The crystal structure of glycerol and its conformation

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.

First-principles study of the specific heat of glass at the glass transition with a case study on glycerol

The standard method to determine the transition temperature (T_g) of glasses is the jump in the specific heat,ΔCp. Despite its importance, standard theory for this jump is lacking. The difficulties include lack of proper treatment of the specific heat of liquids, hysteresis, and the timescale issue. The first part of this paper provides a non-empirical method for calculating the specific heat in the glass transition. The method consists of molecular dynamics (MD) simulations based on density-functional theory (DFT) and thermodynamics methods. Calculation of the total energy, which is the heart of DFT, is the most general method for obtaining specific heat for any state of matters. The influence of energy dissipation processes on specific heat is treated by adiabatic MD simulations. The problems of hysteresis and the timescale are alleviated by restricting the scope of calculations to equilibrium states only. The second part of this paper demonstrates the validity and usefulness of the methods by applying to the specific-heat jump of glycerol. By decomposingΔCpinto contributions of the structural, phonon, and thermal expansion energies, an appropriate interpretation for the specific-heat jump has been established: the major contribution toΔCpis the change in the structural energy. From this, a neat energy diagram about the glass transition is obtained. An outcome of this study is verification of the empirical relationship between the fragility and the specific-heat jump. These two quantities scale to the ratiok=Tg/ΔTg, whereΔTgis the width of the transition, through which the two quantities are interrelated.

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.

Elastic properties of the hydrogen-bonded liquid and glassy glycerol under high pressure: comparison with propylene carbonate

We compare elastic properties of the liquid and glassy glycerol and propylene carbonate as the archetypal molecular glass formers with and without hydrogen bonding.

Effects of monohydric alcohols and polyols on the thermal stability of a protein

The thermal stability of a protein is lowered by the addition of a monohydric alcohol, and this effect becomes larger as the size of hydrophobic group in an alcohol molecule increases. By contrast, it is enhanced by the addition of a polyol possessing two or more hydroxyl groups per molecule, and this effect becomes larger as the number of hydroxyl groups increases. Here, we show that all of these experimental observations can be reproduced even in a quantitative sense by rigid-body models focused on the entropic effect originating from the translational displacement of solvent molecules. The solvent is either pure water or water-cosolvent solution. Three monohydric alcohols and five polyols are considered as cosolvents. In the rigid-body models, a protein is a fused hard spheres accounting for the polyatomic structure in the atomic detail, and the solvent is formed by hard spheres or a binary mixture of hard spheres with different diameters. The effective diameter of cosolvent molecules and the packing fractions of water and cosolvent, which are crucially important parameters, are carefully estimated using the experimental data of properties such as the density of solid crystal of cosolvent, parameters in the pertinent cosolvent-cosolvent interaction potential, and density of water-cosolvent solution. We employ the morphometric approach combined with the integral equation theory, which is best suited to the physical interpretation of the calculation result. It is argued that the degree of solvent crowding in the bulk is the key factor. When it is made more serious by the cosolvent addition, the solvent-entropy gain upon protein folding is magnified, leading to the enhanced thermal stability. When it is made less serious, the opposite is true. The mechanism of the effects of monohydric alcohols and polyols is physically the same as that of sugars. However, when the rigid-body models are employed for the effect of urea, its addition is predicted to enhance the thermal stability, which conflicts with the experimental fact. We then propose, as two essential factors, not only the solvent-entropy gain but also the loss of protein-solvent interaction energy upon protein folding. The competition of changes in these two factors induced by the cosolvent addition determines the thermal-stability change.

A combined experimental and computational study of the esterification reaction of glycerol with acetic acid

This work describes theoretical and experimental studies on glycerol esterification to obtain acetins focusing on the obtained isomers. The reaction of glycerol with acetic acid was carried out on Amberlyst 36 wet. Density functional theory calculations on the level of M06-2X functional and 6-311+G(d,p) basis set are carried out and the most stable structures of the reactants and products are located by considering a large number of conformers. The thermodynamics is discussed in terms of the calculated reaction Gibbs free energy. The AIM theory was used to characterize reactants and products. The glycerol esterification with acetic acid is found to be thermodynamically favored, with exothermal property. These agree well with experiments and allow us to explain the relative selectivity of products.

On achieving experimental accuracy from molecular dynamics simulations of flexible molecules: aqueous glycerol

The rotational isomeric states (RIS) of glycerol at infinite dilution have been characterized in the aqueous phase via a 1 micros conventional molecular dynamics (MD) simulation, a 40 ns enhanced sampling replica exchange molecular dynamics (REMD) simulation, and a reevaluation of the experimental NMR data. The MD and REMD simulations employed the GLYCAM06/AMBER force field with explicit treatment of solvation. The shorter time scale of the REMD sampling method gave rise to RIS and theoretical scalar 3J(HH) coupling constants that were comparable to those from the much longer traditional MD simulation. The 3J(HH) coupling constants computed from the MD methods were in excellent agreement with those observed experimentally. Despite the agreement between the computed and the experimental J-values, there were variations between the rotamer populations computed directly from the MD data and those derived from the experimental NMR data. The experimentally derived populations were determined utilizing limiting J-values from an analysis of NMR data from substituted ethane molecules and may not be completely appropriate for application in more complex molecules, such as glycerol. Here, new limiting J-values have been derived via a combined MD and quantum mechanical approach and were used to decompose the experimental 3J(HH) coupling constants into population distributions for the glycerol RIS.

Coupling between lysozyme and glycerol dynamics: Microscopic insights from molecular-dynamics simulations

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.

Role of hydrogen bonds in the fast dynamics of binary glasses of trehalose and glycerol: A molecular dynamics simulation study

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.