Conformational Flexibility and Dynamics of Two (1→6)‐Linked Disaccharides Related to an Oligosaccharide Epitope Expressed on Malignant Tumour Cells

The conformational flexibility and dynamics of two (1→6)‐linked disaccharides that are related to the action of the glycosyl transferase GnT‐V have been investigated. NMR NOE and T‐ROE spectroscopy experiments, conformation‐dependent coupling constants and molecular dynamics (MD) simulations were used in the analyses. To facilitate these studies, the compounds were synthesised as α‐d‐ [6‐¹³C]‐Manp‐OMe derivatives, which reduced the ¹H NMR spectral overlap and facilitated the determination of two‐ and three‐bond ¹H,¹H, ¹H,¹³C and ¹³C,¹³C‐coupling constants. The population distribution for the glycosidic ω torsion angle in α‐d‐ Manp‐(1→6)‐α‐d‐ Manp‐OMe for gt/gg/tg was equal to 45:50:5, whereas in α‐d‐ Manp‐OMe it was determined to be 56:36:8. The dynamic model that was generated for β‐d‐ GlcpNAc‐(1→6)‐α‐d‐ Manp‐OMe by MD simulations employing the PARM22/SU01 CHARMM‐based force field was in very good agreement with experimental observations. β‐d‐ GlcpNAc‐(1→6)‐α‐d‐ Manp‐OMe is described by an equilibrium of populated states in which the ? torsion angle has the exo‐anomeric conformation, the ψ torsion angle an extended antiperiplanar conformation and the ω torsion angle a distribution of populations predominantly between the gauche–trans and the gauche–gauche conformational states (i.e., gt/gg/tg) is equal to 60:35:5, respectively. The use of site‐specific ¹³C labelling in these disaccharides leads to increased spectral dispersion, thereby making NMR spectroscopy based conformational analysis possible that otherwise might be difficult to attain.     

Conformation analysis of d‐glucaric acid in deuterium oxide by NMR based on its JHH and JCH coupling constants

d ‐Glucaric acid (GA) is an aldaric acid and consists of an asymmetric acyclic sugar backbone with a carboxyl group positioned at either end of its structure (i.e., the C1 and C6 positions). The purpose of this study was to conduct a conformation analysis of flexible GA as a solution in deuterium oxide by NMR spectroscopy, based on J‐resolved conformation analysis using proton–proton (³J_HH) and proton–carbon (²J_CH and ³J_CH) coupling constants, as well as nuclear overhauser effect spectroscopy (NOESY). The ²J_CH and ³J_CH coupling constants were measured using the J‐resolved heteronuclear multiple bond correlation (HMBC) NMR technique. NOESY correlation experiments indicated that H2 and H5 were in close proximity, despite the fact that these protons were separated by too large distance in the fully extended form of the chain structure to provide a NOESY correlation. The validities of the three possible conformers along the three different bonds (i.e., C2? C3, C3? C4, and C4? C5) were evaluated sequentially based on the J‐coupling values and the NOESY correlations. The results of these analyses suggested that there were three dominant conformers of GA, including conformer 1 , which was H2H3:gauche, H3H4:anti, and H4H5:gauche; conformer 2 , which was H2H3:gauche, H3H4:anti, and H4H5:anti; and conformer 3 , which was H2H3:gauche, H3H4: gauche, and H4H5:anti. These results also suggested that all three of these conformers exist in equilibrium with each other. Lastly, the results of the current study suggested that the conformational structures of GA in solution were ‘bent’ rather than being fully extended. Copyright © 2016 John Wiley & Sons, Ltd.     

Conformational analysis ofortho-substituted diphenyl ethers and diphenylmethanes with linear substituents

Conformational analysis of di-ortho-substituted diphenylmethanes and Biphenyl ethers containing I, CCH, and CCCCH substituents was carried out by the molecular mechanics method using the MM3 program. Several minima on the potential energy surface, which correspond to thegg, gt, tg, andort conformations, were found. An increase in the length of the linear substituent results in a substantial decrease in the difference in the relative energies of conformers. Barriers to conformational transitions between thegt, tg, andort conformers are less than 2 kcal mol^–1. The transitionort-gg requires expenditure of energy of up to 5 kcal mol^–1. Two valleys of centrosymmetric pairs of thegt, tg, andort conformers are separated by a barrier of up to 6 kcal mol^–1.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No, 12, pp, 2882–2885, December, 1996.     

Oligonucleotide Analogues with Integrated Bases and Backbone. Part 13

The self‐complementary UA and AU dinucleotide analogues 41 – 45, 47, 48 , and 51 – 60 were prepared by Sonogashira coupling of 6‐iodouridines with C(5′)‐ethynylated adenosines and of 8‐iodoadenosines with C(5′)‐ethynylated uridines. The dinucleotide analogues associate in CDCl₃ solution. The C(6/I)‐unsubstituted AU dimers 51 and 54 prefer an anti‐oriented uracilyl group and form stretched linear duplexes. The UA propargyl alcohols 41 and 43 – 45 possess a persistent intramolecular O(5′/I)? H???N(3/I) H‐bond and, thus, a syn‐oriented adeninyl and a gt‐ or tg‐oriented ethynyl moiety; they form corrugated linear duplexes. All other dimers form cyclic duplexes characterized by syn‐oriented nucleobases. The preferred orientation of the ethynyl moiety (the C(4′),C(5′) torsion angle) defines a conformation between gg and one where the ethynyl group eclipses O(4′/I). The UA dimers 42, 47 , and 48 form Watson–Crick H‐bonds, the AU dimers 56 and 58 – 60 H‐bonds of the Watson–Crick‐type, the AU dimers 53 and 55 reverse‐Hoogsteen, and 57 Hoogsteen H‐bonds. The pairing mode depends on the substituent of C(5′/I) (H, OSiⁱPr₃; OH) and on the H‐bonds of HO? C(5′/I) in the AU dimers. Association constants were derived from the concentration‐dependent chemical shift for HN(3) of the uracilyl moiety; they vary from 45–104 M ^?1 for linear duplexes to 197–2307 M ^?1 for cyclic duplexes. The thermodynamic parameters were determined by van't Hoff analysis of the temperature‐dependence of the (concentration‐dependent) chemical shift for HN(3) of the uracilyl moiety. Neglecting stacking energies, one finds an average energy of 3.5–4.0 kcal/mol per intermolecular H‐bond. Base stacking is evidenced by the temperature‐dependent CD spectra. The crystal structure of 54 shows two antiparallel chains of dimers connected by Watson‐Crick H‐bonds. The chains are bridged by a strong H‐bond between the propargylic OH and O?C(4) and by weak reverse A ? A Hoogsteen H‐bonds.     

Détermination par RMN 1H et 13C des Couplages J(CH) et J(CC) dans des Monomères Precurseurs de Lignine: Vanilline,Férulate d'Ethyle et Alcool Coniférylique Sélectivement Enrichis en 2H et 13C

Some monomer model compounds of lignin have been selectively ²H and ¹³C labelled: vanillin, ethyl ferulate, coniferyl alcohol and ethyl hydrogen malonate. Deuterium isotope effects on the ¹³C chemical shifts in [formyl-²H]vanillin, [5-²H]vanillin and [α,α,5-²H₃]coniferyl alcohol made the unambiguous assignment of the aromatic ¹³C signals possible. Absolute ^1,2,3J(CC) values have been determined on ¹³C spectra of [formyl-¹³C]vanillin, and of ethyl ferulate and coniferyl alcohol in which the vinylic C-γ and C-β carbons were ¹³C enriched. It has been possible to measure ⁴J(C?O, C-4) in vanillin and ⁴J(C-γ, C-4) in ethyl ferulate. The determination of ^1,2,3,4J (CH) absolute values was done by means of gated decoupled ¹³C spectra of the non-labelled compounds. When second order effects made the use of this technique impossible we determined certain J(CH) values and their signs either by analysing the ¹H NMR spectra of ¹³C labelled coniferyl alcohol [²J(C-β, H-γ), ²J(C-β, H-α), ²J(C-γ, H-β), ³J(C-γ, H-α)] or by a double irradiation experiment on the 250 MHz ¹H NMR spectrum of ethyl [β-¹³C] ferulate [for ²J(C-β, H-γ)].     

Conformational analysis and molecular dynamics simulation of cellobiose and larger cellooligomers

The conformational behavior of cellobiose (D -glc-ß(1→4)-D -glc), cellotetraose, and cellooctaose was studied by a combination of energy minimization and molecular dynamics simulations in vacuo at 400 K. These diand oligosaccharide models have considerable flexibility and exhibit a variety of different motions in glycosidic and exocyclic torsions. The glycosidic ?, ψ torsions moved frequently between two local minima on the cellobiose energy surface in the region of known crystal structures. Transitions of the hydroxymethyl side chain were observed between gt,gg, and tg conformations accompanied by changes in intramolecular hydrogen bonding patterns. A reasonable fit to the experimental optical rotation and nuclear magnetic resonance vicinal coupling data of cellobiose in solution required a distribution of its conformations. The oligomers, although generally extended, assumed a more coiled or twisted shape than is observed in the crystalline state of cellulose and exhibited considerable backbone motion due to local ring rotations about the glycosidic bonds. Long-lived transitions to structures having torsion angles 180° from the major minima (ring flips) introduced kinks and bends into the tetramer and octamer. While the glucose rings of the structures remained primarily in the ⁴C₁ conformation, twist and boat structures were also observed in the tetramer and octamer structures. Reducing the simulation temperature to 300 K eliminated some of the transitions seen at 400 K. © 1993 John Wiley & Sons, Inc.     

Conformational analysis of thia crown ether derivatives by NMR spectroscopy and molecular mechanics calculations

Summary Addition of sulfur dichloride to tetrachlorocatechol-bisallylether (1) yields the 9- and 10-ring thia crown ether derivatives2 and3, respectively, together with the dithia-18-crown-6-ether4. The 10-membered ring compound3 represents the first thia macrocycle containing bothMarkovnikov andanti-Markovnikov constitution of the -chloro-thio structural segments in the same molecule. By¹H and¹³C NMR spectroscopy, equal amounts of two preferred conformers of the only isolated diastereomer of3 were observed at temperatures below –50°C. The signals were assigned to these conformers using COSY, HETCOR, and phase sensitive NOESY spectra at low temperatures. The preferred conformations and the relative configuration were determined using the different effects of _gauche -and _anti -positions in¹³C NMR chemical shifts and analyzing vicinal³ J _H,H coupling constants. These results were confirmed by molecular mechanics calculations.Dedicated to Prof. Dr.Rolf Borsdorf on the occasion of his 65^th birthday     

Rigid gt Conformation of the C5/C6 Bond in a Gluco Derivative

Abstract

The rotational freedom of the C5/C6 bond of hexopyranosides very often governs the conformation of oligosaccharides, especially when 1→6 linkages are present in the saccharide. Conformational analysis may be complicated by the existence of a dynamic equilibrium between three staggered rotamers in the C5/C6 fragment.¹ The population of the individual rotamers can be deduced from J_5,6s and J_5,6R coupling constants by ap- plying an equation that connects the experimentally derived time-averaged coupling constants to the populational equilibrium. A prerequisite for this approach is the assign- ment of the prochiral protons H-6R and H-6S² and a correct evaluation of the effects of substituents on the coupling constant.     

The Isomeric Composition of D-Xylo-hexos-5-ulose (5-Keto-glucose) in Aqueous Solution

Abstract

1,2-O-Isopropylidene-α-D-xylo-hexofuranos-5-ulose (2) was deprotected in aqueous acid solution to give a mixture of at least six isomeric forms and one anhydro form of the parent ketoaldohexose, D-xylo-hexos-5-ulose (3), commonly referred to as 5-keto-glucose. Structural assignment of each form was made based on high field ¹H and ¹³C NMR studies of the mixture in aqueous (D₂O) solution. The dominant isomeric form of 3 was observed to have the pyranose structure 1R,5R-D-xlyo-hexo-pyranos-5-ulose (3a, 67 %) with the next most abundant form being an anhydro structure, 1S,5S-l,6-anhydro-D-xylo-hexopyranos-5-ulose (3c, 18 %). Included among the other isomers were the a and β-1,4-furanose (3d, 3e) and 1-aldehydrol β-5,2-furanose (3f) structures. The isomer present in least amount (3g, > 1 %) is assigned as the α-anomer of 3f. Experimentally determined J_C-1,H-1 values were useful in support of assigned isomer structures.     

Use of the Anomeric Carbon-13 Proton One Bond Scalar Coupling Constant as a Tool for Detecting 1,2-Orthoester Formation in Oligosaccharide Synthesis

Abstract

The anomeric ¹J_C,J value has for some time been successfully used for structural elucidation of oligosaccharides. The first recorded spectra on unenriched carbohydrates were published by Bock et al. in 1973 and pointed out that the anomeric ¹J_C,J value could be used for assignment of the anomeric configuration since pyranoses with an axial H-1 have a ¹J_C,J value which is approximately 10 Hz lower than the corresponding value in compounds with an equatorial H-1.^1–3 Their method recording non decoupled ¹³C NMR spectra had the disadvantage of being insensitive and thereby time-consuming. Introduction of INEPT⁴ followed by technical developments, has overcome this disadvantage. Nowadays, with reverse detection techniques, technical skill instead of sensitivity is a limiting factor. In this communication I would like to emphasize that the anomeric ¹J_C,J value can be used for detecting 1,2-orthoester formation as well as for establishing a- or P-configuration.     

The solution conformation of cyclic β-casomorphin-5 analogues

The solution conformation of two cyclic-casomorphin-5 analogues H-Tyr-c(-d-Orn-Phe-Pro-Gly-)1 and H-Tyr-c(-Orn-Phe-Pro-Gly-)2 in DMSO-d ₆ was studied by NMR spectroscopy and accompanying force field calculations. By especially employing¹H,¹³C, and¹⁵N chemical shifts, respectively, the temperature coefficient of the amide proton chemical shifts,³ J _NH,CH andJ _CH.CH coupling constants, respectively, and nuclear Overhauser effects in the rotating frame (ROEs), in the case of1, only one preferred conformer could be identified. In the case of2, two or even more preferred conformers were found, readily interconverting on the NMR time scale. Empirical force field calculations using the SYBYL 6.0 software (TRIPOS) corroborate the experimental NMR results obtained. The conformational behavior of the compounds studied is discussed with respect to the receptor specificity of the-casomorphins studied.     

The conformation of (1R,2S,4R,5S)-2,4-dimethoxybicyclo[3.3.1]nonan-9-one and some related compounds

A mixture of stereoisomers of 2,4-dimethoxybicyclo[3.3.1]nonan-9-one was prepared, separated by column chromatography and characterized by 60 MHz ¹H NMR spectroscopy using Eu(fod)₃. A double chair conformation with axial methoxyl groups is established for (1R,2S,4R,5S)-2,4-dimethoxybicyclo[3.3.1]-nonan-9-one on the basis of the J(12), J(2,H-3 exo) and J(2,3 endo) values and the chemical shifts for H-2(4). The conformation of some related compounds is subsequently inferred.     

Interactions Intramolécularies—XVII Calcul des constantes de couplage en RMN du cyclohexane et de cyclohexanes substitués. Comparaison des méthodes de Pople et Santry et des perturbations finies

Proton–proton ³J, ⁴J and ⁵J NMR coupling constants have been calculated for cyclohexane and monosubstituted cyclohexane conformers (substitiuents: Li, CH₃, OH, F) by the two methods mentioned. Comparing the two methods on the basis of group theory, we show the necessity to use the second. The results from this method are compared with those of the literature.     

Synthese von Nucleosiden aus 2-substituierten Imidazolen

Synthesis of 2-Substituted Imidazole Nucleosides Condensation of the trimethylsilyl derivatives of 2-substituted diethyl and dimethyl imidazole-4,5-dicarboxylates ( 3–5 and 7–9 ) with 1-O-acetyl-2,3,5-tri-O-benzoyl-β-D -ribofuranose ( 2 ) in the presence of trimethysilyl trifluoromethanesulfonate provided the 2-substituted diethyl and dimethyl 1-(2′,3′, 5′-tri-O-benzoyl-β-D -ribofuranosyl)imidazole-4, 5-dicarboxylates 10–15 . These were treated with ammonia to afford the 2-substituted 1-(β-D -ribofuranosyl)imidazole-4,5-dicarboxamides 16–21 . Treatment of 2-methyl-( 16 ) and 2-ethyl-1-(β-D -ribofuranosyl)imidazole-4,5-dicarboxamide ( 17 ) with fuming nitric acid in oleum at ?30° yielded the nitric acid esters 23 and 24 . Besides the esterification of the sugar hydroxyl groups one H-atom of the imidazolecarboxamide function at C(5) in these nucleosides was also substituted by the NO₂ group. The conformations in solution of 16 and 23 have been determined by ¹H- and ¹³C-NMR. spectroscopy. These studies indicate that the nucleosides exist in dimethyl-sulfoxide solution preferentially in the S-gg-syn-conformation ( 16 ) and N-gt-conformation ( 23 ). In the crystal structure of nucleoside 23 , the ribose was found to be in the O(1′)_endo, C(1′)_exo twist conformation. The conformation about C(4′), C(5′) is gauche-trans and the molecule exists in the syn form.     

1,7-dithioxo-substituted systems. Synthesis,structure, and photoconductivity of bis(5,5-dimethyl-3-hydrazonocyclohex-1-enyl) sulfide

Bis(5,5-dimethyl-3-hydrazonocyclohex-1-enyl) sulfide was synthesized by the reaction of bis(5,5-dimethyl-3-thioxocyclohex-1-enyl) sulfide or its oxygen analog with hydrazine. Conformational lability of the molecule of dihydrazone was studied by the DFT(B3LYP) method using expanded basis sets 6–311G and 6–11G(d,p). Analysis of vibration IR and Raman spectra of the most stable conformers of the isolated molecule of dihydrazone was performed at the harmonic approximation. Using the Onsager SCRF solvation model the absence of solvent effect on the relative stability of the conformers was shown. The photoconductivity of dihydrazone was studied. Low value of the ratio of photocurrent to dark current (J _p/J _d = 2.5–3.5) for dyhydrazone was assigned to the lability of its stereoelectronic structure, which was in line with the data of ¹H, ¹³C, and ¹⁵N NMR spectra.     

Quantum mechanical calculations on cellulose–water interactions: structures,energetics, vibrational frequencies and NMR chemical shifts for surfaces of Iα and Iβ cellulose

Periodic and molecular cluster density functional theory calculations were performed on the Iα (001), Iα (021), Iβ (100), and Iβ (110) surfaces of cellulose with and without explicit H₂O molecules of hydration. The energy-minimized H-bonding structures, water adsorption energies, vibrational spectra, and ¹³C NMR chemical shifts are discussed. The H-bonded structures and water adsorption energies (ΔE_ads) are used to distinguish hydrophobic and hydrophilic cellulose–water interactions. O–H stretching vibrational modes are assigned for hydrated and dry cellulose surfaces. Calculations of the ¹³C NMR chemical shifts for the C4 and C6 surface atoms demonstrate that these δ¹³C4 and δ¹³C6 values can be upfield shifted from the bulk values as observed without rotation of the hydroxymethyl groups from the bulk tg conformation to the gt conformation as previously assumed.     

NMR and Monte Carlo Studies on the Solution Conformation of a Linear Capsular Polysaccharide from a Soybean‐Nodulating Bacterium (Strain B33)

The conformational behavior of the capsular polysaccharide obtained from a fast‐growing soybean‐nodulating rhizobia (strain B33) isolated from Xinjiang Autonomous Region (Eastern China) has been analyzed by NMR and molecular mechanics simulations. This polysaccharide has the repeating unit →6)‐4‐O‐Me‐α‐d‐Glcp‐(1→4)‐3‐O‐Me‐β‐d‐GlcpA‐(1→. The NMR results indicate that the α‐(1→4) linkage may adopt a variety of conformations, and that at least two of the resulting minima must exist in solution. NOE data agree with an 85:10:5 ratio for the lowest‐energy conformations. In the case of the β‐(1→6) linkage, NMR indicates that the rotamer gg is highly populated. Experimental and calculated NOE intensities match well when the global energy minimum conformation for this linkage has exclusively the gg orientation. The influence of the adjacent methyl group on the glycosyloxymethyl population has been evaluated by simulation of a disaccharide without this group. A relative destabilization of gt rotamer has been found. Long chains have been simulated using a Metropolis algorithm at different ratios of the gg and gt rotamers in the glucose moiety. It was observed that the increase in population of the gt rotamer yielded more close contacts in the chain.     

1H and 13C NMR study of α-acetylenic PIII and PIV derivatives. Signs and magnitudes of J(P?C) and J(P?H)

All J(P? H) and J(P? C) values, including signs, have been obtained in acetylenic and propynylic phosphorus derivatives, R₂P(X)? C?C? H and R₂P(X)? C?C? CH₃ (X ? oxygen, lone pair and R ? C₆H₅, N(CH₃)₂, OC₂H₅, N(C₆H₅)₂, Cl) from ¹H and ¹³C NMR spectra. In P^IV derivatives the following signs are obtained: ¹J(P? C)+, ²J(P? C)+, ³J(P? C)+, ³J(P? H)+, ⁴J(P? H)? . Linear relations are observed between ¹J(P? C), ²J(P? C) and ³J(P? C) versus ³J(P? H), indicating that these coupling constants are mainly dependent on the Fermi contact term, though the other terms of the Ramsey theory do not seem to be negligible for ¹J(P? C) and ²J(P? C). In P^III derivatives these signs are: ¹J(P? C)- and +, ²J(P? C)+, ³J(P? C)-, ³J(P? H)-, ⁴J(P? H)+. Only ³J(P? C) and ³J(P? H) reflect a small contribution of the Fermi contact term while in ¹J(P? C) and ²J(P? C) this contribution seems to be negligible relative to the orbital and/or spin dipolar coupling mechanisms.     

Conformational analysis of 2-methyl-5-alkyl- and 5-aryl-1,3,2-dioxaborinanes

Quantum chemical study of conformational isomerization of 2-methyl-5-alkyl- and 5-aryl-1,3,2-dioxaborinanes using RHF/6-31G(d) method led to the conclusion that the equilibrium between equatorial and axial sofa conformers is shifted to the latter form. Based on the experimental and theoretically calculated vicinal coupling constants J _HH the quantitative conformational composition and the values of ΔG ⁰ for substituents at the C⁵ ring atom were established.     

Long-Range 31P-31P Spin Coupling Constants in the 31P NMR Spectra of Phosphite Triesters

Abstract

Data are presented on the magnitudes of ⁵ J _pp and ⁶ J _PP spin-spin coupling constants in the ³¹P NMR spectra of a variety of novel polyphosphite triesters.