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Vladimir G. Tsirelson - One of the best experts on this subject based on the ideXlab platform.
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An anatomy of intramolecular Atomic Interactions in halogen-substituted trinitromethanes
Physical Chemistry Chemical Physics, 2014Co-Authors: Ekaterina V. Bartashevich, Ángel Martín Pendás, Vladimir G. TsirelsonAbstract: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.
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Atomic Interactions in ethylenebis(1-indenyl)zirconium dichloride as derived by experimental electron density analysis.
Acta crystallographica. Section B Structural science, 2005Co-Authors: Adam I Stash, Kiyoaki Tanaka, Kazunari Shiozawa, Hitoshi Makino, Vladimir G. TsirelsonAbstract: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.
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Atomic Interactions in ethylenebis(1-indenyl)zirconium dichloride as derived by experimental electron density analysis
Acta Crystallographica Section B-structural Science, 2005Co-Authors: Adam I Stash, Kiyoaki Tanaka, Kazunari Shiozawa, Hitoshi Makino, Vladimir G. TsirelsonAbstract: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.
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Electron density of KNiF3: analysis of the Atomic Interactions
Acta Crystallographica Section B-structural Science, 2000Co-Authors: Vladimir G. Tsirelson, Yury Ivanov, Elizabeth A. Zhurova, Vladimir V. Zhurov, Kiyoaki TanakaAbstract:The topological analysis of the electron density in the perovskite KNiF3, potassium nickel trifluoride, based on the accurate X-ray diffraction data, has been performed. The topological picture of the Atomic Interactions differs from that resulting from the classic crystal chemistry consideration. The shapes of atoms in KNiF3 defined by zero-flux surfaces in the electron density are, in general, far from spherical. At the same time, their asphericity in the close-packed layer is very small. The topological coordination numbers of K and Ni are the same as the geometrical ones, whereas topological coordination for the F atom (6) differs from the geometrical value. The latter results from a specific shape of the Ni-atom basin preventing the bond-path formation between F atoms in the same Atomic close-packed layer, in spite of the fact that the closest F—F distance is the same as K—F. Judging by the electron density value and curvature at the bond critical points, the K—F interaction in KNiF3 can be considered ionic, while the Ni—F bond belongs to the polar covalent type. No correlation of the topological ionic radii with crystal or ionic radii was found in KNiF3. Critical points in the electrostatic potential have also been studied.
T L Blundell - One of the best experts on this subject based on the ideXlab platform.
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Atomic Interactions and profile of small molecules disrupting protein protein interfaces the timbal database
Chemical Biology & Drug Design, 2009Co-Authors: Alicia P Higueruelo, Adrian Schreyer, Richard G J Bickerton, William R Pitt, Colin R Groom, T L BlundellAbstract: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 - One of the best experts on this subject based on the ideXlab platform.
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Atomic Interactions and profile of small molecules disrupting protein protein interfaces the timbal database
Chemical Biology & Drug Design, 2009Co-Authors: Alicia P Higueruelo, Adrian Schreyer, Richard G J Bickerton, William R Pitt, Colin R Groom, T L BlundellAbstract: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
Todd O Yeates - One of the best experts on this subject based on the ideXlab platform.
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verification of protein structures patterns of nonbonded Atomic Interactions
Protein Science, 1993Co-Authors: Chris Colovos, Todd O YeatesAbstract:A novel method for differentiating between correctly and incorrectly determined regions of protein structures based on characteristic Atomic interaction is described. Different types of atoms are distributed nonrandomly with respect to each other in proteins. Errors in model building lead to more randomized distributions of the different atom types, which can be distinguished from correct distributions by statistical methods. Atoms are classified in one of three categories: carbon (C), nitrogen (N), and oxygen (O). This leads to six different combinations of pairwise noncovalently bonded Interactions (CC, CN, CO, NN, NO, and OO). A quadratic error function is used to characterize the set of pairwise Interactions from nine-residue sliding windows in a database of 96 reliable protein structures. Regions of candidate protein structures that are mistraced or misregistered can then be identified by analysis of the pattern of nonbonded Interactions from each window.
Adam I Stash - One of the best experts on this subject based on the ideXlab platform.
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Atomic Interactions in ethylenebis(1-indenyl)zirconium dichloride as derived by experimental electron density analysis.
Acta crystallographica. Section B Structural science, 2005Co-Authors: Adam I Stash, Kiyoaki Tanaka, Kazunari Shiozawa, Hitoshi Makino, Vladimir G. TsirelsonAbstract: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.
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Atomic Interactions in ethylenebis(1-indenyl)zirconium dichloride as derived by experimental electron density analysis
Acta Crystallographica Section B-structural Science, 2005Co-Authors: Adam I Stash, Kiyoaki Tanaka, Kazunari Shiozawa, Hitoshi Makino, Vladimir G. TsirelsonAbstract: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.