Change all of the ring bonds to double bonds, and press enter. Just for kicks, let’s generate a nonsense structure. This should generate the other Kekulé structure for benzoic acid in both the 3D and 2D windows. (That is, switch the 1’s for 2’s and the 2’s for 1’s in the bond type fields (third column) of the bond table entries for the six ring bonds.) With the cursor still in the text window, press enter. Once you have identified the six ring bonds in the MOL file, manually adjust them to generate the other Kekulé structure of the ring. (You can check yourself by hovering over atoms in the 3D window or clicking the “labels” link above this window.) (These will vary depending on the way that you drew the molecule – the 2D sketch application numbers atoms and bonds in the order that they are drawn.) Remember, the first two columns in each bond table entry refer to rows in the atom table, and the third column gives the bond type (1=single, 2=double, etc.) connecting these two atoms. Identify the atoms and bonds that make up the ring. (See discussion of explicit and implicit H earlier in this module for more information.) You will note that, as a default, Hack-a-Mol includes explicit H in the MOL files it generates. Now, take a look at the MOL file in the text window. (For details on how where this data comes from, see “2D to 3D” and “3D to structure data” sections in “How it Works.”) That should render a 3D structure in the window to the right and generate a MOL file in the text window below. Clear the 2D sketch window using the white box button at the top, second from the left, and then draw benzoic acid. MOL/SDF XYZ PDB CIF Modify the data and press ENTER to see changes above. Think of the following examples, and the exercises that follow, as training in the sort of questions that you would be prudent to ask when it comes to working with digital data about chemical structures. However, it also means that there are ample opportunities for developing clever cheminformatic solutions to the limitations of connection tables.įew of these issues are likely to be solved completely. This can make things tricky for those who want to manipulate chemical structure data across the tens of millions of known chemical compounds (and the limitless space of possible compounds). Other times, different file formats (or different users of the same file format) will adopt different conventions for indicating them. Sometimes these phenomena are not (or even cannot be) represented in the connection table at all.
Working with connection tables can become tricky when it comes to features of chemical identity that are not directly represented as a static collection of atoms and covalent bonds, such as: If all explicit hydrogen was included in this connection table, there would be six more entries in the atoms and bonds blocks, and the counts line would show fifteen atoms and fifteen bonds. Note that benzoic acid has nine atoms and nine bonds, not counting hydrogen.
The following figures illustrate the anatomy of a MOL file (MOL v2000, to be specific): the counts line, the atoms block, the bonds block, and the properties block. Here is a MOL file for benzoic acid, generated by ChemDraw, which provides options to save or to copy sketches in this file format. The MOL file, a widely-used chemical structure file format, contains all of these.
Attributes associated with an entire structure (e.g.R/S configuration of a stereocenter dashed/wedged bond Attributes associated with atoms or bonds (e.g.Counts of the number of atoms and bonds in the molecule.2D or 3D spatial coordinates for each atom (sometimes measured, sometimes calculated often, it’s not clear which).A list of bonds, specifying the atoms that it connects and the bond multiplicity (single, double, triple).A list of atoms, specifying the elemental identity of each atom.Most connection table formats contain one or more of the following:
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