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Scalar Relativistic All-Electron and Pseudopotential Ab Initio Study of a Minimal Nitrogenase [Fe(SH)4H]− Model Employing Coupled-Cluster and Auxiliary-Field Quantum Monte Carlo Many-Body Methods

Vysotskiy, Victor P. LU ; Filippi, Claudia and Ryde, Ulf LU orcid (2024) In Journal of Physical Chemistry A 128(7). p.1358-1374
Abstract

Nitrogenase is the only enzyme that can cleave the triple bond in N2, making nitrogen available to organisms. The detailed mechanism of this enzyme is currently not known, and computational studies are complicated by the fact that different density functional theory (DFT) methods give very different energetic results for calculations involving nitrogenase models. Recently, we designed a [Fe(SH)4H]− model with the fifth proton binding either to Fe or S to mimic different possible protonation states of the nitrogenase active site. We showed that the energy difference between these two isomers (ΔE) is hard to estimate with quantum-mechanical methods. Based on nonrelativistic single-reference coupled-cluster... (More)

Nitrogenase is the only enzyme that can cleave the triple bond in N2, making nitrogen available to organisms. The detailed mechanism of this enzyme is currently not known, and computational studies are complicated by the fact that different density functional theory (DFT) methods give very different energetic results for calculations involving nitrogenase models. Recently, we designed a [Fe(SH)4H]− model with the fifth proton binding either to Fe or S to mimic different possible protonation states of the nitrogenase active site. We showed that the energy difference between these two isomers (ΔE) is hard to estimate with quantum-mechanical methods. Based on nonrelativistic single-reference coupled-cluster (CC) calculations, we estimated that the ΔE is 101 kJ/mol. In this study, we demonstrate that scalar relativistic effects play an important role and significantly affect ΔE. Our best revised single-reference CC estimates for ΔE are 85-91 kJ/mol, including energy corrections to account for contributions beyond triples, core-valence correlation, and basis-set incompleteness error. Among coupled-cluster approaches with approximate triples, the canonical CCSD(T) exhibits the largest error for this problem. Complementary to CC, we also used phaseless auxiliary-field quantum Monte Carlo calculations (ph-AFQMC). We show that with a Hartree-Fock (HF) trial wave function, ph-AFQMC reproduces the CC results within 5 ± 1 kJ/mol. With multi-Slater-determinant (MSD) trials, the results are 82-84 ± 2 kJ/mol, indicating that multireference effects may be rather modest. Among the DFT methods tested, τ-HCTH, r2SCAN with 10-13% HF exchange with and without dispersion, and O3LYP/O3LYP-D4, and B3LYP*/B3LYP*-D4 generally perform the best. The r2SCAN12 (with 12% HF exchange) functional mimics both the best reference MSD ph-AFQMC and CC ΔE results within 2 kJ/mol.

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organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Journal of Physical Chemistry A
volume
128
issue
7
pages
17 pages
publisher
The American Chemical Society (ACS)
external identifiers
  • pmid:38324717
  • scopus:85185707816
ISSN
1089-5639
DOI
10.1021/acs.jpca.3c05808
language
English
LU publication?
yes
id
09be58a4-cb95-429d-a4b2-353a0a9c23b2
date added to LUP
2024-03-27 10:34:03
date last changed
2024-04-24 14:27:05
@article{09be58a4-cb95-429d-a4b2-353a0a9c23b2,
  abstract     = {{<p>Nitrogenase is the only enzyme that can cleave the triple bond in N<sub>2</sub>, making nitrogen available to organisms. The detailed mechanism of this enzyme is currently not known, and computational studies are complicated by the fact that different density functional theory (DFT) methods give very different energetic results for calculations involving nitrogenase models. Recently, we designed a [Fe(SH)<sub>4</sub>H]<sup>−</sup> model with the fifth proton binding either to Fe or S to mimic different possible protonation states of the nitrogenase active site. We showed that the energy difference between these two isomers (ΔE) is hard to estimate with quantum-mechanical methods. Based on nonrelativistic single-reference coupled-cluster (CC) calculations, we estimated that the ΔE is 101 kJ/mol. In this study, we demonstrate that scalar relativistic effects play an important role and significantly affect ΔE. Our best revised single-reference CC estimates for ΔE are 85-91 kJ/mol, including energy corrections to account for contributions beyond triples, core-valence correlation, and basis-set incompleteness error. Among coupled-cluster approaches with approximate triples, the canonical CCSD(T) exhibits the largest error for this problem. Complementary to CC, we also used phaseless auxiliary-field quantum Monte Carlo calculations (ph-AFQMC). We show that with a Hartree-Fock (HF) trial wave function, ph-AFQMC reproduces the CC results within 5 ± 1 kJ/mol. With multi-Slater-determinant (MSD) trials, the results are 82-84 ± 2 kJ/mol, indicating that multireference effects may be rather modest. Among the DFT methods tested, τ-HCTH, r<sup>2</sup>SCAN with 10-13% HF exchange with and without dispersion, and O3LYP/O3LYP-D4, and B3LYP*/B3LYP*-D4 generally perform the best. The r<sup>2</sup>SCAN12 (with 12% HF exchange) functional mimics both the best reference MSD ph-AFQMC and CC ΔE results within 2 kJ/mol.</p>}},
  author       = {{Vysotskiy, Victor P. and Filippi, Claudia and Ryde, Ulf}},
  issn         = {{1089-5639}},
  language     = {{eng}},
  month        = {{02}},
  number       = {{7}},
  pages        = {{1358--1374}},
  publisher    = {{The American Chemical Society (ACS)}},
  series       = {{Journal of Physical Chemistry A}},
  title        = {{Scalar Relativistic All-Electron and Pseudopotential Ab Initio Study of a Minimal Nitrogenase [Fe(SH)<sub>4</sub>H]<sup>−</sup> Model Employing Coupled-Cluster and Auxiliary-Field Quantum Monte Carlo Many-Body Methods}},
  url          = {{http://dx.doi.org/10.1021/acs.jpca.3c05808}},
  doi          = {{10.1021/acs.jpca.3c05808}},
  volume       = {{128}},
  year         = {{2024}},
}