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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 ...
However, the three hydrogen atoms are repelled by the electron lone pair in a way that the geometry is distorted to a trigonal pyramid (regular 3-sided pyramid) with bond angles of 107°. In contrast, boron trifluoride is flat, adopting a trigonal planar geometry because the boron does not have a lone pair of electrons.
Monte Carlo N-Particle Transport (MCNP) [2] is a general-purpose, continuous-energy, generalized-geometry, time-dependent, Monte Carlo radiation transport code designed to track many particle types over broad ranges of energies and is developed by Los Alamos National Laboratory.
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]
In chemistry, trigonal planar is a molecular geometry model with one atom at the center and three atoms at the corners of an equilateral triangle, called peripheral atoms, all in one plane. [1] In an ideal trigonal planar species, all three ligands are identical and all bond angles are 120°. Such species belong to the point group D 3h.
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.
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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).