Hydrophobic molecules slow down the hydrogen-bond dynamics of water

We study the spectral and orientational dynamics of HDO molecules in solutions of tertiary-butyl-alcohol (TBA), trimethyl-amine-oxide (TMAO), and tetramethylurea (TMU) in isotopically diluted water (HDO:D(2)O and HDO:H(2)O). The spectral dynamics are studied with femtosecond two-dimensional infrared spectroscopy and the orientational dynamics with femtosecond polarization-resolved vibrational pump-probe spectroscopy. We observe a strong slowing down of the spectral diffusion around the central part of the absorption line that increases with increasing solute concentration. At low concentrations, the fraction of water showing slow spectral dynamics is observed to scale with the number of methyl groups, indicating that this effect is due to slow hydrogen-bond dynamics in the hydration shell of the methyl groups of the solute molecules. The slowing down of the vibrational frequency dynamics is strongly correlated with the slowing down of the orientational mobility of the water molecules. This correlation indicates that these effects have a common origin in the effect of hydrophobic molecular groups on the hydrogen-bond dynamics of water.     

Using MD snapshots in ab initio and DFT calculations: OH vibrations in the first hydration shell around Li+(aq)

The average OH stretching vibrational frequency for the water molecules in the first hydration shell around a Li(+) ion in a dilute aqueous solution was calculated by a hybrid molecular dynamics + quantum-mechanical ("MD + QM") approach. Using geometry configurations from a series of snapshots from an MD simulation, the anharmonic, uncoupled OH stretching frequencies were calculated for 100 first-shell OH oscillators at the B3LYP and HF/6-31G(d,p) levels of theory, explicitly including the first shell and the relevant second shell water molecules into charge-embedded supermolecular QM calculations. Infrared intensity-weighting of the density-of-states (DOS) distributions by means of the squared dipole moment derivatives (which vary by a factor of 20 over the OH stretching frequency band at the B3LYP level), changes the downshift from approximately -205 to -275 cm(-1) at the B3LYP level. Explicit inclusion of relevant third-shell water molecules in the supermolecular cluster leads to a further downshift by approximately -30 cm(-1). Our final estimated average downshift is approximately -305 cm(-1). The experimental value lies somewhere in the range between -290 and -420 cm(-1). Also, the absolute nu(OH) frequency is well reproduced in our calculations. "In-liquid" instantaneous correlation curves between nu(OH) and various typical H-bond strength parameters such as R(O...O), R(H...O), the intramolecular OH bond length, and the IR intensity are presented. Some of these correlations are robust and persist also for the rather distorted instantaneous geometries in the liquid; others are less so.     

Structure and dynamics at the surface of a concentrated aqueous solution of CsF

A molecular dynamics simulation of a liquid layer of a concentrated CsF solution in water has been performed in order to compare the results with those obtained in an experimental study of our group. The main result of the experiment was the existence of a monolayer of nearly pure water constituting the surface and a homogeneous mixture constituting the bulk of the system. The simulation reveals the same phenomena which can be explained by the circumstance that the ions near the surface mostly keep their first solvation shell intact. The water molecules belonging to these shells and being placed on the vapor side constitute this monolayer. The density profiles of the ions indicate that the Cs ions penetrate further into the surface than the F ions. The orientational structure of the first shell of water molecules around an ion is the same for ions in the surface and ions in the bulk in contrast to the dynamics which is altered. The spectra of the librational motion are shifted to lower frequencies. In addition to that the spectra belonging to libration which involves motion of the dipole moment develop a peak in the low frequency range irrespective of whether the water molecules are bonded to Cs or to F ions. This can be correlated with an overall preferred orientation of the water molecules in the surface which is most pronounced for the dipole moment. The calculation of the diffusion coefficients shows that the top surface layer of nearly pure water is a region of enhanced and extremely anisotropic mobility. The mean residence time of water molecules in the surface in the first shell of an ion is reduced according to the enhanced mobility.     

Azide-water intermolecular coupling measured by two-color two-dimensional infrared spectroscopy

We utilize two-color two-dimensional infrared spectroscopy to measure the intermolecular coupling between azide ions and their surrounding water molecules in order to gain information about the nature of hydrogen bonding of water to ions. Our findings indicate that the main spectral contribution to the intermolecular cross-peak comes from population transfer between the asymmetric stretch vibration of azide and the OD-stretch vibration of D(2)O. The azide-bound D(2)O bleach/stimulated emission signal, which is spectrally much narrower than its linear absorption spectrum, shows that the experiment is selective to solvation shell water molecules for population times up to ~500 fs. The waters around the ion are present in an electrostatically better defined environment. Afterwards, ~1 ps, the sample thermalizes and selectivity is lost. On the other hand, the excited state absorption signal of the azide-bound D(2)O is much broader. The asymmetry in spectral width between bleach/stimulated emission versus excited absorption has been observed in very much the same way for isotope-diluted ice Ih, where it has been attributed to the anharmonicity of the OD potential.     

Hydrogen bond breaking mechanism and water reorientational dynamics in the hydration layer of lysozyme

The mechanism and the rate of hydrogen bond-breaking in the hydration layer surrounding an aqueous protein are important ingredients required to understand the various aspects of protein dynamics, its function, and stability. Here, we use computer simulation and a time correlation function technique to understand these aspects in the hydration layer of lysozyme. Water molecules in the layer are found to exhibit three distinct bond-breaking mechanisms. A large angle orientational jump of the donor water molecule is common among all of them. In the most common ( approximately 80%) bond-breaking event in the layer, the new acceptor water molecule comes from the first coordination shell (initially within 3.5 A of the donor), and the old acceptor water molecule remains within the first coordination shell, even after the bond-breaking. This is in contrast to that in bulk water, in which both of the acceptor molecules involve the second coordination shell. Additionally, the motion of the incoming and the outgoing acceptor molecules involved is not diffusive in the hydration layer, in contrast to their observed diffusive motion in the bulk. The difference in rotational dynamics between the bulk and the hydration layer water molecules is clearly manifested in the calculated time-dependent angular van Hove self-correlation function ( G(theta, t)) which has a pronounced two-peak structure in the layer, and this can be traced to the constrained translational motion in the layer. The longevity of the surrounding hydrogen bond network is found to be significantly enhanced near a hydrophilic residue.     

Vibrational spectroscopy and dynamics of azide ion in ionic liquid and dimethyl sulfoxide water mixtures

Steady-state and time-resolved infrared spectroscopy of the azide (N(3)-) anion has been used to characterize aqueous mixtures both with the ionic liquid (IL) 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF(4)]) and with dimethyl sulfoxide (DMSO). In the DMSO-water mixtures, two anion vibrational bands are observed for low water mole fractions (0 > X(w) > 0.25), which indicates a heterogeneous ion solvation environment. The band at 2000 cm(-1) observed for neat DMSO does not shift but decreases in amplitude as the amount of water is increased. Another band appears at slightly higher frequency at low X(w) (=0.05). As the amount of water is increased, this band shifts to higher frequency and becomes stronger and is attributed to azide with an increasing degree of hydration. At intermediate and high X(w), a single band is observed that shifts almost linearly with water mole fraction toward the bulk water value. The heterogeneity is evident from the infrared pump-probe studies in which the decay times depend on probe frequency at low mole fraction. For the azide spectra in IL-water mixtures, a single azide band is observed for each mole fraction mixture. The azide band shifts almost linearly with mole fraction, indicating nearly ideal mixing behavior. As with the DMSO-water mixtures, the time-resolved IR decay times are probe-frequency-dependent at low mole fraction, again indicating heterogeneous solvation. In both the DMSO and IL mixtures with water, the relaxation times are slower than would be expected from ideal mixing, suggesting that vibrational relaxation of azide is more sensitive than its vibrational frequency to the solvent structure. The results are discussed in terms of preferential solvation and the degree to which the azide shift and vibrational relaxation depend on the degree of water association in the mixtures.     

Hydration of the Calcium Dication: Direct Evidence for Second Shell Formation from Infrared Spectroscopy

Infrared laser action spectroscopy in a Fourier‐transform ion cyclotron resonance mass spectrometer is used in conjunction with ab initio calculations to investigate doubly charged, hydrated clusters of calcium formed by electrospray ionization. Six water molecules coordinate directly to the calcium dication, whereas the seventh water molecule is incorporated into a second solvation shell. Spectral features indicate the presence of multiple structures of Ca(H₂O)₇²⁺ in which outer‐shell water molecules accept either one (single acceptor) or two (double acceptor) hydrogen bonds from inner‐shell water molecules. Double‐acceptor water molecules are predominately observed in the second solvent shells of clusters containing eight or nine water molecules. Increased hydration results in spectroscopic signatures consistent with additional second‐shell water molecules, particularly the appearance of inner‐shell water molecules that donate two hydrogen bonds (double donor) to the second solvent shell. This is the first reported use of infrared spectroscopy to investigate shell structure of a hydrated multiply charged cation in the gas phase and illustrates the effectiveness of this method to probe the structures of hydrated ions.     

Lone pair versus bonding pair electrons: the mechanism of electronic polarization of water in the presence of positive ions

It is commonly accepted that the water molecules in the first solvation shell of a positive ion are strongly polarized because of an elongation of the oxygen lone pair orbitals along the ion-oxygen direction and this is commonly considered the dominant effect. Recent experimental and theoretical works have instead suggested that this is not the dominant aspect and that the problem is by far more complicated. Consistent with the picture given above, here we show that, in particular, an equally important role into the polarization process is played by the bonding pair electrons located along the internal oxygen-hydrogen bond. We also provide some arguments which suggest that the main reason of such a behavior is due to the distortion of the molecular orbitals caused by the interaction between non-hydrogen-bonded water molecules in the first solvation shell of the ion.     

A direct comparison of azide and nitrile vibrational probes

The synthesis of 2'-azido-5-cyano-2'-deoxyuridine, N(3)CNdU (1), from trityl-protected 2'-amino-2'-deoxyuridine was accomplished in four steps with a 12.5% overall yield. The IR absorption positions and profiles of the azide and nitrile group of N(3)CNdU were investigated in 14 different solvents and water/DMSO solvent mixtures. The azide probe was superior to the nitrile probe in terms of its extinction coefficient, which is 2-4 times larger. However, the nitrile IR absorbance profile is generally less complicated by accidental Fermi resonance. The IR frequencies of both probes undergo a substantial red shift upon going from water to aprotic solvents such as THF or DMSO. DFT calculations supported the hypothesis that the molecular origin of the higher observed frequency in water is primarily due to hydrogen bonds between the probes and water molecules.     

Car-Parrinello molecular dynamics simulation of Fe 3+ (aq)

The optimized geometry and energetic properties of Fe(D2O)n 3+ clusters, with n = 4 and 6, have been studied with density-functional theory calculations and the BLYP functional, and the hydration of a single Fe 3+ ion in a periodic box with 32 water molecules at room temperature has been studied with Car-Parrinello molecular dynamics and the same functional. We have compared the results from the CPMD simulation with classical MD simulations, using a flexible SPC-based water model and the same number of water molecules, to evaluate the relative strengths and weaknesses of the two MD methods. The classical MD simulations and the CPMD simulations both give Fe-water distances in good agreement with experiment, but for the intramolecular vibrations, the classical MD yields considerably better absolute frequencies and ion-induced frequency shifts. On the other hand, the CPMD method performs considerably better than the classical MD in describing the intramolecular geometry of the water molecule in the first hydration shell and the average first shell...second shell hydrogen-bond distance. Differences between the two methods are also found with respect to the second-shell water orientations. The effect of the small box size (32 vs 512 water molecules) was evaluated by comparing results from classical simulations using different box sizes; non-negligible effects are found for the ion-water distance and the tilt angles of the water molecules in the second hydration shell and for the O-D stretching vibrational frequencies of the water molecules in the first hydration shell.     

Structure and dynamics of the hydration shells of the Al3+ ion

First principles simulations of the hydration shells surrounding Al3+ ions are reported for temperatures near 300 degrees C. The predicted six water molecules in the octahedral first hydration shell were found to be trigonally coordinated via hydrogen bonds to 12 s shell water molecules in agreement with the putative structure used to analyze the x-ray data, but in disagreement with the results reported from conventional molecular dynamics using two-and three-body potentials. Bond lengths and angles of the water molecules in the first and second hydration shells and the average radii of these shells also agreed very well with the results of the x-ray analysis. Water transfers into and out of the second solvation shell were observed to occur on a picosecond time scale via a dissociative mechanism. Beyond the second shell the bonding pattern substantially returned to the tetrahedral structure of bulk water. Most of the simulations were done with 64 solvating water molecules (20 ps). Limited simulations with 128 water molecules (7 ps) were also carried out. Results agreed as to the general structure of the solvation region and were essentially the same for the first and second shell. However, there were differences in hydrogen bonding and Al-O radial distribution function in the region just beyond the second shell. At the end of the second shell a nearly zero minimum in the Al-O radial distribution was found for the 128 water system. This minimum is less pronounced minimum found for the 64 water system, which may indicate that sizes larger than 64 may be required to reliably predict behavior in this region.     

Dynamics of water confined in the interdomain region of a multidomain protein

Molecular dynamics simulations are performed to study the dynamics of interfacial water confined in the interdomain region of a two-domain protein, BphC enzyme. The results show that near the protein surface the water diffusion constant is much smaller and the water-water hydrogen bond lifetime is much longer than that in bulk. The diffusion constant and hydrogen bond lifetime can vary by a factor of as much as 2 in going from the region near the hydrophobic domain surface to the bulk. Water molecules in the first solvation shell persist for a much longer time near local concave sites than near convex sites. Also, the water layer survival correlation time shows that on average water molecules near the extended hydrophilic surfaces have longer residence times than those near hydrophobic surfaces. These results indicate that local surface curvature and hydrophobicity have a significant influence on water dynamics.     

The arrangement of first- and second-shell water molecules in trivalent aluminum complexes: results from density functional theory and structural crystallography

The structural and energetic features of a variety of gas-phase aluminum ion hydrates containing up to 18 water molecules have been studied computationally using density functional theory. Comparisons are made with experimental data from neutron diffraction studies of aluminum-containing crystal structures listed in the Cambridge Structural Database. Computational studies indicate that the hexahydrated structure Al[H(2)O](6)(3+) (with symmetry T(h)()), in which all six water molecules are located in the innermost coordination shell, is lower in energy than that of Al[H(2)O](5)(3+).[H(2)O], where only five water molecules are in the inner shell and one water molecule is in the second shell. The analogous complex with four water molecules in the inner shell and two in the outer shell undergoes spontaneous proton transfer during the optimization to give [Al[H(2)O](2)[OH](2)](+).[H(3)O(+)](2), which is lower in energy than Al[H(2)O](6)(3+); this finding of H(3)O(+) is consistent with the acidity of concentrated Al(3+) solutions. Since, however, Al[H(2)O](6)(3+) is detected in solutions of Al(3+), additional water molecules are presumed to stabilize the hexa-aquo Al(3+) cation. Three models of a trivalent aluminum ion complex surrounded by a total of 18 water molecules arranged in a first shell containing 6 water molecules and a second shell of 12 water molecules are discussed. We find that a model with S(6) symmetry for which the Al[H(2)O](6)(3+) unit remains essentially octahedral and participates in an integrated hydrogen bonded network with the 12 outer-shell water molecules is lowest in energy. Interactions between the 12 second-shell water molecules and the trivalent aluminum ion in Al[H(2)O](6)(3+) do not appear to be sufficiently strong to orient the dipole moments of these second-shell water molecules toward the Al(3+) ion.     

Molecular orbital theory of the hydrogen bond. 26. The hydration of uracil

Ab initio SCF calculations with the STO -3G basis set have been performed to determine the structure and stability of a 6:1 water:uracil heptamer in which water molecules are hydrogen bonded to uracil at each of the six hydrogen-bonding sites in the uracil molecular plane. The structure of the heptamer describes a stable arrangement of these six water molecules, which are the primary solvent molecules in the first solvation shell, and is suggestive of the arrangement of secondary solvent molecules in that shell in the nonpolar region of the uracil molecular plane. The stabilization energy of the heptamer is 49.6 kcal/mol, or 8.3 kcal/mol per water molecule. The hydrogen bonds between uracil and water are the primary factor in the stabilization of the complex, although water–water interactions and nonadditivity effects are also significant.     

Internal water molecules of the proton-pumping halorhodopsin in the presence of azide

In the FTIR study of rhodopsins, we have so far found that strongly hydrogen-bonded water molecules (O-D stretch at <2400 cm-1) are only present in the proteins exhibiting proton-pumping activity. Halorhodopsin (HR) is a light-driven chloride pump in haloarchaea, which does not possess such water molecules. On the other hand, it is known that addition of azide converts HR into a proton pump. Although the mechanism has not been understood, we observed strongly hydrogen-bonded water molecules in the azide-bound HR of Natronobacterium pharaonis (pHR). This finding is consistent with the previous results, implying that the presence of strongly hydrogen-bonded water molecules is requested for the proton-pumping function of rhodopsins.     

Structure of a Na<Superscript>+</Superscript> cation hydration shell on heating in a planar nanopore

Resistance to heating above the boiling point of water of the molecular structure of a single-charged sodium cation hydration shell growing under the conditions of a model planar nanopore with a width of 5 Å is studied by computer simulation. Monte Carlo calculations of spatial correlation functions are performed in a detailed model with regard to many-body interactions between the ion and water molecules. The system demonstrates an increased resistance to thermal fluctuations along the pore plane and a decreased one in the transverse direction. The heating is accompanied by an enhanced coating effect of molecules around the ion and a diminished effect of extruding the ion out of its own hydration shell. The orientational molecular order due to strong spatial anisotropy inside the nanopore is much more stable than the hydrogen bonds between the molecules.     

Adsorption mechanism of water molecules surrounding Au nanoparticles of different sizes

Molecular dynamic simulation is used to investigate the adsorption mechanism of water molecules surrounding Au nanoparticles with different sizes. Our results show that the adsorption mechanism of the water molecules in the first water shell will be influenced by the size of the Au nanoparticle. For the larger Au nanoparticles, the hydrogen bonding of water molecules adsorbed on the surface of the Au nanoparticles are arranged in a two-dimensional structure, while those adsorbed on the edge of the surface of the Au nanoparticles are arranged in a three-dimensional structure. However, in the case of the smallest Au nanoparticle, the hydrogen bonding of the water molecules on the first adsorbed layer are arranged only in a three-dimensional structure. The arrangement of the water molecules in the first water shell can be determined by orientation order parameter. The water molecules that adsorb on the larger Au nanoparticles tend to arrange in an irregular arrangement, while those adsorbed on the smallest Au nanoparticle tend to arrange a regular arrangement. Interestingly, the water molecules adsorbed on the smallest nanoparticle are arranged in a bulklike structure in the first shell.     

Solvation of tetraalkylammonium chlorides in acetonitrile-water mixtures: mass spectrometry and molecular dynamics simulations.

The solvation of tetramethylammonium chloride (Me4NCl) and tetra-n-butylammonium chloride (Bu4NCl) in water-acetonitrile mixtures was investigated by mass spectrometry of clusters isolated from the solution. As far as the positive ions are concerned, clusters composed of alkylammonium ions and acetonitrile molecules only were observed, even for mixtures with high water content. In contrast, for the negative ions, clusters composed of chloride with both water and/or acetonitrile molecules were observed. For the smaller system (Me4NCl) we performed quantum chemical calculations and molecular dynamics simulations. It was found that even though water is present in the solvation shell of Me4N+, only acetonitrile has a strong electrostatic interaction with the cation. Water molecules around Me4N+ form hydrogen bonds with other water molecules, and they interact with Me4N+ mainly via dispersive interactions. These results indicate that Me4N+ behaves like a hydrophobic solute. On the other hand, the interaction of Cl- with water and acetonitrile is of comparable strength and, in both cases, the electrostatic interaction dominates. Herein we demonstrate experimentally and theoretically that positive and negative ions give rise to characteristic solvation structures in mixed solvents: even a relatively small organic cation, such as Me4N+, exhibits a hydrophobic-like solvation shell.     

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.     

Die Kristallstruktur des Zn(N3)2 · 2,5 H2O

Crystal Structure of Zn(N₃)₂ · 2.5 H₂O The crystal structure of zinc azide 2.5 hydrate, 1975 erroneously described as a trihydrate, was determined by single crystal x-ray diffraction. The crystals are monoclinic, a = 996.2(5), b = 594.8(5), c = 1018.4(9) pm, β 90.16(3)°, space group P2/n, Z = 4, R = 0.043. Zinc is hexacoordinated by four azide groups and two water molecules. The octahedra around zinc share nitrogen atoms as common edges and they are connected to form strings along the b-axis. The water molecules are arranged to chainlike clusters, two of the ten water molecules are not coordinated to zinc. The azide groups are asymmetric and almost linear.