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In a simulation, the potential energy of an atom, , is given by [3] = (()) + (), where is the distance between atoms and , is a pair-wise potential function, is the contribution to the electron charge density from atom of type at the location of atom , and is an embedding function that represents the energy required to place atom of type into the electron cloud.
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 ...
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Electron clouds are created when accelerated charged particles disturb stray electrons already floating in the tube, and bounce or slingshot the electrons into the wall. . These stray electrons can be photo-electrons from synchrotron radiation or electrons from ionized gas molecu
The Rutherford model is a name for the first model of an atom with a compact nucleus. The concept arose from Ernest Rutherford discovery of the nucleus. Rutherford directed the Geiger–Marsden experiment in 1909, which showed much more alpha particle recoil than J. J. Thomson 's plum pudding model of the atom could explain.
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In contrast to the Bohr model of chemical bonding, it turned out that the electron cloud mainly concentrates on the line between the nuclei, providing a Coulomb attraction between them. For many-electron atoms, the valence bond theory, laid down in 1927 by Walter Heitler and Fritz London, was a successful approximation.
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