Vibration animation and molecular database

General Discussion
1

On a second note, has there been thought to provide a database of
ground state molecules, with IR and NMR spectra for the smaller
entities? This would be valuable for the average user, who doesn’t
have access to computational software and/or doesn’t know how to use
computational software.

So, my questions for everyone:

  • is a molecular database a good idea?
  • is it something that can be hosted on Avogadro.net?
  • how should it be done? what format should be adopted?

I believe this is within the scope of the Quixote project:
http://quixote.wikispot.org/Front_Page

It is, and Avogadro is fingered as the code that we intend to do most of our prototyping of querying/accessing the database with, so with any luck, it shouldn’t be too long before there is something people can try.

Best wishes,

Jens

Scanned by iCritical.

2

A colleague asked if In knew of any software for animation of
molecular vibration. (She has explained that she would be flapping her
arms in class if I didn’t know of any … and I am seriously thinking
about claiming ignorance and installing a camera.)

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! The higher settings
actually see the atom vibrate through the molecular geometry! Perhaps
the vibrational motion could be toned down by about a factor of 100?

(I was using a G09 output of hydrogen peroxide, run at M06/6-311++G**)

On a second note, has there been thought to provide a database of
ground state molecules, with IR and NMR spectra for the smaller
entities? This would be valuable for the average user, who doesn’t
have access to computational software and/or doesn’t know how to use
computational software.

So, my questions for everyone:

  • is a molecular database a good idea?
  • is it something that can be hosted on Avogadro.net?
  • how should it be done? what format should be adopted?

Regarding the last: CML doesn’t retain spectral data. It would be very
simple for me to provide a gaussian output file, *.g09, that can be
read by Avogadro. (FYI: DFT is great in that the vibrational
frequencies do not require correction (scaling factor is between 0.98
and 1.02).)

Your thoughts?
Dr. Roy Jensen
(==========)-----------------------------------------¤
Chemistry, Grant MacEwan University
Room 5-172J, 10700-104 Avenue
Edmonton, AB T5J 4S2
780.633.3915

3

“Roy Jensen” JensenRH@MacEwan.ca skrev:

A colleague asked if In knew of any software for animation of
molecular vibration. (She has explained that she would be flapping her
arms in class if I didn’t know of any … and I am seriously thinking
about claiming ignorance and installing a camera.)

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! The higher settings
actually see the atom vibrate through the molecular geometry! Perhaps
the vibrational motion could be toned down by about a factor of 100?

I agree: it would be very educational to have an option where the
displacements were properly scaled according to frequency:

(I was using a G09 output of hydrogen peroxide, run at M06/6-311++G**)

On a second note, has there been thought to provide a database of
ground state molecules, with IR and NMR spectra for the smaller
entities? This would be valuable for the average user, who doesn’t
have access to computational software and/or doesn’t know how to use
computational software.

So, my questions for everyone:

  • is a molecular database a good idea?
  • is it something that can be hosted on Avogadro.net?
  • how should it be done? what format should be adopted?

I believe this is within the scope of the Quixote project:
http://quixote.wikispot.org/Front_Page

Regarding the last: CML doesn’t retain spectral data. It would be very
simple for me to provide a gaussian output file, *.g09, that can be
read by Avogadro. (FYI: DFT is great in that the vibrational
frequencies do not require correction (scaling factor is between 0.98
and 1.02).)

Your thoughts?
Dr. Roy Jensen
(==========)-----------------------------------------¤
Chemistry, Grant MacEwan University
Room 5-172J, 10700-104 Avenue
Edmonton, AB T5J 4S2
780.633.3915

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4

On Wed, Dec 22, 2010 at 11:00 AM, jens.thomas@stfc.ac.uk wrote:

On a second note, has there been thought to provide a database of
ground state molecules, with IR and NMR spectra for the smaller
entities? This would be valuable for the average user, who doesn’t
have access to computational software and/or doesn’t know how to use
computational software.

If you are interested in experimental data then there is
http://wwmm.ch.cam.ac.uk/crystaleye with 200,000 crystal structures
and
nmrshiftDB (http://www.ebi.ac.uk/nmrshiftdb/ ) for NMR shifts

I am not aware of much for IR except NIST webbook

I think’s its a good idea to provide both expt and calculations as then each
helps to calibrate and encourage the other.

–
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069

5

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:
Molecular Modeling Basics: Geometry and molecular motion

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

6

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 O–H 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:
Molecular Modeling Basics: Geometry and molecular motion

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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