OD Stretch Mode Research Articles

Systematic investigation of coupling between symmetric and antisymmetric stretches of D2O in CHCl3 by 2D IR.

The coupling between the symmetric (νs) and antisymmetric (νa) OD stretch modes of monomeric D2O in CHCl3 is investigated using polarization-dependent two-dimensional infrared (2D IR) spectroscopy supported by numerical 2D IR simulations based on the exciton-band theory. The relationship between the local modes' and the exciton states' parameters is systematically studied, including center frequencies, diagonal anharmonicities, coupling, and off-diagonal anharmonicity. The mean coupling between νs and νa is accurately evaluated to be -49.96 ± 0.14cm-1. The degree of relaxation in the harmonic approximation is quantified, and the angle between the exciton-state dipoles is accurately evaluated to be 101.4° ± 3.6°. In addition, the effect of the local-mode frequency correlation on the resulting exciton-state frequency correlation and the spectral shape of the linear and 2D IR spectra are also investigated.

Two-dimensional infrared spectroscopy of aqueous solutions from first principles simulations

Vibrational spectral diffusion of OH/OD modes in liquid water can be influenced by the presence of ions, dipolar solutes or by the change of temperature. In the present work, we have calculated the two-dimensional infrared (2D-IR) spectrum of aqueous NaBr and urea solutions at room temperature and also liquid water at two different temperatures to study the effects of these solutes and varying temperature on the dynamics of vibrational spectral diffusion of OD stretch modes in aqueous media. Time-dependent evolution of the ellipticity of 2D-IR spectra is calculated to obtain timescales of the dynamics of vibrational spectral diffusion.

Vibrational echo spectroscopy of aqueous sodium bromide solutions from first principles simulations.

A theoretical study of the time-dependent vibrational echo spectroscopy of sodium bromide solutions in deuterated water at two different concentrations of 0.5 and 5.0 M and at temperatures of 300 and 350 K is presented using the method of ab initio molecular dynamics simulations. The instantaneous fluctuations in frequencies of local OD stretch modes are calculated using time-series analysis of the simulated trajectories. The third-order polarization and intensities of three pulse photon-echo are calculated from ab initio simulations. The timescales of vibrational spectral diffusion are determined from the frequency time correlation functions (FTCF) and short-time slope of three pulse photon echo (S3PE) calculated within the second-order cumulant and Condon approximations. It is found that under ambient conditions, the rate of vibrational spectral diffusion becomes slower with increase in ionic concentration. Decay of S3PE calculated for different systems give timescales, which are in close agreement with those of FTCF and also with the results of experimental time-dependent vibrational spectroscopic experiments. © 2019 Wiley Periodicals, Inc.

Ab initio molecular dynamics simulation of supercritical aqueous ionic solutions: Spectral diffusion of water in the vicinity of Br− and I− ions

Supercritical aqueous ionic solutions containing bromide (Br−) and iodide (I−) ions have been studied using Car-Parrinello molecular dynamics simulation at two different concentrations and at two different densities. The time dependent trajectory has been used for calculating vibrational spectral diffusion, structural properties and, for other dynamical properties such as hydrogen bond dynamics, orientational relaxation and residence dynamics. The vibrational spectral diffusion of fluctuating OD stretch mode inside the solvation shell of the ions and in the bulk has been studied using frequency-frequency time correlation function. Hydrogen bond dynamics, orientational relaxation and residence dynamics of Sc-water have been investigated using population correlation function approach. The water molecules inside the solvation shell of Br− and I− ions are found to show complex molecular dynamics in comparison to the water-water dynamics. The concentration dependent spectral diffusion has been observed and it occurs in multiple time scales in the solvation shell of Br− and I− ions. At supercritical condition, the ion-water hydrogen bond shows faster dynamics with respect to the same at ambient condition and slower dynamics with respect to the water-water hydrogen bond dynamics at supercritical condition.

Temperature dependence of the ultrafast vibrational echo spectroscopy of OD modes in liquid water from first principles simulations.

The rate of vibrational spectral diffusion of OD/OH stretch modes of water is known to be interconnected with the hydrogen bond rearrangement dynamics in aqueous media as found in several recent experiments and molecular simulations. In the present study, the temperature dependence of vibrational spectral diffusion of OD stretch modes in liquid water is investigated from first principles by using the method of ab initio molecular dynamics. Kinetic rates obtained from the frequency time correlation function (FTCF), the slope of the 3-pulse photon echo (S3PE) and local structure correlation functions are used in the Arrhenius equation to determine the energy barrier for hydrogen bond rearrangement in liquid water. The slope of the 3-pulse photon echo is determined within the cumulant and Condon approximations. Although the trend found at the low temperature is slightly non-Arrhenius, the barrier for hydrogen bond rearrangement is found to be around 4.2 kcal mol-1 from all the metrics considered here. It is in good agreement with the hydrogen bond energy determined from different experiments and theoretical studies. Based on the findings, a strong correlation between the vibrational spectral diffusion timescale and hydrogen bond dynamics is identified, which gets even more pronounced at low temperatures. Spatio-temporal correlations between frequency fluctuations and the local hydrogen bond network are also explored.

Vibrational echo spectral observables and frequency fluctuations of hydration shell water around a fluoride ion from first principles simulations

Aqueous solution of a fluoride ion at 300 K is studied using the method of ab initio molecular dynamics simulation. Instantaneous fluctuations in vibrational frequencies of local OD stretch modes of deuterated water are calculated using a time-series analysis of the simulated trajectory. The vibrational spectral diffusion of OD modes in the first and second solvation shells and also in bulk of the aqueous fluoride ionic solution are studied through calculations of the frequency time correlation function (FTCF), joint probability distributions, slope of three pulse photon echo (S3PE) and two dimensional infrared spectrum (2D-IR). The vibrational spectral dynamics in the first solvation shell shows decay with three components which can be correlated with the dynamics of intact ion-water hydrogen bonds, ion-water hydrogen bond lifetime and the escape dynamics of water molecules from the solvation shell. The vibrational spectral diffusion of OD modes in the second solvation shell and in the bulk show very similar decay behavior. The timescales obtained from FTCF, S3PE and the slope of nodal line (SNL) of 2D-IR are found to be in reasonable agreement with each others. Solvation shell dynamics of water molecules in different solvation shells of fluoride ion is studied using vibrational echo spectral observables from first principles simulations. The decay of FTCF, S3PE and SNL for water molecules in first solvation shell show multiple timescales which can be associated with ion-water hydrogen bond lifetime and residence time of water in the solvation shell.

Studying Water Hydrogen-Bonding Network near the Lipid Multibilayer with Multiple IR Probes.

A critical difference between living and nonliving is the existence of cell membranes, and hydration of membrane surface is a prerequisite for structural stability and various functions such as absorption/desorption of drugs, proteins, and ions. Therefore, a molecular level understanding of water structure and dynamics near the membrane is important to perceive the role of water in such a biologically relevant environment. In our recent paper [ J. Phys. Chem. Lett. 2016 , 7 , 741 ] on the IR pump-probe study of the OD stretch mode of HDO near lipid multibilayers, we have observed two different vibrational lifetime components of OD stretch mode in the phospholipid multibilayer systems. The faster component (0.6 ps) is associated with OD groups interacting with the phosphate moiety of the lipid, while the slower component (1.9 ps) is due to choline-associated water molecules that are close to bulklike water. Here, we additionally use hydrazoic acid (HN3) as another IR probe of which frequency is highly sensitive to its local H-bonding water density. Interestingly, we found that the vibrational lifetime of the asymmetric azido stretch mode of HN3 in the lipid multibilayer system is similar to that in neat water, whereas its orientational relaxation is a bit slower than that in bulk water. This indicates that due to the tight packing of lipid molecules, particularly the head parts, in the gel phase, HN3 molecules mostly stay near the choline group of lipid and interact with water molecules in the vicinity of choline groups. This suggests that membrane surface-adsorbed molecules such as hydrophilic drug molecules may interact with choline-associated water molecules, when the membrane is in the gel phase, instead of phosphate-associated water molecules.

Computational Vibrational Spectroscopy of HDO in Osmolyte-Water Solutions.

The IR absorption and time-resolved IR spectroscopy of the OD stretch mode of HDO in water was successfully used to study osmolyte effects on water H-bonding network. Protecting osmolytes such as sorbitol and trimethylglycine (TMG) make the vibrational OD stretch band red-shifted, whereas urea affects the OD band marginally. Furthermore, we recently showed that, even though sorbitol and TMG cause a slow-down of HDO rotation in their aqueous solutions, urea does not induce any change in the rotational relaxation of HDO in aqueous urea solutions even at high concentrations. To clarify the underlying osmolyte effects on water H-bonding structure and dynamics, we performed molecular dynamics (MD) simulations of a variety of aqueous osmolyte solutions. Using the vibrational solvatochromism model for the OD stretch mode and taking into account the vibrational non-Condon and polarization effects on the OD transition dipole moment, we then calculated the IR absorption spectra and rotational anisotropy decay of the OD stretch mode of HDO for the sake of direct comparisons with our experimental results. The simulation results on the OD stretch IR absorption spectra and the rotational relaxation rate of HDO in osmolyte solutions are found to be in quantitative agreement with experimental data, which confirms the validity of the MD simulation and vibrational solvatochromism approaches. As a result, it becomes clear that the protecting osmolytes like sorbitol and TMG significantly modulate water H-bonding network structure, while urea perturbs water structure little. We anticipate that the computational approach discussed here will serve as an interpretive method with atomic-level chemical accuracy of current linear and nonlinear time-resolved IR spectroscopy of structure and dynamics of water near the surfaces of membranes and proteins under crowded environments.

Water Structure at the Lipid Multibilayer Surface: Anionic Versus Cationic Head Group Effects.

Membrane water interface is a potential reaction site for many biochemical reactions. Therefore, a molecular level understanding of water structure and dynamics that strongly depend on the chemical structure of lipid is prerequisite for elucidating the role of water in biological reactions on membrane surface. Recently, we carried out femtosecond infrared pump-probe studies of water structure and dynamics at multibilayer surfaces of zwitterionic phosphatidylcholine-analogue lipid ( J. Phys. Chem. Lett. 2016 , 7 , 741 ). Here, to further elucidate the anionic and cationic headgroup effects on water, we study vibrational dynamics of water on lipid multibilayers formed by anionic phospho-glycerol lipid molecules as well as by cationic choline-derivatized lipid molecules. We observed two significantly different vibrational lifetime components (very fast 0.5 ps and slow 1.9 ps) of the OD stretch mode of HOD molecules at the negatively charged phospho-lipid multibilayer whereas only one vibrational lifetime component (1.6 ps) was observed at the positively charged choline-derivatized lipid multibilayer. From the detailed analyses about the vibrational energy and rotational relaxations of HOD molecules in lipid multibilayers composed of anionic lipid with phosphate and cationic lipid without phosphate, the role of phosphate group in structuring water molecules at phospholipid membrane interface is revealed.

Changing Hydrogen-Bond Structure during an Aqueous Liquid-Liquid Transition Investigated with Time-Resolved and Two-Dimensional Vibrational Spectroscopy.

We investigate the putative liquid-liquid phase transition in aqueous glycerol solution, using the OD-stretch mode in dilute OD/OH isotopic mixtures to probe the hydrogen-bond structure. The conversion exhibits Avrami kinetics with an exponent of n = 2.9 ± 0.1 (as opposed to n = 1.7 observed upon inducing ice nucleation and growth in the same sample), which indicates a transition from one liquid phase to another. Two-dimensional infrared (2D-IR) spectroscopy shows that the initial and final phases have different hydrogen-bond structures: the former has a single Gaussian distribution of hydrogen-bond lengths, whereas the latter has a bimodal distribution consisting of a broad distribution and a narrower, ice-like distribution. The 2D-IR spectrum of the final phase is identical to that of ice/glycerol at the same temperature. Combined with the kinetic data this suggests that the liquid-liquid transformation is immediately followed by a rapid formation of small (probably nanometer-sized) ice crystals.

First-Principles Simulation Study of Vibrational Spectral Diffusion and Hydrogen Bond Fluctuations in Aqueous Solution of N-Methylacetamide.

We have presented a first-principles simulation study of the vibrational spectral diffusion and hydrogen bond dynamics in an aqueous solution of N-methylacetamide (NMA). We have studied the spectral diffusion of local OD stretch modes of deuterated water in the first hydration shells of the carbonyl (CO) and deuterated amide (ND) modes and their relations to the dynamics of hydrogen bonds formed by water with these groups. The frequency fluctuations of the amide I and amide A modes of the solute are also investigated. It is found that the vibrational spectral diffusion of water molecules in the first hydration shell of the carbonyl oxygen of NMA proceeds with three time scales: A short-time relaxation (∼100 fs) originating from the dynamics of NMA-water hydrogen bonds without breaking, a slower relaxation (∼3.3 ps) arising from the breaking dynamics of NMA(CO)-water hydrogen bonds, and another longer time constant (∼14 ps) coming from the escape dynamics of water from the first hydration shell of carbonyl oxygen. The current results show that the NMA(CO)-water hydrogen bonds have a longer lifetime than those between water molecules, although frequency calculations reveal a slightly higher stretch frequency of the water molecules in the first hydration shell of the carbonyl oxygen of NMA. An analysis of the vibrational spectral diffusion of solute modes is also presented in terms of the dynamics of solute-water hydrogen bonds. Effects of dispersion interactions on various calculated properties of the NMA-water system are also investigated in the present work.

Simultaneous spectral and temporal analyses of kinetic energies in nonequilibrium systems: theory and application to vibrational relaxation of O-D stretch mode of HOD in water.

A time series of kinetic energies (KE) from classical molecular dynamics (MD) simulation contains fundamental information on system dynamics. It can also be analyzed in the frequency domain through Fourier transformation (FT) of velocity correlation functions, providing energy content of different spectral regions. By limiting the FT time span, we have previously shown that spectral resolution of KE evolution is possible in the nonequilibrium situations [Jeon and Cho, J. Chem. Phys. 2011, 135, 214504]. In this paper, we refine the method by employing the concept of instantaneous power spectra, extending it to reflect an instantaneous time-correlation of velocities with those in the future as well as with those in the past, and present a new method to obtain the instantaneous spectral density of KE (iKESD). This approach enables the simultaneous spectral and temporal resolution of KE with unlimited time precision. We discuss the formal and novel properties of the new iKESD approaches and how to optimize computational methods and determine parameters for practical applications. The method is specifically applied to the nonequilibrium MD simulation of vibrational relaxation of the OD stretch mode in a hydrated HOD molecule by employing a hybrid quantum mechanical/molecular mechanical (QM/MM) potential. We directly compare the computational results with the OD band population relaxation time profiles extracted from the IR pump-probe measurements for 5% HOD in water. The calculated iKESD yields the OD bond relaxation time scale ∼30% larger than the experimental value, and this decay is largely frequency-independent if the classical anharmonicity is accounted for. From the integrated iKESD over intra- and intermolecular bands, the major energy transfer pathways were found to involve the HOD bending mode in the subps range, then the internal modes of the solvent until 5 ps after excitation, and eventually the solvent intermolecular modes. Also, strong hydrogen-bonding of HOD is found to significantly hinder the initial intramolecular energy transfer process.

Structure and dynamics of water in nanoscopic spheres and tubes.

We study the reorientation dynamics of liquid water confined in nanometer-sized reverse micelles of spherical and cylindrical shape. The size and shape of the micelles are characterized in detail using small-angle x-ray scattering, and the reorientation dynamics of the water within the micelles is investigated using GHz dielectric relaxation spectroscopy and polarization-resolved infrared pump-probe spectroscopy on the OD-stretch mode of dilute HDO:H2O mixtures. We find that the GHz dielectric response of both the spherical and cylindrical reverse micelles can be well described as a sum of contributions from the surfactant, the water at the inner surface of the reversed micelles, and the water in the core of the micelles. The Debye relaxation time of the core water increases from the bulk value τ(H2O) of 8.2 ± 0.1 ps for the largest reverse micelles with a radius of 3.2 nm to 16.0 ± 0.4 ps for the smallest micelles with a radius of 0.7 nm. For the nano-spheres the dielectric response of the water is approximately ∼6 times smaller than expected from the water volume fraction and the bulk dielectric relaxation of water. We find that the dielectric response of nano-spheres is more attenuated than that of nano-tubes of identical composition (water-surfactant ratio), whereas the reorientation dynamics of the water hydroxyl groups is identical for the two geometries. We attribute the attenuation of the dielectric response compared to bulk water to a local anti-parallel ordering of the molecular dipole moments. The difference in attenuation between nano-spheres and nano-cylinders indicates that the anti-parallel ordering of the water dipoles is more pronounced upon spherical than upon cylindrical nanoconfinement.

An Accurate Classical Simulation of a Two-Dimensional Vibrational Spectrum: OD Stretch Spectrum of a Hydrated HOD Molecule

An accurate computational method for the classical simulation of the two-dimensional vibrational spectra is presented. The method refines our previous computational method for the third order vibrational response function in the classical limit, and it enables capturing the diagonal elongation and its waiting time (T) dependence widely observed in experimental two-dimensional infrared (2D IR) spectra of intramolecular modes. The improvement is achieved by a series of new developments including (i) a block algorithm for the stability matrix computation, (ii) new equations of motion for the position-perturbed molecular dynamics (MD) trajectory, and (iii) enhanced sampling efficiency by exploiting the time-reversal invariance of MD trajectories. The method is applied to the simulation of 2D IR spectra of the OD stretch mode in a hydrated HOD molecule, employing a hybrid quantum mechanical/molecular mechanical force field. The simulated spectra exhibit diagonal elongation of the 2D IR signal at small T, reflecting the correlation of individual transitions among the inhomogeneously broadened ensemble. The slopes of the nodal lines of the elongated signals are found to decay with a time scale of 1.6 ps as T increases, in reasonable agreement with the frequency correlation decay time of 1.2 ps. The amplitudes of the positive and negative peaks also decay as T increases, due to vibrational population relaxation and molecular rotation. The peak positions tend to blue shift with increasing T, reflecting the different relaxation rates of the strongly and weakly solvated HOD species. These results indicate that the present method can reliably predict the waiting-time-dependent changes of 2D IR spectra of a single vibrational chromophore in solution.

Theory of action spectroscopy for single-molecule reactions induced by vibrational excitations with STM

A theory of action spectroscopy, i.e., a reaction rate or yield as a function of bias voltage, is presented for single-molecule reactions induced by the inelastic tunneling current with a scanning tunneling microscope. A formula for the reaction yield is derived using the adsorbate resonance model, which provides a versatile tool to analyze vibrationally mediated reactions of single adsorbates on conductive surfaces. This allows us to determine the energy quantum of the excited vibrational mode, the effective broadening of the vibrational density of states (as described by Gaussian or Lorentzian functions), and a prefactor characterizing the elementary process behind the reaction. The underlying approximations are critically discussed. We point out that observation of reaction yields at both bias voltage polarities can provide additional insight into the adsorbate density of states near the Fermi level. As an example, we apply the theory to the case of flip motion of a hydroxyl dimer (OD)${}_{2}$ on Cu(110) which was experimentally observed by Kumagai et al. [Phys. Rev. B 79, 035423 (2009)]. In combination with density functional theory calculations for the vibrational modes, the vibrational damping due to electron-hole pair generation, and the potential energy landscape for the flip motion, a detailed microscopic picture for the switching process is established. This picture reveals that the predominant mechanism is excitation of the OD stretch modes which couple anharmonically to the low-energy frustrated rotation mode.

Three-dimensional infrared spectroscopy of isotope-diluted ice Ih

Using three-dimensional infrared (3D-IR) spectroscopy, we investigate the vibrational dynamics of isotope-diluted ice Ih. By probing the OD stretch mode of HOD in H2O, we observe an extremely rapid decay (≈200 fs) of the population from the second vibrational excited state. Quantum simulations based on a two-dimensional Lippincott-Schroeder potential agree nearly quantitatively with the experimental 3D-IR lineshapes and dynamics. The model suggests that energy dissipation is enhanced due to nonadiabatic effects between vibrational states, which arise from strong mode-mixing between the OD stretch mode with lattice degrees of freedom. Furthermore, we compare the simulation results to ab initio based potentials, in which the hydrogen bond anharmonicity is too small to reproduce the experimental 3D-IR spectra. We thus conclude that the Lippincott-Schroeder potential effectively coalesces many degrees of freedom of the crystal into one intermolecular coordinate.

Effects of Collisional and Vibrational Velocity on Proton and Deuteron Transfer in the Reaction of HOD+ with CO

Reaction of HOD(+) with CO was studied over the collision energy (E(col)) range between 0.18 and 2.87 eV, for HOD(+) in its ground state and with one quantum in each of its vibrational modes: (001)--predominantly OH stretch; (010)--bend, and (100)--predominately OD stretch. In addition to integral cross sections, product recoil velocity distributions were also measured for each initial condition. The dominant reactions are near-thermoneutral proton and deuteron transfer, generating HCO(+) and DCO(+) product ions by a predominantly direct mechanism. The HCO(+) and DCO(+) channels occur with a combined efficiency of 76% for ground state HOD(+) at our lowest E(col), increasing to 94% for E(col) around 0.33 eV, then falling at high E(col) to ~40%. The HCO(+) and DCO(+) channels have a complicated dependence on the HOD(+) vibrational state. Excitation of the OH or OD stretch modes enhances H(+) or D(+) transfer, respectively, and inhibits D(+) or H(+) transfer. Bend excitation preferentially enhances H(+) transfer, with no effect on D(+) transfer. There is no coupling of energy initially in any HOD(+) vibrational mode to recoil velocity of either of the product ions, even at low E(col) where vibrational excitation doubles or triples the energy available to products. The results suggest that transfer of H or D atoms is enhanced if the atom in question has a high vibrational velocity, and that this effect offsets what is otherwise a general inhibition of reactivity by added energy. HOCO(+) + D and DOCO(+) + H products are also observed, but as minor channels despite being barrierless and exoergic. These channels appear to be complex mediated at low E(col), essentially vanish at intermediate E(col), then reappear with a direct reaction mechanism at high E(col).

Vibrationally induced flip motion of a hydroxyl dimer on Cu(110)

Recent low-temperature scanning-tunneling microscopy experiments [T. Kumagai et al., Phys. Rev. B 79, 035423 (2009)] observed the vibrationally induced flip motion of a hydroxyl dimer (OD)2 on Cu(110). We propose a model to describe two-level fluctuations and current-voltage characteristics of nanoscale systems which undergo vibrationally induced switching. The parameters of the model are based on comprehensive density-functional calculations of the system's vibrational properties. For the dimer (OD)2 the calculated population of the high and low conductance states, the I-V, dI/dV, and d2I/dV2 curves are in good agreement with the experimental results and underlines the different roles played by the free and shared OD stretch modes of the dimer.

An ab initio molecular dynamics study of diffusion, orientational relaxation and hydrogen bond dynamics in acetone–water mixtures

A theoretical study of the dynamics of water–acetone mixtures is carried out by using the methods of ab initio molecular dynamics for trajectory generation, time series analysis for frequency calculations and time correlation function approach for calculations of various dynamical quantities. It is found that diffusion coefficients and orientational relaxation times of water and acetone molecules change in a nonlinear manner with variation of composition of the mixture. The lifetimes of acetone–water hydrogen bonds are found to be shorter than that of water–water hydrogen bonds and both are found to increase with decrease of water concentration. The vibrational spectral diffusion of OD stretch modes of deuterated water molecules is also investigated for the equimolar mixture of water and acetone and the results are correlated with the dynamics of water–water and water–acetone hydrogen bonds and also of dangling OD modes.

Two-dimensional infrared spectroscopy of isotope-diluted ice Ih

We present experimental 2D IR spectra of isotope diluted ice Ih (i.e., the OH stretch mode of HOD in D(2)O and the OD stretch mode of HOD in H(2)O) at T = 80 K. The main spectral features are the extremely broad 1-2 excited state transition, much broader than the corresponding 0-1 groundstate transition, as well as the presence of quantum beats. We do not observe any inhomogeneous broadening that might be expected due to proton disorder in ice Ih. Complementary, we perform simulations in the framework of the Lippincott-Schroeder model, which qualitatively reproduce the experimental observations. We conclude that the origin of the observed line shape features is the coupling of the OH-vibrational coordinate with crystal phonons and explain the beatings as a coherent oscillation of the O···O hydrogen bond degree of freedom.