Molecular modelling studies of binding of DACD derivatives into G-Quadruplex DNA: comparison of force field and quantum polarized ligand docking methods

The DNA G-qadruplexes are one of the targets being actively explored for anti-cancer therapy by inhibiting them through small molecules. This computational study was conducted to predict the binding strengths and orientations of a set of novel dimethyl-amino-ethyl-acridine (DACA) analogues that are designed and synthesized in our laboratory, but did not diffract in Synchrotron light.Thecrystal structure of DNA G-Quadruplex(TGGGGT)4(PDB: 1O0K) was used as target for their binding properties in our studies.We used both the force field (FF) and QM/MM derived atomic charge schemes simultaneously for comparing the predictions of drug binding modes and their energetics. This study evaluates the comparative performance of fixed point charge based Glide XP docking and the quantum polarized ligand docking schemes. These results will provide insights on the effects of including or ignoring the drug-receptor interfacial polarization events in molecular docking simulations, which in turn, will aid the rational selection of computational methods at different levels of theory in future drug design programs. Plenty of molecular modelling tools and methods currently exist for modelling drug-receptor or protein-protein, or DNA-protein interactionssat different levels of complexities.Yet, the capasity of such tools to describevarious physico-chemical propertiesmore accuratelyis the next step ahead in currentresearch.Especially, the usage of most accurate methods in quantum mechanics(QM) is severely restricted by theirtedious nature. Though the usage of massively parallel super computing environments resulted in a tremendous improvement in molecular mechanics (MM) calculations like molecular dynamics,they are still capable of dealing with only a couple of tens to hundreds of atoms for QM methods. One such efficient strategy that utilizes thepowers of both MM and QM are the QM/MM hybrid methods. Lately, attempts have been directed towards the goal of deploying several different QM methods for betterment of force field based simulations, but with practical restrictions in place. One of such methods utilizes the inclusion of charge polarization events at the drug-receptor interface, that is not explicitly present in the MM FF.

Crystallization of random aromatic copolyesters containing flexible spacer chains and side-groups

The crystallization behaviour of a series of random copolymers of varying chemical composition is reported. For polymers containing a high proportion of alternating rigid aromatic units and flexible spacers, conventional liquid crystalline and crystalline phase behaviour is observed. The introduction of a substantial fraction of a second shorter rigid unit containing side-chains leads to a broad endotherm in the d.s.c. scan covering some 150°C. Subsequent isothermal crystallization at any point within the broad endotherm leads to the generation of sharp endotherms at temperatures just above the recrystallization temperature. We attribute this behaviour to the crystallization of clusters of molecules containing similar random sequences. Such crystals are non-periodic along the chain direction.

Evaluating the likelihood of the adoption of an animal welfare assessment system in European agri-food supply chains

Purpose – The purpose of this paper is to analyse the likelihood of adoption of a recently designed Welfare Assessment System in agri-food supply chains and the factors affecting the adoption decision. The application is carried out for pig and poultry chains. Design/methodology/approach – This research consisted of two main components: interviews with retailers in pig and poultry supply chains in eight different EU countries to explore their perceptions towards the adoption possibilities of the welfare assessment system; and a conjoint analysis designed to evaluate the perceived adoption likelihood of the assessment system by different Standards Formulating Organisations (SFOs). Findings – Stakeholders were found to be especially concerned about the costs of implementation of the system and how it could, or should, be merged with existing assurance schemes. Another conclusion of the study is that the presence of a strong third independent party supporting the implementation of the welfare assessment system would be the most important influence on the decision whether, or not, to adopt it. Originality/value – This research evaluates the adoption possibilities of a novel Welfare Assessment System and presents the views of different supply chain stakeholders on an adoption of such a system. The main factors affecting the adoption decision are identified and analysed. Contrary to expectations, the costs of adoption of a new welfare assessment system were not considered to be the most important factor affecting the decision of supply chain stakeholders about the adoption of this new welfare system.

Control of strand registry by attachment of PEG chains to amyloid peptides influences nanostructure

The self-assembly in aqueous solution of PEG-peptide conjugates comprising a model amyloid peptide sequence FFKLVFF that contains the Ab(16–20) KLVFF motif is investigated. X-ray diffraction reveals different packing motifs dependent on PEG chain length. This is correlated to remarkable differences in self-assembled nanostructures. The control of strand registry points to a subtle interplay between aromatic stacking, electrostatic and amphiphilic interactions.

On the quantum mechanical scattering statistics of many particles

The probability of a quantum particle being detected in a given solid angle is determined by the S-matrix. The explanation of this fact in time-dependent scattering theory is often linked to the quantum flux, since the quantum flux integrated against a (detector-) surface and over a time interval can be viewed as the probability that the particle crosses this surface within the given time interval. Regarding many particle scattering, however, this argument is no longer valid, as each particle arrives at the detector at its own random time. While various treatments of this problem can be envisaged, here we present a straightforward Bohmian analysis of many particle potential scattering from which the S-matrix probability emerges in the limit of large distances.

Unusual isotope effect in the reaction of chlorosilylene with trimethylsilane-1-d: Absolute rate studies and quantum chemical and Rice–Ramsperger–Kassel–Marcus calculations provide strong evidence for the involvement of an intermediate complex

Time-resolved studies of chlorosilylene, ClSiH, generated by the 193 nm laser flash photolysis of 1-chloro-1- silacyclopent-3-ene, have been carried out to obtain rate constants for its bimolecular reaction with trimethylsilane-1-d, Me3SiD, in the gas phase. The reaction was studied at total pressures up to 100 Torr (with and without added SF6) over the temperature range of 295−407 K. The rate constants were found to be pressure independent and gave the following Arrhenius equation: log[(k/(cm3 molecule−1 s−1)] = (−13.22 ± 0.15) + [(13.20 ± 1.00) kJ mol−1]/(RT ln 10). When compared with previously published kinetic data for the reaction of ClSiH with Me3SiH, kinetic isotope effects, kD/kH, in the range from 7.4 (297 K) to 6.4 (407 K) were obtained. These far exceed values of 0.4−0.5 estimated for a single-step insertion process. Quantum chemical calculations (G3MP2B3 level) confirm not only the involvement of an intermediate complex, but also the existence of a low-energy internal isomerization pathway which can scramble the D and H atom labels. By means of Rice−Ramsperger−Kassel−Marcus modeling and a necessary (but small) refinement of the energy surface, we have shown that this mechanism can reproduce closely the experimental isotope effects. These findings provide the first experimental evidence for the isomerization pathway and thereby offer the most concrete evidence to date for the existence of intermediate complexes in the insertion reactions of silylenes.

The economic theory of international supply chains: a systems view

This paper offers an integrated analysis of out-sourcing, off-shoring and foreign direct investment within a systems view of international business. This view takes the supply chain rather than the firm as the basic unit of analysis. It argues that competition in the global economy selects supply chains that maximise the joint profit of all the firms in the chain. The systems view is compared with the firm-centred view commonly used in strategy literature. The paper shows that a firm’s strategy must be embedded within an efficient supply chain strategy, and that this strategy must be negotiated with, rather than imposed upon, other firms. The paper analyses the conditions under which various supply chain strategies - and by implication various firm-level strategies - are efficient. Only by adopting a systems view of supply chains is it possible to determine which firm-level strategies will succeed in a volatile global economy.

The interplay of secondary Hg⋯S, Hg⋯N and Hg⋯π bonding interactions in supramolecular structures of phenylmercury(ii) dithiocarbamates

Three new phenylmercury(II) and one mercury(II) dithiocarbamate complexes viz. PhHg S2CN(PyCH2) Bz (1), PhHg S2CN(PyCH2)CH3 (2), PhHg S2CN(Bz)CH3 (3), and [Hg (NCS2(PyCH2)Bz)(2)] (4) (Py = pyridine; Bz = benzyl) have been synthesized and characterized by elemental analyses, IR, electronic absorption, H-1 and C-13 NMR spectroscopy. The crystal structures of 1, 2 and 3 showed a linear S-Hg-C core at the centre of the molecule, in which the metal atom is bound to the sulfur atom of the dithiocarbamate ligand and a carbon atom of the aromatic ring. In contrast the crystal structure of 4 showed a linear S-Hg-S core at the Hg(II) centre of the molecule. Weak intermolecular Hg center dot center dot center dot N (Py) interactions link molecules into a linear chain in the case of 1, whereas chains of dimers are formed in 2 through intermolecular Hg center dot center dot center dot N (Py) and Hg center dot center dot center dot S interactions. 3 forms a conventional face-to-edge dimeric structure through intermolecular Hg center dot center dot center dot S secondary bonding and 4 forms a linear chain of dimers through face-to-face Hg center dot center dot center dot S secondary bonding. In order to elucidate the nature of these secondary bonding interactions and the electronic absorption spectra of the complexes, ab initio quantum chemical calculations at the MP2 level and density functional theory calculations were carried out for 1-3. Complexes 1 and 2 exhibited photoluminescent properties in the solid state as well as in the solution phase. Studies indicate that Hg center dot center dot center dot S interactions decrease and Hg center dot center dot center dot N interactions increase the chances of photoluminescence in the solid phase

Time-resolved gas-phase kinetic, quantum chemical, and RRKM studies of reactions of silylene with alcohols

Time-resolved kinetic studies of silylene, SiH2, generated by laser flash photolysis of 1-silacyclopent-3-ene and phenylsilane, have been carried out to obtain rate constants for its bimolecular reactions with methanol, ethanol, 1-propanol, 1-butanol and 2-methyl-1-butanol. The reactions were studied in the gas phase over the pressure range 1-100 Torr in SF6 bath gas, at room temperature. In the study with methanol several buffer gases were used. All five reactions showed pressure dependences characteristic of third body assisted association reactions. The rate constant pressure dependences were modelled using RRKM theory, based on Eo values of the association complexes obtained by ab initio calculation (G3 level). Transition state models were adjusted to fit experimental fall-off curves and extrapolated to obtain k∞ values in the range 1.9 to 4.5 × 10-10 cm3 molecule-1 s-1. These numbers, corresponding to the true bimolecular rate constants, indicate efficiencies of between 16 and 67% of the collision rates for these reactions. In the reaction of SiH2 + MeOH there is a small kinetic component to the rate which is second order in MeOH (at low total pressures). This suggests an additional catalysed reaction pathway, which is supported by the ab initio calculations. These calculations have been used to define specific MeOH-for-H2O substitution effects on this catalytic pathway. Where possible our experimental and theoretical results are compared with those of previous studies.

The reaction between silylene and ammonia: some gas-phase kinetic and quantum chemical studies

Time-resolved kinetic studies of the reaction of silylene, SiH2, generated by 193 nm laser flash photolysis of silacyclopent-3-ene, have been carried out in the presence of ammonia, NH3. Second order kinetics were observed. The reaction was studied in the gas phase at 10 Torr total pressure in SF6 bath gas at each of the three temperatures, 299, 340 and 400 K. The second order rate constants (laser pulse energy of 60 mJ/pulse) fitted the Arrhenius equation: log(k/cm3 molecule-1 s-1) = (-10.37 ± 0.17) + (0.36 ± 1.12 kJ mol-1)/RTln10 Experiments at other pressures showed that these rate constants were unaffected by pressure in the range 10-100 Torr, but showed small decreases in value at 3 and 1 Torr. There was also a weak intensity dependence, with rate constants decreasing at laser pulse energies of 30 mJ/pulse. Ab initio calculations at the G3 level of theory, show that SiH2 + NH3 should form an initial adduct (donor-acceptor complex), but that energy barriers are too great for further reaction of the adduct. This implies that SiH2 + NH3 should be a pressure dependent association reaction. The experimental data are inconsistent with this and we conclude that SiH2 decays are better explained by reaction of SiH2 with the amino radical, NH2, formed by photodissociation of NH3 at 193 nm. The mechanism of this previously unstudied reaction is discussed.

A parallel quantum histogram architecture

A parallel formulation of an algorithm for the histogram computation of n data items using an on-the-fly data decomposition and a novel quantum-like representation (QR) is developed. The QR transformation separates multiple data read operations from multiple bin update operations thereby making it easier to bind data items into their corresponding histogram bins. Under this model the steps required to compute the histogram is n/s + t steps, where s is a speedup factor and t is associated with pipeline latency. Here, we show that an overall speedup factor, s, is available for up to an eightfold acceleration. Our evaluation also shows that each one of these cells requires less area/time complexity compared to similar proposals found in the literature.

Economic analysis of international supply chains: an internalization perspective

Offshoring and outsourcing in global value chains have been extensively analyzed from a strategic management perspective (Gereffi & Li, 2012; Gereffi, Humphrey & Sturgeon, 2005; Mudambi & Venzin, 2010). This paper examines these issues from an internalization theory perspective by summarizing the contribution of internalization theory to supply chain analysis; considering how a division of labor is coordinated and comparing coordination by management with coordination by the market; and discussing the formal models of supply chains developed by economists. Supply chain researchers possessing an interest in economic principles and good mathematical skills can make an important contribution to internalization theory, and it is hoped that this paper will encourage them to do so.

Noisy Monte Carlo: convergence of Markov chains with approximate transition kernels

Monte Carlo algorithms often aim to draw from a distribution π by simulating a Markov chain with transition kernel P such that π is invariant under P. However, there are many situations for which it is impractical or impossible to draw from the transition kernel P. For instance, this is the case with massive datasets, where is it prohibitively expensive to calculate the likelihood and is also the case for intractable likelihood models arising from, for example, Gibbs random fields, such as those found in spatial statistics and network analysis. A natural approach in these cases is to replace P by an approximation Pˆ. Using theory from the stability of Markov chains we explore a variety of situations where it is possible to quantify how ’close’ the chain given by the transition kernel Pˆ is to the chain given by P . We apply these results to several examples from spatial statistics and network analysis.