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Atomic Interactions

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Vladimir G. Tsirelson – 1st expert on this subject based on the ideXlab platform

  • An anatomy of intramolecular Atomic Interactions in halogen-substituted trinitromethanes
    Physical Chemistry Chemical Physics, 2014
    Co-Authors: Ekaterina V. Bartashevich, Ángel Martín Pendás, Vladimir G. Tsirelson

    Abstract:

    The intramolecular Interactions in substituted trinitromethanes, XC(NO2)3 (X = F, Cl, I, H) are studied and clarified by using a combination of the Quantum Theory of Atoms in Molecules (QTAIM), the non-covalent interaction analysis and the Interacting Quantum Atoms (IQA) methods. The stretching vibration modes are formed by the concerted displacements of atoms involved in the covalent bonds showing the significant multiAtomic influence in substituted trinitromethanes. In agreement with that, the arrangement of the local reduced density gradient minima indicates that the electron density favors the non-covalent intramolecular Interactions X⋯O and N⋯O. However, the corresponding QTAIM bond paths are not formed; instead, contacts, which we call uncompleted links in this context, are accompanied by “quasi-bonding channels” corresponding to the λ2(r) ≤ 0 regions on the sign[λ2(r)]ρ(r) contour maps. The intramolecular IQA energy contributions signal the appreciable electron exchange between the pairs of atoms associated with potential Atomic Interactions or the bond-path-free non-covalent links. The IQA analysis shows that the electrostatic term destabilizes FC(NO2)3 and distinctly stabilizes IC(NO2)3, whereas it is close to neutral in ClC(NO2)3. The exchange energy between the X atom and the NO2 groups, in contrast, stabilizes all the molecules.

  • Atomic Interactions in ethylenebis(1-indenyl)zirconium dichloride as derived by experimental electron density analysis.
    Acta crystallographica. Section B Structural science, 2005
    Co-Authors: Adam I Stash, Kiyoaki Tanaka, Kazunari Shiozawa, Hitoshi Makino, Vladimir G. Tsirelson

    Abstract:

    A topological analysis of the experimental electron density in racemic ethylenebis(1-indenyl)zirconium dichloride, C20H16Cl2Zr, measured at 100 (1) K, has been performed. The Atomic charges calculated by the numerical integration of the electron density over the zero-flux Atomic basins demonstrate the charge transfer of 2.25 e from the Zr atom to the two indenyl ligands (0.19 e to each) and two Cl atoms (0.93 e to each). All the Atomic Interactions were quantitatively characterized in terms of the electron density and the electronic energy-density features at the bond critical points. The Zr-C2 bond paths significantly curved towards the C1-C2 bond were found; no other bond paths connecting the Zr atom and indenyl ligand were located. At the same time, the pi-electrons of the C1-C2 bond are significantly involved in the metal-ligand interaction. The electron density features indicate that the indenyl coordination can be approximately described as eta1 with slippage towards eta2. The ;ligand-opposed’ charge concentrations around the Zr atom were revealed using the Laplacian of the electron density and the one-particle potential; they were linked to the orbital representations. Bonds in the indenyl ligand were characterized using the Cioslowski-Mixon bond-order indices calculated directly from the experimental electron density.

  • Atomic Interactions in ethylenebis(1-indenyl)zirconium dichloride as derived by experimental electron density analysis
    Acta Crystallographica Section B-structural Science, 2005
    Co-Authors: Adam I Stash, Kiyoaki Tanaka, Kazunari Shiozawa, Hitoshi Makino, Vladimir G. Tsirelson

    Abstract:

    A topological analysis of the experimental electron density in racemic ethylenebis(l-indenyl)zirconium dichloride, C 20 H 16 Cl 2 Zr, measured at 100 (1) K, has been performed. The Atomic charges calculated by the numerical integration of the electron density over the zero-flux Atomic basins demonstrate the charge transfer of 2.25 e from the Zr atom to the two indenyl ligands (0.19 e to each) and two Cl atoms (0.93 e to each). All the Atomic Interactions were quantitatively characterized in terms of the electron density and the electronic energy-density features at the bond critical points. The Zr-C2 bond paths significantly curved towards the Cl -C2 bond were found; no other bond paths connecting the Zr atom and indenyl ligand were located. At the same time, the π-electrons of the C1-C2 bond are significantly involved in the metal-ligand interaction. The electron density features indicate that the indenyl coordination can be approximately described as η 1 with slippage towards η 2 . The ‘ligand-opposed’ charge concentrations around the Zr atom were revealed using the Laplacian of the electron density and the one-particle potential; they were linked to the orbital representations. Bonds in the indenyl ligand were characterized using the Cioslowski-Mixon bond-order indices calculated directly from the experimental electron density.

T L Blundell – 2nd expert on this subject based on the ideXlab platform

  • Atomic Interactions and profile of small molecules disrupting protein protein interfaces the timbal database
    Chemical Biology & Drug Design, 2009
    Co-Authors: Alicia P Higueruelo, Adrian Schreyer, Richard G J Bickerton, William R Pitt, Colin R Groom, T L Blundell

    Abstract:

    Growing evidence of the possibility of modulating protein–protein Interactions with small molecules is opening the door to new approaches and concepts in drug discovery. In this paper, we describe the creation of TIMBAL, a hand-curated database holding an up to date collection of small molecules inhibiting multi-protein complexes. This database has been analysed and profiled in terms of molecular properties. Protein–protein modulators tend to be large lipophilic molecules with few hydrogen bond features. An analysis of TIMBAL’s intersection with other structural databases, including CREDO (protein–small molecule from the PDB) and PICCOLO (protein–protein from the PDB) reveals that TIMBAL molecules tend to form mainly hydrophobic Interactions with only a few hydrogen bonding contacts. With respect to potency, TIMBAL molecules are slightly less efficient than an average medicinal chemistry hit or lead. The database provides a resource that will allow further insights into the types of molecules favoured by protein interfaces and provide a background to continuing work in this area. Access at http://www-cryst.bioc.cam.ac.uk/timbal

William R Pitt – 3rd expert on this subject based on the ideXlab platform

  • Atomic Interactions and profile of small molecules disrupting protein protein interfaces the timbal database
    Chemical Biology & Drug Design, 2009
    Co-Authors: Alicia P Higueruelo, Adrian Schreyer, Richard G J Bickerton, William R Pitt, Colin R Groom, T L Blundell

    Abstract:

    Growing evidence of the possibility of modulating protein–protein Interactions with small molecules is opening the door to new approaches and concepts in drug discovery. In this paper, we describe the creation of TIMBAL, a hand-curated database holding an up to date collection of small molecules inhibiting multi-protein complexes. This database has been analysed and profiled in terms of molecular properties. Protein–protein modulators tend to be large lipophilic molecules with few hydrogen bond features. An analysis of TIMBAL’s intersection with other structural databases, including CREDO (protein–small molecule from the PDB) and PICCOLO (protein–protein from the PDB) reveals that TIMBAL molecules tend to form mainly hydrophobic Interactions with only a few hydrogen bonding contacts. With respect to potency, TIMBAL molecules are slightly less efficient than an average medicinal chemistry hit or lead. The database provides a resource that will allow further insights into the types of molecules favoured by protein interfaces and provide a background to continuing work in this area. Access at http://www-cryst.bioc.cam.ac.uk/timbal