The objective of this thesis is to propose modeling techniques that enable the design and optimization of material systems which require descriptions via molecular simulations. These kinds of systems are quite common in materials and engineering research. The first step in performing design and optimization tasks on such systems is the development of accurate simulation models from experimental data. In the first part of this thesis, we present a novel simulation model for the hyperbranched polymerization process of difunctional A2 oligomers, and B3 monomers. Unlike the previous models developed by other groups, our model is able to simulate the evolution of the polymer structure development under a wide range of synthesis routes, and in the presence of cyclization and endcapping reactions. Furthermore, our results are in agreement with the experimental data, and add insight into the underlying kinetic mechanisms of this polymerization process. The second major step in our work is the development of reduced order process models that are suitable for design and optimization tasks, using simulation data. We illustrate our approach on a stochastic simulation model of epitaxial thin film deposition process. Compared to the widely used approach called equation-free modeling, our method requires fewer assumptions about the dynamic system. The assumptions required in equation-free modeling include a wide separation between the time scales of low and high order moments describing the system state, and the accuracy of the time derivatives of system properties computed from molecular simulation data, despite the potentially large amount of fluctuations in stochastic simulations. Unlike the recent similar studies, our study also includes the analysis of prediction error which is important to evaluate the predictions of the reduced order model, compared to the high dimensional molecular simulations. Hence, we address two major issues in this thesis: development of simulation models from molecular experimental data, and derivation of reduced order models from molecular simulation data. These two aspects of modeling are both necessary to design and optimize processing conditions of materials for which continuum level descriptions are not available or accurate enough.

Atoms construct the molecules and molecules construct the material substances (with the exceptions as well, e.g.., metals, where atoms directly construct the material substances). Intermolecular interactions play an important role in most of the branches of sciences, ranging from material sciences to biological sciences. Van der Waals interactions are weak intermolecular interactions while hydrogen bonding varies in strength from weak to strong (1 to 40 kcal/mol). The present work focuses on applying some theoretical methods (ab initio and Atoms in Molecules theory) on these interactions to differentiate them with physically meaningful parameters such as hydrogen bond radii and atoms in molecules theory parameters. 1)Defining and calculating H-bond radii have been done using atoms in molecules theory approach which can explain ruling out the presence or absence of an H-bond in an intermolecular interaction. 2) A blue-shift of 200 cm-1 for a weakly bound complex is unprecedented. Our studies on weakly bound complexes showed the blue-shift of 200 cm-1 for H3C•••CIF and shift has been found to be purely from the mixing of normal modes and not because of an interaction. 3)Methane, a symmetric top molecule can act both as H-bond acceptor and donor. The present work shows that methane is rather a better H-bond acceptor than a donor and all the calculated parameters are in favor of this description. 4) Microwave spectrometer is an ultimate tool (at least at present) for structural characterization of the weakly bound complexes accurately. The rotational spectrum of the weakly bound isotopomer weakly bound complexes accurately. The rotational spectrum of the weakly bound isotopomer 13CC5H6•••Ar, which is a symmetric top and gives only “B” rotational constant. Moreover, the A rotational constant of the complex is the same as the rotational constant for 13CC5H6, which has no dipole moment. C2H2 molecule is an astrophysically important molecule as it is present in asymptotic giant branch and T-type stars (Teff<3000K). Due to its various infrared active vibrational modes, C2H2 is one of the most important sources in cool stars. The production of C2H2 infrared spectroscopic data at high temperature is therefore essential to trace back physical characteristics of these objects and to model the radiative transfer in their envelope. The databases such as “HITRAN”, do not have enough data available for stimulating high temperature spectra. Keeping all these objectives in mind, high temperature emission spectrum of acetylene has been recorded around 3µm region of acetylene.

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No. of bitstreams: 1 charlaneciminicorrea.pdf: 11668631 bytes, checksum: a7ab701003fdf688b49377e542ceb430 (MD5) Previous issue date: 2011-03-04 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Este trabalho de tese de doutorado consistiu na síntese e caracterização de arranjos supramoleculares com os metais Mn2+, Co2+, Cu2+ e Zn2+ da primeira série de transição contendo ligantes nitrogenados 1,3-bis(4-piridil)propano (BPP), sulfeto de di(4-piridila) (DPS) e dissulfeto de di(4-piridila) (DPSS) e policarboxilatos 1,2,4,5-benzenotetracarboxilato (BT), p-sulfobenzoato (SF) e 1,3,5-benzenotricarboxilato (BTC). Foram obtidos vinte e seis compostos que foram caracterizados por técnicas analíticas e espectroscópicas, tais como, análise elementar (CHN), análise térmica (TG/DTA) e espectroscopia vibracional (infravermelho e Raman). Dentre esses, vinte e dois compostos foram obtidos na forma de monocristais e tiveram suas estruturas determinadas por difração de raios X de monocristal. A análise térmica mostrou que todos os compostos apresentam-se hidratados, com moléculas de água de coordenação e/ou de cristalização. A espectroscopia vibracional foi importante para inferir sobre os modos de coordenação dos grupos carboxilatos através do cálculo do ∆ν (νassimCOO-νsimCOO). Nos compostos contendo o ligante BT, o grupo carboxilato atuou sempre de modo monodentado. Para os compostos com o ligante SF foram observados os modos monodentado e quelato e para o ligante BTC os modos monodentado, quelato e em ponte syn-syn e syn-anti. Foram descritas a síntese e caracterização dos compostos envolvendo o carboxilato BT e os ligantes nitrogenados BPP, DPS e DPSS que originaram onze complexos inéditos nomeados como: MnBTBPP, CoBTBPP, CuBTBPP, ZnBTBPP, MnBTDPS, CoBTDPS, CuBTDPS, ZnBTDPS, MnBTDPSS, CoBTDPSS e ZnBTDPSS. O ligante BT está presente em todos estes compostos e, com exceção do CoBTDPSS, apresentaram o ligante nitrogenado coordenado em ponte. Todos os compostos exceto o ZnBTBPP tiveram suas estruturas determinadas por difração de raios X de monocristal. Em especial, MnBTDPS e CoBTDPS são isoestruturais e os compostos ZnBTDPS e ZnBTDPSS apresentam estruturas semelhantes inclusive com a mesma topologia de rede. Realizou-se o estudo da síntese e caracterização de nove compostos utilizando o carboxilato SF e os ligantes nitrogenados BPP, DPS e DPSS nomeados, MnSFBPP, CoSFBPP, CuSFBPP, ZnSFBPP, CoSFDPS, CuSFDPS, ZnSFDPS, CoSFDPSS e ZnSFDPSS. Todos os compostos com exceção do CoSFDPSS tiveram suas estruturas determinadas por difração de raios X de monocristal. Em todas as estruturas analisadas os ligantes nitrogenados se coordenaram aos centros metálicos em ponte. No composto MnSFBPP o ligante SF não estava presente. Nos compostos CoSFBPP e CoSFDPS este ligante permaneceu na rede agindo como ânion estabilizando estas estruturas. Os arranjos bidimensional e tridimensional dos compostos foram observados pela presença de ligações de hidrogênio clássicas e não-clássicas, mostrando a importância das interações não covalentes na formação do arranjo supramolecular, bem como da estabilização das estruturas. Por fim, através das sínteses envolvendo o carboxilato BTC com os ligantes nitrogenados BPP, DPS e DPSS, seis complexos foram descritos como MnBTCBPP, CoBTCBPP, ZnBTCBPP, MnBTCDPS, ZnBTCDPS e ZnBTCDPSS. Os complexos CoBTCBPP, MnBTCDPS e ZnBTCDPS não apresentaram o ligante nitrogenado na estrutura, sendo que em todos eles pôde-se observar a presença do ligante BTC. Os complexos MnBTCBPP, CoBTCBPP, ZnBTCBPP e ZnBTCDPSS foram obtidos na forma de monocristais e tiveram suas estruturas cristalinas determinadas por difração de raios X de monocristal. Confirmaram-se então diversos modos de coordenação do ligante BTC nestes complexos tais como monodentado, quelato e em ponte syn-syn e syn-anti. / This work presents the synthesis and characterization of supramolecular arrays with Mn2+, Co2+, Cu2+ and Zn2+ first row transition metal ions, polydentate nitrogen ligands 1,3-bis(4-pyridyl) propane (BPP); di(4-pyridyl)sulfide (DPS) and di(4-pyridyl)disulfide (DPSS) and polycarboxylates 1,2,4,5-benzenotetracarboxylate (BT), p-sulfobenzoate (SF) and 1,3,5-benzenotricarboxylate (BTC). Twenty six compounds were synthesized and characterized of elemental analysis (CHN), thermal analysis (TG/DTA) and vibrational spectroscopy (infrared and Raman). Among these, twenty two compounds were isolated as single crystals and had their structures determined by single crystal X-ray diffraction analysis. Thermal analysis showed that all compounds are hydrated with coordination and/or lattice water molecules. Vibrational spectroscopy was very important to inform about the carboxylate groups coordination mode through ∆ν (νasymCOO - νsymCOO) value. In compounds containing BT ligand, the carboxylate group always acted in monodentate mode. For compounds containing SF ligands, monodentate and bidentatechelate modes were observed and for BTC ligand, monodentate, bidentate-chelate and syn-syn and syn-anti bridging modes were noted. The synthesis and characterization of compounds involving the BT carboxylate ligand and BPP, DPS and DPSS nitrogen ligands gives rise to eleven complexes described as MnBTBPP, CoBTBPP, CuBTBPP, ZnBTBPP, MnBTDPS, CoBTDPS, CuBTDPS, ZnBTDPS, MnBTDPSS, CoBTDPSS and ZnBTDPSS. BT ligand is present in all compounds and, except CoBTDPSS, they showed the nitrogen ligand in bridging coordination mode. All compounds, except ZnBTBPP, had their structures determined by single crystal X-ray diffraction analysis. In particular, MnBTDPS and CoBTDPS are isostructural and ZnBTDPS and ZnBTDPSS present similar structures with the same network topology. Studies of the synthesis and characterization of nine compounds using SF carboxylate and BPP, DPS and DPSS nitrogen ligands were realized, appointed as MnSFBPP, CoSFBPP, CuSFBPP, ZnSFBPP, CoSFDPS, CuSFDPS, ZnSFDPS, CoSFDPSS and ZnSFDPSS. All compounds, except CoSFDPSS, had their structures determined by single crystal X-ray diffraction analysis. In all structures the nitrogenated ligands coordinate to the metal centers in the bridging mode. For MnSFBPP the absence of ligand SF was noted. In CoSFBPP and CoSFDPS, this ligand remained uncoordinated, acting as a counter anion stabilizing these structures. The two- and three-dimensional arrays of the compounds were observed by the presence of classic and non-classic hydrogen bondings showing the importance of non-covalent interactions in the supramolecular arrangement, as well as in the structure stabilization. Finally, through the syntheses involving the BTC carboxylate with nitrogenated ligands BPP, DPS and DPSS, six complexes are described as MnBTCBPP, CoBTCBPP, ZnBTCBPP, MnBTCDPS, ZnBTCDPS and ZnBTCDPSS. CoBTCBPP, MnBTCDPS and ZnBTCDPS do not present nitrogen ligands in their structures and in all of them the presence of BTC ligand is observed. MnBTCBPP, CoBTCBPP, ZnBTCBPP and ZnBTCDPSS were obtained as single crystals and had their crystal structures determined by X-ray diffraction analysis. Great diversity of BTC ligand coordination modes as monodentate, chelate and syn-syn, syn-anti bridging modes were confirmed.

Three distinct aspects, disorder, polymorphism and co-crystal formation have been addressed in molecular crystals in terms of intra- and intermolecular interactions involving halogens, weak hydrogen bonds and van der Waals interactions. A basic introductory chapter highlights the importance of these three aspects followed by a foreword to the contents. Chapter 1 employs in situ cryo-crystallization techniques to study the crystal and molecular structures of compounds which are liquids at room temperature. Section 1.1 deals with the crystal structure analyses of low melting chloro- and bromo-substituted anilines which reveal both the importance of hydrogen bonds and weak interactions involving different halogens. The halogen⋅⋅⋅halogen interactions are compared with fluorine and iodine substituted compounds to bring out the relevance of both size and polarizability characteristics. Section 1.2 describes the crystal structures of benzyl derivative compounds utilizing the concept of in situ cryo-crystallization. This analysis brings out the correlation between acidity of benzyl derivative compounds with its preference of either a (sp2)C-H⋅⋅⋅π or (sp3)C-H⋅⋅⋅π interactions in the crystal packing. Chapter 2 consists of two sections dealing with the preference of halogen⋅⋅⋅halogen interactions in supramolecular chemistry. Section 2.1 discusses a statistically large number of crystal structures in halogen substituted benzanilide compounds. It reveals the importance of hetero halogen F⋅⋅⋅X (Cl, Br), homo halogen X⋅⋅⋅X (F, Cl, Br, I), C-X⋅⋅⋅π and C-H⋅⋅⋅F interactions in terms of their directionality and preferences to complement a primary N-H⋅⋅⋅O hydrogen bond in directing the three-dimensional supramolecular assembly. Section 2.2 deals with solvent induced polymorphism which highlights the role of weak interactions in two case studies. The preference and directionality of C-H⋅⋅⋅F and Cl⋅⋅⋅Cl interactions lead to dimorphic modifications in case of 3-chloro-N-(2-fluorophenyl)benzamide whereas in case of 2-iodo-N-(4-bromophenyl)benzamide the interactions are through C-H⋅⋅⋅π and I⋅⋅⋅I contacts. Further, the analysis is supported using morphological evidence, DSC (Differential scanning calorimetry) and Powder X-ray diffraction data. Chapter 3 has three sections, concentrating on disorder and its consequence in crystal structures. Section 3.1 discusses the apparent shortening of the C(sp3)–C(sp3) bond analysed via a variable temperature X-ray diffraction study in racemic 1,1′-binaphthalene-2,2′-diyl diethyl bis(carbonate). Variable temperature single crystal X-ray diffraction studies show that the shortening is entirely due to positional disorder and not due to thermal effects. A supercell formation at T≤150 K depicts the formation of a Z'= 2 structure. Section 3.2 deals with crystal structure analysis of Ethyl-4-(2-fluorophenyl)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate which clarifies the discrepancy in the higher value of the residual electron density in the literature in terms of positional disorder of fluorine at ortho sites. The existence of fluorine atom at the para position on the phenyl ring of another isomeric molecule leads to disorder induced conformational polymorphism through the involvement of the ethyl group. The static disorder of ethyl group which is associated with only one molecule (Z′=2) could be resolved at 120 K. This supports the results of the previous section (3.1). Section 3.3 reports crystal structure analysis of disordered fluorine in benzanilide compounds. The preference of interactions involving fluorine in either ortho sites or meta sites could be one of the reasons for the positional disorder of both possible sites. With one of the structure showing high Z′ value due to differences in the occupancy of disordered fluorine atom. CSD (Cambridge Structural Database) analysis indicates that the percentage of disorder in halogenated crystal structures having halogen atom at either ortho site or meta site decreases from fluorine to iodine. Further, the analysis points out that the disorder in fluorine containing compounds is mostly localized at the fluorine position whereas for other halogenated disordered structures, the disorder appears at other parts of the molecule. Chapter 4 discusses co-crystal formation and analysis of intermolecular interactions. It consists of two sections. Section 4.1 discusses co-crystal formation of nicotinamide with benzoic acid and seven other derivatives by changing the functional group at different positions of benzoic acid. Hydroxyl (-OH) group at 4/3-postion of benzoic acid prefers phenol⋅⋅⋅pyridine synthon when at 2-position it prefers acid⋅⋅⋅pyridine synthon. The preference of amide anticatemer over dimer synthon is supported by additional C-H⋅⋅⋅O hydrogen bonds. In case of 3,5-dinitro-2-hydroxy benzoic acid, the disorder in hydroxyl (-OH) group at ortho site leads to salt formation. Section 4.2 describes co-crystal study of adenine and thymine (AT) as free nucleobases. This result reveals the formation of AT (2:1) complex with both Hoogsteen and “quasi-Watson-Crick” hydrogen bonds. The hydrogen bonded bases using the Hoogsteen and the “quasi-Watson-Crick” interactions generate a hexagonal supramolecular motif. Four water molecules are located inside the hexagonal void of this complex. A high temperature study on the same crystal shows that at 313K, one of the water molecules escapes from the lattice resulting in the small change in unit cell parameters. However, the space group remains the same and the hexagonal void remains unaltered. With further increase in temperature, the crystal deteriorates irreversibly which clearly brings out the importance of water molecule in the molecular recognition of adenine-thymine complex. Chapter 5 discusses crystal structure analysis of trans-atovaquone (antimalarial drug), its new polymorph form including one stereoisomer (cis) and five other derivatives with different functional groups. Based on the conformational features of these compounds and the characteristics of the nature of hydrogen bonding and other weak intra and intermolecular interactions, docking studies with cytochrome bc1 complex provide valuable insight into the atomistic details of protein-inhibitor interactions. The docking results reveal that atovaquone and its derivatives, owing to their nature of hydrogen bond and the propensity towards the formation of weaker hydrogen bonds involving the chlorine atom as well appear as good candidates for drug evaluation.

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Das Verständnis über die Ausbildung der Grenzfläche eines hybriden Bauteils aus thermoplastischem Kunststoff und Metall sowie die maßgeblichen Faktoren zum Erreichen einer hohen Verbundhaftung und Mediendichtheit in der Grenzfläche stellen nach wie vor eine große Herausforderung dar. Am Beispiel einer spritzgegossenen Kunststoff-Metall-Verbundprobe werden diese Zusammenhänge untersucht und bewertet. Es wird eine Methode zur Herstellung stoffschlüssig gefügter Verbunde mit hoher Mediendichtheit auf Basis einer hohen Kontakttemperatur beim Fügen entwickelt, indem Verbundspritzgießen und nachträgliches thermisches Fügen durch Induktionsheizen kombiniert werden. Eine stoffschlüssige Verbindung mit hoher Mediendichtheit zwischen thermoplastischem Kunststoff und Metall erfordert eine Haftung in der Grenzfläche der Verbundpartner auf Basis intermolekularer Wechselwirkungen. Die Quantifizierung der Mediendichtheit in der Grenzfläche erfolgt über eine eigens entwickelte Messmethode. Die entwickelte Vorgehensweise ermöglichet die Differenzierung zwischen intermolekularen Wechselwirkungen und mechanischen Verklammerungen als Ursache für eine Haftungsausbildung und deren Einfluss auf die Grenzflächeneigenschaften. Die gewonnenen Erkenntnisse tragen zum Verständnis der Grenzflächenausbildung, insbesondere zum Einfluss der Oberflächenbeschaffenheit des metallischen Verbundpartners sowie der Fügeprozessbedingungen zur Fertigung von Kunststoff-Metall-Verbunden mit hoher Mediendichtheit, bei.:1 Einleitung und Motivation 2 Stand der Technik und Forschung 3 Zielsetzung und Lösungsansatz 4 Experimentelles 5 Analytik 6 Ergebnisse 7 Diskussion der Ergebnisse 8 Zusammenfassung und Ausblick / Understanding the formation of the interface of a hybrid component made of thermoplastic and metal as well as the decisive factors for achieving high adhe-sion and media tightness in the interface still represent a major challenge. These relationships are investigated and elucidated using the example of an injection-molded plastic-metal part. A method for the production of firmly bonded hybrid parts with high media tightness based on a high contact temperature during joining of the hybrid part is developed by combining injection molding and subsequent thermal joining by induction heating. A firm bond with high media tightness between a thermoplastic and a metal requires an adhesion in the inter-face of the joint materials based on molecular interactions. The quantification of the media tightness in the interface is done by using a specially developed measurement method. The investigations enable the differentiation between molecular interactions and mechanical interlocking as the cause of adhesion formation and their influence on the properties of the interface. The gained knowledge contributes to the understanding of interface formation and its prop-erties, in particular the influence of the surface properties of the metallic bond partner and the joining process conditions for the production of plastic-metal parts with high media tightness.:1 Einleitung und Motivation 2 Stand der Technik und Forschung 3 Zielsetzung und Lösungsansatz 4 Experimentelles 5 Analytik 6 Ergebnisse 7 Diskussion der Ergebnisse 8 Zusammenfassung und Ausblick