Modulation of molecular conductance induced by electrode atomic species and interface geometry

We present a systematic theoretical investigation of the interaction of an organic molecule with gold and palladium electrodes. We show that the chemical nature of the electrode elicits significant geometrical changes in the molecule. These changes, which are characteristic of the electrode atomic species and the interface geometry, are shown to occur at distances as great as 10 Angstrom from the interface, leading to a significant modification of the inherent electronic properties of the molecule. In certain interface geometries, the highest occupied molecular orbital (HOMO) of the palladium-contacted molecule exhibits enhanced charge delocalization at the center of the molecule, compared to gold. Also, the energy gap between the conductance peak of the lowest unoccupied molecular orbital (LUMO) and the Fermi level is smaller for the case of the palladium electrode, thereby giving rise to a higher current level at a given bias than the gold-contacted molecule. These results indicate that an optimal choice of the atomic species and contact geometry could lead to significantly enhanced conductance of molecular devices and could serve as a viable alternative to molecular derivatization.     

Molecular binding at gold transport interfaces. III. Field dependence of electronic properties

The behavior of the electronic structure in a metal/molecular/metal junction as a function of the applied electric field is studied using density functional methods. Although the calculations reported here do not include the electrode bulk, or intermolecular interactions, and do not permit actual transport to occur, nevertheless they illuminate the charging, energy shift, polarization and orbital occupation changes in the molecular junction upon the application of a static electric field. Specifically, external electric fields generally induce polarization localization on the two cluster ends. The HOMO/LUMO gap usually decreases and, for large enough fields, energy levels can cross, which presages a change of electronic state and, if found in molecular electronic circuits, a change in transmission. The calculations also show changes in the geometry both of the molecule and the molecule/cluster interface upon application of the electric field. These effects should be anticipated in whole circuit studies.     

Koopmans' theorem for large molecular systems within density functional theory

It is shown that in density functional theory (DFT), Koopmans' theorem for a large molecular system can be stated as follows: The ionization energy of the system equals the negative of the highest occupied molecular orbital (HOMO) energy plus the Coulomb electrostatic energy of removing an electron from the system, or equivalently, the ionization energy of an N-electron system is the negative of the arithmetic average of the HOMO energy of this system and the lowest unoccupied molecular orbital (LUMO) energy of the (N - 1)-electron system. Relations between this DFT Koopmans' theorem and its existing counterparts in the literature are discussed. Some of the previous results are generalized and some are simplified. DFT calculation results of a fullerene molecule, a finite single-walled carbon nanotube and a finite boron nitride nanotube are presented, indicating that this Koopmans' theorem approximately holds, even if the orbital relaxation is taken into consideration.     

Electron smearing in DFT calculations: A case study of doxorubicin interaction with single‐walled carbon nanotubes

To address the choice of an appropriate value of electron smearing to facilitate self‐consistent field (SCF) convergence, we studied the interaction of doxorubicin with short armchair and zigzag single‐walled carbon nanotube models with closed caps, at the PWC/DNP level of density functional theory. By gradually reducing the electron smearing value from a large and most commonly used one of 0.005 Ha to zero (Fermi occupation), we monitored the changes in close contacts between the interacting species, total energy of the molecular system, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy and isosurfaces, HOMO‐LUMO gap energy, and plots of electrostatic potential. It became evident that the commonly used smearing values of ≥0.001 Ha can alter the results significantly (for example, by one order of magnitude for HOMO–LUMO gap energy). We suggest the setting of electron smearing value at 0.0001 Ha, which does not imply too high computation cost and can guarantee the results close to the ones obtained with Fermi occupation. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

DFT Theoretical Calculation of the Site Selectivity of Dihydroxylated (5, 0) Zigzag Carbon Nanotube

Functionalization is an important method to change electrical and thermodynamic properties of carbon nanotubes. In this study, the effect of functionalization of a single-walled carbon nanotube (SWCNT) was investigated with the aid of density functional theory. For this case, a (5, 0) zigzag SWCNT model containing 60 C atoms with 10 hydrogen atoms added to the dangling bonds of the perimeter carbons was used. To model hydroxyl CNT two terminal H atoms were replaced by two –OH groups. All the functionalized CNTs are thermodynamically more stable and have higher dipole moment with respect to the pristine CNT. Depending on the positions of hydroxyl groups on CNT five isomers of C₆₀H₈(OH)₂ were obtained. The structure of these five isomers and molecular properties such as the HOMO–LUMO gaps, the dipole moments, and the density of state were calculated. Our results indicate that the HOMO–LUMO gap strongly depends on the placement of the hydroxyl groups on the nanotubes. The isomers were hydroxyl groups locate on the anti-position show the highest distortions in the structure of the CNT.

     

First-principles investigation of the electronic and field emission properties of C-doped ZnO nanotube

In order to search for novel field emitter nanomaterial, a density functional theory investigation is performed to understand electronic structures and field emission properties of carbon doped–ZnO nanotube. It has been revealed that electron transport through ZnONT is significantly increased in the presence of the carbon atom due to the reduced HOMO–LUMO energy gap, which makes the electrons easily excited from HOMO to LUMO, and then the electrons can easily emit. Comparing the ionization potentials of the pure and doped ZnONT, at the same external electric field strength, the ionization potential of C–doped ZnO nanotube is lower than that of pure one. Also, after the doping of carbon atom, the Fermi level of ZnONT increases, which indicates that the Fermi level shifts toward the conduction band. These results indicate that the field emission properties of ZnONT can be enhanced by the doping of ZnO nanotube with the carbon atom.     

The effect of 3d-metal intercalation on the electronic structure of metallic and semiconducting nanotubes

The electronic structure of 3d-metal-intercalated metallic (5,5) and semiconducting (10,0) nanotubes has been studied by quantum-chemical methods. The total and partial densities of states of nanotubes as a function of metal concentration and nature and the carbon-shell structure have been calculated by the linear augmented-cylindrical-wave method. Metalized nanowires based on armchair (5,5) and zigzag (10,0) nanotubes with one, two, three, and four metal atoms in the cross-section have been calculated. The introduction of the metal is accompanied by a sharp increase in the density of states at the Fermi level of the nanowire, which determines the concentration of free electrons involved in charge transfer in the nanotube. The 3d electrons of the metal and the carbon shell are nearly equally involved in electron transport in intercalated wires. Both the 3d electrons of a metal and the carbon shell should be nearly equally involved in electron transport in intercalated wires. The introduction of metals not only affects the conductive state of the carbon nanotube but also changes the entire pattern of its valence band, in particular, increases the valence band width of the nanotube by 5–10 eV owing to the low-energy shift of the 2s(C) states.     

Study of noncovalent interactions of end-caped sulfur-doped carbon nanotubes using DFT,QTAIM, NBO and NCI calculations

In the current study, the interactions of carbon nanotube and sulfur-doped carbon nanotubes (SCNTs) with methanol, methanethiol, water and dihydrogen sulfide at on-body and dead-end positions of nanotubes have been studied. Interaction energies in the gas and solvent (via PCM model) were calculated using density functional theory calculations. Atomic charges, interaction energies, electron densities and their Laplacians at bond critical points have been calculated. Moreover, noncovalent interaction isosurfaces have been visualized using NCI index calculations. Interactions in gaseous phase were more favorable than those in solvent phase, and among considered solvents (benzene, chloroform and cyclohexane), cyclohexane showed the most preferred interactions. In addition, oxygen-bearing molecules (methanol and water) showed more favorable interactions compared with sulfur-bearing ones. NBO analyses revealed the stronger donor–acceptor interactions with methanol and methanethiol. QTAIM calculation results indicated the reasonable electron densities at BCPs, and the Laplacians of electron densities showed ionic-like (closed shell) interactions. Moreover, isosurfaces of these interactions were also studied to depict the interaction surfaces, and DOS plots for SCNTs were obtained to define their HOMO–LUMO levels and electric conduction properties. The increasing of the global softness and decreasing of total hardness was resulted by sulfur doping of nanotubes, which causes the heterodoped nanotubes to become less electrophilic species.     

Comparative study of Li, Na, and K adsorptions on graphite by using ab initio method

A comprehensive study has been conducted to compare the adsorptions of alkali metals (including Li, Na, and K) on the basal plane of graphite by using molecular orbital theory calculations. All three metal atoms prefer to be adsorbed on the "middle hollow site" above a hexagonal aromatic ring. A novel phenomenon was observed, that is, Na, instead of Li or K, is the weakest among the three types of metal atoms in adsorption. The reason is that the SOMO (single occupied molecular orbital) of the Na atom is exactly at the middle point between the HOMO and the LUMO of the graphite layer in energy level. As a result, the SOMO of Na cannot form a stable interaction with either the HOMO or the LUMO of the graphite. On the other hand, the SOMO of Li and K can form a relatively stable interaction with either the HOMO or the LUMO of graphite. Why Li has a relatively stronger adsorption than K on graphite has also been interpreted on the basis of their molecular-orbital energy levels.     

金钯二元小团簇的几何结构与电子性质

在UBP86/LANL2DZ和UB3LYP/def2-TZVP水平下详细研究了AumPdn(m+n≤6)团簇的几何结构和电子性质.阐明了团簇的结构特征、平均结合能、垂直电离势、垂直电子亲和能、电荷转移以及成键特征.除单取代混合团簇(AunPd和AuPdn,n=5或6)外,五和六原子混合团簇中钯原子趋于聚集到一起形成Pdcore,金原子分布在Pdcore周围形成PdcoreAushell结构.含一个和两个钯原子团簇的电子性质与纯金团簇类似,呈现一定奇偶振荡.混合团簇的电子性质,如最高占据分子轨道(HOMO),最低未占据分子轨道(LUMO),垂直电离势,垂直电子亲和能,Fermi能级和化学硬度等均与团簇空间结构和金、钯原子数之比直接相关.混合团簇中存在钯原子到金原子间的电荷转移,表明团簇中存在明显金钯间成键作用.分析团簇的电荷分布、前线轨道和化学硬度表明,金钯混合团簇对小分子如O2、H2和CO等的反应活性要强于纯金团簇.     

Al7Ag and Al7Au clusters with large highest occupied molecular orbital-lowest unoccupied molecular orbital gap

The candidate structures for the ground-state geometry of the Al(7)M (M = Li, Cu, Ag, and Au) clusters are obtained within the spin-polarized density functional theory. Absorption energy, vertical ionization potential, vertical electron affinity, and the energy gap between the highest occupied molecular orbital (HOMO) level and the lowest unoccupied molecular orbital (LUMO) level have been calculated to investigate the effects of doping. Doping with Ag or Au can lead to a large HOMO-LUMO gap, low electron affinity, and increased ionization potential of Al(7) cluster. In the lowest-energy structure of the Al(7)Au cluster, the Al atom binding to the Al(6)Au acts monovalent and the other six Al atoms are trivalent. Thus, the Al(7)Au cluster has 20 valence electrons, and its enhanced stability may be due to the electronic shell closure effect.     

A band dispersion mechanism for Pt alloy compositional tuning of linear bound CO stretching frequencies

The C-O stretching frequency (nu(CO)) of atop CO/Pt in PtRu alloys is compositionally tuned in proportion to the Pt mole percent. The application of a Blyholder-Bagus type mechanism (i.e., increased back-donation from the metal d-band to the hybridized 2pi CO molecular orbitals (MOs)) to compositional tuning has been paradoxical because (1) a Pt-C bond contraction, expected with increased back-donation as the Pt mole percent is reduced, is not observed (i.e., calculated Pt-C bond is either elongated or insensitive to alloying and the binding energies of CO/Pt decrease with alloying) and (2) the lowering d-band center and increased d-band vacancies upon alloying (suggesting less back-donation to the higher energy metal hybridized 2pi CO MOs) must be reconciled with the alloy-induced red shift of the nu(CO). A library of spin-optimized Pt and Pt alloy clusters was the basis of density functional theory (DFT) calculations of CO binding energies, nu(CO) values, shifts, and broadening of 5sigma/2pi CO MO upon hybridization with the alloy orbitals and a DFT derived Mulliken electron population analysis. The DFT results, combined with FEFF8 local density of states (LDOS) calculations, validate a 5sigma donation-2pi back-donation mechanism, reconciling the direction of alloy compositional tuning with the lowering of the d-band center and increased vacancies. Although the d-band center decreases in energy with alloying, an asymmetric increase in the dispersion of the d-band is accompanied by an upshift of the metal cluster HOMO level. Concomitantly, the hybridization and renormalization of the CO 5sigma/2pi states results in a broadening of the 5sigma/2pi manifold with additional lower energy states closer to the upshifted (with respect to the pure Pt cluster) HOMO of the alloy cluster. The dispersion toward higher energies of the alloy d-density of states results in more 5sigma/2pi CO filled states (i.e., enhanced 2pi-back-donation). Finally, Mulliken and FEFF8 electron population analysis shows that the increase of the average d-band vacancies upon alloying and additional 2pi back-donation are not mutually exclusive. The d-electron density of the CO-adsorbed Pt atom increases with alloying while the average d-electron density throughout the cluster is reduced. The localized electron density is manifested as an electrostatic wall effect, preventing the Pt-C bond contractions expected with increased back-donation to the 2pi CO MOs.     

Structure, stability, electronic and magnetic properties of Ni4 clusters containing impurity atoms

Using a gradient-corrected density functional method, we studied computationally how single impurity atoms affect the structure and the properties of a Ni4 cluster. H and O atoms coordinate at a Ni-Ni bond, inducing small changes to the structure of bare Ni4 which is essentially a tetrahedron. For a C impurity, we found three stable structures at a Ni4 cluster. In the most stable geometry, the carbon atom cleaves a Ni-Ni bond of Ni4, binding to all Ni atoms. Inclusion of the impurity atom leads to a partial oxidation of the metal atoms and, in the most stable structures, reduces the spin polarization of the cluster compared to bare Ni4. An H impurity interacts mainly with the Ni 4s orbitals, whereas the Ni 3d orbitals participate strongly in the bonding with O and C impurity atoms. For these impurity atoms, Ni 3d contributions dominate the character of the HOMO of the ligated cluster, in contrast to the HOMO of bare Ni4 where Ni 4s orbitals prevail. We also discuss a simple model which relates the effect of a H impurity on the magnetic state of metal clusters to the spin character (minority or majority) of the LUMO or HOMO of the bare metal cluster.     

Coaxial carbon nanotubes as shielded nanowires

We report transverse polarizabilities of coaxial carbon nanotubes using first principles density functional theory. These results demonstrate a shielding of the inner nanotube from electric fields by the outer nanotube. This study has implications for nanoelectronics, specifically for the possibility of using coaxial nanotubes as nanoelectrical wires. Shielding is predicted to be on the order of 95% by high-level polarizability calculations. This shielding occurs regardless of whether the outer nanotube is metallic or semiconducting. In addition, a series of calculations on coaxial nanotubes where the inner nanotube is not centered show that the shielding still occurs with approximately the same magnitude. These calculations therefore indicate that it would be possible to use a coaxial carbon nanotube as a shielded nanowire.     

Sensor activity with respect to alkali metals of a carbon nanotube edge-modified with amino group

The work is devoted to the theoretical study of sensor activity of nanosystems based on a carbon nanotube modified with a functional amino group, with respect to certain metal atoms and ions. The calculations were performed within the molecular cluster model using the semiempirical MNDO scheme and density functional theory DFT. The mechanism of attachment of an amino group to the open edge of zigzag single-walled carbon nanotubes possessing cylindrical symmetry was studied to design a chemically active sensor based on them. The key geometric and electron-energy characteristics of the constructed systems have been determined. The interaction of the sensors thus constructed with atoms and ions of some metals—potassium, sodium, and lithium—has been studied. The scanning of arbitrary surfaces containing selected atoms or ions has been modeled; from the interaction energies, and the activity of the single-walled carbon nanotube + amino group probe system has been determined with respect to the selected elements to be initialized. Analysis of the charge state of the system has established that the sensor action mechanism is realized, as a result of which the number of charge carriers in the resulting nanotubular system serving as a sensor probe changes, which provides the appearance of conductivity in the system. The presence of metallic atoms can be experimentally detected by the change in the potential in a probe system based on a nanotube with a functional group. The theoretical studies have proved the possibility of creating highly sensitive sensors based on the most promising nanomaterial— carbon nanotubes functionalized with active chemical groups, including the amino group NH₂.     

A theoretical study of dibenzothiophene absorbed on open-ended carbon nanotubes

The (7,7) and (10,5) carbon nanotubes were studied in the context of the Density Functional Theory (DFT) within a generalized gradient approximation (GGA). The Becke's exchange functional along with the correlation functional of Lee, Yang, and Parr (BLYP) were used with the DZVP basis set aided via auxiliary functions for the electron density. In both materials, the global indexes were calculated from the optimized structure with Kopmanns' theorem. The energy values calculated for the physisorption and chemisorption processes suggested that the physisorption process is more likely to occur for the (7,7) than for the (10,5) carbon nanotube, as well as for the achiral than chiral structure for both nanotubes and for both surface phenomena. This effect may be ascribed to the more homogeneous distribution of molecular orbital for the achiral carbon nanotube, which seems to be supported by the DOS calculations.     

Molecular orbital analysis of chemical carcinogens

Simple molecular orbital calculations are employed in searching electronic parameters which may characterize the chemical carcinogens. Using frontier orbitals, the carcinogen-DNA bond formation is described as an electron transfer from the highest occupied molecular orbital (HOMO) of DNA to the lowest unoccupied molecular orbital (LUMO) of the carcinogen. Analysis of the DNA bases units shows that the electron donation occurs preferentially at the guanine site. The calculated low LUMO energy of several carcinogens indicate correctly the electrophilic character of these compounds. The difference between the carcinogen and the ultimate carcinogen is analyzed. Epoxides, free radicals, alkylating agents, and other metabolite forms are studied. A reasonable correlation is found between the LUMO energy and the carcinogenic function. © 1997 John Wiley & Sons, Inc.     

Structures and electronic properties of peanut-shaped dimers and carbon nanotubes

The structures and electronic properties of peanut-shaped dimers and carbon nanotubes constructed from C60 molecules are investigated using ab initio self-consistent field molecular and crystal orbital methods based on the density-functional theory. The calculations show that the formation of peanut-shaped structures without octagonal carbon rings is energetically favorable. The obtained band structures indicate that the peanut-shaped nanotube can be a semiconductor or a metal.     

氟硼二吡咯类pH荧光探针PET光谱特性的理论计算

氟硼二吡咯(BODIPY)类pH荧光探针分子是基于光诱导电子转移(PET)的荧光探针分子, 识别基团氮原子上引入不同取代基可呈现不同的光学灵敏度. 本文应用密度泛函理论(DFT)及含时密度泛函理论(TD-DFT)方法对六种含不同取代基的探针分子进行了几何构型优化及激发态计算, 探讨了不同取代基对PET效应影响. 计算结果表明: 基态时这些探针分子的最高占有分子轨道(HOMO)和最低未占有分子轨道(LUMO)都在荧光母体BODIPY的π, π^*轨道, 而识别基团上氮原子孤对电子所在的轨道为HOMO-1轨道. 但是在激发态, 当氮原子上有两个取代基时, HOMO-1→LUMO跃迁的激发能都小于荧光团的HOMO→LUMO跃迁, 这将有可能产生PET效应并导致荧光熄灭, 而当氮原子上有一个取代基时不会出现这种现象. 通过激发态结构优化可以发现, 无论识别基团氮原子上有一个还是两个取代基, N原子的轨道对称性都发生变化, 由sp³→sp², 孤对电子占据在p轨道上, 其轨道能级升高至荧光团的HOMO和LUMO轨道之间, 将导致不同程度的PET效应, 与实验结果一致.