Reaction mechanism of the acidic hydrolysis of highly twisted amides: Rate acceleration caused by the twist of the amide bond

We present an ab initio study of the acid hydrolysis of a highly twisted amide and a planar amide analogue. The aim of these studies is to investigate the effect that the twist of the amide bond has on the reaction barriers and mechanism of acid hydrolysis. Concerted and stepwise mechanisms were investigated using density functional theory and polarizable continuum model calculations. Remarkable differences were observed between the mechanism of twisted and planar amide, due mainly to the preference for N-protonation of the former and O-protonation of the latter. In addition, we were also able to determine that the hydrolytic mechanism of the twisted amide will be pH dependent. Thus, there is a preference for a stepwise mechanism with formation of an intermediate in the acid hydrolysis, whereas the neutral hydrolysis undergoes a concerted-type mechanism. There is a nice agreement between the characterized intermediate and available X-ray data and a good agreement with the kinetically estimated rate acceleration of hydrolysis with respect to analogous undistorted amide compounds. This work, along with previous ab initio calculations, describes a complex and rich chemistry for the hydrolysis of highly twisted amides as a function of pH. The theoretical data provided will allow for a better understanding of the available kinetic data of the rate acceleration of amides upon twisting and the relation of the observed rate acceleration with intrinsic differential reactivity upon loss of amide bond resonance.     

Combined Inhibitor Free‐Energy Landscape and Structural Analysis Reports on the Mannosidase Conformational Coordinate

Mannosidases catalyze the hydrolysis of a diverse range of polysaccharides and glycoconjugates, and the various sequence‐based mannosidase families have evolved ingenious strategies to overcome the stereoelectronic challenges of mannoside chemistry. Using a combination of computational chemistry, inhibitor design and synthesis, and X‐ray crystallography of inhibitor/enzyme complexes, it is demonstrated that mannoimidazole‐type inhibitors are energetically poised to report faithfully on mannosidase transition‐state conformation, and provide direct evidence for the conformational itinerary used by diverse mannosidases, including β‐mannanases from families GH26 and GH113. Isofagomine‐type inhibitors are poor mimics of transition‐state conformation, owing to the high energy barriers that must be crossed to attain mechanistically relevant conformations, however, these sugar‐shaped heterocycles allow the acquisition of ternary complexes that span the active site, thus providing valuable insight into active‐site residues involved in substrate recognition.     

Computational spectroscopy of ubiquitin: comparison between theory and experiments

Using the constrained molecular dynamics simulation method in combination with quantum chemistry calculation, Hessian matrix reconstruction, and fragmentation approximation methods, the authors have established computational schemes for numerical simulations of amide I IR absorption, vibrational circular dichroism (VCD), and two-dimensional (2D) IR photon echo spectra of the protein ubiquitin in water. Vibrational characteristic features of these spectra in the amide I vibration region are discussed. From the semiempirical quantum chemistry calculation results on an isolated ubiquitin, amide I local mode frequencies and vibrational coupling constants were fully determined. It turns out that the amide I local mode frequencies of ubiquitin in both gas phase and aqueous solution are highly heterogeneous and site dependent. To directly test the quantitative validity of thus obtained spectroscopic properties, they compared the experimentally measured amide I IR, 2D IR, and electronic circular dichroism spectra with experiments, and found good agreements between theory and experiments. However, the simulated VCD spectrum is just qualitatively similar to the experimentally measured one. This indicates that, due to delicate cancellations between the positive and negative VCD contributions, the prediction of protein VCD spectrum is critically relied on quantitative accuracy of the theoretical model for predicting amide I local mode frequencies. On the basis of the present comparative investigations, they found that the site dependency of amide I local mode frequency, i.e., diagonal heterogeneity of the vibrational Hamiltonian matrix in the amide I local mode basis, is important. It is believed that the present computational methods for simulating various vibrational and electronic spectra of proteins will be of use in further refining classical force fields and in addressing the structure-spectra relationships of proteins in solution.     

Nickel‐Catalyzed Synthesis of Dialkyl Ketones from the Coupling of N‐Alkyl Pyridinium Salts with Activated Carboxylic Acids

While ketones are among the most versatile functional groups, their synthesis remains reliant upon reactive and low‐abundance starting materials. In contrast, amide formation is the most‐used bond‐construction method in medicinal chemistry because the chemistry is reliable and draws upon large and diverse substrate pools. A new method for the synthesis of ketones is presented here that draws from the same substrates used for amide bond synthesis: amines and carboxylic acids. A nickel terpyridine catalyst couples N‐alkyl pyridinium salts with in situ formed carboxylic acid fluorides or 2‐pyridyl esters under reducing conditions (Mn metal). The reaction has a broad scope, as demonstrated by the synthesis of 35 different ketones bearing a wide variety of functional groups with an average yield of 60±16 %. This approach is capable of coupling diverse substrates, including pharmaceutical intermediates, to rapidly form complex ketones.     

Hydrolysis of Amides Catalyzed by 4‐Heterocyclohexanones: Small Molecule Mimics of Serine Proteases

The base‐promoted hydrolysis of amide substrates that contain a thiol substituent in the position α to the amide carbonyl group is effectively catalyzed by 4‐heterocyclohexanones [Eq. (1)]. The proposed mechanism of the hydrolysis reaction mimics that employed by serine proteases, and involves equilibrium binding of the substrate to the catalyst, formation of an acyl‐catalyst intermediate, and deacylation of the intermediate to release the product and regenerate the catalyst.     

Mechanical Activation Drastically Accelerates Amide Bond Hydrolysis,Matching Enzyme Activity

Amide bonds, which include peptide bonds connecting amino acids in proteins and polypeptides, give proteins and synthetic polyamides their enormous strength. Although proteins and polyamides sustain mechanical force in nature and technology, how forces affect amide and peptide bond stability is still unknown. Using single‐molecule force spectroscopy, we discover that forces of only a few hundred pN accelerate amide hydrolysis 10⁹‐fold, an acceleration hitherto only known from proteolytic enzymes. The drastic acceleration at low force precedes a moderate additional acceleration at nN forces. Quantum mechanochemical ab initio calculations explain these experimental results mechanistically and kinetically. Our findings reveal that, in contrast to previous belief, amide stability is strongly force dependent. These calculations provide a fundamental understanding of the role of mechanical activation in amide hydrolysis and point the way to potential applications from the recycling of macromolecular waste to the design of bioengineered proteolytic enzymes.     

Unveiling the Neutral Forms of Glutamine

Neutral glutamine has been evaporated by laser ablation of its solid sample to seed a rare gas carrier prior to a supersonic expansion and proved by Fourier transform microwave techniques. We report on three distinct neutral conformers that show a singular non‐interacting and flexible amide sidechain in contrast with the other proteinogenic aliphatic amino acids. It could explain the essential biological role of glutamine as a nitrogen source, and its unique ability to form a variety of hydrogen bonds with peptide backbones. Common computational methods fail to predict the delicate balance of intramolecular interactions controlling the geometry of the most stable conformer. The spectroscopic data here reported can be used to benchmark novel computational methods in quantum chemistry.     

Ab Initio Calculation of Rate Constants for Molecule–Surface Reactions with Chemical Accuracy

The ab initio prediction of reaction rate constants for systems with hundreds of atoms with an accuracy that is comparable to experiment is a challenge for computational quantum chemistry. We present a divide‐and‐conquer strategy that departs from the potential energy surfaces obtained by standard density functional theory with inclusion of dispersion. The energies of the reactant and transition structures are refined by wavefunction‐type calculations for the reaction site. Thermal effects and entropies are calculated from vibrational partition functions, and the anharmonic frequencies are calculated separately for each vibrational mode. This method is applied to a key reaction of an industrially relevant catalytic process, the methylation of small alkenes over zeolites. The calculated reaction rate constants (free energies), pre‐exponential factors (entropies), and enthalpy barriers show that our computational strategy yields results that agree with experiment within chemical accuracy limits (less than one order of magnitude).     

Polyamide synthesis from 6-aminocapronitrile, part 1: N-alkyl amide formation by amine amidation of a hydrolyzed nitrile

The synthesis of N-hexylpentanamide from a stoichiometric amount of pentanenitrile and hexylamine has been studied as a model reaction for the synthesis of nylon-6 from 6-aminocapronitrile. The reaction was carried out under mild hydrothermal conditions and in the presence of a homogeneous ruthenium catalyst. For the mild hydrothermal conditions the presence of hexylamine distinctively increases the nitrile hydrolysis compared to the nitrile hydrolysis in the absence of hexylamine. Amine-catalyzed nitrile hydrolysis mainly produces the N-substituted amide. A clear product development is observed, consisting of first the terminal amide formation and second the accumulation of N-hexylpentanamide. With a maximum conversion of only 80 % after 18 h, the nitrile hydrolysis rate at 230 degrees C is still much too low for nylon-6 synthesis. Ruthenium dihydride phosphine was therefore used as a homogeneous catalyst, which significantly increases the nitrile hydrolysis rate. At a temperature of 140 degrees C and with only 0.5 mol % [RuH(2)(PPh(3))(4)] a 60 % nitrile conversion is already reached within 2 h. Initially the terminal amide is the sole product, which is gradually converted into N-hexylpentanamide. The reaction has a high initial rate, however, for higher conversions a strong decrease in hydrolysis rate is observed. This is ascribed to product inhibition, which results from the equilibrium nature of the reaction.     

Efficient Formation of Luminescent Lanthanide(III) Complexes by Solid‐Phase Synthesis and On‐Resin Screening

Time‐resolved luminescence measurements of luminescent lanthanide complexes have advantages in biological assays and high‐throughput screening, owing to their high sensitivity. In spite of the recent advances in their energy‐transfer mechanism and molecular‐orbital‐based computational molecular design, it is still difficult to estimate the quantum yields of new luminescent lanthanide complexes. Herein, solid‐phase libraries of luminescent lanthanide complexes were prepared through amide‐condensation and Pd‐catalyzed coupling reactions and their luminescent properties were screened with a microplate reader. Good correlation was observed between the time‐resolved luminescence intensities of the solid‐phase libraries and those of the corresponding complexes that were synthesized by using liquid‐phase chemistry. This method enabled the rapid and efficient development of new sensitizers for Sm^III, Eu^III, and Tb^III luminescence. Thus, solid‐phase combinatorial synthesis combined with on‐resin screening led to the discovery of a wide variety of luminescent sensitizers.     

Carbonyl Compounds′ Journey to Amide Bond Formation

The formation of amide bonds is one of the most stimulating emerging areas in organic and medicinal chemistry. Amides are recognized as central building blocks in a plethora of interesting pharmaceuticals, proteins, peptides, polymers, natural products, functional materials, and biologically relevant carbocyclic or heterocyclic molecules, and they are also found in a variety of industrial fields. Therefore, a review of recent developments and challenges in the formation of amide bonds from carbonyl compounds is particularly important. Herein, we have scrutinized a range of metal‐catalyzed and metal‐free approaches for the synthesis of amides from aldehydes, ketones, and oximes. In addition, this Minireview highlights relevant mechanistic studies, as well as the potential applications of these methods in the synthesis of candidate drug molecules. We hope that the data compiled herein will encourage further progress in this notable area of chemistry research.     

Water-promoted hydrolysis of a highly twisted amide: rate acceleration caused by the twist of the amide bond

The water-promoted hydrolysis of a highly twisted amide is studied using density functional theory in conjunction with a continuum dielectric method to introduce bulk solvent effects. The aim of these studies is to reveal how the twisting of the C-N bond affects the neutral hydrolysis of amides. To do so, both concerted and stepwise mechanisms are studied and the results compared to the ones from the hydrolysis of an undistorted amide used as reference. In addition, an extra explicit water molecule that assists in the required proton-transfer processes is taken into account. Our results predict important rate accelerations of the neutral hydrolysis of amides when the C-N bond is highly twisted, the corresponding barrier relaxation depending on the specific reaction pathway and transition state involved. Moreover, our calculations strongly suggest a change in reaction mechanism with degree of amide bond twist, and clearly point to a concerted mechanism at neutral pH for the hydrolysis of highly twisted amides. In addition, the twisting of the amide bond also provokes a higher dependence on an auxiliary water molecule for the concerted mechanism, due to the orthogonality of the lone pair of the nitrogen and the carbonyl pi orbital. There is a direct implication of these findings for biological catalytic mechanism of peptide cleavage reactions that undergoes ground-state destabilization of the peptide.     

Quantitative α‐Alkylation of Primary Nitriles

A synthetic pathway that produces alkyl α,ω‐cyanodiolefins in quantitative yield is described, applying chemistry that is based on simple α‐alkylation of alkyl nitriles. Three amide bases, lithium 2,2,6,6‐tetramethylpiperidide, lithium diisopropylamide, and sodium amide, are used to create the α‐carbanions that undergo substitution with various alkylating agents. Optimization leads to essentially quantitative conversions for every substrate/example reported herein, which will prove useful in many synthetic schemes.     

Living cationic polymerization of amide‐functional vinyl ethers: Specific properties of SnCl4‐based initiating system

Living cationic copolymerization of amide‐functional vinyl ethers with isobutyl vinyl ether (IBVE) was achieved using SnCl₄ in the presence of ethyl acetate at 0 °C: the number–average molecular weight of the obtained polymers increased in direct proportion to the monomer conversion with relatively low polydispersity, and the amide‐functional monomer units were introduced almost quantitatively. To optimize the reaction conditions, cationic polymerization of IBVE in the presence of amide compounds, as a model reaction, was also examined using various Lewis acids in dichloromethane. The combination of SnCl₄ and ethyl acetate induced living cationic polymerization of IBVE at 0 °C when an amide compound, whose nitrogen is adjacent to a phenyl group, was used. The versatile performance of SnCl₄ especially for achieving living cationic polymerization of various polar functional monomers was demonstrated in this study as well as in our previous studies. Thus, the specific properties of the SnCl₄ initiating system are discussed by comparing with the Et_xAlCl_3?x systems from viewpoints of hard and soft acids and bases principle and computational chemistry. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 6129–6141, 2008     

Amide‐Directed Tandem C?C/C?N Bond Formation through C?H Activation

The transformation of C? H bonds into other chemical bonds is of great significance in synthetic chemistry. C? H bond‐activation processes provide a straightforward and atom‐economic strategy for the construction of complex structures; as such, they have attracted widespread interest over the past decade. As a prevalent directing group in the field of C? H activation, the amide group not only offers excellent regiodirecting ability, but is also a potential C? N bond precursor. As a consequence, a variety of nitrogen‐containing heterocycles have been obtained by using these reactions. This Focus Review addresses the recent research into the amide‐directed tandem C? C/C? N bond‐formation process through C? H activation. The large body of research in this field over the past three years has established it as one of the most‐important topics in organic chemistry.     

Kinetics of alkaline hydrolysis of organic esters and amides in neutrally-buffered solution

Reaction rate constants for the hydrolysis of organic esters and amides were determined at temperatures of 100–240°C in aqueous solutions buffered at pH values between 5.5 and 7.3. Experiments are modeled assuming alkaline hydrolysis with a thermodynamic solution model included to account for the temperature dependence of hydroxide ion concentration. In most cases, the ester hydrolysis second order rate constants agree well with published values from experiments in strongly basic solutions at pH values from 11 to 14 and temperatures from 25–80°C, despite the large extrapolations required to compare the data sets. The amide hydrolysis rate constants are about one order of magnitude higher than the extrapolated results from other investigators, but the reaction rate increased proportionally with hydroxide ion concentration, suggesting that an alkaline hydrolysis mechanism is also appropriate. These data establish the validity of the alkaline hydrolysis mechanism and can be used to predict hydrolysis reaction rates in neutrally-buffered solutions such as many groundwater and geothermal fluids.     

The Nature of Crosslinking in N‐Vinylformamide Free‐Radical Polymerization

N‐Vinylformamide (NVF) free‐radical polymerization was found to form polymer gels at high conversions both in bulk and in solution. The polymerization was conducted at different temperatures, monomer and initiator concentrations to show the gelation conditions. Gel fractions and gel swelling ratios were also measured after separating the gel from the polymer samples. In order to confirm the crosslinking unit, a series of hydrolysis experiments were conducted on the gel samples. The hydrolysis results showed that the crosslinks in PNVF gels could be destroyed by alkaline hydrolysis. The most appropriate explanation to this fact is that crosslinking takes place via the amide group.     

Composition and structure of activated complexes in stereoselective deprotonation of cyclohexene oxide by a mixed dimer of chiral lithium amide and lithiated imidazole

Stereoselective deprotonation of cyclohexene oxide, using a mixed dimer built of the chiral lithium amide, lithium (1R,2S)-N-methyl-1-phenyl-2-pyrrolidinyl-propanamide, and 2-lithio-1-methylimidazole, has been studied. The composition of the rate limiting activated complex was determined by kinetics to be built from one mixed dimer molecule and one epoxide molecule. Based on this knowledge computational chemistry has been applied to gain insight into possible structures of the activated complexes.     

A Versatile Approach to Dynamic Amide Bond Formation with Imine Nucleophiles

Dynamic covalent chemistry has rapidly become an important approach to access supramolecular structures. While the products generated in these reactions are held together by covalent bonds, the reversible nature of the transformations can limit the utility of many these systems in creating robust materials. We describe herein a method to form stable and commonly employed amide bonds by exploiting the reversible coupling of imines and acyl chlorides. The reaction employs easily accessible reagents, is dynamic under ambient conditions, without catalysts, and can be trapped with simple hydrolysis. This offers an approach to create broad families of amide products under thermodynamic control, including the selective formation of amide macrocycles or polymers.     

Kinetic isotope effects in the active site of B. subtilis chorismate mutase

Kinetic isotope effects are determined for the enzyme‐catalyzed Claisen rearrangement of chorismate to prephenate using computational methods. The calculated kinetic isotope effects (KIEs) compare reasonably with the few available experimental values with both the theory and experiment obtaining a large KIE for the ether oxygen, indicating large polarization of the transition‐state geometry. Because there is a question of the extent that the experimental rate constants are for chemistry as the rate‐limiting step, the KIEs for all the atoms of the substrate are reported with the exception of the carboxylate groups. A substantial number of large regular and inverse isotope effects are predicted for the hydrogens on the cyclohexadienyl ring related to activation of the reactant and charge reorganization in the transition state. A large KIE is predicted for the hydrogen atom bound to the ether carbon atom because the largest valency change and charge transfer occurs at the ether bond in both the reactant and tansition state. Observation of the overall pattern of predicted KIEs would ensure that conditions are favorable for the rate‐limiting chemistry. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 287–292, 2003