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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]

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]

Two cyclic (alkyl)(amino)carbene (cAAC) stabilized mononuclear neutral radicals of aluminum have been synthesized. They contain an ethyl [(cAAC)2AlClEt (1)] and as well a diethyl group [(cAAC)2AlEt2 (2)], and have been prepared from the reduction of EtAlCl2 and Et2AlCl, respectively, with KC8. Compounds 1 and 2 are monoradicals, which were confirmed by EPR measurements to have the spin located on the carbene carbon of one of the cAAC ligands. [ABSTRACT FROM AUTHOR]

The cyclic alkyl(amino) carbene (cAAC) [:C{N-C6H3(2,6-IPr2)}(CMe2)2CH2] stabilized MeGeGeMe has been isolated in the molecular form with composition (cAAC)MeGe–GeMe(cAAC) (1) at room temperature. Compound 1 was synthesized from the reduction of MeGeCl3 using three equivalents of KC8 in the presence of one equivalent of cAAC. The corresponding silicon compound (cAAC)MeSi–SiMe(cAAC) (2) was also prepared. Compounds 1 and 2 are the first examples of REER compounds (E = Ge, Si) carrying the smallest organic group. Furthermore the structures of compounds 1 and 2 have been investigated by using theoretical methods. The theoretical analysis of the structure of 1 is in agreement with the formation as an unprecedented carbene stabilized bis-germylene whereas compound 2 can be equally described as carbene stabilized bis-silylene with coordinate bonds as with classical double bonds of a 2,3-disila-1,3-butadiene. The compounds were also characterized by X-ray crystallography. [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]

(cAAC)Ge(GeL)2 (1) (cAAC = cyclic alkyl(amino) carbene; L = PhC(tBuN)2), a functionalized Ge3-compound was prepared. Quantum mechanical studies on 1 show a reciprocal relationship between the electronic state of the central tri-coordinated Ge atom and its reactivity towards protons, viz. tetravalent Ge(0) in terms of bonding and divalent Ge(0) in terms of reactivity. Thus the central Ge atom can be considered as having a hidden but highly reactive lone pair of electrons. However, the terminal Ge atoms can be considered as tri-coordinated divalent Ge(i) with an active lone pair of electrons. [ABSTRACT FROM AUTHOR]

The methyl ester of mandelic acid is investigated by a wide range of techniques to unravel its aggregation pattern and the influence of relative chirality of the aggregating monomers. Matrix isolation confirms that a single monomer conformation prevails. The electronic spectrum of the dimers is strongly affected by the relative monomer chirality. Vibrational effects are more subtle and can be explained in terms of the most stable homo- and heteroconfigurational dimer structures, when compared to results of MP2 and DFT-D computations. Selective IR/UV double resonance techniques and wide-band FTIR spectroscopy provide largely consistent spectroscopic fingerprints of the chirality discrimination phenomena. The dominant homochiral dimer has two intermolecular O–HOC hydrogen bonds whereas the more strongly bound heterochiral dimer involves only one such hydrogen bond. This is a consequence of the competition between dispersion and intramolecular or intermolecular hydrogen bonding. Aromatic interactions also play a role in trimers and larger clusters, favoring homochiral ring arrangements. Analogies and differences to the well-investigated methyl lactate system are highlighted. Bulk phases show a competition between different hydrogen bond patterns. The enantiopure, racemic, and 3 : 1 crystals involve infinite hydrogen-bonded chains with different arrangements of the aromatic groups. They exhibit significantly different volatility, the enantiopure compound being more volatile than the racemic crystal. The accumulated experimental and quantum-chemical evidence turns methyl mandelate into a model system for the role of competition between dispersion forces and hydrogen bond interactions in chirality discrimination. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The cyclic alkyl(amino) carbene (cAAC) [:C{N-C 6 H 3 (2,6-IPr 2 )}(CMe 2 ) 2 CH 2 ] stabilized MeGeGeMe has been isolated in the molecular form with composition (cAAC)MeGe-GeMe(cAAC) (1) at room temperature. Compound 1 was synthesized from the reduction of MeGeCl 3 using three equivalents of KC 8 in the presence of one equivalent of cAAC. The corresponding silicon compound (cAAC)MeSi-SiMe(cAAC) (2) was also prepared. Compounds 1 and 2 are the first examples of REER compounds (E = Ge, Si) carrying the smallest organic group. Furthermore the structures of compounds 1 and 2 have been investigated by using theoretical methods. The theoretical analysis of the structure of 1 is in agreement with the formation as an unprecedented carbene stabilized bis-germylene whereas compound 2 can be equally described as carbene stabilized bis-silylene with coordinate bonds as with classical double bonds of a 2,3-disila-1,3-butadiene. The compounds were also characterized by X-ray crystallography.

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 (cAAC˙)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.

(cAAC)Ge(GeL)2 (1) (cAAC = cyclic alkyl(amino) carbene; L = PhC-(tBuN)2), a functionalized Ge3-compound was prepared. Quantum mechanical studies on 1 show a reciprocal relationship between the electronic state of the central tri-coordinated Ge atomand its reactivity towards protons, viz. tetravalent Ge(0) in terms of bonding and divalent Ge(0) in terms of reactivity. Thus the central Ge atomcan be considered as having a hidden but highly reactive lone pair of electrons. However, the terminal Ge atoms can be considered as tri-coordinated divalent Ge(I) with an active lone pair of electrons.

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.

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 example of a siladiaziridine compound.

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.

An abnormal N-heterocyclic carbene (aNHC) has been used as a Lewis base to initiate dismutation of trichlorosilane. This report presents the reactivity differences of a normal N-heterocyclic carbene (NHC) versus aNHC with heavier group 14 elements. Three novel compounds (NHC)(2)·SiCl(2)H(2) (2), aNHC·SiCl(2)H(2) (3), and aNHC·GeCl(2) (4) have been synthesized and characterized by single crystal X-ray analysis, solid-state NMR and DFT calculations.

The generation of amphiphiles 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 metalloamphiphiles with a variety of metal ions. Structural studies have been made of one of the free (protonated) ligands and some of their complexes.

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.

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.