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

First Example

When you start up the program, the Assemble 2.0 input window appears.

This is the central part of the user interface. In the first row, on the top of the window, you enter the molecular formula. You have to do this under all circumstances. Assemble will not run without this knowledge.

To start with a simple example, enter the molecular formula C7H14O by clicking into the text field and typing the formula with the keyboard. If no further input is given, Assemble will generate all constitutional isomers corresponding to that molecular formula. Assemble knows a number of structural features that lead to molecules too strained to be stable. You can choose for each of the strained features whether you want to have it detected. From the "Edit" pulldown menu choose "Forbidden Fragments"

After releasing the mouse button, a window pops up showing the various strained features.

Click the field "Allow All" at the bottom of the window. This will switch off the strained features detector. When you click the "Apply" field, the window vanishes. To start the generator, use the "Project" pull-down menu in the main input window. Select "Calculate with BC ...".

The input to Assemble is stored on disk for later reference. Have a new project created by clicking the corresponding button. Choose or type a project name. You can reload the input later when selecting the project by name.

Assemble makes certain obvious assumptions about the valencies of the elements. Hydrogen and carbon atoms have fixed valencies 1 and 4 respectively. The valencies of hetero atoms can be changed. As you just entered a formula with an oxygen atom, you can set the valency to a value different from the default value of 2. Leave it as it is and click into the "OK" bar. After 2 seconds or so a new window will pop up displaying the first 9 structures generated out of a total of 596 isomers, as you can read in the title bar of the window.

Click into the "Next Page" and "Prev. Page" fields to look at some of the other structures.

Generating all isomers corresponding to a molecular formula is of little use. If you are in a structure elucidation process, you certainly have additional information out of various sources to restrict the number of candidate structures generated. By looking at the main input window you quickly get the idea, how to enter some of this information. For several features a minimum and maximum value can be entered.

Assume you know there is a double bond in your molecule. You may have seen its traces in the IR spectrum, or there are signals with appropriate chemical shifts in the C-13 nmr spectrum. You can enter this information by clicking into the text field corresponding to the minimum value at the "Double bonds" row and enter 1.

If you want to specify a maximum value, you can do so, but it is of no use in this example. The molecular formula you entered corresponds to a single double bond equivalent, which can be a double bond or a ring. Leaving the "max" field blank does not impose an upper limit. When you now restart the generator as shown before, you are first asked where to save the input. Choose a new project name or have the latest version of the current project overwritten.

After starting the kernel, the structures appear in a new window. All of the 294 structures generated have a double bond, as you requested.

The multiplicity of the signals in the off-resonance C-13 nmr spectrum yield information on the number of hydrogens immediately bonded to a carbon atom. In addition the hybridization of the atom may be derived from the chemical shift of the signal. Similarly you may know how many OH groups there are in the molecule, by interpreting the integral of their signal in the H-1 nmr spectrum. This kind of information is most easily entered as atom constraints. There is a text field titled "Atoms:" devoted to them. When you click into the field with the right mouse button, a pop-up menu appears. Select the "Add New Atom" line.

A new input window appears, where you can specify the element, the number of hydrogen atoms immediately bonded, the hybridization, and the minimum and maximum number of such atoms in the molecule.

Pressing the "Add" button will add a line in the main input window, in the "Atoms" field. As an example, request the presence of an OH group. You enter the element symbol "O" in the first field, the number of hydrogens is 1, leave blank the hybridization field (or clear it, if there is already an entry), then enter the minimum value 1. Omit the maximum. When you click the "Add" button, you will see a new line in the "Atoms:" text field.

Start the generator and see that 149 structures are generated. Each of them has an OH group and a double bond.

When you know about the presence of larger fragments, you cannot enter them as atom constraints. Assume you know that there is an ethyl group present in the molecule. The large field in the bottom part of the main input window is devoted to larger fragments. Click into the field with the right mouse button. A pop-up menu appears. Select the line "Draw New Fragment".

Drawing substructures with the JUME editor is straightforward. You best learn how to do it by practicing. Have a look at the help text by clicking the question mark in the toolbar. For the moment just follow these steps. Click into the appropriate fields on the left side of the window to reproduce the selections as shown in this picture.

With the left mouse button click into the editor field. A methane molecule is formed. You see the following picture:

Whenever you make a mistake, you can reverse the latest few actions by clicking the "undo" button in the toolbar (fourth from left) once or several times. You can have a look at the meaning of the toolbar symbols by moving the mouse pointer over a symbol without depressing a button. A text field appears below the symbol.

To continue drawing, move the mouse pointer over the CH4 group until it changes from black to white. Then depress the left mouse button and keep it down. A yellow circle around the carbon atom appears:

Move the mouse pointer to the right, keeping it depressed. A blue line appears, connecting the start point of the move with the current mouse pointer position.

After crossing the circle, release the mouse button. An ethane molecule has formed:

When you look at the "Atoms" field to the left of the drawing area you see the carbon atom highlighted. Change this by clicking into the "R" field. R means free valence. JUME handles it exactly the same way as an atom. Move the mouse pointer over the right methyl group so it turns white. Depress the left mouse button and move it to the right, as you did before. After releasing the mouse button the ethyl fragment is finally formed.

To move the fragment to the main input window of Assemble, move the mouse pointer into the drawing area and depress the right mouse button. A menu pops up. Select the line "Add to Assemble Fragments".

Release the mouse button. The fragment appears now in the "Fragments:" field of the main input window.

Ignore the "min", "max", and "overlapping" fields for the moment. You will learn about their meaning later. Start the generator. A total of 80 structures is generated from which the first 9 are shown as the window pops up. They combine the requested structural features, ethyl group, OH group, and double bond.

When you briefly look at the structures, you find some that are chemically unstable. The enole group would tautomerize to the corresponding carbonyl form. As there are too many structures generated to be handled individually, you may want to eliminate the enoles. You can do this by forbidding the group. First draw the enole as a substructure in JUME. Clear the old input by clicking the delete symbol in the toolbar (third from left).

Start over by selecting the carbon element symbol in the "Atoms" field. Repeat the drawing steps as in the example before until you reach the ethane molecule. You can change the bond type between the carbon atoms by clicking the bond with the left mouse button. It turns into a double bond while the number of hydrogen atoms is adjusted appropriately. By clicking repeatedly you can circle through the sequence single, double, triple, unspecified. After forming a double bond you get the ethene molecule. To add the OH group, first select the oxygen element symbol in the "Atoms" field. Click onto the right carbon atom and move the mouse pointer to the right. After releasing the mouse button, an OH group is formed.

The hydrogen atoms must now be replaced by free valences except for the hydrogen of the OH group. Select the R symbol in the "Atoms" field. Replace all the hydrogens by free valences. The final result may look like this:

Move the substructure to the Assemble input window as you did before. Click into the drawing field with the right mouse button and select "Add To Assemble Fragments" from the pop-up menu.

As the substructure is not completely visible, drag down the scroll bar of the window or resize the Assemble input window. You want to forbid the substructure. You learn about the difference of non-overlapping fragments and potentially overlapping substructure constraints later. Tick the box "overlapping" and change the minimum and maximum from 1 to 0 with mouse and keyboard.

After starting the generator, you see that 54 structures are generated, still not really manageable.

A number of phenomena cause the nmr chemical shifts of two or more atoms to coincide. Among the phenomena is symmetry within the molecule. Assemble can predict the number of signals observed in the broadband-decoupled C-13 nmr spectrum by exploring the topological symmetry of the molecule. As topological symmetry considerations are not sufficient to predict the number of signals exactly, the feature is tricky. Use it with care. You needn't specify exact numbers, you can give a range. This allows a certain conservatism. Assume there is some symmetry in the molecule giving rise to 6 signals in the spectrum. Therefore, from the 7 carbon atoms in the molecular formula, 2 have the same chemical shift. You can enter this information in the main input window. At the bottom of the list of features for which you can specify upper and lower limits you find an entry "C13-NMR Signals". Set both minimum and maximum to 6 and start the generator. You find only 2 structures generated.

You now reached the point where you don't need any more computational aid. You look at the structures and decide.