First-principles study on the structural and electronic properties of graphene upon benzene and naphthalene adsorption

Within the framework of the local density approximation (LDA) of the density functional theory (DFT) and the pseudopotential method, we have carried out ab initio calculations to investigate the structural and electronic properties of graphene upon the adsorption of benzene and naphthalene molecules. Our total-energy calculations suggest that, for both benzene and naphthalene adsorbed on graphene, the stack configuration is the most stable structure. The corresponding adsorption energies at different sites are estimated for both molecular adsorbates. The equilibrium parameters and the electronic band structure for the stable geometries have been calculated and compared with the available findings.     

Scattering of surface state electrons at large organic molecules

The scattering of surface state electrons at Lander-type molecules on Cu(111) is investigated by means of scanning tunneling microscope (STM) experiments at low temperature and model calculations. Specific information concerning the electronic interaction of the different internal groups of the molecule with the surface is obtained. Remarkably, the central molecular wire of the molecule, although decoupled from the surface by spacer groups and therefore not visible in STM images, is the main one responsible for scattering of surface state electrons.     

分子间相互作用对硫醇分子膜电输运性质的影响

利用密度泛函理论和弹性散射格林函数方法,对硫醇分子膜的电学特性进行模拟.计算结果表明,由于分子间的相互作用,导致分子膜的导电能力比单分子提高2~3个数量级.分子结的导电能力随着压力增加而增加,电极距离的变化使分子与电极以及分子间的耦合增强、分子结的链内隧穿和链间隧穿几率增大,导致电流增加.     

The first-principles calculation of molecular conduction

We used the self-consistent method-based density functional theory (DFT) and non-equilibrium Green’s function (NEGF) to simulate molecular transport. Our numerical calculations for the organic molecular measurement made by Reichert et al. (Phys. Rev. Lett., 2002, 88: 176804) and for the alkanedithiols measurement made by Xu et al. (Science, 2003, 301: 1221) met the related experimental values quite well. This means that the first-principles calculations based on DFT and NEGF can well explain the conduction measurements of some large molecules. The numerical study reveals the fact that molecular conduction does not obey the classic law; in stead it illustrates the quantum behavior. We designed active molecular transistors controlled by the gate bias with high working frequency. They may be the next generation electronic devices.      

Enhancement of electronic,photophysical and optical properties of 5,5′-Dibromo-2,2′-bithiophene molecule: new aspect to molecular design

The aims of this study were to enhance electronic, photophysical and optical properties of molecular semiconductors. For this purpose, the isomers of the B-doped molecule (5,5′-Dibromo-2,2′-bithiophene) have been investigated by density functional theory (DFT) based on B3LYP/6-311++G** level of theory. The isomers were first calculated using kick algorithm. The most stable isomers of the B-doped molecule are presented depending on the binding energy, fragmentation energy, ionization potential, electron affinity, chemical hardness, refractive index, radial distribution function and HOMO-LUMO energy gap based on DFT. Ultraviolet-visible (UV–vis) spectra have been also researched by time-dependent (TD) DFT calculations. The value of a band gap for isomer with the lowest total energy decreases from 4.20 to 3.47 eV while the maximum peaks of the absorbance and emission increase from 292 to 324 nm and 392 to 440 nm with boron doped into 5,5′-Dibromo-2,2′-bithiophene. Obtained results reveal that the B-doped molecule has more desirable optoelectronic properties than the pure molecule.     

FT‐Raman,IR and UV‐visible spectral investigations and ab initio computations of a nonlinear food dye amaranth

Amaranth (E123, Food Red 9, FD & C Red 2) is a sulfonated azo dye used as a color additive in foodstuffs, pharmaceuticals and cosmetics. FT‐IR and FT‐Raman spectra of amaranth were recorded and analyzed. Density functional theory (DFT) calculations were performed to derive the equilibrium geometry, vibrational wavenumbers, intensities and first hyperpolarizability. The results of the optimized molecular structure gave clear evidence for the intramolecular charge transfer (ICT) and intramolecular hydrogen bonding in the molecule. Azo stretching wavenumbers are lowered owing to conjugation and π‐electron delocalization. Time‐dependent density functional theory (TD‐DFT) calculations of the electronic spectra were performed on the optimized structure and compared with the experimental UV‐visible spectrum. Vibrational spectra, natural bonding orbitals (NBO) analysis and optimized geometry indicate C H·N hydrogen bonding in the molecule. The first hyperpolarizability of the molecule was calculated. The optical nonlinearity of the dye is due to the donation of the electron density from the hydroxyl group of the conjugated system via naphthalene ( 2 ) ring into π*‐orbital of the azo moiety. Copyright © 2008 John Wiley & Sons, Ltd.     

The generalized SIC‐OEP formalism and the generalized SIC‐Slater approximation (stationary and time‐dependent cases)

We present a generalized formulation of the Optimized Effective Potential (OEP) approach to the Self Interaction Correction (SIC) problem in Time Dependent (TD) Density Functional Theory (DFT). The formulation relies on the introduction of a double set of single electron orbitals. It allows the derivation of a generalized Slater approximation to the full OEP formulation, which extends the domain of validity of the standard Slater approximation. We discuss both formal aspects and practical applications of the new formalism and give illustrations in cluster and molecules. The new formalism provides a valuable ansatz to more elaborate (and computationally very demanding) full TD OEP and full TD SIC calculations especially in the linear domain.     

Features in the electronic structure and photoemission spectra of organic molecular semiconductors: The molecules of metal-phthalocyanines and PTCDA

The role of many-electron effects in the formation of electronic quasiparticle spectra in organic molecular semiconductors (OMS) is analyzed. Many-body perturbation theory, ab initio calculations of metal phthalocyanines and PTCDA molecules, and experimental photoemission spectra are applied to this analysis. It is shown that density functional theory (DFT) poorly reproduces the electronic spectra of OMS. The use of a hybrid functional method (HFM) provides precise reproduction of both valence and conducting bands, while the HOMO-LUMO gap remains underestimated. The correct gap width is obtained in both DFT and HFM, when it is calculated through ionization and affinity energies. It is shown that such an approach gives a formula for gap correction due to electron correlations, which is close to an expression derived from the GW approximation.     

Orbital selection of the double [CuO2] layer compound Ca3Cu2O4Cl2

We present a first-principles investigation on the dynamics and mechanism of the oxidation reaction between water molecules and the reduced PuO_2(110) surface using ab initio molecular dynamics(AIMD) simulations in combination with density functional theory(DFT) + U calculations. We find a dominating dissociation preference of water molecules for the vacancy defect sites on the PuO_2(110) surface, irrespective of the water or vacancy coverage. Due to hybridizations between the frontier orbitals of water molecule and the electronic states of the vacancy vicinity, partial water dissociation at the vacancy sites is exothermic and barrierless. The dissociation product, an OH group, further hydrogenates the PuO_2(110) surface by occupying the vacancy site.We also observe surface vacancy diffusion induced by the interactions between the water molecules and the surface oxygen atom in the proximity of the defect sites.     

Adsorption of 1,3,5-Triphenylbenzene Molecules and Growth of Graphene Nanoflakes on Cu(100) Surface

Adsorption of 1,3,5-triphenylbenzene(TPB) molecules on Cu( 100) surface is studied using ultraviolet photoelectron spectroscopy(UPS) and density functional theory(DFT) calculations. Researches on the bottom-up fabrication of graphene nanoflakes(GNFs) with TPB as a precursor on the Cu(100) surface are carried out based on UPS and DFT calculations. Three emission features d, e and f originating from the TPB molecules are located at 3.095, 7.326 and 9.349 eV below the Fermi level, respectively. With the increase of TPB coverage on the Cu(100) substrate, the work function decreases due to the formation of inter facial dipoles and charge(electron)rearrangement at the TPB/Cu(100) interface. Upon the formation of GNFs, five emission characteristic peaks of g, h, i, j and k originating from the GNFs are located at 1.100, 3.529, 6.984, 8.465 and 9.606 eV below the Fermi level, respectively. Angle resolved ultraviolet photoelectron spectroscopy(ARUPS) and DFT calculations indicate that TPB molecules adopt a lying-down configuration with their molecular plane nearly parallel to the Cu(100) substrate at the monolayer stage. At the same time, the lying-down configuration for the GNFs on the Cu(100) surface is also unveiled by ARUPS and DFT calculations.     

取代基对2-(2-羟基苯基)苯并噻唑分子内氢键及质子转移的影响:密度泛函理论研究

运用密度泛函(DFT)和含时密度泛函(TD DFT)理论方法研究了在2-(2-羟基苯基)苯并噻唑(HBT)苯环羟基的邻位或对位分别引入羟基和醛基后的衍生物分子内质子转移过程,考察了取代基的电子效应及取代位置对分子内氢键和质子转移反应的影响,模拟计算了各分子的IR振动光谱和电子光谱.研究发现,HBT及其衍生物分子可以形成分子内氢键,且激发态时氢键增强.基态时以醇式构型稳定存在,激发态时酮式结构为优势构象.分子的最大吸收峰和发射峰主要源于电子从前线分子轨道HOMO到LUMO之间的跃迁.基态分子内质子转移需要越过较高的能垒因而难以发生,而激发态时只需越过较低能垒就很容易发生激发态分子内质子转移.取代基的电子效应和取代位置对HBT分子氢键强度、互变异构体的相对稳定性、电子光谱及质子转移反应的能垒均有一定影响.     

Raman and SERS study of metoclopramide at different pH values

Conjugate acid–base forms of the drug metoclopramide were investigated by Raman spectroscopy in aqueous solutions and by surface‐enhanced Raman scattering (SERS), when the molecules were adsorbed on colloidal silver surfaces. Raman spectra were recorded at pH values below 8, metoclopramide being poorly water soluble at higher pH values. The SERS spectra of metoclopramide were recorded in the 3–11 pH range, even in spite of its low solubility at basic pH values. The Raman and SERS spectra were assigned by means of density functional theory (DFT) calculations. By monitoring several SERS marker bands, the protonated, neutral or the coexistence of both molecular species adsorbed on the colloidal silver particles could be evidenced. The adsorbate orientation was deduced to be perpendicular to the metal surface for the protonated molecular species and tilted for the neutral metoclopramide molecular species. Copyright © 2009 John Wiley & Sons, Ltd.     

STM simulation of molecules on ultrathin insulating overlayers using tight-binding: Au-pentacene on NaCl bilayer on Cu

We present fast and efficient tight-binding (TB) methods for simulating scanning tunneling microscopy (STM) imaging of adsorbate molecules on ultrathin insulating films. Due to the electronic decoupling of the molecule from the metal surface caused by the presence of the insulating overlayer, STM can be used to image the frontier molecular orbitals of the adsorbate. These images can be simulated with a very efficient scheme based on hopping integrals which also enables the analysis of phase shifts in the STM current. Au-pentacene complex adsorbed on a NaCl bilayer on Cu substrate provides an intricate model system which has been previously studied both experimentally and theoretically. Our calculations indicate that the complicated shape of the molecular orbitals may cause multivalued constant current surfaces - leading to ambiguity of the STM image. The results obtained using the TB methods are found to be consistent with both DFT calculations and experimental data.     

The electronic structure of Be and BeO: benchmark EMS measurements and LCAO calculations

The electronic band structures of Be and BeO have been measured by transmission electron momentum spectroscopy (EMS). The low atomic number of beryllium and the use of ultrathin solid films in these experiments reduce the probability of electron multiple scattering within the sample, resulting in very clean ‘benchmark’ measurements for the EMS technique. Experimental data are compared to tight-binding (LCAO) electronic structure calculations using Hartree–Fock , and local density (LDA-VWN), gradient corrected (PBE) and hybrid (PBE0) density functional theory. Overall, DFT calculations reproduce the EMS data for metallic Be reasonably well. PBE predictions for the valence bandwidth of Be are in excellent agreement with EMS data, provided the calculations employ a large basis set augmented with diffuse functions. For BeO, PBE calculations using a moderately sized basis set are in reasonable agreement with experiment, slightly underestimating the valence bandgap and overestimating the O(2s) and O(2p) bandwidths. The calculations also underestimate the EMS intensity of the O(2p) band around the Γ-point. Simulation of the effects of multiple scattering in the calculated oxide bandstructures do not explain these systematic differences.     

氢原子吸附对金表面金属酞菁分子的吸附位置、自旋和手征性的调控

实现单个功能有机分子构型、电子结构和自旋态的可逆调控, 是未来分子电子学和分子自旋电子学应用的关键. 近年来, 我们利用极低温强磁场超高真空扫描隧道显微镜系统, 结合第一性原理计算, 系统研究了氢原子吸附对金表面吸附的金属酞菁分子的自旋、手性和吸附位置的调控. 通过将金表面吸附的酞菁锰分子暴露于氢气或氢原子环境, 使得分子中心的磁性离子吸附单个氢原子, 从而实现了体系近藤效应由“开”到“关”的转变. 基于密度泛函理论的第一性原理计算表明, 氢原子吸附使得锰离子3d轨道内的电荷重排导致了分子的自旋由3/2降为1; 同时分子与金基底的间距增大, 使得近藤效应消失. 通过施加局域电压脉冲或者给样品加热, 可以实现单个或所有分子脱氢, 从而恢复体系的自旋态和近藤效应. 氢原子吸附还导致分子的优先吸附位置从金表面的面心立方堆垛区域变成了六角密排堆垛区域. 三个氢原子吸附于同一酞菁锰分子上, 可导致分子对称性的降低及分子镜面对称轴与金基底镜面对称轴的偏离, 从而导致手征性的出现. 这种分子吸附结构的手征性, 导致分子轨道也呈现出手征性. 这项工作为金属酞菁未来在分子电子学、自旋电子学、气体传感器等方面的应用提供了新思路.     

NO与C2H2的康普顿轮廓研究

基于第三代同步辐射光源, 在20 keV的入射X射线能量下测量了NO与C₂H₂分子的康普顿轮廓. 考虑到本次实验结果在p_z ≈ 0附近的统计精度达到了0.2%, 本文报道的NO和C₂H₂的康普顿轮廓可以作为严格检验理论的实验基准. 除此之外, 还分别采用HF方法及密度泛函方法选用不同的基组计算了NO 与C₂H₂康普顿轮廓. 通过对比实验结果与理论计算, 发现对于NO分子, 加入弥散函数基组理论计算结果与实验符合更好, 说明NO分子基态的电子分布较为弥散. 对于C₂H₂分子, HF方法理论计算的结果与实验符合较好.     

Manipulating charge‐transfer character and tuning emission color with electron‐withdrawing main‐group moieties in iridium‐based electrophosphors: a theoretical investigation

A new way has been investigated for tuning the optical and electronic performance of cyclometalated iridium(III) phosphors by simple tailoring of the phenyl ring of ppy (Hppy = 2‐phenylpyridine) with various main group moieties in [Ir(ppy‐X)₂(acac)] (X = POPh₂, SO₂Ph, GePh₃, OPh, OPh(CF₃)₃, SOPh). The geometric and electronic structures of the complexes in the ground state are studied with time‐dependent density functional theory (TD‐DFT) and Hartree–Fock method, whereas the lowest singlet and triplet excited states are optimized by the configuration interaction singles method. At the TD‐DFT level, absorptions and phosphorescence properties of the studied molecules were calculated on the basis of the optimized ground‐ and excited‐state geometries, respectively. The various main group moieties produce a remarkable influence on their optoelectronic properties. The calculated data reveal that the studied molecules have improved charge transfer rate and balance and can be used as hole and electron transport materials in organic light‐emitting devices. In particular, the work can provide valuable insight toward future design of new and relatively rare luminescent materials with enhanced electron‐injection and electron‐transporting features. Copyright © 2012 John Wiley & Sons, Ltd.     

Assessment of oscillator strengths with multiconfigurational short-range density functional theory for electronic excitations in organic molecules

ABSTRACT

We have in a series of recent papers investigated electronic excited states with a hybrid between a complete active space self-consistent field (CASSCF) wave function and density functional theory (DFT). This method has been dubbed the CAS short-range DFT method (CAS–srDFT). The previous papers have primarily focused on the excitation energies, and not on the oscillator strengths, although they comprise an important part of the absorption spectrum. In this study, we have carried out a quantitative analysis of oscillator strengths obtained with CAS–srDFT. As target molecules, we have considered the large collection of organic molecules whose excited states were investigated with a range of electronic structure methods by Thiel et al. As a by-product of our calculations of oscillator strengths, we also obtain electronic excitation energies, which enable us to compare the performance of CAS–srPBE for excitation energies, using a larger set of chromophores compared to previous studies.     

Comparison of the electronic structure of a thermoelectric skutterudite before and after adding rattlers: an electron energy loss study

Skutterudites, with rattler atoms introduced in voids in the crystal unit cell, are promising thermoelectric materials. We modify the binary skutterudite with atomic content Co(8)P(24) in the cubic crystal unit cell by adding La as rattlers in all available voids and replacing Co by Fe to maintain charge balance, resulting in La(2)Fe(8)P(24). The intention is to leave the electronic structure unaltered while decreasing the thermal conductivity due to the presence of the rattlers. We compare the electronic structure of these two compounds by studying the L-edges of P and of the transition elements Co and Fe using electron energy loss spectroscopy (EELS). Our studies of the transition metal white lines show that the 3d electron count is similar for Co and Fe in these compounds. As elemental Fe has one electron less than Co, this supports the notion that each La atom donates three electrons. The L-edges of P in these two skutterudites are quite similar, signalling only minor differences in electronic structure. This is in reasonable agreement with density functional theory (DFT) calculations, and with our multiple scattering FEFF calculations of the near edge structure. However, our experimental plasmon energies and dielectric functions deviate considerably from predictions based on DFT calculations.     

Differential cross sections for muonic hydrogen scattering on hydrogen molecules

The results of first calculations of the differential cross sections for muonic hydrogen scattering on hydrogen molecules are presented. They are functions of the initial and final kinetic energy of the system and the scattering angle. These calculations are based on the respective set of cross sections for muonic hydrogen scattering on hydrogen nuclei, obtained within the framework of the adiabatic method. The Fermi pseudopotential method is used to estimate the molecular binding effects. The influence of electrons on the cross sections under consideration is described in terms of the effective screening potential. Rotational and vibrational transitions are taken into account. The calculated molecular differential cross sections show a strong angular dependence. This effect is very significant for the electronic contributions to the cross sections, e.g. for collision energies above approximately 0.1 eV only the cross sections of small scattering angles are influenced considerably by the screening. Since these differential cross sections give detailed information about the final energies and complicated angular distributions of the scattered muonic atoms they are the proper basis for calculations concerning the deceleration of muonic hydrogen atoms in molecular hydrogen targets and for Monte Carlo simulations of different experiments in muonic physics.