Solvent effects on electron-driven proton-transfer processes: adenine-thymine base pairs

Time-Dependent Density Functional Theory (TD-DFT) computations, with M05-2X and PBE0 functionals, have been employed for a detailed study of the Electron-Driven Proton-Transfer (PT) processes in an Adenine-Thymine Watson-Crick Base Pair in the gas phase and in solution, with the bulk solvent described by the polarizable continuum model. In the gas phase, TD-DFT computations predict that the Adenine → Thymine Charge Transfer (CT) excited state undergoes a barrierless PT reaction, in agreement with CC2 computations (S. Perun, A. Sobolewski, W. Domcke, J. Phys. Chem. A, 2006, 110, 9031.). The good agreement between the TD-DFT approach and CC2 results validates the former for the studies of excited state properties, excited state proton transfer reaction, and deactivation mechanisms in the DNA base pairs. Next, it is shown that inclusion of solvent effects significantly influences the possibility of both barrier-less excited state proton transfer and radiation-less deactivation through conical intersection with the ground state, affecting the energy of the CT excited state in the Franck-Condon region, the energy barrier associated to the PT process and the energy gap with the ground electronic state. These findings clearly indicate that environmental effects, with a special attention to proper treatment of dynamical solvation effects, have to be included for reliable computational analysis of photophysical and photochemical processes occurring in condensed phases.     

Vibrational dephasing and hydrodynamic effects on vibrational relaxation rates in acetophenone: Raman bandshape analysis

The isotropic component of Raman band for C=O stretching mode of acetophenone in solution was analyzed by estimating the correlation coefficient with reference to Lorentzian lineshape. In the intermediate region of solute/solvent concentration there is a sharp decrease in the correlation coefficient and there appears to be a transition from non-Lorentzian to Lorentzian lineshape. The vibrational relaxation rates have been estimated from the isotropic component of Raman band in different solvents. The rate is shown to be dependent on several macroscopic as well as microscopic properties of the solute-solvent system and intermolecular interactions. The hydrodynamic and dispersion forces appear to play a major role in determining the vibrational relaxation rate and the broadening of the bands.     

Butyrate production from carbon monoxide byButyribacterium methylotrophicum

Applied Biochemistry and Biotechnology - Carbon monoxide is produced in high concentrations by gasification of coal or biomass, and is a potentially inexpensive feedstock for biological processes....     

Thermal analytical and infrared spectroscopic investigations on polymorphic organic compounds—IV

Twenty-four polymorphic compounds which show between two and four modifications are cited. The compounds described in detail are tetrabutylammonium iodide, tetraheptylammonium bromide, tetraoctylammonium bromide, 3-(3,4,5-trimethoxyphenyl)-2-propenoic acid andl-tyrosine ethyl ester hydrochloride. For the remaining nineteen compounds, only the number of modifications found, and their melting points where possible, are given.     

Phase transition studies in symmetric dimeric liquid crystals

As a part of the systematic studies on symmetric liquid crystal dimer homologous series, α,ω-bis-(4-n-alkylaniline benzylidene-4′-oxy) alkanes, (referred to as m.OnO.m with m = 3, 4, and 5; and n = 8, 9, and 10), we present in this article the nature of phase transitions across isotropic–nematic and nematic–smectic-A (N–SmA) phases exhibited by the just mentioned compounds. The methods employed are differential scanning calorimetry and dilatometry. The compounds studied were 3.O8O.3, 4.O8O.4, and 5.O8O.5; and 3.O9.03, 5.O9O.5, 3.O10O.3, 4.O10O.4, and 5.O10O.5. Different from the case of their corresponding monomers, all these compounds exhibit a nematic phase only with the exception of 5.O8O.5 which exhibits a SA phase in addition to the nematic phase. The phase transitions viz., isotropic–nematic transitions studied in all these compounds were confirmed to be of first-order nature, whereas the N–SmA transition exhibited by the compound 5.O8O.5 only was found to be of second-order nature. We also report in this article the calculated density jumps, thermal expansion coefficient maxima, and pressure dependence of transition temperatures which are analyzed in the light of the available literature data.     

Controlled buckling and crumpling of nanoparticle-coated droplets

We introduce a new experimental approach to study the structural transitions of large numbers of nanoparticle-coated droplets as their volume is reduced. We use an emulsion system where the dispersed phase is slightly soluble in the continuous phase. By adding a fixed amount of unsaturated continuous phase, the volume of the droplets can be controllably reduced, causing them to buckle or crumple, thereby becoming nonspherical. The resultant morphologies depend both on the extent of volume reduction and the average droplet size. The buckling and crumpling behavior implies that the droplet surfaces are solid.     

Pulsed field gradient NMR study of phenol binding and exchange in dispersions of hollow polyelectrolyte capsules

The distribution and exchange dynamics of phenol molecules in colloidal dispersions of submicron hollow polymeric capsules is investigated by pulsed field gradient NMR (PFG-NMR). The capsules are prepared by layer-by-layer assembly of polyelectrolyte multilayers on silica particles, followed by dissolution of the silica core. In capsule dispersion, (1)H PFG echo decays of phenol are single exponentials, implying fast exchange of phenol between a free site and a capsule-bound site. However, apparent diffusion coefficients extracted from the echo decays depend on the diffusion time, which is typically not the case for the fast exchange limit. We attribute this to a particular regime, where apparent diffusion coefficients are observed, which arise from the signal of free phenol only but are influenced by exchange with molecules bound to the capsule, which exhibit a very fast spin relaxation. Indeed, relaxation rates of phenol are strongly enhanced in the presence of capsules, indicating binding to the capsule wall rather than encapsulation in the interior. We present a quantitative analysis in terms of a combined diffusion-relaxation model, where exchange times can be determined from diffusion and spin relaxation experiments even in this particular regime, where the bound site acts as a relaxation sink. The result of the analysis yields exchange times between free phenol and phenol bound to the capsule wall, which are on the order of 30 ms and thus slower than the diffusion controlled limit. From bound and free fractions an adsorption isotherm of phenol to the capsule wall is extracted. The binding mechanism and the exchange mechanism are discussed. The introduction of the global analysis of diffusion as well as relaxation echo decays presented here is of large relevance for adsorption dynamics in colloidal systems or other systems, where the standard diffusion echo decay analysis is complicated by rapidly relaxing boundary conditions.     

The influence of mobile phase demixion on thin-layer chromatographic enantioseparation of ibuprofen and naproxen

In our earlier article we presented the results of tracing the enantioseparation of the two test analytes (ibuprofen and naproxen) by means of video densitometry and scanning densitometry. In that way we demonstrated an excellent performance of this combined approach to the thin-layer chromatographic detection in the area of enantioseparation. In this paper we study an impact of the four different mobile phases on the enantioseparation of the scalemic mixtures of ibuprofen and naproxen on the silica gel layers impregnated with L-arginine as chiral selector. The main component of all the investigated mobile phases is 2-propanol. Mobile phase 1 consists of pure 2-propanol, while mobile phases 2-4 contain, respectively, ca. 0.66, 1.32, and 1.98 g/L of glacial acetic acid in 2-propanol. Acetic acid is used to protonate L-arginine, as the involved retention mechanism consists of the ion pair formation between L-arginine in the cationic form and the chiral 2-arylpropionic acids (2-APAs), ibuprofen and naproxen, in the anionic form. It is shown that in the absence of glacial acetic acid no enantioseparation can be obtained. Then with adding of 0.66 g/L glacial acetic acid partial enantioseparation of the naproxen and ibuprofen antimers is obtained, with a simultaneous effect of the mobile phase demixion. With the amount of acetic acid increasing, the effect of demixion becomes increasingly perceptible. In that case the displacement effect is observed (and mathematically modeled), which results in compressing of the antimer pairs by the second front of mobile phase. The obtained results allow a deeper insight into the mechanism of enantioseparation with the two test 2-APAs. A combined impact of the crystalline chirality of silica gel and the molecular chirality of L-arginine on the vertical and the horizontal enantioseparation of ibuprofen and naproxen is also discussed.     

Metallo-organic domino reactions: C-H versus C-C bond breaking

HL and MeL are prepared by condensing benzil dihydrazone with 2-formylpyridine and 2-acetylpyridine, respectively, in 1:2 molar proportions. While in a reaction with [Ru(C(6)H(6))Cl(2)]2, HL yields the cation [Ru(C(6)H(6)){5,6-diphenyl-3-(pyridin-2-yl)-1,2,4-triazine}Cl]+, MeL gives the cation [Ru(C(6)H(6))(MeL)Cl]+. Both the cations are isolated as their hexafluorophosphate salts and characterised by X-ray crystallography. In the case of HL, double domino electrocyclic/elimination reactions are found to occur. The electrocyclic reaction occurs in a C=N-N=C-C=N fragment of HL and the elimination reaction involves breaking of a C-H bond of HL. Density functional calculations on model complexes indicate that the identified electrocyclic reaction is thermochemically as well as kinetically feasible for both HL and MeL in the gas phase. For a double domino reaction, similar to that operative in HL, to occur for MeL, breaking of a C-C bond would be required in the elimination step. Our model calculations show the energy barrier for this elimination step to be much higher (329.1 kJ mol(-1)) for MeL than that for HL (96.3 kJ mol(-1)). Thus, the domino reaction takes place for HL and not for MeL. This accounts for the observed stability of [Ru(C(6)H(6))(MeL)Cl]+ under the reaction conditions employed.     

Two-dimensional electrophoresis of membrane proteins

One third of all genes of various organisms encode membrane proteins, emphasizing their crucial cellular role. However, due to their high hydrophobicity, membrane proteins demonstrate low solubility and a high tendency for aggregation. Indeed, conventional two-dimensional gel electrophoresis (2-DE), a powerful electrophoretic method for the separation of complex protein samples that applies isoelectric focusing (IEF) in the first dimension and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) in the second dimension, has a strong bias against membrane proteins. This review describes two-dimensional electrophoretic techniques that can be used to separate membrane proteins. Alternative methods for performing conventional 2-DE are highlighted; these involve replacing the IEF with electrophoresis using cationic detergents, namely 16-benzyldimethyl-n-hexadecylammonium chloride (16-BAC) and cetyl trimethyl ammonium bromide (CTAB), or the anionic detergent SDS. Finally, the separation of native membrane protein complexes through the application of blue and clear native gel electrophoresis (BN/CN-PAGE) is reviewed, as well as the free-flow electrophoresis (FFE) of membranes.