Dynamics of nanoscopic water: vibrational echo and infrared pump-probe studies of reverse micelles

The dynamics of water in nanoscopic pools 1.7-4.0 nm in diameter in AOT reverse micelles were studied with ultrafast infrared spectrally resolved stimulated vibrational echo and pump-probe spectroscopies. The experiments were conducted on the OD hydroxyl stretch of low-concentration HOD in the H2O, providing a direct examination of the hydrogen-bond network dynamics. Pump-probe experiments show that the vibrational lifetime of the OD stretch mode increases as the size of the reverse micelle decreases. These experiments are also sensitive to hydrogen-bond dissociation and reformation dynamics, which are observed to change with reverse micelle size. Spectrally resolved vibrational echo data were obtained at several frequencies. The vibrational echo data are compared to data taken on bulk water and on a 6 M NaCl solution, which is used to examine the role of ionic strength on the water dynamics in reverse micelles. Two types of vibrational echo measurements are presented: the vibrational echo decays and the vibrational echo peak shifts. As the water nanopool size decreases, the vibrational echo decays become slower. Even the largest nanopool (4 nm, approximately 1000 water molecules) has dynamics that are substantially slower than bulk water. It is demonstrated that the slow dynamics in the reverse micelle water nanopools are a result of confinement rather than ionic strength. The data are fit using time-dependent diagrammatic perturbation theory to obtain the frequency-frequency correlation function (FFCF) for each reverse micelle. The results are compared to the FFCF of water and show that the largest differences are in the slowest time scale dynamics. In bulk water, the slowest time scale dynamics are caused by hydrogen-bond network equilibration, i.e., the making and breaking of hydrogen bonds. For the smallest nanopools, the longest time scale component of the water dynamics is approximately 10 times longer than the dynamics in bulk water. The vibrational echo data for the smallest reverse micelle displays a dependence on the detection wavelength, which may indicate that multiple ensembles of water molecules are being observed.     

Ultrafast to slow orientational dynamics of a homeotropically aligned nematic liquid crystal

The orientational dynamics of a homeotropically aligned nematic liquid crystal, 4'-pentyl-4-biphenylcarbonitrile (5-CB), is studied over more than six decades of time (500 fs to 2 mus) using optical heterodyne detected optical Kerr effect experiments. In contrast to the dynamics of nematogens in the isotropic phase, the data do not decay as a highly temperature-dependent exponential on the longest time scale, but rather, a temperature-independent power law spanning more than two decades of time, the final power law, is observed. On short time scales (approximately 3 ps to approximately 1 ns) another power law, the intermediate power law, is observed that is temperature dependent. The power law exponent of the correlation function associated with the intermediate power law displays a linear dependence on the change in the nematic order parameter with temperature. Between the intermediate power law and the final power law, there is a crossover region that displays an inflection point. The temperature-dependent orientational dynamics in the nematic phase are shown to be very different than those observed in the isotropic phase.     

Three homeotropically aligned nematic liquid crystals: comparison of ultrafast to slow time-scale dynamics

The dynamics of two nematic liquid crystals, 4-(trans-4(')-n-octylcyclohexyl)isothiocyanatobenzene and 4-(4-pentyl-cyclohexyl)-benzonitrile, are investigated as a function of temperature both in the homeotropically aligned nematic phase and in the isotropic phase using optical heterodyne-detected optical Kerr effect experiments, which measures the time derivative of the polarizability-polarizability-correlation function (orientational relaxation). Data are presented over a time range of 500 fs-70 micros for the nematic phase and 500 fs to a few hundred nanoseconds for the isotropic phase. The nematic dynamics are compared with a previously studied liquid crystal in the nematic phase. All three liquid crystals have very similar dynamics in the nematic phase that are very different from the isotropic phase. On the slowest time scale (20 ns-70 micros), a temperature-independent power law, the final power law, t(-f) with f approximately 0.5, is observed. On short time scales (approximately 3 ps to approximately 1 ns), a temperature-dependent intermediate power law is observed with an exponent that displays a linear dependence on the nematic order parameter. Between the intermediate power law and the final power law, there is a crossover region that has an inflection point. For times that are short compared to the intermediate power law (approximately <2 ps), the data decay much faster, and can be described as a third power law, although this functional form is not definitive. The isotopic phase data have the same features as found in previous studies of nematogens in the isotropic phase, i.e., the temperature-independent intermediate power law and von Schweidler power law at short to intermediate times, and a highly temperature-dependent long time exponential decay that is well described by the Landau-de Gennes theory. The results show that liquid-crystal dynamics in the nematic phase exhibit universal behavior.     

Dielectric relaxation of aqueous solutions of hydrophilic versus amphiphilic peptides

We report on molecular dynamics simulations of the frequency-dependent dielectric relaxation spectra at room temperature for aqueous solutions of a hydrophilic peptide and an amphiphilic peptide at two concentrations. We find that only the high-concentration amphiphilic peptide solution exhibits an anomalous dielectric increment over that of pure water, while the hydrophilic peptide exhibits a significant dielectric decrement. The dielectric component analysis carried out by decomposing these peptide solutions into peptide, hydration layer, and outer layer(s) of water clearly shows the presence of a unique dipolar component with a relaxation time scale on the order of approximately 25 ps (compared to the bulk water time scale of approximately 11 ps) that originates from the interaction between the hydration layer water and the outer layer(s) of water. Results obtained from the dielectric component analysis further show the emergence of a distinct and much lower frequency relaxation process for the high-concentration amphiphilic peptide compared to the hydrophilic peptide due to strong peptide dipolar couplings to all constituents, accompanied by a slowing of the structural relaxation in all water layers, giving rise to time scales close to approximately 1 ns. We suggest that the molecular origin of the dielectric relaxation anomalies is due to frustration in the water network arising from the amphiphilic chemistry of the peptide that does not allow it to reorient on the picosecond time scale of bulk water motions. This explanation is consistent with the idea of the "slaving" of residue side chain motions to protein surface water, and furthermore offers the possibility that the anomalous dynamics observed from a number of spectroscopies arises at the interface of hydrophobic and hydrophilic domains on the protein surface.     

Electron solvation in water clusters following charge transfer from iodide

The dynamics following charge transfer to solvent from iodide to a water cluster are studied using time-resolved photoelectron imaging of I-(H2O)n and I-(D2O)n clusters with n< or =28. The results show spontaneous conversion, on a time scale of approximately 1 ps, from water cluster anions with surface-bound electrons to structures in which the excess electron is more strongly bound and possibly more internalized within the solvent network. The resulting dynamics provide valuable insight into the electron solvation dynamics in water clusters and the relative stabilities between recently observed isomers of water cluster anions.     

Femtosecond pump-probe transient absorption study of the photolysis of [Cp'Mo(CO)3]2 (Cp' = eta5-C5H4CH3): role of translational and rotational diffusion in the radical cage effect

Femtosecond pump-probe studies of the photodissociation and subsequent radical cage pair recombination dynamics of the organometallic dimer [Cp'Mo(CO)3]2 (Cp' = eta5-C5H4CH3) are reported. The dynamics following photodissociation were studied in numerous noncoordinating hydrocarbon solvents. The results indicate that primary geminate recombination occurs on an ultrafast time scale (tau approximately 5 ps) and the efficiency of cage escape is inversely proportional to solvent viscosity. Investigation of the time-dependent anisotropy in this system allowed for an estimate of the rotational correlation time of the radical fragments (tau approximately 5-25 ps). Comparison of the rates of rotational motion with the population kinetics shows that the primary solvent cage dynamics and recombination efficiency are controlled by radical diffusion and not by radical rotation.     

Dynamics of charge-transfer-to-solvent precursor states in I- (water)n (n = 3-10) clusters studied with photoelectron imaging

The dynamics of charge-transfer-to-solvent states are studied in I- (H2O)(n=3-10) clusters and their deuterated counterparts using time-resolved photoelectron imaging. The photoelectron spectra for clusters with n > or = 5 reveal multiple time scales for dynamics after their electronic excitation. An increase in the vertical detachment energy (VDE) by several hundred millielectronvolts on a time scale of approximately 1 ps is attributed to stabilization of the excess electron, primarily through rearrangement of the solvent molecules, but a contribution to this stabilization from motion of the I atom cannot be ruled out. The VDE drops by approximately 50 meV on a time scale of tens of picoseconds; this is attributed to loss of the neutral iodine atom. Finally, the pump-probe signal decays with a time constant of 60 ps-3 ns, increasing with cluster size. This decay is commensurate with the growth of very slow electrons and is attributed to autodetachment. Smaller clusters (n = 3, 4) display simpler dynamics. Anisotropy parameters are reported for clusters n = 4-9.     

Methyl group dynamics and the onset of anharmonicity in myoglobin

The role of methyl groups in the onset of low-temperature anharmonic dynamics in a crystalline protein at low temperature is investigated using atomistic molecular dynamics (MD) simulation. Anharmonicity appears at approximately 150 K, far below the much-studied solvent-activated dynamical transition at approximately 220 K. A significant fraction of methyl groups exhibit nanosecond time scale rotational jump diffusion at 150 K. The splitting and shift in peak position of both the librational band (around 100 cm(-1)) and the torsional band (around 270-300 cm(-1)) also differ significantly among methyl groups, depending on the local environment. The simulation results provide no evidence for a correlation between methyl dynamics and solvent exposure, consistent with the hydration-independence of the low-temperature anharmonic dynamics observed in neutron scattering experiments. The calculated proton mean-square fluctuation and methyl NMR order parameters show a systematic nonlinear dependence on the rotational barrier which can be described using model functions. The methyl groups that exhibit many rotational excitations are located near xenon cavities, suggesting that cavities in proteins act as activation centers of anharmonic dynamics. The dynamic heterogeneity and the environmental sensitivity of motional parameters and low-frequency spectral bands of CH(3) groups found here suggest that methyl dynamics may be used as a probe to investigate the relation between low-energy structural fluctuations and packing defects in proteins.     

Solvent and lipid dynamics of hydrated lipid bilayers by incoherent quasielastic neutron scattering

The microscopic dynamics of the planar, multilamellar lipid bilayer system 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) has been investigated using quasielastic neutron scattering. The DMPC was hydrated to a level corresponding to approximately nine water molecules per lipid molecule. Selective deuteration has been used to separately extract the dynamics of the water, the acyl chains, and the polar head groups from the strong incoherent scattering of the remaining hydrogen atoms. Furthermore, the motions parallel and perpendicular to the bilayers were probed by using two different sample orientations relative to the incident neutron beam. For both sample orientations, the results showed an onset of water motions at 260 K on the experimental time scale of about 100 ps. From lack of wave-vector dependence of the onset temperature for water motions, it is evident that the observed water dynamics is of mainly rotational character at such low temperatures. At 290 K, i.e., slightly below the gel-to-liquid transition around 295 K, the nature of the water dynamics had changed to a more translational character, well described by a jump-diffusion model. On the limited experimental time and length (about 10 A) scales, this jump-diffusion process was isotropic, despite the very anisotropic system. The acyl chains exhibited a weak onset of anharmonic motions already at 120 K, probably due to conformational changes (trans-gauche and/or syn-anti) in the plane of the lipid bilayers. Other anharmonic motions were not observed on the experimental time scale until temperature had been reached above the gel-to-liquid transition around 295 K, where the acyl chains start to show more substantial motions.     

Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: the case of domain motions

Protein dynamics on a long time scale was investigated using all-atom molecular dynamics (MD) simulation and time-structure based independent component analysis (tICA). We selected the lysine-, arginine-, ornithine-binding protein (LAO) as a target protein and focused on its domain motions in the open state. A MD simulation of the LAO in explicit water was performed for 600 ns, in which slow and large-amplitude domain motions of the LAO were observed. After extracting domain motions by rigid-body domain analysis, the tICA was applied to the obtained rigid-body trajectory, yielding slow modes of the LAO's domain motions in order of decreasing time scale. The slowest mode detected by the tICA represented not a closure motion described by a largest-amplitude mode determined by the principal component analysis but a twist motion with a time scale of tens of nanoseconds. The slow dynamics of the LAO were well described by only the slowest mode and were characterized by transitions between two basins. The results show that tICA is promising for describing and analyzing slow dynamics of proteins.     

Femtosecond/picosecond time-resolved fluorescence study of hydrophilic polymer fine particles

Femtosecond/picosecond time-resolved fluorescence study of hydrophilic polymer fine particles (polyacrylamide, PAAm) was reported. Ultrafast fluorescence dynamics of polymer/water solution was monitored using a fluorescent probe molecule (C153). In the femtosecond time-resolved fluorescence measurement at 480 nm, slowly decay components having lifetimes of tau(1) approximately 53 ps and tau(2) approximately 5 ns were observed in addition to rapid fluorescence decay. Picosecond time-resolved fluorescence spectra of C153/PAAm/H2O solution were also measured. In the time-resolved fluorescence spectra of C153/PAAm/H2O, a peak shift from 490 to 515 nm was measured, which can be assigned to the solvation dynamics of polymer fine particles. The fluorescence peak shift was related to the solvation response function and two time constants were determined (tau(3) approximately 50 ps and tau(4) approximately 467 ps). Therefore, the tau(1) component observed in the femtosecond time-resolved fluorescence measurement was assigned to the solvation dynamics that was observed only in the presence of polymer fine particles. Rotational diffusion measurements were also carried out on the basis of the picosecond time-resolved fluorescence spectra. In the C153/PAAm/H2O solution, anisotropy decay having two different time constants was also derived (tau(6) approximately 76 ps and tau(7) approximately 676 ps), indicating the presence of two different microscopic molecular environments around the polymer surface. Using the Stokes-Einstein-Debye (SED) equation, microscopic viscosity around the polymer surface was evaluated. For the area that gave a rotational diffusion time of tau(6) approximately 76 ps, the calculated viscosity is approximately 1.1 cP and for tau(7) approximately 676 ps, it is approximately 10 cP. The calculated viscosity values clearly revealed that there are two different molecular environments around the polyacrylamide fine particles.     

Vibrational spectral diffusion and hydrogen bond dynamics in heavy water from first principles

We present a first-principles theoretical study of vibrational spectral diffusion and hydrogen bond dynamics in heavy water without using any empirical model potentials. The calculations are based on ab initio molecular dynamics simulations for trajectory generation and a time series analysis using the wavelet method for frequency calculations. It is found that, in deuterated water, although a one-to-one relation does not exist between the instantaneous frequency of an OD bond and the distance of its associated hydrogen bond, such a relation does hold on average. The dynamics of spectral diffusion is investigated by means of frequency-time correlation and spectral hole dynamics calculations. Both of these functions are found to have a short-time decay with a time scale of approximately 100 fs corresponding to dynamics of intact hydrogen bonds and a slower long-time decay with a time constant of approximately 2 ps corresponding to lifetimes of hydrogen bonds. The connection of the slower time scale to the dynamics of local structural relaxation is also discussed. The dynamics of hydrogen bond making is shown to have a rather fast time scale of approximately 100 fs; hence, it can also contribute to the short-time dynamics of spectral diffusion. A damped oscillation is also found at around 150-200 fs, which is shown to have come from underdamped intermolecular vibrations of a hydrogen-bonded water pair. Such assignments are confirmed by independent calculations of power spectra of intermolecular motion and hydrogen bond kinetics using the population correlation function formalism. The details of the time constants of frequency correlations and spectral shifts are found to depend on the frequencies of chosen OD bonds and are analyzed in terms of the dynamics of hydrogen bonds of varying strengths and also of free non-hydrogen-bonded OD groups.     

Temperature-dependent mechanistic transition for photoinduced electron transfer modulated by excited-state vibrational relaxation dynamics

The electron transfer (ET) dynamics of an unusually rigid pi-stacked (porphinato)zinc(II)-spacer-quinone (PZn-Q) system, [5-[8'-(4' '-[8' '-(2' ' ',5' ' '-benzoquinonyl)-1' '-naphthyl]-1' '-phenyl)-1'-naphthyl]-10,20-diphenylporphinato]zinc(II) (2a-Zn), in which sub-van der Waals interplanar distances separate juxtaposed porphyryl, aromatic bridge, and quinonyl components of this assembly, have been measured by ultrafast pump-probe transient absorption spectroscopy over a 80-320 K temperature range in 2-methyl tetrahydrofuran (2-MTHF) solvent. Analyses of the photoinduced charge-separation (CS) rate data are presented within the context of several different theoretical frameworks. Experiments show that at higher temperatures the initially prepared 2a-Zn vibronically excited S1 state relaxes on an ultrafast time scale, and ET is observed exclusively from the equilibrated lowest-energy S1 state (CS1). As the temperature decreases, production of the photoinduced charge-separated state directly from the vibrationally unrelaxed S1 state (CS2) becomes competitive with the vibrational relaxation time scale. At the lowest experimentally interrogated temperature ( approximately 80 K), CS2 defines the dominant ET pathway. ET from the vibrationally unrelaxed S1 state is temperature-independent and manifests a subpicosecond time constant; in contrast, the CS1 rate constant is temperature-dependent, exhibiting time constants ranging from 4x10(10) s(-1) to 4x10(11) s(-1) and is correlated strongly with the temperature-dependent solvent dielectric relaxation time scale over a significant temperature domain. Respective electronic coupling matrix elements for each of these photoinduced CS1 and CS2 pathways were determined to be approximately 50 and approximately 100 cm-1. This work not only documents a rare, if not unique, example of a system where temperature-dependent photoinduced charge-separation (CS) dynamics from vibrationally relaxed and unrelaxed S1 states can be differentiated, but also demonstrates a temperature-dependent mechanistic transition of photoinduced CS from the nonadiabatic to the solvent-controlled adiabatic regime, followed by a second temperature-dependent mechanistic evolution where CS becomes decoupled from solvent dynamics and is determined by the extent to which the vibrationally unrelaxed S1 state is populated.     

Nanosecond folding dynamics of a three-stranded beta-sheet

We studied conformational stability and folding kinetics of a three-stranded beta-sheet containing two rigid turns. Static infrared measurements indicate that this beta-sheet undergoes a broad but cooperative thermal unfolding transition with a midpoint at approximately 53 degrees C. Interestingly, time-resolved infrared experiments show that its relaxation kinetics in response to a temperature-jump (T-jump) occur on the nanosecond time scale (e.g., the relaxation time is approximately 140 ns at 35.0 degrees C), thereby suggesting that the conformational relaxation encounters only a small free energy barrier or even proceeds in a downhill manner. Further Langevin dynamics simulations suggest that the observed T-jump relaxation kinetics could be modeled by a conformational diffusion process along a single-well free energy profile, which allowed us to determine the effective diffusion constant and also the roughness of the folding energy landscape.     

Watching Na atoms solvate into (Na+,e-) contact pairs: untangling the ultrafast charge-transfer-to-solvent dynamics of Na- in tetrahydrofuran (THF)

With the large dye molecules employed in typical studies of solvation dynamics, it is often difficult to separate the intramolecular relaxation of the dye from the relaxation associated with dynamic solvation. One way to avoid this difficulty is to study solvation dynamics using an atom as the solvation probe; because atoms have only electronic degrees of freedom, all of the observed spectroscopic dynamics must result from motions of the solvent. In this paper, we use ultrafast transient absorption spectroscopy to investigate the solvation dynamics of newly created sodium atoms that are formed following the charge transfer to solvent (CTTS) ejection of an electron from sodium anions (sodide) in liquid tetrahydrofuran (THF). Because the absorption spectra of the sodide reactant, the sodium atom, and the solvated electron products overlap, we first examined the dynamics of the ejected CTTS electron in the infrared to build a detailed model of the CTTS process that allowed us to subtract the spectroscopic contributions of the sodide bleach and the solvated electron and cleanly reveal the spectroscopy of the solvated atom. We find that the neutral sodium species created following CTTS excitation of sodide initially absorbs near 590 nm, the position of the gas-phase sodium D-line, suggesting that it only weakly interacts with the surrounding solvent. We then see a fast solvation process that causes a red-shift of the sodium atom's spectrum in approximately 230 fs, a time scale that matches well with the results of MD simulations of solvation dynamics in liquid THF. After the fast solvation is complete, the neutral sodium atoms undergo a chemical reaction that takes place in approximately 740 fs, as indicated by the observation of an isosbestic point and the creation of a species with a new spectrum. The spectrum of the species created after the reaction then red-shifts on a approximately 10-ps time scale to become the equilibrium spectrum of the THF-solvated sodium atom, which is known from radiation chemistry experiments to absorb near approximately 900 nm. There has been considerable debate as to whether this 900-nm absorbing species is better thought of as a solvated atom or a sodium cation:solvated electron contact pair, (Na+,e-). The fact that we observe the initially created neutral Na atom undergoing a chemical reaction to ultimately become the 900-nm absorbing species suggests that it is better assigned as (Na+,e-). The approximately 10-ps solvation time we observe for this species is an order of magnitude slower than any other solvation process previously observed in liquid THF, suggesting that this species interacts differently with the solvent than the large molecules that are typically used as solvation probes. Together, all of the results allow us to build the most detailed picture to date of the CTTS process of Na- in THF as well as to directly observe the solvation dynamics associated with single sodium atoms in solution.     

Multiple time scales in solvation dynamics of DNA in aqueous solution: the role of water, counterions, and cross-correlations

Recent time domain experiments have explored solvation dynamics of a probe located inside a DNA duplex, in an effort to gain information, e.g., on the dynamics of water molecules in the DNA major and minor grooves and their environment. Multiple time constants in the range of a few picoseconds to several nanoseconds were obtained. We have carried out 15 ns long atomistic molecular dynamics simulations to study the solvation dynamics of bases of a 38 base-pair long DNA duplex in an aqueous solution containing counterions. We have computed the energy-energy time correlation function (TCF) of the four individual bases (A, T, G, and C) to characterize the solvation dynamics. All the TCFs display highly nonexponential decay with time. When the trajectories are analyzed with 100 fs time resolution, the TCF of each base shows initial ultrafast decay (with tau1 approximately equal 60-80 fs) followed by two intermediate components (tau2 approximately equal 1 ps, tau3 approximately equal 20-30 ps), in near complete agreement with a recent time domain experiment on DNA solvation. Interestingly, the solvation dynamics of each of the four different nucleotide bases exhibit rather similar time scales. To explore the existence of slow relaxation at longer times reported recently in a series of experiments, we also analyzed the solvation TCFs calculated with longer time trajectories and with a larger time resolution of 1 ps. In this case, an additional slow component with a time constant of the order of 250 ps is observed. Through an analysis of partial solvation TCFs, we find that the slow decay originates mainly from the interaction of the nucleotides with the dipolar water molecules and the counterions. An interesting negative cross-correlation between water and counterions is observed, which makes an important contribution to relaxation at intermediate to longer times.     

Molecular dynamics investigation with the time resolved optical Kerr effect on the CS2-C6H6 mixtures

An investigation of the molecular dynamics in pure liquids and in mixtures through the technique of time resolved optical Kerr effect is performed. The samples studied were the mixtures of carbon disulfide (CS(2)) with benzene (C(6)H(6)). The molecular dynamics of the pure liquids is briefly discussed while the main results are obtained for the mixtures. A slow dynamics component is observed for the optical heterodyne detected optical Kerr effect transient decaying exponentially with time constants on picosecond time scale. The fast subpicosend time relaxations are analyzed in terms of the nondiffusive component of the spectral response that is associated with the molecular dynamics. The modifications of the spectrum are quantified, and the explanation of the observed changes is given in terms of the structural interaction configurations that produced changes in the intermolecular potential within which the molecules execute librational motions.     

Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water

In this article, we analyze the folding dynamics of an all-atom model of a polyphenylacetylene (pPA) 12-mer in explicit solvent for four common organic and aqueous solvents: acetonitrile, chloroform, methanol, and water. The solvent quality has a dramatic effect on the time scales in which pPA 12-mers fold. Acetonitrile was found to manifest ideal folding conditions as suggested by optimal folding times on the order of approximately 100-200 ns, depending on temperature. In contrast, chloroform and water were observed to hinder the folding of the pPA 12-mer due to extreme solvation conditions relative to acetonitrile; chloroform denatures the oligomer, whereas water promotes aggregation and traps. The pPA 12-mer in a pure methanol solution folded in approximately 400 ns at 300 K, compared relative to the experimental 12-mer folding time of approximately 160 ns measured in a 1:1 v/v THF/methanol solution. Requisite in drawing the aforementioned conclusions, analysis techniques based on Markov state models are applied to multiple short independent trajectories to extrapolate the long-time scale dynamics of the 12-mer in each respective solvent. We review the theory of Markov chains and derive a method to impose detailed balance on a transition-probability matrix computed from simulation data.     

Ultrafast intermolecular dynamics of liquid water: a theoretical study on two-dimensional infrared spectroscopy

Physical and chemical properties of liquid water are dominated by hydrogen bond structure and dynamics. Recent studies on nonlinear vibrational spectroscopy of intramolecular motion provided new insight into ultrafast hydrogen bond dynamics. However, our understanding of intermolecular dynamics of water is still limited. We theoretically investigated the intermolecular dynamics of liquid water in terms of two-dimensional infrared (2D IR) spectroscopy. The 2D IR spectrum of intermolecular frequency region (<1000 cm(-1)) is calculated by using the equilibrium and nonequilibrium hybrid molecular dynamics method. We find the ultrafast loss of the correlation of the libration motion with the time scale of approximately 110 fs. It is also found that the energy relaxation from the libration motion to the low frequency motion takes place with the time scale of about 180 fs. We analyze the effect of the hindered translation motion on these ultrafast dynamics. It is shown that both the frequency modulation of libration motion and the energy relaxation from the libration to the low frequency motion significantly slow down in the absence of the hindered translation motion. The present result reveals that the anharmonic coupling between the hindered translation and libration motions is essential for the ultrafast relaxation dynamics in liquid water.     

Cation and anion transport through hydrophilic pores in lipid bilayers

To understand the origin of transmembrane potentials, formation of transient pores, and the movement of anions and cations across lipid membranes, we have performed systematic atomistic molecular dynamics simulations of palmitoyl-oleoyl-phosphatidylcholine (POPC) lipids. A double bilayer setup was employed and different transmembrane potentials were generated by varying the anion (Cl-) and cation (Na+) concentrations in the two water compartments. A transmembrane potential of approximately 350 mV was thereby generated per bilayer for a unit charge imbalance. For transmembrane potential differences of up to approximately 1.4 V, the bilayers were stable, over the time scale of the simulations (10-50 ns). At larger imposed potential differences, one of the two bilayers breaks down through formation of a water pore, leading to both anion and cation translocations through the pore. The anions typically have a short residence time inside the pore, while the cations show a wider range of residence times depending on whether they bind to a lipid molecule or not. Over the time scale of the simulations, we do not observe the discharge of the entire potential difference, nor do we observe pore closing, although we observe that the size of the pore decreases as more ions translocate. We also observed a rare lipid flip-flop, in which a lipid molecule translocated from one bilayer leaflet to the opposite leaflet, assisted by the water pore.