Zindo

8       Tutorial--Standalone Mode

This section contains lessons on using the Zindo commands in the standalone environment and using the Insight interface as an aid to preparing molecules and analyzing results. (These tutorials are not available on-screen, since Pilot functions only via the Insight program.)

In Lesson 1: Geometry optimization, you will be introduced to the process of setting up a Zindo job and will perform a geometry optimization on pyridazine.

The topics covered in this lesson include:

• Creating a Zindo input file to do a geometry optimization.

• Creating an options file for the Zindo optimizer.

• Running a Zindo geometry optimization.

The topics covered in this lesson include:

• Creating a Zindo input file to do an energy calculation.

• Telling Zindo to calculate electron density and molecular orbitals.

• Using the Insight interface to display the calculated electron density and molecular orbitals.

• Applying the self-consistent reaction field method to the ground state.

The topics covered in this lesson include:

• Creating a Zindo input file to do a CI calculation.

• Using the Insight interface to display the calculated UV/visible spectrum.

You should create a directory in which to run your tutorials and store their output files:

Enter the following at the operating system prompt, while in a directory in which you have write permission: > mkdir zindo_tutorial > cd zindo_tutorial

2. Starting the Insight II program

Start the Insight program by entering insightII at the operating system prompt.

It takes a few moments for the Insight program to start up.

3. Building a pyridazine model

Go to the Builder module, by clicking the MSI logo and then selecting Builder from the list that appears.

A second set of pulldown names appears on the lower menu bar (A toolbox of icons may also appear, depending on your default settings.).

Select the Fragment/Get command by clicking Fragment and choosing Get from the menu that appears.

The Get Fragment parameter block appears. (There are several ways to build molecules within the Insight program--you may use any method that gives the required molecule.)

Set Type Of Fragment to Rings. Pick the benzene fragment that appears near the top of the Insight screen by clicking any of its atoms.

This fills in the Fragment Name parameter box with BENZ.

Enter pyridazine in the Get Molecuyle parameter box and select Execute or press <Enter>.

A benzene molecule appears in the display area of the Insight window, and the Bond parameter block appears automatically. You may put it away by selecting Cancel, since we do not need this command

Select the Atom/Replace command. When the Replace Atom parameter block and the Periodic Table window appear, click N in the Periodic Table to fill in the Element Type parameter box and pick the two top atoms in the benzene ring. Select the Atom/Delete command and click the H atoms attached to each N atom.

You should now have a model that looks like:

4. Symmetrizing the model

Go to the Zindo module (click the MSI logo--and Execute the Potentials parameter block when it appears) and select the Setup/System command. The Object Name should already be PYRIDAZINE. Select Execute to inform Zindo of the molecule that you want to work on. Now select the Symmetry/Find_Pt_Group command. When its parameter block appears, the Object Name should already be PYRIDAZINE. Confirm that Symmetry_Threshold is set to 0.005 and toggle Snap_Symmetry to on (indicated by a pushed-in appearance and yellow highlighting). The Snap_Orientation parameter should also be on. Select Execute.

The model is moved so that it lies in the xz plane, and symmetry information is printed in the information area near the bottom of the Insight window.

5. Saving your model

Select the Molecule/Put command. When its parameter block appears, confirm that the following parameter values are set: Put File Type = Biosym Assembly/Molecule = PYRIDAZINE Transformed = off Displayed = off PBC_File = off Enter pyrz in the File Name parameter box and select Execute.

6. Exiting the Insight II program

To exit the Insight interface, type quit on on the command line below the graphics display area and press <Enter>.

7. Creating a Zindo input file

Create a file named pyrz.input containing the following lines:

 $TITLEI

!  this title block can be any length.  This is a comment.

   Optimization of Pyridazine using ZINDO.

 $END

 $CONTRL

! Type of SCF calculation; one of RHF, ROHF or UHF.
  SCFTYP   RHF

! Type of Optimisation.
  RUNTYP   GEOM

! Type of structure input. COORD for Cartesians; 
  ENTTYP   COORD

! Type of units used.
  UNITS    ANGS

! Point group.
  ASYM     = C2V

! Definition of Gammas.
! Here we choose Theoretical Gammas since we are doing an optimization.
  INTTYP  0

! Electronic structure method, INDO/1.
  IAPX    3

! Interaction factors.
  INTFA(1) = 1.0 1.0 1.0 1.0 1.0 1.0

! Basis set and CI Size allocation.
  DYNAL(1) = 0   4   6   0   0 000  00

! Output file name.
  ONAME = pyridazine

! Number of atoms.
  NAT   10

! Number of valence electrons in molecule.
  NEL   30

! Multiplicity, i.e., number of unpaired electron + 1.
  MULT  1

! Max number of iterations.
  ITMAX   50

! SCF tolerance.
  SCFTOL = 0.000010

! OPTIMIZE UBOYT SECTUIB
  Locate			minimum
  Opt_Coordinate_System			auto
  Opt_Use_Symmetry			on
  Nax_Displacement			0.30
  Hessian_Update			BFGS
  Opt_Print			2
  Gradient_Convergence			0.0003
  Displacement_Convergence				0.0003
  Opt_Energy_Convergence				0.000001
  Opt_Cycles			50

 $END

At this point the files you should have in your current directory are pyrz.input, pyrz.opt, pyrz.car, and pyrz.mdf.

Run Zindo by entering at the operating system prompt: > zindo pyrz

The calculation completes in a few seconds. The final geometry will be in the file pyrz.car, and your starting geometry is moved to pyrz.orig.car. The series of conformations calculated during the optimization are written into the archive file pyrz.arc, and the output from the calculation appears in the outmol file.

9. Displaying the optimization trajectory (optional)

Make sure you are still in the zindo_tutorial directory and start the Insight program as in Step 2. After the program is loaded, select the File/Import (or Molecule/Get) command. When its parameter block appears, choose pyrz.car from the Files value-aid. This fills in the File_Name parameter box with pyrz.car. Execute the command.

Go to the Analysis module (by clicking the MSI logo). Select the Trajectory/Get command. In the Trajectory File parameter box, enter pyrz.arc. Fill in Trajectory Object with PYRZ, if necessary. Select Execute.

Select the Trajectory/Animate command. Select Execute.

The molecule in the display area is animated according to the optimization trajectory (you'll probably want to rotate it about the x axis to see it better).

When you are finished, quit the Insight program as in Step 6.

Lesson 2: Energy calculation

You need to finish Lesson 1 before starting Lesson 2, so that you have the required molecular specification files. Confirm that your current working directory is zindo_tutorial.

Use a text editor to create the following input file, which should be named pyrz2.input. You may start with a copy of the pyrz.input file that you used in Lesson 1.

 $TITLEI

   Energy Calcn. of Pyridazine using ZINDO.

   We will plot the HOMO (15) and the LUMO (16)

  MOLIST = 15,16

 $END

 $CONTRL

! Type of SCF calculation; one of RHF, ROHF or UHF.
  SCFTYP   RHF

! Type of Optimization; one of GEOM ENERGY or CI
  RUNTYP   ENERGY

! Type of structure input: COORD for Cartesians; ZMAT for internals.
  ENTTYP   COORD

! Type of units used; one of ANGS or BOHRS.
  UNITS    ANGS

! Point group.
  ASYM     = C2V

! Definition of Gammas.
! Now we choose Spectroscopic Gammas.
  INTTYP  1

! Electronic structure method, INDO/1.
  IAPX    3

! Interaction factors.
  INTFA(1) = 1.0 1.267 0.585 1.0 1.0 

! Basis set and CI Size allocation.
  DYNAL(1) = 0   4   6   0   0 000  00

! Output file name.
  ONAME = pyridazine

! Number of atoms.
  NAT   10

! Number of valence electrons in molecule.
  NEL   30

! Multiplicity, i.e., number of unpaired electron + 1.
  MULT   1

! Max number of iterations.
  ITMAX   50

! SCF tolerance.
  SCFTOL = 0.000001

 $END

1. RUNTYP becomes ENERGY.

2. INTTYP becomes 1, i.e., use spectroscopic gammas.

3. INTFA is not initialized to the spectroscopic singlet values, recommended for nearly all cases, especially UV/visible spectra.

4. SCF convergence tolerance SCFTOL was tightened.

The only files you now need are pyrz2.input, pyrz2.car, and pyrz2.mdf.

Make the pyrz2.car and pyrz2.mdf files by copying from pyrz.carorig and pyrz.mdf, respectively.

Since no optimization is taking place, there is no need to have the optimization keywords file pyrz2.input.

Enter at the operating system prompt: > zindo pyrz2

You should receive the following message from Zindo when the run is finished:

ZINDO MAIN  SCF Energy is -41.933849737 hartree

>	cp pyrz2.car pyrz2.car.vac
>	cp pyrz2.input pyrz2.input.vac
>	cp pyrz2.outmol pyrz2.outmol.vac
>	cp pyridazine.con pyridazine.con.vac

3. Performing a self-consistent reaction field calculation

The SCRF method of solvent modeling places the molecule within a spherical bubble of virtual solvent.

If an SCRF calculation is to be performed, the keyword ISCRF # (where #is a positive integer) must be added to the $CONTROL section, and a $SCRFIN block must be added to the Zindo input file. Since we are interested in the effect of solvent upon the ground state, ISCRF takes the value 1. Energy E(SCF) is the sum of the solute and solvent energies.

FORMAT 3I5, 6F10.6:

N1   N2   N3  F1       F2         F3

N1 is a repetition of ISCRF and must match the value in the $CONTRL section (default 0).

N2 is the number of terms in the multipole expansion (default 2).

N3 is the dispersion term, IDISP (default 0).

F1 is the radius of the solvent cavity, A0.

F2 is the static dielectric constant for the solvent.

F3 is the refractive index for the solvent.

ISCRF = 1

 $SCRFIN

   1    2    0  2.450000 78.500000  1.332870

 $END

Enter at the operating system prompt: > zindo pyrz2

Near the end of the run, you should see:

ZINDO MAIN  SCF Energy is -41.964363136 hartree

Unless instructed otherwise, Zindo calculates only the frontier molecular orbitals. You should see the following new files:

pyrz2_homo.grd
pyrz2_lumo.grd

The total number of valence electrons is C 4 x 4 + H 1 x 4 + N 5 x 2 = 16 + 4 + 10 = 30. Therefore, orbital 15 is the HOMO and orbital 16 is the LUMO.

5. Starting the Insight II program

With zindo_tutorial as your current working directory, start the Insight program by entering insightII at the operating system prompt.

It takes a few moments for the Insight program to start up.

6. Reading in the model of pyridazine

Select the Molecule/Get command and set the File Name parameter to pyrz2.car by clicking its name in the value-aid. Execute the command.

The pyridazine model appears in the display area. You may dismiss the parameter block by selecting Cancel.

7. Visualizing the highest occupied molecular orbital

Select the Grid/Get command by clicking the Grid icon in the icon palette. When its parameter block appears, assure that the following parameter values are set: File Name = pyrz2_homo.grd (choose from the value-aid) Sampling Rate = 1 Scalar Grid Name = PYR_HOMO Reference = on (highlighted yellow) Object Name = PYRZ2 Select Execute.

A box indicating the grid for the HOMO appears around the molecule.

Go to the Zindo module (by clicking the MSI logo). Select the Analyze/Orbital_Contour command from the lower menu bar. After its parameter block appears, assure that the following parameter values are set: Scalar Grid Name = PYR_HOMO Contour Name = HOMO Orbital_Amplitude = 0.08 Plus Contour Color = (any color desired for the plus phase) Minus Contour Color = (any color desired for the minus phase) Select Execute.

The HOMO for pyridazine appears.

8. Visualizing the lowest occupied molecular orbital

Select the Grid/Get command by clicking the Grid icon in the icon palette. When its parameter block appears, assure that the following parameter values are set: File Name = pyrz2_lumo.grd (choose from the value-aid) Sampling Rate = 1 Scalar Grid Name = PYR_LUMO Reference = on (highlighted yellow) Object Name = PYRZ2 Select Execute.

A box indicating the grid for the LUMO appears around the molecule.

Select the Analyze/Orbital_Contour command, and assure that the following parameter values are set: Scalar Grid Name = PYR_LUMO Contour Name = LUMO Orbital_Amplitude = 0.08 Plus Contour Color = (any color desired for the plus phase) Minus Contour Color = (any color desired for the minus phase) Select Execute.

The LUMO for pyridazine appears.

9. Exiting the Insight II program

To exit the Insight interface, type quit on on the command line below the graphics display area and press <Enter>.

Lesson 3: Configuration interaction

You need to finish Lesson 2 before starting Lesson 3, so that you have the required molecular specification files. Assure that your current working directory is zindo_tutorial.

Use a text editor to create the following input file, which should be named pyrz3.input. You may start with a copy of the pyrz2.input file that you used in Lesson 2.

The following changes will be made:

1. RUNTYP becomes CI--The type of calculation is changed to CI.

2. INTTYP is 1, i.e., use spectroscopic gammas.

3. Interaction Factors become INTFA(1) = 1.0 1.267 0.585 1.0 1.0

4. Basis set and CI size allocation are: DYNAL(1) = 0 4 6 0 0 250 30

N1 is the number of atoms having 0 basis functions (i.e., point charges).

N2 is the number of atoms having 1 basis function (S).

N3 is the number of atoms having 4 basis functions (S,P).

N4 is the number of atoms having 9 basis functions (S,P,D).

N5 is the number of atoms having 16 basis functions (S,P,D,F).

N6--If RUNTYP is CI, size of CI basis.

N7--If RUNTYP is CI, number of active orbitals in the CI.

Explanation of CI input block:

 $CIINPU

   2    1   10    1    0    0    0    1    1    2   
10
 -60000.00 0.0000000
   0
   1   15   15
  21   04   15   16   27

 $END

There are eleven switches in 11I5 FORMAT:

   N1    N2    N3    N4    N5    N6    N7    N8    N9   N10   N11

N1 is 2--Calculate CI for only SINGLET states from closed shell reference.
N2 is 1--The number of reference determinants to be used to generate the excited configurations.
N3 is 10--The number of roots of the CI matrix to calculate. The default value for N3 is the ten lowest.
N4 is 1--The multiplicity of the CI. It need not be the same as that of the reference SCF.

Transition moment section

N8 is 1--Calculate transition moments for states N9 through N10 into N10 through N11.

For further details see Methodology--Standalone Mode.

Criteria section

Criteria to reduce the number of configurations included in the CI:

ECUT      COMP      FORMAT 2F10.6

Point group symmetry information

No symmetry information is used therefore this card is left blank.

CI specification block

The number of generating cards and the reference determinant in FORMAT 3I5:

1   15   15

21   04   15   16   27

Self-consistent reaction field

In this calculation it is possible to apply the SCRF to the excited states and observe the effects of "solvation" upon the energies of the excited states:

Add these lines to the $CONTRL block of your input file: ! SCRF type. ISCRF 5 A formatted SCRF Input block must be added to your input file: FORMAT 3I5,6F10.6 $SCRFIN 5 1 0 2.450000 78.500000 1.332870 $END

Where:

N1 is 5 = Repeat of ISCRF. SCRF on excited states (absorption spectra).

N2 is 1 = Number of terms in the multipole expansion.

A0 is 2.45 = Cavity radius in angstroms.

EPS is 78.500000 = Dielectric constant for water.

XND is 1.332870 = Refractive index for water.

 $TITLEI

    Configuration Interaction Calcn. of Pyridazine using ZINDO.

 $END

 $CONTRL

! Type of SCF calculation; one of RHF, ROHF or UHF.
  SCFTYP   RHF

! Type of Optimization; one of GEOM ENERGY or CI
  RUNTYP   CI

! Type of structure input: COORD for Cartesians; ZMAT for internals.
  ENTTYP   COORD

! Type of units used; one of ANGS or BOHRS.
  UNITS    ANGS

! Point group.
  ASYM     = C2V

! Definition of Gammas.
! Now we choose Spectroscopic Gammas since we are doing CI
  INTTYP  1

! Electronic structure method, INDO/1.
  IAPX    3

! Interaction factors.
  INTFA(1) = 1.0 1.267 0.585 1.0 1.0 

! Basis set and CI Size allocation.
  DYNAL(1) = 0   4   6   0   0 250  30

! Output file name.
  ONAME = pyridazine

! Number of atoms.
  NAT   10

! Number of valence electrons in molecule.
  NEL   30

! Multiplicity, i.e., number of unpaired electron + 1.
  MULT   1

! Max number of iterations.
  ITMAX   50

! SCF tolerance.
  SCFTOL = 0.000001

 $END

 $CIINPU

   2    1   10    1    0    0    0    1    1    2   10
 -60000.00 0.0000000
   0
   1   15   15
  21   04   15   16   27

 $END

To do a CI calculation, you need a .car and .mdf pair of files (pyrz3.car and pyrz3.mdf) and an input file pyrz3.input. You can copy the .car and .mdf files from pyrz2carorig and pyrz2.mdf. Enter at the operating system prompt: > zindo pyrz3

When the run ends, you should see the message:

ZINDO MAIN  SCF Energy is -42.047108031 hartree

pyrz3.outmol
pyridazine.con
pyrz3.tab

The CI information is in pyrz3.tab.

3. Preparing to analyze the results

The calculation should produce a file called pyrz3.tab. The results that this file contains can be displayed as a graph of wavelength (in nanometers or reciprocal wavenumbers) versus oscillator strength.

With zindo_tutorial as your current working directory, start the Insight program by entering insightII at the operating system prompt.

It takes a few moments for the Insight program to start up.

4. Displaying a graph of the calculated UV/visible spectrum of pyridazine

Select the Analyze/CI_Spectrum command on the lower menu bar. From the list of .tab files that appears, choose pyrz3.tab.

A spreadsheet window appears (behind the main Insight window) and then a graph of the spectrum appears in the display area of the Insight window.

The graph is a representation of the calculated UV/visible spectrum of pyridazine. Notice that there are several peaks with very low oscillator strengths.

5. Exiting the Insight II program

To exit the Insight interface, type quit on on the command line below the graphics display area and press <Enter>.