Search arXivSearch

arXiv · 2305.07227

Multireference protonation energetics of a dimeric model of nitrogenase iron-sulfur clusters

Abstract

Characterizing the electronic structure of the iron--sulfur clusters in nitrogenase is necessary to understand their role in the nitrogen fixation process. One challenging task is to determine the protonation state of the intermediates in the nitrogen fixing cycle. Here, we use a dimeric iron--sulfur model to study relative energies of protonation at C, S or Fe. Using a composite method based on coupled cluster and density matrix renormalization group energetics, we converge the relative energies of four protonated configurations with respect to basis set and correlation level. We find that accurate relative energies require large basis sets, as well as a proper treatment of multireference and relativistic effects. We have also tested ten density functional approximations for these systems. Most of them give large errors in the relative energies. The best performing functional in this system is B3LYP, which gives mean absolute and maximum errors of only 10 and 13 kJ/mol with respect to our correlated wavefunction estimates, respectively. Our work provides benchmark results for the calibration of new approximate electronic structure methods and density functionals for these problems.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Huanchen Zhai, Seunghoon Lee, Zhi-Hao Cui, Lili Cao, Ulf Ryde, Garnet Kin-Lic Chan. 2023-11-25. Multireference protonation energetics of a dimeric model of nitrogenase iron-sulfur clusters. https://doi.org/10.1021/acs.jpca.3c06142

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

Intrinsic Matching Frustration in Fluctuating Finite Systems

We formulate intrinsic matching frustration (IMF), a fluctuation-induced, kinetics-independent reduction in the mean capacity permitted by a prescribed matching rule. For complementary one-to-one matching, the instantaneous capacity is set by the minority population, so fluctuations produce a nonzero mean deficit even when the two populations are balanced on average. At finite size, this deficit depends on the full distribution of the population difference and is determined by its variance alone only in the Gaussian limit. Compartmentalization hides matching capacity by preventing cancellation between local imbalances of opposite sign. Fusion releases this hidden capacity monotonically under coarse graining, producing a measurable recovery of product yield following local reaction to completion.

physics.chem-ph

Phonon chirality as an additive control of CISS: a symmetry-protected law

Chirality-induced spin selectivity (CISS) is usually associated with molecular handedness. The possible contribution of chiral phonons is less established. We study a helical tight-binding model in which local phonon angular momentum modulates spin-dependent nearest-neighbor hopping. Fewest-switches surface hopping calculations give the transmitted spin polarization $\mathrm{SP}=aC+b\mathrm{PH}$. Here $C$ is the molecular chirality and $\mathrm{PH}$ is the phonon chirality. A mirror symmetry reverses $C$, $\mathrm{PH}$, and $\mathrm{SP}$ simultaneously. This symmetry excludes both a chirality-independent offset and a $C\cdot\mathrm{PH}$ term. The phonon contribution can therefore enhance, cancel, or reverse the molecular CISS signal.

physics.chem-ph

A fast physics-based matrix model for the impedance of a PEM fuel cell: Incorporating functionally graded catalyst layer and channel impedances

We extend a recent physics-based matrix model for calculating PEM fuel cell impedance (doi:10.1149/2754-2734/ad6ce8) to cases of low air flow stoichiometry and functionally graded cathode catalyst layers (CCLs). We demonstrate that the matrix model produces accurate spectra and is almost three orders of magnitude faster than a model based on the standard boundary-value problem solver. The physics-based matrix model can compete with equivalent circuit models for fitting experimental EIS spectra, particularly those measured from cells with functionally graded CCL.

physics.chem-ph