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The electron density distribution (EDD) of a plant cyclic nonapeptide of orbitide type was studied. Crystal X-ray diffraction data was obtained from the Cambridge Structural Database (CSD) and refitted using scattering factors of the invariom library, thereby providing aspherical electron density. Bond topological, atomic properties and molecular surfaces (electrostatic potential and Hirshfeld surfaces) were derived. The partial double bond character of the peptide bond was confirmed by the ellipticity ε = 0.25. For eight N–H⋯O hydrogen bonds, atomic charges of contributing atoms differ depending on the type of the accepting oxygen atom. Atomic charge differences between negative main and positive side chains of this nonapeptide result in characteristic features of the electrostatic potential, which shows a positive isosurface around the molecule leading to repulsive interactions in the solid state structure. Weak intermolecular interactions are indicated by insignificant ED concentrations on the Hirshfeld surface except for weak signals at sites of intermolecular N–H⋯O and C–H⋯O hydrogen bonds. [ABSTRACT FROM AUTHOR]

The electron density distribution (EDD) of a cyclic tetrasaccharide composed of four benzoylated galactopyranosyl units was calculated from refinement with scattering factors from the invariom library based on X-ray diffraction data downloaded from the Crystal Structural Data Base (CSD). Bond topological and atomic properties have been derived. Benzoyl substituents cause weak intermolecular interactions. These are also visible from low electron density concentrations on the Hirshfeld surface and have an influence on a low X-ray density compared to that of non-substituted carbohydrates, where hydrogen bonds allow a 20% more dense packing. On the electrostatic potential (ESP) surface, a strong polarization between the positive outer belt of 12 benzoyl groups and a negative core region composed of the four galactose sugar molecules exists. The positive benzoyl exterior establishes a repulsive wall between adjacent molecules in the structure. [ABSTRACT FROM AUTHOR]

Active pharmaceutical ingredients (APIs) and selected coformers were studied in crystalline self-environment, in selected co-crystal structures, and gas phase. To obtain comparable geometries from experimental crystal structures, we rely on fast quantum mechanical GFN2-XTB molecule-in-cluster optimizations. Optimized crystal structures are first analysed in terms of molecule-pair interaction energies, by subdividing a cluster generated from asymmetric unit content through space-group symmetry into pairs of molecules. Accurate energies are then obtained by single-point molecular orbital (MO/MO) two layer "ONIOM" energy partitioning, comparing the same molecules in different crystal environments. Clusters approximate the local environment of a crystal structure for ONIOM. The pre-processor program BAERLAUCH (Acta. Cryst. A 2012) was used to set up all cluster computations. Solid-state computations using dispersion-corrected density functional theory provide reference results. ONIOM partitioned energies shed light on the driving force of co-crystal formation, with the energy gain from the complementarity of molecule-pair wavefunctions in such structures being the main driving force. It follows that improving prediction of co-crystal structure formation beyond current approaches, e.g. COSMO-RS excess enthalpies, statistics from structural databases or full crystal structure prediction is possible by finding complementary molecule-pairs through conformational sampling, as ultimately exemplified. [ABSTRACT FROM AUTHOR]

The electron density of a 1:2 complex of valinomycin with calcium triflate consisting of 10 substructures and a total of 279 atoms was examined using the invariom formalism. In addition to geometric properties, sites and strengths of hydrogen bonds were identified from bond topological properties and from electron density concentrations mapped onto Hirshfeld surfaces. In contrast to free valinomycin and corresponding complexes with potassium the hydrogen bonds are all intermolecular and evenly distributed over the complex. A series of electrostatic potential (ESP) surfaces show the mutual influence in the ensemble of this high Z′ structure. [ABSTRACT FROM AUTHOR]

Rotaxanes as well as catenanes are known as potential building blocks of molecular machines. The nanohoop [2]rotaxane investigated is composed of a macrocycle derived from a [6]cycloparaphenylene (CCP, designated as a carbon nanohoop), where one of the six para-linked phenyl rings is replaced by a 2,6-substituted pyridyl ring. This macrocycle is mechanically interlocked with a thread, a linear rod-shaped diyne fragment sitting in the cavity of the macrocycle. Two bulky 3,5-di-t-butyl-phenyl rests as end groups keep the thread fixed. The interplay between macrocycle and thread was examined by means of the electron density distribution (EDD) obtained by application of the invariom formalism, relying on X-ray diffraction data collected earlier. The so-obtained EDD was subjected to topological analysis using the QTAIM formalism. Moreover, molecular Hirshfeld and electrostatic potential (ESP) surfaces were calculated. The 73 C–C bonds were analysed in terms of bond topological properties. For the 46 single and the 22 aromatic bonds, the analysis gave average bond orders of 1.03 and 1.61. The five C–C bonds in the diyne fragment can clearly be distinguished into three types: formal triple bonds with bond orders above 3.0, arene bonds with bond orders of 1.6 and finally bond orders of 1.3 in the adjacent C–C bonds, which indicate a considerable electron delocalization in this fragment. Mapping the ED onto the Hirshfeld surfaces of the macrocycle and the thread does not show strong signals. This shows that in between the molecules only weak non-covalent interactions are present. The electrostatic potentials (ESPs) were mapped onto molecular EDD isosurfaces. For all phenyl rings, small regions of negative ESP are visible on the delocalized π systems. A potential gradient between the mostly positive ESP of the macrocycle and the diyne region of the thread exist, which can be considered the dominant force to hold this rotaxane together. [ABSTRACT FROM AUTHOR]

Optimizing structures with computations on clusters of molecules permits generation of structure-specific restraints for refinement. Equally importantly, retrospective structure validation and addition of hydrogen atoms consistent with quantum chemistry is possible for experimental structures or the solvent molecules in them, should they be missing in earlier CIF depositions. Revisiting the drug subset structures of the CCDC demonstrates that structure validation through ab initio cluster computations is a tremendous validation tool. The time required for optimization can be similar to the time required to carry out least-squares refinement for small-molecule structures, and becomes feasible for large structures. Several questions arise: is it valid to augment experimental structures with structure-specific restraints, ideally through accompanying refinement with computation? Do energy minimized structures (using the experimental determinations as a starting point) still constitute an experimental result? When re-refinement is impossible in retrospect, like for most of the drug-subset molecules, then additional value lies in completion and validation of existing structures so that they are chemically and crystallographically correct, and contain missing water or solvent hydrogen atoms. Our results suggest that retroactive validation and addition of hydrogen atoms becomes possible for the entire Cambridge Structural Database. Generation of database entries of optimized alongside existing structures will provide the flexibility needed to make full use of the information gained by computation. [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 nonapeptides cyclo(Val-Leu-Pro-Ile-Leu-Leu-Leu-Val-Leu) (I) and cyclo(Val-Leu-Pro-Ala-Leu-Leu-Leu-Val-Leu) (II) were identified as promising candidates for the development as potential anti-cancer drugs. We report a re-refinement of deposited single-crystal X-ray diffraction data with aspherical scattering factors from the invariom database. A subsequent evaluation of the molecular electron density distribution and of the differences in their molecular electrostatic potentials provides insight in their activities. The sequences differ only in residue 4, Ile in (I) and Ala in (II). Since the anti-tumor potency is reduced for the Ala peptide (II), the causes for the differences seen in activity between (I) and (II) were examined from a structural and from an electron density (ED) point of view. The exchange at residue 4 does not lead to significant changes in molecular geometry. Molecular Hirshfeld surfaces and electrostatic potential (ESP) isosurfaces show accumulations of intermolecular interactions in regions adjacent to the Ile/Ala residues indicating preferred interactions with a potential receptor in these regions. The concentrations of intermolecular interactions were localized on the Hirshfeld surfaces through an extended basin of ED concentration close to the Ile/Ala residues. Differences in the electrostatic potentials (ESPs) between (I) and (II) were only found at the Ile/Ala site and were very close to zero otherwise. [ABSTRACT FROM AUTHOR]

The nonapeptides cyclo(Val-Leu-Pro-Ile-Leu-Leu-Leu-Val-Leu) (I) and cyclo(Val-Leu-Pro-Ala-Leu-Leu-Leu-Val-Leu) (II) were identified as promising candidates for the development as potential anti-cancer drugs. We report a re-refinement of deposited single-crystal X-ray diffraction data with aspherical scattering factors from the invariom database. A subsequent evaluation of the molecular electron density distribution and of the differences in their molecular electrostatic potentials provides insight in their activities. The sequences differ only in residue 4, Ile in (I) and Ala in (II). Since the anti-tumor potency is reduced for the Ala peptide (II), the causes for the differences seen in activity between (I) and (II) were examined from a structural and from an electron density (ED) point of view. The exchange at residue 4 does not lead to significant changes in molecular geometry. Molecular Hirshfeld surfaces and electrostatic potential (ESP) isosurfaces show accumulations of intermolecular interactions in regions adjacent to the Ile/Ala residues indicating preferred interactions with a potential receptor in these regions. The concentrations of intermolecular interactions were localized on the Hirshfeld surfaces through an extended basin of ED concentration close to the Ile/Ala residues. Differences in the electrostatic potentials (ESPs) between (I) and (II) were only found at the Ile/Ala site and were very close to zero otherwise. [ABSTRACT FROM AUTHOR]

Catenanes are of considerable interest as potential building blocks for molecular machines. The simplest [2]catenanes, Hopf links, consist of two macrocycles that are mechanically interlocked. This unusual architecture cannot be opened without breaking at least one covalent bond. Based on these structural characteristics, unusual properties on Hirshfeld or electrostatic potential surfaces could be expected. For a comparison of their structural and electronic properties, the electron densities (EDs) of two [2]catenanes, coded H22 and H4L7 in the original papers, were examined after application of the invariom formalism, relying on X-ray diffraction data collected earlier. The obtained electron density distributions were subjected to an analysis using the QTAIM formalism to yield bond and atomic properties. Moreover, molecular Hirshfeld surfaces and electrostatic potentials (ESP) were calculated. There are different types of intra- and intermolecular interactions in these two [2]catenanes. In addition to classical N–H···N and C–H···O hydrogen bonds, various types of π···π interactions in H22 and in H4L7 exist. Most of them are verified by local ED concentrations visible on the corresponding Hirshfeld surfaces, except for the parallel π···π interactions in H22, which are either too weak or too diffuse to generate an ED signal on the Hirshfeld surface between the contributing aromatic rings. The electrostatic potentials (ESPs) were calculated and displayed on molecular surfaces. The interaction in the cavity of one macrocycle with the penetrated fragment of the second one was examined and it was found that corresponding to the above-mentioned contacts attractive and repulsive interactions exist. Additionally the ED was examined using results of density functional calculations, including non-covalent interaction index (NCI) and electron localizability indicator (ELI-D) surface analysis, complementing experimental findings. [ABSTRACT FROM AUTHOR]

Motivated by the medical interest in methylene blue as potential anti-Alzheimer agent, the charge densities of three salt structures containing the methylene blue cation with nitrate (as dihydrate), chloride (as pentahydrate) and thiocyanate counter-ions were generated by application of the invariom formalism and examined. The so-obtained charge density distributions were analyzed using the QTAIM formalism to yield bond topological and atomic properties. The atomic charges on the methylene blue cation indicate a delocalized charge distribution; only a small positive charge on the sulfur atom was found. Electrostatic potentials mapped onto iso-surfaces of electron density for the cations, and for the methylene blue cations with anions, were compared. The effect of hydrogen disorder on the molecular electrostatic potential was investigated for the thiocyanate 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]

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. [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]

The title compounds have raised considerable medical and broad public interest in that sildenafil is used as an agent against male erectile dysfunction; iso-sildenafil is not in clinical use. A comparison of their structural and electronic properties therefore seems of interest. The electron densities of iso-sildenafil and the cationic and neutral forms of sildenafil were examined by the application of the invariom formalism relying on diffraction data reported in the literature. The electron-density distributions obtained were subjected to topological analysis using the quantum theory of atoms in molecules (QTAIM) formalism to yield bond topological and atomic properties. Moreover, molecular Hirshfeld surfaces and electrostatic potentials (ESPs) were calculated. A number of structural and electronic differences were thus identified between sildenafil and the iso-analog. In both sildenafil structures, the phenyl ring and the pyrazolopyrimidine fragment are practically coplanar (planar conformation), whereas in the iso-analog they exhibit an angle of 44° (inclined form). Related to differences in molecular structure are completely different hydrogen bonding patterns and differences in the ESPs, the latter ones being influenced by different methylation at the pyrazolopyrimidine fragment. Iso-sildenafil is present as a hydrogen-bond dimer in the crystal, and the ESP of this dimer is dominated by a surrounding positive potential. [ABSTRACT FROM AUTHOR]

Routines to facilitate the treatment of disorder in invariom modeling have been implemented in the open-source program M olecoolQ t, a visualization program for charge-density work, and I nvariomT ool, a pre-processor program. Two published structures of an amino acid and a dipeptide and the new structure of cefaclor, a cephalosporin antibiotic, provide examples with increasing amounts of disorder, which can now be successfully modeled with invarioms. Like for ordered structures, these non-spherical scattering factors predicted by density functional theory significantly improve the structural model (figures of merit and standard deviations) also in these cases. Furthermore, they allow rapid calculation and comparison of the electrostatic potential and the molecular dipole moment for the different conformers present in the crystal structures. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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, C13H12F2N6O·H2O, a case study on different model refinements is reported, based on single-crystal X-ray diffraction data measured at 100 K with Cu Kα 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. [ABSTRACT FROM AUTHOR]

In the search for new compounds to protect plants from fungi, an endophytic fungus, Epicoccum sp. CAFTBO, obtained from Theobroma cacao was found to produce three polyoxygenated polyketides, namely epicolactone ( 1) and epicoccolides A ( 2) and B ( 3), together with seven known metabolites. The structures of these compounds were elucidated by a combination of detailed spectroscopic and spectrometric analyses as well as DFT calculations of the electronic circular dichroism spectra and the single-crystal X-ray diffraction analysis of 1. Compounds 1- 3 showed potent antimicrobial activities and significant inhibitory effects on the mycelial growth of two peronosporomycete phytopathogens, Pythium ultimum and Aphanomyces cochlioides, and the basidiomycetous fungus Rhizoctonia solani. [ABSTRACT FROM AUTHOR]

The rigid-bond model [Hirshfeld (1976). Acta Cryst. A 32, 239-244] states that the mean-square displacements of two atoms are equal in the direction of the bond joining them. This criterion is widely used for verification (as intended by Hirshfeld) and also as a restraint in structure refinement as suggested by Rollett [ Crystallographic Computing (1970), edited by F. R. Ahmed et al., pp. 167-181. Copenhagen: Munksgaard]. By reformulating this condition, so that the relative motion of the two atoms is required to be perpendicular to the bond, the number of restraints that can be applied per anisotropic atom is increased from about one to about three. Application of this condition to 1,3-distances in addition to the 1,2-distances means that on average just over six restraints can be applied to the six anisotropic displacement parameters of each atom. This concept is tested against very high resolution data of a small peptide and employed as a restraint for protein refinement at more modest resolution ( e.g. 1.7 Å). [ABSTRACT FROM AUTHOR]

In a screening for natural products with mosquito larvicidal activities, the endophytic fungus Podospora sp. isolated from the plant Laggera alata (Asteraceae) was conspicuous. Two xanthones, sterigmatocystin ( 1) and secosterigmatocystin ( 2), and an anthraquinone derivative ( 3) 13-hydroxyversicolorin B were isolated after fermentation on M medium. These compounds were characterised using spectroscopic and X-ray analysis and examined against third instar larvae of Anopheles gambiae. The results demonstrated that compound 1 was the most potent one with LC and LC values of 13.3 and 73.5 ppm, respectively. Over 95% mortality was observed at a concentration 100 ppm after 24 h. These results compared farvourably with the commercial larvicide pylarvex® that showed 100% mortality at the same concentration. Compound 3 was less potent and had an LC of 294.5 ppm and over 95% mortality was achieved at a concentration of 1,000 ppm. Secosterigmatocystin ( 2) revealed relatively weak activity and therefore LC values were not determined. [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]

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 samples 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. [ABSTRACT FROM AUTHOR]

A high-resolution dataset of the tripeptidel-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. [ABSTRACT FROM AUTHOR]

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-2H,6H-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. [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]

Describes the structure of L-tryptophan formic acid solvate at 183 K. Formic acid molecule; Carboxylate group of the tryptophan molecule; Zwitterionic form of L-tryptophan.

Silicon is one of the most important components of electronic devices. Surface passivation of a silicon wafer is an active area of research. The Si(OH)2 sites of partially oxidized silicon surface could exist as hydroxylated [Si(OH)2] or hydrated silanone [SiO∙(OH2)]. The previously reported disiladicarbene (cAAC)2Si2 has been reacted here with water to obtain elusive, hydrated silanone (3) co-crystallized with its silanol analog (2) in a 1:3 molar ratio. The mass spectrometric characterization of acyclic silanone, followed by the isolation and characterization of the zwitterionic hydrated silanone, has been achieved. The detailed energy decomposition analysis coupled with natural orbital for chemical valence (EDA-NOCV) calculations revealed that the central Si(O)OH unit of the hydrated silanone possesses a covalent electron sharing σ- and a dative σ-bonds (CL−Si, Si←CL) with hydrogen-containing cyclic alkyl(amino) carbene ligands. These two bonds are stabilized by 49% coulombic interaction and 47.8% orbital interaction. The presence of N-atoms at the hydrogenated and/or protonated carbene part (cAACH/cAACH2) has reduced the stability of these species. The electron pair on the N-atom of the cAACH unit displays a sort of anomeric effect relevant to the cyclic form of the sugar molecule. A disiladicarbene containing two Si(0) centres reacts with water to produce a mixture of co-crystallized products in a 3:1 molar ratio. EDA-NOCV analyses further analysed the bonding and stability of zwitterionic-hydrate-silanone to probe the nature of chemical bonds in it. This species has further been characterized by ES-MS spectrometry. [ABSTRACT FROM AUTHOR]

Abstract: Die Selbstassemblierung von 8 PdII‐Kationen und 16 Phenanthren‐basierten, verbrückenden Liganden mit einem Bisswinkel von 60° führt zur Bildung einer neuartigen metallosupramolekularen M8L16‐Struktur aus zwei ineinander verflochtenen, D4h‐symmetrischen, fassförmigen Containern. Mit Massenspektrometrie, NMR‐Spektroskopie und Einkristallröntgenstrukturanalyse konnte die Bildung eines sehr großen Catenans mit “Hopf‐Link”‐Topologie nachgewiesen werden, das Kanal‐ähnliche Kavitäten aufweist, in denen sich NO3−‐Anionen befinden. Die Relevanz der Anionen als Templatmoleküle für die Catenierung ergibt sich aus der Beobachtung, dass in einer Mischung von M3L6‐ und M4L8‐Strukturen, die sich in Gegenwart von BF4−‐Anionen bilden, durch Versetzen mit Nitrat eine Strukturänderung zum ineinander verflochtenen Catenan induziert wurde. Das dicht gepackte M8L16‐Catenan fungierte als Vorlage zur Herstellung eines Hexyloxy‐funktionalisierten Analogons, für das eine weiterführende, reversible Aggregation zu vesikulären Überstrukturen beobachtet wurde. [ABSTRACT FROM AUTHOR]

Abstract: The self‐assembly of eight PdII cations and sixteen phenanthrene‐derived bridging ligands with 60° bite angles yielded a novel M8L16 metallosupramolecular architecture composed of two interlocked D4h‐symmetric barrel‐shaped containers. Mass spectrometry, NMR spectroscopy, and X‐ray analysis revealed this self‐assembled structure to be a very large “Hopf link” catenane featuring channel‐like cavities, which are occupied by NO3− anions. The importance of the anions as catenation templates became imminent when we observed the nitrate‐triggered structural rearrangement of a mixture of M3L6 and M4L8 assemblies formed in the presence of BF4− anions into the same interlocked molecule. Furthermore, the densely packed structure of the M8L16 catenane was exploited in the preparation of a hexyloxy‐functionalized analogue, which further self‐assembled into vesicle‐like aggregates in a reversible manner. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 example 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. [ABSTRACT FROM AUTHOR]

Ein einfacher selbstorganisierter [Pd2 L4]-Koordinationskäfig bestehend aus vier Carbazol-basierten Liganden dimerisiert nach Zugabe von 1.5 Äquivalenten eines Halogenidions (X=Cl−, Br−) zu einem verflochtenen Doppelkäfig [3 X@Pd4 L8]. Die Halogenidionen agieren als Template, eingelagert in den drei Taschen der verschlungenen Käfigstruktur und umgeben von vier PdII Kationen. Zugabe höherer Mengen desselben Halogenidions bewirkt eine weitere strukturelle Umwandlung, die in einer dreifach verschlungenen Verbindung resultiert. Letztere enthält trans-koordinierte PdII-Zentren, die von zwei Pyridin-Donor- und zwei Halogenidliganden umgeben sind. Dieses einfache System zeigt eindrucksvoll, wie molekulare Komplexität aus der graduellen Änderung der relativen Konzentrationen einer geringen Zahl an Reaktionspartnern erwachsen kann, insbesondere, wenn diese unterschiedliche strukturelle Rollen einnehmen können. [ABSTRACT FROM AUTHOR]

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 PdII 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 PdII 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. [ABSTRACT FROM AUTHOR]

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°). [ABSTRACT FROM AUTHOR]

Abstract: Three α-pyrone derivatives, campyrones A–C (1–3), were isolated from Aspergillus niger, an endophytic fungus occurring in Zanthoxylum lemairei leaves. Their structures were elucidated by detailed spectroscopic and spectrometric analyses and confirmed by X-ray diffraction. The absolute configurations were assigned by a combination of circular dichroism (CD) spectra and X-ray analyses. Biosynthetically, pyrophen (4) and the new derivatives may be derived in a mixed biosynthesis from l-phenylalanine (for 4), l-isoleucine (for 1), l-leucine (for 2), and l-valine (for 3) as starter units, respectively. In bioassays, the new compounds exhibited weak toxicity on brine shrimp larvae (Artemia salina). [Copyright &y& Elsevier]

Reaction of heteroleptic silylenes LSiX (L = PhC(NtBu)2; X = PPh2(1),NPh2(2), NMe2(3),OtBu (4)) with N2O resultedin the oxidizeddimeric product [LSi(X)(μ-O)]2(X = PPh2(5), NPh2(6), NMe2(7), OtBu (8)), whichcontains a four-membered Si2O2ring. Compounds 5–8were characterized by spectroscopicand spectrometric techniques. The molecular structures of 5–8were established by single-crystal X-ray structureanalysis. [ABSTRACT FROM AUTHOR]

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 ( Fo) and difference density ( Fo- Fc) 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. [ABSTRACT FROM AUTHOR]

Pentacoordinate silicon fluorides L1SiF3 (2a), L2SiF3 (2b), and (L3SiF2)2 (2c)2 based on amidinate (L1 = PhC(NtBu)2), guanidinate (L2 = 1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidinate), and triazapentadienate (L3 = NC(NMe2)NC(NMe2)NAr; Ar = 2,6-iPr2C6H3) ligands were prepared by fluorination of the corresponding chlorosilanes L1SiCl3 (1a), L2SiCl3 (1b), and L3SiCl2 (1c) with Me3SnF at ambient temperature. Compounds 1b, 1c, 2a, 2b, and (2c)2 were characterized by 1H, 13C, 19F, and 29Si 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 L3SiF2 (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 Si2Cl6 led to the formation of the silane (1a) and the silylene L1SiCl (3). Reaction of Si2Cl6 with N-heterocyclic carbenes (NHC) afforded NHC adducts of dichlorosilylene and SiCl4. A one pot method for the preparation of base-stabilized silylenes from Si2Cl6 is discussed. [ABSTRACT FROM AUTHOR]

Abstract: The reaction of protected uridine 5′-aldehydes with sulfur ylides has been reinvestigated. Further transformation of the resulting epoxide product provided a compound of which a single crystal for X-ray diffraction was obtained. As a consequence from the elucidated structure, the stereochemical configuration of the epoxide furnished by the sulfur ylide reaction was revised. Based on these results, an efficient synthesis of the core structure of the naturally occurring muraymycin and caprazamycin nucleoside antibiotics was developed. [Copyright &y& Elsevier]

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]

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]