Jan H. Jensen
@janhjensen.bsky.social
Computational chemist at the University of Copenhagen. Editor-in-Chief PeerJ Physical Chemistry. #compchem
A Software Framework for Physics- and AI-Driven Homogeneous Catalyst Design and Reactivity Optimization | ChemRxiv - doi.org/10.26434/che... #compchem
A Software Framework for Physics- and AI-Driven Homogeneous Catalyst Design and Reactivity Optimization
Identifying molecular catalysts that simultaneously exhibit high selectivity, high turnover frequency, and robust stability remains a major challenge in homogeneous catalysis. Traditionally, catalyst ...
doi.org
November 17, 2025 at 8:59 AM
A Software Framework for Physics- and AI-Driven Homogeneous Catalyst Design and Reactivity Optimization | ChemRxiv - doi.org/10.26434/che... #compchem
Reposted by Jan H. Jensen
#RobSelects paper of the week #j_a_c_s: Frustrated Lewis pair catalyst for coupling formate esters with vinyl and aryl organoboranes. #catalysis https://doi.org/10.1021/jacs.5c17878
November 9, 2025 at 6:24 PM
#RobSelects paper of the week #j_a_c_s: Frustrated Lewis pair catalyst for coupling formate esters with vinyl and aryl organoboranes. #catalysis https://doi.org/10.1021/jacs.5c17878
Reposted by Jan H. Jensen
This week's #RDKit blog post looks at LOBSTER, a nice molecular superposition data set that came out last year. Now that everything's loaded into a database using lwreg, I can start playing with the data in future posts.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
Working with the LOBSTER Data set I – RDKit blog
Registering and working with a 3D data set using lwreg
greglandrum.github.io
November 8, 2025 at 4:38 PM
This week's #RDKit blog post looks at LOBSTER, a nice molecular superposition data set that came out last year. Now that everything's loaded into a database using lwreg, I can start playing with the data in future posts.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
Toward lab-ready AI synthesis plans with protection strategies and route scoring | ChemRxiv - doi.org/10.26434/che... #compchem
Toward lab-ready AI synthesis plans with protection strategies and route scoring
AI-driven synthesis planning tools are developed to automatically create synthesis routes and thereby aid chemists in making novel molecules. However, these tools frequently produce reaction trees wit...
doi.org
November 7, 2025 at 12:00 PM
Toward lab-ready AI synthesis plans with protection strategies and route scoring | ChemRxiv - doi.org/10.26434/che... #compchem
Reaction Database for Catalysis and Organometallics via Freely Available Supplementary Information | ChemRxiv - doi.org/10.26434/che... #compchem
Reaction Database for Catalysis and Organometallics via Freely Available Supplementary Information
Chemical reaction databases have become core scientific infrastructure. Most prominent datasets focus on or- ganic reactions, or only include reactants and product rather than full reaction pathways, ...
doi.org
November 7, 2025 at 11:51 AM
Reaction Database for Catalysis and Organometallics via Freely Available Supplementary Information | ChemRxiv - doi.org/10.26434/che... #compchem
Reposted by Jan H. Jensen
Oh, sorry, I made a mistake. I copied the TS3 structure into TS1. The corrected figure should be. As for wB97M-V/def2-TZVPD, its relative energy of TS1 is very close to M06-2X/def2-TZVPP (within <0.1 kcal/mol). I will share the notebook, IRC and data very soon.
November 2, 2025 at 7:38 PM
Oh, sorry, I made a mistake. I copied the TS3 structure into TS1. The corrected figure should be. As for wB97M-V/def2-TZVPD, its relative energy of TS1 is very close to M06-2X/def2-TZVPP (within <0.1 kcal/mol). I will share the notebook, IRC and data very soon.
Reposted by Jan H. Jensen
A failure case for deep-learning potential: the TS1 geometry is so weird that UMA and Orb-v3 underestimate the barrier by ~15 kcal/mol, likely because it far from the training set. Handling chemical reactions is extremely hard for general deep learning models.
#compchem #compchemsky
#compchem #compchemsky
November 2, 2025 at 1:40 AM
A failure case for deep-learning potential: the TS1 geometry is so weird that UMA and Orb-v3 underestimate the barrier by ~15 kcal/mol, likely because it far from the training set. Handling chemical reactions is extremely hard for general deep learning models.
#compchem #compchemsky
#compchem #compchemsky
New highlight: Electron flow matching for generative reaction mechanism prediction
www.compchemhighlights.org/2025/10/elec... #compchem
www.compchemhighlights.org/2025/10/elec... #compchem
October 31, 2025 at 9:46 AM
New highlight: Electron flow matching for generative reaction mechanism prediction
www.compchemhighlights.org/2025/10/elec... #compchem
www.compchemhighlights.org/2025/10/elec... #compchem
Reposted by Jan H. Jensen
Save the date! Next year's European #RDKit UGM will take place from 16-18 September in Darmstadt, Germany.
Pre-registration will open in early 2026.
Pre-registration will open in early 2026.
October 21, 2025 at 3:25 PM
Save the date! Next year's European #RDKit UGM will take place from 16-18 September in Darmstadt, Germany.
Pre-registration will open in early 2026.
Pre-registration will open in early 2026.
Reposted by Jan H. Jensen
Do you want to invent the future of Chemistry with us? We‘re looking for a "Digital Native” Organic Chemist to join our team at Microsoft Research AI for Science. We offer an amazing environment where you can do deep research with passionate and talented colleagues to solve problems that matter! 1/2
October 16, 2025 at 10:06 PM
Do you want to invent the future of Chemistry with us? We‘re looking for a "Digital Native” Organic Chemist to join our team at Microsoft Research AI for Science. We offer an amazing environment where you can do deep research with passionate and talented colleagues to solve problems that matter! 1/2
Reposted by Jan H. Jensen
Skala is now available to everyone!
Why are we releasing it? Because we’re not just aiming to publish a cool paper — we’re on a mission to bring DFT to chemical accuracy using deep learning. And to make real progress, we need the community’s feedback.
#compchem
Why are we releasing it? Because we’re not just aiming to publish a cool paper — we’re on a mission to bring DFT to chemical accuracy using deep learning. And to make real progress, we need the community’s feedback.
#compchem
The wait is over! Microsoft Research is sharing Skala, the new exchange-correlation functional, marking a major milestone in the accuracy/cost trade-off in DFT. Help us learn from your testing so we can improve. Available on Azure AI Foundry and GitHub. msft.it/6016sFDLY
October 9, 2025 at 4:46 PM
Skala is now available to everyone!
Why are we releasing it? Because we’re not just aiming to publish a cool paper — we’re on a mission to bring DFT to chemical accuracy using deep learning. And to make real progress, we need the community’s feedback.
#compchem
Why are we releasing it? Because we’re not just aiming to publish a cool paper — we’re on a mission to bring DFT to chemical accuracy using deep learning. And to make real progress, we need the community’s feedback.
#compchem
Reposted by Jan H. Jensen
I have a fully funded PhD position available in my group in Copenhagen: candidate.hr-manager.net/ApplicationI...
PhD fellowship in Organic Synthesis and Supramolecular Chemistry
The Department of Chemistry at the University of Copenhagen invites applicants for a PhD fellowship in Organic chemistry with a particular focus on supramolecul
candidate.hr-manager.net
October 9, 2025 at 6:51 AM
I have a fully funded PhD position available in my group in Copenhagen: candidate.hr-manager.net/ApplicationI...
Reposted by Jan H. Jensen
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
Want 70x fast, 2x accurate Hessians for any equivariant machine learning force field? We got you!
#compchemsky #chemsky #machinelearning #mlff
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! 🤠
[1/4]
The problem is, accurate Hessians are really expensive, even with MLIPs. We say, just shoot 'em from the HIP! 🤠
[1/4]
October 8, 2025 at 6:14 PM
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
Want 70x fast, 2x accurate Hessians for any equivariant machine learning force field? We got you!
#compchemsky #chemsky #machinelearning #mlff
Reposted by Jan H. Jensen
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
October 8, 2025 at 8:06 AM
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
Reposted by Jan H. Jensen
I know this has been one of the most widely requested features. Should be in the release on 10/23
#chemsky #compchemsky #opensource
#chemsky #compchemsky #opensource
If you've been wondering about the status of the AutoOptimize interactive optimization in Avogadro2 - coming later this month 👀
October 6, 2025 at 2:02 PM
I know this has been one of the most widely requested features. Should be in the release on 10/23
#chemsky #compchemsky #opensource
#chemsky #compchemsky #opensource
Reposted by Jan H. Jensen
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...
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
October 6, 2025 at 3:53 AM
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...
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...
Jan Jensen: Can you find hits by screening only 100 molecules?
YouTube video by RDKit
youtu.be
October 5, 2025 at 9:09 AM
Fundamental Study of Density Functional Theory Applied to Triplet State Reactivity: Introduction of the TRIP50 Dataset
www.compchemhighlights.org/2025/09/fund... #compchem
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
September 25, 2025 at 1:41 PM
Fundamental Study of Density Functional Theory Applied to Triplet State Reactivity: Introduction of the TRIP50 Dataset
www.compchemhighlights.org/2025/09/fund... #compchem
www.compchemhighlights.org/2025/09/fund... #compchem
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. 👇
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
September 18, 2025 at 9:08 AM
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...
Highlights include support for constraints for geometry optimizations, tweaking bond lengths when changing elements, and more...
discuss.avogadro.cc/t/avogadro-1...
September 16, 2025 at 5:00 AM
Reposted by Jan H. Jensen
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...
From: dm.dk/media/ams/36...
September 15, 2025 at 5:47 AM
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...
From: dm.dk/media/ams/36...
Reposted by Jan H. Jensen
Pretty sure it would translate to French Universities the same way.
"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...
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...
September 14, 2025 at 10:49 PM
Pretty sure it would translate to French Universities the same way.
September 14, 2025 at 7:15 AM
Reposted by Jan H. Jensen
