ORCID Profile
0000-0002-4306-5918
Current Organisations
Freie Universität Berlin
,
Novartis Pharma AG
,
Heinrich-Heine-Universitat Düsseldorf
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Publisher: International Union of Crystallography (IUCr)
Date: 16-05-2007
DOI: 10.1107/S0108768107014838
Abstract: The structure of L-ornithine hydrochloride, C 5 H 13 N 2 O_2^+Cl − , has been redetermined at 100 K by single-crystal X-ray diffraction within a project that aims to generate accurate bond-distance restraints for the invariom refinement of proteins. The high-resolution data were subject to an invariom and a multipole refinement, and the resulting electron densities on a grid were compared. Improvements in the conventional R factor obtained by multipole modelling were smaller than in other structures containing solely the elements CHNO owing to Cl core scattering. Cruickshank's diffraction-component precision index and Stevens & Coppens suitability factor are discussed.
Publisher: Elsevier BV
Date: 03-2013
DOI: 10.1016/J.FITOTE.2013.01.009
Abstract: A new hopene-type triterpenoid, namely sonhafouonic acid 1a was isolated from Zehneria scabra camerunensis, together with eight known compounds. The structure of 1a was established by extensive NMR and high resolution MS techniques and confirmed by single-crystal X-ray crystallographic analysis. Compound 1a exhibited inhibitory activity against mycelial growth of two peronosporomycete phytopathogens Pythium ultimum and Aphanomyces cochliodes and cytotoxicity towards brine shrimp larvae (Artemia salina) at 10 μg/mL.
Publisher: International Union of Crystallography (IUCr)
Date: 15-05-2008
DOI: 10.1107/S0108768108005776
Abstract: From a high-resolution X-ray data set (sin θ/λ = 1.1 Å −1 ) measured at 20 K the electron-density distribution of the nucleoside thymidine was derived by a classical multipole refinement and by application of the invariom formalism. Owing to the presence of the heteroaromatic thymine ring system two invariom models were compared which considered the nearest and next-nearest neighbors for the invariom assignments. Differences between the two invariom models were small for the bond topological and atomic properties – about five times smaller than differences with the classical multipole refinement. Even the latter differences are in the uncertainty ranges which are commonly observed in experimental charge-density work and were found in molecular regions involved in intermolecular contacts. The application of the constrained wavefunction-fitting approach allowed the electron localization function (ELF) to be obtained from the experimental X-ray data, which was graphically represented and topologically analyzed. ELF basin populations were derived from experiment for the first time. The electron populations in the disynaptic valence basins were related quantitatively to bond orders.
Publisher: Wiley
Date: 13-09-2013
Publisher: American Chemical Society (ACS)
Date: 17-10-2013
DOI: 10.1021/JA4072139
Abstract: A 1,4-diamino-2,3-disila-1,3-butadiene derivative of composition (Me2-cAAC)2(Si2Cl2) (Me2-cAAC = :C(CMe2)2(CH2)N-2,6-iPr2C6H3) was synthesized by reduction of the Me2-cAAC:SiCl4 adduct with KC8. This compound is stable at 0 °C for 3 months in an inert atmosphere. Theoretical studies reveal that the silicon atoms exhibit pyramidal coordination, where the Cl-Si-Si-Cl dihedral angle is twisted by 43.3° (calcd 45.9°). The two silicon-carbon bonds are intermediates between single and double Si-C bonds due to twisting of the C-Si-Si-C dihedral angle (163.6°).
Publisher: American Chemical Society (ACS)
Date: 29-03-2011
DOI: 10.1021/OL103076Y
Abstract: ent-Homoabyssomicins A (1) and B (2) are new complex polycyclic spirotetronate metabolites isolated from Streptomyces sp. isolate Ank 210. The structures of 1 and 2 were elucidated by detailed spectroscopic analyses of 1D and 2D NMR data. The absolute configuration of 1 was established by subsequent single-crystal X-ray diffraction studies.
Publisher: Wiley
Date: 15-03-2017
Publisher: International Union of Crystallography (IUCr)
Date: 14-04-2006
Publisher: International Union of Crystallography (IUCr)
Date: 05-2012
Publisher: Springer Science and Business Media LLC
Date: 31-07-2017
Publisher: Wiley
Date: 12-2017
Publisher: International Union of Crystallography (IUCr)
Date: 16-11-2009
DOI: 10.1107/S0108768109046060
Abstract: Bergenin, which has been isolated from a variety of tropical plants, has several pharmacological applications in traditional Asian medicine. Its electron-density distribution was obtained from a room-temperature low-resolution X-ray data set measured with point detection making use of multipole populations from the invariom library. Two refinement models were considered. In a first step, positional parameters and ADPs were refined with fixed library multipoles (model E1). This model was suitable to be input into a second refinement of multipoles (model E2), which converged smoothly although based on Cu K α room-temperature data. Quantitative results of a topological analysis of the electron density from both models were compared with Hartree–Fock and density-functional calculations. With respect to the independent atom model (IAM) more information can be extracted from invariom modelling, including the electrostatic potential and hydrogen-bond energies, which are highly useful, especially for biologically active compounds. The reliability of the applied invariom formalism was assessed by a comparison of bond-topological properties of sucrose, for which high-resolution multipole and invariom densities were available. Since a conventional X-ray diffraction experiment using basic equipment was combined with the easy-to-use invariom formalism, the procedure described here for bergenin illustrates how it can be routinely applied in pharmacological research.
Publisher: International Union of Crystallography (IUCr)
Date: 15-05-2007
DOI: 10.1107/S0021889807016524
Abstract: The program InvariomTool can be used to obtain high-quality X-ray structures of organic molecules by automating both invariom modelling and the modelling process employed in experimental charge density studies. InvariomTool is a preprocessor program for the XD package [Koritsánszky et al. (2003), Technical Report, Freie Universität Berlin] and allows the analysis of a structure in terms of the local atomic bonding environment in order to assign Hansen–Coppens pseudoatoms that are transferable from one molecule to another (invarioms). It relies on a database of invariom entries, each containing the invariom name, local atomic site symmetry, coordinate system, model-compound name and theoretically predicted multipole population parameters. The information on chemical equivalence and local atomic site symmetry determines which multipole parameters are to be refined in the least-squares procedure of an experimental charge density study. InvariomTool allows the user to generate input files either for invariom refinement, where parameters are fixed and taken from the database, or for an experimental refinement of multipole parameters.
Publisher: Wiley
Date: 12-06-2019
Publisher: Wiley
Date: 05-04-2007
Publisher: Wiley
Date: 13-11-2014
Abstract: Single-crystal X-ray diffraction (XRD) is often considered the gold standard in analytical chemistry, as it allows element identification as well as determination of atom connectivity and the solid-state structure of completely unknown s les. Element assignment is based on the number of electrons of an atom, so that a distinction of neighboring heavier elements in the periodic table by XRD is often difficult. A computationally efficient procedure for aspherical-atom least-squares refinement of conventional diffraction data of organometallic compounds is proposed. The iterative procedure is conceptually similar to Hirshfeld-atom refinement (Acta Crystallogr. Sect. A- 2008, 64, 383-393 IUCrJ. 2014, 1,61-79), but it relies on tabulated invariom scattering factors (Acta Crystallogr. Sect. B- 2013, 69, 91-104) and the Hansen/Coppens multipole model disordered structures can be handled as well. Five linear-coordinate 3d metal complexes, for which the wrong element is found if standard independent-atom model scattering factors are relied upon, are studied, and it is shown that only aspherical-atom scattering factors allow a reliable assignment. The influence of anomalous dispersion in identifying the correct element is investigated and discussed.
Publisher: American Chemical Society (ACS)
Date: 21-06-2002
DOI: 10.1021/JP0145199
Publisher: American Chemical Society (ACS)
Date: 14-10-2011
DOI: 10.1021/JA206702E
Abstract: A stable silicon analogue of an acid anhydride {PhC(Bu(t)N)(2)}Si{═O·B(C(6)F(5))(3)}O-Si(H){═O·B(C(6)F(5))(3)}{(NBu(t))(HNBu(t))CPh} (4) with a O═Si-O-Si═O core has been prepared by treating monochlorosilylene PhC(Bu(t)N)(2)SiCl (1) with H(2)O·B(C(6)F(5))(3) in the presence of NHC (NHC = 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene). Compound 4 has been characterized by elemental analysis and multinuclear NMR spectroscopic investigations. The molecular structure of 4 has been established by single-crystal X-ray diffraction studies, and DFT calculations support the experimental results.
Publisher: Wiley
Date: 19-09-2017
Publisher: Royal Society of Chemistry (RSC)
Date: 2017
DOI: 10.1039/C7CC06358J
Abstract: Synthesis, structure, EPR and theoretical calculations of cyclic (alkyl)(amino)carbene stabilized mononuclear neutral radicals of aluminum containing mono- and di-organo groups.
Publisher: International Union of Crystallography (IUCr)
Date: 17-07-2008
DOI: 10.1107/S0108768108017497
Abstract: A corrigendum to the paper by Meents et al. (2008), Acta Cryst. B 64 , 42–49 to correct the nomenclature for CL-20.
Publisher: American Chemical Society (ACS)
Date: 12-05-2015
DOI: 10.1021/JACS.5B03407
Abstract: A cyclic alkyl(amino) carbene (cAAC) stabilized dimer [(cAAC)Si(P-Tip)]2 (2) (Tip = 2,4,6-triisopropylphenyl) is reported. 2 can be considered as a dimer of the heavier ketenimine (R2C═C═N-R) analogue. The dark-red rod-shaped crystals of 2 were synthesized by reduction of the precursor, cAAC-dichlorosilylene-stabilized phosphinidene (cAAC)SiCl2→P-Tip with sodium napthalenide. The crystals of 2 are storable at room temperature for several months and stable up to 215 °C under an inert atmosphere. X-ray single-crystal diffraction revealed that 2 contains a cyclic nonplanar four-membered SiPSiP ring. Magnetic susceptibility measurements confirmed the singlet spin ground state of 2. Cyclic voltammetry of 2 showed a quasi-reversible one-electron reduction indicating the formation of the corresponding radical anion 2(•-), which was further characterized by EPR measurements in solution. The electronic structure and bonding of 2 and 2(•-) were studied by theoretical calculations. The experimentally obtained data are in good agreement with the calculated values.
Publisher: Elsevier BV
Date: 04-2010
Publisher: American Chemical Society (ACS)
Date: 27-04-2009
DOI: 10.1021/OL900694M
Abstract: The first synthesis of anti-fused oligoannelated THF moieties is reported. The key transformation of the synthetic sequence, consisting of cyclopropanation, reduction and oxidation, is the expansion of a push-pull-substituted three-membered ring into a five-membered enol ether system. A repetition of the sequence allows the creation of oligoacetals up to a nonacyclic system.
Publisher: Wiley
Date: 14-03-2013
Publisher: International Union of Crystallography (IUCr)
Date: 18-10-2006
Publisher: International Union of Crystallography (IUCr)
Date: 19-07-2013
Publisher: Wiley
Date: 04-05-2015
Abstract: An elegant general synthesis route for the preparation of two coordinate palladium(0) and platinum(0) complexes was developed by reacting commercially available tetrakis(triphenylphosphine)palladium latinum with π-accepting cyclic alkyl(amino) carbenes (cAACs). The complexes are characterized by NMR spectroscopy, mass spectrometry, and single-crystal X-ray diffraction. The palladium complexes exhibit sharp color changes (crystallochromism) from dark maroon to bright green if the C-Pd-C bond angle is sharpened by approximately 6°, which is chemically feasible by elimination of one lattice THF solvent molecule. The analogous dark orange-colored platinum complexes are more rigid and thus do not show this phenomenon. Additionally, [(cAAC)2 Pd/Pt] complexes can be quasi-reversibly oxidized to their corresponding [(cAAC)2 Pd/Pt](+) cations, as evidenced by cyclic voltammetry measurements. The bonding and stability are studied by theoretical calculations.
Publisher: International Union of Crystallography (IUCr)
Date: 13-11-2008
Publisher: Wiley
Date: 07-2006
Publisher: International Union of Crystallography (IUCr)
Date: 29-08-2014
DOI: 10.1107/S2052252514014845
Abstract: Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the ex le of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly–L-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree–Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints – even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu's), all other structural parameters agree within less than 2 csu's. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below for hydrogen-atom ADPs it is better than 0.006 Å 2 as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements – an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å.
Publisher: American Chemical Society (ACS)
Date: 16-01-2015
DOI: 10.1021/JA5130379
Abstract: Molecular encapsulation processes under the control of an external trigger play a major role in biological signal transduction processes and enzyme catalysis. Here, we present an artificial mimic of a controllable host system that forms via self-assembly from a simple bis-monodentate ligand and Pd(II) cations. The resulting interpenetrated double cage features three consecutive pockets which initially contain one tetrafluoroborate anion, each. Activation of this host system with two halide anions triggers a conformational change that renders the central pocket susceptible to the uptake of small neutral guest molecules. Thereby, the pentacationic cage expels the central anion and replaces it with a neutral molecule to give a hexacationic species. The cage structures prior and after the halide triggered binding of benzene were examined by X-ray crystallography, ESI MS, and NMR techniques. The kinetics and thermodynamics of the encapsulation of benzene, cyclohexane, and norbornadiene are compared.
Publisher: Wiley
Date: 26-09-2007
Abstract: Although reliable determination of the molecular dipole moment from experimental charge density analyses on molecular crystals is a challenging undertaking, these values are becoming increasingly common experimental results. We collate all known experimental determinations and use this database to identify broad trends in the dipole moment enhancements implied by these measurements as well as outliers for which enhancements are pronounced. Compelling evidence emerges that molecular dipole moments from X-ray diffraction data can provide a wealth of information on the change in the molecular charge distribution that results from crystal formation. Most importantly, these experiments are unrivalled in their potential to provide this information in such detail and deserve to be exploited to a much greater extent. The considerable number of experimental determinations now available has enabled us to pinpoint those studies that merit further attention, either because they point unequivocally to a considerable enhancement in the crystal (of 50 % or more), or because the experimental determinations suggest enhancements of 100 % or more--much larger than independent theoretical estimates. In both cases further detailed experimental and theoretical studies are indicated.
Publisher: Royal Society of Chemistry (RSC)
Date: 2010
DOI: 10.1039/C003378B
Publisher: Royal Society of Chemistry (RSC)
Date: 2006
DOI: 10.1039/B514717D
Abstract: A 20 K high resolution X-ray data set of L-Ala-L-Ala-L-Ala*1/2 H2O was measured using an ultra-low temperature laboratory setup, that combines area detection and a closed cycle helium cryostat. The charge density determination includes integration of atomic basins and topological analysis according to Bader's quantum theory of atoms in molecules. Two tripeptide units are found in the asymmetric unit, allowing the assessment of transferability of bond topological and atomic properties taking also into consideration previous data of oligopeptides. With respect to invariom modeling the limits of such transferability are investigated and the results of this study show the validity of the nearest/next-nearest neighbour approximation and support the use of database approaches for electron density modeling of macromolecules.
Publisher: International Union of Crystallography (IUCr)
Date: 17-05-2012
DOI: 10.1107/S0108768112017831
Abstract: The structure of ceftazidime pentahydrate, a third generation cephalosporin antibiotic, is reported. Data collection was carried out in a remarkably short time with synchrotron radiation and the latest detector technology, illustrating that single-crystal X-ray diffraction can be used as a technique for screening hundreds of compounds in a short amount of time. Structure refinement made use of invarioms, namely non-spherical scattering factors, which allow more information to be derived from a diffraction experiment. Properties that can be screened are bond-topological parameters, empirical hydrogen-bond energies, molecular dipole moments and electrostatic potentials.
Publisher: International Union of Crystallography (IUCr)
Date: 18-09-2006
DOI: 10.1107/S0108768106019616
Abstract: The accurate X-ray single-crystal structures of the isoflavone compounds 4- O -methylalpinumisoflavone, O , O -dimethylalpinumisoflavone and 5- O -methyl-4- O -(3-methylbut-2-en-1-yl)alpinumisoflavone {alpinumisoflavone = 5-hydroxy-7-(4-hydroxyphenyl)-2,2-dimethyl-2 H ,6 H -benzo[1,2- b :5,4- b ′]dipyran-6-one} from data sets measured at cryogenic temperature have been obtained from invariom modelling using theoretically predicted Hansen and Coppens multipole-model form factors, which describe the aspherical electron density distribution. Molecular dipole moments and electrostatic potentials obtained from invariom modelling are discussed and compared with results from ab initio theoretical calculations. All three studied compounds are solvent extracts of root bark or seed powder of Millettia thonningii ( leguminosae ), a plant molluscicide and cercaricide used in Franco West Africa as medication against various diseases. The compounds' toxicities to brine shrimp have been determined and their different potencies tentatively related to conformation differences, intramolecular contacts, dipole moments and electrostatic potential features.
Publisher: Wiley
Date: 13-09-2013
Publisher: Elsevier BV
Date: 11-2012
Publisher: International Union of Crystallography (IUCr)
Date: 18-02-2011
Publisher: International Union of Crystallography (IUCr)
Date: 18-04-2008
Publisher: Royal Society of Chemistry (RSC)
Date: 2013
DOI: 10.1039/C3CC43199A
Abstract: Functionalization of N-heterocyclic carbenes (NHCs) has an important influence on their stability, Lewis donor, and acceptor properties. In this study, we report on the selective functionalization of a four-membered N-heterocyclic bis-silylene (2,6-Ar2C6H3NSi:)2 (1) (Ar = 2,4,6-iPr3C6H2) with mono-oxygen sources N2O and Me3NO. Treatment of 1 with N2O results in the selective formation of mono-silylene (2,6-Ar2C6H3NSi(OH)2)(2,6-Ar2C6H3NSi:) (2) as a major product, along with a small amount of further oxidized product (2,6-Ar2C6H3NSi(OH)2)2 (3). Compound 2 is the first four-membered mono-silylene with a di-coordinate silicon atom.
Publisher: American Chemical Society (ACS)
Date: 07-2009
DOI: 10.1021/JP902433X
Abstract: The electron densities of the three natural B(12)-vitamins, two of them being essential cofactors for animal life, were determined in a procedure combining high-order X-ray data collection at low to very low temperatures with high-level density functional calculations. In a series of extensive experimental attempts, a high-order data set of adenosylcobalamin (AdoCbl) could be collected to a resolution of sin theta/lambda = 1.00 A(-1) at 25 K. This modification contains only minor disorder at the solvent bulk. For methylcobalamin (MeCbl), only a severely disordered modification was found (sin theta/lambda = 1.00 A(-1), 100 K, measured with synchrotron radiation). The already published data set of cyanocobalamin (CNCbl) (sin theta/lambda = 1.25 A(-1), 100 K) was reintegrated to guarantee similar treatment of the three compounds and cut to sin theta/lambda = 1.11 A(-1) to obtain a higher degree of completeness and redundancy. On the basis of these accurate experimental geometries of AdoCbl, MeCbl, and CNCbl, state-of-the-art density functional calculations, single-point calculations, and geometry optimizations were performed on model compounds at the BP86/TZVP level of theory to evaluate the electronic differences of the three compounds. AdoCbl and MeCbl are known to undergo different reaction paths in the body. Thus, the focus was directed toward the characterization of the dative Co-C(ax) and Co-N(ax) bonds, which were quantifed by topological parameters, including energy densities the source function including local source and the electron localizability indicator (ELI-D), respectively. The source function reveals the existence of delocalized interactions between the corrin macrocycle and the axial ligands. The ELI-D indicates unsaturated Co-C(ax) bonding basins for the two biochemically active cofactors, but not for CNCbl, where a population of 2.2e is found. This may be related to significant pi-backbonding, which is supported by the delocalization index, delta, of 0.15 between the Co atom and the N atom of the cyano ligand. Considering all results, the inherent electronic differences between AdoCbl and MeCbl are found to be small thus, supporting earlier findings that the interaction with the protein site mainly controls the type of Co-C(ax) bond cleavage.
Publisher: American Chemical Society (ACS)
Date: 16-06-2014
DOI: 10.1021/JA504821U
Abstract: A disiladicarbene, (Cy-cAAC)2Si2 (2), was synthesized by reduction of Cy-cAAC:SiCl4 adduct with KC8. The dark-colored compound 2 is stable at room temperature for a year under an inert atmosphere. Moreover, it is stable up to 190 °C and also can be characterized by electron ionization mass spectrometry. Theoretical and Raman studies reveal the existence of a Si═Si double bond with a partial double bond between each carbene carbon atom and silicon atom. Cyclic voltammetry suggests that 2 can quasi-reversibly accept an electron to produce a very reactive radical anion, 2(•-), as an intermediate species. Thus, reduction of 2 with potassium metal at room temperature led to the isolation of an isomeric neutral rearranged product and an anionic dimer of a potassium salt via the formation of 2(•-).
Publisher: International Union of Crystallography (IUCr)
Date: 18-02-2021
DOI: 10.1107/S2052252521000531
Abstract: Distinguishing disorder into static and dynamic based on multi-temperature X-ray or neutron diffraction experiments is the current state of the art, but is only descriptive, not predictive. Here, several disordered structures are revisited from the Cambridge Crystallographic Data Center `drug subset', the Cambridge Structural Database and own earlier work, where experimental intensities of Bragg diffraction data were available. Using the molecule-in-cluster approach, structures with distinguishable conformations were optimized separately, as extracted from available or generated disorder models of the respective disordered crystal structures. Re-combining these `archetype structures' by restraining positional and constraining displacement parameters for conventional least-squares refinement, based on the optimized geometries, then often achieves a superior fit to the experimental diffraction data compared with relying on experimental information alone. It also simplifies and standardizes disorder refinement. Ten ex le structures were analysed. It is observed that energy differences between separate disorder conformations are usually within a small energy window of RT ( T = crystallization temperature). Further computations classify disorder into static or dynamic, using single experiments performed at one single temperature, and this was achieved for propionamide.
Publisher: Royal Society of Chemistry (RSC)
Date: 2009
DOI: 10.1039/B819157C
Abstract: The X-ray single-crystal structure of methyl 2-aminoisobutyrate hydrochloride (Me-AIB), a non-standard amino acid, is reported at 10, 30, 50, 70 and 100 K. Fourier maps indicate the presence of rotational disorder of the hydrogen atoms of the ester methyl group. To study this effect in detail, high resolution data were collected with synchrotron radiation. The non-spherical molecular electron density was predicted with invariom scattering factors and subtracted from the density obtained from a full multipole refinement. This allows disorder to be distinguished from the molecular electron density at each temperature. The disorder is reduced between 100 K and 30 K, but still detectable even at 10 K. Hence, difference densities can be applied for the purpose of electronic structure validation and have the advantage of an absence of noise over Fourier methods. Ultra-low temperature experiments are foreseen to be useful in reducing such kinds of disorder in ultra-high resolution protein crystallography. Molecular dynamics simulations of Me-AIB at temperatures between 10 and 100 K confirm the temperature dependence of the rotational motion of the methyl group seen experimentally. Modeling disorder in X-ray structure analysis will be an interesting future application of molecular dynamics simulations.
Publisher: International Union of Crystallography (IUCr)
Date: 10-08-2002
Publisher: Wiley
Date: 09-04-2013
Abstract: The 3+3-type synthesis of a pyrazole-based expanded porphyrin 22 H4, a hexaphyrin analogue named Siamese-twin porphyrin, and its homobimetallic diamagnetic nickel(II) and paramagnetic copper(II) complexes, 22 Ni2 and 22 Cu2, are described. The structure of the macrocycle composed of four pyrroles and two pyrazoles all linked by single carbon atoms, can be interpreted as two conjoined porphyrin-like subunits, with the two opposing pyrazoles acting as the fusion points. Variable-temperature 1D and 2D NMR spectroscopic analyses suggested a conformationally flexible structure for 22 H4. NMR and UV/Vis spectroscopic evidence as well as structural parameters proved the macrocycle to be non-aromatic, though each half of the molecule is fully conjugated. UV/Vis and NMR spectroscopic titrations of the free base macrocycle with acid showed it to be dibasic. In the complexes, each metal ion is coordinated in a square-planar fashion by a dianionic, porphyrin-like {N4} binding pocket. The solid-state structures of the dication and both metal complexes were elucidated by single-crystal diffractometry. The conformations of the three structures are all similar to each other and strongly twisted, rendering the molecules chiral. The persistent helical twist in the protonated form of the free base and in both metal complexes permitted resolution of these enantiomeric helimers by HPLC on a chiral phase. The absolute stereostructures of 22 H6(2+), 22 Ni2, and 22 Cu2 were assigned by a combination of experimental electronic circular dichroism (ECD) investigations and quantum-chemical ECD calculations. The synthesis of the first member of this long-sought class of expanded porphyrin-like macrocycles lays the foundation for the study of the interactions of the metal centers within their bimetallic complexes.
Publisher: Springer Science and Business Media LLC
Date: 09-09-2016
DOI: 10.1038/NCOMMS12809
Abstract: Determining the structures of nanoparticles at atomic resolution is vital to understand their structure–property correlations. Large metal nanoparticles with core diameter beyond 2 nm have, to date, eluded characterization by single-crystal X-ray analysis. Here we report the chemical syntheses and structures of two giant thiolated Ag nanoparticles containing 136 and 374 Ag atoms (that is, up to 3 nm core diameter). As the largest thiolated metal nanoparticles crystallographically determined so far, these Ag nanoparticles enter the truly metallic regime with the emergence of surface plasmon resonance. As miniatures of fivefold twinned nanostructures, these structures demonstrate a subtle distortion within fivefold twinned nanostructures of face-centred cubic metals. The Ag nanoparticles reported in this work serve as excellent models to understand the detailed structure distortion within twinned metal nanostructures and also how silver nanoparticles can span from the molecular to the metallic regime.
Publisher: Royal Society of Chemistry (RSC)
Date: 2017
DOI: 10.1039/C7DT01796K
Abstract: An unique molecular ex le of interconnected bis-germylene with the smallest organic group stabilized by cyclic alkyl(amino) carbene.
Publisher: International Union of Crystallography (IUCr)
Date: 28-05-2014
DOI: 10.1107/S2053273314010626
Abstract: The temperature dependence of H- U iso in N -acetyl-L-4-hydroxyproline monohydrate is investigated. Imposing a constant temperature-independent multiplier of 1.2 or 1.5 for the riding hydrogen model is found to be inaccurate, and severely underestimates H- U iso below 100 K. Neutron diffraction data at temperatures of 9, 150, 200 and 250 K provide benchmark results for this study. X-ray diffraction data to high resolution, collected at temperatures of 9, 30, 50, 75, 100, 150, 200 and 250 K (synchrotron and home source), reproduce neutron results only when evaluated by aspherical-atom refinement models, since these take into account bonding and lone-pair electron density both invariom and Hirshfeld-atom refinement models enable a more precise determination of the magnitude of H-atom displacements than independent-atom model refinements. Experimental efforts are complemented by computing displacement parameters following the TLS+ONIOM approach. A satisfactory agreement between all approaches is found.
Publisher: American Chemical Society (ACS)
Date: 02-12-2010
DOI: 10.1021/IC1020548
Abstract: Pentacoordinate silicon fluorides L(1)SiF(3) (2a), L(2)SiF(3) (2b), and (L(3)SiF(2))(2) (2c)(2) based on amidinate (L(1) = PhC(N(t)Bu)(2)), guanidinate (L(2) = 1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidinate), and triazapentadienate (L(3) = NC(NMe(2))NC(NMe(2))NAr Ar = 2,6-(i)Pr(2)C(6)H(3)) ligands were prepared by fluorination of the corresponding chlorosilanes L(1)SiCl(3) (1a), L(2)SiCl(3) (1b), and L(3)SiCl(2) (1c) with Me(3)SnF at ambient temperature. Compounds 1b, 1c, 2a, 2b, and (2c)(2) were characterized by (1)H, (13)C, (19)F, and (29)Si NMR spectroscopic studies. Molecular structures of 1b, 1c, 2a, and (2c)(2) were determined by single crystal X-ray structural analysis. Invariom refinement involving non-spherical scattering factors of the Hansen-Coppens multipole model was performed for 1b. Compound L(3)SiF(2) (2c) is dimeric both in the solid state and in solution, whereas its chloro-analogue 1c is monomeric. The attempted synthesis of diamidinatotetrachlorodisilane by reaction of lithium amidinate with Si(2)Cl(6) led to the formation of the silane (1a) and the silylene L(1)SiCl (3). Reaction of Si(2)Cl(6) with N-heterocyclic carbenes (NHC) afforded NHC adducts of dichlorosilylene and SiCl(4). A one pot method for the preparation of base-stabilized silylenes from Si(2)Cl(6) is discussed.
Publisher: International Union of Crystallography (IUCr)
Date: 13-10-2015
DOI: 10.1107/S2053229615015739
Abstract: In the crystal structure of the title homoleptic Cr II complex, [Cr(CH 3 CN) 6 ](C 24 H 20 B) 2 ·CH 3 CN, the [Cr(CH 3 CN) 6 ] 2+ cation is a high-spin d 4 complex with strong static, rather than dynamic, Jahn–Teller distortion. The electron density of the cation was determined by single-crystal X-ray refinements using aspherical structure factors from wavefunction calculations. The detailed picture of the electronic density allowed us to assess the extent and directionality of the Jahn–Teller distortion of the Cr II cation away from idealized octahedral symmetry. The topological analysis of the aspherical d -electron density about the Cr II cation showed that there are significant valence charge concentrations along the axial Cr—N axes. Likewise, there were significant valence charge depletions about the Cr II cation along the equatorial Cr—N bonds. These charge concentrations are in accordance with a Jahn–Teller-distorted six-coordinate complex.
Publisher: Royal Society of Chemistry (RSC)
Date: 2010
DOI: 10.1039/C0NJ00142B
Publisher: International Union of Crystallography (IUCr)
Date: 30-07-2002
DOI: 10.1107/S0108768102005839
Abstract: The charge density of a hexapeptide was determined from high-resolution CCD area-detector experiments at 100 K. Two datasets, one from a rotating anode and a second one from synchrotron radiation, were measured and the results are compared. The data are interpreted in terms of the `rigid pseudoatom' model. The topology of the experimental density is analyzed and compared with the topology of the constituting amino acids, and shows good agreement. All critical points of the electron density at the covalent and hydrogen bonds, as well as those of the Laplacian, were located. With respect to the transferability of electronic and bond topological properties the six peptide bonds were compared with values given in the literature.
Publisher: International Union of Crystallography (IUCr)
Date: 18-03-2004
DOI: 10.1107/S0108768104001739
Abstract: A high-resolution X-ray diffraction data set was collected within 48 h at 100 K with synchrotron radiation and area detection. A full topological analysis was applied to the resulting electron-density model. This analysis was followed by a Bader partitioning making use of the zero-flux surfaces of the electron-density gradient vector field. The atomic and bonding properties obtained were compared with the results of previous experimental studies, and with theoretical calculations for the title complex and free tryptophan as reported in the literature. The agreement between experiment and theory is similar to the agreement between different theoretical calculations. There is no charge transfer via the strong hydrogen bond however, its strength is indicated by the very small atomic volume of the H atom involved.
Publisher: International Union of Crystallography (IUCr)
Date: 17-05-2014
DOI: 10.1107/S2053229614010195
Abstract: For the structure of fluconazole [systematic name: 2-(2,4-difluorophenyl)-1,3-bis(1 H -1,2,4-triazol-1-yl)propan-2-ol] monohydrate, C 13 H 12 F 2 N 6 O·H 2 O, a case study on different model refinements is reported, based on single-crystal X-ray diffraction data measured at 100 K with Cu K α radiation to a resolution of sin θ/λ of 0.6 Å −1 . The structure, anisotropic displacement parameters (ADPs) and figures of merit from the independent atom model are compared to `invariom' and `Hirshfeld atom' refinements. Changing from a spherical to an aspherical atom model lowers the figures of merit and improves both the accuracy and the precision of the geometrical parameters. Differences between results from the two aspherical-atom refinements are small. However, a refinement of ADPs for H atoms is only possible with the Hirshfeld atom density model. It gives meaningful results even at a resolution of 0.6 Å −1 , but requires good low-order data.
Publisher: Royal Society of Chemistry (RSC)
Date: 2012
DOI: 10.1039/C1CE05966A
Publisher: International Union of Crystallography (IUCr)
Date: 29-09-2017
DOI: 10.1107/S2052520617010745
Abstract: Modelling coordination compounds has been shown to be feasible using the invariom method for the best fit to a given set of diffraction data, additional steps other than using lookup tables of scattering factors need to be carried out. Here such procedures are applied to a number of `duplicate structures', where structures of two or more supposedly different coordination complexes with identical ligand environments, but with different 3 d metal ions, were published. However, only one metal atom can be plausibly correct in these structures, and other spectroscopic data are unavailable. Using aspherical scattering factors, a structure can be identified as correct from the deposited Bragg intensities alone and modelling only the ligand environment often suffices to make this distinction. This is not possible in classical refinements using the independent atom model. Quantum-chemical computations of the better model obtained after aspherical-atom refinement further confirm the assignment of the element in the respective figures of merit.
Publisher: Royal Society of Chemistry (RSC)
Date: 2013
DOI: 10.1039/C3CC44437F
Abstract: Si-enterobactin (2a), a hexacoordinated complex of the siderophore enterobactin (2b) with silicon as the central atom, was isolated from an endophytic Streptomyces sp. occurring in Piper guinensis roots. The structure and absolute configuration were determined from NMR and MS data, and by X-ray diffraction. The orientation of the molecule along the pseudo-3-fold axis shows that the coordination environment of the silicon atom complexed with three bidentate ligands is Δ. We assume that 2a or related complexes may be involved in the transport of silicon in plants, diatoms, or other silicon-dependent organisms.
Publisher: Royal Society of Chemistry (RSC)
Date: 2004
DOI: 10.1039/B312550E
Abstract: High-resolution X-ray diffraction data have been collected on the cubic polymorph of antimony(III) oxide (senarmontite) to determine the charge distribution in the crystal. The results are in quantitative agreement with crystal Hartree-Fock calculations for this polymorph, and have been compared with theoretical calculations on the orthorhombic polymorph (valentinite). Information about the nature of bonding and relative bond strengths in the two polymorphs has been extracted in a straightforward manner via topological analysis of the electron density. All the close contacts in both polymorphs are found to be similar in nature based on the value of the Laplacian, the magnitude of the electron density and the local energy density at the bond critical points, and these characterise the observed interactions as substantially polar covalent, similar to molecular calculation results on Si-O and Ge-O. Electrostatic potential isosurfaces reveal the octopolar nature of this function for senarmontite, and shed light on the observed packing arrangement of Sb4O6 molecules in the crystal.
Publisher: International Union of Crystallography (IUCr)
Date: 25-02-2009
DOI: 10.1107/S0909049509002192
Abstract: Radiation damage is one of the major impediments in obtaining high-resolution structural information utilizing ionizing radiation. From electron microscopy it is known that electron irradiation of biological s les results in the formation of molecular hydrogen. In the present work radiation-induced structural changes of the polypeptide cyclosporine A were observed at a temperature of 100 K. Bond length changes are thought to be due to radiation-induced hydrogen abstraction which chemically modifies the molecules in an irreversible way. The resulting formation of molecular hydrogen might explain the observed increase of the crystal mosaicity, which has also been reported in many previous radiation damage studies.
Publisher: American Chemical Society (ACS)
Date: 14-01-2013
DOI: 10.1021/JP309985E
Abstract: In the charge density study of 9-diphenylthiophosphinoylanthracene the thermal motion of several atoms needed an anharmonic description via Gram-Charlier coefficients even for data collected at 15 K. As several data sets at different temperatures were measured, this anharmonic model could be proved to be superior to a disorder model. Refinements against theoretical data showed the resemblance of an anharmonic model and a disorder model with two positions very close to each other (~0.2 Å), whereas these two models could be clearly distinguished if the second position is 0.5 Å apart. The refined multipole parameters were distorted when the anharmonic motion was not properly refined. Therefore, this study reveals the importance of detecting and properly handling anharmonic motion. Unrefined anharmonic motion leads to typical shashlik-like residual density patterns. Therefore, careful analysis of the residual density and the derived probability density function after the refinement of the Gram-Charlier coefficients proved to be the most useful tools to indicate the presence of anharmonic motion.
Publisher: Royal Society of Chemistry (RSC)
Date: 2020
DOI: 10.1039/D0CE00300J
Abstract: Disorder in crystal structures can disappear, depending on the circumstances, as shown by multi-temperature measurements, aspherical-atom refinement and computational analyses.
Publisher: American Chemical Society (ACS)
Date: 17-04-2018
DOI: 10.1021/ACS.JNATPROD.7B00958
Abstract: Three new alkaloids, janetinine (1a), pleiokomenine A (2), and huncaniterine B (3a), and 13 known compounds, pleiomutinine (3b), huncaniterine A (3c), 1-carbomethoxy-β-carboline (4), evoxanthine (5), deformyltalbotine acid lactone (6), pleiocarpamine (7), N
Publisher: Wiley
Date: 04-12-2017
Publisher: Springer Science and Business Media LLC
Date: 05-10-2010
Publisher: Wiley
Date: 6
Abstract: The synthesis of a centrally functionalized, ribbon-shaped [6]polynorbornane ligand L that self-assembles with Pd(II) cations into a {Pd2 L4 } coordination cage is reported. The shape-persistent {Pd2 L4 } cage contains two axial cationic centers and an array of four equatorial H-bond donors pointing directly towards the center of the cavity. This precisely defined supramolecular environment is complementary to the geometry of classic octahedral complexes [M(XY)6 ] with six diatomic ligands. Very strong binding of [Pt(CN)6 ](2-) to the cage was observed, with the structure of the host-guest complex {[Pt(CN)6 ]@Pd2 L4 } supported by NMR spectroscopy, MS, and X-ray data. The self-assembled shell imprints its geometry on the encapsulated guest, and desymmetrization of the octahedral platinum species by the influence of the D4h -symmetric second coordination sphere was evidenced by IR spectroscopy. [Fe(CN)6 ](3-) and square-planar [Pt(CN)4 ](2-) were strongly bound. Smaller octahedral anions such as [SiF6 ](2-) , neutral carbonyl complexes ([M(CO)6 ] M=Cr, Mo, W) and the linear [Ag(CN)2 ](-) anion were only weakly bound, showing that both size and charge match are key factors for high-affinity binding.
Publisher: Wiley
Date: 09-09-2010
Abstract: The synthesis of oligocyclic oligoacetals using five‐membered rings as repetitive unit is described. Furan was used as the starting material, which is converted by a three‐step procedure consisting of twofold cyclopropanation, reduction, and oxidative ring enlargement into a tricyclic bis(enol ether). A repetition of this synthetic procedure leads to the formation of extended oligoacetal systems. Insights into the structures were gained by X‐ray crystallographic investigations and revealed helical arrangements of the subunits in the solid‐state. DFT (B3LYP) calculations have been carried out to elucidate the transition state of the ring enlargement and the flexibility of the annelated oligocyclic systems. Strain energies and topologies of potential cyclically condensed oligoacetals are predicted.
Publisher: Wiley
Date: 05-05-2004
Publisher: International Union of Crystallography (IUCr)
Date: 03-10-2009
DOI: 10.1107/S0021889809034621
Abstract: The limiting factor for charge-density studies is crystal quality. Although area detection and low temperatures enable redundant data collection, only compounds that form well diffracting single crystals without disorder are amenable to these studies. If thermal motion and electron density ρ( r ) were de-convoluted, multipole parameters could also be refined with lower-resolution data, such as those commonly collected for macromolecules. Using the invariom database for first refining conventional parameters ( x , y , z and atomic displacement parameters), de-convolution can be achieved. In a subsequent least-squares refinement of multipole parameters only, information on the charge density becomes accessible also for data not fulfilling charge-density requirements. A critical aspect of this procedure is the missing information on the correlation between refined and non-refined parameters. This correlation is investigated in detail by comparing a full multipole refinement on high-resolution and a blocked refinement on `normal-resolution' data sets of ciprofloxacin hexahydrate. Topological properties and dipole moments are shown to be in excellent agreement for the two refinements. A `normal-resolution' data set of ciprofloxacin hydrochloride 1.4-hydrate is also evaluated in this manner.
Publisher: Wiley
Date: 19-09-2017
Abstract: Ferrocene, Cp
Publisher: Elsevier BV
Date: 06-2010
DOI: 10.1016/J.BMC.2010.03.004
Abstract: Herein we describe the synthesis of highly substituted chromans and isochromans using carbohydrates as starting materials. The key step of our synthetic approach is the annelation of the benzene moiety via a highly efficient Pd-catalyzed domino reaction. This powerful approach led to a small library of highly substituted chromans and isochromans by making use of a variety of different diynes and bromoglycals. We investigated several Pd-catalysts in order to improve the yields and to enlarge the scope of the domino reaction. Furthermore, we elucidated the mechanistic picture of the reaction with isotope-labelling experiments. Most probably the reaction proceeds via an oxidative addition followed by two carbopalladation steps and a final cyclization reaction.
Publisher: Wiley
Date: 22-07-2014
Abstract: Compound (Me2 -cAAC:)2 Co(0) (2 Me2 -cAAC:=cyclic (alkyl) amino carbene :C(CH2 )(CMe2 )2 N-2,6-iPr2 C6 H3 ) was synthesized by the reduction of the precursor (Me2 -cAAC:)2 Co(I) Cl (1) with KC8 in THF. The cyclic voltammogram of 1 exhibited one-electron reduction, which suggests that synthesis of a bent 2-metallaallene (2) from 1 should be possible. Compound 2 contains one cobalt atom in the formal oxidation state zero, which is stabilized by two Me2 -cAAC: ligands. Bond lengths from X-ray diffraction are 1.871(2) and 1.877(2) Å with a C-Co-C bond angle of 170.12(8)°. The EPR spectrum of 2 exhibited a broad resonance attributed to the unique quasi-linear structure, which favors near degeneracy and gives rise to very rapid relaxation conditions. The cAACCo bond in 2 can be considered as a typical Dewar-Chatt-Duncanson type of bonding, which in turn retains 2.5 electron pairs on the Co atom as nonbonding electrons.
Publisher: International Union of Crystallography (IUCr)
Date: 23-09-2014
DOI: 10.1107/S2052252514018867
Abstract: This article reviews efforts in accurate experimental charge-density studies with relevance to medicinal chemistry. Initially, classical charge-density studies that measure electron density distribution via least-squares refinement of aspherical-atom population parameters are summarized. Next, interaction density is discussed as an idealized situation resembling drug–receptor interactions. Scattering-factor databases play an increasing role in charge-density research, and they can be applied both to small-molecule and macromolecular structures in refinement and analysis software development facilitates their use. Therefore combining both of these complementary branches of X-ray crystallography is recommended, and ex les are given where such a combination already proved useful. On the side of the experiment, new pixel detectors are allowing rapid measurements, thereby enabling both high-throughput small-molecule studies and macromolecular structure determination to higher resolutions. Currently, the most ambitious studies compute intermolecular interaction energies of drug–receptor complexes, and it is recommended that future studies benefit from recent method developments. Selected new developments in theoretical charge-density studies are discussed with emphasis on its symbiotic relation to crystallography.
Publisher: American Chemical Society (ACS)
Date: 19-12-2012
DOI: 10.1021/OM301062D
Publisher: International Union of Crystallography (IUCr)
Date: 26-01-2011
Publisher: American Chemical Society (ACS)
Date: 03-04-2015
DOI: 10.1021/JACS.5B02403
Abstract: Intermediate species dichlorosilylene was generated in situ from trichlorosilane and inserted into the P-Cl bond of diphenylchlorophosphine (Ph2P-Cl) to obtain Ph2P-SiCl3 (1). Monodechlorination of 1 by cyclic alkyl(amino) carbenes (cAACs)/KC8 in THF at low temperature led to the formation of stable radicals Ph2P-Si(cAAC·)Cl2 (2a,b). Compounds 2a,b were characterized by X-ray single crystal diffraction, mass spectrometry and studied by cyclic voltammetry and theoretical calculations. Radical properties of 2 are confirmed by EPR measurements that suggest the radical electron in 2 couples with (14)N (I = 1), (35/37)Cl (I = 3/2), and (31)P (I = 1/2) nuclei leading to multiple hyperfine lines. Hyperfine coupling parameters computed from DFT calculations are in good agreement with those of experimental values. Electronic distributions obtained from the theoretical calculations suggest that the radical electron mostly resides on the carbene C of 2.
Publisher: Royal Society of Chemistry (RSC)
Date: 2012
DOI: 10.1039/C2DT31326J
Abstract: The three-membered silacyclic ring compounds LSi[N(2)(Ph)(2)]tBu (1), LSi[HCN(Ph)(2)]tBu (2) and LSi[C(2)(Ph)(2)]tBu (3) were obtained by the treatment of base stabilized monoalkylsilylenes LSitBu (L = PhC(NtBu)(2)) with PhN=NPh, PhN=CHPh and PhC≡CPh. The reaction of PhN=NPh and PhC≡CPh with LSitBu shows a different reactivity pattern with base stabilized monochlorosilylene LSiCl. The arrangement of the three-membered ring (SiNN) in 1 is the first structurally isolated ex le of a siladiaziridine compound.
Publisher: Elsevier BV
Date: 03-1913
Publisher: International Union of Crystallography (IUCr)
Date: 18-03-2017
DOI: 10.1107/S2052520617006680
Abstract: Topological analysis using Bader and co-worker's Atoms in Molecules theory has seen many applications in theoretical chemistry and experimental charge-density research. A brief overview of successful early developments, establishing topological analysis as a research tool for characterizing intramolecular chemical bonding, is provided. A lack of vision in many `descriptive but not predictive' subsequent studies is discussed. Limitations of topology for providing accurate energetic estimates of intermolecular interaction energies are put into perspective. It is recommended that topological analyses of well understood bonding situations are phased out and are only reported for unusual bonding. Descriptive studies of intermolecular interactions should have a clear research focus.
Publisher: American Chemical Society (ACS)
Date: 07-09-2011
DOI: 10.1021/OL202247E
Publisher: Wiley
Date: 28-01-2016
Abstract: Reduction of the neutral carbene tetrachlorosilane adduct (cAAC)SiCl4 (cAAC=cyclic alkyl(amino) carbene :C(CMe2)2 (CH2)N(2,6-iPr2C6H3) with potassium graphite produces stable (cAAC)3Si3, a carbene-stabilized triatomic silicon(0) molecule. The Si-Si bond lengths in (cAAC)3Si3 are 2.399(8), 2.369(8) and 2.398(8) Å, which are in the range of Si-Si single bonds. Each trigonal pyramidal silicon atom of the triangular molecule (cAAC)3Si3 possesses a lone pair of electrons. Its bonding, stability, and electron density distributions were studied by quantum chemical calculations.
Publisher: American Chemical Society (ACS)
Date: 12-03-2002
DOI: 10.1021/JA011492Y
Abstract: The charge densities rho(r) of the six amino acids L-Asn.H(2)O, DL-Glu.H(2)O, DL-Lys.HCl, DL-Pro.H(2)O, DL-Ser, and DL-Val were determined from high-resolution X-ray diffraction experiments at 100 K using synchrotron radiation and area detection (CCD) techniques. Bond topological parameters derived from these densities and from those of six additional amino acids published earlier are compared to each other and to the results of ab initio calculations. Experimental and theoretical properties for each chemically equivalent bond are in a fair agreement, and their variances are of similar magnitude. A noticeable outlier is the positive curvature of the density at the bond critical point, for which no correlation between the experimental and theoretical values can be established. The location of nonbonded valence shell charge concentrations derived from the crystalline densities scatter in a wider range than those obtained for the isolated molecules.
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C4NJ01503G
Abstract: A combination of pseudoreceptor modeling and electrostatic complementarity maps properties of a native pocket for an enzyme ligand.
Publisher: American Chemical Society (ACS)
Date: 21-08-2003
DOI: 10.1021/JP022584S
Publisher: International Union of Crystallography (IUCr)
Date: 05-2012
Publisher: International Union of Crystallography (IUCr)
Date: 23-08-2018
DOI: 10.1107/S2052520618010120
Abstract: The molecular and solid-state structure of azulene both raise fundamental questions. Therefore, the disordered crystal structure of azulene was re-refined with invariom non-spherical atomic scattering factors from new single-crystal X-ray diffraction data with a resolution of d = 0.45 Å. An unconstrained refinement results in a molecular geometry with C s symmetry. Refinements constrained to fulfill C 2 v symmetry, as observed in the gas phase and in high-level ab initio calculations, lead to similar figures of merit and residual densities as unconstrained ones. Such models are consistent with the structures from microwave spectroscopy and electron diffraction, albeit they are not the same. It is shown that for the disorder present in azulene, the invariom model describes valence electron density as successfully as it does for non-disordered structures, although the disorder still leads to high correlations mainly between positional parameters. Lattice-energy minimizations on a variety of ordered model structures using dispersion-corrected DFT calculations reveal that the local deviations from the average structure are small. Despite the molecular dipole moment there is no significant molecular ordering in any spatial direction. A superposition of all ordered model structures leads to a calculated average structure, which explains not only the experimental determined atomic coordinates, but also the apparently unusual experimental anisotropic displacement parameters.
Publisher: American Chemical Society (ACS)
Date: 02-08-2012
DOI: 10.1021/OL301932D
Abstract: An efficient total synthesis of (+)-(R)-Pinnatolide is described. As a key step an asymmetric multicomponent domino allylation reaction of methyl levulinate is used to form the quaternary stereogenic center in a highly selective way.
Publisher: Royal Society of Chemistry (RSC)
Date: 2020
DOI: 10.1039/D0CE00488J
Abstract: Optimizing structures with computations on clusters of molecules permits generation of structure-specific restraints for refinement and structure validation.
Publisher: American Chemical Society (ACS)
Date: 22-07-2011
DOI: 10.1021/IC201096C
Abstract: Reactions of N-heterocyclic carbene stabilized dichlorosilylene IPr·SiCl(2) (1) (IPr = 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene) with (η(5)-C(5)H(5))V(CO)(4), (η(5)-C(5)H(5))Co(CO)(2), and Fe(2)(CO)(9) afford dichlorosilylene complexes IPr·SiCl(2)·V(CO)(3)(η(5)-C(5)H(5)) (2), IPr·SiCl(2)·Co(CO)(η(5)-C(5)H(5)) (3), and IPr·SiCl(2)·Fe(CO)(4) (4), respectively. Complexes 2-4 are stable under an inert atmosphere, are soluble in common organic solvents, and have been characterized by elemental analysis and multinuclear ((1)H, (13)C, and (29)Si) NMR spectroscopy. Molecular structures of 2-4 have been determined by single crystal X-ray crystallographic studies and refined with nonspherical scattering factors.
Publisher: Royal Society of Chemistry (RSC)
Date: 2010
DOI: 10.1039/C001072C
Publisher: International Union of Crystallography (IUCr)
Date: 20-02-2009
Publisher: American Chemical Society (ACS)
Date: 28-10-2009
DOI: 10.1021/JO901902G
Publisher: International Union of Crystallography (IUCr)
Date: 14-09-2007
DOI: 10.1107/S0108768107030388
Abstract: A high-resolution dataset of the tripeptide L-alanyl-L-prolyl-L-alanine hydrate was measured at 100 K using synchrotron radiation and CCD area detection. Electron densities were obtained from a full multipole refinement of the X-ray experimental data, from an invariom transfer and from a theoretical calculation. Topological and atomic properties were derived via an AIM analysis [Atoms in Molecules see Bader (1990). Atoms in Molecules: A Quantum Theory , No. 22 in International Series of Monographs on Chemistry , 1st ed. Oxford: Clarendon Press] of these densities and compared with each other, as well as with results from the literature of other oligopeptides and amino acids. By application of the invariom formalism to a dataset of limited resolution, its performance was compared with a conventional spherical refinement, highlighting the possibility of aspherically modelling routine structure-determination experiments. The hydrogen-bonding scheme was subject to a detailed analysis according to the criteria of Koch & Popelier [(1995), J. Phys. Chem. 99 , 9747–9754] as well as to the characterization of Espinosa et al. [(1998), Chem. Phys. Lett. 285 , 170–173 (1999), Acta Cryst. B 55 , 563–572 (2002), J. Chem. Phys. 117 , 5529–5542] using the results from the refined and invariom multipole densities as well as the spherical-density model, which are critically compared.
Publisher: International Union of Crystallography (IUCr)
Date: 04-09-2010
DOI: 10.1107/S0108768110026480
Abstract: Multipole refinements of larger organic molecules have so far been limited to a few exceptional cases. We report an investigation of the detailed experimental electron-density distribution (EDD) of roxithromycin, a macrolide antibiotic consisting of 134 atoms. Although the experimental multipole refinement on high-resolution synchrotron data converged smoothly, validation of the electron density by calculation of an `experiment minus invariom' difference density revealed conformational disorder of the H atoms. Hydrogen disorder is shown to affect the EDD, the electrostatic potential and atomic properties as defined by Bader's quantum theory of atoms in molecules. A procedure to obtain the electron density distribution in the presence of disorder is proposed.
Publisher: International Union of Crystallography (IUCr)
Date: 30-05-2014
DOI: 10.1107/S1399004714007603
Abstract: Protein–DNA interactions play a major role in all aspects of genetic activity within an organism, such as transcription, packaging, rearrangement, replication and repair. The molecular detail of protein–DNA interactions can be best visualized through crystallography, and structures emphasizing insight into the principles of binding and base-sequence recognition are essential to understanding the subtleties of the underlying mechanisms. An increasing number of high-quality DNA-binding protein structure determinations have been witnessed despite the fact that the crystallographic particularities of nucleic acids tend to pose specific challenges to methods primarily developed for proteins. Crystallographic structure solution of protein–DNA complexes therefore remains a challenging area that is in need of optimized experimental and computational methods. The potential of the structure-solution program ARCIMBOLDO for the solution of protein–DNA complexes has therefore been assessed. The method is based on the combination of locating small, very accurate fragments using the program Phaser and density modification with the program SHELXE . Whereas for typical proteins main-chain α-helices provide the ideal, almost ubiquitous, small fragments to start searches, in the case of DNA complexes the binding motifs and DNA double helix constitute suitable search fragments. The aim of this work is to provide an effective library of search fragments as well as to determine the optimal ARCIMBOLDO strategy for the solution of this class of structures.
Publisher: Royal Society of Chemistry (RSC)
Date: 2023
DOI: 10.1039/D2CE00148A
Abstract: Energy partitioning of pharmaceutical cocrystals by molecule-pair interaction and ONIOM energies identifies the driving force of their formation, leading to in silico conformational s ling for predicting API-cocrystal combinations for experiment.
Publisher: International Union of Crystallography (IUCr)
Date: 11-11-2011
Publisher: American Chemical Society (ACS)
Date: 17-04-2014
DOI: 10.1021/JA502521B
Abstract: Two (cAAC)2Cu complexes, featuring a two-coordinate copper atom in the formal oxidation state zero, were prepared by reducing (Et2-cAAC)2Cu(+)I(-) with metallic sodium in THF, and by a one-pot synthesis using Me2-cAAC, Cu(II)Cl2, and KC8 in toluene in a molar ratio of 2:1:2, respectively. Both complexes are highly air and moisture sensitive but can be stored in the solid state for a month at room temperature. DFT calculations showed that in these complexes the copper center has a d(10) electronic configuration and the unpaired electron is delocalized over two carbene carbon atoms. This was further confirmed by the EPR spectra, which exhibit multiple hyperfine lines due to the coupling of the unpaired electron with (63,65)Cu isotopes, (14)N, and (1)H nuclei.
Publisher: Wiley
Date: 15-06-2004
Abstract: Two penicillin derivatives, the active penamecillin and the inactive penamecillin-1beta-sulfoxide, were used to study the relationship between their charge density and their activity. Single crystals of both compounds were measured at the synchrotron beamline F1 at the HASYLAB/DESY, at 100 K and up to resolutions of around 0.4 A. Experimental charge densities were obtained by using the Hansen-Coppens multipole formalism. The cleavage of the amide bond in the beta-lactam ring is of paramount importance in the mechanism of action of penicillins. Topological analysis of this bond in terms of Bader's AIM theory showed that its strength is equal in both compounds therefore a direct influence of bond strength on the activity can be ruled out. However, the two derivatives differ significantly in their experimental electrostatic potentials. These differences are discussed and provide further insight into the chemistry and activity of penicillins.
Publisher: International Union of Crystallography (IUCr)
Date: 07-02-2011
DOI: 10.1107/S0021889810042482
Abstract: MoleCoolQt is a molecule viewer for charge-density research. Features include the visualization of local atomic coordinate systems in multipole refinements based on the Hansen and Coppens formalism as implemented, for ex le, in the XD suite. Residual peaks and holes from XDfft are translated so that they appear close to the nearest atom of the asymmetric unit. Critical points from a topological analysis of the charge density can also be visualized. As in the program MolIso , color-mapped isosurfaces can be generated with a simple interface. Apart from its visualization features the program interactively helps in assigning local atomic coordinate systems and local symmetry, which can be automatically detected and altered. Dummy atoms – as sometimes required for local atomic coordinate systems – are calculated on demand XD system files are updated after changes. When using the invariom database, potential scattering factor assignment problems can be resolved by the use of an interactive dialog. The following file formats are supported: XD , MoPro , SHELX , GAUSSIAN (com, FChk, cube), CIF and PDB. MoleCoolQt is written in C++ using the Qt4 library, has a user-friendly graphical user interface, and is available for several flavors of Linux, Windows and MacOS.
Publisher: International Union of Crystallography (IUCr)
Date: 10-11-2015
DOI: 10.1107/S1600576715018075
Abstract: Invariom partitioning and notation are used to estimate anisotropic hydrogen displacements for incorporation in crystallographic refinement models. Optimized structures of the generalized invariom database and their frequency computations provide the information required: frequencies are converted to internal atomic displacements and combined with the results of a TLS (translation–libration–screw) fit of experimental non-hydrogen anisotropic displacement parameters to estimate those of H atoms. Comparison with TLS+ONIOM and neutron diffraction results for four ex le structures where high-resolution X-ray and neutron data are available show that electron density transferability rules established in the invariom approach are also suitable for streamlining the transfer of atomic vibrations. A new segmented-body TLS analysis program called APD-Toolkit has been coded to overcome technical limitations of the established program THMA . The influence of incorporating hydrogen anisotropic displacement parameters on conventional refinement is assessed.
Publisher: Wiley
Date: 19-05-2016
Abstract: A set of look-up point charges for generating molecular electrostatic potentials is provided. The set relies on atom classification of the invariom database, which has already been applied to assign aspherical scattering factors in single-crystal X-ray diffraction. The focus of the investigation is on improving the accuracy of electrostatic potentials calculated by using tabulated point charges. In this respect, the performance of invariom point charges is compared with 1) those from a restrained fit to the electrostatic potential directly following quantum-chemical DFT computations, 2) semi-empirical AM1-bcc charges, and 3) conceptually similar TPACM4 look-up charges. Invariom classification gives charges that perform better than those from TPACM4, although tabulated charges remain inferior to those from molecule-specific computations. Point-charge electrostatic potentials also agree favorably with those from charge-density studies on the basis of X-ray experiments, without requiring the considerable effort of the latter.
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C5DT03742E
Abstract: cAAC-ligand stabilized monomeric siliconthiodichloride (cAAC)SiSCl 2 ( 3 ) is prepared via reaction of (cAAC˙) 2 Si 2 Cl 4 ( 1 ) or (cAAC) 2 Si 2 Cl 2 ( 2 ) with elemental sulfur (S 8 ).
Publisher: Royal Society of Chemistry (RSC)
Date: 2010
DOI: 10.1039/B921930G
Abstract: The generation of hiphiles derived from macrobicyclic hexamines of the "sarcophagine" class can be prepared through efficient and selective reactions involving the reductive alkylation, using long-chain aldehydes, of amino-functionalised sarcophagines when bound to Cu(ii) or Mg(ii). The Mg(ii) pathway is particularly convenient for the ultimate isolation of the free ligands, which can then be used to form metallo hiphiles with a variety of metal ions. Structural studies have been made of one of the free (protonated) ligands and some of their complexes.
Publisher: Wiley
Date: 12-03-2014
Abstract: A neutral C4 cumulene 1 that includes a cyclic alkyl(amino) carbene (cAAC), its air-stable radical cation 1(·+) , and dication 1(2+) have been synthesized. The redox property of 1(·+) was studied by cyclic voltammetry. EPR and theoretical calculations show that the unpaired electron in 1(·+) is mainly delocalized over the central C4 backbone. The commercially available CBr4 is utilized as a source of dicarbon in the cumulene synthesis.
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C5SC01516B
Abstract: Silicondiselenide is a semiconductor and exists as an insoluble polymer (SiSe 2 ) n which is prepared by reacting elemental silicon with selenium powder in the temperature range of 400–850 °C.
Publisher: American Chemical Society (ACS)
Date: 26-06-2014
DOI: 10.1021/JA505817U
Abstract: One and a half decades ago the formation of Si2Cl4 from the intermediate species SiCl2 was theoretically predicted to be exothermic. The hypothetical Si2Cl4 has never been experimentally synthesized and isolated. Herein, we report that the Si2Cl4 species was stabilized as singlet biradical (Cy-cAAC·)2Si2Cl4 utilizing two cAAC (cyclic alkyl(amino) carbene). This compound is stable, isolable, and storable at rt under an inert atmosphere. The electronic structure and bonding were studied by theoretical calculations which revealed that the molecule possesses a singlet biradical ground state with an unpaired electron on each carbene C atom having opposite spin.
Publisher: Future Science Ltd
Date: 07-2012
DOI: 10.4155/FMC.12.85
Abstract: Background: The crystal structures of a very large number of compounds with biological relevance are known. Application of the invariom formalism provides the aspherical electron density distribution. Results and discussion: The electron density distribution of the anti-Alzheimer’s disease drug donepezil was derived from its x-ray structure reported in the literature, using the invariom database. The electrostatic potential mapped on the electron density isosurface shows how the positive charge of the donepezilium cation is distributed over a wide surface range. The presence of intermolecular contacts can be illustrated by the Hirshfeld surface. Comparable interactions are found in both the small-molecule structure and an acetylcholinesterase complex with donezepil from the literature. Conclusion: The electron density of donepezil in the small-molecule crystal structure mimics the intermolecular interactions within the receptor site. Complementing steric properties with electronic information can be a valuable procedure in the examination of molecular recognition of systems with biological activity.
Publisher: International Union of Crystallography (IUCr)
Date: 17-01-2008
DOI: 10.1107/S0108768107055292
Abstract: Experimental electron densities and derived properties have been determined for the two energetic materials CL-20 (3,5,9,11-tetraacetyl-14-oxo-1,3,5,7,9,11-hexaazapentacyclo-[5.5.3.02,6.04,10.08,12]pentadecane), and FOX-7 (1,1-diamino-2,2-dinitroethylene) from single-crystal diffraction. Synchrotron data extending to high scattering angles were measured at low temperature. Low figures-of-merit and excellent residuals were obtained. The Hansen & Coppens multipole-model electron density was compared with results from theoretical calculations via structure factors simulating an experiment. Chemical bonding in the molecules is discussed and a topological analysis gives insight especially into the character of those bonds that are thought to play a key role in the decomposition of the molecules. A comparison of theoretical and experimental electrostatic potentials shows no obvious evidence supporting earlier findings on other nitroheterocyclic molecules that electron-density maxima near the C—NO 2 bonds mapped on the electron-density isosurface can be correlated with impact sensitivities. For FOX-7 periodic Hartree–Fock calculations were performed to investigate the influence of the crystal field on the electron density distribution.
Publisher: Wiley
Date: 09-04-2013
Publisher: Royal Society of Chemistry (RSC)
Date: 2012
DOI: 10.1039/C2DT31578E
Abstract: Two silylene transition metal complexes were prepared by reacting stable N-heterocyclic silylene L {L = PhC(NtBu)(2)SiNPh(2)}with Mn(2)(CO)(10) and Re(2)(CO)(10) respectively in a 2 : 1 ratio to yield [L(2)Mn(CO)(4)](+)[Mn(CO)(5)](-) (1) and [L(2)Re(CO)(4)](+)[Re(CO)(5)](-) (2). Both complexes and were characterized by NMR spectroscopy, EI-MS spectrometry and elemental analysis. The molecular structures of complexes 1 and 2 were established by single crystal X-ray analysis.
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C5OB00728C
Abstract: Hirshfeld surfaces of haloperidol hydropicrate (left) and sila-haloperidol hydrochloride (right) show comparable sites of ED concentrations due to comparable intermolecular environments.
Publisher: Royal Society of Chemistry (RSC)
Date: 2009
DOI: 10.1039/B822987B
Publisher: American Chemical Society (ACS)
Date: 05-01-2011
DOI: 10.1021/OM101066W
Publisher: Walter de Gruyter GmbH
Date: 28-01-2016
Abstract: A mixture of two compounds with potent antiplasmodial activity in vitro against the W2 strain of Plasmodium falciparum (half maximal inhibitory concentration, 1.12 μg/mL) was obtained in a previous investigation of the CH 2 Cl 2 -MeOH extract of the seeds of Salacia longipes var. camerunensis. Separation by column chromatography led now to the isolation of salaterpene E ( 1 ) and (1 R ,2 R ,4 S ,5 S ,6 R ,7 R ,9 S ,10 R )-2-acetoxy-1,6,9-tribenzoyloxy-4-hydroxy-dihydro- β -agarofuran ( 2 ). The structure of 1 was elucidated by spectroscopic analysis, and its absolute configuration was established unambiguously by means of single-crystal X-ray diffraction. Also the absolute configurations of the recently described salaterpenes A ( 2a ) and D ( 2b ) were determined by this method using the anomalous scattering of the oxygen atoms only.
Publisher: International Union of Crystallography (IUCr)
Date: 17-08-2007
Publisher: Wiley
Date: 13-11-2014
Abstract: A simple self-assembled [Pd2 L4 ] coordination cage consisting of four carbazole-based ligands was found to dimerize into the interpenetrated double cage [3 X@Pd4 L8 ] upon the addition of 1.5 equivalents of halide anions (X=Cl(-) , Br(-) ). The halide anions serve as templates, as they are sandwiched by four Pd(II) cations and occupy the three pockets of the entangled cage structure. The subsequent addition of larger amounts of the same halide triggers another structural conversion, now yielding a triply catenated link structure in which each Pd(II) node is trans-coordinated by two pyridine donors and two halide ligands. This simple system demonstrates how molecular complexity can increase upon a gradual change of the relative concentrations of reaction partners that are able to serve different structural roles.
Publisher: Royal Society of Chemistry (RSC)
Date: 2012
DOI: 10.1039/C2CC32887A
Abstract: Formyl chloride (H(Cl)C=O) is unstable at room temperature and decomposes to HCl and CO. Silicon analogue of formyl chloride, silaformyl chloride IPr·SiH(Cl)=O·B(C(6)F(5))(3) (3) (IPr = 1,3-bis(2,6-diisopropyl-phenyl)imidazol-2-ylidene), was stabilized by Lewis donor-acceptor ligands. Compound 3 is not only the first stable acyclic silacarbonyl compound but also the first silacarbonyl halide reported so far.
Publisher: International Union of Crystallography (IUCr)
Date: 2019
DOI: 10.1107/S2053273318013840
Abstract: A new aspherical scattering factor formalism has been implemented in the crystallographic least-squares refinement program SHELXL . The formalism relies on Gaussian functions and can optionally complement the independent atom model to take into account the deformation of electron-density distribution due to chemical bonding and lone pairs. Asphericity contributions were derived from the electron density obtained from quantum-chemical density functional theory computations of suitable model compounds that contain particular chemical environments, as defined by the invariom formalism. Thanks to a new algorithm, invariom assignment for refinement in SHELXL is automated. A suitable parameterization for each chemical environment within the new model was achieved by metaheuristics. Figures of merit, precision and accuracy of crystallographic least-squares refinements improve significantly upon using the new model.
Publisher: Walter de Gruyter GmbH
Date: 03-06-2020
Abstract: The solid-state structures of three H-bonded enol forms of 5-substituted 9-hydroxyphenalenones were investigated to accurately determine the H atom positions of the intramolecular hydrogen bond. For this purpose, single-crystal X-ray diffraction (SC-XRD) data were evaluated by invariom-model refinement. In addition, QM/MM computations of central molecules in their crystal environment show that results of an earlier standard independent atom model refinement, which pointed to the presence of a resonance-assisted hydrogen bond in unsubstituted 9-hydroxyphenalone, are misleading: in all our three and the earlier solid-state structures the lowest energy form is that of an asymmetric hydrogen bond (C S form). Apparent differences of results from SC-XRD and other analytical methods are explained.
Publisher: Elsevier BV
Date: 09-2014
DOI: 10.1016/J.BMCL.2014.08.016
Abstract: X-ray crystallographic characterization of products derived from natural and fully synthetic trioxacarcins, molecules with potent antiproliferative effects, illuminates aspects of their reactivity and mechanism of action. Incubation of the fully synthetic trioxacarcin analog 3, which lacks one of the carbohydrate residues present in the natural product trioxacarcin A (1) as well as oxygenation at C2 and C4 yet retains potent antiproliferative effects, with the self-complimentary duplex oligonucleotide d(AACCGGTT) led to production of a crystalline covalent guanine adduct (6). Adduct 6 is closely analogous to gutingimycin (2), the previously reported guanine adduct derived from incubation of natural trioxacarcin A (1) with duplex DNA, suggesting that 3 and 1 likely share a common basis of cytotoxicity. In addition, we isolated a novel, dark-red crystalline guanine adduct (7) from incubation of trioxacarcin A itself with the self-complimentary duplex oligonucleotide d(CGTATACG). Crystallographic analysis suggests that 7 is an anthraquinone derivative, which we propose arises by a sequence of guanosine alkylation within duplex DNA, depurination, base-catalyzed elimination of the trioxacarcinose A carbohydrate residue, and oxidative rearrangement to form an anthraquinone. We believe that this heretofore unrecognized chemical instability of natural trioxacarcins may explain why trioxacarcin analogs lacking C4 oxygenation exhibit superior chemical stabilities yet, as evidenced by structure 3, retain a capacity to form lesions with duplex DNA.
Publisher: Walter de Gruyter GmbH
Date: 11-2012
Abstract: Phytochemical investigation of the roots and fruits of Mitragyna inermis (Rubiaceae) resulted in the isolation of a new indole alkaloid, named naucleactonin D (1), together with fourteen known compounds: nauclefiline (2), naucleficine (3), nauclefidine (4), angustoline (5), angustine (6), barbinervic acid (7), quinovic acid 3-O-a-L-rhamnopyranoside (8), betulinic acid (9), a mixture of ursolic (10) and oleanolic acid (11), a mixture of stigmasterol and b-sitosterol, b-sitosterol 3-O- b-D-glucopyranoside, and strictosamide (12) as the major compound. The structures of the isolated compounds were elucidated by detailed spectroscopic analysis and by comparison with published data. No 13 C NMR data for 2 and 3 exist in the literature and compounds 2, 3, 5, 7, and 12 are reported for the first time from the genus Mitragyna. The crude extract and isolated compounds were tested in vitro for their preliminary cytotoxicity against brine shrimps (Artemia salina).
Publisher: International Union of Crystallography (IUCr)
Date: 08-11-2008
DOI: 10.1107/S0108768108032163
Abstract: Three L-hydroxylysine structures have been determined at 100 K by single-crystal X-ray diffraction. High-resolution data using either a laboratory or synchrotron source were collected and subjected to invariom- and independent atom-model (IAM) refinements. Anisotropic displacement parameters (ADPs) obtained from invariom refinement were compared (i) with results from a full multipole and (ii) with an IAM high-order refinement. Differences were visualized with the program PEANUT and were complemented by quantitative results from a Hirshfeld test. Influences of scale factor differences, and of refinement against F^2 versus F, have been investigated. Systematic errors were observed in the IAM, especially when only low-order data were available. Although these errors were reduced in high-order IAM refinements, they only disappeared in charge density – and likewise – invariom refinements.
Publisher: MDPI AG
Date: 15-05-2018
DOI: 10.3390/CRYST8050213
Publisher: International Union of Crystallography (IUCr)
Date: 21-04-2005
Publisher: International Union of Crystallography (IUCr)
Date: 14-10-2006
Publisher: Wiley
Date: 24-04-2013
Abstract: The controversy over the absolute configuration of (+)-erythro-mefloquine, the less psychosis-causing enantiomer of the anti-malarial drug Lariam, has been resolved by Mosher ester crystallization. The configuration determined previously by physical methods is correct, whereas the configuration determined by three enantioselective syntheses is wrong.
Publisher: Wiley
Date: 23-11-2017
Abstract: In this work, the quality of the electron density in crystals reconstructed by the multipolar model (MM) and by X-ray wavefunction refinement (XWR) is tested on a set of high-resolution X-ray diffraction data sets of four amino acids and six tripeptides. It results in the first thorough validation of XWR. Agreement statistics, figures of merit, residual- and deformation-density maps, as well as atomic displacement parameters are used to measure the quality of the reconstruction relative to the measured structure factors. Topological analysis of the reconstructed density is carried out to obtain atomic and bond-topological properties, which are subsequently compared to the values derived from benchmarking periodic DFT geometry optimizations. XWR is simultaneously in better agreement than the MM with both benchmarking theory and the measured diffraction pattern. In particular, the obvious problems with the description of polar bonds in the MM are significantly reduced by using XWR. Similarly, modeling of electron density in the vicinity of hydrogen atoms with XWR is visibly improved.
Publisher: Wiley
Date: 12-06-2019
Abstract: Deprotonation usually occurs as an unwanted side reaction in the Lewis pair polymerization of Michael acceptors, for which the conjugated addition of the Lewis base to the acid-activated monomer is the commonly accepted initiation mechanism. This has also been reported for B-P-based bridged Lewis pairs (BLPs) that form macrocyclic addition products. We now show that the formerly unwanted deprotonation is the likely initiation pathway in the case of Al-P-based BLPs. In a detailed study of a series of Al-P-based BLPs, using a combination of single-crystal diffraction experiments (X-ray and neutron) and mechanistic investigations (experimental and computational), an active role of the methylene bridge was revealed, acting as a base towards the α-acidic monomers. Additionally, the polymerization studies proved a living behavior combined with significantly high activities, narrow molecular mass distributions, and the possibility of copolymerization.
Publisher: International Union of Crystallography (IUCr)
Date: 12-11-2011
DOI: 10.1107/S0021889811043202
Abstract: ShelXle is a graphical user interface for SHELXL [Sheldrick, G. M. (2008). Acta Cryst. A 64 , 112–122], currently the most widely used program for small-molecule structure refinement. It combines an editor with syntax highlighting for the SHELXL -associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density ( F o ) and difference density ( F o – F c ) maps. Special features of ShelXle include intuitive atom (re-)naming, a strongly coupled editor, structure visualization in various mono and stereo modes, and a novel way of displaying disorder extending over special positions. ShelXle is completely compatible with all features of SHELXL and is written entirely in C++ using the Qt4 and FFTW libraries. It is available at no cost for Windows, Linux and Mac-OS X and as source code.
No related grants have been discovered for Birger Dittrich.