Click-free imaging of carbohydrate trafficking in live cells using an azido photothermal probe.

Real-time tracking of intracellular carbohydrates remains challenging. While click chemistry allows bio-orthogonal tagging with fluorescent probes, the reaction permanently alters the target molecule and only allows a single snapshot. Here, we demonstrate click-free mid-infrared photothermal (MIP) imaging of azide-tagged carbohydrates in live cells. Leveraging the micromolar detection sensitivity for 6-azido-trehalose (TreAz) and the 300-nm spatial resolution of MIP imaging, the trehalose recycling pathway in single mycobacteria, from cytoplasmic uptake to membrane localization, is directly visualized. A peak shift of azide in MIP spectrum further uncovers interactions between TreAz and intracellular protein. MIP mapping of unreacted azide after click reaction reveals click chemistry heterogeneity within a bacterium. Broader applications of azido photothermal probes to visualize the initial steps of the Leloir pathway in yeasts and the newly synthesized glycans in mammalian cells are demonstrated.

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.

A Maxwell relation for dynamical timescales with application to the pressure and temperature dependence of water self-diffusion and shear viscosity.

A Maxwell relation for a reaction rate constant (or other dynamical timescale) obtained under constant pressure, p, and temperature, T, is introduced and discussed. Examination of this relationship in the context of fluctuation theory provides insight into the p and T dependence of the timescale and the underlying molecular origins. This Maxwell relation motivates a suggestion for the general form of the timescale as a function of pressure and temperature. This is illustrated by accurately fitting simulation results and existing experimental data on the self-diffusion coefficient and shear viscosity of liquid water. A key advantage of this approach is that each fitting parameter is physically meaningful.

Untangling the Interactions between Anionic Polystyrene Nanoparticles and Lipid Membranes Using Laurdan Fluorescence Spectroscopy and Molecular Simulations.

Several classes of synthetic nanoparticles (NPs) induce rearrangements of cell membranes that can affect membrane function. This paper describes the investigation of the interactions between polystyrene nanoparticles and liposomes, which serve as model cell membranes, using a combination of laurdan fluorescence spectroscopy and coarse-grained molecular dynamics (MD) simulations. The relative intensities of the gel-like and fluid fluorescent peaks of laurdan, which is embedded in the liposome membranes, are quantified from the areas of deconvoluted lognormal laurdan fluorescence peaks. This provides significant advantages in understanding polymer-membrane interactions. Our study reveals that anionic polystyrene NPs, which are not cross-linked, induce significant membrane rearrangement compared to other cationic or anionic NPs. Coarse-grained MD simulations demonstrate that polymer chains from the anionic polystyrene NP penetrate the liposome membrane. The inner leaflet remains intact throughout this process, though both leaflets show a decrease in lipid packing that is indicative of significant local rearrangement of the liposome membrane. These results are attributed to the formation of a hybrid gel made up of a combination of polystyrene (PS) and lipids that forces water molecules away from laurdan. Our study concludes that a combination of negative surface charge to interact electrostatically with positive charges on the membrane, a hydrophobic core to provide a thermodynamic preference for membrane association, and the ability to extend non-cross linked polymer chains into the liposome membrane are necessary for NPs to cause a significant rearrangement in the liposomes.

Machine Learning-Assisted Phase Transition Temperatures from Generalized Replica Exchange Simulations of Dry Martini Lipid Bilayers.

Accurate estimation of phase transition temperatures has been a longstanding challenge for molecular simulations. Recently, the generalized Replica Exchange technique for estimating phase transition temperatures has allowed for improved sampling of the phase transition; however, it requires a significant number of simultaneous replicas both inside and outside of the transition region leading to costly computational expense. In this work, the recently developed machine learning-assisted lipid phase analysis technique for learning the phase of individual lipids has been combined with generalized Replica Exchange Molecular Dynamics to reduce the overall computational expense of evaluating transition temperatures. This technique is then applied to eight different Dry Martini lipids to demonstrate its ability to describe transition temperatures as a function of chain length and tail saturation.

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.

Identical Water Dynamics in Acrylamide Hydrogels, Polymers, and Monomers in Solution: Ultrafast IR Spectroscopy and Molecular Dynamics Simulations.

The dynamics and structure of water in polyacrylamide hydrogels (PAAm-HG), polyacrylamide, and acrylamide solutions are investigated using ultrafast infrared experiments on the OD stretch of dilute HOD/H2O and molecular dynamics simulations. The amide moiety of the monomer/polymers interacts strongly with water through hydrogen bonding (H-bonding). The FT-IR spectra of the three systems indicate that the range of H-bond strengths is relatively unchanged from bulk water. Vibrational population relaxation measurements show that the amide/water H-bonds are somewhat weaker but fall within the range of water/water H-bond strengths. A previous study of water dynamics in PAAm-HG suggested that the slowing observed was due to increasing confinement with concentration. Here, for the same concentrations of the amide moiety, the experimental results demonstrate that the reorientational dynamics (infrared pump-probe experiments) and structural dynamics (two-dimensional infrared spectroscopy) are identical in the three acrylamide systems studied. Molecular dynamics simulations of the water orientational relaxation in aqueous solutions of the acrylamide monomer, trimer, and pentamer are in good agreement with the experimental results and are essentially chain length independent. The simulations show that there is a slower, low-amplitude (<7%) decay component not accessible by the experiments. The simulations examine the dynamics and structure of water H-bonded to acrylamide, in the first solvent shell, and beyond for acrylamide monomers and short chains. The experiments and simulations show that the slowing of water dynamics in PAAm-HG is not caused by confinement in the polymer network but rather by interactions with individual acrylamide moieties.

Molecular Simulations of Phase Equilibria and Transport Properties in a Model CO2-Expanded Lithium Perchlorate Electrolyte.

Carbon-dioxide (CO2)-expanded liquids, in which a significant mole fraction of CO2 is dissolved into an organic solvent, have been of significant interest, especially as catalytic support media. Because the CO2 mole fraction and density can be controlled over a significant range by changing the CO2 partial pressure, the transport properties of these solvents are highly tunable. Recently, these liquids have garnered interest as potential electrolyte solutions for catalytic electrochemistry; however, little is currently known about the influence of the electrolyte on CO2 expansion. In the present work, we use molecular-dynamics simulations to study diffusion and viscosity in a model lithium perchlorate electrolyte in CO2-expanded acetonitrile and demonstrate that these properties are highly dependent on the concentration of the electrolyte. Our present results indicate that the electrolyte slows down diffusion of both CO2 and MeCN, and that the slowed diffusion in the former is driven by changes in the activation entropy, whereas slowed diffusion in the latter is driven by changes in the activation energy.

Examining the Role of Different Molecular Interactions on Activation Energies and Activation Volumes in Liquid Water.

There are a large number of force fields available to model water in molecular dynamics simulations, which each have their own strengths and weaknesses in describing the behavior of the liquid. One particular weakness in many of these models is their description of dynamics away from ambient conditions, where their ability to reproduce measurements is mixed. To investigate this issue, we use the recently developed fluctuation theory for dynamics to directly evaluate measures of the local temperature and pressure dependence: the activation energy and the activation volume. We examine these activation parameters for hydrogen-bond jump exchange times, OH reorientation times, and diffusion coefficients calculated from the SPC/E, SPC/Fw, TIP3P-PME, TIP3P-PME/Fw, OPC3, TIP4P/2005, TIP4P/Ew, E3B2, and E3B3 water models. Activation energy decompositions available through the fluctuation theory approach provide mechanistic insight into the origins of different temperature dependences between the various models, as well as the influence of three-body effects and flexibility.

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.

Examining the Hofmeister Series through Activation Energies: Water Diffusion in Aqueous Alkali-Halide Solutions.

The effect of ions on the properties of aqueous solutions is often categorized in terms of the Hofmeister series that ranks them from chaotropes ("structure-breakers"), which weaken the surrounding hydrogen-bond network to kosmotropes ("structure-makers"), which enhance it. Here, we investigate the Hofmeister series in ∼1 M sodium-halide solutions using molecular dynamics simulations to calculate the effect of the identity and proximity of the halide anion on both the water diffusion coefficient and its activation energy. A recently developed method for calculating the activation energy from a single-temperature simulation is used, which also permits a rigorous decomposition into contributions from different interactions and motions. The mechanisms of the salt effects on the water dynamics are explored by separately considering water molecules based on their location relative to the ions. The results show that water diffusion is accelerated moving down the halide group from F- to I-. The behavior of the diffusion activation energy, Ea, is more complex, indicating a significant role for entropic effects. However, water molecules in the first or second solvation shell of an ion exhibit a decrease in Ea moving down the halide series and Na+ exhibits a larger effect than any of the anions. The Ea for water molecules within the second solvation shell of an ion are modest, indicating a short-ranged nature of the ion influence.

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.

Temperature Dependence of the Water Infrared Spectrum: Driving Forces, Isosbestic Points, and Predictions.

The temperature derivative of the infrared (IR) spectrum of HOD/D2O is directly calculated from simulations at a single temperature using a fluctuation theory approach. It is demonstrated, on the basis of an energetic decomposition of the derivative, that the blue shift with increasing temperature is associated with the competition between electrostatic and Lennard-Jones interactions. The same competition gives rise, where their contributions cancel, to a near isosbestic point. The derivative is further used to define an effective internal energy (and entropy) associated with the IR spectrum, and it is shown how a van't Hoff relation can be used to accurately predict the spectrum over a wide range of temperatures. These predictions also explain why a precise isosbestic point is not observed.

The dynamics of supercooled water can be predicted from room temperature simulations.

There is strong interest in understanding the behavior of water in its supercooled state. While many of the qualitative trends of water dynamical properties in the supercooled regime are well understood, the connections between the structure and dynamics of room temperature and supercooled water have not been fully elucidated. Here, we show that the reorientational time scales and diffusion coefficients of supercooled water can be predicted from simulations of room temperature liquid water. Specifically, the derivatives of these dynamical time scales with respect to inverse temperature are directly calculated using the fluctuation theory applied to dynamics. These derivatives are used to predict the time scales and activation energies in the supercooled regime based on the temperature dependence in one of two forms: that based on the stability limit conjecture or assuming an equilibrium associated with a liquid-liquid phase transition. The results indicate that the retarded dynamics of supercooled water originate from structures and mechanisms that are present in the liquid under ambient conditions.

On the temperature dependence of liquid structure.

We introduce a straightforward method for predicting an equilibrium distribution function over a wide range of temperatures from a single-temperature simulation. The approach is based on a simple application of fluctuation theory and requires only a standard equilibrium molecular dynamics (or Monte Carlo) simulation. In addition, it provides mechanistic insight into the origin of the temperature-dependent behavior. We illustrate the method by predicting the structure of liquid water, as represented by the O-O radial distribution function, for temperatures from 235 to 360 K from a room temperature molecular dynamics simulation.

Tests of the Stokes-Einstein Relation through the Shear Viscosity Activation Energy of Water.

A method for calculating the activation energy for the shear viscosity of a liquid from simulations at a single temperature is demonstrated. Importantly, the approach provides a route to the rigorous decomposition of the activation energy into contributions due to different motions and interactions, e.g., kinetic, Coulombic, and Lennard-Jones energies, that are otherwise not accessible. The method is illustrated by application to the case of liquid water under ambient conditions. The shear viscosity activation energy and its components are examined and compared to the analogous results for the time scales of diffusion and reorientation that have been previously calculated, providing a test of the Stokes-Einstein relation for water.

Activation Energies and Beyond.

Recent advances in the calculation and interpretation of the activation energy for a dynamical process are described. Specifically, new approaches that apply the fluctuation theory of statistical mechanics to dynamics enable the direct determination of the activation energy for an arbitrary dynamical time scale from simulations at a single temperature. This opens up significant new possibilities for understanding activated processes in cases where a traditional Arrhenius analysis is not possible. The methods also enable a rigorous decomposition of the activation energy into contributions associated with the different interactions and motions present in the system. These components can be understood in the context of Tolman's interpretation of the activation energy. Specifically, they provide insight into how energy can be most effectively deposited to accelerate the dynamics of interest, promising important new mechanistic information for a broad range of chemical processes. The general approach can be extended beyond activation energies to the examination of non-Arrhenius behavior as well as the changes in dynamical time scales with respect to other thermodynamic variables such as pressure.

The activation energy for water reorientation differs between IR pump-probe and NMR measurements.

Molecular reorientation dynamics in liquid water are typically probed using either infrared (IR) pump-probe anisotropy experiments or the NMR spin-echo technique. While it is widely appreciated that the two yield different reorientation times based on the nature of the measurements, little attention has been paid to the implications for the corresponding activation energies. Here, the activation energies associated with reorientation of the OH bond vector in liquid water are calculated to high accuracy directly from simulations at a single temperature using a recently developed method [Z. A. Piskulich et al., J. Chem. Phys. 147, 134103 (2017)]. The results indicate that the reorientation times obtained from IR anisotropy and NMR measurements have different activation energies that, with improved accuracy, should be experimentally distinguishable. The origins of the differences in the two activation energies are examined in detail, including by a decomposition into the contributions to the activation energies due to the kinetic energy and the intermolecular interactions.

Expanding the calculation of activation volumes: Self-diffusion in liquid water.

A general method for calculating the dependence of dynamical time scales on macroscopic thermodynamic variables from a single set of simulations is presented. The approach is applied to the pressure dependence of the self-diffusion coefficient of liquid water as a particularly useful illustration. It is shown how the activation volume associated with diffusion can be obtained directly from simulations at a single pressure, avoiding approximations that are typically invoked.