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.

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.

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.

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.

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.

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.

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.

Thermal Adaptation of Enzymes: Impacts of Conformational Shifts on Catalytic Activation Energy and Optimum Temperature.

Thermal adaptation of enzymes is essential for both living organism development in extreme conditions and efficient biocatalytic applications. However, the molecular mechanisms leading to a shift in catalytic activity optimum temperatures remain unclear, and there is increasing experimental evidence that thermal adaptation involves complex changes in both structural and reactive properties. Here, a combination of enhanced protein conformational sampling with an explicit chemical reaction description was applied to mesophilic and thermophilic homologues of the dihydrofolate reductase enzyme, and a quantitative description of the stability and catalytic activity shifts between homologues was obtained. The key role played by temperature-induced shifts in protein conformational distributions is revealed. In contrast with pictures focusing on protein flexibility and dynamics, it is shown that while the homologues' reaction free energies are similar, the striking discrepancy between their activation energies is caused by their different conformational changes with temperature. An analytic model is proposed that combines catalytic activity and structural stability, and which quantitatively predicts the shift in homologue optimum temperatures. It is shown that this general model provides a molecular explanation of changes in optimum temperatures for several other enzymes.

Water dynamics at electrified graphene interfaces: a jump model perspective.

The reorientation dynamics of water at electrified graphene interfaces was recently shown [J. Phys. Chem. Lett., 2020, 11, 624-631] to exhibit a surprising and strongly asymmetric behavior: positive electrode potentials slow down interfacial water reorientation, while for increasingly negative potentials water dynamics first accelerates before reaching an extremum and then being retarded for larger potentials. Here we use classical molecular dynamics simulations to determine the molecular mechanisms governing water dynamics at electrified interfaces. We show that changes in water reorientation dynamics with electrode potential arise from the electrified interfaces' impacts on water hydrogen-bond jump exchanges, and can be quantitatively described by the extended jump model. Finally, our simulations indicate that no significant dynamical heterogeneity occurs within the water interfacial layer next to the weakly interacting graphene electrode.

Differences in thermal structural changes and melting between mesophilic and thermophilic dihydrofolate reductase enzymes.

A key aspect of life's evolution on Earth is the adaptation of proteins to be stable and work in a very wide range of temperature conditions. A detailed understanding of the associated molecular mechanisms would also help to design enzymes optimized for biotechnological processes. Despite important advances, a comprehensive picture of how thermophilic enzymes succeed in functioning under extreme temperatures remains incomplete. Here, we examine the temperature dependence of stability and of flexibility in the mesophilic monomeric Escherichia coli (Ec) and thermophilic dimeric Thermotoga maritima (Tm) homologs of the paradigm dihydrofolate reductase (DHFR) enzyme. We use all-atom molecular dynamics simulations and a replica-exchange scheme that allows to enhance the conformational sampling while providing at the same time a detailed understanding of the enzymes' behavior at increasing temperatures. We show that this approach reproduces the stability shift between the two homologs, and provides a molecular description of the denaturation mechanism by identifying the sequence of secondary structure elements melting as temperature increases, which is not straightforwardly obtained in the experiments. By repeating our approach on the hypothetical TmDHFR monomer, we further determine the respective effects of sequence and oligomerization in the exceptional stability of TmDFHR. We show that the intuitive expectation that protein flexibility and thermal stability are correlated is not verified. Finally, our simulations reveal that significant conformational fluctuations already take place much below the melting temperature. While the difference between the TmDHFR and EcDHFR catalytic activities is often interpreted via a simplified two-state picture involving the open and closed conformations of the key M20 loop, our simulations suggest that the two homologs' markedly different activity temperature dependences are caused by changes in the ligand-cofactor distance distributions in response to these conformational changes.

Activation energies and the extended jump model: How temperature affects reorientation and hydrogen-bond exchange dynamics in water.

Hydrogen-bond exchanges drive many dynamical processes in water and aqueous solutions. The extended jump model (EJM) provides a quantitative description of OH reorientation in water based on contributions from hydrogen-bond exchanges, or jumps, and the "frame" reorientation of intact hydrogen-bond pairs. Here, we show that the activation energies of OH reorientation in bulk water can be calculated accurately from the EJM and that the model provides a consistent picture of hydrogen-bond exchanges based on molecular interactions. Specifically, we use the recently developed fluctuation theory for dynamics to calculate activation energies, from simulations at a single temperature, of the hydrogen-bond jumps and the frame reorientation, including their decompositions into contributions from different interactions. These are shown to be in accord, when interpreted using the EJM, with the corresponding activation energies obtained directly for OH reorientation. Thus, the present results demonstrate that the EJM can be used to describe the temperature dependence of reorientational dynamics and the underlying mechanistic details.

Water Dynamics in the Hydration Shells of Biomolecules.

The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics simulations as well as in ultrafast vibrational spectroscopy has led to new and detailed insight into fluctuations of water structure, elementary water motions, electric fields at hydrated biointerfaces, and processes of vibrational relaxation and energy dissipation. Here, we review recent advances in both theory and experiment, focusing on hydrated DNA, proteins, and phospholipids, and compare dynamics in the hydration shells to bulk water.

Dynamical Disorder in the DNA Hydration Shell.

The reorientation and hydrogen-bond dynamics of water molecules within the hydration shell of a B-DNA dodecamer, which are of interest for many of its biochemical functions, are investigated via molecular dynamics simulations and an analytic jump model, which provide valuable new molecular level insights into these dynamics. Different sources of heterogeneity in the hydration shell dynamics are determined. First, a pronounced spatial heterogeneity is found at the DNA interface and explained via the jump model by the diversity in local DNA interfacial topographies and DNA-water H-bond interactions. While most of the hydration shell is moderately retarded with respect to the bulk, some water molecules confined in the narrow minor groove exhibit very slow dynamics. An additional source of heterogeneity is found to be caused by the DNA conformational fluctuations, which modulate the water dynamics. The groove widening aids the approach of, and the jump to, a new water H-bond partner. This temporal heterogeneity is especially strong in the minor groove, where groove width fluctuations occur on the same time scale as the water H-bond rearrangements, leading to a strong dynamical disorder. The usual simplifying assumption that hydration shell dynamics is much faster than DNA dynamics is thus not valid; our results show that biomolecular conformational fluctuations are essential to facilitate the water motions and accelerate the hydration dynamics in confined groove sites.

Orientational Dynamics of Water at an Extended Hydrophobic Interface.

We report on the orientational dynamics of water at an extended hydrophobic interface with an octadecylsilane self-assembled monolayer on fused silica. The interfacial dangling OH stretch mode is excited with a resonant pump, and its evolution followed in time by a surface-specific, vibrationally resonant, infrared-visible sum-frequency probe. High sensitivity pump-probe anisotropy measurements and isotopic dilution clearly reveal that the decay of the dangling OH stretch excitation is almost entirely due to a jump to a hydrogen-bonded configuration that occurs in 1.61 ± 0.10 ps. This is more than twice as fast as the jump time from one hydrogen-bonded configuration to another in bulk H2O but about 50% slower than the reported out-of-plane reorientation at the air/water interface. In contrast, the intrinsic population lifetime of the dangling OH stretch in the absence of such jumps is found to be >10 ps. Molecular dynamics simulations of air/water and hexane/water interfaces reproduce the fast jump dynamics of interfacial dangling OH with calculated jump times of 1.4 and 1.7 ps for the air and hydrophobic interfaces, respectively. The simulations highlight that while the air/water and hydrophobic/water surfaces exhibit great structural similarities, a small stabilization of the OH groups by the hydrophobic interface produces the pronounced difference in the dynamics of dangling bonds.