Topological Anisotropy of Stone-Wales Waves in Graphenic Fragments

Stone-Wales operators interchange four adjacent hexagons with two pentagon-heptagon 5|7 pairs that, graphically, may be iteratively propagated in the graphene layer, originating a new interesting structural defect called here Stone-Wales wave. By minimization, the Wiener index topological invariant evidences a marked anisotropy of the Stone-Wales defects that, topologically, are in fact preferably generated and propagated along the diagonal of the graphenic fragments, including carbon nanotubes and graphene nanoribbons. This peculiar edge-effect is shown in this paper having a predominant topological origin, leaving to future experimental investigations the task of verifying the occurrence in nature of wave-like defects similar to the ones proposed here. Graph-theoretical tools used in this paper for the generation and the propagation of the Stone-Wales defects waves are applicable to investigate isomeric modifications of chemical structures with various dimensionality like fullerenes, nanotubes, graphenic layers, schwarzites, zeolites

Computations on Endohedral Metallofullerenes: Characterization, Properties and Growth

Els ful•lerens són caixes closes de carboni formades per un nombre parell d’àtoms. Una de les propietats mes interessants és la capacitat d’encapsular àtoms i petites molècules en la cavitat interior. El primer ful•lerè endoèdric fou proposat just després del descobriment del C60. Els metal•loful•lerens endoèdrics han atret atenció de gran part de la comunitat científica per les seves propietats i potencials aplicacions en camps com la medicina o la ciència de materials. En aquesta tesi s’hi mostra un extensiu treball combinant experiments i computació per a la caracterització i modelatge de noves especies de metal•loful•lerens endoèdrics. En la majoria dels casos, la síntesi de noves espècies necessita d’aquesta combinació d’experiments i computació per poder la identificació i caracterització de les estructures. Així doncs, aquí es presenta el treball per l’estudi de les propietats i caracterització des de sistemes petits com Ti@C2n (2n =26-50) i altres endoedres monometàl•lics (M@C2n), així com l’estudi detallat dels sistemes Sc2S@C70, Sc2S@C72, Ti2S@C78 i la modelització d’algunes de les seves propietats mes rellevants.Los fulerenos son poliedros esféricos formados por un nombre par de átomos de carbono distribuidos en pentágonos y hexágonos. Una de sus propiedades más atractiva es la capacidad de atrapar átomos y pequeñas moléculas en su interior. Estos fueron descubiertos rápidamente después del descubrimiento del C60. El Sc3N@C80 es el fulereno endoédrico más abundante, y el tercer sistema más abundante en toda la familia de fulerenos, solo por detrás de C60 y C70. Los fulerenos endoédricos han captado la atención de gran parte de la comunidad científica debido a sus propiedades y potenciales aplicaciones en campos como la medicina y la ciencia de materiales. La caracterización de nuevas especies es difícil debido al bajo rendimiento, por eso, la combinación de experimentos con trabajos computacionales es esencial para la exitosa identificación de nuevos sistemas. En esta tesis se incluye un extenso trabajo combinando estudios computacionales con varios tipos de experimentos. Entre las especies estudiadas y caracterizadas se encuentran desde los pequeños fulerenos monometálicos Ti@C2n (2n=26-50), hasta especies más grandes cómo Sc2S@C70, Sc2S@C72 y [email protected] are closed carbon cages constituted by an even number of atoms. One of the attractive properties of the hollow carbon clusters is the possibility to use them as robust containers for other species. The first proposal of an endohedral fullerene was given only a few days after the discovery of C60. Endohedral metallofullerenes have attracted the attention of the scientific community not only because their unique host-guest behaviors, but also because the properties and, thus, the applications are significantly different from those of the empty cages. The formal electron transfer that has been found to happen between the trapped unit and the carbon cages is determinant for the understanding of these new properties. Herein we report an extensive study combining computations and experiments. This combination is a powerful tool for the structural characterization of new species. The computation of the structures and the modeling of the properties, allow us to compare the experimental and computational data to identify the new systems. In this thesis the reader will find a complete study from small endohedrals, Ti@C2n (2n=26-50) and other M@C2n, to larger fullerenes as Sc2S@C70, Sc2S@C72 and Ti2S@C78

The topology of fullerenes

Fullerenes are carbon molecules that form polyhedral cages. Their bond structures are exactly the planar cubic graphs that have only pentagon and hexagon faces. Strikingly, a number of chemical properties of a fullerene can be derived from its graph structure. A rich mathematics of cubic planar graphs and fullerene graphs has grown since they were studied by Goldberg, Coxeter, and others in the early 20th century, and many mathematical properties of fullerenes have found simple and beautiful solutions. Yet many interesting chemical and mathematical problems in the field remain open. In this paper, we present a general overview of recent topological and graph theoretical developments in fullerene research over the past two decades, describing both solved and open problems. WIREs Comput Mol Sci 2015, 5:96–145. doi: 10.1002/wcms.1207 Conflict of interest: The authors have declared no conflicts of interest for this article. For further resources related to this article, please visit the WIREs website

Reactor R&D: Synthesis and Optimization of Metallic Nitride Fullerenes and the Introduction of Two New Classes of Endohedral Metallofullerenes, Metallic Nitride Azafullerenes and Oxo-metallic Fullerenes

Metallic nitride fullerenes (MNFs) were discovered in 1999. This class of endohedral fullerenes show promise in a new diverse range of useful applications. Since then, focus has shifted to the selective synthesis of these molecules with yields that would accommodate adequate sample distribution. Using the electric arc method, the traditional yield of these molecules has been very low (i.e. \u3c 5 mg), and only a small percentage of the fullerene products (i.e. \u3c 5%). This dissertation introduces the novel CAPTEAR (Chemically Adjusting Plasma Temperature, Energy, And Reactivity) method that allows the targeted synthesis of MNFs in high purity and yield. This method utilizes a nontraditional oxidizing method for fullerene synthesis that has not only provided optimization of MNFs, but also resulted in the discovery of two new classes of fullerenes: metallic nitride azafullerenes (MNAFs) and oxo-metallic fullerenes (OMFs). Evidence suggests that the nitrogen of the MNAF cage provides stability for the trimetallic nitride clusters, while the OMFs are the first fullerenes to encapsulate oxygen and incorporate a seven atom cluster inside a Cgo cage. Other efforts to increase yields resulted from scaling up production of fullerenes by using larger quantities of starting materials. These larger quantities required energy (electrical current) beyond the capacity of the traditional electric arc generator. Therefore, a new electric arc generator was designed and fabricated to accommodate these demands. This scale-up process resulted in yield increases by an average of 400%. However, to reduce the waste of scaling up as well as costs, our lab developed a recycling method for the expensive metal oxide starting materials. This method has greatly improved cost effectiveness and waste reduction

Cluster-based redox activity in Endohedral Metallofullerenes:: Electrochemical and EPR studies

Endohedral fullerenes are closed carbon shells encapsulating molecular or ionic species in their inner space. Obtained for the first time in 1985, endohedral metallofullerenes (EMFs) remain in focus of research for many years with a broad variety of metal atoms, endohedral cluster and cage sizes being reported. Electrochemical studies of endohedral metallofullerenes are of particular interest because of the more complex redox behavior in comparison to empty fullerenes. The EMF molecules can be considered as a combinations of positively charged cluster and negatively charged carbon shell “ligand”, and both constituents can be redox active. A cage-based electrochemical activity is more common, in particular, the most abundant nitride clusterfullerenes generally have redox-active cages. Cluster-based electrochemical activity is less common and can be revealed via unexpected redox behavior (e.g., shifted potential when compared to analogous molecules, potential metal dependence) and with the use of spectroscopic methods. Here we report electrochemical and EPR studies of three EMF families: (i) M2@C82-C3v and M2@C82-Cs dimetallofullerenes with a covalent bonding between two metal atoms, (ii) M2@C80(CH2Ph) dimetallofullerene derivatives with single-occupied metal-bonding orbital, and (iii) M2TiC@C80 EMFs with endohedral Ti(IV) (M is either Sc or Y or a lanthanide). For the first two families, the metal-metal bonding orbital has been found to be redox active: in M2@C82, the double-occupied M-M bonding orbital is involved in the first oxidation process, while in M2@C80(CH2Ph) the unoccupied component of single-occupied metal-bonding orbital acts as the LUMO, accepting one electron during the first reduction step. Thus, single electron transfer reactions in both cases lead to the changes in the magnetic properties of EMFs, which is especially well revealed by EPR spectroscopy. For the series of M2TiC@C80 EMFs, the first reduction predominantly occurs on internal Ti atom and can be described as TiIV/TiIII redox process. Due to the variation of the size of the Ti ion in different oxidation states, reduction changes the inner strain of the cluster, leading to a large variability of the TiIV/TiIII reduction potential in dependence on the size of the formally inert lanthanide metal in M2TiC@C80

Synthesis and chemistry of highly distorted polycyclic aromatic hydrocarbons

A significant feature of smaller cyclophanes and buckminsterfullerenes is the presence of nonplanar aromatic rings. Such compounds are of considerable interest due to both the synthetic challenge they pose and to their unusual conformational, spectroscopic, and chemical behavior. A great deal of work has focussed on determining the extent to which an aromatic ring can be distorted from planarity while remaining isolable under ambient conditions. Although this question has been examined in detail for isolated benzene rings (for example, through investigations of [n]paracyclophanes), analogous studies of polycyclic aromatic hydrocarbon (PAH) frameworks have never been pursued. -- Here the first systematic examination of the distortion from planarity of a PAH moiety is reported. The synthesis of a number of [n](2,7)pyrenophanes from [3.3]dithiacyclophane precursors is described. Some physical, spectroscopic, and chemical properties of these molecules are also described, and a number of X-ray structures of markedly nonplanar aromatic moieties are reported. From this data, it is concluded that the end-to-end bend of the most strained pyrenophane prepared is greater than the average end-to-end bend of the pyrene moiety. However, POAV analysis of the pyramidalization of pyrenophane sp² carbon atoms reveals markedly lower pyramidalizations than are observed in D₅h C₇₀. Attempts at the functionalization of [n](2,7)pyrenophanes in the hope of using them as precursors for larger nonplanar PAHs were made. However, suitable conditions for functionalization of pyrenophanes were not found. A synthetic approach to a C₂-chiral 1,6-[n]pyrenophane is also described. -- An attempted synthesis of a derivative of the buckybowl pinakene using a tandem Bergman cycloaromatization/free radical conjugate addition is presented. -- The experimental work is preceded by reviews of the literature concerning the concept of aromaticity, nonplanar aromatic molecules (especially [n]paracyclophanes) and fullerene fragments

Thermal rearrangements of linear carbon chains: Theoretical and experimental studies

The potential energy surface of linear hydrocarbons has been extensively investigated by experiments and the use of molecular modeling. Linear C4 structures have demonstrated the potential to scramble their inner carbon atoms leading to the formation of novel strained intermediates. Long-range carbon atom topomerization in a 1,3-diyne has been demonstrated for the first time. 1-Phenyl-4-p-tolyl-1,3-butadiene, 13C enriched at C-1, was synthesized and subjected to flash vacuum pyrolysis. Under high temperature and at low pressure, this resulted in nearly complete 13C label equilibration among all of the sp hybridized carbons, as seen by NMR analysis. It has been proposed that 1,3-diynes rearrange to form several unprecedented strained intermediates in order to support carbon transpositions. As investigated computationally, 1,3-butadiene forms trialene, (bicyclo[1.1.0]-1,3-butadiene), a highly strained organic intermediate. Trialene serves as a key intermediate in the long-range carbon scrambling. Density functional (B3LYP/6-311+G(2d,p)), and Moller-Plesset, theory calculations support the possible formation of trialene. Long-range carbon topomerization in butatrienes has been investigated as well. Density functional and Moller-Plesset theory calculations predict a low-energy pathway that leads to carbon scrambling of the inner sp hybridized carbons of butatriene. We predict a thermal rearrangement of butatriene to form methylenecyclopropylidene, followed by carbene insertion to form bicyclo[1.1.0]but-1(3)-ene. Ring opening and reformation of butatriene is an overall degenerate process that leads to carbon scrambling. All of these structures have been found computationally as true energy minima along this reaction pathway. Control pyrolysis experiments with tetraarylbutatrienes have established compound stability up to approximately 800°C. A suitable synthesis of 13C labeled unsymmetrical butatriene and pyrolysis experiments are needed in order to support our calculations

Synthesis and characterization of new flavin systems with biomimetic and photovoltaic applications

This thesis describes the incorporation of a flavin unit into a range of systems spanning photovoltaics and biomimetic self-assembly. The flavin unit is better known as a cofactor in a range of enzymes. However, the unique physical and self-assembly properties were exploited in this research programme to develop new systems with photovoltaic and biomimetic self-assembly applications. In Chapter 1 a general introduction relating to flavins and photovoltaics is provided. In Chapter 2, the aim was to explore the effect of the addition of fullerene to a range of acceptors in the expectation of forming new acceptor materials with a wide range of LUMO energies. In Chapter 3, the aim was to investigate the effect of coupling a flavin unit to a naphthalenediimides (NDI) unit in the expectation of forming hybrid materials for solar energy conversion. Chapter 4 describes the formation of conjugated polymers featuring a flavin moiety, in the expectation that these materials will have photovoltaic properties. Chapter 5 describes the synthesis of push-pull flavin systems with pH dependent visisble light absorption characteristics. Finally Chapter 6 describes the synthesis of water soluble ammonium salts to furnish new micelle based systems with hydrogen bonding recognition properties

Large and multi scale mechanistic modeling of Diels-Alder reactions

The [4+2] cycloaddition reaction between conjugated dienes and substituted alkenes is known as the Diels-Alder (DA) reaction, in honor of two German chemists, Otto Diels and Kurt Alder, who first reported this marvelous chemical transformation. The DA reaction is one of the most popular reactions in organic chemistry, allowing for the regio- and stereospecific establishment of six-membered rings with up to four stereogenic centers. This pericyclic reaction has found many applications in areas as diverse as natural products chemistry, polymer chemistry, and agrochemistry. Over the past decades, the mechanism of the Diels-Alder (DA) reaction has been the subject of numerous studies, dealing with questions as diverse as the mechanistic pathway, the synchronicity, the use of catalysts, the effect of solvents and salts, etc. On the other hand, as an example, fullerenes (and particularly [60] fullerene) have been found to act as good dienophiles in DA reactions to the extent that many functionalized fullerenes with interesting applications are still synthesized by reacting C60 with dienes. However, despite the very abundant literature about the mechanism of the DA reaction, some pertinent questions have been still pending, including, without being restricted to, the prediction of transition state (TS) geometries and the modeling of DA reactions involving large systems, such as those of C60 fullerene. It must be emphasized that TSs are not easy to predict and the main reason is that many existing algorithms require that the search is initiated from a good starting point (guess TS), which must be very similar to the actual TS. This problem is even more difficult when many TSs are to be located as may be the case in large-scale studies. Moreover, due to the large size of the C60 molecule, the usage of accurate high-level computational methods in the investigation of its reactivity towards dienes is computationally costly, implying the need to find the best threshold between accuracy and computational cost. Therefore, the present study was carried out to contribute to solving the problems of large-scale prediction of DA transition state geometries and the multi-scale modeling of C60 fullerene DA reactions. To address the first problem (large-scale prediction of TSs), we have developed a python program named “AMADAR”, which predicts an unlimited number of DA transition states, using only the SMILES strings of the cycloadducts. AMADAR is customizable and allows for the description of intramolecular DA reactions as well as systems resulting in competing paths. In addition, The AMADAR tool contains two separate modules that perform reaction force analyses and atomic decomposition of energy derivatives from the predicted Intrinsic Reaction Coordinates (IRC) paths. The performance of AMADAR was assessed using 2000 DA cycloadducts and showed a success rate of ~ 95%. Most of the errors were due to basis set inconsistencies or convergence issues that we are still working on. Furthermore, a set of 150 IRC paths generated by the AMADAR program were analyzed to get insight into the (a)synchronicity of DA reactions. This investigation confirmed that the reaction force constant (second derivatives of the system energy with respect to the reaction coordinate) was a good indicator of synchronicity in DA reactions. A close inspection of the profile of has enabled us to propose an alternative classification of DA reactions based on their synchronicity degree, in terms of (quasi)-synchronous, moderate asynchronous, asynchronous, and likely two-steps DA reactions. Natural population analyses seemed to indicate that the global maximum of the reaction force constant could be identified with the formation of all the bonds in the reaction site. Finally, the atomic resolution of energy derivatives suggested that the mechanism of the DA reaction involves two inner elementary processes associated with the formation of each C-C bond. A striking mechanistic difference between synchronous and asynchronous DA reactions emerging from this study is that, in asynchronous reactions, the driving and retarding forces are mainly caused by the fast and slow-forming bonds (elementary process) respectively, while in the case of synchronous ones both elementary processes retard and drive the process concomitantly and equivalently. Regarding the DA reaction of C60 fullerene that was considered to illustrate the problem of multiscale modeling, we have constructed 12 ONIOM2 and 10 ONIOM3 models combining five semi-empirical methods (AM1, PM3, PM3MM, PDDG, PM6) and the LDA(SVWN) functional in conjunction with the B3LYP/6-31G(d) level. Then, their accuracy and efficiency were assessed in comparison with the pure B3LYP/6-31G(d) level considering first the DA reaction between C60 and cyclopentadiene whose experimental data are available. Further, different DFT functionals were employed in place of the B3LYP functional to describe the higher-layer of the best ONIOM partition, and the results obtained were compared to experimental data. At this step, the ONIOM2(M06-2X/6-31 G(d): SVWN/STO-3G) model, where the higher layer encompasses the diene and pyracyclene portion of C60, was found to provide the best tradeoff between accuracy and cost, with respect to experimental data. This model showed errors lower than 2.6 and 2.0 kcal/mol for the estimation of the activation and reaction enthalpies respectively. We have also demonstrated, by comparing several ONIOM2(DFT/6-31G(d): SVWN/STO-3G) models, the importance of dispersion corrections in the accurate estimation of reaction and activation energies. Finally, we have considered a set of 21 dienes, including anthracene, 1,3-butadiene, 1,3-cyclopentadiene, furan, thiophene, selenothiophene, pyrrole and their mono-cyano and hydroxyl derivatives to get insight into the DA reaction of C60 using the best ONIOM2(M06-2X/6-31 G(d): SVWN/STO-3G) model. For a given diene and its derivatives, the analysis of frontier molecular orbitals provides a consistent explanation for the substituent effect on the activation barrier. It revealed that electron-donating (withdrawing) groups such as -OH (–CN) cut down on the activation barrier of the reaction by lowering (extending) of the HOMOdiene – LUMOC60 gap and consequently enhancing (weakening) the interaction between the two reactants. Further, the decomposition of the activation energy into the strain and interaction components suggested that, for a given diene, electron-donating groups (here –OH) diminish the height of the activation barrier not only by favoring the attractive interaction between the diene and C60, but also by reducing the strain energy of the system; the opposite effect is observed for electron-withdrawing groups (here –CN). In contrast with some previous findings on typical DA reactions, we could not infer any general rule applicable to the entire dataset for the prediction of activation energies because the latter does not correlate well with either of the TS polarity, electrophilicity of the diene, or the reaction energy.Thesis (MSc) -- Faculty of Science, Chemistry, 202