Why Does Thioformamide Have a Larger Rotational Barrier Than Formamide?

Binding Mechanisms and Therapeutic Activity of Heterocyclic Substituted Arylazothioformamide Ligands and Their Cu(I) Coordination Complexes

Finding new sources of biologically active compounds for anticancer or antimicrobial therapies remains an active area of research. Azothioformamides (ATFs) with a 1,3 N=N-C=S heterodiene backbone are a new class of biologically active compounds that chelate metals (e.g., Cu) forming stable ATF metal coordination complexes. In this study, ATF ligands were prepared with pyrrolidine, piperidine, N-methylpiperazine, and morpholine substituents on the formamide as to add more heterocyclic drug-like character for biological studies. Formamide derivatives were then complexed with various Cu(I) salts to form coordination complexes. Cu(I) salts were selected as to create potential bioactive compounds with less toxicity. Binding association constants of each Cu(I) salt to ATF ligands were extrapolated from UV-vis titration studies and were corroborated with DFT calculations using a hybrid functional B3LYP method. It was observed that the smaller pyrrolidine functionalized ATFs bound to the Cu(I) salts had stronger binding than any of the larger six-membered-ring heterocycles with association values in the 104 - 105 M-1 range. The ATF-Cu(I) salt coordination complexes were then evaluated for antimicrobial activity against two bacteria (Staphylococcus aureus, Escherichia coli), one yeast (Candida albicans), four human cancer lines (A-549, K-562, HT-1080, MDA-MB-231), and two normal human lines (MRC-5, HFF). The ATF ligands themselves were inactive against all microbes and most human lines except K-562 cells, which were sensitive to three of the four ligands (IC50's = 7.0-25.5 μM). Most ATF-Cu(I) complexes showed low to medium micromolar activity against Candida albicans (IC50's 2.6-24.8 μM) and Staphylococcus aureus (IC50's = 3.4-37.7 μM), with increasing activity corresponding to complexes with higher binding association constants. The antiproliferative properties of ATF-Cu(I) metal salt complexes against mammalian cells were mixed, with low to medium micromolar activity across all cell lines. Notably, several ATF-Cu(I) salt coordination complexes showed submicromolar activity against the HT-1080 fibrosarcoma line (0.52-0.69 μM). The results demonstrate promising activity of ATF-Cu(I) complexes, particularly with pyrrolidine as the formamide component. These studies suggest that the stronger binding association values correlate to higher levels of biological activity.

Variable temperature-nuclear magnetic resonance experiment and high-resolution MS/MSn measurement of hydroxycarbodenafil, and its PDE5 inhibitory activity

Hydroxycarbodenafil, an analogue of carbodenafil, was detected in a dietary supplement in China in 2020. However, previous reports have not identified some carbon signals from the piperazine ring in nuclear magnetic resonance (NMR) experiments. Because the compound contains an amide bond, the reaction was suggested to be characteristic of compounds with rotational isomers. Variable-temperature NMR is used to determine the rotational barrier between different conformations by changing the measurement temperature. Using this technique, we succeeded in obtaining the first distinct data, including the carbon signals of the piperazine ring in the NMR spectrum of hydroxycarbodenafil. We also confirmed that this technique could be applied to other carbodenafil analogues. Multi-stage mass spectrometry (MSn) measurements with a high-resolution mass spectrometer specific to the substructures were performed to develop a protocol for the structural determination of the carbodenafil analogues. In addition, hydroxycarbodenafil was analysed using X-ray crystallography, and its inhibitory activity against phosphodiesterase type 5 (PDE5) was measured. The IC50 value of the inhibitory activity of hydroxycarbodenafil for PDE5A1, a PDE5 isoform, of 2.9 nM was lower than the 4.5 nM for sildenafil, a positive control.

A Small Change in Structure, a Big Change in Flexibility

Studies of the rotational barrier energy of the amide bond using quantum computing and nuclear magnetic resonance (NMR) are focused mainly on its use as a model of the peptide bond. The results of these studies are valuable not only in terms of the fundamental conformational properties of amide bonds, but also in the design of molecular machines, which have recently attracted interest. We investigate the fluxionality of the amide and enamide bonds of compound 3-[(E)-(dimethylamino)methylidene]-1,1-dimethylurea using advanced dynamic NMR experiments and a theoretical evaluation of the density functional theory (DFT) calculation. The dynamic NMR study shows restricted rotation around the amide group (16.4 kcal/mol) and a very high barrier around the enamine group (18.6 kcal/mol). In a structurally similar compound, (E)-3-(dimethylamino)-N,N-dimethylacrylamide (N atom is replaced by CH), the amide barrier is 12.4 kcal/mol and the enamine barrier is 11.7 kcal/mol. The DFT studies of both compounds reveal the electronic origin of this phenomenon. Theoretical calculations reveal the origin of the higher enamine barrier. The better delocalization of the lone pair of electrons on the end nitrogen atom into the antibonding orbital of the neighboring C-N double bond leads to the better stabilization of the ground state, and this leads to a greater increase in the enamine barrier.

Chemoselective cycloisomerization of O-alkenylbenzamides via concomitant 1,2-aryl migration/elimination mediated by hypervalent iodine reagents

As an ambident nucleophile, controlling the reaction selectivities of nitrogen and oxygen atoms in amide moiety is a challenging issue in organic synthesis. Herein, we present a chemodivergent cycloisomerization approach to construct isoquinolinone and iminoisocoumarin skeletons from o-alkenylbenzamide derivatives. The chemo-controllable strategy employed an exclusive 1,2-aryl migration/elimination cascade, enabled by different hypervalent iodine species generated in situ from the reaction of iodosobenzene (PhIO) with MeOH or 2,4,6-tris-isopropylbenzene sulfonic acid. DFT studies revealed that the nitrogen and oxygen atoms of the intermediates in the two reaction systems have different nucleophilicities and thus produce the selectivity of N or O-attack modes.

Synthesis and Receptor Binding Studies of α5 GABAAR Selective Novel Imidazodiazepines Targeted for Psychiatric and Cognitive Disorders

GABA mediates inhibitory actions through various GABA_A receptor subtypes, including 19 subunits in human GABAAR. Dysregulation of GABAergic neurotransmission is associated with several psychiatric disorders, including depression, anxiety, and schizophrenia. Selective targeting of α2/3 GABAARs can treat mood and anxiety, while α5 GABAA-Rs can treat anxiety, depression, and cognitive performance. GL-II-73 and MP-III-022, α5-positive allosteric modulators have shown promising results in animal models of chronic stress, aging, and cognitive disorders, including MDD, schizophrenia, autism, and Alzheimer's disease. Described in this article is how small changes in the structure of imidazodiazepine substituents can greatly impact the subtype selectivity of benzodiazepine GABAAR. To investigate alternate and potentially more effective therapeutic compounds, modifications were made to the structure of imidazodiazepine 1 to synthesize different amide analogs. The novel ligands were screened at the NIMH PDSP against a panel of 47 receptors, ion channels, including hERG, and transporters to identify on- and off-target interactions. Any ligands with significant inhibition in primary binding were subjected to secondary binding assays to determine their K_i values. The newly synthesized imidazodiazepines were found to have variable affinities for the benzodiazepine site and negligible or no binding to any off-target profile receptors that could cause other physiological problems.

Structures of the Most Twisted Thioamide and Selenoamide: Effect of Higher Chalcogens of Twisted Amides on N-C(X) Resonance

Amide bond replacement with planar isosteric chalcogen analogues has an important implication for the properties of the N-C(X) linkage in structural chemistry, biochemistry and organic synthesis. Herein, we report the first higher chalcogen derivatives of non-planar twisted amides. The synthesis of twisted thioamide in a versatile system has been accomplished by direct thionation without cleavage of the σ N-C bond. The synthesis of twisted selenoamide has been accomplished by selenation with Woollins' reagent. The structures of higher chalcogen analogues of non-planar amides were unambiguously confirmed by X-ray crystallography. Reactivity studies were conducted to determine the effect of isologous N-C(O) to N-C(X) replacement on the properties of the amide linkage. Computational studies were employed to evaluate structural and energetic parameters of amide bond alteration in higher chalcogen amides. The study provides the first experimental evidence on the effect of chalcogen isologues on the structural and electronic properties of the non-planar amide N-C(X) linkage.

How the Chalcogen Atom Size Dictates the Hydrogen‐Bond Donor Capability of Carboxamides, Thioamides, and Selenoamides

The amino groups of thio‐ and selenoamides can act as stronger hydrogen‐bond donors than of carboxamides, despite the lower electronegativity of S and Se. This phenomenon has been experimentally explored, particularly in organocatalysis, but a sound electronic explanation is lacking. Our quantum chemical investigations show that the NH₂ groups in thio‐ and selenoamides are more positively charged than in carboxamides. This originates from the larger electronic density flow from the nitrogen lone pair of the NH₂ group towards the lower‐lying π*_C=S and π*_C=Se orbitals than to the high‐lying π*_C=O orbital. The relative energies of the π* orbitals result from the overlap between the chalcogen np and carbon 2p atomic orbitals, which is set by the carbon‐chalcogen equilibrium distance, a consequence of the Pauli repulsion between the two bonded atoms. Thus, neither the electronegativity nor the often‐suggested polarizability but the steric size of the chalcogen atom determines the amide's hydrogen‐bond donor capability.

Chemoselective Transamidation of Thioamides by Transition-Metal-Free N-C(S) Transacylation

Thioamides represent highly valuable isosteric in the strictest sense "single-atom substitution" analogues of amides that have found broad applications in chemistry and biology. A long-standing challenge is the direct transamidation of thioamides, a process which would convert one thioamide bond (R-C(S)-NR¹ R² ) into another (R-C(S)-NR³ N⁴ ). Herein, we report the first general method for the direct transamidation of thioamides by highly chemoselective N-C(S) transacylation. The method relies on site-selective N-tert-butoxycarbonyl activation of 2° and 1° thioamides, resulting in ground-state-destabilization of thioamides, thus enabling to rationally manipulate nucleophilic addition to the thioamide bond. This method showcases a remarkably broad scope including late-stage functionalization (>100 examples). We further present extensive DFT studies that provide insight into the chemoselectivity and provide guidelines for the development of transamidation methods of the thioamide bond.

Contribution of Solvents to Geometrical Preference in the Z/E Equilibrium of N-Phenylthioacetamide

We studied the Z/E preference of N-phenylthioacetamide (thioacetanilide) derivatives in various solvents by means of ¹H NMR spectroscopy, as well as molecular dynamics (MD) and other computational analyses. Our experimental results indicate that the Z/E isomer preference of secondary (NH)thioamides of N-phenylthioacetamides shows substantial solvent dependency, whereas the corresponding amides do not show solvent dependency of the Z/E isomer ratios. Detailed study of the solvent effects based on molecular dynamics simulations revealed that there are two main modes of hydrogen (H)-bond formation between solvent and (NH)thioacetamide, which influence the Z/E isomer preference of (NH)thioamides. DFT calculations of NH-thioamide in the presence of one or two explicit solvent molecules in the continuum solvent model can effectively mimic the solvation by multiple solvent molecules surrounding the thioamide in MD simulations and shed light on the precise nature of the interactions between thioamide and solvent. Orbital interaction analysis showed that, counterintuitively, the Z/E preference of NH-thioacetamides is mainly determined by steric repulsion, while that of sterically congested N-methylthioacetamides is mainly determined by thioamide conjugation.

Asymmetric Catalysis Mediated by Synthetic Peptides, Version 2.0: Expansion of Scope and Mechanisms

Low molecular weight synthetic peptides have been demonstrated to be effective catalysts for an increasingly wide array of asymmetric transformations. In many cases, these peptide-based catalysts have enabled novel multifunctional substrate activation modes and unprecedented selectivity manifolds. These features, along with their ease of preparation, modular and tunable structures, and often biomimetic attributes make peptides well-suited as chiral catalysts and of broad interest. Many examples of peptide-catalyzed asymmetric reactions have appeared in the literature since the last survey of this broad field in Chemical Reviews (Chem. Rev. 2007, 107, 5759-5812). The overarching goal of this new Review is to provide a comprehensive account of the numerous advances in the field. As a corollary to this goal, we survey the many different types of catalytic reactions, ranging from acylation to C-C bond formation, in which peptides have been successfully employed. In so doing, we devote significant discussion to the structural and mechanistic aspects of these reactions that are perhaps specific to peptide-based catalysts and their interactions with substrates and/or reagents.

Electrophile dependent mechanisms in the asymmetric trapping of α-lithio-N-(tert-butoxythiocarbonyl)azetidine

Sn-Li exchange and 'poor man's Hoffmann tests' establish asymmetric trapping of α-lithio-N-(tert-butoxythiocarbonyl) (Botc) azetidine to be controlled by dynamic thermodynamic resolution or dynamic kinetic resolution, depending on the electrophile. Unusually, different configurational stability is seen for the anion generated by lithiation compared to transmetallation. Configurational stability of α-lithio-N-Boc azetidine indicates instability with the N-Botc system is due to the C[double bond, length as m-dash]S group.

Selenoamides modulate dipole-dipole interactions in hydrogen bonded supramolecular polymers of 1,3,5-substituted benzenes

We report the synthesis and self-assembly behavior of a chiral C₃-symmetrical benzene-tricarboselenoamide. The introduction of the selenoamide moiety enhances the dipolar character of the supramolecular interaction and confers a remarkable thermal stability to the supramolecular polymers obtained.

Evolution of the atomic valence observed by the reaction fragility spectra on the reaction path

The computational fragility spectra of atoms on the reaction path are presented for a selection of canonical processes represented by an amino group rotation around the (X)HC-NH(Y) bond (X = O, S; Y=H, CH₃). Calculated spectra are found to very accurately describe the variation of atomic valence. Significant linear correlation is also demonstrated between the Wiberg bond indices and the corresponding elements of the connectivity matrix, instrumental for calculation of the spectra. Demonstrated atomic fragility spectra contain rich and subtle information on the variation of the bonding status of all atoms, including the weak interacting individual hydrogens. Correlation with the atomic valences confirm the earlier finding that the spectra contain a picture of the electron density flow upon a reaction.

Biosynthesis and Chemical Applications of Thioamides

Thioamidation as a posttranslational modification is exceptionally rare, with only a few reported natural products and exactly one known protein example (methyl-coenzyme M reductase from methane-metabolizing archaea). Recently, there has been significant progress in elucidating the biosynthesis and function of several thioamide-containing natural compounds. Separate developments in the chemical installation of thioamides into peptides and proteins have enabled cell biology and biophysical studies to advance the current understanding of natural thioamides. This review highlights the various strategies used by Nature to install thioamides in peptidic scaffolds and the potential functions of this rare but important modification. We also discuss synthetic methods used for the site-selective incorporation of thioamides into polypeptides with a brief discussion of the physicochemical implications. This account will serve as a foundation for the further study of thioamides in natural products and their various applications.

Origins of the Endo and Exo Selectivities in Cyclopropenone, Iminocyclopropene, and Triafulvene Diels-Alder Cycloadditions

The endo and exo stereoselectivities of Diels-Alder reactions of cyclopropenone, iminocyclopropene, and substituted triafulvenes with butadiene were rationalized using density functional theory calculations. When cyclopropenone is the dienophile, there is a 1.8 kcal/mol preference for the exo cycloaddition with butadiene, while the reaction of 3-difluoromethylene triafulvene with butadiene favors the endo cycloaddition by 2.8 kcal/mol. The influence of charge transfer and secondary orbital interactions on the stereoselectivity of Diels-Alder reactions involving triafulvenes and heteroanalogs is discussed. The predicted stereoselectivity correlates with both the charge and highest occupied molecular orbital (HOMO) coefficient at the C3 carbon of the triafulvene motif.

Increasing the bioactive space of peptide macrocycles by thioamide substitution

We show that substituting a single atom, O to S (amide to thioamide), in a peptide bond results in global restriction of the conformational flexibility in peptide macrocycles with minimal perturbation of the parent conformation. The van der Waals interactions between the C 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 S group and the surrounding atoms are the major driving force in inducing the conformational restriction, resulting in well-defined structures of these cyclic peptides with static 3-D presentation of the pharmacophores. Utilizing this property of thioamides, we report the development of a superactive antagonist of pro-angiogenic αvβ3, αvβ5 and α5β1 integrins, which are responsible for cancer cell proliferation and survival. Using simple thio-scanning and spatial screening of a non-efficacious and conformationally flexible cyclic peptide, we could achieve a more than 10⁵ fold enhancement in its efficacy in cellulo via a single O to S substitution. The developed peptide shows better efficacy in inhibiting the pro-angiogenic integrins than the drug candidate cilengitide, with a significantly enhanced serum half-life of 36 h compared to that of cilengitide (12 h). The long shelf-life, absence of non-specific toxicity and resistance to degradation of the thioamidated macrocyclic peptides in human serum suggest the promise of thioamides in markedly improving the affinity, efficacy and pharmacology of peptide macrocycles.

Post-translational thioamidation of methyl-coenzyme M reductase, a key enzyme in methanogenic and methanotrophic Archaea

Methyl-coenzyme M reductase (MCR), found in strictly anaerobic methanogenic and methanotrophic archaea, catalyzes the reversible production and consumption of the potent greenhouse gas methane. The α subunit of MCR (McrA) contains several unusual post-translational modifications, including a rare thioamidation of glycine. Based on the presumed function of homologous genes involved in the biosynthesis of thioviridamide, a thioamide-containing natural product, we hypothesized that the archaeal tfuA and ycaO genes would be responsible for post-translational installation of thioglycine into McrA. Mass spectrometric characterization of McrA from the methanogenic archaeon Methanosarcina acetivorans lacking tfuA and/or ycaO revealed the presence of glycine, rather than thioglycine, supporting this hypothesis. Phenotypic characterization of the ∆ycaO-tfuA mutant revealed a severe growth rate defect on substrates with low free energy yields and at elevated temperatures (39°C - 45°C). Our analyses support a role for thioglycine in stabilizing the protein secondary structure near the active site.

Access to divergent benzo-heterocycles via a catalyst-dependent strategy in the controllable cyclization of o-alkynyl-N-methoxyl-benzamides

A chemo- and regio-selectively controllable approach for construction of diverse benzo-heterocycles is established. The ligand controls the regioselectivity and the metal dominates the chemoselectivity.

Effects of isosteric substitutions on the conformational preference and cis–trans isomerization of proline-containing peptides

Isosteric substitutions of the peptide CO group by CS and CSe groups increased thetranspopulation and rotational barrier to the prolylcis–transisomerization of proline-containing peptides.

Pyrolysis of azetidinones. Part 2. Kinetics and mechanism of thermolysis of β-lactams and β-thiolactams

The kinetics of the gas-phase thermolysis reaction of seven β-lactams and their thione analogues were investigated over the temperature range 533–603 K for the β-lactams and 463–542 K for the β-thiolactams. The average values of the energy of activation (Ea) (kJ mol−1) and Arrhenius log A (s–1) were, respectively, 170.8 ± 18.6 and 12.4 ± 1.6 for the lactams and 131.7 ± 18.2 and 11.0 ± 2.0 for the thione analogues. The entropy of activation (ΔS#) was negative for of the substrates and slightly positive for three. The rate constants (k) (s−1) were calculated for 510 K and compared for the two series of azetidinones. The effects of substituents on rates and the novel role played by the C=O and C=S moieties on the relative reactivities of the cyclic amides are rationalized on the basis of a formal retro[2+2]cycloaddition mechanism used earlier to explain the products of the gas-phase thermolysis reaction of the present azetidinones.

Thioamides in the collagen triple helix

To probe noncovalent interactions within the collagen triple helix, backbone amides were replaced with a thioamide isostere. This subtle substitution is the first in the collagen backbone that does not compromise thermostability. A triple helix with a thioamide as a hydrogen bond donor was found to be more stable than triple helices assembled from isomeric thiopeptides.

Enhanced anion binding by heteroatom replacement in bambusurils

Calculations predict that protonated aza-bambusurils would bind multiple anions along their main axis and may also function as synthetic anion channels.

R, Krishnamurthy M, Sureshbabu VV. Thionation of di and tripeptides employing thiourea as a sulphur transfer reagent

Thiopeptides have been prepared by thionation employing DMF/PCl₅ and thiourea as a sulphur transfer reagent. The protocol was also successfully used for the thionation of two peptide bonds, amino acid derived arylamides.

α- and α'-Lithiation-Electrophile Trapping of N-Thiopivaloyl and N-tert-Butoxythiocarbonyl α-Substituted Azetidines: Rationalization of the Regiodivergence Using NMR and Computation

(1)H NMR and computational analyses provide insight into the regiodivergent (α- and α'-) lithiation-electrophile trapping of N-thiopivaloyl- and N-(tert-butoxythiocarbonyl)-α-alkylazetidines. The magnitudes of the rotation barriers in these azetidines indicate that rotamer interconversions do not occur at the temperature and on the time scale of the lithiations. The NMR and computational studies support the origin of regioselectivity as being thiocarbonyl-directed lithiation from the lowest energy amide-like rotameric forms (cis for N-thiopivaloyl and trans for N-tert-butoxythiocarbonyl).

Conformational preferences for isomeric N,N′-bis(pyridin-n-ylmethyl)ethanedithiodiamides, n = 2, 3 and 4: a combined crystallographic and DFT study

Crystal structure analysis of the isomeric N,N′-bis(pyridin-n-ylmethyl)ethanedithioamides, n = 2 (1), 3 (2) and 4 (3), show a planar conformation for 1 and conformations whereby the pyridyl rings lie orthogonal and to either side of the central residue for each of 2 and 3. The universal adoption of the all ZZ conformation about the central C–N bonds, which have double bond character, is ascribed to the presence of intramolecular N–H…S hydrogen bonds that close S(5) rings. The gas-phase geometry optimised structure for 1 is the same as the experimental structure which features intramolecular amine-N–H…N(pyridyl) hydrogen bonds. The open structures found for 2 and 3 differ from the somewhat flattened optimised structures. Systematic variations in the geometric parameters characterising the central C2N2S2 residue, in particular the double-bond character of the C–N bond and the elongation of the central C–C bond are shown by theory to be due to conjugative nN → π*C=S interactions and nS → σ*C-C hyperconjugation, respectively.

n→π* interactions of amides and thioamides: implications for protein stability

Carbonyl-carbonyl interactions between adjacent backbone amides have been implicated in the conformational stability of proteins. By combining experimental and computational approaches, we show that relevant amidic carbonyl groups associate through an n→π* donor-acceptor interaction with an energy of at least 0.27 kcal/mol. The n→π* interaction between two thioamides is 3-fold stronger than between two oxoamides due to increased overlap and reduced energy difference between the donor and acceptor orbitals. This result suggests that backbone thioamide incorporation could stabilize protein structures. Finally, we demonstrate that intimate carbonyl interactions are described more completely as donor-acceptor orbital interactions rather than dipole-dipole interactions.