It looks like you need to put the black background behind it. You can do that either by drawing a square or rectangle with the Rectangle tool; or draw it with the Pen/Bezier tool.
With the Pen/Bezier tool:
-- click once to start the path
-- move the mouse to the next corner (if you hold the Ctrl key, the mouse movement will be restricted to horizontal or vertical movement)
-- click once to place a new node
-- moving on, place a new node at the next corner
-- finally, place the mouse inside the tiny square which you can see at the beginning of the path, and click once (to close and end the path)
-- click on the black chip in the palette to fill it with black
-- Object menu > Lower to Bottom, or switch to Selection tool, and this button on the control bar
But before you do that, you probably should deal with making the....I guess they are the bonds?....white.
-- with the Node tool, select 2 opposing paths
-- drag a selection box around the 2 end nodes, at either the left or right, or top or bottom, of the bond
-- click "Join selected nodes with a new segment" button on the control bar, looks like this
-- repeat for the other end
-- click the white chip in the palette, to color it white
-- Object menu > Lower to bottom (if necessary) or switch to the Selection tool and click this button on the control bar
-- repeat for all the bonds
Note that there are a few ways to approach this, and others may have better or faster techniques.
