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I. Ceric ammonium nitrate (CAN) mediated thiocyanate radical additions to glycals
In this dissertation, a facile entry was developed for the synthesis of 2-thiocarbohydrates and their transformations. Initially, CAN mediated thiocyanation of carbohydrates was carried out to obtain the basic building blocks (2-thiocyanates) for the entire studies. Subsequently, 2-thiocyanates were reduced to the corresponding thiols using appropriate reagents and reaction conditions. The screening of substrates, stereochemical outcome and the reaction mechanism are discussed briefly (Scheme I).
Scheme I. Synthesis of the 2-thiocyanates II and reductions to 2-thiols III & IV.
An interesting mechanism was proposed for the reduction of 2-thiocyanates II to 2-thiols III via formation of a disulfide intermediate. The water soluble free thiols IV were obtained by cleaving the thiocyanate and benzyl groups in a single step. In the subsequent part of studies, the synthetic potential of the 2-thiols was successfully expanded by simple synthetic transformations.
II. Transformations of the 2-thiocarbohydrates
The 2-thiols were utilized for convenient transformations including sulfa-Michael additions, nucleophilic substitutions, oxidation to disulfides and functionalization at the anomeric position. The diverse functionalizations of the carbohydrates at the C-2 position by means of the sulfur linkage are the highlighting feature of these studies. Thus, it creates an opportunity to expand the utility of 2-thiocarbohydrates for biological studies.
Reagents and conditions: a) I2, pyridine, THF, rt, 15 min; b) K2CO3, MeCN, rt, 1 h; c) MeI, K2CO3, DMF, 0 °C, 5 min; d) Ac2O, H2SO4 (1 drop), rt, 10 min; e) CAN, MeCN/H2O, NH4SCN, rt, 1 h; f) NaN3, ZnBr2, iPrOH/H2O, reflux, 15 h; g) NaOH (1 M), TBAI, benzene, rt, 2 h; h) ZnCl2, CHCl3, reflux, 3 h.
Scheme II. Functionalization of 2-thiocarbohydrates.
These transformations have enhanced the synthetic value of 2-thiocarbohydrates for the preparative scale. Worth to mention is the Lewis acid catalyzed replacement of the methoxy group by other nucleophiles and the synthesis of the (2→1) thiodisaccharides, which were obtained with complete β-selectivity. Additionally, for the first time, the carbohydrate linked thiotetrazole was synthesized by a (3 + 2) cycloaddition approach at the C-2 position.
III. Synthesis of thiodisaccharides by thiol-ene coupling.
In the final part of studies, the synthesis of thiodisaccharides by a classical photoinduced thiol-ene coupling was successfully achieved.
Reagents and conditions: 2,2-Dimethoxy-2-phenylacetophenone (DPAP), CH2Cl2/EtOH, hv, rt.
Scheme III. Thiol-ene coupling between 2-thiols and exo-glycals.
During the course of investigations, it was found that the steric hindrance plays an important role in the addition of bulky thiols to endo-glycals. Thus, we successfully screened the suitable substrates for addition of various thiols to sterically less hindered alkenes (Scheme III). The photochemical addition of 2-thiols to three different exo-glycals delivered excellent regio- and diastereoselectivities as well as yields, which underlines the synthetic potential of this convenient methodology.
The field of nanophotonics focuses on the interaction between electromagnetic radiation and matter on the nanometer scale. The elements of nanoscale photonic devices can transfer excitation energy non-radiatively from an excited donor molecule to an acceptor molecule by Förster resonance energy transfer (FRET). The efficiency of this energy transfer is highly dependent on the donor-acceptor distance. Hence, in these nanoscale photonic devices it is of high importance to have a good control over the spatial assembly of used fluorophores. Based on molecular self-assembly processes, various nanostructures can be produced. Here, DNA nanotechnology and especially the DNA origami technique are auspicious self-assembling methods. By using DNA origami nanostructures different fluorophores can be introduced with a high local control to create a variety of nanoscale photonic objects. The applications of such nanostructures range from photonic wires and logic gates for molecular computing to artificial light harvesting systems for artificial photosynthesis.
In the present cumulative doctoral thesis, different FRET systems on DNA origami structures have been designed and thoroughly analyzed. Firstly, the formation of guanine (G) quadruplex structures from G rich DNA sequences has been studied based on a two-color FRET system (Fluorescein (FAM)/Cyanine3 (Cy3)). Here, the influences of different cations (Na+ and K+), of the DNA origami structure and of the DNA sequence on the G-quadruplex formation have been analyzed. In this study, an ion-selective K+ sensing scheme based on the G-quadruplex formation on DNA origami structures has been developed. Subsequently, the reversibility of the G-quadruplex formation on DNA origami structures has been evaluated. This has been done for the simple two-color FRET system which has then been advanced to a switchable photonic wire by introducing additional fluorophores (FAM/Cy3/Cyanine5 (Cy5)/IRDye®700). In the last part, the emission intensity of the acceptor molecule (Cy5) in a three-color FRET cascade has been tuned by arranging multiple donor (FAM) and transmitter (Cy3) molecules around the central acceptor molecule. In such artificial light harvesting systems, the excitation energy is absorbed by several donor and transmitter molecules followed by an energy transfer to the acceptor leading to a brighter Cy5 emission. Furthermore, the range of possible excitation wavelengths is extended by using several different fluorophores (FAM/Cy3/Cy5). In this part of the thesis, the light harvesting efficiency (antenna effect) and the FRET efficiency of different donor/transmitter/acceptor assemblies have been analyzed and the artificial light harvesting complex has been optimized in this respect.
This cumulative doctoral dissertation, based on three publications, is devoted to the investigation of several aspects of azobenzene molecular switches, with the aid of computational chemistry.
In the first paper, the isomerization rates of a thermal cis → trans isomerization of azobenzenes for species formed upon an integer electron transfer, i.e., with added or removed electron, are calculated from Eyring’s transition state theory and activation energy barriers, computed by means of density functional theory. The obtained results are discussed in connection with an experimental study of the thermal cis → trans isomerization of azobenzene derivatives in the presence of gold nanoparticles, which is demonstrated to be greatly accelerated in comparison to the same isomerization reaction in the absence of nanoparticles.
The second paper is concerned with electronically excited states of (i) dimers, composed of two photoswitchable units placed closely side-by-side, as well as (ii) monomers and dimers adsorbed on a silicon cluster. A variety of quantum chemistry methods, capable of calculating molecular electronic absorption spectra, based on density functional and wave function theories, is employed to quantify changes in optical absorption upon dimerization and covalent grafting to a surface. Specifically, the exciton (Davydov) splitting between states of interest is determined from first-principles calculations with the help of natural transition orbital analysis, allowing for insight into the nature of excited states.
In the third paper, nonadiabatic molecular dynamics with trajectory surface hopping is applied to model the photoisomerization of azobenzene dimers, (i) for the isolated case (exhibiting the exciton coupling between two molecules) as well as (ii) for the constrained case (providing the van der Waals interaction with environment in addition to the exciton coupling between two monomers). For the latter, the additional azobenzene molecules, surrounding the dimer, are introduced, mimicking a densely packed self-assembled monolayer. From obtained results it is concluded that the isolated dimer is capable of isomerization likewise the monomer, whereas the steric hindrance considerably suppresses trans → cis photoisomerization.
Furthermore, the present dissertation comprises the general introduction describing the main features of the azobenzene photoswitch and objectives of this work, theoretical basis of the employed methods, and discussion of gained findings in the light of existing literature. Also, additional results on (i) activation parameters of the thermal cis → trans isomerization of azobenzenes, (ii) an approximate scheme to account for anharmonicity of molecular vibrations in calculation of the activation entropy, as well as (iii) absorption spectra of photoswitch–silicon composites obtained from time-demanding wave function-based methods are presented.
Lignin valorization
(2017)
The topic of this project is the use of lignin as alternative source of aromatic building blocks and oligomers to fossil feedstocks. Lignin is known as the most abundant aromatic polymer in nature and is isolated from the lignocellulosic component of plants by different possible extraction treatments. Both the biomass source and the extraction method affect the structure of the isolated lignin, therefore influencing its further application. Lignin was extracted from beech wood by two different hydrothermal alkaline treatments, which use NaOH and Ba(OH)2 as base and by an acid-catalyzed organosolv process. Moreover, lignin was isolated from bamboo, beech wood and coconut by soda treatment of the biomasses. A comparison of the structural features of such isolated lignins was performed through the use of a wide range of analytical methods. Alkaline lignins resulted in a better candidate as carbon precursor and macromonomers for the synthesis of polymer than organosolv lignin. In fact, alkaline lignins showed higher residual mass after carbonization and higher content of the reactive hydroxy functionalities. In contrast, the lignin source turned out to slightly affect the lignin hydroxyl content.
One of the most common lignin modifications is its deconstruction to obtain aromatic molecules, which can be used as starting materials for the synthesis of fine chemicals. Lignin deconstruction leads to a complex mixture of aromatic molecules. A gas chromatographic analytical method was developed to characterize the mixture of products obtained by lignin deconstruction via heterogeneous catalytic hydrogenolysis. The analytical protocol allowed the quantification of three main groups of molecules by means of calibration curves, internal standard and a preliminary silylation step of the sample. The analytical method was used to study the influence of the hydrogenolysis catalyst, temperature and system (flow and batch reactor) on the yield and selectivity of the aromatic compounds.
Lignin extracted from beech wood by a hydrothermal process using Ba(OH)2 as base, was functionalized by aromatic nitration in order to add nitrogen functionalities. The final goal was the synthesis of a nitrogen doped carbon. Nitrated lignin was reduced to the amino form in order to compare the influence of different nitrogen functionalities on the porosity of the final carbon. The carbons were obtained by ionothermal treatment of the precursors in the presence of the eutectic salt mixture KCl/ZnCl2 Such synthesized carbons showed micro-, macro- and mesoporosity and were tested for their electrocatalytic activity towards the oxygen reduction reaction. Mesoporous carbon derived from nitro lignin displayed the highest electrocatalytic activity.
Lignins isolated from coconut, beech wood and bamboo were used as macromonomers for the synthesis of biobased polyesters. A condensation reaction was performed between lignin and a hyper branched poly(ester-amine), previously obtained by condensation of triethanolamine and adipic acid. The influence of the lignin source and content on the thermochemical and mechanical properties of the final material was investigated. The prepolymer showed adhesive properties towards aluminum and its shear strength was therefore measured. The gluing properties of such synthesized glues turned out to be independent from the lignin source but affected by the amount of lignin in the final material.
This work shows that, although still at a laboratory scale, the valorization of lignin can overcome the critical issues of lignin´s structure variability and complexity.