Implementing “Ab initio” approach in molecular mechanics method

  • #1
Spathi
75
7
TL;DR Summary
We carry out a calculation with a quantum chemical method, for example DFT, and then use the calculation results as a sample for training the molecular mechanics functional;
Experts in physics, physical chemistry and organic chemistry are invited to the thread. I work in the field of quantum chemistry, and have plans of implementing molecular mechanics calculations in my program Chemcraft. Some people say that molecular mechanics can work rather well in some cases, e.g. for finding conformations of organic molecules. And I have a feeling that I can implement something new.

The general idea is as follows. We carry out a calculation with a quantum chemical method, for example DFT, and then use the calculation results as a sample for training the molecular mechanics functional; we adjust the parameters of our MM functional so that we get the best agreement with the results of the DFT calculation. And then we use the resulting custom MM functional to perform calculations for a more complex problem for which the original DFT method is too expensive.

As an example: firstly we calculate the vibrational spectrum with DFT (the second derivatives of energy with respect to the coordinates of atoms), then we use the force field and other parameters to fit the MM functional, and then we use the resulting MM functional to calculate the anharmonic force field (the third derivatives with respect to energy), and this allows you to predict overtones in the vibrational spectrum, or for example more accurate vibrational entropy.

So, for such an approach, it is necessary to implement the MM model in such a way that the MM calculation in it is rather not “good”, but “non-empirical” (“ab initio”). In other words, this MM model should be based on some universal, fundamental principles; then, in the general case, fitting the parameters of the MM functional will work well. What do I mean by fundamental principles? For example, steric repulsion: unbound atoms at distances near the van der Waals radius usually repel each other. An example of another universal principle is the Lennard-Jones potential. How versatile is its formula?

I will write more specifically about my ideas and questions later.
 
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  • #2
Spathi said:
The general idea is as follows. We carry out a calculation with a quantum chemical method, for example DFT, and then use the calculation results as a sample for training the molecular mechanics functional; we adjust the parameters of our MM functional so that we get the best agreement with the results of the DFT calculation. And then we use the resulting custom MM functional to perform calculations for a more complex problem for which the original DFT method is too expensive.
What is novel about that approach?

Note that PhysicsForums is not a place to do research.
 
  • #3
DrClaude said:
What is novel about that approach?
Can you tell more where this approach is implemented?

DrClaude said:
Note that PhysicsForums is not a place to do research.
Even a research in applied science? I thought you just struggle with people like anti-relativists.
 
  • #4
Spathi said:
Can you tell more where this approach is implemented?
A quick literature search returned results such as

G. A. Kaminski et al., Development of an Accurate and Robust Polarizable Molecular Mechanics Force Field from ab Initio Quantum Chemistry, J. Phys. Chem. A 2004, 108, 4, 621–627

G. D. Smith and W. Paul, United Atom Force Field for Molecular Dynamics Simulations of 1,4-Polybutadiene Based on Quantum Chemistry Calculations on Model Molecules, J. Phys. Chem. A 1998, 102, 7, 1200–1208

J. Sabolović, Modeling Anhydrous and Aqua Copper(II) Amino Acid Complexes:  A New Molecular Mechanics Force Field Parametrization Based on Quantum Chemical Studies and Experimental Crystal Data, Inorg. Chem. 2003, 42, 7, 2268–2279

Spathi said:
Even a research in applied science? I thought you just struggle with people like anti-relativists.
From the Physics Forums Global Guidelines:
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Greg Bernhardt said:
Physics Forums is not intended as an alternative to the usual professional venues for discussion and review of new ideas, e.g. personal contacts, conferences, and peer review before publication. If you have a new theory or idea, this is not the place to look for feedback on it or help in developing it.
 
  • #5
Currently I have the following question. As far as I understand, the energies of covalent bonds are usually described by Morse potential or MLR potential:

https://en.m.wikipedia.org/wiki/Morse_potential

The energies of nonbonding interaction are described by the Lennard-Jones potential or Mie potential:

https://en.m.wikipedia.org/wiki/Lennard-Jones_potential

$$U(R)=4\varepsilon*(\frac{\sigma}{r^{12}}-\frac{\sigma}{r^{6}})$$

Did anyone suggest to include the $$r^{-6}$$ term (and maybe the $$r^{-12}$$ term too) for bonding (covalent) interactions in addition to the Morse/MLR term? I mean, that even when atoms are bonded, possibly this do not prevent other interactions between then, in particularly the London dispersion force ($$r^{-6}$$).
And one more question - are the London dispersion forces taken info account in usual DFT functionals like B3LYP, or the dispersion correction (D3, D4) must be used for this?
 
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