chem1000/lectures/ds-intro-to-ml.ipynb at main · ghutchis/chem1000 Jupyter Noteboks for lecture and assignments for CHEM 1000: Mathematics for Chemistry at University of Pittsburgh - ghutchis/chem1000

For anyone interested, here's the current version of the lecture notebook, although I'm sure I'll revise heavily after this week:

github.com/ghutchis/che...

Wish me luck - for my undergrad "Math for Chemistry" class (for @pittchemistry.bsky.social majors) .. I'm going to give a lecture tomorrow about ML and LLMs.

I think I fit the basics in…

Discussion question:
"Why can a model like ChatGPT give fluent but wrong chemistry answers?

#chemsky

This won’t help the whispers that the awardees on this one are pre-determined.

When Biden took office, he suggested that international students receiving a PhD in the US should get a green card if they want one. Several students in my program were really excited - they wanted to stay.

It never materialized.

Not every job wants to sponsor an H1B, particularly now.

The David M. Hercules Fellowship Award recognizes an outstanding graduate student or postdoctoral researcher, with particular emphasis on scientific creativity, independence, leadership, and the ability to collaborate across disciplines. Our 2026 awardee is Shubhankar Kundu! Congrats Shubhankar!

We have VCD capabilities here @pittchemistry.bsky.social - if you're interested, I can put you in touch with some folks.

Chemist Brett Pollard and colleagues found roughly 20 papers citing water safety standards attributed to the WHO and EPA that, according to the researchers, those agencies never produced.

I mean, N6 seems like it could qualify. Carbon-free, even!

One week of Avogadro 2.0 highlights - and we're just getting started…

Download: avogadro.cc/install/
Join the community: discuss.avogadro.cc

Thanks to everyone who helped make this release happen. Open science is a team effort! Got ideas on where to go next? 🧪 ⚗️

#opensource #openscience #compchem

Otherwise the pace of development is limited by how much free time I find...

While interoperability with other file formats, InChI, etc, are also important, that was secondary - I want to get feedback on the builder first, ligand library, etc.

I'm happy to work towards interconversion, etc. particularly if people want to collaborate or can find funding

Our main goal was "can we make it easy and intuitive" to click into place specific ligands and geometries to build 3D geometries of inorganic and organometallic species, including defining the formal charge and spin states.

Most @avogadro.cc use is for simulations (e.g., DFT) so getting the XYZ out

Happy to talk - there's a JSON-RPC protocol to get the current molecule in CJSON, or molfile and we can certainly add more end-points (e.g., return a message when the user is done)

There's probably some need to improve the Avogadro v3000 support for organometallics, etc. first

Got ideas? Or know a Python package that could use a GUI? Let me know…

Good to know at least some social media posts are fact-checked. 😃

Even though it's using a CSVR thermostat, it's not intended for production runs. Mostly teaching and getting something closer to a good starting geometry.

I'm sure we still have subtle bugs!

IIRC we clicked around and generated some random positions for the oxygen atoms. So they're almost certainly starting in a 2D plane.

Serves us right for not picking an accurate water box for posts. 😀

I'll go find a good water box and post something amended.

Sometimes you just want to see a molecule move.

Run a quick MD simulation without leaving Avogadro — no scripts, no setup. The new auto-optimize tool includes a dynamics mode. Watch it move in real time. Great for teaching. Great for intuition. Just fun to watch.

#openscience #compchem #opensource

You shouldn’t- the initial passport screening, etc. happens at the first airport and then all transfers inside the US don’t require another screening.

I know there were some issues when we switched to a different package for graphs.

Volumetric rendering has been on my wish list for years, and we’ve got a 20-25x speed up coming this summer for orbitals and electron density.

Unfortunately ChemDraw uses some weird shortcuts IMHO, likely because they wanted to keep everything to one character.

We decided some things are more intuitive as longer shortcuts like no2 = nitro, etc.

There was an example posted here recently in which a user clearly wanted boron but got Br.

Rendering of Ziegler–Natta zirconium catalyst with blue-green translucent sphere representing the Zr atom, and ball-and-stick rendering of cyclopentadienyl (Cp) rings and methyl group

Screenshot of Avogadro 2 template tool, indicating a tab for Element: Formal Charge: and the options for Coordination selected, with options 1: Linear, 2: Linear, 3: Trigonal Planar, 4: Tetrahedral, 4: Square Planar, 5: Trigonal Bipyramidal, 5: Square Pyramidal, 6: Octahedral, 6: Trigonal Prism, 7: Pentagonal Bipyramidal, 8: Square Antiprism

Ball and stick rendering of chlorophyll c2 molecule with larger green sphere representing the Mg(II) ion

Screenshot of symmetric (D5d) ferrocene with rotation axes illustrated as red cylinders. Orange sphere is an iron atom, and grey-white cylinders indicate the cyclopentadienyl ligands. Dialog text indicates D5d symmetry, tabs for "Molecule", "Operations", "Subgroups" with operations active, indicating a table of symmetry elements, classes, and element. At the bottom of the dialog is Tolerance: Normal and a button "Detect Symmetry"

Inorganic and organometallic chemists — Avogadro 2.0 is for you...

A new template tool lets you build octahedral, tetrahedral, and other complexes in seconds. Click to add functional groups. Avogadro also detects symmetry and displays symmetry elements

#compchem #openscience #opensource

There's also a walkthrough on the website. We added a whole bunch of keyboard shortcuts. Want a Cp- ligand? Type e5 or cp.

Want a c8 chain? Type c8.

And if you type "b" .. you get boron. So you can build your borates 😀

avogadro.cc/docs/tutoria...

Building Molecules with Templates YouTube video by Avogadro Project

This is one of my favorite new features.

I'll put up another video on building inorganic and organometallic species, but this one goes through the basics.

youtu.be/RC4NZp6nnD8

Avogadro2 rendering of PDB entry 9MBO reconstructed assembly

Thanks! That was interesting. Once I got it in, the rendering wasn't breaking a sweat even with real-time shadows.

OTOH, it attempted to guess bond orders which would have been pretty slow, so I hacked the code to turn that off.

(I'll add support for assemblies too.)

If you've got something really big - 100,000 atoms, a million atoms? I'd really like to try it out.

No fooling, Avogadro 2.0.0 is finally here!

Rebuilt from the ground up: fast modern rendering, improved stability, designed for the next generation of molecular, biomolecule, and materials research & education. 🧪 ⚗️

avogadro.cc/install/
discuss.avogadro.cc

#opensource #openscience #compchem

On this day, let us continue to uphold everyone's fundamental right to just be themselves.

"You’ve made this day a very special day. Just by you being yourself." -Fred Rogers

This.

We get used to our molecular models. Sure, it's great to load something up in PyMol or @avogadro.cc or some other program. But it's way too easy to internalize our static 3D (or 2D) renderings.