First-principles calculation on the conductance of a single 1,4-diisocyanatobenzene molecule with single-walled carbon nanotubes as the electrodes

The conductance of a single 1,4-diisocyanatobenzene molecule sandwiched between two single-walled carbon nanotube (SWCNT) electrodes are studied using a fully self-consistent ab initio approach which combines nonequilibrium Green's function formalism with density functional theory calculations. Several metallic zigzag and armchair SWCNTs with different diameters are used as electrodes; dangling bonds at their open ends are terminated with hydrogen atoms. Within the energy range of a few eV of the Fermi energy, all the SWCNT electrodes couple strongly only with the frontier molecular orbitals that are related to nonlocal pi bonds. Although the chirality of SWCNT electrodes has significant influences on this coupling and thus the molecular conductance, the diameter of electrodes, the distance, and the torsion angle between electrodes have only minor influences on the conductance, showing the advantage of using SWCNTs as the electrodes for molecular electronic devices.     

Dithiocarbamate anchoring in molecular wire junctions: a first principles study

Recent experimental realization [J. Am. Chem. Soc., 127 (2005) 7328] of various dithiocarbamate self-assembly on gold surface opens the possibility for use of dithiocarbamate linkers to anchor molecular wires to gold electrodes. In this paper, we explore this hypothesis computationally. We computed the electron transport properties of 4,4'-bipyridine (BP), 4,4'-bipyridinium-1,1'-bis(carbodithioate) (BPBC), 4-(4'-pyridyl)-peridium-1-carbodithioate (BPC) molecule junctions based on the density functional theory and nonequilibrium Green's functions. We demonstrated that the stronger molecule-electrode coupling associated with the conjugated dithiocarbamate linker broadens transmission resonances near the Fermi energy. The broadening effect along with the extension of the pi conjugation from the molecule to the gold electrodes lead to enhanced electrical conductance for BPBC molecule. The conductance enhancement factor is as large as 25 at applied voltage bias 1.0 V. Rectification behavior is predicted for BPC molecular wire junction, which has the asymmetric anchoring groups.     

Direct estimate of the strength of conjugation and hyperconjugation by the energy decomposition analysis method

The intrinsic strength of pi interactions in conjugated and hyperconjugated molecules has been calculated using density functional theory by energy decomposition analysis (EDA) of the interaction energy between the conjugating fragments. The results of the EDA of the trans-polyenes H2C=CH-(HC=CH)n-CH=CH2 (n = 1-3) show that the strength of pi conjugation for each C=C moiety is higher than in trans-1,3-butadiene. The absolute values for the conjugation between Si=Si pi bonds are around two-thirds of the conjugation between C=C bonds but the relative contributions of DeltaE pi to DeltaE orb in the all-silicon systems are higher than in the carbon compounds. The pi conjugation between C=C and C=O or C=NH bonds in H2C=CH--C(H)=O and H2C=CH-C(H)=NH is comparable to the strength of the conjugation between C=C bonds. The pi conjugation in H2C=CH-C(R)=O decreases when R = Me, OH, and NH2 while it increases when R = halogen. The hyperconjugation in ethane is around a quarter as strong as the pi conjugation in ethyne. Very strong hyperconjugation is found in the central C-C bonds in cubylcubane and tetrahedranyltetrahedrane. The hyperconjugation in substituted ethanes X3C-CY3 (X,Y = Me, SiH3, F, Cl) is stronger than in the parent compound particularly when X,Y = SiH3 and Cl. The hyperconjugation in donor-acceptor-substituted ethanes may be very strong; the largest DeltaE pi value was calculated for (SiH3)3C-CCl3 in which the hyperconjugation is stronger than the conjugation in ethene. The breakdown of the hyperconjugation in X3C-CY3 shows that donation of the donor-substituted moiety to the acceptor group is as expected the most important contribution but the reverse interaction is not negligible. The relative strengths of the pi interactions between two C=C double bonds, one C=C double bond and CH3 or CMe3 substituents, and between two CH3 or CMe3 groups, which are separated by one C-C single bond, are in a ratio of 4:2:1. Very strong hyperconjugation is found in HC[triple bond]C-C(SiH3)3 and HC[triple bond]C-CCl3. The extra stabilization of alkenes and alkynes with central multiple bonds over their terminal isomers coming from hyperconjugation is bigger than the total energy difference between the isomeric species. The hyperconjugation in Me-C(R)=O is half as strong as the conjugation in H2C=CH-C(R)=O and shows the same trend for different substituents R. Bond energies and lengths should not be used as indicators of the strength of hyperconjugation because the effect of sigma interactions and electrostatic forces may compensate for the hyperconjugative effect.     

Concerning the molecular and electronic structure of a tungsten-tungsten quadruply bonded complex supported by two 6-carboethoxy-2-carboxylatoazulene ligands

The preparation and molecular structure of a W2(4+)-quadruply bonded complex is reported wherein two mutually trans azulene-2-carboxylato ligands are shown to be strongly coupled by ligand pi-M2delta-ligand pi conjugation.     

2,3-Diphenylbutadiene and donor-acceptor functionalized derivatives: exploring the competition between conjugation paths in branched pi-systems

2,3-Diphenylbutadiene and its donor-acceptor functionalized derivatives represent branched pi systems consisting of three overlapping linearly conjugated units, namely a 1,3-butadiene and two phenylethene subsystems. The evaluation of pi conjugation using a scheme based on the natural bond orbital analysis shows that the details of the structure of these compounds is governed by electron delocalization. The potential energy surface of 2,3-diphenylbutadiene shows two minima, each one representing a distinct combination of conjugation patterns. These minima are shown to be connected by a low-energy path with transition structures that have one conjugation path fully activated, while conjugation is completely disrupted along the other path. We will show that, in response to donor-accptor functionalization, the 2,3-diphenylbutadiene backbone will switch to other conformations, which come along with substantial changes in the electronic structure.     

Giant macrocycles composed of thiophene, acetylene, and ethylene building blocks

Fully conjugated giant macrocyclic oligothiophenes with 60pi, 90pi,120pi, 150pi, and 180pi frames (1, 2, 3, 4 and 5) have been designed, and their butyl-substituted derivatives (1a, 2a, 3a, 4a, and 5a) have been synthesized using modified Sonogashira and McMurry coupling reactions as key steps. The 60-180pi systems 1-5 are circular with 1.8-6 nm inner cavities and 3.3-7.5 nm outside molecular diameters. Compound 1a containing ten 3,4-dibutyl-2,5-thienylene, eight ethynylene, and two vinylene units has been converted into macrocyclic oligo(3,4-dibutyl-2,5-thienylene-ethynylene) 6a using bromination/dehydrobromination procedure. Giant macrocycles 1a-6a exhibit a red shift of their absorption spectra and a fairly strong fluorescence with a large Stokes shift as compared to a linear conjugated counterpart having five thiophene rings. Compounds 1a-6a exhibit multistep reversible redox behaviors with fairly low first oxidation potentials, reflecting their cyclic conjugation. Furthermore, chemical oxidation of 1a-6a with FeCl3 shows drastic changes of spectroscopic properties due to intramolecular and intermolecular pi-pi interactions. Doping of 1a-3a with iodine forms semiconductor due to its pi-donor properties and pi-pi stacking ability. X-ray analysis of 1a confirmed a round, planar structure with nanoscale inner cavity, and revealed host ability for alkanes and unique packing structure. Interestingly, 2a and 3a self-aggregate in the solid state to form "molecular wires," which are about 200 nm thick and more than 1 mm long. The internal structures of fibrous aggregates have been investigated by optical microscope, scanning electron microscopy, atomic force microscopy, and X-ray diffraction analyses.     

How the pi conjugation length affects the fluorescence emission efficiency

How the pi conjugation length affects the fluorescence emission efficiency is elucidated by examination of the theoretical and experimental relationship between absolute quantum yield (Phi(f)) and magnitude (Api) of the pi conjugation length in the excited singlet state, which provides a novel concept for molecular design for highly fluorescent organic compounds. As a tool to predict Phi(f) from a structural model, (nu(a) - nu(f))1/2 x a3/2 (nu(a): wavenumber of absorption maximum, nu(f): wavenumber of emission maximum, a: molecular radius) could be used instead of Api. The concept should be valuable for potential applications to (1) examination of an excited singlet state structure (for example, coplanarity of excited-state molecules) and (2) molecular design of novel materials, in which the excited singlet state plays an important role, such as highly efficient fluorophores, electroluminescent materials, photoconducting materials, and nonlinear optical materials. A remarkably intense green fluorophore (Phi(f) 0.88, log epsilon 4.72, lambda(em) 527 nm) is created based on this concept, which is of great interest in relation to a green fluorescent protein (Topaz, T203Y type, Phi(f) 0.60, log epsilon 4.98, lambda(em) 527 nm).     

扩展苯基衍生物分子器件的电子输运的理论研究

通过结合杂化密度泛函和前线轨道理论与弹性散射格林函数方法研究了三种苯基衍生物分子器件的电子输运性质. 基于杂化密度泛函方法计算扩展分子电子结构的基础上, 计算了苯基衍生物三分子结的输运性质. 计算结果表明, 在低偏压下, 电流与电压呈线性变化; 分子结的电阻的对数与苯环的数目呈线性增加关系.     

Synthesis, characterization, and properties of subporphyrazines: a new class of nonplanar, aromatic macrocycles with absorption in the green region

Novel subphthalocyanine analogues that display strong absorption in the green region have been synthesized by using a boron template cyclotrimerization of maleonitrile derivatives. The spectroscopic properties of these macrocycles indicate that, like subphthalocyanines, they have 14 pi electrons and are aromatic compounds with a conical shape. The removal of the three fused benzene rings from the subphthalocyanine skeleton produces a 75-80 nm blue shift of the Q-band and a slight lowering of the absorption coefficients for this band. In addition, the reduction of the pi system from 18 to 14 electrons that accompanies progression from porphyrazines to subporphyrazines causes a hypsochromic shift of the Q-band of around 100 nm. Subporphyrazines that are peripherally functionalized with six thioether chains, and in which the sulfur atoms are attached directly to the pyrrole moieties, exhibit optical features that may be explained in terms of the extension of pi conjugation over the six thiolene groups, as well as strong pi donation from the sulfur lone pairs to the macrocycle. These two effects are quantitatively and qualitatively very similar to those observed for porphyrazines that possess the same type of substitution. In addition, the mesomorphic behavior at low temperatures of a macrocycle that is substituted with six thiododecyl chains was demonstrated by using differential scanning calorimetry and optical polarising microscopy.     

Influence of functional groups on charge transport in molecular junctions

Using density functional theory (DFT), we analyze the influence of five classes of functional groups, as exemplified by NO(2), OCH(3), CH(3), CCl(3), and I, on the transport properties of a 1,4-benzenedithiolate (BDT) and 1,4-benzenediamine (BDA) molecular junction with gold electrodes. Our analysis demonstrates how ideas from functional group chemistry may be used to engineer a molecule's transport properties, as was shown experimentally and using a semiempirical model for BDA [Nano Lett. 7, 502 (2007)]. In particular, we show that the qualitative change in conductance due to a given functional group can be predicted from its known electronic effect (whether it is sigma/pi donating/withdrawing). However, the influence of functional groups on a molecule's conductance is very weak, as was also found in the BDA experiments. The calculated DFT conductances for the BDA species are five times larger than the experimental values, but good agreement is obtained after correcting for self-interaction and image charge effects.     

Theoretical study of the source-drain current and gate leakage current to understand the graphene field-effect transistors

We designed acene molecules attached to two semi-infinite metallic electrodes to explore the source-drain current of graphene and the gate leakage current of the gate dielectric material in the field-effect transistors (FETs) device using the first-principles density functional theory combined with the non-equilibrium Green's function formalism. In the acene-based molecular junctions, we modify the connection position of the thiol group at one side, forming different electron transport routes. The electron transport routes besides the shortest one are defined as the cross channels. The simulation results indicate that electron transport through the cross channels is as efficient as that through the shortest one, since the conductance is weakly dependent on the distance. Thus, it is possible to connect the graphene with multiple leads, leading the graphene as a channel utilized in the graphene-based FETs in the mesoscopic system. When the conjugation of the cross channel is blocked, the junction conductance decreases dramatically. The differential conductance of the BA-1 is nearly 7 (54.57 μS) times as large as that of the BA-4 (7.35 μS) at zero bias. Therefore, the blocked graphene can be employed as the gate dielectric material in the top-gated graphene FET device, since the leakage current is small. The graphene-based field-effect transistors fabricated with a single layer of graphene as the channel and the blocked graphene as the gate dielectric material represent one way to overcome the problem of miniaturization which faces the new generation of transistors.     

Mechanism of the electronic stabilization of the 3MR and divalent carbon of bis(diisopropylamino)cyclopropenylidene

Analysis of the topology of the electron density of bis(dimethylamino)cyclopropenylidene as a model of the recently synthesized, stable bis(diisopropylamino)cyclopropenylidene with the quantum theory of atoms in molecules is used to investigate the stabilizing electronic effects at the reactive carbene site by amino substitution. This work demonstrates that the plane perpendicular lone pairs of nitrogen utilize in-plane sigma-aromaticity as a conduit to delocalize charge to the carbene carbon C2, where it is transferred preferentially back into the pi-plane at the site through sigma-pi polarization. C2 is thus stabilized relative to the parent cyclopropenylidene, c-C(3)H(2), by a very different mechanism than that suggested in the orbital view of n(pi)(N) and pi(C=C) conjugation and n(pi)(N) --> p(pi)*(C2) hyperconjugation. Validation of this premise is also found in properties of asymmetric atomic quadrupole tensors, bond path ellipticities, and diamagnetic/paramagnetic components of NMR shielding tensors.     

trans versus geminal electron delocalization in tetra- and diethynylethenes: a new method of analysis

trans-Diethynylethene [(E)-hex-3-ene-1,5-diyne (1 a)], geminal-diethynylethene [3-ethynyl-but-3-ene-1-yne (1 b)], and tetraethynylethene [3,4-diethynyl-hex-3-ene-1,5-diyne (2)] are flexible molecular building blocks for pi-conjugated polymers with interesting electronic and photonic properties. The type of functionalization, the length of the polymer chain, and the choice of pi-conjugation pattern, play a crucial role in determining the properties of these compounds. To rationalize the impact of the different delocalization pathways in the various types of isomers (trans or geminal) on the molecular and electronic structure, a detailed theoretical investigation is presented. We develop a method based on the natural bond orbital (NBO) analysis of Weinhold, which allows one to correlate electron delocalization with molecular and electronic structure observables. The method reveals that the difference between trans (or through) and geminal (or cross) conjugation is not only due to the vertical pi conjugation, but also to the in-plane sigma hyperconjugation. The method is used to correlate the changes in molecular and electronic observables, such as the bond lengths or the absorption frequencies, with the electronic structure of the compounds under investigation. Moreover, this method allows us to predict how a certain substituent will affect the molecular structure and the electronic properties of a given backbone.     

Electronic decay constant of carotenoid polyenes from single-molecule measurements

The conductance of carotenoid polyenes chemically bound at each end to gold contacts has been measured for single molecules containing 5, 7, 9, and 11 carbon-carbon double bonds in conjugation. The electronic decay constant, beta, is determined to be 0.22 +/- 0.04 A-1, in close agreement with the value obtained from first principles simulations (0.22 +/- 0.01 A-1). The absolute values of the molecular conductance are within a factor of 3 of those calculated from first principles. The small value of beta demonstrates that conductivity drops off only slowly with chain length, confirming that carotenoid conjugated chains are relatively good molecular "wires".     

Structure-Independent Conductance of Thiophene-Based Single-Stacking Junctions

The experimental investigation of intermolecular charge transport in π-conjugated materials is challenging. Herein, we describe the investigation of charge transport through intermolecular and intramolecular paths in single-molecule and single-stacking thiophene junctions by the mechanically controllable break junction (MCBJ) technique. We found that the ability for intermolecular charge transport through different single-stacking junctions was approximately independent of the molecular structure, which contrasts with the strong length dependence of conductance in single-molecule junctions with the same building blocks, and the dominant charge-transport path of molecules with two anchors transited from an intramolecular to an intermolecular path when the degree of conjugation increased. An increase in conjugation further led to higher binding probability owing to the variation in binding energies, as supported by DFT calculations.     

How the surrounding water changes the electronic and magnetic properties of DNA

We study the influence of humidity on the transport and magnetic properties of DNA within the quantum chemistry methods. Strong influence of water molecules on these properties, observed in this study, opens up opportunities for application of DNA in molecular electronics. Interaction of the nucleobases with water molecules leads to breaking of some of the pi bonds and appearance of unbound pi electrons. These unbound electrons contribute significantly to the charge transfer at room temperature by up to 10(3) times, but at low temperature the efficiency of charge transfer is determined by the spin interaction of two unbound electrons located on the intrastrand nucleobases. The charge exchange between the nucleobases is allowed only when the spins of unbound electrons are antiparallel. Therefore, the conductance of DNA molecule can be controlled by a magnetic field. That effect has potentials for applications in developing nanoscale spintronic devices based on the DNA molecule, where efficiency of spin interaction will be determined by the DNA sequence.     

Single-Molecule Charge-Transport Modulation Induced by Steric Effects of Side Alkyl Chains

The experimental investigation of side-chain effects on intramolecular charge transport in π-conjugated molecules is essential but remains challenging. Herein, the dependence of intra-molecular conductance on the nature of branching alkyl chains is investigated through a combination of the scanning tunneling microscope break junction (STM-BJ) technique and density functional theory. Three thiophene-flanked diketopyrrolopyrrole (DPP) derivatives with different branching alkyl chains (isopentane, 3-methylheptane, and 9-methylnonadecane) are used with phenylthiomethyl groups as the anchoring groups. The results of single-molecule conductance measurements show that as the alkyl chain becomes longer, the torsional angles between the aromatic rings increase due to steric crowding, and therefore, the molecular conductance of DPP decreases due to reduction in conjugation. Both theoretical simulations and ¹H NMR spectra demonstrate that the planarity of the DPPs is directly reduced after introducing longer branching alkyl chains, which leads to a reduced conductance. This work indicates that the effect of the insulating side chain on the single-molecule conductance cannot be neglected, which should be considered for the design of future organic semiconducting materials.     

Substituent effects in the iron 2p and carbon 1s edge near-edge X-ray absorption fine structure (NEXAFS) spectroscopy of ferrocene compounds

The iron 2p and carbon 1s near-edge X-ray absorption fine structure (NEXAFS) spectra of substituted ferrocene compounds (Fe(Cp-(CH3)5)2, Fe(Cp)(Cp-COOH), Fe(Cp-COOH)2, and Fe(Cp-COCH3)2) are reported and are interpreted with the aid of extended Hückel molecular orbital (EHMO) theory and density functional theory (DFT). Significant substituent effects are observed in both the Fe 2p and C 1s NEXAFS spectra. These effects can be related to the electron donating/withdrawing properties of the cyclopentadienyl ligands and their substituents as well as the presence of pi* conjugation between the cyclopentadienyl ligand and unsaturated substituents.     

Charge Transport through Molecular Rods with Reduced π‐Conjugation

A series of oligophenylene rods of increasing lengths is synthesized to investigate the charge‐transport mechanisms. Methyl groups are attached to the phenyl rings to weaken the electronic overlap of the π‐subsystems along the molecular backbones. Out‐of‐plane rotation of the phenyl rings is confirmed in the solid state by means of X‐ray analysis and in solution by using UV/Vis spectroscopy. The influence of the reduced π‐conjugation on the resonant charge transport is studied at the single‐molecule level by using the mechanically controllable break‐junction technique. Experiments are performed under ultra‐high‐vacuum conditions at low temperature (50 K). A linear increase of the conductance gap with increasing number of phenyl rings (from 260 meV for one ring to 580 meV for four rings) is revealed. In addition, the absolute conductance of the first resonant peaks does not depend on the length of the molecular wire. Resonant transport through the first molecular orbital is found to be dominated by charge‐carrier injection into the molecule, rather than by the intrinsic resistance of the molecular wire length.     

Aromaticity in metallabenzenes

The electronic structure and bonding situation in 21 metallabenzenes (metal=Os, Ru, Ir, Rh, Pt, and Pd) were investigated at the DFT level (BP86/TZ2P) by using an energy decomposition analysis (EDA) of the interaction energy between various fragments. The aim of the work is to estimate the strength of the pi bonding and the aromatic character of the metallacyclic compounds. Analysis of the electronic structure shows that the metallacyclic moiety has five occupied pi orbitals, two with b1 symmetry and three with a2 symmetry, which describe the pi-bonding interactions. The metallabenzenes are thus 10 pi-electron systems. This holds for 16-electron and for 18-electron complexes. The pi bonding in the metallabenzenes results mainly from the b1 contribution, but the a2 contribution is not negligible. Comparison of the pi-bonding strength in the metallacyclic compounds with acylic reference molecules indicates that metallabenzenes should be considered as aromatic compounds whose extra stabilization due to aromatic conjugation is weaker than in benzene. The calculated aromatic stabilization energies (ASEs) are between 8.7 kcal mol(-1) for 13 and 37.6 kcal mol(-1) for 16 which is nearly as aromatic as benzene (ASE=42.5 kcal mol(-1)). The classical metallabenzene model compounds 1 and 4 exhibit intermediate aromaticity with ASE values of 33.4 and 17.6 kcal mol(-1). The greater stability of the 5d complexes compared with the 4d species appears not to be related to the strength of pi conjugation. From the data reported here there is no apparent trend or pattern which indicates a correlation between aromatic stabilization and particular ligands, metals, coordination numbers or charge. The lower metal-C5H5 binding energy of the 4d complexes correlates rather with weaker sigma-orbital interactions.