Linear dichroism in Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy has been used to determine molecular orientation at surfaces and in microscopic domains. However, the molecular orientation of n-alkanes cannot be derived unambiguously from their NEXAFS spectra due to the inadequate understanding of the character of the relevant spectroscopic features in the NEXAFS spectra of n-alkanes (i.e. C 1s to sigma*C-H, C 1s to sigma*C-C transitions).<p>We have studied the linear dichroism in the NEXAFS spectra of n-alkane thin films by using angular dependent NEXAFS spectroscopy to explore the molecular orientation of hexacontane (HC, n-C60H122). The HC thin films were epitaxially grown onto the cleaved NaCl (001) surfaces by physical vapor deposition. NEXAFS spectra of the HC thin film were acquired at different angles using STXM microscopy. A detailed analysis of the angular dependence of the NEXAFS spectra of the HC thin film helps to understand the relationship between the linear dichroism and the molecular orientation in n-alkane molecules. This linear dichroism in the NEXAFS spectroscopy of n-alkanes is relevant for quantitative measurements of molecular orientation, such as for the microanalysis of crystalline organic materials. <p>The linear dichroism of the NEXAFS resonances for n-alkanes has also been studied by ab initio calculations. These calculations were carried out on an isolated n-alkane molecule and a cluster of n-alkane molecules. The calculations on an isolated n-alkane molecule are used to study the linear dichroism for the NEXAFS resonances above the C 1s IP. The cluster calculations account for matrix effects in the NEXAFS features of condensed n-alkanes. A comparison of calculations on an isolated molecule and on a cluster of molecules provides information on how the NEXAFS spectra change from gas phase to condensed phase and determines the linear dichroism of each NEXAFS feature below the C 1s IP.<p>In the process of preparing n-alkane thin films for the study of linear dichroism, the morphology and molecular orientation of n-alkane thin films with different chain length (n-C36H74 and n-C60H122) have also been investigated by the NEXAFS spectroscopy and microscopy. These thin films were epitaxially grown onto cleaved NaCl (001) surfaces by physical vapor deposition. The results revealed that the morphology and molecular orientation of n-alkane thin films depend on the chain length and deposition parameters, such as substrate temperature. These observations have been rationalized by the thermodynamics of nucleation and the kinetics of growth.

Linear dichroism in Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy has been used to determine molecular orientation at surfaces and in microscopic domains. However, the molecular orientation of n-alkanes cannot be derived unambiguously from their NEXAFS spectra due to the inadequate understanding of the character of the relevant spectroscopic features in the NEXAFS spectra of n-alkanes (i.e. C 1s to sigma*C-H, C 1s to sigma*C-C transitions).<p>We have studied the linear dichroism in the NEXAFS spectra of n-alkane thin films by using angular dependent NEXAFS spectroscopy to explore the molecular orientation of hexacontane (HC, n-C60H122). The HC thin films were epitaxially grown onto the cleaved NaCl (001) surfaces by physical vapor deposition. NEXAFS spectra of the HC thin film were acquired at different angles using STXM microscopy. A detailed analysis of the angular dependence of the NEXAFS spectra of the HC thin film helps to understand the relationship between the linear dichroism and the molecular orientation in n-alkane molecules. This linear dichroism in the NEXAFS spectroscopy of n-alkanes is relevant for quantitative measurements of molecular orientation, such as for the microanalysis of crystalline organic materials. <p>The linear dichroism of the NEXAFS resonances for n-alkanes has also been studied by ab initio calculations. These calculations were carried out on an isolated n-alkane molecule and a cluster of n-alkane molecules. The calculations on an isolated n-alkane molecule are used to study the linear dichroism for the NEXAFS resonances above the C 1s IP. The cluster calculations account for matrix effects in the NEXAFS features of condensed n-alkanes. A comparison of calculations on an isolated molecule and on a cluster of molecules provides information on how the NEXAFS spectra change from gas phase to condensed phase and determines the linear dichroism of each NEXAFS feature below the C 1s IP.<p>In the process of preparing n-alkane thin films for the study of linear dichroism, the morphology and molecular orientation of n-alkane thin films with different chain length (n-C36H74 and n-C60H122) have also been investigated by the NEXAFS spectroscopy and microscopy. These thin films were epitaxially grown onto cleaved NaCl (001) surfaces by physical vapor deposition. The results revealed that the morphology and molecular orientation of n-alkane thin films depend on the chain length and deposition parameters, such as substrate temperature. These observations have been rationalized by the thermodynamics of nucleation and the kinetics of growth.

Controlling molecular orientation is of great importance in organic thin films due to the fact that the fundamental properties of functional nanomaterials depend on molecular orientation at the nanoscale. However, controlling molecular orientation cannot be achieved without having an extensive understanding about the controlling factors in the organic film growth processes. Most previous studies have been devoted to monolayer structures. The structure of multilayer films has not been well investigated. This study was performed using a phenomenological approach, in which the morphology and orientation of n-alkane thin films were studied as a function of substrate identity, interface treatment, substrate temperature and deposition rate. The experimental techniques that were used include IR-spectroscopy, polarized optical microscopy, and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and X-ray microscopy. The kinetic and thermodynamic factors that govern the orientation of organic thin films were extracted from the experimental results, and generalized to make a framework by which the morphology and orientation of organic films can be predicted. Epitaxial growth was specifically considered as a method to pattern organic thin films. In epitaxial growth, the oriented crystals of an organic film grow on a crystalline substrate such that the structure of the substrate is copied by the deposit crystals. For epitaxy it is required that the lattice planes of two crystals are parallel and similar in the lattice points spacing. A minor part of this dissertation is devoted to epitaxy in an inorganic system. One of the favorable consequences of epitaxial growth in inorganic systems is lattice strain that alters the electronic properties of semiconductor devices. A synchrotron based experimental method has been developed to quantitatively measure the degree of strain in Si1-xGex alloy films grown epitaxially on the Si(100) substrate.

The objectives of this study were to characterize residual feed intake (RFI) in growing bulls and heifers and in mid-gestation females to examine relationships with performance, body composition, feeding behavior, digestibility (DMD) and heart rate (HR) and evaluate the impact of RFI on bull fertility and cow forage utilization. Additionally, use of the n-alkane method to predict individual animal variations in intake was investigated. To accomplish these objectives, multiple RFI studies were conducted. In all studies RFI was computed as the difference between actual and expected DMI from linear regression of DMI on mid-test metabolic BW and ADG. To evaluate phenotypic relationships between feed efficiency, scrotal circumference (SC) and semen-quality an experiment was conducted with yearling bulls (N=204). Residual feed intake was not correlated with BW and ADG, but was positively associated with 12th-rib back fat (BF) such that the more efficient bulls were leaner. Bulls with low RFI had similar SC and progressive motility of sperm compared to high-RFI bulls. However percent normal sperm were weakly associated with RFI in a negative manner. To examine phenotypic relationships between heifer postweaning RFI, and performance, efficiency, HR, and DMD of mid-gestation cows, RFI was measured in growing Bonsmara heifers (N=175). Forty-eight heifers with divergent RFI were retained for breeding. Subsequently, intake, performance and feeding behavior was measured on mid-gestation females. Pregnant females classified as having low postweaning RFI continued to consume 22% less feed, spent 25% less time eating, and had 7% lower HR while maintaining similar BW, ADG and body composition compared to high RFI females. A moderate association between RFI in growing heifers and subsequent efficiency of forage utilization in pregnant cows was found. Growing heifers identified as efficient had greater DMD, however DMD in mature cows was similar between RFI groups. The n-alkane method of predicting intake detected differences in intake between divergent RFI groups in mid-gestation females. Results from this study indicate that inclusion of RFI as a component of a multi-trait selection program will improve feed efficiency of growing animals and mid-gestation females with minimal impacts on growth, body composition, and fertility traits.

京都大学 / 0048 / 新制・課程博士 / 博士(エネルギー科学) / 甲第19819号 / エネ博第325号 / 新制||エネ||65(附属図書館) / 32855 / 京都大学大学院エネルギー科学研究科エネルギー社会・環境科学専攻 / (主査)教授 東野 達, 教授 坂 志朗, 准教授 亀田 貴之 / 学位規則第4条第1項該当 / Doctor of Energy Science / Kyoto University / DFAM

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Polymers possess bulk elastic properties due to entanglement of the polymer chains, not due to an inherit elasticity found within the monomers. An appropriately disubstituted bicyclo[8.8.8]hexacosane monomer should impart inherit elasticity when utilized in a polymer. A stochastic search of disubstituted bicyclo[m.m.m]alkanes demonstrated that these systems will adopt an out,out configuration and bicycles with medium and large values of m possess variable bridgehead-bridgehead distances. A stochastic search of disubstituted bicyclo[8.8.n]alkanes demonstrated an even-odd effect within the bite-angle of the bicycle. Two model compounds with methyl and hydroxyl groups at the bridgehead carbons were synthesized that demonstrated solid-state structures that correlated extremely well with the computational search. The solid-state structures were observed with both an out,out configuration and variable bridgehead-bridgehead distances. To investigate this hypothesis, polyurethanes will be made from the following diol monomers: 1,10-decanediol, a monocyclic diol, and a bicyclo[8.8.8]hexacosane diol.

Submitted by Biblioteca de Pós-Graduação em Geoquímica BGQ (bgq@ndc.uff.br) on 2016-09-05T17:15:32Z No. of bitstreams: 1 MARTINS G.S. 2016.pdf: 11805657 bytes, checksum: 112f32d3100030fafec5c3f6222a4b72 (MD5) / Made available in DSpace on 2016-09-05T17:15:32Z (GMT). No. of bitstreams: 1 MARTINS G.S. 2016.pdf: 11805657 bytes, checksum: 112f32d3100030fafec5c3f6222a4b72 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Universidade Federal Fluminense. Instituto de Química. Programa de Pós-Graduação em Geociências - Geoquímica. Niterói, RJ / Este trabalho consiste na reconstrução paleoambiental de dois lagos amazônicos através de dados sedimentares e geoquímicos com especial ênfase a geoquímica orgânica e isotópica. Os lagos estudados apresentam-se em duas área climáticas distintas da Amazônia, sendo o Lago do Saci localizado ao sul do estado do Pará, em área de clima tropical com estação seca definida; e a Lagoa da Pata, localizada no extremo norte do Amazonas em regime de clima sempre úmido. O registro do Lago Saci abrange o intervalo entre 35.000 cal AP até o último milênio e o registro da Lagoa da Pata abrange os últimos 7500 cal AP. Na lagoa da Pata observou-se a existência de condições secas durante o Holoceno Inferior (7.500 – 6.500 anos cal AP) e o Holoceno Médio (6.500 – 3.600 anos cal AP) com baixos valores de COT (Carbono orgânico Total) e altos valores de 13C, sugerindo baixo nível do lago e aumento na contribuição de plantas C4. Durante o Holoceno Superior (3.600 anos cal AP até o presente) a estabilização de um clima mais úmido é observado na Lagoa da Pata, suportado pelo aumento significativo nos valores de COT e redução nos valores de 13C, sugerindo um aumento no nível do lago e contribuição de plantas C3. O registro molecular da Lagoa da Pata sugere a existência de uma vegetação adaptada a condições de alto estresse hídrico em função do tipo de solo presente na região do Morro dos Seis Lagos. A composição isotópica de carbono do n-alcano apresentou um range de valores característicos de vegetação C3 (-33,6‰ e -36,9‰) durante os últimos 7.500 anos cal AP. No Pleistoceno Superior, o Lago do Saci é caracterizado pelos menores valores de COT e valores mais enriquecidos de 13C sedimentar, sugerindo um baixo nível lacustre e grandes contribuições de plantas C4. O ápice do clima seco acontece entre 22.000 – 21.000 anos cal AP, com ocorrências significativas de incêndios, indicado pelos valores de BC (Carbono Grafítico). A transição para o Holoceno é marcado pela ausência de sedimentação entre 18.200-9.200 anos cal AP, sugerindo a ocorrência de uma fase seca severa ou evento erosivo atuante no fim do período glacial. O Holoceno no Lago do Saci marca um aumento no nível do lago, refletido pelo aumento na produtividade e acumulação da matéria orgânica. Esse período tem como característica a ocorrência de eventos de transporte de material da bacia de drenagem, representado pelos pulsos de areia.Os dados de biomarcadores moleculares sugerem condições de estresse hídrico durante o Pleistoceno e o Holoceno Médio na Lago do Saci, em função dos altos valores de ACL (Comprimento médio da Cadeia), sendo esses períodos os com maiores contribuições de plantas C4 como indicado pela razão C33:(C27+C29). Os valores de 13C dos n-alcanos (- 33.2‰ e -35.7‰) sugerem que a região foi coberta por vegetação C3 durante todo o período e mostram uma variação significativa entre o Pleistoceno Superior e o Holoceno, associada a alterações fisiológicas da vegetação. O registro de D sugere um período de precipitação reduzida no Pleistoceno e um período de chuvas mais abundantes no Holoceno. Ambos os registros (Lago do Saci e na Lagoa da Pata) sugerem condições ligeiramente mais úmidas durante o Holoceno, com a existência de uma fase seca no Holoceno Médio, caracterizados por uma redução significativa no nível lacustre e maior contribuição de plantas C4. As chuvas se tornam mais abundantes na Lagoa da Pata e o Lago do Saci a partir de 4.000 anos cal AP onde ocorre a expansão da floresta. Em Ambos os sítios, o sinal isotópico de biomarcadores, apesar de indicar alterações na precipitação, apresentou um enriquecimento do sinal isotópico em função da evapotranspiração ou alteração na vegetação fonte (C3 ou C4), alterando o processo de fracionamento do deutério. / In this work we present the paleoenvironmental reconstruction of two Amazonian lakes based in sedimentary and geochemical data with focus on organic and isotopic geochemistry.The lakes are presented in two distinct climatic area of the Amazon, the Saci Lake are located in south of Para state, in tropical area with dry season; and Pata Lake, located on the northern of the Amazon in a humid climate regime. The Saci lake core covers the range between 35,000 cal BP until the last millennium and Pata Lake covers the last 7,500 cal BP. Pata lake record dry conditions during the Early Holocene (7,500-6,500 cal years BP) and the Middle Holocene (6,500-3,600 cal years BP) with low TOC values (Total Organic Carbon) and high 13C values, suggesting low lake level and an increase of C4 plants contribution. During the Late Holocene (3,600 years cal BP to the present) is observed a stabilization of humid conditions, supported by the increase in TOC values and reduction in 13C values, suggesting an increase in lake level and C3 plants. The molecular record of Pata Lake suggests the existence of a vegetation adapted to high water stress conditions due the soil characteristic in the Six Lakes Morro region. The isotopic composition of n-alkane carbon presented a range of C3 vegetation (-33.6 ‰ and -36.9 ‰) over the last 7,500 years AP. In the Late Pleistocene, Saci lake is characterized by lower TOC values and more enriched 13C values, suggesting a low lake level and more C4 plants contributions. The dry climate occurs between 22,000 to 21,000 cal years BP, with significant occurrences of fires, indicated by the BC (Black Carbon) values. The transition to the Holocene is marked by the absence of sedimentation between 18,200-9,200 cal years BP, suggesting the occurrence of a severe drought phase or active erosive event at the end of the glacial period. The Holocene in Saci Lake is marked by an increase in lake level, reflected by the increase of productivity and organic matter accumulation. This period is characterized by the occurrence of runoff events, represented by sand pulses. The molecular biomarker data suggest water stress during the Pleistocene and the Middle Holocene in Lake Saci, with high ACL values (Average Chain Length), and more C4 plants contributions as indicated by the reason C33: (C27 + C29). The 13C values of nalkanes (-33.2 and -35.7 ‰ ‰) suggest that the area was covered by C3 vegetation during the whole period and show a significant variation between the Pleistocene and Holoceno associated with physiological changes in the C3 vegetation. The D record suggests a reduced precipitation in the Pleistocene and a period of more abundant rainfall in the Holocene. Both records (Saci lake and Pata Lake) suggest wetter conditions during the Holocene, with the existence of a dry phase in the Middle Holocene, characterized by a significant reduction in lake levels and greater contribution of C4 plants. The rains become more abundant in Pata Lake and Saci Lake after 4,000 cal years BP, where the forest expansion occurs. In both sites, the isotopic biomarkers indicate changes in precipitation, however the D enrichment could be explained by the evapotranspiration processes or change in vegetation source (C3 or C4), which interfers the deuterium fractionation process.

The study of adsorption of n-alkanes in zeolite pores represents both a fundamental problem in molecular thermodynamics and also a problem with substantial industrial importance. Until mid 19th century, adsorption was mainly used for purification processes such as removal of H2S and mercaptans from natural gas and organic matter from water. However, with the emergence of molecular sieves, especially zeolites, adsorption processes have become an attractive alter- native to distillation in large scale separation of mixtures that have low relative volatility into streams each enriched in one of the components. The pore di- ameters of molecular sieves are of the order of molecular diameters and hence selective adsorption can be achieved by both a difference in adsorbate-adsorbent interactions of various species and obstruction by the pore walls to some of the species in the mixture. The existing adsorption theories such as Henry’s law, Langmuir adsorption model and BET isotherm are incapable of predicting the adsorption isotherms of n-alkanes in zeolite pores. The reason is that in microporous adsorbents, the sorbate molecular mechanisms are influenced by geometrical constraints also. This limitation in the use of theory can be overcome by developing a molecular model and using computers to mimic the real system. This nature of simulation is called molecular simulations. With the development of advanced algorithms, improved force-field parameters and very high computational power of present day computers, molecular simulations have become an important tool in studying adsorption on micro-porous materials. Adsorption experiments of mixtures of long chain alkanes into silicalite under liquid phase conditions show selectivity inversion and azeotrope formation. These effects are due to the subtle interplay between the size of the adsorbed molecules and pore topology of the adsorbent. The underlying molecular mechanisms responsible for selective uptake of one of the components cannot be obtained from experiments but can be realized through simulations. Therefore, in this study, the selective uptake of lighter component during liquid phase adsorption of C14/C15 and C15/C16 n-alkane binary mixtures in the zeolite silicalite is understood through configurational bias grand canonical Monte Carlo (CB- GCMC) molecular simulation technique and a course-grained siting analysis. The simulations are conducted under conditions of low and high loading. The siting pattern of the adsorbates inside the zeolite pores is used to explain the selectivity as seen in experiments.

In dieser Arbeit werden neue Strategien zur Wachstumskontrolle funktionaler organischer Dünnschichtmaterialien aufgezeigt, mit denen sich die Eigenschaften molekularer Schichtsysteme gezielt beeinflussen lassen. Ein Fokus liegt dabei auf der Untersuchung des Einflusses von optischen Feldern auf das Wachstumsverhalten. Ein weiterer Schwerpunkt wird auf das Grundlagenverständnis von thermisch aktivierten, kinetischen Prozessen, die die Morphologie während und nach dem Schichtwachstum beeinflussen, gelegt. Zuerst wird am Beispiel des molekularen Halbleiters Sexithiophen (6T) gezeigt, wie sich Kontrolle über das Kristallphasengleichgewicht während des Wachstums auf Kaliumchlorid (KCl) erzielen lässt. Im zweiten Teil der Arbeit wird eine neue Herangehensweise zur direkten Ausrichtung von Molekülkristallen im optischen Feld während ihrer Entstehung studiert. Am Beispiel von Tetracene wird gezeigt wie sich so optische anisotrope Absorptionseigenschaften von Molekülen dazu nutzen lassen den Brechungsindex eines polykristallinen Films lokal durch ein photolitographisches Verfahren zu beeinflussen. Im dritten Teil wird der Einfluss von dynamisch variierenden Wachstumsbedingungen während des Schichtwachstums von PTCDI-C8 studiert. Es wird gezeigt, dass sich die Oberflächenrauigkeit stark reduzieren lässt, indem zu Beginn des Wachstums jeder individuellen molekularen Monolage die Nukleationsdichte stark erhöht und in den darauf folgenden Wachstumsphasen die Diffusivität gezielt gesteigert wird. Im vierten Teil wird das Diffusionsverhalten von n-Alkan Schichten unter thermischen Einflüssen betrachtet. Es wird gezeigt, dass die inhärente molekulare Anisotropie von C44H90 Molekülen (TTC) sowie die sehr geringe, stark anisotrope, Oberflächenenergie dieses Materials ein ungewöhnliches Diffusionsverhalten auslöst. / The research performed in the framework of this thesis focuses on new strategies to effectively control the growth of crystalline thin films of functional organic molecules and attributes the quest for additional growth control parameters in organic molecular beam deposition (OMBD). First the influence of light on the growth process of the sexithiophene (6T) is studied. We find that 6T thin films deposited as conventional in dark environments on KCl exhibit a bimodal growth with phase coexistence of two crystal polymorphs. In contrast, films grown under illumination with 532 nm light show increased phase purity. Further, we establish light-directed molecular self-assembly (LDSA) to generate permanently aligned thin films of tetracene (C18H12) and demonstrate direct patterning with light. Polarized light illumination leads to azimuthally photoaligned films on isotropic, amorphous substrates. Thus, LDSA can be regarded as a new degree of freedom in the quest for control-parameters in organic thin film growth. Next the impact of dynamic temperature oscillations on the time scales of molecular monolayer growth during organic molecular beam deposition is discussed. We strongly increase the island density during nucleation and selectively increase interlayer diffusion at later stages of monolayer growth. We analyse the interplay between molecular interlayer transport and island sizes to understand kinetic processes during growth. In a fourth experiment we show how thermal annealing can be used to improve smoothness and to increase the lateral size of crystalline islands of n-alkane (TTC, C44H90) films. We employ real-time optical phase contrast microscopy to track the diffusion across monomolecular step edges which causes the unusual smoothing during annealing. We rationalise the smoothing behaviour with the highly anisotropic attachment energies and low surface energies of TTC.