Perfluorinated Trialkoxysilanol with Dramatically Increased Brønsted Acidity

The Brønsted acidity of the perfluorinated trialkoxysilanol {(F₃C)₃CO}₃SiOH 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.

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.

Relativistic Hirshfeld atom refinement of an organo-gold(I) compound

The main goal of this study is the validation of relativistic Hirshfeld atom refinement (HAR) as implemented in Tonto for high-resolution X-ray diffraction datasets of an organo-gold(I) compound. The influence of the relativistic effects on statistical parameters, geometries and electron density properties was analyzed and compared with the influence of electron correlation and anharmonic atomic motions. Recent work in this field has indicated the importance of relativistic effects in the static electron density distribution of organo-mercury compounds. This study confirms that differences in electron density due to relativistic effects are also of significant magnitude for organo-gold compounds. Relativistic effects dominate not only the core region of the gold atom, but also influence the electron density in the valence and bonding region, which has measurable consequences for the HAR refinement model parameters. To study the effects of anharmonic motion on the electron density distribution, dynamic electron density difference maps were constructed. Unlike relativistic and electron correlation effects, the effects of anharmonic nuclear motion are mostly observed in the core area of the gold atom.

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.

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.

On the Role of Hydrogen Bonding in Gas-Phase SN2 Reactions at Silicon

The shape of the potential energy surface (PES) of gas-phase S_N2 reactions at silicon is determined by the type of nucleophile, the leaving group, and substituents which remain bonded to silicon. In this study, we present PES scans along the reaction coordinate of six symmetrical S_N2 reactions: X^- + SiR₃X → XSiR₃ + X^-, where X = Cl or F and R = H, Me, or OMe. While the fluorine systems and the ClSiH₃Cl system only give single-well PESs, ClSiMe₃Cl and ClSi(OMe)₃Cl give triple- and double-well PESs with stable pre- and post-reaction complexes. A complementary bonding analysis (energy decomposition analysis, quantum theory of atoms in molecules, and natural bond orbitals) reveals that the leaving group (X^-) is stabilized by hydrogen bonding in the XSiMe₃X and XSi(OMe)₃X systems. It is shown that this so far neglected stabilizing contribution, along with σ-hole bonding, is responsible for the shapes of the PESs of ClSiMe₃Cl and ClSi(OMe)₃Cl in the gas phase.

Synthesis, X-ray Structure Determination, and Comprehensive Photochemical Characterization of (Trifluoromethyl)diazirine-Containing TRPML1 Ligands

Potential (trifluoromethyl)diazirine-based TRPML1 ion channel ligands were designed and synthesized, and their structures were determined by single-crystal X-ray diffraction analysis. Photoactivation studies via ¹⁹F NMR spectroscopy and HPLC-MS analysis revealed distinct kinetical characteristics in selected solvents and favorable photochemical properties in an aqueous buffer. These photoactivatable TRPML activators represent useful and valuable tools for TRPML photoaffinity labeling combined with mass spectrometry.

Similarities and Differences between Crystal and Enzyme Environmental Effects on the Electron Density of Drug Molecules

The crystal interaction density is generally assumed to be a suitable measure of the polarization of a low-molecular weight ligand inside an enzyme, but this approximation has seldomly been tested and has never been quantified before. In this study, we compare the crystal interaction density and the interaction electrostatic potential for a model compound of loxistatin acid (E64c) with those inside cathepsin B, in solution, and in vacuum. We apply QM/MM calculations and experimental quantum crystallography to show that the crystal interaction density is indeed very similar to the enzyme interaction density. Less than 0.1 e are shifted between these two environments in total. However, this difference has non-negligible consequences for derived properties.

HgH2 meets relativistic quantum crystallography. How to teach relativity to a non-relativistic wavefunction

The capability of X-ray constrained wavefunction (XCW) fitting to introduce relativistic effects into a non-relativistic wavefunction is tested. It is quantified how much of the reference relativistic effects can be absorbed in the non-relativistic XCW calculation when fitted against relativistic structure factors of a model HgH₂ molecule. Scaling of the structure-factor sets to improve the agreement statistics is found to introduce a significant systematic error into the XCW fitting of relativistic effects.

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.

NoSpherA2 brings quantum crystallography to routine structure determination and to the analysis of chemical properties for any class of materials.

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.

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.

On the accuracy and precision of X-ray and neutron diffraction results as a function of resolution and the electron density model

X-ray diffraction is the main source of three-dimensional structural information. In total, more than 1.5 million crystal structures have been refined and deposited in structural databanks (PDB, CSD and ICSD) to date. Almost 99.7% of them were obtained by approximating atoms as spheres within the independent atom model (IAM) introduced over a century ago. In this study, X-ray datasets for single crystals of hydrated α-oxalic acid were refined using several alternative electron density models that abandon the crude spherical approximation: the multipole model (MM), the transferable aspherical atom model (TAAM) and the Hirshfeld atom refinement (HAR) model as a function of the resolution of X-ray data. The aspherical models (MM, TAAM, HAR) give far more accurate and precise single-crystal X-ray results than IAM, sometimes identical to results obtained from neutron diffraction and at low resolution. Hence, aspherical approaches open new routes for improving existing structural information collected over the last century.

Properties of gaseous closo-[B6X6]2- dianions (X = Cl, Br, I)

Electronic structure, collision-induced dissociation (CID) and bond properties of closo-[B₆X₆]^2- (X = Cl-I) are investigated in direct comparison with their closo-[B₁₂X₁₂]^2- analogues. Photoelectron spectroscopy (PES) and theoretical investigations reveal that [B₆X₆]^2- dianions are electronically significantly less stable than the corresponding [B₁₂X₁₂]^2- species. Although [B₆Cl₆]^2- is slightly electronically unstable, [B₆Br₆]^2- and [B₆I₆]^2- are intrinsically stable dianions. Consistent with the trend in the electron detachment energy, loss of an electron (e^- loss) is observed in CID of [B₆X₆]^2- (X = Cl, Br) but not for [B₆I₆]^2-. Halogenide loss (X^- loss) is common for [B₆X₆]^2- (X = Br, I) and [B₁₂X₁₂]^2- (X = Cl, Br, I). Meanwhile, X˙ loss is only observed for [B₁₂X₁₂]^2- (X = Br, I) species. The calculated reaction enthalpies of the three competing dissociation pathways (e^-, X^- and X˙ loss) indicated a strong influence of kinetic factors on the observed fragmentation patterns. The repulsive Coulomb barrier (RCB) determines the transition state for the e^- and X^- losses. A significantly lower RCB for X^- loss than for e^- loss was found in both experimental and theoretical investigations and can be rationalized by the recently introduced concept of electrophilic anions. The positive reaction enthalpies for X^- losses are significantly lower for [B₆X₆]^2- than for [B₁₂X₁₂]^2-, while enthalpies for X˙ losses are higher. These observations are consistent with a difference in bond character of the B-X bonds in [B₆X₆]^2- and [B₁₂X₁₂]^2-. A complementary bonding analysis using QTAIM, NPA and ELI-D based methods suggests that B-X bonds in [B₁₂X₁₂]^2- have a stronger covalent character than in [B₆X₆]^2-, in which X has a stronger halide character.

First steps towards a stable neon compound: observation and bonding analysis of [B12(CN)11Ne]. Chem Commun (Camb) 2020;56:4591-4594. [PMID: 32207481 DOI: 10.1039/d0cc01423k]

Noble gas (Ng) containing molecular anions are much scarcer than Ng containing cations. No neon containing anion has been reported so far. Here, the experimental observation of the molecular anion [B₁₂(CN)₁₁Ne]^- and a theoretical analysis of the boron-neon bond is reported.

Non-Oxido-Vanadium(IV) Metalloradical Complexes with Bidentate 1,2-Dithienylethene Ligands: Observation of Reversible Cyclization of the Ligand Scaffold in Solution

Derivatives of 1,2‐dithienylethene (DTE) have superb photochromic properties due to an efficient reversible photocyclization reaction of their hexatriene structure and, thus, have application potential in materials for optoelectronics and (multi‐responsive) molecular switches. Transition‐metal complexes bearing switchable DTE motifs commonly incorporate their coordination site rather distant from the hexatriene system. In this work the redox active ligand 1,2‐bis(2,5‐dimethylthiophen‐3‐yl)ethane‐1,2‐dione is described, which reacts with [V(TMEDA)₂Cl₂] to give a rare non‐oxido vanadium(IV) species 3(M,M/P,P). This blue complex has two bidentate en‐diolato ligands which chelate the V^IV center and give rise to two five‐membered metallacycles with the adjacent hexatriene DTE backbone bearing axial chirality. Upon irradiation with UVA light or prolonged heating in solution, the blue compound 3(M,M/P,P) converts into the purple atropisomer 4(para,M/para,P). Both complexes were isolated and structurally characterized by single‐crystal X‐ray diffraction analysis (using lab source and synchrotron radiation). The antiparallel configuration (M or P helicity) present in both 3(M,M/P,P) and 4(para,M/para,P) is a prerequisite for (reversible) 6π cyclization reactions. A CW EPR spectroscopic study reveals the metalloradical character for 3(M,M/P,P) and 4(para,M/para,P) and indicates dynamic reversible cyclization of the DTE backbone in complex 3(M,M/P,P) at ambient temperature in solution.