Large Bond Length Research Articles

Stability of the Bulk Phase of Layered ZnO

Recently a novel phase of ZnO has been synthesized which is analogous to α-boron nitride, although more three dimensional, and consists of planar hexagonal sheets of ZnO. Examining the dynamic stability of the structure, we find unstable phonon modes over a considerable part of the Brillouin zone. Local-density approximation (LDA) and generalized gradient approximation level calculations have usually been able to predict the structural stability of s-p bonded systems. The failure in the present case is a surprise and is traced to the self-interaction error which incorrectly locates the localized Zn d states in the valence band of ZnO. Correcting for this with a Hubbard-like U on the Zn d states, the optimized structure is predicted to be stable. This highlights the fact that the large bond length contraction that one finds in going from sp(3)- to sp(2)-type bonding results in an increased necessity to correct for self-interaction errors.

Diffusion of the Cu monomer and dimer on Ag(111): Molecular dynamics simulations and density functional theory calculations

We present results of molecular dynamics (MD) simulations and density functional theory (DFT) calculations of the diffusion of Cu adatom and dimer on Ag(111). We have used potentials generated by the embedded-atom method for the MD simulations and pseudopotentials derived from the projected-augmented-wave method for the DFT calculations. The MD simulations (at three different temperatures: 300, 500, and 700 K) show that the diffusivity has an Arrhenius behavior. The effective energy barriers obtained from the Arrhenius plots are in excellent agreement with those extracted from scanning tunneling microscopy experiments. While the diffusion barrier for Cu monomers on Ag(111) is higher than that reported (both in experiment and theory) for Cu(111), the reverse holds for dimers [which, for Cu(111), has so far only been theoretically assessed]. In comparing our MD result with those for Cu islets on Cu(111), we conclude that the higher barriers for Cu monomers on Ag(111) results from the comparatively large Ag-Ag bond length, whereas for Cu dimers on Ag(111) the diffusivity is taken over and boosted by the competition in optimization of the Cu-Cu dimer bond and the five nearest-neighbor Cu-Ag bonds. Our DFT calculations confirm the relatively large barriers for the Cu monomer on Ag(111)---69 and 75 meV---compared to those on Cu(111) and hint a rationale for them. In the case of the Cu dimer, the relatively long Ag-Ag bond length makes available a diffusion route whose highest relevant energy barrier is only 72 meV and which is not favorable on Cu(111). This process, together with another involving an energy barrier of 83 meV, establishes the possibility of low-barrier intercell diffusion by purely zigzag mechanisms.

Use of complex configuration interaction calculations and the stationary principle for the description of metastable electronic states of HCl−

The complex multireference single- and double-excitation configuration interaction method has been employed to compute potential curves for the anion of the hydrogen chloride molecule. First, conventional CI calculations with real basis functions have been carried out to determine the potential curves of both HCl and its anion over a large range of internuclear distance. It is shown that adding basis functions with very small exponents leads to sharply avoided crossings for the HCl(-) potentials that greatly complicate the search for resonance states thought to be responsible for features observed in electron collision experiments. By limiting the number of such diffuse-type functions it is possible to describe resonance states at a highly correlated level and still account for their interaction with the continuum in which they are embedded. In the present study of the HCl(-) anion the complex basis function technique of Moiseyev-Corcoran and McCurdy-Resigno is employed to calculate the energy positions and line-widths of the resonance states. Two states of (2)Sigma(+) symmetry are calculated which have potentials that have significantly different shapes than that of the neutral ground state and thus contribute to the cross section for vibrational excitation of the neutral HCl molecule induced by low-energy electron collisions. The lower of these (1 (2)Sigma(+)) correlates smoothly with the bound anionic ground state at large internuclear distances and is seen to be responsible for the sharp peaks observed in the low-energy region of the spectrum. The upper state (3 (2)Sigma(+)) has a much larger bond length and is assigned to the broad bands observed with a maximum in the 2.5-3.0 eV range. The present calculations thus stand in contradiction to earlier claims that the above peaks are caused by so-called virtual states without a definite autoionization lifetime.

Adsorption of molecular oxygen on doped graphene: Atomic, electronic, and magnetic properties

Adsorption of molecular oxygen on B-, N-, Al-, Si-, P-, Cr- and Mn-doped graphene is theoretically studied using density functional theory in order to clarify if O2 can change the possibility of using doped graphene for gas sensors, electronic and spintronic devices. O2 is physisorbed on B-, and Ndoped graphene with small adsorption energy and long distance from the graphene plane, indicating the oxidation will not happen; chemisorption is observed on Al-, Si-, P-, Cr- and Mn-doped graphene. The local curvature caused by the large bond length of X-C (X represents the dopants) relative to CC bond plays a very important role in this chemisorption. The chemisorption of O2 induces dramatic changes of electronic structures and localized spin polarization of doped graphene, and in particular, chemisorption of O2 on Cr-doped graphene is antiferromagnetic. The analysis of electronic density of states shows the contribution of the hybridization between O and dopants is mainly from the p or d orbitals. Furthermore, spin density shows that the magnetization locates mainly around the doped atoms, which may be responsible for the Kondo effect. These special properties supply a good choice to control the electronic properties and spin polarization in the field of graphene engineering.

The properties of dimers confined between two charged plates

We consider two like-charged planar surfaces immersed in solution of oppositely charged dimer counterions with a bond length l. To analyze this system, we extend and employ a self-consistent field theory that has been shown to be accurate from the weak to the intermediate through to the strong coupling regimes. In the limit of very short dimers, the results converge to the results for pointlike divalent ions. Near the surfaces, the dimers lie parallel to the charged plates. In the intermediate coupling regime, the dimers are aligned perpendicularly to the surface when they are a distance l from a surface. In the weak coupling regime, the interactions are only repulsive. At slightly higher couplings, there is a minimum in the variation of the free energy with distance at approximately the bond length of the dimers, which arises from bridging conformations of the dimers. In the intermediate coupling regime, an additional minimum in the free energy is observed at much smaller distances, which is due to the correlations between the dimers. For large dimer bond lengths, this minimum is metastable with respect to the previous minimum. However, as the bond length decreases, this minimum becomes the stable, while the minimum associated with the dimer bond length becomes metastable and eventually disappears. For shorter dimer bond length the attractive interaction is the result of correlations between counterions and charges on the surfaces. We find that dimers can mediate attractive interaction between like-charged surfaces in the intermediate coupling regime. The analysis of orientations confirms the bridging mechanism for sufficiently long dimers, whereas at high electrostatic couplings charge correlations contribute to the attraction.

Nanometer interatomic distances in Rydberg Matter clusters confirmed by phase-delay spectroscopy

Recently, rotational spectroscopy in the radio frequency range was used to determine the bond lengths in several types of potassium Rydberg Matter (RM) clusters with high precision (Mol Phy 105: 933–939, 2007). Due to the large bond lengths of a few nm and well-ordered structure of such clusters, it is expected that light scattering can be used to determine their dimensions. A weak carbon dioxide laser beam is introduced collinearly into a tunable RM cavity. When RM is formed, a very pronounced fringe structure with several hundred fringes is observed at the detector as a function of the grating position. These fringes show a phase delay of the carbon dioxide laser light caused by reflections within the RM clusters. The delay lengths derived from the fringe structure give distances between the rows of atoms in the clusters. The excitation level of the most easily observed clusters is n = 5. Clusters with n = 6, 7, and 8 are also commonly detected. The bond distance for n = 5 is found to be 3.804 ± 0.015 nm, while that for n = 6 is 5.525 ± 0.014 nm, in accurate agreement with values from rotational spectroscopy.

First-Principles Langevin Molecular Dynamics Studies of Metallic and Semiconductor Clusters: GGA versus LDA Results

The combination of Langevin molecular dynamics for simulated annealing with realistic quantum-mechanical interactions obtained from first principles supercell calculations within the pseudo potential plane-wave method are applied to examine the structural and electronic properties of the following systems i) pure and mixed GenTem (n, m = 0 - 2), Ge3, Te3 and Ge3Te3 semiconductor clusters, and ii) bimetallic PbNan (n ≤ 7) clusters. Results using the local density approximation (LDA) and the generalized gradient approximation (GGA) for the exchange correlation functional are compared with available experimental data. It is found that the GGA leads to larger bond lengths and smaller binding energies than the LDA, but both approximations lead to the same group symmetry for the ground state of these clusters. Two isomeric configurations for PbNa6, having C3v and Oh symmetries, respectively, are found. The dipole moments of semiconductor clusters are compared with those estimated from recent experiments at room temperature. The dipole moments from GGA calculations are, on average, in better agreement with experiments than those calculated with the LDA.

Ab initio vibrational predissociation dynamics of He–I2(B) complex

Three-dimensional quantum mechanical calculations on the vibrational predissociation dynamics of HeI2 B state complex are performed using a potential energy surface accurately fitted to unrestricted open-shell coupled cluster ab initio data, further enabling extrapolation for large I2 bond lengths. A Lanczos iterative method with an optimized complex absorbing potential is used to determine energies and lifetimes of the vibrationally predissociating He,I2(B,v') complex for v'<or=26 of I2 vibrational excitations. The calculated predissociating state energies agree with recent experimental results within 0.5 cm(-1). This excellent agreement is remarkable since no adjustment was made with respect to the experiments. The present ab initio approach, however, shows its limitations in the fact that the computed lifetimes that are highly sensitive to subtle details of the potential energy surfaces such as anisotropy, are a factor of 1.5 larger than the available experimental data.

Conformational analysis for some nonclassical antagonists of histamine H3 receptor

AbstractA conformational search in vacuum for a series of 1,3‐substituted pyrrolidine derivatives has been performed using the AMBER, AM1, PM3, and MNDO methods. Conformational analysis of the pyrrolidine ligands suggests that these compounds could have many conformers that populate the low‐energy minima on the potential energy surface (PES). The conformational space occupied by the ligands is large and, in vacuum, the rotation barriers of different flexible bonds have energies between 0.5 and thousands of kcal/mol. By optimization, most conformers have energy barriers of 0–5 kcal/mol; thus, they could interconvert easily to obtain better interactions in the receptor active site. Optimized conformers having energy barriers of &gt;5 kcal/mol display bad geometries with very large bond lengths and deformed rings. Shapes and heights of rotation barriers obtained through COSMO–AM1 single‐point calculations in water are similar to those obtained from single‐point calculations in vacuum. However, in water the energy barriers are lower, allowing most conformers to convert in other low‐energy conformers. The best conformers in vacuum and in water are different: the gas phase best conformer has a helical shape, while the best conformer in water has an extended shape. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007

Charging mechanism for the bond elongation observed in suspended chains of gold atoms

Abnormally large bond lengths $(3.5--5.0\phantom{\rule{0.3em}{0ex}}\mathrm{\AA{}})$ between gold atoms forming small chains suspended between two electrodes have been observed in some experiments. Using the density functional theory we explore the possibility that the elongation could arise from the electrical charging of the chains induced in nonequilibrium by the electron beam of the transmission electron microscope used to image the nanowires in those experiments.

Computer simulations in the study of gold nanowires: the effect of impurities

Suspended gold nanowires have recently been made in an ultra-high vacuum ambient and were imaged by electron microscopy. Two puzzles were presented: one atom thick wires are produced and some of the atomic distances between these atoms before their breaking were too large. Simulations using realistic molecular dynamics method were able to unveil some processes to explain the mechanisms of formation, evolution, and breaking of these atomically thin Au nanowires under stress. The calculations showed how defects induce the formation of constrictions that eventually will form the one-atom chains. Atomically thin chains, five atoms long were obtained, before breaking. The results were in excellent agreement with experimental results except for the large Au-Au distances. In fact no theoretical calculation of pure gold nanowires have been able to produce such large distances. Light impurities that cannot be imaged in these experiments may be responsible for these large Au-Au distances. Using ab initio total energy calculations based on the density functional theory, we have studied the effect of H, C, O, N, B, S, CH, CH2, and H2 impurities on the nanowire’s electronic and structural properties, in particular how they affect the rupture of the nanowire. We find that the impurities tend to locally increase the nanowire’s strength, in such a way that its rupture always occurs at an Au-Au bond and never at an Au-X bond (X being an impurity). In particular, oxygen seems to form very stable bonds that may be used to pull longer Au chains. Regarding the observed large Au-Au bond lengths, it was found, based on quasi-static calculations, that the best candidate to explain the large distances is H. However, some particular experimental conditions may lead to different results.

Second-Order Møller−Plesset Evaluation of the Bond Length Alternation of Several Series of Linear Oligomers

We investigate, at the second-order Møller-Plesset level, the bond length alternation of 30 series of increasingly long linear oligomers for a total of more than 250 compounds, polyacetylene, polymethineimine, polyphosphinoborane, polyaminoborane, polyphosphazene, etc., for which, often for the first time, an accurate estimate of the polymeric bond length alternation is given. The variations induced either by chemical substitution of the backbone atoms or conformational modifications are discussed. Only three polymers present a large bond length alternation (>0.03 A). Systematic basis set effects have been unravelled, i.e., MP2/6-311G(2d) always overshoots the bond length alternation. Best estimates of the bond length alternation are provided for more than a dozen of polymers.

Theoretical analysis on the geometries and electronic structures of coplanar conjugated poly(azomethine)s

In this study, theoretical analysis on the geometries and electronic properties of various conjugated poly(azomethine)s is reported. The theoretical ground-state geometry and electronic structure of the studied poly(azomethine)s are optimized by the hybrid density functional theory (DFT) method treated in periodic boundary conditions at the B3LYP level of theory with 6-31G basis set. The geometry and electronic structure of poly(1,4-phenylenemethylidyneitrilo-1,4-phenylene-nitrilomethylidyne) ( PPI) are compared with those of poly( p-phenylene vinylene) ( PPV) or polyazine ( PAZ). The theoretical results suggest the non-coplanar conformation of PPI but PPV and PAZ with a coplanar conformation. The electronic properties of PPI are in the intermediate between PPV and PAZ. The non-coplanar conformation of PPI could be released if the phenylene ring is replaced by the five-member ring of 3,4-ethylenedioxythiophene ( PEEI), pyrrole ( PYYI), thiophene ( PTTI), furan ( PFFI), or thiadiazole ( PThThI). The theoretical E g of PEEI, PYYI, PFFI, and PTTI are in the range of 1.11–1.67 eV, which is due to the coplanar configuration or donor–acceptor intrachain charge transfer. However, the large bond length alternation or lack of charge transfer characteristic makes the PThThI with a larger E g of 2.47 eV than others. The trend on the IP or EA of the studied conjugated poly(azomethine)s are consistent with the electronic characteristic of the aromatic ring. The upper valence bandwidth of the studied five-member ring based poly(azomethine)s except PThThI is in the range of 562–613 meV, which is larger than that of PPI (247 meV) or PPV (373 meV). The results suggest that the electronic properties of conjugated poly(azomethine)s could be varied through various ring structure. The proposed new coplanar conjugated poly(zomethine)s can be potentially used as transparent conductors or thin film transistors.

Describing static correlation in bond dissociation by Kohn–Sham density functional theory

We show that density functional theory within the RPA (random phase approximation for the exchange-correlation energy) provides a correct description of bond dissociation in H(2) in a spin-restricted Kohn-Sham formalism, i.e., without artificial symmetry breaking. We present accurate adiabatic connection curves both at equilibrium and beyond the Coulson-Fisher point. The strong curvature at large bond length implies important static (left-right) correlation, justifying modern hybrid functional constructions but also demonstrating their limitations. Although exact at infinite separation and accurate near the equilibrium bond length, the RPA dissociation curve displays unphysical repulsion at larger but finite bond lengths. Going beyond the RPA by including the exact exchange kernel (RPA+X), we find a similar repulsion. We argue that this deficiency is due to the absence of double excitations in adiabatic linear response theory. Further analyzing the H(2) dissociation limit we show that the RPA+X is not size consistent, in contrast to the RPA.

Synthesis, structure, and redox properties of crowded triarylphosphines carrying 2,6-diarylphenyl substituents

Crowded triarylphosphines carrying 2,6-diarylphenyl and 2,4,6-trialkylphenyl groups were synthesized by the reaction of arylcopper(I) reagent with the chlorophosphines. The triarylphosphines had large bond angles and lengths around the phosphorus and were reversibly oxidized at significantly low potentials. X-ray crystallography of bis(2,4,6-triisopropylphenyl)[4-methyl-2,6-di(1-naphthyl)phenyl]phosphine revealed that two 1-naphthyl groups took anti conformation in the crystal.

Effect of the nature of mendiaxon−–X+ interactions (X+= Na+, Cu+, H+) and the hydrogen bonding on the ν(CO) behavior: theoretical and spectroscopic study

Theoretical and spectroscopic (IR and Raman) study of different 7-hydroxy-4-methylcoumarin (mendiaxon) systems (mend−, mendNa, mendCu, mendH and mendH · 2H2O) were performed at B3LYP/6-31G(d) and B3LYP/6-31++G(d,p) levels of theory. The geometric and electronic structures as well as the vibrational behavior of the systems studied were discussed: (1) as to the changes that occurred in the anion coumarin ring upon the mend−–X+ (X+ =Na+, Cu+, H+) interactions and (2) as to the changes that occurred in mendH due to hydrogen bondings in mendH · 2H2O. The largest bond length changes in the anion coumarin ring were obtained for mendH and the smallest ones for mendNa. The bond length changes were mainly produced from the electrostatic effect of the positive charge of X. The induced polarization of the CO bond upon the mend−–X+ interactions was found to be opposite to the basic one and it led to shorter CO bond lengths (higher ν(CO) frequencies) in the order: mendNa, mendCu and mendH. Conversely, upon the hydrogen bonding the induced polarization of the CO bond was found in the same direction as the basic one and it produced elongation to the CO bond length (lower ν(CO) frequency). On the basis of the correlations found, the ν(CO) positions in mendNa, mendCu, mendH and mendH · 2H2O were explained.

Water molecule by the self-consistent atomic deformation method

We present a density functional method which expresses the charge density of a system of atoms as a sum over localized atomiclike densities derived from potentials defined variationally from the total energy expression, which includes contributions from overlapping densities. An approach for systematically increasing the variational freedom of the atomiclike densities is introduced and tested for the water molecule. For the water molecule our method results in complete charge transfer for sufficiently small bond lengths and reverses the charge transfer at large bond lengths. In case of complete charge transfer the overlap contributions are zero, allowing a direct comparison with the traditional Kohn--Sham approach.

Model Calculations of Radiation-Induced Damage in Thymine Derivatives

When the thymine base is oxidized, the resulting cation may deprotonate reversibly at N3, or irreversibly at >C5-CH3. In all thymine derivatives studied so far in the solid state, there is always a significant concentration of a radical formed by net H-abstraction from the >C5-CH3. DFT calculations on this allyl-like radical are in good agreement with the experimental results for both the isotropic and anisotropic hyperfine couplings. There is a tendency for the thymine cation to deprotonate at N3 in solution. Calculations on the N3 deprotonated thymine cation yield two structures, one planar radical with an unusually large N1-C2 bond length, and one nonplanar radical with the N3 more than 25° out of the molecular plane. Calculations show that the structure with the lowest energy is the allyl-like radical.

Crossover behavior in dilute polymer solutions: Square-well chains

Monte Carlo simulations for model polymer chains composed of hard spheres with square-well attractions were performed to find a precise relation between the parameters of a crossover theory and the parameters of the square-well chain. For sufficiently large bond lengths, there was a direct relation between the effective parameters of the crossover theory and the second- and third-virial coefficients of the square-well atoms. For the systems under study, the theta temperature is close to the Boyle temperature of the disconnected monomers, is mainly dependent on the details of the monomer–monomer interactions, and is only weakly dependent on the bond length of the chain. Above the theta temperature, the crossover theory is in good agreement with the simulation data. Near the theta point, the main effect of tricritical corrections is a shift in the critical amplitudes. Other effects are extremely small. The simulation data are consistent with the tricritical crossover theory. However, more precise data are needed to quantitatively test the tricritical crossover theory.

Electronic structure of the bulk and layers of thealkaline earths (Be-Ba)

We report the results of electronic structure calculations for the bulk and layers of the alkaline earths (Be-Ba) made using the linearized muffin-tin orbital method within the local density approximation. In agreement with experiments, bulk calcium and strontium are found to undergo a metal-semi-metal transition under compression, whereas for each of these elements a single (100) layer is found to have vanishing density of states at the Fermi energy at normal pressure. A layer of Ba, on the other hand, exhibits a similar behaviour under expansion. As compared to the bond length for the bulk, there is an expansion for a single layer in all of the cases. This expansion is large for Mg, which is consistent with the large bond length of the Mg dimer. The binding energy for a single layer is close to its value for dimers but it increases by a large amount for three layers. These results are discussed in terms of the changes in the s-p/d hybridization with the reduction in the coordination, and its importance for understanding the properties of clusters of transition metals.