Proton transport in biological systems can be probed by two-dimensional infrared spectroscopy

We propose a new method to determine the proton transfer (PT) rate in channel proteins by two-dimensional infrared (2DIR) spectroscopy. Proton transport processes in biological systems, such as proton channels, trigger numerous fundamental biochemical reactions. Due to the limitation in both spatial and time resolution of the traditional experimental approaches, describing the whole proton transport process and identifying the rate limiting steps at the molecular level is challenging. In the present paper, we focus on proton transport through the Gramicidin A channel. Using a kinetic PT model derived from all-atom molecular dynamics simulations, we model the amide I region of the 2DIR spectrum of the channel protein to examine its sensitivity to the proton transport process. We demonstrate that the 2DIR spectrum of the isotope-labeled channel contain information on the PT rate, which may be extracted by analyzing the antidiagonal linewidth of the spectral feature related to the labeled site. Such experiments in combination with detailed numerical simulations should allow the extraction of site dependent PT rates, providing a method for identifying possible rate limiting steps for proton channel transfer.

Second-Harmonic Scattering as a Probe of Structural Correlations in Liquids

Second-harmonic scattering experiments of water and other bulk molecular liquids have long been assumed to be insensitive to interactions between the molecules. The measured intensity is generally thought to arise from incoherent scattering due to individual molecules. We introduce a method to compute the second-harmonic scattering pattern of molecular liquids directly from atomistic computer simulations, which takes into account the coherent terms. We apply this approach to large-scale molecular dynamics simulations of liquid water, where we show that nanosecond second-harmonic scattering experiments contain a coherent contribution arising from radial and angular correlations on a length scale of < 1 nm, much shorter than had been recently hypothesized (Shelton, D. P. J. Chem. Phys. 2014, 141). By combining structural correlations from simulations with experimental data (Shelton, D. P. J. Chem. Phys. 2014, 141), we can also extract an effective molecular hyperpolarizability in the liquid phase. This work demonstrates that second-harmonic scattering experiments and atomistic simulations can be used in synergy to investigate the structure of complex liquids, solutions, and biomembranes, including the intrinsic intermolecular correlations

Solvent Fluctuations and Nuclear Quantum Effects Modulate the Molecular Hyperpolarizability of Water

Second-Harmonic Scatteringh (SHS) experiments provide a unique approach to probe non-centrosymmetric environments in aqueous media, from bulk solutions to interfaces, living cells and tissue. A central assumption made in analyzing SHS experiments is that the each molecule scatters light according to a constant molecular hyperpolarizability tensor $\boldsymbol{\beta}^{(2)}$. Here, we investigate the dependence of the molecular hyperpolarizability of water on its environment and internal geometric distortions, in order to test the hypothesis of constant $\boldsymbol{\beta}^{(2)}$. We use quantum chemistry calculations of the hyperpolarizability of a molecule embedded in point-charge environments obtained from simulations of bulk water. We demonstrate that both the heterogeneity of the solvent configurations and the quantum mechanical fluctuations of the molecular geometry introduce large variations in the non-linear optical response of water. This finding has the potential to change the way SHS experiments are interpreted: in particular, isotopic differences between H$_2$O and D$_2$O could explain recent second-harmonic scattering observations. Finally, we show that a simple machine-learning framework can predict accurately the fluctuations of the molecular hyperpolarizability. This model accounts for the microscopic inhomogeneity of the solvent and represents a first step towards quantitative modelling of SHS experiments

Vibrational Spectra of a Mechanosensitive Channel

We report the simulated vibrational spectra of a mechanosensitive membrane channel in different gating states. Our results show that while linear absorption is insensitive to structural differences, linear dichroism and sum-frequency generation spectroscopies are sensitive to the orientation of the transmembrane helices, which is changing during the opening process. Linear dichroism cannot distinguish an intermediate structure from the closed structure, but sum-frequency generation can. In addition, we find that two-dimensional infrared spectroscopy can be used to distinguish all three investigated gating states of the mechanosensitive membrane channel.

Ab initio Modeling of the Vibrational Sum-Frequency Generation Spectrum of Interfacial Water

Understanding the structural and dynamical features of interfacial water is of greatest interest in physics, chemistry, biology, and materials science. Vibrational sum-frequency generation (SFG) spectroscopy, which is sensitive to the molecular orientation and dynamics on the surfaces or at the interfaces, allows one to study a wide variety of interfacial systems. The structural and dynamical features of interfacial water at the air/water interface have been extensively investigated by SFG spectroscopy. However, the interpretations of the spectroscopic features have been under intense debate. Here, we report a simulated SFG spectrum of the air/water interface based on ab initio molecular dynamics simulations, which covers the OH stretching, bending, and libration modes of interfacial water. Quantitative agreement between our present simulations and the most recent experimental studies ensures that ab initio simulations predict unbiased structural features and electrical properties of interfacial systems. By utilizing the kinetic energy spectral density (KESD) analysis to decompose the simulated spectra, the spectroscopic features can then be assigned to specific hydrogen-bonding configurations of interfacial water molecules. © 2019 American Chemical Societ

Revealing the Solvation Structure and Dynamics of Carbonate Electrolytes in Lithium-Ion Batteries by Two-Dimensional Infrared Spectrum Modeling

Carbonate electrolytes in lithium-ion batteries play a crucial role in conducting lithium ions between two electrodes. Mixed solvent electrolytes consisting of linear and cyclic carbonates are commonly used in commercial lithium-ion batteries. To understand how the linear and cyclic carbonates introduce different solvation structures and dynamics, we performed molecular dynamics simulations of two representative electrolyte systems containing either linear or cyclic carbonate solvents. We then modeled their two-dimensional infrared (2DIR) spectra of the carbonyl stretching mode of these carbonate molecules. We found that the chemical exchange process involving formation and dissociation of lithium-ion/carbonate complexes is responsible for the growth of 2DIR cross peaks with increasing waiting time. In addition, we also found that cyclic carbonates introduce faster dynamics of dissociation and formation of lithium-ion/carbonate complexes than linear carbonates. These findings provide new insights into understanding the lithium-ion mobility and its interplay with solvation structure and ultrafast dynamics in carbonate electrolytes used in lithium-ion batteries. © 2017 American Chemical Society1441sciescopu

Simulation of Two-Dimensional Sum-Frequency Generation Response Functions:Application to Amide I in Proteins

<p>We present the implementation of an approach to simulate the two-dimensional sum frequency generation response functions of systems with numerous coupled chromophores using a quantum-classical simulation scheme that was previously applied successfully to simulate two-dimensional infrared spectra. We apply the simulation to the amide I band of a mechanosensitive channel protein. By examining the signal generated from different segments of the protein, we find that the overall signal is impossible to interpret without the aid of simulations due to the interference of the response generated on different segments of the protein. We do not find significant cross-peaks in the spectra, even when the waiting time is increased. The spectra are thus not sensitive to coupling between different structural elements. Despite this, we conclude that two-dimensional sum frequency generation spectroscopy will be a powerful tool to investigate membrane bound proteins.</p>

Orientational ordering of water in extended hydration shells of cations is ion-specific and is correlated directly with viscosity and hydration free energy

Specific ion effects in aqueous solutions are investigated at the molecular, nanoscopic and macroscopic levels. Femtosecond elastic second harmonic scattering (fs-ESHS) is used here to assess the chemical effects of ions on molecular and nanoscopic length scales of water, probing changes in the charge distribution around ions as well as structural orientational order of water molecules in extended hydration shells. We measured >0.05 M electrolyte solutions with a series of chloride salts (LiCl, NaCl, KCl, CsCl, RbCl, NH4Cl, MgCl2, CaCl2, and SrCl2). Ion specificity is observed in both the local electronic anisotropy and the nanoscopic orientational ordering of water. Both observables are influenced more by cations with larger valencies and smaller sizes and follow a direct Hofmeister trend. These ion-induced structural changes in the hydrogen-bond network of water are strongly correlated with the viscosity B-coefficient and the Gibbs free energy of hydration of ions. Such a connection between the nanoscopic and macroscopic changes provides a possibility to construct a molecular model for specific ion effects in aqueous solutions