Total Energy Of Cluster Research Articles

A computational investigation of XnK(X = Mn, Fe, co; n = 1–8) clusters by density functional theory

The properties of XnK(X = Mn, Fe, Co; n = 1–8) clusters have been systematically investigated using quantum calculations of LANL2DZ basis sets at the PBE1PBE level. By optimizing different structural isomers, we determined the ground state structure of XnK clusters, which tends to be compact as the cluster size increases. In order to study the stability of clusters, the average binding energies, dissociation energies and second-order difference of total energies of XnK clusters are calculated. The results show that the stability of FenK clusters is comparable to that of ConK clusters, and both are higher than that of MnnK clusters. Finally, the chemical activity and magnetic properties of the clusters are discussed. The dissociation energies, second-order difference of total energies, HOMO-LUMO energy gaps, and magnetic moments of the ground-state clusters show an irregular oscillatory behavior with atomic number. Fundamental insights obtained in this study can be useful in the design of Mn-K/Fe-K/Co-K catalysts.

Thermal stability of equiatomic FePt nanoclusters of different habitus with ordered and disordered structure

In this work, the thermal stability of FePt nanoclusters of different habitus is considered using the molecular dynamics method with the multiparticle interaction potential MEAM-2NN. Three variants of determining the temperatures of structural disorder/melting of these nanoclusters are presented: by the normalised per atom total energy of clusters from temperature, with approximation of curves by linear sections, the intersection points of which were used to determine the disorder temperatures; the second by the mean-square displacement of atoms; the third by visualisation of cross sections of atomic planes perpendicular to the face <100>. It is shown that the melting of the cluster occurs layer by layer from the surface to the volume. The temperatures of structural disorder of nanoclusters determined by different methods are in good agreement with each other.

A Computational Study of the Dissociation of CaS Nanoclusters in the Extracellular Fluid of Cancer Cells: the Effect of pH in the Structure and Stability of Protonated CaS Nanoclusters

The acidic pH found in the extracellular fluid of many cancer tumors is an important difference from the slightly basic pH found in the corresponding benign cells. Contrary to common anti‐cancer drugs that have significant side effects in healthy cells, calcium sulfide (CaS) nanoclusters have shown to induce apoptosis selectively in human lung, skin, and breast cancer cell lines in vitro. We hypothesize that CaS nanostructures selectively dissociate in the characteristic acidic extracellular environments of cancer cells into free Ca2+ ions and sulfides such as H2S, HS‐ and S2‐, which can be proved via bench and computational experiments. Theoretical calculations at the DFT/B3LYP/DGVZVP level of theory of bare and protonated (CaS)n clusters (n = 1 to 4) were performed to address this hypothesis using the Gaussian 16W and GaussView 6.0.16 programs by varying the number of protons in a CaS cluster to assess cluster stability and reaction pathways in both acidic and neutral media. The total cluster energy decreases with the number of monomer units (n) in the (CaS)n clusters. The CaS monomer and dimer are more stable in water than in their corresponding standard state by about 336kJ/mol and 390kJ/mol, respectively. A single protonation of a sulfur atom in the solvated monomer results in an increase in the Ca‐S bond length from 2.55Å to 2.73Å, indicative of increasing drive to dissociate. It requires protonation of a sulfur atom by two hydrogen atoms to dissociate the cluster into free Ca2+ and H2S. Water facilitates the dissociation of the clusters when the sulfur atom is bonded by two protons. The products of the reaction of the solvated (CaSH2)2+ is more stable than the corresponding gas phase cluster ion by a significant 1479 kJ/mole. These results are consistent with the dissociation of CaS clusters to free Ca2+ and H2S in acidic media like the one found in the extracellular fluid of malignant tumors. Ca2+ ions are known to cause cell damage in cytosolic concentrations higher than 500nM. The biochemistry of H2S is still under study by several groups worldwide but it is generally accepted that it can be genotoxic and induce apoptosis. Therefore, CaS nanoclusters are promising drugs to selectively inhibit malignant tumor growth with little impact on benign tissue. The results are discussed in terms of the basic requirements of a (CaS)n‐based formulation for cancer treatment.

Decoding the terahertz spectrum of allantoin crystal using DFT simulations and energy decomposition analysis

Decoding the terahertz (THz) spectrum of allantoin crystal measured by terahertz time-domain spectroscopy (THz-TDS) is implemented via density functional theory (DFT), potential energy distribution (PED), and energy decomposition analysis based on molecular forcefield (EDA-FF). The theoretical simulation indicates DFT combined with the cluster model could predict a certain absorption peak of the THz spectrum. The PED shows vibrational modes of allantoin cluster are bond angle bending and dihedral twist. The EDA-FF indicates the contribution of dispersion to the total interaction energy of allantoin cluster is greater than that of electrostatic interaction.

Molecular dynamics simulation of size, temperature, heating and cooling rates on structural formation of Ag-Cu-Ni ternary nanoparticles (Ag34-Cu33-Ni33)

We used molecular dynamics (MD) simulations with embedded atom method (EAM) potential to investigate the effect of size, simulation temperature heating and cooling rates on the nanoparticle formations, elemental distributions, melting, crystallization and phase transitions in equiatomic Ag-Cu-Ni ternary nanoparticle systems. Five model systems consisting of N = 412, 1348, 3173, 6222 and 10,843 total atoms of pure, metallic, single-oriented, spherical silver (Ag), copper (Cu) and nickel (Ni) particles used. A two-step heating process including relaxing and heating with fast, 1 × 1013 K s−1 and slow, 1 × 1011 K s−1 heating rates applied to monometallic Ag, Cu, Ni and ternary AgCuNi clusters to study melting behavior of systems. We obtained melting temperatures for various systems and found structural and morphological changes depend on the number of atoms in ternary cluster. A four-step thermal process including relaxing, heating, annealing and cooling applied to model systems to study effects of temperature (T = 1000, 1500 and 2000 K) and cooling rates (fast, 1 × 1013 K s−1 and slow, 1 × 1011 K s−1) for crystallization. We detected core–shell structure, Ag@CuNi for all simulations because of surface energy. The total energy of ternary clusters decrease linearly with increasing N, revealing similar mechanisms govern for core–shell structure and phase transitions. Energy-Temperature data of slow cooling rate have shown phase transition (crystallization) for monometallic Ag, Cu, Ni and ternary AgCuNi clusters, increasing with N. Fast cooling rate influences energy configuration and result in amorphous phases. Polyhedral template matching method applied to study phase transitions. For slow cooled clusters, face-centered cubic (FCC) and hexagonal close packed (HCP) structures are dominant while for fast cooled clusters, we observed amorphous phases with HCP and icosahedral structures. Furthermore, we used centrosymmetry parameter to identify the origin of the FCC structure. Our data show increasing simulation temperature and decreasing cooling rate favor crystallization of ternary AgCuNi clusters.

Theoretical and experimental study of small potassium-bromide K Br(0,1+) (n = 2–6) and K Br(0,1+) (n = 3–5) clusters

Abstract In the present paper, the results of combined theoretical and experimental investigation of small non-stoichiometric bromine-doped potassium clusters are reported. Potassium-bromide clusters were obtained by the Knudsen cell combined with surface ionization in the temperature range of 1000–1600 K, and selected by a magnetic sector mass spectrometer. Positive ions of KnBr (n = 3–6) and KnBrn-1 (n = 3–5) clusters were detected for the first time in one set measurement. In order to reveal the geometrical structure of each type of detected cluster, the randomized search algorithm was employed to survey the (Born-Oppenheimer) potential energy surface of both the neutral and cationic KnBr(0,1+) (n = 1–6) and KnBrn-1(0,1+) (n=3–5) clusters, followed by Density functional theory geometry optimizations, and many lowest-energy conformational isomers are presented. From the total electronic energies of clusters computed by the ab initio RCCSD(T)/ECP10MDF(K),cc-pVTZ-PP(Br) method at obtained equilibrium nuclear geometries, the following stability parameters of clusters were computed: their relative energies, the adiabatic and vertical ionization energies, binding energies per atom, and dissociation energies. Both experimental and theoretical results have shown that the title clusters belong to the group of “superalkali” clusters.

Computer simulation of phases consisting of Be, B and Li atoms and calculating their elastic properties using quantum mechanical calculation

Chemical elements of groups 1 and 2 have the most pronounced properties in their periods. There is something unique about each of them, inciting substantial interest, especially regarding light-weight alloys of these elements. Young’s modulus to density ratio of beryllium is six times higher than that of steel. Heat-resistance of Be is 600°C. The combination of these physicochemical properties makes beryllium alloys specifically applicable in aerospace. Simulation of material properties is one of the main missions for materials science. Elastic properties are the easiest to calculate compared to other mechanical properties. Elastic properties are characterized by the fifth-fourth digits of the total cluster energy. Here we present the results of the calculation of the elastic constants of hexagonal and cubic beryllium and cubic lithium boride. The calculations were based on the density functional theory (DFT). The results obtained by different techniques (quantum chemical, semi-empirical) and data from the literature were compared.

Structure of transition metal clusters: A force-biased Monte Carlo approach

We present a force-biased Monte Carlo (FMC) method for structural modeling of transition metal clusters of Fe, Ni, and Cu with 5 to 60 atoms. By employing the Finnis-Sinclair potential for Fe and the Sutton-Chen potential for Ni and Cu, the total energy of the clusters is minimized using a method that utilizes atomic forces in Monte Carlo simulations. The structural configurations of the clusters obtained from this biased Monte Carlo approach are analyzed and compared with the same from the Cambridge Cluster Database (CCD). The results show that the total-energy of the FMC clusters is very close to the corresponding value of the CCD clusters as listed in the Cambridge Cluster Database. A comparison of the FMC and CCD clusters is presented by computing the pair-correlation function, the bond-angle distribution, and the distribution of atomic-coordination numbers in the first-coordination shell, which provide information about the two-body and three-body correlation functions, the local atomic structure, and the bonding environment of the atoms in the clusters.

Geometry and electronic structure of (SiO2)3 clusters

Electronic structure of (SiO2)3 clusters was calculated by the density functional method. Charge states were determined using various functionals, bond lengths and total energies of clusters were estimated.

A quantum Monte Carlo study of the structural and electronic properties of small cationic and neutral lithium clusters.

Using the fixed-node diffusion quantum Monte Carlo method, we calculate the total energy of small cationic and neutral lithium clusters. We estimate the ionization potential, atomic binding energy, dissociation energy, and the second difference in energy. We present a critical analysis of the structural and electronic properties of the clusters. The bond lengths and binding and dissociation energies obtained from the calculations are in excellent agreement with the available experimental results. A comparative analysis of the dissociation energy and the second difference in energy indicates that the cationic clusters Li3+, Li5+, and Li7+ are the most stable ones. We have also studied the electron correlation effects in the lithium clusters. The cationic clusters of odd-number size are relatively more favored in terms of correlation energy than their neighbors of even-number size. In the range of cluster sizes under investigation, we find that the contribution of electron correlation to ionization potential is not larger than 28% of its total values, whereas it enhances significantly the dissociation energy of the clusters reaching up to 70% of its total values for the most stable ones.

Revisit of Sin (n = 21–29) Clusters by Ab Initio Global Search

Using our improved genetic algorithm combined with density functional theory calculations, we perform unbiased global search for the most stable structures of Sin clusters with n = 21–29. A new principal direction crossover operation is introduced to search the prolate structures on the potential energy surface. We confirmed previous results for most sized Sin clusters and find more stable structure at n = 23 and 26. In particular, we find a new endohedral cage structure at Si23, which is 0.4 eV lower in energy than previously reported prolate structure and exhibit a distinct peak on the second order difference of total cluster energy. We discuss the competition between prolate and spherical motifs in the medium-sized Sin clusters in light of binding energy and HOMO–LUMO gap. The transition of structural motif from prolate to near spherical in Sin clusters occurs at n = 26. The outer cages are composed of pentagon, hexagon, quadrangle and heptagon, with one to three interior atoms filled inside the cage. These results establish a more complete picture for the structural evolution of the medium-sized silicon clusters. Average bond lengths and Mayer bond order are also discussed.

Three-Dimensional Assignment of the Structures of Atomic Clusters: an Example of Au8M (M=Si, Ge, Sn) Anion Clusters.

Identification of different isomer structures of atomic and molecular clusters has long been a challenging task in the field of cluster science. Here we present a three-dimensional (3D) assignment method, combining the energy (1D) and simulated (2D) spectra to assure the assignment of the global minimum structure. This method is more accurate and convenient than traditional methods, which only consider the total energy and first vertical detachment energies (VDEs) of anion clusters. There are two prerequisites when the 3D assignment method is ultilized. First, a reliable global minimum search algorithm is necessary to explore enough valleys on the potential energy surface. Second, trustworthy simulated spectra are necessary, that is to say, spectra that are in quantitative agreement. In this paper, we demonstrate the validity of the 3D assignment method using Au8M− (M = Si, Ge, Sn) systems. Results from this study indicate that the global minimum structures of Au8Ge− and Au8Sn− clusters are different from those described in previous studies.

Many-Body Basis Set Superposition Effect.

The basis set superposition effect (BSSE) arises in electronic structure calculations of molecular clusters when questions relating to interactions between monomers within the larger cluster are asked. The binding energy, or total energy, of the cluster may be broken down into many smaller subcluster calculations and the energies of these subsystems linearly combined to, hopefully, produce the desired quantity of interest. Unfortunately, BSSE can plague these smaller fragment calculations. In this work, we carefully examine the major sources of error associated with reproducing the binding energy and total energy of a molecular cluster. In order to do so, we decompose these energies in terms of a many-body expansion (MBE), where a "body" here refers to the monomers that make up the cluster. In our analysis, we found it necessary to introduce something we designate here as a many-ghost many-body expansion (MGMBE). The work presented here produces some surprising results, but perhaps the most significant of all is that BSSE effects up to the order of truncation in a MBE of the total energy cancel exactly. In the case of the binding energy, the only BSSE correction terms remaining arise from the removal of the one-body monomer total energies. Nevertheless, our earlier work indicated that BSSE effects continued to remain in the total energy of the cluster up to very high truncation order in the MBE. We show in this work that the vast majority of these high-order many-body effects arise from BSSE associated with the one-body monomer total energies. Also, we found that, remarkably, the complete basis set limit values for the three-body and four-body interactions differed very little from that at the MP2/aug-cc-pVDZ level for the respective subclusters embedded within a larger cluster.

Use of density functional theory method to calculate structures of neutral carbon clusters Cn (3 ≤ n ≤ 24) and study their variability of structural forms.

In this work, we present modifications to the well-known basin hopping (BH) optimization algorithm [D. J. Wales and J. P. Doye, J. Phys. Chem. A 101, 5111 (1997)] by incorporating in it the unique and specific nature of interactions among valence electrons and ions in carbon atoms through calculating the cluster's total energy by the density functional tight-binding (DFTB) theory, using it to find the lowest energy structures of carbon clusters and, from these optimized atomic and electronic structures, studying their varied forms of topological transitions, which include a linear chain, a monocyclic to a polycyclic ring, and a fullerene/cage-like geometry. In this modified BH (MBH) algorithm, we define a spatial volume within which the cluster's lowest energy structure is to be searched, and introduce in addition a cut-and-splice genetic operator to increase the searching performance of the energy minimum than the original BH technique. The present MBH/DFTB algorithm is, therefore, characteristically distinguishable from the original BH technique commonly applied to nonmetallic and metallic clusters, technically more thorough and natural in describing the intricate couplings between valence electrons and ions in a carbon cluster, and thus theoretically sound in putting these two charged components on an equal footing. The proposed modified minimization algorithm should be more appropriate, accurate, and precise in the description of a carbon cluster. We evaluate the present algorithm, its energy-minimum searching in particular, by its optimization robustness. Specifically, we first check the MBH/DFTB technique for two representative carbon clusters of larger size, i.e., C60 and C72 against the popular cut-and-splice approach [D. M. Deaven and K. M. Ho, Phys. Rev. Lett. 75, 288 (1995)] that normally is combined with the genetic algorithm method for finding the cluster's energy minimum, before employing it to investigate carbon clusters in the size range C3-C24 studying their topological transitions. An effort was also made to compare our MBH/DFTB and its re-optimized results carried out by full density functional theory (DFT) calculations with some early DFT-based studies.

Dimers of Dimers (DOD): A New Fragment-Based Method Applied to Large Water Clusters.

We have developed a dimer-based two-body interaction model, denoted "dimers of dimers" (DOD), for the study of water clusters using a fragmentation approach. By including a second layer at a lower level of theory (e.g., Hartree-Fock), our DOD2 model accurately reproduces the total energies of water clusters ranging in size from 16 to 100 molecules using the MP2 method with a variety of basis sets. The mean absolute error in the calculated DOD2 total energy for a broad range of calculations is only 0.83 kcal/mol. The size of the fragments is independent of the cluster size, and the number of fragments grows fairly slowly with the cluster size. Our results suggest that our method should be applicable for the study of large water clusters.

Surface sputtering with nanoclusters: the relevant parameters

In this contribution, we compare the results of our recent molecular dynamics simulations with data already published by us and by other authors to identify the relevant physical parameters governing observables such as the range, the damaged volume, the crater shape, the sputtering yield, the emission of molecules and fragments, and the chemical reactions induced in organic solids by cluster projectiles. Among the considered physical quantities, we show for instance that the total cluster energy, the energy per atom/per nucleon in the cluster and, importantly, the mass matching between the cluster and target constituents have a major effect on the physics of the interaction. The evolution of the observables as a function of these basic physical parameters is illustrated and discussed as well as certain implications for organic surface characterization using cluster ion beams. Copyright © 2012 John Wiley & Sons, Ltd.

Tailoring opto‐electronic properties of small InAsN and InN quantum dots

AbstractElectronic energy level structure (ELS), charge and spin density distributions (CDD and SDD, respectively) of small indium nitride clusters have been studied by means of the first‐principle, many‐body field theoretical methods. Electron charge delocalization due to charge accumulation on nitrogen and dopant nickel atoms, and resulting violation of the octet rule of the valence theory, have been observed. This charge delocalization mechanism provides for minimization of the total cluster energy, and thus is necessary to stabilize small non‐stoichiometric indium nitride systems. It may be used to manipulate opto‐electronic properties of indium nitride clusters, and also to synthesize novel, indium nitride‐based nanostructures with desirable properties (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Computational Insight into the Static and Dynamic Polarizabilities of Aluminum Nanoclusters

The static and dynamic polarizabilities for the lowest-energy structures of pure aluminum clusters up to 31 atoms have been investigated systematically within the framework of density functional theory. The size evolution of several electronic properties such as ionization potential, electron affinity, the energy gap between the highest occupied molecular orbital and lowest unoccupied molecular orbital, and chemical hardness have also been discussed for aluminum clusters. Our primary focus in this article, however, has been upon the study of polarizability of aluminum clusters, although we also looked at the role of other electronic properties. From the energetics point of view, the relative stability of aluminum clusters at different sizes is studied in terms of the calculated second-order difference in the total energy of cluster and fragmentation energy, exhibiting that the magic numbers of stabilities are n = 7, 13, and 20. Moreover, the minimum polarizability principle is used to characterize the stability of aluminum clusters. The results show that polarizabilities and electronic properties can reflect obviously the stability of clusters. Electronically, the size dependence of ionization potential and electron affinity of clusters is determined. On the basis of the Wood and Perdew model these quantities converge asymptotically to the value of the bulk aluminum work function.

Molecular Structures, Energetics, and Electronic Properties of Neutral and Charged HgnClusters (n= 2−8)

The geometric and electronic structures of small mercury clusters, Hg(n), Hg(n)(+), and Hg(n)(-) (n </= 8) have been calculated using a density functional theory. The results indicate that as the cluster size increases, the lowest energy states of neutral and anionic mercury clusters prefer three-dimensional structure whereas those of cationic clusters are peculiarly linear structure due to s-p hybridization. This structural feature has influence on the energetic and electronic properties of cationic clusters which deviate from the characteristics of van der Waals cluster. As the cluster size increases, energetic properties, binding energies per atom and second order difference in total energy of cationic clusters consistently decrease, in contrast to the neutral and anionic clusters. However, neutral and charged mercury clusters show common features in terms of size dependent transition of bonding character, such as the decrease of band gap and vertical ionization potential, and the increase of vertical electron affinity. These various properties are also qualitatively and quantitatively in line with the available experimental and theoretical results, implying the reliability of the ground state geometries of these clusters.

Total cluster energy calculation of lithium ion conductors by the DV‐Xα method

AbstractRecently, several programs for the total cluster energy calculation have been developed in the DV‐Xα method. In this study, we have calculated and compared total cluster energies of several diatomic molecules and model clusters of ionic conductors. The total cluster energies of diatomic molecules are minimum near the equilibrium atomic distance of each molecule though the absolute value of the total cluster energy was slightly different from each other. In the case of the model cluster of the Li3N crystal, which is one of the typical Li ion conductors, we have obtained the energy change as a function of the site during the movement of a Li ion. The energy change with the movement of the Li ion along the conduction path was considerably smaller than along other paths, consistent with the results by the band calculation and experiments. The total cluster energy calculation method was useful enough for the discussion of the cluster energy. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009