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Elements4D – Exploring Chemistry with Augmented Reality


joaquinbarroso:

A bit outside the scope of this blog (maybe), but just too cool to overlook. Augmented reality in chemistry education.

Originally posted on :

This is a guest post from Samantha Morra of EdTechTeacher.org, an advertiser on FreeTech4Teachers.com. 

Augmented Reality (AR) blurs the line between the physical and digital world. Using cues or triggers, apps and websites can “augment” the physical experience with digital content such as audio, video and simulations. There are many benefits to using AR in education such as giving students opportunities to interact with items in ways that spark inquiry, experimentation, and creativity. There are a quite a few apps and sites working on AR and its application in education.

Elements4D, an AR app from Daqri, allows students explore chemical elements in a fun way while learning about real-life chemistry. To get started, download Elements4D and print the cubes.

There are 6 physical paper cubes printed with different symbols from the periodic table. It takes a while to cut out and put together the cubes, but it…

View original 475 more words

Natural Bond Orbitals (NBO) Visualization with Chemcraft


It’s been a long time since I last posted something and so many things have happened in our research group! I should catch up with them in short but times have just been quite hectic.

I’m glad to publicly thank Prof. Frank Weinhold’s gesture to include this blog in the bibliography section of the new NBO6.0 website under the NBO-Related Websites tab.

Here is a contribution from Igor Marques at the University of Aveiro in Portugal (Group Website); the original text can be found as a comment in the original NBO Visualization post but it is pretty much the same thing you can find in this post. Here is a link to Chemcraft’s website. Thanks for sharing this, Igor!

=> Examples provided by Igor Marques used Chemcraft Version 1.7, build 365 <=

In the Gaussian input, with the NBORead option included under the population keyword, we should include the PLOT option as illustrated below. The gfoldprint keyword will print the basis set to the output file in the old G03 format. Some visualization programs require a certain format of the basis set to be printed to the output file in order to plot orbitals and other surfaces like the electron density; therefore, if you want to play safe, use gfoldprint, gfprint and gfinput in the same line. gfprint will print the basis set as a list but in the new G09 format, whereas gfinput will print the basis set using Gaussian’s own input format. (The used level of theory and number of shared processors are shown as illustrations only; also the Opt keyword is not fundamental to the visualization of the NBO’s)

%chk=filename.chk
%nprocshared=8

#P b3lyp/6-311++g** Opt pop=(full,nboread) gfoldprint 
filename

0 1
molecular coordinates
$NBO BNDIDX PLOT $END

this will generate files from *.31 to *.41
For the visualization of NBOs, you’ll need FILE.31 and FILE.37. Open FILE.31 from chemcraft. It will automatically detect FILE.37 (if in the same directory).

Tools > Orbitals > Render molecular orbitals

select the NBOs of interest (whcih are in the same order of the output),

Adjust settings > OK

On the left side of the window, select the NBO of interest and then click on ‘show isosurface’. Adjust the remaining settings. To represent another orbital, click on ‘keep this surface’ and then select another orbital from the rendered set and follow the previous steps.

Some Considerations:

> It’s possible to open a formated checkpoint file, containing the NBOs, in chemcraft.
Gaussian input:

%Chk=filename.chk
%nprocshared=4
#P b3lyp/6-311++g** Opt pop=(full,nboread,savenbo) gfoldprint 
filename

0 1
molecular coordinates
$NBO BNDIDX $END

the procedure is identical, but it is only necessary to read the *fchk file and then render the desired orbitals.
However, two problems might arise:
a) Orbitals in the checkpoint are reordered, thus requiring some careful inspection of the output.
b) Sometimes, for a larger molecule, the checkpoint might not be properly saved and the Gaussian job (as previously reported – http://goo.gl/DrSgA ) will end with:

Failed in SchOr1 in NBStor.
Error termination via Lnk1e in /data/programs/g09/l607.exe at Wed Mar 6 15:27:33 2013.

****

As usual, thanks to all for reading/commenting/rating this and other posts in this blog!


joaquinbarroso:

This is the first time I reblog a post from a fellow computational chemist and the reason why I do it is because of its beautiful simplicity and usefulness. Given the scope this blog has taken I think this post becomes most appropriate. This post will show you how to create an energy level diagram using nothing but MS Excel.
Kudos to ‘Eutactic’, from Australia, for coming up with a nice solution to this problem. Check out his blog at eutactic.wordpress.com.
Thanks for letting me repost it :)

Originally posted on eutactic:

I worked out a very quick and easy way to generate level schemes in Excel, based on a query from one of the other students in the group. Normally I would resort to something like the astonishing TikZ for this sort of task, however our group is very much a Microsoft Office ‘What You See Is A Metaphor For Cosmic Horror‘ group and recommending that a colleague learns two new markup languages to produce a figure is probably not helpful in the short term. One of the issues with charting energy levels in Excel is that levels are typically represented by horizontal bars connected at their vertices with lines representing transitions. Whilst Excel does have a horizontal bar as a marker, it possesses two show-stopping limitations:

  1. It is only uniformly scalable, and can only be scaled so far – we cannot make it anywhere near wide and…

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Download, yes, download Molekel 4.3 (WinXP). Happy New Year!


Due to extensive popular demand, I hereby make available the necessary files to run Molekel in its old 4.3 version. The program has been compiled to work under Windows 32 bit architecture. Just extract it and place the main folder (as provided here) in any location and run the .exe file located inside. You can generate a direct access to it from your desktop and it even includes a small icon to be used for this purpose.

Also, the manual in pdf format is included; in it you can find the proper citation which must be included in any publication that makes use of Molekel. Just in case you can’t find it, here it is:

MOLEKEL 4.3, P. Flükiger, H.P. Lüthi, S. Portmann, J. Weber, Swiss Center for Scientific
Computing, Manno (Switzerland), 2000-2002.
Stefan Portmann & Hans Peter Lüthi. MOLEKEL: An Interactive Molecular Graphics Tool.
CHIMIA (2000) 54 766-770.

Now some considerations:

  1. This is an old program. It was generated back in the WindowsXP days, so it wouldn’t be a surprise if it doesn’t work in more recent platforms or under any other 32 bit OS.
  2. The manual is included. Please read it. This blog is not Molekel’s help desk; I may help but I can’t solve everything, I just don’t have the time for it.
  3. I didn’t participate/collaborate/helped or got involved in any way in the development of this program, i.e., don’t shoot the messenger. The Molekel homepage is: http://molekel.cscs.ch/wiki/pmwiki.php
  4. I strongly recommend to make use of the NEW version. A bit more obscure but also great once you figure it out, plus there is available support for it from the actual developers.
  5. I also strongly recommend to look over the internet for other visualization softwares. I don’t recall having reviewed any in this blog. Perhaps some other time.
  6. Since this is not my development I will remove it from the server upon the request of the rightful owners A.S.A.P! My guess is they wont mind all that much since its an old version and it was given away for free from their server anyway.
  7. I can’t think of anything else to put on this list right now but I reserve the right to come back to it and add something more. I just don’t want any trouble.

So, here it is! Right click on the link and download it; Use it to generate nice plots of your orbitals, densities, electrostatic potentials, etc. Consider this a Happy New Year’s gift!

Molekel4.3.win32 (zip)

Rate and comment this and all the other posts you find interesting in this blog. Please!

UPDATE: Thanks to Yuekui Wang for the following information.

This copy doen’t work on some WinXP machine with ATI monitor card. The original copy is still available on the cscs web site. Download link is as follows:
ftp://ftp.cscs.ch/out/molekel/molekel_4.3
It works fine on many macjines, I am sure.

Calixarenes design – Prezi


Last week I had a presentation at the Chemistry Institute in which I talked about the research I’ve been doing during the last year. Here I insert a link to my prezi presentation in which I make an outline of the project’s scope and goals, so not many results available yet.

Unfortunately wordpress.com doesn’t allow embedding of flash files so here is the link to my presentation (in Spanish, sorry) directly to the prezi website.

(Screenshot only)

I’ve been using Prezi lately (at www.prezi.com) and although I still can’t say I got the hang of it, I like the way this presentations flow way better than Powerpoint slides. With prezi you make a single slide in which all the information is contained and then you zoom back and forth (or just forth) through the topics you want to review. The presentation is created online, making it available for public/private use or online viewing; it may also be saved as a flash file which allows you to play it in almost any computer. If you know your way around mental maps, prezi is definitely for you!

Well, here is hoping to be hired once again by Instituto de Química at UNAM after this presentation.

Some software trickery…


This post will become updated continuously in order to include as much of these useful tips as I find along the way, so if you are interested please subscribe so you don’t have to visit often. Some are old or even a bit obsolete in terms of software versions but I still include them so they can all be gathered in one place; this is basically a summary of some common errors in the use of Gaussian (G03 and G09). Please feel free to comment on this post, sharing your tricks with various programs in whatever branch of computational chemistry you might be working on.

Vibrations calculated with Gaussian 09 can’t be visualized with GaussView 3.x

*Change the lines “Atom  AN” with “Atom AN”. They look the same but there are TWO spaces in the first (this is the way G09 prints the output files) and in the second one there is only ONE space. The credit is entirely due to Jean Poully who posted this trick on the CCL a few months ago.

*Reader John Keller from Alaska suggests to use the formatted chk file (.fchk) to avoid this problem. As usual with formatted chk files make sure you format them in the same computer where you calculated it, or at least make sure both versions are compiled under the same architecture (32 or 64 bits).

Molecules appear flat on Molekel versions previous to 5.x

Molekel 4.x reads Gaussian98 files only. Gaussian03 and Gaussian09 files need to have the header corrected in the following part, right at the beginning of the file:

******************************************
Gaussian 09:  EM64L-G09RevA.02 11-Jun-2009
9-May-2010
******************************************

Change to:

******************************************
Gaussian 98:  EM64L-G09RevA.02 11-Jun-2009
9-May-2010
******************************************

A rather old one and kind of a weird one too but it works and some of us (myself very much included) like the previous Molekel far more than the new 5.x version.

Electrostatic potentials can not be visualized with Molekel 4.x

This is an error that stems from the fact that atomic charges are not read by Molekel, so all electrostatic properties derived from them are not calculated nor visualized. The problem is that Gaussian also changed the header for the charges when going from Gaussian98 to Gaussian03. In Gaussian 98 charges are labeled as “Total Atomic Charges”. In G03 and G09, atomic charges are labeled “Mulliken Atomic Charges”. Therefore find and change this label for the latter. PLEASE NOTE that Molekel will look for the title “Total Atomic Charges” so if your calculation was a geometry optimization then you have to find the set of charges that correspond to the last step of it. Look for the last string and change that one; you may also change them all with the right edition option in your editor, Molekel will use the last one since that should be the one corresponding to the optimized structure.

jbf

I’ll post something else when I find/remember it. Thanks for reading!

Mi amor!!!
Muchísimas felicidades!!! Estoy muy orgulloso de ti, de ser tu novio y tenerte en mi vida. Como persona y como profesional no eres más que admirable. Al igual que quienes te escriben, estoy seguro que este es solo el principio, mi amor, ese negocio en tus manos va a llegar hasta donde tu papá siempre quiso y aun más lejos. Te amo y estoy
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