Approximate ab initio calculations and the method of molecular fragments

A two stage approach to performing ab initio calculations on medium and large sized molecules is described. The first step is to perform SCF calculations on small molecules or molecular fragments using the OPIT Program. This employs a small basis set of spherical and p-type Gaussian functions. The Gaussian functions can be identified very closely with atomic cores, bond pairs, lone pairs, etc. The position and exponent of any of the Gaussian functions can be varied by OPIT to produce a small but fully optimised basis set. The second stage is the molecular fragments method. As an example of this, Gaussian exponents and distances are taken from an OPIT calculation on ethylene and used unchanged in a single SCF calculation on benzene. Approximate ab initio calculations of this type give much useful information and are often preferable to semi-empirical approaches, since the nature of the approximations involved is much better defined.

Anomalous transport in plasmas

The application of stochastic methods to the problem of particle and energy transport in turbulent plasmas is briefly reviewed. The "classical" Corrsin approximation is shown to be valid only in the limit of weak turbulence. The recently developed method of decorrelation trajectories is applicable over the whole range of turbulence intensities and yields the correct asymptotic behavior in the limit of very strong turbulence (subdiffusion). © 2004 Wiley Periodicals, Inc.

Distribution of neutral prilocaine in a phospholipid bilayer: Insights from molecular dynamics simulations

In this work, we report a 20-ns constant pressure molecular dynamics simulation of prilocaine (PLC), in amine-amide local anesthetic, in a hydrated liquid crystal bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine. The partition of PLC induces the lateral expansion of the bilayer and a concomitant contraction in its thickness. PLC molecules are preferentially found in the hydrophobic acyl chains region, with a maximum probability at similar to 12 angstrom from the center of the bilayer (between the C(4) and C(5) methylene groups). A decrease in the acyl chain segmental order parameter, vertical bar S-CD vertical bar, compared to neat bilayers, is found, in good agreement with experimental H-2-NMR studies. The decrease in vertical bar S-CD vertical bar induced by PLC is attributed to a larger accessible volume per lipid in the acyl chain region. (C) 2008 Wiley Periodicals, Inc.

Evaluation of the conductor-like screening model for real solvents for the prediction of the water activity coefficient at infinite dilution in ionic liquids

Ionic liquids (ILs) have attracted great attention, from both industry and academia, as alternative fluids for very different types of applications. The large number of cations and anions allow a wide range of physical and chemical characteristics to be designed. However, the exhaustive measurement of all these systems is impractical, thus requiring the use of a predictive model for their study. In this work, the predictive capability of the conductor-like screening model for real solvents (COSMO-RS), a model based on unimolecular quantum chemistry calculations, was evaluated for the prediction water activity coefficient at infinite dilution, gamma(infinity)(w), in several classes of ILs. A critical evaluation of the experimental and predicted data using COSMO-RS was carried out. The global average relative deviation was found to be 27.2%, indicating that the model presents a satisfactory prediction ability to estimate gamma(infinity)(w) in a broad range of ILs. The results also showed that the basicity of the ILs anions plays an important role in their interaction with water, and it considerably determines the enthalpic behavior of the binary mixtures composed by Its and water. Concerning the cation effect, it is possible to state that generally gamma(infinity)(w) increases with the cation size, but it is shown that the cation-anion interaction strength is also important and is strongly correlated to the anion ability to interact with water. The results here reported are relevant in the understanding of ILs-water interactions and the impact of the various structural features of its on the gamma(infinity)(w) as these allow the development of guidelines for the choice of the most suitable lLs with enhanced interaction with water.

Triple resonance, triple-quantum NMR studies of dipolar coupled spin systems

Multiple quantum-single quantum correlation experiments are employed for spectral simplification and determination of the relative signs of the couplings. In this study, we have demonstrated the excitation of three nuclei, triple quantum coherences and discussed the information obtainable from such experiments. The experiments have been carried out on doubly labeled acetonitrile and fluoroacetonitrile aligned in liquid crystalline media. The experiment is advantageous in providing many spectral parameters from a single experiment. The coherence pathways involved in the pulse sequence are described using product operators. (C) 2011 Elsevier Inc. All rights reserved.

Long-Range Visible Fluorescence Tunability Using Component-Modulated Coupled Quantum Dots

A simple route for tailoring emissions in the visible wavelength region by chemically coupling quantum dots composed of ZnSe and CdS is reported. coupled quantum dots offer a novel route for tuning electronic transitions via band-offset engineering at the material interface. This novel class of asymmetric. coupled quantum structures may offer a basis for a diverse set of building blocks for optoelectronic devices, ultrahigh density memories, and quantum information processing.

Selective excitation and detection of maximum quantum coherence of a group of scalar coupled protons in chiral molecules: an NMR experiment for enantiodiscrimination

The H-1 NMR spectroscopic discrimination of enantiomers in the solution state and the measurement of enantiomeric composition is most often hindered due to either very small chemical shift differences between the discriminated peaks or severe overlap of transitions from other chemically non-equivalent protons. In addition the use of chiral auxiliaries such as, crown ether and chiral lanthanide shift reagent may often cause enormous line broadening or give little degree of discrimination beyond the crown ether substrate ratio, hampering the discrimination. In circumventing such problems we are proposing the utilization of the difference in the additive values of all the chemical shifts of a scalar coupled spin system. The excitation and detection of appropriate highest quantum coherence yields the measurable difference in the frequencies between two transitions, one pertaining to each enantiomer in the maximum quantum dimension permitting their discrimination and the F-2 cross section at each of these frequencies yields an enantiopure spectrum. The advantage of the utility of the proposed method is demonstrated on several chiral compounds where the conventional one dimensional H-1 NMR spectra fail to differentiate the enantiomers.

Seawater carbonate chemistry and calcium carbonate of Padina spp., photosynthesis of Padina pavonica in nature CO2 gradients experiment

Predicting the impacts of ocean acidification on coastal ecosystems requires an understanding of the effects on macroalgae and their grazers, as these underpin the ecology of rocky shores. Whilst calcified coralline algae (Rhodophyta) appear to be especially vulnerable to ocean acidification, there is a lack of information concerning calcified brown algae (Phaeophyta), which are not obligate calcifiers but are still important producers of calcium carbonate and organic matter in shallow coastal waters. Here, we compare ecological shifts in subtidal rocky shore systems along CO2 gradients created by volcanic seeps in the Mediterranean and Papua New Guinea, focussing on abundant macroalgae and grazing sea urchins. In both the temperate and tropical systems the abundances of grazing sea urchins declined dramatically along CO2 gradients. Temperate and tropical species of the calcifying macroalgal genus Padina (Dictyoaceae, Phaeophyta) showed reductions in CaCO3 content with CO2 enrichment. In contrast to other studies of calcified macroalgae, however, we observed an increase in the abundance of Padina spp. in acidified conditions. Reduced sea urchin grazing pressure and significant increases in photosynthetic rates may explain the unexpected success of decalcified Padina spp. at elevated levels of CO2. This is the first study to provide a comparison of ecological changes along CO2 gradients between temperate and tropical rocky shores. The similarities we found in the responses of Padina spp. and sea urchin abundance at several vent systems increases confidence in predictions of the ecological impacts of ocean acidification over a large geographical range.

Sensitivity of the NMR density matrix to pulse sequence parameters : a simplified analytic approach

We present a formalism for the analysis of sensitivity of nuclear magnetic resonance pulse sequences to variations of pulse sequence parameters, such as radiofrequency pulses, gradient pulses or evolution delays. The formalism enables the calculation of compact, analytic expressions for the derivatives of the density matrix and the observed signal with respect to the parameters varied. The analysis is based on two constructs computed in the course of modified density-matrix simulations: the error interrogation operators and error commutators. The approach presented is consequently named the Error Commutator Formalism (ECF). It is used to evaluate the sensitivity of the density matrix to parameter variation based on the simulations carried out for the ideal parameters, obviating the need for finite-difference calculations of signal errors. The ECF analysis therefore carries a computational cost comparable to a single density-matrix or product-operator simulation. Its application is illustrated using a number of examples from basic NMR spectroscopy. We show that the strength of the ECF is its ability to provide analytic insights into the propagation of errors through pulse sequences and the behaviour of signal errors under phase cycling. Furthermore, the approach is algorithmic and easily amenable to implementation in the form of a programming code. It is envisaged that it could be incorporated into standard NMR product-operator simulation packages.

Si quantum dots embedded in an amorphous SiC matrix : nanophase control by non-equilibrium plasma hydrogenation

Nanophase nc-Si/a-SiC films that contain Si quantum dots (QDs) embedded in an amorphous SiC matrix were deposited on single-crystal silicon substrates using inductively coupled plasma-assisted chemical vapor deposition from the reactive silane and methane precursor gases diluted with hydrogen at a substrate temperature of 200 °C. The effect of the hydrogen dilution ratio X (X is defined as the flow rate ratio of hydrogen-to-silane plus methane gases), ranging from 0 to 10.0, on the morphological, structural, and compositional properties of the deposited films, is extensively and systematically studied by scanning electron microscopy, high-resolution transmission electron microscopy, X-ray diffraction, Raman spectroscopy, Fourier-transform infrared absorption spectroscopy, and X-ray photoelectron spectroscopy. Effective nanophase segregation at a low hydrogen dilution ratio of 4.0 leads to the formation of highly uniform Si QDs embedded in the amorphous SiC matrix. It is also shown that with the increase of X, the crystallinity degree and the crystallite size increase while the carbon content and the growth rate decrease. The obtained experimental results are explained in terms of the effect of hydrogen dilution on the nucleation and growth processes of the Si QDs in the high-density plasmas. These results are highly relevant to the development of next-generation photovoltaic solar cells, light-emitting diodes, thin-film transistors, and other applications.

Ge/Si quantum dot formation from non-uniform cluster fluxes

The controlled growth of ultra-small Ge/Si quantum dot (QD) nuclei (≈1 nm) suitable for the synthesis of uniform nanopatterns with high surface coverage, is simulated using atom-only and size non-uniform cluster fluxes. It is found that seed nuclei of more uniform sizes are formed when clusters of non-uniform size are deposited. This counter-intuitive result is explained via adatom-nanocluster interactions on Si(100) surfaces. Our results are supported by experimental data on the geometric characteristics of QD patterns synthesized by nanocluster deposition. This is followed by a description of the role of plasmas as non-uniform cluster sources and the impact on surface dynamics. The technique challenges conventional growth modes and is promising for deterministic synthesis of nanodot arrays.

Controlling electronic and adiabatic isolation of quantum dots from the substrate : an ionization-energy theoretic study

Recent controversy on the quantum dots dephasing mechanisms (between pure and inelastic) is re-examined by isolating the quantum dots from their substrate by using the appropriate limits of the ionization energy theory and the quantum adiabatic theorem. When the phonons in the quantum dots are isolated adiabatically from the phonons in the substrate, the elastic or pure dephasing becomes the dominant mechanism. On the other hand, for the case where the phonons from the substrate are non-adiabatically coupled to the quantum dots, the inelastic dephasing process takes over. This switch-over is due to different elemental composition in quantum dots as compared to its substrate. We also provide unambiguous analysis as to understand why GaAs/AlGaAs quantum dots may only have pure dephasing while InAs/GaAs quantum dots give rise to the inelastic dephasing as the dominant mechanism. It is shown that the elemental composition plays an important role (of both quantum dots and substrate) in evaluating the dephasing mechanisms of quantum dots.

Multiple-quantum artifacts in single-quantum two-dimensional correlated NMR spectra of strongly coupled spins

Artifacts in the form of cross peaks have been observed along two- and three-quantum diagonals in single-quantum two-dimensional correlated (COSY) spectra of several peptides and oligonucleotides. These have been identified as due to the presence of a non-equilibrium state of kind I (a state describable by populations which differ from equilibrium) of strongly coupled spins carried over from one experiment to the next in the COSY algorithm.