Geoff

In the H2O output file, attached, the second (of ten) settings has the

hydrogen atoms disappearing into the oxygen atom. Every higher setting

has the hydrogen atoms appearing out the other side! Vibrations at the

third or higher setting leads to inversion and hydrogen overlap. In a

classical approximation, the hydrogen atom, which moves the most,

moves a maximum of 14 % of the bond length. I am not sure how you are

calculating the displacement, but a range from 5 % to 50 % of the bond

length would be great (from around 5 pm to 75 pm). My calculation of

the displacement is given below:

In classical physics, Hookes law gives

2 * pi * v = SQRT(k/m)

Energy is given by

E = 1/2 * k * x^2 = h * v

Solving Hookes law for k and substituting into the energy equation

gives

x^2 = h/(2 * pi^2 * m * v)

For hydrogen in water at 4000 cm-1, x is 13 pm, which is 14 % of the

95 pm bond length. (m should really be the reduced mass. But then

again, this is an application of *classical* physics to a *quantum*

system.)

The above classical calculation is a reasonable approximation of the

turning points on the OH PES: for a bond length of 97 pm, the first

vibrational energy level turning points are at 82 and 119 pm,

corresponding to -15 pm and +22 pm.

Thanks,

Dr. Roy Jensen

(==========)-----------------------------------------¤

Chemistry, Grant MacEwan University

Room 5-172J, 10700-104 Avenue

Edmonton, AB T5J 4S2

780.633.3915

On Fri, 24 Dec 2010 17:50:19 -0500, you wrote:

On Dec 22, 2010, at 5:27 AM, Jan Halborg Jensen wrote:

That said, I noticed that the animate feature of Avogadro *wildly*

exaggerates the vibrational motion. The lowest setting is actually

about 10 times greater motion than in reality!

I’m always open to suggestions. I generally use a “wildly” exaggerated vibrational motion because I find in lecture demonstrations that 2x or 3x is not usually sufficient for students to understand the modes. They see that the atoms are moving, but have a difficult time differentiating the direction of movement. So I often find myself cranking it up to 20-30x…

Maybe you have smaller lecture halls?

It’s obviously a *very* easy patch. Just give me some feedback on what you think the slider ranges should give.

I agree: it would be very educational to have an option where the

displacements were properly scaled according to frequency:

http://molecularmodelingbasics.blogspot.com/2010/06/geometry-and-molecular-motion.html

Jan, I don’t recall you giving this suggestion before – we previously changed the speed of vibration to scale according to frequency, and it’s again a fairly trivial patch. (Easy enough, I suspect you or one of your students could submit it

)

While Quixote is definitely the way to go for a computational repository, I’m also happy to host a repository of “good teaching examples” on the Avogadro website in whatever file format is desired – it need not be CML, since Avogadro can read such a wide range.

-Geoff

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