Density-matrix renormalization-group study of low-lying excitations of polyacene within a Pariser-Parr-Pople model

We have carried out symmetrized density-matrix renormalization-group calculations to study the nature of excited states of long polyacene oligomers within a Pariser-Parr-Pople Hamiltonian. We have used the C-2 symmetry, the electron-hole symmetry, and the spin parity of the system in our calculations. We find that there is a crossover in the lowest dipole forbidden two-photon state and the lowest dipole allowed excited state with size of the oligomer. In the long system limit, the two-photon state lies below the lowest dipole allowed excited state. The triplet state lies well below the two-photon state and energetically does not correspond to its description as being made up of two triplets. These results are in agreement with the general trends in linear conjugated polymers. However, unlike in linear polyenes wherein the two-photon state is a localized excitation, we find that in polyacenes, the two-photon excitation is spread out over the system. We have doped the systems with a hole and an electron and have calculated the charge excitation gap. Using the charge gap and the optical gap, we estimate the binding energy of the 1(1)B(-) exciton to be 2.09 eV. We have also studied doubly doped polyacenes and find that the bipolaron in these systems, to be composed of two separated polarons, as indicated by the calculated charge-density profile and charge-charge correlation function. We have studied bond orders in various states in order to get an idea of the excited state geometry of the system. We find that the ground state, the triplet state, the dipole allowed state, and the polaron excitations correspond to lengthening of the rung bonds in the interior of the oligomer while the two-photon excitation corresponds to the rung bond lengths having two maxima in the system.

Indian Ocean dipole mode events in an ocean general circulation model

The evolution of the dipole mode (DM) events in the Indian Ocean is examined using an ocean model that is driven by the NCEP fluxes for the period 1975-1998. The positive DM events during 1997, 1994 and 1982 and negative DM events during 1996 and 1984-1985 are captured by the model and it reproduces both the surface and subsurface features associated with these events. In its positive phase, the DM is characterized by warmer than normal SST in the western Indian Ocean and cooler than normal SST in the eastern Indian Ocean. The DM events are accompanied by easterly wind anomalies along the equatorial Indian Ocean and upwelling-favorable alongshore wind anomalies along the coast of Sumatra. The Wyrtki jets are weak during positive DM events, and the thermocline is shallower than normal in the eastern Indian Ocean and deeper in the west. This anomaly pattern reverses during negative DM events. During the positive phase of the DM easterly wind anomalies excite an upwelling equatorial Kelvin wave. This Kelvin wave reflects from the eastern boundary as an upwelling Rossby wave which propagates westward across the equatorial Indian Ocean. The anomalies in the eastern Indian Ocean weaken after the Rossby wave passes. A similar process excites a downwelling Rossby wave during the negative phase. This Rossby wave is much weaker but wind forcing in the central equatorial Indian Ocean amplifies the downwelling and increases its westward phase speed. This Rossby wave initiates the deepening of the thermocline in the western Indian Ocean during the following positive phase of the DM. Rossby wave generated in the southern tropical Indian Ocean by Ekman pumping contributes to this warming. Concurrently, the temperature equation of the model shows upwelling and downwelling to be the most important mechanism during both positive events of 1994 and 1997. (C) 2002 Elsevier Science Ltd. All rights reserved.

A determination of the structure of the intramolecular charge transfer state of 4-dimethylaminobenzonitrile (DMABN) by time-resolved resonance Raman spectroscopy

Picosecond time-resolved resonance Raman spectra of the A (intramolecular charge transfer, ICT) state of DMABN, DMABN-d(6) and DMABN-N-15 have been obtained. The isotopic shifts identify the nu (s)(ph-N) mode as a band at 1281 cm(-1). The similar to 96 cm(-1) downshift of this mode from its ground state frequency rules out the electronic coupling PICT model and unequivocally supports the electronic decoupling TICT model. However, our results suggest some pyramidal character of the A state amino conformation.

Real-time kinetic analysis of hCG-monoclonal antibody interaction using radiolabeled hCG probe: presence of two forms of Ag-mAb complex as revealed by solid phase dissociation studies

Real-time kinetics of ligand-ligate interaction has predominantly been studied by either fluorescence or surface plasmon resonance based methods. Almost all such studies are based on association between the ligand and the ligate. This paper reports our analysis of dissociation data of monoclonal antibody-antigen (hCG) system using radio-iodinated hCG as a probe and nitrocellulose as a solid support to immobilize mAb. The data was analyzed quantitatively for a one-step and a two-step model. The data fits well into the two-step model. We also found that a fraction of what is bound is non-dissociable (tight-binding portion (TBP)). The TBP was neither an artifact of immobilization nor does it interfere with analysis. It was present when the reaction was carried out in homogeneous solution in liquid phase. The rate constants obtained from the two methods were comparable. The work reported here shows that real-time kinetics of other ligand-ligate interaction can be studied using nitrocellulose as a solid support. (C) 2002 Elsevier Science B.V. All rights reserved.

Self-assembled molecular films of tetraamino metal (Co, Cu, Fe) phthalocyanines on gold and silver. Electrochemical and spectroscopic characterization

The formation of molecular films of 2,9,16,23-tetraamino metal phthalocyanines [TAM(II)Pc; M (II) = Co, Cu, and TAM(III)Pc; M = Fe] by spontaneous adsorption on gold and silver surfaces is described. The properties of these films have been investigated by cyclic voltammetry, impedance, and FT-Raman spectroscopy. The charge associated with Co(II) and Co(I) redox couple in voltammetric data leads to a coverage of (0.35+/-0.05) x 10(-10) mol cm(-2), suggesting that the tetraamino cobalt phthalocyanine is adsorbed as a monolayer with an almost complete coverage. The blocking behavior of the films toward oxygen and Fe(CN)(6)(3-/4-) redox couple have been followed by cyclic voltammetry and impedance measurements. This leads to an estimate of the coverage of about 85 % in the case of copper and the iron analogs. FT-Raman studies show characteristic bands around 236 cm(-1) revealing the interaction between the metal substrate and the nitrogen of the -NH2 group on the phthalocyanine molecules.

Amino acid interaction preferences in helical membrane proteins

Membrane proteins are involved in a number of important biological functions. Yet, they are poorly understood from the structure and folding point of view. The external environment being drastically different from that of globular proteins, the intra-protein interactions in membrane proteins are also expected to be different. Hence, statistical potentials representing the features of inter-residue interactions based exclusively on the structures of membrane proteins are much needed. Currently, a reasonable number of structures are available, making it possible to undertake such an analysis on membrane proteins. In this study we have examined the inter-residue interaction propensities of amino acids in the membrane spanning regions of the alpha-helical membrane (HM) proteins. Recently we have shown that valuable information can be obtained on globular proteins by the evaluation of the pair-wise interactions of amino acids by classifying them into different structural environments, based on factors such as the secondary structure or the number of contacts that a residue can make. Here we have explored the possible ways of classifying the intra-protein environment of HM proteins and have developed scoring functions based on different classification schemes. On evaluation of different schemes, we find that the scheme which classifies amino acids to different intra-contact environment is the most promising one. Based on this classification scheme, we also redefine the hydrophobicity scale of amino acids in HM proteins.

Carrier density-dependent transport in poly(3-methylthiophene): from injection-limited to space-charge-limited current

Current-voltage (I-V) and impedance measurements were carried out in doped poly(3-methylthiophene) devices by varying the carrier density. As the carrier concentration reduces the I-V characteristics indicate that the conduction mechanism is limited by metal-polymer interface, as also observed in impedance data. The temperature dependence of I-V in moderately doped samples shows a trap-controlled space-charge-limited conduction (SCLC); whereas in lightly doped devices injection-limited conduction is observed at lower bias and SCLC at higher voltages. The carrier density-dependent quasi-Fermi level adjustment and trap-limited transport could explain this variation in conduction mechanism. Capacitance measurements at lower frequencies and higher bias voltages show a sign change in values due to the significant variations in the relaxation behaviour for lightly and moderately doped samples. The electrical hysteresis increases as carrier density is reduced due to the time scales involved in the de-trapping of carriers.

Entrapment of a Water Wire in a Hydrophobic Peptide Channel with an Aromatic Lining

A one-dimensional water wire has been characterized by X-ray diffraction in single crystals of the tripeptide Ac-Phe-Pro-Trp-OMe. Crystals in the hexagonal space group P6(5) reveal a central hydrophobic channel lined by aromatic residues which entraps an approximately linear array of hydrogen bonded water molecules. The absence of any significant van der Waals contact with the channel walls suggests that the dominant interaction between the ``water wire'' and ``peptide nanotube'' is electrostatic in origin. An energy difference of 16 KJmol(-1) is estimated for the distinct orientations of the water wire dipole with respect to the macrodipole of the peptide nanotube. The structural model suggests that Grotthuss type proton conduction may, through constricted hydrophobic channels, be facilitated by concerted, rotational reorientation of water molecules.