Electron Density in Quantum Theory

2011 ◽  
pp. 99-142 ◽  
Author(s):  
Samuel Fux ◽  
Markus Reiher
Keyword(s):  
Quantum Theory ◽  
Electron Density

On the transferability of electron density in binary vanadium borides VB, V3B4 and VB2

2015 ◽  
Vol 71 (6) ◽  
pp. 777-787 ◽  
Author(s):  
Bürgehan Terlan ◽  
Lev Akselrud ◽  
Alexey I. Baranov ◽  
Horst Borrmann ◽  
Yuri Grin
Keyword(s):  
Quantum Theory ◽  
Crystal Structures ◽  
Electron Density ◽  
Critical Points ◽  
Atoms In Molecules ◽  
Model Systems ◽  
Suitable Model ◽  
Interatomic Distances ◽  
Systematic Analysis ◽  
A Charge

Binary vanadium borides are suitable model systems for a systematic analysis of the transferability concept in intermetallic compounds due to chemical intergrowth in their crystal structures. In order to underline this structural relationship, topological properties of the electron density in VB, V3B4 and VB2 reconstructed from high-resolution single-crystal X-ray diffraction data as well as derived from quantum chemical calculations, are analysed in terms of Bader's Quantum Theory of Atoms in Molecules [Bader (1990). Atoms in Molecules: A Quantum Theory, 1st ed. Oxford: Clarendon Press]. The compounds VB, V3B4 and VB2 are characterized by a charge transfer from the metal to boron together with two predominant atomic interactions, the shared covalent B—B interactions and the polar covalent B—M interactions. The resembling features of the crystal structures are well reflected by the respective B—B interatomic distances as well as by ρ(r) values at the B—B bond critical points. The latter decrease with an increase in the corresponding interatomic distances. The B—B bonds show transferable electron density properties at bond critical points depending on the respective bond distances.

scholarly journals The active site of hen egg-white lysozyme: flexibility and chemical bonding

2014 ◽  
Vol 70 (4) ◽  
pp. 1136-1146 ◽  
Author(s):  
Jeanette Held ◽  
Sander van Smaalen
Keyword(s):  
Quantum Theory ◽  
Electron Density ◽  
Active Site ◽  
Egg White ◽  
Hen Egg White Lysozyme ◽  
Acta Cryst ◽  
Covalent Bonds ◽  
Egg White Lysozyme ◽  
Hen Egg White ◽  
Hen Egg

Chemical bonding at the active site of hen egg-white lysozyme (HEWL) is analyzed on the basis of Bader's quantum theory of atoms in molecules [QTAIM; Bader (1994),Atoms in Molecules: A Quantum Theory.Oxford University Press] applied to electron-density maps derived from a multipole model. The observation is made that the atomic displacement parameters (ADPs) of HEWL at a temperature of 100 K are larger than ADPs in crystals of small biological molecules at 298 K. This feature shows that the ADPs in the cold crystals of HEWL reflect frozen-in disorder rather than thermal vibrations of the atoms. Directly generalizing the results of multipole studies on small-molecule crystals, the important consequence for electron-density analysis of protein crystals is that multipole parameters cannot be independently varied in a meaningful way in structure refinements. Instead, a multipole model for HEWL has been developed by refinement of atomic coordinates and ADPs against the X-ray diffraction data of Wang and coworkers [Wanget al.(2007),Acta Cryst.D63, 1254–1268], while multipole parameters were fixed to the values for transferable multipole parameters from the ELMAM2 database [Domagalaet al.(2012),Acta Cryst.A68, 337–351] . Static and dynamic electron densities based on this multipole model are presented. Analysis of their topological properties according to the QTAIM shows that the covalent bonds possess similar properties to the covalent bonds of small molecules. Hydrogen bonds of intermediate strength are identified for the Glu35 and Asp52 residues, which are considered to be essential parts of the active site of HEWL. Furthermore, a series of weak C—H...O hydrogen bonds are identified by means of the existence of bond critical points (BCPs) in the multipole electron density. It is proposed that these weak interactions might be important for defining the tertiary structure and activity of HEWL. The deprotonated state of Glu35 prevents a distinction between the Phillips and Koshland mechanisms.

scholarly journals A STUDY OF THE ALKYLPROPARGYL RADICAL ELECTRON STRUCTURES IN THE FRAMEWORK OF QTAIM

2020 ◽  
pp. 46-52
Author(s):  
Елена Михайловна Чернова ◽  
Андрей Анатольевич Репин ◽  
Владимир Владимирович Туровцев ◽  
Юрий Димитриевич Орлов
Keyword(s):  
Quantum Theory ◽  
Electron Density ◽  
Spin Density ◽  
Classical Theory ◽  
Propargyl Radical ◽  
Significant Volume

Методом DFT B3LYP/6-311++G(3df,3pd) найдено распределение электронной плотности соединений гомологического ряда пропаргильных радикалов. В рамках квантовой теории атомов в молекуле (QTAIM) проведено исследование их электронного строения, выделен радикальный центр и отмечена делокализация спиновой плотности по значительному объему радикалов, что можно объяснить в рамках классической теории как суперпозицию структур. The electron density of the homologues of the propargyl radical series were found by DFT B3LYP/6-311++G(3df, 3pd) method. Within the “quantum theory of atoms in a molecules” (QTAIM) their electron structures were studied, radical centres were specified and it was shown that the spin density was delocalized over a significant volume of radicals. This phenomenon can be explained in the framework of classical theory as a superposition of structures.

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.

scholarly journals PolaBer: a program to calculate and visualize distributed atomic polarizabilities based on electron density partitioning

2014 ◽  
Vol 47 (4) ◽  
pp. 1452-1458 ◽  
Author(s):  
Anna Krawczuk ◽  
Daniel Pérez ◽  
Piero Macchi
Keyword(s):  
Refractive Index ◽  
Optical Properties ◽  
Dipole Moment ◽  
Quantum Theory ◽  
Electron Density ◽  
Electron Density Distribution ◽  
Atomic Charge ◽  
Atoms In Molecules ◽  
Molecular Dipole ◽  
Atomic Polarizability

This paper describes the program PolaBer, which calculates atomic polarizability tensors from electric field perturbations of a partitioned electron density distribution. Among many possible partitioning schemes, PolaBer is currently using the quantum theory of atoms in molecules and it is interfaced to programs that apply such a partitioning. The calculation of the atomic tensors follows the idea suggested by Keith [The Quantum Theory of Atoms in Molecules: From Solid State to DNA and Drug Design, (2007), edited by C. F. Matta & R. J. Boyd. Weinheim: Wiley-VCH], which enables the removal of the intrinsic origin dependence of the atomic charge contributions to the molecular dipole moment. This scheme allows the export, within chemically equivalent functional groups, of properties calculated from atomic dipoles, such as for example the atomic polarizabilities. The software permits visualization of the tensors and calculation of straightforward optical properties of a molecule (like the molar refractive index) or a crystal (assuming the molecule in a given crystal lattice).

scholarly journals SULFUR-CONTAINING HETEROCYCLES OF BENZENE AND HEXANE IN THE QUANTUM THEORY OF ATOMS IN MOLECULES

2020 ◽  
pp. 53-61
Author(s):  
Наталья Петровна Русакова ◽  
Георгий Александрович Курочкин ◽  
Юлия Ивановна Софронова ◽  
Владимир Владимирович Туровцев
Keyword(s):  
Quantum Theory ◽  
Density Distribution ◽  
Electron Density ◽  
Electron Density Distribution ◽  
Cyclic Compound ◽  
Atoms In Molecules ◽  
Electronic Density ◽  
Donor And Acceptor ◽  
Cyclic Compounds ◽  
Sulfur Containing

Изучено распределение электронной плотности 14 циклических соединений и одного нециклического. Проведен анализ зарядов и объемов групп, найдены группы доноры и акцепторы электронной плотности. Рассмотрено изменение электронной плотности серосодержащих групп под влиянием окружения. The electron density distribution of 14 cyclic compounds and one non-cyclic compound was studied. The group charges and group volumes were analyzed, and the electron density donor and acceptor groups were found. Changes in the electronic density of sulfur-containing groups under the influence of the environment are considered.

scholarly journals Quantum chemistry study on the promoted reactivity of substituted cyclooctynes in bioorthogonal cycloaddition reactions

2021 ◽  
Vol 27 (1) ◽  
pp. 142-154
Author(s):  
Tayebeh Hosseinnejad ◽  
Marzieh Omrani-Pachin
Keyword(s):  
Activation Energy ◽  
Quantum Theory ◽  
Quantum Chemistry ◽  
Electron Density ◽  
Critical Points ◽  
Cycloaddition Reaction ◽  
Electronic Energy ◽  
The Other ◽  
Dipolar Cycloaddition ◽  
Topological Properties

Abstract In the present research, we focus on the energetics and electronic aspects of enhanced reactivity in the regioselective bioorthogonal 1,3-dipolar cycloaddition reaction of various substituted cyclooctynes with methyl azide, applying quantum chemistry approaches. In this respect, we assessed the structural and energetic properties of regioisomeric products and their corresponded transition states and calculated the reaction electronic energy changes and energy barriers through the cycloaddition pathways. The obtained results revealed that the trifluoromethyl substitution and fluorination of cyclooctynes lead to improved reactivity, in conjunction with increased exothermicity and decreased activation energy values. On the other hand, quantum theory of atoms in molecules computations were performed on some key bond and ring critical points that demonstrated the stabilizing topological properties of electron density and its derivatives upon trifluoromethyl substitution and fluorination of propargylic carbon of cyclooctynes which can be regarded as the essential origin of enhanced reactivity.

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