Draw and Edit Reaction Mechanisms with ChemSketch

Stuart Berry  00:00

To start with this partially drawn reaction mechanism that I’ve got here. So as I mentioned, in terms of reaction mechanisms, I’m going to cover how we can add things like our lone pair of electrons, and that’s the first thing I’m going to do here.

Stuart Berry  00:15

So we want to add a lone pair of this nitrogen atom here. And the way to do that is to go to this atom, chemical properties button on the left hand toolbar, I can select the button and then select my nitrogen. This would actually allow me to edit the valence of my atom if I wanted to. I could change the isotope as well if I wanted to. And in this case, I can also edit the charge, and that’s actually going to allow me to display my my lone pairs. So in this case, I have, I can display the lone pair either horizontally or, sorry, horizontally or vertically, depending on how I want it displayed. So if I select the horizontal lone pair there, I can press OK, and then you can see that my lone pair is attached to my nitrogen.

Stuart Berry  01:02

Now, the next thing that I want to do for this reaction mechanism is to add some curly arrows. And you can see I’ve already got some here. To do that, I’m going to switch to draw mode. So structure to draw mode, and the tool we want to use is this arc functionality here. If you click the little white triangle just to the right, lower right corner of the arc, and that will allow us to actually select the degree of curvature that we’re looking at. So either 120, 180, 270… it can be a little bit trial and error. If you want to get the correct curve. I’m going to start in this case with the 120 and if we want to add an arrow onto the end of our curve, we also need to select the arrow functionality. So now you can see I’ve got selected my arrow and my curve functionality, and you’ll see that my cursor has changed to this plus sign here. So what I can do is I can hover my cursor in the middle of my lone pair, and then I’m just going to click, and then that’s going to allow me to draw my curve, either curving up or underneath, depending on how I want it to draw. So I’m actually I’m just going to undo that, and I’m just going to go back up the other way so it curves around the correct way. And I’m just going to draw that up to my water molecule there. And then if I wanted to add another, more, deeper curve, I could change the arc functionality, and then I could just draw that second, that second curly arrow in there. So that’s the way to add curly arrows.

Stuart Berry  02:41

It’s really about selecting the degree of curvature on your arc and making sure that you’ve got this arrow functionality selected. And then that will allow you to draw those, to draw those arrows in. And also you need to make sure that you’re in draw mode for that.

Stuart Berry  02:54

If I wanted to add a reaction arrow so different from a straight arrow, curly arrow, and this will actually be seen elsewhere in our software as a reaction. What I would need to do is I would need to select the reaction arrow button, which is this one here. I’m just going to change this to a standard straight arrow. And what I can do is now I can select my arrow, and I can actually just click and drag to draw that in place. So click and drag, and you’ll see, if I do that, you’ll see that I could actually point this arrow in any direction to get my arrow to be defined nicely horizontally. I can actually hold down the Shift key on my keyboard, and you can see now that there is actually a snap to functionality. So it is snapping to the horizontal, it is also snapping to the vertical. So this means that you’ll always get nice, horizontally or vertically defined arrows, and it will snap to it diagonals as well. So that’s what we want in terms of drawing our arrows.

Stuart Berry  03:53

And so if you need to line them up, use the Shift key to draw, and then you can just release and draw. I’m now going to add an equilibrium error as well. And again, I can do the same thing. So click and drag to define the length, hold the Shift key to find the horizontal or the vertical. And so I can add my equilibrium error in there.

Stuart Berry  04:14

If I wanted to line all of my curly error, sorry, all of my reaction errors up. And this goes for the same for aligning anything up in the software. In ChemSketch, I can hold down the shift key and select the elements that I want to align. Switch to draw mode, and all of my alignment options are available here. So if I wanted to, I could align them all to the left. I’m just going to press Undo. If I want to align them all horizontally, I would select the horizontal sorry, the vertically alignment tool, and that’s going to line them up nicely so they’re more nicely, nicely ready for in our reaction scheme.

Stuart Berry  04:53

The last thing we might want to do in terms of this reaction scheme is we may want to define the drawing style so I’m going to show you how to do that as well. So I’m going to use my Lasso Tool to select the entire reaction. So just drag all the way around that. I’m then going to right click on a on a structure and select Object properties. And now what we can see here is we have the tools to actually change the properties of our of our drawings. So here I could, for example, increase the bond length in terms of the width that it was drawn out. I can bold that. I’ve also got separate options for my single, my double, my single, my, my single bonds. I can change the way that I want atoms to be displayed. So whether I want charges, for example, to be displayed, I can also change the color of any atom and any bond.

Stuart Berry  05:50

But what we also have available is we have some predefined templates that match journal drawing styles. So for example, if I wanted to set this into ACS style, I could simply select the ACS style there and press Apply, and then that would automatically define my reaction scheme based on based on that style. If I wanted to change that, I could change it to something else. For example, I could change it to RSC, and again, press apply. And what you can also do is you can set your style, or your preferred style as the default style if you wanted to continue using that every time if you make any custom changes to these so for example, if you want to have, for example, the valence of your atom displayed, you will press Show there. And if you press Save, you can then save that into your style. So that will be how you would do that.