Inelastic incoherent neutron scattering studies of water interacting with biological macromolecules.

The interaction between water and biological macromolecules in living organisms is of fundamental importance in a range of processes. We have studied water-DNA and water-proteolipid membrane systems over a range of hydration states using inelastic incoherent neutron scattering. We find a relatively sharp transition for both systems at a water concentration above which bulk solvent can be detected. Below this concentration, bulk water is essentially absent, i.e., all the water in the system is interacting with the biological macromolecules. This water is strongly perturbed as judged by its energy transfer spectrum, with a broader and lower energy transition than bulk water in the 50-75 meV (approximately 400-600 cm(-1)) range. Taking into account the differing geometry of (cylindrical) DNA and (planar) membranes, the number of water shells perturbed by each system was estimated. A conclusion is that in living organisms a large proportion of the cellular water will be in a state quite distinct from bulk water. The data add to the growing evidence that water structure in the vicinity of biological macromolecules is unusual and that the proximal water behaves differently compared to the bulk solvent.     

Water-protein dynamic coupling and new opportunities for probing it at low to physiological temperatures in aqueous solutions

Both the structure and dynamics of biomolecules are known to be essential for their biological function. In the dehydrated state, the function of biomolecules, such as proteins, is severely impeded, so hydration is required for bioactivity. The dynamics of the hydrated biomolecules and their hydration water are related - but how closely? The problem involves several layers of complexity. Even for water in the bulk state, the contribution from various dynamic components to the overall dynamics is not fully understood. In biological systems, the effects of confinement on the hydration water further complicate the picture. Even if the various components of the hydration water dynamics are properly understood, which of them are coupled to the protein dynamics, and how? The studies of protein dynamics over the wide temperature range, from physiological to low temperatures, provide some answers to these question. At low temperatures, both the protein and its hydration water behave as solids, with only vibrational degrees of freedom. As the temperature is increased, non-vibrational dynamic components start contributing to the measurable dynamics and eventually become dominant at physiological temperatures. Thus, the temperature dependence of the dynamics of protein and its hydration water may allow probing various dynamic components separately. In order to suppress the water freezing, the low-temperature studies of protein rely on either low-hydrated samples (essentially, hydrated protein powders), or cryo-protective solutions. Both approaches introduce the hydration environments not characteristic of the protein environments in living systems, which are typically aqueous protein solutions of various concentrations. In this paper, we discuss the coupling between the dynamic components of the protein and its hydration water by critical examining of the existing literature, and then propose that proteins can be studied in an aqueous solution that is remarkably similar in its dynamic properties to pure water, yet does not freeze down to about 200 K, even in the bulk form. The first experiment of this kind using quasielastic neutron scattering is discussed, and more experiments are proposed.     

Quasielastic and inelastic neutron scattering on hydrated calcium silicate pastes

Using the inverse geometry spectrometer QENS at the Intense Pulsed Neutron Source of the Argonne National Laboratory, we collected quasielastic and inelastic neutron scattering spectra of hydrated tricalcium and dicalcium silicate, the main components of ordinary Portland cement. Data were obtained at different curing time, from a few hours to several months. Both the quasielastic and inelastic spectra have been analyzed at the same time according to the relaxing cage model, which is a model developed to describe the dynamics of water at supercooled temperatures. Short-time and long-time dynamics of hydration water in hydrated cement pastes as a function of the curing time have been simultaneously obtained. The results confirm the findings reported in previous experiments showing that it is possible to fit consistently the quasielastic and inelastic spectra giving insights on the effect of the curing time on the short-time vibrational dynamics of hydration water.     

Experimental observations of water-framework interactions in a hydrated microporous aluminum phosphate

Differential scanning calorimetry of the hydrated, microporous aluminum phosphate AlPO-14 shows two distinct water losses between room temperature and 120 degrees C, indicating the presence of two types of water in the solid. Multiple-quantum magic angle spinning (MQMAS) (27)Al NMR shows that, while in dehydrated AlPO-14 all aluminum is found in tetrahedral sites, on hydration a significant proportion of the aluminum increases its coordination number to 6. This accounts for the presence of tightly bound water. The first detailed incoherent inelastic neutron scattering (IINS) studies of such a system give a spectrum with distinct and sharp librational bands for bound water, significantly different than seen in ice Ih. Using these data, and by consideration of the crystal structure of dehydrated AlPO-14, we propose a model for the hydrated material in which the tightly bound water bridges pairs of Lewis acidic framework aluminums in a dense region of the structure, while loosely bound water resides in the pores of the solid. Further IINS measurements using a high-incident neutron energy provide data that are in agreement with our model. We can detect two O-H stretching modes for bound water in hydrated AlPO-14, consistent with the model of two types of water present in the material, with the loosely bound water connected to neighboring water molecules by intermolecular hydrogen bonds.     

Single particle scattering and momentum distributions in solid hydrogen

The incoherent inelastic neutron scattering function of solid para-hydrogen was recorded. It was shown that at momentum transfers above 5Å⁻¹ the data can be interpreted as recoil spectra from single particle scattering at hydrogen molecules. The evaluation of the momentum distribution and kinetic energy of the scattering particles from such data is discussed.     

Further evidence that interfacial water is the main "driving force" of protein dynamics: a neutron scattering study on perdeuterated C-phycocyanin

The fundamental role of hydration water (also called interfacial water) is widely recognized in protein flexibility, especially in the existence of the so-called protein "dynamical transition" at around 220 K. In the present study, we take advantage of perdeuterated C-phycocyanin (CPC) and elastic incoherent neutron scattering (EINS) to distinguish between protein dynamics and interfacial water dynamics. Powders of hydrogenated (hCPC) and perdeuterated (dCPC) CPC protein have been hydrated, respectively, with D(2)O or H(2)O and measured by EINS to separately probe protein dynamics (hCPC/D(2)O) and water dynamics (dCPC/H(2)O) at different time- and length-scales. We find that "fast" (<20 ps) local mean-square displacements (MSD) of both protein and interfacial water coincide all along the temperature range, with the same dynamical transition temperature at ~220 K. On higher resolution (<400 ps), two different types of motions can be separated: (i) localized motions with the same amplitude for CPC and hydration water and two transitions at ~170 and ~240 K for both; (ii) large scale fluctuations exhibiting for both water molecules and CPC protein a single transition at ~240 K, with a significantly higher amplitude for the interfacial water than for CPC. Moreover, by comparing these motions with bulk water MSD measured under the same conditions, we show no coupling between bulk water dynamics and protein dynamics all along the temperature range. These results show that interfacial water is the main "driving force" governing both local and large scale motions in proteins.     

Vibrational spectroscopic studies of the interaction of water with serine

The vibrational dynamics of water around serine was investigated by using Raman spectroscopy and inelastic incoherent neutron scattering. Experiments with serine in deuterium oxide were performed to assist the assignment. The study shows that for the serine, the exchange of protons-deuterons on the active -NH3+ and -OH groups were relatively easy, whereas there were hardly any exchanged on the -CH or -CH2- groups. The main features of the spectra for hydrated samples (versus the dry samples) were altered considerably; new sharp peaks in the measured spectra appeared, indicating that the hydrogen bonding between water and serine had disturbed the structure of the serine molecule.     

A polymer surfactant corona dynamically replaces water in solvent-free protein liquids and ensures macromolecular flexibility and activity

The observation of biological activity in solvent-free protein-polymer surfactant hybrids challenges the view of aqueous and nonaqueous solvents being unique promoters of protein dynamics linked to function. Here, we combine elastic incoherent neutron scattering and specific deuterium labeling to separately study protein and polymer motions in solvent-free hybrids. Myoglobin motions within the hybrid are found to closely resemble those of a hydrated protein, and motions of the polymer surfactant coating are similar to those of the hydration water, leading to the conclusion that the polymer surfactant coating plasticizes protein structures in a way similar to hydration water.     

Vibrational density of states of hydration water at biomolecular sites: hydrophobicity promotes low density amorphous ice behavior

Inelastic neutron scattering experiments and molecular dynamics simulations have been used to investigate the low frequency modes, in the region between 0 and 100 meV, of hydration water in selected hydrophilic and hydrophobic biomolecules. The results show changes in the plasticity of the hydrogen-bond network of hydration water molecules depending on the biomolecular site. At 200 K, the measured low frequency density of states of hydration water molecules of hydrophilic peptides is remarkably similar to that of high density amorphous ice, whereas, for hydrophobic biomolecules, it is comparable to that of low density amorphous ice behavior. In both hydrophilic and hydrophobic biomolecules, the high frequency modes show a blue shift of the libration mode as compared to the room temperature data. These results can be related to the density of water molecules around the biological interface, suggesting that the apparent local density of water is larger in a hydrophilic environment.     

Neutron scattering study of the vibrations in vitreous silica and germania

The incoherent approximation for the determination of the vibrational density of states of glasses from inelastic neutron or x-ray scattering data is extended to treat the coherent scattering. The method is applied to new room temperature measurements of vitreous silica and germania on the thermal time-of-flight spectrometer IN4 at the High Flux Reactor in Grenoble. The inelastic dynamic structure factor at the boson peak turns out to agree reasonably well with simulation results, but the long-wavelength fraction exceeds the expectation of the Debye model, in particular, in germania.     

Inelastic neutron scattering studies of the interaction between water and some amino acids

The interaction between water and some of amino acids (glycine, L-glutamine, L-threonine, L-cysteine and L-serine) was studied by inelastic incoherent neutron scattering (IINS). The vibrational spectra of dry amino acids and amino acids with a water content (e.g., 1 mol water/1 mol amino acid) were recorded. Comparing the difference spectra obtained by subtracting the spectrum of dry sample from those of wet sample with the spectra of ice Ih, we obtained that the difference spectrum for serine changed greatly from normal ice spectrum; but on the other hand, the difference spectra for the other amino acids such as glycine, glutamine, threonine, and cysteine changed slightly. The results demonstrate that serine has stronger hydrophilic character than glycine, glutamine, threonine, and cysteine. This is the first time the hydrophilic or hydrophobic character of amino acids was studied by using inelastic neutron scattering techniques, which provides important information for theoretical modeling and force field refinement for the interaction between water and the amino acids studied here.     

Time and depth dependent fluxes due to 14 MeV neutrons impinging soil

A spectroscopy system measuring inelastic neutron scattering and thermal neutron capture induced gamma-rays is being developed for in-situ soil analysis. Because a pulsed fast D-T neutron source is utilized, fast neutron induced inelastic neutron scattering reactions are separated in time from thermal neutron capture events. Models utilizing the MCNPX code have been developed to study the time and energy variations of the neutrons in the soil matrix.     

Ultrafast hydration dynamics in the lipidic cubic phase: Discrete water structures in nanochannels

We report here our studies of hydration dynamics of confined water in aqueous nanochannels (approximately 50 A) of the lipidic cubic phase. By systematically anchoring the hydrocarbon tails of a series of tryptophan-alkyl ester probes into the lipid bilayer, we mapped out with femtosecond resolution the profile of water motions across the nanochannel. Three distinct time scales were observed, revealing discrete channel water structures. The interfacial water at the lipid surface is well-ordered, and the relaxation dynamics occurs in approximately 100-150 ps. These dynamically rigid water molecules are crucial for global structural stability of lipid bilayers and for stabilization of anchored biomolecules in membranes. The adjacent water layers near the lipid interface are hydrogen-bonded networks and the dynamical relaxation takes 10-15 ps. This quasi-bound water motion, similar to the typical protein surface hydration relaxation, facilitates conformation flexibility for biological recognition and function. The water near the channel center is bulklike, and the dynamics is ultrafast in less than 1 ps. These water molecules freely transport biomolecules near the channel center. The corresponding orientational relaxation at these three typical locations is well correlated with the hydration dynamics and local dynamic rigidity. These results reveal unique water structures and dynamical motions in nanoconfinements, which is critical to the understanding of nanoscopic biological activities and nanomaterial properties.     

Water and polymer dynamics in chemically cross-linked hydrogels of poly(vinyl alcohol): a molecular dynamics simulation study

A topologically extended model of a chemically cross-linked hydrogel of poly(vinyl alcohol) (PVA) at high hydration degree has been developed for a molecular dynamics simulation with atomic detail at 323 K. The analysis of the 5 ns trajectory discloses structural and dynamic aspects of polymer solvation and elucidates the water hydrogen bonding and diffusion in the network. The features of local polymer dynamics indicate that PVA mobility is not affected by structural constraints of chemical junctions at the investigated cross-linking density, with a prevailing dumping effect due to water interaction. Simulation results are validated by a favorable comparison with findings of an incoherent quasi-elastic neutron scattering study of the same hydrogel system.     

Temperature-dependent dynamics of water confined in nafion membranes

We performed a neutron scattering study to investigate the dynamical behavior of water absorbed in Nafion at low hydration level as a function of temperature in the range 200-300 K. To single out the spectral contribution of the confined water, the measurements were done on samples hydrated with both H(2)O and D(2)O. Due to the strong incoherent scattering cross section of hydrogen atoms with respect to deuterium, in the difference spectra, the contribution from the Nafion membrane is subtracted out and the signal originates essentially from protons in the liquid phase. The main quantities we extracted as a function of the momentum transfer are the elastic incoherent structure factor (EISF) and the line width of the quasielastic component. Their trend suggests that the motion of hydrogen atoms can be schematized as a random jumping inside a confining region, which can be related to the boundaries of the space where water molecules move in the cluster they form around the sulfonic acid site. Through the calculated EISF, we obtained information on the size of such a region, which increases up to 260 K and then attains a constant value. Above this temperature, the number of water protons that are dynamically activated in the accessible time window increases with a faster rate. The jump diffusion dynamics is characterized by a typical jumping time which is stable at 5.3 ps up to approximately 260 K and then gradually decreases. The ensemble of the findings indicates that, within the limits of the energy resolution of the present experiment, water absorbed in the Nafion membrane undergoes a dynamical transition at around 260 K. We discuss the possible relationship of this dynamical onset with the behavior of the electrical conductivity of the membrane as a function of the temperature.     

Neutron scattering study of dynamically disordered hydrogen bonds: Terephthalic acid

Incoherent neutron scattering experiments have been performed on the disordered hydrogen-bonded dimers of terephthalic acid. An abnormally high Debye-Waller factor is found in contradiction to a simple two-site jump model. The inelastic incoherent neutron spectrum is analyzed by using different isotopically substituted molecules. The results are compared with the Arrhenius parameters of the exchange process obtained by solid-state NMR experiments.     

Molecular view of water dynamics near model peptides

Incoherent quasi-elastic neutron scattering (QENS) has been used to measure the dynamics of water molecules in solutions of a model protein backbone, N-acetyl-glycine-methylamide (NAGMA), as a function of concentration, for comparison with results for water dynamics in aqueous solutions of the N-acetyl-leucine-methylamide (NALMA) hydrophobic peptide at comparable concentrations. From the analysis of the elastic incoherent structure factor, we find significant fractions of elastic intensity at high and low concentrations for both solutes, which corresponds to a greater population of protons with rotational time scales outside the experimental resolution (>13 ps). The higher-concentration solutions show a component of the elastic fraction that we propose is due to water motions that are strongly coupled to the solute motions, while for low-concentration solutions an additional component is activated due to dynamic coupling between inner and outer hydration layers. An important difference between the solute types at the highest concentration studied is found from stretched exponential fits to their experimental intermediate scattering functions, showing more pronounced anomalous diffusion signatures for NALMA, including a smaller stretched exponent beta and a longer structural relaxation time tau than those found for NAGMA. The more normal water diffusion exhibited near the hydrophilic NAGMA provides experimental support for an explanation of the origin of the anomalous diffusion behavior of NALMA as arising from frustrated interactions between water molecules when a chemical interface is formed upon addition of a hydrophobic side chain, inducing spatial heterogeneity in the hydration dynamics in the two types of regions of the NALMA peptide. We place our QENS measurements on model biological solutes in the context of other spectroscopic techniques and provide both confirming as well as complementary dynamic information that attempts to give a unifying molecular view of hydration dynamics signatures near peptides and proteins.     

Dynamic behavior of water within a polymer electrolyte fuel cell membrane at low hydration levels

Protonic conduction across the membrane of a polymer electrolyte fuel cell is intimately related to the dynamic behavior of water present within the membrane. To further the understanding of water dynamics in these materials, quasielastic neutron scattering (QENS) has been used to investigate the picosecond dynamic behavior of water within a perfluorosulfonated ionomer (PFSI) membrane under increasing hydration levels from dry to saturation. Evaluation of the elastic incoherent structure factor (EISF) reveals an increase in the characteristic length-scale of confinement as the number of water molecules in the membrane increases, tending to an asymptotic value at saturation. The fraction of elastic incoherent scattering observed at high Q over all hydration levels is well fit by a simple model that assumes a single, nondiffusing hydronium ion per membrane sulfonic acid site. The quasielastic component of the fitted data indicates confined dynamic behavior for scattering vectors less than 0.7 A(-1). As such, the dynamic behavior was interpreted using continuous diffusion confined within a sphere at Q < 0.7 A(-1) and random unconstrained jump diffusion at Q > 0.7 A(-1). As the number of water molecules in the membrane increases, the characteristic residence times obtained from both models is reduced. The increased dynamical frequency is further reflected in the diffusion coefficients predicted by both models. Between low hydration (2 H2O/SO3H) and saturation (16 H2O/SO3H), the continuous spherical diffusion coefficient changes from 0.46 +/- 0.12 to 1.04 +/- 0.12 (10(-5) cm2/s) and jump diffusion indicates an increase from 1.21 +/- 0.03 to 2.14 +/- 0.08 (10(-5) cm2/s). Overall, the dynamic behavior of water has been quantified over different length scale regimes, the results of which may be rationalized on the basis of the formation of water clusters in the hydrophilic domain that expand toward an asymptotic upper limit with increased hydration.     

nMoldyn: a program package for a neutron scattering oriented analysis of molecular dynamics simulations

We present a new implementation of the program nMoldyn, which has been developed for the computation and decomposition of neutron scattering intensities from Molecular Dynamics trajectories (Comp. Phys. Commun 1995, 91, 191-214). The new implementation extends the functionality of the original version, provides a much more convenient user interface (both graphical/interactive and batch), and can be used as a tool set for implementing new analysis modules. This was made possible by the use of a high-level language, Python, and of modern object-oriented programming techniques. The quantities that can be calculated by nMoldyn are the mean-square displacement, the velocity autocorrelation function as well as its Fourier transform (the density of states) and its memory function, the angular velocity autocorrelation function and its Fourier transform, the reorientational correlation function, and several functions specific to neutron scattering: the coherent and incoherent intermediate scattering functions with their Fourier transforms, the memory function of the coherent scattering function, and the elastic incoherent structure factor. The possibility to compute memory function is a new and powerful feature that allows to relate simulation results to theoretical studies.