(1)H NMR investigation of solvent effects in aromatic stacking interactions

Site-specific protein modification with a dirhodium metallopeptide catalyst

A new method for chemical protein modification is presented utilizing a dirhodium metallopeptide catalyst. The combination of peptide-based molecular recognition and a dirhodium catalyst with broad side-chain scope enables site-specific protein functionalization. The scope and utility of dirhodium-catalyzed biomolecule modification is expanded to allow reaction at physiological pH and in biologically relevant buffer solutions. Specific protein modification is possible directly in E. coli lysate, demonstrating the remarkable activity and specificity of the designed metallopeptide catalyst. Furthermore, a new biotin-diazo conjugate 1b is presented that allows affinity tagging of target proteins.

Local nature of substituent effects in stacking interactions

Popular explanations of substituent effects in π-stacking interactions hinge upon substituent-induced changes in the aryl π-system. This entrenched view has been used to explain substituent effects in countless stacking interactions over the past 2 decades. However, for a broad range of stacked dimers, it is shown that substituent effects are better described as arising from local, direct interactions of the substituent with the proximal vertex of the other ring. Consequently, substituent effects in stacking interactions are additive, regardless of whether the substituents are on the same or opposite rings. Substituent effects are also insensitive to the introduction of heteroatoms on distant parts of either stacked ring. This local, direct interaction viewpoint provides clear, unambiguous explanations of substituent effects for myriad stacking interactions that are in accord with robust computational data, including DFT-D and new benchmark CCSD(T) results. Many of these computational results cannot be readily explained using traditional π-polarization-based models. Analyses of stacking interactions based solely on the sign of the electrostatic potential above the face of an aromatic ring or the molecular quadrupole moment face a similar fate. The local, direct interaction model provides a simple means of analyzing substituent effects in complex aromatic systems and also offers simple explanations of the crystal packing of fluorinated benzenes and the recently published dependence of the stability of protein-RNA complexes on the regiochemistry of fluorinated base analogues [J. Am. Chem. Soc.2011, 133, 3687-3689].

Green fluorescent organic nanoparticles by self-assembly induced enhanced emission of a naphthalene diimide bolaamphiphile

Naphthalene diimide (NDI) bolaamphiphilic molecules (1) self-assemble in water to form organic nanoparticles, which exhibit self-assembly induced preassociated excimer formation and hence an enhanced green fluorescence.

Studies on [3]pseudorotaxane formation from a bis-azacrown derivative as host and imidazolium ion-derivatives as guest

A new host molecule, having two azacrown derivatives bridged by luminescent naphthalene diimide functionality, is found to form a [3]pseudorotaxane derivative with imidazolim ion-based guest molecules in non-polar solvents through hydrogen-bonded adduct formation. Depending upon the length of the covalent linker that links the imidazolium ion and the luminescent naphthalene fragment in the guests, the [3]pseudorotaxane adducts adopt different conformation or orientation with varying π-π/donor-acceptor interaction. The mechanism for the naphthalene-based luminescence quenching by NDI fragment on adduct formation was found to be a combination of static, as well as dynamic with static quenching as the dominant one.

Folding of a donor-containing ionene by intercalation with an acceptor

Cationic ionenes that bear electron-rich 1,5-dialkoxynaphthalene (DAN) units within the alkylene segment were allowed to interact with different types of electron-deficient, acceptor-containing molecules in an effort to realize intercalation-induced folding of the ionenes; the collapse of the chains was expected to occur in such a way that the donor and acceptor units become arranged in an alternating fashion. Several acceptor-bearing molecules were prepared by the derivatization of pyromellitic dianhydride and naphthalene tetracarboxylic dianhydride with two different oligoethylene glycol monomethyl ether monoamines. This yielded acceptor molecules with different water solubility and allowed the examination of solvophobic effects in the folding process. UV/Vis spectroscopic studies were carried out by using a 1:1 mixture of the DAN-ionenes and different acceptor molecules in water/DMSO solvent mixtures. The intensity of the charge-transfer (CT) band was seen to increase with the water content in the solvent mixture, thereby suggesting that the intercalation is indeed aided by solvophobic effects. The naphthalene diimide (NDI) bearing acceptor molecules consistently formed significantly stronger CT complexes when compared to the pyromellitic diimide (PDI) bearing acceptor molecules, which is a reflection of the stronger π-stacking tendency of the former. AFM studies of drop-cast films of different ionene-acceptor combinations revealed that compact folded structures are formed most effectively under conditions in which the strongest CT complex is formed.

Self-sorted assembly in a mixture of donor and acceptor chromophores

A simple and novel supramolecular approach for orthogonal self-assembly of donor and acceptor chromophores has been demonstrated. Suitably designed 1,5-dialkoxynaphthalene (DAN) and naphthalene tetracarboxylic acid diimide (NDI) derivatives were used as the donor and acceptor systems, respectively. The molecular design for self-sorting relies upon the precise control over the placement of the self-complementary hydrogen-bonding units (amide functionality) with respect to the individual chromophore. By design, the distances between the two amide groups in the donor and acceptor chromophores are not identical, and consequently the effect of the hydrogen-bonding interaction cannot be maximised in the case of alternate donor-acceptor-type pi-stacking. Thus a relatively weak charge-transfer interaction is expected to be sacrificed, and segregated assembly among the individual chromophores should be enforced by virtue of the much stronger effects of hydrogen bonding and pi-pi stacking. Detailed spectroscopic studies were carried out to probe the mode of self-assembly in various derivatives of the DAN-NDI donor-acceptor pairs to establish the utility of the molecular design as a generalised one for orthogonal self-assembly.

A systematic study of thermochromic aromatic donor-acceptor materials

Molar mixtures (1:1) of electron-rich dialkoxynapthalene (Dan) and electron-deficient 1,4,5,8-napthalenetetracarboxylic diimide (Ndi) derivatives form highly tunable, columnar mesophases with a dark red color due to a charge transfer absorbance derived from alternating face-centered stacking. Certain Dan-Ndi mixtures undergo a dramatic color change from dark red to an almost colorless material upon crystallizing from the mesophase. Macroscopic morphology of the solid is not changed during this process. In order to investigate the origins of this interesting thermochromic behavior, Dan and Ndi side chains were systematically altered and their 1:1 mixtures were studied. We have previously speculated that the presence or absence of steric interactions due to side chain branching on the aromatic units controlled the level of color change associated with crystallization. Results from the present study further refine this conclusion including a key crystal structure that provides a structural rationale for the observed results.

Probing substituent effects in aryl-aryl interactions using stereoselective Diels-Alder cycloadditions

Stereoselective Diels-Alder cycloadditions that probe substituent effects in aryl-aryl sandwich complexes were studied experimentally and theoretically. Computations on model systems demonstrate that the stereoselectivity in these reactions is mediated by differential pi-stacking interactions in competing transition states. This allows relative stacking free energies of substituted and unsubstituted sandwich complexes to be derived from measured product distributions. In contrast to gas-phase computations, dispersion effects do not appear to play a significant role in the substituent effects, in accord with previous experiments. The experimental pi-stacking free energies are shown to correlate well with Hammett sigma(m) constants (r = 0.96). These substituent constants primarily provide a measure of the inductive electron-donating and -withdrawing character of the substituents, not donation into or out of the benzene pi-system. The present experimental results are most readily explained using a recently proposed model of substituent effects in the benzene sandwich dimer in which the pi-system of the substituted benzene is relatively unimportant and substituent effects arise from direct through-space interactions. Specifically, these results are the first experiments to clearly show that OMe enhances these pi-stacking interactions, despite being a pi-electron donor. This is in conflict with popular models in which substituent effects in aryl-aryl interactions are modulated by polarization of the aryl pi-system.

New strategies for the design of folded peptoids revealed by a survey of noncovalent interactions in model systems

Controlling the equilibria between backbone cis- and trans-amides in peptoids, or N-substituted glycine oligomers, constitutes a significant challenge in the construction of discretely folded peptoid structures. Through the analysis of a set of monomeric peptoid model systems, we have developed new and general strategies for controlling peptoid conformation that utilize local noncovalent interactions to regulate backbone amide rotameric equilibria, including n-->pi*, steric, and hydrogen bonding interactions. The chemical functionalities required to implement these strategies are typically confined to the peptoid side chains, preserve chirality at the side chain N-alpha-carbon known to engender peptoid structure, and are fully compatible with standard peptoid synthesis techniques. Our examinations of peptoid model systems have also elucidated how solvents affect various side chain-backbone interactions, revealing fundamental aspects of these noncovalent interactions in peptoids that were largely uncharacterized previously. As validation of our monomeric model systems, we extended the scope of this study to include peptoid oligomers and have now demonstrated the importance of local steric and n-->pi* interactions in dictating the structures of larger, folded peptoids. This new, modular design strategy has guided the construction of peptoids containing 1-naphthylethyl side chains, which we show can be utilized to effectively eliminate trans-amide rotamers from the peptoid backbone, yielding the most conformationally homogeneous class of peptoid structures yet reported in terms of amide rotamerism. Overall, this research has afforded a valuable and expansive set of design tools for the construction of both discretely folded peptoids and structurally biased peptoid libraries and should shape our understanding of peptoid folding.

Molecular recognition of cationic phenothiazinium and phenoxazinium dyes with pi-extended 2'-deoxyadenosine nucleotides

N(6)-(N'-Arylcarbamoyl)-2'-deoxyadenosine-H-phosphonates displayed molecular recognition towards cationic phenothiazinium and phenoxazinium dyes in aqueous solutions; studies have shown that binding is driven mainly by aromatic interactions and that size and shape-complementarity of the aromatic rings in host and guest provides selectivity.

Dipole effects on molecular and electronic structures in a novel conjugate of oligo(phenyleneethynylene) and helical peptide

A novel conjugate of a helical nonapeptide and an oligo(phenyleneethynylene) (OPE) having a nitro group at a molecular terminal was synthesized. Both components have a dipole. The peptide has a disulfide group at the N-terminal for immobilization on gold. In order to investigate the electric field effect of the helical peptide dipole on the OPE and molecular structure by the dipole-dipole interaction between the two components, the electronic structure of the OPE was spectroscopically studied in solution, the self-assembled monolayer on gold, and Langmuir-Blodgett (LB) layers on a fused quartz surface. The absorption maximum (lambda(max)) of the OPE component in chloroform is red-shifted by 4 nm from the reference OPE derivative without the helical peptide component. The red shifts of the OPE component are also observed in the LB monolayer and bilayer compared with that of the self-assembled monolayer. The observed dipole effect of the peptide on the OPE electronic structure was quantitatively discussed with ab initio calculations. Antiparallel orientation on the dipole directions of the peptide and the OPE components is considered to explain the red shifts via the dipole effect on the electronic structure of the OPE.

Understanding binding selectivity toward trypsin and factor Xa: the role of aromatic interactions

A congeneric series of four bis-benzamidine inhibitors sharing a dianhydrosugar isosorbide scaffold in common has been studied by crystal structure analysis and enzyme kinetics with respect to their binding to trypsin and factor Xa. Within the series, aromatic interactions are an important determinant for selectivity discrimination among both serine proteases. To study the selectivity-determining features in detail, we used trypsin mutants in which the original binding site is gradually substituted to finally resemble the factor Xa binding pocket. The influence of these mutations has been analyzed on the binding of the closely related inhibitors. We present the crystal structures of the inhibitor complexes obtained by co-crystallizing an "intermediate" trypsin mutant. They could be determined to a resolution of up to 1.2 A, and we measured the inhibitory activity (K(i)) of each ligand against factor Xa, trypsin, and the various mutants. From these data we were able to derive a detailed structure-activity relationship which demonstrates the importance of aromatic interactions in protein-ligand recognition and their role in modulating enzyme selectivity. Pronounced preference is experienced to accommodate the benzamidine anchor with meta topology in the S(1) specificity pocket. One ligand possessing only para topology deviates strongly from the other members of the series and adopts a distinct binding mode addressing the S(1)' site instead of the distal S(3)/S(4) binding pocket.

Designing functionalized porphyrins capable of pseudo-2D self-assembly on surfaces

A crystallography-instructed strategy to highly ordered layering of porphyrins with different topologies on HOPG is developed based on meso-tetraarylporphyrins bearing 2-ethoxyethanol side chains as "sticky ends". These sticky ends are capable of displaying directive hydrogen bonding motifs with the inherent D4h symmetry of the porphyrins. Solvent effects are shown to have an important role in fabricating the adsorption. Metalation and subsequent axial ligation was a key controlling factor in the topology of the layer, leading to pseudo-2D structures on HOPG.