Density Functional Study Of Structure Research Articles

Chalcogen-substituted carbenes: a density functional study of structure, stability, and donor ability.

Chalcogen-substituted carbenes are examined computationally using density functional theory. Several approaches are used to assess the stability and reactivity of chalcogenazol-2-ylidene carbenes (NEHCs; E = O, S, Se, Te). The known unsaturated species 1,3-dimethylimidazol-2-ylidene is studied at the same level of theory as the NEHC molecules, as a reference. Electronic structures, stability towards dimerization, and ligand properties are discussed. The results highlight the NEHCs as potentially valuable ancillary ligands for stabilizing low-valent metals or paramagnetic main group molecules. A simple, effective computational method for evaluating σ donor ability and π acidity of carbenes is presented.

Density functional study of structure and dynamics in liquid antimony and Sbn clusters.

Density functional/molecular dynamics simulations have been performed on liquid antimony (588 atoms and six temperatures between 600 K and 1300 K) and on neutral Sb clusters with up to 14 atoms. We study structural patterns (coordination numbers, bond angles, and ring patterns, structure factors, pair distribution functions) and dynamical properties (vibration frequencies, diffusion constants, power spectra, dynamical structure factors, viscosity) and compare with available experimental results and with the results of our previous simulations on Bi. Three short covalent bonds characteristic of pnictogens are common in the clusters, and higher temperatures lead in the liquid to broader bond angle distributions, larger total cavity volumes, and weaker correlations between neighboring bond lengths. There are clear similarities between the properties of Sb and Bi aggregates.

A broken-symmetry density functional study of structures, energies, and protonation states along the catalytic O-O bond cleavage pathway in ba3 cytochrome c oxidase from Thermus thermophilus.

Broken-symmetry density functional calculations have been performed on the [Fea3, CuB] dinuclear center (DNC) of ba3 cytochrome c oxidase from Thermus thermophilus in the states of [Fea3(3+)-(HO2)(-)-CuB(2+), Tyr237(-)] and [Fea3(4+)[double bond, length as m-dash]O(2-), OH(-)-CuB(2+), Tyr237˙], using both PW91-D3 and OLYP-D3 functionals. Tyr237 is a special tyrosine cross-linked to His233, a ligand of CuB. The calculations have shown that the DNC in these states strongly favors the protonation of His376, which is above propionate-A, but not of the carboxylate group of propionate-A. The energies of the structures obtained by constrained geometry optimizations along the O-O bond cleavage pathway between [Fea3(3+)-(O-OH)(-)-CuB(2+), Tyr237(-)] and [Fea3(4+)[double bond, length as m-dash]O(2-)HO(-)-CuB(2+), Tyr237˙] have also been calculated. The transition of [Fea3(3+)-(O-OH)(-)-CuB(2+), Tyr237(-)] → [Fea3(4+)[double bond, length as m-dash]O(2-)HO(-)-CuB(2+), Tyr237˙] shows a very small barrier, which is less than 3.0/2.0 kcal mol(-1) in PW91-D3/OLYP-D3 calculations. The protonation state of His376 does not affect this O-O cleavage barrier. The rate limiting step of the transition from state A (in which O2 binds to Fea3(2+)) to state PM ([Fea3(4+)[double bond, length as m-dash]O(2-), OH(-)-CuB(2+), Tyr237˙], where the O-O bond is cleaved) in the catalytic cycle is, therefore, the proton transfer originating from Tyr237 to O-O to form the hydroperoxo [Fea3(3+)-(O-OH)(-)-CuB(2+), Tyr237(-)] state. The importance of His376 in proton uptake and the function of propionate-A/neutral-Asp372 as a gate to prevent the proton from back-flowing to the DNC are also shown.

DFT study of structure, IR and Raman spectra of dendrimer with P[dbnd]N[sbnd]P[dbnd]S linkages and its complexation with gold

The Fourier transform IR and Raman spectra of the zero generation dendrimer G1 with two PNPS linkages and four terminal aldehyde groups have been recorded. The optimized geometry of low energy isomer of G1 have been calculated by density functional (DFT) method at the PBE/TZ2P level of theory. DFT is used for analyzing the properties of PNPS linkages. DFT results for the structure of G1 are in good agreement with X-ray diffraction measurements. A complete vibrational assignment is proposed for different parts of G1. The global and local reactivity descriptors have been used to characterize the reactivity pattern of the core function and terminal group. Natural bond orbital (NBO) analysis has been applied to comparative study of charge delocalization. Our study reveals that the softness and electrophilicity of sulfur atom in the core of the dendrimer G1 is higher than that of sulfur atoms and of the dendron G2. Thus PNPS linkage has a high electron density on sulfur which allows the regiospecific complexation of gold, whereas the other PS groups do not react this way. This explains why PN bond in PNPS linkage is much more stable than isolated PN bonds, which are easily hydrolyzed.

DFT study of structure, IR and Raman spectra of phosphorus-containing dendron with azide functional group

The Fourier transform IR and Raman spectra of the first generation dendron G1 built from thiophosphoryl core with terminal PCl groups and azide functional group have been recorded. The optimized geometries of low energy isomers of G1 have been calculated by density functional (DFT) method at the PBE/TZ2P level of theory. DFT is used for analyzing the properties of each structural part (core, branches, surface). It was found that the repeated branching units of G1 contain planar OC6H4CHNN(CH3)P< fragments. DFT results for the structure of G1 are in good agreement with recent X-ray diffraction measurements. A complete vibrational assignment is proposed for different parts of G1. The global and local reactivity descriptors have been used to characterize the reactivity pattern of the core function and terminal group. Natural bond orbital (NBO) analysis has been applied to comparative study of charge delocalization. Our study reveals why azide group linked to phosphorus has a different reactivity when compared to organic azides.

A conceptual density functional study of structure, bonding, reactivity and the possibility of bond-stretch isomerism in some neutral sulfur clusters, S n (n=3–8)

Geometries of different isomers of various neutral sulfur clusters, S n (n=3–8) are optimized at the B3LYP/6-311+G* level of theory. Their stability and aromaticity behavior are analyzed in terms of the conceptual density functional theory-based reactivity descriptors and the associated electronic structure principles. The nucleus-independent chemical shift lends additional support. Possibility of bond-stretch isomerism in these clusters is explored.

Density Functional Study of Structures and Electron Affinities of BrO4F/BrO4F-

The structures, electron affinities and bond dissociation energies of BrO4F/BrO4F− species have been investigated with five density functional theory (DFT) methods with DZP++ basis sets. The planar F-Br…O2…O2 complexes possess 3A′ electronic state for neutral molecule and 4A′ state for the corresponding anion. Three types of the neutral-anion energy separations are the adiabatic electron affinity (EAad), the vertical electron affinity (EAvert), and the vertical detachment energy (VDE). The EAad value predicted by B3LYP method is 4.52 eV. The bond dissociation energies De (BrO4F → BrO4-mF + Om) (m = 1–4) and De− (BrO4F− → BrO4-mF− + Om and BrO4F− → BrO4-mF + Om−) are predicted. The adiabatic electron affinities (EAad) were predicted to be 4.52 eV for F-Br…O2…O2 (3A′←4A′) (B3LYP method).

Molecular solvent model of cylindrical electric double layers: A systematic study by Monte Carlo simulations and density functional theory

We present the Monte Carlo simulation and density functional study of structure of cylindrical double layers considering solvent as the third component. We have chosen molecular solvent model, where ions and solvent molecules are considered as charged and neutral hard spheres, respectively, having equal diameter. The polyionic cylinder is modeled as an infinite, rigid, and impenetrable charged hard cylinder surrounded by the electrolyte and the solvent spheres. The theory is partially perturbative where the hard-sphere interactions are treated within the weighted density approach, the corresponding ionic interactions have been evaluated through second-order functional Taylor expansion with respect to the bulk electrolyte. The Monte Carlo simulations have been performed in canonical ensemble. The system is studied at varying concentrations of electrolyte ions and the solvent molecules, at different valences of the electrolyte, at different sizes of hard spheres, and at varying surface charge density. The theory and the simulation results are found to be in good agreement at different parametric conditions. The hard-sphere exclusion effects due to molecular nature of the solvent are shown to have special implications in characterizing diffuse layer phenomena such as layering and charge inversion.

Density functional study of structures and mechanical properties of Y-doped α-SiAlONs

A 2 × 2 × 1 supercell of α-Si 3N 4 is used to model Y-doped α-SiAlON's (silicoalumino oxonitrides). Ab initio total energy calculations are performed at the DFT (GGA) level. A full relaxation of atomic positions is performed for stoichiometric α-Si 3N 4 and for a series of substituted structures with concentrations of Y, Al and O increasing up to the composition Y 0.5Si 9.5Al 2.5O 1.0N 15.0, similar to the observed solubility limits. The avoidance of neighboring AlX 4 (X = N,O) tetrahedra in highly doped structures indicates that the distribution of Al atoms in the framework of α-SiAlON's obeys the same Loewenstein rule as in aluminosilicate zeolite structures. An increase of the lattice parameters and cell volumes is observed with increasing degree of the doping. Changes are more pronounced for the insertion of Y than for Si-N/Al-O substitution. An introduction of a Y 3+ cation into the interstitial position in the cage, however, causes a local contraction of the structure. Via the contraction a more efficient Y–N bonding is formed, leading to the stabilization of the Y-doped structure. The pronounced increase of the cell volume and the lattice parameters with Y-doping is due to three framework Al/Si framework substitutions compensating the extraframework Y 3+ cation. The calculated bulk modulus ( B 0) ranges from 223 GPa for pure α-Si 3N 4 to 197 GPa for Y 0.5Si 9.5Al 2.5O 1.0N 15.0. The slope of the decrease of B 0 with the degree of doping depends on the Y-content. For constant concentration of Y an increasing content of O causes a linear decrease of B 0.

A Density Functional Study of Structures and Vibrations of Ta3O and Ta3O−

Density functional calculations of neutral and anionic tantalum trimer monoxide are presented. The calculations were performed employing scalar quasi–relativistic effective core potentials. Different isomers of Ta3O and Ta3O- were studied in order to determinethe ground state structures. For both systems a planar C2vstructure with an edge-boundoxygen atom was found as ground state. Equilibrium structure parameters, harmonic frequencies, adiabatic electron affinity and Kohn-Sham orbital diagrams are reported. The calculated values are in good agreement with the available experimental data obtained from negative ion photoelectron spectroscopy. The correlation diagram between the neutral and anionic Ta3O shows that, in agreement with the experimental prediction, the extra electron in the anionic system occupies a nonbonding orbital.

A Density Functional Study of Structure and Stability of Ni8, Ni8 + and Ni8 − Cluster

Density functional calculations of neutral, cationic and anionic nickel octamer are presented. The structure optimization and frequency analysis were performed on the local density approximation (LDA) level with the exchange correlation functional by Vosko,Wilk and Nusair (VWN). Improved calculations for the stability were based on the generalized gradient approximation (GGA) where the exchange correlation functional of Perdew and Wang (PW) was used. For neutral, cationic and anionic cluster several isomers and different spin multiplicities were investigated in order to find the lowest structures. Structural parameters, relative energies, binding energies, harmonic frequencies, adiabatic ionization potential and electron affinity will be presented. The calculated values are compared with available experimental data.

Ab initio and Density Functional Study of Structure and Bonding of Cage Compounds Containing Boron, Phosphorus and Group 14 Atoms.

Ab initio and density functional calculations for five vertex cage compounds of the type P2(YB)2EH2, (E=C, Si, Ge, Sn, Y=H, H2N) using 6-311G++(d,p) and 3-21G++(d,p) basis sets, showed that they adopt a trigonal bipyramidal structure of C2v symmetry with the two phosphorus atoms occupying the apical position, the HB or NB groups residing in the trigonal basal plane. The theoretical results agree well with the experimental data for E=Si, Ge and Sn. For the carbon cage P2(HB)2CH2 this structure is a transition state and the minimum is a cage of Cs symmetry with a distorted B–B–C ring in the equatorial plane. Key structural parameters within the cages show a linear dependence on the covalent radii and the diffuseness of the orbitals of the heteroatom E. The results of the natural population analysis (NPA) and the values of nucleus independent chemical shifts (NICS) calculated reveal a bonding description very close to the idealized localized Lewis structure, in contrast to the parent P2(HB)3 cage. This is more pronounced in the case of the NH2 substituted cages.

Density functional study of structures and interaction hyperpolarizabilities of NH 3–HCl–(H 2O) n ( n=0–4) clusters

The optimized structures of NH 3–HCl–(H 2O) n ( n=0–4) clusters have been obtained by B3LYP/d-aug-cc-pVDZ method. In the structure of n=1, proton transfer occurs. It is different from the results of some references. The first hyperpolarizabilities ( β 0) and some other properties of the clusters were calculated and the basis set effects were also studied. On the properties of the clusters, the β 0 value reduces with the increasing number of water molecules. For the subunits NH 3–HCl, the β 0 value increases with the extent of proton transfer that result from an important solvent effects of water molecules.

Ab initio and density functional study of structure and bonding of cage compounds containing boron, phosphorus and group 14 atomsElectronic supplementary information (ESI) available: optimized bond lengths and angles. See http://www.rsc.org/suppdata/nj/b3/b301191g/

Ab initio and density functional calculations for five vertex cage compounds of the type P2(YB)2EH2, (E=C, Si, Ge, Sn, Y=H, H2N) using 6-311G++(d,p) and 3-21G++(d,p) basis sets, showed that they adopt a trigonal bipyramidal structure of C2v symmetry with the two phosphorus atoms occupying the apical position, the HB or NB groups residing in the trigonal basal plane. The theoretical results agree well with the experimental data for E=Si, Ge and Sn. For the carbon cage P2(HB)2CH2 this structure is a transition state and the minimum is a cage of Cs symmetry with a distorted B–B–C ring in the equatorial plane. Key structural parameters within the cages show a linear dependence on the covalent radii and the diffuseness of the orbitals of the heteroatom E. The results of the natural population analysis (NPA) and the values of nucleus independent chemical shifts (NICS) calculated reveal a bonding description very close to the idealized localized Lewis structure, in contrast to the parent P2(HB)3 cage. This is more pronounced in the case of the NH2 substituted cages.

A density functional study of structure and heat of formation for Br 2O 4 and Br 2O 5

The equilibrium structure, and heat of formation for both Br 2O 4 and Br 2O 5 molecules have been investigated using density functional theory. Four isomers for the Br 2O 4 and five isomers for the Br 2O 5 molecules are located. At B3LYP/6-311+G(3df) level of theory the heat of formation of the Br 2O 4 and Br 2O 5 molecules has been estimated to be in the range 68.7– 76.0 kcal mol −1 and 80.8– 107.5 kcal mol −1 , respectively. Analysis of the heat of formation, the structure of the isomers, and bromine–oxygen chemistry suggests that the gaseous Br 2O 4 and Br 2O 5 molecules may have a structure of BrOOBrO 2 and O 2BrOBrO 2/BrOOBrO 3/OBrOBrO 3, respectively.

Density-functional study of structures and electronic properties of Cd clusters

The lowest-energy structures and electronic properties of cadmium clusters are studied by density-functional theory with the generalized gradient approximation. The equilibrium structures of ${\mathrm{Cd}}_{n}$ $(n=2--21)$ clusters are determined from a number of structural isomers, which are generated from genetic algorithm simulations with a tight-binding potential. Various close-packed structures are found for cadmium clusters. ${\mathrm{Cd}}_{n}$ clusters with $n=4,9,10,15,17,20$ show relatively high stability, which can be related to the electron shell model, and agrees with experimental results. The density of states for the magic number clusters can also be associated with the electronic shell. The theoretical ionization potentials of ${\mathrm{Cd}}_{n}$ compare well with experimental values. The size evolution of electronic properties from van der Waals to covalent and bulk metallic behavior in Cd clusters is discussed.

A gradient-corrected density functional study of structure, harmonic vibrational frequencies and charge distribution of benzenesulfonate anion on the ground-state potential energy surface

A density functional study of the structure, harmonic vibrational force field, and charge distribution of benzenesulfonate anion combined with a solid-state FT-IR study of sodium benzenesulfonate is presented. Two combinations of exchange/correlation functionals (BLYP and B3LYP) were employed within the quantum chemical approach, using the standard double-zeta quality 6-31+G(d) basis set for orbital expansion. The DFT predicted structure of the studied species is in a very good agreement with the available crystallographic data (significantly better in comparison with our previous HF SCF results for benzenesulfonate and 4-methylbenzenesulfonate anions). Both the B3LYP and BLYP/6-31+G(d) vibrational analyses of the benzenesulfonate anion confirmed our previously proposed reassignments of several vibrational bands of this system based on the HF SCF/6-31+G(d) vibrational force field. The B3LYP predicted vibrational frequencies are superior to the BLYP ones. The Mulliken population analysis predicts a strong anionic charge delocalization over the phenyl ring (−0.54 and −0.56e, B3LYP and BLYP levels correspondingly), whereas according to the electrostatic potential derived schemes, it is mainly localized within the SO3 group. The latter result seems to be more in line both with the observed hydrogen bonding in the solid crystalline hydrates and with chemical intuition.

Structure and electrical conductivity in fluid high-density hydrogen

We present an ab initio Hohenberg - Kohn - Sham density functional study of structure and electrical conductivity in hot dense hydrogen. Our study covers the density range 0.40 - 1.34 ( = 1.5 - 1, P = 1.5 - 24 Mbar) at temperatures T = 800 - 3000 K. In this range both a molecular - atomic and an insulator - metal transition are expected to take place. Our results are compared with recent double-shock experiments in the hot fluid phase. We observe an increase in of an order of magnitude between and 1. At the lowest density, hydrogen is a molecular liquid below about 1100 K and continuously atomizes with increasing T. At the highest density, the sample is a monatomic liquid metal with high coordination number at all T. The metallic fluid is atomic, not molecular, for all densities investigated.

Density functional study of structure and bonding in lithium clusters Lin and their oxides LinO

Density functional (DF) calculations have been performed for lithium clusters Lin and their monoxides LinO with up to ten atoms. There are numerous stable structures, and new isomers have been found in each family. The structural patterns of the homonuclear and oxide clusters are quite distinct. The combination of DF calculations with molecular dynamics (MD) sheds light on the observed pseudorotation of Li3 and Li5. We compare with available experimental data and discuss the bonding and structural patterns in the clusters and their oxides, which are often described as “hyperlithiated.”