The role of the disulfide bond in amyloid-like fibrillogenesis in a model peptide system

The role of the disulfide bond in amyloid-like fibrillogenesis in a model peptide system Apurba Kumar Das,(a) Michael G. B. Drew,(b) Debasish Haldar(a) and Arindam Banerjee*(a) (a)Department of Biological Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India. E-mail: bcab@mahendra.iacs.res.in; Fax: +91-33-2473-2805 b School of Chemistry, The University of Reading, Whiteknights, Reading, UK RG6 6AD Received 28th June 2005, Accepted 20th July 2005 First published as an Advance Article on the web 11th August 2005

A model for stretch-bend interactions in molecular force fields

Interaction force constants between bond-stretching and angle-bending co-ordinates in polyatomic molecules have been attributed, by some authors, to changes of hybridization due to orbital-following of the bending co-ordinate, and consequent changes of bond length due to the change of hybridization. A method is described for using this model quantitatively to reduce the number of independent force constants in the potential function of a polyatomic molecule, by relating stretch-bend interaction constants to the corresponding diagonal stretching constants. It is proposed to call this model the Hybrid Orbital Force Field. The model is applied to the tetrahedral four co-ordinated carbon atom (as in methane) and to the trigonal planar three coordinated carbon atom (as in formaldehyde).

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-(C6H6)Cl-2](2), HL yields the cation [Ru(C6H6){5,6-diphenyl-3-(pyridin-2-yl)- 1,2,4-triazine}Cl](+), MeL gives the cation [Ru(C6H6)(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(C6H6)-(MeL)Cl](+) under the reaction conditions employed.

Structure of adsorbed organometallic rhodium: model single atom catalysts

We have determined the structure of a complex rhodium carbonyl chloride [Rh(CO)(2)Cl] molecule adsorbed on the TiO2 (110) surface by the normal incidence x-ray standing wave technique. The data show that the technique is applicable to reducible oxide systems and that the dominant adsorbed species is undissociated with Rh binding atop bridging oxygen and to the Cl found close to the fivefold coordinated Ti ions in the surface. A minority geminal dicarboryl species, where Rh-Cl bond scission has occurred, is found bridging the bridging oxygen ions forming a high-symmetry site.

European CMBS pricing: bond, mortgage and real estate characteristics

The recent global economic crisis is often associated with the development and pricing of mortgage-backed securities (i.e. MBSs) and underlying products (i.e. sub-prime mortgages). This work uses a rich database of MBS issues and represents the first attempt to price commercial MBSs (i.e. CMBSs) in the European market. Our results are consistent with research carried out in the US market and we find that bond-, mortgage-, real estate-related and multinational characteristics show different degrees of significance in explaining European CMBS spreads at issuance. Multiple linear regression analysis using a databank of CMBSs issued between 1997 and 2007 indicates a strong relationship with bond-related factors, followed by real estate and mortgage market conditions. We also find that multinational factors are significant, with country of issuance, collateral location and access to more liquid markets all being important in explaining the cost of secured funding for real estate companies. As floater coupon tranches tend to be riskier and exhibit higher spreads, we also estimate a model using this sub-set of data and results hold, hence reinforcing our findings. Finally, we estimate our model for both tranches A and B and find that real estate factors become relatively more important for the riskier investment products.

A comparison between bond graphs switching modelling techniques implemented on a boost dc-dc converter

A Bond Graph is a graphical modelling technique that allows the representation of energy flow between the components of a system. When used to model power electronic systems, it is necessary to incorporate bond graph elements to represent a switch. In this paper, three different methods of modelling switching devices are compared and contrasted: the Modulated Transformer with a binary modulation ratio (MTF), the ideal switch element, and the Switched Power Junction (SPJ) method. These three methods are used to model a dc-dc Boost converter and then run simulations in MATLAB/SIMULINK. To provide a reference to compare results, the converter is also simulated using PSPICE. Both quantitative and qualitative comparisons are made to determine the suitability of each of the three Bond Graph switch models in specific power electronics applications

Three dimensional picture of the local structure of 1,4-Polybutadiene from a complete atomistic model and neutron scattering data

An efficient method of combining neutron diffraction data over an extended Q range with detailed atomistic models is presented. A quantitative and qualitative mapping of the organization of the chain conformation in both glass and liquid phase has been performed. The proposed structural refinement method is based on the exploitation of the intrachain features of the diffraction pattern by the use of internal coordinates for bond lengths, valence angles and torsion rotations. Models are built stochastically by assignment of these internal coordinates from probability distributions with limited variable parameters. Variation of these parameters is used in the construction of models that minimize the differences between the observed and calculated structure factors. A series of neutron scattering data of 1,4-polybutadiene at the region 20320 K is presented. Analysis of the experimental data yield bond lengths for C-C and C=C of 1.54 and 1.35 Å respectively. Valence angles of the backbone were found to be at 112 and 122.8 for the CCC and CC=C respectively. Three torsion angles corresponding to the double bond and the adjacent R and β bonds were found to occupy cis and trans, s(, trans and g( and trans states, respectively. We compare our results with theoretical predictions, computer simulations, RIS models, and previously reported experimental results.

A complete atomistic model of molten polyethylene from neutron scattering data: a new methodology for polymer structure

A new approach to the study of the local organization in amorphous polymer materials is presented. The method couples neutron diffraction experiments that explore the structure on the spatial scale 1–20 Å with the reverse Monte Carlo fitting procedure to predict structures that accurately represent the experimental scattering results over the whole momentum transfer range explored. Molecular mechanics and molecular dynamics techniques are also used to produce atomistic models independently from any experimental input, thereby providing a test of the viability of the reverse Monte Carlo method in generating realistic models for amorphous polymeric systems. An analysis of the obtained models in terms of single chain properties and of orientational correlations between chain segments is presented. We show the viability of the method with data from molten polyethylene. The analysis derives a model with average C-C and C-H bond lengths of 1.55 Å and 1.1 Å respectively, average backbone valence angle of 112, a torsional angle distribution characterized by a fraction of trans conformers of 0.67 and, finally, a weak interchain orientational correlation at around 4 Å.

A detailed single chain model for molten poly(tetrafluoroethylene) from a novel structure refinement technique on neutron scattering data

We present a new methodology that couples neutron diffraction experiments over a wide Q range with single chain modelling in order to explore, in a quantitative manner, the intrachain organization of non-crystalline polymers. The technique is based on the assignment of parameters describing the chemical, geometric and conformational characteristics of the polymeric chain, and on the variation of these parameters to minimize the difference between the predicted and experimental diffraction patterns. The method is successfully applied to the study of molten poly(tetrafluoroethylene) at two different temperatures, and provides unambiguous information on the configuration of the chain and its degree of flexibility. From analysis of the experimental data a model is derived with CC and CF bond lengths of 1.58 and 1.36 Å, respectively, a backbone valence angle of 110° and a torsional angle distribution which is characterized by four isometric states, namely a split trans state at ± 18°, giving rise to a helical chain conformation, and two gauche states at ± 112°. The probability of trans conformers is 0.86 at T = 350°C, which decreases slightly to 0.84 at T = 400°C. Correspondingly, the chain segments are characterized by long all-trans sequences with random changes in sign, rather anisotropic in nature, which give rise to a rather stiff chain. We compare the results of this quantitative analysis of the experimental scattering data with the theoretical predictions of both force fields and molecular orbital conformation energy calculations.

Experimentally driven atomistic model of 1,2 Polybutadiene

We present an efficient method of combining wide angle neutron scattering data with detailed atomistic models, allowing us to perform a quantitative and qualitative mapping of the organisation of the chain conformation in both glass and liquid phases. The structural refinement method presented in this work is based on the exploitation of the intrachain features of the diffraction pattern and its intimate linkage with atomistic models by the use of internal coordinates for bond lengths, valence angles and torsion rotations. Atomic connectivity is defined through these coordinates that are in turn assigned by pre-defined probability distributions, thus allowing for the models in question to be built stochastically. Incremental variation of these coordinates allows for the construction of models that minimise the differences between the observed and calculated structure factors. We present a series of neutron scattering data of 1,2 polybutadiene at the region 120-400K. Analysis of the experimental data yield bond lengths for C-C and C=C of 1.54Å and 1.35Å respectively. Valence angles of the backbone were found to be at 112° and the torsion distributions are characterised by five rotational states, a three-fold trans-skew± for the backbone and gauche± for the vinyl group. Rotational states of the vinyl group were found to be equally populated, indicating a largely atactic chan. The two backbone torsion angles exhibit different behaviour with respect to temperature of their trans population, with one of them adopting an almost all trans sequence. Consequently the resulting configuration leads to a rather persistent chain, something indicated by the value of the characteristic ratio extrapolated from the model. We compare our results with theoretical predictions, computer simulations, RIS models and previously reported experimental results.

Bond graph models of DC-DC converters operating in both CCM and DCM

In this paper, Bond Graphs are employed to develop a novel mathematical model of conventional switched-mode DC-DC converters valid for both continuous and discontinuous conduction modes. A unique causality bond graph model of hybrid models is suggested with the operation of the switch and the diode to be represented by a Modulated Transformer with a binary input and a resistor with fixed conductance causality. The operation of the diode is controlled using an if-then function within the model. The extracted hybrid model is implemented on a Boost and Buck converter with their operations to change from CCM to DCM and to return to CCM. The vector fields of the models show validity in a wide operation area and comparison with the simulation of the converters using PSPICE reveals high accuracy of the proposed model, with the Normalised Root Means Square Error and the Maximum Absolute Error remaining adequately low. The model is also experimentally tested on a Buck topology.

The determinants of a cross market arbitrage opportunity: theory and evidence for the European bond market

This paper examines the determinants of cross-platform arbitrage profits. We develop a structural model that enables us to decompose the likelihood of an arbitrage opportunity into three distinct factors: the fixed cost to trade the opportunity, the level at which one of the platforms delays a price update and the impact of the order flow on the quoted prices (inventory and asymmetric information effects). We then investigate the predictions from the theoretical model for the European Bond market with the estimation of a probit model. Our main finding is that the results found in the empirical part corroborate strongly the predictions from the structural model. The event of a cross market arbitrage opportunity has a certain degree of predictability where an optimal ex ante scenario is represented by a low level of spreads on both platforms, a time of the day close to the end of trading hours and a high volume of trade.