Chemical imaging of single 4,7,12,15-tetrakis[2.2]paracyclophane by spatially resolved vibrational spectroscopy

Single 4,7,12,15-tetrakis[2.2]paracyclophane were deposited on NiAl(110) surface at 11 K. Two adsorbed species with large and small conductivities were detected by the scanning tunneling microscope (STM). Their vibrational properties were investigated by inelastic electron tunneling spectroscopy (IETS) with the STM. Five vibrational modes were observed for the species with the larger conductivity. The spatially resolved vibrational images for the modes show striking differences, depending on the coupling of the vibrations localized on different functional groups within the molecule to the electronic states of the molecule. The vibrational modes are assigned on the basis of ab initio calculations. No IETS signal is resolved from the species with the small conductivity.     

Inelastic tunneling spectroscopy of gold-thiol and gold-thiolate interfaces in molecular junctions: The role of hydrogen

It is widely believed that when a molecule with thiol (S-H) end groups bridges a pair of gold electrodes, the S atoms bond to the gold and the thiol H atoms detach from the molecule. However, little is known regarding the details of this process, its time scale, and whether molecules with and without thiol hydrogen atoms can coexist in molecular junctions. Here, we explore theoretically how inelastic tunneling spectroscopy (IETS) can shed light on these issues. We present calculations of the geometries, low bias conductances, and IETS of propanedithiol and propanedithiolate molecular junctions with gold electrodes. We show that IETS can distinguish between junctions with molecules having no, one, or two thiol hydrogen atoms. We find that in most cases, the single-molecule junctions in the IETS experiment of Hihath et al. [Nano Lett. 8, 1673 (2008)] had no thiol H atoms, but that a molecule with a single thiol H atom may have bridged their junction occasionally. We also consider the evolution of the IETS spectrum as a gold STM tip approaches the intact S-H group at the end of a molecule bound at its other end to a second electrode. We predict the frequency of a vibrational mode of the thiol H atom to increase by a factor ～2 as the gap between the tip and molecule narrows. Therefore, IETS should be able to track the approach of the tip towards the thiol group of the molecule and detect the detachment of the thiol H atom from the molecule when it occurs.     

Communication: Identification of the molecule-metal bonding geometries of molecular nanowires

Molecular nanowires in which a single molecule bonds chemically to two metal electrodes and forms a stable electrically conducting bridge between them have been studied intensively for more than a decade. However, the experimental determination of the bonding geometry between the molecule and electrodes has remained elusive. Here we demonstrate by means of ab initio calculations that inelastic tunneling spectroscopy (IETS) can determine these geometries. We identify the bonding geometries at the gold-sulfur interfaces of propanedithiolate molecules bridging gold electrodes that give rise to the specific IETS signatures that were observed in recent experiments.     

Vibrational features in inelastic electron tunneling spectra

A theoretical analysis of inelastic electron tunneling spectroscopy (IETS) experiments conducted on molecular junctions is presented, where the second derivative of the current with respect to voltage is usually plotted as a function of applied bias. Within the nonperturbative computational scheme, adequate for arbitrary parameters of the model, we consider the virtual conduction process in the off-resonance region. Here we study the influence of few crucial factors on the IETS spectra: the strength of the vibronic coupling, the phonon energy, and the device working temperature. It was also shown that weak asymmetry in the IETS signal with respect to bias polarity is obtained as a result of strongly asymmetric connection with the electrodes.     

分子结的非弹性隧道谱和电子-振动的耦合

研究了分子结的非弹性隧道谱, 给出了基于微扰理论近似的非平衡格林函数. 深入研究了非弹性隧道谱和电子-振动耦合常数的相互关系. 同时, 还计算了OPV和OPE分子结的IETS, 计算结果与有关的实验结果具有很好的可比性.     

Understanding the inelastic electron-tunneling spectra of alkanedithiols on gold

We present results for a simulated inelastic electron-tunneling spectra (IETS) from calculations using the "gDFTB" code. The geometric and electronic structure is obtained from calculations using a local-basis density-functional scheme, and a nonequilibrium Green's function formalism is employed to deal with the transport aspects of the problem. The calculated spectrum of octanedithiol on gold(111) shows good agreement with experimental results and suggests further details in the assignment of such spectra. We show that some low-energy peaks, unassigned in the experimental spectrum, occur in a region where a number of molecular modes are predicted to be active, suggesting that these modes are the cause of the peaks rather than a matrix signal, as previously postulated. The simulations also reveal the qualitative nature of the processes dominating IETS. It is highly sensitive only to the vibrational motions that occur in the regions of the molecule where there is electron density in the low-voltage conduction channel. This result is illustrated with an examination of the predicted variation of IETS with binding site and alkane chain length.     

Gate-controlled current and inelastic electron tunneling spectrum of benzene: a self-consistent study

We use density functional theory based nonequilibrium Green's function to self-consistently study the current through the 1,4-benzenedithiol (BDT). The elastic and inelastic tunneling properties through this Au-BDT-Au molecular junction are simulated, respectively. For the elastic tunneling case, it is found that the current through the tilted molecule can be modulated effectively by the external gate field, which is perpendicular to the phenyl ring. The gate voltage amplification comes from the modulation of the interaction between the electrodes and the molecules in the junctions. For the inelastic case, the electron tunneling scattered by the molecular vibrational modes is considered within the self-consistent Born approximation scheme, and the inelastic electron tunneling spectrum is calculated.     

Inelastic electron tunneling spectroscopy and vibrational coupling

We discuss the relationship between the inelastic electron tunneling spectroscopy (IETS) and vibronic coupling constant within the Green's function formalism at a level of perturbation theory approximation. We also compare our results with experimental measurements. Our results can provide insights into the mechanism of active vibronic modes for IETS.     

Bias-controlled selective excitation of vibrational modes in molecular junctions: a route towards mode-selective chemistry

We show that individual vibrational modes in single-molecule junctions with asymmetric molecule-lead coupling can be selectively excited by applying an external bias voltage. Thereby, a non-statistical distribution of vibrational energy can be generated, that is, a mode with a higher frequency can be stronger excited than a mode with a lower frequency. This is of particular interest in the context of mode-selective chemistry, where one aims to break specific (not necessarily the weakest) chemical bond in a molecule. Such mode-selective vibrational excitation is demonstrated for two generic model systems representing asymmetric molecular junctions and/or scanning tunneling microscopy experiments. To this end, we employ two complementary theoretical approaches, a nonequilibrium Green's function approach and a master equation approach. The comparison of both methods reveals good agreement in describing resonant electron transport through a single-molecule contact, where differences between the approaches highlight the role of non-resonant transport processes, in particular co-tunneling and off-resonant electron-hole pair creation processes.     

基于吡嗪连接的石墨烯电极单分子场效应晶体管

In single-molecule junctions, anchoring groups that connect the central molecule to the electrodes have profound effects on the mechanical and electrical properties of devices. The mechanical strength of the anchoring groups affects the device stability, while their electronic coupling strength influences the junction conductance and the conduction polarity. To design and fabricate high-performance single-molecule devices with graphene electrodes, it is highly desirable to explore robust anchoring groups that bond the central molecule to the graphene electrodes. Condensation of ortho-phenylenediamine terminated molecules with ortho-quinone moieties at the edges of graphene generates graphene-conjugated pyrazine units that can be employed as anchoring groups for the construction of molecular junctions with graphene electrodes. In this study, we investigated the fabrication and electrical characterization of single-molecule field-effect transistors (FETs) with graphene as the electrodes, pyrazine as the anchoring groups, and a heavily doped silicon substrate as the back-gate electrode. Graphene nano-gaps were fabricated by a high-speed feedback-controlled electro-burning method, and their edges were fully oxidized; thus, there were many ortho-quinone moieties at the edges. After the deposition of phenazine molecules with ortho-phenylenediamine terminals at both ends, a large current increase was observed, indicating that molecular junctions were formed with covalent pyrazine anchoring groups. The yield of the single-molecule devices was as high as 26%, demonstrating the feasibility of pyrazine as an effective anchoring group for graphene electrodes. Our electrical measurements show that the ten fabricated devices exhibited a distinct gating effect when a back-gate voltage was applied. However, the gate dependence of the conductance varied considerably from device to device, and three types of different gate modulation behaviors, including p-type, ambipolar, and n-type conduction, were observed. Our observations can be understood using a modified single-level model that takes into account the linear dispersion of graphene near the Dirac point; the unique band structure of graphene and the coupling strength of pyrazine with the graphene electrode both crucially affect the conduction polarity of single-molecule FETs. When the coupling strength of pyrazine with the graphene electrode is weak, the highest occupied molecular orbital (HOMO) of the central molecule dominates charge transport. Depending on the gating efficiencies of the HOMO level and the graphene states, devices can exhibit p-type or ambipolar conduction. In contrast, when the coupling is strong, the redistribution of electrons around the central molecule and the graphene electrodes leads to a realignment of the molecular levels, resulting in the lowest unoccupied molecular orbital (LUMO)-dominated n-type conduction. The high yield and versatility of the pyrazine anchoring groups are beneficial for the construction of single-molecule devices with graphene electrodes.     

On-Surface Synthesis and Determination of the Open-Shell Singlet Ground State of Tridecacene**

The character of the electronic structure of acenes has been the subject of longstanding discussion. However, convincing experimental evidence of their open-shell character has so far been missing. Here, we present the on-surface synthesis of tridecacene molecules by thermal annealing of octahydrotridecacene on a Au(111) surface. We characterized the electronic structure of the tridecacene by scanning probe microscopy, which reveals the presence of an inelastic signal at 126 meV. We attribute the inelastic signal to spin excitation from the singlet diradical ground state to the triplet excited state. To rationalize the experimental findings, we carried out many-body ab initio calculations as well as model Hamiltonians to take into account the effect of the metallic substrate. Moreover, we provide a detailed analysis of how the dynamic electron correlation and virtual charge fluctuation between the molecule and metallic surface reduces the singlet-triplet band gap. Thus, this work provides the first experimental confirmation of the magnetic character of tridecacene.     

Ab initio electron propagator calculations in molecular transport junctions: predictions of negative differential resistance

In this work we study current-voltage characteristics in transport molecular junctions with a 1,4-benzene dithiol molecule as a bridge by using different ab initio electron propagator methods such as OVGF and P3 which are both programs in a Gaussian software package. The current-voltage characteristics are calculated for different values of Fermi energy in various basis sets such as 6-311++G(p,d) and cc-pVDZ and are compared with the experimental data. A good agreement is found in almost the entire voltage range. In addition, the results of our calculations indicate that the accuracy of ab initio electron propagator methods is in the range of 0.2-0.3 eV. Since the computational methods are truly ab initio, implying no adjustable parameters, functions, or functionals, the theoretical predictions can be improved only by changing the model of a transport device. The current-voltage characteristics predict peaks, i.e., negative differential resistances, for the various values of Fermi energy. As shown, the origin of the negative differential resistances is related to the voltage dependences of overlap integrals for the active terminal orbitals, expansion coefficients of partial atomic wavefunctions in Dyson orbitals, and the voltage dependences of Dyson poles (ionization potentials). We find that two peak behavior in the current-voltage characteristics can be explained by the anharmonicity of potential energy surfaces. As a result of our studies, we predict that negative differential resistances can be experimentally found by changing a position of Fermi level, i.e., by using different metal electrodes coated by a gold atomic monolayer.     

Spin transport properties of single metallocene molecules attached to single-walled carbon nanotubes via nickel adatoms

The spin-dependent transport properties of single ferrocene, cobaltocene, and nickelocene molecules attached to the sidewall of a (4,4) armchair single-walled carbon nanotube via a Ni adatom are investigated by using a self-consistent ab initio approach that combines the non-equilibrium Green's function formalism with the spin density functional theory. Our calculations show that the Ni adatom not only binds strongly to the sidewall of the nanotube, but also maintains the spin degeneracy and affects little the transmission around the Fermi level. When the Ni adatom further binds to a metallocene molecule, its density of states is modulated by that of the molecule and electron scattering takes place in the nanotube. In particular, we find that for both cobaltocene and nickelocene the transport across the nanotube becomes spin-polarized. This demonstrates that metallocene molecules and carbon nanotubes can become a promising materials platform for applications in molecular spintronics.     

Effect of the continuity of the pi conjugation on the conductance of ruthenium-octene-ruthenium molecular junctions

The conductance of a family of ruthenium-octene-ruthenium molecular junctions with different pi conjugation are investigated using a fully self-consistent ab initio approach which combines the nonequilibrium Green's function formalism with density functional theory. Our calculations demonstrate that the continuity of the pi conjugation in the contact region as well as along the molecular backbone affects the junction conductance significantly, showing the advantage of using the ruthenium-carbon double bond as the linkage of conjugated organic molecules.     

The coupling constant polarizability and hyperpolarizabilty of 1J(NH) in N-methylacetamide, and its application for the multipole spin-spin coupling constant polarizability/reaction field approach to solvation

We present a benchmark study of a combined multipole spin-spin coupling constant (SSCC) polarizability/reaction field (MJP/RF) approach to the calculation of both specific and bulk solvation effects on SSCCs of solvated molecules. The MJP/RF scheme is defined by an expansion of the SSCCs of the solvated molecule in terms of coupling constant dipole and quadrupole polarizabilities and hyperpolarizabilities derived from single molecule ab initio calculations. The solvent electric field and electric field gradient are calculated based on data derived from molecular dynamics (MD) simulations thereby accounting for solute-solvent dynamical effects. The MJP/RF method is benchmarked against polarizable QM/MM calculations for the one-bond N-H coupling constant in N-methylacetamide. The best agreement between the MJP/RF and QM/MM approaches is found by truncating the electric field expansion in the MJP/RF approach at the linear electric field level. In addition, we investigate the sensitivity of the results due to the choice of one-electron basis set in the ab initio calculations of the coupling constant (hyper-)polarizabilities and find that they are affected by the basis set in a way similar to the coupling constants themselves.     

Propensity rules for inelastic electron tunneling spectroscopy of single-molecule transport junctions

Using a perturbative approach to simple model systems, we derive useful propensity rules for inelastic electron tunneling spectroscopy (IETS) of molecular wire junctions. We examine the circumstances under which this spectroscopy (that has no rigorous selection rules) obeys well defined propensity rules based on the molecular symmetry and on the topology of the molecule in the junction. Focusing on conjugated molecules of C(2h) symmetry, semiquantitative arguments suggest that the IETS is dominated by a(g) vibrations in the high energy region and by out of plane modes (a(u) and b(g)) in the low energy region. Realistic computations verify that the proposed propensity rules are strictly obeyed by medium to large-sized conjugated molecules but are subject to some exceptions when small molecules are considered. The propensity rules facilitate the use of IETS to help characterize the molecular geometry within the junction.     

Linear optical response of current-carrying molecular junction: a nonequilibrium Green's function-time-dependent density functional theory approach

We propose a scheme for calculation of linear optical response of current-carrying molecular junctions for the case when electronic tunneling through the junction is much faster than characteristic time of external laser field. We discuss relationships between nonequilibrium Green's function (NEGF) and time-dependent density functional theory (TDDFT) approaches and derive expressions for optical response and linear polarizability within NEGF-TDDFT scheme. Corresponding results for isolated molecule, derived within TDDFT approach previously, are reproduced when coupling to contacts is neglected.     

Charge Transport Properties of Molecular Junctions Built from Dithiol Polyenes

We present a study of the charge transmission behavior of a series of dithiol polyenes in the context of molecular junctions. Using the Landauer theory and zero voltage approximation the Green’s functions of the inserted molecules are calculated from a fully ab initio wave function based procedure. Various possibilities in approximating the correlation space are explored and quantitatively evaluated. Our results show that the transmission behavior of a molecular junction is not a monotonic function of the length of the employed molecule. Moreover, we introduce the analytic solution of a suitable model system to countercheck the ab initio results and find a remarkable degree of correspondence.     

An efficient molecular orbital approach for self-consistent calculations of molecular junctions

To model electron transport through a molecular junction, we propose an efficient method using an ab initio self-consistent nonequilibrium Green's function theory combined with density functional theory. We have adopted a model close to the extended molecule approach, due to its flexibility, but have improved on the problems relating to molecule-surface couplings and the long-range potential via a systematic procedure for the same ab initio level as that of Green's function. The resulting algorithm involves three main steps: (i) construction of the embedding potential; (ii) perturbation expansion of Green's function in the molecular orbital basis; and (iii) truncation of the molecular orbital space by separating it into inactive, active, and virtual spaces. The above procedures directly reduce the matrix size of Green's function for the self-consistent calculation step, and thus, the algorithm is suitable for application to large molecular systems.     

Inelastic insights for molecular tunneling pathways: bypassing the terminal groups

As an example of the use of inelastic transport to deduce structure in molecular transport junctions, we compute the orientation dependence of the Inelastic Electron Tunneling (IET) spectrum of the 1-pentane monothiolate. We find that upon increasing the tilting angle of the molecule with respect to the normal to the electrode the spectrum changes as the intensity of some vibrations is enhanced. These differences occur because for higher tilting angles the tunneling path that bypasses the terminal group grows in importance. IETS can therefore be used to establish the molecular orientation in junctions terminating with alkyl chains and to investigate experimentally the relative importance of the available tunneling paths.