Electronic and Structural Properties of the Double Cubane Iron-Sulfur Cluster

Elghobashi-Meinhardt, Nadia; Tombolelli, Daria; Mroginski, María Andrea

doi:10.3390/catal11020245

Cited by 9 publications

(4 citation statements)

References 53 publications

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“…Note that it could be very useful any additional experimental data on the E n states to further restrict the mechanistic possibilities of FeMo cofactor for comparison with the calculated data. Nonetheless, the published studies propose a pathway to clarify the mechanism of nitrogenase catalytic role [167][168][169][170][171][172][173][174][175][176][177][178].…”

Section: Discussionmentioning

confidence: 99%

Review on the QM/MM Methodologies and Their Application to Metalloproteins

2022

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The multiscaling quantum mechanics/molecular mechanics (QM/MM) approach was introduced in 1976, while the extensive acceptance of this methodology started in the 1990s. The combination of QM/MM approach with molecular dynamics (MD) simulation, otherwise known as the QM/MM/MD approach, is a powerful and promising tool for the investigation of chemical reactions’ mechanism of complex molecular systems, drug delivery, properties of molecular devices, organic electronics, etc. In the present review, the main methodologies in the multiscaling approaches, i.e., density functional theory (DFT), semiempirical methodologies (SE), MD simulations, MM, and their new advances are discussed in short. Then, a review on calculations and reactions on metalloproteins is presented, where particular attention is given to nitrogenase that catalyzes the conversion of atmospheric nitrogen molecules N₂ into NH₃ through the process known as nitrogen fixation and the FeMo-cofactor.

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Section: Discussionmentioning

confidence: 99%

Review on the QM/MM Methodologies and Their Application to Metalloproteins

2022

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“…Geometry optimization and vibrational analysis using normal mode analysis of the EBn:M z+ complexes was performed with the functional BP86 [43,44] in Gaussian16 [45] . Based on related studies on complexes of (alkali) metals and organic molecules, [46,47] C, N, O and H atoms were treated using the 6-31g* basis set, [48] and the alkaline and alkaline earth metal ions were described using def2-TZVP basis set [49] together with its core potential [50] for Cs + . In addition n-pentadecane was specified as solvent in a polarizable continuum model to mimic the hydrophobic parts of the membrane.…”

Section: Calculations Of Computational Infrared Spectramentioning

confidence: 99%

Cation dependence of enniatin B/membrane-interactions assessed using surface-enhanced infrared absorption spectroscopy

Gonzalez,

Forbrig,

Yao

et al. 2024

Preprint

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Enniatins are mycotoxins with well-known antibacterial, antifungal, antihelmintic and antiviral activity, which have recently come to attention as potential mitochondriotoxic anticancer agents. The cytotoxicity of enniatins is traced back to their ionophoric properties, in which the cyclodepsipeptidic structure results in enniatin:cation-complexes of various stoichiometries proposed as membrane-active species. In this work, we employed a combination of surface-enhanced infrared absorption (SEIRA) spectroscopy, tethered bilayer lipid membranes (tBLMs) and density functional theory (DFT)-based computational spectroscopy to monitor the cation-dependence (Mz+ = Na+, K+, Cs+, Li+, Mg2+, Ca2+) on the mechanism of enniatin B (EB) incorporation into membranes and identify the functionally relevant EBn:Mz+ complexes formed. We find that Na+ promotes a cooperative incorporation, modelled via an autocatalytic mechanism and mediated by a distorted 2:1-EB2:Na+ complex. K+ (and Cs+) leads to a direct but less efficient insertion into membranes due to the adoption of “ideal” EB2:K+ sandwich complexes. In contrast, the presence of Li+, Mg2+, and Ca2+ causes a (partial) extraction of EB from the membrane via the formation of “belted” 1:1-EB:Mz+ complexes, which screen the cationic charge less efficiently. Our results point to a relevance of the cation dependence for the transport into the malignant cells where the mitochondriotoxic anticancer activity is exerted.

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“…95 Feng et al used QM/MM calculations to provide insight into how the reactivity of the SAM enzyme Dph2 is affected by the electronic state of the [4Fe-4S] cluster. 96 More complicated still are the double-cubane cluster protein, 97 featuring an [Fe 8 S 9 ] complex, and the iron-molybdenum cofactor (FeMoco) in molybdenum-dependent nitrogenase [98][99][100] and iron-vanadium cofactor in vanadium-dependent nitrogenase. 101 Thorhallson and Bjornsson have used QM/MM calculations with ChemShell to explore the energy surface of reduced states of FeMoco, showing how the electronic structure changes along a proposed redox-state cycle.…”

Section: Qm/mm Simulations Of Biomoleculesmentioning

confidence: 99%