Tutorial 5: Search for Nonbonded Interactions

 

Objectives

 

•	To draw two chemical fragments.

•	To specify that an intermolecular, nonbonded interaction must occur between the fragments.

•	To find such nonbonded interactions in the CSD.

•	To tabulate some geometrical parameters.

 

Steps Required

 

•	Draw the fragments.

•	Define the required nonbonded contact.

•	Define the geometrical parameters that are to be tabulated.

•	Run the search.

•	Save the file of geometrical parameters.

 

The Example

 

•	ConQuest can find intramolecular or intermolecular contacts between individual atoms, pre-defined groups of atoms, or between the centroids of pre-defined groups of atoms. The tutorial explains how to search for the following intermolecular contact:

where N is bonded to exactly 3 atoms, and there is an intermolecular contact < 2.1Å between O
and H. The following parameters will be saved:

•	O...H, O...N nonbonded distances.

•	O...H-N and C-O...H angles.

•	O and H atom labels.

•	Orthogonal coordinates of the hit fragments.

 

Menu Commands Required

 

1.	Start ConQuest and hit the Draw button to open the Draw window.

 

2.	Draw the two fragments.

 

3.	Constrain N to be 3-coordinate.

•	Right-click on the N atom, select Number of Bonded Atoms, then select 3.

 

4.	Specify nonbonded search criteria.

•	Hit the CONTACT button at the left-hand side of the Draw window.

•	Click on the O and H atoms and hit the Define button:

 

•	Click on the Edit... button in the Non-bonded Contact Definition pop-up:

 

•	By default, the search is for intermolecular contacts, which is what we want in this example.

•	By default, the search will find all contacts shorter than the sum of the van der Waals radii of the interacting atoms. However, in this example, we want to find contacts shorter than 2.1Å. Click on the Distance Range radio button, and type 0 and 2.1 into the From and to boxes, respectively:

 

•	Hit OK and then Done to finish definition of the contact.

 

5.	Define the required geometrical parameters and atom labels.

•

Hit the ADD 3D button and define the O...N distance as a parameter to be tabulated. This is done by clicking on the O and N atoms and hitting the Define button next to the word Distance in the Geometric Parameters pop-up. Hit OK in the Distance Type pop-up that then appears to specify that the defined distance is a contact.

 

 

•	Hit the Define button, OK and then Done in the Geometric Parameters dialogue box to finish the definition.

•	Also define the O...H-N and C-O...H angles as geometrical parameters.

 

•	Also define the Labels of O and H (See Tutorial 3: Defining and Saving Geometric Parameters).

 

6.	Run the search and save the parameters and the coordinates of the hit fragments.

•	Hit Done, if you have not already done so, to close down the Geometric Parameters window, then hit Search.

•	Hit the Advanced Options tab and switch on the Normalise terminal H positions check-box. This will apply a correction to remove systematic errors in N-H bond lengths determined by X-ray diffraction.

•	Hit the Filters tab, select the R factor <= 0.1 filter and hit Start Search.

•	The interacting atoms are highlighted in the chemical diagram and the hydrogen-bond distances can be displayed by switching on the Show Parameters check-box. The intermolecular contact can be viewed in the 3D visualiser.

•	Stop the search when you have a few hits. Select File from the top-level menu and then Export Entries as... from the pull-down menu. Select the file type as COORD.

•

This format enables you to write out either (i) orthogonal or (ii) crystallographic (fractional) atomic coordinates, of either (a) all the atoms in each structure, or (b) just those atoms involved in the contact. Select Orthogonal and Hit Fragment Only to save the Cartesian coordinates of the atoms involved in the hydrogen-bonding interaction.

 

This ends the tutorial.