Optical Excitations and Field Enhancement in Short Graphene Nanoribbons

The optical excitations of elongated graphene nanoflakes of finite length are investigated theoretically through quantum chemistry semiempirical approaches. The spectra and the resulting dipole fields are analyzed, accounting in full atomistic details for quantum confinement effects, which are crucial in the nanoscale regime. We find that the optical spectra of these nanostructures are dominated at low energy by excitations with strong intensity, comprised of characteristic coherent combinations of a few single-particle transitions with comparable weight. They give rise to stationary collective oscillations of the photoexcited carrier density extending throughout the flake and to a strong dipole and field enhancement. This behavior is robust with respect to width and length variations, thus ensuring tunability in a large frequency range. The implications for nanoantennas and other nanoplasmonic applications are discussed for realistic geometries.

A novel set of ss-N-biaryl ether sulfonamide hydroxamates as potential MMPs inhibitors: Molecular dynamics simulations and molecular properties evaluation

Matrix metalloproteinases (MMPs) constitute a family of zinc-dependent proteases involved in the extracellular matrix degradation. MMP-2 and MMP9 are overexpressed in several human cancer types, including melanoma, thus the development of new compounds to inhibit MMPs' activity is desirable. Molecular dynamic simulation and molecular properties calculations were performed on a set of novel beta-N-biaryl ether sulfonamide-based hydroxamates, reported as MMP-2 and MMP-9 inhibitors, for providing data to develop an exploratory analysis. Thermodynamic, electronic, and steric descriptors have significantly discriminated highly active from moderately and less active inhibitors of MMP-2 whereas apparent partition coefficient at pH 1.5 was also significant for the MMP-9 data set. Compound 47 was considered an outlier in all analysis, indicating the presence of a bulky substituent group in R3 is crucial to this set of inhibitors for the establishment of molecular interactions with the S1 subsite of both enzymes, but there is a limit. (C) 2012 Wiley Periodicals, Inc.

Interactions between 1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid and gamma-Al2O3 (100) surface calculated by density functional theory

The main aim of this work is to investigate the 1-butyl-3-methylimidazolium tetrafluoroborate ([C4C1Im]+[BF4]-) ionic liquid (IL) adsorption on the gamma-Al2O3 (100) by density functional theory calculations to try to rationalize the adsorption as an electrostatic phenomenon. Optimized geometries and interaction energies of IL one-monolayer on the gamma-Al2O3 were obtained on high surface coverage (one cationanion pair per 94.96 nm2). A study of dispersion force was made to estimate its contribution to the adsorption. Overall, the process is ruled by electrostatic interaction between ions and surface. Adsorption of the anion [BF4]- and cation [C4C1Im]+ was also studied by Bader charge analysis and charge density difference for supported and unsupported situations. It is suggested that the IL ions have their charges maintained with significant anion cloud polarization inward to the acid aluminum sites. (c) 2012 Wiley Periodicals, Inc.

Advanced QSAR Studies on PPAR delta Ligands Related to Metabolic Diseases

PPAR delta is a nuclear receptor that, when activated, regulates the metabolism of carbohydrates and lipids and is related to metabolic syndrome and type 2 diabetes. To understand the main interactions between ligands and PPAR delta, we have constructed 2D and 3D QSAR models and compared them with HOMO, LUMO and electrostatic potential maps of the compounds studied, as well as docking results. All QSAR models showed good statistical parameters and prediction outcomes. The QSAR models were used to predict the biological activity of an external test set, and the predicted values are in good agreement with the experimental results. Furthermore, we employed all maps to evaluate the possible interactions between the ligands and PPAR delta. These predictive QSAR models, along with the HOMO, LUMO and MEP maps, can provide insights into the structural and chemical properties that are needed in the design of new PPAR delta ligands that have improved biological activity and can be employed to treat metabolic diseases.

Hydrogen bond and the resonance effect on the formamide-water complexes

The interaction of formamide and the two transition states of its amide group rotation with one, two, or three water molecules was studied in vacuum. Great differences between the electronic structure of formamide in its most stable form and the electronic structure of the transition states were noticed. Intermolecular interactions were intense, especially in the cases where the solvent interacted with the amide and the carbonyl groups simultaneously. In the transition states, the interaction between the lone pair of nitrogen and the water molecule becomes important. With the aid of the natural bond orbitals, natural resonance theory, and electron localization function (ELF) analyses an increase in the resonance of planar formamide with the addition of successive water molecules was observed. Such observation suggests that the hydrogen bonds in the formamidewater complexes may have some covalent character. These results are also supported by the quantitative ELF analyses. (C) 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012

The generator coordinate method in the unrestricted Hartree-Fock formalism

The generator coordinate method was implemented in the unrestricted Hartree-Fock formalism. Weight functions were built from Gaussian generator functions for 1s, 2s, and 2p orbitals of carbon and oxygen atoms. These weight functions show a similar behavior to those found in the generator coordinate restricted Hartree-Fock method, i.e., they are smooth, continuous, and tend to zero in the limits of integration. Moreover, the weight functions obtained are different for spin-up and spin-down electrons what is a result from spin polarization. (C) 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012

Isatin-Schiff base copper(II) complexes-A DFT study of the metal-ligand bonding situation

Herein, we report results of calculations based on density functional theory (BP86/TZVP) of a set of isatin-Schiff base copper(II) and related complexes, 1-12, that have shown significant pro-apoptotic activity toward diverse tumor cells. The interaction of the copper(II) cation with different ligands has been investigated at the same level of theory. The strength and character of the Cu(II)-L bonding was characterized by metal-ligand bond lengths, vibrational frequencies, binding energies, ligand deformation energies, and natural population analysis. The metal-ligand bonding situation was also characterized by using two complementary topological approaches, the quantum theory of atoms-in-molecules (QTAIM) and the electron localization function (ELF). The calculated electronic g-tensor and hyperfine coupling constants present significant agreement with the EPR experimental data. The calculated parameters pointed to complex 10 as the most stable among the isatin-Schiff base copper(II) species, in good agreement with experimental data that indicate this complex as the most reactive in the series. (C) 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012

VIBRATIONAL ANALYSIS OF COORDINATION COMPOUNDS OF NICKEL (II): AN APPROACH TO THE TEACHING OF POINT GROUPS

VIBRATIONAL ANALYSIS OF COORDINATION COMPOUNDS OF NICKEL (II): AN APPROACH TO THE TEACHING OF POINT GROUPS. This paper presents an IR and Raman experiment executed during the teaching of the course "Chemical Bonds" for undergraduated students of Science and Technology and Chemistry at the Federal University of ABC, in order to facilitate and encourage the teaching and learning of group theory. Some key aspects of this theory are also outlined. We believe that student learning was more significant with the introduction of this experiment, because there was an increase in the discussions level and in the performance during evaluations. This work also proposes a multidisciplinary approach to include the use of quantum chemistry tools.

The basic antioxidant structure for flavonoid derivatives

An antioxidant structure-activity study is carried out in this work with ten flavonoid compounds using quantum chemistry calculations with the functional of density theory method. According to the geometry obtained by using the B3LYP/6-31G(d) method, the HOMO, ionization potential, stabilization energies, and spin density distribution showed that the flavonol is the more antioxidant nucleus. The spin density contribution is determinant for the stability of the free radical. The number of resonance structures is related to the pi-type electron system. 3-hydroxyflavone is the basic antioxidant structure for the simplified flavonoids studied here. The electron abstraction is more favored in the molecules where ether group and 3-hydroxyl are present, nonetheless 2,3-double bond and carbonyl moiety are facultative.

A Combined Study Using Ligand-Based Design, Synthesis, and Pharmacological Evaluation of Analogues of the Acetaminophen Ortho-Regioisomer with Potent Analgesic Activity

A ligand-based drug design study was performed to acetaminophen regioisomers as analgesic candidates employing quantum chemical calculations at the DFT/B3LYP level of theory and the 6-31G* basis set. To do so, many molecular descriptors were used such as highest occupied molecular orbital, ionization potential, HO bond dissociation energies, and spin densities, which might be related to quench reactivity of the tyrosyl radical to give N-acetyl-p-benzosemiquinone-imine through an initial electron withdrawing or hydrogen atom abstraction. Based on this in silico work, the most promising molecule, orthobenzamol, was synthesized and tested. The results expected from the theoretical prediction were confirmed in vivo using mouse models of nociception such as writhing, paw licking, and hot plate tests. All biological results suggested an antinociceptive activity mediated by opioid receptors. Furthermore, at 90 and 120 min, this new compound had an effect that was comparable to morphine, the standard drug for this test. Finally, the pharmacophore model is discussed according to the electronic properties derived from quantum chemistry calculations.

Gas-phase reactivity of 2-hydroxy-1,4-naphthoquinones: a computational and mass spectrometry study of lapachol congeners

In order to understand the influence of alkyl side chains on the gas-phase reactivity of 1,4-naphthoquinone derivatives, some 2-hydroxy-1,4-naphthoquinone derivatives have been prepared and studied by electrospray ionization tandem mass spectrometry in combination with computational quantum chemistry calculations. Protonation and deprotonation sites were suggested on the basis of gas-phase basicity, proton affinity, gas-phase acidity (?Gacid), atomic charges and frontier orbital analyses. The nature of the intramolecular interaction as well as of the hydrogen bond in the systems was investigated by the atoms-in-molecules theory and the natural bond orbital analysis. The results were compared with data published for lapachol (2-hydroxy-3-(3-methyl-2-butenyl)-1,4-naphthoquinone). For the protonated molecules, water elimination was verified to occur at lower proportion when compared with side chain elimination, as evidenced in earlier studies on lapachol. The side chain at position C(3) was found to play important roles in the fragmentation mechanisms of these compounds. Copyright (c) 2012 John Wiley & Sons, Ltd.

Análise vibracional de compostos de coordenação de niquel(II): uma abordagem ao ensino dos grupos pontuais

This paper presents an IR and Raman experiment executed during the teaching of the course "Chemical Bonds" for undergraduated students of Science and Technology and Chemistry at the Federal University of ABC, in order to facilitate and encourage the teaching and learning of group theory. Some key aspects of this theory are also outlined. We believe that student learning was more significant with the introduction of this experiment, because there was an increase in the discussions level and in the performance during evaluations. This work also proposes a multidisciplinary approach to include the use of quantum chemistry tools.

Theoretical studies of mononuclear non-heme iron active sites

The quantum chemical investigations presented in this thesis use hybrid density functional theory to shed light on the catalytic mechanisms of mononuclear non-heme iron oxygenases, accommodating a ferrous ion in their active sites. More specifically, the dioxygen activation process and the subsequent oxidative reactions in the following enzymes were studied: tetrahydrobiopterin-dependent hydroxylases, naphthalene 1,2-dioxygenase and α-ketoglutarate-dependent enzymes. In light of many experimental efforts devoted to the functional mimics of non-heme iron oxygenases, the reactivity of functional analogues was also examined. The computed energetics and the available experimental data served to assess the feasibility of the reaction mechanisms investigated. Dioxygen activation in tetrahydrobiopterin- and α-ketoglutarate-dependent enzymes were found to involve a high-valent iron-oxo species, which was then capable of substrate hydroxylation. In the case of naphthalene 1,2-dioxygenase, the reactivity of an iron(III)-hydroxperoxo species toward the substrate was investigated and compared to the biomimetic counterpart.

Autoionizing states and their relevance in electron-ion recombination

Atomic physics plays an important role in determining the evolution stages in a wide range of laboratory and cosmic plasmas. Therefore, the main contribution to our ability to model, infer and control plasma sources is the knowledge of underlying atomic processes. Of particular importance are reliable low temperature dielectronic recombination (DR) rate coefficients. This thesis provides systematically calculated DR rate coefficients of lithium-like beryllium and sodium ions via ∆n = 0 doubly excited resonant states. The calculations are based on complex-scaled relativistic many-body perturbation theory in an all-order formulation within the single- and double-excitation coupled-cluster scheme, including radiative corrections. Comparison of DR resonance parameters (energy levels, autoionization widths, radiative transition probabilities and strengths) between our theoretical predictions and the heavy-ion storage rings experiments (CRYRING-Stockholm and TSRHeidelberg) shows good agreement. The intruder state problem is a principal obstacle for general application of the coupled-cluster formalism on doubly excited states. Thus, we have developed a technique designed to avoid the intruder state problem. It is based on a convenient partitioning of the Hilbert space and reformulation of the conventional set of pairequations. The general aspects of this development are discussed, and the effectiveness of its numerical implementation (within the non-relativistic framework) is selectively illustrated on autoionizing doubly excited states of helium.

Simulationen zur Exzitonendiffusion in organischen Halbleitern

Die vorliegende Dissertation dient dazu, das Verständnis des Exzitonentransports in organischen Halbleitern, wie sie in Leuchtdioden oder Solarzellen eingesetzt werden, zu vertiefen. Mithilfe von Computersimulationen wurde der Transport von Exzitonen in amorphen und kristallinen organischen Materialien beschrieben, angefangen auf mikroskopischer Ebene, auf der quantenmechanische Prozesse ablaufen, bis hin zur makroskopischen Ebene, auf welcher physikalisch bestimmbare Größen wie der Diffusionskoeffizient extrahierbar werden. Die Modellbildung basiert auf dem inkohärenten elektronischen Energietransfer. In diesem Rahmen wird der Transport des Exzitons als Hüpfprozess aufgefasst, welcher mit kinetischen Monte-Carlo Methoden simuliert wurde. Die notwendigen quantenmechanischen Übergangsraten zwischen den Molekülen wurden anhand der molekularen Struktur fester Phasen berechnet. Die Übergangsraten lassen sich in ein elektronisches Kopplungselement und die Franck-Condon-gewichtete Zustandsdichte aufteilen. Der Fokus dieser Arbeit lag einerseits darauf die Methoden zu evaluieren, die zur Berechnung der Übergangsraten in Frage kommen und andererseits den Hüpftransport zu simulieren und eine atomistische Interpretation der makroskopischen Transporteigenschaften der Exzitonen zu liefern. rnrnVon den drei untersuchten organischen Systemen, diente Aluminium-tris-(8-hydroxychinolin) der umfassenden Prüfung des Verfahrens. Es wurde gezeigt, dass stark vereinfachte Modelle wie die Marcus-Theorie die Übergangsraten und damit das Transportverhalten der Exzitonen oftmals qualitativ korrekt wiedergeben. Die meist deutlich größeren Diffusionskonstanten von Singulett- im Vergleich zu Triplett-Exzitonen haben ihren Ursprung in der längeren Reichweite der Kopplungselemente der Singulett-Exzitonen, wodurch ein stärker verzweigtes Netzwerk gebildet wird. Der Verlauf des zeitabhängigen Diffusionskoeffizienten zeigt subdiffusives Verhalten für kurze Beobachtungszeiten. Für Singulett-Exzitonen wechselt dieses Verhalten meist innerhalb der Lebensdauer des Exzitons in ein normales Diffusionsregime, während Triplett-Exzitonen das normale Regime deutlich langsamer erreichen. Das stärker anomale Verhalten der Triplett-Exzitonen wird auf eine ungleichmäßige Verteilung der Übergangsraten zurückgeführt. Beim Vergleich mit experimentell bestimmten Diffusionskonstanten muss das anomale Verhalten der Exzitonen berücksichtigt werden. Insgesamt stimmten simulierte und experimentelle Diffusionskonstanten für das Testsystem gut überein. Das Modellierungsverfahren sollte sich somit zur Charakterisierung des Exzitonentransports in neuen organischen Halbleitermaterialien eignen.