The canonical molecular orbital depiction of an electronic transition is often a messy business in terms of a ‘chemical‘ interpretation of ‘which electrons‘ go from ‘which occupied orbitals‘ to ‘which virtual orbitals‘.
Natural Transition Orbitals provide a more intuitive picture of the orbitals, whether mixed or not, involved in any hole-particle excitation. This transformation is particularly useful when working with the excited states of molecules with extensively delocalized chromophores or multiple chromophoric sites. The elegance of the NTO method relies on its simplicity: separate unitary transformations are performed on the occupied and on the virtual set of orbitals in order to get a localized picture of the transition density matrix.
 R. L. Martin, J. Chem. Phys., 2003, DOI:10.1063/1.1558471.
After running a TD-DFT calculation with the keyword TD(Nstates=n) (where n = number of states to be requested) we need to take that result and launch a new calculation for the NTOs but lets take it one step at a time. As an example here’s phenylalanine which was already optimized to a minimum at the B3LYP/6-31G(d,p) level of theory. If we take that geometry and launch a new calculation with the TD(Nstates=40) in the route section we obtain the UV-Vis spectra and the output looks like this (only the first three states are shown):
Excitation energies and oscillator strengths: Excited State 1: Singlet-A 5.3875 eV 230.13 nm f=0.0015 <S**2>=0.000 42 -> 46 0.17123 42 -> 47 0.12277 43 -> 46 -0.40383 44 -> 45 0.50838 44 -> 47 0.11008 This state for optimization and/or second-order correction. Total Energy, E(TD-HF/TD-KS) = -554.614073682 Copying the excited state density for this state as the 1-particle RhoCI density. Excited State 2: Singlet-A 5.5137 eV 224.86 nm f=0.0138 <S**2>=0.000 41 -> 45 -0.20800 41 -> 47 0.24015 42 -> 45 0.32656 42 -> 46 0.10906 42 -> 47 -0.24401 43 -> 45 0.20598 43 -> 47 -0.14839 44 -> 45 -0.15344 44 -> 47 0.34182 Excited State 3: Singlet-A 5.9254 eV 209.24 nm f=0.0042 <S**2>=0.000 41 -> 45 0.11844 41 -> 47 -0.12539 42 -> 45 -0.10401 42 -> 47 0.16068 43 -> 45 -0.27532 43 -> 46 -0.11640 43 -> 47 0.16780 44 -> 45 -0.18555 44 -> 46 -0.29184 44 -> 47 0.43124
The oscillator strength is listed on each Excited State as “f” and it is a measure of the probability of that excitation to occur. If we look at the third one for this phenylalanine we see f=0.0042, a very low probability, but aside from that the following list shows what orbital transitions compose that excitation and with what energy, so the first line indicates a transition from orbital 41 (HOMO-3) to orbital 45 (LUMO); there are 10 such transitions composing that excitation, visualizing them all with canonical orbitals is not an intuitive picture, so lets try the NTO approach, we’re going to take excitation #10 for phenylalanine as an example just because it has a higher oscillation strength:
%chk=Excited State 10: Singlet-A 7.1048 eV 174.51 nm f=0.3651 <S**2>=0.000 41 -> 45 0.35347 41 -> 47 0.34685 42 -> 45 0.10215 42 -> 46 0.17248 42 -> 47 0.13523 43 -> 45 -0.26596 43 -> 47 -0.22995 44 -> 46 0.23277
Each set of NTOs for each transition must be calculated separately. First, copy you filename.chk file from the TD-DFT result to a new one and name it after the Nth state of interest as shown below (state 10 in this case). NOTE: In the route section, replace N with the number of the excitation of interest according to the results in filename.log. Run separately for each transition your interested in:
#chk=state10.chk #p B3LYP/6-31G(d,p) Geom=AllCheck Guess=(Read,Only) Density=(Check,Transition=N) Pop=(Minimal,NTO,SaveNTO) 0 1 --blank line--
By requesting SaveNTO, the canonical orbitals in the state10.chk file are replaced with the NTOs for the 10th excitation, this makes it easier to plot since most visualizers just plot whatever set of orbitals they read in the chk file but if they find the canonical MOs then one would need to do some re-processing of them. This is much more straightforward.
Now we format our chk files into fchk with the formchk utility:
formchk -3 filename.chk filename.fchk
formchk -3 state10.chk state10.fchk
If we open filename.fchk (the file where the original TD-DFT calculation is located) with GaussView we can plot all orbitals involved in excited state number ten, those would be seven orbitals from 41 (HOMO-3) to 47 (LUMO+2) as shown in figure 1.
If we now open state10.fchk we see that the numbers at the side of the orbitals are not their energy but their occupation number particular to this state of interest, so we only need to plot those with highest occupations, in our example those are orbitals 44 and 45 (HOMO and LUMO) which have occupations = 0.81186; you may include 43 and 46 (HOMO-1 and LUMO+1, respectively) for a much more complete description (occupations = 0.18223) but we’re still dealing with 4 orbitals instead of 7.
The NTO transition 44 -> 45 is far easier to conceptualize than all the 10 combinations given in the canonical basis from the direct TD-DFT calculation. TD-DFT provides us with the correct transitions, NTOs just paint us a picture more readily available to the chemist mindset.
NOTE: for G09 revC and above, the %OldChk option is available, I haven’t personally tried it but using it to specify where the excitations are located and then write the NTOs of interest into a new chk file in the following way, thus eliminating the need of copying the original chk file for each state:
NTOs are based on the Natural Hybrid orbitals vision by Löwdin and others, and it is said to be so straightforward that it has been re-discovered from time to time. Be that as it may, the NTO visualization provides a much clearer vision of the excitations occurring during a TD calculation.
Thanks for reading, stay home and stay safe during these harsh days everyone. Please share, rate and comment this and other posts.
Editing large molecules on a seemingly simple visualizer as GaussView can be a bit daunting. I’m working on a follow up of that project we recently published in JACS but now we require to attach two macrocycles to the organometallic moiety; the only caveat is that this time we don’t have any crystallographic data with which to start. Generating a 3D model of this structure is already hard enough and even when you managed to do it there are many degrees of freedom that in some cases can lead to unrealistic geometries after optimization.
I recently came across a simple way to edit a large complicated molecule by optimizing the fragments separately and then joining them in a new molecule by using the clipboard. This rather simple method, that I for one had never exploited has just saved me a few good hours.
Copy a molecule (CTRL+C) and it will go to the clipboard as a molecular fragment for which you can define a new hot atom and thus bind it to the other fragment as you would with the regular builder. I strongly suggest to use a “New Molecule Group” instead of editing over an existing molecule. Also, if you are using the “paste” button, observe that it has three different options; you may want to use the last one “append to existing molecule” or you will have your fragments in different windows.
And remember, dihedral angles are your best friends.
A couple of weeks ago I posted a solution for a common error regarding .fchk files that will display the error below when opened with GaussView5.0. As I expected, this error has to do with the use of diffuse functions in the basis set and is related to a change of format between Gaussian versions.
CConnectionGFCHK::Parse_GFCHK() Missing or bad data: Alpha Orbital Energies Line Number 1234
Although the method described in the previous post works just fine, the following update is a better approach. Due to a change of spelling between G03 and G09 (which has been corrected for G09 but not available for GV versions prior to 5.0.9) one must change “independent” for “independant”
To make the change directly from the terminal the following command is needed:
sed -i 's/independent/independant/g' file.fchk
Alternatively you can redirect the output to a new file
sed -e 's/independent/independant/g' file.fchk > newfile.fchk
if you want to keep the old version and work with a new one.
Of course this edition can be performed manually with any text editor available (for example if you work in Windows) but solutions from the terminal always seem easier and a lot more fun to me.
Thanks to Dr. Fernando Cortés for sharing his insight into this issue.
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.
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.
> It’s possible to open a formated checkpoint file, containing the NBOs, in chemcraft.
%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!
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:
- 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.
- 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.
- 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
- 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.
- 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.
- 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.
- 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!
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:
It works fine on many macjines, I am sure.