Physically based molecular device model in a transient circuit simulator

Two efficient, physically based models for the real-time simulation of molecular device characteristics of single molecules are developed. These models assume that through-molecule tunnelling creates a steady-state Lorentzian distribution of excess electron density on the molecule and provides for smooth transitions for the electronic degrees of freedom between the tunnelling, molecular-excitation, and charge-hopping transport regimes. They are implemented in the fREEDA™ transient circuit simulator to allow for the full integration of nanoscopic molecular devices in standard packages that simulate entire devices including CMOS circuitry. Methods are presented to estimate the parameters used in the models via either direct experimental measurement or density-functional calculations. The models require 6–8 orders of magnitude less computer time than do full a priori simulations of the properties of molecular components. Consequently, molecular components can be efficiently implemented in circuit simulators. The molecular-component models are tested by comparison with experimental results reported for 1,4-benzenedithiol.     

Antiparallel triple helices. Structural characteristics and stabilization by 8-amino derivatives

The structural, dynamical, and recognition properties of antiparallel DNA triplexes formed by the antiparallel d(G#G.C), d(A#A.T), and d(T#A.T) motifs (the pound sign and dot mean reverse-Hoogsteen and Watson-Crick hydrogen bonds, respectively) are studied by means of "state of the art" molecular dynamics simulations. Once the characteristics of the helix are defined, molecular dynamics and thermodynamic integration calculations are used to determine the expected stabilization of the antiparallel triplex caused by the introduction of 8-aminopurines. Finally, oligonucleotides containing 8-aminopurine derivatives are synthesized and tested experimentally using several approaches in a variety of systems. A very large stabilization of the triplex is found experimentally, as predicted by simulations. These results open the possibility for the use of oligonucleotides carrying 8-aminopurines to bind single-stranded nucleic acids by formation of antiparallel triplexes.     

Texture changes inside smectic-C droplets in azobenzene Langmuir monolayers

Preparation of Langmuir monolayers of a mixture of trans- and cis-isomers of an azobenzene derivative, 4-[4-[(4-octylphenyl)azo]phenoxy]butanoic acid, results in the segregation of birefringent trans-isomer domains embedded in an isotropic medium of cis-isomers. Brewster angle microscopy observations allow us to identify different textures inside the domains depending on surface pressure, temperature, and domain size. The evolution of the monolayer in the dark, from initial droplets formed after spreading to a stable stripe texture, is described. The dynamics of domain coalescence and some morphological transitions induced by temperature and surface pressure changes are also discussed. A simple theoretical model is included to supplement some of these experimental observations.     

Nitrosation of peptide bonds. Cleavage of nitrosated peptides by pyrrolidine and α-amino esters

The reaction of several α-amino acids and peptides (containing Gly, L-Ala, L-Leu, L- or DL-Phe, and/or L- or D-Val) with air-diluted nitrogen oxides has been studied to roughly mimic the N-nitrosation of peptide bonds that the contaminated urban air might produce in pulmonary tissues. Most N-protected α-amino acids give practically quantitative yields of N-nitroso derivatives. N-Protected dipeptides afford either dinitrosated peptides, mixtures of di- and mononitrosated compounds, selectively mononitrosated products, or no reaction at all, depending mainly on steric effects. The same trends are observed for some higher peptides. The (po1y)nitrosated Peptides, which retain the chirality of the starting materials, have been characterized by ¹H and ¹³C NMR spectroscopy and are cleaved by pyrrolidine and amino esters under mild conditions to give (new) amides or peptides plus diazo derivatives.     

Inclusion by a fluorenyl diol host with substituted pyridines

The structures of the inclusion compounds formed by the host 9,9’-(ethyne-1,2-diyl)bis(fluoren-9-01) with pyridine and picolines are similar and display tubular topology. The host discriminates poorly between these guests. The kinetics of desorption of the pyridine compound is governed by the Avrami-Erofe’ev equation A2, with an activation energy of 111(7) kJ mol⁻¹.     

Stopped-flow injection analysis. The influence of diffusion on dispersion of normal and reverse flow injection

A relationship is derived to enable the comparison of the dispersion heights of normal and reverse flow injection analysis (FIA). A single channel flow system is employed in the absence of a chemical reaction. The stopped-flow injection method is used to probe the influence of molecular diffusion on the overall dispersion of normal and reverse FIA, which appeared to demonstrate fundamentally different diffusion behaviors. Small discrepancies are observed between the dispersion heights, which are enhanced by the stopped-flow period, especially when unmatched matrix ionic compositions of the indicator and counter solutions were involved. For these conditions, the diffusion flux rate is enhanced considerably, displaying a peak, in addition to the transient, for both methods. The influence of diffusion on the dispersion characteristics of normal and reverse FIA is discussed theoretically. Diffusion in the proposed model is postulated to oppose dispersion by convection. The latter initiates concentration gradients in the injection zone and propagates it with flow time over the dispersion zone profile. The diffusion flux then reacts in order to confine the indicator dispersion for normal FIA and to enhance it for reverse FIA. This model is consistent with the experimental results and accounts for most of the phenomena encountered. Probably owing to the influence of secondary flow phenomena, the use of coiled tubes has suppressed the effects of diffusion on the overall dispersion behavior.Part of the experimental work was performed at IMI Institute for Research and Development, Haifa, Israel.     

Exciton dissociation dynamics in model donor-acceptor polymer heterojunctions. I. Energetics and spectra

In this paper we consider the essential electronic excited states in parallel chains of semiconducting polymers that are currently being explored for photovoltaic and light-emitting diode applications. In particular, we focus upon various type II donor-acceptor heterojunctions and explore the relation between the exciton binding energy to the band offset in determining the device characteristic of a particular type II heterojunction material. As a general rule, when the exciton binding energy is greater than the band offset at the heterojunction, the exciton will remain the lowest-energy excited state and the junction will make an efficient light-emitting diode. On the other hand, if the offset is greater than the exciton binding energy, either the electron or hole can be transferred from one chain to the other. Here we use a two-band exciton to predict the vibronic absorption and emission spectra of model polymer heterojunctions. Our results underscore the role of vibrational relaxation and suggest that intersystem crossings may play some part in the formation of charge-transfer states following photoexcitation in certain cases.     

Molecular quantum similarity matrix based clustering of molecules using dendrograms

A new scheme for general classification of quantum objects is presented. Based on molecular quantum similarity matrices (MQSM), different algorithms are presented for generating Molecular Quantum Similarity Dendrograms (MQSD). An application of MQSD is presented for a set of steroid molecules.