Finn K. Larsen

Strong N−H⋅⋅⋅O Hydrogen Bonding in a Model Compound of the Catalytic Triad in Serine Proteases

Low-barrier hydrogen bond (LBHB) involvement in enzyme catalysis is examined by analysis of experimental nuclear and electron densities of a model compound for the catalytic triad in serine proteases (shown schematically), which is based on a cocrystal of betaine, imidazole, and picric acid. The three short, strong N-H⋅⋅⋅O hydrogen bonds in the structure have varying degrees of covalent bonding contributions suggesting a gradual transition to the LBHB situation.

A family of heterometallic wheels containing potentially fourteen hundred siblings

The synthesis and structure of new heterometallic wheels are reported, with preliminary studies of selected compounds.

Atomic displacement parameters for Ni(ND3)4(NO2)2 from 9 K X-ray and 13 K time-of-flight neutron diffraction data

Structural parameters derived from 9(1)K X-ray diffraction data and 13(1)K time-of-flight neutron diffraction data on perdeuterated tetraamminedinitro-nickel(II), Ni(ND 3 ) 4 (NO 2 ) 2 , are compared. It is shown that excellent agreement can be obtained for both positional and thermal parameters derived separately from the two experiments, provided that great care is taken in all steps of the process, including data collection, data reduction, and nuclear and electronic structure refinement. The mean difference in the thermal parameters, , is as low as 0.00034 A 2 and 1/2 = 1.92, showing that, even without any form of scaling between the parameters, the same values can be obtained. This, compared with other such studies, indicates that time-of-flight neutron diffraction data can give structural information of a quality comparable to monochromatic neutron diffraction. The excellent correspondence between the thermal parameters derived separately from X-ray and neutron diffraction data gives confidence in the deconvolution of the thermal motion from the X-ray diffraction data, which is necessary for any study of a static electron density distribution.

X-ray and neutron diffraction study of benzoylacetone in the temperature range 8–300 K: comparison with other cis-enol molecules

The crystal structure of benzoylacetone (1-phenyl-1,3-butanedione, C(10)H(10)O(2); P2(1)/c, Z = 4) has been determined at 300, 160 (both Mo Kalpha X-ray diffraction, XRD), 20 (lambda = 1.012 Å neutron diffraction, ND) and 8 K (Ag Kalpha XRD), to which should be added earlier structure determinations at 300 (Mo Kalpha XRD and ND, lambda = 0.983 Å) and 143 K (Mo Kalpha XRD). Cell dimensions have been measured over the temperature range 8-300 K; a first- or second-order phase change does not occur within this range. The atomic displacement parameters have been analyzed using the thermal motion analysis program THMA11. The most marked change in the molecular structure is in the disposition of the methyl group, which has a librational amplitude of approximately 20 degrees at 20 K and is rotationally disordered at 300 K. The lengths of the two C-O bonds in the cis-enol ring do not differ significantly, nor do those of the two C-C bonds, nor do these lengths change between 8 and 300 K. An ND difference synthesis (20 K) shows a single enol hydrogen trough (rather than two half H atoms), approximately centered between the O atoms; analogous results were obtained by XRD (8 K). It is inferred that the enol hydrogen is in a broad, flat-bottomed single-minimum potential well between the O atoms, with a libration amplitude of approximately 0.30 Å at 8 K. These results suggest that at 8 K the cis-enol ring in benzoylacetone has quasi-aromatic character, in agreement with the results of high-level ab initio calculations made for benzoylacetone [Schiøtt et al. (1998). J. Am. Chem. Soc. 120, 12117-12124]. Application [in a related paper by Madsen et al. (1998). J. Am. Chem. Soc. 120, 10040-10045] of multipolar analysis and topological methods to the charge density obtained from the combined lowest temperature X-ray and neutron data provides evidence for an intramolecular hydrogen bond with partly electrostatic and partly covalent character, and large p-delocalization in the cis-enol ring. This is in good agreement with what is expected from the observed bond lengths. Analysis of the total available (through the Cambridge Structural Database, CSD) population of cis-enol ring geometries confirms earlier reports of correlation between the degree of bond localization in the pairs of C-C and C-O bonds, but does not show the dependence of bond localization on d(O.O) that was reported earlier for a more restricted sample. It is suggested that the only reliable method of determining whether the enol hydrogen is found in a single or double potential well is by low-temperature X-ray or (preferably) neutron diffraction.

A direct investigation of thermal vibrations of beryllium in real space through the maximum-entropy method applied to single-crystal neutron diffraction data

The thermal vibrations of beryllium metal were determined directly from the nuclear densities obtained by the maximum-entropy method (MEM) using neutron single-crystal data. A high-resolution nuclear density distribution of beryllium was obtained by applying the MEM to the 48 structure factors with sin θ/λ < 1.41 A−1 from a previous study [Larsen, Lehmann & Merisalo (1980). Acta Cryst. A36, 159–163], which showed small but significant cubic anharmonicity in beryllium by least-squares refinement of the structure factors. In the present study, quartic as well as cubic anharmonicities are clearly visible in the MEM nuclear density. In order to determine anharmonic thermal-vibration parameters, a three-dimensional function was fitted to the MEM nuclear density around the atom site. The one-particle potential was used to model the thermal vibrations up to quartic terms. The least-squares-fit values were γ = −0.306 eV A−3 for the third- and α40 = − 1.02, β20 = 2.95 and γ00 = − 3.28 eV A−4 for the fourth-order anharmonic parameters. Thus, the atomic potential in the basal plane is hardened against the bipyramidal space around the tetrahedral holes of the hexagonal-close-packed structure. It is softened towards the center of the octahedral voids. Least-squares refinement of the MEM nuclear density gives a standard deviation of about 5 for the last digit of the anharmonic parameters. However, there is added uncertainty in the parameters because of the relationship of the reliability of the MEM density distribution to the standard deviations of the measured intensities. Judging from previous studies of the thermal parameters for beryllium based on least-squares refinement of observed structure factors, it is estimated that values determined here for the anharmonic parameters are reliable to the first digit after the decimal point.

Comparative study of X-ray charge-density data on CoSb3.

CoSb3 is an example 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 CoSb3 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.

Reciprocal- and direct-space determination of the temperature dependence of thermal vibrations in magnesium: A neutron diffraction study

Abstract Neutron diffraction measurements have been carried out on metallic magnesium at 11 different temperatures ranging from 125 to 755 K. The data, which were corrected for extinction and thermal diffuse scattering effects, were analysed with both conventional least-squares fitting in reciprocal space and direct-space fitting using the maximum-entropy method (MEM). Both the Gram-Charlier expansion of the harmonic displacement factor and the one-particle potential (OPP) model were used in the analysis of the atomic thermal motion. The reciprocal-space analysis as well as the direct-space analysis show the existence of cubic anharmonicity above 240 K. The cubic OPP anharmonic parameter could also be derived from values of almost forbidden reflections predicted from the MEM nuclear density distribution. The MEM further indicates fourth-order anharmonic effects in the atomic potentials above the Debye temperature (340 K).

Helium cryostat synchrotron charge densities determined using a large CCD detector – the upgraded beamline D3 at DESY

A 165 mm Mar CCD detector has been fitted on a large Huber four-circle diffractometer together with a helium cryostat at beamline D3 at Hasylab, DESY in Hamburg. This setup allows fast collection of accurate, short-wavelength, very low temperature X-ray diffraction data for charge-density analysis. As a test example, diffraction data have been collected in 10 h on a hydrogen-bonded network system with 15 unique atoms, and the electron density was modelled with the multipole formalism in an X–N procedure using matching-temperature neutron diffraction data collected at Institut Laue Langevin, Grenoble in France.

Pressure versus Temperature Effects on Intramolecular Electron Transfer in Mixed‐Valence Complexes

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.

Experimental charge density in an oxidized trinuclear iron complex using 15 K synchrotron and 100 K conventional single-crystal X-ray diffraction

The experimental electron density distribution in a crystal consisting of the simplest conceivable trinuclear carboxylate-bridged iron-mu3-oxo dianion with two alpha-picolinium cations has been determined using both synchrotron (15 K) and conventional (100 K) X-ray diffraction data. The constituent trinuclear oxo-centered molecule consists of six mu2-bridging formate groups between the iron pairs, while the axial ligand for all iron atoms is another formate group. The compound {[FeO(HCOO)5(HCOO)3]2-.H2O.2(alpha-CH3NC5H5)}, (1) crystallizes in the monoclinic space group P2(1)/m with charge assisted hydrogen bonds linking the alpha-picolinium cations to the trinuclear groups. The chemical bonding in the weakly asymmetric Fe3O-core of 1 has been examined through the use of the quantum theory of atoms in molecules, and in combination with experimental d-orbital populations, a significant electron sharing is observed between the Fe atoms and the central oxygen. The central oxygen exhibits clear sp2 hybridization, and the iron atoms have valence shell charge concentrations in all metal-ligand bond directions. The relative bond strengths are evaluated based upon the charge density distribution and found to be in accordance with the geometrical results. Integrated group charges follow expectations from formal chemical valences.