Density Functional Calculation of Structural and Vibrational Properties of Glycerol

Single-Molecule Tracking of Reagent Diffusion during Chemical Reactions

Recent experiments have shown that the diffusion of reagent molecules is inconsistent with what the Stokes-Einstein equation predicts during a chemical reaction. Here, we used single-molecule tracking to observe the diffusion of reactive reagent molecules during click and Diels-Alder (DA) reactions. We found that the diffusion coefficient of the reagents remained unchanged within the experimental uncertainty upon the DA reaction. Yet, diffusion of reagent molecules is faster than predicted during the click reaction when the reagent concentration and catalyst concentration exceed a threshold. A stepwise analysis suggested that the fast diffusion scenario is due to the reaction but not the involvement of the tracer with the reaction itself. The present results provide experimental evidence on the faster-than-expected reagent diffusion during a CuAAC reaction in specific conditions and propose new insights into understanding this unexpected behavior.

Molecular heterogeneities in the thermal expansivity of polyalcohols

Density is the key quantity for nearly all the numerous theories of the (dynamic) glass transition of supercooled liquids and melts. As mean field quantity, it is used to describe correlations and heterogeneities between regions consisting of several molecules. In contrast, the question how density is created by the interactions (i.e., bonds) within a molecule and to its nearest neighbors is almost unexplored. To investigate this for the example of a homologous series of polyalcohols (glycerol, threitol, xylitol, and sorbitol), Fourier-Transform InfraRed (FTIR) spectroscopy is carried out in a wide range of temperatures from far above to far below the calorimetric glass transition T_g. This enables us to determine the potentials and hence the bond lengths of specific intramolecular and intermolecular interactions. While the former has an expansion coefficient of (∼0.1 pm/100 K) with only smooth changes, the latter shows a 30-40 times stronger response with pronounced kinks at T_g. A comparison with the overall expansion based on mass density reveals that one has to separate between strong (OH⋅⋅⋅O) and weak (CH⋅⋅⋅O) intermolecular hydrogen (H)-bridges. Despite the fact that the latter dominates glassy dynamics, their expansivity is 5 times smaller than that of the weak H-bridges. It is to be expected that such heterogeneities on intramolecular and intermolecular scales are a general phenomenon in liquids and glassy systems demonstrating especially the necessity of atomistic simulations.

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.

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.

Structural heterogeneities at the origin of acoustic and transport anomalies in glycerol glass-former

By means of large scale molecular dynamics simulations, we explore mesoscopic properties of prototypical glycerol glass-former above and below the glass transition. The model used, in excellent agreement with various experimental techniques, permits to carefully study the structure and the vibrational dynamics. We find that a medium range order is present in glycerol glass-former and arises from hydrogen bond network extension. The characteristic size of the structural heterogeneities is related to the anomalous properties of acoustic vibrations (Rayleigh scattering, "mode softening," and Boson Peak) in the glassy state. Finally the characteristic size of these heterogeneities, nearly constant in temperature, is also connected to the cross-over between structural relaxation and diffusion in liquid glycerol.

Contribution of high-energy conformations to NMR chemical shifts, a DFT-BOMD study

This paper highlights the relevance of including the high-energy conformational states sampled by Born-Oppenheimer molecular dynamics (BOMD) in the calculation of time-averaged NMR chemical shifts. Our case study is the very flexible glycerol molecule that undergoes interconversion between conformers in a nonrandom way. Along the sequence of structures from one backbone conformer to another, transition states have been identified. The three (13)C NMR chemical shifts of the molecule were estimated by averaging their calculated values over a large set of BOMD snapshots. The simulation time needed to obtain a good agreement with the two signals present in the experimental spectrum is shown to be dependent on the atomic orbital basis set used for the dynamics, with a necessary longer trajectory for the most extended basis sets. The large structural deformations with respect to the optimized conformer geometries that occur along the dynamics are related to a kinetically driven conformer distribution. Calculated conformer type populations are in good agreement with experimental gas phase microwave results.

Suppression of NaNO3 crystal nucleation by glycerol: micro-Raman observation on the efflorescence process of mixed glycerol/NaNO3/water droplets

Although the hygroscopicity of a NaNO(3)/water microdroplet and a polyalcohol/water microdroplet, two of the most important aerosols in atmosphere, has been widely studied, little is known about the relationship between the hygroscopic behavior of mixed NaNO(3)/polyalcohol/water droplets and their structures on the molecular level. In this study, the hygroscopicity of mixed glycerol/NaNO(3)/water droplets deposited on a hydrophobic substrate was studied by micro-Raman spectroscopy with organic-to-inorganic molar ratios (OIRs) of 0.5, 1, and 2. In the mixed glycerol/NaNO(3)/water droplets, glycerol molecules tended to combine with Na(+) and NO(3)(-) ions by electrostatic interaction and hydrogen bonding, respectively. On the basis of the analyses of the changes of symmetric stretching (v(s)-CH(2)), asymmetric stretching (v(a)-CH(2)), their area ratio (Av(a)-CH(2)/Av(s)-CH(2)) of glycerol, and symmetric stretching band of NO(3)(-) (ν(1)-NO(3)(-)) with relative humidity (RH), it was found that the conformation of glycerol was transformed from αα mainly to γγ and partly to αγ with a decreasing RH in the mixed droplets, contrary to the case in the glycerol/water droplet. In addition, the glycerol with γγ and αγ conformation had strong interaction with Na(+) and NO(3)(-) respectively, which suppressed the formation of contact of ions and delayed the efflorescence relative humidity (ERH) for the mixed droplets compared to the NaNO(3)/water droplet.

Structures and reaction mechanisms of glycerol dehydration over H-ZSM-5 zeolite: a density functional theory study

The initial stage of glycerol conversion over H-ZSM-5 zeolite has been investigated using density functional theory (DFT) calculations on an embedded cluster model consisting of 128 tetrahedrally coordinated atoms. It is found that glycerol dehydration to acrolein and acetol proceeds favourably via a stepwise mechanism. The formation of an alkoxide species upon the first dehydration requires the highest activation energy (42.5 kcal mol(-1)) and can be considered as the rate determining step of the reaction. The intrinsic activation energies for the first dehydration are virtually the same for both acrolein and acetol formation, respectively, suggesting the competitive removal of the primary and secondary OH groups. A high selectivity to acrolein at moderate temperatures can be attributed to the selective activation of the stronger adsorption mode of glycerol through the secondary OH group and the kinetically favoured subsequent consecutive steps. In addition, the less reactive nature of acrolein relative to acetol precludes it from being converted to other products upon conversion to glycerol. In accordance with typical endothermic reactions, the forward rate constant for glycerol dehydration significantly increases with increasing reaction temperature.

Structure, dynamics, and energetics of lysobisphosphatidic acid (LBPA) isomers

Lysobisphosphatidic acid (LBPA), or bis(monoacylglycerol)phosphate, is a very interesting lipid, that is mainly found in late endosomes. It has several intriguing characteristics, which differ from those of other animal glycerophospholipids, that may be related to its specific functions, particularly in the metabolism of cholesterol. Its phosphodiester group is bonded at the sn-1 (sn-1') positions of the glycerols rather than at sn-3 (sn-3'); the position of the two fatty acid chains is still under debate but, increasingly, arguments favor the sn-2, sn-2' position in the native molecule, whereas isolation procedures or acidic conditions lead to the thermodynamically more stable sn-3, sn-3' structure. Because of these peculiar features, it can be expected that LBPA shape and interactions with membrane lipids and proteins are related to its structure at the molecular level. We applied quantum mechanical methods to study the structures and stabilities of the 2,2' and 3,3' LBPA isomers, using a step-by-step procedure from glycerol to precursors (in vitro syntheses) and to the final isoforms. The structures of the two positional LBPA isomers are substantially different, showing that the binding positions of the fatty acid chains on the glycerol backbone determine the shape of the LBPA molecule and thus, possibly, its functions. The 3,3' LBPA structures obtained are more stable with respect to the 2,2' form, as expected from experiment. If one argues that the in vivo synthesis starts from the present glycerol conformers and considering the most stable bis(glycero)phosphate structures, the 2,2' isoform should be the most probable isomer.

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.

Structural Evidence of the Similarity of Sb(OH)3 and As(OH)3 with Glycerol: Implications for Their Uptake

Recent experimental results suggest that As(III) and Sb(III) transport in prokaryotes and eukaryotes might be facilitated by aquaglyceroporins. GlpF, the glycerol facilitator in Escherichia coli was the first to be identified as a trivalent metalloid transporter. Quantum calculations have been performed to study the possible existence of common structural properties between As(OH) 3 and Sb(OH) 3 and glycerol. Because the mechanism of substrate migration is primarily related to the successive formation of hydrogen bonds between the substrate and the hydrophilic part of the channel wall, this study has focused on the structural, thermodynamic, and electrostatic comparison of the main As(III) and Sb(III) compounds present in aqueous solution at physiological pH values, As(OH) 3 and Sb(OH) 3, with the glycerol conformation closest to the structures of these As- and Sb-containing compounds. This particular glycerol conformation has then been compared to three known experimental conformations of glycerol present in the protein channel. Besides their stoichiometry and electroneutral condition, As(OH) 3 and Sb(OH) 3 show very strong similarities to both each other and the studied conformation of the glycerol molecule: Namely, they show a similar charge distribution and a slightly smaller volume than glycerol. Their smaller size can be an additional advantage for the transit through the narrowest region of the GlpF channel. However, the metalloid hydroxyl groups lack the flexibility of glycerol, which probably helps this molecule to adapt its conformation to the topology of the GlpF channel.

Mono-, di-, and tri-tert-butyl ethers of glycerol. A molecular spectroscopic study

MS, NMR, IR and Raman molecular spectroscopy techniques were applied to characterize 3-tert-butoxy-propane-1,2-diol, 1,3-di-tert-butoxy-propan-2-ol, and 1,2,3-tri-tert-butoxy-propane. These ethers are the main products of glycerol etherification reaction and are excellent oxygen additives for diesel fuel. Computational DFT/ B3LYP/6-31G** studies were performed to support and rationalize both vibrational spectroscopy analysis and the isomer ratio.

Determination of the Enthalpy of Solute−Solvent Interaction from the Enthalpy of Solution: Aqueous Solutions of Erythritol and l-Threitol

In this work the enthalpy of the solute-solvent interaction of erythritol and L-threitol in aqueous solution was determined from the values obtained for the enthalpy of solvation. The values for this property were calculated from those determined for the enthalpies of solution and sublimation. To determine the values of the enthalpy of solute-solvent interaction, the solvation process is considered as taking place in three steps: opening a cavity in the solvent to hold the solute molecule, changing the solute conformation when it passes from the gas phase into solution, and interaction between the solute and the solvent molecules. The cavity enthalpy was calculated by the scaled particle theory and the conformational enthalpy change was estimated from the value of this function in the gas phase and in solution. Both terms were determined by DFT calculations. The solvent effect on the solute conformation in solution was estimated using the CPCM solvation model. The importance of the cavity and conformational terms in the interpretation of the enthalpy of solvation is noted. While the cavity term has been used by some authors, the conformational term is considered for the first time. The structural features in aqueous solution of erythritol and L-threitol are discussed.

Conformational study of erythritol and threitol in the gas state by density functional theory calculations

Density functional theory calculations using the B3LYP functional and the 6-311++G(d,p) basis set were carried out on the isolated molecules of erythritol and L-threitol. For the meso isomer, a relatively large number of conformers have to be considered to describe the gas state structure. The lowest energy conformer is characterized by the establishment of a strong intramolecular H-bond between the two terminal hydroxyl groups, giving rise to a seven-membered ring and two additional weaker H-bonds between vicinal OH groups. In the case of L-threitol, two conformers are predominant in the gas state, and both are stabilized by the formation of a cyclic system of four intramolecular hydrogen bonds involving all OH groups. The conformational stability in both diastereomers is discussed in terms of the electronic energy and of the Gibbs energy. The weighted mean enthalpy of both diastereomers in the gas state at 298.15 K was obtained from the thermodynamic data and Boltzmann populations of the low-energy conformers.

Computational analysis of the potential energy surfaces of glycerol in the gas and aqueous phases: effects of level of theory, basis set, and solvation on strongly intramolecularly hydrogen-bonded systems

The 126 possible conformations of 1,2,3-propanetriol (glycerol) have been studied by ab initio molecular orbital and density functional theory calculations in the gas and aqueous phases at multiple levels of theory and basis sets. The partial potential energy surface for glycerol as well as an analysis of the conformational properties and hydrogen-bonding trends in both phases have been obtained. In the gas phase at the G2(MP2) and CBS-QB3 levels of theory, the important, low-energy conformers are structures 100 and 95. In the aqueous phase at the SM5.42/HF/6-31G* level of theory, the lowest energy conformers are structures 95 and 46. Boltzmann distributions have been determined from these high-level calculations, and good agreement is observed when these distributions are compared to the available experimental data. These calculations indicate that the enthalpic and entropic contributions to the Gibbs free energy are important for an accurate determination of the conformational and energetic preferences of glycerol. Different levels of theory and basis sets were used in order to understand the effects of nonbonded interactions (i.e., intramolecular hydrogen bonding). The efficiency of basis set and level of theory in dealing with the issue of intramolecular hydrogen bonding and reproducing the correct energetic and geometrical trends is discussed, especially with relevance to practical computational methods for larger polyhydroxylated compounds, such as oligosaccharides.