Molecular dynamics simulation study of glycerol-water liquid mixtures

Micro-Solvation of Propofol in Propylene Glycol-Water Binary Mixtures: Molecular Dynamics Simulation Studies

The water microstructure around propofol plays a crucial role in controlling their solubility in the binary mixture. The unusual nature of such a water microstructure can influence both translational and reorientational dynamics, as well as the water hydrogen bond network near propofol. We have carried out all-atom molecular dynamics simulations of five different compositions of the propylene glycol (PG)/water binary mixture containing propofol (PFL) molecules to investigate the differential behavior of water microsolvation shells around propofol, which is likely to control the propofol solubility. It is evident from the simulation snapshots for various compositions that the PG at high molecular ratio favors the water cluster and extended chainlike network that percolates within the PG matrix, where the propofol is in the dispersed state. We estimated that the radial distribution function indicates higher ordered water microstructure around propofol for high PG content, as compared to the lower PG content in the PG/water mixture. So, the hydrophilic PG regulates the stability of the water micronetwork around propofol and its solubility in the binary mixture. We observed that the translational and rotational mobility of water belonging to the propofol microsolvation shell is hindered for high PG content and relaxed toward the low PG molecular ratio in the PG/water mixture. It has been noticed that the structural relaxation of the hydrogen bond formed between the propofol and the water molecules present in the propofol microsolvation shell for all five compositions is found to be slower for high PG content and becomes faster on the way to low PG content in the mixture. Simultaneously, we calculated the intermittent residence time correlation function of the water molecules belonging to the microsolvation shell around the propofol for five different compositions and found a faster short time decay followed up with long time components. Again, the origin of such long time decay is primarily from the structural relaxation of the microsolvation shell around the propofol, where the high PG content shows the slower structural relaxation that turns faster as the PG content approaches to the other end of the compositions. So, our studies showed that the slower structural relaxation of the microsolvation shell around propofol for a high PG molecular ratio in the PG/water mixture correlate well with the extensive ordering of the water microstructure and restricted water mobility and facilitates the dissolution process of propofol in the binary mixture.

Orientational dynamics in supercooled glycerol computed from MD simulations: self and cross contributions

The orientational dynamics of supercooled glycerol is probed using molecular dynamics simulations for temperatures ranging from 323 K to 253 K, through correlation functions of first and second ranks of Legendre polynomials, pertaining respectively to dielectric spectroscopy (DS) and depolarized dynamic light scattering (DDLS). The self, cross, and total correlation functions are compared with relevant experimental data. The computations reveal the low sensitivity of DDLS to cross-correlations, in agreement with what is found in experimental work, and strengthen the idea of directly comparing DS and DDLS data to evaluate the effect of cross-correlations in polar liquids. The analysis of the net static cross-correlations and their spatial decomposition shows that, although cross-correlations extend over nanometric distances, their net magnitude originates, in the case of glycerol, from the first shell of neighbouring molecules. Accessing the angular dependence of the static correlation allows us to get a microscopic understanding of why the rank-1 correlation function is more sensitive to cross-correlation than its rank-2 counterpart.

Technologies for Vitrification Based Cryopreservation

Cryopreservation is a unique and practical method to facilitate extended access to biological materials. Because of this, cryopreservation of cells, tissues, and organs is essential to modern medical science, including cancer cell therapy, tissue engineering, transplantation, reproductive technologies, and bio-banking. Among diverse cryopreservation methods, significant focus has been placed on vitrification due to low cost and reduced protocol time. However, several factors, including the intracellular ice formation that is suppressed in the conventional cryopreservation method, restrict the achievement of this method. To enhance the viability and functionality of biological samples after storage, a large number of cryoprotocols and cryodevices have been developed and studied. Recently, new technologies have been investigated by considering the physical and thermodynamic aspects of cryopreservation in heat and mass transfer. In this review, we first present an overview of the physiochemical aspects of freezing in cryopreservation. Secondly, we present and catalog classical and novel approaches that seek to capitalize on these physicochemical effects. We conclude with the perspective that interdisciplinary studies provide pieces of the cryopreservation puzzle to achieve sustainability in the biospecimen supply chain.

1H-NMR Karplus Analysis of Molecular Conformations of Glycerol under Different Solvent Conditions: A Consistent Rotational Isomerism in the Backbone Governed by Glycerol/Water Interactions

Glycerol is a symmetrical, small biomolecule with high flexibility in molecular conformations. Using a ¹H-NMR spectroscopic Karplus analysis in our way, we analyzed a rotational isomerism in the glycero backbone which generates three kinds of staggered conformers, namely gt (gauche-trans), gg (gauche-gauche), and tg (trans-gauche), at each of sn-1,2 and sn-2,3 positions. The Karplus analysis has disclosed that the three rotamers are consistently equilibrated in water keeping the relation of 'gt:gg:tg = 50:30:20 (%)' at a wide range of concentrations (5 mM~540 mM). The observed relation means that glycerol in water favors those symmetric conformers placing 1,2,3-triol groups in a gauche/gauche geometry. We have found also that the rotational isomerism is remarkably changed when the solvent is replaced with DMSO-d₆ or dimethylformamide (DMF-d₇). In these solvents, glycerol gives a relation of 'gt:gg:tg = 40:30:30 (%)', which means that a remarkable shift occurs in the equilibrium between gt and tg conformers. By this shift, glycerol turns to also take non-symmetric conformers orienting one of the two vicinal diols in an antiperiplanar geometry.

Confocal Raman Micro-Spectroscopy for Discrimination of Glycerol Diffusivity in Ex Vivo Porcine Dura Mater

Dura mater (DM) is a connective tissue with dense collagen, which is a protective membrane surrounding the human brain. The optical clearing (OC) method was used to make DM more transparent, thereby allowing to increase in-depth investigation by confocal Raman micro-spectroscopy and estimate the diffusivity of 50% glycerol and water migration. Glycerol concentration was obtained, and the diffusion coefficient was calculated, which ranged from 9.6 × 10^-6 to 3.0 × 10^-5 cm²/s. Collagen-related Raman band intensities were significantly increased for all depths from 50 to 200 µm after treatment. In addition, the changes in water content during OC showed that 50% glycerol induces tissue dehydration. Weakly and strongly bound water types were found to be most concentrated, playing a major role in the glycerol-induced water flux and OC. Results show that OC is an efficient method for controlling the DM optical properties, thereby enhancing the in-depth probing for laser therapy and diagnostics of the brain. DM is a comparable to various collagen-containing tissues and organs, such as sclera of eyes and skin dermis.

A Relation between the Formation of a Hydrogen-Bond Network and a Time-Scale Separation of Translation and Rotation in Molecular Liquids

We study the relation between the translational and rotational motions of liquids, which is anticipated in the framework of the Stokes-Einstein-Debye (SED) treatment. For this purpose, we exploit the fact that ¹H field-cycling nuclear magnetic resonance relaxometry and molecular dynamics simulations provide access to both modes of motion. The experimental and computational findings are fully consistent and show that the time-scale separation between translation and rotation increases from the van der Waals liquid o-terphenyl over ethylene glycol to the hydrogen-bonded liquid glycerol, indicating an increasing degree of breakdown of the SED relation. Furthermore, the simulation results for two ethylene glycol models with different molecular conformations indicate that the translation is more retarded than the rotation when the density of intermolecular hydrogen bonds increases. We conclude that an increasing connectivity of a hydrogen-bond network leads to an increasing time-scale separation and, thus, to a stronger SED violation.

Time-Dependent Hydrogen Bond Network Formation in Glycerol-Based Deep Eutectic Solvents

Over the last few years, Deep Eutectic Solvents have gained popularity as a novel class of green solvents, due to their feasible synthesis and overall low production costs. The properties of glycerol (Gly)-based Deep Eutectic Solvents are frequently associated with the formation of an extended hydrogen bond network. In this study, two-dimensional Nuclear Magnetic Resonance (NMR) spectroscopy is employed to analyse the effect of glycerol oversaturation of the hydrogen bond acceptor, choline chloride (ChCl) on the structural arrangement of glyceline (molar ratio 1 : 2 ChCl:Gly), selected to represent Gly-based Deep Eutectic Solvents. The rearrangement of glycerol molecules, additionally trapping water molecules inside of isolated clusters, is revealed during a time-resolved analysis, performed in the presence of various fractions of water added to solvent. 200 % oversaturated Deep Eutectic Solvent (1 : 4 ChCl:Gly) is found to be a suitable cryoprotectant candidate, based on the revealed glycerol-water interactions.

Understanding the Molecular-Level Interactions of Glucosamine-Glycerol Assemblies: A Model System for Chitosan Plasticization

Glycerol is the most widely used plasticizer for the biopolymer chitosan. However, there remains a lack of understanding of the molecular-level interactions between chitosan and glycerol. Here, we describe an in-depth spectroscopic study of the intermolecular interactions between the monomeric repeating unit of chitosan, glucosamine, and the plasticizer glycerol. Infrared and nuclear magnetic resonance spectroscopy were used to probe glucosamine assembly at high and low concentrations to establish diagnostic signals for intra- and intermolecular glucosamine interactions. Systematic addition of glycerol was found to disrupt intramolecular glucosamine hydrogen bonds and promote glucosamine self-assembly. Furthermore, we observed a significant preference for glycerol binding to the amine functionality of glucosamine. These findings indicate that the plasticization of chitosan with glycerol requires a specific binding motif and likely occurs via the gel theory mechanism.

Co-assembly and Structure of Sodium Dodecylsulfate and other n-Alkyl Sulfates in Glycerol: n-Alkyl Sulfate-Glycerol Crystal Phase

HYPOTHESIS

Following the observation of a microfibrillar phase in sodium dodecylsulfate (SDS)-glycerol mixtures, it is hypothesized that this phase is a crystalline structure containing SDS and glycerol, where the interaction between sulfate and glycerol layers mediates the co-assembly, which also could be universal for similar systems formed by n-alkyl sulfate homologues. Experiment. n-alkyl sulfate glycerol solutions were studied using a combination of optical microscopy, small- and wide-angle X-ray scattering (SAXS/WAXS). Time-resolved SAXS was employed to determine the phase formation in SDS-glycerol-water mixtures.

FINDINGS

The microfibrillar crystalline phase was reproduced in even-chained n-alkyl sulfates with a chain length between 12 and 18 carbon atoms, where the phase lamellar period increased uniformly with the alkyl chain length. Reconstruction of electron density profiles from the diffraction patterns allowed the lamellar structural motif of the phase, the glycerol location and stoichiometry to be determined. When SDS-glycerol-water mixtures with water concentration below 6 wt% are isothermally solidified at 20 °C, SDS-glycerol crystals and/or anhydrous SDS form, where the former is inhibited by the latter at higher water concentrations. The learnings from the SDS-glycerol phase formation allows new gels to be created, utilising the glycerol-sulfate motif generating microfibrils. This expands the knowledge of the applicable formulation space for SDS-water containing mixtures.

Hydrophilic and Hydrophobic Effects on the Structure and Themodynamic Properties of Confined Water: Water in Solutions

NMR spectroscopy is used in the temperature range 180–350 K to study the local order and transport properties of pure liquid water (bulk and confined) and its solutions with glycerol and methanol at different molar fractions. We focused our interest on the hydrophobic effects (HE), i.e., the competition between hydrophilic and hydrophobic interactions. Nowadays, compared to hydrophilicity, little is known about hydrophobicity. Therefore, the main purpose of this study is to gain new information about hydrophobicity. As the liquid water properties are dominated by polymorphism (two coexisting liquid phases of high and low density) due to hydrogen bond interactions (HB), creating (especially in the supercooled regime) the tetrahedral networking, we focused our interest to the HE of these structures. We measured the relaxation times (T1 and T2) and the self-diffusion (DS). From these times, we took advantage of the NMR property to follow the behaviors of each molecular component (the hydrophilic and hydrophobic groups) separately. In contrast, DS is studied in terms of the Adam–Gibbs model by obtaining the configurational entropy (Sconf) and the specific heat contributions (CP,conf). We find that, for the HE, all of the studied quantities behave differently. For water–glycerol, the HB interaction is dominant for all conditions; water–methanol, two different T-regions above and below 265 K are observable, dominated by hydrophobicity and hydrophilicity, respectively. Below this temperature, where the LDL phase and the HB network develops and grows, with the times and CP,conf change behaviors leading to maxima and minima. Above it, the HB becomes weak and less stable, the HDL dominates, and hydrophobicity determines the solution.

Molecular dynamics simulations vs field-cycling NMR relaxometry: Structural relaxation mechanisms in the glass-former glycerol revisited

We combine field-cycling (FC) relaxometry and molecular dynamics (MD) simulations to study the rotational and translational dynamics associated with the glassy slowdown of glycerol. The ¹H NMR spin-lattice relaxation rates R₁(ω) probed in the FC measurements for different isotope-labelled compounds are computed from the MD trajectories for broad frequency and temperature ranges. We find high correspondence between experiment and simulation. Concerning the rotational motion, we observe that the aliphatic and hydroxyl groups show similar correlation times but different stretching parameters, while the overall reorientation associated with the structural relaxation remains largely isotropic. Additional analysis of the simulation results reveals that transitions between different molecular configurations are slow on the time scale of the structural relaxation at least at sufficiently high temperatures, indicating that glycerol rotates at a rigid entity, but the reorientation is slower for elongated than for compact conformers. The translational contribution to R₁(ω) is well described by the force-free hard sphere model. At sufficiently low frequencies, universal square-root laws provide access to the molecular diffusion coefficients. In both experiment and simulation, the time scales of the rotational and translational motions show an unusually large separation, which is at variance with the Stokes-Einstein-Debye relation. To further explore this effect, we investigate the structure and dynamics on various length scales in the simulations. We observe that a prepeak in the static structure factor S(q), which is related to a local segregation of aliphatic and hydroxyl groups, is accompanied by a peak in the correlation times τ(q) from coherent scattering functions.

Molecular heterogeneity in aqueous cosolvent systems

Aqueous cosolvent systems (ACoSs) are mixtures of small polar molecules such as amides, alcohols, dimethyl sulfoxide, or ions in water. These liquids have been the focus of fundamental studies due to their complex intermolecular interactions as well as their broad applications in chemistry, medicine, and materials science. ACoSs are fully miscible at the macroscopic level but exhibit nanometer-scale spatial heterogeneity. ACoSs have recently received renewed attention within the chemical physics community as model systems to explore the relationship between intermolecular interactions and microscopic liquid-liquid phase separation. In this perspective, we provide an overview of ACoS spatial segregation, dynamic heterogeneity, and multiscale relaxation dynamics. We describe emerging approaches to characterize liquid microstructure, H-bond networks, and dynamics using modern experimental tools combined with molecular dynamics simulations and network-based analysis techniques.

Interactions of Glycerol, Diglycerol, and Water Studied Using Attenuated Total Reflection Infrared Spectroscopy

In order to examine the mixing properties of glycerol-water and diglycerol-water solutions, these solutions were measured using attenuated total reflection infrared spectroscopy. The absorbance spectra corrected for 1 µm thickness were subtracted by pure polyols for obtaining water spectra, and by pure water for polyol spectra. Both asymmetric and symmetric CH₂ stretching vibration bands (around 2940, 2885 cm^-1) shifted about 10 cm^-1 to lower wavenumber side (redshifts) with increasing polyol concentrations, especially at higher concentrations. Redshifts of C-O-H rocking bands (around 1335 cm^-1) with increasing polyol concentrations are slightly larger for diglycerol-water (10 > 6 cm^-1) than glycerol-water solutions. C-O stretching bands of CHOH groups (1125 and 1112 cm^-1) shift slightly but in opposite sides for glycerol and diglycerol at highest polyol concentrations (90-100 wt%). These shifts of CH₂ stretching, COH rocking, and CO stretching of CHOH at higher polyol concentrations suggest interactions of outer CH₂ with inner CHOH groups of surrounding polyols. The normalized band area changes with polyol concentrations could be fitted by quadratic polynomials possibly due to mixtures of different interactions between water-water, polyol-water, and polyol-polyol molecules. The OH stretching band for diglycerol 90 wt% shows three humps indicating at least three OH components: long, medium, and short H bond water molecules. Short H bond water molecules are the major component possibly between inner CHOH and outer side CH₂OH groups, while the long H component might loosely bind to outer CH₂OH groups.

Field-dependent paramagnetic relaxation enhancement in solutions of Ni(II): What happens above the NMR proton frequency of 1 GHz?

An extended set of paramagnetic relaxation enhancement (PRE) data, up to the field of 32.9 Tesla, is reported for protons in an acidified aqueous solution of a Ni(II) salt in the presence and in the absence of added glycerol. For the 55% w/w glycerol sample, a distinct maximum in the PRE vs magnetic field curve is observed for the first time. The data are analysed using the Swedish slow-motion theory, including both the intramolecular (inner-sphere) and intermolecular (outer-sphere) contributions. The results indicate that estimating the outer-sphere part in the presence of the more efficient inner-sphere term is a difficult task.

From atoms to aerosols: probing clusters and nanoparticles with synchrotron based mass spectrometry and X-ray spectroscopy

Synchrotron radiation provides insight into spectroscopy and dynamics in clusters and nanoparticles.

Molecular Basis of Water Activity in Glycerol-Water Mixtures

Water activity (Aw) is a reliable indication of the microbial growth, enzymatic activity, preservation, and quality of foods. However, a molecular basis of Aw is still under debate in multiple related disciplines. Glycerol-water mixtures can provide a variation of Aws by controlling the ratio of glycerol and water. In this study, the molecular basis of Aw was examined by using differential scanning calorimetry (DSC), attenuated total reflection Fourier-transform infrared spectroscopy (ATR-IR), and incoherent quasi-elastic neutron scattering (IQENS) based on moisture sorption isotherms of glycerol-water mixtures. Three regions were identified and classified based on DSC results. DSC showed that bulk-like water existed at Aw > ≈ 0.7 at 27°C. Hydrogen bonding related molecular vibrations were analyzed by ATR-IR, which indicated that the OH stretching in water molecules is significantly different for Aw > ≈ 0.7. Translational diffusive and/or rotational motions in time and space analyzed by IQENS appeared when Aw > ≈ 0.7, and are correlated with hydrogen bonding related local vibrational dynamics in the glycerol-water mixtures. More importantly, Aw values of glycerol-water mixtures can be explained by the hydrogen bonding network and molecular dynamics of water in the solution. We discuss the implications of Aw in the preservation of food at the molecular level.

Molecular Effects of Glycerol on Lipid Monolayers at the Gas-Liquid Interface: Impact on Microbubble Physical and Mechanical Properties

The production and stability of microbubbles (MBs) is enhanced by increasing the viscosity of both the formation and storage solution, respectively. Glycerol is a good candidate for biomedical applications of MBs, since it is biocompatible, although the exact molecular mechanisms of its action is not fully understood. Here, we investigate the influence glycerol has on lipid-shelled MB properties, using a range of techniques. Population lifetime and single bubble stability were studied using optical microscopy. Bubble stiffness measured by AFM compression is compared with lipid monolayer behavior in a Langmuir-Blodgett trough. We deduce that increasing glycerol concentrations enhances stability of MB populations through a 3-fold mechanism. First, binding of glycerol to lipid headgroups in the interfacial monolayer up to 10% glycerol increases MB stiffness but has limited impact on shell resistance to gas permeation and corresponding MB lifetime. Second, increased solution viscosity above 10% glycerol slows down the kinetics of gas transfer, markedly increasing MB stability. Third, above 10%, glycerol induces water structuring around the lipid monolayer, forming a glassy layer which also increases MB stiffness and resistance to gas loss. At 30% glycerol, the glassy layer is ablated, lowering the MB stiffness, but MB stability is further augmented. Although the molecular interactions of glycerol with the lipid monolayer modulate the MB lipid shell properties, MB lifetime continually increases from 0 to 30% glycerol, indicating that its viscosity is the dominant effect on MB solution stability. This three-fold action and biocompatibility makes glycerol ideal for therapeutic MB formation and storage and gives new insight into the action of glycerol on lipid monolayers at the gas-liquid interface.

Synergy of orientational relaxation between bound water and confined water in ice cold-crystallization

Dehydration/rehydration of some glycerol molecules provides the optimal path for ice cold-crystallization, wherein bound- and confined-water participate in a dynamically synergetic manner.

Influence of glycerol on the cooling effect of pair hydrophobicity in water: relevance to proteins’ stabilization at low temperature

Glycerol reduces the cooling effect of pair hydrophobicity (reduction of hydrophobicity with decreasing temperature) in water.

Exploring Dynamics and Structure of Biomolecules, Cryoprotectants, and Water Using Molecular Dynamics Simulations: Implications for Biostabilization and Biopreservation

Successful stabilization and preservation of biological materials often utilize low temperatures and dehydration to arrest molecular motion. Cryoprotectants are routinely employed to help the biological entities survive the physicochemical and mechanical stresses induced by cold or dryness. Molecular interactions between biomolecules, cryoprotectants, and water fundamentally determine the outcomes of preservation. The optimization of assays using the empirical approach is often limited in structural and temporal resolution, whereas classical molecular dynamics simulations can provide a cost-effective glimpse into the atomic-level structure and interaction of individual molecules that dictate macroscopic behavior. Computational research on biomolecules, cryoprotectants, and water has provided invaluable insights into the development of new cryoprotectants and the optimization of preservation methods. We describe the rapidly evolving state of the art of molecular simulations of these complex systems, summarize the molecular-scale protective and stabilizing mechanisms, and discuss the challenges that motivate continued innovation in this field.

Liquid crystalline droplets in aqueous environments: electrostatic effects

We demonstrate the strong impact of electrostatic properties on radial-bipolar structural transitions in nematic liquid crystal (LC) droplets dispersed in different aqueous environments. In the experimental part of the study, we systematically changed the electrostatic properties of both LC droplets and aqueous solutions. Mixtures of nematics were studied by combining LC materials with negative (azoxybenzene compounds) and strongly positive (cyanobiphenyl) dielectric anisotropy. The aqueous solutions were manipulated by introducing either polyvinyl alcohol, glycerol, electrolyte or amphiphilic anionic surfactant SDS into water. In the supporting theoretical study, we identified the key parameters influencing the dielectric constant and the electric field strength of aqueous solutions. We also estimated the impact of different electrolytes on the Debye length at the LC-aqueous interface. The obtained results are further analysed for chemical and biological sensing applications.

How do glycerol and dimethyl sulphoxide affect local tetrahedral structure of water around a nonpolar solute at low temperature? Importance of preferential interaction

Glycerol and dimethyl sulphoxide (DMSO) have vital roles in cryoprotection of living cells, tissues, etc. The above action has been directly linked with disruption of hydrogen (H-) bond structure and dynamics of water by these cosolvents at bulk region and around various complex units, such as peptide, amino acid, protein, and lipid membrane. However, the disruption of the local structure of the water solvent around a purely hydrophobic solute is still not studied extensively. The latter is also important in the context of stabilization of protein from cold denaturation. Through all-atom molecular dynamics simulation, we have investigated the comparative effect of glycerol and DMSO on the orientational order of water around a nonpolar solute at -5 °C. A steady reduction of the tetrahedral order of water is observed at bulk (>10 Å distance from the solute) and solute interface (<5.5 Å distance from the solute) with increasing the cosolvent concentration. Contrasting roles of glycerol and DMSO have been evidenced. While DMSO affects the H-bond structure of the interfacial water more than that of the bulk water, glycerol affects the water structure almost uniformly at all regions around the solute. Furthermore, while glycerol helps to retain water molecules at the interface, DMSO significantly reduces the water content in that region. We have put forward a plausible mechanism for these contrasting roles of these cosolvents. The solute-cosolvent hydrophobic-interaction-induced orientational alignment of an interfacial cosolvent molecule determines whether the involvement of the cosolvent molecules in H-bonding with solvent water in the interface is akin to the bulk region or not.

1-Butanol as a Solvent for Efficient Extraction of Polar Compounds from Aqueous Medium: Theoretical and Practical Aspects

The extraction of polar molecules from aqueous solution is a challenging task in organic synthesis. 1-Butanol has been used sporadically as an eluent for polar molecules, but it is unclear which molecular features drive its efficiency. Here, we employ free energy simulations to study the partitioning of 15 solutes between water and 1-butanol. The simulations demonstrate that the high affinity of polar molecules to the wet 1-butanol phase is associated with its nanostructure. Small inverse micelles of water are able to accommodate polar solutes and locally mimic an aqueous environment. We verify the simulations based on partition coefficients between water and 1-octanol, and include a blind prediction of the water/1-butanol partition coefficient of cyclohexane-1,2-diol. The calculations are in excellent agreement with experiment, reaching root-mean-square deviations below 0.7 kcal/mol. Actual extractions of cyclohexane-1,2-diol from buffer solutions that mimic cell lysates and suspensions in biocatalytic reactions further exemplify our findings. The yields highlight that extractions with 1-butanol can be significantly more efficient than the conventional protocol based on ethyl acetate.

Slow rheological mode in glycerol and glycerol–water mixtures

Glycerol–water mixtures were studied at molar concentrations ranging from x_gly = 1 (neat glycerol) to x_gly = 0.3 using shear mechanical spectroscopy.

Local diffusion and diffusion-T2 distribution measurements in porous media

Slice-selective pulsed field gradient (PFG) and PFG-T₂ measurements are developed to measure spatially-resolved molecular diffusion and diffusion-T₂ distributions. A spatially selective adiabatic inversion pulse was employed for slice-selection. The slice-selective pulse is able to select a coarse slice, on the order of 1cm, at an arbitrary position in the sample. The new method can be employed to characterize oil-water mixtures in porous media. The new technique has an inherent sensitivity advantage over phase encoding imaging based methods due to signal being localized from a thick slice. The method will be advantageous for magnetic resonance of porous media at low field where sensitivity is problematic. Experimental CPMG data, following PFG diffusion measurement, were compromised by a transient ΔB₀(t) field offset. The off resonance effects of ΔB₀(t) were examined by simulation. The ΔB₀ offset artifact in D-T₂ distribution measurements may be avoided by employing real data, instead of magnitude data.

Communication: Contrasting effects of glycerol and DMSO on lipid membrane surface hydration dynamics and forces

Glycerol and dimethyl sulfoxide (DMSO) are commonly used cryoprotectants in cellular systems, but due to the challenges of measuring the properties of surface-bound solvent, fundamental questions remain regarding the concentration, interactions, and conformation of these solutes at lipid membrane surfaces. We measured the surface water diffusivity at gel-phase dipalmitoylphosphatidylcholine (DPPC) bilayer surfaces in aqueous solutions containing ≤7.5 mol. % of DMSO or glycerol using Overhauser dynamic nuclear polarization. We found that glycerol similarly affects the diffusivity of water near the bilayer surface and that in the bulk solution (within 20%), while DMSO substantially increases the diffusivity of surface water relative to bulk water. We compare these measurements of water dynamics with those of equilibrium forces between DPPC bilayers in the same solvent mixtures. DMSO greatly decreases the range and magnitude of the repulsive forces between the bilayers, whereas glycerol increases it. We propose that the differences in hydrogen bonding capability of the two solutes leads DMSO to dehydrate the lipid head groups, while glycerol affects surface hydration only as much as it affects the bulk water properties. The results suggest that the mechanism of the two most common cryoprotectants must be fundamentally different: in the case of DMSO by decoupling the solvent from the lipid surface, and in the case of glycerol by altering the hydrogen bond structure and intermolecular cohesion of the global solvent, as manifested by increased solvent viscosity.

Molecular dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana

The LEA (late embryogenesis abundant) proteins COR15A and COR15B from Arabidopsis thaliana are intrinsically disordered under fully hydrated conditions, but obtain α-helical structure during dehydration, which is reversible upon rehydration. To understand this unusual structural transition, both proteins were investigated by circular dichroism (CD) and molecular dynamics (MD) approaches. MD simulations showed unfolding of the proteins in water, in agreement with CD data obtained with both HIS-tagged and untagged recombinant proteins. Mainly intramolecular hydrogen bonds (H-bonds) formed by the protein backbone were replaced by H-bonds with water molecules. As COR15 proteins function in vivo as protectants in leaves partially dehydrated by freezing, unfolding was further assessed under crowded conditions. Glycerol reduced (40%) or prevented (100%) unfolding during MD simulations, in agreement with CD spectroscopy results. H-bonding analysis indicated that preferential exclusion of glycerol from the protein backbone increased stability of the folded state.

Glass polymorphism in glycerol-water mixtures: I. A computer simulation study

We perform out-of-equilibrium molecular dynamics (MD) simulations of water-glycerol mixtures in the glass state. Specifically, we study the transformations between low-density (LDA) and high-density amorphous (HDA) forms of these mixtures induced by compression/decompression at constant temperature. Our MD simulations reproduce qualitatively the density changes observed in experiments. Specifically, the LDA-HDA transformation becomes (i) smoother and (ii) the hysteresis in a compression/decompression cycle decreases as T and/or glycerol content increase. This is surprising given the fast compression/decompression rates (relative to experiments) accessible in MD simulations. We study mixtures with glycerol molar concentration χ(g) = 0-13% and find that, for the present mixture models and rates, the LDA-HDA transformation is detectable up to χ(g) ≈ 5%. As the concentration increases, the density of the starting glass (i.e., LDA at approximately χ(g) ≤ 5%) rapidly increases while, instead, the density of HDA remains practically constant. Accordingly, the LDA state and hence glass polymorphism become inaccessible for glassy mixtures with approximately χ(g) > 5%. We present an analysis of the molecular-level changes underlying the LDA-HDA transformation. As observed in pure glassy water, during the LDA-to-HDA transformation, water molecules within the mixture approach each other, moving from the second to the first hydration shell and filling the first interstitial shell of water molecules. Interestingly, similar changes also occur around glycerol OH groups. It follows that glycerol OH groups contribute to the density increase during the LDA-HDA transformation. An analysis of the hydrogen bond (HB)-network of the mixtures shows that the LDA-HDA transformation is accompanied by minor changes in the number of HBs of water and glycerol. Instead, large changes in glycerol and water coordination numbers occur. We also perform a detailed analysis of the effects that the glycerol force field (FF) has on our results. By comparing MD simulations using two different glycerol models, we find that glycerol conformations indeed depend on the FF employed. Yet, the thermodynamic and microscopic mechanisms accompanying the LDA-HDA transformation and hence, our main results, do not. This work is accompanied by an experimental report where we study the glass polymorphism in glycerol-water mixtures prepared by isobaric cooling at 1 bar.

Contribution of fluorophore dynamics and solvation to resonant energy transfer in protein-DNA complexes: a molecular-dynamics study

In Förster resonance energy transfer (FRET) experiments, extracting accurate structural information about macromolecules depends on knowing the positions and orientations of donor and acceptor fluorophores. Several approaches have been employed to reduce uncertainties in quantitative FRET distance measurements. Fluorophore-position distributions can be estimated by surface accessibility (SA) calculations, which compute the region of space explored by the fluorophore within a static macromolecular structure. However, SA models generally do not take fluorophore shape, dye transition-moment orientation, or dye-specific chemical interactions into account. We present a detailed molecular-dynamics (MD) treatment of fluorophore dynamics for an ATTO donor/acceptor dye pair and specifically consider as case studies dye-labeled protein-DNA intermediates in Cre site-specific recombination. We carried out MD simulations in both an aqueous solution and glycerol/water mixtures to assess the effects of experimental solvent systems on dye dynamics. Our results unequivocally show that MD simulations capture solvent effects and dye-dye interactions that can dramatically affect energy transfer efficiency. We also show that results from SA models and MD simulations strongly diverge in cases where donor and acceptor fluorophores are in close proximity. Although atomistic simulations are computationally more expensive than SA models, explicit MD studies are likely to give more realistic results in both homogeneous and mixed solvents. Our study underscores the model-dependent nature of FRET analyses, but also provides a starting point to develop more realistic in silico approaches for obtaining experimental ensemble and single-molecule FRET data.

Manipulating Excited-State Dynamics of Individual Light-Harvesting Chromophores through Restricted Motions in a Hydrated Nanoscale Protein Cavity

Manipulating the photophysical properties of light-absorbing units is a crucial element in the design of biomimetic light-harvesting systems. Using a highly tunable synthetic platform combined with transient absorption and time-resolved fluorescence measurements and molecular dynamics simulations, we interrogate isolated chromophores covalently linked to different positions in the interior of the hydrated nanoscale cavity of a supramolecular protein assembly. We find that, following photoexcitation, the time scales over which these chromophores are solvated, undergo conformational rearrangements, and return to the ground state are highly sensitive to their position within this cavity and are significantly slower than in a bulk aqueous solution. Molecular dynamics simulations reveal the hindered translations and rotations of water molecules within the protein cavity with spatial specificity. The results presented herein show that fully hydrated nanoscale protein cavities are a promising way to mimic the tight protein pockets found in natural light-harvesting complexes. We also show that the interplay between protein, solvent, and chromophores can be used to substantially tune the relaxation processes within artificial light-harvesting assemblies in order to significantly improve the yield of interchromophore energy transfer and extend the range of excitation transport. Our observations have implications for other important, similarly sized bioinspired materials, such as nanoreactors and biocompatible targeted delivery agents.

Hygroscopicity of Mixed Glycerol/Mg(NO3)2/Water Droplets Affected by the Interaction between Magnesium Ions and Glycerol Molecules

Tropospheric aerosols are usually complex mixtures of inorganic and organic components, which can influence the hygroscopicities of each other. In this research, we applied confocal Raman technology combined with optical microscopy to investigate the relationship between the hygroscopic behavior and the molecular interactions of mixed glycerol/Mg(NO3)2/water droplets. Raman spectra provide detailed structural information about the interactions between glycerol molecules and Mg(2+) ions, as well as information about the interactions between glycerol and NO3(-) ions through electrostatic interaction and hydrogen bonding. The change of the CH2 stretching band of glycerol molecules in mixed droplets suggests that the backbone structures of glycerol mainly transform from αα to γγ in the dehumidifying process, and the additional Mg(2+) ions strongly influence the structure of glycerol molecules. Because the existence of glycerol suppresses the crystallization of Mg(NO3)2·6H2O in the dehumidifying process, Mg(NO3)2 molecules in mixed droplets form an amorphous state rather than forming crystals of Mg(NO3)2·6H2O when the relative humidity is lower than 17.8%. Moreover, in mixed droplets, the molar ratio of NO3(-) to glycerol is higher in the center than in the outer region.

Competing intramolecular vs. intermolecular hydrogen bonds in solution

A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with intramolecular vs. intermolecular hydrogen bonds for different types of small organic molecules. In their most stable gas-phase structure, an intramolecular hydrogen bond is possible. In a protic solution, the intramolecular hydrogen bond may disrupt in favor of two solute-solvent intermolecular hydrogen bonds. The balance of the increased internal energy and the stabilizing effect of the solute-solvent interactions regulates the new conformer composition in the liquid phase. The review additionally considers the solvent effects on the stability of simple dimeric systems as revealed from molecular dynamics simulations or on the basis of the calculated potential of mean force curves. Finally, studies of the solvent effects on the type of the intermolecular hydrogen bond (neutral or ionic) in acid-base complexes have been surveyed.

Molecular structure and hydrogen bonding in pure liquid ethylene glycol and ethylene glycol-water mixtures studied using NIR spectroscopy

The molecular structure and hydrogen bonding of ethylene glycol (EG) and EG-water mixtures in the liquid phase were studied by using near-infrared (NIR) spectroscopy. The spectra were evaluated using a two-dimensional (2D) correlation approach, moving-window 2D correlation analysis and chemometric methods. The minor changes for the CH stretching bands indicate that the structures of pure liquid EG and EG-water mixtures are determined by the intermolecular hydrogen bonding through the OH groups. The analysis of the ν2 + ν3 combination band of water reveals that in EG-rich solutions the molecules of water are predominantly bonded with two molecules of EG and this cooperative hydrogen bonding is stronger than that in bulk water. Further increase in the water content leads to formation of small water clusters around OH groups of EG. Comparing results for the binary mixtures of water with different organic solvents one can conclude that the total amount and distribution of the polar groups are the most important factors determining the solubility of water in the organic phase. The distribution of these groups depends on the length and structure of the hydrocarbon chain. Due to high population and relatively uniform distribution of the OH groups of EG water has unlimited solubility in liquid EG.

Polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator

A polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator is presented. The model is optimized with an emphasis on the transferability of the developed parameters among molecules of different sizes in this series and on the condensed-phase properties validated against experimental data. The importance of the explicit treatment of electronic polarizability in empirical force fields is demonstrated in the cases of this series of molecules with vicinal hydroxyl groups that can form cooperative intra- and intermolecular hydrogen bonds. Compared to the CHARMM additive force field, improved treatment of the electrostatic interactions avoids overestimation of the gas-phase dipole moments resulting in significant improvement in the treatment of the conformational energies and leads to the correct balance of intra- and intermolecular hydrogen bonding of glycerol as evidenced by calculated heat of vaporization being in excellent agreement with experiment. Computed condensed phase data, including crystal lattice parameters and volumes and densities of aqueous solutions are in better agreement with experimental data as compared to the corresponding additive model. Such improvements are anticipated to significantly improve the treatment of polymers in general, including biological macromolecules.

The FMO complex in a glycerol-water mixture

Experimental findings of long-lived quantum coherence in the Fenna-Matthews-Olson (FMO) complex and other photosynthetic complexes have led to theoretical studies searching for an explanation of this unexpected phenomenon. Extending in this regard our own earlier calculations, we performed simulations of the FMO complex in a glycerol-water mixture at 310 K as well as 77 K, matching the conditions of earlier 2D spectroscopic experiments by Engel et al. The calculations, based on an improved quantum procedure employed by us already, yielded spectral densities of each individual pigment of FMO, in water and glycerol-water solvents at ambient temperature that compare well to prior experimental estimates. Due to the slow solvent dynamics at 77 K, the present results strongly indicate the presence of static disorder, i.e., disorder on a time scale beyond that relevant for the construction of spectral densities.