Prospects and challenges for computer simulations of monolayer-protected metal clusters

GraphBNC: Machine Learning-Aided Prediction of Interactions Between Metal Nanoclusters and Blood Proteins

Hybrid nanostructures between biomolecules and inorganic nanomaterials constitute a largely unexplored field of research, with the potential for novel applications in bioimaging, biosensing, and nanomedicine. Developing such applications relies critically on understanding the dynamical properties of the nano-bio interface. This work introduces and validates a strategy to predict atom-scale interactions between water-soluble gold nanoclusters (AuNCs) and a set of blood proteins (albumin, apolipoprotein, immunoglobulin, and fibrinogen). Graph theory and neural networks are utilized to predict the strengths of interactions in AuNC-protein complexes on a coarse-grained level, which are then optimized in Monte Carlo-based structure search and refined to atomic-scale structures. The training data is based on extensive molecular dynamics (MD) simulations of AuNC-protein complexes, and the validating MD simulations show the robustness of the predictions. This strategy can be generalized to any complexes of inorganic nanostructures and biomolecules provided that one generates enough data about the interactions, and the bioactive parts of the nanostructure can be coarse-grained rationally.

A molecular dynamics study on the ion-mediated self-assembly of monolayer-protected nanoclusters

We studied the effects of metal and molecular cations on the aggregation of atomically precise monolayer-protected nanoclusters (MPCs) in an explicit solvent using atomistic molecular dynamics simulations. While divalent cations such as Zn2+ and Cd2+ promote aggregation by forming ligand-cation-ligand bridges between the MPCs, molecular cations such as tetraethylammonium and cholinium inhibit their aggregation by getting adsorbed into the MPC's ligand shell and reducing the ligand's motion. Here, we studied the aggregation of Au25(SR)18 nanoclusters with two types of ligands, para-mercaptobenzoic acid and D-penicillamine, as prototypical examples.

Dithiophosphonate-Protected Eight-Electron Superatomic Ag21 Nanocluster: Synthesis, Isomerism, Luminescence, and Catalytic Activity

The structure-property relationship considering isomerism-tuned photoluminescence and efficient catalytic activity of silver nanoclusters (NCs) is exclusive. Asymmetrical dithiophosphonate NH4[S2P(OR)(p-C6H4OCH3)] ligated first atomically precise silver NCs [Ag21{S2P(OR)(p-C6H4OCH3)}12]PF6 {where, R = nPr (1), Et (2)} were established by single-crystal X-ray diffraction and characterized by electrospray ionization mass spectrometry, NMR (31P, 1H, 2H), X-ray photoelectron spectroscopy, UV-visible, energy-dispersive X-ray spectroscopy, Fourier transforms infrared, thermogravimetric analysis, etc. NCs 1 and 2 consist of eight silver atoms in a cubic framework and enclose an Ag@Ag12-centered icosahedron to constitute an Ag21 core of Th symmetry, which is concentrically inscribed within the S24 snub-cube, P12 cuboctahedron, and the O12 truncated tetrahedron formed by 12 dithiophosphonate ligands. These NCs facilitate to be an eight-electron superatom (1S21P6), in which eight capping Ag atoms exhibit structural isomerism with documented isoelectronic [Ag21{S2P(OiPr)2}12]PF6, 3. In contrast to 3, the stapling of dithiophosphonates in 1 and 2 triggered bluish emission within the 400 to 500 nm region at room temperature. The density functional theory study rationalized isomerization and optical properties of 1, 2, and 3. Both (1, and 2) clusters catalyzed a decarboxylative acylarylation reaction for rapid oxindole synthesis in 99% yield under ambient conditions and proposed a multistep reaction pathway. Ultimately, this study links nanostructures to their physical and catalytic properties.

Phytochemical on-line screening and in silico study of Helianthemum confertum: antioxidant activity, DFT, MD simulation, ADME/T analysis, and xanthine oxidase binding

Seven components from the methanol extract of the aerial part of the endemic species Helianthemum confertum were isolated and identified for the first time. Investigating this species and its separated components chemical make-up and radical scavenging capacity, was the main goal. Using an online HPLC-ABTS˙+ test, ORAC, and TEAC assays, the free radical scavenging capacity of the ethyl acetate extract was assessed. The fractionation of these extracts by CC, TLC, and reverse-phase HPLC was guided by the collected data, which was corroborated by TEAC and ORAC assays. Molecular docking studies, DFT at the B3LYP level, and an examination of the ADME/T predictions of all compounds helped to further clarify the phytochemicals' antioxidant potential. Isolation and identification of all components were confirmed through spectroscopy, which revealed a mixture (50-50%) of para-hydroxybenzoic acid 1 and methyl gallate 2, protocatechuic acid 3, astragalin 4, trans-tiliroside 5, cis-tiliroside 6, contaminated by trans-tiliroside and 3-oxo-α-ionol-β-d-glucopyranoside 7, as well as two new compounds for the genus Helianthemum (2 and 7). With a focus on compounds 1, 2, 3, and 4, the results clearly showed that the extract and the compounds tested from this species had a high antioxidant capacity. Within the xanthine oxidase enzyme's pocket, all of the components tested showed strong and stable binding. In light of these findings, the xanthine oxidase/methyl gallate 2 complex was simulated using the Desmond module of the Schrodinger suite molecular dynamics (MD) for 100 ns. Substantially stable receptor-ligand complexes were observed following 1 ns of MD simulation.

Mono-, di- and trimetallic coinage nanoparticles prepared via the Brust-Schiffrin method

The Brust-Schiffrin two-phase method is a facile way to prepare thiolate-protected metal nanoparticles, but its mechanism remains controversial. In this work, we demonstrate the use of the Brust-Schiffrin method based on coordination compound theory. We confirmed that the formation of stable complexes is the driving force for a series chemical reaction in the organic phase. We found that the stable Cu(I)-thiolate complex decreased the half-cell reduction potential of Cu(I)/Cu(0). Thus, when thiol ligands were in excess, thiolate-protected Cu(I) clusters formed rather than Cu(0)-cored nanoparticles. The thiolate-protected metal-hydride nanoclusters were the intermediate between the metal complexes and nanoparticles. The "metallophilic" interactions of the d10 closed-shell electronic configuration of the metal coordination centers were proposed as the driving force for nanocluster and nanoparticle formation. To confirm this mechanism, we synthesized Au, Ag, and Cu monometallic nanoparticles and bi- and trimetallic nanoparticles. We found that although thiolate-protected Cu(I) nanoclusters are not easily reduced, they can combine with Au and/or Ag nanoclusters to form nanoparticles. The proposed mechanism is expected to provide deeper insight into the Brust-Schiffrin method and further extend its application to metals other than Au, Ag and Cu.

N-Heterocyclic Carbene-Stabilized Atomically Precise Metal Nanoclusters

This perspective highlights advances in the preparation and understanding of metal nanoclusters stabilized by organic ligands with a focus on N-heterocyclic carbenes (NHCs). We demonstrate the need for a clear understanding of the relationship between NHC properties and their resulting metal nanocluster structure and properties. We emphasize the importance of balancing nanocluster stability with the introduction of reactive sites for catalytic applications and the importance of a better understanding of how these clusters interact with their environments for effective use in biological applications. The impact of atom-scale simulations, development of atomic interaction potentials suitable for large-scale molecular dynamics simulations, and a deeper understanding of the mechanisms behind synthetic methods and physical properties (e.g., the bright fluorescence displayed by many clusters) are emphasized.

Insights into the Interactions of Peptides with Monolayer-Protected Metal Nanoclusters

Monolayer-protected atomically precise metal nanoclusters (MPCs) have potential applications in catalysis, imaging, and drug delivery. Understanding their interactions with biomolecules such as peptides is of paramount interest for their use in cell imaging and drug delivery. Here we have carried out atomistic molecular dynamics simulations to investigate the interactions between MPCs and an anticancer peptide, melittin. Melittin gets attached to the MPCs surface by the formation of multiple hydrogen bonds between its amino acid residues with MPCs ligands. Additionally, the positively charged Lys, Arg, and peptide's N-terminal strongly anchor the peptide to the MPC metal surface, providing extra stabilization.

Towards structural optimization of gold nanoclusters with quantum Monte Carlo

We study the prospects of using quantum Monte Carlo techniques (QMC) to optimize the electronic wavefunctions and atomic geometries of gold compounds. Complex gold nanoclusters are widely studied for diverse biochemical applications, but the dynamic correlation and relativistic effects in gold set the bar high for reliable, predictive simulation methods. Here we study selected ground state properties of few-atom gold clusters by using density functional theory (DFT) and various implementations of the variational Monte Carlo (VMC) and diffusion Monte Carlo. We show that the QMC methods mitigate the exchange-correlation (XC) approximation made in the DFT approach: the average QMC results are more accurate and significantly more consistent than corresponding DFT results based on different XC functionals. Furthermore, we use demonstrate structural optimization of selected thiolated gold clusters with between 1 and 3 gold atoms using VMC forces. The optimization workflow is demonstrably consistent, robust, and its computational cost scales with nb, where b < 3 and n is the system size. We discuss the implications of these results while laying out steps for further developments.

Silver-Exchanged Zeolite Y Catalyzes a Selective Insertion of Carbenes into C-H and O-H Bonds

Commercially available zeolite Y modulates the catalytic activity and selectivity of ultrasmall silver species during the Buchner reaction and the carbene addition to methylene and hydroxyl bonds, by simply exchanging the counter cations of the zeolite framework. The zeolite acts as a macroligand to tune the silver catalytic site, enabling the use of this cheap and recyclable solid catalyst for the in situ formation of carbenes from diazoacetate and selective insertion in different C-H (i.e., cyclohexane) and C-O (i.e., water) bonds. The amount of catalyst in the reaction can be as low as ≤0.1 mol % silver. Besides, this reactivity allows deeply drying the HY zeolite framework by making the strongly adsorbed water molecules react with the in situ formed carbenes.

Biopolymer-Based Composite Hydrogels Embedding Small Silver Nanoparticles for Advanced Antimicrobial Applications: Experimental and Theoretical Insights

In this work, we report a two-step methodology for the synthesis of small silver nanoparticles embedded into hydrogels based on chitosan (CS) and hydroxypropyl methylcellulose (HPMC) biopolymers. This method uses d-glucose as an external green reducing agent and purified water as a solvent, leading to an eco-friendly, cost-effective, and biocompatible process for the synthesis of silver nanocomposite hydrogels. Their characterization comprises ultraviolet-visible spectroscopy, Fourier-transform infrared spectra, differential scanning calorimetry, scanning electron microscopy with energy-dispersive spectroscopy, and transmission electron microscopy assays. Moreover, the structural stability of the hydrogels was investigated through sequential swelling-deswelling cycles. The nanomaterials showed good mechanical properties in terms of their structural stability and revealed prominent antibacterial properties due to the reduced-size particles that promote their use as new advanced antimicrobial agents, an advantage compared to conventional particles in aqueous suspension that lose stability and effectiveness. Finally, theoretical analyses provided insights into the possible interactions, charge transfer, and stabilization process of nanoclusters mediated by the high-electron-density groups belonging to CS and HPMC, revealing their unique structural properties in the preparation of nano-scaled materials.

Understanding Molecular Aggregation of Ligand-Protected Atomically-Precise Metal Nanoclusters

Monolayer-protected atomically precise nanoclusters (MPCs) are an important class of molecules due to their unique structural features and diverse applications, including bioimaging, sensors, and drug carriers. Understanding the atomistic and dynamical details of their self-assembly process is crucial for designing system-specific applications. Here, we applied molecular dynamics and on-the-fly probability-based enhanced sampling simulations to study the aggregation of Au₂₅(pMBA)₁₈ MPCs in aqueous and methanol solutions. The MPCs interact via both hydrogen bonds and π-stacks between the aromatic ligands to form stable dimers, oligomers, and crystals. The dimerization free energy profiles reveal a pivotal role of the ligand charged state and solvent mediating the molecular aggregation. Furthermore, MPCs' ligands exhibit suppressed conformational flexibility in the solid phase due to facile intercluster hydrogen bonds and π-stacks. Our work provides unprecedented molecular-level dynamical details of the aggregation process and conformational dynamics of MPCs ligands in solution and crystalline phases.

MOF-Triggered Synthesis of Subnanometer Ag02 Clusters and Fe3+ Single Atoms: Heterogenization Led to Efficient and Synergetic One-Pot Catalytic Reactions

The combination of well-defined Fe³⁺ isolated single-metal atoms and Ag₂ subnanometer metal clusters within the channels of a metal-organic framework (MOF) is reported and characterized by single-crystal X-ray diffraction for the first time. The resulting hybrid material, with the formula [Ag⁰₂(Ag⁰)_1.34Fe^III_0.66]@Na^I₂{Ni^II₄[Cu^II₂(Me₃mpba)₂]₃}·63H₂O (Fe³⁺Ag⁰₂@MOF), is capable of catalyzing the unprecedented direct conversion of styrene to phenylacetylene in one pot. In particular, Fe³⁺Ag⁰₂@MOF─which can easily be obtained in a gram scale─exhibits superior catalytic activity for the TEMPO-free oxidative cross-coupling of styrenes with phenyl sulfone to give vinyl sulfones in yields up to >99%, which are ultimately transformed, in situ, to the corresponding phenylacetylene product. The results presented here constitute a paradigmatic example of how the synthesis of different metal species in well-defined solid catalysts, combined with speciation of the true metal catalyst of an organic reaction in solution, allows the design of a new challenging reaction.

Reversible assembly of nanoparticles: theory, strategies and computational simulations

The significant advances in synthesis and functionalization have enabled the preparation of high-quality nanoparticles that have found a plethora of successful applications. The unique physicochemical properties of nanoparticles can be manipulated through the control of size, shape, composition, and surface chemistry, but their technological application possibilities can be further expanded by exploiting the properties that emerge from their assembly. The ability to control the assembly of nanoparticles not only is required for many real technological applications, but allows the combination of the intrinsic properties of nanoparticles and opens the way to the exploitation of their complex interplay, giving access to collective properties. Significant advances and knowledge gained over the past few decades on nanoparticle assembly have made it possible to implement a growing number of strategies for reversible assembly of nanoparticles. In addition to being of interest for basic studies, such advances further broaden the range of applications and the possibility of developing innovative devices using nanoparticles. This review focuses on the reversible assembly of nanoparticles and includes the theoretical aspects related to the concept of reversibility, an up-to-date assessment of the experimental approaches applied to this field and the advanced computational schemes that offer key insights into the assembly mechanisms. We aim to provide readers with a comprehensive guide to address the challenges in assembling reversible nanoparticles and promote their applications.

Molecular Dynamics Characterization of Radiosensitizing Coated Gold Nanoparticles in Aqueous Environment

Functionalized metal nanoparticles (NPs) have been proposed as promising radiosensitizing agents for more efficient radiotherapy treatment using photons and ion beams. Radiosensitizing properties of NPs may depend on many different parameters (such as size, composition, and density) of the metal core, the organic coatings, and the molecular environment. A systematic exploration of each of these parameters on the atomistic level remains a formidable and costly experimental task, but it can be addressed by means of advanced computational modeling. This paper describes a detailed computational procedure for construction and atomistic-level characterization of radiosensitizing metal NPs in explicit molecular media. The procedure is general and is extensible to many different combinations of the core, coating, and environment. As an illustrative and experimentally relevant case study, we consider nanometer-sized gold NPs coated with thiol-poly(ethylene glycol)-amine molecules of different length and surface density and solvated in water at ambient conditions. The radial distribution of different atoms in the coatings as well as distribution and structural properties of water around the coated NPs are analyzed and linked to radiosensitizing properties of the NPs. It is revealed that the structure of the coating layer on the solvated NPs depends strongly on the surface density of ligands. At surface densities below ∼3 molecules/nm² the coating represents a mixture of different conformation states, whereas elongated "brush"-like structures are formed at higher densities of ligands. The water content in denser coatings is significantly lower at distances from 1 nm up to 3 nm from the gold surface depending on the length of ligand molecules. Such dense and thick coatings may suppress the production of hydroxyl radicals by low-energy electrons emitted from the metal NPs and thus diminish their radiosensitizing properties. The presented computational framework provides precise information for a quantitative atomistic-level description of the structural properties of coated metal NPs in biologically relevant environments and so may form a basis for future developments to achieve a more realistic description of irradiation-driven chemistry effects in the vicinity of coated metal NPs.

Engineering Nanointerfaces of Au25 Clusters for Chaperone-Mediated Peptide Amyloidosis

Synthetic nanomaterials possessing biomolecular-chaperone functions are good candidates for modulating physicochemical interactions in many bioapplications. Despite extensive research, no general principle to engineer nanomaterial surfaces is available to precisely manipulate biomolecular conformations and behaviors, greatly limiting attempts to develop high-performance nanochaperone materials. Here, we demonstrate that, by quantifying the length (-SC_xR^±, x = 3-11) and charges (R^- = -COO^-, R⁺ = -NH₃⁺) of ligands on Au₂₅ gold nanochaperones (AuNCs), simulating binding sites and affinities of amyloid-like peptides with AuNCs, and probing peptide folding and fibrillation in the presence of AuNCs, it is possible to precisely manipulate the peptides' conformations and, thus, their amyloidosis via customizing AuNCs nanointerfaces. We show that intermediate-length liganded AuNCs with a specific charge chaperone peptides' native conformations and thus inhibit their fibrillation, while other types of AuNCs destabilize peptides and promote their fibrillation. We offer a microscopic molecular insight into peptide identity on AuNCs and provide a guideline in customizing nanochaperones via manipulating their nanointerfaces.

The 2D or 3D morphology of sub-nanometer Cu5 and Cu8 clusters changes the mechanism of CO oxidation

The mechanism of the CO oxidation reaction catalysed by planar Cu₅, three dimensional (3D) Cu₅, and 3D Cu₈ clusters is theoretically investigated at the B3PW91/Def2TZVP level. All three clusters are able to catalyse the reaction with similar activation energies for the rate determining step, about 16-18 kcal mol^-1, but with remarkable differences in the reaction mechanism depending on cluster morphology. Thus, for 3D Cu₅ and Cu₈ clusters, O₂ dissociation is the first step of the mechanism, followed by two consecutive CO + O reaction steps, the second one being rate determining. In contrast, on planar Cu₅ the reaction starts with the formation of an OOCO intermediate in what constitutes the rate determining step. The O-O bond is broken in a second step, releasing the first CO₂ and leaving one bi-coordinately adsorbed O atom which reacts with CO following an Eley-Rideal mechanism with a low activation energy, in contrast to the higher barriers obtained for this step on 3D clusters.

Ligand Ratio Plays a Critical Role in the Design of Optimal Multifunctional Gold Nanoclusters for Targeted Gastric Cancer Therapy

Nanodrug delivery systems (NDDSs) based on water-soluble and atomically precise gold nanoclusters (AuNCs) are under the spotlight due to their great potential in cancer theranostics. Gastric cancer (GC) is one of the most aggressive cancers with a low early diagnosis rate, with drug therapy being the primary means to overcome its increasing incidence. In this work, we designed and characterized a set of 28 targeted nanosystems based on Au₁₄₄(p-MBA)₆₀ (p-MBA = para-mercaptobenzoic acid) nanocluster to be potentially employed as combination therapy in GC treatment. The proposed multifunctional AuNCs are functionalized with cytotoxic drugs (5-fluorouracil and epirubicin) or inhibitors of different signaling pathways (phosphatidylinositol 3-kinases (PI3K)/protein kinase B (Akt)/mammalian target of the rapamycin (mTOR), vascular endothelial growth factor (VEGF), and hypoxia-inducible factor (HIF)) and RGD peptides as targeting ligands, and we studied the role of ligand ratio in their optimal structural conformation using peptide-protein docking and all-atom molecular dynamics (MD) simulations. The results reveal that the peptide/drug ratio is a crucial factor influencing the potential targeting ability of the nanosystem. The most convenient features were observed when the peptide amount was favored over the drug in most cases; however, we demonstrated that the system composition and the intermolecular interactions on the ligand shell are crucial for achieving the desired effect. This approach helps guide the experimental stage, providing essential information on the size and composition of the nanosystem at the atomic level for ligand tuning in order to increase the desired properties.

Computational Approaches to the Electronic Properties of Noble Metal Nanoclusters Protected by Organic Ligands

Organometallic nanoparticles composed by metal cores with sizes under two nanometers covered with organic capping ligands exhibit intermediate properties between those of atoms and molecules on one side, and those of larger metal nanoparticles on the other. In fact, these particles do not show a peculiar metallic behavior, characterized by plasmon resonances, but instead they have nonvanishing band-gaps, more along molecular optical properties. As a consequence, they are suitable to be described and investigated by computational approaches such as those used in quantum chemistry, for instance those based on the time-dependent density functional theory (TD-DFT). Here, I present a short review of the research performed from 2014 onward at the University of Modena and Reggio Emilia (Italy) on the TD-DFT interpretation of the electronic spectra of different organic-protected gold and/or silver nanoclusters.