We have crystallized some bioactive organic molecules. On the basis of van der Waals radius of oxygen we found them to possess remarkably short intramolecular oxygen...oxygen interaction. Further, the molecular orbital diagram showed pear shaped orbital overlap between two oxygen atoms.
The characterization of the electron density of such O…O interactions is not common in the literature. But a learned gentlemen tells me that the vdW-radius is a poor descriptor for covalently bonded atoms.
Another idea was to conduct theoretical analysis by Bader theory (AIM—‘‘Atoms in Molecules’’) to support the experimental observation. I hope it is capable of detection of weak interactions of any type such as hydrogen bonds, van der Waals, dihydrogen bonds, oxygen-oxygen interactions etc.
However, for that I’m told that any two overlapping spherical electron densities will yield a bond critical point. A pre-requisite for a BCP as an eigenvalue of the diagonalised Hessian matrix of the total electron density is a local maximum in the Laplacian of the density. No rearrangement of the electrons is required for this purely geometrical effect.
In short I’m confused how to go about. I’m an Organic synthetic chemist, who knows Synthesis, characterisation by spectroscopy and crystallography. I’ve also some experience in deterring themal behavior using DSC, TGA and DTA. I know that whether geometric electronic or any other effect, an interaction between O-O if not repulsive is remarkable. However, the theoretical aspect is beyond me, kindly help!!
Dear Chiranjeev,
I do not know if it helps, I work in different field, but I have investigated in the O-O interaction in the gas phase using a model potential. The theory is simple, the interaction potential depends only on some molecular parameters, such as the polarizability of the particles. I you need a rough estimation you can use the same potential we have used, or adapt it considering the local property of the oxygen atom when bonded to a large molecule. Using this approach you introduce a lot of approximations, but you can adjust the parameter according your need. You can look at the attached paper and to the work of F. Pirani. Hope it helps
Gianpiero
Dear Sir,
Thank you for the help and the paper, I've read it. Since, I'm getting the computation part done by someone else. I will forward the manuscript. However, I'm not sure if it would be applicable in our system. It surely must need a lot of approximations and manuplations. We have coordinates from the crystal structure for investigating intramolecular oxygen-oxygen interactions in structurally rigid bioactive molecules.
May I also ask you an opinion on the characterization of an intramolecular interaction on the basis of vdW radii.
What is exactly the distance between these O atoms? Couldn't be the case of Low Barrier Hydrogen Bond?
There is no hydrogen bond for sure, as there is no hydrogen atom present which could play that role. Further, we have crystal structures and we have studied the packing diagrams also. The distances between two oxygen atoms are between 2.539 to 2.847 angstrom.
Dear Chiranjeev
I am not an expert in potential energy curves, therefore I cannot help you much. If you use vdW potential, it can take into account only weak (physical) interaction, not strong interaction (chemical bond). The potential I was suggested account for the perturbation of the electron cloud, that's why it introduces the polarizability. I do not know what use you think of the interaction potential. If you need it only for energy estimation or you need for molecular dynamic simulation. Obviously, if the atom is attached to a larger molecule, the electron wave function is perturbed, and therefore it changes its properties. If you estimate the energy, the phenomenological potential can be of interest, In the case of molecular dynamics it introduces an error. But there can be many things you could neglect such as rotation and vibration of the molecule that can have an important role in the dynamic of the reaction.
If you want more accurate calculations there exists commercial software that, using semi-empirical rules, estimate the interaction potential of complex molecules.
Dear Chiranjeev,
In my group we study weak interactions. We use NBO and AIM analysis, and more recently Interacting Quantum Atoms, IQA, and Electron Localization Function, ELF. IQA is an atom-atom energetic analysis that gives the strength and the origin of an interaction. Also ELF is very useful to clarify the nature of an interaction. The only problem of IQA is the long computational time for a common molecule.
If you need some help, let me know.
Best regards,
Sergio
Dear Chiranjeev,
This is just to allude to what Sergio said, for your kind of investigation the Interacting Quantum atoms method is probably your best option in this case. As Sergio said its only constraint is its long computation times (due to the fact that originally one could only use Hatree-Fock or MP2 wavefunctions to calculate interaction eneegies and given that HF level of theory is not good enough to obtain accurate informations on most molecular systems) . However recently with the AIMALL program of Todd Keith it is possible to carry out IQA calculations on B3LYP optimized structures and that is much faster. Maybe you should explore this option.
Best Regards,
Adedapo
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