Modeling solvent effects on electron-spin-resonance hyperfine couplings by frozen-density embedding

In this study, we investigate the performance of the frozen-density embedding scheme within density-functional theory [J. Phys. Chem. 97, 8050 (1993)] to model the solvent effects on the electron-spin-resonance hyperfine coupling constants (hfcc's) of the H2NO molecule. The hfcc's for this molecule depend critically on the out-of-plane bending angle of the NO bond from the molecular plane. Therefore, solvent effects can have an influence on both the electronic structure for a given configuration of solute and solvent molecules and on the probability for different solute (plus solvent) structures compared to the gas phase. For an accurate modeling of dynamic effects in solution, we employ the Car-Parrinello molecular-dynamics (CPMD) approach. A first-principles-based Monte Carlo scheme is used for the gas-phase simulation, in order to avoid problems in the thermal equilibration for this small molecule. Calculations of small H2NO-water clusters show that microsolvation effects of water molecules due to hydrogen bonding can be reproduced by frozen-density embedding calculations. Even simple sum-of-molecular-densities approaches for the frozen density lead to good results. This allows us to include also bulk solvent effects by performing frozen-density calculations with many explicit water molecules for snapshots from the CPMD simulation. The electronic effect of the solvent at a given structure is reproduced by the frozen-density embedding. Dynamic structural effects in solution are found to be similar to the gas phase. But the small differences in the average structures still induce significant changes in the computed shifts due to the strong dependence of the hyperfine coupling constants on the out-of-plane bending angle.     

Application of molecular models to electronic structure calculations of defects in oxide crystals. I. Parametrization of the modified INDO method

A modified calculation scheme of the INDO method is applied for calculating the electronic structure of perfect and imperfect oxide crystals. In order to obtain a flexible scheme permitting reliable calculation of both the electronic structure and the defect conformations, the INDO parameters for H, Li, Mg, Si, O are fitted directly to reproduce one-electron energies as well as the vicinity of the potential energy curve minima for a series of diatomic molecules and the electronic structure of MgO and -crystoballite form of SiO₂. The method is tested on the Li₂SiO₃ crystal calculated within the framework of the large unit cell model.     

QM:QM embedding using electronic densities within an ONIOM framework: energies and analytic gradients

Accurate calculations of large systems remain a challenge in electronic structure theory. Hybrid energy techniques are a promising family of methods for treating such systems. Expanding on previous developments, we present a QM:QM electronic embedding model whereby the high-level region is polarized by the electron density of the low-level region within an ONIOM framework. A direct Coulomb embedding model as well a more computationally efficient model involving a density fitting expansion are considered. We also develop a generalized theory for the first derivatives of these classes of QM:QM electronic embedding schemes, which requires solution of a single set of self-consistent field response equations. Two initial test cases are presented and discussed.     

Electronic structure, chemical bonding, and spin polarization in ferromagnetic MnAl

The electronic structure of ferromagnetic τ-MnAl has been calculated using density-functional techniques (TB-LMTO-ASA, FLAPW) and quantum-chemically analyzed by means of the crystal orbital Hamilton population tool. While all observable quantities are in good agreement with experiment, the tetragonal structure of ferromagnetic MnAl is interpreted to arise from a nonmagnetic cubic structure by two subsequent steps, namely (a) an electronic distortion due to spin polarization followed by (b) a structural distortion into the tetragonal system. The various strengths of interatomic bonding have been calculated in order to elucidate the competition between electronic and structural distortion.     

Improved description of the structure of molecular and layered crystals: ab initio DFT calculations with van der Waals corrections

The implementation of technique for full structural optimizations of complex periodic systems in the DFT-PAW package VASP, including the volume and shape of the unit cell and the internal coordinates of the atoms, together with a correction that allows an appropriate modeling of London dispersion forces, as given by the DFT-D2 approach of Grimme [Grimme, S. J. Comp. Chem. 2006, 27, 1787], is reported. Dispersion corrections are calculated not only for the forces acting on the atoms, but also for the stresses on the unit cell. This permits a simultaneous optimization of all degrees of freedom. Benchmark results on a series of prototype systems are presented and compared to results obtained by other methods and experimental data. It is demonstrated that the computationally inexpensive DFT-D2 scheme yields reasonable predictions for the structure, bulk moduli, and cohesive energies of weakly bonded materials.     

Theoretical study on isotope and temperature effect in hydronium ion using ab initio path integral simulation

We have applied the ab initio path integral molecular dynamics simulation to study hydronium ion and its isotopes, which are the simplest systems for hydrated proton and deuteron. In this simulation, all the rotational and vibrational degrees of freedom are treated fully quantum mechanically, while the potential energies of the respective atomic configurations are calculated "on the fly" using ab initio quantum chemical approach. With the careful treatment of the ab initio electronic structure calculation by relevant choices in electron correlation level and basis set, this scheme is theoretically quite rigorous except for Born-Oppenheimer approximation. This accurate calculation allows a close insight into the structural shifts for the isotopes of hydronium ion by taking account of both quantum mechanical and thermal effects. In fact, the calculation is shown to be successful to quantitatively extract the geometrical isotope effect with respect to the Walden inversion. It is also shown that this leads to the isotope effect on the electronic structure as well as the thermochemical properties.     

Exploring the ability of frozen-density embedding to model induced circular dichroism

In this study, we present calculations of the circular dichroism (CD) spectra of complexes between achiral and chiral molecules. Nonzero rotational strengths for transitions of the nonchiral molecule are induced by interactions between the two molecules, which cause electronic and/or structural perturbations of the achiral molecule. We investigate if the chiral molecule (environment) can be represented only in terms of its frozen electron density, which is used to generate an effective embedding potential. The accuracy of these calculations is assessed in comparison to full supermolecular calculations. We can show that electronic effects arising from specific interactions between the two subsystems can reliably be modeled by the frozen-density representation of the chiral molecule. This is demonstrated for complexes of 2-benzoylbenzoic acid with (-)-(R)-amphetamine and for a nonchiral, artificial amino acid receptor system consisting of ferrocenecarboxylic acid bound to a crown ether, for which a complex with l-leucine is studied. Especially in the latter case, where multiple binding sites and interactions between receptor and target molecule exist, the frozen-density results compare very well with the full supermolecular calculation. We also study systems in which a cyclodextrin cavity serves as a chiral host system for a small, achiral molecule. Problems arise in that case because of the importance of excitonic couplings with excitations in the host system. The frozen-density embedding cannot describe such couplings but can only capture the direct effect of the host electron density on the electronic structure of the guest. If couplings play a role, frozen-density embedding can at best only partially describe the induced circular dichroism. To illustrate this problem, we finally construct a case in which excitonic coupling effects are much stronger than direct interactions of the subsystem densities. The frozen density embedding is then completely unsuitable.     

An explicit quantum chemical method for modeling large solvation shells applied to aminocoumarin C151

The absorption spectra of aminocoumarin C151 in water and n-hexane solution are investigated by an explicit quantum chemical solvent model. We improved the efficiency of the frozen-density embedding scheme, as used in a former study on solvatochromism (J. Chem. Phys. 2005, 122, 094115) to describe very large solvent shells. The computer time used in this new implementation scales approximately linearly (with a low prefactor) with the number of solvent molecules. We test the ability of the frozen-density embedding to describe specific solvent effects due to hydrogen bonding for a small example system, as well as the convergence of the excitation energy with the number of solvent molecules considered in the solvation shell. Calculations with up to 500 water molecules (1500 atoms) in the solvent system are carried out. The absorption spectra are studied for C151 in aqueous or n-hexane solution for direct comparison with experimental data. To obtain snapshots of the dye molecule in solution, for which subsequent excitation energies are calculated, we use a classical molecular dynamics (MD) simulation with a force field adapted to first-principles calculations. In the calculation of solvatochromic shifts between solvents of different polarity, the vertical excitation energy obtained at the equilibrium structure of the isolated chromophore is sometimes taken as a guess for the excitation energy in a nonpolar solvent. Our results show that this is, in general, not an appropriate assumption. This is mainly due to the fact that the solute dynamics is neglected. The experimental shift between n-hexane and water as solvents is qualitatively reproduced, even by the simplest embedding approximation, and the results can be improved by a partial polarization of the frozen density. It is shown that the shift is mainly due to the electronic effect of the water molecules, and the structural effects are similar in n-hexane and water. By including water molecules, which might be directly involved in the excitation, in the embedded region, an agreement with experimental values within 0.05 eV is achieved.     

On the ordering in new low gap semiconductors: PtSnS, PtSnSe, PtSnTe. Experimental and DFT studies

The crystallographic and electronic structures of PtSnS, PtSnSe and PtSnTe were investigated by X-ray structure analysis and density functional theory (DFT) calculations. Conductivity measurements and diffraction patterns show semiconducting ordered pyrite type related compounds containing SnX (X=S, Se, Te) entities. A scheme is presented to model ordered variants according to the relative orientation of the XY dumbbells. It represents the ullmannite, the cobaltite and a new rhombohedral structure type. The scheme allows for a systematic investigation of ordering preferences from first principles. According to the total electronic energy PtSnTe and PtSnSe prefer the cobaltite, PtSnS the rhombohedral structure type. The structural and electronic properties agree with experimental results. The three compounds are predicted to be narrow gap indirect semiconductors from conductivity measurements and band structure calculations.     

Electron microscopy, spectroscopy, and first-principles calculations of Cs2O

Oxides of cesium play a key role in ameliorating the photoelectron emission of various opto-electronic devices. However, due to their extreme reactivity, their electronic and optical properties have hardly been touched upon. With the objective of better understanding the electronic and optical properties of Cs₂O in relationship to its structure, an experimental and theoretical study of this compound was undertaken. First-principles density functional theory calculations were performed. The preferred structural motif for this compound was found to be anti-CdCl₂. Here three Cs-O-Cs molecular layers are stacked together through relatively weak van-der-Waals forces. The energy bands were also calculated. The lowest transition at 1.45 eV, was found to be between the K point in the valence band to the Γ point in the conduction band. A direct transition at 2 eV was found in the center (Γ) of the Brillouin zone. X-ray powder diffraction, transmission electron microscopy and selected area electron diffraction were used to analyze the synthesized material. These measurements showed good agreement with the calculated structure of this compound. Absorption measurements at 4.2 K indicated two optical transitions with somewhat higher energy (indirect one at 1.65 and a direct transition at 2.2 eV, respectively). Photoluminescence measurements also showed similar transitions, suggesting that the lower indirect transition is enhanced by three nearby minima at 1.5 eV in the Brillouin zone.     

Calculations of molecules,clusters, and solids with a simplified LCAO-DFT-LDA scheme

A simplified LCAO-DFT-LDA scheme for calculations of structure and electronic structure of large molecules, clusters, and solids is presented. Forces on the atoms are calculated in a semiempirical way considering the electronic states. The small computational effort of this treatment allows one to perform molecular dynamics (MD ) simulations of molecules and clusters up to a few hundred atoms as well as corresponding simulations of condensed systems within the Born-Oppenheimer approximation. The accuracy of the method is illustrated by the results of calculations for a series of small molecules and clusters. © 1996 John Wiley & Sons, Inc.     

Three-dimensional Hartree–Fock crystal-orbital calculations on conducting polymers: trans-polyacetylene and polythiophene

Ab initio Hartree–Fock crystal orbital quantum chemical calculations on various structural models of three-dimensional crystals of trans-polyacetylene and polythiophene were carried out. The results provide insight into the actual structure and symmetry of the crystalline polymers under study, which are not easily amenable to experimental determination. Both conducting polymers under study were calculated to form crystals with monoclinic unit cells. A possible molecular basis of the specific electronic properties of these polymers is discussed. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 68: 421–429, 1998     

Benchmarking the performance of density functional theory based Green's function formalism utilizing different self-energy models in calculating electronic transmission through molecular systems

Electronic transmission through a metal-molecule-metal system is calculated by employing a Green's function formalism in the scattering based scheme. Self-energy models representing the bulk and the potential bias are used to describe electron transport through the molecular system. Different self-energies can be defined by varying the partition between device and bulk regions of the metal-molecule-metal model system. In addition, the self-energies are calculated with different representations of the bulk through its Green's function. In this work, the dependence of the calculated transmission on varying the self-energy subspaces is benchmarked. The calculated transmission is monitored with respect to the different choices defining the self-energy model. In this report, we focus on one-dimensional model systems with electronic structures calculated at the density functional level of theory.     

Band structure calculations on the monoclinic bulk and nano-SrAl2O4 crystals

The electronic structure of SrAl₂O₄ is calculated by density functional method and exchange and correlation have been treated by the generalized gradient approximation within the scheme due to Perdew-Burke-Ernzerhof. The bond length and bond covalency are also calculated by chemical bond method. Compared with the SrAl₂O₄ bulk crystal, the bond covalency of nanocrystal has an increasing trend; its band gap also is wider; the bond lengths of SrAl₂O₄ nanocrystal become shorter, which is responsible for the change of the covalency and band gap.     

SPC cluster modeling of metal oxides: ways of determining the values of point charges in the embedded cluster model

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Electronic structure of highly conducting conjugated polymers: evolution upon doping of polyacetylene, polythiophene, and polyemeraldine

The electronic properties of three types of conducting polymers: trans-polyacetylene (proto-typical of systems with a degenerate ground state), polythiophene (as an example of compounds with a nondegenerate ground state), and polyemeraldine (which can be doped via protonation) are reviewed. The structural and electronic band structure properties of these systems are studied at various defect concentrations corresponding to undoped, lightly doped, and highly doped polymers. Geometry optimizations of oligomeric equivalents to the undoped and doped polymers are performed using the semi-empirical MNDO and AM1 methods. The electronic band structures are calculated using the VEH method. The interpretation of the optical absorption data is discussed in terms of interband transitions; for doped trans-polyacetylene including soliton defects and for doped polythiophene including bipolaron defects. For highly doped trans-polyacetylene and polythiophene as well as for protonated polyemeraldine, the electronic structure of a polaron lattice conformation is discussed and shown to be in agreement with existing optical and magnetic data on these polymers.     

苯并-12-冠-4分子的晶体结构和电子结构

冠醚类化合物对金属离子有特殊的络合能力,并已在分析、萃取、催化和高分子化学等方面得到广泛应用,因此有关共结构和性质的基础研究具有理论和实际意义。大量研究结果表明,冠醚分子的环孔穴大小无疑是决定其络合能力的一个重要因素。在已详细研究过的冠醚中,12-冠-4分子的孔穴最小,但它仍然能同一些金属离子形成稳定的配合物。我们在实验工作中发现,苯并-12-冠-4分子络合能力较差,为较深入地揭示其原因,测定了它的晶体结构并对共电子结构进行了量子化学近似计算。     

Ab initio total energy calculations of copper nitride: the effect of lattice parameters and Cu content in the electronic properties

We have studied the structural and electronic properties of bulk copper nitride by performing first principles total energy calculations using the full-potential linearized augmented plane wave (FP-LAPW) method. In our study we have considered two types of cells: the ideal cubic anti-ReO₃ structure corresponding to Cu₃N, and a unit cell with an extra Cu atom at the center of the cube. In the first case, our calculated lattice parameter a=3.82 Å is in excellent agreement with the experimental value a=3.807 Å. The structure is semiconductor with a small indirect band-gap. The increasing of the lattice parameter results in larger band-gaps. An addition of an extra Cu atom at the center of the cell results in a slightly larger lattice parameter a=3.88 Å, and the structure becomes fully metallic. Our calculated value is similar to the experimental lattice parameter corresponding to a metallic copper nitride film.