BOMD calculations with g09

As part of the work in collaboration with Dr. Fernando Cortés we are working in the nature of chemical bonding and chemical interactions, as revealed by the Quantum Theory of Atoms in Molecules (QTAIM) , under dynamic conditions. The basics of this theory could be found in Bader’s book. This have lead to the publication of an article titled “Dynamic Molecular Graphs:“Hopping” Structures” this year, but it is our best hope that more will follow in the near future.

In this article we studied the temporal evolution of the molecular structure of [Fe{C(CH2)3}(CO)3], throughout Born-Oppenheimer molecular dynamics (BOMD). This system was interesting for us because it was not clear the nature of the interactions between the terminal carbons in the trimethylenemethane and the central Iron atom, with QTAIM and Molecular-Orbital theory interpretations contracting each other: the former argues  for a η-4 ligand, while the latter propose a single sigma interaction between the Iron and the central carbon.

We found that the bond paths between the trimethylenemethane carbons and the metallic core are uninterruptedly formed and broken along the simulation. Thus, our results suggest that a single structure is not the best way for describing the system. Why it should be?


System studied [Fe{C(CH2)3}(CO)3]. On the left the initial proposal of a four coordination ligant. On the right the Molecular Orbital suggestion. The reality is something in between.

This is wonderful and all, but the post about using bomd in g09, not about the great article that was published. What’s is BOMD[1]? It’s a molecular dynamics model where the quantum mechanical effect of the electrons is included in the calculation of energy and forces because the trajectories are computed directly using an electronic structure method. This ab initio calculation, however very costly, was in our opinion the best approach to our problem.

BOMD is implemented in many computational structure programs. We choose Gaussian09 because it was easy to use, or it looked like it at the beginning. Unfortunately, the manual is not as extensive and explicative as it could be.  So, maybe a set of examples could be helpful to those of you trying to apply the same methodology it your work.

A simple example, the movement of a water molecule using DFT is:


#p b3lyp/cc-pVDZ BOMD


0 1
O    0.000000    0.000000    0.117493
H    0.000000    0.757756   -0.469971
H    0.000000   -0.757756   -0.469971

Another example, this time  the simulation runs along a selected coordinate, in this case the H-H distance, is carried out using the keyword Phase. This keyword choose a bond if two atom numbers are listed, an angle if three, and a dihedral if four. Besides, a temperature of 300 Kelvin is selected, and 1300 steps are computed.


#p b3lyp/cc-pVDZ BOMD(Phase=(2,3),RTemp=300,MaxPoints=1300)


0 1
O    0.000000    0.000000    0.117493
H    0.000000    0.757756   -0.469971
H    0.000000   -0.757756   -0.469971

So, that’s it. Try them, and have fun.

[1]X. Li, J. M. Millam, H. B. Schlegel, J. Chem. Phys. 2000, 113, 10062.


Acerca de José Manuel

I'm from Mexico and currently in a PhD program in the University of Oviedo, in Spain.
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