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Unformatted text preview: ry I and II Lab Manual Now, I am very comfortable with this shorthand notation since I have been through organic
chemistry, but maybe you are not. If you want to change the way the program displays our
molecule, simply go to “display” and choose “rendering…”. I recommend “balls and cylinders”
which will make the molecule look like it would if you built it out of small plastic balls (like
when I was taking chemistry). Dakota State University Page 31 of 232 Using HyperChem General Chemistry I and II Lab Manual If you are following along on these instructions, I recommend now that you choose some of the
other tools (begin with rotate in 3D, then rotate in the plane and translate) to see what these do.
For example, choose “rotate in 3D”, click and hold the molecule while moving the stylus and
you will see it rotate as you do in any direction you like.
Now, obviously, this technique is suitable only for very simple molecules. If you have a
much more complicated molecule, such as DNA, RNA, proteins or crystals, Hyper Chem comes
with some very powerful tools built into the program to help you with these. They are found
under “Databases”. We will not cover these here because you probably will not need them for
this course, however, I invite you to play with them. You will find they are fairly selfexplanatory; it is a very simple thing to very quickly build a double-stranded DNA of any
sequence that you choose.
Introduction to Hyper Chem calculations
Hyper Chem calculations are basically broken up into three basic steps; (1) define the
calculation, (2) run the calculation, and (3) display the results. We will not go into this in great
detail here as there are a LOT of possible calculations (an exceptionally impressive amount) that
come with this package. However, we’ll run through one simple one so you can see the theory;
molecular dynamics. Molecular dynamics (or MD) simulates the motions of molecules by taking
into account attraction and repulsion of every atom in the system with every other atom. While it
must be remembered that these calculations are only as good as the programmers who developed
Dakota State University Page 32 of 232 Using HyperChem General Chemistry I and II Lab Manual them, through the years they have become so accurate at reproducing experimental outcomes that
some scientists today consider MD calculations to be legitimate experimental result in and of
themselves (I disagree with this philosophy as I recognize that there will always be factors that
we, as human beings, will simply not recognize, regardless of how accurate we try to get the
To run MD simulations on isopropanal, begin by going to “set-up”, and choosing
“Molecular Mechanics…”. Once in there, select one of the options (I usually choose AMBER,
since I am familiar with this potential function). There are two basic ways to run MD calculations, “In Vacuo” (as I’m sure you guessed, Latin for
“In a Vacuum”), or in water. If you want to add water, under “Set Up” choose “p...
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