Jaguar - Fukui Functions Panel

In this panel you can set up and run jobs to calculate Fukui functions.

To open this panel, click the Tasks button and browse to Quantum Mechanics → Fukui Functions.

Using
Features
Additional Resources
Examples

Using the Fukui Panel

The Fukui functions are calculated by finite difference as the derivative of the electron density with respect to the number of electrons. Since the derivative is discontinuous at integer numbers of electrons, there are two functions: one for increasing the number of electrons (f⁺) and one for decreasing the number of electrons (f^-). The derivatives are calculated by incrementing the charge by a fractional amount and running an SCF calculation with a fractional occupation in either the HOMO or LUMO. The functions are generated by taking the difference in electron density for the incremented system and the unperturbed system on a grid of points, which can then be used to display the function as a surface in Maestro. The original density and the incremented and decremented densities are also available. In addition, the f⁰ Fukui function for radical attack is calculated as the average of f⁺ and f^-.

Löwdin populations of the Fukui functions are calculated as atomic properties, Fukui Lowdin f+, Fukui Lowdin f-, and Fukui Lowdin f0, and can be displayed as atom labels in the Workspace (see Labeling Atoms and Bonds). The populations are the (numerical) derivatives of the Löwdin populations with respect to the number of electrons. Fukui indices for f⁺ and f^- are also calculated, based only on the HOMO or LUMO, as as atom-level properties, f-XX-HOMO and f-XX-LUMO, where X is N or S. See Output of Atomic Fukui Indices for more information.

Fukui functions can be calculated with any wave function from which a density can be generated, any basis set, and for either closed-shell or open-shell molecules. For the latter, UHF or UDFT is enforced.

See Fukui Functions for more information.

To write out the input file and a script for running the job from the command line, click the arrow next to the Settings button and choose Write. For information on command usage and options, see fukui.py Command Help. See also fukui.py: Calculate Fukui Functions.

Use structures from option menu

Choose the structure source for the current task.

Project Table (n selected entries)—Use the entries that are currently selected in the Project Table or Entry List. The number of entries selected is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and select entries.
Workspace (included entry)—Use the entry that is currently included in the Workspace. Only one entry must be included in the Workspace.
File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed.

Open Project Table button

Open the Project Table panel, so you can select or include the entries for the structure source.

File name text box and Browse button

Enter the file name in this text box, or click Browse and navigate to the file. The name of the file you selected is displayed in the text box.

Calculate f+ and Calculate f- options

Select these options to calculate the Fukui functions for addition (f+) and removal (f-) of an electron. If both are selected, f⁰ is also calculated.

Fraction of electron text box

Enter the fraction of an electron that is used to increment the charge in the HOMO or LUMO in the finite difference method for the derivative.

Keywords text box

Enter gen section keywords for the calculation. Because of the nature of the calculations, keywords for anything other than an SCF calculation are not allowed.

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

The Job Settings button opens the Jaguar - Fukui Functions - Job Settings Dialog Box, where you can make settings for running the job.

Status bar

The status bar displays information about the current job settings and status for the panel. The settings includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

Use the Reset button to reset the panel to its default settings and clear any data from the panel. You can also reset the panel from the Job toolbar.

The status bar also contains the Help button , which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.

Workflow Examples

Example: Execute fukui.py workflow to calculate Fukui functions for acrolein, which accounts for both changes in the electron density upon charge addition/removal and radical attack

Example input structure file (wflow-fukui-0001.mae):

{ 
 s_m_m2io_version
 :::
 2.0.0 
} 

f_m_ct { 
 s_m_title
 s_m_entry_id
 s_m_entry_name
 s_m_Source_Path
 i_m_Spin_multiplicity
 s_j_Task
 s_j_Jaguar_input_file
 s_j_Jaguar_restart_input_file
 s_j_Jaguar_restart_mae_file
 s_j_Jaguar_output_file
 s_j_Jaguar_log_file
 s_j_Jaguar_mae_file
 s_j_QM_Method
 s_j_QM_Basis
 i_j_Number_of_canonical_orbitals
 i_j_Geometry_convergence_category
 r_j_Gas_Phase_Energy
 r_j_Final_Energy
 r_j_HOMO
 r_j_LUMO
 r_j_Lowest_Frequency_(cm-1)
 r_j_Highest_Frequency_(cm-1)
 r_j_2nd_Lowest_Frequency_(cm-1)
 i_j_Num_Negative_Frequencies
 r_j_Zero_Point_Energy_(kcal/mol)
 r_j_Entropy_(cal/mol/K)_298.15K_1.00E+00atm
 r_j_Enthalpy_(kcal/mol)_298.15K_1.00E+00atm
 r_j_Free_Energy_(kcal/mol)_298.15K_1.00E+00atm
 r_j_Internal_Energy_(kcal/mol)_298.15K_1.00E+00atm
 r_j_Heat_Capacity_(cal/mol/K)_298.15K_1.00E+00atm
 r_j_ln(Q)_298.15K_1.00E+00atm
 r_j_Total_Internal_Energy_(au)_298.15K_1.00E+00atm
 r_j_Total_Enthalpy_(au)_298.15K_1.00E+00atm
 r_j_Total_Free_Energy_(au)_298.15K_1.00E+00atm
 s_m_job_name
 i_m_ct_format
 :::
 Structure1 
  5 
  Structure4 
  /Users/moore1/acrolein_2 
  1
  Optimization 
  /Users/moore1/acrolein_2/acrolein_2.in 
  /Users/moore1/acrolein_2/acrolein_2.01.in 
  /Users/moore1/acrolein_2/acrolein_2.01.mae 
  /Users/moore1/acrolein_2/acrolein_2.out 
  /Users/moore1/acrolein_2/acrolein_2.log 
  /Users/moore1/acrolein_2/acrolein_2.mae 
  DFT(b3lyp-d3) 
  6-31g** 
  80
  0
  -191.918377576693
  -191.918377576693
  -0.257428017269475
  -0.068927593797851
  190.286291200366
  3258.00567238615
  300.640553975799
  0
  38.6386698274699
  66.6197073463929
  3.30734482281728
  -16.5553209225098
  2.71485923399
  13.6326584431937
  27.942149538655
  -191.852476532902
  -191.85153234701
  -191.883185519902
  acrolein_2 
  2
 m_depend[31] { 
  # First column is dependency index #
  i_m_depend_dependency
  s_m_depend_property
  :::
  1 20 i_m_Spin_multiplicity 
  2 20 s_j_Task 
  3 20 s_j_Jaguar_input_file 
  4 20 s_j_Jaguar_restart_input_file 
  5 20 s_j_Jaguar_restart_mae_file 
  6 20 s_j_Jaguar_output_file 
  7 20 s_j_Jaguar_log_file 
  8 20 s_j_Jaguar_mae_file 
  9 20 s_j_QM_Method 
  10 20 s_j_QM_Basis 
  11 20 i_j_Number_of_canonical_orbitals 
  12 20 i_j_Geometry_convergence_category 
  13 20 r_j_Gas_Phase_Energy 
  14 20 r_j_Final_Energy 
  15 20 r_j_HOMO 
  16 20 r_j_LUMO 
  17 20 r_j_Lowest_Frequency_(cm-1) 
  18 20 r_j_Highest_Frequency_(cm-1) 
  19 20 r_j_2nd_Lowest_Frequency_(cm-1) 
  20 20 i_j_Num_Negative_Frequencies 
  21 20 r_j_Zero_Point_Energy_(kcal/mol) 
  22 20 r_j_Entropy_(cal/mol/K)_298.15K_1.00E+00atm 
  23 20 r_j_Enthalpy_(kcal/mol)_298.15K_1.00E+00atm 
  24 20 r_j_Free_Energy_(kcal/mol)_298.15K_1.00E+00atm 
  25 20 r_j_Internal_Energy_(kcal/mol)_298.15K_1.00E+00atm 
  26 20 r_j_Heat_Capacity_(cal/mol/K)_298.15K_1.00E+00atm 
  27 20 r_j_ln(Q)_298.15K_1.00E+00atm 
  28 20 r_j_Total_Internal_Energy_(au)_298.15K_1.00E+00atm 
  29 20 r_j_Total_Enthalpy_(au)_298.15K_1.00E+00atm 
  30 20 r_j_Total_Free_Energy_(au)_298.15K_1.00E+00atm 
  31 30 s_m_job_name 
  :::
 } 
 m_atom[8] { 
  # First column is atom index #
  i_m_mmod_type
  r_m_x_coord
  r_m_y_coord
  r_m_z_coord
  i_m_residue_number
  i_m_color
  i_m_atomic_number
  s_m_color_rgb
  s_m_atom_name
  i_m_minimize_atom_index
  :::
  1 2 -1.135692 2.036962 0.423492 1 24 6 808080  C1  1
  2 2 0.084031 2.222672 0.940163 1 2 6 A0A0A0  C2  2
  3 41 -1.789551 2.866146 0.173368 1 21 1 FFFFFF  H3  3
  4 41 -1.497989 1.028815 0.242441 1 21 1 FFFFFF  H4  4
  5 2 0.962697 1.073071 1.275325 1 2 6 A0A0A0  C5  5
  6 41 0.476380 3.218898 1.133391 1 21 1 FFFFFF  H6  6
  7 15 0.656681 -0.093376 1.113478 1 70 8 FF2F2F  O8  7
  8 41 1.954388 1.344978 1.698811 1 21 1 FFFFFF  H8  8
  :::
 } 
 m_bond[7] { 
  # First column is bond index #
  i_m_from
  i_m_to
  i_m_order
  :::
  1 1 2 2
  2 1 3 1
  3 1 4 1
  4 2 5 1
  5 2 6 1
  6 5 7 2
  7 5 8 1
  :::
 } 
}

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run fukui.py -jobname=wflow_fukui_0001 -plus -minus -k=basis=lacvp*+ -k=dftname=b3lyp-d3 -k=iacc=1 -k=dconv=5e-6 -k=iflinks=1 wflow-fukui-0001.mae -delta 0.01

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input structure: wflow-fukui-0001.mae

Output files

Jaguar - Fukui Functions Panel

Using the Fukui Panel

Fukui Panel Features

Related Topics

Workflow Examples