Jan H. Jensen
@janhjensen.bsky.social
Computational chemist at the University of Copenhagen. Editor-in-Chief PeerJ Physical Chemistry. #compchem
Reposted by Jan H. Jensen
A new preprint from our team @unisouthampton.bsky.social
Can machine learning predict the space group preference of organic molecules?
Work by Hannah Gittins exploring random forest and graph neural network models to predict space group preferences of organic molecules.
doi.org/10.26434/che...
Can machine learning predict the space group preference of organic molecules?
Work by Hannah Gittins exploring random forest and graph neural network models to predict space group preferences of organic molecules.
doi.org/10.26434/che...
November 26, 2025 at 8:27 AM
A new preprint from our team @unisouthampton.bsky.social
Can machine learning predict the space group preference of organic molecules?
Work by Hannah Gittins exploring random forest and graph neural network models to predict space group preferences of organic molecules.
doi.org/10.26434/che...
Can machine learning predict the space group preference of organic molecules?
Work by Hannah Gittins exploring random forest and graph neural network models to predict space group preferences of organic molecules.
doi.org/10.26434/che...
Later today I'll give a talk entitled "Using QM and ML to predict the regioselectivity of C-H functionalisation reactions". Here are the slides: www.dropbox.com/scl/fi/7l2hf... #compchem
November 25, 2025 at 9:58 AM
Later today I'll give a talk entitled "Using QM and ML to predict the regioselectivity of C-H functionalisation reactions". Here are the slides: www.dropbox.com/scl/fi/7l2hf... #compchem
molSimplify 2.0: Improved Structure Generation for Automating Discovery in Inorganic Molecular and Reticular Chemistry | ChemRxiv - doi.org/10.26434/che... #compchem
molSimplify 2.0: Improved Structure Generation for Automating Discovery in Inorganic Molecular and Reticular Chemistry
ABSTRACT: We provide an overview of core molSimplify functionality and recent updates that enhance its capabilities for automated molecular and materials modeling. We describe the mol3D and atom3D cla...
doi.org
November 20, 2025 at 8:46 AM
molSimplify 2.0: Improved Structure Generation for Automating Discovery in Inorganic Molecular and Reticular Chemistry | ChemRxiv - doi.org/10.26434/che... #compchem
Rapid generation of transition-state conformer ensembles via constrained distance geometry | ChemRxiv - doi.org/10.26434/che... #compchem
Rapid generation of transition-state conformer ensembles via constrained distance geometry
The consideration of transition state (TS) conformer ensembles is required to accurately model a reaction, and thus plays a key role in computational catalyst design. While CREST and GOAT are establis...
doi.org
November 20, 2025 at 8:45 AM
Rapid generation of transition-state conformer ensembles via constrained distance geometry | ChemRxiv - doi.org/10.26434/che... #compchem
A General Pythonic Framework for DFT-in-DFT and WF-in-DFT Embedding | ChemRxiv - doi.org/10.26434/che... #compchem
A General Pythonic Framework for DFT-in-DFT and WF-in-DFT Embedding
High-level quantum mechanical (QM) simulations provide accurate electronic information of chemical systems but scale unfavourably with system size, making calculations of applied systems challenging. ...
doi.org
November 19, 2025 at 9:52 AM
A General Pythonic Framework for DFT-in-DFT and WF-in-DFT Embedding | ChemRxiv - doi.org/10.26434/che... #compchem
Exploring Transition Metal Complexes with Large Language Models | ChemRxiv - doi.org/10.26434/che... #compchem
Exploring Transition Metal Complexes with Large Language Models
Here we use a large language model for the exploration of chemical space of transition metal complexes (TMCs), fine-tuning the open-source Llama-3.2-1B model with a variation of the SMILES string repr...
doi.org
November 18, 2025 at 9:43 AM
Exploring Transition Metal Complexes with Large Language Models | ChemRxiv - doi.org/10.26434/che... #compchem
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 18, 2025 at 9:37 AM
Toward lab-ready AI synthesis plans with protection strategies and route scoring | ChemRxiv - doi.org/10.26434/che... #compchem
Reposted by Jan H. Jensen
WooHoo! @chemrxiv.org has just crossed 10,000 papers (preprints) in the Theoretical and computational chemistry section! #compchem This is the largest section so far...
chemrxiv.org/engage/chemr...
chemrxiv.org/engage/chemr...
a close up of a red and white logo for coca cola
ALT: a close up of a red and white logo for coca cola
media.tenor.com
November 17, 2025 at 7:47 PM
WooHoo! @chemrxiv.org has just crossed 10,000 papers (preprints) in the Theoretical and computational chemistry section! #compchem This is the largest section so far...
chemrxiv.org/engage/chemr...
chemrxiv.org/engage/chemr...
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...