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We present the discovery of an unusually large isotope effect in the structural relaxation and the glass transition temperature Tg of water. Dielectric relaxation spectroscopy of low-density as well as of vapor-deposited amorphous water reveal Tg differences of 10 ± 2 K between H2O and D2O, sharply contrasting with other hydrogen-bonded liquids for which H/D exchange increases Tg by typically less than 1 K. We show that the large isotope effect and the unusual variation of relaxation times in water at low temperatures can be explained in terms of quantum effects. Thus, our findings shed new light on water's peculiar low-temperature dynamics and the possible role of quantum effects in its structural relaxation, and possibly in dynamics of other low-molecular-weight liquids.

The emergence of intrinsically disordered proteins (IDPs) as a recognized structural class has forced the community to confront a new paradigm of structure, dynamics, and mechanical properties for proteins. We present novel data on the similarities and differences in the dynamics and nanomechanical properties of IDPs and other biomacromolecules on the picosecond time scale. An IDP, β-casein (CAS), has been studied in a calcium bound and unbound state using neutron and light scattering techniques. We show that CAS partially folds and stiffens upon calcium binding, but in the unfolded state, it is softer than folded proteins such as green fluorescence protein (GFP). We also see that some localized diffusive motions in CAS have a larger amplitude than in GFP at this time scale but are still smaller than those observed in tRNA. In spite of these differences, CAS dynamics are consistent with the classes of motions seen in folded protein on this time scale.

Complementary neutron- and light-scattering results on nine proteins and amino acids reveal the role of rigidity and secondary structure in determining the time- and lengthscales of low-frequency collective vibrational dynamics in proteins. These dynamics manifest in a spectral feature, known as the boson peak (BP), which is common to all disordered materials. We demonstrate that BP position scales systematically with structural motifs, reflecting local rigidity: disordered proteins appear softer than α-helical proteins; which are softer than β-sheet proteins. Our analysis also reveals a universal spectral shape of the BP in proteins and amino acid mixtures; superimposable on the shape observed in typical glasses. Uniformity in the underlying physical mechanism, independent of the specific chemical composition, connects the BP vibrations to nanometer-scale heterogeneities, providing an experimental benchmark for coarse-grained simulations, structure/rigidity relationships, and engineering of proteins for novel applications., (Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

Ionic liquids (ILs) are key materials for the development of a wide range of emerging technologies. Protic ionic liquids, an important class of ILs, have long been envisioned as promising anhydrous electrolytes for fuel cells. It is well known that in comparison to all other cations, protons exhibit abnormally high conductivity in water. Such superprotonic dynamics was expected in protic ionic conductors as well. However, many years of extensive studies led to the disappointing conclusion that this is not the case and most protic ionic liquids display subionic behavior. Therefore, the relatively low conductivity seems to be the main obstacle for the application of protic ionic liquids in fuel cells. Using dielectric spectroscopy, herein we report the observation of highly decoupled conductivity in a newly synthesized protic ionic conductor. We show that its proton transport is strongly decoupled from the structural relaxation, in terms of both temperature dependence and characteristic rates. This finding offers a fresh look on the charge transport mechanism in PILs and also provides new ideas for design of anhydrous materials with exceptionally high proton conductivity.

The slow, Debye-like relaxation in hydrogen-bonded liquids has largely remained a dielectric phenomenon and has thus far eluded observation by other experimental techniques. Here we report the first observation of a slow, Debye-like relaxation by both depolarized dynamic light scattering (DLS) and dielectric spectroscopy in a model hydrogen-bonded liquid, 2-ethyl-4-methylimidazole (2E4MIm). The relaxation times obtained by these two techniques are in good agreement and can be well explained by the Debye model of rotational diffusion. On the one hand, 2E4MIm is analogous to the widely studied monohydroxy alcohols in which transient chain-like supramolecular structure can be formed by hydrogen bonding. On the other hand, the hydrogen-bonded backbone of 2E4MIm is much more optically polarizable, making it possible to apply light scattering to study the dynamics of the supramolecular structure. These findings provide the missing evidence of the slow, Debye-like relaxation in DLS and open the venue for the application of dynamic light scattering to the study of supramolecular structures in hydrogen-bonded liquids.

In order to understand the nature of the exceedingly low ionic conductivity of aprotic ammonium ionic liquids (ILs), we have measured the charge transport and structural dynamics of methyltrioctylammonium bis(trifluoromethylsulfonyl)imide [m3oa][ntf2] over a broad temperature range using broadband dielectric spectroscopy, depolarized dynamic light scattering (DDLS), rheology, and pulsed field gradient nuclear magnetic resonance. We demonstrate that the low level of ionic conductivity in this material is due to the combined effects of reduced ion mobility as well as reduced free ion concentration relative to other types of ILs. Furthermore, detailed analysis of the DDLS spectra reveals a slow process in addition to the structural α relaxation that we attribute to reorientational motion of alkyl aggregates. These findings indicate that hydrophobic aggregation strongly influences the charge transport mechanism of aprotic ammonium ionic liquids with long aliphatic side chains.

The aminoglycoside N3 acetyltransferase-IIIb (AAC) is responsible for conferring bacterial resistance to a variety of aminoglycoside antibiotics. Nuclear magnetic resonance spectroscopy and dynamic light scattering analyses revealed a surprising result; the dynamics of the ternary complex between AAC and its two ligands, an antibiotic and coenzyme A, are dependent upon the order in which the ligands are bound. Additionally, two structurally similar aminoglycosides, neomycin and paromomycin, induce strikingly different dynamic properties when they are in their ternary complexes. To the best of our knowledge, this is the first example of a system in which two identically productive pathways of forming a simple ternary complex yield significant differences in dynamic properties. These observations emphasize the importance of the sequence of events in achieving optimal protein-ligand interactions and demonstrate that even a minor difference in molecular structure can have a profound effect on biochemical processes.

Collective dynamics are considered to be one of the major properties of soft materials, including biological macromolecules. We present coherent neutron scattering studies of the low-frequency vibrations, the so-called boson peak, in fully deuterated green fluorescent protein (GFP). Our analysis revealed unexpectedly low coherence of the atomic motions in GFP. This result implies a low amount of in-phase collective motion of the secondary structural units contributing to the boson peak vibrations and fast conformational fluctuations on the picosecond timescale. These observations are in contrast to earlier studies of polymers and glass-forming systems, and suggest that random or out-of-phase motions of the β-strands contribute greater than two-thirds of the intensity to the low-frequency vibrational spectra of GFP., (Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

There is tremendous interest in understanding the role that secondary structure plays in the rigidity and dynamics of proteins. In this work we analyze nanomechanical properties of proteins chosen to represent different secondary structures: α-helices (myoglobin and bovine serum albumin), β-barrels (green fluorescent protein), and α + β + loop structures (lysozyme). Our experimental results show that in these model proteins, the β motif is a stiffer structural unit than the α-helix in both dry and hydrated states. This difference appears not only in the rigidity of the protein, but also in the amplitude of fast picosecond fluctuations. Moreover, we show that for these examples the secondary structure correlates with the temperature- and hydration-induced changes in the protein dynamics and rigidity. Analysis also suggests a connection between the length of the secondary structure (α-helices) and the low-frequency vibrational mode, the so-called boson peak. The presented results suggest an intimate connection of dynamics and rigidity with the protein secondary structure.

We present analysis of nanosecond-picosecond dynamics of Green Fluorescence Protein (GFP) using neutron scattering data obtained on three spectrometers. GFP has a β-barrel structure that differs significantly from the structure of other globular proteins and is thought to result in a more rigid local environment. Despite this difference, our analysis reveals that the dynamics of GFP are similar to dynamics of other globular proteins such as lysozyme and myoglobin. We suggest that the same general concept of protein dynamics may be applicable to all these proteins. The dynamics of dry protein are dominated by methyl group rotations, while hydration facilitates localized diffusion-like motions in the protein. The latter has an extremely broad relaxation spectrum. The nanosecond-picosecond dynamics of both dry and hydrated GFP are localized to distances of ∼1-3.5 Å, in contrast to the longer range diffusion of hydration water.

Here we report the low-temperature dielectric and viscoelastic properties of phosphoric acids in the range of H2O:P2O5 1.5-5. Both dielectric and viscosity measurements allow us to determine the glass-transition temperatures of phosphoric acids. The obtained glass-transition temperatures are in good agreement with previous differential scanning calorimetric measurements. Moreover, our analysis reveals moderate decoupling of ionic conductivity from structural relaxation in the vicinity of the glass transition.

We analyzed solute and solvent dynamics of sugars and peptides aqueous solutions using extended depolarized light scattering (EDLS) and broadband dielectric spectroscopies (BDS). Spectra measured with both techniques reveal the same mechanism of rotational diffusion of peptides molecules. In the case of sugars, this solute reorientational relaxation can be isolated by EDLS measurements, whereas its contribution to the dielectric spectra is almost negligible. In the presented analysis, we characterize the hydration water in terms of hydration number and retardation ratio ξ between relaxation times of hydration and bulk water. Both techniques provide similar estimates of ξ. The retardation imposed on the hydration water by sugars is ~3.3 ± 1.3 and involves only water molecules hydrogen-bonded (HB) to solutes (~3 water molecules per sugar OH-group). In contrast, polar peptides cause longer range perturbations beyond the first hydration shell, and ξ between 2.8 and 8, increasing with the number of chemical groups engaged in HB formation. We demonstrate that chemical heterogeneity and specific HB interactions play a crucial role in hydration dynamics around polar solutes. The obtained results help to disentangle the role of excluded volume and enthalpic contributions in dynamics of hydration water at the interface with biological molecules.

Using quasielastic neutron scattering spectroscopy, we measured the averaged translational diffusion of water in solutions of biologically relevant salts, NaCl, a kosmotrope, and KCl, a chaotrope. The analysis revealed the striking difference in the influence of these ions on water dynamics. While the averaged water diffusion slows down in the presence of the structure making (kosmotrope) Na(+) ion, the diffusion becomes faster in the presence of the structure breaking (chaotrope) K(+) ion. The latter means that, despite strong Coulombic interactions introduced by the K(+) ions, their disruption of the hydrogen-bonding network is so significant that it leads to faster diffusion of the water molecules.

Frustration in chain packing has been proposed to play an important role in thermodynamic and dynamic properties of polymeric melts and glasses. Based on a quantitative analysis using Voronoi tessellations and large scale molecular dynamics simulations of flexible and semi-flexible polymers, we demonstrate that the rigid polymer chains have higher averaged Voronoi polyhedral volumes and significantly wider distribution of the volume due to frustration in the chain packing. Using these results, we discuss the advantage of the rigid polymers for possible enhancement of transport properties, e.g. for enhancing ionic conductivity in solid polymer electrolytes.

Electrode polarization analysis is frequently used to determine free-ion diffusivity and number density in ionic conductors. In the present study, this approach is critically examined in a wide variety of electrolytes, including aqueous and nonaqueous solutions, polymer electrolytes, and ionic liquids. It is shown that the electrode polarization analysis based on the Macdonald-Trukhan model [J. Chem. Phys. 124, 144903 (2006); J. Non-Cryst. Solids 357, 3064 (2011)] progressively fails to give reasonable values of free-ion diffusivity and number density with increasing salt concentration. This should be expected because the original model of electrode polarization is designed for dilute electrolytes. An empirical correction method which yields ion diffusivities in reasonable agreement with pulsed-field gradient nuclear magnetic resonance measurements is proposed. However, the analysis of free-ion diffusivity and number density from electrode polarization should still be exercised with great caution because there is no solid theoretical justification for the proposed corrections.

Rheological measurement was employed to study the mutarotation of D-fructose in anhydrous state. By monitoring the evolution of shear viscosity with time, rate constants for mutarotation were estimated, and two different stages of this reaction were identified. One of the mutarotation stages is rapid and has a low activation energy, whereas the other is much slower and has a much higher activation energy. Possible conversions corresponding to these two phases are discussed. This work demonstrates that, in addition to the routine techniques such polarimetry and gas-liquid chromatography, rheological measurement can be used as an alternative method to continuously monitor the mutarotation of sugars.

Flexibility, or softness, is crucial for protein function and consists of a conformational component, involving jumps between potential wells, and an elastic component, involving fluctuations within the wells. Combining molecular dynamics simulation with incoherent neutron scattering and light scattering measurements on green fluorescent protein, we reveal a relationship between the intrawell fluctuations and elastic moduli of the protein. This finding leads to a simple means of experimentally separating the conformational from the elastic atomic displacements.

We present a detailed analysis of the picosecond-to-nanosecond motions of green fluorescent protein (GFP) and its hydration water using neutron scattering spectroscopy and hydrogen/deuterium contrast. The analysis reveals that hydration water suppresses protein motions at lower temperatures (<~ 200 K), and facilitates protein dynamics at high temperatures. Experimental data demonstrate that the hydration water is harmonic at temperatures <~ 180-190 K and is not affected by the proteins' methyl group rotations. The dynamics of the hydration water exhibits changes at ~ 180-190 K that we ascribe to the glass transition in the hydrated protein. Our results confirm significant differences in the dynamics of protein and its hydration water at high temperatures: on the picosecond-to-nanosecond timescale, the hydration water exhibits diffusive dynamics, while the protein motions are localized to <~3 Å. The diffusion of the GFP hydration water is similar to the behavior of hydration water previously observed for other proteins. Comparison with other globular proteins (e.g., lysozyme) reveals that on the timescale of 1 ns and at equivalent hydration level, GFP dynamics (mean-square displacements and quasielastic intensity) are of much smaller amplitude. Moreover, the suppression of the protein dynamics by the hydration water at low temperatures appears to be stronger in GFP than in other globular proteins. We ascribe this observation to the barrellike structure of GFP., (Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

Using a combination of light scattering techniques and broadband dielectric spectroscopy, we have measured the temperature dependence of structural relaxation time and self diffusion in three imidazolium-based room temperature ionic liquids: [bmim][NTf(2)], [bmim][PF(6)], and [bmim][TFA]. A detailed analysis of the results demonstrates that self diffusion decouples from structural relaxation in these systems as the temperature is decreased toward T(g). The degree to which the dynamics are decoupled, however, is shown to be surprisingly weak when compared to other supercooled liquids of similar fragility. In addition to the weak decoupling, we demonstrate that the temperature dependence of the structural relaxation time in all three liquids can be well described by a single Vogel-Fulcher-Tamann function over 13 decades in time from 10(-11) s up to 10(2) s. Furthermore, the stretching of the structural relaxation is shown to be temperature independent over the same range of time scales, i.e., time temperature superposition is valid for these ionic liquids from far above the melting point down to the glass transition temperature. We suggest that these phenomena are interconnected and all result from the same underlying mechanism--strong and directional intermolecular interactions.

A water-soluble poly[( m -phenylenevinylene)- alt -( p -phenylenevinylene)] (PmPV) 2 has been synthesized, which exhibits an unsymmetrical substitution pattern on the para -phenylene unit. With one substituent being hydrophilic while the other being hydrophobic, the polymer chain has a higher tendency to fold in aqueous solution, thereby promoting helical conformation. The polymer is found to selectively disperse the single-walled nanotubes (SWNTs) of small diameters ( d = 0.75-0.84 nm), in sharp contrast to PmPV 1 with a symmetrical substitution pattern. The intriguing diameter-based selectivity is believed to be associated with the confined helical conformation, which provides a suitable cavity to host the SWNT of proper sizes. The study thus provides a useful demonstration that the polymer conformation can have a profound impact on the SWNT sorting.

Recent studies have discovered strong differences between the dynamics of nucleic acids (RNA and DNA) and proteins, especially at low hydration and low temperatures. This difference is caused primarily by dynamics of methyl groups that are abundant in proteins, but are absent or very rare in RNA and DNA. In this paper, we present a hypothesis regarding the role of methyl groups as intrinsic plasticizers in proteins and their evolutionary selection to facilitate protein dynamics and activity. We demonstrate the profound effect methyl groups have on protein dynamics relative to nucleic acid dynamics, and note the apparent correlation of methyl group content in protein classes and their need for molecular flexibility. Moreover, we note the fastest methyl groups of some enzymes appear around dynamical centers such as hinges or active sites. Methyl groups are also of tremendous importance from a hydrophobicity/folding/entropy perspective. These significant roles, however, complement our hypothesis rather than preclude the recognition of methyl groups in the dynamics and evolution of biomolecules.Electronic supplementary material The online version of this article (doi:10.1007/s10867-012-9268-6) contains supplementary material, which is available to authorized users.

Dynamics of water, especially in the temperature range of the "no man's land", remain a mystery. We present detailed study of dynamics in aqueous LiCl solution that is often considered as a model for bulk water. We employ broadband dielectric and light scattering spectroscopy in a broad frequency and temperature range. Our analysis reveals no sign of the fragile-to-strong crossover (FSC) neither in structural relaxation nor in translational motions. Our experimental results combined with a large selection of literature data lead to the clear conclusion-there is no FSC in dynamics of aqueous solutions at T ∼ 200-230 K. Instead, our analysis reveals appearance of the so-called excess wing at the high frequency tail of the structural relaxation peak. We discuss the localized nature of the relaxation process that contributes to the excess wing.

We present detailed studies of the relationship between ionic conductivity and segmental relaxation in polymer electrolytes. The analysis shows that the ionic conductivity can be decoupled from segmental dynamics and the strength of the decoupling correlates with the fragility but not with the glass transition temperature. These results call for a revision of the current picture of ionic transport in polymer electrolytes. We relate the observed decoupling phenomenon to frustration in packing of rigid polymers, where the loose local structure is also responsible for the increase in their fragility.

Electronic and mechanic properties of single-walled carbon nanotubes (SWNTs) are uniquely dependent on the tube's chiralities and diameters. Isolation of different type SWNTs remains one of the fundamental and challenging issues in nanotube science. Herein, we demonstrate that SWNTs can be effectively enriched to a narrow diameter range by sequential treatment of the HiPco sample with nitric acid and a π-conjugated copolymer poly(phenyleneethynylene) (PPE)- co -poly(phenylenevinylene) (PPV). On the basis of Raman, fluorescence, and microscopic evidence, the nitric acid is found to selectively remove the SWNTs of small diameter. The polymer not only effectively dispersed carbon nanotubes but also exhibited a good selectivity toward a few SWNTs. The reported approach thus offers a new methodology to isolate SWNTs, which has the potential to operate in a relatively large scale.

The dynamics of RNA contributes to its biological functions such as ligand recognition and catalysis. Using quasielastic neutron scattering spectroscopy, we show that Mg(2+) greatly increases the picosecond to nanosecond dynamics of hydrated tRNA while stabilizing its folded structure. Analyses of the atomic mean-squared displacement, relaxation time, persistence length, and fraction of mobile atoms showed that unfolded tRNA is more rigid than folded tRNA. This same result was found for a sulfonated polystyrene, indicating that the increased dynamics in Mg(2+) arises from improved charge screening of the polyelectrolyte rather than specific interactions with the folded tRNA. These results are opposite to the relationship between structural compactness and internal dynamics for proteins in which the folded state is more rigid than the denatured state. We conclude that RNA dynamics are strongly influenced by the electrostatic environment, in addition to the motions of local waters.

A simplified description of the 295 K dynamics of a globular protein over a wide frequency range (1-1000 GHz) is obtained by combining neutron scattering of lysozyme with molecular dynamics simulation. The molecular dynamics simulation agrees quantitatively with experiment for both the protein and the hydration water and shows that, whereas the hydration water molecules subdiffuse, the protein atoms undergo confined motion decomposable into three distinct classes: localized diffusion, methyl group rotations, and jumps. Each of the three classes gives rise to a characteristic neutron susceptibility signal.

Light scattering and dielectric spectroscopy measurements were performed on the room temperature ionic liquid (RTIL) [C4mim][NTf2] in a broad temperature and frequency range. Ionic conductivity was used to estimate self-diffusion of ions, while light scattering was used to study structural relaxation. We demonstrate that the ionic diffusion decouples from the structural relaxation process as the temperature of the sample decreases toward T(g). The strength of the decoupling appears to be significantly lower than that expected for a supercooled liquid of similar fragility. The structural relaxation process in the RTIL follows well the high-temperature mode coupling theory (MCT) scenario. Using the MCT analysis we estimated the dynamic crossover temperature in [C4mim][NTf2] to be T(c) ~ 225 ± 5 K. However, our analysis reveals no sign of the dynamic crossover in the ionic diffusion process.

The existence of a Debye-type ultraslow process in dielectric spectra of bulk polyalcohols and similar materials has been reported repeatedly in the recent literature. Its loss peak is observed at frequencies that are decades below those of the primary structural relaxation, in a range where the loss signal is usually dominated by dc-conductivity or even electrode polarization. We show that this peak originates from an incomplete filling of the capacitor volume, e.g., as a result of gas bubbles, a situation that gives rise to a Debye process at the conductivity relaxation frequency of the material, where the values of storage and loss components of permittivity are identical. The result implies that these peaks are not endemic to the liquid and can lead to various misinterpretations of the dielectric relaxation spectra. Techniques avoiding the occurrence of such artifacts are discussed.

We propose an explanation for the long-standing puzzles of the microscopic mechanism of chain friction and the failure of time-temperature superposition in polymer melts based on decoupling of macromolecular scale diffusion from local structural relaxation due to spatially heterogeneous dynamics. The proposed physical picture is also relevant for understanding some aspects of dynamic fluctuation and decoupling phenomena in nonpolymeric glass-forming liquids, crystal growth rates, and protein activity in viscous solvents.

Wrapping of a single-walled carbon nanotube (SWNT) was examined by using a poly[( m-phenylenevinylene)- alt-( p-phenylenevinylene)] (PmPV) derivative. The polymer's intrinsic ability in forming a helical conformation was found to play an essential role in the separation of nanotubes. Among about 15 tubes present in the pure SWNT (HiPcoTM) sample, the polymer was found to selectively pick up the tubes (11,6), (11,7) and (12,6), which correspond to tube diameters of 1.19, 1.25 and 1.24 nm, respectively. The SWNTs of smaller diameters were held loosely by the PmPV, and were gradually dropped out under centrifugation. The suspension solution prepared from the SWNT and PmPV was not permanently stable, with precipitation occurring after a few weeks. Irradiation in the UV-vis region exhibited a catalytic effect to shorten the precipitation time to hours. Those tubes, which were held loosely by PmPV, were quickly separated from the suspension during the irradiation process.

We have carried out molecular-dynamics simulations on fully flexible all-atom models of the protein lysozyme immersed in trehalose, an effective biopreservative, with the purpose of exploring the nature and extent of the dynamical coupling between them. Our study shows a strong coupling over a wide range of temperatures. We found that the onset of anharmonic behavior was dictated by changes in the dynamics and relaxation processes in the trehalose glass. The physical origin of protein-trehalose coupling was traced to the hydrogen bonds formed at the interface between the protein and the solvent. Moreover, protein-solvent hydrogen bonding was found to control the structural relaxation of the protein. The dynamics of the protein was found to be heterogeneous; the motions of surface and core atoms had different dependencies on temperature and, in addition, the surface atoms were more sensitive to the dynamics of the solvent than the core atoms. From the solvent perspective we found that the dynamics near the protein surface showed an unexpected enhanced mobility compared to the bulk. These results shed some light on the microscopic origins of the dynamical coupling in protein-solvent systems.

Dynamics of tRNA was studied using neutron scattering spectroscopy. Despite vast differences in the architecture and backbone structure of proteins and RNA, hydrated tRNA undergoes the dynamic transition at the same temperature as hydrated lysozyme. The similarity of the dynamic transition in RNA and proteins supports the idea that it is solvent induced. Because tRNA essentially has no methyl groups, the results also suggest that methyl groups are not the main contributor of the dynamic transition in biological macromolecules. However, they may explain strong differences in the dynamics of tRNA and lysozyme observed at low temperatures.

We explore possible molecular mechanisms behind the coupling of protein and solvent dynamics using atomistic molecular-dynamics simulations. For this purpose, we analyze the model protein lysozyme in glycerol, a well-known protein-preserving agent. We find that the dynamics of the hydrogen bond network between the solvent molecules in the first shell and the surface residues of the protein controls the structural relaxation (dynamics) of the whole protein. Specifically, we find a power-law relationship between the relaxation time of the aforementioned hydrogen bond network and the structural relaxation time of the protein obtained from the incoherent intermediate scattering function. We demonstrate that the relationship between the dynamics of the hydrogen bonds and the dynamics of the protein appears also in the dynamic transition temperature of the protein. A study of the dynamics of glycerol as a function of the distance from the surface of the protein indicates that the viscosity seen by the protein is not the one of the bulk solvent. The presence of the protein suppresses the dynamics of the surrounding solvent. This implies that the protein sees an effective viscosity higher than the one of the bulk solvent. We also found significant differences in the dynamics of surface and core residues of the protein. The former is found to follow the dynamics of the solvent more closely than the latter. These results allowed us to propose a molecular mechanism for the coupling of the solvent-protein dynamics.

Trehalose-glycerol mixtures are known to be effective in the long time preservation of proteins. However, the microscopic mechanism of their effective preservation abilities remains unclear. In this article we present a molecular dynamics simulation study of the short time, less than 1 ns, dynamics of four trehalose-glycerol mixtures at temperatures below the glass transition temperature. We found that a mixture of 5% glycerol and 95% trehalose has the most suppressed short time dynamics (fast dynamics). This result agrees with the experimental analysis of the mean-square displacement of the hydrogen atoms, as measured via neutron scattering, and correlates with the experimentally observed enhancement of the stability of some enzymes at this particular concentration. Our microscopic analysis suggests that the formation of a robust intermolecular hydrogen bonding network is most effective at this concentration and is the main mechanism for the suppression of the fast dynamics.