HBond Panel

The HBond panel enables you to set up and run a calculation of the binding energy for one or more intermolecular hydrogen-bonded complexes. Each input structure must be a complex that consists of two molecules that are held together by hydrogen bonds.

For information on the workflow, see Binding Energies of Hydrogen-Bonded Complexes.

To open this panel, click the Tasks button and browse to Quantum Mechanics → Hydrogen Bond Strength.

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 hydrogen_bond.py Command Help.

When the job finishes, the optimized structure of the complex is incorporated into the project, with the binding energy, in kcal/mol, as a property.

  • Features
  • Additional Resources

HBond Panel Features

 

Use structures from option menu

Choose the structure source for the hydrogen-bonded complexes.

  • 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.
Entry table

This table lists the entries that are used as the input structures for the job.

The table shows the entry ID and the entry title, and also has an In column, which you can use to display the structures in the Workspace, just as in the Project Table panel or the Entry List panel.

The remaining columns in the table specify the charge (molchg in the gen section) and the spin multiplicity (multip in the gen section. The defaults are 0 for the charge and 1 for the spin multiplicity (singlet), and are displayed in italics (to indicate that they are the defaults). You can edit the table cells to set the charge and multiplicity.

Optimization options

These options allow you to specify which structures and coordinates to optimize. There are four options:

  • Optimize all structures—Optimize the complex and the two molecules that make up the complex.
  • Optimize individual molecules, but not the complex—Optimize the two molecules that make up the complex, but not the complex itself, which retains its input geometry.
  • Do not optimize any structures—Use the input geometry for all calculations: do not perform any optimizations.
  • Freeze all torsions during optimizations—Optimize the complex and the two molecules that make up the complex, but freeze all torsions—intramolecular and intermolecular—in the optimization and optimize only the bond lengths and bond angles. This helps convergence with weakly-bound systems.
Fast mode option

This option uses the X3LYP/6-31G** DFT energies instead of performing the LMP2 calculations. The error for this option increases by about 0.5 kcal/mol compared to the normal mode.

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.

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

The Job Settings button opens the HBond - 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.

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