Electrostatic Properties and Thermal Vibrations of Small Molecules Using Neutron and X-Ray Diffraction Data.

The charge density distribution was determined for hexamethylenetetramine (HMT) from 333 X-ray reflections with sintheta/lambda < 1.47 A^{-1} (Ag K_ alpha). Full matrix least-squares refinement with a multipole model shows correlation between certain octapole deformation terms which are predominant for describing the bonding density between atoms of the molecule. This problem will always arise when the multipole model is applied in a noncentrosymmetric space group. The total molecular electrostatic potential and the molecular octapole moment are reliably obtained. Neutron diffraction data collected at 15, 50, 80, 120, 160 and 200 K were used to study the severe extinction effects in HMT. The structure refinement included two extinction parameters and third-order thermal parameters for the H-nuclei. The crystal domain size decreases from 115 mm at 200 K to 85 mm at 15 K using Sabine's extinction theory. The half-width in the mosaic spread (7 ^{''} of arc) is independent of temperature. The nuclear m.s. thermal displacements have been analysed assuming no coupling between the external (rigid body) and internal vibrations. The methylene H-nuclei have internal vibrations independent of temperature and a small anharmonic component above 160 K. The electrostatic properties of adenosine were determined using X-ray data (Ag K_alpha 123 K). Comparing the charge distribution for the adenine part of adenosine with 9methyladenine shows good agreement, the major difference being at N1. The molecular electrostatic potential maps derived in the present study are different from previous studies. The molecular dipole moment results from net atomic charges and atomic dipoles which almost cancel. Puromycin rm ((C_{22 }H_{31}N_7O_5)^ {2+}cdot Cl_2^{-} cdot5 H_2O) crystallizing in space group P2_12_12_1 (Z = 4, a = 28.465(6) A, b = 13.073(2) A, c = 7.827(2) A) gave 18659 independent reflections ((lambda = 0.71073 A, sintheta/lambda < 1.124 A^{-1}) on a crystal ((0.375 x 0.525 x 0.625) mm) at 123 K. Least -squares refinement was carried with deformation terms up to octapoles for C, N and O and to dipoles for H. The electrostatic potential was calculated for puromycin removed from the crystal structure and in the crystal structure. The electrostatic potential was also calculated for a modified puromycin molecule with the protonated adenosine part replaced by a neutral adenosine. Hereby, models for two protonations states in puromycin are provided. The differences in electrostatic potential give an indication of the drug activity in puromycin.