Gallery – Making Molecules | Hacker News Reader

Gallery – Making Molecules

makingmolecules.com

252 pointsHaoZeke38 comments

Out of curiosity, what do professional chemists refer to when they need a quick reference for something like this? Is it all in their heads by that point, or is there special software that they use every day (some sort of knowledge base type thing...?) or how does it all work?

As a software dev I think I take it for granted that I can look up anything I need to in a second or two. How does it work for other professions with special knowledge bubbles?

They debate it at the supper table (my childhood). ;-)

Most of what's in these handouts, and much, much else, is just in their heads--at least the part that's relevant to their field, obviously an organic chemist is going to have slightly different things memorized than a geochemist. For things that you have to look up, for decades the first thing you reach for would be the CRC Handbook https://en.wikipedia.org/wiki/CRC_Handbook_of_Chemistry_and_... although it's on the web now https://hbcp.chemnetbase.com/contents/ContentsSearch.xhtml?d... as well as other reference materials.

MOSTLY UNINFORMED OPINION

A lot of special knowledge is also available within seconds on the internet, but you (solardev) don't know where. Part of being in the bubble is that you know where to find things that are in the bubble.

For an example that comes easily to my mind, a while ago there was an HN thread where someone asked what made a cross-language dictionary (e.g. English-Japanese) good or bad, and I responded with a link to FrameNet ( https://framenet.icsi.berkeley.edu/ ) and the observation that I'd like dictionaries to include information about how to supply relevant semantic roles to the word you're looking up, which they almost never do.

There's nothing stopping anyone else from looking up FrameNet and seeing what it's about. (Though academic papers on frame semantics might be less accessible.) The obstacle is in knowing that it's there in the first place.

Not a professional chemist (by any stretch of the imagination), but for several of these, it's as much in their heads as "what are the keywords in C?" is for C programmers. For at least some of these well, too, software exists already to do things like draw molecules [1]. Databases also exist to do things like find known properties (spectra, physical properties like melting point) for known chemicals.

[1] I guarantee every molecule drawn on the page was drawn with ChemDraw or similar tool.

You develop an intuition and general understanding. It’s like a carpenter sees a chair and can understand how it was built. He doesn’t have to remember every combination of pieces. With chemistry it’s the same. You just see it.

I am a professional chemist (Ph.D.). After a time, one gets a chemical intuition (as I've heard it called). There are just things that you know or you know where to look and how to filter irrelevant information.

All of that depends on your training and experience. I am not particularly strong in the organic department; however, I am quite expert in areas of physical, aqueous, and computational chemistry. I'm also a geochemist, and have significant lab experience in mostly analytical chemistry. Needless to say, I'm a decent programmer, know a bunch of lab stuff, am quote proficient in linear algebra, and so on. Those main and ancillary skills together give me a pretty good idea of what's going on without having to consult any references.

Resources that I use daily: PubChem, ACS journals, my textbooks, visualization tools, and some software if I'm targeting a certain outcome. IUPAC for naming organics (rarely for me).

Also, I answer questions on the Chemistry Stack Exchange site (not so much these days) which requires a decent amount of digging in order to answer coherently.

Learning is always more important than knowing

90% 0f that stuff is second nature if you've gotten a PhD.

Asymmetric boration would need a red for me, but I'd just Google it and look for an undergrad .edu explainer and sample 3-4 answers

If it's more esoteric, I'd just search through a couple of papers. There's usually a paper.

If it's some specific number, pubChem or chemSpider usually have what I'm looking for.

Honestly, I probably look stuff up on Wikipedia as much as anywhere else. They usually have plenty of basic physical properties for common chemicals. And a useful svg structure that's easily stealable for a presentation....

This would be primarily aimed at the large number of students who have to take organic chemistry as a requirement.

For organic chemistry graduate students and professional organic chemists, all this stuff will largely be so ingrained as to not to require these kinds of resources.

There are, however, a large number of people who are in chemistry fields who need occasional refreshers on introductory concepts and for that purpose, these are excellent.

All of the topics in these handouts are the kind of general knowledge that you'd get in a college undergraduate chemistry program, so it would all be familiar, i.e. if you encountered it you'd know where to look up more specific information on your particular problem.

However, a lot of the databases and tools needed to do analysis, say of an unknown compound, aren't readily available to the public, it's often curated proprietary libraries of things like spectra data, for example this is a short interesting discussion of the software used to match an unknown sample to a reference in a library, which I think might now be applying AI approaches as well:

https://youtu.be/_BHhbg9Bv9Q

Usually you're working on some specific problem, and thus you need access to the historical chemical literature on that problem, which as often as not is hidden behind paywalls and not available on sci-hub or similar, so you need access to a university library or similar to get all the old papers (especially their materials/methods/results) on the topic. Industrial chemistry advances might not even be published over IP concerns, which I guess is somewhat like Nvidia proprietary GPU drivers.

Highly specific software and programming information is certainly a lot more accessible, everything that's highly specific in chemistry is often harder to find and/or costs money to access.

My brief extension course introduction to chem and mol bio gave me an enormous appreciation for chemistry illustrations. Molecular Biology of the Cell is one of the best textbooks ever written.

Beautiful book I used it in undergrad. The only problem with the book is its size; it's terrible to lug around in a backpack.

Yep. Big, heavy book.

They really are something, right? My boyfriend had/has an open offer to jump into a career in scientific illustration if he wants to (but he's in love with his museum job). His neighbor has been doing it for decades and her work has been in many of the mass-produced scientific textbooks used at the high-school and college level - it was really cool to see some of her actual sketches and prints when visiting his parents a few years ago

My aunt is a medical illustrator but had to give up the career for lack of work years ago

I find this a little hilarious and probably sorely needed as someone who was handed what the instructor literally referred to as the "art of the clides" (the heading "Chart of the Nuclides" having been cut off via photocopier margins), in what turned out to practically be a graduate-level physics course at a nominally undergraduate institution.

When I was in high school, one of the extracurricular academic competitions was at a local college. I had time to kill and was browsing through the campus bookstore. They had a rack of 8.5x11 laminated "cheat sheets" of chemistry, physics, geometry that these remind me of. They were pretty cheap, and the nerd that I am spent my lunch money on buying a set of these. At first, I wasn't even taking classes for the subject matter, but I knew that I would be and I wasn't sure if I'd be back to this store. After taking the appropriate classes, they were very useful.

In the one in the third column of the second row, "Drawing Molecules" [1], the second box shows how to go from a structural representation to a skeletal diagram. The third step of that is to remove all C-H bonds, removing both the H and the bond.

But in the example given it retains a C-H bond. Why is that?

[1] https://static1.squarespace.com/static/62185f3b81809a6fd03dd...

I would think it's because it's part of the aldehyde functional group.

That C-H bond is part of an aldehyde functional group, normally those hydrogens are not removed (I think because it helps for pattern matching the functional group)

Usually it’s just hydrogens on hydrocarbon chain backbone or aromatic rings that are deleted

Functional group sheet: https://static1.squarespace.com/static/62185f3b81809a6fd03dd...

Another great one is Compound Interest. https://www.compoundchem.com/infographics/

For:

https://static1.squarespace.com/static/62185f3b81809a6fd03dd...

Is there supposed to be a line through some of the center?

It looks like they've copied the template/page from a previous diagram file and forgot to remove one of the lines, probably just an accident.

I got super confused by the "Page 47" logo. Is it the publisher? Sounds like a pretty poor choice: color me dumb but I did look for page 46 and 48...

A google search leads me to think Page 47 is a reference to the National Treasure franchise https://nationaltreasure.fandom.com/wiki/Page_47

I think I actually paid money for similar printed handouts. I think it was for SAT/ACT concepts or some college course.

How naive I was back then.

Back then for me was well before the internet, so these kinds of things were pure gold. Now, if you can't find it in a quick web search, it's probably not important

But they probably didn't have ads on them.

Maybe these are beautiful, but whoever made them is blatantly not a professional graphic designer or typographer. From a graphic design POV, it's hard to justify rating these higher than 8/10.

Why not explain that POV?

Not a garphic designer, but someone who is anal about graphics in papers.

I don't want to detract from how great this is!

But, if you want to be anal about graphics... There are a lot of little mistakes that could be improved on.

The text isn't justified and sort of meanders left and right.

Nothing is quite correctly centered.

Little bugs like stray lines (in the middle top one, TLC).

Capitalization is really inconsistent.

Sometimes there are paragraphs, sometimes there are separate sentences. Sometimes there are sentence fragments.

Some of the graphics don't follow standards for contrast, like the 2nd from the top middle, black on blue is very hard to read for someone with a low vision. Then there's light blue on white.

The spacing is really inconsistent horizontally. There's pretty uniform space on the left (usually) but on the right it's clear things just end when they do sort of squeezed in. Sometimes it's the other way around and the left is squeezed in.

Some of the fonts are basically impossible for me to read, never mind someone with dyslexia. Look at this one, 2nd page, https://static1.squarespace.com/static/62185f3b81809a6fd03dd...

Sometimes arrows are thick and black, sometimes they're hollow, sometimes they're much thicker and red.

That's just a few. Still awesome though!

On one hand I love this level of nitpicking.

On the other hand, by the standards of what an undergraduate organic chemistry student is looking for from a free online resource, and given that it is just one guy doing this, in his spare time, I think this is absolutely fine.

(I have a competing website on organic chemistry and I think this guy does a much better job on graphics than I do.)

Oh I agree entirely. I totally don't want to detract from the work!

I don't think we need to bend over backwards to avoid any kind of criticism of this project. It's clearly a personal passion project and nobody is saying it is less than "fine". I guess it's an American norm to be very circumspect about any kind of negative appraisal.

It takes time and training to pull off design like this, and while it might work as a fun infographic, it is not as polished or beautiful as it could be. There is room for improvement.

As far as the "graphic design POV" goes, that involves intuitive assessments of things like negative space, colour, and density of graphic elements and text. It involves things like the five Gestalt principles, or the CARP principles, although these are not prescriptions that anyone can follow. They're more like rationalisations of what has been found to work.

I am not a graphic designer nor really care about it too much but I can spot a few things that look less than ideal. Of course I might make the same mistakes (that is why we have code reviews etc.)

In the first handout, any idea what this sentence means?:

> For organic chemistry is NEON or 8 valence electrons is key.

I can't tell if I just don't know ochem or what.

Not a chemist, but yeah, that's just a typo.

> All atoms are reactive except the noble gases (group 18). These are stable due to a full outer shell. For organic chemistry is NEON or 8 valence electrons is key.

It should probably say something like. "For organic chemistry, what you see in NEON, attaining those 8 valence electrons, is key." Atoms want to participate in bonds to reach what Neon already has going on, 8 valence electrons. A full valence shell.

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