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.

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.

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.

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.

Attached Nitrogen Test by 13C-14N Solid-State NMR Spectroscopy for the Structure Determination of Heterocyclic Isomers.

Differentiation of heterocyclic isomers by solution 1H, 13C, and 15N NMR spectroscopy is often challenging due to similarities in their spectroscopic signatures. Here, 13C{14N} solid-state NMR spectroscopy experiments are shown to operate as an "attached nitrogen test", where heterocyclic isomers are easy to distinguish based on one-dimensional nitrogen-filtered 13C solid-state NMR. We anticipate that these NMR experiments will facilitate the assignment of heterocyclic isomers during synthesis and natural product discovery.

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.

Investigation of a Series of 2-(2'-Hydroxyaryl)benzazole Derivatives: Photophysical Properties, Excited-State Intramolecular Proton-Transfer Reactions, and Observation of Long-Lived Triplet Excited States.

Excited state intramolecular proton transfer (ESIPT) has drawn much attention for its important applications in a variety of areas. Here, the steady-state and time-resolved absorption spectroscopic experiments as well as DFT/TD-DFT calculations are employed to study the photophysical properties and photochemical reaction mechanisms of 2-(2'-hydroxyphenyl) benzoxazole (HBO) and selected derivatives (compounds 1-3). Because of their larger π-conjugation framework, compounds 1-3 display red-shifted absorbance but blue-shifted fluorescence compared with HBO. A fast ESIPT process is observed directly for HBO while compound 3 has an enol/keto equilibrium type of ESIPT that exhibits dual emission. Interestingly, only the emission of the enol form is observed for compounds 1 and 2 which suggests that the ESIPT process is strongly inhibited. These results indicate the decoration with electron-withdrawing groups such as thiadiazol and pyrazine on the hydroxyphenyl ring (compounds 1 and 2) apparently suppresses the proton-transfer processes in their excited states. Whereas the ESIPT process is rarely increased for compound 3 that modified with the phenanthrol ring, because the effective conjugation is reduced for compound 3 compared with HBO. The work here provides fundamental insights that may be useful for designing novel ESIPT molecules in the future.

Magnetic shielding paints an accurate and easy-to-visualize portrait of aromaticity.

Chemists are trained to recognize aromaticity semi-intuitively, using pictures of resonance structures and Frost-Musulin diagrams, or simple electron-counting rules such as Hückel's 4n + 2/4n rule. To quantify aromaticity one can use various aromaticity indices, each of which is a number reflecting some experimentally measured or calculated molecular property, or some feature of the molecular wavefunction, which often has no visual interpretation or may not have direct chemical relevance. We show that computed isotropic magnetic shielding isosurfaces and contour plots provide a feature-rich picture of aromaticity and chemical bonding which is both quantitative and easy-to-visualize and interpret. These isosurfaces and contour plots make good chemical sense as at atomic positions they are pinned to the nuclear shieldings which are experimentally measurable through chemical shifts. As examples we discuss the archetypal aromatic and antiaromatic molecules of benzene and square cyclobutadiene, followed by modern visual interpretations of Clar's aromatic sextet theory, the aromaticity of corannulene and heteroaromaticity.

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.

Determination of Diffusion Kinetics of Ketamine in Brain Tissue: Implications for in vitro Mechanistic Studies of Drug Actions.

Ketamine has been in use for over 50 years as a general anesthetic, acting primarily through blockade of N-methyl-D-aspartate receptors in the brain. Recent studies have demonstrated that ketamine also acts as a potent and rapid-acting antidepressant when administered at sub-anesthetic doses. However, the precise mechanism behind this effect remains unclear. We examined the diffusion properties of ketamine in brain tissue to determine their effects in in vitro studies related to the antidepressant action of ketamine. Brain slices from adult mice were exposed to artificial cerebrospinal fluid (aCSF) containing ∼17 µM ketamine HCl for varying amounts of time. The amount of ketamine within each slice was then measured by tandem high-performance liquid chromatography - mass spectrometry to characterize the diffusion of ketamine into brain tissue over time. We successfully modeled the diffusion of ketamine into brain tissue using a mono-exponential function with a time constant of τ = 6.59 min. This curve was then compared to a one-dimensional model of diffusion yielding a diffusion coefficient of approximately 0.12 cm2⋅s-1 for ketamine diffusing into brain tissue. The brain:aCSF partition coefficient for ketamine was determined to be approximately 2.76. Our results suggest that the diffusion properties of ketamine have a significant effect on drug concentrations achieved within brain tissue during in vitro experiments. This information is vital to determine the ketamine concentration necessary for in vitro slice preparation to accurately reflect in vivo doses responsible for its antidepressant actions.

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.

Surface-Grafted Polymeric Ionic Liquids with Tunable Morphology via In/Ex Situ Cross-linking Methods.

Surface-grafted poly(ionic liquid) (PIL) films were prepared by both in and ex situ cross-linking methods with reversible addition-fragmentation chain transfer (RAFT) polymerization. Cross-linked brushes are more stable than linear brushes without sacrificing the surface functionality and, therefore, have increased potential for applications in biomedicine and materials chemistry. The two methods, in situ via a bifunctional cross-linker and ex situ via thermal cross-linking, were systematically compared on silicon-wafer substrates. Films obtained through in situ cross-linking were superior to films derived from our ex situ cross-linking technique with respect to responsive behavior and controlling the formation of polymer brushes on the surface. Alternatively, more stable layers were obtained by the ex situ cross-linking method using a cross-linker based on Meldrum's acid, where the film structure could be changed from a brush to collapsed film morphologies with an increasing cross-linker ratio.

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.

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.

Blue-Light Photocleavable Protecting Groups Based on Benzothiadiazole Scaffolds.

An unexpected nucleophilic aromatic substitution lead to a novel benzothiadiazole scaffold that bore the functional group pattern associated with benzyl-type photocleavable protecting groups. The new molecules display efficient photochemical release of leaving groups with blue light. The performance of both ortho- and meta-substituted derivatives was probed through both structural manipulation and computational metrics to improve performance.

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.

A Bottom-Up Approach To Preserve Thioamide Residue Stereochemistry during Fmoc Solid-Phase Peptide Synthesis.

Thioamides are useful biophysical probes for the study of peptide structure and folding. The α-C stereochemistry of thioamide amino acids, however, is easily epimerized during solid-phase peptide synthesis (SPPS), which limits the sequence space that is available to thioamide incorporation. This work demonstrates that the α-C stereochemistry of thioamides can be reversibly protected in a manner that is compatible with the standard methodology of SPPS to enable the facile implementation of thioamide probes.

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.

Synthesis and Spectral Properties of Push-Pull Dyes Based on Isobenzofuran Scaffolds.

A new class of push-pull dyes based on the reactive isobenzofuran core have been synthesized. The new dyes have a smaller HOMO-LUMO gap than a related class of dyes based on benzofurazan and allow for isolation of structural factors that contribute to environmental sensitivity. Experimental and theoretical evidence implicate different photophysical processes are responsible for a reversal of emissive behavior that is observed between isobenzofuran and benzofurazan analogues.