Temperature-induced structural transitions in self-assembling magnetic nanocolloids

With the help of a unique combination of density functional theory and computer simulations, we discover two possible scenarios, depending on concentration, for the hierarchical self-assembly of magnetic nanoparticles on cooling. We show that typically considered low temperature clusters, i.e. defect-free chains and rings, merge into more complex branched structures through only three types of defects: four-way X junctions, three-way Y junctions and two-way Z junctions. Our accurate calculations reveal the predominance of weakly magnetically responsive rings cross-linked by X defects at the lowest temperatures. We thus provide a strategy to fine-tune magnetic and thermodynamic responses of magnetic nanocolloids to be used in medical and microfluidics applications.

Liquid-vapor interfaces of patchy colloids

We investigate the liquid-vapor interface of a model of patchy colloids. This model consists of hard spheres decorated with short-ranged attractive sites ("patches") of different types on their surfaces. We focus on a one-component fluid with two patches of type A and nine patches of type B (2A9B colloids), which has been found to exhibit reentrant liquid-vapor coexistence curves and very low-density liquid phases. We have used the density-functional theory form of Wertheim's first-order perturbation theory of association, as implemented by Yu and Wu [J. Chem. Phys. 116, 7094 (2002)], to calculate the surface tension, and the density and degree of association profiles, at the liquid-vapor interface of our model. In reentrant systems, where AB bonds dominate, an unusual thickening of the interface is observed at low temperatures. Furthermore, the surface tension versus temperature curve reaches a maximum, in agreement with Bernardino and Telo da Gama's mesoscopic Landau-Safran theory [Phys. Rev. Lett. 109, 116103 (2012)]. If BB attractions are also present, competition between AB and BB bonds gradually restores the monotonic temperature dependence of the surface tension. Lastly, the interface is "hairy," i.e., it contains a region where the average chain length is close to that in the bulk liquid, but where the density is that of the vapor. Sufficiently strong BB attractions remove these features, and the system reverts to the behavior seen in atomic fluids.

The key role of coligands in novel ruthenium(II)-cyclopentadienyl bipyridine derivatives: ranging from non-cytotoxic to highly cytotoxic compounds

A new family of eight ruthenium(II)-cyclopentadienyl bipyridine derivatives, bearing nitrogen, sulfur, phosphorous and carbonyl sigma bonded coligands, has been synthesized. Compounds bearing nitrogen bonded coligands were found to be unstable in aqueous solution, while the others presented appropriate stabilities for the biologic assays and pursued for determination of IC50 values in ovarian (A2780) and breast (MCF7 and MDAMB231) human cancer cell lines. These studies were also carried out for the [5: HSA] and [6: HSA] adducts (HSA=human serum albumin) and a better performance was found for the first case. Spectroscopic, electrochemical studies by cyclic voltammetry and density functional theory calculations allowed us to get some understanding on the electronic flow directions within the molecules and to find a possible clue concerning the structural features of coligands that can activate bipyridyl ligands toward an increased cytotoxic effect. X-ray structure analysis of compound [Ru(η(5)-C5H5)(bipy)(PPh3)][PF6] (7; bipy=bipyridine) showed crystallization on C2/c space group with two enantiomers of the [Ru(η(5)-C5H5)(bipy)(PPh3)](+) cation complex in the racemic crystal packing.

Structural investigation of the Bacillus subtilis morphogenic factor RodZ

A thesis to obtain a Master degree in Structural and Functional Biochemistry

Structural, optical and magnetic properties of pulsed laser deposited Co-doped ZnO films

Zn1−xCoxO films with different Co concentrations (with x=0.00, 0.10, 0.15, and 0.30) were grown by pulsed laser deposition (PLD) technique. The structural and optical properties of the films were investigated by grazing incidence X-ray diffraction (GIXRD), Raman spectroscopy and photoluminescence (PL). The magnetic properties were measured by conventional magnetometry using a SQUID and simulated by ab-initio calculations using Korring–Khon–Rostoker (KKR) method combined with coherent potential approximation (CPA). The effect of Co-doping on the GIXRD and Raman peaks positions, shape and intensity is discussed. PL studies demonstrate that Co-doping induces a decrease of the bandgap energy and quenching of the UV emission. They also suggest the presence of Zn interstitials when x≥0.15. The 10% Co-doped ZnO film shows ferromagnetism at 390 K with a spontaneous magnetic moment ≈4×10−5 emu and coercive field ≈0.17 kOe. The origin of ferromagnetism is explained based on the calculations using KKR method.

Dinámica y cinética de los procesos físicos y químicos del radical OH con compuestos orgánicos volátiles (COVs) de relevancia atmosférica. Dynamics and kinetics of the physical and chemical processes of OH radicals with atmospheric relevant volatile organic compounds (VOCs)

El objetivo del presente proyecto es estudiar los procesos físicos y químicos del radical OH con compuestos orgánicos volátiles (COVs), con los cuales sea factible la formación de agregados de van der Waals (vdW) responsables de la curvatura en los gráficos de Arrhenius, empleando técnicas modernas, complementarias entre si y novedosas en el país. El problema será abordado desde tres perspectivas complementarias: 1) estudios cinéticos, 2) estudios mecanísticos y de distribución de productos y 3) estudios de la dinámica de los procesos físicos y químicos. La finalidad es alcanzar una mejor comprensión de los mecanismos que intervienen en el comportamiento químico de especies presentes en la atmósfera y obtener datos cinéticos de alta calidad que puedan alimentar modelos computacionales capaces de describir la composición de la atmósfera, presente y futura. Los objetivos son estudiar: 1) mediante fotólisis láser pulsada con detección por fluorescencia inducida por láser (PLP-LIF), en reactores de flujo, la cinética de reacción del radical OH(v”=0) con COVs que presentan gráficos de Arrhenius curvos con energías de activación negativas, tales como alcoholes insaturados, alquenos halogenados, éteres halogenados, ésteres alifáticos; 2) en una cámara de simulación de condiciones atmosféricas de gran volumen (4500 L), la identidad y el rendimiento de productos de las reacciones mencionadas, a fines de evaluar su impacto atmosférico y dilucidar los mecanismos de reacción; 3) mediante haces moleculares y espectroscopía láser, la estructura y reactividad de complejos de vdW entre alcoholes insaturados o aromáticos (cresoles) y el radical OH, como modelo de los aductos propuestos como responsables de la desviación al comportamiento de Arrhenius de las reacciones mencionadas; 4) mediante PLP-LIF y expansiones supersónicas, las constantes específicas estado a estado (ksts) de relajación/reacción del radical OH(v”=1-4) vibracionalmente excitado con los COVs mencionados. Los resultados experimentales obtenidos serán contrastados con cálculos ab-initio de estructura electrónica, los cuales apoyarán las interpretaciones, permitirán proponer estructuras de estados de transición y aductos colisionales, como así también calcular las frecuencias de vibración de los complejos de vdW para su posterior asignación en los espectros LIF y REMPI. Asimismo, los mecanismos de reacción propuestos y los parámetros cinéticos medidos experimentalmente serán comparados con aquellos obtenidos por cálculos teóricos. The aim of this project is to study the physical and chemical processes of OH radicals with volatile organic compounds (VOCs) with which the formation of van der Waals (vdW) clusters, responsible for the observed curvature in the Arrhenius plots, might be feasible. The problem will be addressed as follow : 1) kinetic studies; 2) products distribution and mechanistic studies and 3) dynamical studies of the physical and chemical processes. The purpose is to obtain a better understanding of the mechanisms that govern the chemical behavior of species present in the atmosphere and to obtain high quality kinetic data to be used as input to computational models. We will study: 1) the reaction kinetics of OH (v”=0) radicals with VOCs such as unsaturated alcohols, halogenated alkenes, halogenated ethers, aliphatic esters, which show curved Arrhenius plots and negative activation energies, by PLP-LIF, in flow systems; 2) in a large volume (4500 L) atmospheric simulation chamber, reaction products yields in order to evaluate their atmospheric impact and reaction mechanisms; 3) using molecular beams and laser spectroscopy, the structure and reactivity of the vdW complexes formed between the unsaturated or aromatic alcohols and the OH radicals as a model of the adducts proposed as responsible for the non-Arrhenius behavior; 4) the specific state-to-state relaxation/reaction rate constants (ksts) of the vibrationally excited OH (v”=1-4) radical with the VOCs by PLP-LIF and supersonic expansions. Ab-initio calculations will be carried out to support the interpretation of the experimental results, to obtain the transition state and collisional adducts structures, as well as to calculate the vibrational frequencies of the vdW complexes to assign to the LIF and REMPI spectra. Also, the proposed reaction mechanisms and the experimentally measured kinetic parameters will be compared with those obtained from theoretical calculations.

Access of extracellular cations to their binding sites in Na,K-ATPase: role of the second extracellular loop of the alpha subunit.

Na,K-ATPase, the main active transport system for monovalent cations in animal cells, is responsible for maintaining Na(+) and K(+) gradients across the plasma membrane. During its transport cycle it binds three cytoplasmic Na(+) ions and releases them on the extracellular side of the membrane, and then binds two extracellular K(+) ions and releases them into the cytoplasm. The fourth, fifth, and sixth transmembrane helices of the alpha subunit of Na,K-ATPase are known to be involved in Na(+) and K(+) binding sites, but the gating mechanisms that control the access of these ions to their binding sites are not yet fully understood. We have focused on the second extracellular loop linking transmembrane segments 3 and 4 and attempted to determine its role in gating. We replaced 13 residues of this loop in the rat alpha1 subunit, from E314 to G326, by cysteine, and then studied the function of these mutants using electrophysiological techniques. We analyzed the results using a structural model obtained by homology with SERCA, and ab initio calculations for the second extracellular loop. Four mutants were markedly modified by the sulfhydryl reagent MTSET, and we investigated them in detail. The substituted cysteines were more readily accessible to MTSET in the E1 conformation for the Y315C, W317C, and I322C mutants. Mutations or derivatization of the substituted cysteines in the second extracellular loop resulted in major increases in the apparent affinity for extracellular K(+), and this was associated with a reduction in the maximum activity. The changes produced by the E314C mutation were reversed by MTSET treatment. In the W317C and I322C mutants, MTSET also induced a moderate shift of the E1/E2 equilibrium towards the E1(Na) conformation under Na/Na exchange conditions. These findings indicate that the second extracellular loop must be functionally linked to the gating mechanism that controls the access of K(+) to its binding site.

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

Basis set and electron correlation effects on initial convergence for vibrational nonlinear optical properties of conjugated organic molecules

The level of ab initio theory which is necessary to compute reliable values for the static and dynamic (hyper)polarizabilities of three medium size π-conjugated organic nonlinear optical (NLO) molecules is investigated. With the employment of field-induced coordinates in combination with a finite field procedure, the calculations were made possible. It is stated that to obtain reasonable values for the various individual contributions to the (hyper)polarizability, it is necessary to include electron correlation. Based on the results, the convergence of the usual perturbation treatment for vibrational anharmonicity was examined

Intramolecular basis set superposition error effects on the planarity of benzene and other aromatic molecules: A solution to the problem

Recently, the surprising result that ab initio calculations on benzene and other planar arenes at correlated MP2, MP3, configuration interaction with singles and doubles (CISD), and coupled cluster with singles and doubles levels of theory using standard Pople’s basis sets yield nonplanar minima has been reported. The planar optimized structures turn out to be transition states presenting one or more large imaginary frequencies, whereas single-determinant-based methods lead to the expected planar minima and no imaginary frequencies. It has been suggested that such anomalous behavior can be originated by two-electron basis set incompleteness error. In this work, we show that the reported pitfalls can be interpreted in terms of intramolecular basis set superposition error (BSSE) effects, mostly between the C–H moieties constituting the arenes. We have carried out counterpoise-corrected optimizations and frequency calculations at the Hartree–Fock, B3LYP, MP2, and CISD levels of theory with several basis sets for a number of arenes. In all cases, correcting for intramolecular BSSE fixes the anomalous behavior of the correlated methods, whereas no significant differences are observed in the single-determinant case. Consequently, all systems studied are planar at all levels of theory. The effect of different intramolecular fragment definitions and the particular case of charged species, namely, cyclopentadienyl and indenyl anions, respectively, are also discussed

Docking to heme proteins.

In silico screening has become a valuable tool in drug design, but some drug targets represent real challenges for docking algorithms. This is especially true for metalloproteins, whose interactions with ligands are difficult to parametrize. Our docking algorithm, EADock, is based on the CHARMM force field, which assures a physically sound scoring function and a good transferability to a wide range of systems, but also exhibits difficulties in case of some metalloproteins. Here, we consider the therapeutically important case of heme proteins featuring an iron core at the active site. Using a standard docking protocol, where the iron-ligand interaction is underestimated, we obtained a success rate of 28% for a test set of 50 heme-containing complexes with iron-ligand contact. By introducing Morse-like metal binding potentials (MMBP), which are fitted to reproduce density functional theory calculations, we are able to increase the success rate to 62%. The remaining failures are mainly due to specific ligand-water interactions in the X-ray structures. Testing of the MMBP on a second data set of non iron binders (14 cases) demonstrates that they do not introduce a spurious bias towards metal binding, which suggests that they may reliably be used also for cross-docking studies.

Mutational and computational analysis of the alpha(1b)-adrenergic receptor. Involvement of basic and hydrophobic residues in receptor activation and G protein coupling.

To investigate their role in receptor coupling to G(q), we mutated all basic amino acids and some conserved hydrophobic residues of the cytosolic surface of the alpha(1b)-adrenergic receptor (AR). The wild type and mutated receptors were expressed in COS-7 cells and characterized for their ligand binding properties and ability to increase inositol phosphate accumulation. The experimental results have been interpreted in the context of both an ab initio model of the alpha(1b)-AR and of a new homology model built on the recently solved crystal structure of rhodopsin. Among the twenty-three basic amino acids mutated only mutations of three, Arg(254) and Lys(258) in the third intracellular loop and Lys(291) at the cytosolic extension of helix 6, markedly impaired the receptor-mediated inositol phosphate production. Additionally, mutations of two conserved hydrophobic residues, Val(147) and Leu(151) in the second intracellular loop had significant effects on receptor function. The functional analysis of the receptor mutants in conjunction with the predictions of molecular modeling supports the hypothesis that Arg(254), Lys(258), as well as Leu(151) are directly involved in receptor-G protein interaction and/or receptor-mediated activation of the G protein. In contrast, the residues belonging to the cytosolic extensions of helices 3 and 6 play a predominant role in the activation process of the alpha(1b)-AR. These findings contribute to the delineation of the molecular determinants of the alpha(1b)-AR/G(q) interface.

Defect study of SnO2 nanostructures by cathodoluminescence analysis: Application to nanowires

Defects in SnO2 nanowires have been studied by cathodoluminescence, and the obtained spectra have been compared with those measured on SnO2 nanocrystals of different sizes in order to reveal information about point defects not determined by other characterization techniques. Dependence of the luminescence bands on the thermal treatment temperatures and pre-treatment conditions have been determined pointing out their possible relation, due to the used treatment conditions, with the oxygen vacancy concentration. To explain these cathodoluminescence spectra and their behavior, a model based on first-principles calculations of the surface oxygen vacancies in the different crystallographic directions is proposed for corroborating the existence of surface state bands localized at energy values compatible with the found cathodoluminescence bands and with the gas sensing mechanisms. CL bands centered at 1.90 and 2.20 eV are attributed to the surface oxygen vacancies 100° coordinated with tin atoms, whereas CL bands centered at 2.37 and 2.75 eV are related to the surface oxygen vacancies 130° coordinated. This combined process of cathodoluminescence and ab initio calculations is shown to be a powerful tool for nanowire defect analysis.

Structure and energetics of mixed 4He-3He drops

Using a finite-range density functional, we have investigated the energetics and structural features of mixed helium clusters. The possibility of doping the cluster with a molecule of sulfur hexafluoride is also considered. It is seen that the repulsion introduced by the impurity strongly modifies the properties of the smallest drops. Although only a qualitative comparison is possible, the gross features displayed by our calculations are in agreement with recent experimental findings.

Spin and density longitudinal response of quantum dots in the time-dependent local-spin-density approximation

The longitudinal dipole response of a quantum dot has been calculated in the far-infrared regime using local-spin-density-functional theory. We have studied the coupling between the collective spin and density modes as a function of the magnetic field. We have found that the spin dipole mode and single-particle excitations have a sizable overlap, and that the magnetoplasmon modes can be excited by the dipole spin operator if the dot is spin polarized. The frequency of the dipole spin edge mode presents an oscillation which is clearly filling factor (v) related. We have found that the spin dipole mode is especially soft for even-n values. Results for selected numbers of electrons and confining potentials are discussed.