xyz2mol converts xyz files to RDKit mol objects and can be used to summarize organometallic compounds from xyz files by determining the charge of metal ions using information from the localized molecular orbitals (LMOs). While LMOs provide information on how electrons are distributed among atoms, xyz2mol is still needed to construct the molecular structure and assign charges to individual metal atoms in multi-metal systems. This allows organometallic structures to be analyzed in cheminformatics tools.

1. xyz2mol for organometallic compounds
xyz2mol
N
N
N
Cl
Cl
O
O
O
Si
N
H
O N
N
N
Cl
Cl
O
O
O
Si
N
H
O
xyx2mol converts an xyz file to an RDKit mol object
(needs the molecular charge)
github.com/jensengroup/xyz2mol

2. Organic examples
X
H
H H
H H
H H
H
* *[4, 4, 1, 1]
H
H H
H
valence
N
H
H
H
O
O
N
H
H
H
O
O
N
H
H
H
O-
O-
[2, 4, 1, …] N
H
H
H
O
O
*
*
N
H
H
H
O
O
N+
H
H
H
O
O-
[1, 3, 1, …]

3. Organometallic SMILES (in RDKit)
There are 2 types of bonds to TMs: covalent and dative
Only dative gives correct total charge

4. One possible xyz2mol implementation
Dative bonds don’t count
Must know charge of metal ions
O HFe[0, 1, 1] O HFe -O HFe+3
+2

5. Organometallic examples
How to determine the charge of the metal?
N
R N C-
R N C-
Pt+4
Charge of metal ion = total charge − ∑ charges on ligands
Number of e- on metal ion = Total number of e- − number of e- on ligands
Charge of metal ion = number of e- on neutral metal− number of e- on metal ion

6. Organometallic examples
Determining the number of e- on ligands using GFN2-xTB Localized MOs
'[Fe+2]<-O' 4 MOs/8 e- primarily on O => 14-8 = 6 e- on Fe => Fe+2
number of electrons : 14
charge : 2
spin : 0.0
LMO Fii/eV ncent charge center contributions...
1 sigma -29.16 1.69 -0.54034 -1.28587 -0.25605 2O : 0.73 3H : 0.25
2 pi -28.03 1.38 0.27859 -0.67166 -1.24648 2O : 0.84 1Fe: 0.16
3 pi -27.79 1.42 0.77640 -0.84137 -0.37201 2O : 0.82 1Fe: 0.18
4 sigma -27.41 1.53 -0.16053 0.10969 -0.26743 2O : 0.79 4H : 0.14
5 sigma -23.13 1.52 1.95856 0.72486 -0.57154 1Fe: 0.79 4H : 0.19
6 LP -22.93 1.00 4.85138 1.58486 -0.69634 1Fe: 1.00
7 LP -22.92 1.00 5.07576 1.29249 -0.49843 1Fe: 1.00

7. Organometallic examples
Determining the number of e- on ligands using GFN2-xTB Localized Mos
xTB does not give occupancy,
so ligand LMOs are assumed to be doubly occupied.
'[Fe+2]<-O' 4 MOs/8 e- primarily on O => 14-8 = 6 e- on Fe => Fe+2
number of electrons : 14
charge : 2
spin : 0.0
LMO Fii/eV ncent charge center contributions...
1 sigma -29.16 1.69 -0.54034 -1.28587 -0.25605 2O : 0.73 3H : 0.25
2 pi -28.03 1.38 0.27859 -0.67166 -1.24648 2O : 0.84 1Fe: 0.16
3 pi -27.79 1.42 0.77640 -0.84137 -0.37201 2O : 0.82 1Fe: 0.18
4 sigma -27.41 1.53 -0.16053 0.10969 -0.26743 2O : 0.79 4H : 0.14
5 sigma -23.13 1.52 1.95856 0.72486 -0.57154 1Fe: 0.79 4H : 0.19
6 LP -22.93 1.00 4.85138 1.58486 -0.69634 1Fe: 1.00
7 LP -22.92 1.00 5.07576 1.29249 -0.49843 1Fe: 1.00

8. If I have LMOs, do I need xyz2mol?
yes
H
H
H
O
O-
LMO Fii/eV ncent charge center contributions...
1 sigma -9.37 2.01 -1.61159 -0.13544 1.38118 6H : 0.50 1C : 0.49
2 sigma -9.34 1.98 -1.76449 -1.08061 -0.68688 7H : 0.50 1C : 0.50
3 sigma -9.34 1.98 -1.76644 1.16814 -0.48379 5H : 0.50 1C : 0.50
4 sigma -8.95 1.94 0.01538 0.00110 -0.02886 1C : 0.56 2C : 0.45
5 pi -8.69 1.84 2.28053 1.43359 0.30010 4O : 0.65 2C : 0.34
6 pi -8.66 1.83 2.26094 1.39605 -0.61388 4O : 0.66 2C : 0.34
7 LP -7.66 1.03 1.66619 3.53830 -0.24102 4O : 0.98
8 pi -7.56 1.81 2.43494 -1.38722 0.38833 3O : 0.67 2C : 0.33
9 pi -7.48 1.80 2.42087 -1.43266 -0.47667 3O : 0.67 2C : 0.32
10 LP -7.37 1.04 4.36348 2.00006 -0.23648 4O : 0.98
11 LP -6.78 1.02 1.91370 -3.63042 0.05796 3O : 0.99
12 LP -6.54 1.03 4.60590 -1.85302 -0.08025 3O : 0.99
H
H
H
O
O

9. Multi metal ion systems
We can only compute an combined charge of metal ions
The assignment to individual atoms will be arbitrary
But won’t affect any QM calculations.

10. Why xyz2mol for organometallics?
Most homogenous catalysts are organometallics