Ring-breaking electron attachment to uracil: following bond dissociations via evolving resonances

Calculations are carried out at various distinct energies to obtain both elastic cross sections and S-matrix resonance indicators (poles) from a quantum treatment of the electron scattering from gas-phase uracil. The low-energy region confirms the presence of pi(*) resonances as revealed by earlier calculations and experiments which are compared with the present findings. They turn out to be little affected by bond deformation, while the transient negative ions (TNIs) associated with sigma(*) resonances in the higher energy region ( approximately 8 eV) indeed show that ring deformations which allow vibrational redistribution of the excess electron energy into the molecular target strongly affect these shape resonances: They therefore evolve along different dissociative pathways and stabilize different fragment anions. The calculations further show that the occurrence of conical intersections between sigma(*) and pi(*)-type potential energy surfaces (real parts) is a very likely mechanism responsible for energy transfers between different TNIs. The excess electron wavefunctions for such scattering states, once mapped over the molecular space, provide nanoscopic reasons for the selective breaking of different bonds in the ring region.     

Comparison of virtual high-throughput screening methods for the identification of phosphodiesterase-5 inhibitors

Reliable and effective virtual high-throughput screening (vHTS) methods are desperately needed to minimize the expenses involved in drug discovery projects. Here, we present an improvement to the negative image-based (NIB) screening: the shape, the electrostatics, and the solvation state of the target protein's ligand-binding site are included into the vHTS. Additionally, the initial vHTS results are postprocessed with molecular mechanics/generalized Born surface area (MMGBSA) calculations to estimate the favorability of ligand-protein interactions. The results show that docking produces very good early enrichment for phosphodiesterase-5 (PDE-5); however, in general, the NIB and the ligand-based screening performed better with or without the added electrostatics. Furthermore, the postprocessing of the NIB screening results using MMGBSA calculations improved the early enrichment for the PDE-5 considerably, thus, making hit discovery affordable.     

Interaction of VO2+ ion and some insulin-enhancing compounds with immunoglobulin G

Complexation of VO(2+) ion with the most abundant class of human immunoglobulins, immunoglobulin G (IgG), was studied using EPR spectroscopy. Differently from the data in the literature which report no interaction of IgG with vanadium, in the binary system VO(2+)/IgG at least three sites with comparable strength were revealed. These sites, named 1, 2, and 3, seem to be not specific, and the most probable candidates for metal ion coordination are histidine-N, aspartate-O or glutamate-O, and serinate-O or threoninate-O. The mean value for the association constant of (VO)(x)IgG, with x = 3-4, is log β = 10.3 ± 1.0. Examination of the ternary systems formed by VO(2+) with IgG and human serum transferrin (hTf) and human serum albumin (HSA) allows one to find that the order of complexing strength is hTf ? HSA ≈ IgG. The behavior of the ternary systems with IgG and one insulin-enhancing agent, like [VO(6-mepic)(2)], cis-[VO(pic)(2)(H(2)O)], [VO(acac)(2)], and [VO(dhp)(2)], where 6-mepic, pic, acac, and dhp indicate the deprotonated forms of 6-methylpicolinic and picolinic acids, acetylacetone, and 1,2-dimethyl-3-hydroxy-4(1H)-pyridinone, is very similar to the corresponding systems with albumin. In particular, at the physiological pH value, VO(6-mepic)(IgG)(OH), cis-VO(pic)(2)(IgG), and cis-VO(dhp)(2)(IgG) are formed. In such species, IgG coordinates nonspecifically VO(2+) through an imidazole-N belonging to a histidine residue exposed on the protein surface. For cis-VO(dhp)(2)(IgG), log β is 25.6 ± 0.6, comparable with that of the analogous species cis-VO(dhp)(2)(HSA) and cis-VO(dhp)(2)(hTf). Finally, with these new values of log β, the predicted percent distribution of an insulin-enhancing VO(2+) agent between the high molecular mass (hTf, HSA, and IgG) and low molecular mass (lactate) components of the blood serum at physiological conditions is calculated.     

Copper(II) complexes of rat amylin fragments

The fragments of rat amylin rIAPP(17-29) (Ac-VRSSNNLGPVLPP-NH(2)), rIAPP(17-22) (Ac-VRSSNN-NH(2)), rIAPP(19-22) (Ac-SSNN-NH(2)) and rIAPP(17-20) (Ac-VRSS-NH(2)) together with the related mutant peptides (Ac-VASS-NH(2) and Ac-VRAA-NH(2)) have been synthesized and their copper(II) complexes studied by potentiometric, UV-Vis, CD and EPR spectroscopic methods. Despite the lack of any common strongly coordinating donor functions some of these fragments are able to bind copper(II) ions in the physiological pH range. The longest fragment rat amylin(17-29) keeps one equivalent copper(II) ion in solution in the whole pH range, while two other peptides Ac-VRSSNN-NH(2) and Ac-SSNN-NH(2) are also able to interact with copper(II) ions in the slightly alkaline pH range. According to the spectral parameters of the complexes, the peptides can be classified into two different categories: (i) the tetrapeptides Ac-VRSS-NH(2), Ac-VASS-NH(2) and Ac-VRAA-NH(2) can interact with copper(II) only under strongly alkaline conditions (pH > 10.0) and the formation of only one species with four amide nitrogen coordination can be detected; (ii) the peptides Ac-VRSSNNLGPVLPP-NH(2), Ac-VRSSNN-NH(2) and Ac-SSNN-NH(2) can form complexes above pH 6.0 with the major stoichiometries [CuH(-2)L], [CuH(-3)L](-) and [CuH(-4)L](2-). These data support that rIAPP(17-29) can interact with copper(II) ions under physiological conditions and the SSNN tetrapeptide fragment can be considered as the shortest sequence responsible for metal binding. Density functional theory (DFT) calculations provide some information on the possible coordination modes of Ac-SSNN-NH(2) towards the copper(II) ion and suggest that for [CuH(-2)L], [CuH(-3)L](-) and [CuH(-4)L](2-), the binding of two, three and four deprotonated amide nitrogens, with NH(-) of the side chain of asparagine as anchoring group, is probable. Moreover, these data reveal that peptides can be effective metal binding ligands even in the absence of anchoring groups, if more polar side chains are present in a specific sequence.     

Disposable roll-to-roll hot embossed electrophoresis chip for detection of antibiotic resistance gene mecA in bacteria

We present a high-throughput roll-to-roll (R2R) manufacturing process for foil-based polymethyl methacrylate (PMMA) chips of excellent optical quality. These disposable, R2R hot embossed microfluidic chips are used for the identification of the antibiotic resistance gene mecA in Staphylococcus epidermidis. R2R hot embossing is an emerging manufacturing technology for polymer microfluidic devices. It is based on continuous feeding of a thermoplastic foil through a pressurized area between a heated embossing cylinder and a blank counter cylinder. Although mass fabrication of foil-based microfluidic chips and their use for biological applications were foreseen already some years ago, no such studies have been published previously.     

Janus-like squaramide-based hosts: dual mode of binding and conformational transitions driven by ion-pair recognition

New tripodal squaramide-based hosts have been synthesised and structurally characterised by spectroscopic methods. In 2.5?% (v/v) [D(6)]DMSO in CDCl(3), compound 4 formed dimeric assemblies [log?K(dim)=3.68(8)] as demonstrated by (1)H?NMR spectroscopy and UV dilution experiments. AFM and SEM analyses revealed the formation of a network of bundled fibres, which indicates a preferential mechanism for aggregation. These C(3)-symmetric tripodal hosts exhibited two different and mutually exclusive modes of binding, each one easily accessible by simultaneous reorientation of the squaramide groups. In the first, a convergent disposition of the NH squaramide protons allowed the formation of an array of N-H???X(-) hydrogen bonds with anions. In the second mode, reorientation of carbonyl squaramide groups allowed multiple C=O???H interactions with ammonium cations. The titration of 4 with different tetraalkylammonium iodides persistently showed the formation of 1:1 complexes, as well as 1:2 and 1:3 complexes. The corresponding stoichiometries and binding affinities of the complexes were evaluated by multi-regression analysis. The formation of high-order complexes, supported by ROESY, NOESY and mass spectrometry experiments, has been attributed to the insertion of NR(4)I ion pairs between the carbonyl and NH protons of the squaramide groups located in adjacent arms of 4. The observed effects reflect the induction of significant conformational changes in the hosts, mainly in relation to the relative orientation of the squaramide groups adapting their geometries to incoming ion-pair complementary substrates. The results presented herein identify and fully describe two different modes of ion-pair recognition aimed at directing conformational transitions in the host, therefore establishing a base for controlling more elaborate movements of molecular devices through ion-pair recognition.     

Hybridization of binary monolayers of single stranded oligonucleotides and short blocking molecules

We have studied the immobilization of single stranded (ss) DNA oligonucleotides of 16-27 base pairs on gold. The oligonucleotides were thiol-modified (SH-ssDNA) or disulfide-modified via a dimethoxytrityl-group (DMT-S-S-ssDNA). Immobilization was performed by adsorption of the probes on the gold surface for 10-15 min, a time within which saturation coverage was obtained for both thiol- and disulfide-modified probes. Hereafter the layer was post-treated with hydroxyalkyl substituted lipoamides also for a time of 10-15 min. The surface density of layers with shorter probes (16-18 mer) was twice (2.4 ± 0.2 × 10¹³ probes/cm²) that of the longer probes (25-27 mer) as studied with surface plasmon resonance. Hybridization of single stranded polymerase chain reaction (PCR) amplified products with a length above 300 base pairs gave a very low hybridization response. For amplicons with about 100 base pairs the response was high. The surface coverage was comparable to that of complementary ssDNA binding (3.0 × 10¹² strands/cm²). Surfaces made from SH-ssDNA showed a 30% higher hybridization response than surfaces made from DMT-S-S-ssDNA. The PCR amplified products used are of relevance in breast cancer diagnosis. The results clearly demonstrate that the single stranded PCR products might be used in label-free cancer diagnostics.     

Ab initio description of high-temperature superconductivity in dense molecular hydrogen

We present a first-principles study of the electron-phonon interaction and the prediction of the superconducting critical temperature in molecular metallic hydrogen. Our study is able to single out the features which drive the system towards superconductivity: mainly, a rich and complex Fermi surface and strongly coupled phonon modes driving the intra- or intermolecular charge transfer. We demonstrate that in this simple system, a very high superconducting critical temperature can be reached via electron-phonon and Coulomb electron-electron interactions.     

Spectral shaping of femtosecond pulses in aperiodic quasi-phase-matched gratings

We analyze the use of cascading second harmonic interactions in quadratic nonlinear crystals to mould the spectral characteristics of broadband near-infrared femtosecond pulses. Using a genetic algorithm, we optimize the design of the aperiodically poled ferroelectric crystal capable of generating the desired femtosecond infrared pulsed radiation.     

Bootstrap approximation for the exchange-correlation kernel of time-dependent density-functional theory

A new parameter-free approximation for the exchange-correlation kernel f(xc) of time-dependent density-functional theory is proposed. This kernel is expressed as an algorithm in which the exact Dyson equation for the response, as well as an approximate expression for f(xc) in terms of the dielectric function, are solved together self-consistently, leading to a simple parameter-free kernel. We apply this to the calculation of optical spectra for various small band gap (Ge, Si, GaAs, AlN, TiO(2), SiC), large band gap (C, LiF, Ar, Ne), and magnetic (NiO) insulators. The calculated spectra are in very good agreement with the experiment for this diverse set of materials, highlighting the universal applicability of the new kernel.