Ab initio study of catalyzed and uncatalyzed amide bond formation as a model for peptide bond formation: Ammonia-Glycine reactions

As a model reaction for peptide and bond formation, the S_N2 reactions between glycine and ammonia have been studied with and without amine catalysis: using ab initio molecular-orbital methods. For each of the catalyzed and uncatalyzed reactions, two reaction mechanisms have been examined: a two-step and a concerted mechanism. The stationary points of each reaction, including intermediate and transition states, have been identified and free energies calculated for all geometry-optimized reaction species to determine the thermodynamics and kinetics of the reaction. The calculations demonstrate that a second ammonia molecule catalyzes amide bond formation, and that the two-step mechanism is more favorable than the concerted one for the catalyzed reaction, while for the uncatalyzed reaction both mechanisms are competitive.     

Enantioselection in peptide bond formation

Selectivity in abiotic condensations of amino acids remains controversial and stereochemically little explored. We find that competitive activated couplings of N-acyl derivatives of glycine, alanine, valine, proline and phenylalanine with binary, ternary and quaternary mixtures of amides and esters of the same group of amino acids show little selectivity among the reactants, except with respect to configuration, where a consistent and significant preference for heterochiral outcomes, mostly > 80%, is observed. One possible explanation of this selectivity predicts a predisposition to homochiral coupling under conditions that would require the two carboxyl functions to be co-facial in the activated complex.     

Quantum-mechanical study on the mechanism of peptide bond formation in the ribosome

Ribosomes transform the genetic information encoded within genes into proteins. In recent years, there has been much progress in the study of this complex molecular machine, but the mechanism of peptide bond formation and the origin of the catalytic power of this ancient enzymatic system are still an unsolved puzzle. A quantum-mechanical study of different possible mechanisms of peptide synthesis in the ribosome has been carried out using the M06-2X density functional. The uncatalyzed processes in solution have been treated with the SMD solvation model. Concerted and two-step mechanisms have been explored. Three main points suggested in this work deserve to be deeply analyzed. First, no zwitterionic intermediates are found when the process takes place in the ribosome. Second, the proton shuttle mechanism is suggested to be efficient only through the participation of the A2451 2'-OH and two crystallographic water molecules. Finally, the mechanisms in solution and in the ribosome are very different, and this difference may help us to understand the origin of the efficient catalytic role played by the ribosome.     

Solid phase peptide templated glycosidic bond formation

Glycosylation reactions performed between a glycosyl donor and acceptor covalently linked to a peptide template both in the solution and solid phase give similar yields and product distributions. The adoption of a solid phase approach opens the way for the synthesis of libraries of peptide templates in an attempt to screen for particular peptide sequences that effect complete regio-and stereochemical control during glycosidic bond formation, whilst the use of second generation donors allows the possibility of an iterative approach.     

Effect of copper salts on peptide bond formation using peptide thioesters

[reaction: see text] In the present paper, systematic studies revealed that Cu(I) salts in general and Cu(II) salts under certain circumstances promote effective reaction between peptide thiol esters and the N-terminal amino function of a second peptide segment to give the native amide bond for both solution- and solid-phase syntheses. Chiral integrity was retained. Reaction conditions were optimized and applied to the synthesis of a small protein, the identity of which was confirmed by NMR analysis.     

Detection of bond formations by DNA-programmed chemical reactions and PCR amplification

A system capable of performing both DNA-templated chemical reactions and detection of bond formations is reported. Photocleavable DNA templates direct reactions. Products from bond-forming events re-ligate original templates, amplifiable by PCR, therefore distinguishing bond formation from background. This system provides a novel approach for discovering potential new chemical reactions.     

Palladium fluoride complexes: one more step toward metal-mediated C-F bond formation

The first molecular complexes of palladium containing a Pd-F bond, both fluorides and bifluorides, were synthesized and fully characterized in the solid state and in solution. Reactivity studies of the Pd fluoride complexes revealed their unexpected stability and unusual chemical properties, different from the hydroxo, chloro, bromo, and iodo analogues. A novel efficient method to generate "naked fluoride" was developed using [(Ph(3)P)(2)Pd(F)Ph]. The naked fluoride from the Pd source fluorinated dichloromethane, deprotonated chloroform, and catalyzed di- and trimerization of hexafluoropropene under uncommonly mild conditions.     

Chemoselective peptide bond formation using formyl-substituted nitrophenylthio ester

A novel method for peptide bond formation utilizing amino acid 2-formyl-4-nitrophenylthio ester has been developed. The reaction can be performed in water-containing media and is compatible with various types of amino acid side-chain functional groups. Use of N-methylmaleinimide as an additive is essential for the reaction to proceed with high efficiency. It captures liberated formyl-substituted thiophenol through 1,4-addition followed by aldol cyclization.     

Carboncarbon bond ligation between β-cyclodextrin and peptide by photo-irradiation

The formation of a stable covalent bond between β-cyclodextrin and different diphenyl-ketones (para-benzoylphenylalanine (pBz)Phe, para-benzoylbenzoic acid, pBzBz, and ketoprofen, KPF, under photo-irradiation is reported. These photo-probes have been incorporated into five peptides PEP1=Ac-Arg-Lys-Asp-Val-(pBz)Phe-NH₂; PEP2=Ac-Arg-Lys-Val-(pBz)Phe-NH₂; PEP3=Arg-Pro-(KPF)Lys-Pro-Gln-Gln-Phe-Phe-Gly-Leu-Met-NH₂; PEP4=N-(KPF)Arg-Pro-Lys-Pro-Gln-Gln-Phe-Phe-Gly-Leu-Met-NH₂; PEP5=Biot(O₂)-Apa-Arg-Arg-Pro-(pBzBz)Lys-Pro-Gln-Gln-Phe-Phe-Gly-Leu-Met(O₂)-NH₂. The carboncarbon ligation occurs both in solution and in solid state and whatever the position of the diphenyl ketone, the ketyl radical is able to recombinate with β-cyclodextrin radical even in solid state. Photochemistry of diphenylketone is a complementary and orthogonal approach to chemical modifications of primary hydroxyl functions of β-cyclodextrin.     

Unusual bond formation in aspartic protease inhibitors: a theoretical study

The origin of the formation of the weak bond N|C...O involved in an original class of aspartic protease inhibitors was investigated by means of the electron localization function (ELF) and explicitly correlated wave-function (MRCI) analysis. The distance between the electrophilic C and the nucleophilic N centers appears to be controlled directly by the polarity and proticity of the medium. In light of these investigations, an unusual dative N-C bonding picture was characterized. Formation of this bond is driven by the enhancement of the ionic contribution C(+)-O(-) induced mainly by the polarization effect of the near N lone pair, and to a lesser extent by a weak charge delocalization N-->CO. Although the main role of the solvating environment is to stabilize the ionic configuration, the protic solvent can enhance the C(+)-O(-) configuration through a slight but cumulative charge transfer towards water molecules in the short N-C distance regime. Our revisited bond scheme suggests the possible tuning of the N-CO interaction in the design of specific inhibitors.     

Staudinger ligation: a peptide from a thioester and azide

[reaction: see text] The technique of native chemical ligation enables the total chemical synthesis of proteins. This method is limited, however, by an absolute requirement for a cysteine residue at the ligation juncture. Here, this restriction is overcome with a new chemical ligation method in which a phosphinobenzenethiol is used to link a thioester and azide. The product is an amide with no residual atoms.     

Theoretical study of environmental effects on proton transfer reaction through the peptide bond in a model system

This study considered the possibility of proton transfer reactions through the peptide bond under different environments using the dipeptide and the 12-mer polyglycine α-helix models, in which diglycine is substituted by the 12-mer polyglycine helix. Ab initio molecular orbital calculations were carried out at the B3LYP/6-31+G(d) level of theory. To evaluate the free energies in solution, calculations of the solvation energies were performed using PCM. The correction functions on the calculated solvation energies were provided to reproduce experimental pKa values. The proton transfer reactions through the peptide bond are concluded to be possible in the protein for a wide range of proton acceptors. His complex has two free energy minima along a putative proton transfer pathway in spite of one minimum in the other complexes. The α-helix is estimated to suppress the proton transfer reactions through the peptide bond at the termini of the helix, although it is possible to proceed when the proton affinity of the acceptor is low. Contribution to the Mark S. Gordon 65th Birthday Festschrift Issue.     

Biomimetic peptide bond formation in water with aminoacyl phosphate esters

Aminoacyl phosphates, biomimetic analogues of aminoacyl adenylates, react efficiently with amino acid esters to form dipeptides with retention of stereochemical integrity. The reactions are selective and occur readily in the presence of nucleophiles other than amino groups on their side chains. Aminoacyl phosphate esters that lack an amino-protecting group are also suitable for peptide bond formation, leading to a simplified overall process.     

A theoretical study of carbon-carbon bond formation by a Michael-type addition

A theoretical study of the Michael-type addition of 1,3-dicarbonyl compounds to α,β-unsaturated carbonyl compounds has been performed in the gas phase by means of the AM1 semiempirical method and by density functional theory (DFT) calculations within the B3LYP and M06-2X hybrid functionals. A molecular model has been selected to mimic the role of a base, which is traditionally used as a catalyst in Michael reactions, an acetate moiety to modulate its basicity, and point charges to imitate the stabilization of the negative charge developed in the substrate during the reaction when taking place in enzymatic environments. Results of the study of six different reactions obtained at the three different levels of calculations show that the reaction takes place in three steps: in the first step the α proton of the acetylacetone is abstracted by the base, then the nucleophilic attack on the β-carbon of the α,β-unsaturated carbonyl compound takes place generating the negatively charged enolate intermediate, and finally the product is formed through a proton transfer back from the protonated base. According to the energy profiles, the rate limiting step corresponds to the abstraction of the proton or the carbon-carbon bond formation step, depending on substituents of the substrates and method of calculation. The effect of the substituents on the acidity of the α proton of the acetylacetone and the steric hindrance can be analyzed by comparing these two separated steps. Moreover, the result of adding a positive charge close to the center that develops a negative charge during the reaction confirms the catalytic role of the oxyanion hole proposed in enzyme catalysed Michael-type additions. Stabilization of the intermediate implies, in agreement with the Hammond postulate, a reduction of the barrier of the carbon-carbon bond formation step. Our results can be used to predict the features that a new designed biocatalyst must present to efficiently accelerate this fundamental reaction in organic synthesis.     

Phosphorus pentoxide for amide and peptide bond formation with minimal by-products

Phosphorus pentoxide and DMAP are used for amide bond formation from carboxylic acids and amines. Dipeptides and amides have been synthesized using this reagent in 42–77% yields and >99% ees. The protocol is attractive as it occurs at ambient temperature, the formation of organic by-products is minimal and the reagent can be readily quenched using water. Furthermore, excellent enantioselectivities are observed without the use of harsh triazole based additives.     

Quantum chemical studies of a model for peptide bond formation. 3. Role of magnesium cation in formation of amide and water from ammonia and glycine

The SN2 reaction between glycine and ammonia molecules with magnesium cation Mg2+ as a catalyst has been studied as a model reaction for Mg(2+)-catalyzed peptide bond formation using the ab initio Hartree-Fock molecular orbital method. As in previous studies of the uncatalyzed and amine-catalyzed reactions between glycine and ammonia, two reaction mechanisms have been examined, i.e., a two-step and a concerted reaction. The stationary points of each reaction including intermediate and transition states have been identified and free energies calculated for all geometry-optimized reaction species to determine the thermodynamics and kinetics of each reaction. Substantial decreases in free energies of activation were found for both reaction mechanisms in the Mg(2+)-catalyzed amide bond formation compared with those in the uncatalyzed and amine-catalyzed amide bond formation. The catalytic effect of the Mg2+ cation is to stabilize both the transition states and intermediate, and it is attributed to the neutralization of the developing negative charge on the electrophile and formation of a conformationally flexible nonplanar five-membered chelate ring structure.     

Self-assembly of peptide scaffolds in biosilica formation: computer simulations of a coarse-grained model

The self-assembly of model peptides is studied using Brownian dynamics computer simulations. A coarse-grained, bead-spring model is designed to mimic silaffins, small peptides implicated in the biomineralization of certain silica diatom skeletons and observed to promote the formation of amorphous silica nanospheres in vitro. The primary characteristics of the silaffin are a 15 amino acid hydrophilic backbone and two modified lysine residues near the ends of the backbone carrying long polyamine chains. In the simulations, the model peptides self-assemble to form spherical clusters, networks of strands, or bicontinuous structures, depending on the peptide concentration and effective temperature. The results indicate that over a broad range of volume fractions (0.05-25%) the characteristic structural lengthscales fall in the range 12-45 nm. On this basis, we suggest that self-assembled structures act as either nucleation points or scaffolds for the deposition of 10-100 nm silica-peptide building blocks from which diatom skeletons and synthetic nanospheres are constructed.     

One-electron reductive template-directed ligation of oligodeoxynucleotides possessing a disulfide bond

Hypoxic X-radiolysis of diluted aqueous solutions was performed to generate hydrated electrons that induced one-electron reduction of oligodeoxynucleotides (ODNs) possessing a disulfide bond. Upon hypoxic irradiation of dinucleotides, two forms of dinucleotides were produced via intermolecular exchange of the disulfides and ligation that proceeded with a multiple turnover. In contrast to the efficient reaction induced by hypoxic irradiation, the reaction efficiency was dramatically decreased when irradiation was performed under aerobic conditions, presumably due to capturing reactive hydrated electrons by molecular oxygen. We subsequently applied these unique reaction characteristics to template-directed ligation. In the presence of a complementary template ODN, two ODNs possessing a disulfide bond produced a prescribed ODN with high regioselectivity via interstrand crossing upon hypoxic irradiation.