The impact of protonation and deprotonation of 3-methyl-2'-deoxyadenosine on N-glycosidic bond cleavage

The enzyme-substrate contacts that are believed to be involved in depurination by proton transfer have been modelled by protonation and deprotonation of 3-methyl-2'-deoxyadenosine (3-MDA) using quantum mechanical calculations in the gas-phase and solution media. The change in the charge distribution on the sugar ring and nucleobase that is introduced by the protonation and deprotonation strongly affects the N-glycosidic bond length. The unimolecular cleavage and hydrolysis of the N-glycosidic bond, involving D(N)*A(N) and A(N)D(N) pathways, have been considered at several levels of theory. The trend in the energy barriers is A(N)D(N) > cleavage > D(N)*A(N). All probable proton transfer reactions resulting from enzyme-substrate contacts do not facilitate the N-glycosidic bond cleavage of 3-MDA. The deprotonation of 3-MDA that may result from the interaction between H6 and enzyme do not facilitate bond cleavage. The protonation at N7 induces more positive charge on the sugar ring and further facilitates the depurination relative to the protonation at N1. The changes in the charges calculated on the ribose and nucleobase are in good relationship with the C1'-C2', C1'-O4', and N-glycosidic bond lengths along the cleavage. The change in energy barrier ΔE of glycosidic bond cleavage from the gas-phase to solution media strongly depends on the charge of the species.     

A novel numerical scheme for the investigation of surface tension effects on growth and collapse stages of cavitation bubbles

In the present study the effects of surface tension on the growth and collapse stages of cavitation bubbles are studied individually for both spherical and nonspherical bubbles. The Gilmore equation is used to simulate the spherical bubble dynamics by considering mass diffusion and heat transfer. For the collapse stage near a rigid boundary, the Navier–Stokes and energy equations are used to simulate the flow domain, and the VOF method is adopted to track the interface between the gas and the liquid phases. Simulations are divided into two cases. In the first case, the collapse stage alone is considered in both spherical and nonspherical situations with different conditions of bubble radius and surface tension. According to the results, surface tension has no significant effects on the flow pattern and collapse rate. In the second case, both the growth and collapse stages of bubbles with different initial radii and surface tensions are considered. In this case surface tension affects the growth stage considerably and, as a result, the jet velocity and collapse time decrease with increasing surface tension coefficient. This effect is more significant for bubbles with smaller radii.     

Queues with Simultaneous Arrival of Customers and the Dependence Structure of the Waiting Times

Methodology and Computing in Applied Probability - We consider a queueing system where some customers decide to simultaneously wait in two queues, rather than in a single queue, to receive their...     

The molecular Hamiltonian in internal coordinates

A systematic approach for the derivation of the exact translational–rovibronic (non-relativistic) Hamiltonian for a polyatomic molecule consisting of N nuclei and n electrons is presented. All coupling terms which contribute to the total energy are identified. The Hamiltonian is greatly simplified by taking the internal coordinates (bond lengths and bond angles) as the vibrational variables. The translational–rovibronic Hamiltonian of triatomic molecules are considered as an application for this general formulation.     

Solid-phase synthesis of arylidene and alkylidene malonates,as versatile intermediates,catalyzed using mesoporous poly-melamine–formaldehyde as a nitrogen-rich porous organic polymer (POP)

Research on Chemical Intermediates - An efficient solid/slurry-state synthesis of arylidene and alkylidene malonates as versatile intermediates is developed in the presence of mesoporous...     

Preparation of Fucoxanthin Nanoemulsion Stabilized by Natural Emulsifiers: Fucoidan,Sodium Caseinate,and Gum Arabic

This study was proposed to investigate the possibility of O/W nanoemulsion stabilization via natural emulsifiers as a delivery system for fucoxanthin. Nanoemulsions were prepared using ultrasonic treatment (150 W, amplitude 80%, 10 min) with different levels (0.5%, 1%, and 2% wt) of fucoidan, gum Arabic, and sodium caseinate as natural emulsifires and they were compared with tween 80. Then, the creaming index, stability, encapsulation efficacy, Fourier-transform infrared (FT-IR) spectroscopy, and in vitro release were evaluated. The best stability and lowest creaming index were observed at 2% wt of emulsifiers. Nanoemulsions with droplet sizes (113.27–127.50 nm) and zeta potentials (−32.27 to −58.87 mV) were prepared. The droplet size of nanoemulsions was reduced by increasing the emulsifier concentration, and the best nanoemulsion stability after 15 days of storage was in the following order: tween 80 > sodium caseinate > fucoidan > gum Arabic. The encapsulation efficacy of nanoemulsions stabilized by sodium caseinate, fucoidan, and gum Arabic were 88.51 ± 0.11%, 79.32 ± 0.09%, and 60.34 ± 0.13%, respectively. The in vitro gastrointestinal fucoxanthin release of nanoemulsion stabilized with tween 80, sodium caseinate, fucoidan, and gum Arabic were 85.14 ± 0.16%, 76.91 ± 0.34%, 71.41 ± 0.14%, and 68.98 ± 0.36%, respectively. The release of fucoxanthin from nanoemulsions followed Fickian diffusion. The FTIR also confirmed the encapsulation of fucoxanthin.     

Energy,exergy and pinch analyses of an integrated cryogenic natural gas process based on coupling of absorption–compression refrigeration system,organic Rankine cycle and solar parabolic trough collectors

Journal of Thermal Analysis and Calorimetry - The natural gas entering the liquefaction cycle usually consists of nitrogen, ethane, propane and also heavier hydrocarbons which are economically...     

Enhanced optical and hydrophilic properties of V and La co-doped ZnO thin films

V and La co-doped and undoped ZnO thin films were deposited on a glass substrate via the sol–gel method to investigate the structural, optical, and wettability of ZnO thin film by changing the V-doping concentration. Microstructure and water contact angles of the films were measured by SEM and contact angle goniometer, respectively. SEM studies revealed that the grain size and surface roughness of the film were changed by doping concentration. In addition, the contact angles were studied to find the possible effects of doping on the hydrophilicity of the film, indicating that the ZnO films were hydrophobic in nature. Finally, a good correlation was observed between the SEM micrographs and contact angle results, and the nature of ZnO film was found to be changed from hydrophobic to hydrophilic.     

Weak Module Amenability for Semigroup Algebras

We study the weak module amenability of Banach algebras which are Banach module over another Banach algebra with compatible actions. As an example we show that the semigroup algebra of a commutative inverse semigroup is always weakly amenable as a module over the semigroup algebra of its subsemigroup of idempotents.     

5 μm thick 3C-SiC layers grown on Ge-modified Si(100) substrates

The effect of the germanium coverage prior to the epitaxial growth of 5 μm thick 3C-SiC on Si(100) substrates were evaluated with Atomic Force Microscopy and μ-Raman spectroscopy. The 3C-SiC layers were grown by atmospheric pressure chemical vapor deposition via a special procedure leading to layers with compressive instead of tensile stress. The Ge amount was varied from 0 up to 2 ML. The obtained results showed that the residual stress inside the layers is shifted in the compressive direction; the crystalline quality is improved with the Ge introduction but on the account of the surface roughness. These results open the route for the use of Ge-modified Si(100) as a potential substrate in order to improve the heteroepitaxial growth of 3C-SiC on silicon substrates.