Tight-binding potentials for transition metals and alloys

An efficient genetic algorithm for structure prediction at the nanoscale

We have developed and implemented a new global optimization technique based on a Lamarckian genetic algorithm with the focus on structure diversity. The key process in the efficient search on a given complex energy landscape proves to be the removal of duplicates that is achieved using a topological analysis of candidate structures. The careful geometrical prescreening of newly formed structures and the introduction of new mutation move classes improve the rate of success further. The power of the developed technique, implemented in the Knowledge Led Master Code, or KLMC, is demonstrated by its ability to locate and explore a challenging double funnel landscape of a Lennard-Jones 38 atom system (LJ₃₈). We apply the redeveloped KLMC to investigate three chemically different systems: ionic semiconductor (ZnO)_1-32, metallic Ni₁₃ and covalently bonded C₆₀. All four systems have been systematically explored on the energy landscape defined using interatomic potentials. The new developments allowed us to successfully locate the double funnels of LJ₃₈, find new local and global minima for ZnO clusters, extensively explore the Ni₁₃ and C₆₀ (the buckminsterfullerene, or buckyball) potential energy surfaces.

Metal Ion Modeling Using Classical Mechanics

Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.

Atomic structure of Mg-based metallic glasses from molecular dynamics and neutron diffraction

We use a combination of classical molecular dynamics simulation and neutron diffraction to identify the atomic structure of five different Mg–Zn–Ca bulk metallic glasses, covering a range of compositions with substantially different behaviour when implantedin vitro.

An adaptive mutation simulated annealing based investigation of Coulombic explosion and identification of dissociation patterns in (CO2)n2+ clusters

In this communication, we would like to discuss the advantages of adaptive mutation simulated annealing (AMSA) over standard simulated annealing (SA) in studying the Coulombic explosion of (CO₂)_n²⁺ clusters for n = 20–68, where ‘n’ is the size of the cluster.

Vibrational density of states and thermodynamics at the nanoscale: the 3D-2D transition in gold nanostructures

Surface enhanced Raman scattering (SERS) is generally and widely used to enhance the vibrational fingerprint of molecules located at the vicinity of noble metal nanoparticles. In this work, SERS is originally used to enhance the own vibrational density of states (VDOS) of nude and isolated gold nanoparticles. This offers the opportunity of analyzing finite size effects on the lattice dynamics which remains unattainable with conventional techniques based on neutron or x-ray inelastic scattering. By reducing the size down to few nanometers, the role of surface atoms versus volume atoms become dominant, and the “text-book” 3D-2D transition on the dynamical behavior is experimentally emphasized. “Anomalies” that have been predicted by a large panel of simulations at the atomic scale, are really observed, like the enhancement of the VDOS at low frequencies or the occurrence of localized modes at frequencies beyond the cut-off in bulk. Consequences on the thermodynamic properties at the nanoscale, like the reduction of the Debye temperature or the excess of the specific heat, have been evaluated. Finally the high sensitivity of reminiscent bulk-like phonons on the arrangements at the atomic scale is used to access the morphology and internal disorder of the nanoparticles.

Controlling Structural Transitions in AuAg Nanoparticles through Precise Compositional Design

We present a study of the transitional pathways between high-symmetry structural motifs for AgAu nanoparticles, with a specific focus on controlling the energetic barriers through chemical design. We show that the barriers can be altered by careful control of the elemental composition and chemical arrangement, with core@shell and vertex-decorated arrangements being specifically influential on the barrier heights. We also highlight the complexity of the potential and free energy landscapes for systems where there are low-symmetry geometric motifs that are energetically competitive to the high-symmetry arrangements. In particular, we highlight that some core@shell arrangements preferentially transition through multistep restructuring of low-symmetry truncated octahedra and rosette-icosahedra, instead of via the more straightforward square-diamond transformations, due to lower energy barriers and competitive energetic minima. Our results have promising implications for the continuing efforts in bespoke nanoparticle design for catalytic and plasmonic applications.

Impurity effects on solid-solid transitions in atomic clusters

We use the harmonic superposition approach to examine how a single atom substitution affects low-temperature anomalies in the vibrational heat capacity (C_V) of model nanoclusters. Each anomaly is linked to competing solidlike "phases", where crossover of the corresponding free energies defines a solid-solid transition temperature (T_s). For selected Lennard-Jones clusters we show that T_s and the corresponding C_V peak can be tuned over a wide range by varying the relative atomic size and binding strength of the impurity, but excessive atom-size mismatch can destroy a transition and may produce another. In some tunable cases we find up to two additional C_V peaks emerging below T_s, signalling one- or two-step delocalisation of the impurity within the ground-state geometry. Results for Ni₇₄X and Au₅₄X clusters (X = Au, Ag, Al, Cu, Ni, Pd, Pt, Pb), modelled by the many-body Gupta potential, further corroborate the possibility of tuning, engineering, and suppressing finite-system analogues of a solid-solid transition in nanoalloys.

Constraints on phase stability, defect energies, and elastic constants of metals described by EAM-type potentials

We demonstrate that the embedded-atom method and related potentials predict many dimensionless properties of simple metals to depend predominantly on a single coefficient μ, which typically lies between 0.3 and 0.45. Among other relations presented in this work, we find that [Formula: see text], [Formula: see text], and [Formula: see text] hold within 25% accuracy and also find a linear dependence of the melting temperature on μ. The used variables are cohesive energy E c, coordination number Z, vacancy energy E v, and bulk modulus B, while G is the average of ordinary and tetragonal shear modulus. We provide analytical arguments for these findings, which are obeyed reasonably well by several metals.

Reconciling simulated melting and ground-state properties of metals with a modified embedded-atom method potential

We propose a modification of the embedded-atom method-type potential aiming at reconciling simulated melting and ground-state properties of metals by means of classical molecular dynamics. Considering titanium, magnesium, gold, and platinum as case studies, we demonstrate that simulations performed with the modified force field yield quantitatively correctly both the melting temperature of the metals and their ground-state properties. It is shown that the accounting for the long-range interatomic interactions noticeably affects the melting point assessment. The introduced modification weakens the interaction at interatomic distances exceeding the equilibrium one by a characteristic vibration amplitude defined by the Lindemann criterion, thus allowing for the correct simulation of melting, while keeping its behavior in the vicinity of the ground state minimum. The modification of the many-body potential has a general nature and can be applicable to metals with different characteristics of the electron structure as well as for many different molecular and solid state systems experiencing phase transitions.

Phase diagram and segregation of Ag-Co nanoalloys: insights from theory and simulation

Understanding the phase diagram is the first step to identifying the structure-performance relationship of a material at the nanoscale. In this work, a modified nanothermodynamical model has been developed to predict the phase diagrams of Ag-Co nanoalloys with the size of 1 ∼ 100 nm, which also overcomes the difference in the predicted results between theory and simulation for the first time. Based on this modified model, the phase diagrams of Ag-Co nanoalloys with various polyhedral morphologies (tetrahedron, cube, octahedron, decahedron, dodecahedron, rhombic dodecahedron, truncated octahedron, cuboctahedron, and icosahedron) have been predicted, showing good agreement with molecular dynamics simulations at the nanoscale of 1 ∼ 4 nm. In addition, the surface segregation of Ag-Co nanoalloys has been predicted with a Co-rich core/Ag-rich surface, which is also consistent with the simulation results. Our results highlight a useful roadmap for bridging the difference between theory and simulation in the prediction of the phase diagram at the nanoscale, which will help both theorists and experimentalists.

Passive fluidic diode for simple fluids using nested nanochannel structures

In this paper, we propose a moving part-free fluidic diode for simple fluids using nested nanochannels, which contain inner and outer channels of different lengths. Molecular dynamics simulations show that the fluidic diode accepts water flows in the forward direction and blocks flows in the backward direction in a wide range of pressure drops. The anisotropic flow rates are generated by the distinct activation pressures in different directions. In the forward direction, the activation pressure is low, which is determined by the infiltration pressure of the inner channel. In the backward direction, the activation pressure is quite high due to the capillary effects when flows are released from the inner to the outer channel. The pressure drop range for the fluidic diode can be varied by changing the channel size or surface wettability. The fluidic diode offers an alternative way for flow control in integrated micro- and nanofluidic devices.

Pd surface and Pt subsurface segregation in Pt1-c Pd c nanoalloys

The structure and chemical arrangement of Pt1-c Pd c nanoalloys with the icosahedral and face centered cubic symmetry are studied using Monte Carlo simulations with a tight binding interatomic potential fitted to density-functional theory calculations. Pd surface segregation from the lowest to the highest coordinated sites is predicted by the theory together with a Pt enrichment at the subsurface, whatever the structure and the size of the nanoparticles, and which subsists when increasing the temperature. The onion-shell chemical configuration is found for both symmetries and is initiated from the Pd surface segregation. It is amplified in the icosahedral symmetry and small sizes but when considering larger sizes, the oscillating segregation profile occurs near the surface on about three to four shells whatever the structure. Pd segregation results from the significant lower cohesive energy of Pd as compared to Pt and the weak ordering tendency leads to the Pt subsurface segregation. The very weak size mismatch does not prevent the bigger atoms (Pt) from occupying subsurface sites which are in compression whereas the smaller ones (Pd) occupy the central site of the icosahedra where the compression is an order of magnitude higher.

Molecular dynamics of sialic acid analogues complex with cholera toxin and DFT optimization of ethylene glycol-mediated zinc nanocluster conjugation

Cholera is an infectious disease caused by cholera toxin (CT) protein of bacterium Vibrio cholerae. A sequence of sialic acid (N-acetylneuraminic acid, NeuNAc or Neu5Ac) analogues modified in its C-5 position is modelled using molecular modelling techniques and docked against the CT followed by molecular dynamics simulations. Docking results suggest better binding affinity of NeuNAc analogue towards the binding site of CT. The NeuNAc analogues interact with the active site residues GLU:11, TYR:12, HIS:13, GLY:33, LYS:34, GLU:51, GLN:56, HIE:57, ILE:58, GLN:61, TRP:88, ASN:90 and LYS:91 through intermolecular hydrogen bonding. Analogues N-glycolyl-NeuNAc, N-Pentanoyl-NeuNAc and N-Propanoyl-NeuNAc show the least XPGscore (docking score) of -9.90, -9.16, and -8.91, respectively, and glide energy of -45.99, -42.14 and -41.66 kcal/mol, respectively. Stable nature of CT-N-glycolyl-NeuNAc, CT-N-Pentanoyl-NeuNAc and CT-N-Propanoyl-NeuNAc complexes was verified through molecular dynamics simulations, each for 40 ns using the software Desmond. All the nine NeuNAc analogues show better score for drug-like properties, so could be considered as suitable candidates for drug development for cholera infection. To improve the enhanced binding mode of NeuNAc analogues towards CT, the nine NeuNAc analogues are conjugated with Zn nanoclusters through ethylene glycol (EG) as carriers. The NeuNAc analogues conjugated with EG-Zn nanoclusters show better binding energy towards CT than the unconjugated nine NeuNAc analogues. The electronic structural optimization of EG-Zn nanoclusters was carried out for optimizing their performance as better delivery vehicles for NeuNAc analogues through density functional theory calculations. These sialic acid analogues may be considered as novel leads for the design of drug against cholera and the EG-Zn nanocluster may be a suitable carrier for sialic acid analogues.

Size-dependent strain and surface energies of gold nanoclusters

Calculation of size-dependent strain and surface energies of gold nanoparticles.

Structure and stability of neutral Al–Mg nanoclusters up to 55 atoms

The geometries of aluminum–magnesium nanoalloys are explored using a genetic algorithm tuned to search for the 10 lowest energy minima for each cluster size and composition.

Growth patterns and structural motifs of cadmium clusters with up to 60 atoms: disordered or not?

A new growth pattern in small to medium-sized cadmium clusters based on the Leary tetrahedron is predicted.

Atomistic Design of Favored Compositions for Synthesizing the Al-Ni-Y Metallic Glasses

For a ternary alloy system promising for obtaining the so-called bulk metallic glasses (BMGs), the first priority issue is to predict the favored compositions, which could then serve as guidance for the appropriate alloy design. Taking the Al-Ni-Y system as an example, here we show an atomistic approach, which is developed based on a recently constructed and proven realistic interatomic potential of the system. Applying the Al-Ni-Y potential, series simulations not only clarify the glass formation mechanism, but also predict in the composition triangle, a hexagonal region, in which a disordered state, i.e., the glassy phase, is favored energetically. The predicted region is defined as glass formation region (GFR) for the ternary alloy system. Moreover, the approach is able to calculate an amorphization driving force (ADF) for each possible glassy alloy located within the GFR. The calculations predict an optimized sub-region nearby a stoichiometry of Al₈₀Ni₅Y₁₅, implying that the Al-Ni-Y metallic glasses designed in the sub-region could be the most stable. Interestingly, the atomistic predictions are supported by experimental results observed in the Al-Ni-Y system. In addition, structural origin underlying the stability of the Al-Ni-Y metallic glasses is also discussed in terms of a hybrid packing mode in the medium-range scale.

Nanofluidic Diode for Simple Fluids without Moving Parts

The fabrication of small scale, fixed structure fluidic diodes for simple fluids is quite challenging and has not yet been achieved. Here, we fabricate a moving part-free nanofluidic diode for simple fluids using heterogeneous nanochannels, half of which is hydrophilic and the other half is hydrophobic. It accepts water flows in the forward (from hydrophilic to hydrophobic) direction, while the flows in the backward direction are blocked for pressure drop range 0<ΔP<0.63 MPa. The diode is ensured by a potential energy barrier at the channel entrance on the hydrophobic side due to the molecular interactions between the water and channel surface. As the upstream pressure becomes higher than 0.63 MPa, the fluidic diode turns to be a rectifier, which allows flows in both the forward and backward directions but with different flow rates. At sufficiently high driving pressures, the fluidic system fails in flow rectification, analogous to the breakdown of electronic diodes. The three different flow modes (diode, rectifier, and breakdown) of the fluidic chip and the underlying rectification mechanisms are confirmed by molecular dynamics simulations.

The Birmingham parallel genetic algorithm and its application to the direct DFT global optimisation of Ir(N) (N = 10-20) clusters

A new open-source parallel genetic algorithm, the Birmingham parallel genetic algorithm, is introduced for the direct density functional theory global optimisation of metallic nanoparticles. The program utilises a pool genetic algorithm methodology for the efficient use of massively parallel computational resources. The scaling capability of the Birmingham parallel genetic algorithm is demonstrated through its application to the global optimisation of iridium clusters with 10 to 20 atoms, a catalytically important system with interesting size-specific effects. This is the first study of its type on Iridium clusters of this size and the parallel algorithm is shown to be capable of scaling beyond previous size restrictions and accurately characterising the structures of these larger system sizes. By globally optimising the system directly at the density functional level of theory, the code captures the cubic structures commonly found in sub-nanometre sized Ir clusters.

How to derive tight-binding spd potentials? Application to zirconium

We propose here a general methodology to derive tight-binding potentials accounting for spd hybridization in transition metals, dealing simultaneously with electronic structure and energy properties. This methodology is illustrated for zirconium which is largely used for technological applications, in particular in the nuclear industry, and whose modelling is known to be complex and challenging. Such potentials are very promising. Their fits have a clear physical meaning with a limited amount of parameters and their complexity can be adjusted as a function of the problem under consideration.

Global optimization and oxygen dissociation on polyicosahedral Ag32Cu6 core-shell cluster for alkaline fuel cells

The structure of 38 atoms Ag-Cu cluster is studied by using a combination of a genetic algorithm global optimization technique and density functional theory (DFT) calculations. It is demonstrated that the truncated octahedral (TO) Ag32Cu6 core-shell cluster is less stable than the polyicosahedral (pIh) Ag32Cu6 core-shell cluster from the atomistic models and the DFT calculation shows an agreeable result, so the newfound pIh Ag32Cu6 core-shell cluster is further investigated for potential application for O2 dissociation in oxygen reduction reaction (ORR). The activation energy barrier for the O2 dissociation on pIh Ag32Cu6 core-shell cluster is 0.715 eV, where the d-band center is -3.395 eV and the density of states at the Fermi energy level is maximal for the favorable absorption site, indicating that the catalytic activity is attributed to a maximal charge transfer between an oxygen molecule and the pIh Ag32Cu6 core-shell cluster. This work revises the earlier idea that Ag32Cu6 core-shell nanoparticles are not suitable as ORR catalysts and confirms that Ag-Cu nanoalloy is a potential candidate to substitute noble Pt-based catalyst in alkaline fuel cells.

Strain-Induced Segregation in Bimetallic Multiply Twinned Particles

We analyze the possibility of strain-induced segregation in bimetallic multiply twinned particles by an analytic first-order expansion within a continuum model. The results indicate that while the change in free energy may be small, there will be a noticeable segregation of larger atoms to the external surface and smaller ones to the core, which could have interesting effects when such nanoparticles are used as heterogeneous catalysts.

Molecular dynamics simulation of the deposition process of cold Ag-clusters under different landing conditions

We present a series of molecular dynamics simulations on the surface deposition process of initially free silver clusters (Agn) with different sizes (n = 100-2000) and morphologies. During the whole deposition process the morphology of the clusters was studied as a function of the landing conditions. These conditions include variations of the depth and range of the substrate potential as well as the thermal coupling to the surface and a variation of the impact velocity of the free clusters. Depending on the applied conditions the clusters' final form ranges from spread out fragments via deformed and restructured heaps to quasi unchanged spherical clusters sitting at the surface. Under certain landing conditions larger clusters retain their initial multiply twinned morphology upon deposition, while smaller ones undergo structural transitions to form single domain particles. Furthermore, the occurrence of a structural transition depends on the initial structure-initially decahedral clusters tend to conserve their morphology better than icosahedral ones. The same behavior can also be observed in our experiments, where silver clusters were grown in helium nanodroplets and subsequently deposited on amorphous carbon substrates.

Quasi-combinatorial energy landscapes for nanoalloy structure optimisation

We formulate nanoalloy structure prediction as a mixed-variable optimisation problem, where the homotops can be associated with an effective, quasi-combinatorial energy landscape in permutation space. We survey this effective landscape for a representative set of binary systems modelled by the Gupta potential. In segregating systems with small lattice mismatch, we find that homotops have a relatively straightforward landscape with few local optima - a scenario well-suited for local (combinatorial) optimisation techniques that scale quadratically with system size. Combining these techniques with multiple local-neighbourhood structures yields a search for multiminima, and we demonstrate that generalised basin-hopping with a metropolis acceptance criterion in the space of multiminima can then be effective for global optimisation of binary and ternary nanoalloys.

Surface specific heats of metal nanocrystals at low temperatures

In order to quantitatively explain the enhanced specific heat of metal nanocrystals measured from 4.2 K to 80 K, an analytical expression has been deduced to determine the surface specific heat in nanocrystals, which is proportional to T(2.5) at low temperatures. The consequently calculated specific heat and surface Debye temperature of copper nanocrystals are in good agreement with the experimental data. This explains why the experimental specific heat of copper nanocrystals is enhanced with respect to the bulk and why it exhibits a different feature as a function of temperature from that of the bulk at low temperatures. The first experimental evidence is presented that the spatial dimension of surfaces should be neither pure 2D nor 3D, but between 2D and 3D, due to the effect of atoms in the core of the nanocrystals.

Fluid infiltration pressure for hydrophobic nanochannels

We investigate water infiltration pressure for hydrophobic nanochannels through molecular dynamics simulations. It is found that the entrance energy barrier significantly raises the infiltration pressure, which makes the classic Young-Laplace equation invalid for nanochannels. As the channel surface is tuned from superhydrophobic to hydrophobic, the infiltration pressure is greatly reduced mainly due to the decrease of the capillary pressure (Young-Laplace equation) caused by the contact angle change, while the contribution of the entrance energy barrier to the infiltration pressure, which is termed entrance barrier pressure, increases from 25% to 60%.

Vibrational properties and specific heat of core–shell Ag–Au icosahedral nanoparticles

The vibrational density of states (VDOS) of metal nanoparticles can be a fingerprint of their geometrical structure and determine their low-temperature thermal properties.

Theoretical study of the structures and chemical ordering of cobalt–palladium nanoclusters

Global optimization of 1 : 1 compositions of (Co–Pd)_N/2 up to N = 150 and all compositions of 34- and 38-atom binary clusters has been performed using a genetic algorithm, coupled with the Gupta empirical potential to model interatomic interactions.