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At least 541 records · Page 30

Polarizable Water Potential Derived from a Model Electron Density

A new empirical potential for efficient, large scale molecular dynamics simulation of water is presented. The HIPPO (Hydrogen-like Intermolecular Polarizable POtential) force field is based upon the model electron density of a hydrogen-like atom. This framework is used to derive and parametrize individual terms describing charge penetration damped permanent electrostatics, damped polarization, charge transfer, anisotropic Pauli repulsion, and damped dispersion interactions. Initial parameter values were fit to Symmetry Adapted Perturbation Theory (SAPT) energy components for ten water dimer configurations, as well as the radial and angular dependence of the canonical dimer. The SAPT-based parameters were then systematically refined to extend the treatment to water bulk phases. The final HIPPO water model provides a balanced representation of a wide variety of properties of gas phase clusters, liquid water, and ice polymorphs, across a range of temperatures and pressures. This water potential yields a rationalization of water structure, dynamics, and thermodynamics explicitly correlated with an ab initio energy decomposition, while providing a level of accuracy comparable or superior to previous polarizable atomic multipole force fields. The HIPPO water model serves as a cornerstone around which similarly detailed physics-based models can be developed for additional molecular species.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Møller–Plesset and Density-Fixed Adiabatic Connections for a Model Diatomic System at Different Correlation Regimes

In recent years, adiabatic connection (AC) interpolations developed within density functional theory (DFT) have been found to provide good performances in the calculation of interaction energies when used with Hartree–Fock (HF) ingredients. The physical and mathematical reasons for such unanticipated performance have been clarified, to some extent, by studying the strong-interaction limit of the Møller–Plesset (MP) AC. In this work, we calculate both the MP and the DFT AC integrand for the asymmetric Hubbard dimer, which allows for a systematic investigation of different correlation regimes by varying two simple parameters in the Hamiltonian: the external potential, Δv, and the interaction strength, U. Notably, we find that, while the DFT AC integrand appears to be convex in the full parameter space, the MP integrand may change curvature twice. Furthermore, we discuss different aspects of the second-order expansion of the correlation energy in each AC, and we demonstrate why the derivative of the λ-dependent density in the MP AC at λ = 0 (i.e., at the HF density) is zero in the model. Concerning the strong-interaction limit of both ACs in the Hubbard dimer setting, we show that the asymptotic value of the MP AC, W ∞ HF , is lower than (or equal to) its DFT analogue, W ∞ KS , if the two are compared at a given density, just like in real space. Furthermore, we also show that this is not always the case if the two quantities are compared at a given external potential.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Diabatization with Electrostatic Embedding for Studying Photophysics in Organic Molecular Crystals

Highly emissive organic molecular crystals find applications in several areas, such as organic electronics, solar cells, and sensors. Understanding the excited-state mechanisms underlying these applications is essential for optimizing and controlling them effectively. Exciton models coupled with nonadiabatic dynamics, particularly quantum dynamics, provide crucial insights into photochemical and photophysical processes in molecular crystals. Nevertheless, there remains a lack of general tools and automated workflows to facilitate such simulations. In this paper, we present a computational strategy to investigate the photoactivated dynamics of organic molecular crystals, bridging methodologies traditionally used for molecular systems and materials science, with a particular focus on the interplay between local excitations and charge transfer (CT) processes. We have implemented an interface between the fromage and Overdia programs, enabling the construction of vibronic Hamiltonians for molecular crystals within an excited-state ONIOM(QM:QM′) framework, incorporating long-range electrostatics through a RESP-based Ewald summation. Fragment-based diabatization provides a route to quantum dynamics simulations in weak-to-intermediate coupling regimes. The method was applied to the photophysics of dibenzo[g,p]chrysene (DBC) crystals using time-dependent DFT. The fromage/ Overdia interface was employed to compute the couplings of local excitations and CT states for 18 unique DBC dimers in the crystal and to quantify the influence of electrostatic embedding, which was found to be modest (10−20%). Simulations on π-stacked dimers reproduced the small red shift observed experimentally from solution to crystal, attributed to electronic interactions among fixed monomers rather than crystal electrostatics. Quantum dynamics simulations revealed ultrafast population transfer from bright local excitations to CT states. This approach establishes a robust framework linking molecular and solid-state excited-state dynamics, with potential applications for studying excitations, defects, and impurities in molecular crystals.

Crystals↗

A Cautionary Tale: Failure of the Valence CASSCF to Describe the Hallmark of Hydrogen Bonding

Valence CASSCF (vCAS) calculations for the hydrogen-bonded (H2O)2, (HF)2, and HF–H2O dimers fail to predict the lengthening of the hydrogen donor bond and the corresponding red shift in the donor bond vibrational stretching frequency. Analysis of the active orbitals in the vCAS calculation reveals that one of the weakly occupied orbitals in each dimer is used to correlate the electrons in the acceptor lone pairs rather than those in the donor bonding orbitals. This has significant implications for subsequent treatments of the dynamical correlation that are based on the vCAS wavefunction.

Nguyen, Long H.↗

Modeling the Solvation and Acidity of Carboxylic Acids Using an Ab Initio Deep Neural Network Potential

Formic and acetic acid constitute the simplest of carboxylic acids, yet they exhibit fascinating chemistry in the condensed phase such as proton transfer and dimerization. The go-to method of choice for modeling these rare events have been accurate but expensive ab-initio molecular dynamics simulations. Here, we present a deep neural network potential trained using accurate ab-initio data that can be used in tandem with enhanced-sampling methods to perform an efficient exploration of the free-energy surface of aqueous solutions of weak carboxylic acids. In particular, we show that our model captures proton dissociation and provides a good estimate of the pK a , as well as the dimerization of formic and acetic acid. This provides a suitable starting point for applications in different research areas where computational efficiency coupled with the accuracy of ab-initio methods is required.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Microcarbonation of Naphthalene: An Experimental and Computational Study of Photoionization in Naphthalene-Carbon Dioxide Clusters

The photoionization of naphthalene (N)-carbon dioxide (CO 2 ) clusters was studied using tunable vacuum ultraviolet (VUV) radiation from a synchrotron in the photon range of 8.0 to 13.7 eV, in combination with time-of-flight mass spectrometry. Clusters of monomer, dimer, and trimer naphthalene with CO 2 (N­(CO 2 ) 0–6 , N 2 ­(CO 2 ) 0–3 , N3) were observed. The lowest-energy conformers were obtained via a conformer search, followed by geometry optimizations at the ωB97X-V2/aug-cc-pVTZ (monomer) and ωB97X-V2/aug-cc-pVDZ (dimer) levels of theory. Carbon dioxide was found to preferentially cluster on top of the naphthalene molecule (in an out-of-plane configuration). From the mass spectra, photoionization intensity curves (PICs) were constructed, and appearance energies (AEs) were determined. No substantial trend in AE was observed with increasing size of the naphthalene-carbon dioxide clusters; rather, AE oscillations around the value for pure naphthalene were observed. These AE oscillations are also observed in a recently studied naphthalene-water cluster system, though in this system a slight downward trend in AE for pure naphthalene clusters (N1/2/3/4) was observed. The differences between the two systems are attributed to differing interaction strengths. In conclusion, understanding these differences may aid in determining how photoprocessing can proceed differently depending on the dominant matrix component in interstellar ices.

Wannenmacher, Anna [Lawrence Berkeley National Lab↗

Evolution of Structure and Magnetism in FeCl 2 and FeCl 3 : From Clusters to Monolayers

In this work, we address one of the most fundamental questions in cluster science─how do the structure and properties evolve from clusters to crystals? Using density functional theory (DFT), we focus our study on the evolution of structure and magnetism in iron-chloride systems, from clusters to monolayers. The choice of this system is motivated by the recent experimental confirmation of one of the author’s earlier theoretical prediction that the FeCl 2 cluster is magnetic with a spin magnetic moment of 4 μ B localized at the Fe site, while its dimer, Fe 2 Cl 4 , is antiferromagnetic. Similarly, FeCl 3 cluster is magnetic with a total spin magnetic moment of 5 μ B , with 4 μ B localized at the Fe site and 1 μ B distributed over the Cl sites. The dimer clusters Fe 2 Cl 4 and Fe 2 Cl 6 have an antiferromagnetic ground state, and upon Li-functionalization, both can be magnetically transformed from antiferromagnetic to ferromagnetic states. In contrast, FeCl 2 and FeCl 3 monolayers exhibit different magnetic ground states in their periodic forms: FeCl 2 is ferromagnetic (FM), but in FeCl 3 , the antiferromagnetic (AFM) and FM states are energetically nearly degenerate. Such a difference arises due to the different chemical coordination of the Fe atoms with the Cl atoms, caused by their different oxidation states, which is +2 in FeCl 2 and +3 in FeCl 3 , respectively. Interestingly, Li-functionalization allows both FeCl 3 and FeCl 2 monolayers to be ferromagnetic. Our study highlights that several, but not all, electronic and magnetic characteristics of isolated clusters are preserved in the extended periodic structures. This systematic investigation of iron-halide clusters is expected to inspire further experimental and theoretical exploration into the magnetism of other transition metal halides.

cluster chemistry↗

Exciton Delocalization in Indolenine Squaraine Aggregates Templated by DNA Holliday Junction Scaffolds

Exciton delocalization plays a prominent role in the photophysics of molecular aggregates, ultimately governing their particular function or application. DNA is a compelling scaffold in which to template molecular aggregates and promote exciton delocalization. As individual dye molecules are the basis of exciton delocalization in molecular aggregates, their judicious selection is important. Motivated by their excellent photostability and spectral properties, here we examine the ability of squaraine dyes to undergo exciton delocalization when aggregated via a DNA Holliday junction (HJ) template. A commercially available indolenine squaraine dye was chosen for the study given its strong structural resemblance to Cy5, a commercially available cyanine dye previously shown to undergo exciton delocalization in DNA HJs. Three types of DNA-dye aggregate configurations—transverse dimer, adjacent dimer, and tetramer—were investigated. Signatures of exciton delocalization were observed in all squaraine-DNA aggregates. Specifically, strong blue shift and Davydov splitting were observed in steady-state absorption spectroscopy and exciton-induced features were evident in circular dichroism spectroscopy. Strongly suppressed fluorescence emission provided additional, indirect evidence for exciton delocalization in the DNA-templated squaraine dye aggregates. To quantitatively evaluate and directly compare the excitonic Coulombic coupling responsible for exciton delocalization, the strength of excitonic hopping interactions between the dyes were obtained by simultaneous fitting the experimental steady-state absorption and CD spectra via a Holstein-like Hamiltonian in which, following the theoretical approach of Kühn, Renger, and May, the dominant vibrational mode is explicitly considered. The excitonic hopping strength within indolenine squaraines was found to be comparable to that of the analogous Cy5 DNA-templated aggregate. The squaraine aggregates adopted primarily an H-type (dyes oriented parallel to each other) spatial arrangement. Extracted geometric details of dye mutual orientation in the aggregates enabled close comparison of aggregate configurations and the elucidation of the influence of dye angular relationship on excitonic hopping interactions in squaraine aggregates. Furthermore, these results encourage the application of squaraine-based aggregates in next generation systems driven by molecular excitons.

36 MATERIALS SCIENCE↗

Mechanism and Reaction Energy Landscape for Apiose Cross-Linking by Boric Acid in Rhamnogalacturonan II

Rhamnogalacturonan II (RG-II)—the most complex polysaccharide known in nature—exists as a borate cross-linked dimer in the plant primary cell wall. Boric acid facilitates the formation of this cross-link on the apiosyl residues of RG-II’s side chain A. Here, we detail the reaction mechanism for the cross-linking process with ab initio calculations coupled with transition state theory. We determine the formation of the first ester linkage to be the rate-limiting step of the mechanism. Our findings demonstrate that the regio- and stereospecific nature of subsequent steps in the reaction itinerary presents four distinct energetically plausible reaction pathways. This has significant implications for the overall structure of the cross-linked RG-II dimer assembly. Finally, our transition state and reaction path analyses reveal key geometric insights that corroborate previous experimental hypotheses on borate ester formation reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Intermediate Species in the Crystallization of Sodium Aluminate Hydroxy Hydrates

In highly alkaline “water-in-salt” Na 2 O/Al 2 O 3 /H 2 O solutions where the monomeric Al(OH) 4 - anion dominates, isolation of transitional species that seed crystallization of sodium aluminate salt hydrates has been challenging. For example, discrimination of dimeric [e.g., Al 2 O(OH) 6 2- ] from species via 27 Al nuclear magnetic resonance (NMR) spectroscopy is limited via fast interconversion through hydrolysis and condensation reactions. Despite this, using magic-angle spinning NMR ( 27 Al MAS NMR) at high magnetic field strengths (14.1 and 20.0 T) on crystals of nonasodium bis(hexahydroxyaluminate) trihydroxide hexahydrate [NSA, Na 9 [Al(OH) 6 ] 2 ·3(OH)·6(H 2 O)], we observed a 27 Al resonance consistent with Na 2 Al 2 O(OH) 6 . This tetrahedral dimeric species was also identified in the mother liquor by Raman spectroscopy while remaining expectedly unresolved by high-field liquid-state 27 Al NMR. Its substantial abundance in the mother liquor and as either an interstitial or an adsorbate on precipitated solids suggest that it plays a crucial role in NSA crystallization. Here, our detailed characterization, which includes single-pulse 27 Al MAS NMR, nutation 27 Al MAS NMR, and multiple quantum 27 Al MAS NMR, provides new molecular insights into how aluminate transitions from tetrahedral in solution to octahedral in solid. This understanding could ultimately lead to better predictions of aluminum phase change behavior in caustic sodium hydroxide with wide-ranging technological and environmental implications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Density Functional Theory Study of the Adsorption and Dissociation of Copper(I) Acetamidinates on Ni(110): The Effect of the Substrate

In order to assess the role of a metal substrates on the thermal chemistry of adsorbed acetamidinate metalorganic compounds, we have studied the surface chemistry of copper(I)–N,N'-dimethylacetamidinate on Ni(110) using density functional theory and contrasted it with similar calculations we previously carried out on Cu(110). At low coverages, it was found that, in its most stable configuration, the molecular adsorption of copper(I)–N,N'-dimethylacetamidinate dimers occurs with the Cu atoms occupying surface hollow sites. In this work, the ligands reorient away from those metal centers, and the N atoms develop new direct bonds with surface Ni atoms. However, this configuration is not stable and decomposes by losing both ligands to the surface. In the final state, the two ligands bind via their N atoms to Ni sites one lattice space away from the sites where the Cu atoms remain, with their molecular planes perpendicular to that of the surface. This is in contrast with what happens in the case of adsorption on Cu(110), where the Cu atoms from the metalorganic complex still occupy hollow sites but where only one of the ligands breaks away and binds directly to the surface; the other remains on top of the two Cu ions. In terms of the energetics of adsorption and decomposition, the reactions on Ni(110) are much more exothermic than on Cu(110). Further analysis of the distribution of charge within the adsorbates shows a minor reduction of the Cu atoms of the dimer upon interaction with the surface; full reduction to metallic copper is complete only when both ligands have fully migrated to their new Ni surface sites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

AlCl 3 -Dosed Si(100)-2 × 1: Adsorbates, Chlorinated Al Chains, and Incorporated Al

The adsorption of AlCl 3 on Si(100) and the effect of annealing the AlCl 3 -dosed substrate were studied to reveal key surface processes for the development of atomic-precision, acceptor-doping techniques. This investigation was performed via scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT) calculations. At room temperature, AlCl 3 readily adsorbed to the Si substrate dimers and dissociated to form a variety of species. Annealing the AlCl 3 -dosed substrate at temperatures below 450 °C produced unique chlorinated aluminum chains (CACs) elongated along the Si(100) dimer row direction. An atomic model for the chains is proposed with supporting DFT calculations. Al was incorporated into the Si substrate upon annealing at 450 °C and above, and Cl desorption was observed for temperatures beyond 450 °C. Al-incorporated samples were encapsulated in Si and characterized by secondary ion mass spectrometry (SIMS) depth profiling to quantify the Al atom concentration, which was found to be in excess of 10 20 cm –3 across a ~2.7 nm-thick δ-doped region. Here, the Al concentration achieved here and the processing parameters utilized promote AlCl 3 as a viable gaseous precursor for novel acceptor-doped Si materials and devices for quantum computing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Is solid copper oxalate a spin chain or a mixture of entangled spin pairs?

Macroscopic assemblies of interacting spins give rise to a broad spectrum of behaviors determined by the spatial arrangement of the magnetic sites and the electronic interactions between them. Compounds of copper (II), in which each copper carries spin 1/2, exhibit a vast variety of physical properties. For antiferromagnetically coupled spin sites, there are two limiting scenarios: spin chains in which the spins can exhibit a long-range order or a mixture of dimers in which the spins within each pair are entangled but do not communicate with the spins from other dimers. In principle, the two types can be distinguished on the basis of experimental observations and modeling using empirically parameterized effective Hamiltonians, but in practice, ambiguity may persist for decades, as is the case for copper oxalate. Here we use high-level ab initio calculations to establish the validity of the nearest-site Heisenberg model and to predict the interaction strength between the magnetic sites. Finally, the computed magnetic susceptibility provides an unambiguous interpretation of magnetic experiments performed throughout half a century, clearly supporting the infinite spin-chain behavior of solid copper oxalate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Fundamental Insights into Cathode Stability: Linking Compositional Tuning and Local Coordination in Complex Metal Oxides under Aqueous Transformations

Compositional tuning of complex metal oxides in Li-ion battery materials influences their performance as well as their end-of-life behavior, in particular, the tendency to release toxic metal cations in aqueous solution. We modeled ternary variants of a parent LiCoO 2 delafossite structure by varying the metal identity and relative amounts. This yielded ten model formulations of Li(A 4/6 B 1/6 C 1/6 )O 2 , where the material is enriched with the A metal and doped with B and C, with Ni, Mn, Co, Fe, Al, V, and Ti as constituent metals. To assess their stability in aqueous conditions, metal release energetics were calculated using a combination of Density Functional Theory calculations and thermodynamics. Metal release in ternary oxides is dictated by subtle variations in the coordination environment of the leaving group. To identify governing chemical features across diverse compositions with varying local coordination environments, we leverage random forest regression and descriptor importance analysis. A key result is that metal–oxygen orbital hybridization, quantified using a projected density-of-states-derived descriptor, H d/p , provides a physically grounded measure of interaction strength that governs metal release energetics. This refined perspective goes beyond conventional oxidation state considerations and offers more robust insights for materials science. Finally, we model defect surface-bound O 2 dimer formation as a proxy for reactive oxygen species (ROS) generation. The results show that Ni-rich compositions more readily stabilize spin-polarized O 2 dimers, corroborating experimental reports of an increased ROS-driven biological response. In conclusion, our results establish a compositional and electronic basis for metal release and surface oxygen reactivity that form a rationale for complex metal oxide design principles.

36 MATERIALS SCIENCE↗

Solvent Induced Proton Polarization within the Nuclear–Electronic Orbital Framework

To explicitly account for nuclear quantum effects and solvent environments in simulations of chemical processes, the nuclear-electronic orbital approach is coupled with a polarizable continuum model (PCM). This NEO–PCM approach is used to explore the influence of solvation on nuclear polarization through applications to a water dimer and a set of protonated water tetramers. Nuclear polarization in these species is analyzed in terms of changes in proton density and oxygen–hydrogen bond length. Solvation is shown to enhance nuclear polarization with increasing dielectric constant. For the water dimer, the internal, hydrogen-bonded proton is shown to polarize more than the external, free proton. Moreover, proton quantization leads to greater solvent polarization through their mutual polarization. Furthermore, these calculations highlight the complex interplay among electronic, nuclear, and solvent polarization in chemical systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Size-Transferable Prediction of Excited State Properties for Molecular Assemblies with a Machine Learning Exciton Model

Computational modeling of the excited states of molecular aggregates faces significant computational challenges and size heterogeneity. Current machine learning (ML) models, typically trained on specific-sized aggregates, struggle with scalability. We found that the exciton model Hamiltonian of large aggregates can be decomposed into dimer pairs, allowing an ML model trained on dimers to reconstruct Hamiltonians for aggregates of any size. We also proposed a new method to address the phase-correction problem by introducing coupling terms’ approximations. Our model accurately predicted the excitation energies of the trimer and tetramer of perylene and tetracene and estimated S1 oscillator strengths of perylene aggregates. Leveraging our ML model, the optical gaps of nanosized perylene aggregates with up to 50 monomers are analyzed, qualitatively revealing the role of different couplings on their size dependency. Future work will explore transferability across different monomers to predict optical properties in heterogeneous assemblies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Acetic Acid Adsorption and Reactions on Ni(110)

Acetic acid adsorption and reactions at multiple surface coverage values on Ni(110) were studied with temperature-programmed desorption (TPD) and infrared reflection absorption spectroscopy (IRAS) at 90–500 K. The experimental measurements were interpreted with density functional theory (DFT) calculations that provided information on adsorbate geometries, energies, and vibrational modes. Below the monolayer saturation coverage of 0.36 ML at 90 K, acetic acid adsorbs mostly molecularly. Above this coverage, a physisorbed layer is formed with dimers and catemers, without detectable monomers. Dimers and catemers desorb as molecular acetic acid at 157 and 172 K, respectively. Between 90 and 200 K, the O–H bond in acetic acid breaks to form bridge-bonded bidentate acetate that becomes the dominant surface species. Desorption-limited hydrogen evolution is observed at 265 K. However, even after the acetate formation, acetic acid desorbs molecularly at 200–300 K due to recombination. Minor surface species observed at 200 K, acetyls or acetates with a carbonyl group, decompose below 350 K and generate adsorbed carbon monoxide. At 350 K, the surface likely undergoes restructuring, the extent of which increases with acetic acid coverage. The initial dominant bridge-bonded bidentate acetate species formed below 200 K remain on the surface, but they now mostly adsorb on the restructured sites. Here, the acetates and all other remaining hydrocarbon species decompose simultaneously at 425 K in a narrow temperature range with concurrent evolution of hydrogen, carbon monoxide, and carbon dioxide. Above 425 K, only carbon remains on the surface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Aggregation of Size-Selected Oxide Clusters Deposited onto Au(111)

Kinetic Monte Carlo (kMC) simulations along with density functional theory (DFT) calculations were used to investigate the aggregation of size-selected Nb 3 O y (y = 5, 6, 7) clusters deposited onto the Au(111) surface. Recent STM experiments showed that the cluster binding sites and sizes of the cluster assemblies on the Nb 3 O y /Au(111) surfaces strongly depend on the stoichiometry of the clusters, i.e., the oxygen-to-niobium ratio. To better understand the origins of these differences, kMC simulations of the nucleation and growth of cluster assemblies were performed using energy barriers for diffusion and intercluster interactions estimated from DFT calculations of cluster binding and dimerization energies, respectively. Comparisons of the kMC simulations with STM images of the as-deposited Nb 3 O y /Au(111) surfaces at RT and after high temperature annealing were used to further optimize the energetics and gauge the importance of nearest neighbor interactions. The kMC simulations demonstrate that the assembly of Nb 3 O y clusters on Au(111) are largely controlled by the magnitude of the barriers for diffusion and interparticle-bond formation, while changes at higher temperatures are sensitive to the binding energies between nearest neighbors. Simulations for the Nb 3 O 5 and Nb 3 O 6 clusters, which exhibit smaller cluster assembly sizes in STM, required larger diffusion barriers as well as different barriers for interparticle binding, which reflected differences in DFT calculated dimerization energies. Furthermore, the results demonstrate the effectiveness of combined DFT and kMC calculations for understanding how the stoichiometry affects the aggregation of small oxide clusters on a metal surface.

36 MATERIALS SCIENCE↗