Hydrogen Bond Basicity Prediction Panel

Using the Hydrogen Bond Basicity Prediction Panel

This panel takes the structures specified in the input file and evaluates the electrostatic potential (ESP) at specific points near hydrogen and halogen bond acceptors and donors for each structure. These points are added to the structure as dummy atoms. The value can be shown in Maestro by displaying the label using the 'Kenny ESP' atom properties for those atoms. The dummy atoms are colored differently for acceptors and donors. The ESP values are reported in kcal/mol. Note that the dummy atoms are not the locations of potential corresponding donor or acceptor atoms, but points whose ESP correlates with the association free energy. To quantify this correlation, you can use any linear regression tool to obtain a fit of your ESP values to experimental values.

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 hbond_basicity_predictor.py Command Help. See also hbond_basicity_predictor.py: Hydrogen Bond Donor Strength and Minimum Detection.

Hydrogen Bond Basicity Prediction Panel Features

• Use structures from option menu
• Open Project Table button
• File name text box and Browse button
• Basis set text box
• Functional option menu
• Number of ESP points per Å text box
• Bounding box extension text box
• Distances from atoms section
• Job toolbar
• Status bar

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 (n included entries)—Use the entries that are currently included in the Workspace, treated as separate structures. The number of entries in the Workspace is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and include or exclude entries.
• 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.

Basis set text box

Specify the basis set for the calculation. The default has both polarization and diffuse functions, which are important for accuracy. For a list of basis sets, see Basis Sets.

Functional option menu

Choose the density functional for the calculation. For more information on the functionals, see The dftname Keyword in the Jaguar Input File.

Number of ESP points per Å text box

Specify the density of the cubic (Cartesian) grid on which the electrostatic potential is evaluated, for determining the V_min values for hydrogen bond acceptors.

Bounding box extension text box

Specify the amount by which the bounding box for the grid is extended. The base grid extent is defined by the van der Waals radii of the atoms in the molecule, and is extended beyond this distance by the value of the specified extension.

Distances from atoms section

Specify the distance from the hydrogen or halogen atoms at which the electrostatic potential is evaluated for the V_α(r) method. For a hydrogen or halogen bond A–X...Y, the distance is measured from the hydrogen or halogen atom X towards the acceptor Y in the direction along the A–X vector. There are text boxes for each of the atoms involved in hydrogen or halogen bonding. The default distances have been determined for good correlation of the ESP with the hydrogen or halogen bonding association free energy.

Job toolbar

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

The Job Settings button opens the Jaguar - Hydrogen Bond Basicity Prediction - 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. It also displays a progress bar for the job.

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.

Related Topics

• HBond Panel
• hbond_basicity_predictor.py: Hydrogen Bond Donor Strength and Minimum Detection
• Jaguar - Hydrogen Bond Basicity Prediction - Job Settings Dialog Box

Workflow Examples

Example: Execute hbond_basicity_predictor.py workflow to calculate ESP values at points around hydrogen bond donors and acceptors of 4-chlorobenzaldehyde. The calculation is performed at the B3LYP/LACVP+** level of theory and is meant to predict hydrogen bond basicity, as described in P.W. Kenny, J. Chem. Inf. Model. 2009, 49, 1234-1244

Note: The grid is set up to calculate five ESP points per Angstrom in a 3.0 Angstrom bounding box. Special distances for the points can be set for the following atoms: H, Cl, Br, and I.

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

{ 
 s_m_m2io_version
 :::
 2.0.0 
} 

f_m_ct { 
 s_m_title
 i_m_ct_enhanced_stereo_status
 s_m_entry_id
 s_m_entry_name
 b_sd_chiral_flag
 i_sd_version
 s_m_Source_Path
 s_m_Source_File
 i_m_Source_File_Index
 i_m_ct_format
 :::
 Structure1 
  0
  7 
  benz_opt_2.1 
  0
  0
  /Users/moore1 
  benz_opt_2.xyz 
  1
  2
 m_atom[14] { 
  # 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
  :::
  1 2 -0.638800 1.177400 0.183000 900 2 6 A0A0A0  C1 
  2 2 0.023100 -0.046900 0.217600 900 2 6 A0A0A0  C2 
  3 2 -0.698200 -1.244500 0.287400 900 2 6 A0A0A0  C3 
  4 2 -2.100000 -1.210200 0.322900 900 2 6 A0A0A0  C4 
  5 2 -2.774000 0.003300 0.289000 900 2 6 A0A0A0  C5 
  6 2 -2.033700 1.188000 0.219200 900 2 6 A0A0A0  C6 
  7 2 0.012700 -2.542800 0.324000 900 2 6 A0A0A0  C7 
  8 15 -0.538300 -3.625500 0.384800 900 70 8 FF2F2F  O8 
  9 57 -2.880200 2.724400 0.176200 900 9 17 006400  Cl9 
  10 41 -0.090700 2.110900 0.128900 900 21 1 FFFFFF  H10 
  11 41 1.109800 -0.072300 0.190100 900 21 1 FFFFFF  H11 
  12 41 -2.640600 -2.149800 0.377100 900 21 1 FFFFFF  H12 
  13 41 -3.857100 0.044100 0.315700 900 21 1 FFFFFF  H13 
  14 41 1.122900 -2.466100 0.291100 900 21 1 FFFFFF  H14 
  :::
 } 
 m_bond[14] { 
  # First column is bond index #
  i_m_from
  i_m_to
  i_m_order
  :::
  1 1 2 2
  2 1 6 1
  3 1 10 1
  4 2 3 1
  5 2 11 1
  6 3 4 2
  7 3 7 1
  8 4 12 1
  9 4 5 1
  10 5 13 1
  11 5 6 2
  12 6 9 1
  13 7 8 2
  14 7 14 1
  :::
 } 
} 

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

$SCHRODINGER/jaguar run hbond_basicity_predictor.py -jobname wflow_hbond_basicity_0001 -basis_set 'LACVP+**' -functional B3LYP -H 0.55 -Cl 1.75 -Br 1.85 -I 1.98 -ppa 5 -extend 3.0 wflow-hbond_basicity-0001.mae wflow-hbond_basicity-0001-out.mae

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-hbond_basicity-0001.mae

Output files