Neste trabalho estudamos o espectro de absorção da clorofila d, incluindo os efeitos do solvente metanol, utilizando a Teoria do Funcional da Densidade Dependente do Tempo em combinação com o método s-QM/MM. Diferentes abordagens para a descrição do meio solvente, que vão desde o modelo contínuo polarizável até a inclusão de moléculas explícitas do solvente, são utilizadas. Observamos que a inclusão do solvente desloca o espectro, em relação ao calculado em vácuo, para o vermelho. A inclusão de 20 moléculas explícitas de metanol e 880 representadas como as cargas pontuais do seus átomos para a descrição do meio solvente foi a que melhor concordou com os valores experimentais. Mediante cálculos de mecânica quântica obtivemos para o complexo composto por a molécula de clorofila d e apenas uma de metanol explícita um deslocamento do átomo de magnésio da clorofila d em relação ao anel de 0,31 Å. Mediante a analise da função de distribuição radial de pares obtida da simulação clássica comprovamos que esse átomo de magnésio é penta-coordenado. Além disso, é usada uma estrutura simplificada da clorofila d baseado na localização dos orbitais moleculares participantes das transições eletrônicas com o objetivo de diminuir o custo computacional dos cálculos de mecânica quântica. Os espectros calculados para a clorofila d não apresentaram diferenças significativas com os calculados para a simplificação proposta. Como complementação o espectro Raman da clorofila d isolada é calculado mediante DFT e alguns dos modos normais são caracterizados. / In this work we study the absorption spectrum of chlorophyll d, including the effects of the solvent methanol, using the Time Dependent Density Functional Theory in combination with the method s-QM/MM. Different approaches for the description of the solvent medium, ranging from the polarizable continuum model to the inclusion of explicit solvent molecules, are used. We note that the inclusion of solvent shifts the spectrum, relative to that calculated in vacuum, to the red side of the spectrum. The inclusion of 20 explicit molecules of methanol and 880 represented as point charges of their atoms for the description of the solvent medium was the one that best agreed with the experimental values. By quantum mechanics calculations we obtained for the complex composed of the molecule of chlorophyll d and only one explicit methanol molecule a displacement of the magnesium atom of chlorophyll d in relation to the ring of 0,31 Å. By means of the analysis of the radial distribution function obtained from the classic simulation we can see that this atom of magnesium is penta-coordinated. In addition, a simplified structure of chlorophyll d is used based on the location of the molecular orbitals involved in the electronic transitions in order to reduce the computational cost of quantum mechanics calculations. The spectra calculated for chlorophyll d did not show significant differences with those calculated for the proposed simplification. As a complement the Raman spectrum of isolated chlorophyll d is calculated by DFT and some of the normal modes are characterized.

Estudamos as propriedades estruturais e eletrônicas da molécula emodina (EM), em diferentes condições, do ponto de vista experimental e teórico. Numa primeira parte, realizamos medidas do espectro eletrônico de absorção da EM, em meio solvente (água, clorofórmio e metanol). Nessa parte, obtivemos que o solvente provoca pouco efeito nos deslocamentos das bandas. Numa segunda parte, estudamos a EM, isoladamente e nos três solventes, através de cálculos quânticos com funcional de densidade (B3LYP), conjunto de função base de Pople (6-31G*) e modelo contínuo polariz ável (PCM). Como principais resultados obtivemos que a EM é rígida a menos da orientação relativa das 3 hidroxilas. A mudança orientacional nessas hidroxilas pode provocar formação de até 2 ligações de hidrogênio intramolecular (o que estabiliza sua geometria) e conseqüente uma diminuição no momento dipolo de 5.5 a 1.7D (o que desestabiliza sua interação com a água). Numa terceira parte, realizamos simulações com método Monte Carlo e Dinâmica Molecular em solução. Nessa parte, obtivemos que as ligações de hidrogênio intramoleculares são raramente quebradas devido as interações com o solvente e isso atribui a EM um caráter hidrofóbico. Adicionalmente, utilizando Teoria de Perturbação Termodinâmica nas simulações, calculamos a variação de energia livre de solvatação da EM em partição água/clorofórmio e água/- metanol e obtivemos -2.6 e -4.9 kcal/mol, respectivamente. Esse resultado está em boa concordância com o resultado experimental de -5.6 kcal/mol para partição de água/octanol. Por último, realizamos cálculos do espectro eletrônico de absorção da EM, isoladamente e nos três solventes, considerando as moléculas através do modelo, contínuo de solvente (SCRF) e explícito de solvente, com o método INDO/CIS. Nessa parte, obtivemos que o efeito do solvente é bem descrito teoricamente. / We study the structural and electronic properties of the emodin (EM) in different solvents of experimental and theoretical the point of view. We started performing measurements of the UV-Vis absorption spectrum of the EM in solution (water, chloroform and methanol). Our main result is that the solvent causes little effect on shifts the bands. In the second part of this work, we performing quantum calculations of isolated EM and in the three solutions using density functional (B3LYP), a set of Pople basis function (6-31G*) and the polarizable continuum model (PCM). In this part, our result is that EM presents a rigid conformation unless the orientation of its 3 hydroxyls. The change in these hydroxyls orientation can form up to 2 intramolecular H-bonds (which stabilizes its geometry) and causes a decrease in the dipole moment from 5.5 to 1.7D (which destabilizes its interaction with water). In the third part of this work, we performing Monte Carlo and Molecular Dynamics simulations in solution. Our main result is that the intramolecular H-bonds are rarely broken, even in aqueous solution, and these give to EM a hydrophobic character. Additionally, using Thermodynamics Perturbation Theory in the simulations, we calculate variations of free energy of solvation of EM in partition of water/chloroform and water/methanol and obtained -2.6 and -4.9kcal/mol, respectively. This last result is in good agreement with the experimental result[3] of -5.6kcal/mol for partition of water/octanol. Finally, we performing calculations of UV-Vis absorption spectrum of isolated EM and in the three solutions. In this calculations, we considering the molecules through the continuum solvent (SCRF) and explicit solvent model with the method INDO/CIS. In this part, we obtaining that effect of solvent is well described theoretically.

Neste trabalho estudamos o espectro de absorção da clorofila d, incluindo os efeitos do solvente metanol, utilizando a Teoria do Funcional da Densidade Dependente do Tempo em combinação com o método s-QM/MM. Diferentes abordagens para a descrição do meio solvente, que vão desde o modelo contínuo polarizável até a inclusão de moléculas explícitas do solvente, são utilizadas. Observamos que a inclusão do solvente desloca o espectro, em relação ao calculado em vácuo, para o vermelho. A inclusão de 20 moléculas explícitas de metanol e 880 representadas como as cargas pontuais do seus átomos para a descrição do meio solvente foi a que melhor concordou com os valores experimentais. Mediante cálculos de mecânica quântica obtivemos para o complexo composto por a molécula de clorofila d e apenas uma de metanol explícita um deslocamento do átomo de magnésio da clorofila d em relação ao anel de 0,31 Å. Mediante a analise da função de distribuição radial de pares obtida da simulação clássica comprovamos que esse átomo de magnésio é penta-coordenado. Além disso, é usada uma estrutura simplificada da clorofila d baseado na localização dos orbitais moleculares participantes das transições eletrônicas com o objetivo de diminuir o custo computacional dos cálculos de mecânica quântica. Os espectros calculados para a clorofila d não apresentaram diferenças significativas com os calculados para a simplificação proposta. Como complementação o espectro Raman da clorofila d isolada é calculado mediante DFT e alguns dos modos normais são caracterizados. / In this work we study the absorption spectrum of chlorophyll d, including the effects of the solvent methanol, using the Time Dependent Density Functional Theory in combination with the method s-QM/MM. Different approaches for the description of the solvent medium, ranging from the polarizable continuum model to the inclusion of explicit solvent molecules, are used. We note that the inclusion of solvent shifts the spectrum, relative to that calculated in vacuum, to the red side of the spectrum. The inclusion of 20 explicit molecules of methanol and 880 represented as point charges of their atoms for the description of the solvent medium was the one that best agreed with the experimental values. By quantum mechanics calculations we obtained for the complex composed of the molecule of chlorophyll d and only one explicit methanol molecule a displacement of the magnesium atom of chlorophyll d in relation to the ring of 0,31 Å. By means of the analysis of the radial distribution function obtained from the classic simulation we can see that this atom of magnesium is penta-coordinated. In addition, a simplified structure of chlorophyll d is used based on the location of the molecular orbitals involved in the electronic transitions in order to reduce the computational cost of quantum mechanics calculations. The spectra calculated for chlorophyll d did not show significant differences with those calculated for the proposed simplification. As a complement the Raman spectrum of isolated chlorophyll d is calculated by DFT and some of the normal modes are characterized.

Um procedimento baseado no uso sequencial de simulação Monte Carlo e cálculos de Mecânica Quântica é proposto e usado para o tratamento de efeitos de solvente, com especial atenção parao sovatocromismo no espectro de absorção molecular. A ideia básica é realizar simulações clássicas com o método Monte Carlo para gerar estruturas supermoleculares do sistema em solução e em seguida tratar estas supermoléculas (soluto, solvente e suas interações) com cálculos quânticos. Um modelo totalmente discreto do solvente é utilizado e, portanto, o uso de meios dielétricos contínuos é dispensado. Neste procedimento, as supermoléculas são compostas por uma molécula do soluto rodeada pela primeira camada de solvatação definida através da função distribuição. Os efeitos de solvente são calculados usando médias configuracionais sobre estruturas supermoleculares descorrelacionadas obtidas através de análises estatísticas das simulações. Como aplicação, os deslocamentos espectrais da primeira banda de absorção do benzeno 1B2u(- *), devido a presença de diversos solventes, foram analisados e calculados. Boa concordância com os resultados experimentais foram obtidos. / A approach based on the sequential use of Monte Carlo simulation and Quantum Mechanics is proposed and use for the treatment of solvent effects with special attention to solvatochromic shifts. The basic Idea is to perform a classical Monte Carlo simulation to generate supermolecular structures of the system, then to treat these supermolecules (solute, solvent and all its interaction) by quantum mechanics. This is a totally discrete modelo f the solvent that avoids the use of a dielectric continuum. In this approach, the supermolecules are composed by the solute molecule surrounded by the first solvation Shell as determined by the distribution function. The solvent effects are calculated using ensemble average over uncorrelated supermolecular structures obtained by statistical analysis. As na application, the spectral shifts of the 1B2u(- *) trnsition of benzene in different solvents are investigated. Good agreement with the experimental results are obtained.

In this licentiate thesis the luminescence properties of two flexible conjugated dyes have been studied. The first, Pt1, is a platinum(II) acetylide chromophore used in optical power limiting materials. The second is a set of optical probes known as luminescent conjugated oligothiophenes (LCOs), which are used to detect and characterize the protein structures associated with amyloid diseases such as Alzheimer’s disease. MM3 and CHARMM force field parameters have been derived for the Pt1 chromophore and LCOs, respectively, based on potential energy surface references calculated at the density functional theory (DFT)/B3LYP level of theory. The parameters have been used to perform room temperature molecular dynamics simulations of the chromophores in solvent, where tetrahydrofuran was used for Pt1 and water for the LCOs. Conformationally averaged absorption spectra were obtained, based on response theory calculations at the time-dependent DFT(TDDFT)/CAM-B3LYP level of theory for a selection of structures from the simulations. For one of the LCOs, p-HTAA, force field parameters were also created describing the dominant first excited state, based on TDDFT/B3LYP reference potential energy surfaces. These were used for molecular dynamics simulations of the chromophore in the excited state, allowing the creation of an emission spectrum. A theoretically obtained Stokes shift of 112 nm could be computed based on the absorption and emission spectra, which is in good agreement with the experimental value of 124 nm. In addition, a quantum mechanics/molecular mechanics study of the effects of solvation on the absorption properties of the p-HTAA chromophore in water has been conducted, resulting in two models for including these effects in the averaged spectra. The first includes explicit water molecules in the form of point charges and polarizable dipole moments, and results in an absorption wavelength that is blueshifted by 2 nm from a high quality reference calculation. The second model involves the complete removal of the solvent as well as the ionic groups of the chromophore. The resulting absorption wavelength is blueshifted by an additional 4 nm as compared to the first model, but requires only one fifth of the computational resources.

<p>Early processes following photon absorption by the photosynthetic pigment-protein complex photosystem I (PS I) have been the subject of decades of research, yet many questions remain in this area of study. Among the trickiest to investigate is the role of the PS I reaction center’s (RC’s) two accessory (A_‑1) chlorophyll (Chl) cofactors as primary electron donors or acceptors, oxidizing the special pair (P₇₀₀) of Chls or reducing a nominal primary electron acceptor (A₀) Chl in the first electron transfer step. Such processes, which occur on a picosecond timescale, have long been studied via ultrafast spectroscopy, though difficulty lies in distinguishing among signals from early processes, which have similar lifetimes and involve many identical pigments. In this work, we used steady-state and ultrafast optical pump-probe spectroscopies on PS I trimers from wildtype and mutant strains of the cyanobacterium <i>Synechocystis</i> sp. PCC 6803 in which an asparagine amino acid residue near A_‑1 had been replaced with methionine on one or both sides of the RC. We also conducted an identical set of experiments on mutants in which A₀ was similarly targeted, as well as studied the effects on the A₀ absorption spectrum of a third category of mutations in which a peripheral H‑bond to A₀ was lost. Steady-state absorption spectroscopy revealed that many of these mutations caused mild Chl deficiencies in the light-capturing antenna of PS I without necessarily preventing organisms’ growth. More importantly, we determined that contrary to certain hypotheses, A_‑1 is the most likely true first electron acceptor, as reasoned from observing rapid triplet state formation in double A_‑1 mutants. We also concluded from non-additive detrimental effects of single-side mutations that if one RC branch is damaged at the level of A₀ or A_‑1, electron transfer may be redirected along the intact branch. This may help explain the conservation of two functional RC branches in PS I over many generations of natural selection, despite the additional cost to organisms of manufacturing both.</p>

No description available.

<div>Self-assembled templates allow the creation of many complex arrays of nanostructures, which would be extremely difficult and expensive, if not impossible, to realize using any of the other available fabrication techniques. The complexity of these advanced nanostructures, synthesized using the various template assisted electrodeposition techniques, can be controlled to nanometer scale range by tuning the structural properties of the template, which is achieved by adjusting its various growth parameters during the self-assembly process.</div><div>Electrodeposition allows the creation of arrays of various metallic and semiconducting nanostructures. Monitoring the electrodeposition conditions permit the creation of single crystalline nanostructures of a particular material, or the formation of heterostructures using multiple electrodeposition steps. This work demonstrates the template assisted electrodeposition of vertically aligned nanowire arrays, both straight and branched, of metals, and a direct bandgap, III-V semiconductor, indium antimonide (InSb), which has one of the smallest known bandgap of any material. The template assisted electrodeposition of metallic, and InSb inverse opal (IO) structures is also shown, and the fabrication of a novel zipper shaped nanostructure by laser photomodification of a Ni IO structure is reported.</div><div>The optical characterization of the various nanostructures realized in this work have been examined. The results from this work confirm the ability to tune the optical spectra of nanostructures of the same material with similar volume fill fractions by structural modulation, where the different optical responses can be attributed to the structural differences of the actual structure as opposed to the material properties of the solid.</div>

Aggregate aus Molekülen, in denen die Moleküle über ihre elektronischen Übergangsdipole miteinander wechselwirken, finden wegen ihrer besonderen optischen und Energietransfer-Eigenschaften vielfach Anwendung in Natur, Technik, Biologie und Medizin. Beispiele sind die wechselwirkenden Farbstoffmoleküle, die in den Lichtsammelkomplexen Photosynthese betreibender Lebewesen Sonnenlicht absorbieren und die Energie als elektronische Anregung hocheffizient zu Reaktionszentren weiterleiten, oder Aggregate aus tausenden von organischen Farbstoffmolekülen in einem flüssigen Lösungsmittel. Die Wechselwirkung der Moleküle (Monomere) führt zu über mehrere Moleküle delokalisierten angeregten elektronischen Zuständen, die die Energietransfer-Dynamik und die Absorptionsspektren der Aggregate prägen. Die Lichtabsorption und der Energietransfer in molekularen Aggregaten werden oft stark von Vibrationen beeinflusst, sowohl von internen Vibrationsfreiheitsgraden der Monomere als auch von Vibrationen der Umgebung (z. B. das Proteingerüst in Lichtsammelkomplexen oder eine Flüssigkeitsumgebung), an die die elektronische Anregung koppelt. Da es schwierig ist, diese Vibrationen in die theoretische Beschreibung des Transfers und der Spektren einzubeziehen, ist ihr genauer Einfluss noch nicht gut verstanden. Um dieses Verständnis zu verbessern, entwickeln wir in dieser Arbeit neue Berechnungsmethoden und untersuchen damit die Auswirkungen der Vibrationen. Zuerst betrachten wir die diskreten internen Vibrationsfreiheitsgrade der Monomere. Dazu haben wir eine effiziente numerische Methode entwickelt, die es uns erlaubt, mehrere Freiheitsgrade pro Monomer explizit einzubeziehen und die volle Schrödinger-Gleichung zu lösen. Mit den Modellrechnungen können wir experimentelle Aggregat-Spektren der Helium-Nanotröpfchen-Isolation-Spektroskopie, mit der man die einzelnen Vibrationslinien der Monomere auflösen kann, zum ersten Mal quantitativ reproduzieren. In früheren theoretischen Behandlungen wurde oft nur ein einziger Vibrationsfreiheitsgrad pro Monomer berücksichtigt – nun zeigen wir, dass die Einbeziehung möglichst vieler Freiheitsgrade für eine realistische Beschreibung von Aggregat-Spektren wichtig ist. Um neben den internen Vibrationen auch den Einfluss der Umgebung beschreiben zu können, nutzen wir den Zugang offener Quantensysteme und nehmen an, dass die elektronische Anregung an ein strukturiertes Kontinuum von Vibrationsfreiheitsgraden koppelt. Erstmals wenden wir die sogenannte nicht-markovsche Quanten-Zustands-Diffusion auf die molekularen Aggregate an, wodurch wir mit Hilfe einer Näherung Spektren und Transfer mit einer sehr effizienten stochastischen Schrödinger-Gleichung berechnen können. So können wir Merkmale gemessener Aggregat-Spektren, wie das schmale J-Band und das breite strukturierte H-Band, in Abhängigkeit der Anzahl der Monomere und der Wechselwirkungsstärke zwischen den Monomeren beschreiben. Auch können wir den Übergang von kohärentem zu inkohärentem Transfer erfassen. Eine für den Transfer relevante Größe ist die Anzahl der kohärent gekoppelten Monomere im Aggregat. Diese schätzt man häufig aus der Verschmälerung des Aggregat-Spektrums ab. Wir finden jedoch für verschiedene Spektraldichten des Vibrationskontinuums sehr unterschiedliche Verschmälerungen des Aggregat-Spektrums, die wir analytisch erklären. So zeigen wir, dass die bisherige einfache Abschätzung der Anzahl der kohärent gekoppelten Monomere nicht gerechtfertigt ist, da die Verschmälerung stark vom angenommenen Modell abhängt.

Aggregate aus Molekülen, in denen die Moleküle über ihre elektronischen Übergangsdipole miteinander wechselwirken, finden wegen ihrer besonderen optischen und Energietransfer-Eigenschaften vielfach Anwendung in Natur, Technik, Biologie und Medizin. Beispiele sind die wechselwirkenden Farbstoffmoleküle, die in den Lichtsammelkomplexen Photosynthese betreibender Lebewesen Sonnenlicht absorbieren und die Energie als elektronische Anregung hocheffizient zu Reaktionszentren weiterleiten, oder Aggregate aus tausenden von organischen Farbstoffmolekülen in einem flüssigen Lösungsmittel. Die Wechselwirkung der Moleküle (Monomere) führt zu über mehrere Moleküle delokalisierten angeregten elektronischen Zuständen, die die Energietransfer-Dynamik und die Absorptionsspektren der Aggregate prägen. Die Lichtabsorption und der Energietransfer in molekularen Aggregaten werden oft stark von Vibrationen beeinflusst, sowohl von internen Vibrationsfreiheitsgraden der Monomere als auch von Vibrationen der Umgebung (z. B. das Proteingerüst in Lichtsammelkomplexen oder eine Flüssigkeitsumgebung), an die die elektronische Anregung koppelt. Da es schwierig ist, diese Vibrationen in die theoretische Beschreibung des Transfers und der Spektren einzubeziehen, ist ihr genauer Einfluss noch nicht gut verstanden. Um dieses Verständnis zu verbessern, entwickeln wir in dieser Arbeit neue Berechnungsmethoden und untersuchen damit die Auswirkungen der Vibrationen. Zuerst betrachten wir die diskreten internen Vibrationsfreiheitsgrade der Monomere. Dazu haben wir eine effiziente numerische Methode entwickelt, die es uns erlaubt, mehrere Freiheitsgrade pro Monomer explizit einzubeziehen und die volle Schrödinger-Gleichung zu lösen. Mit den Modellrechnungen können wir experimentelle Aggregat-Spektren der Helium-Nanotröpfchen-Isolation-Spektroskopie, mit der man die einzelnen Vibrationslinien der Monomere auflösen kann, zum ersten Mal quantitativ reproduzieren. In früheren theoretischen Behandlungen wurde oft nur ein einziger Vibrationsfreiheitsgrad pro Monomer berücksichtigt – nun zeigen wir, dass die Einbeziehung möglichst vieler Freiheitsgrade für eine realistische Beschreibung von Aggregat-Spektren wichtig ist. Um neben den internen Vibrationen auch den Einfluss der Umgebung beschreiben zu können, nutzen wir den Zugang offener Quantensysteme und nehmen an, dass die elektronische Anregung an ein strukturiertes Kontinuum von Vibrationsfreiheitsgraden koppelt. Erstmals wenden wir die sogenannte nicht-markovsche Quanten-Zustands-Diffusion auf die molekularen Aggregate an, wodurch wir mit Hilfe einer Näherung Spektren und Transfer mit einer sehr effizienten stochastischen Schrödinger-Gleichung berechnen können. So können wir Merkmale gemessener Aggregat-Spektren, wie das schmale J-Band und das breite strukturierte H-Band, in Abhängigkeit der Anzahl der Monomere und der Wechselwirkungsstärke zwischen den Monomeren beschreiben. Auch können wir den Übergang von kohärentem zu inkohärentem Transfer erfassen. Eine für den Transfer relevante Größe ist die Anzahl der kohärent gekoppelten Monomere im Aggregat. Diese schätzt man häufig aus der Verschmälerung des Aggregat-Spektrums ab. Wir finden jedoch für verschiedene Spektraldichten des Vibrationskontinuums sehr unterschiedliche Verschmälerungen des Aggregat-Spektrums, die wir analytisch erklären. So zeigen wir, dass die bisherige einfache Abschätzung der Anzahl der kohärent gekoppelten Monomere nicht gerechtfertigt ist, da die Verschmälerung stark vom angenommenen Modell abhängt.