion and solve Fokker-Planck diffusion equations. These models of motion provide better agreement with relaxation data, mechanistic insight, and a direct link to configuration entropy.

Acids at the Edge: Why Nitric and Formic Acid Dissociations at Air-Water Interfaces Depend on Depth and on Interface Specific Area.

Whether the air-water interface decreases or increases the acidity of simple organic and inorganic acids compared to the bulk is critically important in a broad range of environmental and biochemical processes. However, a consensus has not yet been achieved on this key question. Here we use machine learning-based reactive molecular dynamics simulations to study the dissociation of paradigmatic nitric and formic acids at the air-water interface. We show that the local acidity profile across the interface is determined by changes in acid and conjugate base solvation and that the acidity decreases abruptly over a transition region of a few molecular layers. At the interface, both acids are weaker than in the bulk due to desolvation. In contrast, acidities below the interface reach a plateau and are all the stronger compared to those in the bulk as the surface to volume ratio of the aqueous phase is large, due to the growing impact of the stabilization of the released proton at the surface of the water. These results imply that the measured degree of dissociation sensitively depends on the experimental probing length and system size and suggest a molecular explanation for the contrasting experimental results. The aerosol size dependence of acidity has important consequences for atmospheric chemistry.

Water Diffusion Proceeds via a Hydrogen-Bond Jump Exchange Mechanism.

The self-diffusion of water molecules plays a key part in a broad range of essential processes in biochemistry, medical imaging, material science, and engineering. However, its molecular mechanism and the role played by the water hydrogen-bond network rearrangements are not known. Here we combine molecular dynamics simulations and analytic modeling to determine the molecular mechanism of water diffusion. We establish a quantitative connection between the water diffusion coefficient and hydrogen-bond jump exchanges, and identify the features that determine the underlying energetic barrier. We thus provide a unified framework to understand the coupling between translational, rotational, and hydrogen-bond dynamics in liquid water. It explains why these different dynamics do not necessarily exhibit identical temperature dependences although they all result from the same hydrogen-bond exchange events. The consequences for the understanding of water diffusion in supercooled conditions and for water transport in complex aqueous systems, including ionic, biological, and confined solutions, are discussed.

Using Activation Energies to Elucidate Mechanisms of Water Dynamics.

Recent advances in the calculation of activation energies are shedding new light on the dynamical time scales of liquid water. In this Perspective, we examine how activation energies elucidate the central, but not singular, role of the exchange of hydrogen-bond (H-bond) partners that rearrange the H-bond network of water. The contributions of other motions to dynamical time scales and their associated activation energies are discussed along with one case, vibrational spectral diffusion, where H-bond exchanges are not mechanistically significant. Nascent progress on outstanding challenges, including descriptions of non-Arrhenius effects and activation volumes, are detailed along with some directions for future investigations.

A Model Electron Transfer Reaction in Confined Aqueous Solution.

Liquid water confined within nanometer-sized channels exhibits a strongly reduced local dielectric constant perpendicular to the wall, especially at the interface, and this has been suggested to induce faster electron transfer kinetics at the interface than in the bulk. We study a model electron transfer reaction in aqueous solution confined between graphene sheets with classical molecular dynamics. We show that the solvent reorganization energy is reduced at the interface compared to the bulk, which explains the larger rate constant. However, this facilitated solvent reorganization is due to the partial desolvation by the graphene sheet of the ions involved in the electron transfer and not to a local dielectric constant reduction effect.

Confined Water's Dielectric Constant Reduction Is Due to the Surrounding Low Dielectric Media and Not to Interfacial Molecular Ordering.

Liquid water confined within nanometer-sized channels exhibits a surprisingly low dielectric constant along the direction orthogonal to the channel walls. This is typically assumed to result from a pronounced heterogeneity across the sample: the dielectric constant would be bulk-like everywhere except at the interface, where it would be dramatically reduced by strong restrictions on interfacial molecules. Here we study the dielectric properties of water confined within graphene slit channels via classical molecular dynamics simulations. We show that the permittivity reduction is not due to any important alignment of interfacial water molecules, but instead to the long-ranged anisotropic dipole correlations combined with an excluded-volume effect of the low-dielectric confining material. The bulk permittivity is gradually recovered only over several nanometers due to the impact of long-range electrostatics, rather than structural features. This has important consequences for the control of, e.g., ion transport and chemical reactivity in nanoscopic channels and droplets.

On the role of hydrogen-bond exchanges in the spectral diffusion of water.

The dynamics of a vibrational frequency in a condensed phase environment, i.e., the spectral diffusion, has attracted considerable interest over the last two decades. A significant impetus has been the development of two-dimensional infrared (2D-IR) photon-echo spectroscopy that represents a direct experimental probe of spectral diffusion, as measured by the frequency-frequency time correlation function (FFCF). In isotopically dilute water, which is perhaps the most thoroughly studied system, the standard interpretation of the longest timescale observed in the FFCF is that it is associated with hydrogen-bond exchange dynamics. Here, we investigate this connection by detailed analysis of both the spectral diffusion timescales and their associated activation energies. The latter are obtained from the recently developed fluctuation theory for the dynamics approach. The results show that the longest timescale of spectral diffusion obtained by the typical analysis used cannot be directly associated with hydrogen-bond exchanges. The hydrogen-bond exchange time does appear in the decay of the water FFCF, but only as an additional, small-amplitude (<3%) timescale. The dominant contribution to the long-time spectral diffusion dynamics is considerably shorter than the hydrogen-bond exchange time and exhibits a significantly smaller activation energy. It thus arises from hydrogen-bond rearrangements, which occur in between successful hydrogen-bond partner exchanges, and particularly from hydrogen bonds that transiently break before returning to the same acceptor.