Changes of coupling between the electrodes and the molecule under external bias bring negative differential resistance

We report a first-principles study of electrical transport and negative differential resistance (NDR) in a single molecular conductor consisting of a borazine ring sandwiched between two Au(100) electrodes with a finite cross section. The projected density of states (PDOS) and transmission coefficients under various external voltage biases are analyzed, and it suggests that the variation of the coupling between the molecule and the electrodes with external bias leads to NDR. Therefore, we propose that one origin of NDR in molecular devices is caused by the characteristics of both the molecule and the electrodes as well as their cooperation, not necessarily only by the inherent properties of certain species of molecules themselves. The changes of charge state of the molecule have minor effects on NDR in this device because the Mulliken population analysis shows that electron occupation variation on the molecule is very small when different external biases are applied.     

Theoretical evaluation of atomic charges to be integrated into conformational analyses of neutral lipids

Conformational analyses of large molecules as fatty acids and triglycerides are usually amenable by molecular mechanics. A correct evaluation of the electrostatic energy term is thus crucial in determining reliable results. In this contribution, we have considered the most abundant fatty acids in biomembranes, i.e., lauric, stearic, oleic, and elaidic acid, and the corresponding triglycerides, i.e., trilaurin, tristearin, triolein, and trielaidin, and estimated the Mulliken and potential-derived charges both at the semiempirical AM 1 and ab initio HF MO STO -3G level. Atomic charges obtained by the Mulliken population analysis do not take into account the full geometry of the molecule. On the contrary, the change of conformation, due to different chains length or the presence of a trans or cis double bond, greatly influences the repartition of the potential-derived charges. A systematic comparative analysis shows that charges calculated by AM 1 are not suitable because as they do not reproduce potential-derived charges obtained by ab initio. © 1993 John Wiley & Sons, Inc.     

Conduction modulation of π-stacked ethylbenzene wires on Si(100) with substituent groups

For the realization of molecular electronics, one essential goal is the ability to systematically fabricate molecular functional components in a well-controlled manner. Experimental techniques have been developed such that π-stacked ethylbenzene molecules can now be routinely induced to self-assemble on an H-terminated Si(100) surface at precise locations and along precise directions. Electron transport calculations predict that such molecular wires could indeed carry an electrical current, but the Si substrate may play a considerable role as a competing pathway for conducting electrons. In this work, we investigate the effect of placing substituent groups of varying electron donating or withdrawing strengths on the ethylbenzene molecules to determine how they would affect the transport properties of such molecular wires. The systems consist of a line of π-stacked ethylbenzene molecules covalently bonded to a Si substrate. The ethylbenzene line is bridging two Al electrodes to model current through the molecular stack. For our transport calculations, we employ a first-principles technique where density functional theory (DFT) is used within the non-equilibrium Green’s function formalism (NEGF). The calculated density of states suggest that substituent groups are an effective way to shift molecular states relative to the electronic states associated with the Si substrate. The electron transmission spectra obtained from the NEGF–DFT calculations reveal that the transport properties could also be extensively modulated by changing substituent groups. For certain molecules, it is possible to have a transmission peak at the Fermi level of the electrodes, corresponding to high conduction through the molecular wire with essentially no leakage into the Si substrate.     

A finite expansion method for the calculation and interpretation of molecular electrostatic potentials

Because it is useful to have the molecular electrostatic potential as an element in a complex scheme to assess the toxicity of large molecules, efficient and reliable methods are needed for the calculation and characterization of these potentials. A multicenter multipole expansion of the molecular electron charge density calculated with a limited Gaussian basis set is shown here to have only a finite number of nonzero terms from which the molecular electrostatic potential can be calculated. The discrete contributions to the electrostatic potentials from the terms of this expansion provide a physically meaningful decomposition of the potential and a means for its characterization. With pyrrole as an example, the electrostatic potential calculated from this finite expansion of the electron density is compared to that obtained from exact calculations from the same wave function. Good agreement is obtained at distances greater than 1.5 A from any atom in the molecule. In contrast, rearrangement of the terms into an expansion corresponding only to Mulliken atomic charges and dipoles yields a decomposition that produces electrostatic potentials which agree less well with the exact potential. This discrepancy is attributable to the neglect of terms due to higher moments.     

Using multipole point charge distributions to provide the electrostatic potential in the variational explicit polarization (X-Pol) potential

The equations defining the variational explicit polarization (X-Pol) potential introduced in earlier work are modified in the present work so that multipole point charge distributions are used instead of Mulliken charges to polarize the monomers that comprise the system. In addition, when computing the electrostatic interaction between a monomer whose molecular orbitals are being optimized and a monomer whose electron density is being used to polarize the first monomer, the electron densities of both monomers are represented by atom-centered multipole point charge distributions. In the original formulation of the variational X-Pol potential, the continuous electron density of the monomer being optimized interacts with external Mulliken charges, but this corresponds to the monopole truncation in a multipole expansion scheme in the computation of the Fock matrix elements of the given monomer. The formulation of the variational X-Pol potential introduced in this work (which we are calling the “multipole variational X-Pol potential”) represents the electron density of the monomer whose wave function is being variationally optimized in the same way that it represents the electron densities of external monomers when computing the Coulomb interactions between them.     

Atomic charges,dipole moments,and Fukui functions using the Hirshfeld partitioning of the electron density

In the Hirshfeld partitioning of the electron density, the molecular electron density is decomposed in atomic contributions, proportional to the weight of the isolated atom density in the promolecule density, constructed by superimposing the isolated atom electron densities placed on the positions the atoms have in the molecule. A maximal conservation of the information of the isolated atoms in the atoms-in-molecules is thereby secured. Atomic charges, atomic dipole moments, and Fukui functions resulting from the Hirshfeld partitioning of the electron density are computed for a large series of molecules. In a representative set of organic and hypervalent molecules, they are compared with other commonly used population analysis methods. The expected bond polarities are recovered, but the charges are much smaller compared to other methods. Condensed Fukui functions for a large number of molecules, undergoing an electrophilic or a nucleophilic attack, are computed and compared with the HOMO and LUMO densities, integrated over the Hirshfeld atoms in molecules.     

Adsorption studies of dimethyl and methyl-ethyl ester molecules on silicene nanoring: Application of DFT study

The electronic and adsorption properties of dimethyl and methyl-ethyl ester molecules on a silicene nanoring (SiNR) are studied using first-principles calculations. The adsorption properties of dimethyl and methyl-ethyl ester molecules on the surface of a silicene nanoring is investigated in terms of density of states spectrum, adsorption energy, average energy gap variation, Mulliken charge and Bader charge transfer. The structural stability of the SiNR is ensured using formation energy. The variation in the electron density and energy gap is noticed upon adsorption of dimethyl and methyl-ethyl ester molecules in the SiNR base material compared with its isolated counterpart. The highlights of the present work are silicene nanoring is used as a base material for ester molecule adsorption. The adsorption behavior of ester molecules is studied using energy band structure. The DOS spectrum confirms the transfer of electrons between the SiNR and ester molecules. The findings suggest that a SiNR can be used as a base material for the detection of dimethyl and methyl-ethyl ester molecules.     

二氢吲哚类染料用于染料敏化太阳能电池光敏剂的比较

采用密度泛函理论(DFT)和含时密度泛函理论(TD-DFT)对四种二氢吲哚染料进行研究, 从中筛选出相对优秀的染料敏化太阳能电池光敏剂. 对前线分子轨道的计算表明, 二氢吲哚染料的前线分子轨道结构非常有利于染料激发态向TiO2电极的电子注入. 对真空中的紫外和可见光吸收光谱的计算表明, 二氢吲哚染料的吸收光谱与太阳辐射光谱匹配较好. 对染料分子的能级计算表明, 二氢吲哚染料的能级结构比较适合于I-/I-3作电解液的TiO2纳米晶太阳能电池的光敏剂. 二氢吲哚染料最低未占据分子轨道(LUMO) 能级均比TiO2晶体导带边能级高, 能够保证激发态染料分子高效地向TiO2电极转移电子. 二氢吲哚染料最高占据分子轨道(HOMO)的能级比I-/I-3能级低, 保证了失去电子的染料分子能够顺利地从电解液中得到电子. 与实验数据比较, 得出在提高染料敏化太阳能电池转换效率方面, 对染料的关键要求是LUMO能级的位置. 染料分子的稳定性是染料敏化太阳能电池使用寿命的关键因素. 通过对化学键键长的比较表明, 二氢吲哚染料的分子稳定性基本相同. 对计算结果的分析表明, 二氢吲哚染料1(ID1)的LUMO能级最高, 分子稳定性最好, 在酒精溶液中的吸收光谱与太阳辐射光谱匹配很好, 在同类染料中是较好的染料敏化太阳能电池光敏剂.     

Rapid Estimation of Basis Set Error and Correlation Energy Based on Mulliken Charges and Mulliken Matrix with the Small 6-31g* Basis Set

Good, density functional quality (B3LYP/6-31G*) ground state total electronic energies have been approximated using single point Hartree–Fock-self consistent field (HF-SCF/6-31G*) total energies and Mulliken partial charges versus. Mulliken matrix (electrons assigned to atoms and atoms pairs from Mulliken population analysis). This is a development of our rapid estimation of basis set error and correlation energy from partial charges (REBECEP) method, published earlier (see references [21,22,30]. The development is as follows: (1) A larger set of atoms (H, C, N, O, F, Si, P and S) are considered as building blocks for closed shell, neutral, ground state molecules at their equlibrium geometry; (2) geometries near equilibrium geometry are also considered; (3) A larger set, containing 115 molecules, was used to fit REBECEP parameters; (4) most importantly, electrons belonging to chemical bonds (between atom pairs) are also considered (Mulliken matrix) in addition to the atoms (Mulliken charges), using more REBECEP parameters to fit and yielding a more flexible algorithm. With these parameters a rather accurate closed shell ground state electronic total energy can be obtained from a small basis set HF-SCF calculation in the vicinity of optimal geometry. The 3.3 kcal/mol root mean square deviation of REBECEP improves to 1.5 kcal/mol when using Mulliken matrix instead of Mulliken charges.     

On the charge distribution in ethanes and disilanes and correlations with equilibrium bond lengths; an ab initio study

The equilibrium electronic wave-functions for a series of fluoro- and chloro-ethanes and disilanes of general formula M₂H_6−nX_n, (M=C, Si; X=F, Cl), were analysed by the most commonly used methods for electron distribution, using the Mulliken and Löwdin populations, natural atomic orbital (NAO) populations and atoms in molecules (AIM) electron densities. Although the numerical values for local atomic charges vary greatly, all the methods correlate, but in markedly differing ways. The Mulliken charges seem the most selective in relation to systematic change of substituents in the current type of molecular structure. A number of examples occur where the AIM charges at C, Si centres are effectively identical in different molecules, where some differences might have been anticipated. These are often distinguished by Mulliken populations. The fluoroethanes exemplify this, since a plot of the AIM charges (for example on either the F or H centres) against the Mulliken charges for all members of the series, shows three nearly parallel lines, corresponding to those centres with 0, 1 or 2 fluorine atoms on the centre under study. The bond critical points at which the AIM charges are determined seem to be counter to intuition in some cases. This is a density rather than atomic orbital size issue however. The Mulliken and NAO charges seem more reasonable than those from the AIM method. There is an unexpected correlation of the local bond dipoles from the Mulliken analyses, with the calculated equilibrium bond lengths. These correlations lead to bond length values for the non-polarised bonds MX, which agree with data based on covalent radii for some bonds.     

A localized molecular-orbital assembler approach for Hartree-Fock calculations of large molecules

We describe an alternative fragment-based method, the localized molecular-orbital assembler method, for Hartree-Fock (HF) calculations of macromolecules. In this approach, a large molecule is divided into many small-size fragments, each of which is capped by its local surroundings. Then the conventional HF calculations are preformed on these capped fragments (or subsystems) and the canonical molecular orbitals of these systems are transferred into localized molecular orbitals (LMOs). By assembling the LMOs of these subsystems into a set of LMOs of the target molecule, the total density matrix of the target molecule is constructed and correspondingly the HF energy or other molecular properties can be approximately computed. This approach computationally achieves linear scaling even for medium-sized systems. Our test calculations with double-zeta and polarized double-zeta basis sets demonstrate that the present approach is able to reproduce the conventional HF energies within a few millihartrees for a broad range of molecules.     

A theoretical study of molecular conduction. II. A Hartree-Fock approach to transmission probability

In this paper, we discuss molecular conductivity based on Green's function methods. In our calculations, we adopted the self-energy formalism to accommodate semi-infinite electrodes connected to a molecule, and the self-energy was obtained from the surface Green's function of the electrodes. We adopted the formalism of the surface Green's function derived by Sanvito et al. [Phys. Rev. B 59, 11936 (1999)] and Krstic et al. [Phys. Rev. B 66, 205319 (2002)], and although their formalisms for the surface Green's function were different, we were able to demonstrate that these formalisms are mathematically identical. We analyzed the electron transmission probability by using the spectrum expression of Green's function, instead of using the inverse matrix of the effective Hamiltonian that includes an isolated molecule and the electrodes. Finally, we calculated the transmission probability of benzenedithiol based on the Hartree-Fock method and analyzed the disappearance of the transmission probability due to the orbital interference.     

Optimal population analysis

An easy method of approximating the electron density of a molecule by expressing it as a sum of squares of atomic orbitals is described. The coefficients are determined by minimizing the error in the electric field. The optimal population analysis is an integration of this optimized density over the orbitals belonging to one atom. The Mulliken population analysis can be interpreted as the integral of a Mulliken density that is a similar expression with fixed coefficients. The two densities are compared in détail using calculations on the water molecule and, more briefly, HF, LiH, BH, and C₂H₄. The error in the densities is identified and examined. The optimal population analysis is strongly recommended as a practical improvement to the Mulliken populations.     

从分子水平研究电子传递

有机分子中电子传递受到诸多因素的影响, 纳米电极、界面、环境和分子本身都是必须要系统考察的因素. 本文从理论模拟和实验研究两个方面总结了在分子尺度上电子传递研究的最新进展. 着重讨论了分子动力学方法模拟纳米电极的制备, 量子化学方法研究电场作用下的分子构象及分子电导, 另外还讨论了扫描隧道显微术和电化学方法研究单分子结的电子传递. 分子电子传递的研究不仅涉及微观的实验测量, 从宏观的实验结果通过合理的分析推导, 也可以得到微观的信息.     

Electronegativity equalization method: parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme

The electronegativity equalization method (EEM) was developed by Mortier et al. as a semiempirical method based on the density-functional theory. After parameterization, in which EEM parameters A(i), B(i), and adjusting factor kappa are obtained, this approach can be used for calculation of average electronegativity and charge distribution in a molecule. The aim of this work is to perform the EEM parameterization using the Merz-Kollman-Singh (MK) charge distribution scheme obtained from B3LYP/6-31G* and HF/6-31G* calculations. To achieve this goal, we selected a set of 380 organic molecules from the Cambridge Structural Database (CSD) and used the methodology, which was recently successfully applied to EEM parameterization to calculate the HF/STO-3G Mulliken charges on large sets of molecules. In the case of B3LYP/6-31G* MK charges, we have improved the EEM parameters for already parameterized elements, specifically C, H, N, O, and F. Moreover, EEM parameters for S, Br, Cl, and Zn, which have not as yet been parameterized for this level of theory and basis set, we also developed. In the case of HF/6-31G* MK charges, we have developed the EEM parameters for C, H, N, O, S, Br, Cl, F, and Zn that have not been parameterized for this level of theory and basis set so far. The obtained EEM parameters were verified by a previously developed validation procedure and used for the charge calculation on a different set of 116 organic molecules from the CSD. The calculated EEM charges are in a very good agreement with the quantum mechanically obtained ab initio charges.     

紫罗碱衍生物分子结的电学性质理论研究

本文基于密度泛函(DFT)结合非平衡格林函数(NEGF)的方法,以具有氧化还原中心的紫罗碱衍生物(N,N'-bis(4-thioalkyl)-4,4'-bipyridinium,HS-4V4-SH)功能分子构造Au(111)/S-4V4-S/Au(111)分子结,详细分析了分子在三种价态V、V+和V2+下的电学性质与分...     

分子团簇的量子化学研究

采用Hartree-Fock方法、密度泛函(DFT)方法(BLYP、B3LYP)和MP2方法对Se4分子团簇的各种可能构型进行了结构优化和频率分析, 结果表明有5种构型是势能面上的稳定驻点, 同时对上述4种量子化学方法计算结果的差异进行了分析。并对这5种构型的结构稳定性、几何构型、前线分子轨道、Mulliken布局分析和偶极矩进行了分析, 根据分析结果对Se4分子的某些物理和化学性质进行了预测。     

Dielectric and vibrational properties of amino acids

We calculate polarizability tensors and normal mode frequencies for the amino acids alanine, leucine, isoleucine, and valine using density functional perturbation theory implemented within the plane wave pseudopotential framework. It is found that the behavior of the electron density under external fields depends to a large extent on the geometrical structure of the molecule in question, rather than simply on the constituent functional groups. The normal modes are able to help distinguish between the different types of intramolecular hydrogen bonding present, and help to explain why leucine is found in the zwitterionic form for the gaseous phase. Calculated IR spectra show a marked difference between those obtained for zwitterionic and nonzwitterionic molecules. These differences can be attributed to the different chemical and hydrogen bonds present. Effective dynamical charges are calculated, and compared to atomic charges obtained from Mulliken population analysis. It is found that disagreement exists, largely due to the differing origins of these quantities.