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DOE OSTI2024

Electron transfer in a crystalline cytochrome with four hemes

Diffusion of electrons over distances on the order of 100 μm has been observed in crystals of a small tetraheme cytochrome (STC) from Shewanella oneidensis [J. Huang et al . J. Am. Chem. Soc. 142, 10459–10467 (2020)]. Electron transfer between hemes in adjacent subunits of the crystal is slower and more strongly dependent on temperature than had been expected based on semiclassical electron-transfer theory. Here, in this work, we explore explanations for these findings by molecular-dynamics simulations of crystalline and monomeric STC. New procedures are developed for including time-dependent quantum mechanical energy differences in the gap between the energies of the reactant and product states and for evaluating fluctuations of the electronic-interaction matrix element that couples the two hemes. Rate constants for electron transfer are calculated from the time- and temperature-dependent energy gaps, coupling factors, and Franck–Condon-weighted densities of states using an expression with no freely adjustable parameters. Back reactions are considered, as are the effects of various protonation states of the carboxyl groups on the heme side chains. Interactions with water are found to dominate the fluctuations of the energy gap between the reactant and product states. The calculated rate constant for electron transfer from heme IV to heme Ib in a neighboring subunit at 300 K agrees well with the measured value. However, the calculated activation energy of the reaction in the crystal is considerably smaller than observed. We suggest two possible explanations for this discrepancy. The calculated rate constant for transfer from heme I to II within the same subunit of the crystal is about one-third that for monomeric STC in solution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Constrained HRT Surfaces and their Entropic Interpretation

Abstract Consider two boundary subregionsAandBthat lie in a common boundary Cauchy surface, and consider also the associated HRT surfaceγ B forB. In that context, the constrained HRT surfaceγ A:B can be defined as the codimension-2 bulk surface anchored toAthat is obtained by a maximin construction restricted to Cauchy slices containingγ B . As a result,γ A:B is the union of two pieces,$$ {\gamma}_{A:B}^B $$ γ A : B B and$$ {\gamma}_{A:B}^{\overline{B}} $$ γ A : B B ¯ lying respectively in the entanglement wedges ofBand its complement$$ \overline{B} $$ B ¯ . Unlike the area$$ \mathcal{A}\left({\gamma}_A\right) $$ A γ A of the HRT surfaceγ A , at least in the semiclassical limit, the area$$ \mathcal{A}\left({\gamma}_{A:B}\right) $$ A γ A : B ofγ A:B commutes with the area$$ \mathcal{A}\left({\gamma}_B\right) $$ A γ B ofγ B . To study the entropic interpretation of$$ \mathcal{A}\left({\gamma}_{A:B}\right) $$ A γ A : B , we analyze the Rényi entropies of subregionAin a fixed-area state of subregionB. We use the gravitational path integral to show that then ≈1 Rényi entropies are then computed by minimizing$$ \mathcal{A}\left({\gamma}_A\right) $$ A γ A over spacetimes defined by a boost angle conjugate to$$ \mathcal{A}\left({\gamma}_B\right) $$ A γ B . In the case where the pieces$$ {\gamma}_{A:B}^B $$ γ A : B B and$$ {\gamma}_{A:B}^{\overline{B}} $$ γ A : B B ¯ intersect at a constant boost angle, a geometric argument shows that then ≈1 Rényi entropy is then given by$$ \frac{\mathcal{A}\left({\gamma}_{A:B}\right)}{4G} $$ A γ A : B 4 G . We discuss how then ≈1 Rényi entropy differs from the von Neumann entropy due to a lack of commutativity of then→ 1 andG →0 limits. We also discuss how the behaviour changes as a function of the width of the fixed-area state. Our results are relevant to some of the issues associated with attempts to use standard random tensor networks to describe time dependent geometries.

Physics↗

DOE OSTI2019

Understanding the nature of mean-field semiclassical light-matter dynamics: An investigation of energy transfer, electron-electron correlations, external driving, and long-time detailed balance

Semiclassical electrodynamics (with quantum matter plus classical electrodynamics fields) is an appealing approach for studying light-matter interactions, especially for realistic molecular systems. However, there is no unique semiclassical scheme. On the one hand, intermolecular interactions can be described instantaneously by static two-body interactions connecting two different molecules, while a classical transverse E field acts as a spectator at short distance; we will call this Hamiltonian no. I. On the other hand, intermolecular interactions can also be described as effects that are mediated exclusively through a classical one-body Ε field without any quantum effects at all (assuming we ignore electronic exchange); we will call this Hamiltonian no. II. Moreover, one can also mix these two different Hamiltonians into a third, hybrid Hamiltonian, which preserves quantum electron-electron correlations for lower excitations but describes higher excitations in a mean-field way. To investigate which semiclassical scheme is most reliable for practical use, here we study the real-time dynamics of a minimalistic many-site model—a pair of identical two-level systems (TLSs)—undergoing either resonance energy transfer (RET) or collectively driven dynamics. While both approaches (no. 1 and no. 2) perform reasonably well when there is no strong external excitation, we find that no single approach is perfect for all conditions (and all methods fail when a strong external field is applied). Each method has its own distinct problems: Hamiltonian no. I performs best for RET but behaves in a complicated manner for driven dynamics; Hamiltonian no. II is always stable, but obviously fails for RET at short distances. One key finding is that, for externally driven dynamics, a full configuration-interaction description of Hamiltonian no. I strongly overestimates the long-time electronic energy, highlighting the not obvious fact that, if one plans to merge quantum molecules with classical light, a full, exact treatment of electron-electron correlations can actually lead to worse results than a simple mean-field electronic structure treatment. Future work will need to investigate (i) how these algorithms behave in the context of more than a pair of TLSs and (ii) whether or not these algorithms can be improved in general by including crucial aspects of spontaneous emission.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Microscopic-macroscopic level densities for low excitation energies

Level density ρ(E,Q) is derived within the micro-macroscopic approximation (MMA) for a system of strongly interacting Fermi particles with the energy E and additional integrals of motion Q , in line with several topics of the universal and fruitful activity of A. S. Davydov. Within the extended Thomas Fermi and semiclassical periodic orbit theory beyond the Fermi-gas saddle-point method, we obtain ρ ∝ I ν (S)/S ν , where I ν (S) is the modified Bessel function of the entropy S . For small shell-structure contribution, one finds ν = κ/2 + 1, where κ is the number of additional integrals of motion. This integer number is a dimension of Q, Q = { N, Z , …} for the case of two-component atomic nuclei, where N and Z are the numbers of neutrons and protons, respectively. For much larger shell structure contributions, one obtains ν = κ /2 + 2. The MMA level density ρ reaches the well-known Fermi gas asymptote for large excitation energies and the finite micro-canonical combinatoric limit for low excitation energies. Further, the additional integrals of motion can also be the projection of the angular momentum of a nuclear system for nuclear rotations of deformed nuclei, number of excitons for collective dynamics, and so on. Fitting the MMA total level density ρ( E , Q) for a set of the integrals of motion Q = { N, Z }, to experimental data on a long nuclear isotope chain for low excitation energies, one obtains the results for the inverse level-density parameter K , which differs significantly from those of neutron resonances due to shell, isotopic asymmetry, and pairing effects.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Water-mediated ion transport in an anion exchange membrane

Water is a critical component in polyelectrolyte anion exchange membranes (AEMs). It plays a central role in ion transport in electrochemical systems. Gaining a better understanding of molecular transport and conductivity in AEMs has been challenged by the lack of a general methodology capable of capturing and connecting water dynamics, water structure, and ionic transport over time and length scales ranging from those associated with individual bond vibrations and molecular reorientations to those pertaining to macroscopic AEM performance. In this work, we use two-dimensional infrared spectroscopy and semiclassical simulations to examine how water molecules are arranged into successive solvation shells, and we explain how that structure influences the dynamics of bromide ion transport processes in polynorbornene-based materials. We find that the transition to the faster transport mechanism occurs when the reorientation of water molecules in the second solvation shell is fast, allowing a robust hydrogen bond network to form. Our findings provide molecular-level insights into AEMs with inherent transport of halide ions, and help pave the way towards a comprehensive understanding of hydroxide ion transport in AEMs.

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