Determination and refinement of the structures of some chlorinated carbohydrates
Creators: name: Hoge, Reinhold
Publisher: name: University of British Columbia
Year: 2011

description: The crystal and molecular structures of three chlorinated carbohydrates whose formal nomenclatures are methyl 2-chloro-2-deoxy-α-D-galactopyranoside methyl 4,6-dichloro-4,6-dideoxy- α -D-glucopyranoside, and methyl 4,6-diohloro-4,6-dideoxy- α -D-galactopyranoside have been determined by X-ray diffraction using various methods. A scintillation counter was used in each case to collect the data: for the first, CuK[subscript α] radiation was used; for the second and third, MoK[subscript α] radiation was used. The structure of the 2-chloro-galactoslde was solved by a combination of the Patterson method and trial and error methods. Two possible positions of the chlorine atom found from the Patterson function were differentiated by minimizing R (using h k 0 projection data only) in rotation of a model of the molecule about each chlorine position. A model was used to go from the solved two dimensional structure to three dimensions. Successive Fourier summations and block diagonal least squares refinement established the crystal to be composed of a mixture of the α and β anomers of methyl 2-chloro-2-deoxy-D-galaotopyranoside In the approximate ratio of 2 α: lβ. Both the α and β anomers are in their expected C-l (chair) conformations. Hydrogen bonding involving 0(3), 0(4) and 0(6) links molecules together into infinite sheets, two molecules thick and perpendicular to the x-axis. Mean bond distances are: C-C = 1.53 A, C-0 = 1.42 A and C-Cl - 1.75 A. The structure of the 4,6-dlchloro-glucoside was solved by a combination of the Patterson method (to locate the two chlorines), successive Fourier summations (to locate the carbons and oxygens), block diagonal least squares refinement, and a difference synthesis (to locate eight of the hydrogens). The absolute configuration was determined by the anomalous dispersion method (CuK[subscript α] radiation). The molecule is in the expected C-l conformation. Hydrogen bonding, involving 0(2) and 0(3), links molecules together into infinite chains parallel to the y-axis; the mean planes of the molecules are approximately perpendicular to the direction of these chains. Mean bond distances are C-C = 1.52 A, C-0 = 1.42 A and C-Cl = 1.78 A. The structure of the 4,6-dichloro-galactoside was solved by direct methods applied to the two dimensional data of two centrosymmetric projections. A series of programs, employing the Vand-Pepinsky method of phasing reflexions contained in Sayre relationships, was written to do this. After refinement using block diagonal least squares, the two solutions were combined into the three dimensional solution, which was further refined. A difference Fourier summation revealed the position of six hydrogens. The molecule is again in the expected C-l conformation. Hydrogen bonding Involved 0(1), 0(2), and 0(3) in a complicated network which includes a bifurcated hydrogen bond. As in the 2-chloro-galactoside, molecules are linked by hydrogen bonds into infinite sheets, two molecules thick and perpendicular to the x-axis, but whereas in that structure the baslo symmetry elements propagating the networks of bonding were unit cell translations and two-fold rotation axes, the basic elements propagating the networks in 4,6-dlchloro-galaoto side are unit cell translations and two-fold screw axes. Mean bond distances in this structure are: C-C = 1.53 A, C-0 = 1.45 A, and C-Cl =1.80 A.