Sum Of vdW Radii Research Articles

Salts based on perchlorinated closo-dodecaborate anion: First 35Cl NQR studies and crystal structure

Three salts based on perchlorinated closo-dodecaborate anion, Cs2[B12Cl12]∗2MeCN (1), K2[B12Cl12]∗7MeCN (2), and (Ph4P)2[B12Cl12] (3) were synthesized and characterized using 11В, 1Н, 13С NMR, X-ray diffraction and 35Cl nuclear quadrupole resonsnce (NQR) spectroscopy. The latter was for the first time applied for identification of noncovalent interactions Cl⋯X in closo-dodecaborate clusters. Subtle perturbations of the cluster electron density caused by weak noncovalent Cl⋯X interactions were detected hence selecting from the whole totality of measured interatomic ​« ​short ​» ​contacts those which really participated in noncovalent interactions. It has been shown that X-ray structural information based on measuring the distances between atomic nuclei can be substantially supplemented with the 35Cl NQR data on the features of the electronic distribution in these compounds. According to the 35Cl NQR results, the alkali cations in 2∗7MeCN, unlike in 1∗2MeCN, do not participate in noncovalent interactions with Cl atoms whereas the X-ray diffraction analysis found a number of K⋯Cl distances shorter than the sum of vdW radii.

The Se … Hal halogen bonding: Co-crystals of selenoureas with fluorinated organohalides

Synthesis and structural characterization of binary co-crystals 1–4 is reported in the present paper. Selenourea and 1,1-dimethylselenourea were used as selenium-containing halogen bond (XB) acceptors and iodopentafluorobenzene (IPFB), 1,4-diiodotetrafluorobenzene (1,4-DIFB) and 1,4-dibromotetrafluorobenzene (1,4-DBrFB) as XB donors. A comparative analysis of the similar binary co-crystals of selenourea and thiourea with a halogen donor revealed that Se … Hal halogen bonds are up to 13.12% shorter than the sum of vdW radii, while in case of S … Hal halogen bonds this value is 11.4%. Therefore, selenium tends to form stronger bonds with halogens than sulfur does. Comparisons of XB interaction energies, Hirschfeld and QTAIM analyses of the Se and S systems supported this observation that selenium based XB acceptor results in slightly stronger Ch⋅⋅⋅Hal halogen bonding.

Fluorinated vs Nonfluorinated PR2(biaryl) Ligands and Their [AuCl(L)] Complexes: Synthesis, X-ray Structures, and Computational Study of Weak Interactions. Bond, No Bond, and Beyond.

Six fluorinated PR2(biaryl) phosphines, Ln, with R = Ph, Cy and biaryl = C6H4-C6F5, C6F4-C6H5, C6F4-C6F5, have been prepared. Their [AuCl(Ln)] complexes and H congeners with PhJohnPhos or CyJohnPhos have been studied in order to examine the interactions that bring the distal aryl close to the Au-Cl bond region. X-ray, DFT structure optimization, QTAIM, and NCI methods allow for some understanding of the forces involved. The "no bond" noncovalent distal-aryl/Au-Cl weak interactions are produced at forced short distances achieved under intramolecular structural ligand pressure. Enhanced vdW distal-aryl/Au interactions at "no bond" distances shorter than the sum of Au and C vdW radii and weaker distal-aryl/Cl interactions at "no bond" distances beyond the sum of Cl and C vdW radii counterbalance the unfavorable structural distortion of the free ligand, providing some extra stability of the molecule on the order of 2-10 kcal mol-1. The F substituents in the distal aryl induce shorter aryl distances to the Au-Cl zone, pointing overall to stronger π-aryl polarization as being mainly responsible for the NCIs with gold. The interactions in the C···Cl zone, where the distances are larger than the sum of vdW radii, contribute only about 5%, according to energy estimations using NBOs.

Noncovalent Interactions in Compounds Based on Perchlorinated Boron Cluster as Monitored by 35Cl NQR (Review)

The article surveys the first 35Cl NQR results on detecting and characterizing noncovalent interactions in systems assembling [B10Cl10]2− clusters via halogen atoms. A number of compounds of decachloro-closo-decaborates with alkali metal or organic cations as well as with silver(I), copper(II) and iron(II) complexes were studied using 35Cl NQR and X-ray diffraction. The main interest of this survey is a capability of chlorine atoms to participate in noncovalent interactions with organic cations, ligand and solvent molecules without touching upon issues of synthesis. Whereas X-ray diffraction establishes the noncovalent interactions relying on the sum of vdW radii which serves as the basic and sometimes the only experimental criterion for identifying such interactions, the 35Cl NQR technique registers subtle perturbations in electron density distribution on the chlorine site caused by secondary interactions Cl···X. They adequately split the 35Cl NQR spectra thus selecting from the entire set of interatomic contacts those actually induced by noncovalent interactions.

Solvent effects on the crystal growth structure and morphology of the pharmaceutical dirithromycin

Solvent effects on the crystal structure and morphology of pharmaceutical dirithromycin molecules were systematically investigated using both experimental crystallization and theoretical simulation. Dirithromycin is one of the new generation of macrolide antibiotics with two polymorphic forms (Form I and Form II) and many solvate forms. Herein, six solvates of the dirithromycin, including acetonitrile, acetonitrile/water, acetone, 1-propanol, N,N-dimethylformamide (DMF) and cyclohexane, were studied. Experimentally, we crystallized the dirithromycin molecules in different solvents by the solvent evaporating method and measured the crystal structures with the X-ray diffraction (XRD). We compared these crystal structures of dirithromycin solvates and analyzed the solvent property-determined structure evolution. The solvents have a strong interaction with the dirithromycin molecule due to the formation of inter-molecular interactions (such as the hydrogen bonding and close contacts (sum of vdW radii)). Theoretically, we calculated the ideal crystal habit based on the solvated structures with the attachment growth (AE) model. The predicted morphologies and aspect ratios of dirithromycin solvates agree well with the experimental results. This work could be helpful to better understand the structure and morphology evolution of solvates controlled by solvents and guide the crystallization of active pharmaceutical ingredients in the pharmaceutical industry.

Characteristics of a σ-Hole and the Nature of a Halogen Bond.

The nature of halogen bonding in 128 complexes was investigated using advanced quantum mechanical calculations. First, isolated halogen donors were studied and their σ-holes were described in terms of size and magnitude. Later, both partners in the complex were considered and their interaction was described in terms of DFT-SAPT decomposition. The whole set of complexes under study was split into two categories on the basis of their stabilisation energy. The first subset with 38 complexes possesses stabilisation energies in the range 7-32 kcal/mol, while the second subset with 90 complexes has stabilisation energies smaller than 7 kcal/mol. The first subset is characterised by small intermolecular distances (less than 2.5 Å) and a significant contraction of van der Waals (vdW) distance (sum of vdW radii). Here the polarisation/electrostatic energy is dominant, mostly followed by induction and dispersion energies. The importance of induction energy reflects the charge-transfer character of the respective halogen bonds. Intermolecular distances in the second subset are large and the respective contraction of vdW distance upon the formation of a halogen bond is much smaller. Here the dispersion energy is mostly dominant, followed by polarisation and induction energies. Considering the whole set of complexes, we conclude that the characteristic features of their halogen bonds arise from the concerted action of polarisation and dispersion energies and neither of these energies can be considered as dominant. Finally, the magnitude of the σ-hole and DFT-SAPT stabilisation energy correlates only weakly within the whole set of complexes.