This suggests that the optimal structure for C4H4 is not D4h. Notice the regions of extra electron density. It has good molecular superposition and surface and electrostatic display. Electron density doesn't always tell the whole story Examine the electrostatic potential surface. However more recent packages will do things that Jmol cant and produce a.Steric strain vs electrostatic attraction.
The plots were generated by Jmol embedded in APBS. (a) Electrostatic potential of chain A of 2min, (b) Electrostatic potential of chain B of 2min, (c) Electrostatic potential of chains A and B of 2min.
The default surface is a solvent accessible surface, which is slightly larger than the van der Waals surface.Ī static and interactive version of the Avogadro and Jmol electrostatic potential map, respectively, can be found here. Isosurface solvent color range -0.05 0.05 map mepĪnd this set of commands can thus be used to control the color range and the nature of the surface. The electrostatic potential option in the Jmol menu corresponds to the following set of commands (as far as I can determine): Jmol is not able to determine the charges, but the information can be transferred from Avogadro by saving a mol2 file. It is currently not possible to alter the color range as far as I can see.
#ELECTROSTATIC SURFACE JMOL ISO#
An Iso Value of 0 seems to correspond to the van der Waals sphere surface. It is possible to change the surface using the so-called "Iso Value" but I could not find any documentation on how that actually works.
#ELECTROSTATIC SURFACE JMOL HOW TO#
The screencast above shows how to make such electrostatic potential maps using Avogadro and Jmol.Īvogadro uses an empirical method to determine the atomic charges (an integral part of the MMFF force field). Similarly, the electrostatic potential due to atomic charges can be a reasonable substitute for the electrostatic potential due to the electronic density. Previous posts ( such as this one) have demonstrated that the van der Waals surface is a reasonable substitute for the 0.002 isodensity surface. In a previous post I showed how to compute an electrostatic potential map superimposed on the 0.002 isodensity surface of a molecule based on data computed using quantum chemical methods such as RHF/6-31G(d).
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