Made available in DSpace on 2014-06-12T15:51:55Z (GMT). No. of bitstreams: 2 arquivo872_1.pdf: 4987624 bytes, checksum: fe10b068072d15ab53986d95b266443d (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) Previous issue date: 2010 / Conselho Nacional de Desenvolvimento Científico e Tecnológico / Cálculos de orbitais moleculares usando a Teoria do Funcional de Densidade (DFT) em nível BLYP com funções de base LanL1mb e LanL1dz foram executados para os supercondutores: Nb3Ge, MgB2, LaBa2Cu3Oy, La2-xSrxCuO4, YBa2Cu3Oy, TlBa2Ca2Cu3O8+δ, HgBa2Ca2Cu3O8+δ, LaO1-xFxFeAs e o Ba1-xKxFe2As2. Utilizamos modelos de cluster (aglomerado) baseados na célula unitária com os átomos de fronteira saturados com hidrogênio, o que minimiza o excesso de elétrons no cluster devido às ligações flutuantes. O cluster foi considerado diamagnético. Foram avaliados a distribuição de cargas atômicas e o gap de energia HOMO-LUMO (Highest Occupied Molecular Orbital - Lowest Unoccupied Molecular Orbital: Orbital Molecular de Mais Alta Energia Ocupado - Orbital Molecular de Mais Baixa Energia Desocupado). Os resultados foram interpretados à luz da teoria da ressonância não-sincronizada das ligações covalentes (RVB), como originalmente proposta por Linus Pauling. Uma característica de todos os sistemas investigados neste trabalho é a existência de um gap HOMO-LUMO da ordem de meV e uma distribuição de cargas compatível com a RVB. Apesar de não ser clara sua relação com a supercondutividade, o gap de energia HOMO-LUMO é da mesma ordem de magnitude do gap supercondutor medido experimentalmente. Em adição, verificou-se que os metais presentes nos sistemas investigados se encontram nos três estados de oxidação e na proporção requerida pelo princípio da eletroneutralidade de Pauling. Estes resultados reforçam o modelo RVB e convalidam esta proposta como uma teoria alternativa para a compreensão da supercondutividade. A coerência entre os argumentos da RVB e os resultados dos cálculos para a distribuição de cargas são discutidos

Mutageniciteten för olika ämnen bestäms vanligtvis med hjälp av konventionella in vivo och in vitro metoder. Att övergå till in silico metoder vore både etiskt och miljö- mässigt gynnsamt. Flera olika parametrar kan användas för att förutse mutagenicitet. Bland dessa ingår energin för lägsta oockuperade molekylorbitalen (LUMO), aktiveringsenergin, lokala min/max i elektrostatiska potentialen (Vs,min/Vs,max), lokala min i ”electron attachment energy” (Es,min ), med flera. Aktiveringsenergin är en parameter som kan förutspå mutagenicitet med hög noggrannhet, förutsatt att reaktionsmekanismen antingen är känd eller kan antas. Däremot är beräkningskostnaden för aktiveringsenergin hög. Mutagen-X (MX) och dess analoger (föreningar med samma grundstruktur men olika funktionella grupper, totalt 29 olika föreningar), är föreningar vars mutagenicitet har bestämts med hjälp av traditionella metoder men har nyligen också kunnat bestämmas genom kvantkemiskmodellering. Kvantkemiskmodellering har med framgång implementerats i studien av Kari Tuppurainen [1]; där LUMO har bestämts för MX och dess analogier. Utöver detta visades även en statistiskt signifikant korrelation mellan LUMO för MX och dess analoger och den biologiska aktiviteten som bestämdes med hjälp av Ames test. Målet med detta arbete har varit att undersöka vare sig mutageniciteten för MX och dess analogier kan även bestämmas genom att beräkna Es,min, Vs,max och aktiveringsenergin. Reaktionen som undersöktes var en Michael additionsreaktion  mellan amingruppen på kvävebasen guanin och betapositionen på MX och dess analogier. Av den anledningen utvärderades parametrarna (Es,min, Vs,max och aktiveringsenergin) vid betapositionen. De beräknade värdena för Es,min var korrelerade med biologiska aktiviteten. Även aktiveringsenergierna för MX och dess analogier beräknades vid betapositionen och korrelerades sedan med biologiska aktiviteten och Es,min värdena. Om en statistiskt signifikant korrelation observerades mellan aktiveringsenergin och Es,min värdena, hade detta varit en indikation att Es,min värden kan användas för att ersätta aktiveringsenergin. Es,min värden har en jämförelsevis låg beräkningskostnad. Dock observerades ingen statistiskt signifikant korrelation mellan Es,min värdena och biologiska aktiviteten. Vidare observerades ingen statistiskt signifikant korrelation mellan aktiveringsenergin och biologiska aktiviteten och/eller Es,min värdena. Därmed fanns flera indikationer att den tänkta reaktionsmekanismen var felaktig. Under efterforskningen hittades en studie som visade att en-elektronreduktionsmekanismen var den mest troliga reaktionsmekanismen för den undersökta reaktionen. Detta kan vara en förklaring till varför en statistiskt signifikant korrelation kunde observeras mellan LUMO och biologiska aktiviteten, medan ingen korrelation observerades för Es,min, Vs,max och aktiveringsenergin mot biologiska aktiviteten. Avsaknaden av en korrelation för dessa parametrar anses bero på att den föreslagna reaktionsmekanismen var felaktig. Vidare studier hade behövts för att undersöka dessa parametrars förmåga att kunna förutse mutagenicitet. / Mutagenicity of various compounds is traditionally predicted by conventional in vivo and in vitro methods. However, transitioning to in silico methods would be beneficial both ethically and environmentally. The descriptors that can be used to predict mutagenicity are the lowest unoccupied molecular orbital (LUMO) energy, activation energy, the local minimum / maximum electrostatic potential energy (Vs,min/Vs,max), the minimum local electron attachment energy (Es,min), etc. The activation energy is a descriptor that can predict mutagenicity accurately provided that the reaction mechanism is known or can be assumed. However, determining the activation energy is computationally costly. Mutagen-X (MX) and its analogues (compounds with the same backbone but different functional groups, 29 compounds in total), are compounds of which the mutagenicity had been characterized by traditional means but recently also using an in silico method – molecular modeling. Molecular modeling had been successively employed in the study by Kari Tuppurainen [Source]; the LUMO of MX and its analogues had been computed and, importantly, the obtained values demonstrated a statistically significant correlation with the biological activity determined using Ames test. The aim of this thesis was to investigate whether the mutagenicity of MX and its analogues could also be determined by computing Es,min, Vs,max and the activation energy. The studied reaction was a Michael addition reaction between an amine group on the guanine nucleobase and the beta position of MX and its analogues. Therefore, the studied parameters (Es,min, Vs,max and the activation energy) were evaluated at the beta position. The computed Es,min values were correlated with the biological activity. Activation energies for MX and its analogues were also computed at the beta position and then correlated with the biological activity and Es,min values.  If a highly statistically significant correlation between the activation energy and Es,min values at the beta position would have been observed, that would indicate that Es,min values  could be used as a substitute for the activation energy. Es,min values have comparatively low computational cost. However, no statistically significant correlation between Es,min values and the biological activity was observed. Furthermore, no statistically significant correlation was observed between the activation energy and biological activity and/or Es,min values, respectively. Thus, there were several indications that the proposed reaction mechanism was incorrect. After consulting literature, we learned that the one electron reduction mechanism would be a more probable reaction mechanism. This could be an explanation as to why a highly statistically significant correlation could be observed for LUMO vs. the biological activity, whereas no correlation was observed for Es,min, Vs,max, the activation energy versus the biological activity. The absence of a correlation for these parameters is thought to be due to the proposed reaction mechanism being inaccurate. Additional studies would have to be performed to further investigate the predictive abilities for mutagenicity of the studied parameters.

Synthesis of antiaromatic polycyclic hydrocarbons (PHs) is challenging because the high energy of their highest occupied molecular orbital and low energy of their lowest unoccupied molecular orbital cause them to be reactive and unstable. In this work, two large antiaromatic acene analogues, namely, cyclopenta[pqr]indeno[2,1,7-ijk]tetraphene (CIT, 1a) and cyclopenta[pqr]indeno[7,1,2-cde]picene (CIP, 1b), as well as a curved antiaromatic molecule with 48 πelectrons, dibenzo[a,c]diindeno[7,1,2-fgh:7′,1′,2′-mno]-phenanthro[9,10-k]tetraphene (DPT, 1c), are synthesized on the basis of the corona of indeno[1,2-b]fluorene. These three antiaromatic PHs possess a narrow energy gap down to 1.55 eV and exhibit high kinetic stability under ambient conditions. Moreover, these compounds display reversible electron transfer processes in both the cathodic and anodic regimes. Their cation and anion radicals are characterized by in situ vis−NIR absorption and electron paramagnetic resonance spectroelectrochemistry. The X-ray crystallographic analysis confirms that while CIP and CIT manifest planar structures, DPT shows a curved πconjugated carbon skeleton. The synthetic strategy starting from ortho-substituted benzene units to construct five-membered rings in this work provides a unique entry to novel pentagon-embedding or curved antiaromatic polycyclic hydrocarbons. In addition, besides the detailed chemical and physical investigations, microscale single-crystal fiber field-effect transistors were also fabricated.

The knowledge on the conformations of amino acids is essential to understand the biochemical behaviors and physical properties of proteins. Comprehensive computational study is focused to understand the conformational landscape of three aromatic amino acids (AAAs): tryptophan, tyrosine, and phenylalanine. Three different density functionals (B3LYP, M06-2X and wB97X-D) were used with two basis sets of 6-31G(d) and 6-31+G(d,p) for geometry optimizations of the conformers of AAAs followed by the vibrational frequencies. The goal was to identify the right choice of density functional theory (DFT) level for conformational analysis of amino acids by comparing the computational data against the available experimental results. Calculated infrared (IR) frequency values indicated that wB97X-D/6-31+G(d,p) level is less favorable than other DFT levels in case of O-H and N-H stretching frequencies for the conformers of AAAs. The C=O stretching frequencies at different computational levels were in good agreement with the experimental results. Interactions of AAAs (tryptophan, tyrosine, and phenylalanine) and two cyclic amino acids (histidine and proline) individually with two finite-sized graphene sheets (C62H20 and C186H36) were explored using M06-2X/6-31G(d) level. Computational investigations of the binding of amino acids with graphene provide knowledge for designing of new graphene-based biological/biocompatible materials. Selected conformers for each amino acid with different orientations on the surface of graphene were examined. The purpose of computational study on graphene-amino acids interactions was to identify the preferred conformer of amino acid to bind on graphene as well as to find the influence of amino acid binding on the band gap of graphene. Different conformers of AAAs generally prefer parallel orientation through π-π interactions to bind with graphene. However, bent orientation is more preferred over parallel to bind on the surface of graphene in case of conformer having relative energy approximately equal to 5 kcal/mol for all three AAAs. Histidine generally exhibits higher binding affinity than proline to form complex with graphene. The binding energies in the aqueous medium were slightly lower than those obtained in the gas phase with some exceptions. The adsorption of amino acids did not affect the band gap of graphene.

Aus der riesigen Vielfalt organischer Materialien sind gerade die Phthalocyanine dafür bekannt geworden, auf verschiedenen kristallinen Substraten geordnete Strukturen auszubilden. Außerdem dienen diese Moleküle als Modellsysteme für grundlegende Untersuchungen zur Einstellung elektronischer und struktureller Eigenschaften durch gezielten Einbau eines Metallatoms in den zentralen Hohlraum. Die Strukturen der Adsorptionsschichten von verschiedenen Metallphthalocyaninen, funktionalisierten Phthalocyaninen und Naphthalocyaninen auf der Basaldebene des Graphits werden verglichen, um die Adsorptionsstruktur der einzelnen Moleküle innerhalb der Adsorptionsschicht zu verstehen. Das erlaubt uns die Untersuchung der Molekül-Molekül- und Molekül-Substrat-Wechselwirkungen in Abhängigkeit von Molekularadsorption des zentralen Metallatoms, der Geometrie, einzelner funktionellen Gruppen oder ähnlichem am Molekül. Der Vergleich der Adsorptionsstrukturen von Phthalocyaninen wie PdPc und PtPc, welche d8-Metalle enthalten, dient dem Verständnis für den Effekt des Metallatoms, speziell bei großen Ordnungszahlen. Während beide Moleküle ähnliche Arten von Adsorptionsstrukturen ausbilden weist die PtPc-Adsorptionsschicht eine außergewöhnlich hohe thermische Stabilität auf. Das wurde auf die stark Molekül-Molekül-Wechselwirkung zurückgeführt, die durch die Metallatome in der Adsorptionsschicht vermittelt wird. Der Effekt langer molekularer ‚Flügel’ wird durch den Vergleich der Adsorptionsstrukturen ebener Naphthalocyanine mit denen von ebenen Metallphthalocyaninen demonstriert. Naphthalocyanine bilden viel lockerer gepackte Adsorptionsschichten als Phthalocyanine, was von der stärkeren sterischen Abstoßung zwischen den Wasserstoffatomen in benachbarten molekularen ‚Flügeln’ herrührt. Cyano-funktionalisierte metallfreie Phthalocyanine zeigen als Adsorptionsschicht eine poröse Netzwerkstruktur. Es konnte gezeigt werden, dass durch die Sondenspitze hervorgerufene Störungen dieser Struktur durch die elektrostatische Wechselwirkung zwischen den Molekülen in der Adsorptionsschicht bald weider ausheilen. Schließlich ist durch den Vergleich von Adsorptionsstrukturen ebener Naphthalocyanine und nichtebener Zinn-Naphthalocyanine auch der Geometrieeffekt untersucht worden. Abweichend von allen anderen untersuchten ebenen Molekülen haben Zinn-Naphthalocyanine eine Adsorptionstruktur, die der des Graphits ähnlich ist (hexagonal). Deshalb überwiegt in diesem Fall die Wechselwirkung zwischen Molekül und Substrat, und die Adsorptionsstruktur folgt der Geometrie des Graphitsubstates. Darüberhinaus sind mit der Tunnelspektroskopie in Abhängigkeit vom Abstand zwischen der Spitze und der Probe die elektronischen Eigenschaften der Molekül-Substrat-Grenzfläche für Naphthalocyanin und Zinn-Naphthalocyanin untersucht worden.

Submitted by Etelvina Domingos (etelvina.domingos@ufpe.br) on 2015-03-12T18:57:13Z No. of bitstreams: 2 TESE Marconi Bezerra Costa.pdf: 4071497 bytes, checksum: 5ff606ff53fab5504c1ac18294e33669 (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) / Made available in DSpace on 2015-03-12T18:57:13Z (GMT). No. of bitstreams: 2 TESE Marconi Bezerra Costa.pdf: 4071497 bytes, checksum: 5ff606ff53fab5504c1ac18294e33669 (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Previous issue date: 2014-02 / CNPq / Baseados em cálculos DFT (Density Functional Theory) B3LYP/LANL1dz e na análise da distribuição de cargas atômicas para cupratos, metálicos e pnictídeos, demonstramos a ocorrência de ressonâncias não-sincronizadas de ligações covalentes no estado supercondutor, conforme prevê a teoria RVB (Resonating-Valence-Bond). Os modelos de cluster com as dangling bonds saturadas com hidrogênio nos átomos de fronteira, mostraram-se bastante apropriados para descrever os sistemas investigados. Para caracterizar o estado supercondutor, usamos como critério o gap de energia HOMO-LUMO, que deve ser da mesma ordem de grandeza do gap supercondutor. Para os cupratos, os resultados confirmam as previsões da RVB para a transferência de carga dos elementos hipereletrônicos para os hipoeletrônicos e o efeito da vacância de oxigênio na indução do estado supercondutor. Nos sistemas metálicos, encontramos a separação e o ordenamento de cargas em planos distintos, conforme previsto qualitativamente por Pauling. Nos pnictídeos, o gap HOMO-LUMO só é da mesma ordem de grandeza do gap experimental para os clusters dopados, e a dopagem induz uma separação de cargas no plano em que o dopante é inserido. Baseados nestes resultados, propomos combinações de elementos hipo e hipereletrônicos visando a obtenção de novos sistemas supercondutores que podem apresentar temperaturas críticas maiores do que as conhecidas atualmente. Estes resultados reforçam a teoria RVB como uma alternativa para descrever o fenômeno da supercondutividade.

Semiconducting aromatic-boron carbide composite/alloyed films formed by plasma enhanced chemical vapor deposition from carborane and aromatic precursors have been demonstrated to be excellent detectors for thermal neutrons because of the large 10B cross section. The electronic properties of these films derived from XPS show that the properties of boron carbide can be tuned by co-deposition of aromatic compounds and carborane. Aromatic doping results in narrower indirect band gaps (1.1 - 1.7 eV vs ~3 eV for orthocarborane-derived boron carbide without aromatics) and average charge transport lifetimes (as long as 2.5 ms for benzene-orthocarborane and 1.5 - 2.5 ms for indole-orthocarborane) that are superior to those of boron carbide (35 µs). The films also show enhanced electron-hole separation that is also superior to those of boron carbide where the states at the top of the valence band is made of aromatic components while states at the bottom of the conduction band is a combination of aromatic and carborane moeities. These properties result in greatly enhanced (~850%) charge collection, relative to films without aromatic content, in thermal neutron exposures at zero-bias, and are gamma-blind. Such films are therefore excellent candidates for zero-bias neutron detector applications. These properties also show little variation with increasing aromatic content beyond a critical concentration, indicating that at some point, excess aromatic results in the formation of regions of polymerized aromatic within the film, rather than in additional carborane/aromatic linkages. While previous studies on these aromatic-boron carbide materials indicate the potential for neutron detection due to the narrowed band gap, enhanced electron-hole separation and charge transport lifetimes compared to the boron carbide counterpart, the mechanisms of charge transport and photoconductivity (important for photovoltaic applications) of these materials have remained unexplored. Properties such as narrowed band gap, efficient electron-hole separation and long charge transport lifetimes, are also desirable in photovoltaic applications. This, plus ease of fabrication and environmental robustness makes aromatic-boron carbide films promising candidates for photovoltaic applications. Plasma enhanced chemical vapor deposition (PECVD) has been used to synthesize these aromatic-boron carbide composite films by co-deposition of pyridine, aniline or indole with orthocarborane/metacarborane. Film chemical composition and bonding were characterized by X-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), variable angle spectroscopic ellipsometry (VASE) and (in collaboration with Dowben Group at UNL) charge transport and photoconductivity measurements. Results show narrowed band gaps (indirect) where the top of the valence band is made up of the aromatic moiety and the conduction band minimum us made of aromatic and carborane moeities, improved charge carrier mobilities that is stoichiometry and frequency dependent (aniline-orthocarborane films). Photoconductivity measurement results obtained from ~2.6:1 indole-orthocarborane film show fourth quadrant conductivity. I(V) curves indicate a photocurrent of 2.36 µA at zero bias, with an appreciable open-circuit voltage of 1V. The ability for these aromatic-boron carbide films to operate at zero bias for both neutron detection and photovoltaic applications is an excellent advantage that indicates low cost of operation of these materials.

Computational investigations on semiconductor (silicon or germanium) clusters (Sinor Gen) in combination with transition metal (M) impurities are reviewed in this contribution. Emphasis is placed on investigations that focus on the size evolution features of MmSi n(or MmGen) such as the critical ligand number for the transition from exohedral to endohedral equilibrium geometry. Geometric, energetic, electronic, and magnetic characteristics of MmSi n or MmGen systems are discussed. It is pointed out that selected MmSin systems with n = 12 and n = 16 and MmGen with n = 10 or 12 and n = 16 emerge from present computational research in the size region of n ≤ 20 as the most promising candidates for building blocks of novel nanomaterials. In addition, comparison is made between MmSin and MmGen clusters.

Yes / Pharmaceutical salt, nitrofurantoin–4-dimethylaminopyridine (NF-DMAP), along with its native components NF and DMAP are scrutinized by FT-IR and FT-Raman spectroscopy along with density functional theory so that an insight into the H-bond patterns in the respective crystalline lattices can be gained. Two different functionals, B3LYP and wB97X-D, have been used to compare the theoretical results. The FT-IR spectra obtained for NF-DMAP and NF clearly validate the presence of C33–H34⋅⋅⋅O4 and N23–H24⋅⋅⋅N9 hydrogen bonds by shifting in the stretching vibration of –NH and –CH group of DMAP+ towards the lower wavenumber side. To explore the significance of hydrogen bonding, quantum theory of atoms in molecules (QTAIM) has been employed, and the findings suggest that the N23–H24⋅⋅⋅N9 bond is a strong intermolecular hydrogen bond. The decrement in the HOMO-LUMO gap, which is calculated from NF → NF-DMAP, reveals that the active pharmaceutical ingredient is chemically less reactive compared to the salt. The electrophilicity index (ω) profiles for NF and DMAP confirms that NF is acting as electron acceptor while DMAP acts as electron donor. The reactive sites of the salt are plotted by molecular electrostatic potential (MEP) surface and calculated using local reactivity descriptors. / SERB, DST, India, for providing the National Post-doctoral Fellowship (Project File Number: PDF/2016/003162); Central Facility for Computational Research (CFCR), University of Lucknow; Newton-Bhabha Ph.D. placement award (2017); Royal Society seed corn research grant (2018-19)

Une étude théorique basée sur la théorie de la fonctionnelle de la densité (DFT) a été réalisée sur un ensemble de complexes organométalliques mono, di et trinucléaires à base de fer, de ruthénium ou de platine. Les résultats obtenus sur les complexes mononucléaires à base de fer révèlent que la longueur du chaînon π de carbone n'a qu'une influence mineure sur les propriétés électroniques mais affectent les propriétés spectroscopiques. Une étude entreprise sur des systèmes contenant un ligand aromatique polycyclique a montré que la présence de molécules de solvant coordonnant abaisse les barrières énergétiques et par conséquence, facilite le réarrangement haptotropique du greffon organoruthénium sur le ligand organique. L'étude théorique réalisée sur des nouveaux systèmes de type [2]rotaxane a révélé que la longueur du chaînon π du fil moléculaire enfilé au travers d'un macrocycle influence les énergies d'interaction non covalente dans ces systèmes. Il a été montré que ces interactions non covalentes sont principalement dues à des liaisons hydrogène formées entre le macrocycle et le fil moléculaire. / A theoretical study based on density functional theory (DFT) was performed on several series of organometallic mono, bi and trinuclear iron, ruthenium and platinum based complexes. The results on mononuclear iron based complexes indicate that the length of the π carbon bridge in these systems has only a minor influence on the electronic properties but affect somewhat the spectroscopic properties. A study was conducted on systems containing polycyclic aromatic ligand showing that the presence of a coordinating solvent molecule in the viscinity of the metal atom bound on top of the polycycle strongly lowers the energy barriers and consequently facilitates the haptotropic rearrangement of the grafted organoruthenium entity. The theoretical study of new systems of [2]rotaxane type has revealed that the length of the π bridge of the molecular wire threaded in a macrocycle influences the weak noncovalent interaction energies in these systems. It has been shown that these noncovalent interactions are mainly due to hydrogen bonds formed between the macrocycle and the threaded molecular wire.