Role of Conjugation in the Stabilities and Rotational Barriers of Formamide and Thioformamide. An ab Initio Valence-Bond Study

Direct esterification of amides by the dimethylsulfate-mediated activation of amide C-N bonds

Amides are important intermediates in organic chemistry and the pharmaceutical industry, but their low reactivity requires catalysts and/or severe reaction conditions for esterification. Here, a novel approach was devised to convert amides into esters without the use of transition metals. The method effectively overcomes the inherent low reactivity of amides by employing dimethylsulfate-mediated reaction to activate the C-N bonds. To confirm the proposed reaction mechanism, control experiments and density functional theory (DFT) calculations were conducted. The method demonstrates a wide array of substrates, including amides with typical H/alkyl/aryl substitutions, N,N-disubstituted amides, amides derived from alkyl, aryl, or vinyl carboxylic acids, and even amino acid substrates with stereocentres. Furthermore, we have shown the effectiveness of dimethylsulfate in removing acyl protective groups in amino derivatives. This study presents a method that offers efficiency and cost-effectiveness in broadening the esterification capabilities of amides, thereby facilitating their increased utilization as synthetic compounds in diverse transformations.

Chemical kinetic mechanisms and scaling of two-dimensional polymers via irreversible solution-phase reactions

Two-dimensional (2D) polymers are extended networks of multi-functional repeating units that are covalently linked together but confined to a single plane. The past decade has witnessed a surge in interest and effort toward producing and utilizing 2D polymers. However, facile synthesis schemes suitable for mass production are yet to be realized. In addition, unifying theories to describe the 2D polymerization process, such as those for linear polymers, have not yet been established. Herein, we perform a chemical kinetic simulation to study the recent synthesis of 2D polymers in homogeneous solution with irreversible chemistry. We show that reaction sites for polymerization in 2D always scale unfavorably compared to 3D, growing as molecular weight to the 1/2 power vs 2/3 power for 3D. However, certain mechanisms can effectively suppress out-of-plane defect formation and subsequent 3D growth. We consider two such mechanisms, which we call bond-planarity and templated autocatalysis. In the first, although single bonds can easily rotate out-of-plane to render polymerization in 3D, some double-bond linkages prefer a planar configuration. In the second mechanism, stacked 2D plates may act as van der Waals templates for each other to enhance growth, which leads to an autocatalysis. When linkage reactions possess a 1000:1 selectivity (γ) for staying in plane vs rotating, solution-synthesized 2D polymers can have comparable size and yield with those synthesized from confined polymerization on a surface. Autocatalysis could achieve similar effects when self-templating accelerates 2D growth by a factor β of 10⁶. A combined strategy relaxes the requirement of both mechanisms by over one order of magnitude. We map the dependence of molecular weight and yield for the 2D polymer on the reaction parameters, allowing experimental results to be used to estimate β and γ. Our calculations show for the first time from theory the feasibility of producing two-dimensional polymers from irreversible polymerization in solution.

Ring Opening/Site Selective Cleavage in N-Acyl Glutarimide to Synthesize Primary Amides

A LiOH-promoted hydrolysis selective C-N cleavage of twisted N-acyl glutarimide for the synthesis of primary amides under mild conditions has been developed. The reaction is triggered by a ring opening of glutarimide followed by C-N cleavage to afford primary amides using 2 equiv of LiOH as the base at room temperature. The efficacy of the reactions was considered and administrated for various aryl and alkyl substituents in good yield with high selectivity. Moreover, gram-scale synthesis of primary amides using a continuous flow method was achieved. It is noted that our new methodology can apply under both batch and flow conditions for synthetic and industrial applications.

Supramolecular assembly and spectroscopic characterization of indolenine–barbituric acid zwitterions

The intermolecular hydrogen bonding of barbiturates assists in the supramolecular aggregation and a hypsochromic shift is shown in protic solvents.

Carbamate group as structural motif in drugs: a review of carbamate derivatives used as therapeutic agents

Due to their very good chemical and proteolytic stability, ability to penetrate cell membranes, and resemblance to a peptide bond, carbamate derivatives have received much attention in recent years and got an important role in modern drug discovery and medicinal chemistry. Today, carbamates make structural and/or functional part of many drugs and prodrugs approved and marketed for the treatment of various diseases such as cancer, epilepsy, hepatitis C, HIV infection, and Alzheimer's disease. In drugs they can play a role in drug-target interaction or improve the biological activity of parent molecules. In prodrugs they are mainly used to delay first-pass metabolism and enhance the bioavailability and effectiveness of compounds. This brief review takes a look at the properties and use of carbamates in various fields of medicine and provides quick insights into the mechanisms of action for some of them.

Application of carbamyl in structural optimization

Carbamyl is considered a privileged structure in medicinal chemistry. It has a wide range of biological activities such as antimicrobial, anticancer, anti-epilepsy, for which the best evidence is a number of marketed carbamyl-containing drugs. Carbamyl is formed of primary amine and carbonyl moieties that act as hydrogen bond donors and hydrogen acceptors with residues of targets respectively, which are benefit for improving pharmacological activities. In other cases, the introduced carbamyl improves drug-like properties including oral bioavailability. In this review, we introduce the carbamyl-containing drugs and the application of carbamyl in structural optimization as a result of enhancing activities or/and drug-like properties.

Density Functional Studies on Secondary Amides: Role of Steric Factors in Cis/Trans Isomerization

Cis/trans isomerization of amide bonds is a key step in a wide range of biological and synthetic processes. Occurring through C-N amide bond rotation, it also coincides with the activation of amides in enzymatic hydrolysis. In recently described QM studies of cis/trans isomerization in secondary amides using density functional methods, we highlighted that a peptidic prototype, such as glycylglycine methyl ester, can suitably represent the isomerization and complexities arising out of a larger molecular backbone, and can serve as the primary scaffold for model structures with different substitution patterns in order to assess and compare the steric effect of the substitution patterns. Here, we describe our theoretical assessment of such steric effects using tert-butyl as a representative bulky substitution. We analyze the geometries and relative stabilities of both trans and cis isomers, and effects on the cis/trans isomerization barrier. We also use the additivity principle to calculate absolute steric effects with a gradual increase in bulk. The study establishes that bulky substitutions significantly destabilize cis isomers and also increases the isomerization barrier, thereby synergistically hindering the cis/trans isomerization of secondary amides. These results provide a basis for the rationalization of kinetic and thermodynamic properties of peptides with potential applications in synthetic and medicinal chemistry.

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.

Peptide Bond Isomerization in High-Temperature Simulations

Force fields for molecular simulation are generally optimized to model macromolecules such as proteins at ambient temperature and pressure. Nevertheless, elevated temperatures are frequently used to enhance conformational sampling, either during system setup or as a component of an advanced sampling technique such as temperature replica exchange. Because macromolecular force fields are now put upon to simulate temperatures and time scales that greatly exceed their original design specifications, it is appropriate to re-evaluate whether these force fields are up to the task. Here, we quantify the rates of peptide bond isomerization in high-temperature simulations of three octameric peptides and a small fast-folding protein. We show that peptide octamers with and without proline residues undergo cis/trans isomerization every 1-5 ns at 800 K with three classical atomistic force fields (AMBER99SB-ILDN, CHARMM22/CMAP, and OPLS-AA/L). On the low microsecond time scale, these force fields permit isomerization of nonprolyl peptide bonds at temperatures ≥500 K, and the CHARMM22/CMAP force field permits isomerization of prolyl peptide bonds ≥400 K. Moreover, the OPLS-AA/L force field allows chiral inversion about the Cα atom at 800 K. Finally, we show that temperature replica exchange permits cis peptide bonds developed at 540 K to subsequently migrate back to the 300 K ensemble, where cis peptide bonds are present in 2 ± 1% of the population of Trp-cage TC5b, including up to 4% of its folded state. Further work is required to assess the accuracy of cis/trans isomerization in the current generation of protein force fields.

The ω, φ, and ψ Space of N-Hydroxy-N-methylacetamide and N-Acetyl-N '-hydroxy-N '-methylamide of Alanine and Their Boron Isosteres

The conformational space of N-hydroxy-N-methylacetamide [CH3-CO-N(OH)CH3, NMAOH] and its boron isostere [CH3-CO-B(OH)CH3, BMAOH] has been studied by quantum chemical methods. The potential energy surface of NMAOH and BMAOH has been built at the HF, B3LYP, and MP2 levels of theory with the 6-31+G* basis set. The minima and transition states for rotations about various torsional angles have been located, and the energy barriers have been estimated. The global minimum energy structure of both peptides exhibits an intramolecular hydrogen bond between the carbonyl oxygen and the hydroxyl group, imparting a conformational rigidity to the peptides. The omega rotation barrier is lower in the boron isostere than in NMAOH. The difference in the rotation barrier has been attributed to second-order orbital interactions, like negative hyperconjugation, as revealed by NBO calculations. In contrast, the rotation barrier around the torsion angle tau (torsion governing rotation about the N-O and B-O bonds) is relatively higher in the boron analogue. This difference is due to the double bond character in the B-O bond as opposed to the N-O bond which has the character of a single bond. As an extension, N-acetyl-N'-hydroxy-N'-methylamide of alanine (Ala-NOH) and its boron isostere (Ala-BOH) have been adopted as model peptides to study the conformational preferences about the φ and ψ torsion angles. The study reveals a strong preference for a Type I beta turn as well as inclinations for a left-handed alpha helix, for positive phi torsions, and for extended psi conformations for Ala-NOH; Ala-BOH, on the other hand, shows a leaning toward positive phi and extended psi, with no preference for any regular secondary structure motifs. The replacement of nitrogen by boron changes the electronic and conformational properties of the peptide, extending greater flexibility around the omega angle, a strong preference for positive phi values, and a shift in the site of nucleophilic attack from the carbonyl group to boron.

Organic carbamates in drug design and medicinal chemistry

The carbamate group is a key structural motif in many approved drugs and prodrugs. There is an increasing use of carbamates in medicinal chemistry and many derivatives are specifically designed to make drug-target interactions through their carbamate moiety. In this Perspective, we present properties and stabilities of carbamates, reagents and chemical methodologies for the synthesis of carbamates, and recent applications of carbamates in drug design and medicinal chemistry.

On the large σ-hyperconjugation in alkanes and alkenes

The conventional view that the σCC and σCH bonds in alkanes and unsaturated hydrocarbons are so highly localized that their non-steric interactions are negligible is scrutinized by the block-localized wavefunction (BLW) method. Even molecules considered conventionally to be "strain free" and "unperturbed" have surprisingly large and quite significant total σ-BLW-delocalization energies (DEs) due to their geminal and vicinal hyperconjugative interactions. Thus, the computed BLW-DEs (in kcal mol(-1)) for the antiperiplanar conformations of the n-alkanes (C(N)H(2N+2), N = 1-10) range from 11.6 for ethane to 82.2 for n-decane and are 50.9 for cyclohexane and 91.0 for adamantane. Although σ-electron delocalization in unsaturated hydrocarbons usually is ignored, the σ-BLW-DEs (in kcal mol(-1)) are substantial, as exemplified by D2h ethylene (9.0), triplet D2d ethylene (16.4), allene (19.3), butadiene (19.0), hexatriene (28.3), benzene (28.1), and cyclobutadiene (21.1). While each individual geminal and vicinal hyperconjugative interaction between hydrocarbon σ-bonding and σ-antibonding orbitals tends to be smaller than an individual π conjugative interaction (e.g., 10.2 kcal mol(-1) in anti-1,3-butadiene, the presence of many σ-hyperconjugative interactions (e.g., a total of 12 in anti-1,3-butadiene, see text), result in substantial total σ-stabilization energies (e.g., 19.0 kcal mol(-1) for butadiene), which may surpass those from the π interactions. Although large in magnitude, σ-electron delocalization energies often are obscured by cancellation when two hydrocarbons are compared. Rather than being strain-free, cyclohexane, adamantane, and diamantane suffer from their increasing number of intramolecular 1,4-C…C repulsions resulting in elongated C-C bond lengths and reduced σ-hyperconjugation, compared to the (skew-free) antiperiplanar n-alkane conformers. Instead of being inconsequential, σ-bond interactions are important and merit consideration.

Characterization of amide bond conformers for a novel heterocyclic template of N-acylhydrazone derivatives

Herein we describe NMR experiments and structural modifications of 4-methyl-2-phenylpyrimidine-N-acylhydrazone compounds (aryl-NAH) in order to discover if duplication of some signals in their ¹H- and ¹³C-NMR spectra was related to a mixture of imine double bond stereoisomers (E/Z) or CO-NH bond conformers (syn and anti-periplanar). NMR data from NOEdiff, 2D-NOESY and ¹H-NMR spectra at different temperatures, and also the synthesis of isopropylidene hydrazone revealed the nature of duplicated signals of a 4-methyl-2-phenylpyrimidine-N-acylhydrazone derivative as a mixture of two conformers in solution. Further we investigated the stereoelectronic influence of substituents at the ortho position on the pyrimidine ring with respect to the carbonyl group, as well as the electronic effects of pyrimidine by changing it to phenyl. The conformer equilibrium was attributed to the decoplanarization of the aromatic ring and carbonyl group (generated by an ortho-alkyl group) and/or the electron withdrawing character of the pyrimidine ring. Both effects increased the rotational barrier of the C-N amide bond, as verified by the ΔG^≠ values calculated from dynamic NMR. As far as we know, it is the first description of aryl-NAH compounds presenting two CO-NH bond- related conformations.

Why Cyclooctatetraene Is Highly Stabilized: The Importance of "Two-Way" (Double) Hyperconjugation

Despite its highly nonplanar geometry, the tub-shaped D2d cyclooctatetraene (COT) minimum is far from being an unconjugated polyene model devoid of important π interactions. The warped skeleton of D2d COT results in the large stabilization (41.1 kcal/mol) revealed by its isodesmic bond separation energy (BSE). This originates largely from the "two-way" hyperconjugation, back and forth across the C-C single bonds, between the CC/CH σ(σ*) and the C═C (π*)π orbitals. These hyperconjugative effects compensate for the substantial, but not complete, loss of π conjugation upon ring puckering. C-C single bond rotation of 1,3-butadiene involves a similar interplay between π conjugation and "two-way" double hyperconjugation and serves as a simple model for the inversion of D2d to D4h COT. The perpendicular rotational transition states of many other systems, e.g., the allyl cation, styrene, biphenyl, and ethene, are stabilized similarly by "two-way" hyperconjugation.

ELECTRONIC DELOCALIZATION: A QUANTITATIVE STUDY FROM MODERN AB INITIO VALENCE BOND THEORY

An ab initio spin-free valence bond code called Xiamen-99 has been developed based on an efficient algorithm called paired-permanent-determinant approach, where Hamiltonian and overlap matrix elements are expressed in terms of paired-permanent-determinants. With this tool, we probed the electronic delocalization phenomenon in a few typical examples including benzene, formamide and ethane. Our computations revealed that ab initio valence bond methods are able to estimate the energetic contribution from the delocalization effect to the stabilization of molecules, thus pave the way to illuminate the resonance theory at the quantitative level. In particular, we analyzed the cyclic electronic delocalization in benzene and showed that different understandings on the resonance may originate from the different usage of one-electron orbitals in the valence bond theory. Our investigation into the hyperconjugative interaction in ethane demonstrated that the hyperconjugation effect is not the dominating factor in the preference of the staggered conformer of ethane.

Peptide bond distortions from planarity: new insights from quantum mechanical calculations and peptide/protein crystal structures

By combining quantum-mechanical analysis and statistical survey of peptide/protein structure databases we here report a thorough investigation of the conformational dependence of the geometry of peptide bond, the basic element of protein structures. Different peptide model systems have been studied by an integrated quantum mechanical approach, employing DFT, MP2 and CCSD(T) calculations, both in aqueous solution and in the gas phase. Also in absence of inter-residue interactions, small distortions from the planarity are more a rule than an exception, and they are mainly determined by the backbone ψ dihedral angle. These indications are fully corroborated by a statistical survey of accurate protein/peptide structures. Orbital analysis shows that orbital interactions between the σ system of C(α) substituents and the π system of the amide bond are crucial for the modulation of peptide bond distortions. Our study thus indicates that, although long-range inter-molecular interactions can obviously affect the peptide planarity, their influence is statistically averaged. Therefore, the variability of peptide bond geometry in proteins is remarkably reproduced by extremely simplified systems since local factors are the main driving force of these observed trends. The implications of the present findings for protein structure determination, validation and prediction are also discussed.

Cooperative activation of alkyne and thioamide functionalities; direct catalytic asymmetric conjugate addition of terminal alkynes to α,β-unsaturated thioamides

A detailed study of the direct catalytic asymmetric conjugate addition of terminal alkynes to α,β-unsaturated thioamides is described. A soft Lewis acid/hard Brønsted base cooperative catalyst, comprising [Cu(CH(3)CN)(4)]PF(6), bisphosphine ligand, and Li(OC(6)H(4)-p-OMe) simultaneously activated both substrates to compensate for the low reactivity of copper alkynylide. A series of control experiments revealed that the intermediate copper-thioamide enolate functioned as a Brønsted base to generate copper alkynylide from the terminal alkyne, thus driving the catalytic cycle through an efficient proton transfer between substrates. These findings led to the identification of a more convenient catalyst using potassium hexamethyldisilazane (KHMDS) as the Brønsted base, which was particularly effective for the reaction of silylacetylenes. Divergent transformation of the thioamide functionality and a concise enantioselective synthesis of a GPR40 receptor agonist AMG-837 highlighted the synthetic utility of the present catalysis.

Stability of medium-bridged twisted amides in aqueous solutions

"Twisted" amides containing nonstandard dihedral angles are typically hypersensitive to hydrolysis, a feature that has stringently limited their utility in water. We have synthesized a series of bridged lactams that contain a twisted amide linkage but exhibit enhanced stability in aqueous environments. Many of these compounds were extracted unchanged from aqueous mixtures ranging from the strongly basic to the strongly acidic. NMR experiments showed that tricyclic lactams undergo reversible hydrolysis at extreme pH ranges but that a number of compounds in this structure class are indefinitely stable under physiologically relevant pH conditions; one bicyclic example was additionally water-soluble. We examined the effect of structure on the reversibility of amide bond hydrolysis, which we attributed to the transannular nature of the amino acid analogs. These data suggest that medium-bridged lactams of these types should provide useful platforms for studying the behavior of twisted amides in aqueous systems.

Computational evidence that hyperconjugative interactions are not responsible for the anomeric effect

The 'anomeric effect' is the thermodynamic preference for polar substituents to occupy the axial position in the chair conformation of various heterocycles. The most common explanation given for this effect at present is hyperconjugation from the lone pairs on the ring heteroatom to the antibonding orbital between the anomeric carbon and its linking substituent. Alternatively, the anomeric effect could be explained by intramolecular electrostatic interactions between local dipoles. Few models can provide convincing data for either theory at the quantum-mechanical level. Now, using the extended block-localized wavefunction method, which is the simplest form of valence bond theory, we have evaluated the degree of hyperconjugation in various compounds that display the anomeric effect and have interpreted their conformational preferences in terms of steric, hyperconjugation and dispersion effects. The results provide strong evidence that hyperconjugative interactions are not responsible for the anomeric effect and that it is better interpreted in terms of electrostatic interactions.

Synthesis and binding studies of two new macrocyclic receptors for the stereoselective recognition of dipeptides

We present here the design, synthesis, and analysis of a series of receptors for peptide ligands inspired by the hydrogen-bonding pattern of protein β-sheets. The receptors themselves can be regarded as strands 1 and 3 of a three-stranded β-sheet, with cross-linking between the chains through the 4-position of adjacent phenylalanine residues. We also report on the conformational equilibria of these receptors in solution as well as on their tendency to dimerize. ¹H NMR titration experiments are used to quantify the dimerization constants, as well as the association constant values of the 1:1 complexes formed between the receptors and a series of diamides and dipeptides. The receptors show moderate levels of selectivity in the molecular recognition of the hydrogen-bonding pattern present in the diamide series, selecting the α-amino acid-related hydrogen-bonding functionality. Only one of the two cyclic receptors shows modest signs of enantioselectivity and moderate diastereoselectivity in the recognition of the enantiomers and diastereoisomers of the Ala-Ala dipeptide (ΔΔG⁰₁ (DD-DL) = −1.08 kcal/mol and ΔΔG⁰₁ (DD-LD) = −0.89 kcal/mol). Surprisingly, the linear synthetic precursors show higher levels of stereoselectivity than their cyclic counterparts.