Experimental charge density study of estrogens: 17beta-estradiol.urea

To relate the molecular electrostatic potential to the biological activities of estrogens, a comparative charge density study of different derivatives has been initiated. The second completed charge density analysis of this series for 17beta-estradiol*urea is presented here. This is a large organic system with 52 atoms in a noncentrosymmetric space group, therefore special tools such as an optimal coordinate system and slow, initially constrained refinement have been used to accomplish this study. Our results for the urea molecule reasonably agree with previous experimental and theoretical results. In the 17beta-estradiol molecule, the oxygen atoms appear to be close to sp3 in shape, exhibiting two consistent, distinct lone pairs despite different chemical environments. No significant interaction of the hydroxyl group oxygen with the orbitals of the aromatic ring is observed. Analysis of the electrostatic potential revealed that the negative potential in the lone pair region of the two oxygen atoms is quite different. The topological analysis of the electron density has been performed, and the atomic charges have been estimated.     

Variable temperature neutron diffraction and X-ray charge density studies of tetraacetylethane

Single crystal neutron diffraction data have been collected on a sample of enolized 3,4-diacetyl-2,5-hexanedione (tetraacetylethane, TAE) at five temperatures between 20 and 298 K to characterize the temperature-dependent behavior of the short, strong, intramolecular hydrogen bond. Upon decreasing the temperature from 298 K to 20 K, the O2-H1 distance decreases from 1.171(11) to 1.081(2) A and the O1...H1 distance increases from 1.327(10) to 1.416(6) A. The convergence of the C-O bond lengths from inequivalent distances at low temperature to identical values (1.285(4) A) at 298 K is consistent with a resonance-assisted hydrogen bond. However, a rigid bond analysis indicates that the structure at 298 K is disordered. The disorder vanishes at lower temperatures. Short intermolecular C-H...O contacts may be responsible for the ordering at low temperature. The intramolecular O...O distance (2.432 +/- 0.006 A) does not change with temperature. X-ray data at 20 K were measured to analyze the charge density and to gain additional insight into the nature of the strong hydrogen bond. Quantum mechanical calculations demonstrate that periodic boundary conditions provide significant enhancement over gas phase models in that superior agreement with the experimental structure is achieved when applying periodicity. One-dimensional potential energy calculations followed by quantum treatment of the proton reproduce the location of the proton nearer to the O2 site reasonably well, although they overestimate the O-H distance at low temperatures. The choice of the single-point energy calculation strategy for the proton potential is justified by the fact that the proton is preferably located nearer to O2 rather than being equally distant to O1 and O2 or evenly distributed (disordered) between them.     

Structure and bonding in beta-HMX-characterization of a trans-annular N...N interaction

Chemical bonding in the beta-phase of the 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane (HMX) crystal based on the experimental electron density obtained from X-ray diffraction data at 20 K, and solid state theoretical calculations, has been analyzed in terms of the quantum theory of atoms in molecules. Features of the intra- and intermolecular bond critical points and the oxygen atom lone-pair locations are discussed. An unusual N...N bonding interaction across the 8-membered ring has been discovered and characterized. Hydrogen bonding, O...O and O...C intermolecular interactions are reported. Atomic charges and features of the electrostatic potential are discussed.     

Secondary ion yields produced by keV atomic and polyatomic ion impacts on a self-assembled monolayer surface

A suite of keV polyatomic or 'cluster' projectiles was used to bombard unoxidized and oxidized self-assembled monolayer surfaces. Negative secondary ion yields, collected at the limit of single ion impacts, were measured and compared for both molecular and fragment ions. In contrast to targets that are orders of magnitude thicker than the penetration range of the primary ions, secondary ion yields from polyatomic projectile impacts on self-assembled monolayers show little to no enhancement when compared with monatomic projectiles at the same velocity. This unusual trend is most likely due to the structural arrangement and bonding characteristics of the monolayer molecules with the Au(111). Copyright 1999 John Wiley & Sons, Ltd.     

Experimental and theoretical electron density study of estrone

The electron density and the electrostatic potential (ESP) distributions of estrone have been determined using X-ray diffraction analysis and compared with theoretical calculations in the solid and gas phases. X-ray diffraction measurements are performed with a Rigaku Rapid rotating anode diffractometer at 20 K. The electron density in the estrone crystal has been described with the multipole model, which allowed extensive topological analysis and calculation of the ESP. From DFT calculations in the solid state a theoretical X-ray diffraction data set has been produced and treated in the same way as the experimental data. Two sets of single molecule DFT calculations were performed: (a) An electron density distribution was obtained via a single-point calculation with a large basis set at the experimental geometry and subsequently analyzed according to the quantum theory of atoms in molecules (AIM) to obtain the bond and most atomic properties, and (b) another electron density distribution was obtained with a smaller basis set, but at a geometry optimized using the same basis set for the analysis of atomic energies. An interesting locally stabilizing hydrogen-hydrogen bond path linking H(1) and H(11B) is found which represents the first characterization of such bonding in a steroid molecule. AIM delocalization indices were shown to be well correlated to the experimental electron density at the bond critical points through an exponential relationship. The aromaticity of ring A, chemical bonding, the O(1)...O(2) distance necessary for estrogenic activity, and the electrostatic potential features are also discussed.