How would you describe briefly your own mental modeling of chemistry?

[sbrothy]

I admit it was a little tongue in cheek. Hence the smiley. I'm more of a assembler/c/c++ fan though. I kinda regard all these new languages, Tcl, python, what have we - heck even Perl - as glue to make "real" programs work together. Probably not a popular view, but then again, I am pretty old school.


EDIT: Also, I fear quantum chemistry is way beyond me. I'm not as smart and educated as I may look to the casual observer. Darn, even @TensorCalculus triggers my inferiority complex!

EDIT: And it just occurred to me that the word “even” in that sentence might be misconstrued as derogative, which was in no way my intention. I apologize for any misunderstanding.

 

[TensorCalculus]

At some points - like Pauli working out the exclusion principle - it's an interplay between physics, maths and chemistry - which really are almost arbitrary classifications at times like that, IMO.

Formulating the rules: of course this will require looking deeper, using physics and maths.
Just like developing functions in python: someone has had to write the code for it in a lower-level language or machine code at some point :)

On a slightly unrelated note: it's interesting how the Pauli exclusion principle is used/perceived differently by different subjects. My friend who is passionate about chemistry kept calling it the "bus filling principle". Took me a while to figure out what she was talking about.

Sometimes - but on other occasions, like when Peter Mitchell was doing his Nobel Prize-winning work identifying how life captures energy - https://en.wikipedia.org/wiki/Chemiosmosis - transforming the understanding of bioenergetics, I think he probably did need to to worry about what's going on "behind the scenes" in terms of the electron transport chain, proton pumps and electrochemical gradients, not just the chemical surface scenery of adenosine triphosphate (ATP) and its diphosphate (ADP).

Ah yeah, sometimes they do need to look deeper. Hence the "too much" when talking about people not having to worry about what's going on behind the scenes :D

Take a look at quantum chemistry, then - it's nothing but equations: from calculus and Lie algebra to group theory and beyond, eventually realised as computer programs - mainly FORTRAN, C AND C++ - and of interest to TensorCalculus - Python,: so you might consider Python at two levels in chemistry.

Ooh I should: I'm curious as to how it differs form quantum physics!
The thing is, as someone who knows basically 0 chemistry, I don't consider Quantum in the fundamentals: if I did, my analogy would be different.

I admit it was a little tongue in cheek. Hence the smiley. I'm more of a assembler/c/c++ fan though. I kinda regard all these new languages, Tcl, python, what have we - heck even Perl - as glue to make "real" programs work together. Probably not a popular view, but then again, I am pretty old school.

Honestly fair enough: I don't use C/C++ because python and rust are more preferable OK I admit I don't have admin rights on my computer and in order to get C++ working on VSCode you need admin rights (there's probably an alternative way to do it but I never bothered to find it) so I just stick with python....

EDIT: Also, I fear quantum chemistry is way beyond me. I'm not as smart and educated as I may look to the casual observer. Darn, even @TensorCalculus triggers my inferiority complex!

Hmm so he says, but I beg to differ: he's a pretty big nerd: even if it's not the type of nerd most people on PF are :D. He wrote... thousands of lines of code... just to cheat on wordle... if that's not a nerd I don't know what is.

(I'll take the compliment - appreciated but it shouldn't be True!)

EDIT: And it just occurred to me that the word “even” in that sentence might be misconstrued as derogative, which was in no way my intention. I apologize for any misunderstanding.

Never occurred to me to think of it that way: it was one hell of a compliment considering my age!

 

[berkeman]

My friend who is passionate about chemistry kept calling it the "bus stop principle".

Can you elaborate? So far I'm not getting the analogy. Thanks.

 

[TensorCalculus]

Can you elaborate? So far I'm not getting the analogy. Thanks.

Whoops, typo. She called it the "bus filling principle" (which might make more sense... sort of. I don't really get the name either)

She was explaining something to me before the chemistry Olympiad: I think we were revising orbital bonding or something, I can't remember anymore... essentially she was explaining how something worked and kept referring to the Pauli exclusion principle as the "bus filling principle": when I asked her what it was she thought I was joking:

"You're a physics nerd: of course you know the bus filling principle, don't you?"
"No... what on Earth is that"
"<provides a description of the Pauli exclusion principle>"
"You mean... the Pauli Exclusion Principle?"
"Uh... I think so? I've rarely heard it called that though (pulls out textbook and shows me it being described as the 'bus filling principle')"
"Riiiight... chemists are weird sometimes"
"I could say that about physicists too"

That comment about Chemistry students vs Physics students perceiving the Pauli Exclusion principle differently was just a little slightly unrelated note of mine, don't really know why I included it but...

 

[berkeman]

Whoops, typo. She called it the "bus filling principle"

Oh, that could make more sense. Only one student per seat on the bus...

https://skagwaynews.com/2022/02/25/dog-bus-captures-hearts-attention-of-internet/

 

[pellis]

With thanks to all contributors so far, here is my own answer to the question, with an explanation after it, for anyone interested in how I reached it. Even though I would now make some small changes as I can see that it's not quite as clear as it seemed to me at first, I've left it as I first wrote it, with whatever faults you feel able to point out.

“THE ESSENCE OF CHEMISTRY resides in the dynamics of electrons interacting with the electro magnetic (em) field - primarily that provided by nuclei – while also being constrained by the Exclusion Principle. The influence of gravity can usually be ignored.

One can then visualise chemical activity as the rearrangement of nuclei within the em field of its accompanying electrons, subject to the thermodynamics of changing conformations and reactivities.

The thermodynamics of changing conformations and reactivities depends, in turn, on the affinities of atomic and molecular species that result from electronegativities - the net effect of the electronic structure enveloping the nuclei, providing the influences for the essential dynamics outlined above."

This summary is a shortened version of a minor epiphany that occurred to me, as an improvement in my own mental model of what chemistry is about, some time after being stimulated by reading https://www.newscientist.com/article/dn25894-meet-the-electric-life-forms-that-live-on-pure-energy/

[The final year of my undergraduate degree specialised in physical and inorganic chemistry, omitting organic chemistry, and consequently I never developed any real sense of biochemistry.]

But as a former quantum chemist, I felt that the idea that life could “feed off electrons” was something that I should have some familiarity with. After nagging at me for a few years I recently got round to looking into this subject in sufficient detail.

At first, I couldn’t see beyond the biochemical explanation that “life runs on electron transfer” from the potential energy drop down the https://en.wikipedia.org/wiki/Electron_transport_chain Etc (pun intended) resulting in “cells using the free energy of ATP”.

[ I should mention that my way of understanding scientific ideas (and most other things) is generally based on being able to visualise something.]

So, it wasn’t until I could finally bridge my visual/conceptual gap by mentally seeing how the free energy from ATP enables key cellular tasks: by donating one of its phosphate groups in a way that “changes the shape or reactivity of biomolecules” e.g. by something as straight-forward as the mechanical work of muscle contraction via actin-myosin interactions www.ncbi.nlm.nih.gov/books/NBK9961/

So, ATP can cause changes in the conformation of some biomolecules and by understanding that I finally felt (!) that I had achieved a satisfying understanding of how, ultimately, it can be said that life feeds off electrons.

I look forward to learning more from any points where you think I could improve it (using the remaining 41 words).

 

[erobz]

Chemistry as I took the required course ( just Chem 1 ) felt like organized chaos. "Here we are, but there is no clear record of where we've been, nor any logical indication of where we will go"...I felt like that at every section. Still have the textbook though.

 

[pellis]

Chemistry as I took the required course ( just Chem 1 ) felt like organized chaos. "Here we are, but there is no clear record of where we've been, nor any logical indication of where we will go"...I felt like that at every section. Still have the textbook though.

Sounds like poor lecturer/tutor support.

 

[pellis]

Ooh I should: I'm curious as to how it differs form quantum physics!
The thing is, as someone who knows basically 0 chemistry, I don't consider Quantum in the fundamentals: if I did, my analogy would be different.

@TensorCalculus As the name implies, https://en.wikipedia.org/wiki/Quantum_chemistry is the application of quantum physics to chemical systems/problems.

In my day that often boiled down to using large computer programs to solve, by energy minimisation, approximations to Schrödinger's equation (from Hartree-Fock to a range of "semi-empirical" methods, most of which tried to avoid dealing with the complication of "overlap integals" to varying degrees, from "CNDO" (Complete Neglect of Differential Overlap) to "MINDO") together with approximate orbital models, such as Gaussian orbitals, all in order to find things like electron density distributions or to vary the angles of molecules to find the most stable conformations.

I haven't kept up with modern QC, except to note that it now takes account of relativistic effects in the motions of electrons in heavy elements, which among other things accounts for the colour of metallic gold.

 

[erobz]

Sounds like poor lecturer/tutor support.

I think it needed to be taught with more weaving of demos in like this:



Ours was lecture and 1 lab a week if I recall correctly, but there was a distinct lack of demos in the lab (none in the lecture). It was mostly "see if you can follow these steps" - the whole experience was very unmotivated/unmotivating. Also, you get what you pay for - and I didn't pay terribly much.

 

[TensorCalculus]

@TensorCalculus As the name implies, https://en.wikipedia.org/wiki/Quantum_chemistry is the application of quantum physics to chemical systems/problems.

In my day that often boiled down to using large computer programs to solve, by energy minimisation, approximations to Schrödinger's equation (from Hartree-Fock to a range of "semi-empirical" methods, most of which tried to avoid dealing with the complication of "overlap integals" to varying degrees, from "CNDO" (Complete Neglect of Differential Overlap) to "MINDO") together with approximate orbital models, such as Gaussian orbitals, all in order to find things like electron density distributions or to vary the angles of molecules to find the most stable conformations.

I haven't kept up with modern QC, except to note that it now takes account of relativistic effects in the motions of electrons in heavy elements, which among other things accounts for the colour of metallic gold.

Aaaaaagh!


Still sounds fun, but sort of scary fun.

 

[sbrothy]

@sbrothy @TensorCalculus

Take a look at quantum chemistry, then - it's nothing but equations: from calculus and Lie algebra to group theory and beyond, eventually realised as computer programs - mainly FORTRAN, C AND C++ - and of interest to TensorCalculus - Python,: so you might consider Python at two levels in chemistry.

Wow. Lie algebra! The fact that you think I have any hope of understanding that, beyond admiring the shadows it casts into our world, feels me with a warm fuzzy feeling.

(And maybe an idea of using my bluff skills to play professional poker!)

 

[TensorCalculus]

Wow. Lie algebra! The fact that you think I have any hope of understanding that, beyond admiring the shadows it casts into our world, feels me with a warm fuzzy feeling.

(And maybe an idea of using my bluff skills to play professional poker!)

Hmmm... maybe... though I can confirm my poker face is abysmal (we were playing with fake money being kids, don't worry) and @pellis got the idea that I am also capable of something like lie algebra... for context someone or something mentioned it like a year ago or so, I searched it up, opened the Wikipedia, saw the diagram, and instantly closed the Wikipedia

 

[pellis]

Hmmm... maybe... though I can confirm my poker face is abysmal (we were playing with fake money being kids, don't worry) and @pellis got the idea that I am also capable of something like lie algebra... for context someone or something mentioned it like a year ago or so, I searched it up, opened the Wikipedia, saw the diagram, and instantly closed the Wikipedia

Unless you're a natural mathematician, which I am not, it takes a lot of study to get to the point of being able to make some sense of these topics, and I'm still learning - its the buzz of that moment when it finally clicks that makes it all worthwhile

 

[TensorCalculus]

Unless you're a natural mathematician, which I am not, it takes a lot of study to get to the point of being able to make some sense of these topics, and I'm still learning - its the buzz of that moment when it finally clicks that makes it all worthwhile

...very well said :)
EDIT: A handful on minutes ago I went back to the Wiki site and had the same reaction which does not bode well...

 

[sbrothy]

All this talk about Lie algebras reminds me of all the hype surrounding Garret Lisi’s paper An Explicit Embedding of Gravity and the Standard Model in E8. His idea had a certain beauty to it, as I understand is often the case with multidimensional Lie manifolds(?). I think though, that Jacques Distler, from Texas University, shot [sic] it down, dare I say, vehemently? Maybe some of his critique is still available at his blog “Musings”.

Apparently he suffers “fools” at least as badly as @Vanadium 50!

It’s not the same person is it?! Naaaah….

I’m just joking you guys. I hope I’m not being too personal!

EDIT: I actually mean this paper:

An Exceptionally Simple Theory of Everything

 

[pellis]

All this talk about Lie algebras reminds me of all the hype surrounding Garret Lisi’s paper An Explicit Embedding of Gravity and the Standard Model in E8. His idea had a certain beauty to it, as I understand is often the case with multidimensional Lie manifolds(?). I think though, that Jacques Distler, from Texas University, shot [sic] it down, dare I say, vehemently? Maybe some of his critique is still available at his blog “Musings”.

Apparently he suffers “fools” at least as badly as @Vanadium 50!

It’s not the same person is it?! Naaaah….

I’m just joking you guys. I hope I’m not being too personal!

EDIT: I actually mean this paper:

An Exceptionally Simple Theory of Everything

@sbrothy Thanks for the reminder - I was intrigued by the idea of E8 at the time but didn't follow it up till now.

Recent online evaluation, in summary (GPT):

"Lisi’s proposal attracted media attention as a refreshing departure from mainstream approaches—but the physics community judged it overwhelmingly speculative, with substantive mathematical and physical criticisms unresolved. Lisi remains undeterred, and the theory continues to inspire discussions, though it is not considered a viable unification model in its current form."

 

[renormalize]

Recent online evaluation, in summary (GPT):

AI answers are prohibited on Physics Forums. Please cite actual published references that evaluate and discuss Lisi's proposal.

 

[sbrothy]

This one: C, P, T, and Triality may in fact be a part of his defense to Jacques Distler's arguments (Mr. Distler seemed very adamant that it wouldn't fly, but scientists often express themselves using at least some hyperbole as discussions get heated.). I vividly remember the critique ran along something involving trialities, but then again I'm in way over my head here. It's just so interesting I can't help but read and take away what I can. I'm annoyingly dependent on the arguments from people with higher educations than myself.

 

[pellis]

AI answers are prohibited on Physics Forums. Please cite actual published references that evaluate and discuss Lisi's proposal.

AGAINST: Distler & Garibaldi (2009, peer-reviewed), SABINE HOSSENFELDER https://backreaction.blogspot.com/2007/11/theoretically-simple-exception-of.html
ATTEMPTS TO ENGAGE: “The Plebanski action extended to a unification of gravity and Yang–Mills theory” by Lee Smolin (Physical Review D, 2007). AND Unification of gravity, gauge fields,and Higgs bosons, A. Garrett Lisia, Lee Smolin, and Simone Speziale, Journal of Physics A: Mathematical and Theoretical, 2010. (ATTACHED)

 

[sbrothy]

Yes. I was just about to say that Mr. Distler wasn't the only one involved and that there was another side trying to make it work.

 

[sbrothy]

Also, this discussion is, in fact, veering into "Beyond Standard Model" land....

EDIT: The hijack was truly unintentional. Sorry.

 

[pellis]

@Mayhem @TensorCalculus @DaveE @berkeman @Borek @mjc123 @sbrothy @erobz @renormalize

To try to bring this discussion back on course, just briefly, I would appreciate any comments on what you think my answer (#36, Tuesday 3:07pm) omits or gets wrong.

I take mentions of a few points, especially kinetics (Mayhem). A few more may help me refocus my summary.

With thanks to all who've contributed so far - and anyone else tempted to do so in the future.

 

[Muu9]

There are a few metaphors/mental models/mnemonics I like to use for general chemistry, like thinking of chemical energy minimization as being similar to gravitational energy minimization. Another example is how electronegative atoms are "greedy", so they "hog" the electrons, leading to their region of the molecule being more negatively charged. It reminds me of when I was much younger and thought of arithmetic with positive and negative numbers as good guys vs bad guys...

But in my opinion, this isn't what chemistry is "about" any more than math is about the alligator always eating the bigger number.

 

[sbrothy]

I can relate to the visual understanding. My brain works the same way. In fact, if I'm unsure how to spell a word I can usually write different versions of it down and my brain will somehow recognize the correct one.

I assume you're mostly concerned with organic chemistry. Not that it makes a lot of difference for a fundamental understanding. But I think we can all agree that the carbon element is special as basis for life as we know it, and for it's willingness to interact in so many ways with so many other elements.

Electron bonding and the electron shell picture is still the way I picture chemical syntheses, then again my chemistry lessons were more than 20 years ago! The "shells" have become much more diffuse since Niels Bohr's simplified picture was overtaken by the quantum one - eh now I'm going there anyway - but I'm not sure it really means something for everyday chemistry. It's a little like Newton is adequate for most of the day to day physics needed, relativistic effects only becoming necessary in extreme cases.

Thermodynamics was mentioned (and of course no matter what you study there's no way around it). First time I experienced an endothermic reaction was really fascinating. As are catalysts.

There are so many rules and exceptions to them as only nature can do. And that is before we get into quantum chemistry! Hypervalence, electron deficiency, stereochemistry... and spectroscopy is so useful it almost reminds me of the babel fish from Hitchhiker's Guide to the Galaxy.

Richard Feynman, in his book What Do You Care What Other People Think?": Further Adventures of a Curious Character explains that he is a synesthete, (There's a small article which mentions it here: The Brain of a Synesthete). I'm sure it can be a gift as well as a curse, either useless or useful - perhaps downright debilitating!

I don't know if such a thing is possible with elements and molecules but it could be illuminating to examine how many gifted scientist benefitted from this syndrome.

EDIT: Yeah, and that's another thing. I doubt gravity will ever be relevant for everyday chemistry (possible on the nanoscale and lower) with electromagnetism being so much stronger.

 

[pellis]

There are a few metaphors/mental models/mnemonics I like to use for general chemistry, like thinking of chemical energy minimization as being similar to gravitational energy minimization. Another example is how electronegative atoms are "greedy", so they "hog" the electrons, leading to their region of the molecule being more negatively charged. It reminds me of when I was much younger and thought of arithmetic with positive and negative numbers as good guys vs bad guys...

But in my opinion, this isn't what chemistry is "about" any more than math is about the alligator always eating the bigger number.

@Muu9 Agree about electronegativity. As for energy minimisation, Peter W Atkins (well known text writer at Oxford U) reckons all energy is PE or KE, with one exception - if I remember correctly, he can't decide how to consider photons... But energy minimisation is central to quantum chemistry, at least for ground state properties.

 

[pellis]

I assume you're mostly concerned with organic chemistry.

Richard Feynman, in his book What Do You Care What Other People Think?": Further Adventures of a Curious Character explains that he is a synesthete, (There's a small article which mentions it here: The Brain of a Synesthete). I'm sure it can be a gift as well as a curse, either useless or useful - perhaps downright debilitating!

EDIT: Yeah, and that's another thing. I doubt gravity will ever be relevant for everyday chemistry (possible on the nanoscale and lower) with electromagnetism being so much stronger.

Organic chemistry is only a focus as it is the gap in my studies that limits my understanding of the bigger issues relating to the origin of life, but I think it's just as subject to the same points as the ones my summary covers.

I only mentioned gravity as I'd mentioned the em field, but in retrospect it really isn't directly relevant except when it pulls enough matter together to create metastable environments in which chemistry can happen; more relevant are the ElectroWeak and Strong Nuclear Force, which do impact chemistry via radioactivity/isotope decay etc. I'll have to think about whether to insert some references to them (as one other contributor here did earliuer).

Thanks for the ref to The Brain of a Synesthete. I used to keep a list of words in the colours I felt they were best represented by "Philip" was brown, "Maupertuisian" was pale blue, and "sushumna" was red - there were others but It was decades ago. Then there's the famour Stroop test https://en.wikipedia.org/wiki/Stroop_effect

 

[sbrothy]

As an aside I tried to search for "scientists with synesthesia". Wiki has a short list but surprisingly it looks like it's mostly artists. But if notes translates to colors I guess that makes sense. I can't really find any other scientists than Feynman.

Sorry. Carry on.

 

[pellis]

AI answers are prohibited on Physics Forums. Please cite actual published references that evaluate and discuss Lisi's proposal.

AGAINST: Distler & Garibaldi (2009, peer-reviewed), SABINE HOSSENFELDER https://backreaction.blogspot.com/2007/11/theoretically-simple-exception-of.html
ATTEMPTS TO ENGAGE: “The Plebanski action extended to a unification of gravity and Yang–Mills theory” by Lee Smolin (Physical Review D, 2007). AND Unification of gravity, gauge fields,and Higgs bosons, A. Garrett Lisia, Lee Smolin, and Simone Speziale, Journal of Physics A: Mathematical and Theoretical, 2010. (ATTACHED)

@renormalize @sbrothy @TensorCalculus In order to find those references, aside from my own files I could have found them in https://en.wikipedia.org/wiki/An_Exceptionally_Simple_Theory_of_Everything, and you likely wouldn't have objected.

Does the fact that I used the newly released ChatGPT5.0 to find the references actually contravene PF's rules? It was certainly more convenient and provided additional context that was reassuring (not copied into the refs listed).

I can understand that purists and those who see it as merely a token manipulator will be doubtful of its use. But I think we're all going to find, quite soon, that AI assistance will become more widely accepted, and is probably being used far more already than some people realise.

Given that humans also make mistakes, does openly-acknowledged use of AI assistance really make any difference, if used judiciously and checked carefully?

Note also that over a year ago (before learning that AI assisted answers were not allowed there either) I posted on Physcis Stack Exchange, as an experiment, an answer to the highly technical question:
https://physics.stackexchange.com/q...rs-under-vielbein-redefinitions/812257#812257
...which was upvoted and accepted, has been viewed over 100 times and never challenged beyond a request for clarification (also answered). It's more advanced theoretical./mathematical physics than I am familar with but I checked it as carefully as I could before posting it, having felt free to do so as no-one else had even tried to answer the question since it had been posted 5 days earlier.

 

[sbrothy]

I suspect it would have perfectly acceptable (I'm not a modertor) if you had also linked to the arXiv paper. But I may be wrong. I'm myself a little new to this AI stuff and I don't use it much.