Leveraging Halogen Interactions for a Supramolecular Nanotube.

We demonstrate the formation of supramolecular nanotubes from molecular triangles in a single crystal by balancing the hydrogen bonds and halogen interactions between individual macrocycles. Thereby, we template the supramolecular nanotube growth by intermolecular interactions encoded directly in the macrocycles instead of those provided by the crystallization solvent. Ultimately, we show that replacing bromines for iodines in the macrocycle is necessary to achieve this supramolecular organization by enhancing the strength of the halogen interactions and concomitant reduction of the detrimental hydrogen bonds. We investigated the nature and the interplay of the individual intermolecular interactions by analysis of the experimental single crystal data and quantum chemical calculations. This work enriches the available toolbox of supramolecular interactions and will aid and abet the development of rationally-designed materials with a long-range 1D tubular organization.

Lattice response to the radiation damage of molecular crystals: radiation-induced versus thermal expansivity.

The interaction of intense synchrotron radiation with molecular crystals frequently modifies the crystal structure by breaking bonds, producing fragments and, hence, inducing disorder. Here, a second-rank tensor of radiation-induced lattice strain is proposed to characterize the structural susceptibility to radiation. Quantitative estimates are derived using a linear response approximation from experimental data collected on three materials Hg(NO3)2(PPh3)2, Hg(CN)2(PPh3)2 and BiPh3 [PPh3 = triphenylphosphine, P(C6H5)3; Ph = phenyl, C6H5], and are compared with the corresponding thermal expansivities. The associated eigenvalues and eigenvectors show that the two tensors are not the same and therefore probe truly different structural responses. The tensor of radiative expansion serves as a measure of the susceptibility of crystal structures to radiation damage.

Deciphering Iron-Catalyzed C-H Amination with Organic Azides: N2 Cleavage from a Stable Organoazide Complex.

Catalytic C-N bond formation by direct activation of C-H bonds offers wide synthetic potential. En route to C-H amination, complexes with organic azides are critical precursors towards the reactive nitrene intermediate. Despite their relevance, α-N coordinated organoazide complexes are scarce in general, and elusive with iron, although iron complexes are by far the most active catalysts for C-H amination with organoazides. Herein, we report the synthesis of a stable iron α-N coordinated organoazide complex from [Fe(N(SiMe3 )2 )2 ] and AdN3 (Ad=1-adamantyl) and its crystallographic, IR, NMR and zero-field 57 Fe Mössbauer spectroscopic characterization. These analyses revealed that the organoazide is in fast equilibrium between the free and coordinated state (Keq =62). Photo-crystallography experiments showed gradual dissociation of N2 , which imparted an Fe-N bond shortening and correspond to structural snapshots of the formation of an iron imido/nitrene complex. Reactivity of the organoazide complex in solution showed complete loss of N2 , and subsequent formation of a C-H aminated product via nitrene insertion into a C-H bond of the N(SiMe3 )2 ligand. Monitoring this reaction by 1 H NMR spectroscopy indicates the transient formation of the imido/nitrene intermediate, which was supported by Mössbauer spectroscopy in frozen solution.

Dynamic Covalent Bonds in the Ebselen Class of Antioxidants Probed by X-ray Quantum Crystallography.

Dynamic bonds are essential structural ingredients of dynamic covalent chemistry that involve reversible cleavage and formation of bonds. Herein, we explore the electronic characteristics of Se-N bonds in the organo-selenium antioxidant ebselen and its derivatives for their propensity to function as dynamic covalent bonds by employing high-resolution X-ray quantum crystallography and complementary computational studies. An analysis of the experimentally reconstructed X-ray wavefunctions reveals the salient electronic features of the Se-N bonds with very low electron density localized at the bonding region and a positive Laplacian value at the bond critical point. Bond orders and percentage covalency and ionicity estimated from the X-ray wavefunctions, along with localized orbital locator (LOL) and electron localization function (ELF) analyses show that the Se-N bond is unique in its closed shell-like features, despite being a covalent bond. Time-dependent DFT calculations simulate the cleavage of Se-N bonds in ebselen in the excited state, further substantiating their nature as dynamic bonds.

An investigation into the Brønsted acidity of the perfluorinated alkoxy silanes {(F3C)3CO}3SiH and {(F6C5)3CO}2Si(Cl)H.

The perfluorinated alkoxy silanes {(F3C)3CO}3SiH (1) and {(F5C6)3CO}2Si(Cl)H (2) were prepared and fully characterized. Despite the high calculated Brønsted acidities, all attempts to deprotonate 1 and 2 to give the conjugate silanide ions failed due to the exceptionally short and strong Si-H bonds. In the solid state, the Si-H units are not involved in any intermolecular interactions, but instead the crystal packing consists of exceptionally short and strong F⋯F interactions. The cohesive energies are entirely comprised of London dispersion interactions, similarly as in the crystal structures of noble gases.

Towards Hexagonal Planar Nickel: A Dispersion-Stabilised Tri-Lithium Nickelate.

Advancing the understanding of lithum nickelate complexes, here we report a family of homoleptic organonickelate complexes obtained by reacting Ni(COD)2 and lithium aryl-acetylides in the presence of the bidentate donor TMEDA. These compounds represent rare examples of low-valent transition-metals supported solely by organolithium ligands. Whilst the solid-state structures indicate a hexagonal planar geometry around Ni0 with Ni-Li bonds, bonding analysis via QTAIM, NCI, NBO and ELI methods reveals that the Ni-Li interactions are repulsive in nature, characterising these complexes as tri-coordinated. London dispersion forces between TMEDA and the organic substituents on nickel are found to play a crucial role in the stabilisation and thus isolation of these complexes. Preliminary reactivity studies demonstrate that the homoleptic lithium nickelates undergo stoichiometric cross-coupling with PhI to give dinickel clusters containing both anionic acetylide and neutral alkyne ligands.

Unmasking the constitution and bonding of the proposed lithium nickelate "Li3NiPh3(solv)3": revealing the hidden C6H4 ligand.

More than four decades ago, a complex identified as the planar homoleptic lithium nickelate "Li3NiPh3(solv)3" was reported by Taube and co-workers. This and subsequent reports involving this complex have lain dormant since; however, the absence of an X-ray diffraction structure leaves questions as to the nature of the Ni-PhLi bonding and the coordination geometry at Ni. By systematically evaluating the reactivity of Ni(COD)2 with PhLi under different conditions, we have found that this classical molecule is instead a unique octanuclear complex, [{Li3(solv)2Ph3Ni}2(µ-η2:η2-C6H4)] (5). This is supported by X-ray crystallography and solution-state NMR studies. A theoretical bonding analysis from NBO, QTAIM, and ELI perspectives reveals extreme back-bonding to the bridging C6H4 ligand resulting in dimetallabicyclobutane character, the lack of a Ni-Ni bond, and pronounced σ-bonding between the phenyl carbanions and nickel, including a weak σC-Li → sNi interaction with the C-Li bond acting as a σ-donor. Employing PhNa led to the isolation of [Na2(solv)3Ph2NiCOD]2 (7) and [Na2(solv)3Ph2(NaC8H11)Ni(COD)]2 (8), which lack the benzyne-derived ligand. These findings provide new insights into the synthesis, structure, bonding and reactivity of heterobimetallic nickelates, whose prevalence in organonickel chemistry and catalysis is likely greater than previously believed.

Nickel and Palladium Complexes of a PP(O)P Pincer Ligand Based upon a peri-Substituted Acenaphthyl Scaffold and a Secondary Phosphine Oxide.

A PP(O)P pincer ligand based upon a peri-substituted acenaphthyl (Ace) scaffold and a secondary phosphine oxide, (5-Ph2P-Ace-6-)2P(O)H, was prepared and fully characterized including a neutron diffraction study. The reaction with [Ni(H2O)6]Cl2 and PdCl2 produced ionic metal(II) complexes [κ3-P,P',P''((5-Ph2P-Ace-6-)2P(OH))MCl]Cl, which upon addition of Et3N gave rise to zwitterionic metal(II) complexes κ3-P,P',P''((5-Ph2P-Ace-6-)2P(O))MCl (M = Ni, Pd). The reaction with Ni(COD)2 (COD = cyclooctadiene) provided the η3-cyclooctenyl Ni(II) complex κ3-P,P',P''((5-Ph2P-Ace-6-)2P(O))Ni(η3-C8H13). A detailed complementary bonding analysis of the P-H, P-O, and P-M interactions was carried out (M = Ni, Pd).

BN-Substitution in Dithienylpyrenes Prevents Excimer Formation in Solution and in the Solid State.

Boron-nitrogen substitutions in polycyclic aromatic hydrocarbons (PAHs) have a strong impact on the optical properties of the molecules due to a significantly more heterogeneous electron distribution. However, besides these single-molecule properties, the observed optical properties of PAHs critically depend on the degree of intermolecular interactions such as π-π-stacking, dipolar interactions, or the formation of dimers in the excited state. Pyrene is the most prominent example showing the latter as it exhibits a broadened and strongly bathochromically shifted emission band at high concentrations in solution compared to the respective monomers. In the solid state, the impact of intermolecular interactions is even higher as it determines the crystal packing crucially. In this work, a thiophene-flanked BN-pyrene (BNP) was synthesized and compared with its all-carbon analogue (CCP) in solution and in the solid state by means of crystallography, NMR spectroscopy, UV-vis spectroscopy, and photoluminescence (PL) spectroscopy. In solution, PL spectroscopy revealed the solvent-dependent presence of excimers of CCP at high concentrations. In contrast, no excimers were found in BNP. Clear differences were also observed in the single-crystal packing motifs. While CCP revealed overlapped pyrene planes with centroid distances in the range of classical π-stacking interactions, the BNP scaffolds were displaced and significantly more spatially separated.

Perfluorinated Trialkoxysilanol with Dramatically Increased Brønsted Acidity.

The Brønsted acidity of the perfluorinated trialkoxysilanol {(F3 C)3 CO}3 SiOH is more than 13 orders of magnitude higher than that of orthosilicic acid, Si(OH)4 , and even more for most previously known silanols. It is easily deprotonated by simple amines and pyridines to give the conjugate silanolates [OSi{OC(CF3 )3 }3 ]- , which possess extremely short Si-O bonds, comparable to those of silanones.

The advanced treatment of hydrogen bonding in quantum crystallography.

Although hydrogen bonding is one of the most important motifs in chemistry and biology, H-atom parameters are especially problematic to refine against X-ray diffraction data. New developments in quantum crystallography offer a remedy. This article reports how hydrogen bonds are treated in three different quantum-crystallographic methods: Hirshfeld atom refinement (HAR), HAR coupled to extremely localized molecular orbitals and X-ray wavefunction refinement. Three different compound classes that form strong intra- or intermolecular hydrogen bonds are used as test cases: hydrogen maleates, the tripeptide l-alanyl-glycyl-l-alanine co-crystallized with water, and xylitol. The differences in the quantum-mechanical electron densities underlying all the used methods are analysed, as well as how these differences impact on the refinement results.

lamaGOET: an interface for quantum crystallography.

In quantum crystallography, theoretical calculations and crystallographic refinements are closely intertwined. This means that the employed software must be able to perform both quantum-mechanical calculations and crystallographic least-squares refinements. So far, the program Tonto is the only one able to do that. The lamaGOET interface described herein deals with this issue since it interfaces dedicated quantum-chemical software (the widely used Gaussian package and the specialized ELMOdb program) with the refinement capabilities of Tonto. Three different flavours of quantum-crystallographic refinements of the dipetide glycyl-l-threonine dihydrate are presented to showcase the capabilities of lamaGOET: Hirshfeld atom refinement (HAR), HAR-ELMO, namely HAR coupled with extremely localized molecular orbitals, and X-ray constrained wavefunction fitting.

Investigating Complex Magnetic Anisotropy in a Co(II) Molecular Compound: A Charge Density and Correlated Ab Initio Electronic Structure Study.

Understanding magnetic anisotropy and specifically how to tailor it is crucial in the search for high-temperature single-ion magnets. Herein, we investigate the magnetic anisotropy in a six-coordinated cobalt(II) compound that has a complex geometry and distinct triaxial magnetic anisotropy from the perspective of the electronic structure, using electronic spectra, ab initio calculations, and an experimental charge density, of which the latter two provides insight into the d-orbital splitting. The analysis showed that the d-orbital splitting satisfactorily predicted the complex triaxial magnetic anisotropy exhibited by the compound. Furthermore, a novel method to directly compare the ab initio results and the d-orbital populations obtained from the experimental charge density was developed, while a topological analysis of the density provided insights into the metal-ligand bonding. This work thus further establishes the validity of using d-orbitals for predicting magnetic anisotropy in transition metal compounds while also pointing out the need for a more frequent usage of the term triaxial anisotropy in the field of single-molecule magnetism.

Sila-Ibuprofen.

The synthesis, characterization, biological activity, and toxicology of sila-ibuprofen, a silicon derivative of the most common nonsteroidal anti-inflammatory drug, is reported. The key improvements compared with ibuprofen are a four times higher solubility in physiological media and a lower melting enthalpy, which are attributed to the carbon-silicon switch. The improved solubility is of interest for postsurgical intravenous administration. A potential for pain relief is rationalized via inhibition experiments of cyclooxygenases I and II (COX-I and COX-II) as well as via a set of newly developed methods that combine molecular dynamics, quantum chemistry, and quantum crystallography. The binding affinity of sila-ibuprofen to COX-I and COX-II is quantified in terms of London dispersion and electrostatic interactions in the active receptor site. This study not only shows the potential of sila-ibuprofen for medicinal application but also improves our understanding of the mechanism of action of the inhibition process.

Intramolecular Reaction of Transient Phosphenium and Arsenium Ions Giving Rise to Isolable 9-Phospha- and 9-Arsena-Fluorenium Ions.

Transient phosphenium and arsenium ions, generated by fluoride abstraction from bis(m-terphenyl)fluoropnictogens, underwent intramolecular electrophilic attack prior to methyl group migration and gave rise to isolable 9-phospha- and 9-arsena-fluorenium ions.

Accurate crystal structures and chemical properties from NoSpherA2.

The relationship between the structure and the properties of a drug or material is a key concept of chemistry. Knowledge of the three-dimensional structure is considered to be of such importance that almost every report of a new chemical compound is accompanied by an X-ray crystal structure - at least since the 1970s when diffraction equipment became widely available. Crystallographic software of that time was restricted to very limited computing power, and therefore drastic simplifications had to be made. It is these simplifications that make the determination of the correct structure, especially when it comes to hydrogen atoms, virtually impossible. We have devised a robust and fast system where modern chemical structure models replace the old assumptions, leading to correct structures from the model refinement against standard in-house diffraction data using no more than widely available software and desktop computing power. We call this system NoSpherA2 (Non-Spherical Atoms in Olex2). We explain the theoretical background of this technique and demonstrate the far-reaching effects that the improved structure quality that is now routinely available can have on the interpretation of chemical problems exemplified by five selected examples.

The Bis(ferrocenyl)phosphenium Ion Revisited.

The bis(ferrocenyl)phosphenium ion, [Fc2 P]+ , reported by Cowley et al. (J. Am. Chem. Soc. 1981, 103, 714-715), was the only claimed donor-free divalent phosphenium ion. Our examination of the molecular and electronic structure reveals that [Fc2 P]+ possesses significant intramolecular Fe⋅⋅⋅P contacts, which are predominantly electrostatic and moderate the Lewis acidity. Nonetheless, [Fc2 P]+ undergoes complex formation with the Lewis bases PPh3 and IPr to give the donor-acceptor complexes [Fc2 P(PPh3 )]+ and [Fc2 P(IPr)]+ (IPr=1,3-bis(2,6-diisopropylphenyl)imidazole-2-ylidene).

Proximity Enforced Agostic Interactions Involving Closed-Shell Coinage Metal Ions.

A proximity enforcing diarylsilane ligand is reported, which gives rise to unusual Si-H···M interactions with the d10 metal ions Cu+ and Ag+ upon complexation. These interactions are studied in detail both experimentally and computationally and can be classified to be weakly agostic in nature for the Si-H···Cu interaction. The Si-H···Ag interaction has more signatures of an electrostatic contact.

Complementary bonding analysis of the N-Si interaction in pentacoordinated silicon compounds using quantum crystallography.

The N-Si interaction in two pentacoordinated silicon compounds is investigated based on a complementary bonding analysis, which consists of bonding descriptors from real space and orbital space. These are derived from X-ray wavefunction refinements of high-resolution X-ray diffraction data of single crystals and from isolated-molecule theoretical wavefunctions. The two pentacoordinated compounds only differ in one methylene group, so that the amino substituent is more flexible in one of the structures, hence probing the attractive or repulsive character of the N-Si interaction. All studies suggest weak dative interactions, which do, however, greatly influence the character of the Si-F bond: A strong N-Si interaction results in a weakened Si-F bond, which is quantified in this study experimentally and theoretically.

Fast and Accurate Quantum Crystallography: From Small to Large, from Light to Heavy.

The coupling of the crystallographic refinement technique Hirshfeld atom refinement (HAR) with the recently constructed libraries of extremely localized molecular orbitals (ELMOs) gives rise to the new quantum-crystallographic method HAR-ELMO. This method is significantly faster than HAR but as accurate and precise, especially concerning the free refinement of hydrogen atoms from X-ray diffraction data, so that the first fully quantum-crystallographic refinement of a protein is presented here. However, the promise of HAR-ELMO exceeds large molecules and protein crystallography. In fact, it also renders possible electron-density investigations of heavy elements in small molecules and facilitates the detection and isolation of systematic errors from physical effects.