Glycerol Conformation Research Articles

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.

Computational Study of Glycerol Binding within the Active Site of Coenzyme B12-Dependent Diol Dehydratase.

Molecular dynamics (MD) simulations have been employed for the first time to gain insight into the geometry of glycerol (GOL) bound within the active site of B12-dependent diol dehydratase (B12-dDDH). A peculiar feature of the B12-dDDH enzyme is that it undergoes suicidal inactivation by the substrate glycerol. To fully understand the inactivation mechanism, it is crucial to identify all possible interactions between GOL and the surrounding amino acid residues in the enzyme-substrate complex. Particularly important is the orientation of the C3-OH group in GOL since the presence of this OH group is the only difference between GOL and propanediol (PDO), a substrate for B12-dDDH that does not induce suicidal inactivation. The MD simulations indicate that glycerol can adopt two conformations that differ with respect to the orientation of the C3-OH group; in one conformer, the C3-OH group is oriented toward Ser301 (C3-OH···Ser301), and in the other toward Asp335 (C3-OH···Asp335). Although the former configuration is consistent with the crystal structure of B12-dDDH crystallized with cyanocobalamin (CNCbl) as the cofactor, MD simulations of this system suggest a substantial predominance of the latter conformer. A similar result with an even higher preference for the latter conformer is obtained for B12-dDDH with 5'-deoxyadenosylcobalamin (AdoCbl) as a cofactor. Employing QM/MM calculations it is found that the energy difference between the two conformers of GOL is very small in CNCbl B12-dDDH, where the slightly preferred conformer is C3-OH···Ser301. However, in AdoCbl B12-dDDH, this energy difference is higher, implying that GOL exists predominantly as the C3-OH···Asp335 conformer. These findings offer a new perspective for investigations of substrate-induced inactivation of the B12-dDDH enzyme.

Binary Phase Behavior of Saturated-Unsaturated Mixed-Acid Triacylglycerols-A Review.

Most natural lipids contain a complex mixture of individual triacylglycerols (TAGs). An in-depth knowledge of the mixing behavior of TAGs is necessary for the rational design and engineering of food materials. The binary phase diagram of TAGs is a simplified model that can be explored to help foster an understanding of the phase behavior of complex fats and oils. This article reviews recent research on the binary phase behavior of saturated-unsaturated mixed-acid TAGs, with special emphasis on the stearicunsaturated and palmitic-unsaturated diacid TAGs. The occurrence of polymorphic forms and mutual solubility of TAG mixtures are strongly related to the glycerol conformation of the saturated-oleic diacid TAGs; it appears to be most influenced by the chain-length mismatch in saturated-elaidic diacid TAGs. In addition, the polymorphism of pure enantiomers and racemic mixture of chiral TAGs was also reviewed, while the effect of chirality on mixing behavior was discussed.

Computational Mutation Design of Diol Dehydratase: Catalytic Ability toward Glycerol beyond the Wild-Type Enzyme

Abstract A computational mutation analysis based on quantum mechanical/molecular mechanical (QM/MM) calculations is performed for the elucidation of catalytic functions of amino acid residues at the active site of diol dehydratase in the dehydration of glycerol to afford 3-hydroxypropionaldehyde. While the wild-type diol dehydratase is subject to suicide inactivation in the dehydration process, mutants Gln336Ala and Ser301Ala are more resistant to the inactivation by glycerol (Yamanishi et al., FEBS J.2012, 279, 793). In the present study the impact of the mutation is discussed on the basis of energy profiles of two reaction pathways for the dehydration of glycerol and the inactivation of the enzyme. Both the mutants efficiently distinguish between two possible binding conformations of glycerol, the GS and GR conformations, where the former is known to mainly contribute to the inactivation of the enzyme. The improved resistance to the inactivation observed for the mutants can be explained by a hydrogen-bonding interaction between an OH group of glycerol and Ser301 as well as steric repulsion between glycerol and Val300. The computational mutation analysis first unveils the vital role of Val300 in the discrimination of the GS and GR conformations, which was not clearly viewed in the wild-type enzyme. The present findings will encourage the application of computational mutation approach to the rational design of enzymes optimized for desired organic synthesis.

Acid catalyzed first dehydration of glycerol at the secondary site: The effect of glycerol conformation

The first dehydration of protonated glycerol taking place at its secondary site was investigated by density functional calculations by considering different conformations of glycerol. Five parallel reaction pathways via different conformers of protonated glycerol were found. One of these pathways leads to a direct formation of protonated 3-hydroxylpropanal (HPA), another one of these pathways produces protonated glycidol, and the other three produce protonated 3-hydroxy-1,1-propanediol (HPD). One of these pathways producing protonated HPD was found to have obviously larger relative reaction rate than other pathways. The dehydration of protonated HPD to afford protonate HPA requires a rather low reaction barrier (12 kcal/mol). These results show that the production of HPA via a stepwise process with protonated HPD as a key intermediate, is energetically favorable than via a one-step concerted process producing HPA.

Structures and Binary Mixing Characteristics of Enantiomers of 1‐Oleoyl‐2,3‐dipalmitoyl‐sn‐glycerol (S‐OPP) and 1,2‐Dipalmitoyl‐3‐oleoyl‐sn‐glycerol (R‐PPO)

AbstractWe performed differential scanning calorimetry (DSC) and synchrotron radiation X‐ray diffraction (SR‐XRD) experiments of polymorphic structures and binary mixing characteristics of the enantiomers of 1‐oleoyl‐2,3‐dipalmitoyl‐sn‐glycerol (S‐OPP) and 1,2‐dipalmitoyl‐3‐oleoyl‐sn‐glycerol (R‐PPO). In the two enantiomers, oleic and palmitic acid moieties are asymmetrically connected at the sn‐1 and sn‐3 positions of the glycerol groups, with palmitic acid moiety at the sn‐2 position. Pure enantiomer samples (>99 %) were synthesized and employed throughout this study. The following results were obtained. (1) A basic feature of the mixture systems of S‐OPP and R‐PPO is of a eutectic nature due to different polymorphic structures of two enantiomers and the racemic compound of PPO (rac‐PPO). (2) Polymorphic behavior of S‐OPP and R‐PPO was quite similar, both having α‐2 and β′‐3, whereas rac‐PPO contained α rac‐3, β′rac‐2, and β′rac‐3. The DSC measurements showed that the melting points of β′‐3 (S‐OPP = 35.3 °C and R‐PPO = 34.9 °C) were higher than that of β′rac‐3 (31.0 °C). β was not crystallized in the pure enantiomers, and rac‐PPO. (3) αrac‐3 was crystallized at low cooling rates (~2 °C/min), whereas α‐2 of the two enantiomers was crystallized only with very rapid cooling (~10 °C/min). (4) Triple‐chain‐length structures were formed in αrac‐3, β′S‐3 (=β′R‐3), and β′rac‐3; α‐2 with a double‐chain‐length structure was formed in both enantiomers. These results indicate the importance of the relationship between subcell packing and glycerol conformation in the polymorphism and mixing characteristics of asymmetric unsaturated–saturated‐saturated mixed‐acid triacylglycerols.

Conformational Preferences of Glycerol in the Gas Phase and in Water

E-mail: ykkang@chungbuk.ac.krReceived January 2, 2012, Accepted January 5, 2012The conformational study of glycerol has been carried out using the M06-2X/cc-pVTZ level of theory in thegas phase and the SMD M06-2X/cc-pVTZ level of theory in water in order to understand its conformationalpreferences and solvation effects. Most of the preferred conformers of glycerol have two C

Microwave spectrum of glycerol: Observation of a tunneling chiral isomer

The microwave spectrum of the sugar alcohol glycerol (CH 2OHCHOHCH 2OH) has been measured over the frequency range 8.2–26.5 GHz with a pulsed-beam Fourier-transform microwave spectrometer. Five conformers of glycerol have been assigned and identified with the aid of ab initio electronic structure calculations. One of the higher energy conformers exhibits tunneling of the three hydroxyl groups along a chiral inversion pathway similar to the tunneling of the C2 polyol, ethylene glycol. Stark effect measurements were carried out on several of the lowest energy conformers to provide accurate determinations of the dipole moment components.

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.

Binary Phase Behavior of 1,3‐Dipalmitoyl‐2‐oleoyl‐sn‐glycerol and 1,2‐Dioleoyl‐3‐palmitoyl‐rac‐glycerol

Abstract1,3‐Dipalmitoyl‐2‐oleoyl‐sn‐glycerol (POP) and 1,2‐dioleoyl‐3‐palmitoyl‐rac‐glycerol (OOP) are two major molecular species that account for roughly half of the total triacylglycerols in palm oil. The binary phase behavior of a POP/OOP mixture plays an important role in the crystallization of palm oil. We conducted thermodynamic and kinetic studies of OOP and its mixtures with POP using differential scanning calorimetry and X‐ray diffraction with a conventional generator and synchrotron radiation. We found that OOP has two polymorphs, α as a metastable form and β′ as the most stable form, and that the two forms are stacked in a triple‐chain‐length structure. The POP/OOP mixtures exhibited immiscible eutectic natures in both their metastable and their most stable states, in contrast to POP/1,2‐dipalmitoyl‐3‐oleoyl‐rac‐glycerol and POP/1,3‐dioleoyl‐2‐palmitoyl‐sn‐glycerol mixtures, in which molecular compounds of a double‐chain‐length structure were formed. A time‐resolved synchrotron radiation X‐ray diffraction study undertaken during the cooling and heating processes indicated that the α and β′ forms of the POP and OOP fractions crystallized and melted in separate manners, and that crystallization of the β′ form and the polymorphic transformation from α to β′ of POP and OOP are promoted in the presence of another component. The absence of molecular compound crystals in the binary mixtures of POP/OOP is explained by taking into account the molecular interactions of acyl chain packing, glycerol conformation, and methyl end stacking, among which glycerol conformation appeared to be most influential.

Molecular orbital computations on lipids: an ab initio exploratory study on the conformations of glycerol and its fluorine congeners

In order to characterize the set of topologically probable glycerol-3-phosphate backbone conformers, ab initio calculations were performed on glycerol as a preliminary study. Ab initio calculations were also completed for selected congeners of glycerol, such as 1,2-difluoro-3-hydroxylpropane and 1,2,3-trifluoropropane, in order to model the effects of changing electron densities on the glycerol-3-phosphate backbone geometry. The results show that conformations having intramolecular hydrogen bonds have a lower relative energy. The O–H stretching frequencies computed in different glycerol conformations were largely dependent on ϕ i and ψ i backbone dihedrals.

Molecular orbital computations on lipids: modular numbering

Ab initio molecular orbital calculations have been carried out on selected phospholipids models to explore their structural properties. A modular numbering of constituent molecular components has been employed to effectively model all MDCA-predicted conformers. This system defines a phospholipid into five fragments consisting of the glycerol, the phosphate group (for phospholipids) and three substituents (X-group and two fatty acid chains). Each fragment is converted into distinct section of an internal coordinates matrix. The relative spatial orientation of all atoms in a given fragment will all be defined in an explicit manner. With a multi-lipid system, several of these modules may be used as a macro-module representing one lipid molecule. Subsequently, several macro-modules may be assembled into a lipid bilayer model. All macro-modules may then be combined to create an internal coordinate matrix describing a multi-lipid system without the loss of an explicit definition of every 3N-6 degree of freedom as well as intermolecular coupling and interaction. Molecular orbitals computations are completed on four selected conformations of glycerol. The results reveal that the dihedral values are not ideal as predicted by MDCA, implying that dihedrals properties are coupled to other inter-atomic interactions within the glycerol module.

Ab initio stochastic optimization of conformational and many-body degrees of freedom.

Moderate to large size molecules in solution have complex energy surfaces due to intramolecular (conformational) and intermolecular (many-body) interactions. The first principles Monte Carlo (FPMC) method, previously shown to effectively locate minimum-energy structures for systems with only many-body complexity, has been extended to address conformational flexibility by adding three new Monte Carlo move types. The primary advantage of the FPMC method is the ability to efficiently locate minimum energy structures of molecules with conformational flexibility in the presence of explicit solvent molecules using highly accurate quantum chemical calculations. The additions to FPMC were validated by studying conformers of glycerol, glyceraldehyde, and a large humic acid monomer unit. The structure of glyceraldehyde in the presence of one and two water molecules was also explored to demonstrate the power of FPMC to study systems with both conformational and many-body degrees of freedom.

Density Functional Calculation of Structural and Vibrational Properties of Glycerol

The conformational distribution of glycerol is still an open question both in gas and in liquid phase. Density functional calculations on different conformers of glycerol are reported and compared to the experimental infrared spectra of the gas and of the liquid. The experimental infrared spectra of gas and liquid glycerol are fitted by a linear combination of the single conformer ab initio spectra, obtaining the relative conformer concentrations. For the gas the results are in agreement with electron diffraction experiments and with molecular dynamics simulation data. The conformational distribution of glycerol in liquid phase is less accurate but always indicative. Some results about the role of the intramolecular hydrogen bonding in stabilization and in structural features of the conformers are discussed.

Crystal structure of a mixed chain diacylglycerol, 1-stearoyl-3-oleyl-glycerol.

Diacylglycerols composed of one saturated and one unsaturated chain make up the hydrophobic core of many biological membranes. We report here the first crystalline structure of such a mixed chain diacylglycerol. The mixed chain diacylglycerol, 1-stearoyl-3-oleyl-glycerol (1,3-SODG) was produced by solution isomerization of 1-stearoyl-2-oleyl-sn-glycerol. 1,3-SODG was isolated by flash chromatography and crystallized by slow evaporation in ethyl acetate at 4 degrees C. The melting point was 42.5 degrees C and the enthalpy was 18.0 kcal/mol. The crystal structure was determined to a final R factor of 0.127. Four molecules are present in the monoclinic unit cell: space group Cc, a = 9.362(2), b = 5.495(2), c = 77.92(3)A, beta = 91.46(2), V = 4007(4)A3, Z = 4, D = 1.032 g/cm3. The molecule forms an extended V-shaped conformation with the oleate and stearate chains coming off the two ends of the glycerol with an angle between their planes of 94 degrees. The two chains pack separately in individual layers and do not interact. The hydrogen bonds between the free hydroxyl group on the glycerol-2 position and the carbonyl oxygen on the oleyl chain of an adjacent molecule are 2.78 A in length and stabilize the glycerol layers. The stearoyl chain is roughly straight and packed in a triclinic parallel subcell. Both portions of the oleyl chain also pack in triclinic parallel packing. The torsion angle sequence along the double bond extending from the oleyl carbons C7 to C13 is tscsst (173 degrees, -152 degrees, -17 degrees, -157 degrees, -163 degrees, -178 degrees). This sequence is different from other monounsaturates. The torsion angle sequence around the glycerol region shows that the glycerol conformation is quite similar to the A conformer of racemic alpha monolaurin, and to 1,3-di-11-bromoundecanoyl glycerol, but completely unlike 1,2-diacyl-sn-glycerols. Thus the glycerol conformation appears to be driven by the hydrogen bond formation, which in turn determines whether chains interact or are segregated. In 1,3-diacylglycerols the two acyl chains point in different directions and are segregated. In 1,2-diacylglycerols the acyl chains lie side by side and must interact. When the two chains are quite different, then serious problems in packing occur, giving rise to disordered crystal packing. Probably as a result of the disordered chain packing in 1-stearoyl-2-oleyl-sn-glycerol (Di, L. and D.M. Small. 1993. J. Lipid Res. 34: 1611-1623) we were not successful in growing adequate crystals suitable for crystallographic structure determination of this 1,2 mixed chain diacylglycerol.

Conformational effects of metal salt binding to the polar head of phosphatidylcholines investigated by FTIR spectroscopy

FTIR spectra of DPPC multibilayers with metal salts incorporated (EuCl 3, Eu(NO 3) 3, UO 2(NO 3) 2, CaCl 2, Ca(NO 3) 2, MgCl 2, NaCl, NaNO 3, LiCl, LiNO 3), dry and hydrated, were investigated with particular attention to bands that are expected to be indicative of the conformation of choline, phosphate and acyl ester moieties. Some egg lecithin and DOPC complexes were also examined. The band at 875 cm −1, assigned to a mixed mode involving CN stretching of the choline chain with sc conformation in α 5 appears in all samples suggesting that no major conformational changes in α 5 occur on complexing. This is in agreement with the Raman spectroscopic work of Akutsu (H. Akutsu et al. (1986) Biochim. Biophys. Acta 854, 213–218). The symmetric CN(CH 3) 3 stretching mode gives rise to three bands near 930, 916 and 906 cm −1 which are assigned to distinct rotamers in α 4. Relative intensities of these bands permit an estimation of the rotamer populations. Metal salt binding favours the ap conformation in α 4. Exceptions to this general result appear with some nitrate complexes (Ca, UO 2) in dry multibilayer preparations in which the ac rotamers are dominant. However, in the aqueous dispersions the ap rotamers are dominant throughout. The critical examination of the phosphate bands shows the effects of cation binding to exceed the expected conformational effects and therefore it is not possible to infer anything definite about the latter. The behaviour of the antisymmetric PO 2 − stretching frequencies is discussed in terms of the nature of binding of the cations. The components of the carbonyl absorption exhibit, upon metal salt binding, pronounced changes of the relative intensities that are interpreted in terms of changes of subpopulations concerning the glycerol conformation. In dry multibilayer complexes with chlorides, the low frequency of the N(CH 3) 3 stretching indicates the interaction of chloride with the quaternary choline terminal group. Hydration influences the cation binding and its conformational consequences but, on the whole, the present results are in fair agreement with those obtained by NMR methods. The relation of the present results to those derived from NMR techniques is discussed.

Single crystal structure of a mixed-chain triacylglycerol: 1,2-dipalmitoyl-3-acetyl-sn-glycerol.

The mixed chain triacylglycerol 1,2-dipalmitoyl-3-acetyl-sn-glycerol was synthesized and its crystal structure was determined to a final reliability factor (R) of 0.11. Two molecules are present in the monoclinic unit cell: space group P2(1); a = 5.375(1), b = 8.286(2), c = 42.96(1) A; beta = 93.30(2) degrees, V = 1910 A3, rho = 1.065 g/cm3, and mu = 5.7 cm-1. The structure is a trilayer: a bilayer of palmitate chains packed in the beta mode (T parallel) and an interdigitated monolayer of acetates. The glycerol backbone and acetate extend roughly linearly from the sn-1 chain. The sn-2 chain bends around the C-2 carbon to lie next to the sn-1 chain. Analysis of the torsion angles indicate that the glycerol conformation of 1,2-dipalmitoyl-3-acetyl-sn-glycerol is markedly different from single acid triacylglycerols and from 1,2-diacyl-sn-glycerols but very similar to 1,2-dimyristoyl-sn-glycero-3-phosphocholine.

Ab initio studies of structural features not easily amenable to experiment: Part 41. Molecular geometries of hydrogen-bonded six-membered ring structures of glycerol

The geometries of eight conformations of glycerol, which contain hydrogen-bonded six-membered ring structures, were refined by the ab initio gradient method on the 4-21G level. The two most stable forms in 4-21G space are both of type γγ; the energy difference between them is 1 kcal mol −1, and the barrier to conversion is 1.3 kcal mol −1. In this and a previous study four conformations were found, including αγ-forms, whose energies are within approximately 2 kcal mol −1. The results suggest that the system represents a complex dynamic process. In addition to the interconversion of different conformers, which differ both in HOCC and OCCO torsional arrangements, the dynamic equilibrium of glycerol can involve the concerted exchange of the conformational arrangements of inequivalent CH 2OH-groups within a given conformer.

Ab initio studies of structural features not easily amenable to experiment: Part 26. Conformational analysis and study of the self-induced molecular asymmetry of glycerol

The structures of ten conformations of glycerol have been refined without any geometrical constraints by ab initio gradient relaxation on the 4-21G level. The compound can exist in forms which possess a symmetry plane, and in forms in which asymmetry is induced by intramolecular interactions. The two most stable forms are of type αγ (Fig. 1) and γγ (Fig. 9). The latter is characterized by a chair-type six-membered ring closed by hydrogen bonding. The calculations make it possible to estimate the positions of the hydrogen atoms which are not known from experimental work. Intramolecular hydrogen bonds are approximately oriented along the directions conventionally defined for σ-,π-and sp 3-type electron lone pairs on oxygen. The results also make it possible to describe the differences in local geometry which can cause the central carbon atom to be chiral. This is in contrast to presentations in which the chemical equivalence of the terminal CH 2OH groups in glycerol is correlated with the assumption that the central carbon atom is symmetric. It is postulated that, rather, the chemical equivalence of the terminal groups can involve the rapidly interconverting equilibrium of asymmetric, enantiomeric forms. The results thus demonstrate that details of molecular local geometries can be important in interpretations of chemical reactivity.

Glycerol Conformation and the Crystal Structure of Lipids II. A Further Study of Tripalmitin and Conformationally Fixed Analogs by Small-Angle X-Ray Diffraction and Reflection Electron Diffraction

Abstract The utility of analogs to glycerol-containing lipids based on the configurational isomers of cyclo-pentane-1,2,3-triol for ab initio crystal structure analysis via electron diffraction is assessed further. Such analogs of tripalmitin are examined with the natural triglyceride via low angle X-ray diffraction. The 1,3/2 (all-trans) and 1,2/3 (cis-trans) analogs give long spacing dimensions some 23 Å greater than found for the β-2 form of the natural compound, consistent with the long spacing observed for a β-3 form. The 1,2,3/0 (all-cis) analog gives a long spacing near that of the a-form of the triglyceride. Reflection electron diffraction measurements on the 1,3/2 and 1,2/3 analogs reveal a chain tilt near 60° for both and untilted chains for 1,2,3/0. A more accurate tilt determination from X-ray long spacings of the homologous series of 1,3/2 pseudotrilaurin to 1,3/2 pseudo-tripalmitin confirm the 67° tilt expected for the β-3 form. Therefore, given the same T,, methylene subcell, the molecular packing is very close to natural triglycerides. The subtle influences of the cyclopentane ring are overcome for 1,3/2 analogs based on stearic and arachidic acids. This emphasizes the utility of these structural analogs for ab initio crystal structure determinations of glycerol containing lipids.