General Installation of (4H)-Imidazolone cis-Amide Bioisosteres Along the Peptide Backbone.

Imidazolones represent an important class of heterocycles present in a wide range of pharmaceuticals, metabolites, and bioactive natural products and serve as the active chromophore in green fluorescent protein. Recently, imidazolones have received attention for their ability to act as a nonaromatic amide bond bioisotere which improves pharmacological properties. Herein, we present a tandem amidine installation and cyclization with an adjacent ester to yield (4H)-imidazolone products. Using amino acid building blocks, we can access the first examples of α-chiral imidazolones that have been previously inaccessible. Additionally, our method is amenable to on-resin installation which can be seamlessly integrated into existing solid-phase peptide synthesis protocols. Finally, we show that peptide imidazolones are potent cis-amide bond surrogates that preorganize linear peptides for head-to-tail macrocyclization. This work represents the first general approach to the backbone and side-chain insertion of imidazolone bioisosteres at various positions in linear and cyclic peptides.

Anomeric Answer to Sulfenamide Stability and α-Nucleophilicity.

The S-N bond remains a synthetically challenging motif for organic chemists to access. The problem arises from instability in many sulfenamide derivatives, which has led to fewer S-N bond surrogate molecules compared to their hydroxylamine (NH2OH) and hydrazine (NH2NH2) analogues. In turn, sulfenamides have often been omitted in studies regarding α-nucleophilicity. Herein, we provide factors responsible for the stability of the sulfenamide motif and provide new insights on the nucleophilic properties of sulfenamides as they relate to the α-effect.

A General Strategy to Install Amidine Functional Groups Along the Peptide Backbone.

Amidines are a structural surrogate for peptide bonds, yet have received considerably little attention in peptides due to limitations in existing methods to access them. The synthetic strategy developed in this study represents the first robust and general procedure for the introduction of amidines into the peptide backbone. We exploit and further develop the utility and efficiency of thioimidate protecting groups as a means to side-step reactivity that ultimately renders existing methods unsuitable for the installation of amidines along the main-chain of peptides. This work is significant because it describes a generally applicable path to access unexplored peptide designs and architectures for new therapeutics made possible by the unique properties of amidines.

Molecular Conformation in Charge Tunneling across Large-Area Junctions.

Self-assembled monolayers are predicated on thermodynamic equilibrium; hence, their properties project accessible relaxation pathways. Herein, we demonstrate that charge tunneling correlates with conformational degrees of freedom(s). Results from open chain and cyclic head groups show that, as expected, distribution in tunneling data correlates with the orientation of the head group, akin to the odd-even effect and more importantly the degree of conformational freedom, but fluctuates with applied bias. Trends in nature of distributions in current density illuminate the need for higher statistical moments in understanding these rather dynamic systems. We employ skewness, kurtosis, and estimation plots to show that the conformational degree of freedom in the head group significantly amplifies the odd-even effect and may lead to enhanced or perturbed tunneling based on whether the head group is on an odd- or even-parity spacer.

Hydrogen Bond and Geometry Effects of Thioamide Backbone Modifications.

Thioamide substitution of backbone peptide bonds can probe interactions along the main chain of proteins. Despite theoretical predictions of the enhanced hydrogen bonding propensities of thioamides, previous studies often do not consider the geometric constraints imposed by folded peptide secondary structure. This work addresses drawbacks in previous studies that ignored the geometry dependence and local dielectric properties of thioamide hydrogen bonding and identifies cases where thioamides may be either stronger or weaker hydrogen-bonding partners than amides.

Fast Acquisition of Proton-Detected HETCOR Solid-State NMR Spectra of Quadrupolar Nuclei and Rapid Measurement of NH Bond Lengths by Frequency Selective HMQC and RESPDOR Pulse Sequences.

Fast magic-angle spinning (MAS), frequency selective (FS) heteronuclear multiple quantum coherence (HMQC) experiments which function in an analogous manner to solution SOFAST HMQC NMR experiments, are demonstrated. Fast MAS enables efficient FS excitation of 1 H solid-state NMR signals. Selective excitation and observation preserves 1 H magnetization, leading to a significant shortening of the optimal inter-scan delay. Dipolar and scalar 1 H{14 N} FS HMQC solid-state NMR experiments routinely provide 4- to 9-fold reductions in experiment times as compared to conventional 1 H{14 N} HMQC solid-state NMR experiments. 1 H{14 N} FS resonance-echo saturation-pulse double-resonance (RESPDOR) allowed dipolar dephasing curves to be obtained in minutes, enabling the rapid determination of NH dipolar coupling constants and internuclear distances. 1 H{14 N} FS RESPDOR was used to assign multicomponent active pharmaceutical ingredients (APIs) as salts or cocrystals. FS HMQC also provided enhanced sensitivity for 1 H{17 O} and 1 H{35 Cl} HMQC experiments on 17 O-labeled Fmoc-alanine and histidine hydrochloride monohydrate, respectively. FS HMQC and FS RESPDOR experiments will provide access to valuable structural constraints from materials that are challenging to study due to unfavorable relaxation times or dilution of the nuclei of interest.

Highly selective staining and quantification of intracellular lipid droplets with a compact push-pull fluorophore based on benzothiadiazole.

A robust lipophilic dye, based on the structures of the benzothiadiazole heterocycle, was shown to be a potent fluorescent stain for the selective imaging of lipid droplets (LDs) within both live and fixed human cells. Its small molecular framework, large Stokes shift, and vastly improved photostability over that of the current status quo, Nile Red, highlight its tremendous potential as a versatile chemical tool for facilitating LD imaging and research.

Detailed Visualization of Aromaticity Using Isotropic Magnetic Shielding.

For many years, Clar's aromatic sextet theory has served as a qualitative method for assessing the aromatic character of polycyclic aromatic hydrocarbons. A new approach, based on the calculation of isotropic magnetic shielding (IMS) contour plots, is shown to provide a feature-rich picture of aromaticity that is both quantitative yet still easily interpreted. Chemists are visual creatures who are adept at discerning reactivity and chemical behavior from molecular structures. To quote Roald Hoffmann, "People like pictures. Chemists live off them." Thus, the detailed image analysis we present simultaneously provides quantitative assessment of electronic structure, which is still easy-to-understand through visual inspection, embedded in an aesthetically appealing and intuitive picture that draws the reader in. We provide novel computed IMS contour plots for a representative selection of aromatic molecules. Where Clar's static drawings capture only a partial sketch of the electronic properties of a molecule, IMS contour plots present a detailed, global landscape of a molecule that sums all possible resonance structures. This novel analysis allows us to correct certain drawbacks of Clar's analysis with respect to polycyclic aromatics and quantitatively assess the bonding and electronic structure of acene hydrocarbons.

Probing O-H Bonding through Proton Detected 1H-17O Double Resonance Solid-State NMR Spectroscopy.

The ubiquity of oxygen in organic, inorganic, and biological systems has stimulated the application and development of 17O solid-state NMR spectroscopy as a probe of molecular structure and dynamics. Unfortunately, 17O solid-state NMR experiments are often hindered by a combination of broad NMR signals and low sensitivity. Here, it is demonstrated that fast MAS and proton detection with the D-RINEPT pulse sequence can be generally applied to enhance the sensitivity and resolution of 17O solid-state NMR experiments. Complete 2D 17O → 1H D-RINEPT correlation NMR spectra were typically obtained in less than 10 h from less than 10 mg of material, with low to moderate 17O enrichment (less than 20%). Two-dimensional 1H-17O correlation solid-state NMR spectra allow overlapping oxygen sites to be resolved on the basis of proton chemical shifts or by varying the mixing time used for 1H-17O magnetization transfer. In addition, J-resolved or separated local field (SLF) blocks can be incorporated into the D-RINEPT pulse sequence to allow the direct measurement of one-bond 1H-17O scalar coupling constants (1 JOH) or 1H-17O dipolar couplings ( DOH), respectively, the latter of which can be used to infer 1H-17O bond lengths. 1 JOH and DOH calculated from plane-wave density functional theory (DFT) show very good agreement with experimental values. Therefore, the 2D 1H-17O correlation experiments, 1H-17O scalar and dipolar couplings, and plane-wave DFT calculations provide a method to precisely determine proton positions relative to oxygen atoms. This capability opens new opportunities to probe interactions between oxygen and hydrogen in a variety of chemical systems.

Deprotection Strategies for Thioimidates during Fmoc Solid-Phase Peptide Synthesis: A Safe Route to Thioamides.

Thioamides are important biophysical probes of peptide folding but are prone to α-C epimerization during Fmoc solid-phase peptide synthesis. The stereochemical integrity of thioamide-containing peptides can be dramatically improved by protecting the thioamide as a thioimidate during synthesis. A drawback of this approach, however, is that once synthesis of the peptide is complete, regeneration of the thioamide requires the toxic, corrosive, and flammable gas H2S. This work examines several approaches to supplant H2S as a deprotection reagent in favor of a safer and more convenient alternative. Ultimately, a new application of the 4-azidobenzyl protecting group to thioamides was found to provide the most suitable means of both protection of α-C stereochemistry and conversion back to thioamide.

Tuning the Electrochemical Redox Potentials of Catechol with Boronic Acid Derivatives.

A strategy to control the oxidation potential of catechol using borinic acids is presented. Borinic acids reversibly bind catechol to form boron "ate" complexes (BACs) that alter the electron density on the oxygen atoms of catechol and, in turn, the propensity of the catechol toward electrochemical oxidation. The effect of different substituents on the borinic acid are investigated to determine their efficacy in tuning the electron density within the BAC and the resulting oxidation potential.

A designed protein binding-pocket to control excited-state intramolecular proton transfer fluorescence.

Excited-state intramolecular proton transfer involves a photochemical isomerization and creates the opportunity for the emission of two distinct wavelengths of light from a single fluorophore. The selectivity between these two wavelengths of emission is dependent on the environment around the fluorophore and suggests the possibility for ratiometric monitoring of protein microenvironments. Unfortunately, nonspecific binding of ESIPT fluorophores does not often lead to dramatic changes in the ratio between the two wavelengths of emission. A protein binding pocket was designed to selectively discriminate between the two channels of emission available to an ESIPT fluorophore. This work is significant because it demonstrates that specific interactions between the protein and the fluorophore are essential to realize strong ratiometric differences between the two possible wavelengths of emission. The design strategies proposed here lead to an ESIPT fluorophore that can discern subtle differences in the interface between two proteins.

Demonstration of Baird's rule complementarity in the singlet state with implications for excited-state intramolecular proton transfer.

The aromatic character of an arene is proposed to switch from aromatic in the ground state (S0) to antiaromatic in the S1 and T1 excited states. This behavior is known as Baird's rule and has been invoked to explain excited-state properties, primarily in the triplet state, whereas rationalization of antiaromaticity in the singlet state is less developed. This work demonstrates the first application of Baird's rule to rationalize previously unexplained experimental behavior of the singlet state process known as excited-state intramolecular proton transfer (ESIPT). Further, by analyzing the variations in isotropic magnetic shielding around the base arenes (benzene and naphthalene) of ESIPT fluorophores in the S0 and S1 electronic states, different shielding distributions indicate a complementarity to Baird's rule: greater aromaticity in S0 leads to greater antiaromaticity in S1 and vice versa. These findings have immediate application in the design of functional ESIPT fluorophores and, more generally, for photochemical reactions that are driven by the relief of antiaromaticity in the excited state. Notably, a tenet of traditional chromophore design states that expansion of conjugation generally leads to a red-shift in absorbance and emission wavelengths. The results of this study show that ESIPT fluorophores run contrary to those conventional design principles and this behavior can only be rationalized by considering Baird's rule.

Open-Resonance-Assisted Hydrogen Bonds and Competing Quasiaromaticity.

The delocalization of electron density upon tautomerization of a proton across a conjugated bridge can alter the strength of hydrogen bonds. This effect has been dubbed resonance-assisted hydrogen bonding (RAHB) and plays a major role in the energetics of the tautomeric equilibrium. The goal of this work was to investigate the role that π-delocalization plays in the stability of RAHBs by engaging other isomerization processes. Similarly, acid-base chemistry has received little experimental attention in studies of RAHB, and we address the role that acid-base effects play in the tautomeric equilibrium. We find that π-delocalization and the disruption of adjacent aromatic rings is the dominant effect in determining the stability of a RAHB.

Understanding interface (odd-even) effects in charge tunneling using a polished EGaIn electrode.

Charge transport across large area molecular tunneling junctions is widely studied due to its potential in the development of quantum electronic devices. Large area junctions based on eutectic gallium indium (used in the form of a conical tip top electrode) have emerged as a reliable platform for delineating structure-property relationships. Discrepancies, however, arise from different tip-morphologies and fabrication techniques. It can be, therefore, challenging to make reliable conclusions based on molecular features. Of particular note is the discrepancy between the behaviors of hydrocarbons containing odd and even numbered carbons across different EGaIn electrodes. Moreover, inconsistencies in tip roughness and oxide thickness can lead to more than a 100× increase in current densities with narrow distribution in data. Besides effects on the precision vs. accuracy of data, a theoretically predicted length-dependent limit to observation of the odd-even effect has not been realized experimentally. We developed a method to chemically polish the EGaIn tip to allow formation of smooth conformal contact due to re-establishment of liquid character at the point of contact though tension-driven reconstruction of a thin oxide layer. To evaluate the polished tip, we measured charge transport behavior across n-alkanethiolate SAMs and observed good correlation in the odd-even oscillation behavior to that observed from wetting studies. Since these molecules are homologues of each other, only differing in the orientation of the terminal CH2CH3 moiety, the odd-even effects are governed by orientation induced differences in the absences of SAM (gauche) defects. Comparison of obtained data with the literature shows significant difference between odd-numbered SAMs across Ag and Au.

Target selection by natural and redesigned PUF proteins.

Pumilio/fem-3 mRNA binding factor (PUF) proteins bind RNA with sequence specificity and modularity, and have become exemplary scaffolds in the reengineering of new RNA specificities. Here, we report the in vivo RNA binding sites of wild-type (WT) and reengineered forms of the PUF protein Saccharomyces cerevisiae Puf2p across the transcriptome. Puf2p defines an ancient protein family present throughout fungi, with divergent and distinctive PUF RNA binding domains, RNA-recognition motifs (RRMs), and prion regions. We identify sites in RNA bound to Puf2p in vivo by using two forms of UV cross-linking followed by immunopurification. The protein specifically binds more than 1,000 mRNAs, which contain multiple iterations of UAAU-binding elements. Regions outside the PUF domain, including the RRM, enhance discrimination among targets. Compensatory mutants reveal that one Puf2p molecule binds one UAAU sequence, and align the protein with the RNA site. Based on this architecture, we redesign Puf2p to bind UAAG and identify the targets of this reengineered PUF in vivo. The mutant protein finds its target site in 1,800 RNAs and yields a novel RNA network with a dramatic redistribution of binding elements. The mutant protein exhibits even greater RNA specificity than wild type. The redesigned protein decreases the abundance of RNAs in its redesigned network. These results suggest that reengineering using the PUF scaffold redirects and can even enhance specificity in vivo.

A Small Push-Pull Fluorophore for Turn-on Fluorescence.

A new class of push-pull dyes is reported based on the structures of benzoxa- and benzothiadiazole heterocycles. This new class of dyes displays red-shifted wavelengths of emission and greater sensitivity to polarity and hydrogen bonding solvents relative to previously known derivatives.

Convenient synthesis of collagen-related tripeptides for segment condensation.

Chromatography is a common step in the solution-phase synthesis of typical peptides, as well as peptide fragments for subsequent coupling on a solid support. Combining known reagents that form readily separable byproducts is shown to eliminate this step, which wastes time and other resources. Specifically, activating carboxyl groups with isobutyl chloroformate or as pentafluorophenyl esters and using N-methyl morpholine as a base enable chromatography-free synthetic routes in which peptide products are isolated from byproducts by facile evaporation, extraction, and trituration. This methodology was used to access tripeptides related to collagen, such as Fmoc-Pro-Pro-Gly-OH and Fmoc-Pro-Hyp(tBu)-Gly-OH, in a purity suitable for solid-phase segment condensation to form collagen mimetic peptides.

Thioimidate Solutions to Thioamide Problems during Thionopeptide Deprotection.

Thioamides have structural and chemical similarity to peptide bonds, offering valuable insights when probing peptide backbone interactions, but are prone to side reactions during solid-phase peptide synthesis (SPPS). Thioimidates have been demonstrated to be effective protecting groups for thioamides during peptide elongation. We further demonstrate how thioimidates can assist thioamides through the most yield-crippling step of thionopeptide deprotection, allowing for the first isolation of an important benchmark α-helical peptide that had previously eluded synthesis and isolation.

Thioimidates provide general access to thioamide, amidine, and imidazolone peptide-bond isosteres.

Thioamides, amidines, and heterocycles are three classes of modifications that can act as peptide-bond isosteres to alter the peptide backbone. Thioimidate protecting groups can address many of the problematic synthetic issues surrounding installation of these groups. Historically, amidines have received little attention in peptides due to limitations in methods to access them. The first robust and general procedure for the introduction of amidines into peptide backbones exploits the utility of thioimidate protecting groups as a means to side-step reactivity that ultimately renders existing methods unsuitable for the installation of amidines along the main-chain of peptides. Further, amidines formed on-resin can be reacted to form (4H)-imidazolone heteorcycles which have recently been shown to act as cis-amide isosteres. General methods for heterocyclic installation capable of geometrically restricting peptide conformation are also under-developed. This work is significant because it describes a generally applicable and divergent approach to access unexplored peptide designs and architectures.