---------- Forwarded message ---------From: Bailey Qin . . .
Date: Fri, Jan 23, 2015 at 4:06 PM
Subject: Re: Rotations and Vibrations
To: paul matsumoto <psmatsu@gmail.com>
Hi Matsumoto,
I've never used odyssey before but hopefully I can be of some help deciphering this.
1.I believe from the first one, he doesn't really know what you mean by "internal energy" so he just told you
what total energy is equal to.
2. I think very simply, he is just saying that you can call any point in energy "zero". A value being "positive"
or "negative" is simply saying it is bigger or smaller than the "zero" that you picked. He is saying that the
value of energy is kind of meaningless. It is only when you take differences between energies that they become
meaningful.
An example of this is in physics, when you use conservation of energy. with a ball dropping from some height
KE1 + mgh1 = KE2 +mgh2
now drawing a picture out.
------------- O
<- ball
---------------
some time passes
and ball drops
--------------
--------------- O <- ball
where you call "zero" potential energy is arbitrary. (ie. you can call either the when the ball is at the top
mgh=0 or when the ball is on the bottom mgh=0 or even somewhere in between it doesn't matter. What
matters is that the difference in the two mgh will account for the ball's velocity at the end.)
Again, to recap, what you call "zero" potential energy is arbitrary, so saying that a value is "positive" or
"negative" has no significance. What is important are the relative energies (ie. the difference in energy between
things).
Attached is a picture incase the email messes up my format and what i drew doesn't look like what it does on
my screen.
I hope that helps,
Bailey
On Fri, Jan 23, 2015 at 11:42 AM, paul matsumoto <psmatsu@gmail.com> wrote:
Bailey & Bryan,
Wondering if your students are using Odyssey, a chemistry visualization simulation software, based activity
about molecular rotation & vibration ? While the activity's focus is not on the concept of internal energy, based
on my understanding of the concept, this activity would be of relevance. I developed a thermodynamics
(http://chem-is-try.us/class/ap/supplement/odyssey_v5/thermo/internal-energy.odylab) activity and am
wondering if you can check / explain stuff to me - see below colored text / content. If you have access to the
software, you could see the actual activity.
Thank you.
Context: trying to develop a thermodynamics assignment about internal energy, then later, about the 1st law of
thermodynamics, where envision simulating changes in (i) q by changing the system's temperature and (ii) w by
changing the system's volume. Don't know if the 1st law assignment would work, but want to establish internal
energy assignment before working on 1st law of thermo assignment.
---------- Forwarded message ---------From: Jurgen Schnitker <jurgen@wavefun.com>
Date: Thu, Jan 22, 2015 at 12:17 PM
Subject: Rotations and Vibrations
To: paul matsumoto <psmatsu@gmail.com>
Cc: Sean Ohlinger <sean@wavefun.com>, Tyler Netherton <tyler@wavefun.com>
Hi Paul,
> thermal energy (in text panel) = kinetic energy (molar; from properties panel) = energy due to
translational, rotational, & vibrational motion
> trans kin energy (molar; from properties panel) = energy due to translational motion only
Yes
> total energy (from properties panel) = internal energy
Total Energy = Kinetic energy (all terms) + Intramolecular Potential Energy (flexible only) +
Intermolecular Potential Energy (all systems)
is that person's response saying that I'm correct ?
> 3 trans = motion along x-, y-, & z- axis ?
Yes.
> 3 rotat = rotation, where (i) S follows a circular path / clockwise; S follows a cicrcule path / counter
clockwise; F rotate, while S is stationary ?
Rotation around the three principal axes of the moment of inertia tensor. Your description sounds right for a
bent and fully symmetric object.
> 3 vibr = single S - F bond vibrate; other single S - F bond vibrate; both S - F bonds vibrate ?
It's just like the normal modes of water--symmetric stretch, asymmetric stretch, and bending.
> In regards to Kr, Cl2(rigid), & SF2(rigid), why is the potential energy (molar; in the properties panel) a
(small) negative value ?
The fact that the Kr (g) potential energy is slightly negative is physically correct. The description is at the
Lennard-Jones potential level (*not* an ideal gas). There are minor attractive interactions for particles that are
sufficiently close (and at a sufficiently high density things condense, don't they!?!).
Potential energy of the other 5 systems in this lab, and incidentally most other *condensed (!) phase* models in
Odyssey: The numbers are difficult to interpret in that the zero of energy is different from model to model. The
default force field in Odyssey is MMFF ( = Merck Molecular Force Field, although we are not allowed to call it
that way). MMFF was parametrized for the *conformational* degrees of freedom of a large number of
primarily organic molecules, i.e., for something intra(!)molecular. Condensed phase properties didn't enter into
the picture, and the zero of energy was basically of no interest to Tom Halgren at Merck who did the
parametrization. Maybe you didn't explicitly notice it, but the potential energy is usually *hidden* in the
Properties table. You have to go to EXPERT mode to get access to it--I guess you now understand why this is
the case. Again, it's the *zero of energy* that is "wrong" (or rather arbitrary), not the relative change of the
energy with the conditions. The latter is not necessarily great, but as good as you can expect from a general
purpose program. (Even now Odyssey is still the only program in the world that will easily simulate everything
from hydrogen to DNA and do this from a unified perspective!)
"translate" the entire preceding response; i.e. what's potential energy ? simplistically, thought it was related to
the interactions among the parts of the atom, e.g. electrostatic force between electron & protons & strong
nuclear force between the proton & neutron.
More on the potential energy
For a few hundred models in Odyssey (only prebuilt ones, nothing that you build yourself with the builder), we
have either extended the MMFF force field with custom parameters or replaced it by something entirely
different so as to get the potential energy right even in the absolute sense. For those systems the potential energy
is available even without going to EXPERT. For example, the potential energy of NaCl and elemental copper is
very close to the experimental value.
> why is the potential energy of the flexible molecule greater than the rigid molecule ?
The rigid molecule is forced to be at the minimum energy of the springs. Most of the flexible molecules will be
away from the minimum, the spring energy drives up the potential energy.
I'll respond to your "editing files" e-mail shortly--thank you for your patience.
Jurgen
From: paul matsumoto [mailto:psmatsu@gmail.com]
Sent: Wednesday, January 21, 2015 7:10 AM
To: support@wavefun.com
Subject: odyssey
Re. Odyssey; college level; version 5; lab 13 Rotation & vibration
Please confirm:

thermal energy (in text panel) = kinetic energy (molar; from properties panel) = energy due to
translational, rotational, & vibrational motion

trans kin energy (molar; from properties panel) = energy due to translational motion only

total energy (from properties panel) = internal energy
In regards to flexible SF2, please describe the various degrees of freedom
3 trans = motion along x-, y-, & z- axis ?
3 rotat = rotation, where (i) S follows a circular path / clockwise; S follows a cicrcule path / counter clockwise;
F rotate, while S is stationary ?
3 vibr = single S - F bond vibrate; other single S - F bond vibrate; both S - F bonds vibrate ?
In regards to Kr, Cl2(rigid), & SF2(rigid), why is the potential energy (molar; in the properties panel) a (small)
negative value ? why is the potential energy of the flexible molecule greater than the rigid molecule ?