Polyunsaturated hydrocarbon chains: computer study of the characteristics of intramolecular ordering of chains

The conformational properties of isolated unbranched hydrocarbon polyunsaturated molecules of cis-C18:4 and cis-C18:5 under theta-conditions (T = 298 K) were studied using Monte Carlo simulations. The conformations were generated by a computer (the continuum model was used; the energy of nonbonded interactions and torsion and electrostatic terms were taken into account). A molecule-fixed coordinate system with the axes along inertia tensor eigenvectors of each molecule conformation (principal axes of inertia) were used for the calculations. C-H and C-C bond orientation distribution functions rho and ordering parameters S with respect to the maximum molecule span axis were calculated. It was shown that the presence of five methylene-interrupted cis double bonds in C18 chain has a maximum effect on the intramolecular ordering properties of the molecule. The widths of function rho CH for pentaenes differed significantly from those of other C18-chains: the widths of function rho for all CH2-groups were nearly twice as large as that for C-H-bonds flanking the double bonds C=C, and roughly constant along the chain sequence. The mean magnitudes of magnitudes of SCH in the molecule decreased when unsaturation increased.     

A computer investigation of intramolecular bond ordering: unsaturated chains of natural lipids

Computer simulations (by the Monte Carlo method) of unperturbed linear hydrocarbon chains of 18-22 carbon atoms with methylene-interrupted cis-double bonds (18:0, 20:0, 22:0, 18:1delta11cis, 18:2delta9, 12cis, 18:3delta9, 12, 15cis, 20:3delta5, 8, 11cis, 20:4delta5, 8, 11, 14cis, 20:5delta5, 8, 11, 14, 17cis, 22:6delta4, 7, 10, 13, 16, 19cis), typical components of natural lipids, at a temperature of 298 K have been carried out. The conformations generated with continuous variation of all single C-C bond rotation angles within the (0, 360 degrees) range have been considered. The energy of nonbonded interactions and torsion and electrostatic terms have been taken into account. The intramolecular bond order parameters S(CC) and S(CH) about the axes along inertia tensor eigenvectors and bond orientation distributions rho(theta) with respect to the maximum molecule span axis (theta is the angle between the bond and the axis) have been calculated. The relation of the bond orientation distributions rho(theta) to the order parameters S are analyzed in terms of angles thetamax (a "geometric" factor, rho(thetamax) = max) and widths deltatheta of the distributions (factor of "fluctuations"). The results indicate that fluctuation factors depend on both the segment chemical structure and location in the chain; fluctuations increase from the centre of the chain towards the terminals, all things being equal. The two deltatheta values of C-H bonds flanking the cis-double bond are smaller than that obtained for adjacent CH2 groups by a factor of 1.5-2. Defining these properties is a necessary step to gaining a more complete understanding of polyunsaturated lipid hydrocarbon chains significance. The mean molecule magnitudes of ?S(CH)? decrease when unsaturation increases. The cis-double bond parameters S(CC) are found to be higher than those of adjacent single C-C bonds: the parameter S(CC) odd-even effect in the polyunsaturated molecules of such structure changes the "sign" between double bonds. The order parameter profiles -S(CH) of cis-18:1 and cis-18:2 obtained from the simulations (at the portion which corresponds to the double bonds location) are in qualitative agreement with experimental data on bilayers in the liquid-crystal phase. This has made possible the quantitative prognosis of the ordering properties of experimentally uninvestigated unsaturated lipids.     

Molecular Dynamics Investigation of Bond Ordering of Unsaturated Lipids in Monolayers

Molecular dynamics simulations of three model lipid monolayers of 2,3-diacyl-D-glycerolipids, that contained stearoyl (18:0) in the position 3 and oleoyl (18:9cis), linoleoyl (18:26cis), or linolenoyl (18:33cis) in the position 2, have been carried out. The simulation systems consisted of 24 lipid molecules arranged in a rectangular simulation cell, with periodic boundary conditions in the surface plane. 1 nanosecond simulations were performed at T = 295 K. C-C and C-H bond order parameter profiles and the bond orientation distributions about the monolayer normal have been calculated. The relation of the distributions to the order parameters was analyzed in terms of maxima and widths of the distributions. The cis double bond order parameter is found to be higher than those of adjacent single C-C bonds. The widths of the two distributions of C-H bonds of the cis double bond segment in di- and triunsaturated molecules are much smaller than that obtained for methylene group located between the double bonds. The bond orientation distribution function widths depend on both the segment location in the chain and the segment chemical structure.     

Effect of cholesterol on the bond ordering in hydrated unsaturated lipid bilayers

Molecular dynamics computer simulations of hydrated bilayers of unsaturated phosphatidylcholines in which double bonds are in the states: 18:0/18:1(n-9)cis (PC), 18:0/18:2(n-6)cis (PC), 18:0/18:3(n-3)cis (PC), 18:0/20:4(n-6)cis (PC), and 18:0/22:6(n-3)cis in the presence of cholesterol (40 mol%) and its absence have been performed. The simulation have been performed at 303 K and 1 atm, under the conditions corresponding to the experimentally observed liquid-crystalline state of the bilayer from phosphatidylcholine. The C-C and C-H bond order parameter profiles with respect to the bilayer normal and the C-C bond orientation distribution functions have been calculated. The widths of the functions and positions of their maxima have been determined. The dependence of these characteristics on the type of the bond, the degree of unsaturation of the chain, the presence of cholesterol in the bilayer, and the bond order parameters have been analyzed.     

Temperature dependence of conformational properties of natural lipid oligomer chains: computer simulation

The conformational properties of several oligomeric chain molecules at T = 278 and T = 403 K have been studied using Monte Carlo computer simulations. Hydrocarbon oligomers with methylene-interrupted cis double bonds in the main chain were considered. These oligomers are typical constituents of natural lipid molecules. The characteristics of the shape of C-H and C-C bond orientation distribution functions with respect to the principal axis of inertia of the chains and their temperature dependences were studied. It was found that the temperature sensitivity of not only the common geometric characteristics of the polyunsaturated chain is significantly reduced compared with the saturated one, but also that of local characteristics, i. e., the shape of each bond orientation distribution function of the polyunsaturated chain. The relationship between the properties of lipid polyunsaturated hydrocarbon chains and their functions in natural membrane systems, in particular their possible role in the stabilization or optimization of lipid-protein interactions, was discussed.     

Synthesis, structural studies, and cytostatic evaluation of 5,6-di-O-modified L-ascorbic acid derivatives

The 5,6-di-O-tosylated derivative of l-ascorbic acid was synthesized by selective protection and deprotection of 2,3- and 5,6-dihydroxy functional groups involving 5,6-ditosylation in the final step, while the novel 6-acetoxy, 6-hydroxy, and 6-chloro derivatives of 4,5-didehydro-l-ascorbic acid were obtained by reaction of ditosylated compound with nucleophilic reagents. The analysis of 3JH-4-H-5 homonuclear coupling constants shows that all l-ascorbic acid derivatives except for epoxy and 4,5-didehydro compounds exist in high population as gauche conformers across C-4-C-5 bonds, while 3JC-3-H-5 heteronuclear coupling constants in 4,5-didehydro derivatives indicate cis geometry along C-4-C-5 double bond. The X-ray crystal structure analysis of 2,3-di-O-benzyl-5,6-epoxy- and 5,6-isopropylidene-l-ascorbic acid shows that the oxygen atoms attached at positions 2 and 3 of the lactone ring are disposed in a synperiplanar fashion. Besides that, the dioxolane ring adopts half-chair conformation. The molecules of epoxy derivative are joined into infinite chains by one weak hydrogen bond of C-H...O type. Two O-H...O, and C-H...O hydrogen bonds link the molecules of 5,6-di-O-isopropylidene compound into two-dimensional network. 6-Chloro derivative of 2,3-di-O-benzyl-l-ascorbic acid showed the best cytostatic effects against all tested malignant tumor cells (IC50: approximately 18 microM).     

Properties of unsaturated phospholipid bilayers: Effect of cholesterol

Properties of hydrated unsaturated phosphatidylcholine (PC) lipid bilayers containing 40 mol % cholesterol and of pure PC bilayers have been studied. Various methods were applied, including molecular dynamics simulations, self-consistent field calculations, and the pulsed field gradient nuclear magnetic resonance technique. Lipid bilayers were composed of 18:0/18:1(n-9)cis PC, 18:0/18:2(n-6)cis PC, 18:0/18:3(n-3)cis PC, 18:0/20:4(n-6)cis PC, and 18:0/22:6(n-3)cis PC molecules. Lateral self-diffusion coefficients of the lipids in all these bilayers, mass density distributions of atoms and atom groups with respect to the bilayer normal, the C-H and C-C bond order parameter profiles of each phospholipid hydrocarbon chain with respect to the bilayer normal were calculated. It was shown that the lateral self-diffusion coefficient of PC molecules of the lipid bilayer containing 40 mol % cholesterol is smaller than that for a corresponding pure PC bilayer; the diffusion coefficients increase with increasing the degree of unsaturation of one of the PC chains in bilayers of both types (i.e., in pure bilayers or in bilayers with cholesterol). The presence of cholesterol in a bilayer promoted the extension of saturated and polyunsaturated lipid chains. The condensing effect of cholesterol on the order parameters was more pronounced for the double C=C bonds of polyunsaturated chains than for single C-C bonds of saturated chains.     

Langevin dynamics studies of unsaturated phospholipids in a membrane environment.

Computer simulations of three unsaturated phospholipids in a membrane environment have been carried out using Langevin dynamics and a mean-field based on the Marcelja model. The applicability of the mean-field to model unsaturated lipids was judged by comparison to available experimental NMR data. The results show that the mean-field methodology and the parameters developed for saturated lipids are applicable in simulations of unsaturated molecules, indicating that these simulations have good predictive capabilities. Single molecule simulations, each 100 ns in length, of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1-palmitoyl-2-elaidoyl-sn-glycero-3-phosphocholine (PEPC), and 1-palmitoyl-2-isolinoleoyl-sn-glycero-3-phosphocholine (PiLPC) reveal similarities between PEPC and DPPC. The presence of the trans double bond in PEPC has a minimum impact on the structural and dynamic properties of the molecule, which is probably the reason that isolated trans double bonds are rare in biological lipids. POPC exhibits different behavior, especially in the calculated average interchain distances, because of the cis double bond. The position of the two double bonds in PiLPC imparts special properties to the molecule.     

Average structural and motional properties of a diunsaturated acyl chain in a lipid bilayer: effects of two cis-unsaturated double bonds

Isolinoleic acid (18:2 delta 6,9) deuterated at 10 different positions was esterified to form 1-palmitoyl-2-isolinoleoyl-sn-glycero-3-phosphocholine (PiLPC), and the average structural and motional properties of the diunsaturated chain, in aqueous dispersions of PiLPC, were examined by 2H NMR spectroscopy. For each sample, 2H spectra were acquired over a temperature range of 1-40 degrees C and the quadrupolar splittings interpreted in terms of carbon-deuterium bond order parameters, SCD. Furthermore, definition of the average orientation of the C8 methylene unit with respect to the bilayer normal [Baenziger, J. E., Smith, I. C. P., Hill, R. J., & Jarrell, H. C. (1988) J. Am. Chem. Soc. 110, 8229-8231] provided sufficient information to calculate both the average orientations and the molecular order parameters, Smol (which reflects the amplitudes of motion), for the C6-C7 and the C9-C10 double bonds. The results indicate that both the motional freedom (reflected in the order profile) and the average structure (reflected in the orientation of carbon segments with respect to the bilayer normal) are strongly affected by the presence of two cis-unsaturated double bonds. The data were interpreted in terms of two possible models whereby, in each case, the chain adopts a conformation consistent with the low-energy conformation of 1,4-pentadiene [Applegate, K. R., & Glomset, J. A. (1986) J. Lipid Res. 27, 658-680] but undergoes a two-site jump between the conformations. The jump motion arises mainly from rotations about the C7-C8 and the C8-C9 single bonds that disorder the C8 and the C9-C10 segments (Smol = 0.15 and 0.08, respectively) but leave the C6-C7 double bond relatively immobile (Smol = 0.55; all at 40 degrees C). It is suggested that acyl chains containing three or more double bonds could not undergo a similar jump motion and therefore would be highly ordered and not "fluid" as is generally thought.     

Double coned inverse sandwich complexes [M-(η4-C4H4)-M′] of Gr-IA and Gr-IIA Metals: theoretical study of electronic of structure and second hyperpolarizability

Molecular interaction between dioxane and methanol involves certain polar and nonpolar bonding to form a one to one complex. Interatomic distances between hydrogen and oxygen within 3 Å have been considered as hydrogen bonding. Optimizations of the structures of dioxane-methanol complexes were carried out considering any spatial orientation of a methanol molecule around a chair/boat/twisted-boat conformation of dioxane. From 45 different orientations of dioxane and water, 23 different structures with different local minima were obtained and the structural characteristics like interatomic distances, bond angles, dihedral angles, dipole moment of each complex were discussed. The most stable structure, i.e., with minimum heat of formation is found to have a chair form dioxane, one O-H…O, and two C-H…O hydrogen bonds. In general, the O-H…O hydrogen bonds have an average distance of 1.8 Å while C-H…O bonds have 2.6 Å. The binding energy of the dioxane-methanol complex is found to be a linear function of number of O-H…O and C-H…O bonds, and hydrogen bond length. Graphical Abstract

Sixteen orientations of methanol around dioxane converge to six local minima including the global minima with one H-O…H and two C-H…O hydrogen bonds.     

Theoretical study of the triangular bonding complex formed by carbon tetrabromide, a halide, and a solvent molecule in the gas phase

MP2(full)/aug-cc-pVDZ(-PP) computations predict that new triangular bonding complexes (where X^? is a halide and H–C refers to a protic solvent molecule) consist of one halogen bond and two hydrogen bonds in the gas phase. Carbon tetrabromide acts as the donor in the halogen bond, while it acts as an acceptor in the hydrogen bond. The halide (which commonly acts as an acceptor) can interact with both carbon tetrabromide and solvent molecule (CH₃CN, CH₂Cl₂, CHCl₃) to form a halogen bond and a hydrogen bond, respectively. The strength of the halogen bond obeys the order CBr₄???Cl^? > CBr₄???Br^? > CBr₄???I^?. For the hydrogen bonds formed between various halides and the same solvent molecule, the strength of the hydrogen bond obeys the order C-H???Cl^? > C-H???Br^? > C-H???I^?. For the hydrogen bonds formed between the same halide and various solvent molecules, the interaction strength is proportional to the acidity of the hydrogen in the solvent molecule. The diminutive effect is present between the hydrogen bonds and the halogen bond in chlorine and bromine triangular bonding complexes. Complexes containing iodide ion show weak cooperative effects.

A new crystal form of beta-cyclodextrin-ethanol inclusion complex: channel-type structure without long guest molecules

A new crystal form of beta-cyclodextrin (beta-CD)[bond]ethanol[bond]dodecahydrate inclusion complex [(C(6)H(10)O(5))(7).0.3C(2)H(5)OH.12H(2)O] belongs to monoclinic space group C2 (form II) with unit cell constants a=19.292(1), b=24.691(1), c=15.884(1) A, beta=109.35(1) degrees. The beta-CD macrocycle is more circular than that of the complex in space group P2(1) [form I: J. Am. Chem. Soc. 113 (1991) 5676]. In form II, a disordered ethanol molecule (occupancy 0.3) is placed in the upper part of beta-CD cavity (above the O-4 plane) and is sustained by hydrogen bonding to water site W-2. In form I, an ethanol molecule located below the O-4-plane is well ordered because it hydrogen bonds to surrounding O-3[bond]H, O-6[bond]H groups of the symmetry-related beta-CD molecules. In the crystal lattice of form I, beta-CD macrocycles are stacked in a typical herringbone cage structure. By contrast, the packing structure of form II is a head-to-head channel that is stabilized at both O-2/O-3 and O-6 sides of each beta-CD by direct O(CD)...O(CD) and indirect O(CD)...O(W)...(O(W))...O(CD) hydrogen bonds. The 12 water molecules are disordered in 18 positions both inside the channel-like cavity of beta-CD dimer (W-1[bond]W-6) and in the interstices between the beta-CD macrocycles (W-7[bond]W-18). The latter forms a cluster that is hydrogen bonded together and to the neighboring beta-CD O[bond]H groups.     

On the conformational, physical properties and functions of polyunsaturated acyl chains

The conformational properties of the acyls of biological membranes--hydrocarbon chains with isolated cis double bonds--were studied by computer simulation. The Monte Carlo method was used, with continuous variation of bond rotation angles within the (0, 360 degree) range considered. It has been shown, that if all double bonds of molecules are separated only by one methylene group, and their number in the chain is maximum, the molecule is characterized by the highest equilibrium flexibility (at temperatures only encountered by biological systems) as compared to any similar molecules. It is such a structure which is inherent to docosahexaenoic acid. The above molecule coefficient that characterizes the temperature sensitivity of the molecule sizes is 10-times lower than that of a saturated chain. The polyunsaturated chain segment with high probability assumes the extended (in perfect crystal structures the 'angle iron-shaped') conformation when all the molecules are efficiently packed below the phase-transition temperatures. The annular lipid layer of embedded enzymes is assumed to be enriched with polyunsaturated fatty acid acyls. The above physical properties of polyunsaturated chains are bound to favour the maintenance of the proper conformational mobility of biomembrane enzymes, to relax the negative influence of environmental temperature changes on their activity. When freezing biological membranes they are bound to provide the molecule packing which is free of high tensions.     

Proline-containing beta-turns. IV. Crystal and solution conformations of tert.-butyloxycarbonyl-L-prolyl-D-alanine and tert.-butyloxycarbonyl-L-prolyl-D-alanyl-L-alanine

The conformations of the dipeptide t-Boc-Pro-DAla-OH and the tripeptide t-Boc-Pro-DAla-Ala-OH have been determined in the crystalline state by X-ray diffraction and in solution by CD, n.m.r. and i.r. techniques. The unit cell of the dipeptide crystal contains two independent molecules connected by intermolecular hydrogen bonds. The urethane-proline peptide bond is in the cis orientation in both the molecular forms while the peptide bond between Pro and DAla is in the trans orientation. The single dipeptide molecule exhibits a "bent" structure which approximates to a partial beta-turn. The tripeptide adopts the 4----1 hydrogen-bonded type II beta-turn with all trans peptide bonds. In solution, the CD and i.r. data on the dipeptide indicate an ordered conformation with an intramolecular hydrogen bond. N.m.r. data indicate a significant proportion of the conformer with a trans orientation at the urethane-proline peptide bond. The temperature coefficient of the amide proton of this conformer in DMSO-d6 points to a 3----1 intramolecular hydrogen bond. Taken together, the data on the dipeptide in solution indicate the presence (in addition to the cis conformer) of a C7 conformation which is absent in the crystalline state. The spectral data on the tripeptide indicate the presence of the type II beta-turn in solution in addition to the nonhydrogen-bonded conformer with the cis peptide bond between the urethane and proline residues. The relevance of these data to studies on the substrate specificity of collagen prolylhydroxylase is pointed out.     

Unique side chain conformation of a Leu residue in a triple-helical structure

Single crystal structures of host-guest peptides, (Pro-Hyp-Gly)(4)-Leu-Hyp-Gly-(Pro-Hyp-Gly)(5) (LOG1) and (Pro-Hyp-Gly)(4)- (Leu-Hyp-Gly)(2)-(Pro-Hyp-Gly)(4) (LOG2), have been determined at 1.6 A and 1.4 A resolution, respectively. In these crystals, the side chain conformations of the Leu residues were (+)gauche-trans. This conformational preference for the Leu side chain in the Leu-Hyp-Gly sequence was explained by stereochemical considerations together with statistical analysis of Protein Data Bank data. In the (+)gauche-trans conformation, the Leu side chain can protrude along the radial direction of the rod-like triple-helical molecule. One strong hydrophobic interaction of the Leu residue was observed between adjacent molecules in the LOG2 crystal. Because the Leu-Hyp-Gly sequence is one of the most frequently occurring triplets in Type I collagen, this strong hydrophobic interaction can be expected in a fibrillar structure of native collagen. All the Leu residues in the asymmetric unit of the LOG1 and LOG2 crystals had water molecules hydrogen bonded to their NH. These water molecules made three additional hydrogen bonds with the Hyp OH, the Gly O[double bond]C, and a water molecule in the second hydration shell, forming a tetrahedral coordination of hydrogen bonds, which allows a smaller mean-square displacement factor of this water oxygen atom than those of other water molecules. These hydrogen bonds stabilize the molecular and packing structures by forming one O[double bond]C(Gly)---W---OH(Hyp) intra-molecular linkage and two NH(Leu)---W---O[double bond]C(Gly) and NH(Leu)---W---OH(Hyp) inter-molecular linkages.     

Conformational flexibility in a triazole nucleoside derivative: 4-cyano-5-cyanomethyl-1-(2,3,5-tri-O-acetyl-beta-D-ribofuranosyl)-1,2,3-triazole

The crystal-structure determination of the molecular structure of the hydrophobic compound, 4-cyano-5-cyanomethyl-1-(2,3,5-tri-O-acetyl-beta-D-ribofuranosyl)-1,2,3-triazole, C16H17N5O7, provides us with two different conformations of ribofuranosyl moieties [(C2'-exo, C3'-endo) and C2'-exo] with two markedly different N-glycosidic angles. There are two molecules in the asymmetric unit of the crystal and the overall stereochemistry of the molecules are influenced predominantly by weak intramolecular bifurcated and trifurcated hydrogen bonds of the type C-H...O and C-H...N, where endo-H atoms attached to C2' and C3' are involved. The molecules in the crystal are interconnected with longer intermolecular bonds of the same type. There are empty channels (occupying 14.0% of the whole volume of the unit cell), which are extended along b-axis of the entire crystal.     

Glutathione conjugation of synthetic steroids in isolated rat hepatocytes

When designing steroid drugs with multiple double bonds, the influence of glutathione conjugation on the pharmacodynamics of drug action should be considered. We have examined the effect of canrenone, a mineralocorticoid receptor antagonist, on isolated rat hepatocytes and found that 1 mM canrenone injured the hepatocytes during shortterm incubation at 37 C, while an analogue of canrenone which bears 4 double bonds (delta 1,11-CAN) did not manifest such toxicity. To further pursue this, we prepared testosterone analogues comprising multiple double bonds as model compounds, and incubated them with freshly isolated rat hepatocytes. The viability of the hepatocytes was not influenced by any of the steroids, but some of them having a double bond at the C6-C7 position reduced the cellular glutathione levels. This was found to be due to conjugation of glutathione to the C7 position of the steroid molecule, and the rate of conjugation was accelerated when an additional double bond was introduced at C1-C2 or C11-C12 positions. The finding is interesting as glucuronidation or sulfation are common as conjugation processes of steroids.     

Non-aromatic stabilised form of 3,4-difluoropyrrole at triosmium clusters: N-H and C-H versus C-F activation

Reaction of 3,4-difluoropyrrole with the labile triosmium cluster [Os₃(CO)₁₀(CH₃CN)₂] affords products in which C-H, N-H and C-F bonds are cleaved under mild conditions. C-H and N-H bonds are cleaved to give [Os₃H(NCCFCFCH₂)(CO)₁₀] (1) a non-aromatic stabilised form of 3,4-difluoropyrrole. Thermolysis of 1 affords in moderate yields the compounds [Os₃H₂(CCCFCHNH)(CO)₉] (2) and [Os₃H₂(NCHCFCFC)(CO)₉] (3). For compound 3, C-H and N-H bonds are cleaved with concomitant migration of H atoms to the metal framework. In contrast, for compound 2 activation of C-H and C-F bonds leads to coordination of the ligand through the carbon atoms, acting as a four-electron donating species.     

Density functional theory investigation of cocaine water complexes

Twenty cocaine–water complexes were studied using density functional theory (DFT) B3LYP/6-311++G** level to understand their geometries, energies, vibrational frequencies, charge transfer and topological parameters. Among the 20 complexes, 12 are neutral and eight are protonated in the cocaine-water complexes. Based on the interaction energy, the protonated complexes are more stable than the neutral complexes. In both complexes, the most stable structure involves the hydrogen bond with water at nitrogen atom in the tropane ring and C?=?O groups in methyl ester. Carbonyl groups in benzoyl and methyl ester is the most reactive site in both forms and it is responsible for the stability order. The calculated topological results show that the interactions involved in the hydrogen bond are electrostatic dominant. Natural bond orbital (NBO) analysis confirms the presence of hydrogen bond and it supports the stability order. Atoms in molecules (AIM) and NBO analysis confirms the C-H?·?·?·?O hydrogen bonds formed between the cocaine-water complexes are blue shifted in nature.