Biomedical subjects

Mark A Ratner

Publications and source records attributed to Mark A Ratner.

At least 19 recordsLinked to original sources

PubMed2006

Steered molecular dynamics studies of the potential of mean force of a Na+ or K+ ion in a cyclic peptide nanotube.

Potential of mean force (PMF) profiles of a single Na+ or K+ ion passing through a cyclic peptide nanotube, cyclo[-(D-Ala-Glu-D-Ala-Gln)2-], in water are calculated to provide insight into ion transport and to understand the conductance difference between these two ions. The PMF profiles are obtained by performing steered molecular dynamics (SMD) simulations that are based on the Jarzynski equality. The computed PMF profiles for both ions show barriers of around 2.4 kcal/mol at the channel entrances and exits and energy wells in the middle of the tube. The energy barriers, so-called dielectric energy barriers, arise due to the desolvation of water molecules when ions move across the nanotube, and the energy wells appear as a result of attractive interactions between the cations and negatively charged carbonyl oxygens on the backbone of the tube. We find more and deeper energy wells in the PMF profile for Na+ than for K+, which suggests that Na+ ions have a longer residence time inside the nanotube and that permeation of Na+ ions is reduced compared to K+ ions. Calculations of the radial distribution functions (RDF) between the ions and oxygens in the water molecules and in carbonyl groups on the tube and an investigation of the orientations of the carbonyl groups show that, in contrast with the dynamic carbonyl groups observed in the selectivity filter of the KcsA ion channel, the carbonyl groups in the cyclic peptide nanotube are relatively rigid, with only slight reorientation of the carbonyl groups as the cations pass through. The rigidity of the carbonyl groups in the cyclic peptide nanotube can be attributed to their role in hydrogen bonding, which is responsible for the tube structure. Comparison of the PMF profiles with the electrostatic energy profiles calculated from the Poisson-Boltzmann (PB) equation, a dielectric continuum model, reveals that the dielectric continuum model breaks down in the confined region within the tube that governs ion transport.

Nanotechnology↗

PubMed2006

Singlet fission for dye-sensitized solar cells: can a suitable sensitizer be found?

We discuss possible improvements in the efficiency of dye-sensitized photovoltaic cells using dyes capable of singlet fission into two triplets, thus producing two electron-hole pairs from a single photon. It is pointed out that, in addition to derivatives of large alternant hydrocarbons, those of biradicals are also likely candidates for a favorable ordering of excited-state energy levels, E(T2), E(S1) > 2E(T1). A large number of potentially favorable structures has been examined by the semiempirical Pariser-Parr-Pople method and some also by the time-dependent density functional theory method. Several likely candidates have been identified for experimental examination.

Journal Article↗

PubMed2006

Time-resolved EPR studies of photogenerated radical ion pairs separated by p-phenylene oligomers and of triplet states resulting from charge recombination.

Photoexcitation of a series of donor-bridge-acceptor (D-B-A) systems, where D = phenothiazine (PTZ), B = p-phenylene (Phn), n = 1-5, and A= perylene-3,4:9,10-bis(dicarboximide) (PDI) results in rapid electron transfer to produce 1(PTZ+*-Phn-PDI-*). Time-resolved EPR (TREPR) studies of the photogenerated radical pairs (RPs) show that above 150 K, when n = 2-5, the radical pair-intersystem crossing mechanism (RP-ISC) produces spin-correlated radical ion pairs having electron spin polarization patterns indicating that the spin-spin exchange interaction in the radical ion pair is positive, 2J > 0, and is temperature dependent. This temperature dependence is most likely due to structural changes of the p-phenylene bridge. Charge recombination in the RPs generates PTZ-Phn-3*PDI, which exhibits a spin-polarized signal similar to that observed in photosynthetic reaction-center proteins and some biomimetic systems. At temperatures below 150 K and/or at shorter donor-acceptor distances, e.g., when n = 1, PTZ-Phn-3*PDI is also formed from a competitive spin-orbit-intersystem crossing (SO-ISC) mechanism that is a result of direct charge recombination: 1(PTZ+*-Phn-PDI-*) --> PTZ-Phn-3*PDI. This SO-ISC mechanism requires the initial RP intermediate and depends strongly on the orientation of the molecular orbitals involved in the charge recombination as well as the magnitude of 2J.

Biphenyl Compounds↗

PubMed2006

Quantum chemical analysis of electronic structure and n- and p-type charge transport in perfluoroarene-modified oligothiophene semiconductors.

Density-functional theory (DFT) is employed to investigate the structural, electronic, and transport properties of several isomeric fluoroarene-oligothiophene-based semiconductors. Three oligothiophene systems varying in the perfluoroarene group positions within the molecule are studied to understand the electronic structure leading to the observed mobility values and to the n- or p-type behavior in these structures. Analyses of both intermolecular interactions in dimers and extended interactions in crystalline structures afford considerable insight into the electronic properties and carrier mobilities of these materials, as well as the polarity of the charge carriers. From the calculated carrier effective masses, we find that sterically governed molecular planarity plays a crucial role in the transport properties of these semiconductors. Our calculations correlate well with experimentally obtained geometries, highest-occupied molecular orbital (HOMO)/lowest-unoccupied molecular orbital (LUMO) energies, and the experimental carrier mobility trends among the systems investigated.

Journal Article↗

PubMed2006

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.

Journal Article↗

PubMed2006

High-capacitance organic nanodielectrics: effective medium models of their response.

Molecular and macromolecular high-permittivity organic gate dielectric materials have been the focus of recent experimental research as a consequence of their promising properties for organic and inorganic field effect transistor (FET) applications. Two types of molecular thin films, self-assembled nanodielectrics (SANDs) and cross-linked polymer blends (CPBs), have been shown experimentally to afford high capacitances and low FET operating voltages. In an effort to design optimized nanostructures having even larger capacitances, lower leakage current densities, and further reduced FET operating voltages, we discuss approaches for computing the effective permittivities of each nanodielectric motif and investigate how molecular arrangements impact overall device capacitance. The calculated frequency-dependent capacitances, derived from Maxwell-Wagner theory applied to the Maxwell-Garnett effective medium approximation, agree fairly well with the experimental values for the two types of nanodielectrics. Predictions of larger capacitance SANDs are made with the two-capacitors-in-series equivalent circuit, where the layered, self-assembled structure is viewed as two different capacitors. The Maxwell-Garnett and Polder-Van Santen effective medium approximations are used to predict the dielectric response of higher permittivity polymer cross-linked blends. In calculations showing good agreement between theory and experiment, and with all parameters being equal, it is found that greater capacitances should be achievable with cross-linked composites than with layered composites.

Journal Article↗

PubMed2006

Single molecule electron transport junctions: charging and geometric effects on conductance.

A p-benzenedithiolate (BDT) molecule covalently bonded between two gold electrodes has become one of the model systems utilized for investigating molecular transport junctions. The plethora of papers published on the BDT system has led to varying conclusions with respect to both the mechanism and the magnitude of transport. Conductance variations have been attributed to difficulty in calculating charge transfer to the molecule, inability to locate the Fermi energy accurately, geometric dispersion, and stochastic switching. Here we compare results obtained using two transport codes, TRANSIESTA-C and HUCKEL-IV, to show that upon Au-S bond lengthening, the calculated low bias conductance initially increases by up to a factor of 30. This increase in highest occupied molecular orbital (HOMO) mediated conductance is attributed to charging of the terminal sulfur atom and a corresponding decrease in the energy gap between the Fermi level and the HOMO. Addition of a single Au atom to each terminal of the extended BDT molecule is shown to add four molecular states near the Fermi energy, which may explain the varying results reported in the literature.

Journal Article↗

PubMed2006

Electron transfer in multiply bridged donor-acceptor molecules: Dephasing and quantum coherence.

We present a simple theoretical treatment of nonadiabatic electron transfer in multiply bridged donor-bridge-acceptor molecules using the density matrix formalism. Destructive interference can result from different signed couplings between bridge sites, with the simplest system being a four-site Joachim-type molecular interferometer. Previous work has shown that deposition of energy on the bridge sites erases the interference and recovers transport. We show that pure local dephasing, a completely elastic process, is also capable of eliminating destructive interference and regaining transport. Destructive interference as a result of system connectivity can explain the familiar ortho-meta-para reactivity of benzene bridges. We also show that pure dephasing can yield a coalescence of ortho, meta, and para effective coupling strengths and suggest a system to observe this effect experimentally.

Journal Article↗

PubMed2006

Effects of hydration on molecular junction transport.

The study of charge transport through increasingly complex small molecules will benefit from a detailed understanding of how contaminants from the environment affect molecular conduction. This should provide a clearer picture of the electronic characteristics of molecules by eliminating interference from adsorbed species. Here we use magnetically assembled microsphere junctions incorporating thiol monolayers to provide insight into changing electron transport characteristics resulting from exposure to air. Using this technique, current-voltage analysis and inelastic electron tunnelling spectroscopy (IETS) demonstrate that the primary interaction affecting molecular conduction is rapid hydration at the gold-sulphur contacts. We use IETS to present evidence for changing mechanisms of charge transport as a result of this interaction. The detrimental effects on molecular conduction discussed here are important for understanding electron transport through gold-thiol molecular junctions once exposed to atmospheric conditions.

Electrochemistry↗

PubMed2006

Geometry dependent features of optically induced forces between silver nanoparticles.

A recently devised, discrete-dipole approximation (DDA) based method for computing optical forces is used to explore geometry dependent aspects of the light induced interactions between pairs of silver nanoparticles, including the influence of particle shape, relative positioning of the particles, and incident field orientation. The interactions are observed to have a large degree of generic character, independent of the details of the particle shape. The size of the optical forces is also compared to estimates for the van der Waals forces, and the results are used to assess the potential importance of radiation forces on recent experiments demonstrating photoinduced self-assembly of triangular silver nanoprisms.

Journal Article↗

PubMed2006

Stability and phase separation in mixed self-assembled monolayers.

Recent single molecule experiments rely on the self-assembly of binary mixtures of molecules with very different properties in a stable monolayer, in order to probe the characteristics of the interspersed molecule of interest in a controlled environment. However, not all efforts at coassembly have been successful. To study systematically the behavior of such systems, we derive the free energy of multicomponent systems of rods with configurational degrees of freedom, localized on a surface, starting from a generalized van der Waals description. The molecular parameters are determined by geometrical factors of the molecules and by their pairwise van der Waals interactions computed using molecular mechanics. Applying the model to two experimental situations, we are able to use the stability analysis of the respective mixtures to explain why coassembly was successful in one set of experiments (carotene and alkanethiol) and not in another (benzenethiols and alkanethiol). We outline general guidelines for suitable choices of molecules to achieve coassembly.

Journal Article↗

PubMed2006

Spin dynamics of photogenerated triradicals in fixed distance electron donor-chromophore-acceptor-TEMPO molecules.

The stable free radical 2,2,6,6-tetramethylpiperidinoxyl (TEMPO, T*) was covalently attached to the electron acceptor in a donor-chromophore-acceptor (D-C-A) system, MeOAn-6ANI-Phn-A-T*, having well-defined distances between each component, where MeOAn = p-methoxyaniline, 6ANI = 4-(N-piperidinyl)naphthalene-l,8-dicarboximide, Ph = 2,5-dimethylphenyl (n = 0,1), and A = naphthalene-1,8:4,5-bis(dicarboximide) (NI) or pyromellitimide (PI). Using both time-resolved optical and EPR spectroscopy, we show that T* influences the spin dynamics of the photogenerated triradical states 2,4(MeOAn+*-6ANI-Phn-A-*-T*), resulting in modulation of the charge recombination rate within the triradical compared with the corresponding biradical lacking T*. The observed spin-spin exchange interaction between the photogenerated radicals MeOAn+* and A-* is not altered by the presence of T*, which interacts most strongly with A-* and accelerates radical pair intersystem crossing. Charge recombination within the triradicals results in the formation of 2,4(MeOAn-6ANI-Phn-3*NI-T*) or 2,4(MeOAn-3*6ANI-Phn-PI-T*) in which T* is strongly spin polarized in emission. Normally, the spin dynamics of correlated radical pairs do not produce a net spin polarization; however, the rate at which the net spin polarization appears on T* closely follows the photogenerated radical ion pair decay rate. This effect is attributed to antiferromagnetic coupling between T* and the local triplet state 3NI, which is populated following charge recombination. These results are explained using a switch in the spin basis set between the triradical and the three-spin charge recombination product having both T* and 3*NI or 3*6ANI present.

Journal Article↗

PubMed2006

Molecular transport junctions: current from electronic excitations in the leads.

Using a model comprising a two-level bridge connecting free electron reservoirs we show that coupling of a molecular bridge to electron-hole excitations in the leads can markedly effect the source-drain current through a molecular junction. In some cases, e.g., molecules that exhibit strong charge transfer transitions, the contribution from electron-hole excitations can exceed the Landauer elastic current and dominate the observed conduction.

Journal Article↗

PubMed2006

Ion current calculations based on three dimensional Poisson-Nernst-Planck theory for a cyclic peptide nanotube.

Ion current calculations based on Poisson-Nernst-Planck (PNP) theory are performed for a synthetic cyclic peptide nanotube that consists of eight or ten cyclo[(-L-Trp-D-Leu-)4] embedded in a lipid bilayer membrane to investigate the ion transport properties of the nanotube. To explore systems with arbitrary geometries, three-dimensional PNP theory is implemented using a finite difference method. The influence of dipolar lipid molecules on the ion currents is also examined by turning on or off the charges of the lipid dipoles in dipalmitoylphosphatidylcholine (DPPC). Comparisons between the calculated and experimentally measured ion currents show that the PNP approach agrees well with the measurements at low ion concentrations but overestimates the currents at higher concentrations. Concentration profiles reveal the selectivity of the peptide nanotube to cations, which is attributed to the negatively charged carbonyl oxygens inside the nanotube. The dominant cation and the minimum anion concentrations inside the cyclic peptide nanotube suggest that these cyclic peptide nanotubes can be employed as ion sensors. In the case of the polar DPPC bilayer, smaller currents are obtained in the calculation. The variation of current with polarity of the lipids implies that both polar and nonpolar lipid bilayer membranes can be utilized to regulate ion currents in the peptide nanotube and other ion channels. Strengths and limitations of the PNP theory are also discussed.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed2006

Electron donor-bridge-acceptor molecules with bridging nitronyl nitroxide radicals: influence of a third spin on charge- and spin-transfer dynamics.

Appending a stable radical to the bridge molecule in a donor-bridge-acceptor system (D-B-A) is potentially an important way to control charge- and spin-transfer dynamics through D-B-A. We have attached a nitronyl nitroxide (NN*) stable radical to a D-B-A system having well-defined distances between the components: MeOAn-6ANI-Ph(NN*)-NI, where MeOAn = p-methoxyaniline, 6ANI = 4-(N-piperidinyl)naphthalene-1,8-dicarboximide, Ph = phenyl, and NI = naphthalene-1,8:4,5-bis(dicarboximide). MeOAn-6ANI, NN*, and NI are attached to the 1, 3, and 5 positions of the Ph bridge. Using both time-resolved optical and EPR spectroscopy, we show that NN* influences the spin dynamics of the photogenerated triradical states (2,4)(MeOAn(+)*-6ANI-Ph(NN*)-NI(-)*), resulting in slower charge recombination within the triradical compared to the corresponding biradical lacking NN*. The observed spin-spin exchange interaction between the photogenerated radicals MeOAn(+)(*) and NI(-)(*) is not altered by the presence of NN*, which only accelerates radical pair intersystem crossing. Charge recombination within the triradical results in the formation of (2,4)(MeOAn-6ANI-Ph(NN*)-(3)NI), in which NN* is strongly spin-polarized. Normally, the spin dynamics of correlated radical pairs do not produce a net spin polarization; however, net spin polarization appears on NN* with the same time constant as describes the photogenerated radical ion pair decay. This effect is attributed to antiferromagnetic coupling between NN* and the local triplet state (3)NI, which is populated following charge recombination. This requires an effective switch in the spin basis set between the triradical and the three-spin charge recombination product having both NN* and (3)NI present.

Journal Article↗

PubMed2006

A theoretical study of molecular conduction. III. A nonequilibrium-Green's-function-based Hartree-Fock approach.

Many recent experimental and theoretical studies have paid attention to the conductivity of single molecule transport junctions, both because it is fundamentally important and because of its significance in the development of molecular-based electronics. In this paper, we discuss a nonequilibrium Green's function (NEGF)-based Hartree-Fock (HF) approach; the NEGF method can appropriately accommodate charge distributions in molecules connected to electrodes. In addition, we show that a NEGF-based density matrix can reduce to an ordinary HF density matrix for an isolated molecule if the molecule does not interact with electrodes. This feature of the NEGF-based density matrix also means that NEGF-based Mulliken charges can be reduced to ordinary Mulliken charges in those cases. Therefore, the NEGF-based HF approach can directly compare molecules that are connected to electrodes with isolated ones, and is useful in investigating complicated features of molecular conduction. We also calculated the transmission probability and conduction for benzenedithiol under finite electrode biases. The coupling between the electrodes and molecule causes electron transfer from the molecule to the electrodes, and the applied bias modifies this electron transfer. In addition, we found that the molecule responds capacitively to the applied bias, by shifting the molecular orbital energies.

Journal Article↗

PubMed2006

Electron transfer mechanism and the locality of the system-bath interaction: a comparison of local, semilocal, and pure dephasing models.

We simulate the effects of two types of dephasing processes, a nonlocal dephasing of system eigenstates and a dephasing of semilocal eigenstates, on the rate and mechanism of electron transfer (eT) through a series of donor-bridge-acceptor systems, D-B(N)-A, where N is the number of identical bridge units. Our analytical and numerical results show that pure dephasing, defined as the perturbation of system eigenstates through the system-bath interaction, does not disrupt coherent eT because it induces no localization; electron transfer may proceed through superexchange in a system undergoing only pure dephasing. A more physically reasonable description may be obtained via a system-bath interaction that reflects the perturbation of more local electronic structure by local nuclear distortions and dipole interactions. The degree of locality of this interaction is guided by the structure of the system Hamiltonian and by the nature of the measurement performed on the system (i.e., the nature of the environment). We compare our result from this "semilocal" model with an even more local phenomenological dephasing model. We calculate electron transfer rate by obtaining nonequilibrium steady-state solutions for the elements of a reduced density matrix; a semigroup formalism is used to write down the dissipative part of the equation of motion.

Journal Article↗

PubMed2006

Effects of anharmonicity on nonadiabatic electron transfer: a model.

The effect of anharmonicity in the intramolecular modes of a model system for exothermic intramolecular nonadiabatic electron transfer is probed by examining the dependence of the transition probability on the exoergicity. The Franck-Condon factor for the Morse potential is written in terms of the Gauss hypergeometric function both for a ground initial state and for the general case, and comparisons are made between the first-order perturbation theory results for transition probability for harmonic and Morse oscillators. These results are verified with quantum dynamical simulations using wave-packet propagations on a numerical grid. The transition-probability expression incorporating a high-frequency quantum mode and low-frequency medium mode is compared for Morse and harmonic oscillators in different temperature ranges and with various coarse-graining treatments of the delta function from the Fermi golden rule expression. We find that significant deviations from the harmonic approximation are expected for even moderately anharmonic quantum modes at large values of exoergicity. The addition of a second quantum mode of opposite displacement negates the anharmonic effect at small energy change, but in the inverted regime a significantly flatter dependence on exoergicity is predicted for anharmonic modes.

Journal Article↗