Conformational domino effect in saccharides. 2. Anomeric configuration control

A series of alkyl beta-D-glucopyranosyl-(1-->6)-alpha-D-glucopyranosides were synthesized and analyzed by NMR and CD techniques. As in their beta-anomer series, the rotational populations of the hydroxymethyl group involved in the interglycosidic linkage (torsion angle omega) are shown to depend on the aglycon and the solvent. However, for this alpha-anomer series the rotational dependence arises directly from steric effects. Correlations between rotational populations and molar refractivity (MR) steric parameters, but not Taft's steric parameters (beta-anomers), of the alkyl substituents were observed. The conformational domino effect previously predicted from alkyl beta-(1-->6)-diglucopyranosides is now supported by the conformational properties of their alpha-anomers, the anomeric configuration controlling the domino effect. In addition, the rotational populations around the C5'-C6' bond (torsion angle omega') depend weakly on the structure of the aglycon and the anomeric configuration.     

Stereochemical properties of glucosyl sulfoxides in solution

A series of alkyl β-glucosyl sulfoxides were synthesized and characterized in order to study their stereochemical properties. The dependence of the aglycon, solvent and absolute configuration of the sulfinyl group on the conformational properties around the glucosidic and C5-C6 (hydroxymethyl group) bonds were studied. The results for R(S) sulfoxides show linear correlations between the rotamer populations of the hydroxymethyl group and the corresponding Taft's steric parameter (E(S)) of the alkyl group attached to the sulfinyl group in polar and apolar solvents, an increase in the absolute value of E(S) leading to an increase in the gt population. In addition, NOE experiments reveal that as the bulkiness of the alkyl group increases the population of the g- rotamer increases, the latter stabilized by the exo-anomeric effect. These results are in complete agreement with the participation of the exo-anomeric effect in both conformational properties of R(S) sulfoxides. Sulfoxides with the S(S) configuration show different behavior to their R(S) epimers; thus, an increase in the E(S) value of the alkyl group leads to similar or lower gt populations in apolar solvents and to increases in gt in polar solvents. Their NOE studies reveal a conformational equilibrium (in polar and apolar solvents) between g- and g+, dependent on the size of the alkyl group R attached to the sulfinyl group. All these results for both epimers support the general hypothesis that the exo-anomeric effect modifies the conformation of the hydroxymethyl group, fulfills the stereoelectronic requirements, and shows dependence on the solvent.     

Conformational properties of glucosyl-thioglucosides and their S-oxides in solution

A stereochemical study of a series of alkyl glucosyl-β-(1→6)-thioglucosides and their S-oxides by means of nuclear magnetic resonance and circular dichroism revealed that the populations around the thioglucosidic bond (ring I) as well as those of the interglycosidic linkage ω depend on the aglycone, the solvent and, in the S-oxides, on the absolute configuration of the sulfur atom. The results for the thio-disaccharides showed the strong influence of the solvent polarity on the conformational preferences of the interglycosidic bond. In polar solvents, the magnitudes of the rotamer populations, P_gg and P_gt, remained practically constant through the series, while in non-polar solvents a clear predominance of gt conformation was observed as well as the influence of the aglycone on the conformational equilibrium. The results for both (S_S)- and (R_S)-alkyl thiogentiobiosyl S-oxide series showed a clear predominance of the gt rotamer, P_gt always having a higher magnitude in the latter series than in the former. Both series exhibited linear correlations between interglycosidic P_gg and P_gt and Taft’s steric parameter (E_S) for the alkyl group attached to the sulfinyl group, especially in non-polar solvents. The stereochemical study around the C1–S bond established that the flexibility around this linkage depends on aglycone size, solvent polarity, and the absolute configuration of the sulfur, derivatives of the S_S series showing higher flexibility in both polar and non-polar media. The conformational properties of these compounds in solution are explained in terms of stereoelectronic, steric, and solvent effects.     

Hydroxymethyl rotamer populations in disaccharides

Sixteen methyl glucopyranosyl glucopyranoside disaccharides (methyl beta-d-Glcp(p-Br-Bz)-(1-->x)-beta/alpha-d-Glcp) containing beta-glycosidic linkages (1-->2, 1-->3, 1-->4, and 1-->6) were synthesized and analyzed by means of CD and NMR spectroscopy in three different solvents. For each of these four types of disaccharides, a correlation was observed between the hydroxymethyl rotational populations around the C5-C6 bond of the glucopyranosyl residue II with the substituents and the anomeric configuration of the methoxyl group in residue I, as well as with the solvent. Nonbonded interactions, the stereoelectronic exo-anomeric effect, and hydrogen bonding were found to be responsible for the observed rotameric differences. Whereas the rotational populations of the (1-->6)-linked disaccharides are mainly dependent on the exo-anomeric effect, the (1-->2)-bonded disaccharides are strongly dependent on the anomeric configuration at C1, and the (1-->3)- and (1-->4)-linked disaccharides are mainly dependent on the substituents and the solvent. The population of the gt rotamer decreases as nonbonded interactions increase but increases as the exo-anomeric effect becomes greater, as well as in the presence of intramolecular hydrogen bonding to the endocyclic oxygen O5'. Comparison of the hydroxymethyl rotational preferences between our model disaccharides revealed a dependence on the glycosidic linkage type. Thus the population of the gg and gt rotamers decreases/increases from (1-->2)- (beta series), to (1-->6)-, to (1-->2)- (alpha series), to (1-->4)-, and to (1-->3)-bonded disaccharides respectively, while the tg rotamer population remains almost constant (around 20%), except for the (1-->3)- and (1-->4)-linked disaccharides with the intramolecular hydrogen bonding to O5', where this population decreases to 10%.     

A conformational study of the trisaccharide beta-D-Glcp-(1-->2)[beta-D-Glcp-(1-->3)]alpha-D-Glcp-OMe by NMR NOESY and TROESY experiments, computer simulations, and X-ray crystal structure analysis

Proton-proton cross-relaxation rates have been measured for the trisaccharide beta-D-Glcp-(l --> 2)[beta-D-Glcp-(1 --> 3)]alpha-D-Glcp-OMe in D2O as well as in D2O/[D6]DMSO 7:3 solution at 30 degrees C by means of one-dimensional NMR pulsed field gradient 1H,1H NOESY and TROESY experiments. Interatomic distances for the trisaccharide in D2O were calculated from the cross-relaxation rates for two intraresidue and three interglycosidic proton pairs, using the isolated spin-pair approximation. In the solvent mixture one intraresidue and three interglycosidic distances were derived without the use of a specific molecular model. In this case the distances were calculated from the cross-relaxation rates in combination with "model-free" motional parameters previously derived from 13C relaxation measurements. The proton-proton distances for interglycosidic pairs were compared with those averaged from Metropolis Monte Carlo and Langevin Dynamics simulations with the HSEA, PARM22, and CHEAT95 force fields. The crystal structure of the trisaccharide was solved by analysis of X-ray data. Interresidue proton pairs from the crystal structure and those observed by NMR experiments were similar. However, the corresponding proton-proton distances generated by computer simulations were longer. For the (1 --> 2) linkage the glycosidic torsion angles of the crystal structure were found in a region of conformational space populated by all three force fields, whereas for the (1 --> 3) linkage they occupied a region of low population density, as seen from the simulations.     

Structure characterization of flavonoid O-diglycosides by positive and negative nano-electrospray ionization ion trap mass spectrometry.

Isomeric flavonoid O-diglycosides were analyzed by positive and negative nano-electrospray ionization (ESI) ion trap mass spectrometry (ITMS) in order to evaluate whether the two most common interglycosidic linkage types, i.e. 1 --> 2 and 1 --> 6, found for glycosides containing a rhamnosylglucose glycan part can be differentiated. In the positive ion mode the degree of internal glucose residue loss was found to be strongly dependent on the aglycone type and was very pronounced for aglycones of the flavanone type. The relative abundance of the Y-type ions formed by fragmentation at glycosidic bonds only allows one to infer the interglycosidic linkage types in the case of flavone O-diglycosides. In contrast, the negative ion mode makes a clear differentiation between a rutinoside (1 --> 6) and a neohesperidoside (1 --> 2) glycan residue possible for all aglycone types. The neohesperidose-containing compounds could be characterized by additional product ions. When the compounds were dissolved in pure methanol a molecular radical ion was found to be the base peak in nano-ESI.     

A generic rotamer model to explain the temperature dependence of BSA protein fluorescence

Protein fluorescence signals essential information about the conformational dynamics of proteins. Different types of intrinsic fluorophores reflect different protein local or global structural changes. Bovine Serum Albumin (BSA) is a transport protein that contains two intrinsic fluorophores: Tryptophan134 (Trp134) and Tryptophan213 (Trp213). This protein displays an interesting temperature dependence of the tryptophan fluorescence. However, the molecular mechanism of the temperature dependence is still unclear. In this work, we propose a generic rotamer model to explain this phenomenon. The model assumes the presence of rotamer-specific fluorescence lifetimes. The fluorescence temperature dependence is caused by the population shifts between different rotamers due to thermal effects. As a proof of concept, we show that the tryptophan's two fluorescence lifetimes (𝜏₁ = 0.4–0.5 ns and 𝜏₂ = 2-4 ns) are sufficient to qualitatively explain the fluorescence intensity change at different temperatures, both in buffer solution (water) and in the protein. To computationally verify our rotamer hypothesis, we use an all-atom molecular dynamics simulation to study the effects of temperature on the two tryptophans' rotamer dynamics. The simulations show that Trp134 is more sensitive to temperature, consistent with experimental observations. Overall, the results support that the temperature dependence of fluorescence in the protein BSA is due to local conformational changes at the residue level. This work sheds light on the relationship between tryptophan's rotamer dynamics and its ability to fluorescence.     

New insights into the conformational properties of α-C-glucosides

A series of alkyl α-d-C-glucopyranosides were synthesized and their conformational properties analyzed by CD and NMR spectroscopy. The conformational analysis revealed that the hydroxymethyl group populations (torsion angle ω, O1–C1–C2–O2) and those around the C-glucopyranosidic bond (torsion angle Φ; O2–C6–C7–C8) depend on the structural nature of the C-aglycon. The gt and the exo–syn populations increased as the C-aglycon became more substituted. Linear correlations between these rotational populations and proton chemical shifts versus the Taft’s steric parameters revealed the significant role of the C-aglycon in the overall conformation of C-glucosides. The stereoelectronic exo-deoxoanomeric effect, affecting the rotation of the hydroxymethyl group, becomes more important as the steric hindrance of motion increases. A pseudo-anomer rotational comparison study was also performed.     

On the magnetic non-equivalence of methylene protons in some propane derivatives, and its variation with solvent and temperature

The magnetic non-equivalence, δ ab, of methylene protons in 1,2-disubstituted and 1,2,3-trisubstituted propanes (same substituent) shows a marked dependence on solvent and temperature that allows a correlation with conformational equilibrium. Results indicate that symmetry is a necessary, but not a sufficient, condition for observation of δ ab. Factors that affect rotamer population such as medium, temperature, and nature of substituents, contribute substantially to the magnitude of δ ab.     

Enzymatic α(1→2)-l-fucosylation: investigation of the specificity of the α(1→2)-l-galactosyltransferase from Helix pomatia

The α(1→2)-l-galactosyltransferase from Helix pomatia transfers an l-fucosyl residue from GDP-l-Fucose to a terminal, non-reducing d-galactopyranosyl moiety of an oligosaccharide. The extent of the enzyme's specificity towards the stereochemistry at the d-galactopyranosyl anomeric centre, the site of interglycosidic linkage and the nature of the subterminal oligosaccharide residue has been investigated using HPAEC-PAD and MALDI-TOF technology. This α(1→2)-l-galactosyltransferase is specific for d-galactopyranosyl β-linkages, independent of the site of the interglycosidic linkage and aglycone configuration and with limited specificity for the nature of the subterminal sugar residue.     

Hindered rotation in five-membered cyclic nitrosamines: A 13C NMR study

The equilibrium rotamer populations and N? N rotational barriers of N-nitrosopyrrolidine (1), N-nitrosothiazolidine (2), N-nitrosooxazolidine (3) and their 2-methyl derivatives, 4, 5 and 6, were determined by ¹³C NMR spectroscopy. While equal rotamer populations occur in 1 and 2, the E rotamers predominate in the other four compounds, with the highest percentage (92%) of E rotamer occurring in N-nitroso-2-methyloxazolidine (6). The average barrier to N? N bond rotation varies over a range of 4.1 kcal mol^?1in these compounds, decreasing in the order N-nitrosopyrrolidine > N-nitrosothiazolidine > N-nitrosooxazolidine. The compounds which contain an exocyclic 2-methyl group have average rotational barriers which are 0.1–0.9 kcal mol^?1 higher than those of the corresponding unmethylated derivatives. The results are interpreted in terms of the relative effects of steric hindrance by the 2-methyl substituents and electron induction by the heterocyclic sulfur and oxygen atoms on both the rotamer populations and the N? N rotational barriers.     

Restricted rotation in unbridged sandwich complexes: rotational behavior of closo-[Co(eta 5-NC4H4)(C2B9H11)] derivatives

Rotation about the centroid/metal/centroid axis in ferrocene is facile; the activation energy is 1-5 kcal mol(-1). The structurally similar sandwich complexes derived from closo-[3-Co(eta5-NC4H4)-1,2-C2B9H11] (1) have a different rotational habit. In 1, the cis rotamer in which the pyrrolyl nitrogen atom bisects the carboranyl cluster atoms is 3.5 kcal mol(-1) more stable in energy than the rotamer that is second lowest in energy. This cis rotamer is wide, spanning 216 degrees , and may be split into three rotamers of almost equal energy by substituting the N and the carboranyl carbon atoms adequately. To support this statement, closo-[3-Co(eta5-NC4H4)-1,2-(CH3)2-1,2-C2B9H9] (2), closo-[3-Co(eta5-NC4H4)-1,2-(mu-CH2)3-1,2-C2B9H9] 3, 2-->BF3, and 3-->BF3 have been prepared. Two rotamers are found at low temperature for 2-->BF(3) and 3-->BF3. Compounds 2, 3, and 1-->BF3 behave similarly to 1. Rotational energy barriers and the relative populations of the different energy states are calculated from 1H DNMR spectroscopy (DNMR, dynamic NMR). These results agree with those of semiempirical calculations. Without exception, the cis rotamer is energetically the more stable. The fixed conformation of 1 assists in elucidating the rotational preferences of the [3,3'-Co(1,2-C2B9H11)2]- ion in the absence of steric hindrance; the [3,3'-Co(1,2-C2B9H11)2]- ion is commonly accepted to present a cisoid orientation. Complex 1 is electronically similar to the [3,3'-Co(1,2-C2B9H11)2]- ion. Both have heteroatoms in the pi ligands, and they have the same electronegativity difference between the constituent atoms. This leads to a view of the [NC4H4]- as [7,8-C2B9H11]2- ion, with no steric implications. Therefore the [3,3'-Co(1,2-C2B9H11)2]- ion should be considered to have a cisoid structure, and the different rotamers observed to be the result of steric factors and of the interaction of the counterion with either B-H groups and/or ancillary ligands. The rotamer adopted is the one with the atoms holding the negative charges furthest apart.     

Substituent Effects And Structure-Reactivity Relationship of Organophosphorus Compounds

To evaluate the substituent effect in organophosphorus compounds, a series of model compounds, namely 4-substituted-2,6,7-trioxa-1-phosphabicyclo[2.2.2] octane-1-oxides, alkyl hydrogen p-substituted phenyl-phosphonates, dialkyl p-substituted phenylphosphonates, as well as alkyl hydrogen alkylphosphonates, were synthesized and studied. Since in these compounds the substituents are located far away from reaction centre and the contribution of the steric effect of substituents can thus be eliminated, the substituent polar effect was evaluated based on ³¹P NMR, pKa and charge density of phosphoryl oxygen of these compounds calculated by the quantum mechanies MNDO method. The results showed that the polar effects of substituent in carboxylic and organophosphorus esters are similar, and the variation in polar effect among the alkyl groups is not significant. In the meantime, some steric parameters E_s^p of substituents were suggested for organophosphorus compounds, which are different from the Taft's E_s and Charton's υ parameters^[1,2].     

Carbohydrate solution simulations: producing a force field with experimentally consistent primary alcohol rotational frequencies and populations

We present a CHARMM Carbohydrate Solution Force Field (CSFF) suitable for nanosecond molecular dynamics computer simulations. The force field was derived from a recently published sugar parameter set.1 Dihedral angle parameters for the primary alcohol as well as the secondary hydroxyl groups were adjusted. Free energy profiles of the hydroxymethyl group for two monosaccharides (beta-D-glucose and beta-D-galactose) were calculated using the new parameter set and compared with similar force fields. Equilibrium rotamer populations obtained from the CSFF are in excellent agreement with NMR data (glucose gg:gt:tg approximately 66:33:1 and galactose gg:gt:tg approximately 4:75:21). In addition, the primary alcohol rotational frequency is on the nanosecond time scale, which conforms to experimental observations. Equilibrium population distributions of the primary alcohol conformers for glucose and galactose are reached within 10 nanoseconds of molecular dynamics simulations. In addition, gas phase vibrational frequencies computed for beta-D-glucose using this force field compare well with experimental frequencies. Carbohydrate parameter sets that produce both conformational energies and rotational frequencies for the pyranose primary alcohol group that are consistent with experimental observations should allow for increased accuracy in modeling the flexibility of biologically important (1-6)-linked saccharides in solution.     

Free energy surfaces for the alpha(1 --> 4)-glycosidic linkage: implications for polysaccharide solution structure and dynamics

We present a potential of mean force surface for rotation about phi and psi dihedral angles of the alpha(1 --> 4)-glycosidic linkage in the maltose disaccharide (4-O-alpha-d-glucopyranosyl-d-glucopyranose) in aqueous solution. Comparison of the vacuum and solution free energy surfaces for maltose shows the principal effects of water to be an increase in the rotational freedom of the alpha(1 --> 4) linkage brought about by lowering the energy barrier for syn to anti conformational changes as well as expansion of the range of low-energy phi,psi conformations. This free energy analysis thus provides a thermodynamic and conformational rationale for the effects of water on alpha(1 --> 4)-linked polysaccharides and carbohydrate glasses.     

Synthesis, inhibitory effects on nitric oxide and structure-activity relationships of a glycosphingolipid from the marine sponge Aplysinella rhax and its analogues

The novel glycosphingolipid, β-D-GalNAcp(1-->4)[α-D-Fucp(1-->3)]-β-D-GlcNAcp(1-->)Cer (A), isolated from the marine sponge Aplysinella rhax has a unique structure, with D-fucose and N-acetyl-D-galactosamine moieties attached to a reducing-end N-acetyl-D-glucosamine through an α1-->3 and β1-->4 linkage, respectively. We synthesized glycolipid 1 and some non-natural di- and trisaccharide analogues 2-6 containing a D-fucose residue. Among these compounds, the natural type showed the most potent nitric oxide (NO) production inhibitory activity against LPS-induced J774.1 cells. Our results indicate that both the presence of a D-Fucα1-3GlcNAc-linkage and the ceramide aglycon portion are crucial for optimal NO inhibition.     

The conformational behaviour and P-selectin inhibition of fluorine-containing sialyl LeX glycomimetics

A combination of experimental J/NOE NMR data with molecular mechanics and dynamics calculations has been used to examine the conformational behaviour and assign the configuration of synthetically prepared epimeric 3-carboxymethyl-O-Gal-(1-->1)-alpha-Man-fluoro-C-glycosides. It is shown that the population distributions around the glycosidic linkages strongly depend on the configuration at the fluorinated carbon of the pseudoacetal residue. It is also shown that these compounds resemble the inhibition ability of sialyl LeX towards P-selectin.     

Solvent-dependent stabilization of the E configuration of propargylic secondary amides

Secondary amides typically exist 98-99% in the Z rotamer to avoid steric repulsion between the substituent on the carbonyl carbon and the nitrogen. In contrast, secondary amide 3a displays 24% E rotamer at room temperature in aqueous solution. The analogous ester displays 6% E rotamer in chloroform, which suggests that the relatively high E conformer population observed for 3a in water results in part from the low steric bulk of the sp-hybridized carbons and in part from the hydrophobic effect.