JAGUAR/Q-site TUTORIAL

Trp-(Pro)3-Trp peptide (step by step)


You can check here the Jaguar manual(pdf)


THE REACTION

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.

    OPTIMIZATION


    1. Open maestro and load the maestro file


    2. Prepare the system in its red/red form according with the hole transfer mechanism.


    3. 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*.


    4. 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.


    SINGLE POINT

    1. Include the following keywords in the input:

      ip102=8 to print molcular orbitals

      ldips=3 ip499=2 to print dipole matrix (GMH)

      ip18=2 to print overlap matrix matrix

      iplotspn=1 to print HOMO and LUMO orbitals

      iorb2b=lumo+n to print n beta orbitals from LUMO (for example: iorb2b=lumo+4)

      iorb2a=lumo+n to print n alpha orbitals from LUMO

      iorb1a=homo-n to print n alpha orbitals from HOMO

      iorb1b=lumo-n to print n beta orbitals from HOMO


    2. Run a single point calculation from the optimized structure, using the same theory level and basis set.

      Check the full JAGUAR input file input_JAGUAR.01.in for the Trp-Trp peptide example.
      For the ecoupling calculation you should submit the last input file generated by Jaguar/Qsite (.01.in ; 02.in ; 03.in, etc)


    PREPARE THE E-COUPLING CALCULATION

    1. Identify atom numbers from donor and acceptor

      With Maestro: Label>> residue number

    2. Visualize orbitals involved in the reaction.

      Open the optimized structure .mae with maestro

      Workspace > Surface > Import

      Open the orbitals (format .vis) , you will see a window similar like that:



      Click in each square in the Manage Surface window to visualize each orbital , its energy, the occupancy (1 or 0) and the orbital type (alpha or beta)



    3. 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)