Magdalena Woińska

Hydrogen atoms can be located accurately and precisely by x-ray crystallography

Hydrogen atoms cannot hide from x-rays anymore but can instead be detected very reliably in routine measurements. Precise and accurate structural information on hydrogen atoms is crucial to the study of energies of interactions important for crystal engineering, materials science, medicine, and pharmacy, and to the estimation of physical and chemical properties in solids. However, hydrogen atoms only scatter x-radiation weakly, so x-rays have not been used routinely to locate them accurately. Textbooks and teaching classes still emphasize that hydrogen atoms cannot be located with x-rays close to heavy elements; instead, neutron diffraction is needed. We show that, contrary to widespread expectation, hydrogen atoms can be located very accurately using x-ray diffraction, yielding bond lengths involving hydrogen atoms (A–H) that are in agreement with results from neutron diffraction mostly within a single standard deviation. The precision of the determination is also comparable between x-ray and neutron diffraction results. This has been achieved at resolutions as low as 0.8 Å using Hirshfeld atom refinement (HAR). We have applied HAR to 81 crystal structures of organic molecules and compared the A–H bond lengths with those from neutron measurements for A–H bonds sorted into bonds of the same class. We further show in a selection of inorganic compounds that hydrogen atoms can be located in bridging positions and close to heavy transition metals accurately and precisely. We anticipate that, in the future, conventional x-radiation sources at in-house diffractometers can be used routinely for locating hydrogen atoms in small molecules accurately instead of large-scale facilities such as spallation sources or nuclear reactors.

Contrasting Elastic Properties of Heavily B- and N-doped Graphene with Random Impurity Distributions Including Aggregates

We focused on elastic properties of B- and N-doped graphene in a wide range of concentrations up to 20%. The Young’s, bulk, and shear moduli and Poisson’s ratio have been calculated by means of density functional theory for a representative set of supercells with disordered impurity patterns including aggregates. In contrast to earlier work, it is demonstrated that doping with nitrogen strengthens the graphene layers, whereas incorporation of boron induces large structural and morphological changes seen in simulated STM images. Young’s and shear moduli increase or decrease with the doping concentration for nitrogen or boron, respectively, while bulk modulus and Poisson’s ratio exhibit opposite trends. Elastic properties of samples for both types of impurities are strongly related to the electronic structures, especially for heavy doping (>12%). Local arrangements of dopants and an aggregation or separation of impurities play crucial roles in the determination of stiffness in the investigated systems. Inte...

Electronic structure of graphene functionalized with boron and nitrogen

We present a theoretical study of the structural and electronic properties of graphene monolayer functionalized with boron and nitrogen atoms substituting carbon atoms. Our study is based on the ab initio calculations in the framework of the density functional theory. We calculate the binding energies of the functionalized systems, changes in the morphology caused by functionalization, and further the band gap energy as a function of the concentration of dopants. Moreover, we address the problem of possible clustering of dopants at a given concentration. We define the clustering parameter to quantify the dependence of the properties of the functionalized systems on the distribution of B/N atoms. We show that clustering of B/N atoms in graphene is energetically unfavorable in comparison to the homogenous distribution of dopants. For most of the structures, we observe a nonzero energy gap that is only slightly dependent on the concentration of the substituent atoms. (© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

Transferability of Atomic Multipoles in Amino Acids and Peptides for Various Density Partitions

Multipole expansion of electron density distribution is an efficient tool for evaluating the energy of interactions in molecules. In as much as atoms in macromolecules such as peptides are modeled with certain types of atoms derived from small organic molecules, investigating transferability of atomic multipoles for various partitions of molecular electron density is an important issue. In this study, multipole moments up to hexadecapoles for types of atoms present in selected amino acids, as well as di- and tripeptides composed of these amino acids, are computed using three density partitions: Hansen-Coppens aspherical pseudoatoms formalism, Hirshfelds stockholder partition, and Baders atoms in molecules theory. Electron density of relevant molecules is derived in a procedure including molecular wave function ab initio calculation for isolated molecules in geometry from X-ray measurements, calculation of theoretical structure factors for molecules put in a pseudocubic cell, and multipole refinement as in crystallographic data processing and computation of multipoles. The results were compared to calculations of multipole moments in AIM and in stockholder density partitions obtained directly from molecular wave functions. The presented comparison does not point unambiguously to any particular influence of multipole refinement on moments obtained from these two partitions. The advantage of stockholder partitioning in terms of transferability of atomic multipoles is affirmed. AIM and pseudoatoms provide slightly less transferable multipoles of lower order. Higher rank of multipole expansion reveals a transferability improvement in the case of AIM and meaningful deterioration for pseudoatoms.

N,N'-(Pyridine-2,6-di-yl)dibenzamide.

The molecule of the title compound, C19H15N3O2, is completed by the application of crystallographic twofold symmetry, with the pyridine N atom lying on the rotation axis. The molecular structure is approximately planar, the dihedral angle between the mean planes of the pyridine and benzene rings being 7.53 (11)°. In the crystal, N—H⋯O hydrogen bonds link the molecules into a two-dimensional array perpendicular to the c axis.

Structure, charge density and energetic features of quinoline derivatives

Quinoline derivatives are common among many natural compounds; moreover, quinoline is a structural subunit which plays an important role in the design and synthesis of pharmaceutically active substances. This makes investigation of its derivatives and their properties particularly interesting and is the motivation for the presented X-ray diffraction and computational study of crystal structure, electron density (ED) and intermolecular interactions of four quinoline derivatives. The derivatives differ in the substituent at position 8 which is either a halogen atom (Cl, Br, I) or -S-Ph moiety. Highresolution X-ray measurements were performed in each case, resulting in experimental data of varying quality, possibly characterized by the presence of anharmonic motion, which makes them suitable for verifying capabilities of two different charge density models compared in this work.

Precision and accuracy of single-crystal X-ray results

Krzysztof Wozniak1, W. Fabiola Sanjuan-Szklarz1, Magdalena Woinska1, Paulina Dominiak1, Simon Grabowsky2, Dylan Jayatilaka3, Matthias Gutmann4 1Chemistry Department, University Of Warsaw, Warszawa, Poland, 2Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Bremen, Germany, 3School of Chemistry and Biochemistry, University of Western Australia, Perth, Australia, 4Rutherford Appleton Laboratory, ISIS Facility,, Chilton, Didcot, Oxfordshire, United Kingdom E-mail: kwozniak@chem.uw.edu.pl

Hydrogen maleate salts: Precise and accurate determination of the hydrogen atom position in short hydrogen bonds using X-ray diffraction at extremely low temperatures

Hydrogen maleate salts offer the unique opportunity to follow a pseudo-reaction pathway of a proton transfer not only in theoretical simulations but also experimentally because the hydrogen position in the strong and short intramolecular O-H-O hydrogen bond is highly flexible dependent on the cation. There are numerous crystal structures of hydrogen maleate salts in the literature showing that the O-O distance is constant around 2.45 A, but the O-H distances vary from 0.83 A/1.63 A in highly asymmetric hydrogen bonds to 1.22A in symmetric hydrogen bonds with a large variety of intermediate distances. This means that snapshots along a pseudo-reaction pathway can be measured and with the symmetric hydrogen bonds, even a model for a possible transition state is accessible. Experimental electron-density modelling of high-resolution low-temperature (20K) synchrotron X-ray data of nine different compounds (4-aminopyridinium, 8-hydroxyquinolinium, barium, calcium, potassium, lithium, magnesium, sodium and phenylalaninium hydrogen maleates) measured at SPring-8, Japan, will give electronic information on the pseudo-reaction mechanism. For these detailed electron-density analyses, it is crucial to obtain accurate positional and displacement parameters of the hydrogen atoms. It is a widespread notion that this can only be achieved using neutron-diffraction techniques. Therefore we have collected Laue-diffraction neutron data at the Bragg institute of ANSTO, Australia. Using those data as a reference, we will show that we can obtain hydrogen atom positions and bond lengths involving hydrogen atoms with the same accuracy and precision from X-ray data as from neutron data even from X-ray data of routinely achievable resolution if an advanced X-ray refinement technique is used. This new technique is called Hirshfeld Atom Refinement (HAR) [1]. [1] S. C. Capelli, H.-B. Bürgi, B. Dittrich, S. Grabowsky, D. Jayatilaka: Hirshfeld atom refinement. IUCrJ 2014, 1, 361-379.

Applications of X-ray Wavefunction Refinement

X-ray wavefunction refinement (XWR) is a way of modeling the total aspherical electron density from an X-ray diffraction experiment on a single crystal of a molecular compound. It is a combination of existing quantum-crystallographical techniques: In the first step, geometry is determined using Hirshfeld atom refinement,[1] which is based on a stockholder partitioning of quantum-mechanical aspherical electron densities. In the second step, the same wavefunction is fitted to the experimental data to reproduce the diffraction pattern and simultaneously minimize the molecular energy.[2] The XWR protocol involves embedding the molecule into a field of point charges and dipoles as well as termination strategies to avoid overfitting.[3] Results from an X-ray wavefunction refinement are not restricted to the analysis of electron density: the full reconstructed density matrix is available. Therefore, chemical problems can be tackled with suitable tools for any given question including, e.g., experimentally derived bond orders, electron-pair localisation information, or energetics. We will present first applications of this protocol for a selection of organic (hydrogen maleate salts, sulfur-containing protease inhibitors) and inorganic (siloxanes, sulfur dioxide) compounds, for which we measured high-resolution low-temperature X-ray diffraction data at various synchrotron facilities. We will show geometry improvements, anisotropic displacement parameters for hydrogens, anharmonic motion parameters for sulfur and chlorine atoms, and improved total electron-density distributions in comparison to results from multipole modeling. Moreover, we will discuss the contribution of the experimental data to the final constrained wavefunction (defect density) and demonstrate how the experimentally derived orbital-based descriptors assist in solving fundamental chemical problems.

Ab initio modeling of graphene layer functionalized with boron and nitrogen

We present a computational study of the phenomenon of opening the band gap in graphene by means of functionalization with boron and nitrogen atoms. For most of the considered structures, we observe a nonzero energy gap with the width slightly dependent on the concentration of the substituent atoms. Additionally, elastic properties for graphene functionalized with B/N atoms for concentrations of 2% and 4% have been predicted. N-substitution almost does not influence the elastic moduli of graphene, while changes caused by B-substitution are more remarkable.