Tom Fay

#compchemsky

GitHub - tomfay/openespf: A python toolkit for performing polarizable QM/MM simulations. A python toolkit for performing polarizable QM/MM simulations. - tomfay/openespf

This opens the door to studying more complex processes like charge transfer and non-adiabatic dynamics in the condensed phase. The methods are implemented in the OpenESPF code available here: github.com/tomfay/opene... It combines PySCF for QM calculations and OpenMM for GPU accelerated MM.

We've also developed the machinery to treat periodic boundary conditions and calculate forces for ground and excited states. In the paper we demonstrate that we can calculate fluorescence spectra with tens of nanoseconds of excited state QM/MM molecular dynamics with state-specific MM polarisation.

Analytic Gradients and Periodic Boundary Conditions for Direct Reaction Field Polarizable QM/MM with Electrostatic Potential Fitting Our recently developed Direct Reaction field with ESPF Embedding Model (DREEM) method offers an efficient and physically rigorous framework for incorporating polarizable molecular mechanics (MM) environments into quantum mechanics/molecular mechanics (QM/MM) simulations. By coupling the QM and MM regions through the instantaneous MM electrostatic polarization response to QM charge density fluctuations, DREEM enables consistent treatment of ground and excited electronic states, capturing electronic state-specific polarization and dispersion effects absent in conventional mean-field or linear response approaches. The use of the electrostatic potential fitting (ESPF) approximation method to describe charge density fluctuations significantly improves the computational efficiency compared to the integral-exact direct reaction field. In this work, we present two methodological advancements to extend the applicability of DREEM to realistic condensed-phase simulations: first, the development of efficient analytic energy gradients, enabling geometry optimization, transition state searches, and molecular dynamics; and second, a formulation of periodic boundary conditions (PBC) compatible with the DREEM framework. These capabilities are implemented in the open-source OpenESPF code, interfacing PySCF and OpenMM for high-performance QM and MM calculations. We demonstrate that the resulting implementation enables practical simulations of excited-state optical properties in periodic polarizable environments, where we calculate the fluorescence spectrum of acetone in water, including quantum vibronic and non-Condon effects. This paves the way for predictive modeling of photochemical reactivity and spectroscopy in complex systems where environment polarization is important.

The last paper from my postdoc at Aix-Marseille has just been published in the Journal of Chemical Theory and Computation! doi.org/10.1021/acs....

We developed an efficient method, which we call DREEM, QM/MM simulations including electronic polarisability in MM atoms in a QM state specific way.

I'm also going to take this opportunity to advertise again that I'm recruiting postdocs to work in my group. If you have an interest in quantum dynamics, excited states, electron/energy transfers, or other things my group does (see here faygroupucla.github.io) please do get in touch.

This work describes a new mechanism by which reactions of spin-polarised radicals, high energy intermediates encountered in lots of chemistry, can selectively react to form different chiral products. This could implications for the chemistry of the origin of life.

Enantioselective Radical Reactions Can Be Induced by Electron Spin Polarization: A Quantum Mechanism for Nature’s Emergent Homochirality? Biomolecules that constitute life on Earth are chiral, but the precise mechanism by which homochirality emerged remains a mystery. In this work, it is demonstrated that reactions of radical pairs, whe...

I'm very pleased to say the first paper from my group at UCLA has been published in @pubs.acs.org JPCL doi.org/10.1021/acs.... #chemsky

University fees could be linked to teaching standards, regulator says England's universities regulator says some institutions might have to charge less than others.

There are lots of great things about the British university system, but I do worry what effect something like this would have on early career researchers and in general the scientific research output from universities.
www.bbc.com/news/article...

Research Fellow in Theoretical Quantum Chemistry at UCL Apply for the Research Fellow in Theoretical Quantum Chemistry role on jobs.ac.uk, the top job board for academic positions in higher education. View details and apply now.

New PostDoc opportunity in #CompChem at
@uclchemistry.bsky.social

Join our exciting research to develop novel wavefunction theory for open-shell ground and excited states in molecules. Find out more about our group at www.hughburton.com

Please share widely!

www.jobs.ac.uk/job/DOE518/r...

Fascinating to see that French "tacos" have made to LA as the "FrenchFold".

#chemsky

#theoreticalchemistry #theochem #chemistry #quantum #quantumbiology #physchem

On the origins of life’s homochirality: Inducing enantiomeric excess with spin-polarized electrons | PNAS Life as we know it is homochiral, but the origins of biological homochirality on early Earth remain elusive. Shallow closed-basin lakes are a plaus...

This idea may have implications for why all of life's molecules have a particular chirality over another. This work was inspired by work from Ozturk and Sasselov which I'd thoroughly recommend. doi.org/10.1073/pnas...

Probably my zaniest preprint to date just came out. I've explored the possibility that reactions of radical pairs can become enantioselective when one of the radicals is spin-polarised.
arxiv.org/abs/2507.08287

Introducing CECAM-US-WEST, a new CECAM node located at UC Berkeley. Programing starting next calendar year! @cecamevents.bsky.social @ucberkeleyofficial.bsky.social chemistry.berkeley.edu/news/new-int...

GitHub - tomfay/openespf: A python toolkit for performing polarizable QM/MM simulations. A python toolkit for performing polarizable QM/MM simulations. - tomfay/openespf

All of this is implemented in the freely available OpenESPF code: github.com/tomfay/opene... . This interfaces PySCF for QM calculations and OpenMM for polarisable MM calculations (with GPU acceleration). Lots of examples are included in the git repo!

With this we've been able to run 10s of picoseconds of excited state, polarisable QM/MM molecular dynamics, with rigorously treated periodic boundary conditions. We can also run calculations with well over 100,000 polarisable MM atoms.

Analytic gradients and periodic boundary conditions for direct reaction field polarizable QM/MM Our recently developed Direct Reaction field with ESPF Embedding Model (DREEM) method offers an efficient and physically rigorous framework for incorporating polarizable molecular mechanics (MM) envir...

New pre-print with @huixrotllant.bsky.social and Nicolas Ferré! We've been making some big developments for the DREEM method for polarisable QM/MM, including analytic energy gradients for SCF and TD-DFT and periodic boundary conditions. #compchemsky #chemsky
doi.org/10.26434/che...

If I want to send a message to my bank I first need to start a chat with a chatbot, which I need to persuade to connect me to a second AI chatbot which I then need to persuade to connect me to a person... 🙃

Based on the outcomes of our project, we have created a pamphlet designed to be used in research laboratories. #researchintegrity #researchclimate #researchmisconduct

Hope you're enjoying your trip! When you're next in the US you'd be welcome to come visit UCLA as well!

A PhD position in theoretical chemistry (2025-2028) is available in my group starting in October. Info&Apply: huixrotllant.github.io/openings.html #academicjobs #compchem Please RT

pyTTN: An Open Source Toolbox for Open and Closed System Quantum Dynamics Simulations Using Tree Tensor Networks We present the Python Tree Tensor Network package (pyTTN) for the evaluation of dynamical properties of closed and open quantum systems that makes use of Tree Tensor Network (TTN), or equivalently the...

A great preprint from Lachlan Lindoy and co where they present a powerful new tree tensor network package! Super impressive stuff! arxiv.org/abs/2503.15460 #compchemsky

#ChemSky

Molecular Engineering of Emissive Molecular Qubits Based on Spin-Correlated Radical Pairs Spin chemistry of photogenerated spin-correlated radical pairs (SCRPs) offers a practical approach to control chemical reactions and molecular emissions by using weak magnetic fields. This capability ...

I'm very happy to have contributed theory to this paper from Tomo Mani's group (@ManiGroup) at UConn out now in JACS. A big shout-out to Neo, Miu, Tomo and everyone else in the Mani group who spearheaded this work! doi.org/10.1021/jacs...

A very cool paper from Tomo Mani's group out in JACS using spin-correlated radical pairs to produce up to 70% magnetic field effects on triplet-triplet annihilation photon upconversion. Even a fridge magnet has a visible effect! #ChemSky

doi.org/10.1021/jacs...

Quantum Biology Institute on LinkedIn: Big Quantum Bio Meeting, tomorrow Thu February 20, 7am PT/10am ET! This… Big Quantum Bio Meeting, tomorrow Thu February 20, 7am PT/10am ET! This week the @QuantumBioOrg welcomes Thomas Fay from Aix-Marseille University, to talk…

I'll be speaking at tomorrow's Big Quantum Biology meeting, about quantum coherence effects in biological electron transfer. Specifically chirality induced spin selectivity and quenching of excitons in photosynthesis. 4pm CET on zoom! #quantum #biology #ChemSky www.linkedin.com/posts/quantu...

Determination of exchange coupling constants in the electronic ground and excited states of molecular multi-spin systems The interaction between unpaired electrons determines the magnetic properties of molecular materials and consequently their applicability. In particular, for ap

Interested in exchange interactions? Our new review article is now online: doi.org/10.1063/5.02...

I'll be recruiting postdoc(s) to start from July 2025 onwards at UCLA. Potential projects are very flexible, and can be tailored to your interests, but will be broadly in the area of quantum dynamics of chemical systems. Contact info is on the group site faygroupucla.github.io. #chemsky #compchemsky

We invite applications for a tenure-track position of Assistant Professor as part of an HSI cluster hire. Join us in advancing research, mentoring, and diversity in STEM with a focus on U.S. Latinx experiences. Apply here by 1/3/25: recruit.apo.ucla.edu/JPF10039