Trp-(Pro)3-Trp peptide (step by step)
You can download here the ORCA manual (pdf)
We propose an example of hole transfer mechanism in order to explain how calculate the electron coupling by e-coupling server. In the model Trp-(Pro)3-Trp a hole is transfered from one radical Trp to the other Trp.
Prepare the system in its red/red form according with the hole transfer mechanism.
Run an optimization of the molecule. In this example the molecule has charge 0, multiplicity 1 and we optimized at Hartree Fock level of theory (HF) and basis set 6-31g*.
Include the following keywords in the input:
Print [P_Overlap] 1 to print the Overlap matrix
Print[ P_MOs ] 1 to print molecular orbitals
Print[ P_Density ] 1 to print density matrix
Print[ P_SpinDensity ] 1 to compute the spin density
Run a single point calculation from the optimized structure, using the same theory level and basis set.
Check the full ORCA input file input_ORCA.in for the Trp-Trp peptide example.
Identify atom numbers from donor and acceptor
Load the structure (molden input) and click button label >> atom number
Load the structure (.log file) and click right button in the mouse style >> label >> with atom number. In this example, first Trp (donor) is from atom 1 to 15 and the second (acceptor) from 16 to 30.
Visualize orbitals involved in the reaction.
From the loaded structure press Density mode >> Orbital >> and click in the window Molden Orbital Select to visualize the orbitals. The reaction in the example is hole transfer and for this reason, we visualize the HOMOs.
JSMOL: Click the buttons to visualize different HOMO/LUMO orbitals. Detail information about each orbital appears in the left corner.
- Select orbitals involved in the electronic coupling
Select the number of more stable degenerated HOMOs (in case of hole transfer) or LUMOs (electron transfer) placed in both donor (Trp5) and acceptor (Trp1).
Consider degenerated orbitals when the difference is lower than 0.005eV (or decide the value using your own criteria and depending on your system)
In the example, HOMO is placed on the donor (Trp5) and the HOMO-1 is placed on the acceptor (Trp1). The orbital HOMO-2 is placed on the acceptor (Trp 1) but is not degenerated (comparing with the HOMO-1) and we do not consider it in the calculation. We use the same reasoning to reject HOMO-3.
As a conclusion, in the example we take one orbital from donor (HOMO) and one for the acceptor(HOMO-1)
Note. Choose an appropiate level of theory and basis set accurate to your system.
The number of optimization steps depends on the system. Not enough optimization steps could give a spin contaminated wave function. The Spin operator <S2> measures the spin contamination and estimates the quality of the wave function.
S = (M-1)/2 (M = multiplicity)
<S2> = S*(S+1) (0, ¾, 2... etc)
For example, in a doublet state the spin operator without contamination should have a value of 0.75. If the computed value differs largely from this number ( >0.05), consider reoptimizing the wave function.
PREPARE THE E-COUPLING CALCULATION
From the output file identify donor and acceptor atom numbers and localize orbitals involved in the electronic coupling using a visualization program like Molden or JSMOL (directly from e-coupling server).
First ,transform the output file .gbw from ORCA into a molden readable file (.mkl ) using orca_2mkl from the orca package.
orca_2mkl input -molden (where input is the name of the .gbw file)