Aromatic Oligoamide β-Sheet Foldamers

Synthesis of a glycan hairpin

The primary sequence of a biopolymer encodes the essential information for folding, permitting to carry out sophisticated functions. Inspired by natural biopolymers, peptide and nucleic acid sequences have been designed to adopt particular three-dimensional (3D) shapes and programmed to exert specific functions. In contrast, synthetic glycans capable of autonomously folding into defined 3D conformations have so far not been explored owing to their structural complexity and lack of design rules. Here we generate a glycan that adopts a stable secondary structure not present in nature, a glycan hairpin, by combining natural glycan motifs, stabilized by a non-conventional hydrogen bond and hydrophobic interactions. Automated glycan assembly enabled rapid access to synthetic analogues, including site-specific 13C-labelled ones, for nuclear magnetic resonance conformational analysis. Long-range inter-residue nuclear Overhauser effects unequivocally confirmed the folded conformation of the synthetic glycan hairpin. The capacity to control the 3D shape across the pool of available monosaccharides has the potential to afford more foldamer scaffolds with programmable properties and functions.

A folded π-system with supramolecularly oriented dipoles: single-component piezoelectric relaxor with NLO activity

Organic molecules with an active dipole moment have a natural propensity to align in an antiparallel fashion in the solid state, resulting in zero macroscopic polarization. This primary limitation makes the material unresponsive to switching with electric fields, mechanical forces, and to intense laser light. A single-component organic material that bestows macroscopic dipole-driven electro-mechanical and optical functions, e.g., piezoelectric, ferroelectric and nonlinear optical (NLO) activity, is unprecedented due to the design challenges imparted by crystal symmetry and dipole orientations. Herein we report a crystalline organic material that self-assembles with a polar order (P ₁), and is endowed with a high piezoelectric coefficient (d ₃₃-47 pm V^-1), as well as ferroelectric and Debye-type relaxor properties. In addition, it shows second harmonic generation (SHG) activity, which is more than five times that of the benchmark potassium dihydrogen phosphate. Piezoelectric force microscopy (PFM) images validated electro-mechanical deformations. Piezoresponse force spectroscopy (PFS) studies confirmed a signature butterfly-like amplitude and a phase loop. To the best of our knowledge, this is the first report of a folded supramolecular π-system that manifests unidirectionally oriented dipoles and exhibits piezoelectricity, ferroelectricity, and has excellent ability to generate second harmonic light. These findings can herald new design possibilities based on folded architectures to explore opto-, electro- and mechano-responsive multifaceted functions.

A new amino acid, hybrid peptides and BODIPY analogs: synthesis and evaluation of 2-aminotroponyl-L-alanine (ATA) derivatives

Natural aromatic α-amino acid residues play critical roles in the structural and functional organization of proteins owing to π-interactions. Their aromatic residues are derived from benzenoid scaffolds. Non-benzenoid aromatic scaffolds such as tropone and tropolone are also constituents of troponoid natural products. Tropolone has also the ability to exhibit π-interactions along with additional hydrogen bonding. Thus, amino acids comprising troponyl could be potential building blocks of novel peptidomimetics. This report describes the synthesis of the L-aminotroponylalanine amino acid (ATA) and its unusual activity with the peptide coupling agent EDC. Importantly, its di-peptides form β-sheet/-turn type secondary structures in organic solvents owing to the troponyl residue. This amino acid is an excellent scaffold for the synthesis of fluorescent amino acids such as BODIPY amino acid analogs. Nevertheless, this amino acid and its BODIPY derivatives can enter HeLa cells without exhibiting significant cytotoxicity at low concentrations (∼50 μM). Hence, ATA and its BODIPY derivatives are promising aromatic amino acids for the construction of potential peptidomimetics and fluorescent labelling of target peptides.

Phenazine-Based Oligomers as Redox-Responsive Molecular Actuators

Nanosized butterfly-coil foldamers containing alternating phenazine-1,6-dicarboxamide and 2,5-dialkoxyterephthalamide moieties have been demonstrated to undergo extension-contraction in response to changing their oxidation state. Both the chemical (catalytic hydrogenation/aerial oxidation) and electrochemical versions of this process have been shown to be clean and fully reversible.

Miniature β-Hairpin Mimetic by Intramolecular Hydrogen Bond and C-H···π Interactions

Canonically, protein β-hairpin motifs are stabilized by intramolecular hydrogen bonds. Here, we attempt to develop a rational design recipe for a miniature hairpin structure stabilized by hydrogen bonding as well as C-H···π interaction and try to understand how such a stabilization effect varies with different functional groups at each terminus. Database analysis shows that the α-amino acids with an aromatic side chain will not favor that kind of C-H···π stabilized hairpin structure. However, hybrid tripeptides with an N-terminal Boc-Trp-Aib corner residue and C-terminal aromatic ω-amino acids fold into the hairpin conformation with a central β-turn/open-turn that is reinforced by a C-H···π interaction. The CCDC database analysis further confirms that this C-H···π stabilized hairpin motif is general for Boc-protected tripeptides containing Aib in the middle and aromatic functionality at the C-terminus. The different α-amino acids like Leu/Ala/Phe/Pro/Ser at the N-terminus have a minor influence on the C-H···π interaction and stabilities of the folded structures in solid-state. However, the hybrid peptides exhibit different degrees of conformational heterogeneity both in the solid and solution phase, which is common for this kind of flexible small molecule. Conformational heterogeneity in the solution phase including the C-H···π stabilized β-hairpin structures are characterized by the molecular dynamics (MD) simulations explaining their plausible origin at an atomistic level.

Selective and Cooperative Photocycloadditions within Multistranded Aromatic Sheets

A series of aromatic helix-sheet-helix oligoamide foldamers composed of several different photosensitive diazaanthracene units have been designed and synthesized. Molecular objects up to 7 kDa were straightforwardly produced on a 100 mg scale. Nuclear magnetic resonance and crystallographic investigations revealed that helix-sheet-helix architectures can adopt one or two distinct conformations. Sequences composed of an even number of turn units were found to fold in a canonical symmetrical conformation with two helices of identical handedness stacked above and below the sheet segment. Sequences composed of an odd number of turns revealed a coexistence between a canonical fold with helices of opposite handedness and an alternate fold with a twist within the sheet and two helices of identical handedness. The proportions between these species could be manipulated, in some cases quantitatively, being dependent on solvent, temperature, and absolute control of helix handedness. Diazaanthracene units were shown to display distinct reactivity toward [4 + 4] photocycloadditions according to the substituent in position 9. Their organization within the sequences was programmed to allow photoreactions to take place in a specific order. Reaction pathways and kinetics were deciphered and product characterized, demonstrating the possibility to orchestrate successive photoreactions so as to avoid orphan units or to deliberately produce orphan units at precise locations. Strong cooperative effects were observed in which the photoreaction rate was influenced by the presence (or absence) of photoadducts in the structure. Multiple photoreactions within the aromatic sheet eventually lead to structure lengthening and stiffening, locking conformational equilibria. Photoproducts could be thermally reverted.

Folding of aromatic polyamides into a rare intrachain β-sheet type structure and further reinforcement of the secondary structure through host–guest interactions

We report the design, synthesis, and folding of aromatic polyamides into an intrachain β-sheet-like structure. Additionally, the effect of a guest molecule in stabilizing the β-sheet structure has also been demonstrated here.

Improvement of the antimicrobial potency, pharmacokinetic and pharmacodynamic properties of albicidin by incorporation of nitrogen atoms

The worrisome development and spread of multidrug-resistant bacteria demands new antibacterial agents with strong bioactivities particularly against Gram-negative bacteria. Albicidins were recently structurally characterized as highly active antibacterial natural products from the bacterium Xanthomonas albilineans. Albicidin, which effectively targets the bacterial DNA-gyrase, is a lipophilic hexapeptide mostly consisting of para amino benzoic acid units and only one α-amino acid. In this study, we report on the design and synthesis of new albicidins, containing N-atoms on each of the 5 different phenyl rings. We systematically introduced N-atoms into the aromatic backbone to monitor intramolecular H-bonds and for one derivative correlated them with a significant enhancement of the antibacterial activity and activity spectrum, particularly also towards Gram-positive bacteria. In parallel we conducted DFT calculations to find the most stable conformation of each derivative. A drastic angle-change was observed for the lead compound and shows a preferred planarity through H-bonding with the introduced N-atom at the D-fragment of albicidin. Finally, we went to the next level and conducted the first in vivo experiments with an albicidin analogue. Our lead compound was evaluated in two different mouse experiments: In the first we show a promising PK profile and the absence of toxicity and in the second very good efficiency and reduction of the bacterial titre in an E. coli infection model with FQ-resistant clinically relevant strains. These results qualify albicidins as active antibacterial substances with the potential to be developed as a drug for treatment of infections caused by Gram-negative and Gram-positive bacteria.

N-Alkylated Aromatic Poly- and Oligoamides

N-alkylated aromatic poly- and oligoamides are a particular class of abiotic foldamers that is deprived of the capability of forming intramolecular hydrogen-bonding networks to stabilize their tri-dimensional structure. The alkylation of the backbone amide nitrogen atoms greatly increases the chemical diversity accessible for aromatic poly- and oligoamides. However, the nature and the conformational preferences of the N,N-disubstituted amides profoundly modify the folding properties of these aromatic poly- and oligoamides. In this Review, representative members of this class of aromatic poly- and oligoamides will be highlighted, among them N-alkylated phenylene terephthalamides, benzanilides, pyridylamides, and aminomethyl benzamide oligomers. The principal synthetic pathways to the main classes of N-alkylated aromatic polyamides with narrow to broad molecular-weight distribution, or oligoamides with specific sequences, will be detailed and their foldameric properties will be discussed. The Review will end by describing the few applications reported to date and future prospects for the field.

Folding and fluorescence enhancement with strong odd-even effect for a series of merocyanine dye oligomers

A series of merocyanine (MC) oligomers with a varying number of chromophores from two to six has been synthesized via a peptide synthesis strategy. Solvent-dependent UV/vis spectroscopic studies reveal folding processes for the MC oligomers driven by strong dipole–dipole interactions resulting in well-defined π-stacks with antiparallel orientation of the dyes. Whilst even-numbered tetramer 4 and hexamer 6 only show partial folding into dimeric units, odd-numbered trimer 3 and pentamer 5 fold into π-stacks of three and five MC units upon decreasing solvent polarity. In-depth 2D NMR studies provided insight into the supramolecular structure. For trimer 3, an NMR structure could be generated revealing the presence of a well-defined triple π-stack in the folded state. Concomitant with folding, the fluorescence quantum yield is increased for all MC oligomers in comparison to the single chromophore. Based on radiative and non-radiative decay rates, this fluorescence enhancement can be attributed to the rigidification of the chromophores within the π-stacks that affords a pronounced decrease of the non-radiative decay rates. Theoretical investigations for the double and triple dye stacks based on time-dependent density functional theory (TD-DFT) calculations indicate for trimer 3 a pronounced mixing of Frenkel and charge transfer (CT) states. This leads to significant deviations from the predictions obtained by the molecular exciton theory which only accounts for the Coulomb interaction between the transition dipole moments of the chromophores.

A series of merocyanine (MC) oligomers with a varying number of chromophores from two to six has been synthesized via a peptide synthesis strategy.

Secondary Structure in Nonpeptidic Supramolecular Block Copolymers

Proteins contain a level of complexity-secondary and tertiary structures-that polymer chemists aim to imitate. The bottom-up synthesis of protein-mimicking polymers mastering sequence variability and dispersity remains challenging. Incorporating polymers with predefined secondary structures, such as helices and π-π stacking sheets, into block copolymers circumvents the issue of designing and predicting one facet of their 3D architecture. Block copolymers with well-defined secondary-structure elements formed by covalent chain extension or supramolecular self-assembly may be considered for localized tertiary structures.In this Account, we describe a strategy toward block copolymers composed of units bearing well-defined secondary structures mixed in a "plug-and-play" manner that approaches a modicum of the versatility seen in nature. Our early efforts focused on the concept of single-chain collapse to achieve folded secondary structures through either hydrogen bonding or quadrupole attractive forces. These cases, however, required high dilution. Therefore, we turned to the ring-opening metathesis polymerization (ROMP) of [2.2]paracyclophane-1,9-dienes (pCpd), which forms conjugated, fluorescent poly(p-phenylenevinylene)s (PPVs) evocative of β-sheets. Helical building blocks arise from polymers such as poly(isocyanide)s (PICs) or poly(methacrylamide)s (PMAcs) containing bulky, chiral side groups while the coil motif can be represented by any flexible chain; we frequently chose poly(styrene) (PS) or poly(norbornene) (PNB). We installed moieties for supramolecular assembly at the chain ends of our "sheets" to combine them with complementary helical or coil-shaped polymeric building blocks.Assembling hierarchical materials tantamount to the complexity of proteins requires directional interactions with high specificity, covalent chain extension, or a combination of both chemistries. Our design is based on functionalized reversible addition-fragmentation chain-transfer (RAFT) agents that allowed for the introduction of recognition motifs at the terminus of building blocks and chain-terminating agents (CTAs) that enabled the macroinitiation of helical polymers from the chain end of ROMP-generated sheets and/or coils. To achieve triblock copolymers with a heterotelechelic helix, we relied on supramolecular assembly with helix and coil-shaped building blocks. Our most diverse structures to date comprised a middle block of PPV sheets, parallel or antiparallel, and supramolecularly or covalently linked, respectively, end-functionalized with molecular recognition units (MRUs) for orthogonal supramolecular assembly. We explored PPV sheets with multiple folds achieved by chain extension using alternating pCpd and phenyl-pentafluorophenyl β-hairpin turns. Using single-molecule polarization spectroscopy, we showed that folding occurs preferentially in multistranded over double-stranded PPV sheets. Our strategy toward protein-mimicking and foldable polymers demonstrates an efficient route toward higher ordered, well-characterized materials by taking advantage of polymers that naturally manifest secondary structures. Our studies demonstrate the retention of distinct architectures after complex assembly, a paradigm that we believe may extend to other polymeric folding systems.

Role of intramolecular hydrogen bonds in promoting electron flow through amino acid and oligopeptide conjugates

Elucidating the factors that control charge transfer rates in relatively flexible conjugates is of importance for understanding energy flows in biology as well as assisting the design and construction of electronic devices. Here, we report ultrafast electron transfer (ET) and hole transfer (HT) between a corrole (Cor) donor linked to a perylene-diimide (PDI) acceptor by a tetrameric alanine (Ala)₄ Selective photoexcitation of the donor and acceptor triggers subpicosecond and picosecond ET and HT. Replacement of the (Ala)₄ linker with either a single alanine or phenylalanine does not substantially affect the ET and HT kinetics. We infer that electronic coupling in these reactions is not mediated by tetrapeptide backbone nor by direct donor-acceptor interactions. Employing a combination of NMR, circular dichroism, and computational studies, we show that intramolecular hydrogen bonding brings the donor and the acceptor into proximity in a "scorpion-shaped" molecular architecture, thereby accounting for the unusually high ET and HT rates. Photoinduced charge transfer relies on a (Cor)NH^…O=C-NH^…O=C(PDI) electronic-coupling pathway involving two pivotal hydrogen bonds and a central amide group as a mediator. Our work provides guidelines for construction of effective donor-acceptor assemblies linked by long flexible bridges as well as insights into structural motifs for mediating ET and HT in proteins.

Applications of Discrete Synthetic Macromolecules in Life and Materials Science: Recent and Future Trends

In the last decade, the field of sequence-defined polymers and related ultraprecise, monodisperse synthetic macromolecules has grown exponentially. In the early stage, mainly articles or reviews dedicated to the development of synthetic routes toward their preparation have been published. Nowadays, those synthetic methodologies, combined with the elucidation of the structure-property relationships, allow envisioning many promising applications. Consequently, in the past 3 years, application-oriented papers based on discrete synthetic macromolecules emerged. Hence, material science applications such as macromolecular data storage and encryption, self-assembly of discrete structures and foldamers have been the object of many fascinating studies. Moreover, in the area of life sciences, such structures have also been the focus of numerous research studies. Here, it is aimed to highlight these recent applications and to give the reader a critical overview of the future trends in this area of research.

Fluorinated Triazole Foldamers: Folded or Extended Conformational Preferences

The Ministère de l'Enseignement Supérieur et de la Recherche (MESR) is thanked for financial support for José Laxio Arenas. The China Scholarship Council is thanked for financial support for Yaochun Xu. The authors thank Pr. Vadim Soloshonok and TOSOH F-TECH, Inc. for the kind gift of N-terbutyl-sulfinylimine.

Large-Amplitude Conformational Changes in Self-Assembled Multi-Stranded Aromatic Sheets

The orchestration of ever larger conformational changes is made possible by the development of increasingly complex foldamers. Aromatic sheets, a rare motif in synthetic foldamer structures, have been designed so as to form discrete stacks of intercalated aromatic strands through the self‐assembly of two identical subunits. Ion‐mobility ESI‐MS confirms the formation of compact dimers. X‐ray crystallography reveals the existence of two distinct conformational dimeric states that require large changes to interconvert. Molecular dynamics simulation validates the stability of the two conformations and the possibility of their interconversion.

Oligo-Quinolylene-Vinylene Foldamers

Quinoline based aromatic amide foldamers are known to adopt stable folded conformations. We have developed a synthetic approach to produce similar oligomers where all amide bonds, or part of them, have been replaced by an isosteric vinylene group. The results of solution and solid state structural studies show that oligomers exclusively containing vinylene linkages are not well folded, and adopt predominantly flat conformations. In contrast, a vinylene segment flanked by helical oligoamides also folds in a helix, albeit with a slightly lower curvature. The presence of vinylene functions also result in an extension of π-conjugation across the oligomer that may change charge transport properties. Altogether, these results pave the way to foldamers in which both structural control and specific electronic properties may be engineered.

Oligo(5-amino-N-acylanthranilic acids): Amide Bond Formation without Coupling Reagent and Folding upon Binding Anions

Oligomers of 5-amino-N-acylanthranilic acid, previously unknown aromatic oligoamides that cannot be obtained with known amide coupling methods, are synthesized based on a new, highly efficient amide-bond formation strategy that takes advantage of the ring-opening of benzoxazinone derivatives. These oligoamides offer multiple backbone NH groups as H-bond donors which, in the presence of iodide or chloride ion, are convergently arranged and H-bonded, which enforces a folded, crescent conformation. These aromatic oligoamides provide a versatile platform based on which anion-dependent foldamers, or anion binders with tunable affinity and specificity, are being constructed.

Structure-Dependent Guest Recognition with Flexible Ferrocene-Based Aromatic Oligoamide β-Sheet Mimics

A series of aromatic oligoamides incorporating an inherently flexible ferrocene dicarboxylic acid unit was synthesized. Solid state, solution, and computational studies on these systems indicated that the aromatic strands can adopt a syn parallel stacked conformation. This results in modular β-sheet-like molecular clefts that display structure-dependent recognition of small polar molecules. NMR and theoretical studies of the host-guest interaction support an in cleft binding mode and allowed the selectivity of the oligomers to be rationalized on the basis of minor changes in functional-group presentation on the edge of the aromatic strands.

Prodrugs for nitroreductase-based cancer therapy-3: Antitumor activity of the novel dinitroaniline prodrugs/Ssap-NtrB enzyme suicide gene system: Synthesis, in vitro and in silico evaluation in prostate cancer

Prodrugs for targeted tumor therapies have been extensively studied in recent years due to not only maximising therapeutic effects on tumor cells but also reducing or eliminating serious side effects on healthy cells. This strategy uses prodrugs which are safe for normal cells and form toxic metabolites (drugs) after selective reduction by enzymes in tumor tissues. In this study, prodrug candidates (1-36) containing nitro were designed, synthesized and characterized within the scope of chemical experiments. Drug-likeness properties of prodrug candidates were analyzed using DS 2018 to investigate undesired toxicity effects. In vitro cytotoxic effects of prodrug canditates were performed with MTT assay for human hepatoma cells (Hep3B) and prostate cancer cells (PC3) and human umbilical vein endothelial cells (HUVEC) as healthy control. Non-toxic compounds (3, 5, 7, 10, 12, 15, 17, 19 and 21-23), and also compounds (1, 2, 5, 6, 9, 11, 14, 16, 20 and 24) which had low toxic effects, were selected to examine their suitability as prodrug canditates. The reduction profiles and kinetic studies of prodrug/Ssap-NtrB combinations were performed with biochemical analyses. Then, selected prodrug/Ssap-NtrB combinations were applied to prostate cancer cells to determine toxicity. The results of theoretical, in vitro cytotoxic and biochemical studies suggest 14/Ssap-NtrB, 22/Ssap-NtrB and 24/Ssap-NtrB may be potential prodrug/enzyme combinations for nitroreductase (Ntr)-based prostate cancer therapy.

Macrocycles of higher ortho-phenylenes: assembly and folding

The sizes and geometries of macrocycles assembled from ortho-phenylenes are predicted by the stabilities and bite angles of possible conformers.

Higher-order structure in abiotic foldamer systems represents an important but largely unrealized goal. As one approach to this challenge, covalent assembly can be used to assemble macrocycles with foldamer subunits in well-defined spatial relationships. Such systems have previously been shown to exhibit self-sorting, new folding motifs, and dynamic stereoisomerism, yet there remain important questions about the interplay between folding and macrocyclization and the effect of structural confinement on folding behavior. Here, we explore the dynamic covalent assembly of extended ortho-phenylenes (hexamer and decamer) with rod-shaped linkers. Characteristic ¹H chemical shift differences between cyclic and acyclic systems can be compared with computational conformer libraries to determine the folding states of the macrocycles. We show that the bite angle provides a measure of the fit of an o-phenylene conformer within a shape-persistent macrocycle, affecting both assembly and ultimate folding behavior. For the o-phenylene hexamer, the bite angle and conformer stability work synergistically to direct assembly toward triangular [3 + 3] macrocycles of well-folded oligomers. For the decamer, the energetic accessibility of conformers with small bite angles allows [2 + 2] macrocycles to be formed as the predominant species. In these systems, the o-phenylenes are forced into unusual folding states, preferentially adopting a backbone geometry with distinct helical blocks of opposite handedness. The results show that simple geometric restrictions can be used to direct foldamers toward increasingly complex folds.

Side-Chain-Driven Dual Structural System of Poly-Arylopeptide: Selective Helical Formation Derived from Aromatic Ring Flips on the Backbone

A methodology for producing dual structural systems of macromolecules, which involves flipping the unsymmetrical aromatic rings on the main chain is presented. Previously, we reported a non-natural polypeptide containing an aromatic ring on the peptide backbone, called a poly "arylopeptide". Herein, we used 2,6-naphthalene rings as axially unsymmetrical spacers, which has two geometrical isomers, anti and syn, to create dual structural properties. The miniscule energy difference between the two geometrical isomers can be amplified by incorporating the 2,6-naphthylene units into the polypeptide backbone, which creates a thermodynamic driving force for the formation of two specific global structures (i.e., 3₁-helix or 4₁-helix) biased toward one side geometrical isomer depending on the side chain. Additionally, the 3₁-helix can be switched to the 4₁-helix upon addition of a small amount of additives, indicating a conformational conversion from an identical sequence. The developmental dual helical systems exploit basic molecular geometry and can serve as a design platform for synthetic polymers.

Aromatic β-sheet foldamers based on tertiary squaramides

Suitably substituted aryl-methyl tertiary squaramides are convenient and efficient at promoting hairpin turns in aromatic amide sequences.

Synthesis and folding behaviour of poly(p-phenylene vinylene)-based β-sheet polychromophores

This contribution describes the design and synthesis of β-sheet-mimicking synthetic polymers comprising distinct poly(p-phenylene vinylene) (PPV) and poly(norbornene) (PNB) backbones with multiple turns.

This contribution describes the design and synthesis of β-sheet-mimicking synthetic polymers comprising distinct poly(p-phenylene vinylene) (PPV) and poly(norbornene) (PNB) backbones with multiple turns. The rod–coil–coil–rod tetrablock copolymers, synthesized using ring-opening metathesis polymerization (ROMP) and featuring orthogonal face-to-face π–π stacking and phenyl/perfluorophenyl interactions, show persistent folding both in bulk and at the single molecule level, irrespective of the number of β-turns. Single molecule polarization studies reveal that the copolymers are more anisotropic than the corresponding homopolymers. Examination of the spectral signatures of the single molecules shows a dominant emissive chromophore in the linked materials compared to the homopolymer. The lack of significant spectral changes of the folded materials along with the existence of a dominant emission spectrum supports the proposed structure of well-aligned, minimally-interacting chromophores. Utilization of this reliably folding, phenyl/perfluorophenyl functionality could provide an extremely useful tool in future functional materials design.

Intramolecular Natural Energy Decomposition Analysis: Applications to the Rational Design of Foldamers

We describe an intramolecular version of the natural energy decomposition analysis (NEDA), with the aim of evaluating interactions between molecular fragments across covalent bonds. The electronic energy in intramolecular natural energy decomposition analysis (INEDA) is divided into electrical, core, and charge transfer components. The INEDA method describes the fragments using the nonfragmented electronic density, and, therefore, there are no limitations in how to choose the boundary orbital. We used INEDA to evaluate the interaction energies that give origin to barriers of rotation around C_amide C_aromatic (C_am C_ar ) and N_amide C_aromtaic (N_am C_ar ) bonds in arylamide-foldamer building blocks. We found that differences of barrier height between models with different ortho-aryl substituents stem from charge transfer and core interactions. In three-center hydrogen-bond (H-bond) models with an NH proton donor H-bound to two electronegative ortho-aryl substituents, the interaction energy of the three-center system is larger than in either of the two-center H-bond subsystem alone, indicating an increase of overall rigidity. The combination of INEDA and NEDA allows the evaluation of intermolecular and intramolecular interactions using a consistent theoretical framework. © 2018 Wiley Periodicals, Inc.

Exploiting the interactions of aromatic units for folding and assembly in aqueous environments

A variety of non-covalent interactions (including hydrogen bonding, ionic interactions, metal coordination and desolvation/solvation) have been utilized to organize oligomers into well-defined structures. Herein is described a survey of aromatic foldamers that capitalize on electrostatic complementarity of substituted aromatic units to drive folding and assembly in aqueous environments. A brief description of recent advances in the understanding of aromatic interactions is provided, followed by examples of foldamers that exploit interactions between aromatic units to drive their assembly in predictable fashion. The history of our aromatic foldamers is traced from the first structure designed to fold into a pleated structure in an aqueous environment to a heteroduplex system more related to nucleic acids. Taken together, the results demonstrate that electrostatic complementarity of aromatic units provides a versatile framework for driving predictable folding and assembly in aqueous environments.

Effect of conformational flexibility on photophysics of bis-coumarins

The fluorescence of bis-coumarins linked via CONH and COO functionalities is strongly dependant on solvent polarity.

N1-(5-Fluoro-2,4-dinitrophenyl)-N2-phenyl-4-(trifluoromethyl)benzene-1,2-diamine

Treating 1,5-difluoro-2,4-dinitrobenzene (1) with N1-phenyl-5-(trifluoromethyl)benzene-1,2-diamine (4) and N,N-diisopropylethylamine in EtOH at ca. 0 °C for 4 h affords a mixture of N1-(5-ethoxy-2,4-dinitrophenyl)-N2-phenyl-4-(trifluoromethyl)benzene-1,2-diamine (5) (38%) and N1-(5-fluoro-2,4-dinitrophenyl)-N2-phenyl-4-(trifluoromethyl)benzene-1,2-diamine (6) (51%) that can be separated by chromatography. Repeating the reaction in dichloromethane led to the sole formation of N1-(5-fluoro-2,4-dinitrophenyl)-N2-phenyl-4-(trifluoromethyl)benzene-1,2-diamine (6) in 96% yield.

Optimizing side chains for crystal growth from water: a case study of aromatic amide foldamers

The growth of crystals of aromatic compounds from water much depends on the nature of the water solubilizing functions that they carry. Rationalizing crystallization from water, and structure elucidation, of aromatic molecular and supramolecular systems is of general value across various fields of chemistry. Taking helical aromatic foldamers as a test case, we have validated several short polar side chains as efficient substituents to provide both solubility in, and crystal growth ability from, water. New 8-amino-2-quinolinecarboxylic acids bearing charged or neutral aminomethyl, carboxymethyl, sulfonic acid, or bis(hydroxymethyl)-methoxy side chains in position 4 or 5, were prepared on a multi gram scale. Fmoc protection of the main chain amine and suitable protections of the side chains ensured compatibility with solid phase synthesis. One tetrameric and five octameric oligoamides displaying these side chains were synthesized and shown to be soluble in water. In all cases but one, crystals were obtained using the hanging drop method, thus validating the initial design principle to combine polarity and rigidity. The only case that resisted crystallization appeared to be due to exceedingly high water solubility endowed by eight sulfonic acid functions. The neutral side chain did provide crystal growth ability from water but contributed poorly to solubility.