Anders Ø. Madsen

Atomic structures of amyloid cross-β spines reveal varied steric zippers

Amyloid fibrils formed from different proteins, each associated with a particular disease, contain a common cross-β spine. The atomic architecture of a spine, from the fibril-forming segment GNNQQNY of the yeast prion protein Sup35, was recently revealed by X-ray microcrystallography. It is a pair of β-sheets, with the facing side chains of the two sheets interdigitated in a dry ‘steric zipper’. Here we report some 30 other segments from fibril-forming proteins that form amyloid-like fibrils, microcrystals, or usually both. These include segments from the Alzheimer’s amyloid-β and tau proteins, the PrP prion protein, insulin, islet amyloid polypeptide (IAPP), lysozyme, myoglobin, α-synuclein and β2-microglobulin, suggesting that common structural features are shared by amyloid diseases at the molecular level. Structures of 13 of these microcrystals all reveal steric zippers, but with variations that expand the range of atomic architectures for amyloid-like fibrils and offer an atomic-level hypothesis for the basis of prion strains.

Discovery of a cyclic 6 + 6 hexamer of D-biotin and formaldehyde

The discovery of receptors using templated synthesis enables the selection of strong receptors from complex mixtures. In this contribution we describe a study of the condensation of D-biotin and formaldehyde in acidic water. We have discovered that halide anions template the formation of a single isomer of a 6 + 6 macrocycle. The macrocycle (biotin[6]uril) is water-soluble, chiral and binds halide anions (iodide, bromide and chloride) with selectivity for iodide in water, and it can be isolated on a gram scale in a one-pot reaction in 63% yield.

Three-dimensional coherent X-ray diffractive imaging of whole frozen-hydrated cells

Since its first experimental demonstration in 1999, coherent diffractive imaging (CDI) has been applied to image a broad range of samples using advanced synchrotron radiation, X-ray free-electron lasers, high harmonic generation and electrons. Here, the first experimental demonstration of cryogenic CDI for quantitative three-dimensional imaging of whole frozen-hydrated cells is reported. As a proof of principle, the three-dimensional mass density of the sub-cellular organization of a Neospora caninum cell is determined based on its natural contrast.

Anisotropic displacement parameters for molecular crystals from periodic Hartree–Fock and density functional theory calculations

Fully periodic Hartree–Fock and density functional theory calculations have been used to compute the anisotropic displacement parameters (ADPs) of molecular crystals at different temperatures by using the CRYSTAL code. Crystalline urea was adopted as a benchmark system to investigate the dependence on basis set and Hamiltonian. The results were compared with ADPs derived from neutron diffraction experiments. The approach can estimate the internal ADPs, corresponding to the contributions of high-frequency intramolecular vibrations, and for these internal contributions the results are almost independent of the basis set and Hamiltonian. Much larger variations and discrepancies from neutron diffraction experiments are seen for the external, low-frequency modes, which become dominant at higher temperatures. The approach was then tested on benzene and urotropine. Finally, ADPs of l-alanine were predicted at the B3LYP/6-31G(d,p) level of theory. The total ADPs, including low-frequency external modes, are underestimated, but can be brought into good agreement with the experimental ADPs by introducing a Gruneisen parameter, which partly accounts for anharmonicity of the potential energy surface, but likely also contains contributions from other deficiencies of the calculations.

Synthesis and Characterization of Tetrathiafulvalene-Substituted Di- and Tetraethynylethenes with p-Nitrophenyl Acceptors

Novel di- and tetraethynylethene (DEE and TEE) compounds functionalized with tetrathiafulvalene (TTF) donor groups and p-nitrophenyl acceptor groups were synthesized by palladium-catalyzed cross-coupling reactions under various conditions. The molecules are strong chromophores and were investigated for their optical properties. Placement of two TTFs and two p-nitrophenyls about a central TEE core provides a molecule with a high third-order optical nonlinearity. The molecules experience reversible oxidations of the TTF units, and the optical properties of the oxidized species were elucidated by spectroelectrochemistry. The degree of quinoid character of the p-nitrophenyl in the molecules was determined by X-ray crystallography.

The phosphorylation site in double helical amylopectin as investigated by a combined approach using chemical synthesis, crystallography and molecular modeling

The only known in planta substitution of starch is phosphorylation. Whereas the function of starch phosphorylation is poorly understood, phosphorylated starch possesses improved functionality in vitro. Molecular models of native crystalline starch are currently being developed and the starch phosphorylating enzyme has recently been discovered. Accordingly, it is desirable to obtain a more exact description of the molecular structures of phosphorylated starch. We have determined the crystal structure of methyl α‐D‐glucopyranoside 6‐O‐phosphate as its potassium salt which is thought to be the starch phosphate counterion in vivo. From this structure and previously known glucophosphate structures we describe the possible 6‐O‐phosphate geometries and through modeling extrapolate the results to the double helical structure of the crystalline part of amylopectin. The geometries of the existing crystal structures of 6‐O‐phosphate groups were found to belong to two main adiabatic valleys. One of these conformations could be fitted into the double helical amylopectin part without perturbing the double helical amylopectin structure and without creating steric problems for the hexagonal chain–chain packing.

Understanding Thermodynamic Properties at the Molecular Level: Multiple Temperature Charge Density Study of Ribitol and Xylitol

X-ray diffraction data of high quality measured to high resolution on crystals of the two pentitol epimers ribitol (centric) and xylitol (acentric) at 101, 141, and 181 K and data on the two compounds previously recorded at 122 K have formed the basis for multipole refinements with the VALRAY system. Our analysis showed that it is possible to obtain a reliable crystal electron density for an acentric compound (xylitol) from X-ray diffraction data and that the thermal motion can be deconvoluted from the static density in this temperature range. The Bader-type topological analysis of the static electron densities revealed virtually identical intramolecular interactions as well as very similar hydrogen bond interactions of ribitol and xylitol; the only minor differences are found in the weaker intermolecular interactions. The high-level periodic DFT calculations are in accordance with the thermodynamic measurements that show that the two pentitols have identical sublimation energies. A rigid body normal coordinate analysis was performed on the atomic displacement parameters obtained at the four different temperatures. The translational and librational mean square deviations derived through this analysis were used in a quantum statistical approach to derive frequencies of the corresponding harmonic oscillators. The analysis showed a consistent vibrational model for all temperatures. The frequencies were subsequently used to calculate crystal entropies assuming an Einstein-type behavior. These calculations show that the crystal entropy of ribitol is 8 J K(-1) mol(-1) higher than the crystal entropy of xylitol, confirming that it is a difference in the entropy of the two compounds that causes the difference in their free energy. Our results presented in this Article show the potential to use X-ray diffraction data to obtain physicochemical properties of crystals.

A pH-Metric, UV, NMR, and X-ray Crystallographic Study on Arsenous Acid Reacting with Dithioerythritol

The aqueous solutions of arsenous acid with the meso and racemic forms of 1,4-dithiol-butane-2,3-diol, namely, dithioerythritol (dte) and dithiothreitol (dtt), respectively, were titrated pH-metrically in different molar ratios. The p K a values determined for As(OH) 3, and dtt were in good accordance with the literature data, and we determined for the first time the p K a value of dte. The deprotonation steps of both M (As(OH) 3 considered as a central metal ion) and H 2L components dte and dtt (considered as ligands) appeared at a higher pH in the titration curves of the ternary systems (M, H 2L, H (+)) than in the individual component. This unusual observation is explained by the condensation reactions between the reagents taking place in the pH < 8 range. In the solutions of c As(III) > 5.10 (-3) M, the precipitate formed upon mixing the arsenous acid and H 2L solutions in neutral medium, and the formation of the precipitate shifted toward acidic pH on the increase of the total concentrations. This indicated that pH-metry can follow the reactions only in an indirect way. Useful, but not satisfactory, information can be obtained by means of this method alone. Combined with NMR and UV spectroscopic measurements it is revealed that depending on the As(III)/H 2L molar ratio, different complexes form in the solutions. In the species with 1:2 composition, one of the ligands is strongly bound to the arsenic(III) probably via its two thiolate, while the second one is attached only weakly. The crystal structure of an As(III)-dte crystal of 1:1 composition, grown from ethanolic solution, shows that As(III) binds the ligand through its three p-orbitals in a manner similar to that expected in aqueous solution. While the uptake of the second ligand cannot be detected by pH-metry, the decomposition of thioether bonds above pH approximately 10 is confirmed by the change in UV spectra at approximately 265 nm to be a base-consuming process. In such alkaline solutions, most probably, rearrangement of the bonding scheme occurs, resulting in ligands being bound to the arsenic(III) through the oxygen donor atoms.

Modeling and Analysis of Hydrogen Atoms

Hydrogen atoms are elusive seen from the point of view of the X-ray crystallographer. But they are also extremely important, being involved in a wealth of intermolecular interactions and thereby defining the way molecules interact. Most experimental charge density studies are performed on compounds containing hydrogen, yet a commonly accepted strategy to deal with these elusive but so important atoms is only just about to surface. We review the efforts to determine a strategy for the modeling of hydrogen atoms, as well as a number of recent studies where the modeling of hydrogen atoms has had a major impact on the chemical conclusions drawn from analysis of the experimental charge densities.

Yes, one can obtain better quality structures from routine X-ray data collection

Single-crystal X-ray diffraction data should be collected to the highest resolution as this allows for refinement of more reliable structural, thermal and dependent parameters. The results of refinements using a Transferable Aspherical Atomic Model of electron density (TAAM) appear to be in far better agreement with neutron results than the corresponding Independent Atom Model (IAM) results for all parameters, all resolutions and all compounds, and we advocate the use of this approach instead of IAM.