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Shiv Nadar University

(SoNS) School of Natural Sciences

Chemistry

A Matter of Density: Exploring the Electron Density Concept in the Chemical, Biological, and Materials Sciences

The Electron Density

We investigated Ru mirror contamination and subsequent EUV reflectivity loss using the IMPACT facility at Purdue University. Because Ru can either be used as a grazing mirror or as a capping layer for multilayer normal mirror, we examined the angular dependency of XPS peak area intensity at the O 1s and Ru 3d regions as well as the effects of sputtering. Although no change in intensity has been observed at lower take-off angles from the target surface, the peak area intensity starts changing with increasing θ(i.e., emission observation angle, representing the angle between the target surface plane and detector entrance). Among different components, the effect of water and oxidized carbon are found to be most notable when viewed at lower θ, and primarily responsible for degrading the reflectivity of the Ru layer. On the other hand, the effect of OH becomes dominant with increasing observation angle θ, and thus plays a key role to suppress optical transmission. Moreover, atomic carbon effect is found to peak when observed at 30°, and most likely plays an important role in degrading both reflectivity and transmission. This is also because of the total photon path length in the Ru film at different angles. During the contamination process, the EUV reflectivity of the Ru film is found to significantly degrade in the presence of additional secondary electrons from the focusing Ru mirror of the EUV setup. This effect could be explained in the light of a competition between oxidation and carbonization processes on Ru surface. © 2012 SPIE.

World University root node

Physics

Proceedings of SPIE - The International Society for Optical Engineering

Mirror contamination and secondary electron effects during EUV reflectivity analysis

The impact of secondary electrons induced contamination of the Ru surface was investigated. Mirror-like Ru sample was bombarded with low energy (100 eV) electrons and the change in surface chemistry was investigated using Xray photoelectron spectroscopy (XPS).Along with XPS studies the corresponding effect on in-situ EUV reflectivity was examined by exposing the Ru surface to photons at a wavelength of 13.5 nm in an ultrahigh vacuum chamber. Detailed XPS analyses showed a sudden increase in carbon concentrations on the Ru surface in the first 60 min, followed by a slow but linear growth in carbon concentration. In parallel, a noticeable decrease in water content was observed during the time of electrons irradiation along with slight oxidation of pure Ru surface. All chemical changes were discussed in terms of the electrons bombardment mediated dissociation of water and hydrocarbon molecules. A time dependent EUV reflectivity measurements show insignificant change in reflectivity up to 510 min of electrons bombardment. The impact of water molecules on the Ru surface and the accumulation of carbon through dissociation of residual hydrocarbons is discussed in details. © 2012 SPIE.

Low energy electron bombardment induced surface contamination of Ru mirrors

Telomeric ends of chromosomes, which comprise noncoding repeat sequences of guanine-rich DNA, which are the fundamental in protecting the cell from recombination and degradation. Telomeric DNA sequences can form four stranded quadruplex structures, which are involved in the structure of telomere ends. The formation and stabilization of telomeric quadruplexes has been shown to inhibit the activity of telomerase, thus establishing telomeric DNA quadrulex as an attractive target for cancer therapeutic intervention. Molecular dynamic simulation offers the prospects of detailed description of the dynamical structure with ion and water at molecular level. In this work we have taken a oligomeric part of human telomeric DNA, d(TAGGGT) to form different monomeric quadruplex structures d(TAGGGT) 4. Here we report the relative stabilities of these structures under K+ ion conditions and binding interaction between the strands, as determined by molecular dynamic simulations followed by energy calculation. We have taken locked nucleic acid (LNA) in this study. The free energy molecular mechanics Poission Boltzman surface area calculations are performed for the determination of most stable complex structure between all modified structures. We calculated binding free energy for the combination of different strands as the ligand and receptor for all structures. The energetic study shows that, a mixed hybrid type quadruplex conformation in which two parallel strands are bind with other two antiparallel strands, are more stable than other conformations. The possible mechanism for the inhibition of the cancerous growth has been discussed. Such studies may be helpful for the rational drug designing. © Springer Science+Business Media B.V. 2012.

Journal of Computer-Aided Molecular Design

Stability and free energy calculation of LNA modified quadruplex: A molecular dynamics study

Abl kinase plays a decisive role in the mechanism of the most fatal human pathogen chronic mylogenous leukemia (CML). Here, we have carried out a comprehensive study about the conformational flexibility, role of salt bridge and the protein- ligand interaction for this kinase with its well-known inhibitor, Imatinib. We have performed molecular dynamics simulations for conformational behavior, investigated the salt bridges and calculated the binding free energy of Imatinib with MM-PB/SA method for Abl kinase complex. We also explored the role of salt-bridge in the kinase complex and its effect on binding activity of inhibitors. Furthermore, to investigate the importance of those residues which form salt bridges, we mutated them by Alanine with the help of Alanine scanning program. We noticed significant variations in total free energy of Imatinib in all possible mutations. The binding free energy of ligand for kinase receptor was analyzed by molecular mechanics Poission Boltzmann surface area (MM-PB/SA) method. These results suggest that conserved glutamic acid and lysine are necessary for stability of complex. © Springer-Verlag 2011.

Journal of Molecular Modeling

Conformational flexibility, binding energy, role of salt bridge and alanine-mutagenesis for c-Abl kinase complex

Semiconducting transition metal dichalcogenides (TMDs) are emerging as the potential alternatives to graphene. As in the case of graphene, the monolayer of TMDs can easily be exfoliated using mechanical or chemical methods, and their properties can also be tuned. At the same time, semiconducting TMDs (MX 2; M = Mo, W and X = S, Se, Te) possess an advantage over graphene in that they exhibit a band gap whose magnitude is appropriate for applications in the opto-electronic devices. Using ab initio simulations, we demonstrate that this band gap can be widely tuned by applying mechanical strains. While the electronic properties of graphene remain almost unaffected by tensile strains, we find TMDs to be sensitive to both tensile and shear strains. Moreover, compared to that of graphene, a much smaller amount of strain is required to vary the band gap of TMDs. Our results suggest that mechanical strains reduce the band gap of semiconducting TMDs causing an direct-to-indirect band gap and a semiconductor-to-metal transition. These transitions, however, significantly depend on the type of applied strain and the type of chalcogenide atoms. The diffuse nature of heavier chalcogenides require relatively more tensile and less shear strain (when the monolayer is expanded in y-direction and compressed in x-direction) to attain a direct-to-indirect band gap transition. In addition, our results demonstrate that the homogeneous biaxial tensile strain of around 10% leads to semiconductor-to-metal transition in all semiconducting TMDs, while through pure shear strain this transition can only be achieved by expanding and compressing the monolayer of MTe 2 in the y- and x-directions, respectively. Our results highlight the importance of tensile and pure shear strains in tuning the electronic properties of TMDs by illustrating a substantial impact of the strain on going from MS 2 to MSe 2 to MTe 2. © 2012 American Chemical Society.

ACS Nano

Tuning the electronic properties of semiconducting transition metal dichalcogenides by applying mechanical strains

We report a Ni impurity induced reversible ferromagnetism and surface conduction in rutile TiO 2 crystals subjected to specific thermal annealing. For annealing in vacuum at 800 °C, a growing ferromagnetic signal is seen with time while for a similar annealing in air, the magnetism vanishes. The magnetism is concomitant with a surface conductivity which at low temperatures shows tunneling characteristics. Here, we show that Ni magnetic impurity (in TiO 2 crystals at &lt;100 ppm) under vacuum annealing segregates to the surface over a 50 nm layer where the Ni concentration exceeds 10-20 and drops with subsequent air annealing. © 2012 American Institute of Physics.

Fulltext

Applied Physics Letters

Reversible ferromagnetism in rutile TiO 2 single crystals induced by nickel impurities

Furan substituted diketopyrrolopyrrole (DBF) combined with benzothiadiazole based polymer semiconductor PDPP-FBF has been synthesized and evaluated as an ambipolar semiconductor in organic thin-film transistors. Hole and electron mobilities as high as 0.20 cm2 V−1 s−1 and 0.56 cm2 V−1 s−1, respectively, are achieved for PDPP-FBF. © 2012 The Royal Society of Chemistry.

Chemical Communications

A furan-containing conjugated polymer for high mobility ambipolar organic thin film transistors

A new diketopyrrolopyrrole (DPP)-containing donor-acceptor polymer, poly(2,5-bis(2-octyldodecyl)-3,6-di(furan-2-yl)-2,5-dihydro-pyrrolo[3,4-c] pyrrole-1,4-dione-co-thieno[3,2-b]thiophene) (PDBF-co-TT), is synthesized and studied as a semiconductor in organic thin film transistors (OTFTs) and organic photovoltaics (OPVs). High hole mobility of up to 0.53 cm 2 V -1 s -1 in bottom-gate, top-contact OTFT devices is achieved owing to the ordered polymer chain packing and favoured chain orientation, strong intermolecular interactions, as well as uniform film morphology of PDBF-co-TT. The optimum band gap of 1.39 eV and high hole mobility make this polymer a promising donor semiconductor for the solar cell application. When paired with a fullerene acceptor, PC 71BM, the resulting OPV devices show a high power conversion efficiency of up to 4.38\% under simulated standard AM1.5 solar illumination. © 2012 the Owner Societies.

Physical Chemistry Chemical Physics

Poly(2,5-bis(2-octyldodecyl)-3,6-di(furan-2-yl)-2,5-dihydro-pyrrolo[3,4-c] pyrrole-1,4-dione-co-thieno[3,2-b]thiophene): A high performance polymer semiconductor for both organic thin film transistors and organic photovoltaics

Background: The adolescent girls are more vulnerable, particularly in developing countries including India, due to various adverse socio-cultural and economic reasons. Majority of the health problems affecting adolescent girls are preventable by promotion of hygienic practices through proper health education by the teachers. Aim: This study was designed to examine the various factors influencing the prevalence of morbidity among school-going adolescent girls of Lucknow district in north India. Materials and Methods: A cross-sectional study was carried out in urban and rural schools of Lucknow district from 2008 to 2009. Multistage random sampling was used to select the requisite number of girls. A total of 847 adolescent girls between 10 and 19 years of age were interviewed, and information regarding their socio-demographic characteristics was collected and clinical examination was carried out. Statistical analyses were done using percentage and Chi-square test. Results: Of 847 adolescent girls, around 64.8% were found to be sick at the time of the study. Significant association of morbidity was observed with caste, birth order, type of family, socioeconomic status (SES), living status with parents/guardian, and general personal hygiene (P<0.05). Conclusion: This study reveals a high prevalence of morbidity. A strong need exists for planning and programming intervention activities for health needs in the area.