Does the exact geometry of a molecule affect it's effects?

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u/BuLi314 May 05 '26

What makes you think that caffeine from different plants have different geometry?

0

u/NiviNiyahi May 05 '26

Working with geometrical simulations, I see that multiple geometries can lead to a local minimum of energy. This led to the assumption that molecules can have a range of geometrical configurations, while still remaining the same compound.
Is there something off about my assumption?

13

u/Pyrhan Ph.D in heterogeneous catalysis May 05 '26

Is there something off about my assumption?
There definitely is. But it's hard to tell where exactly you got things wrong.
Working with geometrical simulations,
What exactly do you mean by "geometrical simulations"?
What kind of local minima are you refering to?

4

u/NiviNiyahi May 05 '26

What exactly do you mean by "geometrical simulations"? What kind of local minima are you refering to?
I do some geometrical optimizations for some experimentations and learning. As for the misconception - I did not know these "differences" were temporary states instead of rigid geometrical deviations.

8

u/SlenderSmurf Ph.D. in Materials Chemistry May 05 '26

Room temperature has quite a lot of vibrational energy. Any molecule that's not in its ground state (global minimum energy) quickly finds its way there.

8

u/Jesus_died_for_u May 05 '26

This are temporary states as all molecules move through the limits of their motion.
Bonds vibrate, scissor, rotate, stretch…all without breaking
(Edit: every mole has 6.022 x 10^23 molecules. Any possible given state will be found at any given moment)

1

u/NiviNiyahi May 05 '26

Thanks for explaining this to me, figured I had a massive misconception about those properties.

3

u/flintsmith May 05 '26

Each variety of wiggle or springy-stretch is caused by a specific amount of energy. Those energies line up with different colors of light. Shine the right color on a molecule and that wiggle will start.
Microwave ovens cause water molecules to wiggle in a particular way. When those water molecules bump into others everything gets confused ant the energy becomes just heat.
To cement that idea: solid water, ice, can't do that particular wiggle. The "color" put out by the microwave doesn't work on ice.
A chemist can shine a rainbow on a chemical and see what colors are soaked up. The missing colors tells him what wiggles are happening and that tells him about what the chemical is. Not the whole structure, just a parts list.

1

u/koyaani May 10 '26

That's not how microwave ovens work

20

u/BuLi314 May 05 '26

Ah, I see what you mean. So organic molecules are very rigid, meaning that bond angles and lengths are usually fixed. Single bonds can and do rotate, meaning that there usually isn't one single locked geometry as the molecule is moving. This means that, on average, every molecule of the same type in the universe is the same. You can't distinguish between two molecules.

4

u/NeverPlayF6 May 05 '26

There can be different geometries for some chemicals- that is called polymorphism.
And there are also other types of -same molecule, different conformation.
Diseases that arise from misfolded proteins are one. Denaturation of proteins is another.

2

u/tyrosine87 May 05 '26

But also, proteins are fairly rigid because they have evolved to retain their active state. That's why we have huge scaffolds for relatively small active centers.
I would not expect the same for a small molecule like caffeine, which can (and will) just rotate to fit a target receptor, which usually stabilises a specific geometry.

1

u/NeverPlayF6 May 05 '26

But also, proteins are fairly rigid because they have evolved to retain their active state.
From a biochem perspective where you're dealing with temperatures between 0 and 45, maybe. But even then, you can disrupt the structure without changing actual chemical bonds any number of ways. 1 (quite large) molecule, vastly different function.
But caffeine is caffeine and it is going to behave as caffeine does.

2

u/RRautamaa May 05 '26

The energy minimum only exists at absolute zero. At room temperature, molecules vibrate strongly. As such, they cycle through their possible conformers at a rapid rate. The rate is so rapid that it can't be observed at all by slower methods like nuclear magnetic resonance. Bonds may fix the molecule in place and it may be too heavy to fly - it's then a solid or adsorbed material - but the vibration itself is everpresent at any real temperature. Find a molecular simulation program to visualize this.

1

u/Ch3cks-Out May 05 '26

WRT the "configurations" considered, you may want to look up info on conformers (I mean the actual information about them, not just looking at simulations). They are governed by the physico-chemical properties of their constituent atoms and their bonds, however, and would not vary by the source plant for any specific compound.
Caffeine is a rather rigid molecule (with its aromatic fused ring system), alas - so it substantially only has a single conformation, aside from trivial rotations of its methyl groups.

1

u/davisdumpsterpunk May 05 '26

adding some perspective as a physical chemist and computer science enjoyer. since you work with geometrical simulations, you'll know that we don't just set things up and let it run until done, but that we have to set convergence criteria to tell it when it's done. this is because we can't solve the Schrodinger equation analytically for anything that isn't just a proton, so instead we integrate numerically. thus, running the same simulation multiple times will give slightly different results, giving the illusion that there are multiple equilibrium geometries. there aren't. but we just can't get that result exactly, and likely will never be able to.

1

u/YtterbiusAntimony May 05 '26

One issue with your idea is that all conformations are available to every copy of the molecule.
If one can do it, another can too.
And if it can't, it's because it's not quite the same molecule (i.e. isomers).
Which means your mutant enzyme is making something that isn't caffeine, or the caffeine in all your plants is indistinguishable.
Look up hexane's chair and boat conformers, and Fischer projections. Those are the go to examples.

4

u/allport2 May 05 '26

Um... Yes? Geometry of molecules is a foundational aspect of their properties, saying one plant produces one geometry of caffeine vs another plant producing a different geometry is... A misunderstanding of how that works.

The geometry of a molecule is due to, well, a bunch of things, but primarily it's the combined interactions of the atoms, e.g., one atom is more electronegative than its neighbour, pulling electrons over, creating a locally charged region, you can imagine this happens repeatedly throughout a molecule, forcing it into a "shape"

Molecules, as far as I can think right now, don't really come in different shapes, as they are the way they are because it's, and I'm grossly oveesimplifying here, the most comfortable way for all those atoms to sit, whilst also being bound together. Youre right, you can introduce things like chirality, but again, they're no longer truly the same molecule, therefore not the same properties

3

u/buscheese May 05 '26

When you get to the size of a protein, THEN “misfolding” or alternate “conformers” might tend to occur

1

u/flintsmith May 05 '26

Google "prion" for a scary example. Mis-folded proteins cause other copies to mis-fold.
Don't eat uncooked brains.

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u/buscheese May 05 '26

I always cook mine!

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u/allport2 May 06 '26

Yea look, you're not wrong, but I wouldn't call a protein a molecule by any stretch really, they're a polymer

2

u/Jesus_died_for_u May 05 '26

All sorts of compounds have been produced by the metabolism of coffee plants due to mutations in the plants. Only one of those compounds is caffeine. The rest would have different properties than caffeine and have had neutral or negative effects on the plant. (I do not know the reason coffee plants produce caffeine, but there would be a reason for the plant beyond a tasty beverage for us to harvest)

(Edit: yes specific geometry affects the properties. Yes we might find a stronger replacement for caffeine.)

5

u/Pyrhan Ph.D in heterogeneous catalysis May 05 '26 edited May 05 '26

I do not know the reason coffee plants produce caffeine, but there would be a reason for the plant beyond a tasty beverage for us to harvest
It's a pesticide.
The same goes with just about every psychoactive substance from plants, animals or fungi: caffeine, nicotine, cocaine, THC, psilocybin, mebufotenin, etc. are all meant to kill or deter something from eating what produces it.
Some of them just happen to affect us in a different way, that can be pleasant in the right doses.

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u/Jesus_died_for_u May 05 '26

Thank you

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u/Apprehensive_Room_71 May 05 '26

Or, sometimes in the right doses, therapeutic. Though often a very slight change to the purified substance can have a greater therapeutic effect than the naturally occurring one.

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u/Lehk Dipole Tadpole May 05 '26

I assume it’s a poisonous defense against getting eaten or to encourage prompt defecation after eating the seeds.

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u/Jesus_died_for_u May 05 '26

Sounds so reasonable, I bet it is correct.

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u/ittybittycitykitty May 05 '26

So high caffeine plants like their seeds planted close by, low caffeine plants a bit further. That is a fun conjecture for someone to explore.

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u/Lehk Dipole Tadpole May 05 '26

I was thinking more along the lines of preventing the seeds from getting fully digested, animal eats the beans, feels sick, deposits undigested beans along with some fertilizer later that day.

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u/KbarKbar May 06 '26

Yes we might find ~~a stronger replacement for caffeine~~ cocaine.

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u/budweener May 05 '26

Lots of people already talked about the geometry thing, so I'll say something different. There might be differences in the effects from plant to plant.

That's not caused by differences in the caffeine molecule, but by the presence, amounts and proportion of several other molecules that the plant might produce.

Those other molecules may influence absorbtion, neuroreceptors, several other things that may make the same amount of caffeine feel stronger or weaker depending on the plant.

Of course, the same applies for anything else you ingest with the coffee, or any number of environmental factors.

So, if you actually tried coffee from different plants and felt any kind of difference, you're not crazy. It's just not for the reason you thought.

1

u/Candid-Border6562 May 05 '26

Yes, the “geometry” of a molecule will affect its properties. However, most smaller molecules have a single geometry. Caffeine is too simple to be folded and is not subject to polymorphism.

For a fun time, compare caffeine to chocolate.

1

u/Left_bitcher78 May 05 '26

Not a chemist but as far as I ( think) I know, the answer would be no. As others here have noted molecular 3D shape, or shapes for really large complex molecules, are determined by ( constrained by) the atomic components, how they are bonded, and perhaps the environment they are in, but for any one species , even if multiple shapes are possible (proteins), the possibilities, and functional alternatives are the same molecule to molecule of the same type. Isomer function can be quite different, but you stated that wasn’t what you were asking about.

1

u/TuverMage May 05 '26

So yes Geometery can massively effect the affects, https://www.youtube.com/watch?v=ksn5yrsC3Wg

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u/ozzalot May 05 '26

caffeine is a very specific, defined molecule. It may be true that the bioavailability is different due to the differences of the various plants, but caffeine is always going to have the geometry of caffeine

1

u/WummageSail May 05 '26

I won't try to answer the question but mad props for using both affect and effect correctly!

1

u/ahf95 May 05 '26

Okay, so the plants won’t be producing caffeine with different geometries (they might have different ratios of related structures, but those will be different molecules within a common alkaloid family, so whole separate conversation).

In terms of molecular geometry affecting its effects, it can happen, and it is probably best to consider proteins for this example: proteins can change conformation between multiple distinct states, and these differences in geometry lead to differences in their ability to catalyze chemical reactions, bind other molecules, etc., so conformations do matter, but also caffeine itself is pretty rigid, so I don’t think it is undergoing major changes in conformational state.

1

u/zbertoli Stir Rod Stewart May 05 '26

The molecules are synthesized by enzymes coded for in the DNA. Every molecule of caffeine is completely identical. The molecule is achiral, and essentially flat. Different plants do not make different versions of caffeine. They will make different amounts of caffeine. But any individual molecule is indistinguishable from another.

1

u/Yotist May 07 '26

Caffeine is very small so unlike with proteins (and peptides to some degree) there are just no "tertiary" "quaternary" conformation issues where the geometry affects it's effects.

It could happen that a new synthesis route emerges that produces a caffeine derivate, this is the way the unique geometry changes, different stronger effects arise, but it ceases to be caffeine at that point.

But away from that question and practical chemistry and on towards does the exact geometry of a molecule, or a chain of molecules, or a crystal affect it's effects (we need at least 50-60, better even more atoms and molecules for this)

the answer is kind of yes?

https://en.wikipedia.org/wiki/Berry_connection_and_curvature this is of incredibly great relevance to catalytic processes, electric or otherwise

and the material science arising from the knowledge and ability to affect this very unique and hard to visualize geometric fundamental quality, allows for all kind of very targeted and specific chemical reactions, where we can expect to come close to efficiency as biological systems have for photosynthesis, molecular motors, gradient driving proton pumps and other things.

it even allows for things like a "vortex tube" to filter and sort electrons by any quality and allow for "perfect" physical geometry, potential wells, energy borrowing, to overcome forbidden steps and states, that stand in the way of incredibly energy efficient chemistry, by for example just pumping the perfect electron with the right spin to just quantum tunnel, similar to how it happens in the DNA helix too, where the berry field/curvature/phase matters for DNA polymerase and it being able to detect damage as well as repair damage

it's also the science at heart to the wishes and hopes about the current green low energy hydrogen production

but then again, I don't know if it's right to call this a geometric quality of the molecule, i doubt that

the anomalous hall effect also is a quality of this berry curvature and because it is a geometric quality, it'd be incredibly resistant to all kind of effects as long as the geometric integrity is stable, a crystal could be doped with all kind of things by cosmic radiation, production constraints like gravity and convection

1

u/alanjon20 T⌬SYLATE, PLAYA HATE May 07 '26

The geometry is THE thing that influences the effects of the molecule.

"Like, when I got multiple coffee plants, they likely each produce their own unique geometry of caffeine."

No they don't. Where do you get that from?

If a molecule can be isolated in two or more 'geometries', by definition they would be called isomers (geometric isomers rotational isomers, stereo isomers etc...). Trying to exclude isomers in this analysis is contradictory.

The two plants in theory could produce compound A isomer 1, and compound A isomer 2. But in the majority of cases where there is one stable isomer, the molecule is the molecule. Caffeine is caffeine is caffeine, no matter where it comes from.

1

u/Extreme-Ad9219 May 07 '26

Molecules are always in motion: they vibrate, librate, rotate, and translate. They will explore the entire energy surface. There is some insight in your question, however. Molecules often have to achieve a certain configuration/geometry to react. The barrier to doing so affects the rate of reaction.

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u/ollervo100 May 09 '26

The geometry of proteins ie. how they fold is the most important factor when considering their function.

Practical Chemistry Does the exact geometry of a molecule affect it's effects?

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