Numerical modeling of interaction between surface radiation and natural convection of atmospheric aerosol in presence of transverse magnetic field

After the era of industrialization, technology is developing daily since the last century. Urbanization, communication, and transportation have grown rapidly and simultaneously deforestation and volcanic eruptions take place on a large scale. As result every moment tons of foreign particles like soot, dust, ash, and bio-fuel contaminants are released into the atmosphere. These contaminants mix with air and various green house gases, form a blanket structure in atmosphere. This mixture of ultrafine particle suspension with atmospheric air is known as aerosol. In the present study, numerical simulations of hydrodynamic single cell buoyant convection of atmospheric aerosol sample enclosed within a gray enclosure in the presence of a transverse magnetic field and surface radiation is addressed. Flow of the aerosol over deserts and industrial belts is a practical example of such a condition, where the thermal radiation emanating from the surface, affects the flow mechanism of the aerosol transport. The emphasis of the present study is only on carbon-black solid particles of a size in the nanometer range present in atmospheric air. The aerosol is treated as nanofluid for the numerical simulation. A comprehensive study on the controlling parameters that affect the flow and heat transfer characteristics are delineated. The governing equations are solved using modified MAC method and SIMPLER algorithm has been used to solve pressure velocity coupling employing relaxation technique. The transport equation for surface radiation is solved using the net radiation method. The cross string method is used to evaluate the view factor. The most striking result is that the heat transfer rate increases with increase in the volume fraction of the carbon-black particles, which has an adverse effect on both the climate and living creatures. The results are presented in tabular and graphical form. The heat transfer and flow characteristics are depicted in the form of isotherms and streamlines revealing the physics of this complex phenomenon.     

Interaction of guanine, its anions, and radicals with lysine in different charge states

Modification in DNA or protein structure can severely affect DNA-protein interactions and the functioning of biological systems. Some new insights into radiation-induced effects of guanine-lysine interactions have been obtained here by theoretical investigations. Geometries of zwitterionic and non-zwitterionic lysine in different charge states (neutral, radical cation, and protonated cation) were optimized employing the B3LYP/6-31G** and B3LYP/AUG-cc-pVDZ levels of hybrid density functional theory (DFT) and using the second-order M?ller-Plesset perturbation theory along with the 6-31G** basis set. In the case of neutral lysine in the gas phase, no zwitterionic structure was obtained. The non-zwitterionic structures of lysine in radical and protonated cationic forms are appreciably more stable than the corresponding zwitterionic structures in the gas phase as obtained at all levels of theory employed here. Binding of guanine and different dehydrogenated guanine radicals with lysine in different charge states was studied at the B3LYP/6-31G** level of DFT. When guanine makes a complex with the lysine radical cation, large amounts of spin and positive charge densities are transferred from the lysine radical cation to guanine and the guanine is thus converted from its normal form to the radical cationic form. Complexation of the lysine radical cation with the H1-hydrogen-abstracted guanine radical leads to CO2 liberation and proton transfer from lysine. These results are compared with the available experimental ones.     

Methyl groups at dielectric and metal surfaces studied by sum-frequency generation in co- and counter-propagating configurations

The optimum experimental geometry for visible-infrared sum-frequency generation experiments depends rather sensitively on the molecules adsorbed at the surface, their orientation, and the nature of the adjacent bulk media. We consider the commonly encountered case of methyl groups situated at air-water, air-gold, and polymer-water interfaces. We provide expressions that may be used to determine the optimal visible and IR beam incident angles, considering the symmetric and antisymmetric modes separately and then together. The analysis is carried out for co-propagating (collinear and non-collinear geometries) and counter-propagating configurations. We first consider that one or more vibrational modes are of interest, and the goal is to study them quantitatively under a single polarization scheme; our results enable the user to set the beam angles for such an experiment. In the second case, molecular orientation information is desired, and so the calibrated response is required in all accessible polarization schemes for full characterization of the nonlinear susceptibility tensor.     

Structures and photoelectron spectroscopy of Cu(n)(BO2)m-(n, m=1, 2) clusters: observation of hyperhalogen behavior

The electronic structures of CuBO(2)(-), Cu(BO(2))(2)(-), Cu(2)(BO(2))(-), and Cu(2)(BO(2))(2)(-) clusters were investigated using photoelectron spectroscopy. The measured vertical and adiabatic detachment energies of these clusters revealed unusual properties of Cu(BO(2))(2) cluster. With an electron affinity of 5.07 eV which is larger than that of its BO(2) superhalogen (4.46 eV) building-block, Cu(BO(2))(2) can be classified as a hyperhalogen. Density functional theory based calculations were carried out to identify the ground state geometries and study the electronic structures of these clusters. Cu(BO(2)) and Cu(BO(2))(2) clusters were found to form chainlike structures in both neutral and anionic forms. Cu(2)(BO(2)) and Cu(2)(BO(2))(2) clusters, on the other hand, preferred a chainlike structure in the anionic form but a closed ringlike structure in the neutral form. Equally important, substantial differences between adiabatic detachment energies and electron affinities were found, demonstrating that correct interpretation of the experimental photoelectron spectroscopy data requires theoretical support not only in determining the ground state geometry of neutral and anionic clusters, but also in identifying their low lying isomers.     

Pressure-induced local structure distortions in Cu(pyz)F2(H2O)2

We employed infrared spectroscopy along with complementary lattice dynamics and spin density calculations to investigate pressure-driven local structure distortions in the copper coordination polymer Cu(pyz)F(2)(H(2)O)(2). Here, pyz is pyrazine. Our study reveals rich and fully reversible local lattice distortions that buckle the pyrazine ring, disrupt the bc-plane O-H···F hydrogen-bonding network, and reinforce magnetic property switching. The resiliency of the soft organic ring is a major factor in the stability of this material. Interestingly, the collective character of the lattice vibrations masks direct information on the Cu-N and Cu-O linkages through the series of pressure-induced Jahn-Teller axis switching transitions, although Cu-F bond softening is clearly identified above 3 GPa. These findings illustrate the importance of combined bulk and local probe techniques for microscopic structure determination in complex materials.     

Reaction-induced magnetic transition in Mn2 dimers

The magnetic coupling between Mn atoms in Mn(2) dimers embedded in a rare gas matrix is antiferromagnetic but undergoes ferromagnetic transition at a higher temperature or when ionized to the Mn(2)(+) state. By use of density functional theory and hybrid functional for exchange-correlation potentials, we show that ferromagnetic transition can also be induced when Mn(2) reacts with Cl and/or BO(2). Because of their highly electronegative character, both Cl and BO(2) draw electrons from the Mn(2) dimer leaving it in a positively charged state. The resulting shrinkage in the Mn-Mn bond brought about by the removal of an antibonding electron causes the magnetic transition. We further show that the coupling between Mn atoms remains ferromagnetic when two Mn(2)Cl units are allowed to interact with each other. The ability to induce a magnetic transition through a chemical reaction provides a way to synthesize new magnetic materials.     

All‐Metal Clusters that Mimic the Chemistry of Halogens

Owing to their s²p⁵ electronic configuration, halogen atoms are highly electronegative and constitute the anionic components of salts. Whereas clusters that contain no halogen atoms, such as AlH₄, mimic the chemistry of halogens and readily form salts (e.g., Na⁺(AlH₄)^?), clusters that are solely composed of metal atoms and yet behave in the same manner as a halogen are rare. Because coinage‐metal atoms (Cu, Ag, and Au) only have one valence electron in their outermost electronic shell, as in H, we examined the possibility that, on interacting with Al, in particular as AlX₄ (X=Cu, Ag, Au), these metal atoms may exhibit halogen‐like properties. By using density functional theory, we show that AlAu₄ not only mimics the chemistry of halogens, but also, with a vertical detachment energy (VDE) of 3.98 eV in its anionic form, is a superhalogen. Similarly, analogous to XHX superhalogens (X=F, Cl, Br), XAuX species with VDEs of 4.65, 4.50, and 4.34 eV in their anionic form, respectively, also form superhalogens. In addition, Au can also form hyperhalogens, a recently discovered species that show electron affinities (EAs) that are even higher than those of their corresponding superhalogen building blocks. For example, the VDEs of M(AlAu₄)₂^? (M=Na and K) and anionic (FAuF)? Au? (FAuF) range from 4.06 to 5.70 eV. Au‐based superhalogen anions, such as AlAu₄^? and AuF₂^?, have the additional advantage that they exhibit wider optical absorption ranges than their H‐based analogues, AlH₄^? and HF₂^?. Because of the catalytic properties and the biocompatibility of Au, Au‐based superhalogens may be multifunctional. However, similar studies that were carried out for Cu and Ag atoms have shown that, unlike AlAu₄, AlX₄ (X=Cu, Ag) clusters are not superhalogens, a property that can be attributed to the large EA of the Au atom.     

Is FapyG Mutagenic?: Evidence from the DFT Study

2,6‐diamino‐4‐oxo‐5‐formamidopyrimidine (FapyG) is an oxidatively damaged product of guanine (G), which is mainly formed through metabolic processes that produce OH radicals. It has been proposed that in bacterial cells, FapyG retains the coding properties of G, and is, therefore, not mutagenic. However, in mammalian cells, FapyG induces G to thymine (T) mutation more dominantly than another ubiquitous oxidative lesion, that is, 8‐oxoguanine (8‐oxoG). The exact reasons for these coding properties of FapyG are not properly understood. In order to rationalize the cause of FapyG‐mediated mutagenesis, all of the possible base‐pair interactions of FapyG with cytosine (C), adenine (A), and T, in both anti‐ and syn‐ conformations, are studied in detail by using density functional theory (DFT). The effects of solvation on the coding properties of FapyG are also evaluated. We demonstrate that the anti‐FapyG:C base pair has the highest binding energy, and that the base‐pair alignment is similar to that of the normal G:C base pair. Therefore, insertion of C opposite anti‐FapyG is preferred over the other DNA bases. This could be the reason for the non‐mutagenic behavior of FapyG in bacterial cells. However, as the binding patterns and energies of anti‐FpyG:A and syn‐FapyG:A base pairs are similar, and these are also similar to those of the T:A base pair, mammalian polymerases may not distinguish between FapyG and T. As a result, A would be mistakenly inserted opposite either anti‐FapyG or syn‐FapyG, resulting in G to T transverse mutation.     

Aromatic interaction profile to understand the molecular basis of raltegravir resistance

Integrase (IN) is the enzyme of human immunodeficiency virus (HIV) which inserts the viral DNA (vDNA) into the host genome for successful viral replication leading to the infection. However, the chemical basis of HIV IN catalysis is speculative due to lack of complete co-crystal structure. Using the recently published prototype foamy virus IN crystal structure, we developed a model structure of HIV IN showing interaction of vDNA, the metal (Mg²⁺) cofactor, and raltegravir (RLT) in the active site. Molecular docking and dynamics simulations studies showed that RLT uses it core central ring with diketo motif for Mg²⁺ chelation and bridge interaction with DDE motif. The triple arene interactions mediated by RLT with neighboring molecular motifs (Y143, cytosine, and adenine) is maintained during long simulation in wild type (WT). The fluorobenzyl and oxadiazole moieties of RLT forms aromatic stacking with cytosine base (head stacking) aromatic side chain of Y143 (tail stacking), respectively, while central ring further establishes aromatic stacking with distorted adenine base of vDNA (central stacking). The novel triple stacking systems were further explored to understand the molecular basis of drug resistance by molecular simulation. The in silico mutation (N155H, Q148H, and Q148H + G140S) and simulation studies elucidated the structural mechanism of resistance to RLT. The simulation studies provided the molecular basis for interdependency observed for the primary and secondary (Q148H and G140S) mutations and also explained the mechanism of viral fitness regain. Our study reveals that triple stacking and its consequence in terms of VdW energetic profile acts as a critical point to understand the drug-resistance. Here, we demonstrate that the root mean square deviation of centroid system (aromatic stacking) can be used as a major determinant of RLT binding toward the fold resistance. This is first kind of report, which discloses a strategy to explore the molecular level of drug resistance profile using aromatic interactions.     

Highly sensitive and selective electrochemical detection of sub-ppb level chromium(VI) using nano-sized gold particle

Gold nanoparticle based nanostructured electrode has been developed for the amperometric detection of ultratrace amount of toxic Cr(VI). The nano-sized Au particles have been grown on a conducting substrate modified with sol-gel-derived thiol functionalized silicate network and used for the electroanalysis of Cr(VI). The nanostructured interface show well-defined voltammetric peak for the reduction of Cr(VI) at approximately 0.4 V. The voltammetric behavior of Cr(VI) strongly depends on the coverage of nanoparticle on the electrode surface. Constant potential amperometry has been used for the detection of Cr(VI) at well below the guideline value set by World Health Organization (WHO). This electrode is highly sensitive (30+/-0.2 nA/ppb) and the detection limit (S/N=9) was 0.1 ppb. Cr(III) and coexisting other metal ions and surface active agent present in water do not interfere with the amperometric measurement of Cr(VI). This nanostructured electrode is highly stable and it can be used for continuous measurement of Cr(VI) without using any pretreatment or activation procedures. The accuracy of the measurement has been validated by measuring the concentration of Cr(VI) in the certified reference material (CRM).