Instantaneous normal mode analysis of liquid water

Force Fields for Deep Eutectic Mixtures: Application to Structure, Thermodynamics and 2D-Infrared Spectroscopy

Parametrizing energy functions for ionic systems can be challenging. Here, the total energy function for an eutectic system consisting of water, SCN-, K+ and acetamide is improved vis-a-vis experimentally measured properties. Given the importance of electrostatic interactions, two different types of models are considered: the first (model M0) uses atom-centered multipole whereas the other two (models M1 and M2) are based on fluctuating minimal distributed charges (fMDCM) that respond to geometrical changes of SCN-. The Lennard-Jones parameters of the anion are adjusted to best reproduce experimentally known hydration free energies and densities, which are matched to within a few percent for the final models irrespective of the electrostatic model. Molecular dynamics simulations of the eutectic mixtures with varying water content (between 0 and 100%) yield radial distribution functions and frequency correlation functions for the CN-stretch vibration. Comparison with experiments indicates that models based on fMDCM are considerably more consistent than those using multipoles. Computed viscosities from models M1 and M2 are within 30% of measured values and their change with increasing water content is consistent with experiments. This is not the case for model M0.

Unraveling the Structure-Spectrum Relationship of Yeast Phenylalanine Transfer RNA: Insights from Theoretical Modeling of Infrared Spectroscopy

Yeast phenylalanine tRNA (tRNAphe) is a paradigmatic model in structural biology. In this work, we combine molecular dynamics simulations and spectroscopy modeling to establish a direct link between its structure, conformational dynamics, and infrared (IR) spectra. Employing recently developed vibrational frequency maps and coupling models, we apply a mixed quantum/classical treatment of the line shape theory to simulate the IR spectra of tRNAphe in the 1600-1800 cm-1 region across its folded and unfolded conformations and under varying concentrations of Mg2+ ions. The predicted IR spectra of folded and unfolded tRNAphe are in good agreement with experimental measurements, validating our theoretical framework. We then elucidate how the characteristic L-shaped tertiary structure of the tRNA and its modulation in response to diverse chemical environments give rise to distinct IR absorption peaks and line shapes. These calculations effectively bridge IR spectroscopy experiments and atomistic molecular simulations, unraveling the molecular origins of the observed IR spectra of tRNAphe. This work presents a robust theoretical protocol for modeling the IR spectroscopy of nucleic acids, which will facilitate its application as a sensitive probe for detecting the fluctuating secondary and tertiary structures of these essential biological macromolecules.

On the temperature dependence of the density of states of liquids at low energies

We report neutron-scattering measurements of the density of states (DOS) of water and liquid Fomblin in a wide range of temperatures. In the liquid phase, we confirm the presence of a universal low-energy linear scaling of the experimental DOS as a function of the frequency, g ( ω ) = a ( T ) ω , which persists at all temperatures. The low-frequency scaling of the DOS exhibits a sharp jump at the melting point of water, below which the standard Debye's law, g ( ω ) ∝ ω 2 , is recovered. On the contrary, in Fomblin, we observe a continuous transition between the two exponents reflecting its glassy dynamics, which is confirmed by structure measurements. More importantly, in both systems, we find that the slope a(T) grows with temperature following an exponential Arrhenius-like form, a ( T ) ∝ exp ( - ⟨ E ⟩ / T ) . We confirm this experimental trend using molecular dynamics simulations and show that the prediction of instantaneous normal mode (INM) theory for a(T) is in qualitative agreement with the experimental data.

Terahertz spectroscopy of thick and diluted water solutions

While bright terahertz sources are used to perform nonlinear experiments, they can be advantageous for high-precision linear measurements of opaque samples. By placing the sample away from the focus, nonlinearities can be suppressed, and sizeable amounts of transmitted radiation detected. Here, this approach is demonstrated for a 0.5 mm thick layer of liquid water in a static sample holder. Variations of the index of refraction as small as (7 ± 2) · 10-4 were detected at 0.58 THz for an aqueous salt solution containing ten millimoles of sodium chloride. To my knowledge, this precision is unprecedented in time-domain spectroscopy studies of diluted aqueous systems or other optically thick and opaque materials.

Evidence of Excited-State Vibrational Mode Governing the Photorelaxation of a Charge-Transfer Complex

Modern, nonlinear, time-resolved spectroscopic techniques have opened new doors for investigating the intriguing but complex world of photoinduced ultrafast out-of-equilibrium phenomena and charge dynamics. The interaction between light and matter introduces an additional dimension, where the complex interplay between electronic and vibrational dynamics needs the most advanced theoretical-computational protocols to be fully understood on the molecular scale. In this study, we showcase the capabilities of ab initio molecular dynamics simulation integrated with a multiresolution wavelet protocol to carefully investigate the excited-state relaxation dynamics in a noncovalent complex involving tetramethylbenzene (TMB) and tetracyanoquinodimethane (TCNQ) undergoing charge transfer (CT) upon photoexcitation. Our protocol provides an accurate description that facilitates a direct comparison between transient vibrational analysis and time-resolved spectroscopic signals. This molecular level perspective enhances our understanding of photorelaxation processes confined in the adiabatic regime and offers an improved interpretation of vibrational spectra. Furthermore, it enables the quantification of anharmonic vibrational couplings between high- and low-frequency modes, specifically the TCNQ "rocking" and "bending" modes. Additionally, it identifies the primary vibrational mode that governs the adiabaticity between the ground state and the CT state. This comprehensive understanding of photorelaxation processes holds significant importance in the rational design and precise control of more efficient photovoltaic and sensor devices.

Visualizing and characterizing excited states from time-dependent density functional theory

Time-dependent density functional theory (TD-DFT) is the most widely-used electronic structure method for excited states, due to a favorable combination of low cost and semi-quantitative accuracy in many contexts, even if there are well recognized limitations. This Perspective describes various ways in which excited states from TD-DFT calculations can be visualized and analyzed, both qualitatively and quantitatively. This includes not just orbitals and densities but also well-defined statistical measures of electron-hole separation and of Frenkel-type exciton delocalization. Emphasis is placed on mathematical connections between methods that have often been discussed separately. Particular attention is paid to charge-transfer diagnostics, which provide indicators of when TD-DFT may not be trustworthy due to its categorical failure to describe long-range electron transfer. Measures of exciton size and charge separation that are directly connected to the underlying transition density are recommended over more ad hoc metrics for quantifying charge-transfer character.

Conformational Dynamics in Proteins: Entangled Slow Fluctuations and Nonequilibrium Reaction Events

Proteins exhibit conformational fluctuations and changes over various time scales, ranging from rapid picosecond-scale local atomic motions to slower microsecond-scale global conformational transformations. In the presence of these intricate fluctuations, chemical reactions occur and functions emerge. These conformational fluctuations of proteins are not merely stochastic random motions but possess distinct spatiotemporal characteristics. Moreover, chemical reactions do not always proceed along a single reaction coordinate in a quasi-equilibrium manner. Therefore, it is essential to understand spatiotemporal conformational fluctuations of proteins and the conformational change processes associated with reactions. In this Perspective, we shed light on the complex dynamics of proteins and their role in enzyme catalysis by presenting recent results regarding dynamic couplings and disorder in the conformational dynamics of proteins and rare but rapid enzymatic reaction events obtained from molecular dynamics simulations.

Infrared Spectroscopy of Liquid Solutions as a Benchmarking Tool of Semiempirical QM Methods: The Case of GFN2-xTB

The accurate description of large molecular systems has triggered the development of new computational methods. Due to the computational cost of modeling large systems, the methods usually require a trade-off between accuracy and speed. Therefore, benchmarking to test the accuracy and precision of the method is an important step in their development. The typical gold standard for evaluating these methods is isolated molecules, because of the low computational cost. However, the advent of high-performance computing has made it possible to benchmark computational methods using observables from more complex systems such as liquid solutions. To this end, infrared spectroscopy provides a suitable set of observables (i.e., vibrational transitions) for liquid systems. Here, IR spectroscopy observables are used to benchmark the predictions of the newly developed GFN2-xTB semiempirical method. Three different IR probes (i.e., N-methylacetamide, benzonitrile, and semiheavy water) in solution are selected for this purpose. The work presented here shows that GFN2-xTB predicts central frequencies with errors of less than 10% in all probes. In addition, the method captures detailed properties of the molecular environment such as weak interactions. Finally, the GFN2-xTB correctly assesses the vibrational solvatochromism for N-methylacetamide and semiheavy water but does not have the accuracy needed to properly describe benzonitrile. Overall, the results indicate not only that GFN2-xTB can be used to predict the central frequencies and their dependence on the molecular environment with reasonable accuracy but also that IR spectroscopy data of liquid solutions provide a suitable set of observables for the benchmarking of computational methods.

Infrared Spectra in the 1000-100 cm-1 Region Combined with 4000-3000 cm-1 Region to Evaluate the States of Water

In this study, we evaluated the state of water by performing infrared (IR) spectroscopic analysis in the 4000-100 cm-1 region. The effects of ions on the structure of water molecules were investigated by analyzing specific IR bands of salt solutions in the 1000-100 cm-1 region. Chloride solutions of Li, Na, K, Cs, Ba, and Ca were prepared at different concentrations, and their IR spectra were recorded by the attenuated total reflection method. The isosbestic point was observed in the 1000-100 cm-1 region, and the position was related to the ratio of the Stokes radius and effective ionic radius of each ion. Two bands were identified at around 660 and 400 cm-1 by curve fitting, and the intensity ratio increased linearly with a decrease in water activity. Thus, this demonstrates the potential of the 1000-100 cm-1 region as a marker for the evaluation of water structure subjected to ions. Moreover, it is possible to evaluate different states of water simultaneously by combining this with the band in the 4000-3000 cm-1 region. These results successfully demonstrate the effectiveness of the spectra in the 1000-100 cm-1 region to evaluate the state of water in ionic solutions.

Atomic dynamics in fluids: Normal mode analysis revisited

Developing microscopic understanding of the thermal properties of liquids is challenging due to their strong dynamic disorder, which prevents characterization of the atomic degrees of freedom. There have been significant research interests in the past few decades to extend the normal mode analysis for solids to instantaneous structures of liquids. However, the nature of normal modes that arise from these unstable structures is still elusive. In this paper, we explore the instantaneous eigenmodes of dynamical matrices of various Lennard-Jones argon liquid and gas systems at high temperatures and show that the normal modes can be interpreted as an interpolation of T→∞ (gas) and T=0 (solid) mode descriptions. We find that normal modes become increasingly collisional and translational, recovering atomistic gaslike behavior rather than vibrational with increase in temperature, suggesting that normal modes in liquids may be described by both solidlike and gaslike modes.

Theoretical Simulations of Kinetic Isotope Effects on Decarboxylation of 3-Carboxybenzisoxazole

Kinetic isotope effect values on the decarboxylation of 3-carboxybenzisoxazole have been computed using the second-order Kleinert's variational perturbation theory in the framework of Feynman's path integrals along with the potential energy surface obtained at the MP2/6-31+G(d) level. Good agreement with the experimental data was obtained, demonstrating that this novel computational approach for computing KIE values of organic reaction is a viable alternative to the traditional method employing the Bigeleisen equation and harmonic vibrational frequencies. Compared with the experimental measurements, consideration of anharmonicity and tunneling effects can significantly improve the calculated KIE values, reducing the root-mean-square deviation from 1.19 % for traditional method to 0.20 % for path-integral method.

Discontinuous Tension-Controlled Transition between Collective Actuations in Active Solids

The recent finding of collective actuation in active solids-solids embedded with active units-is a new promise for the design of multifunctional materials with genuine autonomy, and a better understanding of dense biological systems. Here, we combine the experimental study of centimetric model active solids, the numerical study of an agent-based model, and theoretical arguments to reveal a new form of collective actuation and how mechanical tension can serve as a general mechanism for transitioning between different collective actuation regimes. The presence of hysteresis when varying tension back and forth highlights the nontrivial selectivity of collective actuations.

Structure, Organization, and Heterogeneity of Water-Containing Deep Eutectic Solvents

The spectroscopy and structural dynamics of a deep eutectic mixture (KSCN/acetamide) with varying water content is investigated from 2D IR (with the C-N stretch vibration of the SCN^- anions as the reporter) and THz spectroscopy. Molecular dynamics simulations correctly describe the nontrivial dependence of both spectroscopic signatures depending on water content. For the 2D IR spectra, the MD simulations relate the steep increase in the cross-relaxation rate at high water content to the parallel alignment of packed SCN^- anions. Conversely, the nonlinear increase of the THz absorption with increasing water content is mainly attributed to the formation of larger water clusters. The results demonstrate that a combination of structure-sensitive spectroscopies and molecular dynamics simulations provides molecular-level insights into the emergence of heterogeneity of such mixtures by modulating their composition.

From Networked to Isolated: Observing Water Hydrogen Bonds in Concentrated Electrolytes with Two-Dimensional Infrared Spectroscopy

Superconcentrated electrolytes have emerged as a promising class of materials for energy storage devices, with evidence that high voltage performance is possible even with water as the solvent. Here, we study the changes in the water hydrogen bonding network induced by the dissolution of lithium bis(trifluoromethane sulfonyl)imide (LiTFSI) in concentrations ranging from the dilute to the superconcentrated regimes. Using time-resolved two-dimensional infrared spectroscopy, we observe the progressive disruption of the water-water hydrogen bond network and the appearance of isolated water molecules interacting only with ions, which can be identified and spectroscopically isolated through the intermolecular cross-peaks between the water and the TFSI^- ions. Analyzing the vibrational relaxation of excitations of the H₂O stretching mode, we observe a transition in the dominant relaxation path as the bulk-like water vanishes and is replaced by ion-solvation water with the rapid single-step relaxation of delocalized stretching vibrations into the low frequency modes being replaced by multistep relaxation through the intramolecular H₂O bend and into the TFSI^- high frequency modes prior to relaxing to the low frequency structural degrees of freedom. These results definitively demonstrate the absence of vibrationally bulk-like water in the presence of high concentrations of LiTFSI and especially in the superconcentrated regime, while additionally revealing aspects of the water hydrogen bond network that have been difficult to discern from the vibrational spectroscopy of the neat liquid.

OH Stretching and Libration Bands of Solitary Water in Ionic Liquids and Dipolar Solvents Share a Single Dependence on Solvent Polarity

Ionic liquids are an emerging class of materials which are finding application in a variety of technologically important areas. Because of their hydrophilic character, at least a small concentration of water is often present when ionic liquids are used in practical applications. This study employs infrared spectroscopy in the OH stretching and libration regions together with DFT calculations to better characterize the state of dilute water in ionic liquids. Water mole fractions (x_w ∼ 0.1) are chosen such that nearly all water occurs in monomeric form and spectra probe the solvation structure and dynamics of solitary water molecules. New data are reported for a series of 1-ethyl-3-methylimidazolium liquids [Im₂₁][X] with X^- = (C₂F₅)₃F₃P^-, (CF₃SO₂)₂N^-, BF₄^-, B(CN)₄^-, CF₃SO₃^-, C₂H₅SO₄^-, NO₃^-, SCN^-, and CH₃CO₂^-, as well as for the two 1-hexyl-3-methylimidazolium liquids [Im₆₁][Cl] and [Im₆₁][I]. For comparison, spectra are also recorded in a variety of dipolar solvents, and much of the available literature data are summarized, providing a comprehensive perspective on monomeric water in homogeneous solution. Most prior studies of dilute water in ionic liquids interpreted OH stretching spectra only in terms of water being specifically bonded to two anions in A^-···H-O-H···A^- type solvates. The more detailed analysis presented here indicates the additional presence of asymmetrically solvated water, which in some cases includes both singly solvated (A^-···H-O-H) and more subtle forms of asymmetric solvation. The same pattern of solvation also pertains to dipolar solvents capable of accepting hydrogen bonds from water. No clear distinction is found between OH spectra in high-polarity conventional solvents and ionic liquids. In all solvents, OH frequencies are strongly correlated to measures of solvent basicity or hydrogen bond accepting ability. Far-infrared spectra of the water libration band also show common trends in ionic and dipolar solvents. Despite the different character of the libration and OH modes, the frequencies of these vibrations show virtually the same solvent dependence (apart from sign) except in weakly polar or nonpolar solvents.

Correlation lengths in nanoconfined water and transport properties

We report the existence of disparate static and dynamic correlation lengths that could describe the influence of confinement on nanoconfined water (NCW). Various aspects of viscous properties, such as anisotropy and viscoelasticity, of NCW are studied by varying the separation distance "d" between two confining hydrophobic plates. The transverse component of the mean square stress exhibits slow spatial decay (measured from the surface) beyond ∼1.8 nm, which was not reported before. The static correlation length obtained from fitting the exponential decay of the transverse mean-square stress with d is 0.75 nm, while the decay time of the stress-stress time correlation function gives a dynamic correlation length of only 0.35 nm. The shortness of the dynamic correlation length seems to arise from the low sensitivity of orientational relaxation to confinement. In the frequency-dependent viscosity, we observe a new peak at about 50 cm^-1 that is not present in the bulk. This new peak is prominent even at 3 nm separations. The peak is absent in the bulk, although it is close to the intermolecular -O-O-O- bending mode well known in liquid water. We further explore the relationship between diffusion and viscosity in NCW by varying d.

Experimental Confirmation of the Universal Law for the Vibrational Density of States of Liquids

An analytical model describing the vibrational density of states (VDOS) of liquids has long been elusive, owing to the complexities of liquid dynamics. Nevertheless, Zaccone and Baggioli have recently developed such a model which was proposed to be the universal law for the vibrational density of states of liquids. Distinct from the Debye law, g(ω) ∝ ω², for solids, the universal law for liquids reveals a linear relationship, g(ω) ∝ ω, in the low-energy region. We have confirmed this universal law with experimental VDOS measured by inelastic neutron scattering on real liquid systems including water, liquid metal, and polymer liquids, and have applied this model to extract the effective relaxation rate for the short time dynamics for each liquid. The model has also been further evaluated in the prediction of the specific heat with comparison to existing experimental data as well as with values obtained by different approaches.

Understanding cytoskeletal avalanches using mechanical stability analysis

Eukaryotic cells are mechanically supported by a polymer network called the cytoskeleton, which consumes chemical energy to dynamically remodel its structure. Recent experiments in vivo have revealed that this remodeling occasionally happens through anomalously large displacements, reminiscent of earthquakes or avalanches. These cytoskeletal avalanches might indicate that the cytoskeleton's structural response to a changing cellular environment is highly sensitive, and they are therefore of significant biological interest. However, the physics underlying "cytoquakes" is poorly understood. Here, we use agent-based simulations of cytoskeletal self-organization to study fluctuations in the network's mechanical energy. We robustly observe non-Gaussian statistics and asymmetrically large rates of energy release compared to accumulation in a minimal cytoskeletal model. The large events of energy release are found to correlate with large, collective displacements of the cytoskeletal filaments. We also find that the changes in the localization of tension and the projections of the network motion onto the vibrational normal modes are asymmetrically distributed for energy release and accumulation. These results imply an avalanche-like process of slow energy storage punctuated by fast, large events of energy release involving a collective network rearrangement. We further show that mechanical instability precedes cytoquake occurrence through a machine-learning model that dynamically forecasts cytoquakes using the vibrational spectrum as input. Our results provide a connection between the cytoquake phenomenon and the network's mechanical energy and can help guide future investigations of the cytoskeleton's structural susceptibility.

Multipolar Force Fields for Amide-I Spectroscopy from Conformational Dynamics of the Alanine Trimer

The dynamics and spectroscopy of N-methyl-acetamide (NMA) and trialanine in solution are characterized from molecular dynamics simulations using different energy functions, including a conventional point charge (PC)-based force field, one based on a multipolar (MTP) representation of the electrostatics, and a semiempirical DFT method. For the 1D infrared spectra, the frequency splitting between the two amide-I groups is 10 cm^-1 from the PC, 13 cm^-1 from the MTP, and 47 cm^-1 from self-consistent charge density functional tight-binding (SCC-DFTB) simulations, compared with 25 cm^-1 from experiment. The frequency trajectory required for the frequency fluctuation correlation function (FFCF) is determined from individual normal mode (INM) and full normal mode (FNM) analyses of the amide-I vibrations. The spectroscopy, time-zero magnitude of the FFCF C(t = 0), and the static component Δ₀² from simulations using MTP and analysis based on FNM are all consistent with experiments for (Ala)₃. Contrary to this, for the analysis excluding mode-mode coupling (INM), the FFCF decays to zero too rapidly and for simulations with a PC-based force field, the Δ₀² is too small by a factor of two compared with experiments. Simulations with SCC-DFTB agree better with experiment for these observables than those from PC-based simulations. The conformational ensemble sampled from simulations using PCs is consistent with the literature (including P_II, β, α_R, and α_L), whereas that covered by the MTP-based simulations is dominated by P_II with some contributions from β and α_R. This agrees with and confirms recently reported Bayesian-refined populations based on 1D infrared experiments. FNM analysis together with a MTP representation provides a meaningful model to correctly describe the dynamics of hydrated trialanine.

Terahertz pump-probe of liquid water at 12.3 THz

The dynamical complexity of the hydrogen-bonded water network can be investigated with intense Terahertz (THz) spectroscopy, which can drive the liquid into the nonlinear response regime and probe anharmonicity effects. Here we report single-color and polarization-dependent pump–probe experiments at 12.3 THz on liquid water, exciting the librational mode. By comparing results obtained on a static sample and a free-flowing water jet, we are able to disentangle the distinct contributions by thermal, acoustic, and nonlinear optical effects. We show that the transient transmission by the static water layer on a time scale of hundreds of microseconds can be described by thermal (slow) and acoustic (temperature-dependent) effects. In addition, during pump probe overlap we observe an anisotropic nonlinear optical response. This nonlinear signal is more prominent in the liquid jet than in the static cell, where temperature and density perturbations are more pronounced. Our measurements confirm that the THz excitation resonates with the rotationally-damped motion of water molecules, resulting in enhanced transient anisotropy. This model can be used to explain the non-linear response of water in the frequency range between about 1 and 20 THz.

The excitation on the librational band of liquid water at 12.3 THz resonates with the rotationally-damped motion of water molecules.

Quantification of Starch Order in Physically Modified Rice Flours Using Small-Angle X-ray Scattering (SAXS) and Fourier Transform Infrared (FT-IR) Spectroscopy

The purpose of this study was to understand the ordered structure of starch in rice flour based on a physical modification with non-heating, milling, and water sorption through the structural evaluation of rice flour using small-angle X-ray scattering (SAXS) and infrared spectroscopy within the 4000-100 cm^-1 region. The SAXS pattern of the samples with low moisture contents subjected to milling yield a band within the 0.4-0.9 nm^-1 of the q range owing to a lamellar repeat of starch with an ordered structure in rice flour. We proposed an order parameter using the intensity of the SAXS band to quantify the order structure of starch in rice flour, and the true density was negatively correlated with the order parameter. Infrared band at 990 cm^-1 in COH bending mode applied to the hydroxyl group of C6 shifted to a low wavenumber corresponding to the order parameter. A linear correlation was found between the order parameter and the 990 cm^-1 and band at 861 cm^-1 owing to COC symmetrical stretching of glycoside bond and CH₂ deformation of the glucose unit of starch, 572, 472, and 436 cm^-1, owing to the pyranose ring in the glucose unit of starch. The identified infrared bands are effective for quantifying the ordered structure of starch at the lamellar level. When subjected to water sorption, the band position at 990 cm^-1 shifted to a higher wavenumber above a water activity of 0.7. This result revealed that the water-induced transition of glass to rubber of starch in rice flour can be clearly evaluated through infrared spectroscopy using the band at 990 cm^-1. In addition, the band at 861 cm^-1 also shifted to a higher wavenumber, whereas those at 572 and 436 cm^-1 did not show a significant shift. These results indicate that water sorption slightly affects the internal structure and may mainly affect the surface of starch.

Exploring the Franck-Condon region of a photoexcited charge transfer complex in solution to interpret femtosecond stimulated Raman spectroscopy: excited state electronic structure methods to unveil non-radiative pathways

We present electronic structure methods to unveil the non-radiative pathways of photoinduced charge transfer (CT) reactions that play a main role in photophysics and light harvesting technologies. A prototypical π-stacked molecular complex consisting of an electron donor (1-chloronaphthalene, 1ClN) and an electron acceptor (tetracyanoethylene, TCNE) was investigated in dichloromethane solution for this purpose. The characterization of TCNE:π:1ClN in both its equilibrium ground and photoinduced low-lying CT electronic states was performed by using a reliable and accurate theoretical-computational methodology exploiting ab initio molecular dynamics simulations. The structural and vibrational time evolution of key vibrational modes is found to be in excellent agreement with femtosecond stimulated Raman spectroscopy experiments [R. A. Mathies et al., J. Phys. Chem. A, 2018, 122, 14, 3594], unveiling a correlation between vibrational fingerprints and electronic properties. The evaluation of nonadiabatic coupling matrix elements along generalized normal modes has made possible the interpretation on the molecular scale of the activation of nonradiative relaxation pathways towards the ground electronic state. In particular, two low frequency vibrational modes such as the out of plane bending and dimer breathing and the TCNE central C[double bond, length as m-dash]C stretching play a prominent role in relaxation phenomena from the electronic CT state to the ground state one.

Modeling the structure and infrared spectra of omega-3 fatty acid esters

Omega-3 dietary supplements provide a rich source of the active moieties eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), which exist in the form of triacylglycerols or ethyl esters. Infrared (IR) spectroscopy provides a rapid and quantitative tool to assess the quality of these products as specific normal modes, in particular the ester carbonyl stretch modes, exhibit characteristic spectral features for the two ester forms of omega-3 fatty acids. To uncover the origin of the observed spectra, in this work, we perform molecular dynamics simulations of EPA and DHA ethyl esters and triacylglycerols to characterize their conformation, packing, and dynamics in the liquid phase and use a mixed quantum/classical approach to calculate their IR absorption spectra in the ester carbonyl stretch region. We show that the ester liquids exhibit slow dynamics in spectral diffusion and translational and rotational motion, consistent with the diffusion ordered NMR spectroscopy measurements. We further demonstrate that the predicted IR spectra are in good agreement with experiments and reveal how a competition between intermolecular and intramolecular interactions gives rise to distinct absorption peaks for the fatty acid esters.

Persistent Protein Motions in a Rugged Energy Landscape Revealed by Normal Mode Ensemble Analysis

Proteins are allosteric machines that couple motions at distinct, often distant, sites to control biological function. Low-frequency structural vibrations are a mechanism of this long-distance connection and are often used computationally to predict correlations, but experimentally identifying the vibrations associated with specific motions has proved challenging. Spectroscopy is an ideal tool to explore these excitations, but measurements have been largely unable to identify important frequency bands. The result is at odds with some previous calculations and raises the question what methods could successfully characterize protein structural vibrations. Here we show the lack of spectral structure arises in part from the variations in protein structure as the protein samples the energy landscape. However, by averaging over the energy landscape as sampled using an aggregate 18.5 μs of all-atom molecular dynamics simulation of hen egg white lysozyme and normal-mode analyses, we find vibrations with large overlap with functional displacements are surprisingly concentrated in narrow frequency bands. These bands are not apparent in either the ensemble averaged vibrational density of states or isotropic absorption. However, in the case of the ensemble averaged anisotropic absorption, there is persistent spectral structure and overlap between this structure and the functional displacement frequency bands. We systematically lay out heuristics for calculating the spectra robustly, including the need for statistical sampling of the protein and inclusion of adequate water in the spectral calculation. The results show the congested spectrum of these complex molecules obscures important frequency bands associated with function and reveal a method to overcome this congestion by combining structurally sensitive spectroscopy with robust normal mode ensemble analysis.

Multiresolution continuous wavelet transform for studying coupled solute-solvent vibrations via ab initio molecular dynamics

Vibrational analysis in solution and the theoretical determination of infrared and Raman spectra are of key importance in many fields of chemical interest. Vibrational band dynamics of molecules and their sensitivity to the environment can also be captured by these spectroscopies in their time dependent version. However, it is often difficult to provide an interpretation of the experimental data at the molecular scale, such as molecular mechanisms or the processes hidden behind them. In this work, we present a theoretical-computational protocol based on ab initio molecular dynamics simulations and a combination of normal-like (generalized) mode analysis of solute-solvent clusters with a wavelet transform, for the first time. The case study is the vibrational dynamics of N-methyl-acetamide (NMA) in water solution, a well-known model of hydration of peptides and proteins. Amide modes are typical bands of peptide and protein backbone, and their couplings with the environment are very challenging in terms of the accurate prediction of solvent induced intensity and frequency shifts. The contribution of water molecules surrounding NMA to the composition of generalized and time resolved modes is introduced in our vibrational analysis, showing unequivocally its influence on the amide mode spectra. It is also shown that such mode compositions need the inclusion of the first shell solvent molecules to be accurately described. The wavelet analysis is proven to be strongly recommended to follow the time evolution of the spectra, and to capture vibrational band couplings and frequency shifts over time, preserving at the same time a well-balanced time-frequency resolution. This peculiar feature also allows one to perform a combined structural-vibrational analysis, where the different strengths of hydrogen bond interactions can quantitatively affect the amide bands over time at finite temperature. The proposed method allows for the direct connection between vibrational modes and local structural changes, providing a link from the spectroscopic observable to the structure, in this case the peptide backbone, and its hydration layouts.

Low-Frequency (Gigahertz to Terahertz) Depolarized Raman Scattering Off n-Alkanes, Cycloalkanes, and Six-Membered Rings: A Physical Interpretation

Molecular liquids have long been known to undergo various distinct intermolecular motions, from fast librations and cage-rattling oscillations to slow orientational and translational diffusion. However, their resultant gigahertz to terahertz spectra are far from simple, appearing as broad shapeless bands that span many orders of magnitude of frequency, making meaningful interpretation troublesome. Ad hoc spectral line shape fitting has become a notoriously fine art in the field; a unified approach to handling such spectra is long overdue. Here we apply ultrafast optical Kerr-effect (OKE) spectroscopy to study the intermolecular dynamics of room-temperature n-alkanes, cycloalkanes, and six-carbon rings, as well as liquid methane and propane. This work provides stress tests and converges upon an experimentally robust model across simple molecular series and range of temperatures, providing a blueprint for the interpretation of the dynamics of van der Waals liquids. This will enable the interpretation of low-frequency spectra of more complex liquids.

Molecular Structure and Modeling of Water-Air and Ice-Air Interfaces Monitored by Sum-Frequency Generation

From a glass of water to glaciers in Antarctica, water-air and ice-air interfaces are abundant on Earth. Molecular-level structure and dynamics at these interfaces are key for understanding many chemical/physical/atmospheric processes including the slipperiness of ice surfaces, the surface tension of water, and evaporation/sublimation of water. Sum-frequency generation (SFG) spectroscopy is a powerful tool to probe the molecular-level structure of these interfaces because SFG can specifically probe the topmost interfacial water molecules separately from the bulk and is sensitive to molecular conformation. Nevertheless, experimental SFG has several limitations. For example, SFG cannot provide information on the depth of the interface and how the orientation of the molecules varies with distance from the surface. By combining the SFG spectroscopy with simulation techniques, one can directly compare the experimental data with the simulated SFG spectra, allowing us to unveil the molecular-level structure of water-air and ice-air interfaces. Here, we present an overview of the different simulation protocols available for SFG spectra calculations. We systematically compare the SFG spectra computed with different approaches, revealing the advantages and disadvantages of the different methods. Furthermore, we account for the findings through combined SFG experiments and simulations and provide future challenges for SFG experiments and simulations at different aqueous interfaces.

On the role of intermolecular vibrational motions for ice polymorphs. II. Atomic vibrational amplitudes and localization of phonons in ordered and disordered ices

We investigate the vibrational amplitudes and the degree of the phonon localization in 19 ice forms, both crystalline and amorphous, by a quasi-harmonic approximation with a reliable classical intermolecular interaction model for water. The amplitude in the low pressure ices increases with compression, while the opposite trend is observed in the medium and high pressure ices. The amplitude of the oxygen atom does not differ from that of hydrogen in low pressure ices apart from the contribution from the zero-point vibrations. This is accounted for by the coherent but opposite phase motions in the mixed translational and rotational vibrations. A decoupling of translation-dominant and rotation-dominant motions significantly reduces the vibrational amplitudes in any ice form. The amplitudes in ice III are found to be much larger than any other crystalline ice form. In order to investigate the vibrational mode characteristics, the moment ratio of the atomic displacements for individual phonon modes, called the inverse participation ratio, is calculated and the degree of the phonon localization in crystalline and amorphous ices is discussed. It is found that the phonon modes in the hydrogen-ordered ice forms are remarkably spread over the entire crystal having propagative or diffusive characteristic, while many localized modes appear at the edges of the vibrational bands, called dissipative modes, in the hydrogen-disordered counterparts. The degree of localization is little pronounced in low density amorphous and high density amorphous due to disordering of oxygen atoms.

Ab Initio Investigation of the Resonance Raman Spectrum of the Hydrated Electron

According to the conventional picture, the aqueous or "hydrated" electron, e^-(aq), occupies an excluded volume (cavity) in the structure of liquid water. However, simulations with certain one-electron models predict a more delocalized spin density for the unpaired electron, with no distinct cavity structure. It has been suggested that only the latter (non-cavity) structure can explain the hydrated electron's resonance Raman spectrum, although this suggestion is based on calculations using empirical frequency maps developed for neat liquid water, not for e^-(aq). All-electron ab initio calculations presented here demonstrate that both cavity and non-cavity models of e^-(aq) afford significant red-shifts in the O-H stretching region. This effect is nonspecific and arises due to electron penetration into frontier orbitals of the water molecules. Only the conventional cavity model, however, reproduces the splitting of the H-O-D bend (in isotopically mixed water) that is observed experimentally and arises due to the asymmetric environments of the hydroxyl moieties in the electron's first solvation shell. We conclude that the cavity model of e^-(aq) is more consistent with the measured resonance Raman spectrum than is the delocalized, non-cavity model, despite previous suggestions to the contrary. Furthermore, calculations with hybrid density functionals and with Hartree-Fock theory predict that non-cavity liquid geometries afford only unbound (continuum) states for an extra electron, whereas in reality this energy level should lie more than 3 eV below vacuum level. As such, the non-cavity model of e^-(aq) appears to be inconsistent with available vibrational spectroscopy, photoelectron spectroscopy, and quantum chemistry.

Hydrogen-Bonding in Liquid Water at Multikilobar Pressures

High-precision THz (30 to 360 cm^-1) spectra of bulk liquid water are presented from ambient conditions up to hydrostatic pressures of 10 kbar. In concert with ab initio simulations, this allows us to characterize the molecular-level changes of the H-bond network under solvent stress conditions. Both the experimental and theoretical THz spectra reveal a blue shift in the intermolecular translational mode at 180 cm^-1 by 40 cm^-1 at 10 kbar and a blue shift together with an intensity increase in the relaxation mode. These changes can be traced back to a pressure-induced increase of the population of so-called short H-bond double donor configurations at the expense of those with longer such intermolecular bonds. Distinct electronic polarization effects are critical to capture the characteristic intensity changes of the THz line shape function. These advances in high-pressure THz spectroscopy open the door to investigate the pressure response of solvation shells and solute-solvent couplings.

Pressure response of the THz spectrum of bulk liquid water revealed by intermolecular instantaneous normal mode analysis

The radial distribution functions of liquid water are known to change significantly their shape upon hydrostatic compression from ambient conditions deep into the kbar pressure regime. It has been shown that despite their eye-catching changes, the fundamental locally tetrahedral fourfold H-bonding pattern that characterizes ambient water is preserved up to about 10 kbar (1 GPa), which is the stability limit of liquid water at 300 K. The observed increase in coordination number comes from pushing water molecules into the first coordination sphere without establishing an H-bond, resulting in roughly two such additional interstitial molecules at 10 kbar. THz spectroscopy has been firmly established as a powerful experimental technique to analyze H-bonding in aqueous solutions given that it directly probes the far-infrared lineshape and thus the prominent H-bond network mode around 180 cm^-1. We, therefore, set out to assess pressure effects on the THz response of liquid water at 10 kbar in comparison to the 1 bar (0.1 MPa) reference, both at 300 K, with the aim to trace back the related lineshape changes to the structural level. To this end, we employ the instantaneous normal mode approximation to rigorously separate the H-bonding peak from the large background arising from the pronounced librational tail. By exactly decomposing the total molecular dynamics into hindered translations, hindered rotations, and intramolecular vibrations, we find that the H-bonding peak arises from translation-translation and translation-rotation correlations, which are successively decomposed down to the level of distinct local H-bond environments. Our utmost detailed analysis based on molecular pair classifications unveils that H-bonded double-donor water pairs contribute most to the THz response around 180 cm^-1, whereas interstitial waters are negligible. Moreover, short double-donor H-bonds have their peak maximum significantly shifted toward higher frequencies with respect to such long H-bonds. In conjunction with an increasing relative population of these short H-bonds versus the long ones (while the population of other water pair classes is essentially pressure insensitive), this explains not only the blue-shift of the H-bonding peak by about 20-30 cm^-1 in total from 1 bar to 10 kbar but also the filling of the shallow local minimum of the THz lineshape located in between the network peak and the red-wing of the librational band at 1 bar. Based on the changing populations as a function of pressure, we are also able to roughly estimate the pressure-dependence of the H-bond network mode and find that its pressure response and thus the blue-shifting are most pronounced at low kbar pressures.

Mechanism of Solvent Control of Protein Dynamics

We find that the coupled interactions between protein and water polarization fluctuations play a dominant role in driving the configuration space random walk of solvated proteins. We perform atomistic molecular dynamics simulations on five proteins. Owing to a very low dielectric constant of protein, its dipolar groups experience forces from water along with local forces due to protein atoms. Energy fluctuations reveal a pronounced anticorrelation between protein and water contributions. The protein energy spectrum shows bimodal 1/f noise, which can be attributed to the influence of water on the dynamics of protein.

Reconsideration of the relaxational and vibrational line shapes of liquid water based on ultrabroadband dielectric spectroscopy

The Debye relaxation function is widely used to describe the large dielectric dispersion of ambient water around 20 GHz. However, from a theoretical point of view, this function is supposed to give incorrect predictions at high frequencies owing to the inappropriate assumption that inertial effects and intermolecular interactions do not affect the relaxation dynamics. Our ultrabroadband spectroscopy investigation of liquid water ranging from 500 MHz to 400 THz did demonstrate that the Debye function is inaccurate far above the microwave region. As an alternative, we tried a stochastic frequency modulation (SFM) model assuming instantaneous modification of the line shapes by the correlation with the surrounding system. The SFM relaxation model reproduced the experimental dielectric spectra up to 400 THz, showing that the hydrogen-bond dynamics are associated with the inertial effect that causes the non-exponential relaxation behaviour in a very short time (typically 25 fs). Within the framework of this relaxation model, the hindered translation modes are able to be approximated as fast modulation (homogeneous) line shapes because the interaction time with frequency modulation is too short. Compared with them, the libation mode is found to have a relatively slow modulation (inhomogeneous) origin, where disturbance of water hydrogen bonds induced by the hindered translations leads to fluctuations in the libration frequency.

Delocalization and stretch-bend mixing of the HOH bend in liquid water

Liquid water's rich sub-picosecond vibrational dynamics arise from the interplay of different high- and low-frequency modes evolving in a strong yet fluctuating hydrogen bond network. Recent studies of the OH stretching excitations of H₂O indicate that they are delocalized over several molecules, raising questions about whether the bending vibrations are similarly delocalized. In this paper, we take advantage of an improved 50 fs time-resolution and broadband infrared (IR) spectroscopy to interrogate the 2D IR lineshape and spectral dynamics of the HOH bending vibration of liquid H₂O. Indications of strong bend-stretch coupling are observed in early time 2D IR spectra through a broad excited state absorption that extends from 1500 cm^-1 to beyond 1900 cm^-1, which corresponds to transitions from the bend to the bend overtone and OH stretching band between 3150 and 3550 cm^-1. Pump-probe measurements reveal a fast 180 fs vibrational relaxation time, which results in a hot-ground state spectrum that is the same as observed for water IR excitation at any other frequency. The fastest dynamical time scale is 80 fs for the polarization anisotropy decay, providing evidence for the delocalized or excitonic character of the bend. Normal mode analysis conducted on water clusters extracted from molecular dynamics simulations corroborate significant stretch-bend mixing and indicate delocalization of δ_HOH on 2-7 water molecules.

Nanoscale Mobility of Aqueous Polyacrylic Acid in Dental Restorative Cements

Hydrogen dynamics in a time range from hundreds of femtoseconds to nanoseconds can be directly analyzed using neutron spectroscopy, where information on the inelastic and quasi-elastic scattering, hereafter INS and QENS, can be obtained. In this study, we applied these techniques to understand how the nanoscale mobility of the aqueous solution of polyacrylic acid (PAA) used in conventional glass ionomer cements (GICs) changes under confinement. Combining the spectroscopic analysis with calorimetric results, we were able to separate distinct motions within both the liquid and the GICs. The QENS analysis revealed that the self-diffusion translational motion identified in the liquid is also visible in the GIC. However, as a result of the formation of the cement matrix and its setting, both translational diffusion and residence time differed from the PAA solution. When comparing the local diffusion obtained for the selected GIC, the only noticeable difference was observed for the slow dynamics associated with the polymer chain. Additionally, over short-term aging, progressive water binding to the polymer chain occurred in one of the investigated GICs. Finally, a considerable change in the density of the GIC without progressive water binding indicates an increased polymer cross-linking. Taken together, our results suggest that accurate and deep understanding of polymer-water binding, polymer cross-linking, as well as material density changes occurring during the maturation process of GIC are necessary for the development of advanced dental restorative materials.