Themed collection Quantum Bio-Inorganic Chemistry
Perspective: multi-configurational methods in bio-inorganic chemistry
Transition metals play crucial roles in many proteins. Historically, density functional theory has dominated this field, but recent advancements have now made multiconfigurational wave functions accessible. We discuss these recent advancements.
Phys. Chem. Chem. Phys., 2024,26, 17443-17455
https://doi.org/10.1039/D4CP01297F
Binding modes of a flexible ruthenium polypyridyl complex to DNA
Ruthenium(II) polypyridyl complexes are attractive binders to DNA.
Phys. Chem. Chem. Phys., 2024,26, 27116-27130
https://doi.org/10.1039/D4CP02782E
Influence of graphene on the electronic and magnetic properties of an iron(III) porphyrin chloride complex
An electronic and magnetic structure analysis of an iron(III) porphyrin chloride complex in the absence and presence of a graphene layer was carried out by integrating molecular and periodic DFT approaches.
Phys. Chem. Chem. Phys., 2024,26, 26370-26376
https://doi.org/10.1039/D4CP01551G
Insights into dioxygen binding on metal centers: an ab initio multireference electronic structure analysis
Why does binding of dioxygen (O2) to metal centers, the initial step of O2 storage, transportation, and activation, almost inevitably induce metal-to-O2 single-electron transfer and generate superoxo (O2−˙) species, instead of genuine O02 adducts?
Phys. Chem. Chem. Phys., 2024,26, 25057-25068
https://doi.org/10.1039/D4CP02915A
Extensive reference set and refined computational protocol for calculations of 57Fe Mössbauer parameters
A refined protocol for scalar relativistic quantum chemical calculations of Mössbauer spectroscopic parameters is developed on the basis of a new and chemically complete reference set of iron compounds.
Phys. Chem. Chem. Phys., 2024,26, 23322-23334
https://doi.org/10.1039/D4CP00431K
Ligand engineering of tetra N-heterocyclic carbenes for boosting catalytic aziridination
A comprehensive computational study on the underlying reactivity of iron tetra-NHC complexes for C2 + N1 aziridination catalysis is presented.
Dalton Trans., 2024,53, 14665-14677
https://doi.org/10.1039/D4DT01084A
Synthesis, photophysical characterisation, quantum-chemical study and in vitro antiproliferative activity of cyclometalated Ir(III) complexes based on 3,5-dimethyl-1-phenyl-1H-pyrazole and N,N-donor ligands
Cyclometalated complexes of Ir(III) and phenyl-1H-pyrazole derivatives with N^N auxiliary ligands have been synthesised and fully characterised physicochemically. The resulting complexes exhibit interesting luminescence and are highly potent cytotoxic.
Dalton Trans., 2024,53, 14438-14450
https://doi.org/10.1039/D4DT01796J
Extension of the D3 and D4 London dispersion corrections to the full actinides series
Extension of the DFT-D3 and -D4 London dispersion corrections to francium, radium, and the full actinides series, with minimal modifications to the existing parameterization strategy.
Phys. Chem. Chem. Phys., 2024,26, 21379-21394
https://doi.org/10.1039/D4CP01514B
Synergy of experimental and computational chemistry: structure and biological activity of Zn(II) hydrazone complexes
Zn(II) hydrazone complexes: combining computational chemistry and biological activity.
Dalton Trans., 2024,53, 13436-13453
https://doi.org/10.1039/D4DT01353K
Chemical accuracy for ligand-receptor binding Gibbs energies through multi-level SQM/QM calculations
The semi-empirical quantum chemical exploration of the conformational space of ligand-receptor complexes followed by systematic QM refinement of poses leads to Gibbs energies of binding with thermochemical accuracy.
Phys. Chem. Chem. Phys., 2024,26, 21197-21203
https://doi.org/10.1039/D4CP01529K
Unravelling Mn4Ca cluster vibrations in the S1, S2 and S3 states of the Kok–Joliot cycle of photosystem II
QMMM-MD dipole partitioning and dipole correlation fourier transform for Mn4Ca cluster vibrations assignment in metastable stetes of Kok–Joliot’s cycle.
Phys. Chem. Chem. Phys., 2024,26, 20598-20609
https://doi.org/10.1039/D4CP01307G
The trials and triumphs of modelling X-ray absorption spectra of transition metal phthalocyanines
This study explores the electronic structure of Co, Fe, and Mn phthalocyanines and their fluorinated counterparts. Their metal L-edge and ligand (N,F) K-edge X-ray absorption spectra (XAS) are simulated in an angle-resolved manner.
Phys. Chem. Chem. Phys., 2024,26, 20376-20387
https://doi.org/10.1039/D4CP01900H
Elucidation of factors shaping reactivity of 5′-deoxyadenosyl – a prominent organic radical in biology
SAM enzymes harness inherent HAA activity of 5′dAdo˙ via in situ formation of the radical and by hindering its self-decay reactions.
Phys. Chem. Chem. Phys., 2024,26, 20280-20295
https://doi.org/10.1039/D4CP01725K
Towards reliable and efficient modeling of [Cu2O2]2+-based compound electronic structures with the partially fixed reference space protocols
This work reports a computationally efficient approach for reliable modeling of complex electronic structures based on [Cu2O2]2+ moieties.
Phys. Chem. Chem. Phys., 2024,26, 19742-19754
https://doi.org/10.1039/D4CP01309C
Mechanism of non-phenolic substrate oxidation by the fungal laccase Type 1 copper site from Trametes versicolor: the case of benzo[a]pyrene and anthracene
The reactivity of laccases towards non-phenolic polycyclic aromatic hydrocarbons remains unclear. Using molecular modelling the oxidation of anthracene and benzo[a]pyrene by Trametes versicolor fungal laccase is investigated.
Dalton Trans., 2024,53, 12152-12161
https://doi.org/10.1039/D4DT01377H
The effect of ionic versus covalent functionalization of polyoxometalate hybrid materials with coordinating subunits on their stability and interaction with DNA
The nature of the polyoxometalate (POM) and coordinating subunit (CSU) modulate the stability of the POM-CSU hybrid and the DNA binding.
Dalton Trans., 2024,53, 11678-11688
https://doi.org/10.1039/D4DT00965G
Delving into the catalytic mechanism of molybdenum cofactors: a novel coupled cluster study
In this work, we use modern electronic structure methods to model the catalytic mechanism of different variants of the molybdenum cofactor (Moco).
Phys. Chem. Chem. Phys., 2024,26, 18918-18929
https://doi.org/10.1039/D4CP01500B
Putative reaction mechanism of nitrogenase with a half-dissociated S2B ligand
With QM/MM calculations we study whether dissociation of the S2B sulfide ligand from one of its two coordinating Fe ions may affect later parts of the reaction mechanism of nitrogenase.
Dalton Trans., 2024,53, 11500-11513
https://doi.org/10.1039/D4DT00937A
Ligand field theory, Pauli shields and ultra-covalency in organometallic chemistry
The d-orbital-only, implicit-bonding picture of LFT applies equally well to organometallic and coordination compounds: one concept to rule them all?
Phys. Chem. Chem. Phys., 2024,26, 18138-18148
https://doi.org/10.1039/D4CP00764F
Predicting spin states of iron porphyrins with DFT methods including crystal packing effects and thermodynamic corrections
Which DFT methods can most reliably predict the observed spin state in iron porphyrins with thermodynamics and crystal packing included?
Phys. Chem. Chem. Phys., 2024,26, 18182-18195
https://doi.org/10.1039/D4CP01327A
A new MOF@bioactive glass composite reinforced with silver nanoparticles – a new approach to designing antibacterial biomaterials
A new approach to overcoming the problem of infected bone defects has been developed by combining three components: bioactive glass, a Cu-based MOF, and AgNPs. Ag@Cu-MOF@BG exhibits antibacterial properties while being bioactive and biocompatible.
Dalton Trans., 2024,53, 10928-10937
https://doi.org/10.1039/D4DT01190B
Machine learning-aided engineering of a cytochrome P450 for optimal bioconversion of lignin fragments
Using molecular dynamics, machine learning, and density functional theory calculations we make predictions on engineered cytochrome P450 structures and their product distributions.
Phys. Chem. Chem. Phys., 2024,26, 17577-17587
https://doi.org/10.1039/D4CP01282H
Exploring novel Cd(II) complexes with 5-methyl-4-imidazolecarboxaldehyde: synthesis, structure, computational insights, and affinity to DNA through switchSense methodology
The study of four Cd(II) complexes with 5-methyl-4-imidazolecarboxaldehyde and different anions (Cl−, Br−, I− and PF6−) using experimental and computational methods including interaction with DNA using the switchSense technique was carried out.
Dalton Trans., 2024,53, 10347-10360
https://doi.org/10.1039/D4DT00879K
Gaseous inhibition of the transsulfuration pathway by cystathionine β-synthase
This work investigates the signalling mechanism found in human CBS. Quantum chemical calculations give an atomistic insight into gas binding to heme, and molecular dynamics simulations show the allosteric signalling pathway initiated by gas binding.
Phys. Chem. Chem. Phys., 2024,26, 16579-16588
https://doi.org/10.1039/D4CP01321B
Application of a modern theoretical approach to the study of the interaction of KR-12 peptides derived from human cathelicidins with Cu(II) ions
Modern theoretical analysis (GFN2-xTB/ALPB) was used to determine the complexing properties towards Cu(II) ions of the antimicrobial peptide called KR-12 and the most probable ways of coordinating Cu(II) ions with this peptide were proposed.
Dalton Trans., 2024,53, 9942-9951
https://doi.org/10.1039/D4DT01027B
Role of Lewis acid/base anchor atoms in catalyst regeneration: a comprehensive study on biomimetic EP3Fe nitrogenases
Exploration of anchor atoms in Fe-nitrogenase catalysts demonstrates superior N2 reduction with Lewis acidic atoms (B, Al, Ga), particularly boron, over Lewis basic counterparts (N, P).
Phys. Chem. Chem. Phys., 2024,26, 12520-12529
https://doi.org/10.1039/D4CP00483C
A frontier-orbital view of the initial steps of lytic polysaccharide monooxygenase reactions
The copper enzymes lytic polysaccharide monooxygenases (LPMOs) oxidatively cleave strong C–H bonds in recalcitrant polysaccharide substrates. Based on crystal structures, we analyse the roles of the priming reduction, substrate and H2O2 binding.
Dalton Trans., 2024,53, 5796-5807
https://doi.org/10.1039/D3DT04275H
About this collection
Bioinorganic chemistry focuses on the interactions of metals with organic species, particularly on metalloenzymes and biomimetic compounds. Quantum chemistry plays a prominent role here by first providing a deeper understanding of the structure and reactivity of naturally occurring metalloenzymes, allowing for knowledge-driven biomimetics construction.
This themed collection published across Physical Chemistry Chemical Physics (PCCP) and Dalton Transactions brings together work on quantum bioinorganic chemistry, covering theoretical methods, novel applications, and combined computational/experimental approaches.
Guest Edited by: Marcel Swart (University of Girona), Adam Kubas (Institute of Physical Chemistry, Polish Academy of Sciences) and Ragnar Björnsson (University Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux)