Introduction:

QUEST3D can locate fragments containing one or more intramolecular and/or intermolecular non-bonded contacts defined using distance criteria. Contacts can involve:

• individual atoms
• pre-defined groups of atoms
• centroid of an atomic group

• CONTACT
  defines the non-bonded contact in terms of
  - pair of atoms / atom group / centroid involved in contact.
  - type of contact as intra/inter/any.
  - limiting contact distance.
  
• GROUP
  defines a set of atoms as a group (Gn) so that a contact can be defined to any atom of Gn or to its centroid Cn.
• VDW-RAD
  is used to modify stored van der Waals radii (v_i, v_j) or tolerance limit (t, default 1 Å) in

  dij < vi + vj + t

• Search the CSD for the fragment

  	C           C
  	 \         /
  	  C=O...H-N
  	 /         \
  	C           C
  

  where:

  • N is exactly 3-coordinate.
  • there is an intermolecular contact < 2.1 Å between O and H.
  • the N-H bond length is normalized to th mean distance (1.009 Å) obtained from neutron studies (see Special Notes below).
• Define (and tabulate) the following parameters for each hit:
  • O...H, O...N non-bonded distances
  • O...H-N and C=O...H bond angles
  • O and H atom labels
  • Direction of approach of N-H vector to carbonyl O atom (see 'Special Notes' below)
• Obtain histograms of O...H and O...N, and scattergram of O...H versus O...H-N
• Use entries having R < 10% and that are classified as organic compounds

Special Notes

• Intramolecular Contacts: Shortest Path

  In locating intramolecular non-bonded contacts (INTRA or INTRA + INTER options) QUEST3D will take account of limits placed on the shortest path of covalent bonds that links two atoms in the molecule. Thus:

  

  has a shortest path (S-PATH)of 5 bonds. Minimum and maximum S-PATH values can be input via the NON-BONDED CONTACT command. Default values are 4 and 999, respectively.

• Normalization of Hydrogen Positions (H-NORMALIZE in SEARCH menu)

  In X-ray analyses (but not neutron studies), the position of a proton is usually too close to that of its bonded atom (due to aspherity in the electron-density ditribution) although the bonded vector direction may be acceptable.
  The H-NORMALIZE command will reposition H atoms along the X-H bonded vector at distances that correspond to mean X-H inter-nuclear separations obtained in neutron studies for X=C,N,O. Distances are taken from J.Chem.Soc.Perkin 2 (1987) pp. S1-S19.

• Lone-pair Directionality in H-bond studies (*LP2 and *LP3 in 3D-CONSTRAIN submenu)

  The direction of approach of donor H atoms to acceptor atom A can be quantified in terms of the spherical polar angle and made by the A...H vector with respect to some reference plane that represents the equatorial plane of the sphere.
  For H-bonding studies it is convenient to take this plane as that which is assumed to contain the lone pairs on the acceptor A. The QUEST3D commands *LP2 and *LP3 will calculate , for common situations: an sp²-hybridized acceptor (e.g. O in carbonyl >C=O) or an sp³-hybridized acceptor (e.g. O in C-O-C).
  The DEFINE *LP2, *LP3 commands on the 3D-CONSTRAINsubmenu require the user to specify four atoms (i,j,k,n in the picture below) to define the reference plane. Two parameter names, e.g. THETA, PHI must also be provided.

  

• Draw bonded fragments using the BUILD menu.

                      
  	C1             C7
  	 \            /
  	  C2=O4    H5-N6
  	 /            \
  	C3             C8
  	             
  

• Constrain N to be 3-coordinate:
  • Select 2D-CONSTRAIN
  • Select TOTAL-COORD-NO, type 3 and select the N-atom. The N will get a T3 superscript.
  • Go back to the BUILD menu with TO-BUILD.
• Define non-bonded search criteria:
  • Select 3D-CONSTRAIN
  • Select NON_BONDED CONTACT
  • Select O₄ and H₅
  • Choice intermolecular by typing 2 and a 'return'
  • Type 1.0 2.1 and a 'return' to override the van der Waals defaults of 1.2+1.52+1.0=3.72Å
  The summary area will show the line

  	INTER 4 A 5 A 1.0 2.1
  

  in which 'A' refers to an atom contact (rather than centroid).
• Define required distances, angles and atom labels:
  • Use the DEFINE PARAMETER command to obtain the following lines in the summary area (see previous examples):

    	O..H 4 5
    	O..N 4 6
    	OHN  4 5 6
    	COH  2 4 5
    

    (Note:The numbering of atoms may differ depending on the way of drawing the structure)

  • Select DEFINE ATOM-LABEL, select atoms O₄ and H₅ and reselect ATOM-LABEL The summary area will now include

    	LAB4 4
    	LAB5 5
    

• Calculate the direction of approach of the N-H group to O:
  • Select DEFINE *LP2 (see Special Notes above)
  • Select atoms C₁, C₂, O₄, H₅ in that order.
  • Type THETA and a 'return' for the first parameter.
  • Type PHI and a 'return' for the second parameter, which will give

    	*LP2 THETA PHI 1 2 4 5
    

• Take absolute values of THETA and PHI:
  • Select TRANSFORM to display operators
  • Select ABS, type THETA and a 'return' to construct right-hand side of the equation.
  • Click on '=' to complete and type in the new parameter name, PTHETA and a 'return' at the prompt.
  • Repeat this procedure for PHI to obtain in the summary area:

    	PTHETA = ABS THETA
    	PPHI = ABS PHI
    

• Define histograms and scattergram:
  • Select the HIST command
  • Select O..H and OHN from the summary area
  • Reselect HIST and select SCAT
  • Select O..H and OHN from the summary area again, and the corresponding lines will be written to the summary area.
• The query is complete, so select DEFINE STRUCTURE, and the text screen will tell you the number of screens set (32). Select TO-SEARCH to activate the H-NORMALIZE command as discussed above.
• Select QUEST, then activate T1 and all 'INSIST-' options, and finally, the screen will look like this, take ONLY-ORGANICS before initiating the search with START-SEARCH as in previous examples.

The first hit (using the '95/2 database) is ACMPIM10.
(Note: When using the SAMSAM CSD-subdatabase the first entry found is HESLAS).
Note that the 2D diagram highlights both parts of the search fragment within one subunit:

whereas the corresponding 3D-diagram (select TO-3D) shows the two parts in different subunits of the structure:

Packing the structure is achieved as follows:

• Select RENDER CELL to visualize the unit cell (toggle)
• Select RENDER PACK which displays the unit cell contents plus the non-bonded contact. The non-bonded residue might still be isolated, and
• Selection of RENDER SET-PACK allows you to extend the crystallographic connectivity beyond the single unit cell. Type a 'return' at the prompt for extensions along the a-axis, type -1 1 and a 'return' for the b-axis, and accept the default again for the c-axis. The non-bonded residue is part of a complete molecule.

Last updated on October 19, 1998.