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Tutorial 01 -- Creating Structures


   There are usually several ways to create a given structure using MSC.  The following represents only one possible approach.  


1  To begin, make certain that you are in DRAW mode -- the 'Draw' option button should be selected near the bottom of the palette on the left of the screen, and the Draw state should be indicated at the top to the right of the toolbar.

2  Single bond is selected by default at start up.  Select benzene by clicking on the top middle image on the structure palette.  This ring is in the second column of  the first row [R1,C2].  

3  Move the mouse pointer into the drawing region and then press and hold the left mouse button.  While continuing to hold the mouse button down, move the pointer around the screen.  An outline of the ring will track the pointer as you move it.  When you have the structure located where you want (roughly centered on the screen in this case), release the mouse button and the ring will be drawn at that point.

Note:  the current elemental composition and molecular weight will be updated on the bottom of the screen.  In this case, C6H6 and MW=78.  As the structure is changed, these displays will be continuously updated.

4  Now select the cyclopentane ring with the vertex facing down [R2,C3] on the palette.  Again move the mouse pointer into the drawing region and then press and hold the mouse button.  Move the ring to a position parallel to and about 2 cm to the right of the benzene ring and release the button.  The cyclopentane ring will automatically move and merge with its nearest atomic neighbors in the benzene ring.  This is the default behavior and will always occur unless you force the addition of a separate ring as described below.

5  For the nicotine structure, we want two separate rings.  Undo the last change by clicking on the blue Undo button on the Toolbar. 

6  After Undoing the merged rings structure, press and hold the left mouse button, move the cyclopentane ring into position about 1 cm to the right and about 1 cm above the benzene ring, then depress and hold the <Shift> key while releasing the mouse button.  If the <Shift> key is depressed when the mouse button is released, then the object being added will be drawn at its current location as a separate structure, and will not be merged with the remainder of the molecule.

7   Now select the single bond object ( / ) from the palette [R3, C1], move the mouse pointer over the upper right vertex of the benzene ring, press and hold the left mouse button, and draw a line extending to the lower left vertex of the cyclopentane ring.  If you first click on Edit | Number Atoms, the structure's atoms will be labeled and the two atoms that you want to connect are numbers 6 and 8.  When you release the button, a bond will be formed and the valence H will be corrected as needed.   

You can view valence H on ring carbons at any time by selecting  the 'Show All Atoms' from the Options menu, or from the Popup menu.   In this case,  all implicit ring carbons with their valence hydrogens will be displayed. The default in MSC is to omit ring carbons from the display, although heteroatoms are always displayed as are acyclic carbons unless you check the Implicit Carbons option in the Preferences menu.  To revert to the default format, click on 'Show All Atoms' again to turn it off. 

8    Another way to link two rings is to add the bond first.  Click Undo three times as needed to revert to the original benzene structure.  Select the bond tool and add a methyl group to the #6 carbon in the benzene ring.  Now select the cyclopentane ring again and merge it into the methyl group.

9  Select (click on) the N atom object from the atom palette.  Move the pointer over the bottom carbon of the benzene ring and click the left mouse button.  The carbon will be replaced with a N, converting the benzene to a pyridine ring.  As a heteroatom, the N will be displayed regardless of the state of Show/Hide.  Move the pointer over the bottom vertex of the cyclopentane ring and add another N.

Elements can be replaced at any time by selecting a new element and clicking on the atom to be replaced.  If a replacement would violate valence restrictions, then MSC will abort the change, although you can override this by using the Valence option.

10  To complete the structure, select the single bond again and click on the pyrrolidine nitrogen.  You should now have the structure of nicotine, C10 H14 N2, MW = 162.  Save this structure by clicking on the disc icon on the toolbar.

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