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Coot displays electron density maps and atomic models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, and Ramachandran idealization. The software is designed to be easy-to-learn for novice users, achieved by ensuring that ...
The Bohr model of the hydrogen atom (Z = 1) or a hydrogen-like ion (Z > 1), where the negatively charged electron confined to an atomic shell encircles a small, positively charged atomic nucleus and where an electron jumps between orbits, is accompanied by an emitted or absorbed amount of electromagnetic energy (hν). [1]
Atomic orbitals are basic building blocks of the atomic orbital model (or electron cloud or wave mechanics model), a modern framework for visualizing submicroscopic behavior of electrons in matter. In this model, the electron cloud of an atom may be seen as being built up (in approximation) in an electron configuration that is a product of ...
Chromium and copper have electron configurations [Ar] 3d 5 4s 1 and [Ar] 3d 10 4s 1 respectively, i.e. one electron has passed from the 4s-orbital to a 3d-orbital to generate a half-filled or filled subshell. In this case, the usual explanation is that "half-filled or completely filled subshells are particularly stable arrangements of electrons".
Atomic Spectroscopy, by W.C. Martin and W.L. Wiese in Atomic, Molecular, & Optical Physics Handbook, ed. by G.W.F. Drake (AIP, Woodbury, NY, 1996) Chapter 10, pp. 135–153. This website is also cited in the CRC Handbook as source of Section 1, subsection Electron Configuration of Neutral Atoms in the Ground State.
The MO diagram for diboron (B-B, electron configuration 1σ g 2 1σ u 2 2σ g 2 2σ u 2 1π u 2) requires the introduction of an atomic orbital overlap model for p orbitals. The three dumbbell -shaped p-orbitals have equal energy and are oriented mutually perpendicularly (or orthogonally ).
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This shape is found when there are four bonds all on one central atom, with no extra unshared electron pairs. In accordance with the VSEPR (valence-shell electron pair repulsion theory), the bond angles between the electron bonds are arccos(− 1 / 3 ) = 109.47°. For example, methane (CH 4) is a tetrahedral molecule.