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Molecular mechanism of nitrocefin hydrolysis by the L1 metallo-β-lactamase: a benchmark study.

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Title: Molecular mechanism of nitrocefin hydrolysis by the L1 metallo-β-lactamase: a benchmark study.
Authors: Krivitskaya, Alexandra V.1 (AUTHOR), Polyakov, Igor V.2,3 (AUTHOR), Khrenova, Maria G.1,2,3 (AUTHOR) khrenovamg@my.msu.ru
Source: Molecular Physics. Feb2026, Vol. 124 Issue 3/4, p1-9. 9p.
Subjects: Beta lactamases, Density functionals, Gibbs' energy diagram, Electron density, Beta lactam antibiotics, Biocatalysis, Molecular dynamics
Abstract: Nitrocefin hydrolysis by metallo-β-lactamase is an important model chemical reaction mimicking cephalosporin antibiotic inactivation. Due to the specific chromogenic properties of the nitrocefin, transient kinetic data for this reaction is available. Despite its importance in the understanding of the reaction mechanism, these data can be utilised to verify benchmark calculations. This reaction is complicated from the computational viewpoint as the active site carries two double charged cations and therefore is highly polarised; nucleophilic attack and formation of the electrophilic site should be properly described. We calculate Gibbs-free energy profiles of three chemical steps comprising the entire reaction at the QM(DFT)/MM molecular dynamics level. We compare results obtained with three hybrid functionals differing in the contribution of the exact Hartree–Fock exchange, B3LYP-D3, PBE0-D3 and BHHLYP-D3. Among them, only calculations performed at the QM(PBE0-D3)/MM level were able to properly describe the intermediate accumulation and the limiting step. Laplacian of electron density maps clarify the influence of the computational protocol on the electrophilic site formation and covalent bond polarisation. [ABSTRACT FROM AUTHOR]
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Database: Engineering Source
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Abstract:Nitrocefin hydrolysis by metallo-β-lactamase is an important model chemical reaction mimicking cephalosporin antibiotic inactivation. Due to the specific chromogenic properties of the nitrocefin, transient kinetic data for this reaction is available. Despite its importance in the understanding of the reaction mechanism, these data can be utilised to verify benchmark calculations. This reaction is complicated from the computational viewpoint as the active site carries two double charged cations and therefore is highly polarised; nucleophilic attack and formation of the electrophilic site should be properly described. We calculate Gibbs-free energy profiles of three chemical steps comprising the entire reaction at the QM(DFT)/MM molecular dynamics level. We compare results obtained with three hybrid functionals differing in the contribution of the exact Hartree–Fock exchange, B3LYP-D3, PBE0-D3 and BHHLYP-D3. Among them, only calculations performed at the QM(PBE0-D3)/MM level were able to properly describe the intermediate accumulation and the limiting step. Laplacian of electron density maps clarify the influence of the computational protocol on the electrophilic site formation and covalent bond polarisation. [ABSTRACT FROM AUTHOR]
ISSN:00268976
DOI:10.1080/00268976.2025.2456688