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Reposted by Jan H. Jensen

Alán Aspuru-Guzik @aspuru.bsky.social · 10h

Some non-MOF content today to clean your palate.

Want 70x fast, 2x accurate Hessians for any equivariant machine learning force field? We got you!

#compchemsky #chemsky #machinelearning #mlff

The Matter Lab @thematterlab.bsky.social · 11h

What do transition state search, geometry relaxation, zero point energy corrections, and extrema classification have in common? They all require Hessians!

The problem is, accurate Hessians are really expensive, even with MLIPs. We say, just shoot 'em from the HIP! 🤠
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Reposted by Jan H. Jensen

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 20h

Am at the University of Copenhagen Frontier Research in Denmark meeting celebrating the @erc.europa.eu. Rector David Lassen highlights how his first meeting with the ERC was a grant rejection, and how it's important to tell early career scientists about the CV of failure in addition to successes 1/n

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Reposted by Jan H. Jensen

Geoff Hutchison @geoffhutchison.net · 2d

I know this has been one of the most widely requested features. Should be in the release on 10/23

#chemsky #compchemsky #opensource

Avogadro Project @avogadro.cc · 2d

If you've been wondering about the status of the AutoOptimize interactive optimization in Avogadro2 - coming later this month 👀

Screenshot of Avogadro2 using the interactive AutoOptimize tool to minimize a molecule (n-pentane) using the UFF force field. Text reads UFF ΔE = -229.80 kcal/mol

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Reposted by Jan H. Jensen

Greg Landrum @greglandrum.bsky.social · 3d

I forgot to post over the weekend...
The new #RDKit blog post is a short one showing how to get decent 2D renderings for systems with intramolecular hydrogen bonds.
greglandrum.github.io/rdkit-blog/p...

Rendering intramolecular H bonds in 2D – RDKit blog

A simple approach to get nonbonded atoms close to each other.

greglandrum.github.io

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Jan H. Jensen @janhjensen.bsky.social · 3d

My talk at the #RDKit UGM in Prague youtu.be/TduH7v-biyY?... #compchem

Jan Jensen: Can you find hits by screening only 100 molecules?

YouTube video by RDKit

youtu.be

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Jan H. Jensen @janhjensen.bsky.social · 13d

Fundamental Study of Density Functional Theory Applied to Triplet State Reactivity: Introduction of the TRIP50 Dataset
www.compchemhighlights.org/2025/09/fund... #compchem

Fundamental Study of Density Functional Theory Applied to Triplet State Reactivity: Introduction of the TRIP50 Dataset

William B. Hughes, Mihai V. Popescu, Robert S. Paton (2025) Highlighted by Jan Jensen While this paper presents an interesting and useful be...

www.compchemhighlights.org

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Jan H. Jensen @janhjensen.bsky.social · 17d

I ... that's ... no ... uuuhm #tooclosetohome
youtu.be/8AeCo3AD1cM?...

Confused Teacher Crashes Out Over His Job | Mitchell and Webb Are Not Helping | Channel 4 Comedy

YouTube video by Channel 4 Comedy

youtu.be

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Jan H. Jensen @janhjensen.bsky.social · 20d

#compchem

Janus Juul Eriksen @januseriksen.bsky.social · 20d

New preprint online today - spearheaded by my very talented postdoc, Jonas - on a new reusable, open-source software implementation of the second-order trust region algorithm:

arxiv.org/abs/2509.13931

Here are some of the reasons why this library may be useful for a great many in our community. 👇

A Reusable Library for Second-Order Orbital Optimization Using the Trust Region Method

We present a reusable, open-source software implementation of the second-order trust region algorithm in the new OpenTrustRegion library. We apply the implementation to the general-purpose optimizatio...

arxiv.org

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Jan H. Jensen @janhjensen.bsky.social · 22d

#compchem

Avogadro Project @avogadro.cc · 23d

We've got a new release 1.101, which should particularly fix some bugs with Windows and Mac, and of course a variety of new features.

Highlights include support for constraints for geometry optimizations, tweaking bond lengths when changing elements, and more...

discuss.avogadro.cc/t/avogadro-1...

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Reposted by Jan H. Jensen

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 23d

This is in line with old data from Danish universities. Dark green shows expenses and light green shows revenues from commercialisation. As one example, the Danish Technical University spent 27M DKK and got 11M DKK back. Admittedly this is old data and may have changed.
From: dm.dk/media/ams/36...

Plot showing progress in expenses (dark green) and expenses (light green) for commercialisation from Danish Universities 2004–2015. Taken from https://dm.dk/media/ams/36084/ff-303.pdf

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Reposted by Jan H. Jensen

Gerald Monard @gmonard.bsky.social · 24d

Pretty sure it would translate to French Universities the same way.

Jed Brown @jedbrown.org · 24d

"Do Universities Investing In Technology Transfer Via Patenting Lose Money?"

This study reaches a conclusion I've believed to be true since seeing how tech transfer offices work. The paper calls for closing tech transfer offices and instead open sourcing all innovations.
ttb.sk/clanky/do-un...

ABSTRACT Substantial investments are made in
universities patenting new developments to pursue
a return. To gauge the impact of the holistic costs
of patenting at universities, this study provides a
new methodology for quantifying the investment
in intellectual property (IP) that includes not only
technology transfer staff costs but also direct and
opportunity faculty-related costs. It then uses the
novel methodology and publicly accessible data on
an average American research university case study.
The results found all component costs were higher
than the IP-related income, with the opportunity cost
for writing patents instead of grants being more than
33 times the income realized through IP protection.
Overall, the case study university loses over $9
million per year on IP with a negative ROI of -97.6%.
Research universities have opportunities to increase
research income >10% by ignoring IP. It is clear that
Bayh-Dole Act and similar national legislation, is
harming university economics. It can be concluded
that as generally practiced in the U.S. now, it is not
rational to continue to support university technology
transfer by patents. Instead, to improve the economic
bottom lines of universities, as well as increase the
good that research and development does for society,
universities can open source all innovations.

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Jan H. Jensen @janhjensen.bsky.social · 24d

#compchem

macinchem.bsky.social @macinchem.bsky.social · 25d

jonswain.github.io/ai/cheminfor...

Chemprop-RF: A Hybrid Approach to Chemical Property Prediction

Can we combine d-MPNNs and Random Forests to outperform each of them individually?

jonswain.github.io

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Reposted by Jan H. Jensen

Paul J. Dauenhauer @pauldauenhauer.bsky.social · 25d

www.theatlantic.com/ideas/archiv...

How Teacher Evaluations Broke the University

“We give them all A’s, and they give us all fives.”

www.theatlantic.com

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Reposted by Jan H. Jensen

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 26d

I’m biased 🇩🇰, but this is quite nice to read:

I thought science hinged on prestige. Moving abroad made me reassess my priorities

www.science.org/content/arti...

I thought science hinged on prestige. Moving abroad made me reassess my priorities

In Denmark, this Ph.D. student fell in love with an egalitarian society that values work-life balance

www.science.org

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Reposted by Jan H. Jensen

Jiwoong Lee @jiwoonglee.bsky.social · 25d

Turning plastic bottles into a new carbon capture material cen.acs.org/environment/...

Turning plastic bottles into a new carbon capture material

Aminolyzed PET could help fight both plastic waste and carbon emissions

cen.acs.org

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Reposted by Jan H. Jensen

Frank Glorius @gloriusfrank.bsky.social · Sep 5

JOB ALERT! 🚨MOLECULAR MACHINE LEARNING

2️⃣ fully funded PhD positions🚀🎓 are available in the @gloriusgroup.bsky.social associated with the German Priority Program @spp2363.bsky.social
Your profile:
- MSc in chemistry (knowledge of computational methods) or data science.
- Passion for science.
🙏RT

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Reposted by Jan H. Jensen

Alán Aspuru-Guzik @aspuru.bsky.social · Sep 3

The elephant in the lab: Synthesizablity! Check our new opinion from @thematterlab.bsky.social

The Matter Lab @thematterlab.bsky.social · Sep 3

Ever wondered how to get organic chemists to synthesize the molecules you designed with your newest generative AI model?

Please check out our latest article: “The elephant in the lab: Synthesizability in generative small-molecule design”.

🐘 Link to preprint: chemrxiv.org/engage/chemr...
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Jan H. Jensen @janhjensen.bsky.social · Aug 29

yeah, I think the lack of implicit solvent is currently the biggest limitation. We're also having some practical problems with computing Hessians in parallel using UMA

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Jan H. Jensen @janhjensen.bsky.social · Aug 29

UMA: A Family of Universal Models for Atoms www.compchemhighlights.org/2025/08/uma-... #compchem

UMA: A Family of Universal Models for Atoms

Brandon M. Wood, Misko Dzamba1, Xiang Fu, Meng Gao, Muhammed Shuaibi, Luis Barroso-Luque, Kareem Abdelmaqsoud, Vahe Gharakhanyan, John R. Ki...

www.compchemhighlights.org

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Reposted by Jan H. Jensen

Noel O'Boyle @baoilleach.bsky.social · Aug 21

Want to work with me on cool stuff? #ukchemjobs #chembl #chemjobs

Chemical Biology Services @chembl.bsky.social · Aug 21

Last chance to apply for this pivotal role, taking our services to the next level. Get in touch by end of Aug if interested...

Chemical Biology Services @chembl.bsky.social · Jul 14

We are inviting applications for a 3-year ARISE2 Postdoctoral Fellowship with the team. Read more on our blog at: chembl.blogspot.com/2025/07/invi...

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Reposted by Jan H. Jensen

Jorge Bravo Abad @bravo-abad.bsky.social · Aug 21

Glad to share my new Substack post on the recent Nature paper by Joonyoung F. Joung and coauthors, introducing FlowER, a generative ML model that predicts reaction mechanisms while strictly conserving mass and electrons. open.substack.com/pub/bravoaba...

Predicting reaction mechanisms with electron flow matching

Understanding chemical reactivity ultimately requires understanding mechanisms.

open.substack.com

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Reposted by Jan H. Jensen

WIRED @wired.com · Aug 10

By proving how individual molecules create the complex motion of fluids, three mathematicians have illuminated why time can’t flow in reverse.

Efforts to Ground Physics in Math Are Opening the Secrets of Time

By proving how individual molecules create the complex motion of fluids, three mathematicians have illuminated why time can’t flow in reverse.

wrd.cm

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Reposted by Jan H. Jensen

Robert Pollice @robpollice.mstdn.science.ap.brid.gy · Aug 4

#RobSelects paper of the week #j_a_c_s: Reversible carbon-hydrogen activation of benzene and unactivated arenes with a nickel(0)-silylene complex. #OrgChem https://doi.org/10.1021/jacs.5c10922

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Jan H. Jensen @janhjensen.bsky.social · Jul 31

Computing solvation free energies of small molecules with first principles accuracy www.compchemhighlights.org/2025/07/comp... #compchem

Computing solvation free energies of small molecules with first principles accuracy

J. Harry Moore, Daniel J. Cole, and Gábor Csányi (2025) Highlighted by Jan Jensen Local CCSD(T) has made it possible to reach near chemic...

www.compchemhighlights.org

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Reposted by Jan H. Jensen

Greg Landrum @greglandrum.bsky.social · Jul 24

Today's #RDKit blog post shows a way to store partial charges in SD files. We really should stop using mol2 files.

Thanks to @wpwalters.bsky.social for the inspiration for this one.

greglandrum.github.io/rdkit-blog/p...

Storing partial charges in SD files – RDKit blog

No really, we don’t need mol2 files any more.

greglandrum.github.io

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