Structural Water Molecules Confined in Soft and Hard Nanocavities as Bright Color Emitters

The Importance of Structural Water in HDAC8 for Correct Binding Pose Applied for Drug Design of Anticancer Molecules

AIMS

Validating the docking procedure and maintaining the structural water molecules at HDAC8 catalytic site.

BACKGROUND

Molecular docking simulations play a significant role in Computer-Aided Drug Design, contributing to the development of new molecules. To ensure the reliability of these simulations, a validation process called "self-docking or re-docking" is employed, focusing on the binding mode of a ligand co-crystallized with the protein of interest.

OBJECTIVE

In this study, several molecular docking studies were conducted using five X-ray structures of HDAC8-ligand complexes from the PDB.

METHODS

Ligands initially complexed with HDAC8 were removed and re-docked onto the free protein, revealing a poor reproduction of the expected binding mode. In response to this, we observed that most HDAC8-ligand complexes contained one to two water molecules in the catalytic site, which were crucial for maintaining the cocrystallized ligand.

RESULTS

These water molecules enhance the binding mode of the co-crystallized ligand by stabilizing the proteinligand complex through hydrogen bond interactions between ligand and water molecules. Notably, these interactions are lost if water molecules are removed, as is often done in classical docking methodologies. Considering this, molecular docking simulations were repeated, both with and without one or two conserved water molecules near Zn+2 in the catalytic cavity. Simulations indicated that replicating the native binding pose of co-crystallized ligands on free HDAC8 without these water molecules was challenging, showing greater coordinate displacements (RMSD) compared to those including conserved water molecules from crystals.

CONCLUSION

The study highlighted the importance of conserved water molecules within the active site, as their presence significantly influenced the successful reproduction of the ligands' native binding modes. The results suggest an optimal molecular docking procedure for validating methods suitable for filtering new HDAC8 inhibitors for future experimental assays.

P-Band Intermediate States Mediate Electron Transfer at Confined Nanoscale

In this Perspective, mainly based on the model of structural water molecules (SWs) as bright color emitters, we briefly summarize the development and theoretical elaboration of P-band intermediate state (PBIS) theory as well as its application in several typical catalytic redox reactions. In addition, with a simple equation (2∫ψ2σ1' + ∫ψ2σ2 + ∫ψ2π = 1), we clearly define how the interface states correlate with the three basic parameters of heterogeneous catalysis (conversion, selectivity, and stability), and what is the dynamic nature of catalytic active sites. Overall, the proposal of SW-dominated PBIS theory establishes an internal physical connection between the decay kinetics of excited electrons and the catalytic reaction kinetics and provides new insights into the physical origin of photoluminescence emission of low-dimensional quantum nanodots and the physical nature of nanoconfinement and nanoconfined catalysis.

Green carbon science: fundamental aspects

Carbon energy has contributed to the creation of human civilization, and it can be considered that the configuration of the carbon energy system is one of the important laws that govern the operation of everything in the universe. The core of the carbon energy system is the opposition and unity of two aspects: oxidation and reduction. The operation of oxidation and reduction is based on the ternary elemental system composed of the three elements of carbon, hydrogen and oxygen. Its operation produces numerous reactions and reaction products. Ancient Chinese philosophy helps us to understand in depth the essence of green carbon science, to explore its scientific basis, and to identify the related platforms for technology development.

Structural water molecules dominated p band intermediate states as a unified model for the origin on the photoluminescence emission of noble metal nanoclusters: from monolayer protected clusters to cage confined nanoclusters

In the past several decades, noble metal nanoclusters (NMNCs) have been developed as an emerging class of luminescent materials due to their superior photo-stability and biocompatibility, but their luminous quantum yield is relatively low and the physical origin of the bright photoluminescence (PL) of NMNCs remain elusive, which limited their practical application. As the well-defined structure and composition of NMNCs have been determined, in this mini-review, the effect of each component (metal core, ligand shell and interfacial water) on their PL properties and corresponded working mechanism were comprehensively introduced, and a model that structural water molecules dominated p band intermediate state was proposed to give a unified understanding on the PL mechanism of NMNCs and a further perspective to the future developments of NMNCs by revisiting the development of our studies on the PL mechanism of NMNCs in the past decade.

Ligand effects on the photoluminescence of atomically precise silver nanoclusters

Photoluminescence (PL) is one of the most exciting properties of atomically precise metal nanoclusters (NCs), making them a prime choice for various applications, from sensing to bio-imaging. While there are several advantages of metal NCs for PL-based applications, their PLQY is significantly low compared to other PL-active nanomaterials or organic dyes. It is essential to understand the PL mechanism in detail to tune the PLQY of NCs. There are numerous reports on gold NCs with a known structure where the origin of PL has been explored, and it was found that ligands play a vital role in their PL properties along with the kernel (core). Reports on understanding the ligand effects on PL properties are also evolving for the case of atomically precise silver NCs. This mini-review will summarize the ligands' role in PL of 29 atom Ag NCs, the most reported NCs with diversity in the silver family. The ligands were classified as primary and secondary, and their effects on tuning the PL properties were explained. The review will also address some of the answers to open questions for AgNCs, such as the origin of PL, dynamics, and the tunability of PLQY using ligand modifications.

Activation of H2O Tailored by Interfacial Electronic States at a Nanoscale Interface for Enhanced Electrocatalytic Hydrogen Evolution

Despite the fundamental and practical significance of the hydrogen evolution reaction (HER), the reaction kinetics at the molecular level are not well-understood, especially in basic media. Here, with ZIF-67-derived Co-based carbon frameworks (Co/NCs) as model catalysts, we systematically investigated the effects of different reaction parameters on the HER kinetics and discovered that the HER activity was directly dependent not on the type of nitrogen in the carbon framework but on the relative content of surface hydroxyl and water (OH-/H2O) adsorbed on Co active sites embedded in carbon frameworks. When the ratio of the OH-/H2O was close to 1:1, the Co/NC nanocatalyst showed the best reaction performance under the condition of high-pH electrolytes, e.g., an overpotential of only 232 mV at a current density of 10 mA cm-2 in the 1 M KOH electrolyte. We unambiguously identified that the structural water molecules (SWs) in the form of hydrous hydroxyl complexes absorbed on metal centers {OHad·H2O@M+} were catalytic active sites for the enhanced HER, where M+ could be transition or alkaline metal cations. Different from the traditional hydrogen bonding of water, the hydroxyl (hydroxide) groups and water molecules in the SWs were mainly bonded together via the spatial interaction between the p orbitals of O atoms, exhibiting features of a delocalized π-bond with a metastable state. These newly formed surface bonds or transitory states could be new weak interactions that synergistically promote both interfacial electron transfer and the activation of water (dissociation of O-H bonds) at the electrode surface, i.e., the formation of activated H adducts (H*). The capture of new surface states not only explains pH-, cation-, and transition-metal-dependent hydrogen evolution kinetics but also provides completely new insights into the understanding of other electrocatalytic reductions involving other small molecules, including CO2, CO, and N2.

Dynamic Pt-OH-·H2O-Ag species mediate coupled electron and proton transfer for catalytic hydride reduction of 4-nitrophenol at the confined nanoscale interface

Generally, the catalytic transformation of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP) at heterogeneous metal surfaces follows a Langmuir-Hinshelwood (L-H) mechanism when sodium borohydride (NaBH₄) is used as the sacrificial reductant. Herein, with Pt-Ag bimetallic nanoparticles confined in dendritic mesoporous silica nanospheres (DMSNs) as a model catalyst, we demonstrated that the conversion of 4-NP did not pass through the direct hydrogen transfer route with the hydride equivalents being supplied by borohydride via the bimolecular L-H mechanism, since Fourier transform infrared (FTIR) spectroscopy with the use of isotopically labeled reactants (NaBD₄ and D₂O) showed that the final product of 4-AP was composed of protons (or deuterons) that originated from the solvent water (or heavy water). Combined characterization by X-ray photoelectron spectroscopy (XPS), ¹H nuclear magnetic resonance (NMR) and the optical excitation and photoluminescence spectrum evidenced that the surface hydrous hydroxide complex bound to the metal surface (also called structural water molecules, SWs), due to the space overlap of p orbitals of two O atoms in SWs, could form an ensemble of dynamic interface transient states, which provided the alternative electron and proton transfer channels for selective transformation of 4-NP. The cationic Pt species in the Ag-Pt bimetallic catalyst mainly acts as a dynamic adsorption center to temporally anchor SWs and related reactants, and not as the active site for hydrogen activation.