Triplet energy studies of thiophene and para-phenylene based oligomers

A series of conjugated materials based on oligomers of the para-phenylene type and oligothiophenes was prepared, and their phosphorescence spectra were recorded at 77 K using a pulsed flash-lamp as a light source and gated detection. The triplet energies of the oligomers were estimated and correlated with their chemical structure. It was found that simple changes in the building block sequence in the thiophene-containing oligomers allowed for tuning the triplet energy from 1.86 to 2.35 eV (530-670 nm). Hypsochromic shifts and little variation of the triplet energy were obtained with increasing length of the pi-system for thiophene end-capped oligomers, contrary to the usual behavior of unsubstituted oligomers. The experimental results were supported with theoretical computations from density functional theory (B3LYP/6-31G*) calculations, which indicated that changes in the geometry and delocalization of the triplet excited state account for the trends in the triplet energy evolution.     

Charge and spin transport through nucleic acids

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Intermolecular charge transfer between heterocyclic oligomers. Effects of heteroatom and molecular packing on hopping transport in organic semiconductors

For electron or hole transfer between neighboring conducting polymer strands or oligomers, the intrinsic charge-transfer rate is dictated by the charge-resonance integral and by the reorganization energy due to geometric relaxation. To explain conduction anisotropy and other solid-state effects, a multivariate, systematic analysis of bandwidth as a function of intermolecular orientations is undertaken for a series of oligoheterocycles, using first-principles methods. While cofacial oligomers show the greatest bandwidths at a given intermolecular C-C contact distance, for a fixed center-to-center intermolecular distance, tilted pi-stacking increases pi-overlap (particularly for LUMO orbitals) and decreases electrostatic repulsion, yielding optimum tilt angles for packing of approximately 40-60 degrees at small intermolecular separations. The calculations also reveal that bandwidths and intrinsic mobilities of holes and electrons in conjugated oligoheterocycles can be quite comparable.     

Analytical results on ballistic transport in a periodic molecular wire

In this paper, we study the coherent electronic transport of a periodic quantum wire (P-QW) such as poly-acetylene connected to uniform metallic leads, within the tight-binding (TB) approach and in the ballistic regime. We have calculated the Green’s function (GF), density of states (DOS) and the coherent transmission coefficient (TC) fully exactly for a quantum wire. The quasi gap and the energy and wire-length dependence of the GF and conductance for the system are also derived. Finally, we obtain a non-linear equation which gives the bound state energies. Our calculation can be generalized to arbitrary leads and can be applied to molecular wires, polymers, nanocrystals, where results may be useful in designing future molecular electronic devices.     

Efficient charge transport along phenylene-vinylene molecular wires

We have studied the motion of charge carriers along isolated phenylene-vinylene (PV) chains using a combination of experimental and theoretical methods. The conductive properties of positive charges along PV chains in dilute solution were studied by using the pulse-radiolysis time-resolved microwave conductivity (TRMC) technique. This technique enables the measurement of high-frequency (tens of GHz) charge carrier mobilities along isolated PV chains without the use of electrodes. The charge carrier mobility along PV chains with finite and infinite length was studied theoretically by charge transport simulations with parameters from density functional theory (DFT) calculations. The high-frequency charge carrier mobility is found to depend strongly on the conjugation length of the PV chains and is found to increase both with increasing length of the PV chain and with increasing conjugation fraction. The experimental results are in good agreement with the calculated results. On the basis of this combined experimental and theoretical study an intrachain charge carrier mobility of a few tens of cm2/Vs is expected for an infinitely long PV chain without conjugation breaks.     

Direct detection of spin polarization in photoinduced charge transfer through a chiral bridge

It is well assessed that the charge transport through a chiral potential barrier can result in spin-polarized charges. The possibility of driving this process through visible photons holds tremendous potential for several aspects of quantum information science, e.g., the optical control and readout of qubits. In this context, the direct observation of this phenomenon via spin-sensitive spectroscopies is of utmost importance to establish future guidelines to control photo-driven spin selectivity in chiral structures. Here, we provide direct proof that time-resolved electron paramagnetic resonance (EPR) can be used to detect long-lived spin polarization generated by photoinduced charge transfer through a chiral bridge. We propose a system comprising CdSe quantum dots (QDs), as a donor, and C₆₀, as an acceptor, covalently linked through a saturated oligopeptide helical bridge (χ) with a rigid structure of ∼10 Å. Time-resolved EPR spectroscopy shows that the charge transfer in our system results in a C₆₀ radical anion, whose spin polarization maximum is observed at longer times with respect to that of the photogenerated C₆₀ triplet state. Notably, the theoretical modelling of the EPR spectra reveals that the observed features may be compatible with chirality-induced spin selectivity, but the electronic features of the QD do not allow the unambiguous identification of the CISS effect. Nevertheless, we identify which parameters need optimization for unambiguous detection and quantification of the phenomenon. This work lays the basis for the optical generation and direct manipulation of spin polarization induced by chirality.

Our work provides a first attempt to directly detect the spin polarisation of Chiral-Induced Spin Selectivity (CISS) effect by studying the photoinduced electron transfer in a CdSe Quantum Dot-chiral bridge-fullerene derivative (QD–χ–C₆₀) system.     

Sequence dependence of charge transport through DNA domains

Here we examine the photooxidation of two kinetically fast electron hole traps, N4-cyclopropylcytosine (CPC) and N2-cyclopropylamine-guanosine (CPG), incorporated in DNA duplexes of various sequence using different photooxidants. DNA oxidation studies are carried out either with noncovalently bound [Ru(phen)(dppz)(bpy')]3+ (dppz = dipyridophenazine) and [Rh(phi)2(bpy)]3+ (phi = phenanthrenequinone diimine) or with anthraquinone tethered to DNA. Because the cyclopropylamine-substituted bases decompose rapidly upon oxidation, their efficiency of decomposition provides a measure of relative hole localization. Consistent with a higher oxidation potential for CPC versus CPG in DNA, CPC decomposes with photooxidation by [Rh(phi)2(bpy)]3+, while CPG undergoes ring-opening both with photoexcited [Rh(phi)2(bpy)]3+ and with [Ru(phen)(dppz)(bpy')]3+. Anthraquinone-modified DNA assemblies of identical base composition but different base sequence are also probed. Single and double base substitutions within adenine tracts modulate CPC decomposition. In fact, the entire sequence within the DNA assembly is seen to govern CPC oxidation, not simply the bases intervening between CPC and the tethered photooxidant. These data are reconciled in the context of a mechanistic model of conformationally gated charge transport through delocalized DNA domains. Photooxidations of anthraquinone-modified DNA assemblies containing both CPC and CPG, but with varied distances separating the modified bases, point to a domain size of at least three bases. Our model for DNA charge transport is distinguished from polaron models. In our model, delocalized domains within the base pair stack form transiently based upon sequence-dependent DNA structure and dynamics. Given these results, DNA charge transport is indeed remarkably sensitive to DNA sequence and structure.     

Single-step charge transport through DNA over long distances

Quantum yields for charge transport across adenine tracts of increasing length have been measured by monitoring hole transport in synthetic oligonucleotides between photoexcited 2-aminopurine, a fluorescent analogue of adenine, and N(2)-cyclopropyl guanine. Using fluorescence quenching, a measure of hole injection, and hole trapping by the cyclopropyl guanine derivative, we separate the individual contributions of single- and multistep channels to DNA charge transport and find that with 7 or 8 intervening adenines the charge transport is a coherent, single-step process. Moreover, a transition occurs from multistep to single-step charge transport with increasing donor/acceptor separation, opposite to that generally observed in molecular wires. These results establish that coherent transport through DNA occurs preferentially across 10 base pairs, favored by delocalization over a full turn of the helix.     

Conformations and charge transport characteristics of biphenyldithiol self-assembled-monolayer molecular electronic devices: a multiscale computational study

We report a computational study of conformations and charge transport characteristics of biphenyldithiol (BPDT) monolayers in the (sqrt.3 x sqrt.3)R30 degrees packing ratio sandwiched between Au(111) electrodes. From force-field molecular-dynamics and annealing simulations of BPDT self-assembled monolayers (SAMs) with up to 100 molecules on a Au(111) substrate, we identify an energetically favorable herringbone-type SAM packing configuration and a less-stable parallel packing configuration. Both SAMs are described by the (2sqrt.3 x sqrt.3)R30 degrees unit cell including two molecules. With subsequent density-functional theory calculations of one unit cell of the (i) herringbone SAM with the molecular tilt angle theta approximately 15 degrees , (ii) herringbone SAM with theta approximately 30 degrees , and (iii) parallel SAM with theta approximately 30 degrees, we confirm that the herringbone packing configuration is more stable than the parallel one but find that the energy variation with respect to the molecule tilting within the herringbone packing is very small. Next, by capping these SAMs with the top Au(111) electrode, we prepare three molecular electronic device models and calculate their coherent charge transport properties within the matrix Green's function approach. Current-voltage (I-V) curves are then obtained via the Landauer-Buttiker formula. We find that at low-bias voltages (|V| < or = 0.2 V) the I-V characteristics of models (ii) and (iii) are similar and the current in model (i) is smaller than that in (ii) and (iii). On the other hand, at higher-bias voltages (|V| > or 0.5 V), the I-V characteristics of the three models show noticeable differences due to different phenyl band structures. We thus conclude that the BPDT SAM I-V characteristics in the low-bias voltage region are mainly determined by the -Au [corrected] interaction within the individual molecule-electrode contact, while both intramolecular conformation and intermolecular interaction can affect the BPDT SAM I-V characteristics in the high-bias voltage region.     

Challenges in distinguishing superexchange and hopping mechanisms of intramolecular charge transfer through fluorene oligomers

The temperature dependence of intramolecular charge separation in a series of donor-bridge-acceptor molecules having phenothiazine (PTZ) donors, 2,7-oligofluorene FL(n) (n = 1-4) bridges, and perylene-3,4:9,10-bis(dicarboximide) (PDI) acceptors was studied. Photoexcitation of PDI to its lowest excited singlet state results in oxidation of PTZ via the FL(n) bridge. In toluene, the temperature dependence of the charge separation rate constants for PTZ-FL(n)-PDI, (n = 1-4) is relatively weak and is successfully described by the semiclassical Marcus equation. The activation energies for charge separation suggest that bridge charge carrier injection is not the rate limiting step. The difficulty of using temperature and length dependence to differentiate hopping and superexchange is discussed, with difficulties in the latter topic explored via an extension of a kinetic model proposed by Bixon and Jortner.     

Investigating charge transport in molecular switches with neural networks

The control of charge transport on a polymer chain by impurity molecules working as switches is studied. Charge propagation is estimated using a backpropagation neural network approach. The supervised learning is accomplished using theoretical results in which the chain is modeled by a tight-binding Hamiltonian extended to include the effects of an external electric field. The charge transport through the sites that work like a switch is analyzed by the numerical integration of the equations of motion. For a donor–acceptor pair of impurities, we found that the chain offers a wide range of devices, from simple switches to perfect molecular rectifiers. The influence of the parameters of the molecules on the charge transport, the role of the length of separation between the sites where the impurity molecules bond, as well as the changes they must undergo to characterize each kind of molecular switch are determined. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1060–1066, 1999     

1,3-Diborata-2,4-diphosphoniocyclobutane-1,3-diyls communicate through a para-phenylene linker

The presence of a second 1,3-diborata-2,4-diphosphoniocyclobutane-1,3-diyl in the para-position of a phenylene linker favors the diradical form over the 1,3-diborata-2,4-diphosphoniobicyclo[1.1.0]butane bond stretch isomer, as long as the two planar diradical units are coplanar with the linker. This demonstrates that two BPBP diradicals communicate through the phenyl ring.     

The vibrational reorganization energy in pentacene: molecular influences on charge transport

The reorganization energy in pentacene is reported on the basis of a joint experimental and theoretical study of pentacene ionization using high-resolution gas-phase photoelectron spectroscopy, semiempirical intermediate neglect of differential overlap calculations, and first-principles correlated quantum-mechanical calculations at MP2 and density functional theory levels. The reorganization energy upon positive ionization of pentacene is determined both experimentally and theoretically to be remarkably low. This is one key element that allows one to rationalize the extremely high hole mobilities recently measured in pentacene single crystals.     

Oxidative charge transport through DNA in nucleosome core particles

Eukaryotic DNA is packaged into nucleosomes, made up of 146 bp of DNA wrapped around a core of histone proteins. We used photoexcited rhodium intercalators to explore DNA charge transport within these assemblies. Although histone proteins inhibit intercalation of the rhodium complex within the core particle, they do not prevent 5'-GG-3' oxidation, the signature of oxidative charge transport through DNA. Moreover, using rhodium intercalators tethered to the 5' terminus of the DNA, we found that guanine bases within the nucleosome can be oxidized from a distance of 24 bp. Histone binding did not affect the pattern and extent of this oxidation. Therefore, although the structure of the nucleosome core particle generally protects DNA from damage by solution-borne molecules, packaging within the nucleosome does not protect DNA from charge transfer damage through the base pair stack.     

Anisotropic heat transport in nanoconfined polyamide-6,6 oligomers: atomistic reverse nonequilibrium molecular dynamics simulation

While polymers are known as thermal insulators, recent studies show that stretched single chains of polymers have a very high thermal conductivity. In this work, our new simulation scheme for simulation of heat flow in nanoconfined fluids [H. Eslami, L. Mohammadzadeh, and N. Mehdipour, J. Chem. Phys. 135, 064703 (2011)] is employed to study the effect of chain ordering (stretching) on the rate of heat transfer in polyamide-6,6 nanoconfined between graphene surfaces. Our results for the heat flow in the parallel direction (the plane of surfaces) show that the coefficient of thermal conductivity depends on the intersurface distance and is much higher than that of the bulk polymer. A comparison of results in this work with our former findings on the heat flow in the perpendicular direction, with the coefficient of heat conductivity less than the bulk sample, reveal that well-organized polymer layers between the confining surfaces show an anisotropic heat conduction; the heat conduction in the direction parallel to the surfaces is much higher than that in the perpendicular direction. The origin of such anisotropy in nanometric heat flow is shown to be the dramatic anisotropy in chain conformations (chain stretching) beside the confining surfaces. The results indicate that the coefficients of heat conductivity in both directions, normal and parallel to the surfaces, depend on the degree of polymer layering between the surfaces and the pore width.     

Charge transmission through a molecular wire: the role of terminal sites for the current-voltage behavior

The current-voltage and the conductance-voltage characteristics are analyzed for a particular type of molecular wire embedded between two electrodes. The wire is characterized by internal molecular units where the lowest occupied molecular orbital (LUMO) levels are positioned much above the Fermi energy of the electrodes, as well as above the LUMO levels of the terminal wire units. The latter act as specific intermediate donor and acceptor sites which in turn control the current formation via the superexchange and sequential electron transfer mechanisms. According to the chosen wire structure, intramolecular multiphonon processes may block the superexchange component of the interelectrode current, resulting in a negative differential resistance of the molecular wire. A pronounced current rectification appears if (i) the superexchange component dominates the electron transfer between the terminal sites and if (ii) the multiphonon suppression of distant superexchange charge hopping events between those sites is nonsymmetric.     

Sensing a binding event through charge transport variations using an aromatic oligoamide capsule

The selective binding properties of a 13-mer oligoamide foldamer capsule composed of 4 different aromatic subunits are reported. The capsule was designed to recognize dicarboxylic acids through multiple-point interactions owing to a combination of protonation/deprotonation events, H-bonding, and geometrical constraints imparted by the rigidity of the foldamer backbone. Compared to tartaric acid, binding of 2,2-difluorosuccinic acid or 2,2,3,3-tetrafluorosuccinic acid resulted in symmetry breaking due to deprotonation of only one of the two carboxylic acid groups of the encapsulated species as shown by NMR studies in solution and by single-crystal X-ray diffraction in the solid state. An analogous 14-mer foldamer capsule terminated with a thiol anchoring group was used to probe the complexation event in self-assembled monolayers on Au substrates. Ellipsometry and polarization-modulation infrared absorption-reflection spectroscopy studies were consistent with the formation of a single molecule layer of the foldamer capsule oriented vertically with respect to the surface. The latter underwent smooth complexation of 2,2-difluorosuccinic acid with deprotonation of one of the two carboxylic acid groups. A significant (80-fold) difference in the charge transport properties of the monolayer upon encapsulation of the dicarboxylic acid was evidenced from conducting-AFM measurements (S = 1.1 × 10⁻⁹vs. 1.4 × 10⁻¹¹ ohm⁻¹ for the empty and complexed capsule, respectively). The modulation in conductivity was assigned to protonation of the aromatic foldamer backbone.

Conductance through a monolayer of a helical foldamer host was found to vary by 80-fold depending on the presence or the absence of a guest in the host''s cavity.