arXiv subjects

Thomas P. Fay

Publications and source records attributed to Thomas P. Fay.

18 recordsLinked to original sources

arXiv2026

Solvent Effects on Triplet Yields in BODIPY-Based Photosensitizers

We employ molecular dynamics simulations and quantum rate theories to elucidate the complex condensed-phase dynamics underpinning triplet-state formation in organic photosensitizers. Using models informed by first-principles calculations complete with a molecular representation of solvents of different polarities, we elucidate the interplay of the internal and environmental interactions underlying triplet yield. We find that triplet yields depend sensitively on the dielectric stabilization of the charge transfer intermediate that facilitates a transition into the triplet manifold. Our results illustrate the importance of molecularly detailed models in understanding the excited-state internal charge-transfer dynamics of photochemically-relevant organic molecules.

physics.chem-ph↗

arXiv2024

Efficient polarizable QM/MM using the direct reaction field Hamiltonian with electrostatic potential fitted multipole operators

Electronic polarization and dispersion are decisive actors in determining interaction energies between molecules. These interactions have a particularly profound effect on excitation energies of molecules in complex environments, especially when the excitation involves a significant degree of charge reorganisation. The direct reaction field (DRF) approach, which has seen a recent revival of interest, provides a powerful framework for describing these interactions in quantum mechanics/molecular mechanics (QM/MM) models of systems, where a small subsystem of interest is described using quantum chemical methods and the remainder is treated with a simple MM force field. In this paper we show how the DRF approach can be combined with the electrostatic potential fitted (ESPF) multipole operator description of the QM region charge density, which significantly improves the efficiency of the method, particularly for large MM systems, and for typical calculations effectively eliminates the dependence on MM system size. We also show how the DRF approach can be combined with fluctuating charge descriptions of the polarizable environment, as well as previously used atom-centred dipole-polarizability based models. We further show that the ESPF-DRF method provides an accurate description of molecular interactions in both ground and excited electronic states of the QM system and apply it to predict the gas to aqueous solution solvatochromic shifts in the UV/visible absorption spectrum of acrolein.

physics.chem-ph↗

arXiv2024

Coherent control from quantum committment probabilities

We introduce a general definition of a quantum committor in order to clarify reaction mechanisms and facilitate control in processes where coherent effects are important. With a quantum committor, we generalize the notion of a transition state to quantum superpositions and quantify the effect of interference on the progress of the reaction. The formalism is applicable to any linear quantum master equation supporting metastability for which absorbing boundary conditions designating the reactant and product states can be applied. We use this formalism to determine the dependence of the quantum transition state on coherences in a polaritonic system and optimize the initialization state of a conical intersection model to control reactive outcomes, achieving yields of the desired state approaching 100%. In addition to providing a practical tool, the quantum committor provides a conceptual framework for understanding reactions in cases when classical intuitions fail.

physics.chem-ph↗

arXiv2024

Unraveling the mechanisms of triplet state formation in a heavy-atom free photosensitizer

Triplet excited state generation plays a pivotal role in photosensitizers, however the reliance on transition metals and heavy atoms can limit the utility of these systems. In this study, we demonstrate that an interplay of competing quantum effects control the high triplet quantum yield in a prototypical boron dipyrromethene-anthracene (BD-An) donor-acceptor dyad photosensitizer, which is only captured by an accurate treatment of both inner and outer sphere reorganization energies. Our ab initio-derived model provides excellent agreement with experimentally measured spectra, triplet yields and excited state kinetic data, including the triplet lifetime. We find that rapid triplet state formation occurs primarily via high-energy triplet states through both spin-orbit coupled charge transfer and El-Sayed's rule breaking intersystem crossing, rather than direct spin-orbit coupled charge transfer to the lowest lying triplet state. Our calculations also reveal that competing effects of nuclear tunneling, electronic state recrossing, and electronic polarizability dictate the rate of non-productive ground state recombination. This study sheds light on the quantum effects driving efficient triplet formation in the BD-An system, and offers a promising simulation methodology for diverse photochemical systems.

physics.chem-ph↗

arXiv2023

Exciton dynamics from the mapping approach to surface hopping: Comparison with Förster and Redfield theories

We compare the recently introduced multi-state mapping approach to surface hopping (MASH) with the Förster and Redfield theories of excitation energy transfer. Whereas Förster theory relies on weak coupling between chromophores, and Redfield theory assumes the electronic excitations to be weakly coupled to fast chromophore vibrations, MASH is free from any perturbative or Markovian approximations. We illustrate this with an example application to the rate of energy transfer in a Frenkel-exciton dimer, showing that MASH interpolates correctly between the opposing regimes in which the Förster and Redfield results are reliable. We then compare the three methods for a realistic model of the Fenna-Matthews-Olson complex with a structured vibrational spectral density and static disorder in the excitation energies. In this case there are no exact results for comparison so we use MASH to assess the validity of Förster and Redfield theories. We find that Förster theory is the more accurate of the two on the picosecond timescale, as has been shown previously for a simpler model of this particular light-harvesting complex. We also explore various ways to sample the initial electronic state in MASH and find that they all give very similar results for exciton dynamics.

physics.chem-ph↗

arXiv2023

Kinetics of the xanthophyll cycle and its role in photoprotective memory and response

Efficiently balancing photochemistry and photoprotection is crucial for survival and productivity of photosynthetic organisms in the rapidly fluctuating light levels found in natural environments. The ability to respond quickly to sudden changes in light level is clearly advantageous. In the alga Nannochloropsis oceanica we observed an ability to respond rapidly to sudden increases in light level which occur soon after a previous high-light exposure. This ability implies a kind of memory. In this work, we explore the xanthophyll cycle in N. oceanica as a short-term photoprotective memory system. By combining snapshot fluorescence lifetime measurements with a biochemistry-based quantitative model, we show that short-term "memory" arises from the xanthophyll cycle. In addition, the model enables us to characterize the relative quenching abilities of the three xanthophyll cycle components. Given the ubiquity of the xanthophyll cycle in photosynthetic organisms the model described here will be of utility in improving our understanding of vascular plant and algal photoprotection with important implications for crop productivity.

physics.bio-ph↗

arXiv2023

On the mechanism of polaritonic rate suppression from quantum transition paths

Polariton chemistry holds promise for facilitating mode-selective chemical reactions, but the underlying mechanism behind the rate modifications observed under vibrational strong coupling is not well understood. Using the recently developed quantum transition path theory, we have uncovered a mechanism of resonant suppression of a thermal reaction rate in a simple model polaritonic system, consisting of a reactive mode in a bath confined to a lossless microcavity with a single photon mode. This mechanism was uncovered by resolving the quantum dynamical reactive pathways and identifying their rate limiting transitions. Upon inspecting the wavefunctions associated with the rate limiting transition, we observed the formation of a polariton and identified the concomitant rate suppression as due to hybridization between the reactive mode and the cavity mode, which inhibits bath-mediated tunneling during the reaction. The transition probabilities that define the quantum master equation can be directly translated into a visualisation of the corresponding polariton energy landscape. This landscape exhibits a double funnel structure, with a large barrier between the initial and final states. This mechanism of resonant rate suppression is found to be robust to model parameters and computational details, and thus expected to be general.

physics.chem-ph↗

arXiv2023

Spin selective charge recombination in chiral donor-bridge-acceptor triads

In this paper we outline a physically motivated framework for describing spin-selective recombination processes in chiral systems, from which we derive spin-selective reaction operators for recombination reactions of donor-bridge-acceptor molecules, where the electron transfer is mediated by chirality and spin-orbit coupling. In general the recombination process is selective only for spin-coherence between singlet and triplet states, and it is not in general selective for spin polarisation. We find that spin polarisation selectivity only arises in hopping mediated electron transfer. We describe how this effective spin-polarisation selectivity is a consequence of spin-polarisation generated transiently in the intermediate state. The recombination process also augments the coherent spin dynamics of the charge separated state, which is found to have a significant effect on recombination dynamics and to destroy any long-lived spin polarisation. Although we only consider a simple donor-bridge-acceptor system, the framework we present here can be straightforwardly extended to describe spin-selective recombination processes in more complex systems.

physics.chem-ph↗

arXiv2022

Coupled charge and energy transfer dynamics in light harvesting complexes from a hybrid hierarchical equations of motion approach

We describe a method for simulating exciton dynamics in protein-pigment complexes, including effects from charge transfer as well as fluorescence. The method combines the hierarchical equations of motion, which are used to describe quantum dynamics of excitons, and the Nakajima-Zwanzig quantum master equation, which is used to describe slower charge transfer processes. We study the charge transfer quenching in light harvesting complex II, a protein postulated to control non-photochemcial quenching in many plant species. Using our hybrid approach, we find good agreement between our calculation and experimental measurements of the excitation lifetime. Furthermore our calculations reveal that the exciton energy funnel plays an important role in determining quenching efficiency, a conclusion we expect to extend to other proteins that perform protective excitation quenching. This also highlights the need for simulation methods that properly account for the interplay of exciton dynamics and charge transfer processes.

physics.chem-ph↗

arXiv2021

The origin of chirality induced spin selectivity in photo-induced electron transfer

Here we propose a mechanism by which spin polarization can be generated dynamically in chiral molecular systems undergoing photo-induced electron transfer. The proposed mechanism explains how spin polarization emerges in systems where charge transport is dominated by incoherent hopping, mediated by spin orbit and electronic exchange couplings through an intermediate charge transfer state. We derive a simple expression for the spin polarization that predicts a non-monotonic temperature dependence consistent with recent experiments. We validate this theory using approximate quantum master equations and the numerically exact hierarchical equations of motion. The proposed mechanism of chirality induced spin selectivity should apply to many chiral systems, and the ideas presented here have implications for the study of spin transport at temperatures relevant to biology, and provide simple principles for the molecular control of spins in fluctuating environments.

cond-mat.mes-hall↗

arXiv2021

Spin relaxation in radical pairs from the stochastic Schrödinger equation

We show that the stochastic Schrödinger equation (SSE) provides an ideal way to simulate the quantum mechanical spin dynamics of radical pairs. Electron spin relaxation effects arising from fluctuations in the spin Hamiltonian are straightforward to include in this approach, and their treatment can be combined with a highly efficient stochastic evaluation of the trace over nuclear spin states that is required to compute experimental observables. These features are illustrated in example applications to a flavin-tryptophan radical pair of interest in avian magnetoreception, and to a problem involving spin-selective radical pair recombination along a molecular wire. In the first of these examples, the SSE is shown to be both more efficient and more widely applicable than a recent stochastic implementation of the Lindblad equation, which only provides a valid treatment of relaxation in the extreme-narrowing limit. In the second, the exact SSE results are used to assess the accuracy of a recently-proposed combination of Nakajima-Zwanzig theory for the spin relaxation and Schulten-Wolynes theory for the spin dynamics, which is applicable to radical pairs with many more nuclear spins. An appendix analyses the efficiency of trace sampling in some detail, highlighting the particular advantages of sampling with SU(N) coherent states.

quant-ph↗

arXiv2021

Chirality Induced Spin Coherence in Electron Transfer Reactions

Recently there has been much interest in the chirality induced spin selectivity effect, whereby electron spin polarisation, which is dependent on the molecular chirality, is produced in electrode-molecule electron transfer processes. Naturally, one might consider if a similar effect can be observed in simple molecular charge transfer reactions, for example in light-induced electron transfer from an electron donor to an electron acceptor. In this work we explore the effect of electron transfer on spins in chiral single radicals and chiral radical pairs using Nakajima-Zwanzig theory. In these cases chirality, in conjuction with spin-orbit coupling, does not lead to spin polarisation, but instead the electron transfer generates quantum coherence between spins states. In principle, this chirality induced spin coherence could manifest in a range of experiments, and in particular we demonstrate that the OOP-ESEEM pulse EPR experiment would be able to detect this effect in oriented radical pairs.

physics.chem-ph↗

arXiv2020

Quantum mechanical spin dynamics of a molecular magnetoreceptor

Radical pair recombination reactions are known to be sensitive to extremely weak magnetic fields, and can therefore be said to function as molecular magnetoreceptors. The classic example is a carotenoid-porphyrin-fullerene (C+PF-) radical pair that has been shown to provide a "proof-of-principle" for the operation of a chemical compass [K. Maeda et al., Nature 453, 387 (2008)]. Previous simulations of this radical pair have employed semiclassical approximations, which are routinely applicable to its 47 coupled electronic and nuclear spins. However, calculating the exact quantum mechanical spin dynamics presents a significant challenge, and has not been possible before now. Here we use a recently developed method to perform numerically converged simulations of the C+PF- quantum mechanical spin dynamics, including all coupled spins. Comparison of these quantum mechanical simulations with various semiclassical approximations reveals that, while it is not perfect, the best semiclassical approximation does capture essentially all of the relevant physics in this problem.

physics.chem-ph↗

arXiv2019

Electron spin relaxation in radical pairs: Beyond the Redfield approximation

Relaxation processes can have a large effect on the spin selective electron transfer reactions of radical pairs. These processes are often treated using phenomenological relaxation superoperators or with some model for the microscopic relaxation mechanism treated within Bloch-Redfield-Wangsness theory. Here, we demonstrate that an alternative perturbative relaxation theory, based on the Nakajima-Zwanzig equation, has certain advantages over Redfield theory. In particular, the Nakajima-Zwanzig equation does not suffer from the severe positivity problem of Redfield theory in the static disorder limit. Combining the Nakajima-Zwanzig approach consistently with the Schulten-Wolynes semiclassical method, we obtain an efficient method for modeling the spin dynamics of radical pairs containing many hyperfine-coupled nuclear spins. This is then used to investigate the spin-dependent electron transfer reactions and intersystem crossing of dimethyljulolidine-naphthalenediimide (DMJ-NDI) radical ion pairs. By comparing our simulations with experimental data, we find evidence for a field-independent contribution to the triplet quantum yields of these reactions which cannot be explained by electron spin relaxation alone.

physics.chem-ph↗

arXiv2018

Spin-selective electron transfer reactions of radical pairs: beyond the Haberkorn master equation

Radical pair recombination reactions are normally described using a quantum mechanical master equation for the electronic and nuclear spin density operator. The electron spin state selective (singlet and triplet) recombination processes are described with a Haberkorn reaction term in this master equation. Here we consider a general spin state selective electron transfer reaction of a radical pair and use Nakajima-Zwanzig theory to derive the master equation for the spin density operator, thereby elucidating the relationship between non-adiabatic reaction rate theory and the Haberkorn reaction term. A second order perturbation theory treatment of the diabatic coupling naturally results in the Haberkorn master equation with an additional reactive scalar electron spin coupling term. This term has been neglected in previous spin chemistry calculations, but we show that it will often be quite significant. We also show that beyond second order in perturbation theory, i.e., beyond the Fermi golden rule limit, an additional reactive singlet-triplet dephasing term appears in the master equation. A closed form expression for the reactive scalar electron spin coupling in terms of the Marcus theory parameters that determine the singlet and triplet recombination rates is presented. By performing simulations of radical pair reactions with the exact Hierarchical Equations of Motion (HEOM) method, we demonstrate that our master equations provide a very accurate description of radical pairs undergoing spin-selective non-adiabatic electron transfer reactions. The existence of a reactive electron spin coupling may well have implications for biologically relevant radical pair reactions such as those which have been suggested to play a role in avian magnetoreception.

physics.chem-ph↗

arXiv2018

On the low magnetic field effect in radical pair reactions

Radical pair recombination reactions are known to be sensitive to the application of both low and high magnetic fields. The application of a weak magnetic field reduces the singlet yield of a singlet-born radical pair, whereas the application of a strong magnetic field increases the singlet yield. The high field effect arises from energy conservation: when the magnetic field is stronger than the sum of the hyperfine fields in the two radicals, ${\rm S}\to {\rm T}_{\pm}$ transitions become energetically forbidden, thereby reducing the number of pathways for singlet to triplet interconversion. The low field effect arises from symmetry breaking: the application of a weak magnetic field lifts degeneracies among the zero field eigenstates and increases the number of pathways for singlet to triplet interconversion. However, the details of this effect are more subtle, and have not previously been properly explained. Here we present a complete analysis of the low field effect in a radical pair containing a single proton, and in a radical pair in which one of the radicals contains a large number of hyperfine-coupled nuclear spins. We find that the new transitions that occur when the field is switched on are between ${\rm S}$ and ${\rm T}_0$ in both cases, and not between ${\rm S}$ and ${\rm T}_{\pm}$ as has previously been claimed. We then illustrate this result by using it in conjunction with semiclassical spin dynamics simulations to account for the observation of a biphasic--triphasic--biphasic transition with increasing magnetic field strength in the magnetic field effect on the time-dependent survival probability of a photoexcited carotenoid-porphyrin-fullerene radical pair.

physics.chem-ph↗

arXiv2017

Spin-dependent charge recombination along para-phenylene molecular wires

We have used an efficient new quantum mechanical method for radical pair recombination reactions to study the spin-dependent charge recombination along PTZ$^{\bullet+}$--Ph$_n$--PDI$^{\bullet-}$ molecular wires. By comparing our results to the experimental data of E. Weiss {\em et al.} [J. Am. Chem. Soc. {\bf 126}, 5577 (2004)], we are able to extract the spin-dependent (singlet and triplet) charge recombination rate constants for wires with $n=2-5$. These spin-dependent rate constants have not been extracted previously from the experimental data because they require fitting its magnetic field-dependence to the results of quantum spin dynamics simulations. We find that the triplet recombination rate constant decreases exponentially with the length of the wire, consistent with the superexchange mechanism of charge recombination. However, the singlet recombination rate constant is nearly independent of the length of the wire, suggesting that the singlet pathway is dominated by an incoherent hopping mechanism. A simple qualitative explanation for the different behaviours of the two spin-selective charge recombination pathways is provided in terms of Marcus theory. We also find evidence for a magnetic field-independent background contribution to the triplet yield of the charge recombination reaction, and suggest several possible explanations for it. Since none of these explanations is especially compelling given the available experimental evidence, and since the result appears to apply more generally to other molecular wires, we hope that this aspect of our study will stimulate further experimental work.

physics.chem-ph↗

arXiv2016

An efficient quantum mechanical method for radical pair recombination reactions

The standard quantum mechanical expressions for the singlet and triplet survival probabilities and product yields of a radical pair recombination reaction involve a trace over the states in a combined electronic and nuclear spin Hilbert space. If this trace is evaluated deterministically, by performing a separate time-dependent wavepacket calculation for each initial state in the Hilbert space, the computational effort scales as $O(Z^2\log Z)$, where $Z$ is the total number of nuclear spin states. Here we show that the trace can also be evaluated stochastically, by exploiting the properties of spin coherent states. This results in a computational effort of $O(MZ\log Z)$, where $M$ is the number of Monte Carlo samples needed for convergence. Example calculations on a strongly-coupled radical pair with $Z>10^6$ show that the singlet yield can be converged to graphical accuracy using just $M=200$ samples, resulting in a speed up by a factor of $>5000$ over a standard deterministic calculation. We expect that this factor will greatly facilitate future quantum mechanical simulations of a wide variety of radical pairs of interest in chemistry and biology.

physics.chem-ph↗