Bond orders for intermolecular interactions in crystals: charge transfer, ionicity and the effect on intramolecular bonds

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.

Bicyclic (alkyl)(amino)carbene (BICAAC)-supported phosphinidenes

Herein, the synthesis and characterization of bicyclic (alkyl)(amino)carbene (BICAAC)-stabilized phosphinidenes (1-4) are reported. Compounds 1-3 were obtained by reacting trihalophosphine [PX3, X = Cl (1), Br (2), I (3)] with BICAAC in THF. A BICAAC-stabilized bis-phosphinidene (4) was obtained from the reduction of compound 2. All four compounds were characterized by X-ray crystallography and heteronuclear NMR spectroscopy. Theoretical calculations indicated the predominant C(carbene)P double bond characteristic in compounds 1-4.

Occurrence Modes of Critical Metals (Li+ and Ge4+) in the Organic Molecular Structures of Coal: A Density Functional Theory Study

To explore the mechanism of critical metal (Li⁺ and Ge⁴⁺) occurrence in the organic molecular structures of different rank coals, simulations were investigated using quantum chemical density functional theory. In this paper, Wender lignite, bituminous, and anthracite molecular models were used as organic molecular structures in coal. The electrostatic potential (ESP), frontier molecular orbitals, and Mulliken charges were used to identify adsorption sites in organic molecular structures. Mulliken charge, bond length, Mayer bond order (MBO), and adsorption energy values were used to estimate the binding conformation and strength between organic molecular structures and critical metals (Li⁺ and Ge⁴⁺). The results showed that the negative ESP, the highest occupied molecular orbitals, and negative Mulliken charges in the organic molecular structures were located at the O atom of oxygen functional groups and the aromatic structures, respectively, which were the active sites for critical metal adsorption. Mulliken charge transfer, bond length, MBO, and adsorption energy data suggested that the binding of Li⁺ with organic molecular structures was controlled by the carbonyl group (C=O), while the aromatic structures had less effect on the occurrence of Li⁺ in the organic molecular structures. The maximum adsorption energy value for binding Li⁺ with organic molecular structures was -742.16 kJ/mol. The Ge⁴⁺ ions not only showed strong binding ability with oxygen functional groups, but also Ge⁴⁺ formed thermodynamically stable half-sandwich complexes with aromatic structures. Therefore, the coal rank had little effect on the binding of Ge⁴⁺ with organic molecular structures. Moreover, the binding of Ge⁴⁺ with organic molecule structures was enhanced by the synergistic interactions of oxygen functional groups and aromatic structures. The adsorption energy values were up to -8511.43 kJ/mol. The adsorption of organic matter in coal to critical metals (Li⁺ and Ge⁴⁺) generated changes in the spatial configuration of the organic molecular structure, including local twisting of the organic molecular structure in lignite and bending of the aromatic structure in anthracite.

Definition of the Pnictogen Bond: A Perspective

This article proposes a definition for the term “pnictogen bond” and lists its donors, acceptors, and characteristic features. These may be invoked to identify this specific subset of the inter- and intramolecular interactions formed by elements of Group 15 which possess an electrophilic site in a molecular entity.

ComABAN: refining molecular representation with the graph attention mechanism to accelerate drug discovery

An unsolved challenge in developing molecular representation is determining an optimal method to characterize the molecular structure. Comprehension of intramolecular interactions is paramount toward achieving this goal. In this study, ComABAN, a new graph-attention-based approach, is proposed to improve the accuracy of molecular representation by simultaneously considering atom-atom, bond-bond and atom-bond interactions. In addition, we benchmark models extensively on 8 public and 680 proprietary industrial datasets spanning a wide variety of chemical end points. The results show that ComABAN has higher prediction accuracy compared with the classical machine learning method and the deep learning-based methods. Furthermore, the trained neural network was used to predict a library of 1.5 million molecules and picked out compounds with a classification result of grade I. Subsequently, these predicted molecules were scored and ranked using cascade docking, molecular dynamics simulations to generate five potential candidates. All five molecules showed high similarity to nanomolar bioactive inhibitors suppressing the expression of HIF-1α, and we synthesized three compounds (Y-1, Y-3, Y-4) and tested their inhibitory ability in vitro. Our results indicate that ComABAN is an effective tool for accelerating drug discovery.

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.

An unprecedented interconversion between non-covalent and covalent interactions driven by halogen bonding

The spontaneous interconversion between covalent forces and noncovalent counterparts remains an unexplained mystery to date. Here we have discovered a marvelous transformation between them through halogen bonding using NI 3 as a prototype. Our results show that the interaction strength of the NI 3 dimer is 7.01 kcal mol -1 , demonstrating it is a quite strong halogen bond. Molecular orbital analyses indicate that the frontier MOs result from strong mixing of the fragment MOs, which may be the electronic structure basis of interconversion. Further studies on a series of NI 3 oligomers (5-, 10-, 15-, 20-, 26-, 30-mer) show that the interconversion occurs approximately at 26-mer on the basis on bond distance, ELF, etc.; the interconversion is a gradual transformation not a sudden one. This study provides more insights into the halogen bonding and the high explosivity of NI 3 containing species.

Chalcogen Bonding in the Molecular Dimers of WCh2 (Ch = S, Se, Te): On the Basic Understanding of the Local Interfacial and Interlayer Bonding Environment in 2D Layered Tungsten Dichalcogenides

Layered two-dimensional transition metal dichalcogenides and their heterostructures are of current interest, owing to the diversity of their applications in many areas of materials nanoscience and technologies. With this in mind, we have examined the three molecular dimers of the tungsten dichalcogenide series, (WCh₂)₂ (Ch = S, Se, Te), using density functional theory to provide insight into which interactions, and their specific characteristics, are responsible for the interfacial/interlayer region in the room temperature 2H phase of WCh₂ crystals. Our calculations at various levels of theory suggested that the Te···Te chalcogen bonding in (WTe₂)₂ is weak, whereas the Se···Se and S···S bonding interactions in (WSe₂)₂ and (WS₂)₂, respectively, are of the van der Waals type. The presence and character of Ch···Ch chalcogen bonding interactions in the dimers of (WCh₂)₂ are examined with a number of theoretical approaches and discussed, including charge-density-based approaches, such as the quantum theory of atoms in molecules, interaction region indicator, independent gradient model, and reduced density gradient non-covalent index approaches. The charge-density-based topological features are shown to be concordant with the results that originate from the extrema of potential on the electrostatic surfaces of WCh₂ monomers. A natural bond orbital analysis has enabled us to suggest a number of weak hyperconjugative charge transfer interactions between the interacting monomers that are responsible for the geometry of the (WCh₂)₂ dimers at equilibrium. In addition to other features, we demonstrate that there is no so-called van der Waals gap between the monolayers in two-dimensional layered transition metal tungsten dichalcogenides, which are gapless, and that the (WCh₂)₂ dimers may be prototypes for a basic understanding of the physical chemistry of the chemical bonding environments associated with the local interfacial/interlayer regions in layered 2H-WCh₂ nanoscale systems.

Zero-, one-, two- and three-dimensional supramolecular architectures sustained by Se…O chalcogen bonding: A crystallographic survey

The Cambridge Structural Database was evaluated for crystals containing Se…O chalcogen bonding interactions. These secondary bonding interactions are found to operate independently of complementary intermolecular interactions in about 13% of the structures they can potentially form. This number rises significantly when more specific interactions are considered, e.g. Se…O(carbonyl) interactions occur in 50% of cases where they can potentially form. In about 55% of cases, the supramolecular assemblies sustained by Se…O(oxygen) interactions are one-dimensional architectures, with the next most prominent being zero-dimensional assemblies, at 30%.

A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts

The founding in 1965 of what is now called the Cambridge Structural Database (CSD) has reaped dividends in numerous and diverse areas of chemical research. Each of the million or so crystal structures in the database was solved for its own particular reason, but collected together, the structures can be reused to address a multitude of new problems. In this Review, which is focused mainly on the last 10 years, we chronicle the contribution of the CSD to research into molecular geometries, molecular interactions, and molecular assemblies and demonstrate its value in the design of biologically active molecules and the solid forms in which they are delivered. Its potential in other commercially relevant areas is described, including gas storage and delivery, thin films, and (opto)electronics. The CSD also aids the solution of new crystal structures. Because no scientific instrument is without shortcomings, the limitations of CSD research are assessed. We emphasize the importance of maintaining database quality: notwithstanding the arrival of big data and machine learning, it remains perilous to ignore the principle of garbage in, garbage out. Finally, we explain why the CSD must evolve with the world around it to ensure it remains fit for purpose in the years ahead.

Halogen Bonding: A Halogen-Centered Noncovalent Interaction Yet to Be Understood

In addition to the underlying basic concepts and early recognition of halogen bonding, this paper reviews the conflicting views that consistently appear in the area of noncovalent interactions and the ability of covalently bonded halogen atoms in molecules to participate in noncovalent interactions that contribute to packing in the solid-state. It may be relatively straightforward to identify Type-II halogen bonding between atoms using the conceptual framework of σ-hole theory, especially when the interaction is linear and is formed between the axial positive region (σ-hole) on the halogen in one monomer and a negative site on a second interacting monomer. A σ-hole is an electron density deficient region on the halogen atom X opposite to the R–X covalent bond, where R is the remainder part of the molecule. However, it is not trivial to do so when secondary interactions are involved as the directionality of the interaction is significantly affected. We show, by providing some specific examples, that halogen bonds do not always follow the strict Type-II topology, and the occurrence of Type-I and -III halogen-centered contacts in crystals is very difficult to predict. In many instances, Type-I halogen-centered contacts appear simultaneously with Type-II halogen bonds. We employed the Independent Gradient Model, a recently proposed electron density approach for probing strong and weak interactions in molecular domains, to show that this is a very useful tool in unraveling the chemistry of halogen-assisted noncovalent interactions, especially in the weak bonding regime. Wherever possible, we have attempted to connect some of these results with those reported previously. Though useful for studying interactions of reasonable strength, IUPAC’s proposed “less than the sum of the van der Waals radii” criterion should not always be assumed as a necessary and sufficient feature to reveal weakly bound interactions, since in many crystals the attractive interaction happens to occur between the midpoint of a bond, or the junction region, and a positive or negative site.