Atomic and bond topological properties of the tripeptide l-alanyl–l-alanyl–l-alanine based on its experimental charge density obtained at 20 K

Charge density distribution and theoretical analysis of low and high energy phosphate esters

There is a strict relation between the energy of hydrolysis of phosphate esters and the extent of interactions between the p ester oxygen lone pair and the antibonding orbitals of the rest of the molecule. Its impact on experimental charge density distribution is analyzed.

Validation of experimental charge densities: refinement of the macrolide antibiotic roxithromycin

Multipole refinements of larger organic molecules have so far been limited to a few exceptional cases. We report an investigation of the detailed experimental electron-density distribution (EDD) of roxithromycin, a macrolide antibiotic consisting of 134 atoms. Although the experimental multipole refinement on high-resolution synchrotron data converged smoothly, validation of the electron density by calculation of an `experiment minus invariom' difference density revealed conformational disorder of the H atoms. Hydrogen disorder is shown to affect the EDD, the electrostatic potential and atomic properties as defined by Bader's quantum theory of atoms in molecules. A procedure to obtain the electron density distribution in the presence of disorder is proposed.

Topological properties of hydrogen bonds and covalent bonds from charge densities obtained by the maximum entropy method (MEM)

Charge densities have been determined by the Maximum Entropy Method (MEM) from the high-resolution, low-temperature (T approximately 20 K) X-ray diffraction data of six different crystals of amino acids and peptides. A comparison of dynamic deformation densities of the MEM with static and dynamic deformation densities of multipole models shows that the MEM may lead to a better description of the electron density in hydrogen bonds in cases where the multipole model has been restricted to isotropic displacement parameters and low-order multipoles (l(max) = 1) for the H atoms. Topological properties at bond critical points (BCPs) are found to depend systematically on the bond length, but with different functions for covalent C-C, C-N and C-O bonds, and for hydrogen bonds together with covalent C-H and N-H bonds. Similar dependencies are known for AIM properties derived from static multipole densities. The ratio of potential and kinetic energy densities |V(BCP)|/G(BCP) is successfully used for a classification of hydrogen bonds according to their distance d(H...O) between the H atom and the acceptor atom. The classification based on MEM densities coincides with the usual classification of hydrogen bonds as strong, intermediate and weak [Jeffrey (1997). An Introduction to Hydrogen Bonding. Oxford University Press]. MEM and procrystal densities lead to similar values of the densities at the BCPs of hydrogen bonds, but differences are shown to prevail, such that it is found that only the true charge density, represented by MEM densities, the multipole model or some other method can lead to the correct characterization of chemical bonding. Our results do not confirm suggestions in the literature that the promolecule density might be sufficient for a characterization of hydrogen bonds.

Physicochemical properties of zwitterionic L- and DL-alanine crystals from their experimental and theoretical charge densities

The total experimental electron density distributions rho(r) of zwitterionic L- and DL-alanine crystals, as derived from extensive sets of X-ray diffracted intensities collected at 23 and 19 K, are compared to gain an insight into the different physical properties of the two related chiral compounds in the solid state and to explore the extent of the rho(r) transferability. Relevant parameters that characterize the two crystal forms are obtained, showing differences and similarities in terms of (i) geometric descriptors, (ii) topological indexes, (iii) molecular electrostatic potential Phi(r) distributions, (iv) atomic volumes and charges, (v) molecular electric moments, and (vi) electrostatic interaction energies. To assess the relative stability of the racemate with respect to the pure enantiomer, the crystal lattice energies, as obtained through DFT fully periodic calculations, are also discussed and compared with the experimental sublimation enthalpies after correction for the proton-transfer energies. In-crystal group charges, evaluated with the quantum theory of atoms in molecules, are found to be transferable between the racemic and the pure enantiomer, at variance with group volumes. Similarly, molecular first and third moments are not strictly transferable and indicate that for the zwitterionic alanine molecule the molecular charge distribution in the DL-crystal is more polarized in the c direction by about 10%. By contrast, quantitative agreement is observed for second and fourth moments. Significant differences arise from (1) the crystal packing of the dipole vectors, which are aligned in an antiparallel fashion in the L-crystal, to be compared with a parallel alignment in the racemate, due the polar space group Pna21 of the latter, (2) the strongly attractive electrostatic energy of a homochiral pair in the L-crystal, which is opposed to the corresponding heterochiral pair in the DL-crystal form. The difference between these Ees values amounts to 135-150 kJ mol(-1). Despite this, the two crystal forms are predicted as equally thermodynamically favored by the theoretical P-B3LYP estimates of the crystal lattice energies. Finally, the necessity of an upgrading of the dispersion and exchange-repulsion terms currently adopted within the experimental charge density approach to intermolecular interactions is recognized and discussed.

Fast electron density methods in the life sciences--a routine application in the future?

The understanding of mutual recognition of biologically interacting systems on an atomic scale is of paramount importance in the life sciences. Electron density distributions that can be obtained from a high resolution X-ray diffraction experiment can provide--in addition to steric information--electronic properties of the species involved in these interactions. In recent years experimental ED methods have seen several favourable developments towards successful application in the life sciences. Experimental and methodological advances have made possible on the one hand high-speed X-ray diffraction experiments, and have allowed on the other hand the quantitative derivation of bonding, non-bonding and atomic electronic properties. This has made the investigation of a large number of molecules possible, and moreover, molecules with 200 or more atoms can be subject of experimental ED studies, as has been demonstrated by the example of vitamin B12. Supported by the experimentally verified transferability concept of submolecular electronic properties, a key issue in Bader's The Quantum Theory of Atoms in Molecules, activities have emerged to establish databases for the additive generation of electron densities of macromolecules from submolecular building blocks. It follows that the major aims of any experimental electron density work in the life sciences, namely the generation of electronic information for a series of molecules in a reasonable time and the study of biological macromolecules (proteins, polynucleotides), are within reach in the near future.

Reproducibility and transferability of topological data: experimental charge density study of two modifications ofl-alanyl-l-tyrosyl-l-alanine

Two crystalline modifications of the tripeptide L-Ala-L-Tyr-L-Ala, which have different solvent molecules in the crystal structure (water and ethanol for modifications 1 and 2), were the subject of experimental charge density studies based on high resolution X-ray data collected at ultra-low temperatures of 9 K (1) and 20 K (2), respectively. The molecular structures and the intermolecular interactions were found to be rather similar in the two crystal lattices, so that this study allowed the reproducibility of the charge density of a given molecule in different (but widely comparable) crystalline environments to be examined. With respect to bond topological and atomic properties, the agreement between the two modifications of the title tripeptide was in the same range as found from the comparison with the previously reported results of tri-L-alanine. It follows that the reproducibility and transferability of quantitative topological data are comparable and that within the accuracy of experimental charge density work the replacement of the central amino acid residue L-Ala by L-Tyr has no significant influence, neither on bond nor on the atomic properties of the oligopeptide main chain. Intermolecular interactions in the form of hydrogen bonds were characterized quantitatively and qualitatively by topological criteria and by mapping the charge density distribution on the Hirshfeld surface.