(A) Optimization of solid body phase synthesis of RNA using the Cpep chemistry. (B) Synthesis of BODIPY labeled oligonucleotides

(A) Solid phase synthesis of oligonucleotides are well documented and are extensively studied as the demands continue to rise with the development of antisense, anti-gene, RNA interference, and aptamers. Although synthesis of RNA sequences faces many challenges, most notably the choice of the 2' -hydroxy protecting group, modified 2' -O-Cpep protected ribonucleotides were synthesized as alternitive building blocks. Altering phosphitylation procedures to incorporate 3' -N,N-diethyl phosphoramidites enhanced the overall reactivity, thus, increased the coupling efficiency without loss of integrety. Furthermore, technical optimizations of solid phase synthesis cycles were carried out to allow for successful synthesis of a homo UIO sequences with a stepwise coupling efficiency reaching 99% and a final yield of 91 %. (B) Over the past few decades, dipyrrometheneboron difluoride (BODIPY) has gained recognition as one of the most versatile fluorophores. Currently, BODIPY labeling of oligonucleotides are carried out post-synthetically and to date, there lacks a method that allows for direct incorporation of BODIPY into oligonucleotides during solid phase synthesis. Therefore, synthesis of BODIPY derived phosphoramidites will provide an alternative method in obtaining fluorescently labelled oligonucleotides. A method for the synthesis and incorporation of the BODIPY analogues into oligonucleotides by phosphoramidite chemistry-based solid phase DNA synthesis is reported here. Using this approach, BODIPY-labeled TlO homopolymer and ISIS 5132 were successfully synthesized.

Synthesis of well-dispersed nanoparticles within porous solid structures using surface-tethered surfactants in supercritical CO2

We have developed a new method for the synthesis of Pd nanoparticles with controllable sizes within a silica matrix using solid-supported surfactants in supercritical CO2. XRD, HRTEM and CO chemisorption data show that unformly sized Pd nanoparticles are evenly distributed within the porous silica and are chemically tethered by surfactant molecules [poly(oxyethylene stearyl ether) and fluorinated poly(oxyethylene)]. It is postulated that tiny solid-supported surfactant assemblies act as nano-reactors for the template synthesis of nanoparticles or clusters from the soluble precursors therein.

Sequence-controlled synthesis of soluble oligo(p-benzamide)s

This work focused on the synthesis of novel monomers for the design of a series of oligo(p-benzamide)s following two approaches: iterative solution synthesis and automated solid phase protocols. These approaches present a useful method to the sequence-controlled synthesis of side-chain and main-chain functionalized oligomers for the preparation of an immense variety of nanoscaffolds. The challenge in the synthesis of such materials was their modification, while maintaining the characteristic properties (physical-chemical properties, shape persistence and anisotropy). The strategy for the preparation of predictable superstructures was devote to the selective control of noncovalent interactions, monodispersity and monomer sequence. In addition to this, the structure-properties correlation of the prepared rod-like soluble materials was pointed. The first approach involved the solution-based aramide synthesis via introduction of 2,4-dimethoxybenzyl N-amide protective group via an iterative synthetic strategy The second approach focused on the implementation of the salicylic acid scaffold to introduce substituents on the aromatic backbone for the stabilization of the OPBA-rotamers. The prepared oligomers were analyzed regarding their solubility and aggregation properties by systematically changing the degree of rotational freedom of the amide bonds, side chain polarity, monomer sequence and degree of oligomerization. The syntheses were performed on a modified commercial peptide synthesizer using a combination of fluorenylmethoxycarbonyl (Fmoc) and aramide chemistry. The automated synthesis allowed the preparation of aramides with potential applications as nanoscaffolds in supramolecular chemistry, e.g. comb-like-

Solid-state NMR on columnar supramolecular structures

The present work deals with the characterisation of three columnar self-assembled systems, that is, benzene-1,3,5-tricarboxamides, a peripherally thioalkyl-substituted phthalocyanine, and several oligo-(p-phenylenevinylene)s. In order to probe the supramolecular organisation solid-state NMR has been used as the main technique, supported by X-ray measurements, theoretical methods, and thermal analysis. rnrnBenzene-1,3,5-tricarboxamides (BTAs) turned out to be well suited model compounds to study various fundamental supramolecular interactions, such as π-π-interactions, hydrogen bonding, as well as dynamic and steric effects of attached side chains. Six BTAs have been investigated in total, five with a CO-centred amide group bearing different side chains and one with an inverted N-centred amide group. The physical properties of these BTAs have been investigated as a function of temperature. The results indicated that in case of the CO-centred BTAs the stability of the columnar mesophase depends strongly on the nature of the side chains. Further experiments revealed a coplanar orientation of adjacent BTA molecules in the columnar assembly of CO-centred BTAs, whereas the N-centred BTA, showed a deviating not fully coplanar arrangement. These differences were ascribed to distinct hydrogen bonding schemes, involving a parallel alignment of hydrogen bonds in case of CO-centred BTAs and an antiparallel alignment in case of the N-centred counterpart.rnrn The fundamental insights of the supramolecular organisation of BTAs could be partially adapted to an octa-substituted phthalocyanine with thiododecyl moieties. Solid-state NMR in combination with chemical shift calculations determined a tilted herringbone arrangement of phthalocyanine rings in the crystalline phase as well as in the mesophase. Moreover, 1H NMR measurements in the mesophase of this compound suggested an axial rotation of molecules, which is inhibited in the crystalline phase.rnrnAs a third task, the supramolecular assembly of oligo-(p-phenylenevinylene)s of varying length and with different polar head groups have been investigated by a combined X-ray and solid-state NMR study. The results revealed a columnar structure formation of these compounds, being promoted by phase separation of alkyl side chains and aromatic rigid rods. In this system solid-state NMR yielded meaningful insight into the isotropisation process of butoxy and 2-S-methylbutoxy substituted oligo-(p-phenylenevinylene) rods.rn

Preparative solid state chemistry. Recent developments

A survey of recent developments in preparative solid state chemistry shows that, with a knowledge of structural chemistry and reactivity patterns of solids, it is possible to synthesize a variety of new solids possessing novel structures. A distinction is made between synthesis ofnew solids and synthesis of solids bynew methods. Three new routes to solid state synthesis are recognized: the precursor method, and topochemical methods involving redox and ion-exchange reactions. The low-temperature topochemical methods enable synthesis of metastable phases that are inaccessible by the high temperature route. Several illustrative examples of solid state synthesis from the recent literature are presented.

An efficient and flexible synthesis of model lignin oligomers

The use of model compounds in the development of selective lignin depolymerisation processes has been limited by the lack of complexity of these models compared with lignin itself. In this paper we report a convergent and efficient synthetic method for the flexible, multi-gram preparation of model lignin hexamers and octamers containing three of the most common connectivity motifs found within native lignin, namely ß-O-4', 5-5' and ß-5', which will be used to further the mechanistic understanding of lignin depolymerisation processes.

Stepwise self-assembly of a tripeptide from molecular dimers to supramolecular beta-sheets in crystals and amyloid-like fibrils in the solid state

The terminally protected tripeptide Boc-Ala(1)-Leu(2)-Ala(3)-OMe 1 forms antiparallel hydrogen-bonded dimers of two different conformers in the asymmetric unit and the individual dimers then self-associate to form supramolecular beta-sheet structures in crystals and amyloid-like fibrils in the solid state.

Supramolecular helix and beta-sheet through self-assembly of two isomeric tetrapeptides in crystals and formation of filaments and ribbons in the solid state

Single crystal X-ray diffraction studies show that the beta-turn structure of tetrapeptide I, Boc-Gly-Phe-Aib-Leu-OMe (Aib: alpha-amino isobutyric acid) self-assembles to a supramolecular helix through intermolecular hydrogen bonding along the crystallographic a axis. By contrast the beta-turn structure of an isomeric tetrapeptide II, Boc-Gly-Leu-Aib-Phe-OMe self-assembles to a supramolecular beta-sheet-like structure via a two-dimensional (a, b axis) intermolecular hydrogen bonding network and pi-pi interactions. FT-IR studies of the peptides revealed that both of them form intermolecularly hydrogen bonded supramolecular structures in the solid state. Field emission scanning electron micrographs (FE-SEM) of the dried fibrous materials of the peptides show different morphologies, non-twisted filaments in case of peptide I and non-twisted filaments and ribbon-like structures in case of peptide II.

Synthesis of beaded poly(vinyl ether) solid supports with unique solvent compatibility

Poly(vinyl ether) gels SLURPS (Superior Liquid Uptake Resin for Polymer-supported synthesis) with low cross-linking levels have been synthesized for the first time in beaded form using a non-aqueous inverse suspension polymerisation approach. The synthetic protocol was optimized with regards to several parameters including reactions conditions, type and concentration of suspension stabilizer and controlled low temperature addition of co-initiator. Particle size measurements confirm the production of beads with average diameters of 700e950 mm. Optimization of the monomer composition of the poly (vinyl ether) gels resulted in a novel beaded polymer support with considerably improved as well as unique swelling characteristics in solvents ranging from hexane to water. The synthetic utility of the new gel was confirmed by carrying out a set of transformations with complete conversion leading to a useful amino and hydroxy terminated solid-phase precursor resin. Reaction progress could be monitored easily by 1H and 13C gel-phase NMR.

Calixarene and Resorcarene Based Receptors: From Structural and Thermodynamic Studies to the Synthesis of a New Mercury(II) Selective Material

Materials used in current technological approaches for the removal of mercury lack selectivity. Given that this is one of the main features of supramolecular chemistry, receptors based on calix[4]arene and calix[4]resorcarene containing functional groups able to interact selectively with polluting ions while discriminating against biologically essential ones were designed. Thus two receptors, a partially functionalized calix[4]arene derivative, namely, 5,11,17,23-tetra-tert-butyl [25-27-bis(diethyl thiophosphate amino)dihydroxy] calix[4]arene (1) and a fully functionalized calix[4]resorcarene, 4,6,10,12,16,18,22,24-diethyl thiophosphate calix[4]resorcarene (2) are introduced. Mercury(II) was the identified target due to the environmental and health problems associated with its presence in water Thus following the synthesis and characterization of 1 and 2 in solution ((1)HNMR) and in the solid state (X-ray crystallography) the sequence of experimental events leading to cation complexation studies in acetonitrile and methanol ((1)H NMR, conductance, potentiometric, and calorimetric measurements) with the aim of assessing their behavior as mercury selective receptors are described. The cation selectivity pattern observed in acetonitrile follows the sequence Hg(II) > Cu(II) > Ag(I). In methanol 1 is also selective for Hg(II) relative to Ag(I) but no interaction takes place between this receptor and Cu(II) in this solvent. Based on previous results and experimental facts shown in this paper, it is concluded that the complexation observed with Cu(II) in acetonitrile occurs through the acetonitrile-receptor adduct rather than through the free ligand. Receptor 2 has an enhanced capacity for uptaking Hg(II) but forms metalate complexes with Cu(II). These studies in solution guided the inmobilization of receptor 1 into a silica support to produce a new and recyclable material for the removal of Hg(II) from water. An assessment on its capacity to extract this cation from water relative to Cu(II) and Ag (I) shows that the cation selectivity pattern of the inmobilized receptor is the same as that observed for the free receptor in methanol. These findings demonstrate that fundamental studies play a critical role in the selection of the receptor to be attached to silicates as well as in the reaction medium used for the synthesis of the new decontaminating agent.

NMR studies on supramolecular aggregates in solution and the solid state

The aim of this work presented here is the characterization of structure and dynamics of different types of supramolecular systems by advanced NMR spectroscopy. One of the characteristic features of NMR spectroscopy is based on its high selectivity. Thus, it is desirable to exploit this technique for studying structure and dynamics of large supramolecular systems without isotopic enrichment. The observed resonance frequencies are not only isotope specific but also influenced by local fields, in particular by the distribution of electron density around the investigated nucleus. Barbituric acid are well known for forming strongly hydrogen-bonded complexes with variety of adenine derivatives. The prototropic tautomerism of this material facilitates an adjustment to complementary bases containing a DDA(A = hydrogen bond acceptor site, D = hydrogen bond donor site) or ADA sequences, thereby yielding strongly hydrogen-bonded complexes. In this contribution solid-state structures of the enolizable chromophor "1-n-butyl-5-(4-nitrophenyl)-barbituric acid" that features adjustable hydrogen-bonding properties and the molecular assemblies with three different strength of bases (Proton sponge, adenine mimetic 2,6-diaminopyridine (DAP) and 2,6-diacetamidopyridine (DAC)) are studied. Diffusion NMR spectroscopy gives information over such interactions and has become the method of choice for measuring the diffusion coefficient, thereby reflecting the effective size and shape of a molecular species. In this work the investigation of supramolecular aggregates in solution state by means of DOSY NMR techniques are performed. The underlying principles of DOSY NMR experiment are discussed briefly and more importantly two applications demonstrating the potential of this method are focused on. Calix[n]arenes have gained a rather prominent position, both as host materials and as platforms to design specific receptors. In this respect, several different capsular contents of tetra urea calix[4]arenes (benzene, benzene-d6, 1-fluorobenzene, 1-fluorobenzene-d5, 1,4-difluorobenzene, and cobaltocenium) are studied by solid state NMR spectroscopy. In the solid state, the study of the interaction between tetra urea calix[4]arenes and guest is simplified by the fact that the guests molecule remains complexed and positioned within the cavity, thus allowing a more direct investigation of the host-guest interactions.

NON-CHROMATOGRAPHIC PURIFICATION OF SYNTHETIC BIO-OLIGOMERS

Synthetic oligonucleotides and peptides have found wide applications in industry and academic research labs. There are ~60 peptide drugs on the market and over 500 under development. The global annual sale of peptide drugs in 2010 was estimated to be $13 billion. There are three oligonucleotide-based drugs on market; among them, the FDA newly approved Kynamro was predicted to have a $100 million annual sale. The annual sale of oligonucleotides to academic labs was estimated to be $700 million. Both bio-oligomers are mostly synthesized on automated synthesizers using solid phase synthesis technology, in which nucleoside or amino acid monomers are added sequentially until the desired full-length sequence is reached. The additions cannot be complete, which generates truncated undesired failure sequences. For almost all applications, these impurities must be removed. The most widely used method is HPLC. However, the method is slow, expensive, labor-intensive, not amendable for automation, difficult to scale up, and unsuitable for high throughput purification. It needs large capital investment, and consumes large volumes of harmful solvents. The purification costs are estimated to be more than 50% of total production costs. Other methods for bio-oligomer purification also have drawbacks, and are less favored than HPLC for most applications. To overcome the problems of known biopolymer purification technologies, we have developed two non-chromatographic purification methods. They are (1) catching failure sequences by polymerization, and (2) catching full-length sequences by polymerization. In the first method, a polymerizable group is attached to the failure sequences of the bio-oligomers during automated synthesis; purification is achieved by simply polymerizing the failure sequences into an insoluble gel and extracting full-length sequences. In the second method, a polymerizable group is attached to the full-length sequences, which are then incorporated into a polymer; impurities are removed by washing, and pure product is cleaved from polymer. These methods do not need chromatography, and all drawbacks of HPLC no longer exist. Using them, purification is achieved by simple manipulations such as shaking and extraction. Therefore, they are suitable for large scale purification of oligonucleotide and peptide drugs, and also ideal for high throughput purification, which currently has a high demand for research projects involving total gene synthesis. The dissertation will present the details about the development of the techniques. Chapter 1 will make an introduction to oligodeoxynucleotides (ODNs), their synthesis and purification. Chapter 2 will describe the detailed studies of using the catching failure sequences by polymerization method to purify ODNs. Chapter 3 will describe the further optimization of the catching failure sequences by polymerization ODN purification technology to the level of practical use. Chapter 4 will present using the catching full-length sequence by polymerization method for ODN purification using acid-cleavable linker. Chapter 5 will make an introduction to peptides, their synthesis and purification. Chapter 6 will describe the studies using the catching full-length sequence by polymerization method for peptide purification.

Two-dimensional supramolecular polymers: controlled formation and visualization on the surface

Self – assembly is a powerful tool for the construction of highly organized nanostructures. Therefore, the possibility to control and predict pathways of molecular ordering on the nanoscale level is a critical issue for the production of materials with tunable and adaptive macroscopic properties. 2D polymers are attractive objects for the field of material sciences due to their exceptional properties. [1] As shown before, amphiphilic oligopyrenotides (produced via automated solid-phase synthesis) form rod–like supramolecular polymers in water. [2] These assemblies form 1D objects. [3] By applying certain changes to the design of the oligopyrenotide units the dimensionality of the formed assemblies can be influenced. Herein, we demonstrate that Py3 (see Figure 1) forms defined supramolecular assemblies under thermodynamic conditions in water. To study Py3 self-assembly, we carried out whole set of spectroscopic (UV/vis, fluorescence, DLS) and microscopic experiments (AFM). The obtained results suggest that oligopyrenotides with the present type of geometry and linker length leads to formation of 2D supramolecular assemblies.

The Design and Synthesis of Versatile Molecular Building Blocks: Working Towards the Controlled Self-Assembly of Novel Functional Materials

Our research goals are focused on the preparation of novel molecule-based materials that possess specifically designed properties in solution or in the solid state e.g. self-assembly, magnetism, conductivity and spin crossover phenomena. Most of our systems incorporate paramagnetic transition metal ions and the search for new molecule-based magnetic materials is a prominent theme. Specific areas of research include the preparation and study of oxalate based 2D and 3D magnets, probing the versatility of octacyanometalate building blocks as precursors for new molecular magnets, and the preparation of new tetrathiafulvalene (TIF) derivatives for applications in molecular and supramolecular chemistry.

Hierarchical self-assembly of the DNA-grafted supramolecular polymers

Conjugation of functional entities with a specific set of optical, mechanical or biological properties to DNA strands allows engineering of sophisticated DNA-containing architectures. Among various hybrid systems, DNA-grafted polymers occupy an important place in modern materials science. In this contribution we present the non-covalent synthesis and properties of DNA-grafted linear supramolecular polymers (SPs), which are assembled in a controllable manner from short chimeric DNA-pyrene oligomers. The synthetic oligomers consist of two parts: a 10 nucleotides long DNA chain and a covalently attached segment of variable number of phosphodiester-linked pyrenes. The temperature-dependent formation of DNA-grafted SPs is described by a nucleation-elongation mechanism. The high tendency of pyrenes to aggregate in water, leads to the rapid formation of SPs. The core of the assemblies consists of stacked pyrenes. They form a 1D platform, to which the DNA chains are attached. Combined spectroscopic and microscopic studies reveal that the major driving forces of the polymerization are π-stacking of pyrenes and hydrophobic interactions, and DNA pairing contributes to a lesser extent. AFM and TEM experiments demonstrate that the 1D SPs appear as elongated ribbons with a length of several hundred nanometers. They exhibit an apparent helical structure with a pitch-to-pitch distance of 50±15 nm. Since DNA pairing is a highly selective process, the ongoing studies are aimed to utilize DNA-grafted SPs for the programmable arrangement of functional entities. For example, the addition of non-modified complementary DNA strands to the DNA-grafted SPs leads to the cooperative formation of higher-order assemblies. Also, our experiments suggest that the fluorescent pyrene core of 1D ribbons serves as an efficient donor platform for energy transfer applications.