Prakash P. Neelakandan

Stimuli-Responsive Metal-Ligand Assemblies.

The Engineering and Physical Sciences Research Council and the European Research Council are acknowledged for financial support.

Hydrophobic self-assembly of a perylenediimide-linked DNA dumbbell into supramolecular polymers.

The self-assembly of DNA dumbbell conjugates possessing hydrophobic perylenediimide (PDI) linkers separated by an eight-base pair A-tract has been investigated. Cryo-TEM images obtained from dilute solutions of the dumbbell in aqueous buffer containing 100 mM NaCl show the presence of structures corresponding to linear end-to-end assemblies of 10-30 dumbbell monomers. The formation of assemblies of this size is consistent with analysis of the UV-vis and fluorescence spectra of these solutions for the content of PDI monomer and dimer chromophores. Assembly size is dependent upon the concentration of dumbbell and salt as well as the temperature. Kinetic analysis of the assembly process by means of salt-jump stopped-flow measurements shows that it occurs by a salt-triggered isodesmic mechanism in which the rate constants for association and dissociation in 100 mM NaCl are 3.2 × 10(7) M(-1)s(-1) and 1.0 s(-1), respectively, faster than the typical rate constants for DNA hybridization. TEM and AFM images of samples deposited from solutions having higher concentrations of dumbbell and NaCl display branched assemblies with linear regions >1 μm in length and diameters indicative of the formation of small bundles of dumbbell end-to-end assemblies. These observations provide the first example of the use of hydrophobic association for the assembly of small DNA duplex conjugates into supramolecular polymers and larger branched aggregates.

Effect of Bridging Units on Photophysical and DNA Binding Properties of a Few Cyclophanes

A few novel anthracene‐based cyclophanes CP‐1, CP‐2 and CP‐3 were synthesized and their interactions with DNA were investigated employing photophysical and biophysical techniques. In methanol and acetonitrile, these systems exhibited optical properties characteristic of the anthracene chromophore. However, in the aqueous medium, the symmetric cyclophane CP‐1 showed a dual emission having λmax at 430 and 550 nm, due to the monomer and excimer, respectively. In contrast, the cyclophanes CP‐2 and CP‐3 in the aqueous medium showed structured anthracene absorption and emission spectra similar to those obtained in methanol and acetonitrile. DNA binding studies indicate that CP‐1 undergoes efficient nonclassical partial intercalative interactions with DNA resulting in the exclusive formation of a sandwich‐type excimer having enhanced emission intensity and lifetimes. The cyclophane CP‐2 having one anthracene moiety exhibited nonclassical intercalative binding with DNA, albeit with less efficiency compared with CP‐1. In contrast, CP‐3, having sterically bulky viologen bridging group showed DNA electrostatic as well as groove binding interactions. These results demonstrate that the nature of the bridging unit plays an important role in the binding mode of the cyclophanes with DNA and in the formation of the novel sandwich‐type excimer.

Ground and excited state electronic spectra of perylenediimide dimers with flexible and rigid geometries in DNA conjugates

The structure and electronic spectra of six DNA conjugates possessing two face-to-face perylenediimide (PDI) chromophores have been investigated. Structures of hairpins possessing two adjacent PDI base analogues opposite a tetrahydrofuran abasic site on the same or opposite strands were simulated using molecular dynamics. These structures are compared with those previously reported for a duplex and hairpin dimer possessing PDI linkers. The minimized structures all have face-to-face PDI geometries but differ in the torsional angle between PDI long axes and the offset between PDI centers. These structures provide the basis for analysing differences in the electronic spectra of the PDI dimers both in the ground state (UV-Vis and circular dichroism spectra) and excited state (fluorescence and transient absorption) determined in aqueous buffer and in the denaturing solvent dimethyl sulfoxide. PDI dimers with rigid structures and large PDI–PDI torsional angles display large effects of exciton coupling in their UV-Vis and CD spectra and also display split transient absorption bands; whereas PDI dimers with smaller PDI–PDI torsional angles and flexible structures display weaker UV-Vis and CD exciton coupling and a single transient absorption band. The excimer fluorescence maxima and decay times for all of these DNA–PDI constructs are similar.

Excitation Energy Delocalization and Transfer to Guests within MII 4L6 Cage Frameworks

We have prepared a series of MII4L6 tetrahedral cages containing one or the other of two distinct BODIPY moieties, as well as mixed cages that contain both BODIPY chromophores. The photophysical properties of these cages and their fullerene-encapsulated adducts were studied in depth. Upon cage formation, the charge-transfer character exhibited by the bis(aminophenyl)-BODIPY subcomponents disappeared. Strong excitonic interactions were instead observed between at least two BODIPY chromophores along the edges of the cages, arising from the electronic delocalization through the metal centers. This excited-state delocalization contrasts with previously reported cages. All cages exhibited the same progression from an initial bright singlet state (species I) to a delocalized dark state (species II), driven by interactions between the transition dipoles of the ligands, and subsequently into geometrically relaxed species III. In the case of cages loaded with C60 or C70 fullerenes, ultrafast host-to-guest electron transfer was observed to compete with the excitonic interactions, short-circuiting the I → II → III sequence.

Interplay of monomer, intra- and intermolecular excimer fluorescence in cyclophanes and selective recognition of methanol vapours

With an objective to develop simple organic systems for optoelectronic applications, we have investigated photophysical properties of water soluble cyclophane derivatives 1, 2 and model compound 3 in solution and solid state. Of these, the symmetrical cyclophane 1 exhibited monomer emission in methanol, whereas an intramolecular excimer emission was observed in the aqueous medium. Interestingly, in the solid state it showed a highly red-shifted emission maximum when compared to those in the solution. The unsymmetrical cyclophane 2, on the other hand, exhibited monomer emission in both organic and aqueous media, while a dual emission (monomer and excimer) was observed in the solid state. Insights into these unique fluorescence properties were gained by studying the molecular packing of the cyclophanes through single crystal X-ray structure analysis. The cyclophane 1 exhibited a unidirectional sandwich-type packing pattern thereby resulting in strong face-to-face π–π stacking interactions between the anthracene chromophores, whereas 2 exhibited both herringbone and sandwich-type pattern, wherein the interacting anthracene moieties are arranged in an intermolecular T-shaped fashion. By virtue of different molecular packing the cyclophane 1 showed visible fluorescence colour change from yellow to blue when exposed to methanol vapours as compared to ethanol, acetonitrile, hexane and water vapours. Uniquely, this system can detect as low as 1% of methanol in ethanol solution thereby demonstrating its usefulness as an optical probe for the detection of methanol vapours.

Electronic interactions in helical stacked arrays of the modified DNA base pyrrolocytosine

The thermal stability and ultraviolet and circular dichroism spectra of nine synthetic DNA hairpins possessing one or more (P)C-G base pairs ((P)C = pyrrolocytosine) have been investigated. One group of hairpins possess 1-5 sequential (P)C-G base pairs while another group possess two (P)C-G base pairs separated by 1-3 A-T base pairs. The first group displays a nearly linear dependence of UV and exciton-coupled circular dichroism (EC-CD) band intensity upon the number of neighboring chromophores, whereas the second group shows weak EC-CD only at the shortest distances between non-neighboring chromophores. This result stands in marked contrast to the exciton coupling seen between stilbene chromophores separated by as many as a dozen base pairs. The weak exciton coupling between non-neighboring (P)C chromophores, like that of the natural nucelobases, is attributed to their relatively weak electronic transition dipoles.