Nuclear magnetic resonance chemical shifts with the statistical average of orbital-dependent model potentials in Kohn-Sham density functional theory

The performance of the SAOP potential for the calculation of NMR chemical shifts was evaluated. SAOP results show considerable improvement with respect to previous potentials, like VWN or BP86, at least for the carbon, nitrogen, oxygen, and fluorine chemical shifts. Furthermore, a few NMR calculations carried out on third period atoms (S, P, and Cl) improved when using the SAOP potential

Configurational statistical model for the damaged structure of silicon oxide after ion implantation

A configurational model for silicon oxide damaged after a high-dose ion implantation of a nonreactive species is presented. Based on statistics of silicon-centered tetrahedra, the model takes into account not only the closest environment of a given silicon atom, but also the second neighborhood, so it is specified whether the oxygen attached to one given silicon is bridging two tetrahedra or not. The frequencies and intensities of infrared vibrational bands have been calculated by averaging over the distributions and these results are in agreement with the ones obtained from infrared experimental spectra. Likewise, the chemical shifts obtained from x-ray photoelectron spectroscopy (XPS) analysis are similar to the reported values for the charge-transfer model of SiOx compounds.

A chemical Hamiltonian approach study of the basis set superposition error changes on electron densities and one- and two-center energy components

A comparision of the local effects of the basis set superposition error (BSSE) on the electron densities and energy components of three representative H-bonded complexes was carried out. The electron densities were obtained with Hartee-Fock and density functional theory versions of the chemical Hamiltonian approach (CHA) methodology. It was shown that the effects of the BSSE were common for all complexes studied. The electron density difference maps and the chemical energy component analysis (CECA) analysis confirmed that the local effects of the BSSE were different when diffuse functions were present in the calculations

Microscopic calculations of the excitation spectrum of one 3He impurity in liquid 4He

We calculate the chemical potential ¿0 and the effective mass m*/m3 of one 3He impurity in liquid 4He. First a variational wave function including two- and three-particle dynamical correlations is adopted. Triplet correlations bring the computed values of ¿0 very close to the experimental results. The variational estimate of m*/m3 includes also backflow correlations between the 3He atom and the particles in the medium. Different approximations for the three-particle distribution function give almost the same values for m*/m3. The variational approach underestimates m*/m3 by ~10% at all of the considered densities. Correlated-basis perturbation theory is then used to improve the wave function to include backflow around the particles of the medium. The perturbative series built up with one-phonon states only is summed up to infinite order and gives results very close to the variational ones. All the perturbative diagrams with two independent phonons have then been summed to compute m*/m3. Their contribution depends to some extent on the form used for the three-particle distribution function. When the scaling approximation is adopted, a reasonable agreement with the experimental results is achieved.

Could cell membranes produce acoustic streaming? Making the case for synechococcus self-propulsion

Sir James Lighthill proposed in 1992 that acoustic streaming occurs in the inner ear, as part of the cochlear amplifier mechanism. Here we hypothesize that some of the most ancient organisms use acoustic streaming not only for self-propulsion but also to enhance their nutrient uptake. We focus on a motile strain of Synechococcus, a yanobacteria whose mechanism for self-propulsion is not known. Molecular motors could work like piezoelectric transducers acting on the crystalline structure surrounding the outer cell membrane. Our calculations show that a traveling surface acoustic wave (SAW)could account for the observed velocities. These SAW waves will also produce a non-negligible Stokes layer surrounding the cell: motion within this region being essentially chaotic. Therefore, an AS mechanism would be biologically advantageous, enhancing localized diffusion processes and consequently, chemical reactions. We believe that acoustic streaming, produced by nanometer scale membrane vibrations could be widespread in cell biology. Other possible instances are yeast cells and erythrocytes. Flows generated by acoustic streaming may also be produced by silica coated diatoms along their raphe. We note that microelectromechanical (MEMS) acoustic streaming devices were first introduced in the 1990’s. Nature may have preceded this invention by 2.7 Gyr.

The nature of the Cr-C bond: direct estimation of aromaticity in Fischer carbenes

Report for the scientific sojourn at the the Philipps-Universität Marburg, Germany, from september to december 2007. For the first, we employed the Energy-Decomposition Analysis (EDA) to investigate aromaticity on Fischer carbenes as it is related through all the reaction mechanisms studied in my PhD thesis. This powerful tool, compared with other well-known aromaticity indices in the literature like NICS, is useful not only for quantitative results but also to measure the degree of conjugation or hyperconjugation in molecules. Our results showed for the annelated benzenoid systems studied here, that electron density is more concentrated on the outer rings than in the central one. The strain-induced bond localization plays a major role as a driven force to keep the more substituted ring as the less aromatic. The discussion presented in this work was contrasted at different levels of theory to calibrate the method and ensure the consistency of our results. We think these conclusions can also be extended to arene chemistry for explaining aromaticity and regioselectivity reactions found in those systems.In the second work, we have employed the Turbomole program package and density-functionals of the best performance in the state of art, to explore reaction mechanisms in the noble gas chemistry. Particularly, we were interested in compounds of the form H--Ng--Ng--F (where Ng (Noble Gas) = Ar, Kr and Xe) and we investigated the relative stability of these species. Our quantum chemical calculations predict that the dixenon compound HXeXeF has an activation barrier for decomposition of 11 kcal/mol which should be large enough to identify the molecule in a low-temperature matrix. The other noble gases present lower activation barriers and therefore are more labile and difficult to be observable systems experimentally.

Avenços en l'estudi de la litiasi renal: mètodes de chemical imaging i intel·ligencia artificial (ANN) per la caracterització de càlculs renals

La litiasi urinària és un trastorn que implica la formació de precipitats en qualsevol part del tracte urinari. Aquest és un desordre comú que afecta aproximadament a una desena part de la població de la Unió Europea al llarg de la seva vida. A més, durant els cinc anys posteriors a un episodi litiàsic el percentatge de recurrència dels pacients és del 45 al 75%. Aquest trastorn urinari està influït per una gran quantitat de variables, d’origen fisiològic, psicològic i ambiental. Els episodis litiàsics, es poden solucionar espontàniament, amb l’expulsió del càlcul renal, o bé a través de diverses intervencions mèdiques. Els tractaments mèdics derivats de la litiasi urinària; és a dir, la fragmentació del càlcul, intervencions quirúrgiques i tractaments posteriors generen unes grans despeses als sistemes mèdics. Pels motius exposats, la identificació del desordre que ha originat l’episodi litiàsic és de radical importància, per tal de minimitzar el risc de reincidència. Els mètodes més usuals per determinar les causes que desencadenen la formació del càlcul renal són les anàlisis d’orina i l’estudi del càlcul generat. La correcta descripció de la composició i, especialment, l’estructura del càlcul renal pot aportar informació clau sobre les possibles causes de la seva formació, tant de l’inici de nucleació del càlcul com de les successives etapes de creixement cristal·lí. Tenint en compte aquest darrer aspecte, el present estudi s’ha dirigit a la caracterització de càlculs urinaris mitjançant l’aplicació de metodologies d’imatge química (Hyperspectral Imaging), el que va contribuir a determinar les principals característiques espectrals de cada compost majoritari als càlculs renals. D’altra banda, la utilització de mostres de composició coneguda ha possibilitat la creació d’un model amb Xarxes Neuronals Artificials, que permet la classificació de noves mostres de composició desconeguda, de manera més ràpida que el procediment actual. Aquest treball constitueix una nova contribució a la comprensió de l’estructura de les pedres de ronyó, així com les condicions de la seva formació. Els resultats obtinguts destaquen les possibilitats que presenten les tècniques emprades al camp de la litiasi renal, que permeten complementar els coneixements existents enfocats a millorar la qualitat de vida dels pacients.

Bandwidth allocation based on real time calculations using the convolution approach

This paper focuses on one of the methods for bandwidth allocation in an ATM network: the convolution approach. The convolution approach permits an accurate study of the system load in statistical terms by accumulated calculations, since probabilistic results of the bandwidth allocation can be obtained. Nevertheless, the convolution approach has a high cost in terms of calculation and storage requirements. This aspect makes real-time calculations difficult, so many authors do not consider this approach. With the aim of reducing the cost we propose to use the multinomial distribution function: the enhanced convolution approach (ECA). This permits direct computation of the associated probabilities of the instantaneous bandwidth requirements and makes a simple deconvolution process possible. The ECA is used in connection acceptance control, and some results are presented

The chemical variability at the surface of Mars: implications for exogenic processes

The chemical composition of sediments and rocks, as well as their distribution at theMartian surface, represent a long term archive of processes, which have formed theplanetary surface. A survey of chemical compositions by means of Compositional DataAnalysis represents a valuable tool to extract direct evidence for weathering processesand allows to quantify weathering and sedimentation rates. clr-biplot techniques areapplied for visualization of chemical relationships across the surface (“chemical maps”).The variability among individual suites of data is further analyzed by means of clr-PCA,in order to extract chemical alteration vectors between fresh rocks and their crusts andfor an assessment of different source reservoirs accessible to soil formation. Bothtechniques are applied to elucidate the influence of remote weathering by combinedanalysis of several soil forming branches. Vector analysis in the Simplex provides theopportunity to study atmosphere surface interactions, including the role andcomposition of volcanic gases

Full Exploration of the Diels–Alder Cycloaddition on Metallofullerenes M3N@C80 (M=Sc, Lu, Gd): The D5h versus Ih Isomer and the Influence of the Metal Cluster

In this work a detailed investigation of the exohedral reactivity of the most important and abundant endohedral metallofullerene (EMF) is provided, that is, Sc3N@Ih-C80 and its D5h counterpart Sc3N@D5h-C80, and the (bio)chemically relevant lutetium- and gadolinium-based M3N@Ih/D5h-C80 EMFs (M=Sc, Lu, Gd). In particular, we analyze the thermodynamics and kinetics of the Diels–Alder cycloaddition of s-cis-1,3-butadiene on all the different bonds of the Ih-C80 and D5h-C80 cages and their endohedral derivatives. First, we discuss the thermodynamic and kinetic aspects of the cycloaddition reaction on the hollow fullerenes and the two isomers of Sc3N@C80. Afterwards, the effect of the nature of the metal nitride is analyzed in detail. In general, our BP86/TZP//BP86/DZP calculations indicate that [5,6] bonds are more reactive than [6,6] bonds for the two isomers. The [5,6] bond D5h-b, which is the most similar to the unique [5,6] bond type in the icosahedral cage, Ih-a, is the most reactive bond in M3N@D5h-C80 regardless of M. Sc3N@C80 and Lu3N@C80 give similar results; the regioselectivity is, however, significantly reduced for the larger and more electropositive M=Gd, as previously found in similar metallofullerenes. Calculations also show that the D5h isomer is more reactive from the kinetic point of view than the Ih one in all cases which is in good agreement with experiments

Study of chemical modification of alkaline lignin by the glyoxalation reaction

In this study, glyoxalated alkaline lignins with a non-volatile and non-toxic aldehyde, which can be obtained from several natural resources, namely glyoxal, were prepared and characterized for its use in wood adhesives. The preparation method consisted of the reaction of lignin with glyoxal under an alkaline medium. The influence of reaction conditions such as the molar ratio of sodium hydroxide-to-lignin and reaction time were studied relative to the properties of the prepared adducts. The analytical techniques used were FTIR and 1H-NMR spectroscopies, gel permeation chromatography (GPC), differential scanning calorimetry (DSC), and thermogravimetric analysis (TGA). Results from both the FTIR and 1H-NMR spectroscopies showed that the amount of introduced aliphatic hydroxyl groups onto the lignin molecule increased with increasing reaction time and reached a maximum value at 10 h, and after they began to decrease. The molecular weights remained unchanged until 10 h of reaction time, and then started to increase, possibly due to the repolymerization reactions. DSC analysis showed that the glass transition temperature (Tg) decreased with the introduction of glyoxal onto the lignin molecule due to the increase in free volume of the lignin molecules. TGA analysis showed that the thermal stability of glyoxalated lignin is not influenced and remained suitable for wood adhesives. Compared to the original lignin, the improved lignin is reactive and a suitable raw material for adhesive formula

Automatic generation of active coordinates for quantum dynamics calculations: application to the dynamics of benzene photochemistry

A new practical method to generate a subspace of active coordinates for quantum dynamics calculations is presented. These reduced coordinates are obtained as the normal modes of an analytical quadratic representation of the energy difference between excited and ground states within the complete active space self-consistent field method. At the Franck-Condon point, the largest negative eigenvalues of this Hessian correspond to the photoactive modes: those that reduce the energy difference and lead to the conical intersection; eigenvalues close to 0 correspond to bath modes, while modes with large positive eigenvalues are photoinactive vibrations, which increase the energy difference. The efficacy of quantum dynamics run in the subspace of the photoactive modes is illustrated with the photochemistry of benzene, where theoretical simulations are designed to assist optimal control experiments

Determination of vibrational polarizabilities and hyperpolarizabilities using field-induced coordinates

An analytical set of field-induced coordinates is defined and is used to show that the vibrational degrees of freedom required to completely describe nuclear relaxation polarizabilities and hyperpolarizabilities is reduced from 3N-6 to a relatively small number. As this number does not depend upon the size of the molecule, the process provides computational advantages. A method is provided to separate anharmonic contributions from harmonic contributions as well as effective mechanical from electrical anharmonicity. The procedures are illustrated by Hartree-Fock calculations, indicating that anharmonicity can be very important

Electron localization function at the correlated level

The electron localization function (ELF) has been proven so far a valuable tool to determine the location of electron pairs. Because of that, the ELF has been widely used to understand the nature of the chemical bonding and to discuss the mechanism of chemical reactions. Up to now, most applications of the ELF have been performed with monodeterminantal methods and only few attempts to calculate this function for correlated wave functions have been carried out. Here, a formulation of ELF valid for mono- and multiconfigurational wave functions is given and compared with previous recently reported approaches. The method described does not require the use of the homogeneous electron gas to define the ELF, at variance with the ELF definition given by Becke. The effect of the electron correlation in the ELF, introduced by means of configuration interaction with singles and doubles calculations, is discussed in the light of the results derived from a set of atomic and molecular systems