We have performed molecular dynamics simulation on B-DNA duplex (CGCGAATTGCGC) at different temperatures. The DNA was immerged in a salt-water medium with 1 M NaCl concentration to investigate salt effect on the denaturation process. At each temperature, configurational entropy is estimated using the covariance matrix of atom-positional fluctuations, from which the melting temperature (T(m)) was found to be 349 K. The calculated configuration entropy for different bases shows that the melting process involves more peeling (including fraying from the ends) conformations, and therefore the untwisting of the duplex and peeling states form the transition state of the denaturation process. There is a narrow minor groove in the AATT sequence that becomes wider by increasing temperature which disappears at high temperatures, especially above the melting temperature. We have also calculated the fraction of denatured base pairs, f-curve, from which T(m) was found to be 340 K, close to experimental value of 341 K. We found that DNA at high salt concentrations has few hydrogen bonds even at temperatures higher than the T(m). Our calculations show the fact that adding salt leads to increase of T(m) and stabilization of DNA.

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In this paper, an efficient, green and eco-friendly method for synthesis of 3,4-dihydropyrimidin-2(1<em>H</em>)-ones via one-pot multi-component reaction of aldehydes, urea and ethyl acetoacetate is shown at the presence of cuttlebone as an effective, reusable and natural heterogeneous catalyst. The advantages of this method are short reaction times, high yields, simple work-up, and reusable natural catalysts. The structure of cuttlebone was characterized by FT-IR spectrum, scanning electron microscopy (SEM) and energy dispersive spectrometer (SEM-EDS).

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Different equations of state (EOSs) have been used to obtain analytical expressions for the ideal curves, namely, the Joule-Thomson inversion curve (JTIC), Boyle curve (BC), and Joule inversion curve (JIC). The selected EOSs are the Redlich-Kwong (RK), Soave-Redlich-Kwong (SRK), Deiters, linear isotherm regularity (LIR), modified LIR (MLIR), dense system equation of state (DSEOS), and van der Waals (vdW). Analytical expressions have been obtained for the JTIC and BC only by using the LIR, MLIR, and vdW equations of state. The expression obtained using the LIR is the simplest. The experimental data for the JTIC and the calculated points from the empirical EOSs for the BC are well fitted into the derived expression from the LIR, in such a way that the fitting on this expression is better than those on the empirical expressions given by Gunn et al. and Miller. No experimental data have been reported for the BC and JIC; therefore, the calculated curves from different EOSs have been compared with those calculated from the empirical equations. On the basis of the JTIC, an approach is given for obtaining the temperature dependence of an EOS parameter(s). Such an approach has been used to determine the temperature dependences of A 2 of the LIR, a and b parameters of the vdW, and the cohesion function of the RK. Such temperature dependences, obtained on the basis of the JTIC, have been found to be appropriate for other ideal curves as well.