Electron probability density maps

Detailed calculations of cross-sections of the reaction He " + H — He" + in the range 1-8 keV are illustrated with electron probability density maps drawn for different internuclear distances in the course of a reactive collision. The transition from an essentially atomic to a molecular description, with decreasing distance, is clearly seen. " Another feature of recent theoretical work in this... 

In the Bohr model, electrons exist in specific orbits encircling the atom. In the quantum mechanical model, electrons exist in orbitals that are really probability density maps of where the electron is likely to be found. The Bohr model is inconsistent with Heisenberg s uncertainty principle. 

One of the most intriguing recent examples of disordered structure is in tomato bushy stunt virus (Harrison et ah, 1978), where at least 33 N-terminal residues from subunit types A and B, and probably an additional 50 or 60 N-terminal residues from all three subunit types (as judged from the molecular weight), project into the central cavity of the virus particle and are completely invisible in the electron density map, as is the RNA inside. Neutron scattering (Chauvin et ah, 1978) shows an inner shell of protein separated from the main coat by a 30-A shell containing mainly RNA. The most likely presumption is that the N-terminal arms interact with the RNA, probably in a quite definite local conformation, but that they are flexibly hinged and can take up many different orientations relative to the 180 subunits forming the outer shell of the virus particle. The disorder of the arms is a necessary condition for their specific interaction with the RNA, which cannot pack with the icosahedral symmetry of the protein coat subunits. 

Even when this is done, electron density maps usually show, in the regions of low density, irregularities which do not appear to have any significance they are probably due to inaccuracies in the measurement of the intensities of the reflections, or to approximations in calculation. The positions of the atomic centres, however, are not in doubt. 

A more practical representation of the electron distribution in a molecule can be obtained from the probability density contour maps. Isodensity contours in the molecular plane and in a plane parallel to the molecular plane at an altitude of 0.8 atomic unit have been calculated230 for three nucleic acid bases (adenine, thymine, and cytosine) from non-empirical wave functions. The first type of contour gives an overall picture of cr-bonding in the molecule, and the second characterizes the 77-electron density. 

In agreement with the Heisenberg uncertainty principle, the model cannot specify the detailed electron motions. Instead, the square of the wave function represents the probability distribution of the electron in that orbital. This approach allows us to picture orbitals in terms of probability distributions, or electron density maps. 

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