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Reposted by Michael Bogdos

Morandi Research Group @morandilab.bsky.social · 2d

Congrats to @mixalhsmpogdos.bsky.social, @sevenroediger.bsky.social, @fruepp.bsky.social, Nathalie, Patrick, Fabio and Jan on this epic study of C-N red. elim. in @jacs.acspublications.org - using causal inference, organometallics, electrochemistry, kinetics and DFT. pubs.acs.org/doi/full/10....

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Michael Bogdos @mixalhsmpogdos.bsky.social · 2d

Also thanks to @robpollice.mstdn.science.ap.brid.gy for sharing our paper!

bsky.app/profile/robp...

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

#RobSelects paper of the week #j_a_c_s: Deriving a model for estimating rates of C-X reductive elimination from palladium(II) derived via causal inference. #catalysis https://doi.org/10.1021/jacs.5c06124

Michael Bogdos @mixalhsmpogdos.bsky.social · 2d

If we managed to map the causal structure aka "the data generating process", we are on track to refine the models.

I believe what we presented is approaching that; imprecisions remain e.g. treating CN as exposure and not modeling S -> CN. Hopefully these are eventually resolved.

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Michael Bogdos @mixalhsmpogdos.bsky.social · 2d

As one of my favourite papers puts it:

> As a consequence, linear regression results are notoriously unstable – even minor changes in model specification can lead to coefficient estimates that bounce around like a box full of gerbils on methamphetamines.

journals.sagepub.com/doi/10.1177/...

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Sage Journals: Discover world-class research

Subscription and open access journals from Sage, the world's leading independent academic publisher.

journals.sagepub.com

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Michael Bogdos @mixalhsmpogdos.bsky.social · 2d

The biggest takeaway from the paper is not the predictive model we use to infer generalisability, but rather the model structure. The coefficients may change if e.g. we find better descriptors. Even if the model is "retrained" in the lingo of data-driven models, the causal structure remains.

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Michael Bogdos @mixalhsmpogdos.bsky.social · 2d

Causal inference lets us visualise, quantify and compare effects. Prior to now, there was no answer to the question "what affects RE most, ligand sterics, electronics, or coordination number?".

Our analysis indicates that electronics is dominant, particularly when changed by lowering CN.

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Michael Bogdos @mixalhsmpogdos.bsky.social · 2d

Instead, we propose that CN affects electronics; for CN (2n - 1) fewer donating ligands surround the metal compared to CN (2n), making it more e-poor accelerating RE.

The relevant relationships for variation only in the ancillary ligand(s) are captured in a DAG:

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Michael Bogdos @mixalhsmpogdos.bsky.social · 2d

Contrary to textbooks, our data don't support an effect of coordination number on rate, once we condition for metal electronics.

i.e. if we ensure that the metal complexes we compare are equally electron-poor, they eliminate at the same rate, even if one is square-planar and one is T-shaped.

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Michael Bogdos @mixalhsmpogdos.bsky.social · 2d

Great to see this published!

In short, we introduced causal inference logic to test which of metal electronics, ancillary ligand sterics and metal coordination number (CN) directly affect the rate of reductive elimination at Pd(II) (and presumably other metals...)

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Morandi Research Group @morandilab.bsky.social · 2d

Congrats to @mixalhsmpogdos.bsky.social, @sevenroediger.bsky.social, @fruepp.bsky.social, Nathalie, Patrick, Fabio and Jan on this epic study of C-N red. elim. in @jacs.acspublications.org - using causal inference, organometallics, electrochemistry, kinetics and DFT. pubs.acs.org/doi/full/10....

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Michael Bogdos @mixalhsmpogdos.bsky.social · Sep 13

Pleased to have been awarded the ETH Medal this summer for my PhD thesis!

Many thanks to all those who supported me through my journey, especially my PhD supervisor Prof. Bill Morandi.

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Reposted by Michael Bogdos

Morandi Research Group @morandilab.bsky.social · Sep 2

Congrats to @fruepp.bsky.social, Vasily Grebennikov, Mykola Avramenko, Marc-Olivier Ebert "Kinetic, Spectroscopic, and Computational Investigation of Oxidative Aminative Alkene Cleavage Reveals an N-Iodonium-Iminoiodinane Pathway" now @chemrxiv.org - chemrxiv.org/engage/chemr...

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Michael Bogdos @mixalhsmpogdos.bsky.social · Aug 14

Nature Catalysis, my favourite physical chemistry journal

Reposted by Michael Bogdos

Marina Perez Jimenez @perezjimenez-group.bsky.social · May 11

We have two open PhD positions to start our new group at University of Geneva!
If you are interested in organometallic chemistry, heterometallic complexes and mechanistic investigations, please contact me. Check more details here:
jobs.unige.ch/www/wd_porta...

Assistant-e (A2) postes de doctorat en chimie inorganique / organométallique (6378)

jobs.unige.ch

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Michael Bogdos @mixalhsmpogdos.bsky.social · May 12

Thanks for the suggested reading

Michael Bogdos @mixalhsmpogdos.bsky.social · May 12

Could you please walk me through how this works? I've been trying to understand this argument for ages and cannot find sources with hard numbers. It implies that, excluding marketing costs (which are huge), companies are selling at a loss in all other places which I simply cannot find evidence for.

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Reposted by Michael Bogdos

Chemjobber @chemjobber.bsky.social · Apr 25

Blunt letter to the editor on ACS: "If ACS won’t stand up now, it should stand down." cen.acs.org/business/Rea... #chemsky 🧪⚗️

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Michael Bogdos @mixalhsmpogdos.bsky.social · Apr 6

100 %.

Very frustrating that EU institutions increase funding when they eye US researchers, but don't care about scientists in Europe who leave science for other careers in droves. Why endorse American exceptionalism?

That is to say nothing of the intra EU inequality, a whole other can of worms.

Darren Dahly @statsepi.bsky.social · Apr 6

American scientists aren't special. It's the institutions, and willingness to spend on research, that set them apart. Similarly invest here, and you will naturally attract the best talent from *everywhere*.

www.politico.eu/article/euro...

Europe to burned American scientists: We’ll take you in

The EU’s body for scientific research, as well as local, regional and national governments, are mobilizing to poach top U.S. scholars.

www.politico.eu

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Reposted by Michael Bogdos

Derek Lowe @dereklowe.bsky.social · Feb 20

Re-upping this post this morning: Big Pharma CEOs are finally starting to speak out about the Trump administration.

Unfortunately, they’re smiling and clapping.

Pharma CEOS Speaking Up, Damn It

www.science.org

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Reposted by Michael Bogdos

Derek Lowe @dereklowe.bsky.social · Feb 12

Biopharma companies and CEOs are keeping their heads down at their own peril. They should speak up about what’s happening to the NIH and other science agencies before it’s too late.

Silence gives consent. And no one should consent to this.

Stand Up And Be Counted

www.science.org

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Reposted by Michael Bogdos

Carl T. Bergstrom @carlbergstrom.com · Feb 7

When the federal government abandons important areas of funding and leaves a gaping hole in the advancement of science, any prudent funder would fill the hole, not follow suit. I don’t know the rationale here but seriously WTF?

Disclosure: HHMI paid my way through graduate school.

Science Magazine @science.org · Feb 6

The Howard Hughes Medical Institute, the nation’s largest private funder of biomedical research, yesterday killed a $60 million program aimed at making universities’ STEM education more inclusive. scim.ag/3EtS0US

HHMI kills program aimed at boosting inclusivity in STEM education

“Inclusive excellence” program had committed $60 million to 104 institutions

scim.ag

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Reposted by Michael Bogdos

John Trant @trantteam.bsky.social · Jan 27

Hey American PIs. If you have undergrad students who, for whatever personal reasons might find it...appropriate to not do grad school in the good ol' US of A for the next 4+ years, I (and my colleagues at UWindsor Chem) are open to applicants. They pay Canadian domestic rates at UWindsor.

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Reposted by Michael Bogdos

John Trant @trantteam.bsky.social · Jan 27

And you WON'T BELIEVE the incentives the Canadian Government will give you to just do R&D in Canada. It's literally insane. Anyways, happy to talk and connect people if anyone is interested. Things might get rocky for a bit, and staff might be happier living somewhere that thinks they are humans.

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Michael Bogdos @mixalhsmpogdos.bsky.social · Jan 11

How does one include all sources of error for a quantity of interest obtained by fitting a model e.g. rate constants from kinetics?

Simulations give the answer:

atigdnc.netlify.app/post/error_handling/

tldr; fit each dataset, propagate and combine errors (or random effects model). #chemsky

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Michael Bogdos @mixalhsmpogdos.bsky.social · Dec 22

Wrapping up 2024 - quite the year! I defended my PhD, after more than 4 years at ETH.

Here's hoping 2025 has something just as exciting in store!

Michael Bogdos @mixalhsmpogdos.bsky.social · Dec 8

Experimental results here:

foundry.adaptyvbio.com/competition

Adaptyv Foundry

foundry.adaptyvbio.com