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.

1,2,3,4-Tetrafluorobiphenylene: A Prototype Janus-Headed Scaffold for Ambipolar Materials.

The title compound was synthesized by Ullmann cross-coupling in low yield as the first representative of [n]phenylene containing hydrocarbon and fluorocarbon rings. Stille/Suzuki-Miyaura cross-coupling reactions, as well as substitution of fluorine in suitable starting compounds, failed to give the same product. The geometric and electronic structures of the title compound were studied by X-ray diffraction, cyclic voltammetry and density functional theory calculations, together with Hirshfeld surface and reduced density gradient analyses. The crystal structure features head-to-tail π-stacking and other fluorine-related secondary bonding interactions. From the nucleus-independent chemical shifts descriptor, the four-membered ring of the title compound is antiaromatic, and the six-membered rings are aromatic. The Janus molecule is highly polarized; and the six-membered fluoro- and hydrocarbon rings are Lewis π-acidic and π-basic, respectively. The electrochemically-generated radical cation of the title compound is long-lived as characterized by electron paramagnetic resonance, whereas the radical anion is unstable in solution. The title compound reveals electrical properties of an insulator. On expanding its molecular scaffold towards partially fluorinated [n]phenylenes (n≥2), the properties presumably can be transformed into those of semiconductors. In this context, the title compound is suggested as a prototype scaffold for ambipolar materials for organic electronics and spintronics.

The effects of experimentally obtained electron correlation and polarization on electron densities and exchange-correlation potentials.

In X-ray constrained wavefunction (XCW) fitting, external information, such as electron correlation and polarization, is included into a single-determinantal isolated-molecule wavefunction. In a first step, we show that the extraction of these two physical effects by XCW fitting is complete and accurate by comparing to theoretical reference calculations. In a second step, we show that fitting to data from single-crystal x-ray diffraction measurements provides the same results qualitatively and how the physical effects can be separated, although always inherently convolved in the experiment. We further demonstrate that exchange-correlation potentials are systematically affected by XCW fitting in a physically meaningful way, which could be exploited for method development in quantum chemistry, subject to some remaining challenges that we also outline.

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.

Reversing the Bond Length Alternation Order in Conjugated Polyenes by Substituent Effects.

We have synthesised several push-pull substituted conjugated polyenes and determined their accurate C-C bond lengths and charge-density distributions by utilising quantum crystallographic techniques. In a series of alkene, dienes, and triene bearing two (trifluoromethyl)sulfonyl (triflyl) groups on the terminal carbon atom, unique reversal of the bond-length alternation (BLA) order has been observed. This is a pronounced aberration from the molecular structure predicted by the Lewis-structure-based neutral resonance structure. Such reversal of BLA order has not been observed in push-pull compounds bearing conventional electron-withdrawing groups such as carbonyl and cyano groups instead of triflyl groups. Bonding behaviour of both normal and reversed bond length alternating systems has been revealed by complementary bonding analysis using several bond descriptors based on the experimentally fitted wavefunctions.

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.

Influence of modelling disorder on Hirshfeld atom refinement results of an organo-gold(I) compound.

Details of the validation of disorder modelling with Hirshfeld atom refinement (HAR) for a previously investigated organo-gold(I) compound are presented here. The impact of refining disorder on HAR results is discussed using an analysis of the differences of dynamic structure factors. These dynamic structure factor differences are calculated from thermally smeared quantum mechanical electron densities based on wavefunctions that include or exclude electron correlation and relativistic effects. When disorder is modelled, the electron densities stem from a weighted superposition of two (or more) different conformers. Here this is shown to impact the relative importance of electron correlation and relativistic effect estimates expressed by the structure factor magnitudes. The role of disorder modelling is also compared with the effect of the treatment of hydrogen anisotropic displacement parameter (ADP) values and atomic anharmonicity of the gold atom. The analysis of ADP values of gold and disordered carbon atoms showed that the effect of disorder significantly altered carbon ADP values and did not influence those of the gold atom.

X-ray constrained wavefunctions based on Hirshfeld atoms. I. Method and review.

The X-ray constrained wavefunction (XCW) procedure for obtaining an experimentally reconstructed wavefunction from X-ray diffraction data is reviewed. The two-center probability distribution model used to perform nuclear-position averaging in the original paper [Grimwood & Jayatilaka (2001). Acta Cryst. A57, 87-100] is carefully distinguished from the newer one-center probability distribution model. In the one-center model, Hirshfeld atoms are used, and the Hirshfeld atom based X-ray constrained wavefunction (HA-XCW) procedure is described for the first time, as well as its efficient implementation. In this context, the definition of the related X-ray wavefunction refinement (XWR) method is refined. The key halting problem for the XCW method - the procedure by which one determines when overfitting has occurred - is named and work on it reviewed.

X-ray constrained wavefunctions based on Hirshfeld atoms. II. Reproducibility of electron densities in crystals of α-oxalic acid dihydrate.

The Hirshfeld atom-based X-ray constrained wavefunction fitting (HA-XCW) procedure is tested for its reproducibility, and the information content of the fitted wavefunction is critically assessed. Fourteen different α-oxalic acid dihydrate data sets are used for this purpose, and the first joint fitting to 12 of these data sets is reported. There are systematic features in the electron density obtained from all data sets which agree with higher level benchmark calculations, but there are also many other strong systematic features which disagree with the reference calculations, most notably those associated with the electron density near the nuclei. To enhance reproducibility, three new protocols are described and tested to address the halting problem of XCW fitting, namely: an empirical power-function method, which is useful for estimating the accuracy of the structure factor uncertainties; an asymptotic extrapolation method based on ideas from density functional theory; and a `conservative method' whereby the smallest value of the regularization parameter is chosen from a series of data sets, or subsets.

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).

π-Hole bonding in a new co-crystal hydrate of gallic acid and pyrazine: static and dynamic charge density analysis.

A new cocrystal hydrate of gallic acid with pyrazine (4GA, Py, 4H2O; GA4PyW4) was obtained and characterized by single crystal X-ray diffraction. In addition to structure determination, experimental charge density analysis was carried out in terms of Multipole Modelling (MP), X-ray wavefunction refinement (XWR) and maximum entropy method (MEM). As a part of XWR, the structural refinement via Hirshfeld atom refinement was carried out and resulted in O-H bond lengths close to values from neutron diffraction. A systematic comparison of molecular conformations and aromatic interactions in this new cocrystal hydrate was performed with other existing polymorphs of gallic acid. In GA4PyW4, the two symmetry-independent gallic acid molecules have a syn COOH orientation and form the common (COOH)2 dimeric synthon. The carboxyl C atom displays the characteristics of π-holes with electropositive regions above and below the molecular plane and engages in acceptor-donor interactions with oxygen atoms of acidic O-H groups and phenol groups of neighbouring gallic acid molecules. The signature of the π-hole was identified from experimental charge density analysis, both in static density maps in MP and XWR as well as dynamic density in MEM, but it cannot be pinned down to a specific atom-atom interaction. This study presents the first comparison between an XWR and a MEM experimental electron-density determination.

Aurophilic Interactions Studied by Quantum Crystallography.

This is the first use of a wave-function-based crystallographic method to characterize aurophilic interactions from X-ray diffraction data. Theoretical calculations previously suggested the importance of electron correlation and dispersion forces, but no influence of relativistic corrections to the Au...Au interaction energy was found. In this study, we confirm the importance of relativistic corrections in the characterization of aurophilic interactions in addition to electron correlation and dispersion.

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.

Vanishing of the atomic form factor derivatives in non-spherical structural refinement - a key approximation scrutinized in the case of Hirshfeld atom refinement.

When calculating derivatives of structure factors, there is one particular term (the derivatives of the atomic form factors) that will always be zero in the case of tabulated spherical atomic form factors. What happens if the form factors are non-spherical? The assumption that this particular term is very close to zero is generally made in non-spherical refinements (for example, implementations of Hirshfeld atom refinement or transferable aspherical atom models), unless the form factors are refinable parameters (for example multipole modelling). To evaluate this general approximation for one specific method, a numerical differentiation was implemented within the NoSpherA2 framework to calculate the derivatives of the structure factors in a Hirshfeld atom refinement directly as accurately as possible, thus bypassing the approximation altogether. Comparing wR2 factors and atomic parameters, along with their uncertainties from the approximate and numerically differentiating refinements, it turns out that the impact of this approximation on the final crystallographic model is indeed negligible.

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.