scholarly journals Electron Density Geometry and the Quantum Theory of Atoms in Molecules

Author(s):  
Timothy Wilson ◽  
Anastassia Alexandrova ◽  
Mark Eberhart

A novel form of charge density analysis, that of isosurface curvature redistribution, is formulated and applied to the toy problem of carbonyl oxygen activation in formaldehyde. The isosurface representation of the electron charge density allows us to incorporate the rigorous geometric constraints of closed surfaces towards the analysis and chemical interpretation of the charge density response to perturbations. Visual inspection of 2D isosurface motion resulting from applied external electric fields reveals how isosurface curvature flows within and between atoms, and that a molecule can be uniquely and completely partitioned into chemically significant regions of positive and negative curvature. These concepts reveal that carbonyl oxygen activation proceeds primarily through curvature and charge redistribution within rather than between Bader atoms. Using gradient bundle analysis—the partitioning of formaldehyde into infinitesimal volume elements bounded by QTAIM zero flux surfaces—the observations from visual isosurface inspection are verified. The results of the formaldehyde carbonyl analysis are then shown to be transferable to the substrate carbonyl in the ketosteroid isomerase enzyme, laying the groundwork for extending this approach to the problems of enzymatic catalysis.

2021 ◽  
Author(s):  
Timothy Wilson ◽  
Anastassia Alexandrova ◽  
Mark Eberhart

A novel form of charge density analysis, that of isosurface curvature redistribution, is formulated and applied to the toy problem of carbonyl oxygen activation in formaldehyde. The isosurface representation of the electron charge density allows us to incorporate the rigorous geometric constraints of closed surfaces towards the analysis and chemical interpretation of the charge density response to perturbations. Visual inspection of 2D isosurface motion resulting from applied external electric fields reveals how isosurface curvature flows within and between atoms, and that a molecule can be uniquely and completely partitioned into chemically significant regions of positive and negative curvature. These concepts reveal that carbonyl oxygen activation proceeds primarily through curvature and charge redistribution within rather than between Bader atoms. Using gradient bundle analysis—the partitioning of formaldehyde into infinitesimal volume elements bounded by QTAIM zero flux surfaces—the observations from visual isosurface inspection are verified. The results of the formaldehyde carbonyl analysis are then shown to be transferable to the substrate carbonyl in the ketosteroid isomerase enzyme, laying the groundwork for extending this approach to the problems of enzymatic catalysis.


2021 ◽  
Author(s):  
Timothy Wilson ◽  
Anastassia Alexandrova ◽  
Mark Eberhart

A novel form of charge density analysis, that of isosurface curvature redistribution, is formulated and applied to the toy problem of carbonyl oxygen activation in formaldehyde. The isosurface representation of the electron charge density allows us to incorporate the rigorous geometric constraints of closed surfaces towards the analysis and chemical interpretation of the charge density response to perturbations. Visual inspection of 2D isosurface motion resulting from applied external electric fields reveals how isosurface curvature flows within and between atoms, and that a molecule can be uniquely and completely partitioned into chemically significant regions of positive and negative curvature. These concepts reveal that carbonyl oxygen activation proceeds primarily through curvature and charge redistribution within rather than between Bader atoms. Using gradient bundle analysis—the partitioning of formaldehyde into infinitesimal volume elements bounded by QTAIM zero flux surfaces—the observations from visual isosurface inspection are verified. The results of the formaldehyde carbonyl analysis are then shown to be transferable to the substrate carbonyl in the ketosteroid isomerase enzyme, laying the groundwork for extending this approach to the problems of enzymatic catalysis.


2014 ◽  
Vol 70 (a1) ◽  
pp. C674-C674
Author(s):  
Sajesh Thomas ◽  
Rebecca Fuller ◽  
Alexandre Sobolev ◽  
Philip Schauer ◽  
Simon Grabowsky ◽  
...  

The effect of an electric field on the vibrational spectra, the Vibrational Stark Effect (VSE), has been utilized extensively to probe the local electric field in the active sites of enzymes [1, 2]. For this reason, the electric field and consequent polarization effects induced by a supramolecular host system upon its guest molecules attain special interest due to the implications for various biological processes. Although the host-guest chemistry of crown ether complexes and clathrates is of fundamental importance in supramolecular chemistry, many of these multicomponent systems have yet to be explored in detail using modern techniques [3]. In this direction, the electrostatic features associated with the host-guest interactions in the inclusion complexes of halogenated acetonitriles and formamide with 18-crown-6 host molecules have been analyzed in terms of their experimental charge density distribution. The charge density models provide estimates of the molecular dipole moment enhancements which correlate with the simulated values of dipole moments under electric field. The accurate electron density mapping using the multipole formalism also enable the estimation of the electric field experienced by the guest molecules. The electric field vectors thus obtained were utilized to estimate the vibrational stark effect in the nitrile (-C≡N) and carbonyl (C=O) stretching frequencies of the guest molecules via quantum chemical calculations in gas phase. The results of these calculations indicate remarkable elongation of C≡N and C=O bonds due to the electric fields. The electronic polarization in these covalent bonds induced by the field manifests as notable red shifts in their characteristic vibrational frequencies. These results derived from the charge densities are further supported by FT-IR experiments and thus establish the significance of a phenomenon that could be termed as the "supramolecular Stark effect" in crystal environment.


ChemInform ◽  
2010 ◽  
Vol 41 (13) ◽  
Author(s):  
T. Noritake ◽  
M. Aoki ◽  
M. Matsumoto ◽  
K. Miwa ◽  
S. Towata ◽  
...  

Author(s):  
Zhijie Chua ◽  
Bartosz Zarychta ◽  
Christopher G. Gianopoulos ◽  
Vladimir V. Zhurov ◽  
A. Alan Pinkerton

A high-resolution X-ray diffraction measurement of 2,5-dichloro-1,4-benzoquinone (DCBQ) at 20 K was carried out. The experimental charge density was modeled using the Hansen–Coppens multipolar expansion and the topology of the electron density was analyzed in terms of the quantum theory of atoms in molecules (QTAIM). Two different multipole models, predominantly differentiated by the treatment of the chlorine atom, were obtained. The experimental results have been compared to theoretical results in the form of a multipolar refinement against theoretical structure factors and through direct topological analysis of the electron density obtained from the optimized periodic wavefunction. The similarity of the properties of the total electron density in all cases demonstrates the robustness of the Hansen–Coppens formalism. All intra- and intermolecular interactions have been characterized.


2011 ◽  
Vol 67 (a1) ◽  
pp. C99-C100 ◽  
Author(s):  
E. Espinosa ◽  
T. T. T. Bui ◽  
S. Dahaoui ◽  
E. Aubert ◽  
C. Lecomte ◽  
...  

2006 ◽  
Vol 84 (5) ◽  
pp. 771-781 ◽  
Author(s):  
Cina Foroutan-Nejad ◽  
Gholam Hossein Shafiee ◽  
Abdolreza Sadjadi ◽  
Shant Shahbazian

In this study, a detailed topological charge density analysis based on the quantum theory of atoms in molecules (QTAIM) developed by Bader and co-workers, has been accomplished (using the B3LYP method) on the CB62– anion and three planar isomers of the C3B4 species, which had been first proposed by Exner and Schleyer as examples of molecules containing hexacoordinate carbon atoms. The analysis uncovers the strong (covalent) interactions of boron atoms as well as the "nondirectional" interaction of central carbon atom with those peripheral atoms. On the other hand, instabilities have been found in the topological networks of (B6C)2– and B4C3(para) species. A detailed investigation of these instabilities demonstrates that the topology of charge density has a floppy nature near the equilibrium geometries of the species under study. Thus, these species seems to be best described as complexes of a relatively concrete ring containing boron or carbon atoms and a central carbon atom that is confined in the plane of the molecule, but with nondirectional interactions with the surrounding atoms.Key words: hypervalency, hexacoordinate carbon, quantum theory of atoms in molecules, charge density analysis, ab initio methods.


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