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Tailoring chemical bonds to design unconventional glasses.

ABSTRACT: Glasses are commonly described as disordered counterparts of the corresponding crystals; both usually share the same short-range order, but glasses lack long-range order. Here, a quantification of chemical bonding in a series of glasses and their corresponding crystals is performed, employing two quantum-chemical bonding descriptors, the number of electrons transferred and shared between adjacent atoms. For popular glasses like SiO₂, GeSe₂, and GeSe, the quantum-chemical bonding descriptors of the glass and the corresponding crystal hardly differ. This explains why these glasses possess a similar short-range order as their crystals. Unconventional glasses, which differ significantly in their short-range order and optical properties from the corresponding crystals are only found in a distinct region of the map spanned by the two bonding descriptors. This region contains crystals of GeTe, Sb₂Te₃, and GeSb₂Te₄, which employ metavalent bonding. Hence, unconventional glasses are only obtained for solids, whose crystals employ theses peculiar bonds.

SUBMITTER: Raty JY

PROVIDER: S-EPMC10786265 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature

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Tailoring chemical bonds to design unconventional glasses.

Raty Jean-Yves JY Bichara Christophe C Schön Carl-Friedrich CF Gatti Carlo C Wuttig Matthias M

Proceedings of the National Academy of Sciences of the United States of America 20240103 2

Glasses are commonly described as disordered counterparts of the corresponding crystals; both usually share the same short-range order, but glasses lack long-range order. Here, a quantification of chemical bonding in a series of glasses and their corresponding crystals is performed, employing two quantum-chemical bonding descriptors, the number of electrons transferred and shared between adjacent atoms. For popular glasses like SiO<sub>2</sub>, GeSe<sub>2</sub>, and GeSe, the quantum-chemical bo ...[more]

PMID: 38170754

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Project description:The reduction of C=X (X = N, O) bonds is a cornerstone in both synthetic organic chemistry and biocatalysis. Conventional reduction mechanisms usually involve a hydride ion targeting the less electronegative carbon atom. In a departure from this paradigm, our investigation into Old Yellow Enzymes (OYEs) reveals a mechanism involving transfer of hydride to the formally more electronegative nitrogen atom within a C=N bond. Beyond their known ability to reduce electronically activated C=C double bonds, e.g., in α, β-unsaturated ketones, these enzymes have recently been shown to reduce α-oximo-β-ketoesters to the corresponding amines. It has been proposed that this transformation involves two successive reduction steps and proceeds via imine intermediates formed by the reductive dehydration of the oxime moieties. We employ advanced quantum mechanics/molecular mechanics (QM/MM) simulations, enriched by a two-tiered approach incorporating QM/MM (UB3LYP-6-31G*/OPLS2005) geometry optimization, QM/MM (B3LYP-6-31G*/amberff19sb) steered molecular dynamics simulations, and detailed natural-bond-orbital analyses to decipher the unconventional hydride transfer to nitrogen in both reduction steps and to delineate the role of active site residues as well as of substituents present in the substrates. Our computational results confirm the proposed mechanism and agree well with experimental mutagenesis and enzyme kinetics data. According to our model, the catalysis of OYE involves hydride transfer from the flavin cofactor to the nitrogen atom in oximoketoesters as well as iminoketoesters followed by protonation at the adjacent oxygen or carbon atoms by conserved tyrosine residues and active site water molecules. Two histidine residues play a key role in the polarization and activation of the C=N bond, and conformational changes of the substrate observed along the reaction coordinate underline the crucial importance of dynamic electron delocalization for efficient catalysis.

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Tailoring chemical bonds to design unconventional glasses.

Publications

Tailoring chemical bonds to design unconventional glasses.

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