The robustness of nickelocene's (NiCp 2 , Cp = cyclopentadienyl) magnetic anisotropy and addressability of its spin states make this molecular magnet attractive as a spin sensor. However, microscopic understanding of its magnetic anisotropy is still lacking, especially when NiCp 2 is deposited on a surface to make quantum sensing devices. Quantum chemical calculations of such molecule/solid-state systems are limited to density functional theory (DFT) or DFT+U (Hubbard correction to DFT). We investigate the magnetic behavior of NiCp 2 using the spin-flip variant of the equation-of-motion coupled-cluster (EOM-SF-CC) method and use the EOM-SF-CC results to benchmark SF-TD-DFT. Our first-principle calculations agree well with experimentally derived magnetic anisotropy and susceptibility values. The calculations show that magnetic anisotropy in NiCp 2 originates from a large spin−orbit coupling (SOC) between the triplet ground state and the third singlet state, whereas the coupling with lower singlet excited states is negligible. We also considered a set of six ring-substituted NiCp 2 derivatives and a model system of the NiCp 2 /MgO(001) adsorption complex, for which we used SF-TD-DFT method. To gain insight into the electronic structure of these systems, we analyze spinless transition density matrices and their natural transition orbitals (NTOs). The NTO analysis of SOCs explains how spin states and magnetic properties are retained upon modification of the NiCp 2 coordination environment and upon its adsorption on a surface. Such resilience of the NiCp 2 magnetic behavior supports using NiCp 2 as a spin-probe molecule by functionalization of the tip of a scanning tunneling microscope.
This work explores the level of transparency in reporting
the details
of computational protocols that is required for practical reproducibility
of quantum mechanics/molecular mechanics (QM/MM) simulations. Using
the reaction of an essential SARS-CoV-2 enzyme (the main protease)
with a covalent inhibitor (carmofur) as a test case of chemical reactions
in biomolecules, we carried out QM/MM calculations to determine the
structures and energies of the reactants, the product, and the transition
state/intermediate using analogous QM/MM models implemented in two
software packages, NWChem and Q-Chem. Our main benchmarking goal was
to reproduce the key energetics computed with the two packages. Our
results indicate that quantitative agreement (within the numerical
thresholds used in calculations) is difficult to achieve. We show
that rather minor details of QM/MM simulations must be reported in
order to ensure the reproducibility of the results and offer suggestions
toward developing practical guidelines for reporting the results of
biosimulations.
The effect of size and substitution patterns of azobenzene derivatives on the spectroscopic properties and rigidity of the smallest photoswitchable G-quadruplex.
The search for efficient inhibitors of the SARS-CoV-2 enzymes remains important due to the continuing COVID-19 pandemic. We report the results of computational modeling of the reactions of the SARS-CoV-2 main protease (MPro) with four potential covalent inhibitors. Two of them, carmofur and nirmatrelvir, have been shown experimentally the ability to inhibit MPro. Two other compounds, X77A and X77C, were designed computationally in this work, derived from the structure of X77, a non-covalent inhibitor forming a tight surface complex with MPro. We modified the X77 structure by introducing warheads capable of efficient chemical reactions with the catalytic cysteine residue in the MPro active site. The reactions of the four molecules with MPro were investigated by quantum mechanics/molecular mechanics (QM/MM) calculations. According to calculations, the reactions for all four compounds are exothermic, with sufficiently low barriers, suggesting efficient inhibition of the enzyme. From the chemical perspective, the four compounds react with MPro following three distinct mechanisms. In all cases, the reaction is initiated by a nucleophilic attack of the thiolate group of the deprotonated cysteine residue from the catalytic dyad Cys145-His41 of MPro. In the case of carmofur and X77A, the covalent binding of the thiolate to the ligand involves the formation of the fluoro-uracil leaving group. The reaction with X77C follows the nucleophilic aromatic substitution SNAr mechanism. The reaction of MPro with nirmatrelvir, which has a reactive nitrile group, leads to the formation of the covalent thioimidate adduct with the thiolate of the Cys145 residue in the enzyme active site.
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