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Quantum Chemistry | Theoretical and Computational Chemistry | F-Block Chemistry
Expanding Knowledge in the Chemical Sciences | Expanding Knowledge in the Physical Sciences |
Publisher: International Union of Crystallography (IUCr)
Date: 23-04-2020
DOI: 10.1107/S1600576720003775
Abstract: Hybrid photon-counting detectors are widely established at third-generation synchrotron facilities and the specifications of the Pilatus3 X CdTe were quickly recognized as highly promising in charge-density investigations. This is mainly attributable to the detection efficiency in the high-energy X-ray regime, in combination with a dynamic range and noise level that should overcome the perpetual problem of detecting strong and weak data simultaneously. These benefits, however, come at the expense of a persistent problem for high diffracted beam flux, which is particularly problematic in single-crystal diffraction of materials with strong scattering power and sharp diffraction peaks. Here, an in-depth examination of data collected on an inorganic material, FeSb 2 , and an organic semiconductor, rubrene, revealed systematic differences in strong intensities for different incoming beam fluxes, and the implemented detector intensity corrections were found to be inadequate. Only significant beam attenuation for the collection of strong reflections was able to circumvent this systematic error. All data were collected on a bending-magnet beamline at a third-generation synchrotron radiation facility, so undulator and wiggler beamlines and fourth-generation synchrotrons will be even more prone to this error. On the other hand, the low background now allows for an accurate measurement of very weak intensities, and it is shown that it is possible to extract structure factors of exceptional quality using standard crystallographic software for data processing ( SAINT-Plus , SADABS and SORTAV ), although special attention has to be paid to the estimation of the background. This study resulted in electron-density models of substantially higher accuracy and precision compared with a previous investigation, thus for the first time fulfilling the promise of photon-counting detectors for very accurate structure factor measurements.
Publisher: American Chemical Society (ACS)
Date: 14-02-2019
DOI: 10.1021/JACS.8B12927
Abstract: High-resolution synchrotron and neutron single-crystal diffraction data of 18-crown-6/(pentakis)urea measured at 30 K are combined, with the aim of better appreciating the electrostatics associated with intermolecular interactions in condensed matter. With two 18-crown-6 molecules and five different urea molecules in the crystal, this represents the most ambitious combined X-ray/synchrotron and neutron experimental charge density analysis to date on a cocrystal or host-guest system incorporating such a large number of unique molecules. The dipole moments of the five urea guest molecules in the crystal are enhanced considerably compared to values determined for isolated molecules, and 2D maps of the electrostatic potential and electric field show clearly how the urea molecules are oriented with dipole moments aligned along the electric field exerted by their molecular neighbors. Experimental electric fields in the range of 10-19 GV m
Publisher: American Chemical Society (ACS)
Date: 18-09-2014
DOI: 10.1021/IC501152J
Abstract: Four transition metal formate coordination polymers with anionic frameworks, namely, Na[Mn(HCOO)3], K[Mn(HCOO)3], Na2[Cu3(HCOO)8], and K2[Cu5(HCOO)12], were synthesized using a mild solution chemistry approach. Multitemperature single-crystal (100-300 K) and powder X-ray diffraction studies of the compounds reveal structures of large ersity ranging from cubic chiral Na-Mn formate to triclinic Na-Cu formate. The structural variety is caused by the nature of the transition metals, the alkali metal ion templation, and the versatility of the formate group, which offers metal-metal coordination through three different O-C-O bridging modes (syn-syn, syn-anti, anti-anti) in addition to metal-metal bridging via a single oxygen atom. The two manganese(II) compounds contain mononuclear, octahedrally coordinated moieties, but the three-dimensional connectivity between the manganese octahedra is very different in the two structures. The two copper frameworks, in contrast, consist of binuclear and mononuclear moieties (Na-Cu formate) and trinuclear and mononuclear moieties (K-Cu formate), respectively. Procrystal electron density analysis of the compounds indicates one-dimensional K(+)-ion conductivity in K-Mn and K-Cu, and the nature of the proposed potassium ion migration is compared with results from similar analysis on known Na(+) and K(+) ion conductors. K-Mn and Na-Mn were tested as cathode materials, but this resulted in poor reversibility due to low conductivity or structural collapse. The magnetic properties of the compounds were studied by vibrating s le magnetometric measurements, and their thermal stabilities were determined by thermogravimetric analysis and differential thermal analysis. Despite structural differences, the metal formates that contain the same transition metal have similar magnetic properties and thermal decomposition pathways, that is, the nature of the transition metal controls the compound properties.
Publisher: International Union of Crystallography (IUCr)
Date: 15-01-2005
Publisher: American Chemical Society (ACS)
Date: 21-07-2014
DOI: 10.1021/CM501681R
Publisher: International Union of Crystallography (IUCr)
Date: 2018
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C5DT00447K
Abstract: The effects of non-hydrostaticity in n -pentane-isopentane were overcome by annealing, and accurate crystal structures of Co 3 (dpa) 4 Cl 2 ·CH 2 Cl 2 were determined above 10 GPa.
Publisher: International Union of Crystallography (IUCr)
Date: 19-09-2014
DOI: 10.1107/S2053273314015599
Abstract: Accurate atomic displacement parameters (ADPs) are a good indication of high-quality diffraction data. Results from the newly commissioned time-of-flight Laue diffractometer TOPAZ at the SNS are presented. Excellent agreement is found between ADPs derived independently from the neutron and X-ray data emphasizing the high quality of the data from the time-of-flight Laue diffractometer.
Publisher: American Chemical Society (ACS)
Date: 09-2020
Publisher: Royal Society of Chemistry (RSC)
Date: 2022
DOI: 10.1039/D1RA08389A
Abstract: In this study, the 1:1 cocrystal of theophylline and malonic acid originally engineered by Trask undergoes charge density analysis to rationalise the chemical change process seen throughout crystallisation.
Publisher: American Chemical Society (ACS)
Date: 26-07-2012
DOI: 10.1021/IC301372M
Abstract: One of the most basic concepts in chemical bonding theory is the octet rule, which was introduced by Lewis in 1916, but later challenged by Pauling to explain the bonding of third-row elements. In the third row, the central atom was assumed to exceed the octet by employing d orbitals in double bonding leading to hypervalency. Ever since, polyoxoanions such as SO(4)(2-), PO(4)(3-), and ClO(4)(-) have been paradigmatic ex les for the concept of hypervalency in which the double bonds resonate among the oxygen atoms. Here, we examine S-O bonding by investigating the charge density of the sulfate group, SO(4)(2-), within a crystalline environment based both on experimental and theoretical methods. K(2)SO(4) is a high symmetry inorganic solid, where the crystals are strongly affected by extinction effects. Therefore, high quality, very low temperature single crystal X-ray diffraction data were collected using a small crystal (∼30 μm) and a high-energy (30 keV) synchrotron beam. The experimental charge density was determined by multipole modeling, whereas a theoretical density was obtained from periodic ab initio DFT calculations. The chemical bonding was jointly analyzed within the framework of the Quantum Theory of Atoms In Molecules only using quantities derived from an experimental observable (the charge density). The combined evidence suggests a bonding situation where the S-O interactions can be characterized as highly polarized, covalent bonds, with the "single bond" description significantly prevailing over the "double bond" picture. Thus, the study rules out the hypervalent description of the sulfur atom in the sulfate group.
Publisher: International Union of Crystallography (IUCr)
Date: 2018
DOI: 10.1107/S2052252517015548
Abstract: Hirshfeld atom refinement (HAR) is a novel X-ray structure refinement technique that employs aspherical atomic scattering factors obtained from stockholder partitioning of a theoretically determined tailor-made static electron density. HAR overcomes many of the known limitations of independent atom modelling (IAM), such as too short element–hydrogen distances, r ( X —H), or too large atomic displacement parameters (ADPs). This study probes the accuracy and precision of anisotropic hydrogen and non-hydrogen ADPs and of r ( X —H) values obtained from HAR. These quantities are compared and found to agree with those obtained from (i) accurate neutron diffraction data measured at the same temperatures as the X-ray data and (ii) multipole modelling (MM), an established alternative method for interpreting X-ray diffraction data with the help of aspherical atomic scattering factors. Results are presented for three chemically different systems: the aromatic hydrocarbon rubrene (orthorhombic 5,6,11,12-tetraphenyltetracene), a co-crystal of zwitterionic betaine, imidazolium cations and picrate anions (BIPa), and the salt potassium hydrogen oxalate (KHOx). The non-hydrogen HAR-ADPs are as accurate and precise as the MM-ADPs. Both show excellent agreement with the neutron-based values and are superior to IAM-ADPs. The anisotropic hydrogen HAR-ADPs show a somewhat larger deviation from neutron-based values than the hydrogen SHADE-ADPs used in MM. Element–hydrogen bond lengths from HAR are in excellent agreement with those obtained from neutron diffraction experiments, although they are somewhat less precise. The residual density contour maps after HAR show fewer features than those after MM. Calculating the static electron density with the def2-TZVP basis set instead of the simpler def2-SVP one does not improve the refinement results significantly. All HARs were performed within the recently introduced HARt option implemented in the Olex2 program. They are easily launched inside its graphical user interface following a conventional IAM.
Publisher: Wiley
Date: 16-02-2016
Abstract: The energy landscape governing a new pressure-induced phase transition in the hydroquinone-formic acid clathrate is reported in which the host structure collapses, opening up the cavity channels within which the guest molecules migrate and order. The reversible isosymmetric phase transition causes significant changes in the morphology and the birefringence of the crystal. The subtle intermolecular interaction energies in the clathrate are quantified at varying pressures using novel model energies and energy frameworks. These calculations show that the high-pressure phase forms a more stable host network at the expense of less-stable host-guest interactions. The phase transition can be kinetically hindered using a nonhydrostatic pressure-transmitting medium, enabling the comparison of intermolecular energies in two polymorphic structures in the same pressure range. Overall this study illustrates a need for accurate intermolecular energies when analyzing self-assembly structures and supramolecular aggregates.
Publisher: International Union of Crystallography (IUCr)
Date: 31-05-2014
DOI: 10.1107/S2052520614003497
Abstract: Ionothermal reaction between Mn II (acetate) 2 ·4H 2 O and 1,3,5-benzenetricarboxylic acid (H 3 BTC) in either of the two ionic liquids 1-ethyl-3-methylimidazolium bromide (EMIMBr) and 1-ethyl-3-methylimidazolium tosylate (EMIMOTs) resulted in the formation of the new metal–organic framework (MOF) EMIM[Mn II BTC] (BTC = 1,3,5-benzenetricarboxylate). The compound crystallizes in the orthorhombic space group Pbca with unit-cell parameters of a = 14.66658 (12), b = 12.39497 (9), c = 16.63509 (14) Å at 100 K. Multi-temperature single-crystal (15–340 K) and powder X-ray diffraction studies (100–400 K) reveal strongly anisotropic thermal expansion properties. The linear thermal expansion coefficients, α L ( l ), attain maximum values at 400 K along the a - and b -axis, with α L ( a ) = 115 × 10 −6 K −1 and α L ( b ) = 75 × 10 −6 K −1 . At 400 K a negative thermal expansion coefficient of −40 × 10 −6 K −1 is observed along the c -axis. The thermal expansion is coupled to a continuous deformation of the framework, which causes the structure to expand in two directions. Due to the rigidity of the linker, the expansion in the ab plane causes the network to contract along the c -axis. Hirshfeld surface analysis has been used to describe the interaction between the framework structure and the EMIM cation that resides within the channel. This reveals a number of rather weak interactions and one governing hydrogen-bonding interactions.
Publisher: Royal Society of Chemistry (RSC)
Date: 2014
DOI: 10.1039/C3SC52977K
Abstract: The chemical bonding in the pyrite (left) and marcasite (right) polymorphs of FeS 2 is investigated by charge density analysis.
Publisher: International Union of Crystallography (IUCr)
Date: 13-06-2017
DOI: 10.1107/S2052252517005553
Abstract: The crystal structure uniquely imparts the specific properties of a material, and thus provides the starting point for any quantitative understanding of thermoelectric properties. Cu 2− x Se is an intensely studied high performing, non-toxic and cheap thermoelectric material, and here for the first time, the average structure of β-Cu 2− x Se is reported based on analysis of multi-temperature single-crystal X-ray diffraction data. It consists of Se–Cu layers with additional copper between every alternate layer. The structural changes during the peculiar zT enhancing phase transition mainly consist of changes in the inter-layer distance coupled with subtle Cu migration. Just prior to the transition the structure exhibits strong negative thermal expansion due to the reordering of Cu atoms, when approached from low temperatures. The phase transition is fully reversible and group–subgroup symmetry relations are derived that relate the low-temperature β-phase to the high-temperature α-phase. Weak superstructure reflections are observed and a possible Cu ordering is proposed. The structural rearrangement may have a significant impact on the band structure and the Cu rearrangement may also be linked to an entropy increase. Both factors potentially contribute to the extraordinary zT enhancement across the phase transition.
Publisher: American Chemical Society (ACS)
Date: 10-12-2012
DOI: 10.1021/IC301918X
Abstract: We present a combined experimental and theoretical charge density study of the coordination polymer Zn(HCOO)(2)(H(2)O)(2), which serves as a nonmagnetic reference for the isostructural magnetic compounds containing 3d transition metals. The charge density has been modeled using the multipole formalism against a high-resolution single-crystal X-ray diffraction data set collected at 100 K. The theoretical model is based on periodic density functional theory calculations in the experimental geometry. To gauge the degree of systematic bias from the multipole model, the structure factors of the theoretical model were also projected into a multipole model and the two theoretical models are compared with the experimental results. All models, both experiment and theory, show that the Zn atom densities are highly spherical but show small accumulations of charge toward the negative ligands. The metal-ligand interactions are found to be primarily ionic, but there are subtle topological indications of covalent contributions to the bonds. The source function calculated at the bond critical points reveals a rather delocalized picture of the density in the bridging carboxylates, and this presumably reflects the exchange pathway in the magnetic analogues.
Publisher: American Chemical Society (ACS)
Date: 13-12-2018
Publisher: International Union of Crystallography (IUCr)
Date: 2018
Publisher: International Union of Crystallography (IUCr)
Date: 19-05-2010
Publisher: Royal Society of Chemistry (RSC)
Date: 2014
DOI: 10.1039/C3DT52035H
Abstract: Single crystal X-ray diffraction studies of the symmetrical molecular wire compound Co3(dpa)4Cl2·(dcm) have been performed up to a pressure of 3.6 GPa using both synchrotron and conventional sources. It is found that the terminal Co-Cl bond distance initially increases by 0.013(4) Å at 0.32 GPa after which it continuously decreases. Extensive theoretical calculations show that population of a thermally excited state containing increased Co-Cl anti-bonding character is a possibility at 0.32 GPa. The relative occupancy of the disordered dcm solvent molecule changes significantly with pressure and this is explained by the analysis of void spaces and Hirshfeld surfaces at different pressures. At 3.2 GPa, fingerprint plots derived from Hirshfeld surfaces indicate that neighbouring metal chain compounds approach each other such that short H···H interactions appear.
Publisher: Wiley
Date: 15-05-2013
Publisher: American Chemical Society (ACS)
Date: 16-09-2010
DOI: 10.1021/IC100990A
Abstract: The hexagonal polymorph of CeMnNi(4) has been synthesized using cold crucible, high-frequency induction melting with subsequent Czochralski crystal pulling. Single-crystal X-ray diffraction, multitemperature synchrotron powder X-ray diffraction (90 to 600 K), and neutron powder diffraction data have been measured to establish the detailed crystal structure and in particular the location of the Mn atoms. The neutron diffraction data provide sufficient scattering contrast between Mn and Ni to establish that the 2c site has an occupancy of 13% Mn atoms, while the 3g site has an occupancy of 25% Mn atoms. Thus, the crystal structure is complex with considerable disorder. Rietveld refinement of the multitemperature synchrotron data establishes a near linear thermal expansion coefficient of 13.9(3) × 10(-6) K(-1) and 14.9(3) × 10(-6) K(-1) for the a and c axes, respectively. Atomic Hirshfeld surfaces are introduced as a new tool to investigate the atomic coordination and interactions in intermetallic compounds. The atomic displacement parameters (ADPs) are observed to be much larger for the heavy Ce atom than for the lighter Mn and Ni atoms, and this correlates with the large atomic Hirshfeld volume of Ce relative to Mn and Ni. The fit of a Debye model to the ADPs gives θ(D) = 312(3) K. Magnetic susceptibility data measured between 2 and 350 K indicate ferromagnetic ordering at 122(2) K (Weiss constant) based on a linear fit of the inverse magnetic susceptibility in the paramagnetic region. Transport properties were measured on a polycrystalline s le containing CeO(2) (2.8%) and Ni (7.7%) impurities. The electrical conductivity is observed to be metallic with a distinct kink in the data around 120 K coinciding with the observed Curie temperature. The lattice thermal conductivity (κ(L)) increases from 0.5 W/Km at 2 K to 8 W/Km at 50 K, and the relatively moderate value of κ(L) probably reflects the significant structural disorder.
Publisher: Springer Netherlands
Date: 2012
Publisher: Wiley
Date: 22-06-2020
Publisher: International Union of Crystallography (IUCr)
Date: 29-03-2017
DOI: 10.1107/S2052520616019235
Abstract: A variable-temperature single-crystal structural study of five valence tautomeric cobalt molecular complexes, Co II (3,5-DBSQ) 2 (DBPy) 2 (1), Co II (3,5-DBSQ) 2 (DBPy) 2 ·1.33C 7 H 8 (1 S ), Co II (3,5-DBSQ) 2 (DCPy) 2 ·C 7 H 8 (2 S ), Co II (3,5-DBSQ) 2 (TBPy) 2 (3) and Co II (3,5-DBSQ) 2 (TCPy) 2 (4) (S = toluene, 3,5-DBSQ = 3,5-di- tert -butylsemiquinonate, DBPy = 3,5-dibromopyridine, DCPy = 3,5-dichloropyridine, TBPy = 3,4,5-tribromopyridine and TCPy = 3,4,5-trichloropyridine) is reported. The re-crystallization of (1 S ) in toluene at 277 K resulted in a concomitant formation of a solvent-free polymorph, Co II (3,5-DBSQ) 2 (DBPy) 2 (1). Thermally induced valence tautomerism (VT) is observed only in (1 S ), (1) and (2 S ) [hs-Co II (3,5-DBSQ) 2 L 2 ↔ ls-Co III (3,5-DBSQ)(3,5-DBCat)L 2 (hs = high spin, ls = low spin, 3,5-DBCat = 3,5-di- tert -butylcatecholate)], whereas (3) and (4) remain locked in the hs-Co II (3,5-DBSQ) 2 state during cooling of the s le. Multi-temperature single-crystal studies demonstrate the change in cobalt coordination environment during the VT conversion. The non-solvated compound (1) shows a sharp VT transition ( T 1/2 ∼ 245 K with Δ T ∼ 10 K) from hs-Co II (3,5-DBSQ) 2 (DBPy) 2 to ls-Co III (3,5-DBSQ)(3,5-DBCat)(DBPy) 2 oxidation state, whereas the other polymorph with lattice solvent (1 S ) results in a broad transition ( T 1/2 ∼ 150 K with Δ T ∼ 100 K). This increase in the VT transition temperature for (1) relative to (1 S ) illustrates the effect of lattice solvent on the VT transition mechanism. Additionally, the influence of halogen substitutions on the pyridine ring is discussed with respect to observed VT behaviour in the studied compounds.
Publisher: International Union of Crystallography (IUCr)
Date: 15-11-2006
Publisher: Springer Science and Business Media LLC
Date: 12-02-2018
DOI: 10.1038/S41563-017-0012-2
Abstract: Van der Waals (vdW) solids have attracted great attention ever since the discovery of graphene, with the essential feature being the weak chemical bonding across the vdW gap. The nature of these weak interactions is decisive for many extraordinary properties, but it is a strong challenge for current theory to accurately model long-range electron correlations. Here we use synchrotron X-ray diffraction data to precisely determine the electron density in the archetypal vdW solid, TiS
Publisher: American Chemical Society (ACS)
Date: 10-10-2011
DOI: 10.1021/IC2015258
Abstract: Single crystal synchrotron X-ray diffraction measurements have been carried out on [Nd(DMF)(4)(H(2)O)(3)(μ-CN)Fe(CN)(5)]·H(2)O (DMF = dimethyl-formamide), 1 [Y(DMF)(4)(H(2)O)(3)(μ-CN)Fe(CN)(5)]·H(2)O, 2 [Ce(DMF)(4)(H(2)O)(3)(μ-CN)Fe(CN)(5)]·H(2)O, 3 [Sm(DMF)(4)(H(2)O)(3)(μ-CN)Fe(CN)(5)]·H(2)O, 4 [Tb(DMF)(4)(H(2)O)(3)(μ-CN)Fe(CN)(5)]·H(2)O, 5 [Yb(DMF)(4)(H(2)O)(3)(μ-CN)Fe(CN)(5)]·H(2)O, 6 and [Nd(DMF)(4)(H(2)O)(3)(μ-CN)Co(CN)(5)]·H(2)O, 7, at 15(2) K with and without UV illumination of the crystals. Significant changes in unit cell parameters are observed for all of the iron-containing complexes, while compound 7 shows no response to UV illumination. These results are consistent with previous results and are furthermore reproduced by powder synchrotron X-ray diffraction for compounds 1 and 7. Photoexcited crystal structures have been determined for 1-6 from refinements of two-conformer models, and excited state occupancies in the range 80-94% are found. Significant bond length changes are observed for the Fe-ligand bonds (up to 0.06 Å), the cyano bonds (up to 0.02 Å), and the lanthanide-ligand bonds (up to 0.1 Å). On the contrary, powder X-ray diffraction on the simple compound K(3)Fe(CN)(6), 8, upon UV illumination does not show any structural changes, suggesting that the photomagnetic effect requires the presence of both the transition metal and the lanthanide ion. Photomagnetic measurements show an increase in magnetization of the excited state of 1 of up to 3%, which is much diminished compared with previously published values of 45%. Furthermore, they show that the isostructural complex [La(DMF)(4)(H(2)O)(3)(μ-CN)Fe(CN)(5)]·H(2)O, 9, exhibits identical magnetic responses in the UV-induced excited crystal structure.
Publisher: Royal Society of Chemistry (RSC)
Date: 2019
DOI: 10.1039/C9CC00187E
Abstract: Li 2 B 12 H 12 is reported in the molten state for the first time, which enables a range of new research opportunities.
Publisher: International Union of Crystallography (IUCr)
Date: 26-05-2016
DOI: 10.1107/S2052520616005515
Abstract: The effect of pressure on the crystal structure of a coordination polymer, emim[Mn II (btc)] (emim = 1-ethyl,3-methyl imidazolium cation, btc = 1,3,5-benzene-tricarboxylate), was investigated with single-crystal X-ray diffraction. At 4.3 GPa the unit-cell volume had decreased by 14% compared with ambient conditions. The unit-cell contraction is highly anisotropic, with the a - and b -axes decreasing by 5.5 and 9.5%, respectively, and the c -axis compressing a mere 0.25% up to 1.7 GPa followed by a 0.2% expansion between 1.7 and 4.3 GPa. The 0.2% increase in length of the c -axis in this interval happens above the quasi-hydrostatic limit of the pressure-transmitting medium and therefore it might be a consequence of strain gradients. Under ambient conditions, two MnO 6 units are connected by two carboxylate ligands to form dimeric units. On increasing pressure, a non-bonded O atom from a bridging carboxylate group approaches the Mn atom, with the Mn—O distance decreasing from 2.866 (1) Å at 0.3 GPa to 2.482 (6) Å at 4.3 GPa, increasing the coordination environment of the Mn ion from six- to seven-coordinated.
Publisher: International Union of Crystallography (IUCr)
Date: 06-08-2011
Publisher: Royal Society of Chemistry (RSC)
Date: 2011
DOI: 10.1039/C1CC12626A
Abstract: The excited state crystal structure of the ionic complex (Nd(DMA)(4)(H(2)O)(4)-Fe(CN)(6)·3H(2)O (DMA = dimethylacetamide) has been determined at 15 K upon UV illumination by single crystal X-ray diffraction. Significant structural changes are observed around the Fe site in the excited state. These changes are similar to those observed for a related molecular compound exhibiting photomagnetic properties.
Publisher: American Chemical Society (ACS)
Date: 06-2017
Publisher: Wiley
Date: 21-11-2015
DOI: 10.1111/ZSC.12148
Publisher: Royal Society of Chemistry (RSC)
Date: 2023
DOI: 10.1039/D2CC06722F
Abstract: The effects of high-pressure on the structural and magnetic properties of the dysprosocenium cation are analyzed. Combined with periodic calculations, correlations between structural deformations and magnetic relaxation characteristics are obtained.
Publisher: Wiley
Date: 13-12-2012
Publisher: International Union of Crystallography (IUCr)
Date: 2018
Publisher: Wiley
Date: 10-2014
Publisher: Elsevier BV
Date: 07-2012
Publisher: American Chemical Society (ACS)
Date: 11-01-2018
Publisher: International Union of Crystallography (IUCr)
Date: 2018
Publisher: Springer Science and Business Media LLC
Date: 16-12-2019
DOI: 10.1038/S41557-019-0387-6
Abstract: The distribution of electrons in the 4f orbitals of lanthanide ions is often assigned a crucial role in the design of single-molecule magnets, which maintain magnetization in zero external field. Optimal spatial complementarity between the 4f-electron density and the ligand field is key to maximizing magnetic anisotropy, which is an important factor in the ability of lanthanide complexes to display single-molecule magnet behaviour. Here we have experimentally determined the electron density distribution in two dysprosium molecular complexes by interpreting high-resolution synchrotron X-ray diffraction with a multipole model. The ground-state 4f-electron density is found to be an oblate ellipsoid, as is often deduced from a simplified Sievers model that assumes a pure |±15/2> ground-state doublet for the lanthanide ion. The large equatorial asymmetry-determined by a model wavefunction-was found to contain considerable M
Publisher: MDPI AG
Date: 18-01-2018
DOI: 10.3390/CRYST8010046
Publisher: International Union of Crystallography (IUCr)
Date: 08-11-2014
DOI: 10.1107/S2052520614019179
Abstract: The homometallic wheel compound [Cr 8 F 8 (O 2 CCMe 3 ) 16 ] formed with fluorine and pivalic acid ligands can be modified by introducing in the synthesis process a alent cation M capable of octahedral coordination instead of one of the trivalent Cr centres in the ring. Heterometallic mono-anionic species [Cr 7 M F 8 (O 2 CCMe 3 ) 16 ] − can form diethylammonium salts and be crystallized from ethylacetate solution as compounds with the general formula [NH 2 Et 2 ][Cr 7 M F 8 ( t BuCO 2 ) 16 ][C 4 H 8 O 2 ] 0.5 for M = Mn, Fe, Co, Ni, Cu, Zn and Cd. Their structures are isomorphous, belonging to the space group P 2 1 / c . The study has determined the degree of order for the in idual M heterometal over the possible metal positions of the ring in the crystal structure by modelling based on X-ray diffraction data. The model took into account disorder in tert -butyl groups of the pivalate ligands and in the position and orientation of the ethylacetate solvent molecule. The heterometal turned out to be partly ordered in the crystal structure.
Publisher: American Chemical Society (ACS)
Date: 10-11-2014
DOI: 10.1021/IC501603X
Abstract: A combined experimental and theoretical electron density study of the shortest trichromium metal wire, Cr3(dpa)4Cl2·(C2H5OC2H5)(x)(CH2Cl2)(1-x) (1, dpa = bis(2-pyridyl)amido), is reported. High resolution X-ray diffraction data has been collected both at 100 K using a conventional X-ray source (DS1) and at 15 K using a synchrotron X-ray source (DS2). The linear chromium string is terminated by Cl(-) ions at both ends, and each Cr atom is also coordinated by four N atoms from bridging dpa ligands. The two Cr-Cr bond distances are unequal at 100 K (with d(Cr1-Cr2) being 0.029 Å shorter than d(Cr2-Cr3)) but at 15 K they are almost equal (0.002 Å difference). Analysis of the slightly elongated thermal ellipsoids of the Cr2 atom suggests that it is not due to disorder, but the presence of a shallow potential energy surface. Laplacian maps clearly show local valence shell charge concentration (VSCC) in the electron density along the bisector of the equatorial Cr-N bonds. Integration over the atomic basins indicates that Cr2 has smaller atomic charge and volume than Cr1 and Cr3. The topological characterization of the Cr-Cr bonds indicates partly covalent characters with electron density at the bond critical point of ∼0.3 e Å(-3) and negative total energy density. The delocalization index of Cr-Cr is 0.8 for Cr1-Cr2 and 0.08 for Cr1-Cr3. Second-order perturbation analysis shows high stabilization energy of the Cr-Cr bonds (E(2) ∼ 190 kcal mol(-1)). Delocalization indices and source function and natural bond orbital analyses are all indicative of localized Cr-Cr bonding interactions.
Publisher: American Chemical Society (ACS)
Date: 15-12-2010
DOI: 10.1021/JP109547W
Abstract: High-resolution X-ray diffraction data, coupled with theoretical calculations, are used to demonstrate the presence of a non-nuclear local maximum in the electron density of a dimeric Mg(I) molecule. This is the first time such a non-nuclear attractor (NNA) has been observed in a stable molecular species. Multipole modeling of the Mg(I) centers requires use of expansion/contraction (κ) coefficients taken from density functional theory (DFT), since accurate scattering factors for Mg(I) are not available. The model developed accurately accounts for the electron density in the Mg-Mg region and is in excellent agreement with directly calculated DFT data. Within the quantum theory of atoms in molecules (QTAIM), this molecule is not bound by a Mg-Mg bond but rather by two Mg-"pseudo-atom" bonds. The NNA is associated with a large region of negative Laplacian in the Mg-Mg internuclear region and arises from the overlap of 3s orbitals in this long, nonpolar "bond". The pseudoatomic basin associated with the NNA contains 0.8 electrons, which are highly delocalized and hence weakly bound. Possible implications of this unusual electronic structure for the chemistry of such molecules, including their use as excellent reducing agents, are discussed.
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C4CE02224F
Publisher: Wiley
Date: 28-05-2013
Publisher: International Union of Crystallography (IUCr)
Date: 15-03-2006
DOI: 10.1107/S160053680600883X
Abstract: The title compound, [Fe 2 Yb 2 (CN) 12 (C 4 H 9 NO) 5 (H 2 O) 6 ]·2H 2 O, is a tetranuclear complex, where the four metal centres are connected through three cyano bridges, the iron centres making one and two bridges, respectively. Each Fe atom is surrounded by six cyano ligands, forming almost ideal octahedra. The two Yb atoms have different ligand environments both are coordinated by seven ligands, consisting of water molecules, dimethylacetamide (DMA) solvent and cyano groups, but not in the same ratio. Four of the five DMA molecules show various degrees of common structural disorder. The asymmetric unit also includes two solvent water molecules, which take part in hydrogen bonding, forming an extended network of tetramers.
Publisher: International Union of Crystallography (IUCr)
Date: 29-08-2014
DOI: 10.1107/S2052252514018570
Abstract: Synchrotron radiation has many compelling advantages over conventional radiation sources in the measurement of accurate Bragg diffraction data. The variable photon energy and much higher flux may help to minimize critical systematic effects such as absorption, extinction and anomalous scattering. Based on a survey of selected published results from the last decade, the benefits of using synchrotron radiation in the determination of X-ray electron densities are discussed, and possible future directions of this field are examined.
Publisher: International Union of Crystallography (IUCr)
Date: 19-06-2019
DOI: 10.1107/S2052520619005791
Abstract: Carbon nitride materials include functional materials, and their chemical ersity and complexity are becoming increasingly appreciated. Heating of NH 4 SCN leads to a range of new carbon nitride compounds, which have been structurally characterized by single-crystal X-ray diffraction. Heating at ambient pressure to 175°C leads to guanidinium thiocyanate, H 6 CN 3 SCN ( 1 ), and when maintaining that temperature for about 12 h a water-insoluble carbon nitride product is formed, which is a co-crystal between melamine and melamium thiocyanate, [H 6 C 3 N 6 ]·[H 10 C 6 N 11 ] + ·[SCN] − ( 2 ). In situ powder X-ray diffraction measurements of this material reveal a gradual transformation from ( 2 ), via two intermediate products, to a final melon-like end product. The first of these forms between 350 and 400°C, and is an adduct of melam and melamium thiocyanate, [H 9 C 6 N 11 ]·2[H 10 C 6 N 11 ] + ·2[SCN] − ( 3 ). The second forms between 400 and 480°C, and is identified as melem, 2,5,8-triamino-tri- s -triazine, H 6 C 6 N 10 ( 4 ). On heating of ( 2 ) in a sealed oule to 600°C, various crystals were obtained and six crystal structures were determined from the batch: 1,3,5-triazine-2,4,6-triamino, H 6 C 3 N 6 ( 5 ), 1,3,5-triazine-2,4-diamino, H 5 C 3 N 5 ( 6 ), 1,1′,3,3′,5,5′-triazine-2,2′,4,4′-tetraamino, H 8 C 6 N 10 ( 7 ), 2[H 6 C 3 N 6 ]·[H 10 C 6 N 11 ] + ·[SCN] − ( 8 ) and 2[H 6 C 3 N 6 ]·[H 7 C 3 N 6 ] + ·[SCN] − ( 9 ). Finally, a recrystallized decomposition product was found to be [H 6 C 3 N 6 ]·[H 7 C 3 N 6 ] + ·[SCN] − ·[H 2 O] ( 10 ).
Publisher: International Union of Crystallography (IUCr)
Date: 2018
Publisher: Royal Society of Chemistry (RSC)
Date: 2016
DOI: 10.1039/C6CP02690G
Abstract: Experimental charge density analysis of two piroxicam polymorphs has found a redistribution of charge to a non-classical zwitterionic form.
Publisher: Wiley
Date: 28-12-2010
Publisher: International Union of Crystallography (IUCr)
Date: 16-02-2012
Publisher: Royal Society of Chemistry (RSC)
Date: 2016
DOI: 10.1039/C6RA10411H
Abstract: Experimental and theoretical charge density of piroxicam, saccharin and their 1 : 1 co-crystal have been determined using high-resolution X-ray diffraction, multipole refinement and DFT calculations
Publisher: International Union of Crystallography (IUCr)
Date: 17-10-2013
DOI: 10.1107/S0108767313024458
Abstract: CoSb 3 is an ex le of a highly challenging case for experimental charge-density analysis due to the heavy elements (suitability factor of ∼0.01), the perfect crystallinity and the high symmetry of the compound. It is part of a family of host–guest structures that are potential candidates for use as high-performance thermoelectric materials. Obtaining and analysing accurate charge densities of the undoped host structure potentially can improve the understanding of the thermoelectric properties of this family of materials. In a previous study, analysis of the electron density gave a picture of covalent Co–Sb and Sb–Sb interactions together with relatively low atomic charges based on state-of-the-art experimental and theoretical data. In the current study, several experimental X-ray diffraction data sets collected on the empty CoSb 3 framework are compared in order to probe the experimental requirements for obtaining data of high enough quality for charge-density analysis even in the case of very unsuitable crystals. Furthermore, the quality of the experimental structure factors is tested by comparison with theoretical structure factors obtained from periodic DFT calculations. The results clearly show that, in the current study, the data collected on high-intensity, high-energy synchrotron sources and very small crystals are superior to data collected at conventional sources, and in fact necessary for a meaningful charge-density study, primarily due to greatly diminished effects of extinction and absorption which are difficult to correct for with sufficient accuracy.
Publisher: American Chemical Society (ACS)
Date: 14-09-2016
Abstract: Rubrene endoperoxide p-xylene (1) has been obtained in crystalline form from recrystallization and purification of the organic semiconductor, rubrene, and for the first time characterized by single-crystal X-ray diffraction methods. 1 is produced by reaction of rubrene with molecular oxygen to create rubrene endoperoxide, C42H28O2, in which an O2-bridge is joining the two phenyl-substituted C atoms opposite each other in the second of the four aromatic rings in tetracene thereby breaking the resonance along the tetracene moiety. The electron density distribution of 1 reveals that the intramolecular O-O bond is best characterized as charge-shift bonding with loss of electronic concentration in the interatomic region evidenced by the Laplacian. Likewise the ELI-D indicates little electron localization in this region. Furthermore, source function and ELI-D analysis of 1 clearly quantifies the lack of electronic delocalization across the six-membered ring that carries the peroxide-bridge.
Publisher: Wiley
Date: 06-2016
Abstract: The mixed-valence complex Fe3 O(cyanoacetate)6 (H2 O)3 (1) has been studied by single-crystal X-ray diffraction analysis at pressures up to 5.3(1) GPa and by (synchrotron) Mössbauer spectroscopy at pressures up to 8(1) GPa. Crystal structure refinements were possible up to 4.0(1) GPa. In this pressure range, 1 undergoes two pressure-induced phase transitions. The first phase transition at around 3 GPa is isosymmetric and involves a 60° rotation of 50 % of the cyanoacetate ligands. The second phase transition at around 4 GPa reduces the symmetry from rhombohedral to triclinic. Mössbauer spectra show that the complex becomes partially valence-trapped after the second phase transition. This sluggish pressure-induced valence-trapping is in contrast to the very abrupt valence-trapping observed when compound 1 is cooled from 130 to 120 K at ambient pressure.
Publisher: Wiley
Date: 14-05-2014
Abstract: X-ray/neutron (X/N) diffraction data measured at very low temperature (15 K) in conjunction with ab initio theoretical calculations were used to model the crystal charge density (CD) of the host-guest complex of hydroquinone (HQ) and acetonitrile. Due to pseudosymmetry, information about the ordering of the acetonitrile molecules within the HQ cavities is present only in almost extinct, very weak diffraction data, which cannot be measured with sufficient accuracy even by using the brightest X-ray and neutron sources available, and the CD model of the guest molecule was ultimately based on theoretical calculations. On the other hand, the CD of the HQ host structure is well determined by the experimental data. The neutron diffraction data provide hydrogen anisotropic thermal parameters and positions, which are important to obtain a reliable CD for this light-atom-only crystal. Atomic displacement parameters obtained independently from the X-ray and neutron diffraction data show excellent agreement with a |ΔU| value of 0.00058 Å(2) indicating outstanding data quality. The CD and especially the derived electrostatic properties clearly reveal increased polarization of the HQ molecules in the host-guest complex compared with the HQ molecules in the empty HQ apohost crystal structure. It was found that the origin of the increased polarization is inclusion of the acetonitrile molecule, whereas the change in geometry of the HQ host structure following inclusion of the guest has very little effect on the electrostatic potential. The fact that guest inclusion has a profound effect on the electrostatic potential suggests that nonpolarizable force fields may be unsuitable for molecular dynamics simulations of host-guest interaction (e.g., in protein-drug complexes), at least for polar molecules.
Publisher: American Chemical Society (ACS)
Date: 03-08-2011
DOI: 10.1021/JP2041789
Abstract: The crystal structure of the β-polymorph of hydroquinone (β-HQ), the apohost of a large family of clathrates, is reported with a specific focus on intermolecular interactions and the electrostatic nature of its cavity. Hirshfeld surface analysis reveals subtle close contacts between two interconnecting HQ networks, and the local packing and related close contacts were examined by breakdown of the fingerprint plot. An experimental multipole model containing anisotropic thermal parameters for hydrogen atoms has been successfully refined against 15(2) K single microcrystal synchrotron X-ray diffraction data. The experimental electron density model has been compared with a theoretical electron density calculated with the molecule embedded in its own crystal field. Hirshfeld charges, interaction energies and the electrostatic potential calculated for both models are qualitatively in good agreement, but small differences in the electrostatic potential persist due to charge transfer from all hydrogen atoms to the oxygen atoms in the theoretical model. The electrostatic potential in the center of the cavity is positive, very shallow and highly symmetric, suggesting that the inclusion of polar molecules in the void will involve a balance between opposing effects. The electric field is by symmetry zero in the center of the cavity, increasing to a value of 0.0185 e/Å(2) (0.27 V/Å) 1 Å along the 3-fold axis and 0.0105 e/Å(2) (0.15 V/Å) 1 Å along the perpendicular direction. While these values are substantial in a macroscopic context, they are quite small for a molecular cavity and are not expected to strongly polarize a guest molecule.
Publisher: International Union of Crystallography (IUCr)
Date: 11-04-2006
DOI: 10.1107/S1600536806011950
Abstract: The title compound, [Gd(C 4 H 9 NO) 4 (H 2 O) 3 ][Fe(CN) 6 ]·2H 2 O, is a bimetallic complex containing two isolated metal complexes. The Fe atom is bonded to six cyano ligands forming an almost ideal octahedron. One of the cyano groups is also connected through a hydrogen bond to a water molecule bonded to the Ga atom. Aside from three water molecules, gadolinium is also coordinated by four dimethylacetamide molecules, two of which show various degrees of structural disorder. The asymmetric unit also includes two solvent water molecules, which take part in hydrogen bonding, forming an extended network.
Publisher: Royal Society of Chemistry (RSC)
Date: 2011
DOI: 10.1039/C0CC04418K
Abstract: The title compound undergoes two order-disorder transitions between 15 and 299 K, dictated by ordering of the guest molecules in the host cages, and resulting in three related crystal structures. We anticipate behaviour of this kind to be widespread, and speculate that the concept of "the crystal structure" for in idual Dianin's clathrates may be elusive.
Publisher: American Chemical Society (ACS)
Date: 20-04-2020
Publisher: American Chemical Society (ACS)
Date: 26-02-2018
Abstract: Experimental charge density distribution studies, complemented by quantum mechanical theoretical calculations, of a host-guest system composed of a macrocycle (1) and barbital (2) in a 1:1 ratio (3) have been carried out via high-resolution single-crystal X-ray diffraction. The data were modeled using the conventional multipole model of electron density according to the Hansen-Coppens formalism. The asymmetric unit of macrocycle 1 contained an intraannular ethanol molecule and an extraannular acetonitrile molecule, and the asymmetric unit of 3 also contained an intraannular ethanol molecule. Visual comparison of the conformations of the macrocyclic ring shows the rotation by 180° of an amide bond attributed to competitive hydrogen bonding. It was found that the intraannular and extraannular molecules inside were orientated to maximize the number of hydrogen bonds present, with the presence of barbital in 3 resulting in the greatest stabilization. Hydrogen bonds ranging in strength from 4 to 70 kJ mol
Publisher: International Union of Crystallography (IUCr)
Date: 2018
Publisher: Wiley
Date: 25-04-2019
Abstract: The covalent nature of the low-barrier N-H-N hydrogen bonds in the negative thermal expansion material H
Publisher: International Union of Crystallography (IUCr)
Date: 14-08-2015
DOI: 10.1107/S2052252515012130
Abstract: Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically, the presence of C π ...C π interactions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI) analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H—H interactions. The electron density features of H—H bonding, and the interaction energy of molecular dimers connected by H—H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. The quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations.
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C5CC00603A
Abstract: A non-hydrostatic pressure induces ligand to metal charge transfer on the iron site of a 3d–4f photomagnetic material.
Publisher: Wiley
Date: 21-11-2012
Abstract: Mixed-valence trinuclear carboxylates, [M(3)O(O(2)CR)(6)L(3)] (M = metal, L = terminal ligand), have small differences in potential energy between the configurations M(II)M(III)M(III)⇔M(III)M(II)M(III)⇔M(III)M(III)M(II), which means that small external changes can have large structural effects, owing to the differences in coordination geometry between M(2+) and M(3+) sites (e.g., about 0.2 Å for Fe-O bond lengths). It is well-established that the electron transfer (ET) between the metal sites in these mixed-valence molecules is strongly dependent on temperature and on the specific crystal environment however, herein, for the first time, we examine the effect of pressure on the electron transfer. Based on single-crystal X-ray diffraction data that were measured at 15, 90, 100, 110, 130, 160, and 298 K on three different crystals, we first unexpectedly found that our batch of Fe(3)O (O(2)CC(CH(3))(3))(6)(C(5)H(5)N)(3) (1) exhibited a different temperature dependence of the ET process than previous studies of compound 1 have shown. We observed a phase transition at around 130 K that was related to complete valence trapping and Hirshfeld surface analysis revealed that this phase transition was governed by a subtle competition between C-H⋅⋅⋅π and π⋅⋅⋅π intermolecular interactions. Subsequent high-pressure single-crystal X-ray diffraction at pressures of 0.15, 0.35, 0.45, 0.74, and 0.96 GPa revealed that it was not possible to trigger the phase transition (i.e., valence trapping) by a reduction of the unit-cell volume, owing to this external pressure. We conclude that modulation of the ET process requires anisotropic changes in the intermolecular interactions, which occur when various directional chemical bonds are affected differently by changes in temperature, but not by the application of pressure.
Start Date: 03-2021
End Date: 10-2022
Amount: $330,000.00
Funder: Australian Research Council
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