Simulation of the intermolecular vibrational spectra of liquid water and water clusters

Terahertz Spectra of Mannitol and Erythritol: A Joint Experimental and Computational Study

Sugar substitutes, which generally refer to a class of food additives, mostly have vibration frequencies within the terahertz (THz) band. Therefore, THz technology can be used to analyze their molecular properties. To understand the characteristics of sugar substitutes, this study selected mannitol and erythritol as representatives. Firstly, PXRD and Raman techniques were used to determine the crystal structure and purity of mannitol and erythritol. Then, the THz time-domain spectroscopy (THz-TDS) system was employed to measure the spectral properties of the two sugar substitutes. Additionally, density functional theory (DFT) was utilized to simulate the crystal configurations of mannitol and erythritol. The experimental results showed good agreement with the simulation results. Finally, microfluidic chip technology was used to measure the THz spectroscopic properties of the two sugar substitutes in solution. A comparison was made between their solid state and aqueous solution state, revealing a strong correlation between the THz spectra of the two sugar substitutes in both states. Additionally, it was found that the THz spectrum of a substance in solution is related to its concentration. This study provides a reference for the analysis of sugar substitutes.

TMAO perturbs intermolecular vibrational motions of water revealed by low-frequency modes

Trimethylamine N-oxide (TMAO) as a representative natural osmolyte has received much attention because of its unique properties, including enhancement of hydrogen bonding networks in liquid water and stabilization of three-dimensional structures of proteins in living organisms. As a hydrogen bond maker and/or a protein stabilizer, its hydrated structures and orientation dynamics in aqueous solutions have been investigated by various spectroscopic methods. Particularly, distinct from other natural osmolytes, it has been found that TMAO molecules form complexes with water molecules even at low concentrations, showing extraordinarily long lifetimes and much larger effective dipole moments. In this study, we demonstrated that collective motions of water molecules are closely correlated to TMAO molecules, as revealed by the changes of the librational modes observed in hyper-Raman (HR) spectra in the low-frequency region (<1000 cm-1) for the first time. Based on HR spectra of the TMAO solutions at submolar concentrations, we observed that the librational bands originating from water apparently upshift (∼15 cm-1) upon the addition of TMAO molecules. Compared to the OH stretching band of water showing a negligible downshift (<5 cm-1), the librational bands of water are more sensitive to reflect changes in the hydrogen bonding networks in the TMAO solutions, suggesting formation of transient TMAO-water complexes plays an essential role toward surrounding water molecules in perturbing their librational motions. We expect to provide a supplementary approach to understand that water molecules in TMAO aqueous solutions are strongly affected by TMAO molecules, different from other osmolytes.

Lifting Hofmeister's Curse: Impact of Cations on Diffusion, Hydrogen Bonding, and Clustering of Water

Water plays a role in the stability, reactivity, and dynamics of the solutes that it contains. The presence of ions alters this capacity by changing the dynamics and structure of water. However, our understanding of how and to what extent this occurs is still incomplete. Here, a study of the low-frequency Raman spectra of aqueous solutions of various cations by using optical Kerr-effect spectroscopy is presented. This technique allows for the measurement of the changes that ions cause in both the diffusive dynamics and the vibrations of the hydrogen-bond structure of water. It is found that when salts are added, some of the water molecules become part of the ion solvation layers, while the rest retain the same diffusional properties as those of pure water. The slowing of the dynamics of the water molecules in the solvation shell of each ion was found to depend on its charge density at infinite dilution conditions and on its position in the Hofmeister series at higher concentrations. It is also observed that all cations weaken the hydrogen-bond structure of the solution and that this weakening depends only on the size of the cation. Finally, evidence is found that ions tend to form amorphous aggregates, even at very dilute concentrations. This work provides a novel approach to water dynamics that can be used to better study the mechanisms of solute nucleation and crystallization, the structural stability of biomolecules, and the dynamic properties of complex solutions, such as water-in-salt electrolytes.

Chirped pulse Fourier-transform microwave spectroscopy of alcohol and water tetramers

In an effort to build towards quantitative models of alcohol:water microaggregation in liquid mixtures, the present works characterizes the energy landscape and structures of pure ethanol and mixed ethanol:water tetramers using Chirped Pulse Fourier-transform Microwave spectroscopy. Many conformers of each type of tetramer are available, and those with sufficiently strong dipole moments are experimentally examined. This analysis considers, but does not explicitly fit, the splitting of rotational states due to internal rotation of the methyl groups present, as well as utilizes isotopic substitution experiments to verify the conformer variations observed. Implications of the listed results include a suggestion of the stability of micro-aggregated structures as opposed to homogeneously mixed clusters, informing future work on characterization of larger clusters and any potential modeling of the hydrogen bond network at play.

Terahertz spectral properties of glucose and two disaccharides in solid and liquid states

The vibrational and rotational frequencies of most biological macromolecules fall within the terahertz (THz) band; therefore, the THz wave has a strong ability to distinguish substances. Saccharides are important organic substances and the main source of life-sustaining activities. In this study, the spectral characteristics of D-glucose, α-lactose hydrate, and β-maltose hydrate were measured in the solid state through THz time-domain spectroscopy in the frequency range of 0.1–2.5 THz. The crystal configurations of these three saccharides were then simulated using solid-state density functional theory, and the experimental results were found to be in good agreement with the simulation results. Furthermore, the spectral characteristics of the three saccharides in solutions were measured. Each saccharide was found to have unique spectral characteristics, and a correlation existed between the THz absorption spectra of the same substance in the solid state and aqueous solution.

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Solid D-glucose, α-lactose hydrate, and β-maltose hydrate have unique absorption peaks

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The simulated results of the three saccharides are consistent with the experimental ones

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The THz spectra of the three saccharides in solid and aqueous solutions are correlated

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.

Energy transfer within the hydrogen bonding network of water following resonant terahertz excitation

Energy dissipation in water is very fast and more efficient than in many other liquids. This behavior is commonly attributed to the intermolecular interactions associated with hydrogen bonding. Here, we investigate the dynamic energy flow in the hydrogen bond network of liquid water by a pump-probe experiment. We resonantly excite intermolecular degrees of freedom with ultrashort single-cycle terahertz pulses and monitor its Raman response. By using ultrathin sample cell windows, a background-free bipolar signal whose tail relaxes monoexponentially is obtained. The relaxation is attributed to the molecular translational motions, using complementary experiments, force field, and ab initio molecular dynamics simulations. They reveal an initial coupling of the terahertz electric field to the molecular rotational degrees of freedom whose energy is rapidly transferred, within the excitation pulse duration, to the restricted translational motion of neighboring molecules. This rapid energy transfer may be rationalized by the strong anharmonicity of the intermolecular interactions.

Ice-VII-like molecular structure of ambient water nanomeniscus

Structural transformations originating from diverse rearrangements of the hydrogen bonding in water create various phases. Although most phases have been well investigated down to the molecular level, the molecular structure of the nanomeniscus, a ubiquitous form of nanoscale water in nature, still remains unexplored. Here, we demonstrate that the water nanomeniscus exhibits the stable, ice-VII-like molecular structure in ambient condition. Surface-enhanced Raman spectroscopy on trace amounts of water, confined in inter-nanoparticle gaps, shows a narrowed tetrahedral peak at 3340 cm^-1 in the OH-stretching band as well as a lattice-vibrational mode at 230 cm^-1. In particular, the ice-VII-like characteristics are evidenced by the spectral independence with respect to temperature variations and differing surface types including the material, size and shape of nanoparticles. Our results provide un unambiguous identification of the molecular structure of nanoconfined water, which is useful for understanding the molecular aspects of water in various nanoscale, including biological, environments.

Application of classical simulations for the computation of vibrational properties of free molecules

In this study, we investigate the ability of classical molecular dynamics (MD) and Monte-Carlo (MC) simulations for modeling the intramolecular vibrational motion. These simulations were used to compute thermally-averaged geometrical structures and infrared vibrational intensities for a benchmark set previously studied by gas electron diffraction (GED): CS₂, benzene, chloromethylthiocyanate, pyrazinamide and 9,12-I₂-1,2-closo-C₂B₁₀H₁₀. The MD sampling of NVT ensembles was performed using chains of Nose-Hoover thermostats (NH) as well as the generalized Langevin equation thermostat (GLE). The performance of the theoretical models based on the classical MD and MC simulations was compared with the experimental data and also with the alternative computational techniques: a conventional approach based on the Taylor expansion of potential energy surface, path-integral MD and MD with quantum-thermal bath (QTB) based on the generalized Langevin equation (GLE). A straightforward application of the classical simulations resulted, as expected, in poor accuracy of the calculated observables due to the complete neglect of quantum effects. However, the introduction of a posteriori quantum corrections significantly improved the situation. The application of these corrections for MD simulations of the systems with large-amplitude motions was demonstrated for chloromethylthiocyanate. The comparison of the theoretical vibrational spectra has revealed that the GLE thermostat used in this work is not applicable for this purpose. On the other hand, the NH chains yielded reasonably good results.

Water Librations in the Hydration Shell of Phospholipids

The hydrophilic phosphate moiety in the headgroup of phospholipids forms strong hydrogen bonds with water molecules in the first hydration layer. Time-domain terahertz spectroscopy in a range from 100 to 1000 cm^-1 reveals the influence of such interactions on rotations of water molecules. We determine librational absorption spectra of water nanopools in phospholipid reverse micelles for a range from w₀ = 2 to 16 waters per phospholipid molecule. A pronounced absorption feature with maximum at 830 cm^-1 is superimposed on a broad absorption band between 300 and 1000 cm^-1. Molecular dynamics simulations of water in the reverse micelles suggest that the feature at 830 cm^-1 arises from water molecules forming one or two strong hydrogen bonds with phosphate groups, while the broad component comes from bulk-like environments. This behavior is markedly different from water interacting with less polar surfaces.

Proton mobility in aqueous systems: combining ab initio accuracy with millisecond timescales

Development of a combined molecular dynamics/kinetic Monte Carlo scheme for the modeling of excess charge transport in water.

Surface-enhanced infrared absorption studies towards a new optical biosensor

Reflectometric interference spectroscopy (RIfS), which is well-established in the visual regime, measures the optical thickness change of a sensitive layer caused, e.g., by binding an analyte. When operated in the mid-infrared range the sensor provides additional information via weak absorption spectra (fingerprints). The originally poor spectra are magnified by surface-enhanced infrared absorption (SEIRA). This is demonstrated using the broad complex fluid water band at 3300 cm-1, which is caused by superposition of symmetric, antisymmetric stretching vibration, and the first overtone of the bending vibration under the influence of H-bonds and Fermi resonance effect. The results are compared with a similar experiment performed with an ATR (attenuated total reflectance) set-up.

Local, solvation pressures and conformational changes in ethylenediamine aqueous solutions probed using Raman spectroscopy

Raman spectra of 1,2-ethylenediamine (EDA) in aqueous solutions are used to demonstrate that EDA molecules experience an anti-gauche conformational change resulting from the interactions with water. The observed Raman shift reveals a compressive (hydrophobic) effect of water on both methylene and amino groups of EDA. Raman spectra of EDA at high pressures are used as reference to quantify the intermolecular EDA-H₂O interactions in terms of local pressures. These results are compared with macroscopic solvation pressures calculated from the cohesive energy parameter. We compare and discuss all our observations with available computational and experimental studies.

The hydrogen-bond network of water supports propagating optical phonon-like modes

The local structure of liquid water as a function of temperature is a source of intense research. This structure is intimately linked to the dynamics of water molecules, which can be measured using Raman and infrared spectroscopies. The assignment of spectral peaks depends on whether they are collective modes or single-molecule motions. Vibrational modes in liquids are usually considered to be associated to the motions of single molecules or small clusters. Using molecular dynamics simulations, here we find dispersive optical phonon-like modes in the librational and OH-stretching bands. We argue that on subpicosecond time scales these modes propagate through water's hydrogen-bond network over distances of up to 2 nm. In the long wavelength limit these optical modes exhibit longitudinal–transverse splitting, indicating the presence of coherent long-range dipole–dipole interactions, as in ice. Our results indicate the dynamics of liquid water have more similarities to ice than previously thought.

How the local structure of water varies as a function of temperature is a long-studied topic, which is still under debate. Here, the authors show that dielectric susceptibility measurements might be used to probe and identify propagating optical phonon-like modes in the hydrogen-bond network of water.

Infrared and Raman Spectroscopy of Liquid Water through "First-Principles" Many-Body Molecular Dynamics

Vibrational spectroscopy is a powerful technique to probe the structure and dynamics of water. However, deriving an unambiguous molecular-level interpretation of the experimental spectral features remains a challenge due to the complexity of the underlying hydrogen-bonding network. In this contribution, we present an integrated theoretical and computational framework (named many-body molecular dynamics or MB-MD) that, by systematically removing uncertainties associated with existing approaches, enables a rigorous modeling of vibrational spectra of water from quantum dynamical simulations. Specifically, we extend approaches used to model the many-body expansion of interaction energies to develop many-body representations of the dipole moment and polarizability of water. The combination of these "first-principles" representations with centroid molecular dynamics simulations enables the simulation of infrared and Raman spectra of liquid water under ambient conditions that, without relying on any ad hoc parameters, are in good agreement with the corresponding experimental results. Importantly, since the many-body energy, dipole, and polarizability surfaces employed in the simulations are derived independently from accurate fits to correlated electronic structure data, MB-MD allows for a systematic analysis of the calculated spectra in terms of both electronic and dynamical contributions. The present analysis suggests that, while MB-MD correctly reproduces both the shifts and the shapes of the main spectroscopic features, an improved description of quantum dynamical effects possibly combined with a dissociable water potential may be necessary for a quantitative representation of the OH stretch band.

Local hydration pressures in methanol aqueous solution: a Raman spectroscopy analysis

Raman spectra of methanol-water mixtures were measured over the whole composition range at room conditions. The spectra are used to quantify the strength of intermolecular interactions in terms of local internal pressures. The conclusions derived from the spectroscopic analysis are discussed within the framework of the solvation pressure model using values of the cohesion energy density expected in the mixture. This work demonstrates that an appropriate analysis of Raman spectroscopy experiments can be used to quantify the local internal pressures due to intermolecular interactions in liquid mixtures, provided that high pressure results of the pure liquids are available.

Comparison of the interfacial dynamics of water sandwiched between static and free-standing fully flexible graphene sheets

Classical molecular dynamics simulations are used to present a detailed atomistic picture of the instantaneous local structures of water and the structural evolution of stationary and dynamically evolving graphene-water interfaces. The confinement effects are strongly coupled to the nature of the interface, which eventually governs its nanoscopic structural arrangements and interface dynamics. We show that the structure, transport properties, and vibrational densities of states of proximal water molecules are strongly correlated with the nature of the graphene-water interface. We identify and correlate features in vibrational spectra with characteristic structural features observed at the atomic scale for the confined water molecules near a stationary and dynamically evolving hydrophobic surface such as graphene. Our simulations indicate that the local orientation, ordering, and solvation dynamics of interfacial water molecules are a strong function of the graphene slit-width, which is controlled by the nature of the interface (fully flexible vs. static). A monotonic decrease in local ordering with increasing slit-width was observed for the static graphene-water interface, whereas a non-monotonic variation was seen for its fully flexible counterpart. The simulation results offer useful insights into the effect of interfacial dynamics in defining the structure and transport properties at graphene-aqueous media interfaces. Finally these simulations provide a molecular level interpretation of the differential confinement effects arising from the dynamically evolving graphene-water interface.

Atomistic simulations of methane interactions with an atmospheric moisture

Methane is an extremely effective absorber of radiation, i.e., it is a relatively potent greenhouse gas, and the increased concentration of methane in the atmosphere must influence earth's radiation balance. The adsorption of one to six methane molecules by water clusters is studied by the method of molecular dynamics under near-atmospheric conditions. The capture of methane molecules by water clusters produces an increase in the integrated intensity of IR absorbance and the reflection coefficient. The Raman spectrum of the system is considerably depleted due to the addition of methane molecules to the disperse water system. The observed emission power of a dispersed aqueous system with adsorbed methane molecules has appreciably increased relative to the analogous characteristics of the pure water cluster system. The Voronoi polyhedra and simplified ones constructed within the framework of molecular-dynamic model of clusters are used for the analysis of the structure changes occurring with increasing the number of adsorbed CH4 molecules.

Fluctuations and Relaxation Dynamics of Liquid Water Revealed by Linear and Nonlinear Spectroscopy

Many efforts have been devoted to elucidating the intra- and intermolecular dynamics of liquid water because of their important roles in many fields of science and engineering. Nonlinear spectroscopy is a powerful tool to investigate the dynamics. Because nonlinear response functions are described by more than one time variable, it is possible to analyze static and dynamic mode couplings. Here we review the intra- and intermolecular dynamics of liquid water revealed by recent linear and nonlinear spectroscopic experiments and computer simulations. In particular, we discuss the population relaxation, anisotropy decay, and spectral diffusion of the intra- and intermolecular motions of water and their temperature dependence, which play important roles in ultrafast dynamics and relaxations in water.

H-bond network in amino acid cocrystals with H2O or H2O2. The DFT study of serine-H2O and serine-H2O2

The structure, IR spectrum, and H-bond network in the serine-H(2)O and serine-H(2)O(2) crystals were studied using DFT computations with periodic boundary conditions. Two different basis sets were used: the all-electron Gaussian-type orbital basis set and the plane wave basis set. Computed frequencies of the IR-active vibrations of the titled crystals are quite different in the range of 10-100 cm(-1). Harmonic approximation fails to reproduce IR active bands in the 2500-2800 frequency region of serine-H(2)O and serine-H(2)O(2). The bands around 2500 and 2700 cm(-1) do exist in the anharmonic IR spectra and are caused by the first overtone of the OH bending vibrations of H(2)O and a combination vibration of the symmetric and asymmetric bendings of H(2)O(2). The quantum-topological analysis of the crystalline electron density enables us to describe quantitatively the H-bond network. It is much more complex in the title crystals than in a serine crystal. Appearance of water leads to an increase of the energy of the amino acid-amino acid interactions, up to ~50 kJ/mol. The energy of the amino acid-water H-bonds is ~30 kJ/mol. The H(2)O/H(2)O(2) substitution does not change the H-bond network; however, the energy of the amino acid-H(2)O(2) contacts increases up to 60 kJ/mol. This is caused by the fact that H(2)O(2) is a much better proton donor than H(2)O in the title crystals.

Computer study of absorption of oxygen and ozone molecules by water clusters with Cl– and Br–

Infrared absorption and Raman spectra were calculated by using the molecular dynamics method for water clusters with chlorine and bromine ions in a medium of water and either ozone or oxygen molecules. The intensity of IR absorption spectra of clusters with absorbed oxygen increased and that of clusters with absorbed ozone decreased as the number of chlorine ions grew. When Br– were present in the system the inverse behaviour was observed. An increase in the number of ions weakened the intensity of the Raman spectra when either oxygen or ozone was absorbed; for ozone this weakening was more noticeable. A stronger reduction of the integrated intensity of the Raman spectrum with an increase in the number of Br– was observed in the presence of ozone molecules in the system. Cl– ions caused an amplification of the emission power of the IR radiation for both systems in the presence of oxygen and ozone, and Br– strengthened the emission of IR radiation for systems containing ozone, and weakened it for systems with oxygen molecules.

A model proton-transfer system in the condensed phase: NH4(+)OOH(-), a crystal with short intermolecular H-bonds

The crystal structure of NH(4)(+)OOH(-) is determined from single-crystal x-ray data obtained at 150 K. The crystal belongs to the space group P2(1)/c and has four molecules in a unit cell. The structure consists of discrete NH(4)(+) and OOH(-) ions. The OOH(-) ions are linked by short hydrogen bonds (2.533 Å) to form parallel infinite chains. The ammonium ions form links between these chains (the N⋯O distances vary from 2.714 to 2.855 Å) giving a three-dimensional network. The harmonic IR spectrum and H-bond energies are computed at the Perdew-Burke-Ernzerhof (PBE)/6-31G(∗∗) level with periodic boundary conditions. A detailed analysis of the shared (bridging) protons' dynamics is obtained from the CPMD simulations at different temperatures. PBE functional with plane-wave basis set (110 Ry) is used. At 10 K the shared proton sits near the oxygen atom, only a few proton jumps along the chain are detected at 70 K while at 270 K numerous proton jumps exist in the trajectory. The local-minimum structure of the space group Cc is localized. It appears as a result of proton transfer along a chain. This process is endothermic (∼2 kJ/mol) and is described as P2(1)/c↔2Cc. The computed IR spectrum at 10 K is close to the harmonic one, the numerous bands appear at 70 K while at 270 K it shows a very broad absorption band that covers frequencies from about 1000 to 3000 cm(-1). The advantages of the NH(4)(+)OOH(-) crystal as a promising model for the experimental and DFT based molecular dynamics simulation studies of proton transfer along the chain are discussed.