Dimer Bond Length Research Articles

Relativistic Fully Self-Consistent GW for Molecules: Total Energies and Ionization Potentials.

The fully self-consistent GW (scGW) method with an iterative solution of the Dyson equation provides a consistent approach for describing the ground and excited states without any dependence on the mean-field reference. In this work, we present a relativistic version of scGW for molecules containing heavy elements using the exact two-component (X2C) Coulomb approximation. We benchmark SOC-81 data set containing closed shell heavy elements for the first ionization potential using the fully self-consistent GW as well as one-shot GW. The self-consistent GW provides superior results compared to G0W0 with PBE reference and comparable results to G0W0 with PBE0 while also removing the starting point dependence. The photoelectron spectra obtained at the X2C level demonstrate very good agreement with the experimental spectra. We also observe that scGW provides very good estimation of ionization potential for the inner d-shell orbitals. Additionally, using the well-conserved total energy, we investigate the equilibrium bond length and harmonic frequencies of a few halogen dimers using scGW. Overall, our findings demonstrate the applicability of the fully self-consistent GW method for accurate ionization potential, photoelectron spectra, and total energies in finite systems with heavy elements with a reasonable computational scaling.

Reexamination of the ground-state Born-Oppenheimer Yb2 potential

The precision of the photoassociation spectroscopy of Yb dimer in degenerate gases is enough to improve the constraints on the new short-range gravity-like forces if the theoretical knowledge of the Born-Oppenheimer interatomic potential and non-Born-Oppenheimer interactions is refined [M. Borkowski et al. Sci. Rep. A {\bf 9}, 14807 (2019)]. The ground-state interaction potential of ytterbium dimer is investigated at the eXact 2-component core-correlated CCSD(T) level of {\it ab initio} theory in the complete basis set limit with extensive augmentation by diffuse functions. For the small basis set the comparison is made with the four-component relativistic finite-nuclei CCSD(T) calculations to identify the contraction of the dimer bond length as the main unrecoverable consequence of the scalar-relativistic approximation. Empirical constraint on the number of bound vibrational energy levels of the $^{174}$Yb$_2$ dimer is accounted for by representing the global {\it ab initio}-based Born-Oppenheimer potential with the model semianalytical function containing the scale and shift parameters. The results support the previous evaluation of the Yb dimer potentials from the photoassociation spectroscopy data and provide an accurate and flexible reference for future refinement of the constraints on the short-range gravity-like forces by ultracold atomic spectroscopy.

Effects of Mn-substitution on the valence bond solid in Li2RuO3

$Li_{2}RuO_{3}$ with a honeycomb structure undergoes a drastic transition from a regular honeycomb lattice with the $C2/m$ space group to a valence bond solid state of the $P2_{1}/m$ space group with an extremely strong dimerization at 550 K. We synthesized $Li_{2}Ru_{1-x}Mn_{x}O_{3}$ with a full solid solution and investigated doping effects on the valence bond solid state as a function of Mn content. The valence bond solid state is found to be stable up to $x = 0.2$, based on our extensive experiments: structural studies, resistivity, and magnetic susceptibility. On the other hand, the extended x-ray absorption fine structure analyses show that the dimer local structure remains robust even above $x = 0.2$ with a minimal effect on the dimer bond length. This indicates that the locally-disordered dimer structure survives well into the Mn-rich phase even though the thermodynamically stable average structure has the $C2/m$ space group. Our results prove that the dimer formation in $Li_{2}RuO_{3}$ is predominantly a local phenomenon driven by the formation of orbitally-assisted metal-metal bonds and that these dimers are relatively robust against doping-induced disorder.

Estimation of the decay rate of Be7 and Be27 encapsulated in C70

Electron capture ($\ensuremath{\beta}$-decay) rates of $^{7}\mathrm{Be}$ and $^{7}\mathrm{Be}_{2}$ encapsulated in ${\mathrm{C}}_{70}$ have been estimated by calculating the electron density $\ensuremath{\rho}(0)$ at the $^{7}\mathrm{Be}$ nucleus and comparing it with $\ensuremath{\rho}(0)$ and experimental $\ensuremath{\beta}$-decay rates of $^{7}\mathrm{Be}$ inside another fullerene---${\mathrm{C}}_{60}$. For that the endohedral fullerenes $^{7}\mathrm{Be}@{\mathrm{C}}_{70}$ and $^{7}\mathrm{Be}_{2}@{\mathrm{C}}_{70}$ have been examined by means of the ab initio approach using the Hartree-Fock method with the the second order M\o{}ller-Plesset perturbation theory accounting for the Van der Waals foces. Our calculations indicate that the $^{7}\mathrm{Be}_{2}@{\mathrm{C}}_{70}$ complex is stable with the binding energy of 1.3 eV and the $^{7}\mathrm{Be}$ dimer bond length 2.30 \AA{}. It has been found that $\ensuremath{\rho}(0)$ is practically the same in $^{7}\mathrm{Be}@{\mathrm{C}}_{70}$ and $^{7}\mathrm{Be}_{2}@{\mathrm{C}}_{70}$, but larger than in an isolated $^{7}\mathrm{Be}$ atom. The increase of $\ensuremath{\rho}(0)$ however is smaller than in $^{7}\mathrm{Be}@{\mathrm{C}}_{60}$. We also discuss in detail the mechanism underlying the increase of $\ensuremath{\rho}(0)$ and consequently the decrease of the decay rate in $^{7}\mathrm{Be}@{\mathrm{C}}_{70}$ in comparison with the isolated $^{7}\mathrm{Be}$ atom.

Magnetic properties of HoCoC2, HoNiC2 and their solid solutions

Magnetic properties of single crystalline HoCoC2 and the evolution of magnetic and structural features in a series of polycrystalline solid solutions HoCo1−xNixC2(0⩽x⩽1) are investigated by means of X-ray diffraction, magnetization, magnetic susceptibility and specific heat measurements. The crystal structures of all investigated samples refers to the CeNiC2-type structure (space group Amm2 and Pearson symbol oS8). Non-isoelectronic substitution of Co by Ni causes a non-linear increase of the unit cell volume and especially a non-monotonous variation of the a and c lattice parameters as well as a pronounced reduction of the C–C bond length of carbon dimers. Temperature dependent magnetization and specific heat measurements reveal a crossover from a ferromagnetic for HoCoC2 with TC=10.6(1)K to an antiferromagnetic ground state for HoNiC2 with TN=2.78(6)K and a non-monotonous variation of the magnetic ordering temperature with a minimum at intermediate compositions. Crystalline electric field effects of HoCoC2 and HoNiC2 are analysed using combined thermodynamic and magnetic susceptibility data. The electrical resistivity of HoNiC2 displays a distinct anomaly near room temperature which indicates the formation of a charge density wave (CDW) state as earlier reported for several other rare earth nickel dicarbides.

MN15: A Kohn-Sham global-hybrid exchange-correlation density functional with broad accuracy for multi-reference and single-reference systems and noncovalent interactions.

Kohn-Sham density functionals are widely used; however, no currently available exchange-correlation functional can predict all chemical properties with chemical accuracy. Here we report a new functional, called MN15, that has broader accuracy than any previously available one. The properties considered in the parameterization include bond energies, atomization energies, ionization potentials, electron affinities, proton affinities, reaction barrier heights, noncovalent interactions, hydrocarbon thermochemistry, isomerization energies, electronic excitation energies, absolute atomic energies, and molecular structures. When compared with 82 other density functionals that have been defined in the literature, MN15 gives the second smallest mean unsigned error (MUE) for 54 data on inherently multiconfigurational systems, the smallest MUE for 313 single-reference chemical data, and the smallest MUE on 87 noncovalent data, with MUEs for these three categories of 4.75, 1.85, and 0.25 kcal mol-1, respectively, as compared to the average MUEs of the other 82 functionals of 14.0, 4.63, and 1.98 kcal mol-1. The MUE for 17 absolute atomic energies is 7.4 kcal mol-1 as compared to an average MUE of the other 82 functionals of 34.6 kcal mol-1. We further tested MN15 for 10 transition-metal coordination energies, the entire S66x8 database of noncovalent interactions, 21 transition-metal reaction barrier heights, 69 electronic excitation energies of organic molecules, 31 semiconductor band gaps, seven transition-metal dimer bond lengths, and 193 bond lengths of 47 organic molecules. The MN15 functional not only performs very well for our training set, which has 481 pieces of data, but also performs very well for our test set, which has 823 data that are not in our training set. The test set includes both ground-state properties and molecular excitation energies. For the latter MN15 achieves simultaneous accuracy for both valence and Rydberg electronic excitations when used with linear-response time-dependent density functional theory, with an MUE of less than 0.3 eV for both types of excitations.

ChemInform Abstract: Conformational Preferences of 2‐Acylpyrroles in Light of FT‐IR and DFT Studies

AbstractReview: 129 refs.

Conformational Preferences of 2-Acylpyrroles in Light of FT-IR and DFT Studies

Conformations of alpha-substituted pyrroles have been effectively studied using spectroscopic methods assisted by theoretical calculations developed in the recent decade. The question of how to effectively study the conformation of 2-acylpyrrole no longer remains unanswered. The detailed spectroscopic studies conducted in the last decade and interpreted on the basis of theoretical calculations provide a satisfactory answer to that question. Based on the Density Functional Theory (DFT) calculations of conformational properties of 2-acylpyrroles, for which two stable rotameric forms were predicted, syn and anti-conformers have been studied either by experimental or theoretical methods. The family of 2-acylpyrroles have both a proton donor N-H group and a proton acceptor C=O group. This structure favors the formation of doubly hydrogen-bonded cyclic dimers connected by two N-H...O=C bonds. The tendency to form cyclic dimers stabilizes the syn-conformation. Due to these properties 2-acylpyrroles can be used as structural models for the conformational analysis of peptides. This review summarizes recent investigations of conformations of 2-acylpyrroles, with a particular emphasis on the hydrogen bonds forming within these systems. The influence of 2-substitution on different aspects of stability of these molecular systems and the usefulness of infrared spectroscopy supported by theoretical calculations in H-bonds and conformational studies are discussed. Among the molecular properties hydrogen bond energy, structural characteristics such as C=O bond length of dimers and unique spectral features of 2-acylpyrroles that can be used to predict and investigate the conformation and structure of proteins are considered.

Ab initio study of platinum induced reconstructions on Ge(001)–(1×2) surface with dimerization

We present first principle total energy calculation of Pt induced reconstructions on Ge(001)–(1×2) surface with dimerization. Study was undertaken using localized orbitals basis set DFT using SIESTA to compare pure Ge dimerized Ge(001)–(1×2) surface with 0.5 and 1.0 Pt covered dimerized Ge(001)–(1×2) surface with the possibility of homo (Ge–Ge and Pt–Pt) and hetro (Pt–Ge) dimers. From total energy calculation results we calculated dimer bond lengths, buckling angles and formation energy of dimers on Ge(001)–(1×2) surface. By calculating the formation energy of different configurations we find that Ge–Ge buckled dimerized surface has least (−1.23 eV/dimer) and Pt–Pt symmetric dimerized surface has largest (+0.09 eV/dimer) formation energy with respect to unreconstructed surface. We further calculated the electronic DOS and band structure of Ge dimerized as well as Pt dimerized surface to see the change in semiconducting behavior on dimerization. By comparing the DOS and electronic band structure of homo Ge dimerized surface, we found metallicity of Ge(001)–(1×2) surface results from dimer formation. Also by comparing the electronic band structure of homo Ge dimerized surface with unreconstructed surface we find that less number of bands crossing the Fermi level which is perhaps due to the saturation of one dangling bond per Ge surface atom. By introducing Pt at 0.5 and 1.0 coverage in place of Ge, except for homo Pt buckled dimerized surface having 1.0 coverage of Pt, we find in all other cases increase in number of bands are crossing the Fermi level, indicating strong metallic behavior of Ge(001)–(1×2) surface.

Atomic structure and composition of the2×Nreconstruction of the Ge wetting layer on Si(001) investigated by surface x-ray diffraction

The 2 \ifmmode\times\else\texttimes\fi{} $N$ reconstruction of the Ge/Si(001) wetting layer has been investigated by surface x-ray diffraction. At a substrate temperature of $670 {}^{ˆ}\mathrm{C}$, the average $N$ periodicity decreases from $N$ $=$ 11.5 to 8 with an increasing Ge coverage from one to three monolayers (ML). The top layer consists of asymmetric dimers with a bond length in the range of 2.50--2.60 \AA{} and a buckling angle in the range of 9.4\ifmmode^\circ\else\textdegree\fi{}--15.6\ifmmode^\circ\else\textdegree\fi{}, depending on the Ge coverage. The obtained dimer bond lengths are similar to those calculated for alternating asymmetric mixed dimers. Intermixing of Ge with Si is found down to the sixth (eighth) layer for 2 (from 3 to 5) ML coverage. For 2 ML coverage, a quantitative surface x-ray diffraction data set has been measured. It is analyzed using a model describing the atomic structure and Ge occupation probability with a limited set of parameters to bypass the intrinsic lack of appreciable reflections of the 2 \ifmmode\times\else\texttimes\fi{} $N$ ($N$ $=$ 9) reconstruction. The Ge occupation probability varies periodically along the $N$ direction, having its minimum value below the dimer vacancy lines. In addition, a more direct calculation of the Lorentz and detector acceptance corrections is given for rocking and radial scans.

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.

Electric-field effects on the diffusion of Si and Ge adatoms on Si(001) studied by density functional simulations

We present results of density functional theory (DFT) calculations of the electric-field effects on the clean Si(001) surface and the diffusion of Si or Ge adatoms on Si(001) surface. Our results indicate that the electric field only slightly affected the dimer bond lengths and buckling angles of the clean Si(001), implying that the electric field of scanning tunneling microscopy tip should not be responsible for the observation of symmetric dimers and the flip-flop motion of the buckling dimers. Also, the electric field mainly influences the diffusion along the dimer row, and the diffusion barrier could be reduced greatly under a positive electric field. It can be expected that the positive field should make the diffusion of Si or Ge adatoms on the Si(001) surface become more anisotropic.

Solvation pressure in a Lennard-Jones fluid by molecular dynamics simulation

We present molecular dynamics simulations of a simple dimer immersed in a Lennard-Jones (LJ) fluid to test the validity of the solvation pressure model in a system where we attempt to isolate the general and ubiquitous solvation pressure. The solvated dimer acts as a simple pressure gauge in a system where the cohesive energy density (CED) of the solvent is fixed. We study the dimer bond length as a function of uniform hydrostatic pressure and as a function of a scaling parameter $x$ which changes the attractive component of the LJ solvent-solute interaction. For small $x$, or weak solvent-solute attractive interactions, the liquid bond lengths are dominated by repulsive interactions, but at higher values of $x$ strong solvent-solute interactions produce a ``packing effect'' that is the dominant factor. We find that the change in bond length between vapor and liquid is consistent with the solvation pressure model for only a narrow range of $x$. Despite the simplicity of the system, departure from the solvation pressure model and an increase in the dimer bond length with increasing pressure are observed which is consistent with experimental observations of real liquids and normally attributed to masking effects. The existence and impact of these effects are explained in terms of CED, axial forces, and axial pressures.

Charge Dynamics in Thermally and Doping Induced Insulator-Metal Transitions of(Ti1−xVx)2O3

Charge dynamics of (Ti1-xVx)2O3 with x=0-0.06 has been investigated by measurements of charge transport and optical conductivity spectra in a wide temperature range of 2-600 K with the focus on the thermally and doping induced insulator-metal transitions (IMTs). The optical conductivity peaks for the interband transitions in the 3d t_{2g} manifold are observed in both the insulating and metallic states, while their large variation (by approximately 0.4 eV) with change of temperature and doping level scales with that of the Ti-Ti dimer bond length, indicating the weakened singlet bond in the course of IMTs. The thermally and V-doping induced IMTs are driven with the increase in carrier density by band crossing and hold doping, respectively, in contrast with the canonical IMT of correlated oxides accompanied by the whole collapse of the Mott gap.

Calculation of surface energy and simulation of reconstruction for diamond cubic crystals (0 0 1) surface

The energies of the ideal (1 × 1), dimer (2 × 1) and trimer (3 × 1) structures on (0 0 1) surfaces have been calculated by using MEAM for three diamond cubic crystals C, Si and Ge. From energy minimization, the dimer (2 × 1) and trimer (3 × 1) reconstructions can be formed naturally and without any barrier. The dimer corresponding to the lowest energy implies it is the easiest to be formed and the most stable as well. This is consistent with the experimental result and other theoretical prediction. Determined dimer bond length of 2.43 Å for Si drops in the experimental range of 2.20–2.47 Å, and of 2.5 Å for Ge is close to the 2.55 Å measured by X-ray diffraction. The trimer, constructed here firstly, has not been observed in the experimental due to its slightly higher energy than dimer. Its bond lengths have been determined to be 1.96, 2.64 and 2.75 Å for C, Si and Ge, respectively. Further experimental testing is needed.

Electronic Properties of Y2C3 by First-Principles Calculations

The electronic and structural properties of Y 2 C 3 are studied from first principles. We optimize all the structural parameters, the lattice constant and internal atomic positions, assuming the observed crystal structure symmetry. We also examine the lattice-constant and the C dimer bond length dependences of the electronic properties of Y 2 C 3 . It is found that there is a peak structure in close vicinity to the Fermi energy in the density of states for the optimized structure at all the lattice constants studied. This peak structure comes from a flat band along ΓN line.

Density Functionals for Inorganometallic and Organometallic Chemistry

We present a database of 21 bond dissociation energies for breaking metal-ligand bonds. The molecules in the metal-ligand bond energy database are AgH, CoH, CoO+, CoOH+, CrCH3+, CuOH2+, FeH, Fe(CO)5, FeO, FeS, LiCl, LiO, MgO, MnCH3NiCH2+, Ni(CO)4, RhC, VCO+, VO, and VS. We have also created databases of metal-ligand bond lengths and atomic ionization potentials. The molecules used for bond lengths are AgH, BeO, CoH, CoO+, FeH, FeO, FeS, LiCl, LiO, MgO, RhC, VO, and VS and the ionization potentials are for the following atoms: C, Co, Cr, Cu, Ni, O, and V. The data were chosen based on their diversity and expected reliability, and they are used along with three previously developed databases (transition metal dimer bond energies and bond lengths and main-group molecular atomization energies) for assessing the accuracy of several kinds of density functionals. In particular, we report tests for 42 previously defined functionals: 2 local spin density approximation (LSDA) functionals, 14 generalized gradient approximation (GGA) methods, 13 hybrid GGA methods, 7 meta GGA methods, and 8 hybrid meta GGA methods. In addition to these functionals, we also examine the effectiveness of scaling the correlation energy by testing 13 functionals with scaled or no gradient-corrected correlation energy, and we find that functionals of this kind are more accurate for metal-metal and metal-ligand bonds than any of the functionals already in the literature. We also present a readjusted GGA and a hybrid GGA with parameters adjusted for metals. When we consider these 57 functionals for metal-ligand and metal-metal bond energies simultaneously with main-group atomization energies, atomic ionization potentials, and bond lengths we find that the most accurate functional is G96LYP, followed closely by MPWLYP1M (new in this article), XLYP, BLYP, and MOHLYP (also new in this article). Four of these five functionals have no Hartree-Fock exchange, and the other has only 5%. As a byproduct of this work we introduce a convenient diagnostic, called the B1 diagnostic, for ascertaining the multireference character in a bond.

Mechanisms for correlated surface diffusion of weakly bonded dimers

We propose a model for the potential energy of a dimer on a surface that allows to identify the relevant reaction paths for diffusion and assess the favored path as the result of a competition between gain of potential energy due to the atom surface interaction and loss of elastic energy due to stretching of the dimer bond. We show that atoms forming weakly bonded dimers tend to diffuse via individual jumps although they remain bound to each other during the process, giving a rationale for the correlated piecewise diffusion observed on Si(001). For dimer equilibrium lengths smaller than the surface periodicity, the model predicts the not yet considered diffusion path that we call pinched diffusion with a contraction of the dimer bond length. Determination of the few parameters of the model requires only a study of the interaction of a single atom with the surface and of an isolated dimer instead of the complex potential energy of a dimer on a surface.

A cluster study of aluminum adsorption on Ga-rich GaAs(100)(2 × 1) and β (4 × 2) surfaces

Ab initio self-consistent total energy calculations using second order Moller-Plesset perturbation theory and Hay-Wadt effective core potentials with associated basis sets (HWECP’s) for gallium and arsenic have been used to investigate the chemisorption properties of atomic aluminum on the Ga-rich GaAs(100)-(2 × 1) and β(4 × 2) surfaces. Finite sized hydrogen saturated clusters with the experimental zinc-blende lattice constant of 5.654 A and the energy optimized Ga dimer bond length of 2.758 A have been used to model the semiconductor surface. To investigate the effects of the core electrons of aluminum in the adsorption process, we have represented the Al adatom with both HWECP’s and an all electron 6-311++G** basis set. Detailed energetics of chemisorption on the (100) surface, including chemisorption energies, nearest surface neighbor bond lengths, and Mulliken population analysis, have been reported for all considered sites of chemisorption.

Stabilization of pyrite (FeS2), marcasite (FeS2), arsenopyrite (FeAsS) and loellingite (FeAs2) surfaces by polymerization and auto-redox reactions

Abstract A comparative X-ray photoelectron spectrometric (XPS) study of the Fe 2p, S 2p and As 3d spectra of pristine, fractured surfaces of pyrite, marcasite, arsenopyrite and loellingite indicates systematic and predictable change to the surfaces of these minerals. Auto-redox and polymerization reactions stabilize uncompensated surfaces of these 3d transition metal-bearing dichalcogenides. The route to stabilization is predictable through consideration of bulk structure and electronegativity of the elements constituting the dichalcogenides. Stabilization occurs through reconstruction via polymerization of surface ligands, unless inhibited by intervening atoms or by large distances separating adjacent ligand dimers. The cubic structure of pyrite results in adjacent S dimers being separated by a distance about 50% greater than the S dimer bond length and Fe atoms are located sufficiently close to surface S atoms to inhibit S-polymer formation on (0 0 1) surfaces; polymerization on this surface consequently is minimal (if it occurs). The pyrite surfaces are consequently stabilized via an auto-redox reaction. Adjacent As dimers of loellingite (orthorhombic) are separated by a distance only 16% greater than the As dimer bond length and Fe atoms do not separate surface dimers from bulk dimers. Surface stabilization occurs via reconstruction with migration of surface As dimers toward the bulk and bonding with bulk As dimers to produce near-surface tetramers. Polymerization proceeds to such an extent that no surface monomers or dimers are detected at fracture surfaces. The crystal structure of marcasite is orthorhombic like loellingite but contains strongly electronegative S atoms (rather than As atoms). Its fracture surfaces are stabilized by both polymerization reactions (just as observed on loellingite surfaces) and by surface redox reactions (as on pyrite surfaces). The shortest distance separating adjacent S dimers is about 50% greater than the S–S dimer bond length in marcasite. This distance apparently diminishes appreciably the probablility of polymerization of surface S atoms thus allowing auto-redox reactions to occur. Polymerization and redox reactions stabilize Fe dichalcogenide surfaces. The extent to which each type of reaction proceeds is dependent upon bulk structure and electronegativity of the constituent atoms of the compound and favorable redox reaction energetics.