I think = the pointers previously cited give a good overview of the problem of = ontology in computational chemistry. That term is too broad for usefully = defining an ontology. You really need to identify the problem space you = are working in such as cheminformatics based on data extracted from = ELNs, or assay definitions and types that you might troll through in = pulling data from PubChem etc. Or, the various tools used in QM = applications with terms ranging from basis sets to density functionals = etc.

But on = the philosophy side I=E2=80=99ll quibble a bit on what was said. =

The = quantization of physical phenomena is the =E2=80=98law of = nature=E2=80=99. It is captured effectively in Schroedinger=E2=80=99s = equation due to that mathematical formalism. Quantum mechanics is an = approximation to solutions of Schoedinger=E2=80=99s equation. As = computational power has increased over the decades we are increasingly = able to approach useful problem spaces. That is often through the = combination of methods of varying treatment of electron correlation and = dispersion. The severe scaling of problems means that we still can only = approximate fine details of larger problems.

The = question usually comes down to what level of detail matters to your = problem. Do you want to get some idea of how a protein can move around = your ligand? Various approaches to molecular dynamics will do very = nicely. But, you could add a more sophisticated handling of water = through additional DFT evaluation of each step and add correction factor = forces to the MD. Are you trying to model light harvesting proteins and = account for energetics of photon to electron shift? That=E2=80=99s going = to need more.

DFT, = coupled cluster methods, or pure molecular mechanics are simply = empirical formalisms that are useful in the right setting. =

We can = extend this to QSAR in a dramatic example. If you compile enough = examples of a problem space and develop a mathematical model that = represents that space with high confidence, have you identified a = =E2=80=98law of nature=E2=80=99? The recent Nobel Prize on protein = folding is just that. All these =E2=80=98AI=E2=80=99 methods are well = fitted models, often simply with very deep (many layered) neural nets to = model the phenomena. Even in this space though, there are still = exceptions.

So, how = much =E2=80=98truth=E2=80=99 do you want with your ontology? =

Dominic = Ryan

From:<= /b> = owner-chemistry+m.dominic.ryan=3D=3Dgmail.com+*+ccl.net = <owner-chemistry+m.dominic.ryan=3D=3Dgmail.com+*+ccl.net> On = Behalf Of David Young zqmuser]![gmail.com
Sent: Sunday, = November 10, 2024 8:18 AM
To: Ryan, M Dominic = <m.dominic.ryan+*+gmail.com>
Subject: CCL: Computational = Chemistry Ontology

Darren,

Quantum chemistry is an = application of quantum mechanics, which is generally accepted as a law = of nature, so follow the ontology for laws of = nature.

Molecular mechanics & = dynamics are based on other laws of nature (i.e. Hook's Law of = Elasticity), which are not strictly the correct formulation but have = been validated as giving results that match to experiment to a = reasonable accuracy within a certain region (near equilibrium = geometry). The constants in these equations are fitted to = reproduce experimental data.

Some of the cheminformatics = methods, like QSAR and QSPR, are completely empirical. Although they are = not derived from any law of nature, they can give results accurate = enough to be useful for certain research = needs.

Dave Young (he, him, Dr., scientist, fencer, = author)

The wise person tries to find the = truth.

The foolish = person believes whoever tells them what they want to = hear.

<= p class=3DMsoNormal = style=3D'margin-left:.5in'>

On Sun, Nov 10, 2024 at = 6:40=E2=80=AFAM = Darren Rhodes darren.rhodes!^!gmail.com = <owner-chemistry[a]ccl.net&g= t; wrote:

Sent to CCL by: "Darren Rhodes" = [darren.rhodes]|[gmail.com]
Hi All

Can you point me in = the direction of an appropriate ontology for use in
computational = chemistry?

all the = best

Darren.
darren.rhodes.:.REMOVEgmail.com

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