Rafał Szabla

Barbara Lech and Boluwatife Ogunnaiya (3rd and 2nd year PhD students) investigate nonenzymatic RNA self-replication with molecular dynamics and quantum chemical methods. They recently described their work in two exciting research articles:
t.co/uz5Wrnt6qh
t.co/5Mifw9SjY3
t.co/FBzsNvQs6h

The International Day of Women and Girls in Science is an excellent opportunity to share with you some info about the outstanding female PhD students that I have the privilege to work with. Below, Róża Okoń, 1st year PhD student working on kinetics of complex (photo)chemical reactions 🙂. 1/2

Research associate/visiting researcher in computational chemistry Faculty/Unit/Organizational unit: Faculty of Chemistry/ Wroclaw University of Science and Technology

I am looking for a Postdoctoral Researcher who will focus on computational studies of RNA. Topics include studying non-enzymatic RNA self-replication with MD and QM/MM methods, and applying/developing machine learning potentials for RNA. Full info under:

euraxess.ec.europa.eu/jobs/405129

Accurate Prediction of Photoinduced Electron Transfer Timescales with Nonadiabatic Microcanonical Rate Theory Photoinduced electron transfer (PET) lies at the heart of energy conversion from light into chemical reactions. It governs a variety of biological processes including DNA damage and repair and biological photosynthesis. Quantifying PET rates and optimizing them is also crucial for selective photoredox catalysis. However, commonly used rate theories break down for PET operating in the strong coupling and nonequilibrium regimes, while excited-state dynamics simulations are computationally demanding and require complex analysis to extract PET times. Here, we employed surface-hopping nonadiabatic excited-state dynamics simulations and statistical rate theories to characterize ultrafast PET in a dimer of stacked adenine nucleobases. We show that the widely used classical Marcus Theory and Fermi’s Golden Rule fail to describe ultrafast PET or even reproduce qualitative rate trends. Instead, we propose a chromophore-localized variant of nonadiabatic Rice–Rampsperger–Kassel–Marcus (NA-RRKM) theory, which yields PET timescales that are in excellent agreement with excited-state dynamics simulations.

Have you ever wondered what happens to DNA after absorption of light? It could lead to photoinduced electron transfer. Our new approach to the calculation of photoinduced electron timescales was just published!
pubs.acs.org/doi/10.1021/...

See our simulation of this process:
youtu.be/eSzKTzZJgmo

@chemcomm.rsc.org 😊

A-type helicity controls efficient nonenzymatic template copying of nucleic acids We performed classical molecular dynamics simulations for DNA self-replication on an RNA template with phosphoroimidazole activation. We demonstrate that the RNA template imposes A-type helicity on th...

Nonenzymatic self-replication of nucleic acids is driven by helicity type A! The unique structure of RNA is predisposed to nonenzymatic copying, and DNA can be copied on an RNA template. Is this why nature chose RNA?

Great work by Barbara, from my group!

pubs.rsc.org/en/content/a...

High propensity to bind such protective metal cations could have enabled the emergence of first functional peptides. It could have also limited the sequence space.

Overall, it was a fantastic collaboration with the Mansy, Sasselov and Kufner labs as well as other experimenters!

Zinc can stabilize the smallest functional protein motifs. In our @chemicalscience.rsc.org article, we also showed that Zn2+ protects small potentially prebiotic peptides from photodegradation involving photoinduced electron transfer.

pubs.rsc.org/en/content/a...

Quinol–Enedione Rearrangement The quinol–enedione rearrangement enables the synthesis of 2-cyclohexene-1,4-diones from readily available para-quinol substrates. Building on sporadic early reports of this transformation, we have op...

I had a great pleasure to collaborate with @biomimetic-chem.bsky.social , develop and characterize a previously poorly understood reaction - quinol-enedione rearrangement. See the excellent experimental work with a small support of my DFT calculations😉 !

pubs.acs.org/doi/full/10....

@chemistryeurope.bsky.social

We evaluated the binding of activated dinucleotides in nonenzymatic RNA self-replication scenarios using molecular dynamics simulations. See the 1st paper by Basia, a 2nd year PhD student in my lab🥳!

chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1...

Preprint:
chemrxiv.org/engage/chemr...

Check out our 2024 #ChemSciMostPopular chemical biology collection, which is online now! Read the collection here:

pubs.rsc.org/en/jour...

#ChemBio #ChemSky 🧪

📣 The abstract submission deadline for the 32nd International Conference on Photochemistry has been extended to 12 May 2025!

🔬Join us in Aachen, 13–18 July 2025, for great science in a historic setting!

New paper from our lab just out @pnas.org! 🚀
Using free energy simulations, #AIphaFold and #cryoEM refinement, we uncovered a key conformational change in a paradigm-shifting #CRISPR-associated #transposon capable of precise gene knock-ins. 🔍🧬
www.pnas.org/doi/epub/10....

Signs of life on a distant planet? Not so fast, say these astronomers Bold claims of ‘biosignature’ molecules trigger an outpouring of scepticism.

Signs of life on a distant planet? Not so fast, say these astronomers www.nature.com/articles/d41...

Our research article about photoinduced electron transfer in DNA was selected as one of the most popular Chemical Science papers in chemical biology!

pubs.rsc.org/en/content/a...

@chemicalscience.rsc.org @wroclaw-tech.bsky.social

Are you using nonadiabatic dynamics for complex systems? Join us in sunny Spain for the "Future Directions in Non-Adiabatic Dynamics" workshop (Sept 2-5, 2025) at CECAM-Zaragoza! Register by June 3. Check out the event page: tinyurl.com/2nvnanf2

#NAMD #NonAdiabaticDynamics #CECAM

Trump’s siege of science: how the first 30 days unfolded and what’s next The breakneck pace and devastating impact of the administration’s policy changes has shocked researchers.

Trump’s siege of science: how the first 30 days unfolded & what’s next

Once upon a time leaders believed that science was essential to nation’s security, to better health, to more jobs, to a higher standard of living & to cultural progress
🧪 #academicSky
@nature.com
www.nature.com/articles/d41...

Last week to register to the 11th Winter School in Computational Chemistry (27-31 Jan)!

take a look at our great program, register for free and come along to learn a lot about #theochem 😊

winterschool.cc/program

I have a new paper in Dialogues on Climate Change exploring climate outcomes under current policies. I find that we are likely headed toward 2.7C by 2100 (with uncertainties from 1.9C to 3.7C), and that high end emissions scenarios have become much less likely.

journals.sagepub.com...

It was a lot of fun and I'm slowly coming back to shape🏂. Sadly, we do not get to many snowy days anymore.

With ERC grants it's best to celebrate the submission, because you never know if you get it. This week I submitted a ERC proposal for the 4th time (5th time counting Synergy). This time a CoG. Then, I took Thursday off to do some snowboarding, for the 1st time in 10 years 🙂.

Polish scientists describe new type of chemical reaction in formation of DNA building blocks Quantum chemists from the Wrocław University of Science and Technology have described the principles of a completely new class of chemical reactions. It was discovered during research on the formation...

A very nice news item was recently released by the service Science in Poland (in English). It describes our work on the identification of a new type of photoredox reactions, which can be enabled by sulfur-sulfur (chalcogen bonding) interactions 🙂.

scienceinpoland.pl/en/news/news...

To choose a career, I needed to do more than ‘follow my dream’ Practical advice helped this international scientist figure out her post-Ph.D. direction

"[My adviser] told me that instead of focusing on finding a dream job, I should think about what I am good at and what makes me happy at least 80% of the time. This advice surprised me at first, but it ended up being exactly what I needed to hear." scim.ag/3DHtLCc

Oh great! For a moment I thought it was Terraforming Mars, but I didn't recognize some of the pieces :). Great game :)

What's the name of the game :)?

Good Practices in Database Generation for Benchmarking Density Functional Theory Advancements in DFT over the past three decades have been driven by extensive benchmarking studies. This review outlines best practices in database generation, offering guidance on key methodological...

#compchem Good read: Good Practices in Database Generation for Benchmarking Density Functional Theory #compchemsky doi.org/10.1002/wcms...

Okay, can now perform iterative automatic ML potential fitting and finetuning including benchmark (for certain properties).

Looks like I can also easily use both GPUs and CPUs in the same workflow despite the fact that they don't have access to the same hard drive. 🙃 But more on Monday.

We finally had some snowfall and with 5 cm thicker layer I would be nordic skiing already. Still nordic walking in these conditions is a lot of fun ;).