This thesis concerns the construction, use and modulation of various host–guest systems, from small bispidines for binding of inorganic ions to bisporphyrin clips for supramolecular systems. Small flexible molecules undergo fast conformational movements when in solution. These conformational movements generate time-averaged population-weighted chemical shifts, coupling constants and NOEs when analysed by NMR spectroscopy. A bisporphyrin clip was designed to be used as a host for restriction of conformational movements of small flexible molecules by ditopic metal-ligand binding. Based on conformational analysis in combination with NMR analysis of molecular flexibility in solution (NAMFIS), the relative stereochemistry of flexible alditol-derived diamines containing three or four consecutive stereocentres could be determined. To further explore the idea of conformational deconvolution via host–guest binding, two flexible molecular tweezers with photoswitchable moieties were developed. Upon photoswitching cis/trans isomerisation facilitates the opening and closing of these bisporphyrin hosts. A guest molecule could then be exposed to a “catch and stretch” or “catch and release” effect. Preliminary studies have shown that photoisomerisation of the constructed systems is possible without photodecomposition and preliminary binding studies have been conducted. Controlled modulation of molecular conformations is of interest especially if the conformational steering activates a unit working as a nucleator in a larger structure or facilitates a reaction. The protonation-triggered modulation of bispidine conformations has been investigated. In addition to previously reported conformations we have observed that upon diprotonation a bispidine derivative can be driven into the unusual boat-boat conformation. Finally, the unexpected formation of persistent organic radicals with a cyclophane motif from the reaction of N,N´-diphenyl-1-5-diazacyclooctane and AgBF4 is described. Interestingly, these diradicals exhibit features such as intramolecular π-stacking without lateral displacement and also intramolecular spin pairing.

Supramolecular systems comprised of non-covalent interactions are reversible in nature. This intrinsic reversibility of these systems is essential in achieving several functions, making it crucial to understand the dynamics of supramolecular systems. However, studies on the dynamics of supramolecular systems have always lagged behind structural and thermodynamic characterization of innumerable supramolecular systems developed. The first objective of this work was to understand the dynamics leading to a shift in the acidity constant (pKa) for 2-aminoanthracenium cation (AH+) upon binding with cucurbit[7]uril (CB[7]) host molecule. The adiabatic deprotonation of free AH+ in water was found to be inhibited in the complex with CB[7]. Different spectral characteristics for the protonated and deprotonated form of the guest molecule were used to understand the mechanism of this pKa shift associated with the binding to CB[7]. The results suggested that the pKa shift upon binding with CB[7] is a result of the slowing down of the deprotonation step in the complex, whereas the association rate constant did not change very much. The second objective of this work was to understand the role of cations on the binding dynamics of the N-phenyl-2-naphthyl amine (Ph-A-Np) binding to CB[7]. Ph-A-Np has two binding sites, which can lead to 1:1 and 2:1 host-guest complexes. The results indicate a switch in the binding mechanism for Ph-A-Np at low and high concentration regimes of sodium ions. Sodium ion was found to reduce the binding affinity of the naphthyl group to CB[7] whereas the complex formed by the phenyl group with CB[7] bound to one sodium ion was found to be stabilized. The final objective of this work was to study how structural changes to a guest molecule can affect the binding dynamics for the formation of a 2:1 “capsule” like complex with octa acid (OA). The dissociation for the OA capsule with pyrene (Py) as the encapsulated guest was shown to happen in 2.7 s previously. Two pyrene derivatives, 1-methylpyrene (MePy) and 1-pyrenemethanol (PyMeOH) were chosen as guest molecules to study the effect of these substituents on pyrene on the capsule dissociation dynamics. The results show that the residence time for the guests in the OA capsule depends on the substituents. For PyMeOH and MePy a shorter and longer residence time respectively in the capsule was observed when compared to Py. / Graduate / 2019-09-30

The main focus of this thesis is on photochemical modulation of molecular recognition in various host-guest systems. This involves the design, synthesis and integration of light-triggered conformational switches into peptidomimetic guests and molecular tweezer hosts. The impact of the switches on guest and host structures has been assessed by spectroscopic and computational conformational analysis. Effects of photochemical structure modulation on molecular recognition in protein-ligand and supramolecular host-guest systems are discussed. Phototriggerable peptidomimetic inhibitors of the enzyme M. tuberculosis ribonucleotide reductase (RNR) were obtained by incorporation of a stilbene based amino acid moiety into oligopeptides between 3-9 residues long (Paper I). Interstrand hydrogen bond probability in the E and Z forms of the peptidomimetics was used as a tool for predicting conformational preferences. Considerable differences in inhibitory potency for the E and Z photoisomers were demonstrated in a binding assay. In order to advance the concept of photomodulable inhibitors, synthetic routes towards amino acid derivatives based on the more rigid stiff-stilbene chromophore were developed (Paper II).  The effect of E-Z isomerization on the conformational properties of peptidomimetic inhibitors incorporating the stiff-stilbene chromophore was also assessed computationally (Paper III). It was indicated that inhibitors with the more rigid amino acid derivative should display larger conformational divergence between photoisomers than corresponding stilbene derivatives. Bisporphyrin tweezers with enediyne and stiff-stilbene spacers have been synthesized, and the conformational characteristics imposed by the spacers have been studied and compared to a glycoluril linked tweezer. The effects of spacers on tweezer binding of diamine guests and helicity induction by chiral guests have been investigated (Paper IV). Connections between spacer flexibility and host-guest binding strength have been established. The structural properties of the stiff-stilbene spaced tweezer made it particularly susceptible to helicity induction by both monotopic and bitopic chiral guests. Finally, the possibility of photochemical bite-size variation of tweezers with photoswitchable spacers has been assessed. Initial studies have shown that photoisomerization of the tweezers is possible without photochemical decomposition. Conformational analyses indicate that isomerization should impact binding characteristics of the tweezers to a significant extent (Paper V).

<p>Molecular recognition via noncovalent interactions plays a key role in many biological processes such as antigen-antibody interactions, protein folding, the bonding and catalytic transformation of substrates by enzymes, etc. Amongst these noncovalent interactions, electrostatic interactions, hydrogen bonding, π-π interactions, and metal-to-ligand bonding are the most prominent. Exploring noncovalent interactions in host-guest systems that range from small hydrocarbon systems to more complex systems is the main motivation of this thesis. The present study involves the design, synthesis and characterization of clip-shaped molecules as host structures, and an examination of their binding properties with a variety of guests using NMR spectroscopy. </p><p>Several clips with a hydrocarbon or glycoluril backbone were synthesized. The binding of cations to small, hydrocarbon-based clips suggests that binding is enhanced by the rigidity and cooperativity between the two sidewalls of the clip. Binding is also very much dependant on the solvent properties. </p><p>Glycoluril-based clips built with aromatic sidewalls provide a deep cavity for binding guest molecules. The binding properties of these hosts were studied with several guests such as cations, Lewis acids and Lewis bases. Lewis basic binding sites in the acenaphthene-terminated clip were dominating in guest binding. Complexation-induced conformational changes in the wall-to-wall distance were observed for this clip.</p><p>In contrast, for a porphyrin-terminated clip with metal centers, very strong binding to a series of Lewis basic guests of various sizes into the clip cavity was observed. Conformational locking of guests with long alkyl chains was achieved, suggesting that, this clip could be useful as a potential molecular tool for the structural characterization of acyclic molecules with several stereogenic centers. This porphyrin clip was also shown to bind substituted fullerenes in the cavity.</p>

Molecular recognition via noncovalent interactions plays a key role in many biological processes such as antigen-antibody interactions, protein folding, the bonding and catalytic transformation of substrates by enzymes, etc. Amongst these noncovalent interactions, electrostatic interactions, hydrogen bonding, π-π interactions, and metal-to-ligand bonding are the most prominent. Exploring noncovalent interactions in host-guest systems that range from small hydrocarbon systems to more complex systems is the main motivation of this thesis. The present study involves the design, synthesis and characterization of clip-shaped molecules as host structures, and an examination of their binding properties with a variety of guests using NMR spectroscopy. Several clips with a hydrocarbon or glycoluril backbone were synthesized. The binding of cations to small, hydrocarbon-based clips suggests that binding is enhanced by the rigidity and cooperativity between the two sidewalls of the clip. Binding is also very much dependant on the solvent properties. Glycoluril-based clips built with aromatic sidewalls provide a deep cavity for binding guest molecules. The binding properties of these hosts were studied with several guests such as cations, Lewis acids and Lewis bases. Lewis basic binding sites in the acenaphthene-terminated clip were dominating in guest binding. Complexation-induced conformational changes in the wall-to-wall distance were observed for this clip. In contrast, for a porphyrin-terminated clip with metal centers, very strong binding to a series of Lewis basic guests of various sizes into the clip cavity was observed. Conformational locking of guests with long alkyl chains was achieved, suggesting that, this clip could be useful as a potential molecular tool for the structural characterization of acyclic molecules with several stereogenic centers. This porphyrin clip was also shown to bind substituted fullerenes in the cavity.

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