Embedded atom method study of Cu deposition on Ag(111)

A new model is applied to the study of Cu deposition on Ag(111), It links elements from the embedded atom model and Monte Carlo simulations. In agreement with the experiment, the present results favor overpotential upon underpotential deposition. A diffusion coefficient of 1.93 × 10⁻⁶ cm² s⁻¹ is estimated for the system. The predicted structure of the adsorbed monolayer is more compact than the electrochemical observation, a fact which may be due to some simplifications of the model like neglecting the solvent and anion effects or the nature of the potentials employed.     

Interaction of Dihydrogen with Transition Metal (Pd,Ni, Ag,Cu) Clusters

Quantum calculations of interaction of the molecular hydrogen with transition-metal clusters have been performed. The aim of the project is to compare the results for different metals and different methods of calculations. The calculations have been mostly based on the gradient-corrected methods of the density functional theory. The list of the exchange-correlation functionals includes: the gradient corrected functional BP86, the hybrid functionals B3P86, B3LYP, B3PW9, and the local SVWN functional. The calculations of the potential energy surface (PES) for the hydrogen molecule positioned over the planar Pd₅ clusters have been performed. It was found that the H–H bond activation is without barrier for most of the functionals used. However, the results obtained for the B3LYP functional suggest very small potential barrier, of the order of 0.003 eV. The calculations of the PES for dihydrogen in contact with metal clusters have been performed for Ni₅, Ag₅, Cu₅ clusters and for mixed clusters Ag₄Pd, AgPd₄, NiCu₄, and NiPd₄. The dissociation paths for all the cases with the exception of Ag₅ and Cu₅ have been found and the dissociation energies and activation barriers have been estimated.     

Comparison of small metal clusters: Ni, Pd, Pt, Cu, Ag, Au

Structures of small clusters of Ni, Pd, Pt, Cu, Ag, and Au with n=2–34 and n=55 atoms are calculated as functions of number of atoms and temperature by the simulated annealing Monte Carlo method using an embedded atom potential.     

Glucose interaction with Au,Ag, and Cu clusters: Theoretical investigation

Interactions of α‐D ‐glucose with gold, silver, and copper metal clusters are studied theoretically at the density functional theory (CAM‐B3LYP) and MP2 levels of theory, using trimer clusters as simple catalytic models for metal particles as well as investigating the effect of cluster charge by studying the interactions of cationic and anionic gold clusters with glucose. The bonding between α‐D ‐glucose and metal clusters occurs by two major bonding factors; the anchoring of M atoms (M = Cu, Ag, and Au) to the O atoms, and the unconventional M…H? O hydrogen bond. Depending on the charge of metal clusters, each of these bonds contributes significantly to the complexation. Binding energy calculations indicate that the silver cluster has the lowest and gold cluster has the highest affinity to interact with glucose. Natural bond orbital analysis is performed to calculate natural population analysis and charge transfers in the complexes. Quantum theory of atoms in molecules was also applied to interpret the nature of bonds. © 2012 Wiley Periodicals, Inc.     

Anisotropy analysis of the surface stress in Ag stepped surfaces with the modified embedded atom method

The surface stresses in Ag stepped surfaces (910), (710), (510), (410), (310), (210), (320), (430) and (540) have been calculated by using the modified embedded atom method (MEAM). The surface stresses in the surface plane τ_xx (along the step edge) and τ_yy (normal to the step edge) have similar orders of magnitude as the surface energy. For surfaces having the (100) and (110) terraces, the change of τ_xx and τ_yy is very small and the variation of the surface energy is smooth. The stress τ_zz (normal to the surface plane) is always tensile in the unrelaxed state. The linear variation of the change in surface energy per unit change in elastic strain , and (i.e. τ_xx ? γ, τ_yy ? γ and τ_zz) with the angle α between the (hk0) and (100) planes has a turning point corresponding to the (210) surface. The anisotropic ratio in the stepped surface having the (110) terrace is larger than that having the (100) terrace, and the wider the (110) terrace or the narrower the (100) terrace, the larger the ratio τ_yy/τ_xx. Copyright © 2006 John Wiley & Sons, Ltd.     

First-principles calculations of the structural and electronic properties of Cu3MN compounds with M = Ni,Cu, Zn,Pd, Ag,and Cd

We have performed accurate ab initio total energy calculations using the full-potential linearized augmented plane wave (FP-LAPW) method to investigate the structural and electronic properties of copper-transition metal nitrides. In its ground state, Cu₃N crystallizes in an anti-ReO₃ type cell and it is a semiconductor material with a small indirect gap. In this paper, we report a study of Cu₃MN compounds with M = Ni, Cu, Zn, Pd, Ag, and Cd. In the calculations, we have used the same anti-ReO₃ type cell of Cu₃N, but with the extra transition metal atom at the center of the cube. In particular, our calculated lattice parameters for copper nitride (a = 3.82 Å) and copper palladium nitride (a = 3.89 Å) are in excellent agreement with the experimental values of a = 3.807 Å and a = 3.86 Å, respectively. In all the cases we have studied, the addition of the transition metal atom modifies the electronic structure of Cu₃N, turning all copper-transition metal nitrides into metals.     

Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: applications to structural and energetic analysis

Parameters for the zinc ion have been developed in the self-consistent charge density functional tight-binding (SCC-DFTB) framework. The approach was tested against B3LYP calculations for a range of systems, including small molecules that contain the typical coordination environment of zinc in biological systems (cysteine, histidine, glutamic/aspartic acids, and water) and active site models for a number of enzymes such as alcohol dehydrogenase, carbonic anhydrase, and aminopeptidase. The SCC-DFTB approach reproduces structural and energetic properties rather reliably (e.g., total and relative ligand binding energies and deprotonation energies of ligands and barriers for zinc-assisted proton transfers), as compared with B3LYP/6-311+G** or MP2/6-311+G** calculations.     

Structure and stability of coinage metal fluoride and chloride clusters (MnFn and MnCln,M = Cu,Ag, or Au; n = 1–6)

Calculations in the framework of the density functional theory are performed to study the lowest‐energy isomers of coinage metal fluoride and chloride clusters (M_nF_n, M_nCl_n, M = Cu, Ag, or Au, n = 1–6). For all calculated species starting from the trimers the most stable structures are found to be cyclic arrangements. However, planar rings are favored in the case of metal fluorides whereas metal chlorides prefer nonplanar cycles. Calculated bond lengths and infrared frequencies are compared with the available experimental data. The nature of the bonding, involving both covalent and ionic contributions, is characterized. The stability and the fragmentation are also investigated. Trimers are found to be particularly stable when considering the Gibbs free energies. © 2012 Wiley Periodicals, Inc.     

Density functional studies of LiN and LiN+ (N = 2–30) clusters: Structure,binding and charge distribution

Density functional calculations using B3LYP/6‐311G method have been carried out for small to medium‐sized lithium clusters (Li_N, N = 2–30). The optimized geometries of neutral and singly charged clusters, their binding energies, ionization potential, electron affinity, chemical potential, softness, hardness, highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO–LUMO) gap, and static dipole polarizability have been investigated systematically. In addition, we study the distribution of partial charges in detail using natural population analysis (NPA) in small‐sized clusters (Li_N, N = 2–10), both neutral and cationic, and demonstrate the correlation between symmetry and charge. Uniform distribution of charges in cationic clusters confirms them to be energetically more favorable than the neutral counterparts. Whenever possible, results have been compared with available data. An excellent agreement in every case supports new results as reliable predictions. A careful study of optimized geometries shows that Li₉ is derivable from bulk Li structure, i.e., body centered cubic cell, and higher clusters have optimized shapes derived from this. Further, the turnover form two to three dimensional structure occurs at cluster size N = 6. The quantity α^1/3 (α = polarizability) per atom is found to be broadly proportional to softness (per atom) as well as inverse ionization potential (per atom). The present work forms a sound basis for further study of large‐sized clusters as well as other atomic clusters. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

A DFT investigation of the interactions of Pd,Ag, Sn,and Cs with silicon carbide

With a view to understand the diffusion of radionuclides through the silicon carbide layers in tristructural isotropic coated fuel particles, density functional theory calculations are applied to assess the interaction of palladium, silver, tin, and caesium with silicon carbide. The silicon carbide molecule (Si₂C₂), crystalline cubic silicon carbide (β‐SiC), and the (120) ∑5 grain boundary of β‐SiC are investigated to elucidate the differences in the interactions of silicon carbide with these elements. The main stabilizing forces in the PdSi₂C₂ complex were found to be donor‐acceptor charge transfer (covalent) interactions, the Ag and Sn complexes involve significant contributions from both electrostatic and covalent interactions, while the Cs atom is bonded dominantly by electrostatic forces. For the unconstrained M? Si₂C₂ model, the following energetic ordering was obtained: Pd > Sn > Cs > Ag. The steric constraints in the bulk SiC and on the grain boundary change the order of binding energies to Pd > Ag > Sn > Cs in the interstitials and Pd > Sn > Ag > Cs in vacancies and at the grain boundary. By comparing the incorporation energies in the solid phases, it is possible to group these elements by similarities in the patterns of incorporation energies. Silver and palladium form a group with carbon, tin is grouped with silicon, and caesium is on its own. © 2014 European Commission. International Journal of Quantum Chemistry published by Wiley Periodicals, Inc.     

Density functional embedded cluster study of Cu(4), Ag(4) and Au(4) species interacting with oxygen vacancies on the MgO(001) surface

Cu(4), Ag(4), and Au(4) species adsorbed on an MgO(001) surface that exhibits neutral (F(s)) and charged (F(s) (+)) oxygen vacancies have been studied using a density functional approach and advanced embedding models. The gas-phase rhombic-planar structure of the coinage metal tetramers is only moderately affected by adsorption. In the most stable surface configuration, the plane of the tetramers is oriented perpendicular to the MgO(001) surface; one metal atom is attached to an oxygen vacancy and another one is bound to a nearby surface oxygen anion. A very similar structural motif was recently found on defect-free MgO(001), where two O(2-) ions serve as adsorption sites. Following the trend of the interactions with the regular MgO(001) surface, Au(4) and Cu(4) bind substantially stronger to F(s) and F(s) (+) sites than Ag(4). This stronger adsorption interaction at oxygen vacancies, in particular at F(s), is partly due to a notable accumulation of electron density on the adsorbates. We also examined the propensity of small supported metal species to aggregate to adsorbed di-, tri- and tetramers. Furthermore, we demonstrated that core-level ionization potentials offer the possibility for detecting experimentally supported metal tetramers and characterizing them structurally with the help of calculated data.     

Binding affinity prediction with different force fields: examination of the linear interaction energy method

A systematic study of the linear interaction energy (LIE) method and the possible dependence of its parameterization on the force field and system (receptor binding site) is reported. We have calculated the binding free energy for nine different ligands in complex with P450cam using three different force fields (Amber95, Gromos87, and OPLS-AA). The results from these LIE calculations using our earlier parameterization give relative free energies of binding that agree remarkably well with the experimental data. However, the absolute energies are too positive for all three force fields, and it is clear that an additional constant term (gamma) is required in this case. Out of five examined LIE models, the same one emerges as the best for all three force fields, and this, in fact, corresponds to our earlier one apart from the addition of the constant gamma, which is almost identical for the three force fields. Thus, the present free energy calculations clearly indicate that the coefficients of the LIE method are independent of the force field used. Their relation to solvation free energies is also demonstrated. The only free parameter of the best model is gamma, which is found to depend on the hydrophobicity of the binding site. We also attempt to quantify the binding site hydrophobicity of four different proteins which shows that the ordering of gamma's for these sites reflects the fraction of hydrophobic surface area.     

Cu(II), Fe(III)与人血清白蛋白相互作用的荧光光谱研究

通过研究Cu(II),Fe(III)对人血清白蛋白(HSA)内源荧光的猝灭,探讨了Cu(II),Fe(III)与人血清白蛋白的结合机理。基于Forster非辐射能量转移机理。获得了人血清白蛋白第一类Cu(II)结合部位与214位色氨酸残基间的距离为1.8nm,并讨论了Cu(II),Fe(III)与HSA结合的差异。     

Modeling structural recovery in glasses: An analysis of the peak‐shift method

Amorphous polymers below their glass‐transition temperature are inherently not at equilibrium. As a result, their structures continuously relax in an attempt to reach the equilibrium state. The current models of structural recovery can quantitatively describe the process. One of the parameters needed for the models is the nonlinearity parameter x. It has been proposed that x can be obtained from experimental data with the so‐called peak‐shift method. In this work, we use the Tool–Narayanaswamy–Moynihan model to identify the factors that determine the accuracy of the peak‐shift method and to quantify the errors in the value of x obtained from the peak‐shift method. In addition, we determine the influence of the error in x on the evaluation of the nonexponential model parameter β. Finally, the peak‐shift method is compared with the traditional curve‐fitting method for model parameter determination. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 2027–2036, 2002     

Density Functional Theory Study on the Adsorption of CN on Transition Metal M（100） （M = Ni,Pd, Pt,Cu, Ag and Au） Surfaces

The adsorption of cyanide on the top site of a series of transition metal M（100） （M = Cu, Ag, Au, Ni, Pd, Pt） surfaces via carbon and nitrogen atoms respectively, with the CN axis perpendicular to the surface, has been studied by means of density functional theory and cluster model. Geometry, adsorption energy and vibrational frequencies have been determined, and the present calculations show that the adsorption of CN through C-end on metal surface is more favorable than that via N-end for the same surface. The vibrational frequencies of CN for C-down configuration on surface are blue-shifted with respect to the free CN, which is contrary to the change of vibrational frequencies when CN is adsorbed by N-down structure. Furthermore, the charge transfer from surface to CN causes the increase of surface work function.     

Influence of the Charge State on the Structures and Interactions of Vancomycin Antibiotics with Cell‐Wall Analogue Peptides: Experimental and Theoretical Studies

Charge matters! The charge state significantly influences the conformation and the binding energy between vancomycin antibiotic and bacterial cell‐wall analogue peptides (see figure). Surface‐induced dissociation (SID) studies provide a quantitative comparison between the stabilities of different charge states of the complex.

     

Topological analysis of the charge density response of a Ni4 cluster to a probe H2 molecule

Local density self-consistent field (SCF) discrete variationalX calculations are performed on a Ni₄ tetrahedron interacting with a probe H₂ molecule in special geometries. Optimized basis functions generated from the spherically averaged SCF potential are used. Topological charge-density analyses and binding energy calculations are used to study a portion of the energy surface for the approach of the H₂ molecule toward the Ni₄ tetrahedron. The effect of the H₂ molecule on Ni-Ni, Ni-H bonds and changes in the H-H covalent bond are investigated with the help of the field and various data at its critical points. The qualitative relationship between these data and the calculated binding energies is exploited.     

Strain in nonclassical silicon hydrides: An insight into the “ultrastability” of sila‐bi[6]prismane (Si18H12) cluster with the endohedrally trapped silicon atom,Si19H12

The recently postulated concept of “ultrastability” and “electron‐deficient aromaticity” (Vach, Nano Lett 2011, 11, 5477; Vach, J Chem Theory Comput 2012, 8, 2088) in a sila‐bi[6]prismane having an additional entrapped silicon atom, Si₁₉H₁₂, has been disproved on the basis of a careful analysis of the energetic characteristics related to the formation of this and other silicon hydrides. The central silicon atom in Si₁₉H₁₂ is weaker bound to other silicon atoms than in conventional tetrahedral silanes; moreover, Si₁₉H₁₂ possesses a significant amount of strain. The role of strain in the formation of the title compounds has been further rationalized by calculating the relative energies for the transformation to a half‐planar conformation in methane and in silane and by calculating the respective strain energies. The strain energy value in Si₁₈H₁₂ is equal to 9.93 eV whereas the same property for Si₁₉H₁₂ lies in range of 6.42–8.85 eV. Two low‐energy isomers of Si₁₉H₁₂ which lie by 2.77 and 3.42 eV (!) lower in energy than the originally considered sila‐bi[6]prismane‐based structure have been proposed. © 2015 Wiley Periodicals, Inc.     

Primary Fragmentation Pathways of Gas Phase [M(Uracil−H)(Uracil)]+ Complexes (M=Zn,Cu, Ni,Co, Fe,Mn, Cd,Pd , Mg,Ca, Sr,Ba, and Pb): Loss of Uracil versus HNCO

Complexes formed between metal dications, the conjugate base of uracil, and uracil are investigated by sustained off‐resonance irradiation collision‐induced dissociation (SORI‐CID) in a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. Positive‐ion electrospray spectra show that [M(Ura?H)(Ura)]⁺ (M=Zn, Cu, Ni, Co, Fe, Mn, Cd, Pd, Mg, Ca, Sr, Ba, or Pb) is the most abundant ion even at low concentrations of uracil. SORI‐CID experiments show that the main primary decomposition pathway for all [M(Ura?H)(Ura)]⁺, except where M=Ca, Sr, Ba, or Pb, is the loss of HNCO. Under the same SORI‐CID conditions, when M is Ca, Sr, Ba, or Pb, [M(Ura?H)(Ura)]⁺ are shown to lose a molecule of uracil. Similar results were observed under infrared multiple‐photon dissociation excitation conditions, except that [Ca(Ura?H)(Ura)]⁺ was found to lose HNCO as the primary fragmentation product. The binding energies between neutral uracil and [M(Ura?H)]⁺ (M=Zn, Cu, Ni, Fe, Cd, Pd ,Mg, Ca, Sr Ba, or Pb) are calculated by means of electronic‐structure calculations. The differences in the uracil binding energies between complexes which lose uracil and those which lose HNCO are consistent with the experimentally observed differences in fragmentation pathways. A size dependence in the binding energies suggests that the interaction between uracil and [M(Ura?H)]⁺ is ion–dipole complexation and the experimental evidence presented supports this.