Search PubMed⌕ Search

Biomedical subjects

Mark A Ratner

Publications and source records attributed to Mark A Ratner.

69 records · Page 4Linked to original sources

Molecular binding at gold transport interfaces. IV. Thiol chemisorption.

Alkene thiol/coinage metal molecular interfaces are relatively easy to make, and can result in well-ordered self-assembled monolayer films. The energetics of such formation is complex-differing experimental and theoretical accounts have focused on the nature of the binding, the energetics via different pathways (thiol radical, thiol or thiolate) and the geometry of binding. We report density functional theory calculations on a four atom gold cluster interacting with different (alkane, alkene, alkyne) thiolates. We find thiolate addition to be strongly exoergic, thiol radical to be roughly half as favorable, and thiol to be slightly favorable. We also find that the S-H bond can remain when the thiol attaches to the gold cluster, formally resulting in increased coordination on the sulfur atom.

Journal Article↗

Dynamic nature of the intramolecular electronic coupling mediated by a solvent molecule: a computational study.

We present a combined Molecular Dynamics/Quantum Chemical study of the solvent-mediated electronic coupling between an electron donor and acceptor in a C-clamp molecule. We characterize the coupling fluctuations due to the solvent motion for different solvents (acetonitrile, benzene, 1,3-diisopropyl-benzene) for the charge separation and the charge recombination processes. The time scale for solvent-induced coupling fluctuation is approximately 0.1 ps. The effect of these fluctuations on the observed rate is discussed using a recently developed theoretical model. We show that, while the microscopic charge transfer process is very complicated and its computational modeling very subtle, the macroscopic phenomenology can be captured by the standard models. Analyzing the contribution to the coupling given by different solvent orbitals, we find that many solvent orbitals mediate the electron transfer and that paths through different solvent orbitals can interfere constructively or destructively. A relatively small subset of substrate-solvent configurations dominate contributions to solvent-mediated coupling. This subset of configurations is related to the electronic structure of the C-clamp molecule.

Journal Article↗

How narrow can a meniscus be?

A water meniscus naturally forms in air between an atomic force microscope (AFM) tip and a substrate. This nanoscale meniscus produces a capillary force on the AFM, and also serves as a molecular transport channel in dip-pen nanolithography (DPN). A stable meniscus is a necessary condition for DPN and for the validity of the Kelvin equation commonly applied to AFM experiments. Lattice gas Monte Carlo simulations show that, due to thermal fluctuation, a stable meniscus has a lower limit in width. We find a minimum width of 5 molecular diameters (1.9 nm) when the tip becomes atomically sharp (terminated by a single atom).

Journal Article↗

Thermodynamic manifestations of structure fluctuations in liquids.

Fluctuations of pressure and internal energy in a low-temperature liquid, generated by structure fluctuations, are related in a general and straightforward way to the differences between the long- and short-time thermodynamic susceptibilities. The relations are similar to, but not identical with, those between thermodynamic fluctuations and susceptibilities in classical statistical mechanics. The derivation is general and straightforward, and based on the assumption that the local structure is a slow-relaxing mode in low-temperature liquids and may be characterized by an order parameter.

Journal Article↗

Capillary force in atomic force microscopy.

Under ambient conditions, a water meniscus generally forms between a nanoscale atomic force microscope tip and a hydrophilic surface. Using a lattice gas model for water and thermodynamic integration methods, we calculate the capillary force due to the water meniscus for both hydrophobic and hydrophilic tips at various humidities. As humidity rises, the pull-off force rapidly reaches a plateau value for a hydrophobic tip but monotonically increases for a weakly hydrophilic tip. For a strongly hydrophilic tip, the force increases at low humidities (<30%) and then decreases. We show that mean-field density functional theory reproduces the simulated pull-off force very well.

Journal Article↗

Reduced basis set for the gold atom in cluster complexes.

To extend the metal cluster size used in interfacing between bulk metals and molecules in ab initio studies of molecular electronics and chemisorption, a reduced size atomic orbital basis set for the gold atom has been generated. Based on the SKBJ relativistic effective core potential set, the three component 5d Gaussian orbital basis set is completely contracted. Comparisons between the full and reduced basis set in Au atom clusters and cluster complexes for geometry, bond distances, dipole moments, atomic charges, spin, bond dissociation energies, lowest energy harmonic frequencies, electron affinities, ionization energies, and density of states distributions show the contracted set to be a viable replacement for the full basis set. This result is obtained using both the B3LYP and BPW91 exchange-correlation potentials in density functional theory.

Journal Article↗

Electron transport in molecular wire junctions.

Molecular conductance junctions are structures in which single molecules or small groups of molecules conduct electrical current between two electrodes. In such junctions, the connection between the molecule and the electrodes greatly affects the current-voltage characteristics. Despite several experimental and theoretical advances, including the understanding of simple systems, there is still limited correspondence between experimental and theoretical studies of these systems.

Journal Article↗

Capillary force on a nanoscale tip in dip-pen nanolithography.

Monte Carlo simulation has been used to characterize the capillary force due to the condensation of a liquid meniscus between a tip with a nanoscale asperity and a flat surface. To consider both hydrophobic and hydrophilic molecules coating the tip as a model of dip-pen nanolithography, tips with various wettabilities are studied. The capillary force due to the meniscus is calculated for various saturations (humidities). We have implemented a thermodynamic integration technique that can project the force into energetic and entropic contributions. In most cases, the force is mainly energetic in origin. At the snap-off separation where the meniscus disappears, the tip feels a significant entropic force at high saturation. Our calculation shows nonmonotonic behavior of the pull-off force as a function of saturation, which is in qualitative accord with experiments.

Journal Article↗

Molecular rectification through electric field induced conformational changes.

A new approach for the design of a molecular rectifier is proposed. Using a simple model, we have shown that conformational changes induced by the electric field may lead to a rectifying junction. The simplest possible rectifier of this kind presents two almost isoenergetic conformations, with different conductances and dipole moments. A simple equation allows for the estimation of the range of molecular parameters and temperatures that lead to an effective rectification. Examples show that rectification based on this mechanism is also possible at room temperature.

Journal Article↗

Molecular rectification in a metal-insulator-metal junction based on self-assembled monolayers.

An electrical junction formed by mechanical contact between two self-assembled monolayers (SAMs)--a SAM formed from an dialkyl disulfide with a covalently linked tetracyanoquinodimethane group that is supported by silver (or gold) and a SAM formed from an alkanethiolate SAM that is supported by mercury-rectifies current. The precursor to the SAM on silver (or gold) was bis(20-(2-((2,5-cyclohexadiene-1,4-diylidene)dimalonitrile))decyl)) disulfide and that for the SAM on mercury was HS(CH(2))(n-1)CH(3) (n = 14, 16, 18). The electrical properties of the junctions were characterized by current-voltage measurements. The ratio of the conductivity of the junction in the forward bias (Hg cathodic) to that in the reverse bias (Hg anodic), at a potential of 1 V, was 9 +/- 2 when the SAM on mercury was derived from HS(CH(2))(15)CH(3). The ratio of the conductivity in the forward bias to that in the reverse bias increased with decreasing chain length of the alkanethiol used to form the SAM on mercury. These results demonstrate that a single redox center asymmetrically placed in a metal-insulator-metal junction can cause the rectification of current and indicate that a fixed dipole in the insulating region of a metal-insulator-metal junction is not required for rectification.

Disulfides↗

Effect of bond-length alternation in molecular wires.

Current-voltage (I-V) characteristics for metal-molecule-metal junctions formed from three classes of molecules measured with a simple crossed-wire molecular electronics test-bed are reported. Junction conductance as a function of molecular structure is consistent with I-V characteristics calculated from extended Hückel theory coupled with a Green's function approach, and can be understood on the basis of bond-length alternation.

Journal Article↗

Random laser in one dimension.

We present an analytical approach to random lasing in a one-dimensional medium, consistent with transfer matrix numerical simulations. It is demonstrated that the lasing threshold is defined by transmission through the passive medium and thus depends exponentially on the size of the system. Lasing in the most efficient regime of strong three-dimensional localization of light is discussed. We argue that the lasing threshold should have anomalously strong fluctuations from probe to probe, in agreement with recent measurements.

Journal Article↗

Interplay of topology and chemical stability on the electronic transport of molecular junctions.

The coherent electronic transport through molecular junctions is theoretically modeled. The interplay of geometry, topology, and chemistry is explored within the Landauer picture of elastic scattering and various methods of quantum description of the composite system. The emphasis is on obtaining guiding principles for device optimization. Outstanding problems and future directions are outlined.

Electric Conductivity↗