Absorbtion and emission spectra of formaldehyde
Nino Runeberg
CSC – IT Center for Science
March 19, 2013
N. Runeberg
CSC – IT Center for Science
Background
Fomaldehyde is the prototype molecule to
study in order to get a detailed
understanding of the electronic structure
and spectra of an important class of
chromophores. Here is a scematic
presentation of the processes that we are
going to study in this session. R GS and
R ES represent the ground and excited state
minimum geometries, respectively. E GS
and E ES are the corresponding energies.
E abso , E fluo and E adia are the absorbtion,
fluorescence and adiabatic transition
energies, respectively.
From http://dx.doi.org/10.1016/j.cplett.2006.01.068
N. Runeberg
CSC – IT Center for Science
Outline
We are using Turbomole 6.4/TmoleX 3.3/TD-DFT to study formaldehyde in order to:
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Obtain the equilibrium structure of the ground state
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Calculate the vertical absorbtion spctrum of the ground state
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Identify and characterize the first excited state
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Optimize the structure of the first excited state
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Calculate the emission spectrum of the first excited state
N. Runeberg
CSC – IT Center for Science
Download and install TmoleX
Download the TmoleX GUI client from
http://www.cosmologic.de/index.php?cosId=3016&crId=3
(Users who feel more comfortable working from the command line are of course free to
do so)
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CSC – IT Center for Science
Launch TmoleX
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Create a project
A complete Turbomole job is specified by walking through the sequence
Geometry - Atomic Attributes - Molecular Attributes - Method - Start Job - Results
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Build formaldehyde
Open 3D builder and load formaldehyde from the library
Continue with default def-SV(P) basis through ”Atomic Attributes”
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CSC – IT Center for Science
Initial guess MOs
In ”Molecular Attributes” do an EHT calculation to generate an initial guess
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CSC – IT Center for Science
Method
Select the default method (ri-dft pb/m3) and continue to ”Start Job”
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Start Job
In the ”Start Job” define the job type as ground state geometry optimization
Continue to ”Run (network)”
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Remote job
Define the parameters for an external interactive job on Vuori
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GeoOpt
The calculation finished and hopefully converged to a minimum energy structure.
There are various tools to analyze the results
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CSC – IT Center for Science
IR spectrum
In order to verify that the stationary point is a true minimum do frequency calc (Reuse
data by just hitting ”Start Job” )
N. Runeberg
CSC – IT Center for Science
Freq’s
Tabulate all useful information corresponding to the GS minimum such as ”R GS , E GS
and zero-point vibrational energy.
N. Runeberg
CSC – IT Center for Science
Spectra & Excited states
"Start Job" -> "Spectra & Excited states"
Do for singlet states and 10 excitations
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CSC – IT Center for Science
Spectra & Excited states
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CSC – IT Center for Science
Check output for the lowest excitation E abso and the type of excitation this
corresponds to
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CSC – IT Center for Science
Nature of excitation
Plot the dominant orbitals
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Select the relevant ”8a” and ”9a” orbitals
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CSC – IT Center for Science
Orbital ”8a” is a non-bonding electron pair on oxygen
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Orbital ”9a” is an antibonding π orbital over the O=C bond
Excitation is of type n → π ∗
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CSC – IT Center for Science
Optimize excited state structure
The lowest vertical excited state corresponds to the state we are interested in
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CSC – IT Center for Science
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CSC – IT Center for Science
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CSC – IT Center for Science
Stationary point on excited state energy surface, but is it a true minimum?
N. Runeberg
CSC – IT Center for Science
TmoleX not capable of doing NumForce calc’s. Copy the last opt directory to Vuori
and do the Numforce from command line.
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CSC – IT Center for Science
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CSC – IT Center for Science
Copy job folder to Vuori
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CSC – IT Center for Science
On Vuori load the Turbomole environment and start the NumForce Job
salloc -p interactive -n 1 srun NumForce -ri -ex 1 > & Numforce.out &
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Bummer! A saddle point
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New try
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Distort initial guess
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From the ”Gradients” menu confirm that this is a new stationary point corresponding
to a pyramidal structure
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CSC – IT Center for Science
Copy job folder corresponding to the new structure to Vuori and redo NumForce
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CSC – IT Center for Science
On Vuori load the Turbomole environment and start the NumForce Job
salloc -p interactive -n 1 srun NumForce -ri -ex 1 > & Numforce.out &
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CSC – IT Center for Science
A true minimum found
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CSC – IT Center for Science
Emission spectrum
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CSC – IT Center for Science
N. Runeberg
CSC – IT Center for Science
Results
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adia
Tabulate all relevant data such as R GS , R ES , E abso , E fluo , E adia and EZPVE
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Compare your results with experimental data found in the literature
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Compare your results with computational results obtained at more sofisticated
levels of theories
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If you have time, apply the efficient ricc2 implementation in Turbomole on the
system
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If you have time, extend the study to include solvent effects (COSMO)
N. Runeberg
CSC – IT Center for Science
Questions to ask?
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Is the basis set sufficient?
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What is the ultimate choise of functional?
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For this particular physical problem is tddft the method of choise?
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How does the environment interact?
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Should we be more careful when treating dispersion (intra, inter)?
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Relativity?
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Temperature and dynamics?
N. Runeberg
CSC – IT Center for Science