Docking and molecular dynamics studies toward the binding of new natural phenolic marine inhibitors and aldose reductase

Phenolic marine natural product is a kind of new potential aldose reductase inhibitors (ARIs). In order to investigate the binding mode and inhibition mechanism, molecular docking and dynamics studies were performed to explore the interactions of six phenolic inhibitors with human aldose reductase (hALR2). Considering physiological environment, all the neutral and other two ionized states of each phenolic inhibitor were adopted in the simulation. The calculations indicate that all the inhibitors are able to form stable hydrogen bonds with the hALR2 active pocket which is mainly constructed by residues TYR48, HIS110 and TRP111, and they impose the inhibition effect by occupying the active space. In all inhibitors, only La and its two ionized derivatives La_ion1 and La_ion2, in which neither of the ortho-hydrogens of 3-hydroxyl is substituted by Br, bind with hALR2 active residues using the terminal 3-hydroxyl. While, all the other inhibitors, at least one of whose ortho-sites of 3- and 6-hydroxyls are substituted by Br substituent which take much electron-withdrawing effect and steric hindrance, bind with hALR2 through the lactone group. This means that the Br substituent can effectively regulate the binding modes of phenolic inhibitors. Although the lactone bound inhibitors have relatively high RMSD values, our dynamics study shows that both binding modes are of high stability. For each inhibitor molecule, the ionization does not change its original binding mode, but it does gradually increase the binding free energy, which reveals that besides hydrogen bonds, the electrostatic effect is also important to the inhibitor–hALR2 interaction.

通过第一性原理计算研究内地核的结构与成分

The determination of the composition and structure of the Earth’s inner core has long been the major subject in the study of the Earth’s deep interior. It’s widely believed that the Earth’s core is formed by iron with a fraction of nickel. However, light elements must exist in the inner core because the earth core is less dense than pure iron-nickel alloy (~2-3% in the solid inner core and ~6-7% in the liquid outer core). The questions are what and how much light element is there in the iron-nickel alloy. Besides the composition, the crystal structure of the iron with or without light element is also not well known. According to the seismological observations, the sound waves propagate 3-4% faster along the spin axis than in the equatorial plane. That means the inner core is anisotropic. The densest structure of iron-nickel alloy should be h.c.p structure under the very high pressures. However, the h,c,p structure does not propagate waves anisotropic ally. Then what is the structure of the iron-nickel alloy or the iron-nickle-light element alloy. In this study, we tried to predict the composition and the structure of the inner core through ab initio calculation of the Gibbs free energy, which is a function of internal energy, density and entropy. We conclude that the h.c.p structure is more stable than the b.c.c structure under high pressure and 0 K, but with the increase of temperature, the free energy of the b.c.c structure is decreasing much faster than the h.c.p structure caused by the vibration of the atomics, so the b.c.c structure is more stable at high temperatures. With the addition of light elements (S or Si or both), the free energy of b.c.c. decreases even faster, about 3at% of Si not only explains why the inner core is about 2-3 % lighter than the iron-nickle alloy, but also reasons why the inner core is anisotropic, since the b.c.c. structure becomes more stable than the h.c.p structure at 5500-6000K and b.c.c. is anisotropic in propagating seismic waves. Therefore, we infer that the inner core of the earth is formed by b.c.c iron and a fraction of nickel plus ~3at.% Si, with a temperature higher than 5500K, which is consistent with the studies from other approaches.

Heat capacity enhancement and thermodynamic properties of nanostructured amorphous SiO2

The heat capacity of nanostructured amorphous SiO2 (na-SiO2) has been measured by adiabatic calorimetric method over the temperature range 9-354 K. TG and differential scanning calorimeter (DSC) were also employed to determine the thermal stability. Glass transition temperature (T-g) for the two same grain sizes with different specific surface of naSiO(2) samples and one coarse-grained amorphous SiO2 (ca-SiO2) sample were determined to be 1377, 1397 and 1320 K, respectively. The low temperature experimental results show that there are significant heat capacity (C-P) enhancements among na-SiO2 samples and ca-SiO2. Entropy, enthalpy, Gibbs free energy and Debye temperature (theta (D)) were obtained based on the low temperature heat capacity measurement of na-SiO2. The Cp enhancements of na-SiO2 were discussed in terms of configurational and vibrational entropy. (C) 2001 Elsevier Science B.V. All rights reserved.

Prediction of soil adsorption coefficients from retention parameters on three reversed-phase liquid chromatographic columns

Reversed-phase high-performance liquid chromatographic (RP-HPLC) retention parameters, which are determined by the intermolecular interactions in retention process, can be considered as the chemical molecular descriptors in linear free energy relationships (LFERs). On the basis of the characterization and comparison of octadecyl-bonded silica gel (ODS), cyano-bonded silica gel (CN), and phenyl-bonded silica gel (Ph) columns with linear solvation energy relationships (LSERs), a new multiple linear regression model using RP-HPLC retention parameters on ODS and CN columns as variables for estimation of soil adsorption coefficients was developed. It was tested on a set of reference substances from various chemical classes. The results showed that the multicolumn method was more promising than a single-column method was for the estimation of soil adsorption coefficients. The accuracy of the suggested model is identical with that of LSERs.

Characteristics of plasma induced by interaction of a free-oscillated laser pulse with a coal target in air and combustible gas

Plasma in the air is successfully induced by a free-oscillated Nd:YAG laser pulse with a peak power of 10(2-3) W. The initial free electrons for the cascade breakdown process are from the ablated particles from the surface of a heated coal target, likewise induced by the focused laser beam. The laser field compensates the energy loss of the plasma when the corresponding temperature and the images are investigated by fitting the experimental spectra of B-2 Sigma(+) -> X-2 Sigma(+) band of CN radicals in the plasma with the simulated spectra and a 4-frame CCD camera. The electron density is estimated using a simplified Kramer formula. As this interaction occurs in a gas mixture of hydrogen and oxygen, the formation and development of the plasma are weakened or restrained due to the chaining branch reaction in which the OH radicals are accumulated and the laser energy is consumed. Moreover, this laser ignition will initiate the combustion or explosion process of combustible gas and the minimum ignition energy is measured at different initial pressures. The differences in the experimental results compared to those induced by a nanosecond Q-switched laser pulse with a peak power of 10(6-8) W are also discussed. (C) 2009 Professor T. Nejat Veziroglu. Published by Elsevier Ltd. All rights reserved.

Probing the high density behavior of the symmetry energy by using the free neutron-proton ratio

Based on the isospin- and momentum-dependent transport model IBUU04, the transverse momentum distributions of the free neutron-proton ratio in the Sn-132+(124) Sn reaction system at mid-central collisions with beam energies of 400/A MeV, 600/A MeV and 800/A MeV are studied by using two different symmetry energies. It is found that the free neutron-proton ratio as a function of the transverse momentum at the mid-rapidity is very sensitive to the density dependency of the symmetry energy especially at incident energies around 400/AMeV.