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Jovica D Badjić

Publications and source records attributed to Jovica D Badjić.

9 recordsLinked to original sources

Template-directed synthesis of mechanically interlocked molecular bundles using dynamic covalent chemistry.

Mixing the dipyrido[24]crown-8 derivatives carrying one or two formyl group(s) on the 4 position(s) of their pyridine ring(s) with a 3-fold symmetrical trisammonium ion template in a 3:1 ratio in CD3NO2 results in the formation of thermodynamically stable [4]pseudorotaxanes which, upon addition of a 1,3,5-trisaminobenzene cap, form mechanically interlocked molecular bundles with one and two caps, respectively, by virtue of dynamic imine bond formation.

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Allosteric regulation of the conformational dynamics of a cavitand receptor.

[reaction: see text] Inspired by allostery in nature, we synthesized cavitand 1 and investigated regulation of its conformational dynamics. Quantitative 1H NMR studies have revealed that the rate of the conformational isomerization of 1 can be modulated using the external addition of acid. As 1 maintains its vase-like conformation in an acidic environment, ample opportunities for controlling the kinetics of molecular recognition, and thus reactivity, in this and related receptors have arisen.

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Design, synthesis, and conformational dynamics of a gated molecular basket.

We have developed a synthesis and examined the conformational behavior and recognition properties of dynamic molecular containers 1-3. As follows from the 1H NMR dilution, diffusion NMR, and vapor pressure osmometry measurements, compound 1 has a low affinity for intermolecular aggregation and is mostly present in monomeric form in dilute chloroform solutions. Inspecting the O-H chemical shift resonances of 1, 3, and model compound 4 as a function of temperature afforded the deltadelta/deltaT coefficients of 17.0, 17.3, and 4.7 ppb K(-1), respectively. In combination with the results from variable temperature 1H NMR and IR measurements, the existence of conformers of 1 and 3 in equilibrium, each having a different extent of hydrogen bonding, was confirmed. Molecular mechanics calculations suggested 1a as the most favorable conformation, with three additional conformers, 1b, 1c, and 1d, populating local energy minima. Further optimization of each of the four conformers using semiempirical PM3 and ab initio (HF/6-31G) methods allowed a determination of their relative free energies and the corresponding Boltzmann population distributions which were heavily weighted toward 1a. A computed composite IR spectrum of a fraction-weighted mixture of the conformers of 1 reproduced the experimentally observed IR spectrum in its structural features, leading to a conclusion that conformer 1a indeed dominates the equilibrium. The egg-shaped cavity of 1 (136.6 angstroms3) is complementary in size, shape, and electrostatic potential to chloroform (74.9 angstroms3). A single-crystal X-ray study of 2 revealed a disordered chloroform molecule positioned inside the cavitand along its C3 axis.

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Multivalency and cooperativity in supramolecular chemistry.

Multivalent interactions, which rely upon noncovalent bonds, are essential ingredients in the mediation of biological processes, as well as in the construction of complex (super)structures for materials applications. A fundamental understanding of multivalency in supramolecular chemistry is necessary not only to construct motors and devices on the nanoscale but also to synthesize model systems to provide insight into how biological processes work. This Account focuses on the application of multivalency to supramolecular chemistry in particular and the nanosciences in general.

Macromolecular Substances↗

A mechanically interlocked bundle.

The prototype of an artificial molecular machine consisting of a trisammonium tricationic component interlocked with a tris(crown ether) component to form a molecular bundle with averaged C(3v) symmetry has been designed and synthesized. The system is based on noncovalent interactions, which include 1) N(+)-H...O hydrogen bonds; 2) C-H...O interactions between the CH(2)NH(2) (+)CH(2) protons on three dibenzylammonium-ion-containing arms, which are attached symmetrically to a benzenoid core, and three dibenzo[24]crown-8 macrorings fused onto a triphenylene core; and 3) pi...pi stacking interactions between the aromatic cores. The template-directed synthesis of the mechanically interlocked, triply threaded bundle involves post-assembly covalent modification, that is, the efficient conversion of three azide functions at the ends of the arms of the bound and threaded trication into bulky triazole stoppers, after 1,3-dipolar cycloaddition with di-tert-butylacetylenedicarboxylate to the extremely strong 1:1 adduct that is formed in dichloromethane/acetonitrile (3:2), on account of a cluster effect associated with the paucivalent adduct. Evidence for the averaged C(3v) symmetry of the molecular bundle comes from absorption and luminescence data, as well as from electrochemical experiments, (1)H NMR spectroscopy, and mass spectrometry. The photophysical properties of the mechanically interlocked bundle are very similar to those of the superbundle that precedes the formation of the bundle in the process of supramolecular assistance to covalent synthesis. Although weak non-nucleophilic bases (e.g., nBu(3)N and iPr(2)NEt) fail to deprotonate the bundle, the strong tBuOK does, as indicated by both luminescence and (1)H NMR spectroscopy. While deprotonation undoubtedly loosens up the interlocked structure of the molecular bundle by replacing relatively strong N(+)-H...O hydrogen bonds by much weaker N-H...O ones, the pi...pi stacking interactions ensure that any structural changes are inconsequential, particularly when the temperature of the solution of the neutral molecular bundle in dichloromethane is cooled down to considerably below room temperature.

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Can multivalency be expressed kinetically? The answer is yes.

Inspired by the concept of multivalency and in pursuit of ever more intricate artificial molecular machines, we investigated the strict self-assembly of a triply threaded two-component superbundle, starting from a tritopic receptor in which three benzo[24]crown-8 macrorings are fused onto a triphenylene core and a trifurcated trication wherein three bipyridinium units are linked 1,3,5 to a central benzenoid core. The result of the investigation was quite unexpected and surprising. It transpired that the rapid formation of a doubly threaded two-component complex was followed by an extremely slow conversion (a week at 253 K in CD3COCD3 to reach equilibrium) of this kinetically controlled product into a thermodynamically controlled one, namely a triply threaded two-component superbundle. This intriguing observation begs the question: are there instances in nature where multivalency is expressed as a kinetically controlled process, prior to an equilibrium state being reached, and if so, what are the biological implications, if any?

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Conjugate of palladium(II) complex and beta-cyclodextrin acts as a biomimetic peptidase.

We combined the newly discovered ability of [Pd(H2O)4]2+ to residue-selectively hydrolyze X-Pro bonds in peptides at 6 </= pH </= 9 with the known ability of beta-cyclodextrin to recognize aromatic side chains and synthesized a conjugate reagent that acts as a sequence-specific peptidase. This new reagent cleaved the Ser6-Pro7 amide bond in bradykinin at pH 7. ROESY 1H NMR spectra gave evidence for inclusion of the side chain of Phe8 in the beta-cyclodextrin cavity, the interaction that makes the cleavage sequence specific.

Biomimetic Materials↗

Controlling multivalent interactions in triply-threaded two-component superbundles.

We have investigated the (1)H NMR spectra, the absorption spectra, the fluorescence spectra and decays, and the electrochemical properties of i). a tritopic receptor in which three benzo[24]crown-8 macrorings are fused onto a triphenylene core, ii). a trifurcated trication wherein three dibenzylammonium ions are linked 1,3,5 to a central benzenoid core, and iii). their 1:1 adduct which constitutes a triply-threaded, two-component supramolecular bundle. X-Ray crystallography has established the precise geometry of this paucivalent recognition motif in the solid state. In addition to [N(+)-H...O] hydrogen bonding and [C-H...O] interactions between the NH(2) (+) centers on the three dibenzylammonium ion containing arms of the trication and the three crown ether rings in the tritopic receptor, there is a stabilizing [pi...pi] stacking interaction between the two aromatic cores. Mass spectrometry and (1)H NMR spectroscopy have confirmed the integrity of the 1:1 adduct beyond the solid state, provided the solvents are relatively apolar (e.g., chloroform and acetonitrile). The intense fluorescence emissions of the two recognition components are quenched upon association with the concomitant appearance of a lower energy, broad fluorescence band originating from the pi-pi stacking in the 1:1 adduct of the aromatic cores in the two matching components. Titration experiments, including Job plots, establish the 1:1 stoichiometry of the adduct, an observation which is also confirmed by electrochemical experiments. The electrochemical results show that, both in the tritopic receptor and in the superbundle itself, the first oxidation process is associated with the hexaalkoxytriphenylene core. The successive oxidation processes of the peripheral dioxybenzene units are affected by charge-transfer interactions in the tritopic receptor, whereas, in the superbundle, such units are not interacting. In acetonitrile solution, dethreading/rethreading of the 1:1 adduct can be controlled quantitatively by addition of base and acid. Dethreading and rethreading is also observed by (1)H NMR spectroscopy when dimethylsulfoxide is added to a solution of the 1:1 adduct in equal volumes of acetonitrile and chloroform. A trifurcated trication where methyl groups are located on the para positions of the three dibenzylammonium ions, which are linked 1,3,5 to the neutral benzenoid core, has been employed to demonstrate that dethreading of the 1:1 adduct involves doubly-threaded and singly-threaded species, that is, the paucivalent site is dismembered in a sequence of logical steps involving stable intermediates. This molecular recognition system is a rare example of a supramolecular entity based on a cooperative binding motif that can be switched on and off by chemical means.

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