Effects of phase-breaking on long-range charge transfer in DNA: Partially-coherent-tunneling model study

The mechanism of hole charge transfer in DNA of various lengths and sequences is investigated based on a partially coherent tunneling theory (Zhang et al., J Chem Phys 117:4578, 2002), where the effects of phase-breaking in adenine-thymine and guanine-cytosine base pairs are treated on equal foot. This work aims at providing a self-consistent microscopic interpretation for rate experiments on various DNA systems. We will also clarify the condition under which the simple superexchange-mediated-hopping picture is valid, and make some comments on the further development of present theory.

Scattering matrix approach to electronic dephasing in long-range electron transfer

Based on the Buttiker dephasing model, we propose an analytical scattering matrix approach to the long-range electron transfer phenomena. The present efficient scheme smoothly interpolates between the superexchange and the sequential hopping mechanisms. Various properties such as the drastic dephasing-assisted enhancement and turnover behaviors are demonstrated in good agreement with those obtained via the dynamical reduced density-matrix methods. These properties are further elucidated as results of the interplay among the dephasing strength, the tunneling parameter, and the bridge length of the electron transfer system. (C) 2001 American Institute of Physics.

Phase equilibria and plate-fluid interfacial tensions for associating hard sphere fluids confined in slit pores

The excess Helmholtz free energy functional for associating hard sphere fluid is formulated by using a modified fundamental measure theory [Y. X. Yu and J. Z. Wu, J. Chem. Phys. 117, 10156 (2002)]. Within the framework of density functional theory, the thermodynamic properties including phase equilibria for both molecules and monomers, equilibrium plate-fluid interfacial tensions and isotherms of excess adsorption, average molecule density, average monomer density, and plate-fluid interfacial tension for four-site associating hard sphere fluids confined in slit pores are investigated. The phase equilibria inside the hard slit pores and attractive slit pores are determined according to the requirement that temperature, chemical potential, and grand potential in coexistence phases should be equal and the plate-fluid interfacial tensions at equilibrium states are predicted consequently. The influences of association energy, fluid-solid interaction, and pore width on phase equilibria and equilibrium plate-fluid interfacial tensions are discussed.

Ultrafast vibrational and thermal relaxation of dye molecules in solutions

Intra- and intermolecular relaxations of dye molecules are studied after the excitation to the high-lying excited states by a femtosecond laser pulse, using femtosecond time-resolved stimulated emission pumping fluorescence depletion spectroscopy (FS TR SEP FD). The biexponential decays indicate a rapid intramolecular vibrational redistribution (IVR) depopulation followed by a slower process, which was contributed by the energy transfer to the solvents and the solvation of the excited solutes. The time constants of IVR in both oxazine 750 and rhodamine 700 are at the 290-360 fs range, which are insensitive to the characters of solvents. The solvation of the excited solutes and the cooling of the hot solute molecules by collisional energy transfer to the surrounding takes place in the several picoseconds that strongly depend on the properties of solvents. The difference of Lewis basicity and states density of solvents is a possible reason to explain this solvent dependence. The more basic the solvent is, which means the more interaction between the solute and the neighboring solvent shell, the more rapid the intermolecular vibrational excess energy transfer from the solute to the surroundings and the solvation of the solutes are. The higher the states density of the solvent is, the more favorable the energy transfer between the solute and solvent molecules is.

Bis[tris(2,2 '-bipyridyl-kappa N-2,N ')iron(II)] cyclo-tetravanadate decahydrate

The hydrothermal reactions of metavanadate and divalent iron salts in the presence of nitrogen-donor chelating ligands yield the complex [Fe(C10H8N2)(3)](2)[V4O12].10H(2)O, which consists of one centrosymmetric eight-membered ring [V4O12](4-) anion cluster, formed by four VO4 tetrahedra sharing vertices, two discrete octahedral [Fe(C10H8N2)(3)](2+) cations, formed by three 2,2'-bipyridyl ligands coordinated to Fe-II, and ten water molecules of solvation. The anion and coordination cations are isolated and form anion and cation layers, respectively. In the anion layers, these anions and water molecules of solvation are linked to each other, in a two-dimensional motif, through hydrogen-bonding interactions.

Electroactive gold nanoparticles protected by 4-ferrocene thiophenol monolayer

Numerous reports have focused on ferrocene-terminated electroactive self-assembled monolayers (SAMs) on a flat An surface but only a few on ferrocene SAMs on An colloid. In this paper, we employ 4-ferrocene thiophenol as a novel capping agent to produce electroactive gold nanoparticles in consideration of the peculiar pi-conjugated structure. Transmission electron microscopy shows the narrow-dispersed gold core with an average core diameter of ca. 2.5 nm. UV/vis spectra examine the pi-conjugated structure of 4-ferrocene thiophenol and surface plasmon absorbance of the indicated gold nanoparticles. X-ray photoelectron spectroscopy reveals electronic properties of the An core and thiol ligands. Electrochemical measurement shows that the oxidation peak current is proportional to the scan rate, indicating the electrode process is controlled by adsorbed layer reaction. The formal potential of the Fc-MPCs is compared with that of free ferrocene in MeCN solution and the Fc-SAMs. The shifts are attributed to the phenyl moiety in the 4-ferrocene thiophenol and dielectric constant of the solvation environment.

Separation of phenothiazines in aqueous and non-aqueous capillary electrophoresis

Four phenothiazines, promethazine, dioxypromethazine, chlorpromazine, and trifluoperazine have been separated by capillary electrophoresis using N, N, -dimethylformamide (DMF) as separation medium with UV absorbance detection. High voltage and concentrated buffer were used with small current and low electroosmosis. Good resolution and high column efficiency were obtained. Separation selectivity in DMI; was different from that in water because of the different solvation interactions. The influence of buffer composition on separation selectivities and electroosmosis were also studied.

分子水平上研究地质流体的物理化学性质

Geological fluids exist in every geosphere of the Earth and play important roles in many processes of material transformations, energetic interchanges and geochemical interactions. To study the physicochemical properties and geochemical behaviors of geological fluids turn Girt to be one of the challenging issues in geosciences. Compared with conventional approaches of experiments and semi-theoretical modeling, computer simulation on molecular level shows its advantages on quantitative predictions of the physicochemical properties of geological fluids under extreme conditions and emerges as a promising approach to find the characteristics of geological fluids and their interactions in different geospheres of the Earth interior.This dissertation systematically discusses the physicochemical properties of typical geological fluids with state-of-the-art computer simulation techniques. The main results can be summarized as follows: (1) The experimental phase behaviors of the systems CH4-C2H6 and. CO2 have been successfully reproduced with Monte Carlo simulations. (2) Through comprehensive isothermal-isobaric molecular dynamics simulations, the PVT data of water hia^e been extended beyond experimental range to about 2000 K and 20 GPa and an improved equation of state for water has been established. (3) Based on extensive computer simulations, am optimized molecular potential for carbon dioxide have been proposed, this model is expected to predict different properties of carbon dioxide (volumetric properties, phase equilibria, heat of vaporization, structural and dynamical properties) with improved accuracies. (4) On the basis of the above researches of the end-members, a set of parameters for unlike interactions has been proposed by non-linear fitting to the ab initio potential surface of CO2-H2O and is superior to the common used mixing rule and the results of prior workers vs/Ith remarkable accuracies, then a number of simulations of the mixture have been carried out to generate data under high temperatures and pressures as an important complement to the limited experiments. (5) With molecular dynamics simulations, various structural, dynamical and thermodynamical properties of ionic solvations and associations have been oomprehensively analyzed, these results not only agree well with experimental data and first principle calculation results, but also reveal some new insights into the microscopic ionic solvation and association processes.

Prediction of soil adsorption coefficients from retention parameters on three reversed-phase liquid chromatographic columns

Reversed-phase high-performance liquid chromatographic (RP-HPLC) retention parameters, which are determined by the intermolecular interactions in retention process, can be considered as the chemical molecular descriptors in linear free energy relationships (LFERs). On the basis of the characterization and comparison of octadecyl-bonded silica gel (ODS), cyano-bonded silica gel (CN), and phenyl-bonded silica gel (Ph) columns with linear solvation energy relationships (LSERs), a new multiple linear regression model using RP-HPLC retention parameters on ODS and CN columns as variables for estimation of soil adsorption coefficients was developed. It was tested on a set of reference substances from various chemical classes. The results showed that the multicolumn method was more promising than a single-column method was for the estimation of soil adsorption coefficients. The accuracy of the suggested model is identical with that of LSERs.

Retention behavior of hydrophobic organic chemicals as a function of temperature in soil leaching column chromatography

To study the transport mechanism of hydrophobic organic chemicals (HOCs) and the energy change in soil/solvent system, a soil leaching column chromatographic (SLCC) experiment at an environmental temperature range of 20-40 degreesC was carried out, which utilized a reference soil (SP 14696) packed column and a methanol-water (1:4 by volume ratio) eluent. The transport process quickens with the increase of column temperature. The ratio of retention factors at 30 and 40 degreesC (k'(30)/k'(40)) ranged from 1.08 to 1.36. The lower enthalpy change of the solute transfer in SLCC (from eluent to soil) than in conventional reversed-phase liquid chromatography (e.g., from eluent to C-18) is consistent with the hypothesis that HOCs were dominantly and physically partitioned between solvent and soil. The results were also verified by the linear solvation energy relationships analysis. The chief factor controlling the retention was found to be the solute solvophobic partition, and the second important factor was the solute hydrogen-bond basicity, while the least important factors were the solute polarizability-dipolarity and hydrogen-bond acidity. With the increase of temperature, the contributions of the solute solvophobic partition and hydrogen-bond basicity gradually decrease, and the latter decreases faster than the former. (C) 2002 Elsevier Science Ltd. All rights reserved.

THERMODYNMICS AND STRUCTURE OF POLY(ETHYLENE OXIDE) IN MIXTURES OF WATER AND ETHANOL

Poly(ethylene oxide) (PEO) is one of the most researched synthetic polymers due to the complex behavior which arises from the interplay of the hydrophilic and hydrophobic sites on the polymer chain. PEO in ethanol forms an opaque gel-like mixture with a partially crystalline structure. Addition of a small amount of water disrupts the gel: 5 wt % PEO in ethanol becomes a transparent solution with the addition of 4 vol % water. The phase behavior of PEO in mixed solvents have been studied using small-angle neutron scattering (SANS). PEO solutions (5 wt % PEO) which contain 4 vol % - 10 vol % (and higher) water behave as an athermal polymer solution and the phase behavior changes from UCST to LCST rapidly as the fraction of water is increased. 2 wt % PEO in water and 10 wt % PEO in ethanol/ water mixtures are examined to assess the role of hydration. The observed phase behavior is consistent with a hydration layer forming upon the addition of water as the system shifts from UCST to LCST behavior. At the molecular level, two or three water molecules can hydrate one PEO monomer (water molecules form a sheath around the PEO macromolecule) which is consistent with the suppression of crystallization and change in the mentioned phase behavior as observed by SANS. The clustering effect of aqueous PEO solution (M.W of PEO = 90,000 g/mol) is monitored as an excess scattering intensity at low-Q. Clustering intensity at Q = 0.004 Å^-1 is used for evaluating the clustering effect. The clustering intensity is proportional to the inverse temperature and levels off when the temperature is less than 50 ˚C. When the temperature is increased over 50 ˚C, the clustering intensity starts decreasing. The clustering of PEO is monitored in ethanol/ water mixtures. The clustering intensity increases as the fraction of water is increased. Based on the solvation intensity behavior, we confirmed that the ethanol/ water mixtures obey a random solvent mixing rule, whereby solvent mixtures are better at solvating the polymer that any of the two solvents. The solution behavior of PEO in ethanol was investigated in the presence of salt (CaCl2) using SANS. Binding of Ca2+ ions to the PEO oxygens transforms the neutral polymer to a weakly charged polyelectrolyte. We observed that the PEO/ethanol solution is better solvated at higher salt concentration due to the electrostatic repulsion of weakly charged monomers. The association of the Ca2+ ions with the PEO oxygen atoms transforms the neutral polymer to a weakly charged polyelectrolyte and gives rise to repulsive interactions between the PEO/Ca2+ complexes. Addition of salt disrupts the gel, which is consistent with better solvation as the salt concentration is increased. Moreover, SANS shows that the phase behavior of PEO/ethanol changes from UCST to LCST as the salt concentration is increased.

Vibrational spectroscopy and DFT calculations of the di-amino acid peptide L-aspartyl-L-glutamic acid in the zwitterionic state

Solid state IR and Raman as well as aqueous solution state Raman spectra are reported for the linear di-amino acid peptide L-aspartyl-L-glutamic acid (L-Asp-L-Glu); the solution state Raman spectrum has also been obtained for the N,O-deuterated derivative. SCF-DFT calculations at the B3-LYP/cc-pVDZ level established that the structure and vibrational spectra of L-Asp-L-Glu can be interpreted using a model of the peptide with ten hydrogen-bonded water molecules, in conjunction with the conductor-like polarizable continuum solvation method. The DFT calculations resulted in the computation of a stable zwitterionic structure, which displays trans-amide conformation. The vibrational spectra were computed at the optimised molecular geometry, enabling normal coordinate analysis, which yielded satisfactory agreement with the experimental IR and Raman data. Computed potential energy distributions of the normal modes provided detailed vibrational assignments.

Vibrational spectra of α-amino acids in the zwitterionic state in aqueous solution and the solid state: DFT calculations and the influence of hydrogen bonding

The zwitterionic forms of the two simplest alpha-amino acids, glycine and l-alanine, in aqueous solution and the solid state have been modeled by DFT calculations. Calculations of the structures in the solid state, using PW91 or PBE functionals, are in good agreement with the reported crystal structures, and the vibrational spectra computed at the optimized geometries provide a good fit to the observed IR and Raman spectra in the solid state. DFT calculations of the structures and vibrational spectra of the zwitterions in aqueous solution at the B3-LYP/cc-pVDZ level were found to require both explicit and implicit solvation models. Explicit solvation was modeled by inclusion of five hydrogen-bonded water molecules attached to each of the five possible hydrogen-bonding sites in the zwitterion and the integration equation formalism polarizable continuum model (IEF-PCM) was employed, providing a satisfactory fit to observed IR and Raman spectra. Band assignments are reported in terms of potential-energy distributions, which differ in some respects to those previously reported for glycine and l-alanine.

Concertedness and solvent effects in multiple proton transfer reactions: The formic acid dimer in solution

The issue of multiple proton transfer (PT) reactions in solution is addressed by performing molecular dynamics simulations for a formic acid dimer embedded in a water cluster. The reactant species is treated quantum mechanically, within a density functional approach, while the solvent is represented by a classical model. By constraining different distances within the dimer we analyze the PT process in a variety of situations representative of more complex environments. Free energy profiles are presented, and analyzed in terms of typical solvated configurations extracted from the simulations. A decrease in the PT barrier height upon solvation is rationalized in terms of a transition state which is more polarized than the stable states. The dynamics of the double PT process is studied in a low-barrier case and correlated with solvent polarization fluctuations. Cooperative effects in the motion of the two protons are observed in two different situations: when the solvent polarization does not favor the transfer of one of the two protons and when the motion of the two protons is not synchronized. This body of observations is correlated with local structural and dynamical properties of the solvent in the vicinity of the reactant. (C) 2000 American Institute of Physics. [S0021-9606(00)51121-0].

A new route to synthesize high degree polythiophene in a room temperature melt medium

Conducting polymers suffer from folds and kinks because of random nucleation and solvation of a free radical cation to yield a cross linked/disordered polymer and therefore a solvent free electrochemical polymerization in a room temperature melt medium is adopted to yield a high degree polymer with high electronic conductivity. Electropolymerization of thiophene was performed on platinum/ITO substrates using cyclic voltametry or galvenostatic mode in chloroaluminate room temperature melt medium to obtain a reddish brown free standing film which can be peeled off from the electrode surface after a minimum of 10 cycles. The conductivity was found to be around 102 S/cm. The degree of polymerization was calculated to be around 44 from IR studies. A layered structure supportive for high degree of polymerization was witnessed from potential step technique. From UV spectra the charge carriers were found to be bipolarons. The morphology of the film was found to be crystalline from SEM and XRD studies. Capacitative impedance properties for doped samples were interpreted from impedance spectroscopy.