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*LP3

*LP3 is used to define the angular relationship of a vector to an sp3-plane.

Remarks

In practice this command is most often used in studying the approach of a hydrogen atom to an sp3 oxygen atom and the consequent potential for hydrogen bonding.

Consider the following:

The format of the *LP3 command is:

DEFINE *LP3  <parnam1>  <parnam2>  i  j  k  n

<parnam1> : 

The angle between the probe atom vector (k->n) and the plane bisecting the angle i k j, as illustrated in the Figure above. The range of values is -90.0° <= parnam1 <= +90.0°. The plane bisecting the angle i k j generates two hemispheres of parnam1 values. The hemisphere of positive parnam1 values contains the vector k->i.

It should be noted that the definition of parnam1 is different from the polar angle usually found in spherical polar coordinate systems. Parnam1 starts from the plane bisecting the angle i k j instead of the normal to the plane as in the standard spherical polar coordinate system. This modification was made so that the angular parameters have more intuitive chemical meaning. A parnam1 value of 0.0 means the probe atom lies in the plane of the putative lone pairs of the sp3 atom.

<parnam2> : 

The angle between the projections of the vector k-> i and k-> n (the probe atom vector) on to the plane bisecting the angle i j k. The range of values is -180.0 <= parnam2 <= +180.0°. The plane i j k generates two hemispheres of parnam2 values. The hemisphere of positive parnam2 values is identified by the cross product of k->i and k->j (the parnam2 angle identified in the Figure thus has a positive value).

<parnam2> is the same as the azimuth angle in the standard spherical polar coordinate system. A value of +/-125.25 means the probe atom is collinear with an sp3 - lone pair direction.

i  j  k  n :

Atom numbers, centroids and/or dummy points.

i j k specify an sp3 plane with origin k, and n is the probe atom for calculating angular parameters. i and j define the positive hemispheres for parnam1 and parnam2. The order in which i j k n are given is CRITICAL to obtain the correct results.

Example

• Select *LP3

• Select or type items for *LP3. If necessary reselect *LP3 to end
  input.
  Select CANCEL to cancel command.

• Select atom number 2

• 2 appears in the dialogue area

  A red + appears at atom 2 in the fragment.

• Select in turn atoms 4 3 1

  As each atom is selected a red + appears at the atom in the fragment.

  After the selection of the fourth atom these red crosses disappear.

• In the dialogue area we now have:

  DEFINE, *LP3,
  Input *LP3 parameter name no.  1

• Type THETA <RETURN>

• In the dialogue area we now have:

  DEFINE, *LP3, THETA,
  Input *LP3 parameter name no.  2

• Type PHI <RETURN>

• In the summary area we now have:

  *LP3  THETA  PHI  2  4  3  1

  This line is displayed in green to indicate that it is a DEFINE command.

  In the dialogue area we now have the "home" prompt:

  Search for ALL crystal fragments
  OVERLAP of crystal fragments permitted
  Select a menu command or TO-BUILD to return to the BUILD menu.

  The resultant command in the instruction document is:

  DEFINE  *LP3  THETA  PHI  2  4  3  1

The order in which the four atoms, centroids and/or dummy points i j k n are specified is important.

The non-bonded vector must be between the atoms, centroids and/or dummy points k and n.

In a single search test there can be a maximum of 10 *LP3 instructions.

Related Command

DEFINE *LP2

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Volume 2 Chapter 3 3D-Constrain Sub-menu *MASK.