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Undo
Undo the last action. Can be performed multiple times.
Redo
Redo the last action that was undone. Can be performed multiple times.
Lasso
Select atoms by drawing around them (“lassoing”). The selected atoms can be moved, rotated,
deleted, copied.
Move
Move (translate) the selected atoms or the entire structure. Drag in the drawing area to move
the structure. Drag the selection to move the selected atoms. (This is the default action for
dragging a selection, so you do not need to click this button before dragging it.) You can also
move the structure by dragging with the right mouse button.
Rotate
Rotate the selected atoms or the entire structure. Drag in the drawing area to rotate the struc-
ture. The angle through which the structure has been rotated is displayed near the center of
rotation while you are rotating it. If rotation does not seem to be working properly, check
whether you have other structures in the drawing area that are not visible. You can also rotate
the structure by dragging with the middle mouse button.
Cleanup
Clean up the structure (2D coordinates) and normalize orientation and arrangement of groups.
If you have atoms selected, only those atoms are cleaned up.
Draw
Draw a single bond. Click on an atom to draw a bond to a new (carbon) atom, click on a bond
to add another bond between two atoms.
Erase
Delete atoms or bonds. Clicking on a carbon atom deletes it; clicking on a non-carbon atom
changes it back to carbon, then clicking again deletes it. Clicking on a bond removes one
bond.
Wedge Bond
Draw a wedge bond. Clicking on an atom draws a wedge bond to a new (carbon) atom; click-
ing on a single bond converts it to a wedge bond.
Dashed Bond
Draw a dashed bond. Clicking on an atom draws a dashed bond to a new (carbon) atom; click-
ing on a single bond converts it to a dashed bond.
Increase Charge
Increase the formal charge on an atom by 1.
Decrease Charge
Decrease the formal charge on an atom by 1.
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5.5.3
Sketching Molecules
To start drawing, click the
Draw
button.
Drawing creates a carbon-atom framework. You can change the element with the element
buttons, either during drawing or after you have finished drawing, or by typing the element
symbol while the pointer is over an atom.
The first atom is placed by clicking in the drawing area. It is shown as CH
4
. After placing the
first atom, you can draw in several ways:
• Click on an atom to place a new atom and draw a bond to it from the clicked atom. The
bond is placed in a default orientation with respect to existing bonds.
• Drag from an atom in a particular direction, to place a new atom and draw a bond from
the clicked atom to the new atom in the chosen direction.
• Drag from an atom to another atom to create a bond between the two atoms.
• Hold down shift and drag from an atom to add a linear chain to that atom.
• Click on a bond to increase its bond order.
The “active” atom—the one to which a new bond will be attached—is indicated by a gray
filled circle. Likewise, the active bond is indicated by a thicker gray line. The active atom or
bond changes as you move the pointer over the atoms or bonds.
You can also start your drawing with a ring: click on the ring in the toolbar then click in the
drawing area to place the ring.
To draw bonds with a given stereochemistry, click the
Wedge Bond
or
Dashed Bond
button,
and draw in the drawing area. Clicking on a bond changes its stereochemistry; clicking on an
atom adds a new atom with the selected orientation.
To add rings to your system, click on one of the ring buttons, then click in the drawing area.
When you move the pointer into the drawing area, the ring is shown in blue. As you move the
pointer in the drawing area, the ring “snaps” to positions that show a potential attachment of
the ring to the structure. Clicking when the ring is in one of these positions places the ring at
that position, and its color changes to black. You can do the same with the fragments on the
User-defined fragments
toolbar.
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To add a functional group, pause the pointer over the atom you want to add the group to, then
type – followed by its name, and press
ENTER
, e.g. -et to add an ethyl group. Many common
functional groups are recognized: the list is given in
Table 5.1
with the corresponding
SMARTS patterns; the names are case-insensitive. You can also replace an atom with a func-
tional group, by omitting the initial –.
To change the element, you can do one of the following:
• Pause the pointer over the atom, then type the element symbol.
• Click the button for the desired element on the toolbar, then click an atom in the structure.
• Type the element symbol, then click an atom in the structure.
The last two of these choices allow you to click on multiple atoms to change the element; the
first operates only on the active atom.
To assign a formal charge, click the
Increase Charge
button or the
Decrease Charge
button,
then click on an atom. The formal charge is given next to the atom, and any hydrogens are also
shown that are needed to complete the valence for the atom; or a red underline is shown to indi-
cate that the valence is not satisfied. You can also pause the pointer over an atom and type in
the formal charge. Any combination of numbers, +, and – is accepted.
Table 5.1. Functional group names and SMARTS patterns for use in editing 2D structures.
Name
SMARTS
Name
SMARTS
Name
SMARTS
me C
ph C(C=C1)=C-C=C1
coo-
C(=O)[O-]
et CC
bz CC(C=C1)=C-C=C1
no2
[N+](=O)[O-]
pr CCC
chex
C(CC1)CCC1
so2
S(=O)=O
ipr C(C)C
cp C(C=C1)C=C1
so2n
S(=O)(=O)N
nbu CCCC
ome OC
so3 S(=O)(=O)[O-]
ibu CC(C)C
oet OCC
po3 P(=O)([O-])[O-]
sbu C(C)CC
cooh
C(=O)O
con C(=O)N
tbu C(C)(C)C
coome
C(=O)OC
nco NC=O
nhex CCCCCC
cooet C(=O)OCC
cn
C#N