Accurate X-ray Diffraction Data Research Articles

Accurate X-ray diffraction data required for proper evaluation of bond valence sums and global instability indexes: redetermination of the crystal structures of diamond-like Cu2CdSiS4 and Cu2HgSnS4 as a case study.

Our calculations of the global instability index (G) values for some diamond-like materials with the general formula I2-II-IV-VI4 have indicated that the structures may be unstable or incorrectly determined. To compute the G value of a given compound, the bond valence sums (BVSs) must first be calculated using a crystal structure. Two examples of compounds with high G values, based on data from the literature, are the wurtz-stannite-type dicopper cadmium silicon tetrasulfide (Cu2CdSiS4) and the stannite-type dicopper mercury tin tetrasulfide (Cu2HgSnS4), which were first reported in 1967 and 1965, respectively. In the present study, Cu2CdSiS4 and Cu2HgSnS4 were prepared by solid-state synthesis at 1000 and 900 °C, respectively. The phase purity was assessed by powder X-ray diffraction. Optical diffuse reflectance UV/Vis/NIR spectroscopy was used to estimate the optical bandgaps of 2.52 and 0.83 eV for Cu2CdSiS4 and Cu2HgSnS4, respectively. The structures were solved and refined using single-crystal X-ray diffraction data. The structure type of Cu2CdSiS4 was confirmed, where Cd2+, Si4+ and two of the three crystallographically unique S2- ions lie on a mirror plane. The structure type of Cu2HgSnS4 was also verified, where all ions lie on special positions. The S2- ion resides on a mirror plane, the Cu+ ion is situated on a fourfold rotary inversion axis and both the Hg2+ and the Sn4+ ions are located on the intersection of a fourfold rotary inversion axis, a mirror plane and a twofold rotation axis. Using the crystal structures solved and refined here, the G values were reassessed and found to be in the range that indicates reasonable strain for a stable crystal structure. This work, together with some examples gathered from the literature, shows that accurate data collected on modern instrumentation should be used to reliably calculate BVSs and G values.

Special issue celebrating Professor Yu Wang's 80th birthday

Prof. Yu Wang [the middle of the front row] with friends and colleagues at her 70th birthday symposium and celebration, 2013 It is our great pleasure to organize this special issue of the Journal of the Chinese Chemical Society (JCCS) dedicated to the occasion of Professor Yu Wang's 80th birthday. We do appreciate all authors' great efforts in this special issue. Professor Wang was born in June 1943 and grew up in Hsinchu, Taiwan. She received her bachelor degree in chemistry from National Taiwan University (NTU) in 1966 and her Ph.D. degree from University of Illinois, USA in 1973. After completing her post-doctoral research at State University of New York Buffalo for 1 year and assistant researcher at National Research Council of Canada for 5 years, Professor Wang returned to Taiwan and took up her teaching post as an associate professor at NTU in 1979. She became a full professor in 1981 and served as the Dean of the College of Science from 2002 to 2005. She retired in 2013 as an Emeritus Professor and continued to be active in the community. In addition, she served as the Director General at Department of Math and Physical Science, NSC (1998–2001), and as the Vice President of Academia Sinica, 2014–2016. Professor Wang is a world-renowned scientist for her frontier research on crystallography and chemistry. Several pioneer works have been accomplished during her research career. Two areas are worth mentioning: Charge density studies by combining highly accurate X-ray diffraction data and relevant molecular calculations lead to obtain the insights of chemical bonding and physical properties. This area is expanded now to Quantum Crystallography. The other is her works in spin crossover system, where she accomplished a single crystal to single-crystal spin transition via photo excitation (Photo Crystallography). She has published more than 300 papers. Because of her excellence in research, Professor Wang was awarded as an academician of Academia Sinica in 2010. In addition to her research, she also made a great deal of contributions to both local and international academic communities. She played an important role in the development of local crystallographic society and was instrumental in helping Taiwan become a member of IUCr since 1996. She is reputed as the “Mother of crystallography in Taiwan.” Over the years, she served on several prestigious crystallographic societies: Chairman of Crystallographic Committee, Academia Sinica, Taipei (1995–2003), Commission Member of CSMD, IUCr (1996–2002), the President of Asian Crystallographic Association (AsCA) (2002–2004), and Chairman of CSMD, IUCr (2005–2008). She also served as the Editor-in-Chief of the Journal of Chinese Chemical Society, co-published by Wiley in 2006–2014. In addition to her scientific achievement, Professor Wang is also an excellent educator. She is the most gifted educator I have ever known. She always gives her students the best ever-ending love and enthusiasm. Being her student is our greatest reward. To celebrate Professor Wang's 80th birthday, we dedicate this special issue of the JCCS to her. There are 30 cutting-edge articles in this issue contributed from her former students, colleagues, and friends over the years. We are grateful to all authors who have endeavored to bring about a refreshing novelty in this special issue. Dr. Kuan-Jiuh Lin Chairman and Lifetime Distinguished Professor Department of Chemistry National Chung Hsing University Dr. Hwo-Shuenn Sheu Scientist National Synchrotron Radiation Research Center Dr. Biing-Chiau Tzeng Professor Department of Chemistry and Biochemistry National Chung Cheng University

A combined model of electron density and lattice dynamics refined against elastic diffraction data. Thermodynamic properties of crystalline L-alanine.

Thermodynamic stability is an essential property of crystalline materials, and its accurate calculation requires a reliable description of the thermal motion - phonons - in the crystal. Such information can be obtained from periodic density functional theory (DFT) calculations, but these are costly and in some cases insufficiently accurate for molecular crystals. This deficiency is addressed here by refining a lattice-dynamics model, derived from DFT calculations, against accurate high-resolution X-ray diffraction data. For the first time, a normal-mode refinement is combined with the refinement of aspherical atomic form factors, allowing a comprehensive description and physically meaningful deconvolution of thermal motion and static charge density in the crystal. The small and well diffracting L-alanine system was used. Different lattice-dynamics models, with or without phonon dispersion, and derived from different levels of theory, were tested, and models using spherical and aspherical form factors were compared. The refinements indicate that the vibrational information content in the 23 K data is too small to study lattice dynamics, whereas the 123 K data appear to hold information on the acoustic and lowest-frequency optical phonons. These normal-mode models show slightly larger refinement residuals than their counterparts using atomic displacement parameters, and these features are not removed by considering phonon dispersion in the model. The models refined against the 123 K data, regardless of their sophistication, give calculated heat capacities for L-alanine within less than 1 cal mol-1 K-1 of the calorimetric measurements, in the temperature range 10-300 K. The findings show that the normal-mode refinement method can be combined with an elaborate description of the electron density. It appears to be a promising technique for free-energy determination for crystalline materials at the expense of performing a single-crystal elastic X-ray diffraction determination combined with periodic DFT calculations.

Unraveling the Nature of Weak Hydrogen Bonds and Intermolecular Interactions Involving Elements of Group 14–17 via Experimental Charge Density Analysis

Mapping of charge densities in molecular crystals has been contemplated ever since it was recognized that X-rays are scattered by the electron density in the crystal. The methodology both from the experimental and theoretical perspective was standardized and applied extensively only during the last few decades, as technological advances were a prerequisite in both data collection and computation. Multipole formalism developed for accurate X-ray diffraction data is routinely utilized in conjunction with the concept of atoms in molecules to obtain quantitative estimates of the topological properties in molecular crystals which allow the evaluation of both bonded and non-bonded contacts. Recently, with the advent of quantum crystallography, combining Hirshfeld atom refinement along with libraries of extremely localized molecular orbitals, HAR–ELMOs, has emerged as an alternate approach. Apart from the weak hydrogen bonds, other highly directional non-bonded contacts like halogen, pnicogen, chalcogen and carbon bonds have been subjected to charge density analysis to experimentally observe and quantify σ-holes using experimental high-resolution X-ray diffraction data. The recognition of lack of directional preferences in hydrophobic interactions is demonstrated experimentally which might have far reaching consequences in the areas of materials and biology.

Building Blocks for High-Efficiency Organic Photovoltaics: Interplay of Molecular, Crystal, and Electronic Properties in Post-Fullerene ITIC Ensembles.

Accurate single-crystal X-ray diffraction data offer a unique opportunity to compare and contrast the atomistic details of bulk heterojunction photovoltaic small-molecule acceptor structure and packing, as well as provide an essential starting point for computational electronic structure and charge transport analysis. Herein, we report diffraction-derived crystal structures and computational analyses on the n-type semiconductors which enable some of the highest efficiency organic solar cells produced to date, 3,9-bis(2-methylene-(3-(1,1-dicyanomethylene)-indanone))-5,5,11,11-tetrakis(4-hexylphenyl)-dithieno[2,3-d:2',3'-d']-s-indaceno[1,2-b:5,6-b']dithiophene (ITIC) and seven derivatives (including three new crystal structures: 3,9-bis(2-methylene-(3-(1,1-dicyanomethylene)-indanone))-5,5,11,11-tetrakis(4-propylphenyl)-dithieno[2,3-d:2',3'-d']-s-indaceno[1,2-b:5,6-b']dithiophene (ITIC-C3), 3,9-bis(2-methylene-(3-(1,1-dicyanomethylene)-indanone))-5,5,11,11-tetrakis(3-hexylphenyl)-dithieno[2,3-d:2',3'-d']-s-indaceno[1,2-b:5,6-b']dithiophene (m-ITIC-C6), and 3,9-bis(2-methylene-((3-(1,1-dicyanomethylene)-6,7-difluoro)-indanone))-5,5,11,11-tetrakis(4-butylphenyl)-dithieno[2,3-d:2',3'-d']-s-indaceno[1,2-b:5,6-b']dithiophene (ITIC-C4-4F). IDTT acceptors typically pack in a face-to-face fashion with π-π distances ranging from 3.28-3.95 Å. Additionally, edge-to-face packing is observed with S⋯π interactions as short as 3.21-3.24 Å. Moreover, ITIC end group identities and side chain substituents influence the nature and strength of noncovalent interactions (e. g. H-bonding, π-π) and thus correlate with the observed packing motif, electronic structure, and charge transport properties of the crystals. Density functional theory (DFT) calculations reveal relatively large nearest-neighbor intermolecular π-π electronic couplings (5.85-56.8 meV) and correlate the nature of the band structure with the dispersion interactions in the single crystals and core-end group polarization effects. Overall, this combined experimental and theoretical work reveals key insights into crystal engineering strategies for indacenodithienothiophene (IDTT) acceptors, as well as general design rules for high-efficiency post-fullerene small molecule acceptors.

Structural Reasons for the Nonlinear Optical Properties of KTP Family Single Crystals

A brief review focuses on studies into the structural reasons for the nonlinear optical properties of crystals of the potassium titanyl phosphate family, performed at the Shubnikov Institute of Crystallography. Accurate X-ray diffraction data are discussed, providing evidence that the optical susceptibility of crystals is related not only to the alternation of long and short Ti–O bonds in the chains of TiO6 octahedra, but to the geometry of tetrahedral anions and the alkaline cation arrangement in the structure channels, as well. The contribution of each of the three structural components depends on the crystal composition.

Experimental Observation of the Nature of Weak Chemical Bonds in Labile Compounds.

Accurate single-crystal X-ray diffraction data afford a total electron density distribution for crystalline materials by employing an aspherical atomic model with comparable accuracy to that of theoretical calculations. Chemical bonds and intermolecular interactions in the crystalline state are characterized based on the electron density distribution of valence electrons, as well as structural parameters. Herein, the bonding nature of weak chemical bonds in labile compounds, such as hypervalent bonds and delocalized π-bonds, is explored on the basis of electronic structures derived from experimental electron density distribution analyses. In addition, the visualization of a radicalic orbital distribution on an sp2 -hydridized carbon atom is demonstrated.

Interaction and dynamics of ionic liquids based on choline and amino acid anions.

The combination of amino acid anions with the choline cation gives origin to a new and potentially important class of organic ionic liquids that might represent a viable and bio-compatible alternative with respect to the traditional ones. We present here a detailed study of the bulk phase of the prototype system composed of the simplest amino acid (alanine) anion and the choline cation, based on ab initio and classical molecular dynamics. Theoretical findings have been validated by comparing with accurate experimental X-ray diffraction data and infrared spectra. We find that hydrogen bonding (HB) features in these systems are crucial in establishing their local geometric structure. We have also found that these HBs once formed are persistent and that the proton resides exclusively on the choline cation. In addition, we show that a classical force field description for this particular ionic liquid can be accurately performed by using a slightly modified version of the generalized AMBER force field.

Monoclinic–Orthorhombic Phase Transition in ZSM-5 Zeolite: Spontaneous Strain Variation and Thermodynamic Properties

Modeling the ferroelastic properties of the monoclinic–orthorhombic phase transition of ZSM-5 zeolites is very relevant to the understanding of the effects of lattice strain on adsorption and diffusion properties of these microporous materials widely used in catalysis and water treatment. Using very accurate synchrotron X-ray diffraction data, we report here the analysis of spontaneous strain variation across the transition. According to the Landau theory, the behavior of the order parameter reveals the tricritical character of this transition from ferroelastic to paraelastic phase in ZSM-5. Combination of results from Landau analysis with calorimetric data allows the calculation of thermodynamic quantities which are in good agreement with the experimentally derived ones.

Electron Properties of Carbamazepine Drug in Form III

The experimental electron and electrostatic properties of carbamazepine drug molecule (form III) were determined from accurate high-resolution X-ray diffraction data collected at 100 K. The results are compared to quantum mechanics calculations for gas-phase molecule and multimers. The experimental electron density was refined using the Hansen–Coppens multipole formalism, and the deformation electron density maps are compared to the theoretical ones. Both experimental and theoretical deformation electron density maps presented here are based on Clementi’s promolecule densities used as a reference. The topological analysis of the carbamazepine electron density using Bader’s theory has been carried out, and the integrated atomic charges are presented and compared to those obtained for molecules with equivalent chemical fragments. The charge values compare qualitatively well with those obtained by theoretical calculations. The electrostatic potential features and the interaction electrostatic energies are also discussed.

VALTOPO: a program for the determination of atomic and molecular properties from experimental electron densities

VALTOPOis a program for the multipole refinement of accurate X-ray diffraction data and for the determination of electrostatic properties. It is a new version ofVALRAY, including the quantum theory of atoms in molecules analysis as implemented in theTOPOND98program. Two test structures, L-alanine and the complex of (E)-1,2-bis(4-pyridyl)ethylene with 1,4-diiodotetrafluorobenzene, have been analysed in order to illustrate some of the potentialities of the program.

Can topological analysis of intermolecular interactions explain differences in the physico-chemical properties of related chiral compounds?

Interactions between chiral molecules play a fundamental role for the most biological and many chemical processes. Due to the complexity of the interactions that range from normal hydrogen bonds to weaker interactions like C-H—O hydrogen bonds and stacking, it can be difficult to relate overall thermodynamic properties to the nature of the intermolecular interactions. The topological analysis developed by R.W. Bader for theoretical electron densities has proven to be a powerful tool to analyse intermolecular interactions in crystals based on an analysis of experimental electron densities obtained from accurate high resolution X-ray diffraction data. Our recent investigations of the molecular crystal naphthalene revealed that the topological analysis could reveal and characterize unexpected interatomic interactions [1]. The two pentose epimers xylitol and ribitol differ in the physico-chemical properties, the acentric xylitol being the higher melting and the less dense than ribitol. All possible hydrogen bond donors participate in the hydrogen bond interactions in both compounds, and the topological analysis confirms the energetic similarity of these interactions. The investigations suggest that the origin of the differences in physico-chemical properties is related to differences in the weaker intermolecular interactions and in the entropy. Crystallization of a racemate may lead to racemic compound composed of equal amounts of the two enantiomers or to a spontaneous resolution of crystals that are formed by the pure enantiomers, and the outcome of the process depends on differences in enthalpy and entropy. We have investigated the intermolecular interactions in closely related crystal structures, e.g. a racemic para-fluoromandelic acid and its corresponding enantiomer. The racemic para-fluoromandelic acid showing the unusual behaviour of being the higher melting. An earlier investigation showed that the two forms have an identical hydrogen bond pattern. This was confirmed by the topological analyses based on accurate X-ray diffraction data. Though additional features were revealed from the topological analysis it also showed the significance of supplementing the investigations with theoretical calculations.

On functions and quantities derived from the experimental electron density.

Calculation of properties of molecules and crystals as obtained from a multipole electron-density model restored from the accurate X-ray diffraction data is considered. Electronic and exchange energy-density distributions are presented along with those of local temperature and local entropy. Integration of the local functions over atomic basins defined by the zero-flux condition allows properties of molecules and crystals to be expressed in terms of atomic contributions derived directly from X-ray diffraction experiments. Distributions of local Fermi momentum and one-electron potential are considered as well. The approach has been applied to diamond, sodium fluoride, sodium chloride, solid chlorine, alpha-oxalic acid dihydrate and YBa(2)Cu(3)O(6.98).

An experimental (120 K) and theoretical electron-density study of KMnO4 and KClO4.

The experimental electron density rho(r) of the two isomorphic salts KMnO(4) and KClO(4) was determined by a multipole analysis of accurate X-ray diffraction data at 120 K. The quantum theory of atoms in molecules was applied to rho(r) and to its Laplacian nabla(2)rho(r). The bonds were characterized using the topological parameters at the bond critical points of the density rho(r), nabla(2)rho(r), G(r) (kinetic energy density), V(r) (potential energy density) and H(r) (total energy density). According to the classification recently proposed by Espinosa, Alkorta, Elguero & Molins [J. Chem. Phys. (2002), 117, 5529-5542], the K-O and Cl-O bonds have a pure ionic and covalent character, respectively, while the Mn-O bonds show an intermediate behaviour. The results of the topological analysis of the experimental and theoretical (fully periodic Hartree-Fock and density functional calculations) electron density are in good agreement, even on a quantitative level. The atomic charges, determined by performing an integration over the topological basins, are about +2 e for Mn and Cl atoms. The ionic radius, estimated with the distance of the bond critical point from the nucleus, is in agreement with a charge of +2 e for the Mn atom.

Structure of incommensurate ammonium tetrafluoroberyllate studied by structure refinements and the maximum entropy method.

Incommensurately modulated ammonium tetrafluoroberyllate (AFB) occurs in a narrow temperature interval between the paraelectric room-temperature phase with space group Pnma (Ti = 178 K) and the ferroelectric low-temperature phase with space group Pna2(1) (Tc = 173 K). The structure is determined from accurate single-crystal X-ray diffraction data collected with synchrotron radiation at 175 K. The superspace group of the structure is Pnma(alpha00)0ss with alpha = 0.4796 (4). Both structure refinements and the maximum entropy method lead to the same structure model, which involves only single harmonic modulations. The building units of the structure are BeF4(2-) and NH4+ complex ions with approximately tetrahedral point symmetry. They are relatively rigid and the modulations consist mainly of translations of the tetrahedra and their rotations around a fixed axis. The modulation is related to changes in the network of the hydrogen bonds. The low-temperature superstructure can be described as a commensurately modulated structure with the same superspace symmetry. The first harmonic modulations of the low-temperature and incommensurate phases are related by a scale factor with a value of approximately two. In addition, the low-temperature phase exhibits a second harmonic modulation that is responsible for shifts along c and the ferroelectricity in this phase. The experimental data of the incommensurate phase do not contain any evidence for the presence of a second harmonic in the modulation functions. This suggests that the development of the second harmonic, i.e. the development of the spontaneous polarization, is responsible for the lock-in transition.

Experimental and Theoretical Charge Density Studies of Tetrafluorophthalonitrile and Tetrafluoroisophthalonitrile

The experimental electron density distributions (EDD) in tetrafluorophthalonitrile and tetrafluoroisophthalonitrile have been determined from a multipole refinement with use of accurate X-ray diffraction data collected at 100 K. As hydrogen atoms pose a serious challenge to a successful X-ray based EDD determination due to their diminishing diffraction power, the absence of any such atoms in the studied complexes is an important advantage. The experimental EDD is compared with theoretical densities resulting from high-level ab initio and DFT calculations using the atoms in molecules theory. Topological analysis of the electron density was used to compare the two different isomers and to estimate the similarity of identical functional groups in different crystalline environments. Comparison with theoretical results reveals subtle differences in C−F bonds. The experimental molecular electrostatic potential satisfactorily explains the observed differences in the patterns of weak intermolecular interactions.

Structural investigation of Fe2O3–SiO2nanocomposites through radial distribution functions analysis

Two Fe2O3–SiO2 nanocomposites containing 50% by weight of iron oxide were prepared by a sol–gel method. By changing the surface to volume ratio of the gelling mass from 0.04 (sample A) to 0.3 cm−1 (sample B), gelation times changed, resulting in nanoparticles of average size of about 10 and 4 nm, respectively. Accurate X-ray diffraction (XRD) data were collected and used to calculate total structure and correlation functions. The analysis of these functions unequivocally proved that in both samples maghemite is the iron oxide formed. The result demonstrated that decreasing the gelation time gives rise to the formation of smaller and smaller nanoparticles of the same phase. The possibility of interpreting the XRD pattern of sample B in terms of occurrence of 2-line ferrihydrite was discussed.

Simultaneous variation of multipole parameters and Gram-Charlier coefficients in a charge-density study of tetrafluoroterephthalonitrile based on X-ray and neutron data.

Difficulties encountered in modelling the scattering of fluorine in organic compounds have been investigated through refinements of accurate X-ray and neutron diffraction data measured on tetrafluoroterephthalonitrile, TFT, at 122.4 K. Multipole refinements led to a highly contracted octopole on fluorine. The subsequent analysis revealed that fluorine does not possess a valence octopole but exhibits anharmonic thermal motion that can be modelled by the octopole multipole parameters. The scattering contribution from the octopole shows the same cubic dependence in the scattering vector as the Gram-Charlier expansion of the nuclear displacements to third order. The analysis also showed that refinement of third-order Gram-Charlier coefficients on fluorine requires data to at least 0.93 A(-1) resolution in sinthetas/lambda. The X-ray data extending to 1.27 A(-1) were of sufficient resolution to include third-order Gram-Charlier coefficients for N, F and the cyano C atoms in the refinement, whereas the neutron data only enabled refinement of the third-order Gram-Charlier coefficients for nitrogen. The refinements of the neutron and X-ray diffraction data yielded identical atomic displacement parameters for all the atoms. Though inclusion of anharmonic motion for N and F atoms provides the best model, it does not affect the crystal electron density, and all intramolecular bond critical points have identical features. Application of the anharmonic model, however, leads to small differences in the intermolecular interactions, which is illustrated by the electrostatic potential adjacent to the N atom. The characteristics of the C-F bond were elucidated by the topological analysis of the crystal electron density, which also supported the proposed quinonoid structure of the benzene ring.

Experimental and Theoretical Electron Density Studies in Large Molecules: NAD+, β-Nicotinamide Adenine Dinucleotide

NAD+ is the oxidized form of the coenzyme redox pair NAD+/NADH and plays a main role in catalysis of biological processes. Accurate X-ray diffraction data have been collected at 100 K from a crystal of the free acid form of the coenzyme NAD+ with a CCD area detector up to 0.55 A resolution. A multipole refinement was carried out, and the electron density of the molecule has been analyzed in order to further model its interaction with enzymes. The electron density of NAD+ has also been computed by a DFT (density functional theory) approach. The charge density and electrostatic potential obtained from experiment and theory compare well. There is a very good agreement between the theoretical and experimental charge densities for all the C−C and C−N type connections of the NAD+ molecule; this is less the case for the pyrophosphate region. The experimental electron density lone pairs of the pyrophosphate lateral oxygen atoms are distorted by hydrogen bonds effects. The electrostatic potential has large spatial...

Electronic topological transition in AuX2 (X = In, Ga and Al) compounds at highpressures

We present accurate x-ray diffraction data at high pressures for AuIn2,AuGa2 andAuAl2, obtained using a diamond anvil cell with the ELETTRA synchrotron source. Theresulting P–V data obtainedfrom the d-valueswere used to get the universal equation of state (UEOS), which is compared withtheoretical estimates. Deviation from linearity is evident in the UEOS curves ofAuIn2 and AuGa2, thus verifying that some of the observed anomalies inthese systems below 5 GPa are due to electronic topological transitions.