The role of van der Waals interactions in the case of H2 adsorption on ruthenium (0001) surface

Computational material science with the Density Functional Theory (DFT) has recently gained a method for describing, for the first time the non local bonding i.e., van der Waals (vdW) bonding. The newly proposed van der Waals-Density Functional (vdW-DF) is employed here to address the role of non local interactions in the case of H2 adsorption on Ru(0001) surface. The later vdW-DF2 implementation with the DFT code VASP (Vienna Ab-initio Simulation Package) is used in this study. The motivation for studying H2 adsorption on ruthenium surface arose from the interest to hydrogenation processes. Potential energy surface (PES) plots are created for adsorption sites top, bridge, fcc and hcp, employing the vdW-DF2 functional. The vdW-DF yields 0.1 eV - 0.2 eV higher barriers for the dissociation of the H2 molecule; the vdW-DF seems to bind the H2 molecule more tightly together. Furthermore, at the top site, which is found to be the most reactive, the vdW functional suggests no entrance barrier or in any case smaller than 0.05 eV, whereas the corresponding calculation without the vdW-DF does. Ruthenium and H2 are found to have the opposite behaviors with the vdW-DF; Ru lattice constants are overestimated while H2 bond length is shorter. Also evaluation of the CPU time demand of the vdW-DF2 is done from the PES data. From top to fcc sites the vdW-DF computational time demand is larger by 4.77 % to 20.09 %, while at the hcp site it is slightly smaller. Also the behavior of a few exchange correlation functionals is investigated along addressing the role of vdW-DF. Behavior of the different functionals is not consistent between the Ru lattice constants and H2 bond lengths. It is thus difficult to determine the quality of a particular exchange correlation functional by comparing equilibrium separations of the different elements. By comparing PESs it would be computationally highly consuming.

Desenvolupament, implementació i aplicació de noves metodologies per a l'estudi de la reactivitat química i de les propietats òptiques no lineals

El coneixement de la superfície d'energia potencial (PES) ha estat essencial en el món de la química teòrica per tal de discutir tant la reactivitat química com l'estructura i l'espectroscòpia molecular. En el camp de la reactivitat química es hem proposat continuar amb el desenvolupament de nova metodologia dins el marc de la teoria del funcional de la densitat conceptual. En particular aquesta tesis es centrarà en els següents punts: a) El nombre i la naturalesa dels seus punts estacionaris del PES poden sofrir canvis radicals modificant el nivell de càlcul utilitzats, de tal manera que per estar segurs de la seva naturalesa cal anar a nivells de càlcul molt elevats. La duresa és una mesura de la resistència d'un sistema químic a canviar la seva configuració electrònica, i segons el principi de màxima duresa on hi hagi un mínim o un màxim d'energia trobarem un màxim o un mínim de duresa, respectivament. A l'escollir tot un conjunt de reaccions problemàtiques des del punt de vista de presència de punts estacionaris erronis, hem observat que els perfils de duresa són més independents de la base i del mètode utilitzats, a més a més sempre presenten el perfil correcte. b) Hem desenvolupat noves expressions basades en les integracions dels kernels de duresa per tal de determinar la duresa global d'una molècula de manera més precisa que la utilitzada habitualment que està basada en el càlcul numèric de la derivada segona de l'energia respecte al número d'electrons. c) Hem estudiat la validesa del principis de màxima duresa i de mínima polaritzabiliat en les vibracions asimètriques en sistemes aromàtics. Hem trobat que per aquests sistemes alguns modes vibracionals incompleixen aquests principis i hem analitzat la relació d'aquest l'incompliment amb l'efecte de l'acoblament pseudo-Jahn-Teller. A més a més, hem postulat tot un conjunt de regles molt senzilles que ens permetien deduir si una molècula compliria o no aquests principis sense la realització de cap càlcul previ. Tota aquesta informació ha estat essencial per poder determinar exactament quines són les causes del compliment o l'incompliment del MHP i MPP. d) Finalment, hem realitzat una expansió de l'energia funcional en termes del nombre d'electrons i de les coordenades normals dintre del conjunt canònic. En la comparació d'aquesta expansió amb l'expansió de l'energia del nombre d'electrons i del potencial extern hem pogut recuperar d'una altra forma diferent tot un conjunt de relacions ja conegudes entre alguns coneguts descriptors de reactivitat del funcional de la densitat i en poden establir tot un conjunt de noves relacions i de nous descriptors. Dins del marc de les propietats moleculars es proposa generalitzar i millorar la metodologia pel càlcul de la contribució vibracional (Pvib) a les propietats òptiques no lineals (NLO). Tot i que la Pvib no s'ha tingut en compte en la majoria dels estudis teòrics publicats de les propietats NLO, recentment s'ha comprovat que la Pvib de diversos polímers orgànics amb altes propietats òptiques no lineals és fins i tot més gran que la contribució electrònica. Per tant, tenir en compte la Pvib és essencial en el disseny dels nous materials òptics no lineals utilitzats en el camp de la informàtica, les telecomunicacions i la tecnologia làser. Les principals línies d'aquesta tesis sobre aquest tema són: a) Hem calculat per primera vegada els termes d'alt ordre de Pvib de diversos polímers orgànics amb l'objectiu d'avaluar la seva importància i la convergència de les sèries de Taylor que defineixen aquestes contribucions vibracionals. b) Hem avaluat les contribucions electròniques i vibracionals per una sèrie de molècules orgàniques representatives utilitzant diferents metodologies, per tal de poder de determinar quina és la manera més senzilla per poder calcular les propietats NLO amb una precisió semiquantitativa.

Quantitative evaluation of three reconfiguration strategies on FPGAs: a case study

Reconfigurable computing is becoming an important new alternative for implementing computations. Field programmable gate arrays (FPGAs) are the ideal integrated circuit technology to experiment with the potential benefits of using different strategies of circuit specialization by reconfiguration. The final form of the reconfiguration strategy is often non-trivial to determine. Consequently, in this paper, we examine strategies for reconfiguration and, based on our experience, propose general guidelines for the tradeoffs using an area-time metric called functional density. Three experiments are set up to explore different reconfiguration strategies for FPGAs applied to a systolic implementation of a scalar quantizer used as a case study. Quantitative results for each experiment are given. The regular nature of the example means that the results can be generalized to a wide class of industry-relevant problems based on arrays.

Propriedades física de molécilas orgânicas e compostos do tipo perovskita CdSiO3 e CaPbO3

In the first part of this work our concern was to investigate the thermal effects in organic crystals using the theory of the polarons. To analyse such effect, we used the Fröhlich s Hamiltonian, that describes the dynamics of the polarons, using a treatment based on the quantum mechanics, to elucidate the electron-phonon interaction. Many are the forms to analyzing the polaronic phenomenon. However, the measure of the dielectric function can supply important information about the small polarons hopping process. Besides, the dielectric function measures the answer to an applied external electric field, and it is an important tool for the understanding of the many-body effects in the normal state of a polaronic system. We calculate the dielectric function and its dependence on temperature using the Hartree-Fock decoupling method. The dieletric function s dependence on the temperature is depicted by through a 3D graph. We also analyzed the so called Arrhenius resistivity, as a functionof the temperature, which is an important tool to characterize the conductivity of an organic molecule. In the second part we analyzed two perovskita type crystalline oxides, namely the cadmium silicate triclinic (CdSiO3) and the calcium plumbate orthorhombic (CaPbO3), respectively. These materials are normally denominated ABO3 and they have been especially investigated for displaying ferroelectric, piezoelectric, dielectrics, semiconductors and superconductors properties. We found our results through ab initio method within the functional density theory (DFT) in the GGA-PBE and LDA-CAPZ approximations. After the geometry optimization for the two structure using the in two approximations, we found the structure parameters and compared them with the experimental data. We still determined further the angles of connection for the two analyzed cases. Soon after the convergence of the energy, we determined their band structures, fundamental information to characterize the nature of the material, as well as their dielectrics functions, optical absorption, partial density of states and effective masses of electrons and holes

Computer-aided design of a novel ligand for retinoic acid receptor in cancer chemotherapy

The isotypes of RAR and RXR are retinoic acid and retinoid X acid receptors, respectively, whose ligand-binding domain contains the ligand-dependent activation function, with distinct pharmacological targets for retinoids, involved in the treatment of various cancers and skin diseases. Due to the major challenge which cancer treatment and cure still imposes after many decades to the international scientific community, there is actually considerable interest in new ligands with increased bioactivity. We have focused on the retinoid acid receptor, which is considered an interesting target for drug design. In this work, we carried out density functional geometry optimizations, and different docking procedures. We performed screening in a large database (hundreds of thousands of molecules which we optimized at the AM1 level) yielding a set of potential bioactive ligands. A new ligand was selected and optimized at the B3LYP/6-31G* level. A flexible docking program was used to investigate the interactions between the receptor and the new ligand. The result of this work is compared with several crystallographic ligands of RAR. Our theoretically more bioactive new-ligand indicates stronger and more hydrogen bonds as well as hydrophobic interactions with the receptor. (c) 2005 Wiley Periodicals, Inc.

Estudo teórico das propriedades estruturais e eletrônicas do GaN e do semicondutor magnético Ga1-xMnxN no bulk e na superfície

Pós-graduação em Ciência e Tecnologia de Materiais - FC

Synthese und Charakterisierung zylindrischer Poly(2-oxazolin)bürsten als Nanocarrier für Drug Delivery Systeme

Inspiriert durch natürlich vorkommende Peptide, sind Poly(2-oxazoline) vielversprechende Kandidaten für Anwendungen in Bereichen des kontrollierten Wirkstoff- bzw. Gentransportes, wie die moderne Biomedizin dies fordert. Da Polyoxazoline als strukturisomere Amide von natürlichen Polypeptiden aufgefasst werden können, zeigen diese synthetischen Polymere in direktem Vergleich erhebliche Vorteile etwa hinsichtlich Zytotoxizät und Effizienz, was wesentlich dazu beitragen kann, aktuelle Hürden biomedizinischer Fragestellungen hinsichtlich Transport und Targeting zu überwinden. Darüber hinaus sollten zylindrische Polymerbürsten aufgrund ihrer molekularen, architekturbedingten Formanisotropie und jüngsten Ergebnissen insbesondere zur formabhängigen Endozytose sehr aussichtsreiche Kandidaten für den Einsatz zum Wirkstofftransport sein.rnrnDie vorliegende Arbeit widmete sich deshalb der Synthese und Charakterisierung von biokompatiblen zylindrischen Poly(2-oxazolin)bürsten als potentielle Nanotransporter von Wirkstoffen, Biomolekülen oder genetischem Material. Als Monomer wurde zunächst 2-Isopropyloxazolin gewählt, da das Polymer eine Phasenübergangstemperatur von 37 °C besitzt, was für Konjugatsynthesen wie auch diverse biomedizinische Applikationen interessant sein kann. Durch terminierende Methacrylamid Funktionalisierung der lebenden kationischen Oxazolinpolymerisation bzw. nachfolgende Endgruppen Transferreaktionen sind Makromonomere im Bereich 1000-5000 g/mol zugänglich. Erstmals gelang es so 2-Oxazolin basierte, hochmolekulare zylindrische Bürsten mit Konturlängen im Bereich von 250 nm mittels „Grafting Through“ Technik in freier radikalischer Polymerisation herzustellen.rnrnAusgehend von der entwickelten Syntheseroute konnten so neben Homo- und Blockcopolymerbürsten von 2-Ethyl-2-oxazolin und 2-Isopropyl-2-oxazolin auch Bürstenmoleküle aus statistischen Copolymeren von 2-Ethyl-2-oxazolin und unsubstituiertem 2-Oxazolin hergestellt werden. Während letztere die Einführung kationischer Gruppen durch selektivere Abspaltmethoden der Formylreste erlauben und so etwa DNA/RNA Komplexierungen ermöglichen können, bietet andererseits der in dieser Arbeit erstmalig demonstrierte Einsatz Azid-funktionalisierter Initiatoren zur kationischen Oxazolinpolymerisation unter Beibehaltung aller anderen sonstigen Reaktionsschritte auch die Möglichkeit der Synthese Azid-Endgruppen-funktionalisierter Makromonomere. Die „Grafting Through“ Methodik der freien radikalischen Makromonomer Polymerisation ist selbst bei diesen funktionalisierten Systemen von großem Vorteil, erlaubt sie auch hier den Zugang zu hochmolekularen Substraten mit einem Pfropfungs- bzw. Funktionalisierungsgrad von 100 %, da jede Seitenkette dieser zylindrischen Bürsten die aussenliegende, und damit sterisch leichter zugängliche funktionale Gruppe trägt. Dabei gelang es die Syntheseroute so zu gestalten, dass es möglich war alle vorgestellten Polymerbürsten mittels statischer und dynamischer Lichtstreuung hinsichtlich absoluter Molmasse und molekularer Dimension zu charakterisieren.rnIn weitereren Reaktionen konnten dann reaktive Fluoreszenzfarbstoffe mit Hilfe kupferfreier 1,3 dipolarerer Addition (kupferfreie „Click-Chemie“) an die Azid-funktionalisierten Polymerbürsten angebunden werden, so dass eine wesentliche Voraussetzung für die Detektion in in vivo und in vitro Experimenten erfüllt werden kann. Darüber hinaus gelingt die quantitative polymeranaloge Umsetzung der Azid- zu Aminogruppen durch eine polymeranalog geführte Reduktion nach Staudinger; damit können an diesen Systemen auch etablierte Konjugationstechniken an Aminogruppen durchgeführt werden. Zudem erlauben die Aminogruppen-haltigen Polymerbürsten durch Protonierung schon bei physiologischem pH die Komplexierung von DNA oder RNA. rnrnErste Lichtstreumessungen in Blutserum zeigen im Falle der kationischen Aminogruppen tragenden Polymerbürsten zwar Aggregation, was aber durch entsprechende Umsetzung nach Konjugation wahrscheinlich unterdrückt werden kann, zeigen doch die entsprechenden Precursorpolymerbürsten mit Azidgruppen in Serum keinerlei Aggregation.rnrnZellaufnahmestudien in dendritische Zellen zeigen nur im Falle einer Azid-funktionalisierten Poly(2-isopropyl-2-oxazolin)bürste eine unspezifische Aufnahme. Die hydrophileren Poly(2-oxazolin)bürsten weise keine unspezifische Aufnahme auf, was eine wichtige Anfoderung für die Verwendung als Polymercarrier in der Krebsimmuntherapie ist.rn

Analyzing the n→π* Electronic Transition of Formaldehyde in Water. A Sequential Monte Carlo/Time-Dependent Density Functional Theory

The n→π* absorption transition of formaldehyde in water is analyzed using combined and sequential classical Monte Carlo (MC) simulations and quantum mechanics (QM) calculations. MC simulations generate the liquid solute-solvent structures for subsequent QM calculations. Using time-dependent density functional theory in a localized set of gaussian basis functions (TD-DFT/6-311++G(d,p)) calculations are made on statistically relevant configurations to obtain the average solvatochromic shift. All results presented here use the electrostatic embedding of the solvent. The statistically converged average result obtained of 2300 cm-1 is compared to previous theoretical results available. Analysis is made of the effective dipole moment of the hydrogen-bonded shell and how it could be held responsible for the polarization of the solvent molecules in the outer solvation shells.

Density functional theory study of Fe(3)Ga

First-principles scalar relativistic calculations in supercells of 16 atoms are used to represent disordered B2 ordering of Fe(3)Ga in order to observe the effect of Ga-Ga pairs on the electronic structure of this alloy. From a comparison with pure bcc Fe it is observed that the energy position and occupation of e(g) and t(2g) states are largely affected by the Ga-Ga pairs and strengthened intraplane interactions takes place. The results show that a larger hybridization of the conduction band is in the source of the magnetostriction enhancement experimentally observed in Galfenol. (C) 2011 American Institute of Physics. [doi:10.1063/1.3525609]

Combining Monte Carlo simulation and density-functional theory to describe the spectral changes of Na(2) in liquid helium

Spectral changes of Na(2) in liquid helium were studied using the sequential Monte Carlo-quantum mechanics method. Configurations composed by Na(2) surrounded by explicit helium atoms sampled from the Monte Carlo simulation were submitted to time-dependent density-functional theory calculations of the electronic absorption spectrum using different functionals. Attention is given to both line shift and line broadening. The Perdew, Burke, and Ernzerhof (PBE1PBE, also known as PBE0) functional, with the PBE1PBE/6-311++G(2d,2p) basis set, gives the spectral shift, compared to gas phase, of 500 cm(-1) for the allowed X (1)Sigma(+)(g) -> B (1)Pi(u) transition, in very good agreement with the experimental value (700 cm(-1)). For comparison, cluster calculations were also performed and the first X (1)Sigma(+)(g) -> A (1)Sigma(+)(u) transition was also considered.

Mn-doped cubic BN as an atomiclike memory device: A density functional study

We investigate the electronic properties of Mn(B) substitutional doping in cubic boron nitride (BN), for different charge states, using density functional theory (DFT) calculations. We show that the neutral Mn has a nonmagnetic ground state (S=0). Upon charge injection, it is unambiguously shown that the Mn(B)(-) has a high-spin configuration with a strong, localized magnetic moment of 5 mu(Bohr). We developed a simple model, parameterized by the DFT results, that allows us to interpret the rules played by the crystal-field and exchange-correlation splitting in the magnetization process.

Edge effects in bilayer graphene nanoribbons: Ab initio total-energy density functional theory calculations

We show that the ground state of zigzag bilayer graphene nanoribbons is nonmagnetic. It also possesses a finite gap, which has a nonmonotonic dependence with the width as a consequence of the competition between bulk and strongly attractive edge interactions. All results were obtained using ab initio total-energy density functional theory calculations with the inclusion of parametrized van der Waals interactions.

Approximation to density functional theory for the calculation of band gaps of semiconductors

The local-density approximation (LDA) together with the half occupation (transitionstate) is notoriously successful in the calculation of atomic ionization potentials. When it comes to extended systems, such as a semiconductor infinite system, it has been very difficult to find a way to half ionize because the hole tends to be infinitely extended (a Bloch wave). The answer to this problem lies in the LDA formalism itself. One proves that the half occupation is equivalent to introducing the hole self-energy (electrostatic and exchange correlation) into the Schrodinger equation. The argument then becomes simple: The eigenvalue minus the self-energy has to be minimized because the atom has a minimal energy. Then one simply proves that the hole is localized, not infinitely extended, because it must have maximal self-energy. Then one also arrives at an equation similar to the self- interaction correction equation, but corrected for the removal of just 1/2 electron. Applied to the calculation of band gaps and effective masses, we use the self- energy calculated in atoms and attain a precision similar to that of GW, but with the great advantage that it requires no more computational effort than standard LDA.

Spin gaps and spin-flip energies in density-functional theory

Energy gaps are crucial aspects of the electronic structure of finite and extended systems. Whereas much is known about how to define and calculate charge gaps in density-functional theory (DFT), and about the relation between these gaps and derivative discontinuities of the exchange-correlation functional, much less is known about spin gaps. In this paper we give density-functional definitions of spin-conserving gaps, spin-flip gaps and the spin stiffness in terms of many-body energies and in terms of single-particle (Kohn-Sham) energies. Our definitions are as analogous as possible to those commonly made in the charge case, but important differences between spin and charge gaps emerge already on the single-particle level because unlike the fundamental charge gap spin gaps involve excited-state energies. Kohn-Sham and many-body spin gaps are predicted to differ, and the difference is related to derivative discontinuities that are similar to, but distinct from, those usually considered in the case of charge gaps. Both ensemble DFT and time-dependent DFT (TDDFT) can be used to calculate these spin discontinuities from a suitable functional. We illustrate our findings by evaluating our definitions for the Lithium atom, for which we calculate spin gaps and spin discontinuities by making use of near-exact Kohn-Sham eigenvalues and, independently, from the single-pole approximation to TDDFT. The many-body corrections to the Kohn-Sham spin gaps are found to be negative, i.e., single-particle calculations tend to overestimate spin gaps while they underestimate charge gaps.

Density-functional description of superconducting and magnetic proximity effects across a tunneling barrier

A density-functional formalism for superconductivity and magnetism is presented. The resulting relations unify previously derived Kohn-Sham equations for superconductors and for noncollinear magnetism. The formalism, which discriminates Cooper-pair singlets from triplets, is applied to two quantum liquids coupled by tunneling through a barrier. An exact expression is derived, relating the eigenstates and eigenvalues of the Kohn-Sham equations, unperturbed by tunneling, on one side of the barrier to the proximity-induced ordering potential on the other.