VOID & SOLV Calculations
Overview
PLATON offers two options to detect and analyse solvent accessible voids
in a crystal structure. SOLV is a faster version of VOID. VOID is useful
when, in addition to the detection of solvent areas, a packing coefficient
(Kitaigorodski) is to be calculated. The SOLV option is used as part of a
SQUEEZE calculation.
Some background information may be obtained from the
paper: P. van der Sluis & A.L.Spek, Acta Cryst (1990) A46, 194-201.
The algorithm used to detect solvent accessible areas in the VOID
incarnation may be summarised as follows.
- The unitcell is filled with atoms of the (symmetry expanded) structural
model with van der Waals radii assigned to each atom involved.
- A grid search (with approximately 0.2 Angstrom grid steps is set up to
generate a list of all gridpoints (list #1) in the unitcell with the
property to
be at a minimum distance of 1.2 Angstrom from the nearest van der Waals
surface.
- The list generated under 2) is used to grow lists of gridpoints (possibly
supplemented with gridpoints within 1.2 Angstrom around list #1 points)
constituting (isolated) solvent accessible areas.
- For each set of 'connected gridpoints' a number of quantities are
calculated.
- The center of gravity
- The volume of the void
- The second moment of the distribution (The center of gravity can be
seen as a first moment). The corresponding properties of the second
moment (ellipsoid) can be calculated via the eigenvalue/eigenvector
algorithm. The shape of the ellipsoid can be guessed from the
square-root of the eigenvalues: a sphere will give three equal values.
- For each void in the structure a list of shortest distances of
centre-of-gravity of the void to atoms
surrounding the void is calculated. Short contacts to potential H-bond
donors/acceptors may point to solvents with donor/acceptor properties.
As a general remark it can be stated that crystal structures do not contain
solvent accessible voids larger than in the order of 25 Ang**3. However
it may happen that solvent of crystallisation leaves the lattice without
disrupting the structure. This can be the case with strongly H-bonded
structures or framework structures such as zeolites.
Packing Index
The Kitaigorodskii type of packing index is calculated as a 'free' extra
for the VOID calculation. Use the SOLV option when neither the packing
index nor a map-section listing is needed.
It should be remarked that structures have a typical packing index of in the
order of 65 %. However, the missing space is in small pockets, too small to
include isolated atoms.
VOID TOOLS
PLATON HOMEPAGE
05-Feb-2001 A.L.Spek