Search

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.

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 (CS form). Apparent differences of results from SC-XRD and other analytical methods are explained. [ABSTRACT FROM AUTHOR]

Single crystal X-ray diffraction is the method of choice to resolve difficult solid-state problems. This is exemplified by analysis of three disordered structures that cease to be disordered depending on the circumstances. Interesting research questions of relevance for the pharmaceutical industry, including possible issues of intellectual property, emerge from disappearing disorder phenomena. Its relationship to polymorphism is discussed, and the term 'archetype structure' that includes both polymorphs and disorder components is recommended for use. X-ray structural studies reported here benefit from refinement with aspherical scattering factors that improve accuracy and precision of the results, thereby providing the confidence required in interpreting comparably small residual electron density features. Full understanding of the mechanism of how disorder can come into existence and disappear with temperature or time (pressure being another factor not exploited here) requires computing the relative energy differences of archetype structures by ONIOM cluster or solid-state computations. [ABSTRACT FROM AUTHOR]

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 (CS form). Apparent differences of results from SC-XRD and other analytical methods are explained. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The structure of glutathione, γ-l-Glutamyl-l-cysteinyl-glycine (C10H17N3O6S), was studied by multi-temperature single-crystal X-ray diffraction. Residual density maps from conventional independent atom model refinement gave indication of anharmonic motion in the molecule. This was further investigated by invariom refinement with anisotropic displacement parameters for all atoms, which described asphericity due to chemical bonding and lone pairs; afterwards only the residual-density signal of anharmonic motion remained. Treating anharmonicity with third-order Gram-Charlier displacement parameters led to regions with unphysical negative electron density. In contrast, a maximum entropy method (MEM) determination of the electron density successfully takes the features into account. Respective difference electron density plots (MEM minus prior and [Invariom+GC] minus invariom) agree well with each other. Challenges in treating and understanding the phenomenon are discussed. A procedure is proposed how unphysical negative electron density can be avoided. It is closely related to the free lunch algorithm. [ABSTRACT FROM AUTHOR]

Ferrocene, Cp2Fe, is quantitatively protonated in a mixture of liquid HF/PF5 to yield [Cp2FeH](PF6), which was characterized by 1H/13C NMR and 57Fe Mössbauer spectroscopy as well as single-crystal X-ray diffraction analysis. X-ray diffraction analysis at 100 K revealed a disordered, iron-coordinated hydrido ligand, which was unambiguously located by aspherical atom refinement at 100 K, and by analyzing the non-disordered crystal structure at 30 K, revealing a non-agostic structure. [ABSTRACT FROM AUTHOR]

Although compounds undergoing thermally induced spin crossover have been widely studied, their experimental d-orbital populations from single-crystal X-ray diffraction have rarely been reported. Three pairs of structures of iron/manganese coordination compounds were re-evaluated. Least-squares refinements relied on aspherical scattering factors obtained from molecular quantum-mechanical DFT single-point computations of the respective solid-state conformation, initiated by accurate starting structures from preliminary invariom refinements of the ligand environment. Further evaluation concerned d-orbital populations of metal ions from (a) single-point computations projected onto the Hansen-Coppens multipole model and from (b) experimental refinements of the metal atoms only. The latter were successful for good-quality data, independent of temperature, and provided only one spin state was exclusively present in the crystal. Crystals that underwent light-induced excited spin state trapping were not showing the expected d-orbital populations. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Amino acid structures are an ideal test set for method-development studies in crystallography. High-resolution X-ray diffraction data for eight previously studied genetically encoding amino acids are provided, complemented by a non-standard amino acid. Structures were re-investigated to study a widely applicable treatment that permits accurate X−H bond lengths to hydrogen atoms to be obtained: this treatment combines refinement of positional hydrogen-atom parameters with aspherical scattering factors with constrained 'TLS+INV' estimated hydrogen anisotropic displacement parameters (H-ADPs). Tabulated invariom scattering factors allow rapid modeling without further computations, and unconstrained Hirshfeld atom refinement provides a computationally demanding alternative when database entries are missing. Both should incorporate estimated H-ADPs, as free refinement frequently leads to over-parameterization and non-positive definite H-ADPs irrespective of the aspherical scattering model used. Using estimated H-ADPs, both methods yield accurate and precise X−H distances in best quantitative agreement with neutron diffraction data (available for five of the test-set molecules). This work thus solves the last remaining problem to obtain such results more frequently. Density functional theoretical QM/MM computations are able to play the role of an alternative benchmark to neutron diffraction. [ABSTRACT FROM AUTHOR]

Chemical investigation of terrestrial and marine streptomycete isolates led to the identification of two new natural pigments, namely, 6-hydroxyisatin ( 3) and 6-hydroxy-5-methoxyisatin ( 4). Additionally, the strains delivered numerous known compounds, among them N β-acetyltryptamine, N-acetyltyramine, phenylacetamide, N-(2-phenethyl)acetamide, 1-acetyl- β-carboline, tyrosol, 2′-deoxyadenosine, 2′-deoxythymidine, anthranilic acid, 2′-deoxyuridine, indolyl-3-acetic acid, indolyl-3-carboxylic acid, and p-hydroxybenzoic acid. The isatin structures were deduced by NMR and mass studies and further confirmed by synthesis and by X-ray diffraction of the isomeric 5-hydroxy-6-methoxyisatin ( 5). [ABSTRACT FROM AUTHOR]

Thiophosgene (CSCl2), a chemical reagent used in numerous organic syntheses, exists in the monomeric form while its heavier silicon analogue [siliconthiodichloride (SiSCl2)] has been isolated so far as a dimer at room temperature and as a tetramer at 180 °C. Herein, we report on the first synthesis, isolation, and characterization of cyclic alkyl(amino) carbene (cAAC) stabilized siliconthiodichloride (cAAC)SiSCl2 (3) in the neutral monomeric form. 3 is synthesized via reaction of (cAACṖ)2Si2Cl4 (1) or (cAAC)2Si2Cl2 (2) with S8 in the temperature range of −78 to 20 °C. An NHC [NHC = N-heterocyclic carbene] analogue of 3 is not isolated when (NHC)SiCl2 is reacted with S8. The bright yellow colored compound 3 is soluble in polar organic solvents. It is stable at room temperature for a month under an inert atmosphere. 3 decomposes above 160 °C. The monomeric molecular structure of 3 has been unambiguously confirmed by X-ray single crystal diffraction. 3 is also characterized by NMR, UV-vis, and IR spectroscopy. The bonding and electron density distributions of 3 have been further studied by theoretical calculations. [ABSTRACT FROM AUTHOR]

Compound (Me2-cAAC:)2Co0 ( 2; Me2-cAAC:=cyclic (alkyl) amino carbene; :C(CH2)(CMe2)2N-2,6- iPr2C6H3) was synthesized by the reduction of the precursor (Me2-cAAC:)2CoICl ( 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 cAACCo 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. [ABSTRACT FROM AUTHOR]

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 El). This model was suitable to be input into a second refinement of multipoles (model E2), which converged smoothly although based on Cu Kαroom-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 (JAM) 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. [ABSTRACT FROM AUTHOR]

The article provides a comprehensive description of the computer program MoleCoolQt designed for the visualization of molecular structures from single-crystal X-ray diffraction.

The structure ofl-valinol [( S)-(+)-2-amino-3-methyl­butan-1-ol or hydroxy­latedl-valine], C5H13NO, has been determined at 100 K by single-crystal X-ray diffraction. The independent atom model geometry, Flack parameter and figures of merit are compared with results from an invariom structure refinement. The latter provides H-atom positions free of independent atom model bias and therefore yields a more accurate hydrogen-bond pattern, and the geometry from invariom refinement shows an improved agreement with results from a quantum chemical geometry optimization. [ABSTRACT FROM AUTHOR]

The cyclic alkyl(amino) carbene (cAAC) stabilized monoanionic phosphorus atom in the form of lithium phosphinidene [cAACPLi(THF)[sub 2] ][sub 2] (l) has been isolated as a molecular species and characterized by single crystal X-ray structure analysis. Furthermore, the structure and bonding of compound l has been investigated by theoretical methods. The utilization of the lithium phosphinidene as a phosphorus transfer reagent for a wide range of organic and inorganic substrates has been investigated. Herein, we report on the preparation of fascinating compounds containing P -- C, P -- Si, P -- Ge, and P -- P bonds using a single step with a base-stabilized phosphorus atom. [ABSTRACT FROM AUTHOR]

Eight compounds were isolated from the stem bark of Antrocaryon klaineanum , and their structures determined by chemical and spectroscopic methods. Among these compounds, the ergostane-type antrocarine E ( 1a ) is a new compound, although the structure had already been published by mismatching the spectroscopic data with those of 2 . In this paper, we are reporting the valid spectroscopic values for antrocarine E and X-ray diffraction results. [ABSTRACT FROM AUTHOR]

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 CH2Cl2-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. [ABSTRACT FROM AUTHOR]

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 14N (I = 1), 35/37Cl (I = 3/2), and 31P (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. [ABSTRACT FROM AUTHOR]

A stable silicon analogue of an acid anhydride {PhC(ButN)2}Si{-O·B(C6F5)3}O-Si(H){-O·B(C6F5)3}{(NBut)(HNBut)CPh} (4) with a O-Si-O-Si-O core has been prepared by treating monochlorosilylene PhC(ButN)2SiCl (1) with H2O·B(C6F5)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. [ABSTRACT FROM AUTHOR]