Themed collection Quantum Bio-Inorganic Chemistry

27 items
Perspective

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.

Graphical abstract: Perspective: multi-configurational methods in bio-inorganic chemistry
From the themed collection: Quantum Bio-Inorganic Chemistry
Open Access Paper

Binding modes of a flexible ruthenium polypyridyl complex to DNA

Ruthenium(II) polypyridyl complexes are attractive binders to DNA.

Graphical abstract: Binding modes of a flexible ruthenium polypyridyl complex to DNA
From the themed collection: Quantum Bio-Inorganic Chemistry
Open Access Paper

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.

Graphical abstract: Influence of graphene on the electronic and magnetic properties of an iron(iii) porphyrin chloride complex
From the themed collection: Quantum Bio-Inorganic Chemistry
Open Access Paper

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?

Graphical abstract: Insights into dioxygen binding on metal centers: an ab initio multireference electronic structure analysis
From the themed collection: Quantum Bio-Inorganic Chemistry
Open Access Paper

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.

Graphical abstract: Extensive reference set and refined computational protocol for calculations of 57Fe Mössbauer parameters
From the themed collection: Quantum Bio-Inorganic Chemistry
Paper

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.

Graphical abstract: Ligand engineering of tetra N-heterocyclic carbenes for boosting catalytic aziridination
From the themed collection: Quantum Bio-Inorganic Chemistry
Paper

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.

Graphical abstract: 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
From the themed collection: Quantum Bio-Inorganic Chemistry
Open Access Paper

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.

Graphical abstract: Extension of the D3 and D4 London dispersion corrections to the full actinides series
From the themed collection: 2024 PCCP HOT Articles
Paper

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.

Graphical abstract: Synergy of experimental and computational chemistry: structure and biological activity of Zn(ii) hydrazone complexes
From the themed collection: Quantum Bio-Inorganic Chemistry
Open Access Paper

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.

Graphical abstract: Chemical accuracy for ligand-receptor binding Gibbs energies through multi-level SQM/QM calculations
From the themed collection: Quantum Bio-Inorganic Chemistry
Open Access Paper

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.

Graphical abstract: Unravelling Mn4Ca cluster vibrations in the S1, S2 and S3 states of the Kok–Joliot cycle of photosystem II
From the themed collection: Quantum Bio-Inorganic Chemistry
Open Access Paper

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.

Graphical abstract: The trials and triumphs of modelling X-ray absorption spectra of transition metal phthalocyanines
From the themed collection: Quantum Bio-Inorganic Chemistry
Open Access Paper

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.

Graphical abstract: Elucidation of factors shaping reactivity of 5′-deoxyadenosyl – a prominent organic radical in biology
From the themed collection: Quantum Bio-Inorganic Chemistry
Paper

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.

Graphical abstract: Towards reliable and efficient modeling of [Cu2O2]2+-based compound electronic structures with the partially fixed reference space protocols
From the themed collection: Quantum Bio-Inorganic Chemistry
Open Access Paper

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.

Graphical abstract: 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
From the themed collection: Quantum Bio-Inorganic Chemistry
Paper

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.

Graphical abstract: The effect of ionic versus covalent functionalization of polyoxometalate hybrid materials with coordinating subunits on their stability and interaction with DNA
From the themed collection: Quantum Bio-Inorganic Chemistry
Paper

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).

Graphical abstract: Delving into the catalytic mechanism of molybdenum cofactors: a novel coupled cluster study
From the themed collection: Quantum Bio-Inorganic Chemistry
Open Access Paper

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.

Graphical abstract: Putative reaction mechanism of nitrogenase with a half-dissociated S2B ligand
From the themed collection: Quantum Bio-Inorganic Chemistry
Open Access Paper

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?

Graphical abstract: Ligand field theory, Pauli shields and ultra-covalency in organometallic chemistry
From the themed collection: Quantum Bio-Inorganic Chemistry
Paper

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?

Graphical abstract: Predicting spin states of iron porphyrins with DFT methods including crystal packing effects and thermodynamic corrections
From the themed collection: Quantum Bio-Inorganic Chemistry
Paper

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.

Graphical abstract: A new MOF@bioactive glass composite reinforced with silver nanoparticles – a new approach to designing antibacterial biomaterials
From the themed collection: Quantum Bio-Inorganic Chemistry
Open Access Paper

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.

Graphical abstract: Machine learning-aided engineering of a cytochrome P450 for optimal bioconversion of lignin fragments
Paper

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.

Graphical abstract: Exploring novel Cd(ii) complexes with 5-methyl-4-imidazolecarboxaldehyde: synthesis, structure, computational insights, and affinity to DNA through switchSense methodology
From the themed collection: Quantum Bio-Inorganic Chemistry
Open Access Paper

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.

Graphical abstract: Gaseous inhibition of the transsulfuration pathway by cystathionine β-synthase
From the themed collection: Quantum Bio-Inorganic Chemistry
Paper

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.

Graphical abstract: Application of a modern theoretical approach to the study of the interaction of KR-12 peptides derived from human cathelicidins with Cu(ii) ions
From the themed collection: Quantum Bio-Inorganic Chemistry
Paper

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).

Graphical abstract: Role of Lewis acid/base anchor atoms in catalyst regeneration: a comprehensive study on biomimetic EP3Fe nitrogenases
From the themed collection: Quantum Bio-Inorganic Chemistry
Paper

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.

Graphical abstract: A frontier-orbital view of the initial steps of lytic polysaccharide monooxygenase reactions
From the themed collection: Quantum Bio-Inorganic Chemistry
27 items

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)

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