Molecular modeling is a constantly growing field of theoretical chemistry and in general should be left to the Pros! However, ChemPup does have the ability to do some basic molecular modeling which serves as an excellent resource for chemistry students of all levels.
For the beginner, simple models can be built, viewed and minimized easily with the Avogadro molecular builder. The student will readily be able to see steric interactions using a built-in force-field minimizer (Ghemical, MMFF, etc) with a "steepest decent" algorithm.
For the more advanced user, Avogadro and JMol both readily generate Gaussian input files (.gjf, .com) which may be very useful to those that have access to the Gaussian Suite of Programs.
Registered users of ChemToolBox.com also have access to a download repository which currently has dozens of hard to get fullerene coordinates (.pdb format) and a ready to view (.xyz format) cyclacene. PDB files may be converted to .xyz files using the following steps:
1. download the .pdf file, open it with a "text editor" and enter a space after each atom symbol (i.e. C, H, N, O, S, etc)
2. copy the contents to A1 in a spreadsheet (merge delimiters: tab, space)
3. omit rows 1 and 2 as well as columns D, E, F
4. copy columns C, D, E, F to a text editor
5. enter the total number of atoms at the top followed by an empty line and the coordinates and save as filename.xyz
6. open file with JMol or Avogadro
Please consider uploading your converted .xyz files back to the ChemToolBox.com repository for others to use!
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