0000000001203533
AUTHOR
Jaakko Akola
Density functional study of Cu2+-phenylalanine complex under micro-solvation environment
Abstract We present an atomistic study carried out using density functional calculations including structural relaxations and Car–Parrinello Molecular Dynamics (CPMD) simulations, aiming to investigate the structures of phenylalanine-copper (II) ([Phe-Cu] 2+ ) complexes and their micro-solvation processes. The structures of the [Phe-Cu] 2+ complex with up to four water molecules are optimized using the B3LYP/6-311++G** model in gas phase to identify the lowest energy structures at each degree of solvation ( n = 0–4). It is found that the phenylalanine appears to be in the neutral form in isolated and mono-hydrated complexes, but in the zwitterionic form in other hydrated complexes (with n …
First-principles simulations of hydrogen peroxide formation catalyzed by small neutral gold clusters.
Energetics and dynamical pathways for hydrogen peroxide formation from H(2) and O(2) bound to neutral gold dimers and tetramers have been investigated by applying several strategies: T = 0 K geometry optimizations, constrained Car-Parrinello molecular dynamics simulations at T = 300 K and metadynamics at T = 300 K. The competing reaction channels for water and hydrogen peroxide formation have been found and characterized. In each case, the reaction barriers for Au cluster catalyzed proton transfer are less than 1 eV. Water formation is a competitive reaction channel, and the relative weight of H(2)O and H(2)O(2) products may depend on the chosen Au cluster size. Dynamic simulations demonstr…
Metallic evolution of small magnesium clusters
Structural and electronic properties of small magnesium clusters (N≤13) are studied using a first-principles simulation method in conjunction with the density functional theory and generalized gradient correction approximation for the exchange-correlation energy functional. It is observed that the onset of metallization of magnesium clusters is hard to assign since both the s-p hybridization and the energy gap between the valence and conduction bands do not evolve rapidly towards the known bulk properties. Instead these quantities show a slow and nonmonotonic evolution.
CLEASE: a versatile and user-friendly implementation of cluster expansion method
Materials exhibiting a substitutional disorder such as multicomponent alloys and mixed metal oxides/oxyfluorides are of great importance in many scientific and technological sectors. Disordered materials constitute an overwhelmingly large configurational space, which makes it practically impossible to be explored manually using first-principles calculations such as density functional theory due to the high computational costs. Consequently, the use of methods such as cluster expansion (CE) is vital in enhancing our understanding of the disordered materials. CE dramatically reduces the computational cost by mapping the first-principles calculation results on to a Hamiltonian which is much fa…
Quantum size effects in ambient CO oxidation catalysed by ligand-protected gold clusters
Finely dispersed nanometre-scale gold particles are known to catalyse several oxidation reactions in aerobic, ambient conditions. The catalytic activity has been explained by various complementary mechanisms, including support effects, particle-size-dependent metal-insulator transition, charging effects, frontier orbital interactions and geometric fluxionality. We show, by considering a series of robust and structurally well-characterized ligand-protected gold clusters with diameters between 1.2 and 2.4 nm, that electronic quantum size effects, particularly the magnitude of the so-called HOMO-LUMO energy gap, has a decisive role in binding oxygen to the nano-catalyst in an activated form. T…
Structural phase transitions on the nanoscale: The crucial pattern in the phase-change materialsGe2Sb2Te5and GeTe
Phase-change materials are of immense importance for optical recording and computer memory, but the structure of the amorphous phases and the nature of the phase transition in the nanoscale bits pose continuing challenges. Massively parallel density functional simulations have been used to characterize the amorphous structure of the prototype materials ${\mathrm{Ge}}_{2}{\mathrm{Sb}}_{2}{\mathrm{Te}}_{5}$ and GeTe. In both, there is long-ranged order among Te atoms and the crucial structural motif is a four-membered ring with alternating atoms of types $A$ (Ge and Sb) and $B$ (Te), an ``$ABAB$ square.'' The rapid amorphous-to-crystalline phase change is a reorientation of disordered $ABAB$ …
Cationic Au Nanoparticle Binding with Plasma Membrane-like Lipid Bilayers: Potential Mechanism for Spontaneous Permeation to Cells Revealed by Atomistic Simulations
Despite being chemically inert as a bulk material, nanoscale gold can pose harmful side effects to living organisms. In particular, cationic Au nanoparticles (AuNP+) of 2 nm diameter or less permeate readily through plasma membranes and induce cell death. We report atomistic simulations of cationic Au nanoparticles interacting with realistic membranes and explicit solvent using a model system that comprises two cellular compartments, extracellular and cytosolic, divided by two asymmetric lipid bilayers. The membrane-AuNP+ binding and membrane reorganization processes are discovered to be governed by cooperative effects where AuNP+, counterions, water, and the two membrane leaflets all contr…
A unified view of ligand-protected gold clusters as superatom complexes
Synthesis, characterization, and functionalization of self-assembled, ligand-stabilized gold nanoparticles are long-standing issues in the chemistry of nanomaterials. Factors driving the thermodynamic stability of well documented discrete sizes are largely unknown. Herein, we provide a unified view of principles that underlie the stability of particles protected by thiolate (SR) or phosphine and halide (PR 3 , X) ligands. The picture has emerged from analysis of large-scale density functional theory calculations of structurally characterized compounds, namely Au 102 (SR) 44 , Au 39 (PR 3 ) 14 X 6 − , Au 11 (PR 3 ) 7 X 3 , and Au 13 (PR 3 ) 10 X 2 3+ , where X is either a halogen or a thiol…
Bright Beaches of Nanoscale Potassium Islands on Graphite in STM Imaging
We demonstrate, via scanning tunneling microscopy (STM) measurements performed at 48 K, the existence of "bright beaches" at the edges of K islands (diameter approximately 5-500 nm) on the graphite surface. The enhanced tunneling current is only observed in monolayer-high islands on graphite, and not in islands of similar geometry on top of a K monolayer film. First-principles density functional calculations and STM simulations suggest that this is an STM field effect, which appears as the positive tip attracts donated electrons back to the metallic K islands. The restored charge accumulates preferentially at the island edges.
Structure and dynamics in amorphous tellurium and Te-n clusters: A density functional study
Density functional/molecular dynamics simulations have been performed on amorphous tellurium (a meltquenched sample of 343 atoms at 300 K) and on Te clusters with up to 16 atoms. The former extend our calculations on liquid Te at 560, 625, 722, and 970 K [Phys. Rev. B 81, 094202 (2010)]. We discuss trends in structures (including those of other group-16 elements), electronic densities of states, and vibration frequencies. Chain structures are common in S and Se, but the chains in amorphous Te are short, and branching sites with threefold-coordinated atoms are common. The energy difference between two- and threefold local coordination depends sensitively on the exchange-correlation functiona…
Experimentally constrained density-functional calculations of the amorphous structure of the prototypical phase-change materialGe2Sb2Te5
Phase change materials involve the rapid and reversible transition between nanoscale amorphous $(a\text{\ensuremath{-}})$ and crystalline $(c\text{\ensuremath{-}})$ spots in a polycrystalline film and play major roles in the multimedia world, including nonvolatile computer memory. The materials of choice are alloys of Ge, Sb, and Te, e.g., ${\text{Ge}}_{2}{\text{Sb}}_{2}{\text{Te}}_{5}$ (GST) in digital versatile disk--random access memory. There has been much speculation about the structure of $a\text{\ensuremath{-}}$ GST, but no model has yet received general acceptance. Here we optimize the structure by combining the results of density-functional calculations with high-energy x-ray diffr…
On the Structure of Thiolate-Protected Au25
Density functional theory is used to explore the structure of Au25(RS)18. The preferred structure consists of an icosahedral Au13 core protected by 6 RS-Au-RS-Au-RS units. The enhanced stability of the structure as an anion is found to originate from closure of an eight-electron shell for delocalized Au(6s) electrons. The evaluated XRD pattern and optical spectra are in good agreement with experimental data.
Structure and dynamics in amorphous tellurium and Te-n clusters: A density functional study
Density functional/molecular dynamics simulations have been performed on amorphous tellurium (a melt-quenched sample of 343 atoms at 300 K) and on Te clusters with up to 16 atoms. The former extend our calculations on liquid Te at 560, 625, 722, and 970 K [Phys. Rev. B 81, 094202 (2010)]. We discuss trends in structures (including those of other group-16 elements), electronic densities of states, and vibration frequencies. Chain structures are common in S and Se, but the chains in amorphous Te are short, and branching sites with threefold-coordinated atoms are common. The energy difference between two- and threefold local coordination depends sensitively on the exchange-correlation function…
Real-space Wigner-Seitz Cells Imaging of Potassium on Graphite via Elastic Atomic Manipulation
Atomic manipulation in the scanning tunnelling microscopy, conventionally a tool to build nanostructures one atom at a time, is here employed to enable the atomic-scale imaging of a model low-dimensional system. Specifically, we use low-temperature STM to investigate an ultra thin film (4 atomic layers) of potassium created by epitaxial growth on a graphite substrate. The STM images display an unexpected honeycomb feature, which corresponds to a real-space visualization of the Wigner-Seitz cells of the close-packed surface K atoms. Density functional simulations indicate that this behaviour arises from the elastic, tip-induced vertical manipulation of potassium atoms during imaging, i.e. el…
Ionization potential of Al6 and Al7 as a function of temperature
The temperature-depence of the ionization potential of Al6 and Al7 clusters is studied by using ab initio molecular dynamics. The threshold regions of theoretical photoionization efficiency curves are obtained from the calculated ionization potential distributions by integration and the determined ionization potentials are compared with the experimental ones. Two important effects, which complicate the determination of ionization potential from photoionization efficiency curves, are observed: the thermal tail effect and the isomerization. Also a link between the adiabatic ionization potential and the threshold of the photoionization efficiency curve is discussed. In the case of Al7, this of…
Silver Sulfide Nanoclusters and the Superatom Model
The superatom model of electron-shell closings has been widely used to explain the stability of noble-metal nanoclusters of few nanometers, including thiolate-protected Au and Ag nanoclusters. The presence of core sulfur atoms in silver sulfide (Ag–S) nanoclusters renders them a class of clusters with distinctive properties as compared to typical noble-metal clusters. Here, it is natural to ask whether the superatom model is still applicable for the Ag–S nanoclusters with mixed metal and nonmetal core atoms. To address this question, we applied density functional simulations to analyze a series of Ag–S nanoclusters: Ag14S(SPh)12(PPh3)8, Ag14(SC6H3F2)12(PPh3)8, Ag70S16(SPh)34(PhCO2)4(triphos…
Electronic structure of triangular, hexagonal and round graphene flakes near the Fermi level
The electronic shell structure of triangular, hexagonal and round graphene quantum dots (flakes) near the Fermi level has been studied using a tight-binding method. The results show that close to the Fermi level the shell structure of a triangular flake is that of free massless particles, and that triangles with an armchair edge show an additional sequence of levels ("ghost states"). These levels result from the graphene band structure and the plane wave solution of the wave equation, and they are absent for triangles with an zigzag edge. All zigzag triangles exhibit a prominent edge state at the Fermi level, and few low-energy conduction electron states occur both in triangular and hexagon…
Electronic properties of single-walled carbon nanotubes inside cyclic supermolecules
Possible ways for manipulating carbon nanotubes (CNTs) with cyclic supermolecules are studied using density functional theory. Electronic structure calculations with structure optimizations have been performed for the (4,4) and (8,0) single-walled carbon nanotubes (SWNTs) complexed with crown ethers as well as for the (4,0) SWNT with beta-cyclodextrin. A slight polarization of charge in both the nanotube and the supermolecule is observed upon rotaxane complexation, but the interaction is mainly repulsive, and the systems stay 2.8-3.5 A apart. The supermolecule does not affect the electronic band structure of the nanotube significantly within such a configuration. The situation differs notic…
Ionization potential of aluminum clusters
Structure, electronic structure, and ionization potential of aluminum clusters of 2–23 atoms are studied with a total energy method based on the density-functional theory. The calculated adiabatic ionization potentials agree remarkably well with the data from threshold photoionization measurements. The analysis of results gives insight into hybridization effects in the smallest clusters as well as reveals certain clusters that exhibit a clear jellium-type shell structure. An explanation of the experimental results in the size region of 12–23 atoms is given in terms of coexisting, competing icosahedral, decahedral, and fcc-based clusters. @S0163-1829~98!00228-8#
Structure and dynamics in liquid bismuth and Bin clusters: A density functional study
Density functional/molecular dynamics simulations with more than 500 atoms have been performed on liquid bismuth at 573, 773, 923, and 1023 K and on neutral Bi clusters with up to 14 atoms. There are similar structural patterns (coordination numbers, bond angles, and ring patterns) in the liquid and the clusters, with significant differences from the rhombohedral crystalline form. We study the details of the structure (structure factor, pair, and cavity distribution functions) and dynamical properties (vibration frequencies, diffusion constants, power spectra), and compare with experimental results where available. While the three short covalent bonds typical to pnictogens are characteristi…
Nucleus-driven crystallization of amorphous Ge2Sb2Te5: A density functional study
Early stages of nucleus-driven crystallization of the prototype phase change material Ge${}_{2}$Sb${}_{2}$Te${}_{5}$ have been studied by density functional/molecular dynamics simulations for amorphous samples (460 and 648 atoms) at 500, 600, and 700 K. All systems assumed a fixed cubic seed of 58 atoms and 6 vacancies. Crystallization occurs within 600 ps for the 460-atom system at 600 and 700 K, and signs of crystallization (nucleus growth, percolation) are present in the others. Crystallization is accompanied by an increase in the number of ``$ABAB$ squares'' ($A$: Ge, Sb, $B$: Te), and atoms of all elements move significantly. There is no evidence of cavity movement to the crystal-glass…
Density functional study of gold atoms and clusters on a graphite (0001) surface with defects
Adsorption of gold atoms and clusters $(N=6)$ on a graphite (0001) surface with defects has been studied using density functional theory. In addition to perfect graphite (0001), three types of surface defects have been considered: a surface vacancy (hole), a pyridinelike defect comprising three grouped nitrogen atoms, and a substitutional doping by N or B. Results for Au and ${\mathrm{Au}}_{6}$ indicate that the surface vacancy can form chemical bonds with Au as the three nearby carbons align their dangling bonds towards the gold particle (binding energy 2.4--$2.6\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$). A similar chemically saturated holelike construction with three pyridinic N atoms resul…
Structure of amorphousGe8Sb2Te11:GeTe-Sb2Te3alloys and optical storage
The amorphous structure of ${\text{Ge}}_{8}{\text{Sb}}_{2}{\text{Te}}_{11}$, an alloy used in the Blu-ray Disc, the de facto successor to digital versatile disk (DVD) optical storage, has been characterized by large-scale (630 atoms, 0.4 ns) density-functional/molecular-dynamics simulations using the new PBEsol approximation for the exchange-correlation energy functional. The geometry and electronic structure agree well with available x-ray diffraction data and photoelectron measurements. The total coordination numbers are Ge: 4.0, Sb: 3.7, and Te: 2.9, and the Ge-Ge partial coordination number is 0.7. Most atoms (particularly Sb) prefer octahedral coordination but 42% of Ge atoms are ``tet…
Aluminum cluster anions: Photoelectron spectroscopy andab initiosimulations
Atomic structures and geometries, electronic structure, and temperature-dependent photoelectron spectra of ${\mathrm{Al}}_{N}^{\ensuremath{-}} (N=19\ensuremath{-}102)$ clusters are studied both theoretically via ab initio local-density-functional simulations, and experimentally with high-resolution measurements. The use of a theoretically well-defined energy shift in conjunction with a generalized Koopmans' theorem enables direct comparisons between the calculated density of states and the experimental photoelectron spectrum. Such comparisons, using photoelectron spectra calculated for various relaxed cluster geometries, enables a determination of the optimal structures of the clusters. The…
Density variations in liquid tellurium: Roles of rings, chains and cavities
Liquid tellurium has been studied by density-functional/molecular-dynamics simulations at 560, 625, 722, and 970 K and by high-energy x-ray diffraction (HEXRD) at 763 K and 973 K. The HEXRD measurements agree very well with earlier neutron-scattering data of Menelle et al. The density maximum near the melting point (722 K) reflects the competition between twofold and threefold local coordination, which results in chain formation and changed ring statistics at lower $T$, and the variation with $T$ of the volume of cavities ($26--35\text{ }\mathrm{%}$ of the total). A higher-order gradient expansion of the exchange-correlation functional is needed to describe structural details. Changes in th…
Bright beaches of nanoscale potassium islands on graphite in STM imaging,
We demonstrate, via scanning tunneling microscopy (STM) measurements performed at 48 K, the existence of “bright beaches” at the edges of K islands (diameter ∼ 5 – 500 nm ) on the graphite surface. The enhanced tunneling current is only observed in monolayer-high islands on graphite, and not in islands of similar geometry on top of a K monolayer film. First-principles density functional calculations and STM simulations suggest that this is an STM field effect, which appears as the positive tip attracts donated electrons back to the metallic K islands. The restored charge accumulates preferentially at the island edges. peerReviewed
Aluminum-lithium clusters: First-principles simulation of geometries and electronic properties
The geometries and electronic properties of small lithium-rich ${\mathrm{Al}}_{N}{\mathrm{Li}}_{5N}$ $(N=1--6,10)$ clusters are studied using first-principles simulations. Aluminum ions form a compact inner core configuration in the clusters that changes into a chainlike skeleton embedded in a lithium surrounding as the cluster size increases. This behavior restricts $s\ensuremath{-}p$ hybridization effects and causes separate s and p bands in the electronic energy spectrum. A significant charge transfer from Li ions and nearby Al ions strengthens ionic Al-Li bonds, while Al-Al bonds gain a more covalent nature. The evolution of some bulk properties of $B2$ and $B32$ phases of AlLi alloys i…
Comment on “Formation of Large Voids in the Amorphous Phase-Change MemoryGe2Sb2Te5Alloy”
A Comment on the Letter by Zhimei Sun, Jian Zhou, Andreas Blomqvist, Borje Johansson, and Rajeev Ahuja, Phys. Rev. Lett. 102, 075504 (2009). The authors of the Letter offer a Reply. (See also preceding Comment and Reply in this issue.)
A density functional investigation of thiolate-protected bimetal PdAu24(SR)18z clusters: doping the superatom complex
Structure, electronic properties, optical absorption and charging properties of methylthiolate-protected bimetal PdAu(24)(SR)(18)(z) (R = Me) clusters with various charge states (-3or=zor= +3) are investigated by using density functional theory. The results are compared to properties of the well-understood singly anionic pure gold complex Au(25)(SR)(18)((-1)) [J. Akola, M. Walter, H. Häkkinen and H. Grönbeck, J. Am. Chem. Soc., 2008, 130, 3756]. The atomic structure of this all-gold complex can be written in a "divide-and-protect" way [H. Häkkinen, M. Walter and H. Grönbeck, J. Phys. Chem. B, 2006, 110, 9927] as Au(13)[Au(2)(SR)(3)](6)((-1)) where 6 v-shaped Au(2)(SR)(3) ligands protect the…
Probing the Atomic-Scale Structure of Monolayer-Protected Au38 Clusters
Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.
Edge-dependent selection rules in magic triangular graphene flakes
The electronic shell and supershell structure of triangular graphene quantum dots has been studied using density functional and tight-binding methods. The density functional calculations demonstrate that the electronic structure close to the Fermi energy is correctly described with a simple tight-binding model, where only the ${p}_{z}$ orbitals perpendicular to the graphene layer are included. The results show that (i) both at the bottom and at the top of the ${p}_{z}$ band, a supershell structure similar to that of free electrons confined in a triangular cavity is seen, (ii) close to the Fermi level, the shell structure is that of free massless particles, (iii) triangles with armchair edge…
Atomistic Simulations of Functional Au_{144}(SR)_{60} Gold Nanoparticles in Aqueous Environment
Charged monolayer-protected gold nanoparticles (AuNPs) have been studied in aqueous solution by performing atomistic molecular dynamics simulations at physiological temperature (310 K). Particular attention has been paid to electrostatic properties that modulate the formation of a complex comprised of the nanoparticle together with surrounding ions and water. We focus on Au-144 nanoparticles that comprise a nearly spherical Au core (diameter similar to 2 nm), a passivating Au-S interface, and functionalized alkanethiol chains. Cationic and anionic AuNPs have been modeled with amine and carboxyl terminal groups and Cl-/Na+ counterions, respectively. The radial distribution functions show tha…
Amorphous Ge15Te85: density functional, high-energy x-ray and neutron diffraction study
The structure and electronic properties of amorphous Ge15Te85 have been studied by combining density functional (DF) simulations with high-energy x-ray and neutron diffraction measurements. Three models with 560 atoms have been constructed using reverse Monte Carlo methods constrained to (1) agree with the experimental structure factors S(Q), and have (2) energies close to the DF minimum and (3) a semiconducting band structure. The best structure is based on the melt-quenched DF structure and has a small number of Ge–Ge bonds. It shows interlocking networks of Te and GeTe with a significant fraction (22–24%) of voids (cavities). Ge occurs with both tetrahedral and 3 + 3 defective octahedral…
From local structure to nanosecond recrystallization dynamics in AgInSbTe phase-change materials
Phase-change optical memories are based on the astonishingly rapid nanosecond-scale crystallization of nanosized amorphous 'marks' in a polycrystalline layer. Models of crystallization exist for the commercially used phase-change alloy Ge(2)Sb(2)Te(5) (GST), but not for the equally important class of Sb-Te-based alloys. We have combined X-ray diffraction, extended X-ray absorption fine structure and hard X-ray photoelectron spectroscopy experiments with density functional simulations to determine the crystalline and amorphous structures of Ag(3.5)In(3.8)Sb(75.0)Te(17.7) (AIST) and how they differ from GST. The structure of amorphous (a-) AIST shows a range of atomic ring sizes, whereas a-GS…
Close packing of clusters: Application toAl100
The lowest energy configurations of close-packed clusters up to N=110 atoms with stacking faults are studied using the Monte Carlo method with Metropolis algorithm. Two types of contact interactions, a pair-potential and a many-atom interaction, are used. Enhanced stability is shown for N=12, 26, 38, 50, 59, 61, 68, 75, 79, 86, 100 and 102, of which only the sizes 38, 75, 79, 86, and 102 are pure FCC clusters, the others having stacking faults. A connection between the model potential and density functional calculations is studied in the case of Al_100. The density functional calculations are consistent with the experimental fact that there exist epitaxially grown FCC clusters starting from…
Sodium atoms and clusters on graphite by density functional theory
Sodium atoms and clusters $(Nl~5)$ on graphite (0001) are studied using density functional theory, pseudopotentials and periodic boundary conditions. A single Na atom is observed to bind at a hollow site 2.45 \AA{} above the surface with an adsorption energy of 0.51 eV. The small diffusion barrier of 0.06 eV indicates a flat potential energy surface. Increased Na coverage results in a weak adsorbate-substrate interaction, which is evident in the larger separation from the surface in the cases of ${\mathrm{Na}}_{3},$ ${\mathrm{Na}}_{4},$ ${\mathrm{Na}}_{5},$ and the $(2\ifmmode\times\else\texttimes\fi{}2)$ Na overlayer. The binding is weak for ${\mathrm{Na}}_{2},$ which has a full valence el…
Density functional study of alkali-metal atoms and monolayers on graphite (0001)
Alkali metal atoms (Li, Na, K, Rb, Cs), dimers and (2$\times$2) monolayers on a graphite (0001) surface have been studied using density functional theory, pseudopotentials, and a periodic substrate. The adatoms bind at the hollow site (graphite hexagon), with Li lying closest to (1.84 ��) and Cs farthest (3.75 ��) from the surface. The adsorption energies range between $0.55-1.21$ eV, and the energy ordering of the alkali adatoms is Li$>$Cs$\ge$Rb$\ge$K$>$Na. The small diffusion barriers (0.02-0.21 eV for the C-C bridge) decrease as the atom size increases, indicating a flat potential energy surface. The formation (cohesion) energies of (2$\times$2) monolayers range between 0.55-0.81 …
Density functional study of amorphous, liquid and crystalline Ge(2)Sb(2)Te(5): homopolar bonds and/or AB alternation?
The amorphous, liquid and crystalline phases of the phase change material Ge(2)Sb(2)Te(5) (GST) have been studied by means of density functional/molecular dynamics simulations. The large sample (460 atoms and 52 vacancies in the unit cell) and long simulations (hundreds of picoseconds) provide much new information. Here we extend our original analysis (2007 Phys. Rev. B 76 235201) in important ways: partial coordination numbers and radial distribution functions, bond angle distributions, new local order parameters, vibration frequencies, and the charges on atoms and vacancies. The valence band densities of states in amorphous and crystalline GST are compared with ones from x-ray photoemissi…
Atomistic Simulations of Functional Gold Nanoparticles Au144(Sr)60 Interacting with Membranes
Gold nanoparticles (AuNps) are used in nanomedicine in, e.g., drug delivery and bio-imaging. However, it is regrettable that the understanding of nanoparticle properties in cellular surroundings is incompletely understood. Here, we have complemented our previous studies [1] by performing extensive atomistic molecular dynamics simulations of lipid membranes interacting with charged gold nanoparticles. We have elucidated the action of these nanoparticles on membranes characterized by lipid compositional asymmetry in the two leaflets, thereby unraveling the interactions of AuNPs with both the extracellular and the cytosolic sides of plasma membranes of eukaryotic cells. We have found that ther…
Heating ofAl13−andAl14clusters
Dynamical properties of ${\mathrm{Al}}_{13}^{\ensuremath{-}}$ and ${\mathrm{Al}}_{14}$ clusters at a high-temperature regime are studied using a density functional theory based first-principles simulations method. During the heating ${\mathrm{Al}}_{13}^{\ensuremath{-}}$ shows a significantly different behavior than ${\mathrm{Al}}_{14}$ due to its double-magic nature. We also demonstrate that it is hard to assign any distinct melting transition for the studied cluster sizes. For ${\mathrm{Al}}_{13}^{\ensuremath{-}}$ we observe a solidlike behavior well after the melting temperature of bulk aluminum. In contradiction with the rare gas clusters we notice that the outermost atom of icosahedral …
Polymorphism in phase-change materials: melt-quenched and as-deposited amorphous structures in Ge2Sb2Te5from density functional calculations
The as-deposited (AD) amorphous structure of the prototype phase change material Ge${}_{2}$Sb${}_{2}$Te${}_{5}$ (GST-225) has been studied by density functional calculations for a 648-atom sample generated by computer-aided deposition at 300 K. The AD sample differs from a melt-quenched (MQ) sample in essential ways: (1) Ge atoms are predominantly tetrahedrally coordinated, and (2) homopolar and Ge-Sb bonds are more common and reduce the number of $\mathit{ABAB}$ squares ($A=\mathrm{Ge}$, Sb; $B=\mathrm{Te}$), the characteristic building blocks of the material. The first observation resolves the contradiction between measured (EXAFS) and calculated Ge-Te bond lengths, and the latter explain…
Role of the central gold atom in ligand-protected biicosahedral Au 24 and Au25 clusters
The crystal structures of the ligand-protected clusters [Au24(PPh3)10(SC2H4Ph)5Cl2]+ and [Au25(PPh3)10(SC2H4Ph)5Cl2]2+ have been elucidated recently, and they comprise the same biicosahedral structural motif for the Au core. The only difference is the central Au atom joining two icosahedra which is absent in the Au24 cluster. On the basis of density functional simulations, we have evaluated the structural, electronic, optical, and vibrational properties of the clusters in question with a full presentation for the thiolate and phosphine side groups. Our spherical harmonics analysis of the electronic structure shows that the chemical stability of both clusters can be understood based on an 8 …
Photoelectron spectra of aluminum cluster anions: Temperature effects and ab initio simulations
Photoelectron (PES) spectra from aluminum cluster anions (from 12 to 15 atoms) at various temperature regimes, were studied using ab-initio molecular dynamics simulations and experimentally. The calculated PES spectra, obtained via shifting of the simulated electronic densities of states by the self-consistently determined values of the asymptotic exchange-correlation potential, agree well with the measured ones, allowing reliable structural assignments and theoretical estimation of the clusters' temperatures.
Thermal Expansion in Small Metal Clusters and its Impact on the Electric Polarizability
The thermal expansion coefficients of $\mathrm{Na}_{N}$ clusters with $8 \le N \le 40$ and $\mathrm{Al}_{7}$, $\mathrm{Al}_{13}^-$ and $\mathrm{Al}_{14}^-$ are obtained from {\it ab initio} Born-Oppenheimer LDA molecular dynamics. Thermal expansion of small metal clusters is considerably larger than that in the bulk and size-dependent. We demonstrate that the average static electric dipole polarizability of Na clusters depends linearly on the mean interatomic distance and only to a minor extent on the detailed ionic configuration when the overall shape of the electron density is enforced by electronic shell effects. The polarizability is thus a sensitive indicator for thermal expansion. We …
Interaction of Au16 Nanocluster with Defects in Supporting Graphite: A Density-Functional Study
Soft-landed adsorption of Au-16 on bilayered graphene is investigated using density functional theory. The orientation of the Au-16 cluster and number of neighboring surface vacancies affect the overall structural and electronic properties of the cluster. The results of the PBE, vdW-DF, and vdW-DF2 exchange-correlation functionals are compared for the cluster-substrate interaction for systems with and without defects. In the presence of defects size two and greater, an Au atom adsorbs into the topmost graphene layer; this strongly influences the binding energy (>3 eV), while inducing substantial bending in the carbon plane and altering electronic properties of the system. Though the T-d-sym…
Ionization potential of Al6 and A17 as a function of temperature
The temperature-depence of the ionization potential of Al6 and Al7 clusters is studied by using ab initio molecular dynamics. The threshold regions of theoretical photoionization eciency curves are ob- tained from the calculated ionization potential distributions by integration and the determined ionization potentials are compared with the experimental ones. Two important eects, which complicate the determin- ation of ionization potential from photoionization eciency curves, are observed: the thermal tail eect and the isomerization. Also a link between the adiabatic ionization potential and the threshold of the photoion- ization eciency curve is discussed. In the case of Al7, this often use…
Binary alloys of Ge and Te: order, voids, and the eutectic composition
The liquid and amorphous structures of ${\mathrm{Ge}}_{0.15}{\mathrm{Te}}_{0.85}$ and GeTe alloys are characterized using combined density functional/molecular dynamics simulations. Te is threefold coordinated, in contrast with predictions of the ``8-$N$ rule,'' and Ge atoms (fourfold coordinated) show octahedral and tetrahedral bonding angles. Cubic local environment occurs in both materials, and GeTe shows a pronounced alternation of atomic types. Tetrahedral Ge coordination is more common in the eutectic ${\mathrm{Ge}}_{0.15}{\mathrm{Te}}_{0.85}$, which comprises corner- and edge-sharing ${\mathrm{GeTe}}_{4}$ units surrounded by Te. There is no Te segregation, and the material resembles …
Density functional simulations of structure and polymorphism in Ga/Sb films.
Thin films of gallium/antimony alloys are promising candidates for phase change memories requiring rapid crystallization at high crystallization temperatures. Prominent examples are the stoichiometric form GaSb and alloys near the eutectic composition GaSb(7), but little is known about their amorphous structures or the differences between the 'as-deposited' (AD) and 'melt-quenched' (MQ) forms. We have generated these structures using 528-atom density functional/molecular dynamics simulations, and we have studied in detail and compared structural parameters (pair distribution functions, structure factors, coordination numbers, bond and ring size distributions) and electronic properties (dens…
CPMD simulation of Cu2+ -- phenylalanine complex under micro-solvated environment
The study combines DFT calculations and CPMD simulations to investigate the structures of phenylalanine-copper (II) ([Phe-Cu]2+) complexes and the micro-solvation processes. ....It is found that the phenylalanine moiety appears to be in the neutral form in isolated and mono-hydrated complexes, but in the zwitterionic form in other hydrated complexes (with n no less than 2). .... The present CPMD simulations reveal that the maximum coordination of Cu2+ in the presence of the Phe ligand does not exceed four: the oxygen atoms from three water molecules and one carboxyl oxygen atom of Phe. Any excess water molecules will migrate to the second solvation shell. Moreover a unique structural motif …
Densified low-hygroscopic form of P2O5 glass
P2O5 compound is an archetypical glass-forming oxide with a record-high hygroscopicity, which makes both the study and potential industrial uses of the glass extremely difficult. We found that the quenching from the P2O5 melt under ultrahigh pressures enables obtaining densified P2O5 glasses with a residual densification up to 12% at normal conditions. These glasses have a low hygroscopicity and can exist under air conditions for several weeks. An examination of the structure of the new form of P2O5 glass reveals a significant increase in neighbors of terminal oxygen atoms in the second coordination sphere and a cardinal decrease of the volume of nanovoids in the glassy matrix. The research…
Topology and structure of Au144(SRNH3+)60 from "Atomistic Simulations of Functional Au144(SR)60 Gold Nanoparticles in Aqueous Environment"
Positively charged monolayer-protected gold nanoparticles (AuNPs) structure and topology files for GROMACS used in DOI: 10.1021/jp301094m. The final structure of the simulation reported in DOI: 10.1021/jp301094m for the neutral case is provided. The gold nanoparticle contain a core of 144 Au atoms and 60 functionalized alkanethiol side groups (undecanyl chain, R = C11H22), each possessing a positively charged amonium terminal group. When using this structure do not forget to cite DOI: 10.1021/jp301094m. NOTE1: Different versions for the topology files are provided of both AuNPs. All versions were used for the publication. The changes only affect the core surface and therefore had no influ…
Topology and structure of Au144(SRCOO-)60 from "Atomistic Simulations of Functional Au144(SR)60 Gold Nanoparticles in Aqueous Environment"
Negatively charged monolayer-protected gold nanoparticles (AuNPs) structure and topology files for GROMACS used in DOI: 10.1021/jp301094m. The final structure of the simulation reported in DOI: 10.1021/jp301094m for the neutral case is provided. The gold nanoparticle contain a core of 144 Au atoms and 60 functionalized alkanethiol side groups (undecanyl chain, R = C11H22), each possessing a negatively charged carboxylic terminal group. When using this structure do not forget to cite DOI: 10.1021/jp301094m. NOTE1: Different versions for the topology files are provided of both AuNPs. All versions were used for the publication. The changes only affect the core surface and therefore had no in…