Exploring and exploiting polar-π interactions with fluorinated aromatic amino acids

Nitrogen substitution improves the mobility and stability of electron transport materials for inverted perovskite solar cells

A suitable electron transport material (ETM) plays key roles in efficient perovskite solar cells (PSCs), because it is beneficial for exciton dissociation and charge transport at the interface thus increasing the short circuit current density. Based on the experimentally reported efficient electron transport molecule 10,14-bis(5-(2-ethylhexyl)thiophen-2-yl)-dipyrido[3,2-a:2',3'-c][1,2,5]thiadiazolo[3,4-i]phenazine (TDTP), we theoretically design a set of new ETMs (TDTP-1, TDTP-2a, TDTP-2b, TDTP-3a, and TDTP-3b) by introducing a nitrogen atom into the thiophene ring or replacing a hydrogen atom on the methyl with an amino group. Quantum-chemical calculations reveal that the designed molecules behave much better than TDTP in terms of electron mobility, air stability, and solubility, where the electron mobility of TDTP-3b is two orders of magnitude higher than that of TDTP owing to the extra SN interactions in TDTP-3b that lead to the quasi two-dimensional π packing motif which facilitates electron transport evidently. Moreover, we find that the substitution effect of the nitrogen atom strongly depends on the position, where the nitrogen atom at the β-position of the thiophene ring (TDTP-2b and TDTP-3b) is more conducive to electron transport. Importantly, our calculations show that the ETM/perovskite interface interaction is enhanced after the introduction of the nitrogen atom and amino group thanks to the added NPb interaction, which favors electron transport with the newly designed ETMs. Our results not only report a set of novel promising ETMs, but also provide a useful design strategy for efficient ETMs.

Evidence of C--F-P and aromatic π--F-P weak interactions in imidazolium ionic liquids and its consequences

A simple change from alkyl group to alkene in side chain of imidazolium cation with same anion resulted in a drastic impact on physical properties (e.g., melting point) from bmimPF₆ IL to cmimPF₆ IL. The underlying reasons have been elucidated by structural and interaction studies with the help of DSC, SCXRD, vibrational and multi-nuclear NMR spectroscopic techniques. Experiments reveal existence of new weak interactions involving the carbon and π cloud of the imidazolium aromatic ring with fluoride of PF₆ anion (i.e., C₂--F-P and π--F-P) in cmimPF₆ but are absent in structurally similar prototype IL, bmimPF₆. Though weak, these interactions helped to form ladder type supramolecular arrangement, resulting in quite high melting point for cmimPF₆ IL compared to bmimPF₆ IL. These findings emphasize that an IL system can behave uniquely because of the existence of uncommon weak interactions.

Adsorbate-Induced Modification of the Confining Barriers in a Quantum Box Array

Quantum devices depend on addressable elements, which can be modified separately and in their mutual interaction. Self-assembly at surfaces, for example, formation of a porous (metal-) organic network, provides an ideal way to manufacture arrays of identical quantum boxes, arising in this case from the confinement of the electronic (Shockley) surface state within the pores. We show that the electronic quantum box state as well as the interbox coupling can be modified locally to a varying extent by a selective choice of adsorbates, here C₆₀, interacting with the barrier. In view of the wealth of differently acting adsorbates, this approach allows for engineering quantum states in on-surface network architectures.

Hydrolysis, polarity, and conformational impact of C-terminal partially fluorinated ethyl esters in peptide models

Fluorinated moieties are highly valuable to chemists due to the sensitive NMR detectability of the 19F nucleus. Fluorination of molecular scaffolds can also selectively influence a molecule's polarity, conformational preferences and chemical reactivity, properties that can be exploited for various chemical applications. A powerful route for incorporating fluorine atoms in biomolecules is last-stage fluorination of peptide scaffolds. One of these methods involves esterification of the C-terminus of peptides using a diazomethane species. Here, we provide an investigation of the physicochemical consequences of peptide esterification with partially fluorinated ethyl groups. Derivatives of N-acetylproline are used to model the effects of fluorination on the lipophilicity, hydrolytic stability and on conformational properties. The conformational impact of the 2,2-difluoromethyl ester on several neutral and charged oligopeptides was also investigated. Our results demonstrate that partially fluorinated esters undergo variable hydrolysis in biologically relevant buffers. The hydrolytic stability can be tailored over a broad pH range by varying the number of fluorine atoms in the ester moiety or by introducing adjacent charges in the peptide sequence.

Non-additive stabilization by halogenated amino acids reveals protein plasticity on a sub-angstrom scale

It has been a long-standing goal to understand the structure-stability relationship of proteins, as optimal stability is essential for protein function and highly desirable for protein therapeutics. Halogenation has emerged as a minimally invasive strategy to probe the physical characteristics of proteins in solution, as well as enhance the structural stabilities of proteins for therapeutic applications. Although advances in synthetic chemistry and genetic code expansion have allowed for the rapid synthesis of proteins with diverse chemical sequences, much remains to be learned regarding the impact of these mutations on their structural integrity. In this contribution, we present a systematic study of three well-folded model protein systems, in which their structural stabilities are assessed in response to various hydrogen-to-halogen atom mutations. Halogenation allows for the perturbation of proteins on a sub-angstrom scale, offering unprecedented precision of protein engineering. The thermodynamic results from these model systems reveal that in certain cases, proteins can display modest steric tolerance to halogenation, yielding non-additive consequences to protein stability. The observed sub-angstrom sensitivity of protein stability highlights the delicate arrangement of a folded protein core structure. The stability data of various halogenated proteins presented herein should also provide guidelines for using halogenation as a strategy to improve the stability of protein therapeutics.

Organocatalyzed synthesis of fluorinated poly(aryl thioethers)

The preparation of high-performance fluorinated poly(aryl thioethers) has received little attention compared to the corresponding poly(aryl ethers), despite the excellent physical properties displayed by many polysulfides. Herein, we report a highly efficient route to fluorinated poly(aryl thioethers) via an organocatalyzed nucleophilic aromatic substitution of silyl-protected dithiols. This approach requires low catalyst loadings, proceeds rapidly at room temperature, and is effective for many different perfluorinated or highly activated aryl monomers. Computational investigations of the reaction mechanism reveal an unexpected, concerted S_NAr mechanism, with the organocatalyst playing a critical, dual-activation role in facilitating the process. Not only does this remarkable reactivity enable rapid access to fluorinated poly(aryl thioethers), but also opens new avenues for the processing, fabrication, and functionalization of fluorinated materials with easy removal of the volatile catalyst and TMSF byproducts.

Fluorinated poly(aryl thioethers), unlike their poly(aryl ethers) counterparts, have received little attention despite excellent physical properties displayed by many polysulfides. Here the authors show a highly efficient route to fluorinated poly(aryl thioethers) via an organocatalyzed nucleophilic aromatic substitution of silyl-protected dithiols.

SNAr catalysis enhanced by an aromatic donor-acceptor interaction; facile access to chlorinated polyfluoroarenes

Selective catalytic S_NAr reaction of polyfluoroaryl C-F bonds with chloride is shown. Stoichiometric TMSCl makes the reaction exergonic and allows catalysis, which involves ground state elevation of chloride, aromatic donor-acceptor interactions, and stabilization of the Meisenheimer complex. Traditional cross-coupling of the products is now possible and demonstrates the utility.

Substituent Effects That Control Conjugated Oligomer Conformation through Non-covalent Interactions

Although understanding the conformations and arrangements of conjugated materials as solids is key to their prospective applications, predictive power over these structural factors remains elusive. In this work, substituent effects tune non-covalent interactions between side-chain fluorinated benzyl esters and main-chain terminal arenes, in turn controlling the conformations and interchromophore aggregation of three-ring phenylene-ethynylenes (PEs). Cofacial fluoroarene-arene (ArF-ArH) interactions cause twisting in the PE backbone, interrupting intramolecular conjugation as well as blocking chromophore aggregation, both of which prevent the typically observed bathochromic shift observed upon transitioning PEs from solution to solid. This work highlights two structural factors that determine whether the ArF-ArH interactions, and the resulting twisted, unaggregated chromophores, occur in these solids: (i) the electron-releasing characteristic of substituents on ArH, with more electron-releasing character favoring ArF-ArH interactions, and (ii) the fluorination pattern of the ArF ring, with 2,3,4,5,6-pentafluorophenyl favoring ArF-ArH interactions over 2,4,6-trifluorophenyl. These trends indicate that considerations of electrostatic complementarity, whether through a polar-π or substituent-substituent mechanism, can serve as an effective design principle in controlling the interaction strengths, and therefore the optoelectronic properties, of these molecules as solids.

The Cation-π Interaction Enables a Halo-Tag Fluorogenic Probe for Fast No-Wash Live Cell Imaging and Gel-Free Protein Quantification

The design of fluorogenic probes for a Halo tag is highly desirable but challenging. Previous work achieved this goal by controlling the chemical switch of spirolactones upon the covalent conjugation between the Halo tag and probes or by incorporating a “channel dye” into the substrate binding tunnel of the Halo tag. In this work, we have developed a novel class of Halo-tag fluorogenic probes that are derived from solvatochromic fluorophores. The optimal probe, harboring a benzothiadiazole scaffold, exhibits a 1000-fold fluorescence enhancement upon reaction with the Halo tag. Structural, computational, and biochemical studies reveal that the benzene ring of a tryptophan residue engages in a cation−π interaction with the dimethylamino electron-donating group of the benzothiadiazole fluorophore in its excited state. We further demonstrate using noncanonical fluorinated tryptophan that the cation−π interaction directly contributes to the fluorogenicity of the benzothiadiazole fluorophore. Mechanistically, this interaction could contribute to the fluorogenicity by promoting the excited-state charge separation and inhibiting the twisting motion of the dimethylamino group, both leading to an enhanced fluorogenicity. Finally, we demonstrate the utility of the probe in no-wash direct imaging of Halo-tagged proteins in live cells. In addition, the fluorogenic nature of the probe enables a gel-free quantification of fusion proteins expressed in mammalian cells, an application that was not possible with previously nonfluorogenic Halo-tag probes. The unique mechanism revealed by this work suggests that incorporation of an excited-state cation−π interaction could be a feasible strategy for enhancing the optical performance of fluorophores and fluorogenic sensors.

Designing Fluorinated Proteins

As methods to incorporate noncanonical amino acid residues into proteins have become more powerful, interest in their use to modify the physical and biological properties of proteins and enzymes has increased. This chapter discusses the use of highly fluorinated analogs of hydrophobic amino acids, for example, hexafluoroleucine, in protein design. In particular, fluorinated residues have proven to be generally effective in increasing the thermodynamic stability of proteins. The chapter provides an overview of the different fluorinated amino acids that have been used in protein design and the various methods available for producing fluorinated proteins. It discusses model proteins systems into which highly fluorinated amino acids have been introduced and the reasons why fluorinated residues are generally stabilizing, with particular reference to thermodynamic and structural studies from our laboratory. Lastly, details of the methodology we have developed to measure the thermodynamic stability of oligomeric fluorinated proteins are presented, as this may be generally applicable to many proteins.

Folding stability modulation of the villin headpiece helical subdomain by 4-fluorophenylalanine and 4-methylphenylalanine

HP36, the helical subdomain of villin headpiece, contains a hydrophobic core composed of three phenylalanine residues (Phe47, Phe51, and Phe58). Hydrophobic effects and electrostatic interactions were shown to be the critical factors in stabilizing this core and the global structure. To assess the interactions among Phe47, Phe51, and Phe58 residues and investigate how they affect the folding stability, we implanted 4-fluorophenylalanine (Z) and 4-methylphenylalanine (X) into the hydrophobic core of HP36. We chemically synthesized HP36 and its seven variants including four single mutants whose Phe51 or Phe58 was replaced with Z or X, and three double mutants whose Phe51 and Phe58 were both substituted. Circular dichroism and nuclear magnetic resonance measurements show that the variants exhibit a native HP36 like fold, of which F51Z and three double mutants are more stable than the wild type. Molecular modeling provided detailed interaction energy within the phenylalanine residues, revealing that electrostatic interactions dominate the stability modulation upon the introduction of 4-fluorophenylalanine and 4-methylphenylalanine. Our results show that these two non-natural amino acids can successfully tune the interactions in a relatively compact hydrophobic core and the folding stability without inducing dramatic steric effects. Such an approach may be applied to other folded motifs or proteins.

Experimental Binding Energies in Supramolecular Complexes

On the basis of many literature measurements, a critical overview is given on essential noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses with selected proteins. The methods, which can be applied to derive binding increments for single noncovalent interactions, start with the evaluation of consistency and additivity with a sufficiently large number of different host-guest complexes by applying linear free energy relations. Other strategies involve the use of double mutant cycles, of molecular balances, of dynamic combinatorial libraries, and of crystal structures. Promises and limitations of these strategies are discussed. Most of the analyses stem from solution studies, but a few also from gas phase. The empirically derived interactions are then presented on the basis of selected complexes with respect to ion pairing, hydrogen bonding, electrostatic contributions, halogen bonding, π-π-stacking, dispersive forces, cation-π and anion-π interactions, and contributions from the hydrophobic effect. Cooperativity in host-guest complexes as well as in self-assembly, and entropy factors are briefly highlighted. Tables with typical values for single noncovalent free energies and polarity parameters are in the Supporting Information.

Synthesis, structure and optical properties of tetraphenylethene derivatives with through-space conjugation between benzene and various planar chromophores

A series of tetraphenylethene derivatives with through-space conjugation and aggregation-enhanced emission properties are synthesized and studied.

Theoretical study of intermolecular interactions in crystalline arene–perhaloarene adducts in terms of the electron density

The intermolecular interactions in C₆X₆–arene crystals (X = F, Cl) and the halogen substitution effect can be quantified by the electron density.

A Cofacially Stacked Electron-Deficient Small Molecule with a High Electron Mobility of over 10 cm(2) V(-1) s(-1) in Air

A strong, electron-deficient small molecule, F4 -BDOPV, has a lowest unoccupied molecular orbital (LUMO) level down to -4.44 eV and exhibits cofacial packing in single crystals. These features provide F4 -BDOPV with good ambient stability and large charge-transfer integrals for electrons, leading to a high electron mobility of up to 12.6 cm(2) V(-1) s(-1) in air.

Implications of aromatic-aromatic interactions: From protein structures to peptide models

With increasing structural information on proteins, the opportunity to understand physical forces governing protein folding is also expanding. One of the significant non-covalent forces between the protein side chains is aromatic-aromatic interactions. Aromatic interactions have been widely exploited and thoroughly investigated in the context of folding, stability, molecular recognition, and self-assembly processes. Through this review, we discuss the contribution of aromatic interactions to the activity and stability of thermophilic, mesophilic, and psychrophilic proteins. Being hydrophobic, aromatic amino acids tend to reside in the protein hydrophobic interior or transmembrane segments of proteins. In such positions, it can play a diverse role in soluble and membrane proteins, and in α-helix and β-sheet stabilization. We also highlight here some excellent investigations made using peptide models and several approaches involving aryl-aryl interactions, as an increasingly popular strategy in protein and peptide engineering. A recent survey described the existence of aromatic clusters (trimer, tetramer, pentamer, and higher order assemblies), revealing the self-associating property of aryl groups, even in folded protein structures. The application of this self-assembly of aromatics in the generation of modern bionanomaterials is also discussed.

Pyridine-enabled copper-promoted cross dehydrogenative coupling of C(sp2)-H and unactivated C(sp3)-H bonds

The pyridine-enabled cross dehydrogenative coupling of sp2 C-H bonds of polyfluoroarenes and unactivated sp3 C-H bonds of amides was achieved via a copper-promoted process with good functional group compatibility. This reaction showed great site-selectivity by favoring the sp2 C-H bonds ortho to two fluoro atoms of arenes and the sp3 C-H bonds of α-methyl groups over those of the α-methylene, β- or γ-methyl groups of the aliphatic amides. Mechanistic studies revealed that sp3 C-H bond cleavage is an irreversible but not the rate-determining step, and the sp2 C-H functionalization of arenes appears precedent to the sp3 C-H functionalization of amides in this process.

Fluorinated Aromatic Amino Acids Distinguish Cation-π Interactions from Membrane Insertion

Cation-π interactions, where protein aromatic residues supply π systems while a positive-charged portion of phospholipid head groups are the cations, have been suggested as important binding modes for peripheral membrane proteins. However, aromatic amino acids can also insert into membranes and hydrophobically interact with lipid tails. Heretofore there has been no facile way to differentiate these two types of interactions. We show that specific incorporation of fluorinated amino acids into proteins can experimentally distinguish cation-π interactions from membrane insertion of the aromatic side chains. Fluorinated aromatic amino acids destabilize the cation-π interactions by altering electrostatics of the aromatic ring, whereas their increased hydrophobicity enhances membrane insertion. Incorporation of pentafluorophenylalanine or difluorotyrosine into a Staphylococcus aureus phosphatidylinositol-specific phospholipase C variant engineered to contain a specific PC-binding site demonstrates the effectiveness of this methodology. Applying this methodology to the plethora of tyrosine residues in Bacillus thuringiensis phosphatidylinositol-specific phospholipase C definitively identifies those involved in cation-π interactions with phosphatidylcholine. This powerful method can easily be used to determine the roles of aromatic residues in other peripheral membrane proteins and in integral membrane proteins.

Reactivity-based dynamic covalent chemistry: reversible binding and chirality discrimination of monoalcohols

In an effort to develop reactivity-based dynamic covalent bonding and to expand the scope and application of the dynamic covalent chemistry, in situ-generated simple generic iminium ions were utilized for the dynamic covalent binding of monoalcohols with high affinity. Hammett analysis was conducted to manipulate the equilibrium and correlate with the reactivity of reactants. The structural features of aldehydes and secondary amines were identified, and both polar and steric effects have significant impact on the binding. In particular, the substrates which can participate in π-π and polar-π interactions are able to afford apparent equilibrium constants in the magnitude of 10(4) M(-2), demonstrating the power of weak supramolecular forces to stabilize the dynamic covalent assembly. The generality of the assembly was validated with a series of mono secondary alcohols. To showcase the practicality of our system, chirality discrimination and ee measurement of chiral secondary alcohols were achieved.

Photocontrolled chignolin-derived β-hairpin peptidomimetics

The synthesis of novel, chignolin-derived peptides comprising the azobenzene photoswitch [3-(3-aminomethyl)phenylazo]phenylacetic acid (AMPP) is reported.

Electron transport via phenyl–perfluorophenyl interaction in crystals of fluorine-substituted dibenzalacetones

Although substitution with fluorine creates stability in organic electronic materials by altering the molecular crystal packing, the charge transport properties of the materials are significantly affected.

Anti-parallel sheet structures of side-chain-free γ-, δ-, and ε-dipeptides stabilized by benzene–pentafluorobenzene stacking

Benzene–pentafluorobenzene stacking can guide ω-amino acid dipeptides to arrange in an anti-parallel manner.