Molecular theory of solvation and solvation dynamics of a classical ion in a dipolar liquid

A microscopic theory of equilibrium solvation and solvation dynamics of a classical, polar, solute molecule in dipolar solvent is presented. Density functional theory is used to explicitly calculate the polarization structure around a solvated ion. The calculated solvent polarization structure is different from the continuum model prediction in several respects. The value of the polarization at the surface of the ion is less than the continuum value. The solvent polarization also exhibits small oscillations in space near the ion. We show that, under certain approximations, our linear equilibrium theory reduces to the nonlocal electrostatic theory, with the dielectric function (c(k)) of the liquid now wave vector (k) dependent. It is further shown that the nonlocal electrostatic estimate of solvation energy, with a microscopic c(k), is close to the estimate of linearized equilibrium theories of polar liquids. The study of solvation dynamics is based on a generalized Smoluchowski equation with a mean-field force term to take into account the effects of intermolecular interactions. This study incorporates the local distortion of the solvent structure near the ion and also the effects of the translational modes of the solvent molecules.The latter contribution, if significant, can considerably accelerate the relaxation of solvent polarization and can even give rise to a long time decay that agrees with the continuum model prediction. The significance of these results is discussed.

KO2: Realization of Orbital Ordering in a p-Orbital System

KO2 is a molecular solid consisting of oxygen dimers. K present in the lattice donates an electron which goes on to occupy the O p levels.As the basic electronic structure is similar to that of an oxygen molecule, except for broadening due to solid state effects, KO2 represents the realization of the doping of oxygen molecules arranged in a lattice. These considerations alone result in magnetism with high ordering temperatures as our calculations reveal. However, we find that the high temperature structure is unstable to an orbital ordering (OO) transition. The microscopic considerations driving the OO transition, however, are electrostatic interactions instead of the often encountered superexchange driven ordering within the Kugel-Khomskii model often used to describe the OO. This OO transition is also found to preclude any possibility of high magnetic ordering temperatures, which otherwise seemed possible.

Topological analysis off charge density distribution in concomitant polymorphs of 3-acetylcoumarin, a case off packing polymorphism

Detailed investigation of the charge density distribution in concomitant polymorphs of 3-acetylcoumarin in terms of experimental and theoretical densities shows significant differences in the intermolecular features when analyzed based on the topological properties via the quantum theory of atoms in molecules. The two forms, triclinic and monoclinic (Form A and Form B), pack in the crystal lattice via weak C-H---O and C-H---pi interactions. Form A results in a head-to-head molecular stack, while Form B generates a head-to-tail stack. Form A crystallizes in PI (Z' = 2) and Form B crystallizes in P2(1)/n (Z = 1). The electron density maps of the polymorphs demonstrate the differences in the nature of the charge density distribution in general. The charges derived from experimental and theoretical analysis show significant differences with respect to the polymorphic forms. The molecular dipole moments differ significantly for the two forms. The lattice energies evaluated at the HF and DFT (B3LYP) methods with 6-31G** basis set for the two forms clearly suggest that Form A is the thermodynamically stable form as compared to Form B. Mapping of electrostatic potential over the molecular surface shows dominant variations in the electronegative region, which bring out the differences between the two forms.

Interaction between the Z-type DNA duplex and 1,3-propanediamine:crystal structure of d(CACGTG)(2) at 1.2 angstrom resolution

The crystal structure of a hexamer duplex d(CACGTG)(2) has been determined and refined to an R-factor of 18.3% using X-ray data up to 1.2 angstrom resolution. The sequence crystallizes as a left-handed Z-form double helix with Watson-Crick base pairing. There is one hexamer duplex, a spermine molecule, 71 water molecules, and an unexpected diamine (Z-5, 1,3-propanediamine, C3H10N2)) in the asymmetric unit. This is the high-resolution non-disordered structure of a Z-DNA hexamer containing two AT base pairs in the interior of a duplex with no modifications such as bromination or methylation on cytosine bases. This structure does not possess multivalent cations such as cobalt hexaammine that are known to stabilize Z-DNA. The overall duplex structure and its crystal interactions are similar to those of the pure-spermine form of the d(CGCGCG)(2) structure. The spine of hydration in the minor groove is intact except in the vicinity of the T5A8 base pair. The binding of the Z-5 molecule in the minor grove of the d(CACGTG)(2) duplex appears to have a profound effect in conferring stability to a Z-DNA conformation via electrostatic complementarity and hydrogen bonding interactions. The successive base stacking geometry in d(CACGTG)(2) is similar to the corresponding steps in d(CG)(3). These results suggest that specific polyamines such as Z-5 could serve as powerful inducers of Z-type conformation in unmodified DNA sequences with AT base pairs. This structure provides a molecular basis for stabilizing AT base pairs incorporated into an alternating d(CG) sequence.

Characterization of compact ICP ion source for focused ion beam applications

A compact, high brightness 13.56 MHz inductively coupled plasma ion source without any axial or radial multicusp magnetic fields is designed for the production of a focused ion beam. Argon ion current of density more than 30 mA/cm(2) at 4 kV potential is extracted from this ion source and is characterized by measuring the ion energy spread and brightness. Ion energy spread is measured by a variable-focusing retarding field energy analyzer that minimizes the errors due t divergence of ion beam inside the analyzer. Brightness of the ion beam is determined from the emittance measured by a fully automated and locally developed electrostatic sweep scanner. By optimizing various ion source parameters such as RF power, gas pressure and Faraday shield, ion beams with energy spread of less than 5 eV and brightness of 7100 Am(-2)sr(-1)eV(-1) have been produced. Here, we briefly report the details of the ion source, measurement and optimization of energy spread and brightness of the ion beam. (C) 2010 Elsevier B.V. All rights reserved.

A MAS NMR investigation of aluminosilicate, silicophosphate, and aluminosilicophosphate gels and the evolution of crystalline structures on heating the gels

Gels of various composition containing SiO2, Al2O3, and P2O5 have been investigated by employing high resolution magic-angle-spinning (MAS) 27Al, 29Si, and 31P NMR spectroscopy. Changes occurring in the NMR spectra as the gels are progressively heated have been examined to understand the nature of structural changes occurring during the crystallization of the gels. 27Al resonance is sensitive to changes in the coordination number even when the Al concentration is as low as 1 mol%. As the percentage of Al increases, the hydroxyl groups tend to be located on the Al sites while Si remains as SiO4/2 (Q4). Mullite is the major phase formed at higher temperature in the aluminosilicate gels. In the case of the silicophosphate gels, Si is present in the form of Q4 and Q3 species. There is a change in the coordination of Si from four to six as the gel is heated. The formation of six-coordinated Si is facilitated even at lower temperatures (~673 K) when the P2O5 content is high. The phosphorus atoms present as orthophosphoric acid units in the xerogels change over to metaphosphate-like units as the gel is heated to higher temperatures. In aluminosilicophosphates, Si is present as Q4 and Q3 species while P is present as metaphosphate units; Al in these gels seems to be inducted into the tetrahedral network positions.

Performance study of high operating temperature HgCdTe mid wave infrared detector through numerical modeling

The design of present generation uncooled Hg1-xCdxTe infrared photon detectors relies on complex heterostructures with a basic unit cell of type (n) under bar (+)/pi/(p) under bar (+). We present an analysis of double barrier (n) under bar (+)/pi/(p) under bar (+) mid wave infrared (x = 0.3) HgCdTe detector for near room temperature operation using numerical computations. The present work proposes an accurate and generalized methodology in terms of the device design, material properties, and operation temperature to study the effects of position dependence of carrier concentration, electrostatic potential, and generation-recombination (g-r) rates on detector performance. Position dependent profiles of electrostatic potential, carrier concentration, and g-r rates were simulated numerically. Performance of detector was studied as function of doping concentration of absorber and contact layers, width of both layers and minority carrier lifetime. Responsivity similar to 0.38 A W-1, noise current similar to 6 x 10(-14) A/Hz(1/2) and D* similar to 3.1 x 10(10)cm Hz(1/2) W-1 at 0.1 V reverse bias have been calculated using optimized values of doping concentration, absorber width and carrier lifetime. The suitability of the method has been illustrated by demonstrating the feasibility of achieving the optimum device performance by carefully selecting the device design and other parameters. (C) 2010 American Institute of Physics. doi:10.1063/1.3463379]

Thermoelectric properties of electrostatically tunable antidot lattices

We report on the fabrication and characterization of a device which allows the formation of an antidot lattice (ADL) using only electrostatic gating. The antidot potential and Fermi energy of the system can be tuned independently. Well defined commensurability features in magnetoresistance as well as magnetothermopower are observed. We show that the thermopower can be used to efficiently map out the potential landscape of the ADL. (C) 2010 American Institute of Physics. doi: 10.1063/1.3493268]

Crystal structure of hexanediamine-glutamic acid complex

Polyamines are some of the most important and ubiquitous small molecules that modulate several functions of plant, animal and bacterial cells. Despite the simplicity of their chemical structure, their specific interactions with other biomolecules cannot be explained solely on the basis of their electrostatic properties. To evolve a structural understanding on the specificity of these interactions it is necessary to determine the structure of complexes of polyamines with other, representative biomolecules. This paper reports the structure of the 1:2 complex of hexanediamine and L-glutamic acid. The complex crystallizes in the monoclonic space group P2(1) with a = 5.171(1) angstrom, b = 22.044(2) angstrom, c = 10.181(2) angstrom and beta = 104.51(1)-degrees. The structure was refined to an R factor of 6.6%. The structures of these complexes not only suggest the importance of hydrogen-bonding interactions of polyamines but also provide some insight into other complementary interactions probably important for the specificity of biomolecular interactions.

Design and fabrication of an indigenous molecular beam ultraviolet photoelectron spectrometer

An ultraviolet photoelectron spectrometer for the study of van der Waals molecules has been designed and fabricated indigenously. The spectrometer consists of an HeI discharge lamp, a molecular beam sample inlet system, an electrostatic lens, a 180-degrees hemispherical electrostatic analyser and a channeltron detector. Performance of the spectrometer is illustrated with an example.

Heterogeneous nucleation of solidification of cadmium particles embedded in an aluminium matrix

A hypomonotectic alloy of Al-4.5wt%Cd has been manufactured by melt spinning and the resulting microstructure examined by transmission electron microscopy. As-melt spun hypomonotectic Al-4.5wt%Cd consists of a homogeneous distribution of faceted 5 to 120 nm diameter cadmium particles embedded in a matrix of aluminium, formed during the monotectic solidification reaction. The cadmium particles exhibit an orientation relationship with the aluminium matrix of {111}Al//{0001}Cd and lang110rangAlAl//lang11¯20> Cd, with four cadmium particle variants depending upon which of the four {111}Al planes is parallel to {0001}Cd. The cadmium particles exibit a distorted cuboctahedral shape, bounded by six curved {100}Al//{20¯23}Cd facets, six curved {111}Al/{40¯43}Cd facets and two flat {111}Al//{0001}Cd facets. The as-melt spun cadmium particle shape is metastable and the cadmium particles equilibrate during heat treatment below the cadmium melting point, becoming elongated to increase the surface area and decrease the separation of the {111}Al//{0001}Cd facets. The equilibrium cadmium particle shape and, therefore, the anisotropy of solid aluminium-solid cadmium and solid aluminium -liquid cadmium surface energies have been monitored by in situ heating in the transmission electron microscope over the temperature range between room temperature and 420 °C. The anisotropy of solid aluminium-solid cadmium surface energy is constant between room temperature and the cadmium melting point, with the {100}Al//{20¯23}Cd surface energy on average 40% greater than the {111}Al//{0001}Cd surface energy, and 10% greater than the {111}Al//{40¯43Cd surface energy. When the cadmium particles melt at temperatures above 321 °C, the {100}Al//{20¯23}Cd facets disappear and the {111}Al//{40¯43}Cd and {111}A1//{0001}Cd surface energies become equal. The {111}Al facets do not disappear when the cadmium particles melt, and the anisotropy of solid aluminium-liquid cadmium surface energy decreases gradually with increasing temperature above the cadmium melting point. The kinetics of cadmium solidification have been examined by heating and cooling experiments in a differential scanning calorimeter over a range of heating and cooling rates. Cadmium particle solidification is nucleated catalytically by the surrounding aluminium matrix on the {111}Al faceted surfaces, with an undercooling of 56 K and a contact angle of 42 °. The nucleation kinetics of cadmium particle solidification are in good agreement with the hemispherical cap model of heterogeneous nucleation.

Ions in water: Role of attractive interactions in size dependent diffusivity maximum

A molecular dynamics study of model ions in water is reported. The van der Waals diameter of both the cations and anions is varied. We have carried out two sets of simulations-with and without dispersion interaction-between the ion and water. Self-diffusivity of the ions exhibits an anomalous maximum as a function of the van der Waals diameter for both these sets. This existence of a maximum in self-diffusivity when there is no dispersion interaction between the ion and the water is attributed to the attractive term from electrostatic interactions. Detailed analysis of this effect shows that the solvent shell is more strongly defined in the presence of dispersion interactions. A smaller ion exhibits biexponential decay while a single exponential decay is seen for the ion with maximum diffusivity in the self-part of the intermediate scattering function. The solvent structure around the ion appears to determine much of the dynamics of the ion. Interesting trends are seen in the activation energies and these can be understood in terms of the levitation effect. (C) 2010 American Institute of Physics. doi:10.1063/1.3481656]

Sign Of The Order Parameter In Oriented Systems And Its Utility In The Study Of The Dynamic Properties Of Molecules

Novel one and two dimensional NMR techniques are proposed and utilized for the determination of the signs of the order parameters used for the study of the mobility of the fatty acid chains. The experiments designed to extract this information involve the use of the intensities of the side bands in the spectra of oriented systems spinning at the magic angle. Advantages of the two dimensional technique over the one dimensional method are discussed. The utility of the method in the study of the dynamic properties of membranes and model systems is pointed out.

Interactions of tris buffer with nucleotides: the crystal structure of tris(hydroxymethyl)methylammonium adenosine 5'-diphosphate dihydrate

The crystal and molecular structures of the Tris salt of adenosine 5'-diphosphate were determined from X-ray diffraction data. The crystals are monoclinic, space P21, and Z = 2 with a=9.198 (2) A, b=6.894 (1) A, c=18.440 (4) A, and beta = 92.55 (2) degrees. Intensity data were collected on an automated diffractometer. The structure was solved by the heavy-atom technique and refined by least squares to R = 0.047. The ADP molecule adopts a folded conformation. The conformation about the glycosidic bond is anti. The conformation of the ribose ring is close to a perfect C(2')-endo-C-(3')-exo puckering. The conformation about C(4')-C(5') is gauche-gauche, similar to other nucleotide structures. The pyrophosphate chain displays a nearly eclipsed geometry when viewed down the P-P vector, unlike the staggered conformation observed in crystal structures of other pyrophosphates. The less favorable eclipsed conformation probably results from the observed association of Tris molecules with the polar diphosphate chain through electrostatic interactions and hydrogen bonds. Such interactions may play an important role in Tris-buffered aqueous solutions of nucleotides and metal ions.

A nanosecond molecular dynamics study of antiparallel d(G)(7) quadruplex structures: Effect of the coordinated cations

Nanosecond scale molecular dynamics simulations have been performed on antiparallel Greek key type d(G(7)) quadruplex structures with different coordinated ions, namely Na+ and K+ ion, water and Na+ counter ions, using the AMBER force field and Particle Mesh Ewald technique for electrostatic interactions. Antiparallel structures are stable during the simulation, with root mean square deviation values of similar to1.5 Angstrom from the initial structures. Hydrogen bonding patterns within the G-tetrads depend on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate different cations. However, alternating syn-anti arrangement of bases along a chain as well as in a quartet is maintained through out the MD simulation. Coordinated Na+ ions, within the quadruplex cavity are quite mobile within the central channel and can even enter or exit from the quadruplex core, whereas coordinated K+ ions are quite immobile. MD studies at 400 K indicate that K+ ion cannot come out from the quadruplex core without breaking the terminal G-tetrads. Smaller grooves in antiparallel structures are better binding sites for hydrated counter ions, while a string of hydrogen bonded water molecules are observed within both the small and large grooves. The hydration free energy for the K+ ion coordinated structure is more favourable than that for the Na+ ion coordinated antiparallel quadruplex structure.