VOID & SOLV calculations

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 Acta Cryst (1990) A46, 194-201.

The algoritm used to detect solvent accessible areas may be summarised as follows.

The unitcell is filled with atoms of the (symmetry expended) 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 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 b) is used to grow lists of gridpoints (possibly supplemented with gridpoints within 1.2 Angstrom around b-list points) constituting (isolated) solvent accessible areas.

• For each set of 'connected gridpoints' a number of quantities are calculated. 1) The center of gravity 2) The volume of the void 3) 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 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.

  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