Assemble 2.0 Tutorial

Brief Description | First Example | Fundamental difference between non-overlapping fragments and substructure constraints | Atom Tags | Assemble as a tool in structure elucidation | Ranking | Postprocessing

Postprocessing

Occasionally the available structural information is of very different quality. Some information, such as the number of signals in the C-13 nmr spectrum, is almost without any uncertainty. Some other information, such as the presence of a SO2 group according to the bands in the IR spectrum, are much less certain. In this situation one could run Assemble several times, trying all alternatives. However this may become cumbersome, as the execution time for each run may be substantial. A much better possibility is to give only the high-quality information in a first run, thereby naturally generating a large number of candidates. In subsequent runs the list of constitutions is further pruned by entering the weaker information, resulting in shorter execution times. Postprocessing can be nested to any depth.

As an example you may run Assemble with the molecular formula C6H10O2 as you did before. There are again 4869 structures generated. Now select the "Postprocess Output" item from the "Project" pull-down menu.



The subproject window pops up. In postprocessing you cannot change the molecular formula. Therefore the corresponding input field is not shown.



Just for curiosity you may want to find out whether there are some molecules as symmetric to produce only 2 signals in the C-13 nmr spectrum. So enter 2 in the corresponding min and max fields and start a new Assemble run. You are asked to create a new subproject. Give it a name and click into the "OK" field.



There are indeed 6 structures generated. Are you sure that the 3rd structure has 2 kinds of carbon environments? You may prefer to look at a 3-dimensional picture of the molecule. Move the mouse pointer over the structure and depress the right mouse button. Select the "Calculate 3D Coordinates" menu item.



The structure is shown in a window. Move the mouse pointer over it and keep one of the buttons depressed while moving the mouse. The structure rotates according to your mouse movements. There are indeed two carbon environments.