A non-empirical molecular orbital study on the relative stabilities of adenine and guanine tautomers

The relative stabilities of a series of adenine and guanine tautomers have been calculated using anab initio Hartree-Fock-Roothaan SCF MO method. The calculated relative stabilities agree in general with the results of earlier semiempirical studies. According to the present study, tautomeric forms with regular Kekulé structure for the six-membered purine ring are the most stable. The amine-imine tautomerization of purine bases is not likely to be responsible for spontaneous mutations in DNA.     

Infrared Monitoring of Interlayer Water in Stacks of Purple Membranes†

The thermodynamic behavior of films of hydrated purple membranes from Halobacterium salinarum and the water confined in it was studied by Fourier transform infrared spectroscopy in the 180–280 K range. Unlike bulk water, water in the thin layers sandwiched between the biological membranes does not freeze at 273 K but will be supercooled to ～256 K. The melting point is unaffected, leading to hysteresis between 250 and 273 K. In its heating branch, a gradually increasing light‐scattering by ice is observed with rate‐limiting kinetics of tens of minutes. Infrared (IR) spectra decomposition provided extinction coefficients for the confined water vibrational bands and their changes upon freezing. Because of the hysteresis, at any given temperature in the 255–270 K range, the interbilayer water could be either liquid or frozen, depending on thermal history. We find that this difference affects the dynamics of the bacteriorhodopsin photocycle in the hysteresis range: the decay of the M and N states and the redistribution between them are different depending on whether or not the water was initially precooled to below the freezing point. However, freezing of interbilayer water does block the M to N transition. Unlike the water, the purple membrane lipids do not undergo any IR‐detectable phase transition in the 180–280 K range.     

pH-dependent transitions in xanthorhodopsin

Xanthorhodopsin (XR), the light-driven proton pump of the halophilic eubacterium Salinibacter ruber, exhibits substantial homology to bacteriorhodopsin (BR) of archaea and proteorhodopsin (PR) of marine bacteria, but unlike them contains a light-harvesting carotenoid antenna, salinixanthin, as well as retinal. We report here the pH-dependent properties of XR. The pKa of the retinal Schiff base is as high as in BR, i.e. > or =12.4. Deprotonation of the Schiff base and the ensuing alkaline denaturation cause large changes in the absorption bands of the carotenoid antenna, which lose intensity and become broader, making the spectrum similar to that of salinixanthin not bound to XR. A small redshift of the retinal chromophore band and increase of its extinction, as well as the pH-dependent amplitude of the M intermediate indicate that in detergent-solubilized XR the pKa of the Schiff base counterion and proton acceptor is about 6 (compared to 2.6 in BR, and 7.5 in PR). The protonation of the counterion is accompanied by a small blueshift of the carotenoid absorption bands. The pigment is stable in the dark upon acidification to pH 2. At pH < 2 a transition to a blueshifted species absorbing around 440 nm occurs, accompanied by loss of resolution of the carotenoid absorption bands. At pH < 3 illumination of XR with continuous light causes accumulation of long-lived photoproduct(s) with an absorption maximum around 400 nm. The photocycle of XR was examined between pH 4 and 10 in solubilized samples. The pH dependence of recovery of the initial state slows at both acid and alkaline pH, with pKas of 6.0 and 9.3. The decrease in the rates with pKa 6.0 is apparently caused by protonation of the counterion and proton acceptor, and that at high pH reflects the pKa of the internal proton donor, Glu94, at the times in the photocycle when this group equilibrates with the bulk.     

Multiple dual-mode centrifugal partition chromatography, a semi-continuous development mode for routine laboratory-scale purifications

Nowadays, centrifugal partition chromatography (CPC) separations can be routinely achieved at the laboratory scale. The solvent system selection has been made easy, as generic sets of solvent systems are described in publications and books. This approach, however, generally reduces the scope of optimization strategies for two important parameters: selectivity and sample solubility. This can be very limiting for the preparative separation of structurally similar compounds. Multiple dual-mode (MDM) CPC has been developed to provide an easy-to-use alternative technique to circumvent this problem. A MDM separation consists of a succession of dual-mode runs (i.e. multiple inversion of stationary and mobile phase) that can only be achieved because both chromatographic phases are liquids. This original elution mode is thus a semi-continuous process with a classical sample injection and which only requires a single CPC column. Underlying mechanisms of MDM were studied using a model mixture of acenaphthylene and naphthalene. A mixture of two synthetic pairs of diastereomers was then successfully submitted to MDM CPC, in the framework of the synthesis of biologically active compounds.     

Mesh independent superlinear convergence estimates of the conjugate gradient method for some equivalent self-adjoint operators

A mesh independent bound is given for the superlinear convergence of the CGM for preconditioned self-adjoint linear elliptic problems using suitable equivalent operators. The results rely on K-condition numbers and related estimates for compact Hilbert-Schmidt operators in Hilbert space.This research was supported by the Hungarian National Research Fund OTKA under grant No. T043765.     

A new, powerful glycosylation method: activation of thioglycosides with dimethyl disulfide-triflic anhydride

Dimethyl disulfide reacts with triflic anhydride to provide a highly reactive electrophile. Various thioglycosides, differing in their thio aglycons, carbohydrate units, and protecting group pattern, were activated with Me2S2-Tf2O in the presence of different glycosyl acceptors. The reactions proceeded at low temperatures within a short time, affording oligosaccharides in high yields both on primary and secondary hydroxyls. Armed and disarmed glycosyl donors were activated equally efficiently.     

Lectures on the functional renormalization group method

These introductory notes are about functional renormalization group equations and some of their applications. It is emphasised that the applicability of this method extends well beyond critical systems, it actually provides us a general purpose algorithm to solve strongly coupled quantum field theories. The renormalization group equation of F. Wegner and A. Houghton is shown to resum the loop-expansion. Another version, due to J. Polchinski, is obtained by the method of collective coordinates and can be used for the resummation of the perturbation series. The genuinely non-perturbative evolution equation is obtained by a manner reminiscent of the Schwinger-Dyson equations. Two variants of this scheme are presented where the scale which determines the order of the successive elimination of the modes is extracted from external and internal spaces. The renormalization of composite operators is discussed briefly as an alternative way to arrive at the renormalization group equation. The scaling laws and fixed points are considered from local and global points of view. Instability induced renormalization and new scaling laws are shown to occur in the symmetry broken phase of the scaler theory. The flattening of the effective potential of a compact variable is demonstrated in case of the sine-Gordon model. Finally, a manifestly gauge invariant evolution equation is given for QED.