---------- Forwarded message ---------From: Jurgen Schnitker <jurgen@wavefun.com>
Date: Wed, Oct 14, 2015 at 10:11 AM
Subject: Re: Odyssey - dipole moment
To: paul matsumoto <psmatsu@gmail.com>
Cc: Spartan Support <support@wavefun.com>
Hi Paul,
It's the issue of scalar vs. vector: The dipole moment (as a single
number) is the LENGTH of the dipole vector. The vector randomly 1)
changes its orientation and 2) fluctuates in length between zero and
some positive number. No matter what, its length is never negative.
While there are many limitations of the software (or rather: inherent
limitations of our ability to describe a complex reality with
simplistic models), I'd say that we're actually getting this one right
:)
Best regards,
Jurgen
> From: paul matsumoto [mailto:psmatsu@gmail.com]
> Sent: Tuesday, October 13, 2015 10:38 PM
> To: support@wavefun.com
> Subject: Odyssey - dipole moment
>
>
>
> While developing an assignment for my students to explore the nature of
> London intermolecular forces in tetrafluromethane, a nonpoplar compound,
> noticed that
>
>
>
> 1. using: properties --> add property --> electrostatics --> dipole
> moment
>
> 2. using: plots --> add plot --> xy plot .. --> x-axis = time & y-axis =
> dipole moment
>
> upon running the animation / simulation, I was expecting that there would be
> random changes in the molecule's dipole moment (due to random electron
> motion and bond vibrations in the molecule) and its value would be symmetric
> about zero, but such behavior was not observed. While the value of the
> molecule's dipole moment did vary, its value was always positive and not
> symmetric about zero. why ?
>
>
> believe it reflects my lack of understanding of the concept of the London
> IMF. alternatively, is my understanding correct and that it's a limitation
> / bug in the simulation software ?
>
> Thank you.
>
>
> Paul
>
...
***********************************************************
---------- Forwarded message ---------From: Bryan Marten <bdmarten@gmail.com>
Date: Sun, Nov 16, 2014 at 10:10 PM
Subject: Re: odyssey programming bug ?
To: paul matsumoto <psmatsu@gmail.com>
Cc: Jonathan Fong <jonafon@gmail.com>, "Rotter, Katrina" <RotterK@sfusd.edu>, Kevin <HartzogK@sfusd.edu>,
Helen Lee <lothree@gmail.com>, Jessica Wong <wongj@galileoweb.org>
I think Odyssey uses fixed charge models, not fluctuating charge models in its molecular/atomic force fields. I ran the
simulations in that lab and I do see the dipole moment changing for ammonia but not for water as shown by the Properties
info. I think for ammonia the dipole moment is changing just because of geometry changes due to vibrations and the
molecules getting pushed and pulled. For water I see its color change dramatically every so often when color is for dipole
moment magnitude even though the Properties info says the dipole moment isn’t changing. I think this is because the
dipole moment is actually probably changing in the 3rd or 4th decimal place which doesn’t show up in the Properties info
but the color coding might be based on the max range of values and for water in Odyssey that range of values might be
pretty tight. So minor fluctuations which don’t show up in the Properties info (which only displays to 2 decimal places)
might still swing the color from red to blue.
Bryan
> On Nov 15, 2014, at 7:38 PM, paul matsumoto <psmatsu@gmail.com> wrote:
>
> Hi, Odyssey users,
>
> I am planning to use Odyssey for an upcoming lesson on London IMF in polar compounds using lab 97, hydrogen
bonding, in the molecular labs by selecting:
>
> style (in the drop down menu) --> color by property --> dipole moment,
>
> as well as,
>
> properties (in the tool bar) --> add property --> electrostatics --> dipole moment
>
> where it seems to work with ammonia and water, but the behavior of the simulation for water is suspicious, since there's
no change in the properties panel, but there's simultaneous change in the color (corresponding to the molecule's dipole
moment) in the animation panel.
>
> On the other hand, using the halogen module from the stockroom, didn't see any changes in the molecule's dipole
moment, which was unexpected based on my understanding of London IMF.
>
> I'm using the ap chemistry instructor's version of odyssey, version 4, in exploring odyssey. i assume if a feature does
not work in a simulation that it would be disable -- unless, the programmers didn't expect someone to try this feature of
the software in this module.
>
> Do you have any ideas what's going on in these simulations ?
>
> Also, I consider this behavior - of spontaneous changes in a molecule's dipole moment - to be a "real" occurrence - not
some error in the simulation. Please confirm. If true, this simulation could be beneficial for students to acquire this subtle
aspect of IMF.
>
> Paul
>
>