Vibrational spectral diffusion of azide in water

Vibrational spectral diffusion denotes the time-dependent fluctuations of a solute's vibrational frequencies due to local environmental dynamics. Vibrational line shapes are weakly sensitive to spectral diffusion, whereas three-pulse vibrational echoes are much more sensitive. We report here on theoretical studies of spectral diffusion of the asymmetric stretch of the azide anion in heavy water. We run a classical molecular dynamics simulation of rigid azide in rigid water, and at every time step we calculate the azide's anharmonic asymmetric stretch frequency using an optimized quantum mechanics/molecular mechanics method developed earlier. This generates a frequency trajectory, which we use to calculate the absorption line shape and integrated three-pulse echo intensity. Our results for both the line width and the integrated echo intensity are in excellent agreement with experiment. Our calculated frequency time-correlation function is in excellent agreement with experiment for long times (greater than 250 fs) but differs considerably from experiment at short times; our theoretical correlation function has a very pronounced oscillation, presumably due to intermolecular azide-water hydrogen-bond stretching dynamics.     

Spectral characterization of hydrogen bond network dynamics in water

Some computational aspects of the characterization of the complex hydrogen bond network dynamics using power spectral analysis are discussed. In the case of hydrogen-bonded liquids, the tagged molecule potential energy is shown to be a useful quantity for capturing the behavior of the networked liquid on different lengths and time scales. The computation of the tagged potential energy for rigid-body effective pair potentials, such as the TIP5P-E and SPC-E models, is discussed. The more structured nature of the TIP5P-E potential, compared to the SPC/E potential, shows up as differences in the high-frequency librational band of the power spectra of the tagged molecule potential energies. The static distributions of the tagged molecule potential energies are also more structured in the case of TIP5P-E, rather than SPC/E, water. The overall behavior of the key power spectral features remains the same in both the models. The possibility of detailed characterization of the power spectrum, and therefore of the underlying dynamics, using a model-based parametric fitting procedure for the power spectra is also discussed. We show that a parametric fitting can allow one to test alternative models of the dynamics underlying the liquid state dynamics.     

Vibrational spectral signatures of peptide secondary structures: N-methylation and side chain hydrogen bond in cyclosporin A

Molecular dynamics simulations are performed to explore important conformations of cyclosporin A, an immunosuppressive cyclic undecapeptide drug, in different media including gas-phase, chloroform, and acetonitrile. Density functional theory calculations are used to refine the low-lying conformers and to predict their infrared and vibrational circular dichroism spectra. Vibrational spectral signatures in the important amide II, I, and A regions are identified for typical peptide secondary structures including β-turn (type II' or I), antiparallel β-sheet (flat or twisted), inverse γ-turn, N-methylated peptide bond, and side chain H-bond. New insights into the spectral signatures of secondary structures especially with N-methylation and side chain hydrogen bond are provided, which can be very useful for further peptide conformation analysis in general.     

Hydrogen bond dynamics in heavy water studied with quantum dynamical simulations

The structure and dynamics of the hydrogen-bond network in heavy water (D(2)O) is studied as a function of the temperature using quantum dynamical simulations. Our approach combines an ab initio-based representation of the water interactions with an explicit quantum treatment of the molecular motion. A direct connection between the calculated linear and nonlinear vibrational spectra and the underlying molecular dynamics is made, which provides new insights into the rearrangement of the hydrogen-bond network in heavy water. A comparison with previous calculations on liquid H(2)O suggests that tunneling does not effectively contribute to the dynamics of the water hydrogen-bond network above the melting point. However, the effects of nuclear quantization are not negligible at all temperatures and become increasingly important near the melting point, which is in agreement with recent experimental analysis of the structural properties of liquid water as well as of the proton momentum distribution in supercooled water.     

Toward understanding mobile proton behavior from first principles calculation: the short hydrogen bond in crystalline urea-phosphoric acid

The dynamics of the intermolecular short hydrogen bond in the molecular complex of urea and phosphoric acid are investigated using plane-wave density functional theory. Results indicate migration of the proton toward the center of the hydrogen bond as temperature is increased, in line with recent experimental measurements. Computed vibrational frequencies show favorable agreement with experimental measurement. An analysis of existing neutron diffraction data leads us to conclude that the effective potential well experienced by the proton is temperature-dependent. Inspired by our computations and theoretical analysis, we offer a possible explanation for the proton migration phenomenon.     

Exploring DNA groove water dynamics through hydrogen bond lifetime and orientational relaxation

Dynamics of water molecules in the grooves of DNA are of great interest both for practical (functionality of DNA) and fundamental (as examples of confined systems) interest. Here the authors employ atomistic molecular dynamics simulations to understand varying water dynamics at the minor and the major grooves of a 38 base-pair long DNA duplex in water. In order to understand and quantify the diversity in the nature of hydrogen bond due to many hydrogen bond donors and acceptors present in the four bases, they have undertaken study of hydrogen bond lifetime (HBLT) correlation functions of all the specific hydrogen bonds between the base atoms and water molecules. They find that the HBLT correlation functions are in general multiexponential, with the average lifetime depending significantly on the specificity and may thus be biologically relevant. The average hydrogen bond lifetime is longer in the minor groove than that in the major groove by almost a factor of 2. Analysis further shows that water hydrogen bonds with phosphate oxygen have substantially shorter lifetimes than those with the groove atoms. They also compute two different orientational time correlation functions (OTCFs) of the water molecules present at the major and the minor grooves and attempt to correlate OTCF with HBLT correlation function. The OTCFs in the minor groove exhibit three time scales, with the time constant of the slowest component one to two orders of magnitude longer than what is observed for bulk water. A slow component is also present for the major groove water but with shorter time constant. Interestingly, correlation between reformations allowed HBLT correlation function [C(HB)(t)] and the OTCF markedly deviates from each other in the grooves, indicating enhanced rigidity of water molecules in the grooves.     

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.     

Simulating fluid-phase equilibria of water from first principles

Efficient Monte Carlo algorithms and a mixed-basis set electronic structure program were used to compute from first principles the vapor-liquid coexistence curve of water. A water representation based on the Becke-Lee-Yang-Parr exchange and correlation functionals yields a saturated liquid density of 900 kg/m3 at 323 K and normal boiling and critical temperatures of 350 and 550 K, respectively. An analysis of the structural and electronic properties of the saturated liquid phase shows an increase of the asymmetry of the local hydrogen-bonded structure despite the persistence of a 4-fold coordination and decreases of the molecular dipole moment and of the spread of the lowest unoccupied molecular orbital with increasing temperature.     

Effect of ionic solutes on the hydrogen bond network dynamics of water: power spectral analysis of aqueous NaCl solutions

To understand the modifications of the hydrogen bond network of water by ionic solutes, power spectra as well as static distributions of the potential energies of tagged solvent molecules and solute ions have been computed from molecular dynamics simulations of aqueous NaCl solutions. The key power spectral features of interest are the presence of high-frequency peaks due to localized vibrational modes, the existence of a multiple time scale or 1/falpha frequency regime characteristic of networked liquids, and the frequency of crossover from 1/falpha type behavior to white noise. Hydrophilic solutes, such as the sodium cation and the chloride anion, are shown to mirror the multiple time scale behavior of the hydrogen bond network fluctuations, unlike hydrophobic solutes which display essentially white noise spectra. While the power spectra associated with tagged H2O molecules are not very sensitive to concentration in the intermediate frequency 1/falpha regime, the crossover to white noise is shifted to lower frequencies on going from pure solvent to aqueous alkali halide solutions. This suggests that new and relatively slow time scales enter the picture, possibly associated with processes such as migration of water molecules from the hydration shell to the bulk or conversion of contact ion pairs into solvent-separated ion pairs which translate into variations in equilibrium transport properties of salt solutions with concentration. For anions, cations, and solvent molecules, the trends in the alpha exponents of the multiple time scale region and the self-diffusivities are found to be strongly correlated.     

Dielectric spectroscopy of hydrogen bond dynamics and microheterogenity of water + dioxane mixtures

Mixtures of water or D2O + 1,4-dioxane (DX) have been studied at 25 degrees C by dielectric relaxation spectroscopy over a wide range of frequencies (0.2 < or = nu/GHz < or = 89) for DX mole fractions 0 < or = x2 < or = 0.67. The spectra were best fitted by the sum of two Debye terms. The slower process was assigned to the cooperative relaxation of the hydrogen-bond network of water, whereas the faster mode reflects the dynamics of H2O molecules in a DX-rich environment. Analysis of the relaxation parameters revealed a largely microheterogeneous structure of the mixtures. The marked slowing-down of the cooperative mode on addition of DX is ascribed to the reduction of available H-bond acceptor sites and geometrical constraints on the H2O molecules in the water-rich regions.     

Vibrational dynamics of the hydrogen bond in H(2)S-HF: Fourier-transform-infrared spectra and ab initio theory

The rotationally resolved infrared spectrum of the hydrogen bonded complex H(2)S-HF and of its isotopomer D(2)S-DF in the HF/DF stretching range have been observed in a supersonic jet Fourier-transform infrared (FTIR) experiment and indicate a predissociation lifetime of 130 ps for H(2)S-HF. Complementary spectra taken at a temperature of 190 K in a cell without resolved rotational structure indicate the presence of strong anharmonic couplings between low frequency intermolecular modes and the HF donor stretch mode previously observed in other complexes with heavier acceptor molecules without rotational fine structure. The anharmonic analysis of the hot band progressions and of the rotational data confirm the coupling mechanism. The coupling constants and the absolute frequency of the hydrogen bonded stretch mode are in excellent agreement with theoretical predictions based on adiabatic variational calculations on potential surfaces computed at MP2 and CCSD(T) level. Complementary calculations with a perturbational approach further confirm the coupling model.     

Liquid structures of water, methanol, and hydrogen fluoride at ambient conditions from first principles molecular dynamics simulations with a dispersion corrected density functional

Using first principles molecular dynamics simulations in the isobaric-isothermal ensemble (T = 300 K, p = 1 atm) with the Becke-Lee-Yang-Parr exchange/correlation functional and a dispersion correction due to Grimme, the hydrogen bonding networks of pure liquid water, methanol, and hydrogen fluoride are probed. Although an accurate density is found for water with this level of electronic structure theory, the average liquid densities for both hydrogen fluoride and methanol are overpredicted by 50 and 25%, respectively. The radial distribution functions indicate somewhat overstructured liquid phases for all three compounds. The number of hydrogen bonds per molecule in water is about twice as high as for methanol and hydrogen fluoride, though the ratio of cohesive energy over number of hydrogen bonds is lower for water. An analysis of the hydrogen-bonded aggregates revealed the presence of mostly linear chains in both hydrogen fluoride and methanol, with a few stable rings and chains spanning the simulation box in the case of hydrogen fluoride. Only an extremely small fraction of smaller clusters was found for water, indicating that its hydrogen bond network is significantly more extensive. A special form of water with on average about two hydrogen bonds per molecule yields a hydrogen-bonding environment significantly different from the other two compounds.     

Hydration of alkali ions from first principles molecular dynamics revisited

Structural and dynamical properties of the hydration of Li(+), Na(+), and K(+) in liquid water at ambient conditions were studied by first principles molecular dynamics. Our simulations successfully captured the different hydration behavior shown by the three alkali ions as observed in experiments. The present analyses of the dependence of the self-diffusion coefficient and rotational correlation time of water on the ion concentration suggest that Li(+) (K(+)) is certainly categorized as a structure maker (breaker), whereas Na(+) acts as a weak structure breaker. An analysis of the relevant electronic structures, based on maximally localized Wannier functions, revealed that the dipole moment of H(2)O molecules in the first solvation shell of Na(+) and K(+) decreases by about 0.1 D compared to that in the bulk, due to a contraction of the oxygen lone pair orbital pointing toward the metal ion.     

Gadolinium (III) ion in liquid water: structure, dynamics, and magnetic interactions from first principles

We applied first principles molecular dynamics (MD) technique to study structure, dynamics, and magnetic interactions of the Gd(3+) aqua ion dissolved in liquid water, a prototypical system for Gd-based complexes used as contrast agents for magnetic resonance imaging. The first coordination sphere contains eight water molecules with an average Gd-O distance of 2.37 A and an average geometric arrangement close to a square antiprism. The mean tilt angle of the electric dipole vector of these water molecules is theta=145 degrees . In our picosecond time scale simulation we observe no exchange event from the first coordination sphere but only fast "wagging" motions. The second coordination sphere is well pronounced though water molecules in this sphere are subjected to large amplitude dynamic motions. The isotropic hyperfine coupling constants for the inner sphere water molecules [A(iso)((17)O(I))=0.65+/-0.03 MHz, A(iso)((1)H(I))=0.085+/-0.005 MHz] are in good agreement with experimental data and with an earlier study using classical MD. Second sphere Fermi contact hyperfine coupling constants calculated are more than one order of magnitude smaller and of opposite sign as those of the first coordination sphere. The effect of spin polarization induced by the paramagnetic Gd(3+) ion on the dipolar hyperfine interaction was found to be sizable only for the (17)O nuclei of inner sphere water molecules and has a screening character.     

Dynamics and mechanism of structural diffusion in linear hydrogen bond

Dynamics and mechanism of proton transfer in a protonated hydrogen bond (H-bond) chain were studied, using the CH(3)OH(2)(+)(CH(3)OH)(n) complexes, n = 1-4, as model systems. The present investigations used B3LYP/TZVP calculations and Born-Oppenheimer MD (BOMD) simulations at 350 K to obtain characteristic H-bond structures, energetic and IR spectra of the transferring protons in the gas phase and continuum liquid. The static and dynamic results were compared with the H(3)O(+)(H(2)O)(n) and CH(3)OH(2)(+)(H(2)O)(n) complexes, n = 1-4. It was found that the H-bond chains with n = 1 and 3 represent the most active intermediate states and the CH(3)OH(2)(+)(CH(3)OH)(n) complexes possess the lowest threshold frequency of proton transfer. The IR spectra obtained from BOMD simulations revealed that the thermal energy fluctuation and dynamics help promote proton transfer in the shared-proton structure with n = 3 by lowering the vibrational energy for the interconversion between the oscillatory shuttling and structural diffusion motions, leading to a higher population of the structural diffusion motion than in the shared-proton structure with n = 1. Additional explanation on the previously proposed mechanisms was introduced, with the emphases on the energetic of the transferring proton, the fluctuation of the number of the CH(3)OH molecules in the H-bond chain, and the quasi-dynamic equilibriums between the shared-proton structure (n = 3) and the close-contact structures (n ≥ 4). The latter prohibits proton transfer reaction in the H-bond chain from being concerted, since the rate of the structural diffusion depends upon the lifetime of the shared-proton intermediate state.     

Structural fluctuation and dynamics of ribose puckering in aqueous solution from first principles

Using the method of ab initio molecular dynamics, we examine the structural fluctuation and the low-frequency dynamics of beta-ribofuranose puckering in aqueous solution. Our analysis suggests that the distance between the anomeric and hydroxymethyl oxygens is a simple relevant geometrical parameter that dynamically correlates with the phase angle in the north region. The time-frequency analysis using the Hilbert-Huang transform also confirms the correlation, and most of the instantaneous frequencies for the phase angle and the above distance are found to be concentrated on the region below about 100 cm(-1). Our analysis of ab initio molecular dynamics trajectories suggests that the molecular origin of the hydration effects on the low-frequency dynamics of beta-ribofuranose puckering is closely related to this correlation and thus primarily attributed to the relatively local interactions among the anomeric and hydroxymethyl oxygens and the surrounding water molecules near them. Additionally, we discuss the difference in the low-frequency dynamics of beta-ribofuranose puckering between two hydroxymethyl rotamers.     

Nonideality in diffusion of ionic and neutral solutes and hydrogen bond dynamics in dimethyl sulfoxide-chloroform mixtures of varying composition

Molecular dynamics simulations of charged and neutral solutes in dimethyl sulfoxide (DMSO)-chloroform mixtures reveal pronounced nonideality in the solute diffusion with changes of composition of the mixtures. The diffusion coefficient of the anionic solute first decreases, passes through a minimum at DMSO mole fraction of about 0.50, and then increases to reach its value for pure DMSO. The diffusion coefficients of the cationic and neutral solutes are found to decrease with increase in DMSO content of the solvent mixture. The extent of nonideality in the diffusion and orientational relaxation of solvent molecules is found to be somewhat stronger than that in diffusion of the anionic solute in these mixtures. We have also calculated the relaxation of hydrogen bonds formed between DMSO and chloroform molecules. The lifetimes of DMSO-chloroform hydrogen bonds are found to increase monotonically with increase in DMSO concentration. The average number of hydrogen bonds and their average energies are also computed. It is found that an increase in DMSO concentration causes a decrease in the number of DMSO-chloroform hydrogen bonds per DMSO or chloroform molecules but increases the strength of these hydrogen bonds.     

Nonlinear dynamics of a model hydrogen bond

The dynamics of a model triatomic hydrogen bond are analyzed through classical mechanics. The approximate separability of the equations of motion induces the existence of an adiabatic invariant for the intramolecular mode motion. This mode is governed by a Mathieu equation, a feature already present for the antisymmetric mode in symmetric triatomics. The corresponding spectrum readily obtained as the Fourier transform of a classical trajectory shows that the fundamental frequency is shifted to lower values owing to the anharmonicity of the potential. We observe also a substructure of combination lines generated by a nonlinear resonance with the intermolecular mode. These properties are consistent with experimental observation. In a four-atoms model, the lines are split when intramolecular Fermi resonance occurs. When the intermolecular mode becomes chaotic there is no vibrational heating of the intramolecular neighboring mode which tends to behave like a local isolated oscillator.     

Vibrational dynamics and hydrogen bond properties of β-CD nanosponges: an FTIR-ATR, Raman and solid-state NMR spectroscopic study

Cyclodextrin nanosponges (CDNS) are cross-linked polymers with remarkable inclusion/release properties. CDNS show swelling capability and a hydrophilicity/hydrophobicity balance that can be dramatically modified by the type and quantity of cross-linking agents. Here, we focus our attention on samples of β-cyclodextrin nanosponges (β-CDNS) obtained by reacting β-cyclodextrin (β-CD) with the cross-linking agent carbonyldiimidazole at different β-CD:cross-linking agent molar ratio. The vibrational properties of CDNS thus synthesized have been investigated by Fourier transform infrared spectroscopy in attenuated total reflectance geometry and Raman spectroscopy in the dry state at room temperature. The quantitative analysis of the O–H stretching region (3,000–3,800 cm^?1) allowed us to obtain structural information on the role played by primary and secondary OH groups in the hydrogen bond network of the polymer. Also, the contribution of interstitial and intracavity crystallization water molecules is reported. Solid-state NMR spectroscopy is used to study the molecular mobility of the polymer by measuring the ¹H spin–lattice relaxation time in the rotating frame (T_1ρ). The T_1ρ values obtained for the polymer β-CDNS are compared with free β-CD. The observed relaxation parameters point out that the ester formation occurs mainly at the primary OH groups of CDs, also supporting the interpretation of vibrational spectra.     

Quantum diffusion in liquid water from ring polymer molecular dynamics

We have used the ring polymer molecular-dynamics method to study the translational and orientational motions in an extended simple point charge model of liquid water under ambient conditions. We find, in agreement with previous studies, that quantum-mechanical effects increase the self-diffusion coefficient D and decrease the relaxation times around the principal axes of the water molecule by a factor of around 1.5. These results are consistent with a simple Stokes-Einstein picture of the molecular motion and suggest that the main effect of the quantum fluctuations is to decrease the viscosity of the liquid by about a third. We then go on to consider the system-size scaling of the calculated self-diffusion coefficient and show that an appropriate extrapolation to the limit of infinite system size increases D by a further factor of around 1.3 over the value obtained from a simulation of a system containing 216 water molecules. These findings are discussed in light of the widespread use of classical molecular-dynamics simulations of this sort of size to model the dynamics of aqueous systems.