Bond Path

2016 ◽  
Author(s):  
Vladimir I. Minkin
Keyword(s):  
Bond Path

scholarly journals On atom–atom `short contact' bonding interactions in crystals

IUCrJ ◽  
2015 ◽  
Vol 2 (2) ◽  
pp. 161-163 ◽  
Author(s):  
Claude Lecomte ◽  
Enrique Espinosa ◽  
Cherif F. Matta
Keyword(s):  
Intermolecular Interactions ◽  
Structural Stability ◽  
Crystal Engineering ◽  
Alternative View ◽  
Short Contact ◽  
Bond Path ◽  
Individual Atom ◽  
Present Essay

Professor Dunitz questions the usefulness of ascribing crystalline structural stability to individual atom–atom intermolecular interactions viewed as bonding (hence stabilizing) whenever linked by a bond path. An alternative view is expressed in the present essay that articulates the validity and usefulness of the bond path concept in a crystallographic and crystal engineering context.

scholarly journals Halogen and Hydrogen Bonding in Halogenabenzene/NH3 Complexes Compared Using Next-Generation QTAIM

Molecules ◽  
2019 ◽  
Vol 24 (16) ◽  
pp. 2875 ◽  
Author(s):  
Shuman Li ◽  
Tianlv Xu ◽  
Tanja van Mourik ◽  
Herbert Früchtl ◽  
Steven R. Kirk ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Quantum Theory ◽  
Relativistic Effects ◽  
Halogen Bonding ◽  
Atomic Mass ◽  
Atoms In Molecules ◽  
Next Generation ◽  
Bond Path ◽  
Chemical Character ◽  
Effective Core Potentials

Next-generation quantum theory of atoms in molecules (QTAIM) was used to investigate the competition between hydrogen bonding and halogen bonding for the recently proposed (Y = Br, I, At)/halogenabenzene/NH3 complex. Differences between using the SR-ZORA Hamiltonian and effective core potentials (ECPs) to account for relativistic effects with increased atomic mass demonstrated that next-generation QTAIM is a much more responsive tool than conventional QTAIM. Subtle details of the competition between halogen bonding and hydrogen bonding were observed, indicating a mixed chemical character shown in the 3-D paths constructed from the bond-path framework set B. In addition, the use of SR-ZORA reduced or entirely removed spurious features of B on the site of the halogen atoms.

Experimental observation of charge-shift bond in fluorite CaF2

2017 ◽  
Vol 73 (4) ◽  
pp. 643-653 ◽  
Author(s):  
Marcin Stachowicz ◽  
Maura Malinska ◽  
Jan Parafiniuk ◽  
Krzysztof Woźniak
Keyword(s):  
Quantum Theory ◽  
Density Distribution ◽  
Critical Point ◽  
Electron Density ◽  
Closed Shell ◽  
Atoms In Molecules ◽  
Bond Critical Point ◽  
Ionic Radii ◽  
Bond Path ◽  
Charge Shift

On the basis of a multipole refinement of single-crystal X-ray diffraction data collected using an Ag source at 90 K to a resolution of 1.63 Å−1, a quantitative experimental charge density distribution has been obtained for fluorite (CaF2). The atoms-in-molecules integrated experimental charges for Ca2+and F−ions are +1.40 e and −0.70 e, respectively. The derived electron-density distribution, maximum electron-density paths, interaction lines and bond critical points along Ca2+...F−and F−...F−contacts revealed the character of these interactions. The Ca2+...F−interaction is clearly a closed shell and ionic in character. However, the F−...F−interaction has properties associated with the recently recognized type of interaction referred to as `charge-shift' bonding. This conclusion is supported by the topology of the electron localization function and analysis of the quantum theory of atoms in molecules and crystals topological parameters. The Ca2+...F−bonded radii – measured as distances from the centre of the ion to the critical point – are 1.21 Å for the Ca2+cation and 1.15 Å for the F−anion. These values are in a good agreement with the corresponding Shannon ionic radii. The F−...F−bond path and bond critical point is also found in the CaF2crystal structure. According to the quantum theory of atoms in molecules and crystals, this interaction is attractive in character. This is additionally supported by the topology of non-covalent interactions based on the reduced density gradient.

A Quantum Theory of Atoms-in-Molecules Perspective and DFT Study of Two Natural Products: Trans-Communic Acid and Imbricatolic Acid

2017 ◽  
Vol 70 (3) ◽  
pp. 328 ◽  
Author(s):  
Sarvesh Kumar Pandey ◽  
Mohammad Faheem Khan ◽  
Shikha Awasthi ◽  
Reetu Sangwan ◽  
Sudha Jain
Keyword(s):  
Density Functional Theory ◽  
Quantum Theory ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Atoms In Molecules ◽  
Reactivity Index ◽  
Chemical Hardness ◽  
Functional Theory ◽  
Bond Path ◽  
Topological Features

The topological features of the charge densities, ρ(r), and the chemical reactivity of two most biologically relevant and chemically interesting scaffold systems i.e. trans-communic acid and imbricatolic acid have been determined using density functional theory. To identify, characterize, and quantify efficiently, the non-covalent interactions of the atoms in the molecules have been investigated quantitatively using Bader's quantum theory of atoms-in-molecules (QTAIM) technique. The bond path is shown to persist for a range of weak H···H as well as C···H internuclear distances (in the range of 2.0–3.0 Å). These interactions exhibit all the hallmarks of a closed-shell weak interaction. To get insights into both systems, chemical reactivity descriptors, such as HOMO–LUMO, ionization potential, and chemical hardness, have been calculated and used to probe the relative stability and chemical reactivity. Some other useful information is also obtained with the help of several other electronic parameters, which are closely related to the chemical reactivity and reaction paths of the products investigated. Trans-communic acid seems to be chemically more sensitive when compared with imbricatolic acid due to its experimentally observed higher half-maximal inhibitory concentration (bioactivity parameter) value, which is in accordance with its higher chemical reactivity as theoretically predicted using density functional theory-based reactivity index. The quantum chemical calculations have also been performed in solution using different solvents, and the relative order of their structural and electronic properties as well as QTAIM-based parameters show patterns similar to those observed in gas phase only. This study further exemplifies the use and successful application of the bond path concept and the quantum theory of atoms-in-molecules.

scholarly journals Defining the Bounds of Chemical Coupling Between Covalent and Hydrogen-bonds in Small Water Clusters

2021 ◽  
Author(s):  
Zi Li ◽  
Yong Yang ◽  
Xing Nie ◽  
Tianlv Xu ◽  
Steven Kirk ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Water Clusters ◽  
Covalent Bond ◽  
Covalent Bonds ◽  
Bond Path ◽  
Small Water ◽  
Chemical Coupling ◽  
Chemical Character ◽  
Sigma Bond

We seek to determine the two-way transfer of chemical character due to the coupling occurring between hydrogen-bonds and covalent-bonds known to account for the unusual strength of hydrogen-bonds in water. We have provided a vector-based quantification of the chemical character of uncoupled hydrogen-bonds and covalent-bonds and then determined the effects of two-way coupling consistent with the total local energy density H(rb) < 0 for hydrogen-bonds. We have calculated the precessions Kʹ of the eigenvectors around the bond-path for the Ehrenfest Force F(r) and compared with the corresponding QTAIM Kʹ. In doing so we explain why the Ehrenfest Force F(r) provides insights into the coupling between the hydrogen and covalent bonds whilst QTAIM cannot. Conditions for favorable transfer of electron momentum from the hydrogen atom of a sigma bond to the hydrogen-bond are found, with excellent agreement with the hydrogen-bond BCP and covalent-bond BCP separations providing the theoretical bounds for coupling.

scholarly journals A Theoretical Investigation on Chemical Bonding of the Bridged Hydride Triruthenium Cluster: [Ru3 (μ-H)( μ3-κ2-Hamphox-N,N)(CO)9]

2020 ◽  
Vol 17 (2) ◽  
pp. 0488
Author(s):  
Muhsen Al-Ibadi et al.
Keyword(s):  
Transition Metal Complexes ◽  
Chemical Bonding ◽  
Bond Critical Point ◽  
Research Papers ◽  
Bond Path ◽  
Topological Parameters ◽  
The Core ◽  
Bonding Interaction ◽  
Ligand Interactions ◽  
Core Part

Ruthenium-Ruthenium and Ruthenium–ligand interactions in the triruthenium "[Ru3(μ-H)(μ3-κ2-Hamphox-N,N)(CO)9]" cluster are studied at DFT level of theory. The topological indices are evaluated in term of QTAIM (quantum theory of atoms in molecule). The computed topological parameters are in agreement with related transition metal complexes documented in the research papers. The QTAIM analysis of the bridged core part, i.e., Ru3H, analysis shows that there is no bond path and bond critical point (chemical bonding) between Ru(2) and Ru(3). Nevertheless, a non-negligible delocalization index for this non-bonding interaction is calculated. The interaction in the core Ru3H can be described as a (4centre–4electron) type. For Ru-N (oxazoline ring) bond, the calculated topological data propose a pure σ-bond. The computed topological parameters of oxazoline ligand reveal the presence of slightly some double bond characters within ligand ring.

Charge-density analysis of the ground state of a photochromic 1,10-phenanthroline zinc(II) bis(thiolate) complex

2010 ◽  
Vol 66 (3) ◽  
pp. 366-372 ◽  
Author(s):  
Stephan Scheins ◽  
Shao-Liang Zheng ◽  
Jason B. Benedict ◽  
Philip Coppens
Keyword(s):  
Charge Transfer ◽  
Charge Density ◽  
Title Compound ◽  
Theoretical Calculations ◽  
Oscillator Strengths ◽  
Bond Path ◽  
Ligand Charge Transfer ◽  
Density Analysis ◽  
Wavelength Emission ◽  
Phenanthroline Ligand

The charge density of the title compound was determined at 90 K, using a spherical crystal of 150 µm diameter. The proper treatment of the Zn atom in the pseudo-tetrahedral environment is considered in detail. A satisfactory refinement is only obtained when anharmonic Gram–Charlier parameters are included as variables in the refinement. A successful combined anharmonic/multipole refinement indicates a small polarization of the 4s shell in the anisotropic environment. One of the two toluenethiols is approximately π-stacked with the phenanthroline ligand. A bond path is found connecting the two ligands. In addition the Zn—S bond to this ligand is slightly extended compared with the same bond to the second toluenethiol. A separate photocrystallographic and theoretical study indicates the long wavelength emission of the title compound to be due to a ligand-to-ligand charge transfer (LLCT) from a toluenethiol to the phenanthroline ligand. The charge-density results do not provide a basis for deciding which of the thiole ligands is the source of the transferred electron density. This result is in agreement with the theoretical calculations, which show comparable oscillator strengths for charge transfer from either of the ligands.

A charge density study of π-delocalization and intermolecular interactions

2015 ◽  
Vol 17 (21) ◽  
pp. 14177-14184 ◽  
Author(s):  
L.-C. Wu ◽  
W.-C. Chung ◽  
C.-C. Wang ◽  
G.-H. Lee ◽  
S.-I. Lu ◽  
...  
Keyword(s):  
Charge Density ◽  
Intermolecular Interactions ◽  
Critical Points ◽  
Black Line ◽  
Bond Path ◽  
Π Interactions ◽  
Weak Intermolecular Interactions ◽  
A Charge ◽  
Density Study

The location of bond critical points (red dots) and its associated bond path (black line) provide the evidence on the existence of the weak intermolecular interactions of the π–π interactions between triazole rings of atrz molecules in crystal with the close ring distance of 3.17 Å.

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