Linkage Conformation (linkage + conformation)

Distribution by Scientific Domains


Selected Abstracts


Methyl ,-allolactoside [methyl ,- d -galactopyranosyl-(1,6)-,- d -glucopyranoside] monohydrate

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 12 2009
Thomas E. Klepach
Methyl ,-allolactoside [methyl ,- d -galactopyranosyl-(1,6)-,- d -glucopyranoside], (II), was crystallized from water as a monohydrate, C13H24O11·H2O. The ,Galp and ,Glcp residues in (II) assume distorted 4C1 chair conformations, with the former more distorted than the latter. Linkage conformation is characterized by ,, (C2Gal,C1Gal,O1Gal,C6Glc), ,, (C1Gal,O1Gal,C6Glc,C5Glc) and , (C4Glc,C5Glc,C6Glc,O1Gal) torsion angles of 172.9,(2), ,117.9,(3) and ,176.2,(2)°, respectively. The ,, and , values differ significantly from those found in the crystal structure of ,-gentiobiose, (III) [Rohrer et al. (1980). Acta Cryst. B36, 650,654]. Structural comparisons of (II) with related disaccharides bound to a mutant ,-galactosidase reveal significant differences in hydroxymethyl conformation and in the degree of ring distortion of the ,Glcp residue. Structural comparisons of (II) with a DFT-optimized structure, (IIC), suggest a link between hydrogen bonding, pyranosyl ring deformation and linkage conformation. [source]


Methyl ,- d -galactopyranosyl-(1,4)-,- d -allopyranoside tetrahydrate

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 9 2010
Wenhui Zhang
The title compound, C13H24O11·4H2O, (I), crystallized from water, has an internal glycosidic linkage conformation having ,, (O5Gal,C1Gal,O1Gal,C4All) = ,96.40,(12)° and ,, (C1Gal,O1Gal,C4All,C5All) = ,160.93,(10)°, where ring-atom numbering conforms to the convention in which C1 denotes the anomeric C atom, C5 the ring atom bearing the exocyclic hydroxymethyl group, and C6 the exocyclic hydroxymethyl (CH2OH) C atom in the ,Galp and ,Allp residues. Internal linkage conformations in the crystal structures of the structurally related disaccharides methyl ,-lactoside [methyl ,- d -galactopyranosyl-(1,4)-,- d -glucopyranoside] methanol solvate [Stenutz, Shang & Serianni (1999). Acta Cryst. C55, 1719,1721], (II), and methyl ,-cellobioside [methyl ,- d -glucopyranosyl-(1,4)-,- d -glucopyranoside] methanol solvate [Ham & Williams (1970). Acta Cryst. B26, 1373,1383], (III), are characterized by ,, = ,88.4,(2)° and ,, = ,161.3,(2)°, and ,, = ,91.1° and ,, = ,160.7°, respectively. Inter-residue hydrogen bonding is observed between O3Glc and O5Gal/Glc in the crystal structures of (II) and (III), suggesting a role in determining their preferred linkage conformations. An analogous inter-residue hydrogen bond does not exist in (I) due to the axial orientation of O3All, yet its internal linkage conformation is very similar to those of (II) and (III). [source]


Methyl 4- O -,- d -galactopyranosyl ,- d -mannopyranoside methanol 0.375-solvate

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 2 2010
Xiaosong Hu
Methyl ,- d -galactopyranosyl-(1,4)-,- d -mannopyranoside methanol 0.375-solvate, C13H24O11·0.375CH3OH, (I), was crystallized from a methanol,ethanol solvent system in a glycosidic linkage conformation, with ,, (O5Gal,C1Gal,O1Gal,C4Man) = ,68.2,(3)° and ,, (C1Gal,O1Gal,C4Man,C5Man) = ,123.9,(2)°, where the ring is defined by atoms O5/C1,C5 (monosaccharide numbering); C1 denotes the anomeric C atom and C6 the exocyclic hydroxymethyl C atom in the ,Galp and ,Manp residues, respectively. The linkage conformation in (I) differs from that in crystalline methyl ,-lactoside [methyl ,- d -galactopyranosyl-(1,4)-,- d -glucopyranoside], (II) [Pan, Noll & Serianni (2005). Acta Cryst. C61, o674,o677], where ,, is ,93.6° and ,, is ,144.8°. An intermolecular hydrogen bond exists between O3Man and O5Gal in (I), similar to that between O3Glc and O5Gal in (II). The structures of (I) and (II) are also compared with those of their constituent residues, viz. methyl ,- d -mannopyranoside, methyl ,- d -glucopyranoside and methyl ,- d -galactopyranoside, revealing significant differences in the Cremer,Pople puckering parameters, exocyclic hydroxymethyl group conformations and intermolecular hydrogen-bonding patterns. [source]


Methyl ,-allolactoside [methyl ,- d -galactopyranosyl-(1,6)-,- d -glucopyranoside] monohydrate

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 12 2009
Thomas E. Klepach
Methyl ,-allolactoside [methyl ,- d -galactopyranosyl-(1,6)-,- d -glucopyranoside], (II), was crystallized from water as a monohydrate, C13H24O11·H2O. The ,Galp and ,Glcp residues in (II) assume distorted 4C1 chair conformations, with the former more distorted than the latter. Linkage conformation is characterized by ,, (C2Gal,C1Gal,O1Gal,C6Glc), ,, (C1Gal,O1Gal,C6Glc,C5Glc) and , (C4Glc,C5Glc,C6Glc,O1Gal) torsion angles of 172.9,(2), ,117.9,(3) and ,176.2,(2)°, respectively. The ,, and , values differ significantly from those found in the crystal structure of ,-gentiobiose, (III) [Rohrer et al. (1980). Acta Cryst. B36, 650,654]. Structural comparisons of (II) with related disaccharides bound to a mutant ,-galactosidase reveal significant differences in hydroxymethyl conformation and in the degree of ring distortion of the ,Glcp residue. Structural comparisons of (II) with a DFT-optimized structure, (IIC), suggest a link between hydrogen bonding, pyranosyl ring deformation and linkage conformation. [source]


Conformational evaluation of labeled C3,-O-P- 13CH2 -O-C4, phosphonate internucleotide linkage, a phosphodiester isostere

BIOPOLYMERS, Issue 7 2009

Abstract Modified internucleotide linkage featuring the C3,-O-P-CH2 -O-C4, phosphonate grouping as an isosteric alternative to the phosphodiester C3,-O-P-O-CH2 -C4, bond was studied in order to learn more on its stereochemical arrangement, which we showed earlier to be of prime importance for the properties of the respective oligonucleotide analogues. Two approaches were pursued: First, the attempt to prepare the model dinucleoside phosphonate with 13C-labeled CH2 group present in the modified internucleotide linkage that would allow for a more detailed evaluation of the linkage conformation by NMR spectroscopy. Second, the use of ab initio calculations along with molecular dynamics (MD) simulations in order to observe the most populated conformations and specify main structural elements governing the conformational preferences. To deal with the former aim, a novel synthesis of key labeled reagent (CH3O)2P(O)13CH2OH for dimer preparation had to be elaborated using aqueous 13C-formaldehyde. The results from both approaches were compared and found consistent. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 514,529, 2009. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source]


Methyl ,- d -galactopyranosyl-(1,4)-,- d -allopyranoside tetrahydrate

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 9 2010
Wenhui Zhang
The title compound, C13H24O11·4H2O, (I), crystallized from water, has an internal glycosidic linkage conformation having ,, (O5Gal,C1Gal,O1Gal,C4All) = ,96.40,(12)° and ,, (C1Gal,O1Gal,C4All,C5All) = ,160.93,(10)°, where ring-atom numbering conforms to the convention in which C1 denotes the anomeric C atom, C5 the ring atom bearing the exocyclic hydroxymethyl group, and C6 the exocyclic hydroxymethyl (CH2OH) C atom in the ,Galp and ,Allp residues. Internal linkage conformations in the crystal structures of the structurally related disaccharides methyl ,-lactoside [methyl ,- d -galactopyranosyl-(1,4)-,- d -glucopyranoside] methanol solvate [Stenutz, Shang & Serianni (1999). Acta Cryst. C55, 1719,1721], (II), and methyl ,-cellobioside [methyl ,- d -glucopyranosyl-(1,4)-,- d -glucopyranoside] methanol solvate [Ham & Williams (1970). Acta Cryst. B26, 1373,1383], (III), are characterized by ,, = ,88.4,(2)° and ,, = ,161.3,(2)°, and ,, = ,91.1° and ,, = ,160.7°, respectively. Inter-residue hydrogen bonding is observed between O3Glc and O5Gal/Glc in the crystal structures of (II) and (III), suggesting a role in determining their preferred linkage conformations. An analogous inter-residue hydrogen bond does not exist in (I) due to the axial orientation of O3All, yet its internal linkage conformation is very similar to those of (II) and (III). [source]