Hydrogen atom position

First, it is not possible to determine hydrogen atom positions by X-ray crystallography. Thus the coordinates for the many hydrogen atoms in the molecule are missing from X-ray coordinate files. These coordinates must be added to the initial structure before the simulation is started. Several algorithms are available for ensuring reasonable placement of hydrogens. 

The structure was refined by block-diagonal least squares in which carbon and oxygen atoms were modeled with isotropic and then anisotropic thermal parameters. Although many of the hydrogen atom positions were available from difference electron density maps, they were all placed in ideal locations. Final refinement with all hydrogen atoms fixed converged at crystallographic residuals of R=0.061 and R =0.075. 

A search for intermolecular bonds resulted in one possible hydrogen bond between hydroxyl 013 and lactone carbonyl Ol. The distance between 01 and 013 is 2.85 A, a value well within the range expected for OH-O hydrogen bonds (25). The hydrogen atom position for hydroxyl 013 was chosen to be along the 013-01 vector. The hydrogen position was not evident in the difference electron density map, presumably due to problems modeling the 013 position. 

PbTX-1 also cx)ntains the intermolecular hydrogen bond between hydroxyl 013 and carbonyl 01 already discussed. Only for dihydro PbTX-1 was it possible to locate an 012 hydroxyl hydrogen atom position from difference electron density maps. In that structure a peak appeared at 1.1 A from 012 and 2.1 A from symmetry related 05. 

P2j Z = 6 D = 1.56 R = 0.81 for 2,048 intensities. There are three symmetry-independent molecules in the unit cell with almost identical structures. The ribopyranoside conformation is lC4 with Q = 49, 48, 47 pm 6 = 178,177,176°. The P-O distances are 165 pm, longer than in the analogous thiophosphate. The hydrogen-atom positions were not reported. 

P2X Z = 2 D = 1.30 R = 0.10 for 995 intensities. The enopyranoside has the °HS conformation, with Q = 47 pm, 0 = 51°, = 326°. The orientation of the primary alcohol group is gauche-trans, and the a-glyco-sidic bond has the usual + syn orientation. The bond lengths given, which are of low accuracy, do not differ significantly from normal values. The hydrogen-atom positions were not determined. 

P212121 Z = 8 Dx = 1.419 R = 0.068 for 1,373 intensities. The crystal structure contains two symmetry-independent molecules having slightly different conformations. The pyranoside conformations are 1C4 with Q = 57,60 pm, 0=173,177°. The nitro and acetate groups are oriented approximately normal to the mean plane of the pyranoside ring. The atomic coordinates refer to the d enantiomer. The hydrogen-atom positions were not reported. 

P212121 Z = 4 Dx = 1.29 R = 0.11 for 629 intensities from film measurements. The pyranoside conformation is 4C1, with Q = 60 pm, 6 — 6°, dioxane ring is close to an ideal chair, with Q = 53 pm, 0=1°. The phenyl group is axial, and appears to be somewhat distorted from planar. The hydrogen-atom positions were not determined. 

OH-3 and the ring-oxygen atom, 0-5, of the first and second D-glucose residues from the steroid residue. The hydrogen-atom positions were reported in the second publication.135... 

Parameters marked with derive from an alcohol donor and an acid (C = 0) acceptor. Parameters marked with derive from a carboxyl(-OH) donor and carboxyl (C=0) acceptor (intermolecular). Entries not marked represent inverted relations. b For compound designation see Table 11. e No hydrogen atomic positions were determined for these sites. 

Figure 25. Shapes of five alkylated derivatives of adenosine and deoxyadenosine. (a) Adenosine derivative of DMBA (XXXII). (b) Deoxyadenosine derivative of DMBA (XXXIV). No hydrogen atom positions for this diagram, (c) Adenosine derivative of dimethyl anthracene (XXXI). Note the different conformation.

Most of the crystal-structure analyses report hydrogen-atom positions these are less accurate than those of the non-hydrogen atoms by a factor of ten, except in the case of neutron diffraction, where the accuracies are comparable. 

H 0=C hydrogen-bonds, with H O distances of 212 and 220 pm. Some of the hydrogen atom positions were not reported. 

Z = 8 Dx = 1.21 R = 0.118 for 1,694 intensities. The pyranoside conformation is a slightly distorted 4Ci (0 = 7°,

reaction-product was anticipated119). Hydrogen atom positions were not reported. 

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