VOID & SOLV Calculations

Overview

PLATON offers two options for the detection and analyses of solvent accessible voids in a crystal structure. The SOLV option is a faster version of the VOID option and recommended when only the solvent accessible volume is of interest. The additional expense in computing time with the VOID option is useful only when, in addition to the detection of solvent areas, a packing coefficient (Kitaigorodski) is to be calculated (for which also the solvent inaccessible voids between atoms have to be considered). The faster SOLV option is used implicitly as part of a SQUEEZE calculation and CIF-VALIDATION (in order to report about incomplete structures).

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.

  1. 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].

  2. 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.

  3. 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.

  4. 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.

  5. 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 with 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]/GRID [0.2]) (LIST/LISTabc) for 0.2 Angstrom grid steps.

The LIST option produces a printout of the VOID grid.
The default order of x,y&z in the listing may be managed manually with the LISTabc keyword where a,b,c can be X,Y,Z in any order.
E.g. LISTXYZ has X section to section and Z horizontal.
Note: The horizontal grid has 130 steps as a maximum.

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 (#gtp) are listed:

VOIDS&FLIP TOOLS PLATON HOMEPAGE
18-Jan-2005 A.L.Spek