Calculations of the free energy of interaction of the c-Fos−c-Jun coiled coil: Effects of the solvation model and the inclusion of polarization effects

The leucine zipper region of activator protein-1 (AP-1) comprises the c-Jun and c-Fos proteins and constitutes a well-known coiled coil protein−protein interaction motif. We have used molecular dynamics (MD) simulations in conjunction with the molecular mechanics/Poisson−Boltzmann generalized-Born surface area [MM/PB(GB)SA] methods to predict the free energy of interaction of these proteins. In particular, the influence of the choice of solvation model, protein force field, and water potential on the stability and dynamic properties of the c-Fos−c-Jun complex were investigated. Use of the AMBER polarizable force field ff02 in combination with the polarizable POL3 water potential was found to result in increased stability of the c-Fos−c-Jun complex. MM/PB(GB)SA calculations revealed that MD simulations using the POL3 water potential give the lowest predicted free energies of interaction compared to other nonpolarizable water potentials. In addition, the calculated absolute free energy of binding was predicted to be closest to the experimental value using the MM/GBSA method with independent MD simulation trajectories using the POL3 water potential and the polarizable ff02 force field, while all other binding affinities were overestimated.

Photodimerization of coumarins in solid cyclodextrin inclusion complexes

The photodimerizations of coumarin and eight of its derivatives are found to proceed selectively in solid inclusion complexes with beta- and gamma-cyclodextrins (beta- and gamma-CD). The distribution of photodimers from these complexes is compared with those from the neat coumarin solids and their solutions in a variety of solvents. By assuming that the stereochemistry of the dimers reflects the packing arrangements of their precursors in the CD complexes, several hypotheses concering the locations and arrangements of the coumarins in the host toruses have been made. The stoichiometries of the complexes have been assigned on the basis of the presence or absence of photodimers and from NMR integration ratios of characteristic coumarin and saccharide protons. The relative orientations of substituted coumarins within a complex are inferred from the stereochemistry of the photodimers. Depending upon the substitution pattern of the coumarin molecules and the type of CD employed, complexes whose guest-host stoichiometries are 1:1, 2:1, and 2:2 have been identified. In several instances, dimers not available from irradiation of neat solid coumarins or their solutions have been obtained from the CD complexes.

Electrical resistivity studies of benzidine-TCNQ and its inclusion compound under high pressure

Electrical resistivity studies of the charge transfer complex benzidine—TCNQ and its inclusion compound, have been carried out up to pressures 8 GPa. Two types of behaviour were observed in these complexes under high pressure and this difference is interpreted and discussed.

Accommodating Unwelcome Guests in Inorganic Layered Hosts: Inclusion of Chloranil in a Layered Double Hydroxide

The host-guest chemistry of most inorganic layered solids is limited to ion-exchange reactions. The guest species are either cations or anions to compensate for the charge deficit, either positive or negative, of the inorganic layers. Here, we outline a strategy to include neutral molecules like ortho- and para-chloranil, that are known to be good acceptors in donor-acceptor or charge-transfer complexes, within the galleries of a layered solid. We have succeeded in including neutral ortho- and para-chloranil molecules within the galleries of an Mg-Al layered double hydroxide (LDH) by using charge-transfer interactions with preintercalated p-aminobenzoate ions as the driving force. The p-aminobenzoate ions are introduced in the Mg-Al LDH via ion exchange. The intercalated LDH can adsorb ortho- and para-chloranil from chloroform solutions by forming charge-transfer complexes with the p-aminobenzoate anions present in the galleries. We use X-ray diffraction, spectroscopy, and molecular dynamics simulations to establish the nature of interactions and arrangement of the charge-transfer complex within the galleries of the layered double hydroxide.

Charge-transfer-driven inclusion of neutral TCNQ molecules in the galleries of a layered double hydroxide: an experimental and computational study

The layered double hydroxides (LDH) or anionic clays are an important class of ion-exchange materials. They consist of positively charged brucite-like inorganic sheets with charge-compensating exchangeable anions in the interlamellar space. Here we show how neutral TCNQ (7,7,8,8-tetracyanoquinodimethane) molecules can be included within the galleries of an LDH. To do so, we exploit the fact that TCNQ is a good electron acceptor that forms donor acceptor complexes with a variety of donors. The electron donor aniline was intercalated into a Mg-Al LDH as p-aminobenzoate (AB) ions by a conventional ion-exchange reaction. We show here that neutral TCNQ molecules may be driven into the galleries of the layered solid by charge-transfer complex formation with the intercalated p-aminobenzoate anions. We use diffraction and spectroscopic measurements in combination with molecular dynamics simulations and quantum chemical calculations to establish the nature of interactions and arrangement of the charge-transfer complex within the galleries of the layered double hydroxide. Electrostatic interactions between the TCNQ molecules and the anchored AB ions, subsequent to charge transfer, are the driving force for the inclusion of TCNQ molecules in the galleries of the LDH.

Stress-distribution at the rigid circular-arc inclusion end

The elastic plane problem of a rigid co-circular arc inclusion under arbitrary loads is dealt with. Applying Schwarz's reflection principle integrated with the analysis of the singularity of complex stress functions, the general solution of the problem is found and several closed-form solutions to some problems of practical importance are given. Finally, the stress distribution at the arc inclusion end is examined and a comparison is made with that of the rigid line inclusion end to show the effect of curvature.

Double proton transfer and one-electron oxidation behaviors in double H-bonded glycinamide-formamidine complex and comparison with biological base pair

The behaviors of double proton transfer (DPT) occurring in a representative glycinamide-formamidine complex have been investigated employing the B3LYP/6-311++G** level of theory. Computational results suggest that the participation of a formamidine molecule favors the proceeding of the proton transfer (PT) for glycinamide compared with that without mediator-assisted case. The DPT process proceeds with a concerted mechanism rather than a stepwise one since no zwitterionic complexes have been located during the DPT process. The barrier heights are 14.4 and 3.9 kcal/mol for the forward and reverse directions, respectively. However, both of them have been reduced by 3.1 and 2.9 kcal/mol to 11.3 and 1.0 kcal/mol with further inclusion of zero-point vibrational energy (ZPVE) corrections, where the lower reverse barrier height implies that the reverse reaction should proceed easily at any temperature of biological importance. Additionally, the one-electron oxidation process for the double H-bonded glycinamide-formamidine complex has also been investigated. The oxidated product is characterized by a distonic radical cation due to the fact that one-electron oxidation takes place on glycinamide fragment and a proton has been transferred from glycinamide to formamidine fragment spontaneously. As a result, the vertical and adiabatic ionization potentials for the neutral double H-bonded complex have been determined to be about 8.46 and 7.73 eV, respectively, where both of them have been reduced by about 0.79 and 0.87 eV relative to those of isolated glycinamide due to the formation of the intermolecular H-bond with formamidine. Finally, the differences between model system and adenine-thymine base pair have been discussed briefly.

Electrocatalytic reduction of 1,2-diiodoethane by anions of supramolecular complex of (beta-CD)(2)/C-60 in DMF solution

The homogeneous electrocatalytic reduction of 1,2-diiodoethane by anions of the supramolecular complex of (beta-CD)(2)/C-60 in DMF solution is reported. The results show that the trianion of (beta-CD)(2)/C-60 exhibits electrocatalytic behavior towards the reduction of 1,2-diiodoethane, whereas the diani on is unable to reduce the diiodoethane. The second-order catalytic rate constant in DMF solution was determined to be 3.1 x 10(5) M-1 s(-1) by analysis of voltammetric responses under pseudo-first-order conditions with respect to (beta-CD)(2)/C-60. The results suggest that the host beta-cyclodextrin molecules have little effect on the electrocatalytic ability of the encapsulated C-60 toward organic halides.

Studies on beta-cyclodextrin amino acids inclusion complexes by electrospray ionization mass spectrometry

The positive- and negative-ion electrospray ionization mass spectra of beta-cyclodextrin-amino acids complexes in NH4Ac buffer have been reported in this paper. Compared with positive-ion ESI mass spectra of beta-cyclodextrin-amino acids complexes under the same condition, negative-ion mass spectra obtained for inclusion complexes of beta-cyclodextrin (CD) with tyrosine, phenylalanine and tryptophan, respectively, were completely dominated by deprotonated complex ions and [CD-H](-) ion which is the only daughter ion in collision-induced dissociation (CID) experiment of deprotonated complexes, The results indicated that the charged position for protonated and deprotonated complexes is different from each other. In addition, two complex ions for the same complex have similarly relative dissociation energies, which are higher than that of [CD+NH4](+), indicating that complexes observed in gasphase are not electrostatic adducts at all but complexes formed by hydrogen bonds.

STUDY ON THE KINETIC PROCESS OF THE COMPLEX-REACTION BETWEEN BILIRUBIN AND CYCLODEXTRINS

The complex behavior of bilirubin (BR) with beta-CD (cyclodextrin) and gamma-CD in aqueous and dimethylformamide (DMF) solution was investigated by absorption spectroscopy and cyclic voltammetry, respectively. The data shows that the complexation mechanis

Cryptic species diversity in a widespread bumble bee complex revealed using mitochondrial DNA RFLPs

Cryptic species diversity is thought to be common within the class Insecta, posing problems for basic ecological and population genetic studies and conservation management. Within the temperate bumble bee (Bombus spp.) fauna, members of the subgenus Bombus sensu stricto are amongst the most abundant and widespread. However, their species diversity is controversial due to the extreme difficulty or inability morphologically to identify the majority of individuals to species. Our character-based phylogenetic analyses of partial CO1 (700 bp) from 39 individuals spread across their sympatric European ranges provided unequivocal support for five taxa (3-22 diagnostic DNA base pair sites per species). Inclusion of 20 Irish specimens to the dataset revealed >= 2.3% sequence divergence between taxa and 200 m) whilst B. cryptarum was relatively more abundant at higher altitudes. Bombus magnus was rarely encountered at urban sites. Both B. lucorum and B. terrestris are nowadays reared commercially for pollination and transported globally. Our RFLP approach to identify native fauna can underpin ecological studies of these important cryptic species as well as the impact of commercial bumble bees on them.

Regulating Digital Financial Services Agents in Developing Countries to Promote Financial Inclusion

Limited access to bank branches excludes over one billion people from accessing financial services in developing countries. Digital financial services offered by banks and mobile money providers through agents can solve this problem without the need for complex and costly physical banking infrastructures. Delivering digital financial services through agents requires a legal framework to regulate liability. This article analyses whether vicarious liability of the principal is a more efficient regulatory approach than personal liability of the agent. Agent liability in Kenya, Fiji, and Malawi is analysed to demonstrate that vicarious liability of the principal, coupled to an explicit agreement as to agent rewards and penalties, is the more efficient regulatory approach.

Electrospinning and characterization of self-assembled inclusion complexies

L’électrofilage est une technique permettant de fabriquer des fibres polymériques dont le diamètre varie entre quelques nanomètres et quelques microns. Ces fibres ont donc un rapport surface/volume très élevé. Les fibres électrofilées pourraient trouver des applications dans le relargage de médicaments et le génie tissulaire, comme membranes et capteurs chimiques, ou dans les nanocomposites et dispositifs électroniques. L’électrofilage était initialement utilisé pour préparer des toiles de fibres désordonnées, mais il est maintenant possible d’aligner les fibres par l’usage de collecteurs spéciaux. Cependant, il est important de contrôler non seulement l’alignement macroscopique des fibres mais aussi leur orientation au niveau moléculaire puisque l’orientation influence les propriétés mécaniques, optiques et électriques des polymères. Les complexes moléculaires apparaissent comme une cible de choix pour produire des nanofibres fortement orientées. Dans les complexes d’inclusion d’urée, les chaînes polymères sont empilées dans des canaux unidimensionnels construits à partir d’un réseau tridimensionnel de molécules d’urée liées par des ponts hydrogène. Ainsi, les chaînes polymère sonts très allongées à l’échelle moléculaire. Des nanofibres du complexe PEO-urée ont été préparées pour la première fois par électrofilage de suspensions et de solutions. Tel qu’attendu, une orientation moléculaire inhabituellement élevée a été observée dans ces fibres. De tels complexes orientés pourraient être utilisés à la fois dans des études fondamentales et dans la préparation de matériaux hiérarchiquement structurés. La méthode d’électrofilage peut parfois aussi être utilisée pour préparer des matériaux polymériques métastables qui ne peuvent pas être préparés par des méthodes conventionnelles. Ici, l’électrofilage a été utilisé pour préparer des fibres des complexes stables (α) et "métastables" (β) entre le PEO et l’urée. La caractérisation du complexe β, qui était mal connu, révèle un rapport PEO:urée de 12:8 appartenant au système orthorhombique avec a = 1.907 nm, b = 0.862 nm et c = 0.773 nm. Les chaînes de PEO sont orientées selon l’axe de la fibre. Leur conformation est significativement affectée par les ponts hydrogène. Une structure en couches a été suggérée pour la forme β, plutôt que la structure conventionnelle en canaux adoptée par la forme α. Nos résultats indiquent que le complexe β est thermodynamiquement stable avant sa fonte et peut se transformer en forme α et en PEO liquide par un processus de fonte et recristallisation à 89 ºC. Ceci va dans le sens contraire aux observations faites avec le complexe β obtenu par trempe du complexe α fondu. En effet, le complexe β ainsi obtenu est métastable et contient des cristaux d’urée. Il peut subir une transition de phases cinétique solide-solide pour produire du complexe α dans une vaste gamme de températures. Cette transition est induite par un changement de conformation du PEO et par la formation de ponts hydrogène intermoléculaires entre l’urée et le PEO. Le diagramme de phases du système PEO-urée a été tracé sur toute la gamme de compositions, ce qui a permis d’interpréter la formation de plusieurs mélanges qui ne sont pas à l’équilibre mais qui sont été observés expérimentalement. La structure et le diagramme de phases du complexe PEO-thiourée, qui est aussi un complexe très mal connu, ont été étudiés en détail. Un rapport molaire PEO :thiourée de 3:2 a été déduit pour le complexe, et une cellule monoclinique avec a = 0.915 nm, b = 1.888 nm, c = 0.825 nm et β = 92.35º a été déterminée. Comme pour le complexe PEO-urée de forme β, une structure en couches a été suggérée pour le complexe PEO-thiourée, dans laquelle les molécules de thiourée seraient disposées en rubans intercalés entre deux couches de PEO. Cette structure en couches pourrait expliquer la température de fusion beaucoup plus faible des complexes PEO-thiourée (110 ºC) et PEO-urée de forme β (89 ºC) en comparaison aux structures en canaux du complexe PEO-urée de forme α (143 ºC).

Promoting resilience and protective factors in the Children's Fund: supporting children and young people's pathways towards social inclusion?

As part of the broader prevention and social inclusion agenda, concepts of risk, resilience, and protective factors inform a range of U.K. Government initiatives targeted towards children and young people in England, including Sure Start, the Children's Fund, On Track, and Connexions. This paper is based on findings from a large qualitative dataset of interviews conducted with children and their parents or caregiver who accessed Children's Fund services as part of National Evaluation of the Children's Fund research.1 Drawing on the notion of young people's trajectories, the paper discusses how Children's Fund services support children's and young people's pathways towards greater social inclusion. While many services help to build resilience and protective factors for individual children, the paper considers the extent to which services also promote resilience within the domains of the family, school, and wider community and, hence, attempt to tackle the complex, multi-dimensional aspects of social exclusion affecting children, young people, and their families.

The acoustic signature of fluid flow in complex porous media

Effective medium approximations for the frequency-dependent and complex-valued effective stiffness tensors of cracked/ porous rocks with multiple solid constituents are developed on the basis of the T-matrix approach (based on integral equation methods for quasi-static composites), the elastic - viscoelastic correspondence principle, and a unified treatment of the local and global flow mechanisms, which is consistent with the principle of fluid mass conservation. The main advantage of using the T-matrix approach, rather than the first-order approach of Eshelby or the second-order approach of Hudson, is that it produces physically plausible results even when the volume concentrations of inclusions or cavities are no longer small. The new formulae, which operates with an arbitrary homogeneous (anisotropic) reference medium and contains terms of all order in the volume concentrations of solid particles and communicating cavities, take explicitly account of inclusion shape and spatial distribution independently. We show analytically that an expansion of the T-matrix formulae to first order in the volume concentration of cavities (in agreement with the dilute estimate of Eshelby) has the correct dependence on the properties of the saturating fluid, in the sense that it is consistent with the Brown-Korringa relation, when the frequency is sufficiently low. We present numerical results for the (anisotropic) effective viscoelastic properties of a cracked permeable medium with finite storage porosity, indicating that the complete T-matrix formulae (including the higher-order terms) are generally consistent with the Brown-Korringa relation, at least if we assume the spatial distribution of cavities to be the same for all cavity pairs. We have found an efficient way to treat statistical correlations in the shapes and orientations of the communicating cavities, and also obtained a reasonable match between theoretical predictions (based on a dual porosity model for quartz-clay mixtures, involving relatively flat clay-related pores and more rounded quartz-related pores) and laboratory results for the ultrasonic velocity and attenuation spectra of a suite of typical reservoir rocks. (C) 2003 Elsevier B.V. All rights reserved.