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 faster 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 to P1)
structural model with van der Waals radii assigned to each atom involved.
The default van der Waals Radii can be customized with the
SET VDWR ELTYPE radius (ELTYPE radius ..) instruction [e.g.
SET VDWR C 1.7 H 1.3 O 1.8].
- 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.
The relevant keyboard instruction is:
CALC VOID (PROBE rad[1.2]) (PSTEP n[6]) for 0.2 Angstrom grid
steps.
Example Output
......
Search for and Analysis of Solvent Accessible Voids in the Structure -
Grid = 0.20, Probe Radius = 1.20 Angstrom.
========================================================================
van der Waals (or ion) Radii used in the Analysis
================================================================================
C H Cu N O
--------------------------------------------------------------------------------
1.70 1.20 2.32 1.55 1.52
:: Grid: Y-Axis Step = 0.0139 = Points 72, Angstrom Step = 0.19
:: Grid: X-Axis Step = 0.0119 = Points 84, Angstrom Step = 0.20
:: Grid: Z-Axis Step = 0.0119 = Points 84, Angstrom Step = 0.20
:: Potential solvent area Vol = 624.3 Ang^3 /Unit cell Vol of 3939.0 Ang^3
Note: Expected volumes for solvent molecules are:
A hydrogen bonded H2O-molecule 40 Ang^3
Small molecules (e.g. Toluene) 100-300 Ang^3
:: Use the CALC SQUEEZE instruction to calculate and optionally correct for
:: density identified in solvent accessible areas (Reflection data required)
Area #gpt VolPerc Vol(A^3) X(av) Y(av) Z(av) Nr Eigenvector(frac) Sig(Ang)
-------------------------------------------------------------------------------
1 4070> 20126 4.0 156 0.000 0.184 0.750 1 1.000-0.003 0.520 1.74
2 -0.502-0.002 1.000 1.55
3 -0.001-1.000-0.002 1.35
2 4070> 20134 4.0 156 0.500 0.316 0.250 1 1.000-0.006 0.521 1.74
2 -0.503 0.002 1.000 1.55
3 -0.003-1.000-0.001 1.35
3 4070> 20125 4.0 156 0.500 0.684 0.750 1 1.000-0.008 0.522 1.74
2 -0.504-0.005 1.000 1.55
3 -0.003-1.000-0.004 1.35
4 4070> 20131 4.0 156 0.000 0.816 0.250 1 1.000-0.003 0.523 1.74
2 -0.505-0.002 1.000 1.55
3 -0.001-1.000-0.002 1.35
x y z Shortest Contacts within 4.5 Angstrom (Excl. H)
================================================================================
1 0.000 0.184 0.750 C13 4.27; C13 4.27;
2 0.500 0.316 0.250 C13 4.27; C13 4.27;
3 0.500 0.684 0.750 C13 4.27; C13 4.27;
4 0.000 0.816 0.250 C13 4.27; C13 4.27;
......
Note: Two number of gridpoints are listed:
- The first number corresponds to the number of gridpoints that have
the property of being at least 1.2 Angstrom (Default) away from the van
der Waals sulface of the nearest atom.
- The number of gridpoints in the solvent accessible volume.
VOID TOOLS
PLATON HOMEPAGE
01-Mar-2002 A.L.Spek