You can alternately process the coordinates with a tool such as Matlab/Octave: data=[-2.1849 -1.2310 -0.2189 16 0 0 0 0 0 0 0 0 0 0 0 0 The computed distance (not clearly visible in the figure) is $\pu$ The results are 5.42 Å along the x-axis, 5.20 Å along the y-axis, and 0.07 Å along the z-axis.Īnother nice free (but limited in function) tool for this job is NIH PubChem's viewer: VMD will give you the atom-to-atom size along the x, y, and z axis using the following commands: mol new tropolone.mol2 Note that these distances are in angstroms (Å). You can measure distances between pairs of atoms by hitting the "2" key and clicking atoms. mol file natively, but VMD will not, so you can use OpenBabel to convert the. There are many tutorials for using these programs. They are open source and completely free (Avogadro is GPL'd) or free for educational use (VMD, PyMol). Conformers can also be downloaded in different formats from PubChem (maintained by the US National Institutes of Health), which offers many of the same features as ChemSpider.Ĭommonly used standalone programs for visualizing molecular structures are the programs VMD, PyMol, and Avogadro. mol file from ChemSpider by clicking the disk icon below the 3D image. More complex ways of characterizing the size would be better done in a dedicated program. This is only one way to characterize the size. Hydrogen has a radius of 0.11 nm, so the total distance would be 0.558 nm plus the van der Waals radius of the two hydrogen atoms, which would be 0.778 nm. The atoms themselves have size owing to their electron clouds, so a better measure of the size of the molecule could include the van der Waals radius of the atoms, which you can find a value for on the Wikipedia page. The largest distance appears to be 0.588 nm. By moving the mouse to the other atoms, you can see their distances. To get the largest atom-to-atom distance, I've selected the hydroxyl hydrogen. In the JSMol window, you can select an atom by double clicking it. Select the 3D representation by hitting the 3D button. A quick way to do this would be to enter the molecule in name in the search form on ChemSpider (maintained by the UK Royal Society of Chemistry).
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