Water-mediated ion transport through functional nanoporous materials depends on the dynamics of water confined within a given nanostructured morphology. Here, we investigate H-bonding dynamics of interfacial water within a “normal” (Type I) lyotropic gyroid phase formed by a gemini dicarboxylate surfactant self-assembly using a combination of 2DIR spectroscopy and molecular dynamics simulations. Experiments and simulations demonstrate that water dynamics in the normal gyroid phase is 1 order of magnitude slower than that in bulk water, due to specific interactions between water, the ionic surfactant headgroups, and counterions. Yet, the dynamics of water in the normal gyroid phase are faster than those of water confined in a reverse spherical micelle of a sulfonate surfactant, given that the water pool in the reverse micelle and the water pore in the gyroid phase have roughly the same diameters. This difference in confined water dynamics likely arises from the significantly reduced curvature-induced frustration at the convex interfaces of the normal gyroid, as compared to the concave interfaces of a reverse spherical micelle. These detailed insights into confined water dynamics may guide the future design of artificial membranes that rapidly transport protons and other ions.

In this study, we present the third version of a water model that explicitly includes three-body interactions. The major difference between this version and the previous two is in the two-body water model we use as a reference potential; here we use the TIP4P/2005 model (previous versions used the TIP4P water model). We alter four parameters from our previous version of the model by fitting to the diffusion coefficient of the ambient liquid, the liquid and ice densities, and the melting point. We evaluate the performance of this version by calculating many other microscopic and thermodynamic static and dynamic properties as a function of temperature and near the critical point and comparing to experiment, the TIP4P/2005 model and the previous version of our three-body model.

Vibrational sum frequency generation (SFG) has become a very promising technique for the study of proteins at interfaces, and it has been applied to important systems such as anti-microbial peptides, ion channel proteins, and human islet amyloid polypeptide. Moreover, so-called “chiral” SFG techniques, which rely on polarization combinations that generate strong signals primarily for chiral molecules, have proven to be particularly discriminatory of protein secondary structure. In this work, we present a theoretical strategy for calculating protein amide I SFG spectra by combining line-shape theory with molecular dynamics simulations. We then apply this method to three model peptides, demonstrating the existence of a significant chiral SFG signal for peptides with chiral centers, and providing a framework for interpreting the results on the basis of the dependence of the SFG signal on the peptide orientation. We also examine the importance of dynamical and coupling effects. Finally, we suggest a simple method for determining a chromophore’s orientation relative to the surface using ratios of experimental heterodyne-detected signals with different polarizations, and test this method using theoretical spectra.

Polyglutamine (polyQ) sequences are found in a variety of proteins, and mutational expansion of the polyQ tract is associated with many neurodegenerative diseases. We study the amyloid fibril structure and aggregation kinetics of K2Q24K2W, a model polyQ sequence. Two structures have been proposed for amyloid fibrils formed by polyQ peptides. By forming fibrils composed of both 12C and 13C monomers, made possible by protein expression in Escherichia coli, we can restrict vibrational delocalization to measure 2D IR spectra of individual monomers within the fibrils. The spectra are consistent with a β-turn structure in which each monomer forms an antiparallel hairpin and donates two strands to a single β-sheet. Calculated spectra from atomistic molecular-dynamics simulations of the two proposed structures confirm the assignment. No spectroscopically distinct intermediates are observed in rapid-scan 2D IR kinetics measurements, suggesting that aggregation is highly cooperative. Although 2D IR spectroscopy has advantages over linear techniques, the isotope-mixing strategy will also be useful with standard Fourier transform IR spectroscopy.

Using our newly developed explicit three-body (E3B) water model, we simulate the surface of liquid water. We find that the timescale for hydrogen-bond switching dynamics at the surface is about three times slower than that in the bulk. In contrast, with this model rotational dynamics are slightly faster at the surface than in the bulk. We consider vibrational two-dimensional (2D) sum-frequency generation (2DSFG) spectroscopy as a technique for observing hydrogen-bond rearrangement dynamics at the water surface. We calculate the nonlinear susceptibility for this spectroscopy for two different polarization conditions, and in each case we see the appearance of cross-peaks on the timescale of a few picoseconds, signaling hydrogen-bond rearrangement on this timescale. We thus conclude that this 2D spectroscopy will be an excellent experimental technique for observing slow hydrogen-bond switching dynamics at the water surface.

Urea/water is an archetypical “biological” mixture and is especially well-known for its relevance to protein thermodynamics as urea acts as a protein denaturant at high concentration. This behavior has given rise to an extended debate concerning urea’s influence on water structure. On the basis of a variety of methods and of definitions of the water structure, urea has been variously described as a structure-breaker, a structure-maker, or as remarkably neutral toward water. Because of its sensitivity to microscopic structure and dynamics, vibrational spectroscopy can help resolve these debates. We report experimental and theoretical spectroscopic results for the OD stretch of HOD/H2O/urea mixtures (linear IR, 2DIR, and pump–probe anisotropy decay) and for the CO stretch of urea-D4/D2O mixtures (linear IR only). Theoretical results are obtained using existing approaches for water and a modification of a frequency map developed for acetamide. All absorption spectra are remarkably insensitive to urea concentration, consistent with the idea that urea only very weakly perturbs the water structure. Both this work and experiments by Rezus and Bakker, however, show that water’s rotational dynamics are slowed down by urea. Analysis of the simulations casts doubt on the suggestion that urea immobilizes particular doubly hydrogen bonded water molecules.

Noticeable differences between the vibrational (IR and Raman) spectra of neat H2O and D2O ice Ih are observed experimentally. Here, we employ our theoretical mixed quantum/classical approach to investigate these differences. We find reasonable agreement between calculated and experimental line shapes at both high and low temperatures. From understanding the structure of ice Ih and its vibrational exciton Hamiltonian, we provide assignments of the IR and Raman spectral features for both H2O and D2O ice Ih. We find that in H2O ice these features are due to strong and weak intermolecular coupling, not to intramolecular coupling. The differences between H2O and D2O ice spectra are attributed to the significantly stronger intramolecular coupling in D2O ice. Our conclusion for both H2O and D2O ice is that the molecular symmetric and antisymmetric normal modes do not form a useful basis for understanding OH or OD stretch spectroscopy.

Infrared (IR) spectroscopy has been widely utilized for the study of protein folding, unfolding, and misfolding processes. We have previously developed a theoretical method for calculating IR spectra of proteins in the amide I region. In this work, we apply this method, in combination with replica-exchange molecular dynamics simulations, to study the equilibrium thermal unfolding transition of the villin headpiece subdomain (HP36). Temperature-dependent IR spectra and spectral densities are calculated. The spectral densities correctly reflect the unfolding conformational changes in the simulation. With the help of isotope labeling, we are able to capture the feature that helix 2 of HP36 loses its secondary structure before global unfolding occurs, in agreement with experiment.

Phase-sensitive vibrational sum-frequency experiments on the water surface, using isotopic mixtures of water and heavy water, have recently been performed. The experiments show a positive feature at low frequency in the imaginary part of the susceptibility, which has been difficult to interpret, and impossible to reproduce using two-body (pairwise-additive) water simulation models. We have reparameterized a new three-body simulation model for liquid water, and with this model we calculate the imaginary part of the sum-frequency susceptibility, finding good agreement with experiment for dilute HOD in D2O. Theoretical analysis provides a molecular-level structural interpretation of these new and exciting experiments. In particular, we do not find evidence of any special ice-like ordering at the surface of liquid water.

A theoretical/computational framework for determining vibrational energy relaxation rates, pathways, and mechanisms, for small molecules and ions in liquids, is presented. The framework is based on the system—bath coupling approach, Fermi’s golden rule, classical time-correlation functions, and quantum correction factors. We provide results for three specific problems: relaxation of the oxygen stretch in neat liquid oxygen at 77 K, relaxation of the water bend in chloroform at room temperature, and relaxation of the azide ion anti-symmetric stretch in water at room temperature. In each case, our calculated lifetimes are in reasonable agreement with experiment. In the latter two cases, theory for the observed solvent isotope effects illuminates the relaxation pathways and mechanisms. Our results suggest several propensity rules for both pathways and mechanisms.

Infrared (IR) spectroscopy of the amide I band has been widely utilized for the analysis of peptides and proteins. Theoretical modeling of IR spectra of proteins requires an accurate and efficient description of the amide I frequencies. In this paper, amide I frequency maps for protein backbone and side chain groups are developed from experimental spectra and vibrational lifetimes of N-methylacetamide and acetamide in different solvents. The frequency maps, along with established nearest-neighbor frequency shift and coupling schemes, are then applied to a variety of peptides in aqueous solution and reproduce experimental spectra well. The frequency maps are designed to be transferable to different environments; therefore, they can be used for heterogeneous systems, such as membrane proteins.

Vibrational spectroscopy, including infrared, Raman, sum-frequency, and ultrafast, has proven to be an exceptionally useful technique for probing the structure and dynamics of water, in the bulk liquid, and at the liquid/vapor interface. Focusing on the case of dilute HOD in D2O, we have previously analyzed infrared and Raman spectra for the bulk liquid by considering the OH frequency distribution for the ensemble of HOD molecules, and its partitioning into sub-distributions for molecules in different hydrogen-bonding environments, using one particular hydrogen-bonding definition. We have similarly analyzed the sum-frequency spectrum for the liquid/vapor interface by considering the relevant spectral density and its partitions. We show that our conclusions about the molecular origins of spectral features, and the lack of correlation in the hydrogen-bonding region between frequency and hydrogen-bonding environment, are robust, in the sense that qualitatively similar results are obtained for five other, not necessarily closely related, hydrogen-bond definitions.Simulation snapshot of the liquid/vapor interface for dilute HOD in D2O (the green atoms are hydrogen).

Much effort has been directed at developing models for the computer simulation of liquid water. The simplest models involve effective two-molecule interactions, parametrized from experiment, for use in classical molecular dynamics simulations. These models have been very successful in describing the structure and dynamics of liquid water at room temperature and one atmosphere pressure. A completely successful model, however, should be robust enough to describe the properties of liquid water at other thermodynamic points, water’s complicated phase diagram, heterogeneous situations like the liquid/vapor interface, ionic, and other aqueous solutions, and confined and biological water. In this paper, we develop a new classical simulation model with explicit three-molecule interactions. These interactions presumably make the model more robust in the senses described above, and since they are short-ranged, the model is efficient to simulate. The model is formulated as a perturbation from a classical two-molecule interaction model, where the forms of the correction to the two-molecule term and the three-molecule terms result from electronic structure calculations on dimers and trimers. The magnitudes of these perturbations, however, are determined empirically. The resulting model improves upon the well-known two-molecule interaction models for both static and dynamic properties.

We present improvements on our previous approaches for calculating vibrational spectroscopy observables for the OH stretch region of dilute HOD in liquid D₂O. These revised approaches are implemented to calculate IR and isotropic Raman spectra, using the SPC/E simulation model, and the results are in good agreement with experiment. We also calculate observables associated with three-pulse IR echoes: the peak shift and 2D-IR spectrum. The agreement with experiment for the former is improved over our previous calculations, but discrepancies between theory and experiment still exist. Using our proposed definition for hydrogen bonding in liquid water, we decompose the distribution of frequencies in the OH stretch region in terms of subensembles of HOD molecules with different local hydrogen-bonding environments. Such a decomposition allows us to make the connection with experiments and calculations on water clusters and more generally to understand the extent of the relationship between transition frequency and local structure in the liquid.

Various linear and nonlinear vibrational and electronic spectroscopy experiments in liquids are usually analyzed within the second-cumulant approximation, and therefore the fundamental quantity of interest is the equilibrium time-correlation function of the fluctuating transition frequency. In the usual approach the “bath” variables responsible for the fluctuating frequency are treated classically, leading to a classical time-correlation function. Alternatively, sometimes a quantum correction appropriate for relatively high temperatures is included, which adds an imaginary part to the classical time-correlation function. This approach, although appealing, does not satisfy detailed balance. One can consider a similar correction, but where detailed balance is satisfied, by using the harmonic quantum correction factor. In this article, we compare these approaches for a model system and two realistic examples. Our conclusion is that for linear spectroscopy the classical result is usually adequate, whereas for nonlinear spectroscopy it can be more important to include quantum corrections.

We develop a new two-site Lennard-Jones intermolecular potential model for liquid oxygen where the two sites are centered on the nuclear positions. The Lennard-Jones ϵ and σ parameters are determined by fitting experimental thermodynamic data in the liquid region of the phase diagram to results from molecular dynamics simulations. This procedure yields ϵ/k=48 K, and σ=3.006 Å. Using this potential we then calculate, again from molecular dynamics simulations, the static structure factor (or site–site radial distribution function) and the second-rank rotational time-correlation function. In both cases our results are in excellent agreement with experiment (from X-ray scattering and depolarized Raman spectroscopy, respectively).

The pH-controlled M2 protein from influenza A is a critical component of the virus and serves as a target for the aminoadamantane antiflu agents that block its H+ channel activity. To better understand its H+ gating mechanism, we investigated M2 in lipid bilayers with a new combination of IR spectroscopies and theory. Linear Fourier transform infrared (FTIR) spectroscopy was used to measure the precise orientation of the backbone carbonyl groups, and 2D infrared (IR) spectroscopy was used to identify channel-lining residues. At low pH (open state), our results match previously published solid-state NMR and X-ray structures remarkably well. However, at neutral pH when the channel is closed, our measurements indicate that a large conformational change occurs that is consistent with the transmembrane α-helices rotating by one amino acid register—a structural rearrangement not previously observed. The combination of simulations and isotope-labeled FTIR and 2D IR spectroscopies provides a noninvasive means of interrogating the structures of membrane proteins in general and ion channels in particular.