Revisiting Ultrafast Dynamics in Carbonate-Based Electrolytes for Li-Ion Batteries: Clarifying 2D-IR Cross-Peak Interpretation.

Understanding chemical exchange in carbonate-based electrolytes employed in Li-ion batteries (LIBs) is crucial for elucidating ion transport mechanisms. Ultrafast two-dimensional (2D) IR spectroscopy has been widely used to investigate the solvation structure and dynamics of Li-ions in organic carbonate-based electrolytes. However, the interpretation of cross-peaks observed in picosecond carbonyl stretch 2D-IR spectra has remained contentious.

Quantifying tensile forces at cell-cell junctions with a DNA-based fluorescent probe.

Cells are physically contacting with each other. Direct and precise quantification of forces at cell-cell junctions is still challenging. Herein, we have developed a DNA-based ratiometric fluorescent probe, termed DNAMeter, to quantify intercellular tensile forces.

Free Volume Element Sizes and Dynamics in Polystyrene and Poly(methyl methacrylate) Measured with Ultrafast Infrared Spectroscopy.

The size, size distribution, dynamics, and electrostatic properties of free volume elements (FVEs) in polystyrene (PS) and poly(methyl methacrylate) (PMMA) were investigated using the Restricted Orientation Anisotropy Method (ROAM), an ultrafast infrared spectroscopic technique. The restricted orientational dynamics of a vibrational probe embedded in the polymer matrix provides detailed information on FVE sizes and their probability distribution. The probe's orientational dynamics vary as a function of its frequency within the inhomogeneously broadened vibrational absorption spectrum.

Structural Heterogeneity in the Preamyloid Oligomers of β-2-Microglobulin.

In dialysis patients, the protein β2-microglobulin (β2m) forms amyloid fibrils in a condition known as dialysis-related amyloidosis. To understand the early stages of the amyloid assembly process, we have used native electrospray ionization (ESI) together with ion mobility mass spectrometry (IM-MS) to study soluble preamyloid oligomers. ESI-IM-MS reveals the presence of multiple conformers for the dimer, tetramer, and hexamer that precede the Cu(II)-induced amyloid assembly process, results which are distinct from β2m oligomers formed at low pH.

Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation Studies of Nonaqueous Lithium Ion Battery Electrolytes.

Lithium ion battery (LIB) technology is undoubtedly indispensable to modern life. However, despite enormous and extended effort to improve LIB performance, our understanding of the underlying principles and mechanisms of lithium ion transport in nonaqueous LIB electrolytes remained limited until recently. There is a particular lack of knowledge of the microscopic solvation structures and fluctuation dynamics around charge carriers in real electrolytes.

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.

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.

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.

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.

Electrolytes induce long-range orientational order and free energy changes in the H-bond network of bulk water.

Electrolytes interact with water in many ways: changing dipole orientation, inducing charge transfer, and distorting the hydrogen-bond network in the bulk and at interfaces. Numerous experiments and computations have detected short-range perturbations that extend up to three hydration shells around individual ions. We report a multiscale investigation of the bulk and surface of aqueous electrolyte solutions that extends from the atomic scale (using atomistic modeling) to nanoscopic length scales (using bulk and interfacial femtosecond second harmonic measurements) to the macroscopic scale (using surface tension experiments).

Molecular determinants of desensitization in an ENaC/degenerin channel.

Epithelial Na(+) channel (ENaC)/degenerin family members are involved in mechanosensation, blood pressure control, pain sensation, and the expression of fear. Several of these channel types display a form of desensitization that allows the channel to limit Na(+) influx during prolonged stimulation. We used site-directed mutagenesis and chemical modification, functional analysis, and molecular dynamics simulations to investigate the role of the lower palm domain of the acid-sensing ion channel 1, a member of the ENaC/degenerin family.

Simulation of two-dimensional sum-frequency generation response functions: application to amide I in proteins.

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.

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.

Proton transport in a membrane protein channel: two-dimensional infrared spectrum modeling.

We model the two-dimensional infrared (2DIR) spectrum of a proton channel to investigate its applicability as a spectroscopy tool to study the proton transport process in biological systems. Proton transport processes in proton channels are involved in numerous fundamental biochemical reactions. However, probing the proton transport process at the molecular level is challenging, because of the limitation in both spatial and time resolution of the traditional experimental approaches.

An Efficient N(3)-Scaling Propagation Scheme for Simulating Two-Dimensional Infrared and Visible Spectra.

In this paper, we develop and test a new approximate propagation scheme for calculating two-dimensional infrared and visible spectra. The new scheme scales one order more efficiently with the system size than the existing schemes. A Trotter type of approximation is used for the matrix exponent that describes the time evolution of the quantum system.

Proton transport in a binary biomimetic solution revealed by molecular dynamics simulation.

We report the simulation results of the proton transport in a binary mixture of amphiphilic tetramethylurea (TMU) molecules and water. We identify different mechanisms that either facilitate or retard the proton transport. The efficiency of these mechanisms depends on the TMU concentration.

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.

Hydrophobic solvation: a 2D IR spectroscopic inquest.

For decades, the enigma of the hydrophobic force has captured the imagination of scientists. In particular, Frank and Evans' idea that the hydrophobic effect was mainly due to some kind of "iceberg" formation around a hydrophobic solute stimulated many experiments and molecular dynamics simulation studies. A better understanding of hydrophobic interactions will aid understanding in many contexts including protein structural dynamics and functioning in biological systems.

The beta-strand-loop-beta-strand conformation is marginally populated in beta2-microglobulin (20-41) peptide in solution as revealed by replica exchange molecular dynamics simulations.

Solid-state NMR study shows that the 22-residue K3 peptide (Ser(20)-Lys(41)) from beta(2)-microglobulin (beta(2)m) adopts a beta-strand-loop-beta-strand conformation in its fibril state. Residue Pro(32) has a trans conformation in the fibril state of the peptide, while it adopts a cis conformation in the native state of full-length beta(2)m. To get insights into the structural properties of the K3 peptide, and determine whether the strand-loop-strand conformation is encoded at the monomeric level, we run all-atom explicit solvent replica exchange molecular dynamics on both the cis and trans variants.

Structure and aggregation mechanism of beta(2)-microglobulin (83-99) peptides studied by molecular dynamics simulations.

Many human neurodegenerative diseases are associated with amyloid fibril formation. The human 99-residue beta(2)-microglobulin (beta2m) is one of the most intensively studied amyloid-forming proteins. Recent studies show that the C-terminal fragments 72-99, 83-89, and 91-96 form by themselves amyloid fibrils in vitro and play a significant role in fibrillization of the full-length beta2m protein under acidic pH conditions.