SambVca: A Web Application for the Calculation of the Buried Volume of
Organometallic Ligands
by
Albert Poater,a Biagio Cosenza,b Andrea Correa,a Simona Giudice,a Francesco Ragone,a Vittorio Scaranob and Luigi Cavallo*,a
aDepartment of Chemistry, University of Salerno, Fisciano, Italy
bDipartimento di Informatica ed Applicazioni, University of Salerno, Fisciano, Italy
1. What the buried volume, %VBur, is ?
2. How the %VBur is calculated ?
3. Which is the required input ?
4. Which formats can be used to input coordinates ?
5. Which sets of atoms radii are available ?
6. Which sphere radius do you suggest ?
7. Which distance do you suggest for the M-(NHC) bond ?
8. Which mesh spacing should be used ?
9. What about H atoms ?
10. There is a set of tabulated %VBur values ?
12. Terms of use
13. Copyright
11. Citing SambVca
1. What the buried volume, %VBur is ?
The buried volume, %VBur
gives a measure of the space occupied by an organometallic
ligand in the first
coordination sphere of the metal centre, see Figure 1.
Figure 1. Graphical representation of the sphere used to calculate the %VBur.
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2. How the %VBur is calculated ?
Calculating the %VBur
requires the definition of the metal M centre to which the ligand
is coordinated. If the structure to be examined is a transition metal complex,
it can be natural to use the coordinates of the metal centre as in the
structure. Differently, if the structure of the ligand
alone is available, a putative metal centre (M in the following) to which the
NHC ligand is coordinated through the carbene C atom,
see Figure 1, must be defined. Similarly, in the case of phosphines
it is the P atom that is coordinated to the putative metal centre. The M centre
is located on the line passing through the point to be coordinated (C or P in
NHC or PR3, respectively) and the centre of mass of the two N atoms
of the heterocyclic ring in NHCs, or of the three C
(H) atoms bonded to the P atom in phosphines, XN
and XC respectively, see Figure 2. The distance of the M centre from
the coordinating centre of the ligand, d in
the following, is also shown in Figure 2.
Figure 2. Geometrical building of the putative M atom in NHC and PR3
ligands.
Once the position of the M centre is defined, a sphere of
radius R, centred on M, is built. This sphere is sectioned by a regular
3D cubic mesh of spacing s, which defines cubic voxels
vxyz of volume s3.
The distance between the centre of each
voxel with all the atoms in the ligand
is tested to check if any of the atoms is within a van der
Waals distance from the centre of the examined
voxel. If no atom is within a van der
Waals distance, the volume s3 of
the examined voxel is assigned to the free volume
VFree. Conversely, if a single atom is
within a van der Waals
distance, the volume s3 of the examined voxel
is assigned to the buried volume VBur.
With this description, Eq. 1 holds:
1) VSphere =
Σvxyz = Vfree + VBur =
Σvxyz(Free) +
Σvxyz(Buried);
While the VBur
already indicates the amount of the coordination sphere that is occupied by the
considered ligand, we prefer the more intuitive %VBur descriptor
of Eq. 2, which simply is:
2) %VBur = 100*VBur/VSphere.
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3. Which is the required input ?
The input that must be provided is a
file with the coordinates of the ligand to be
examined. If the ligand is part of a complex, ONLY
the coordinates of the ligand must be supplied. In
other words, the user must remove the coordinates of the metal and of all the other
ligands. Beside that, it is mandatory to supply the
following data:
1) The sequence number of the atom that is coordinated to the metal.
2) The number of atoms that
should be used to define the coordination axis, which is 2 for NHC and 3
for PR3, because the 2 N of the NHC or the 3 C bonded to P for PR3
are used to build the axis (see Figure 2.)
3) A space separated list of the sequence number of the atoms defined at step 2.
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4. Which formats can be used to input coordinates ?
Currently, coordinates can be uploaded in 4 different formats.
If other formats are required, please contact us at
lcavallo|@|unisa.it.
1) Simple xyz format
2) Cif format
3) Chem3D format type 1
4) Chem3D format type 2
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5. Which sets of atoms radii are available ?
Currently, three sets of atoms radii are available.
The first one, denoted “Old Set”, is
the set of atoms used in the first %VBur
calculations. It has the disadvantage that the radii are assigned according to
the hybridization state of a given atom. That is, sp2 and
sp3 C atoms are assigned a different radius. This
set of radii is now considered obsolete, and it is kept only for backward compatibility.
The Bondi radii scaled by 1.17 is the set of radii we suggest, based on a fitting of the DFT
binding energy of 33 NHC ligands to the atom in Cp*Ru(NHC)
complexes (see ref. XX).
Unscaled Bondi radii are also available, and finally a user defined set of radii can be
uploaded.
Table 1. Old set, Bondi and scaled Bondi radii, in Å, used to calculate the %VBur.
|
Atom
|
Old set
|
Bondi
|
Bondi*1.17
|
|
H
|
1.16
|
1.20
|
1.40
|
|
C (sp2)
|
1.76
|
1.70
|
1.99
|
|
C (sp3)
|
1.87
|
|
N (sp2)
|
1.65
|
1.55
|
1.81
|
|
N (sp3)
|
1.87
|
|
O
|
1.70
|
1.52
|
1.78
|
|
F
|
1.30
|
1.47
|
1.72
|
|
P
|
1.90
|
1.80
|
2.11
|
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6. Which sphere radius do you suggest ?
We suggest a value of 3.5 Å for the radius, R,
of the sphere built around the metal atom.
This value is based on a fitting of the DFT binding energy of 33 NHC
ligands to the Ru atom in Cp*Ru(NHC)Cl complexes (see ref. XX).
We remark that in the first evaluations of the %VBur
we used a value of 3.0 Å.
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7. Which distance do you suggest for the M-(NHC) bond ?
We suggest a value of 2.10 Å for the M-(NHC) distance, d.
This value is close to the average M-(NHC) distance in the DFT optimized
geometry of a series of (NHC)Ir(CO)2Cl complexes.
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8. Which mesh spacing should be used ?
We suggest a value s = 0.05 Å. This is an optimal trade between accuracy and computing efficiency. As an example of the accuracy, the %VBur of the IMes ligand is 23.645, 23.651 and 23.654 Å3 for s values of 0.1, 0.05 and 0.01 Å, respectively. In terms of computer performances, the calculation of the %VBur for the IMes ligand requires only 0.3 secs on a 3.0 GHz Pentium4, for a value s = 0.05 Å, while it takes some minutes if s is set equal to 0.01 Å.
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9. What about H atoms ?
Normally, H atoms are omitted from the %VBur calculation. However,
they can be included by switching on the “Include H atoms” check-box in the
main SambVca page.
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10. There is a set of tabulated values ?
Below is a set of VBur for the ligands
shown in the table. The NHC geometries have been obtained
from DFT calculations on the (NHC)Ir(CO)2Cl
complexes.
Table 2. VBur for the shown NHC ligands. Bondi radii scaled
by 1.17 for the atoms, radius of the sphere R = 3.5 Å.
|
|
NHC
|
Unsaturated
|
Aromatic
|
Saturated
|
|
|
1
|
18.8
|
18.9
|
19.0
|
|
2
|
24.9
|
25.1
|
25.4
|
|
3
|
26.0
|
26.4
|
25.9
|
|
4
|
31.1
|
30.4
|
31.8
|
|
5
|
35.5
|
38.9
|
36.2
|
|
6
|
36.1
|
40.8
|
36.6
|
|
7
|
30.5
|
30.2
|
31.6
|
|
8
|
30.5
|
30.2
|
32.4
|
|
9
|
31.3
|
30.9
|
32.3
|
|
10
|
31.6
|
31.2
|
32.7
|
|
11
|
33.6
|
31.9
|
35.7
|
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11. Terms of use
Access to the SambVca suite is provided under the following conditions:
* The results obtained from the server shall be used for scientific purposes only, excluding industrial or commercial purposes.
* Proper acknowledgement shall be made to the author of the server in publications resulting from the use of it.
* The results of the server are provided "AS IS" without warranty of any kind.
If you are interested to use the SambVca suite for industrial or commercial purposes, please contact us at lcavallo|@|unisa.it.
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12. Copyright
SambVca - A tool to calculate the buried volume of ligands.
Copyright (C) 2008 Luigi Cavallo
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13. Citing SambVca
Please, cite SambVca and the %VBur as:
Poater, A.; Cosenza, B.; Correa, A.; Giudice, S.; Ragone, F.; Scarano, V.; Cavallo, L.;
SambVca: A Web Application for the Calculation of the Buried Volume of N-Heterocyclic Carbene Ligands
Eur. J. Inorg. Chem. 2009, 1759
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