Relative stability of major types of beta-turns as a function of amino acid composition: a study based on Ab initio energetic and natural abundance data

Folding properties of small globular proteins are determined by their amino acid sequence (primary structure). This holds both for local (secondary structure) and for global conformational features of linear polypeptides and proteins composed from natural amino acid derivatives. It thus provides the rational basis of structure prediction algorithms. The shortest secondary structure element, the beta-turn, most typically adopts either a type I or a type II form, depending on the amino acid composition. Herein we investigate the sequence-dependent folding stability of both major types of beta-turns using simple dipeptide models (-Xxx-Yyy-). Gas-phase ab initio properties of 16 carefully selected and suitably protected dipeptide models (for example Val-Ser, Ala-Gly, Ser-Ser) were studied. For each backbone fold most probable side-chain conformers were considered. Fully optimized 321G RHF molecular structures were employed in medium level [B3LYP/6-311++G(d,p)//RHF/3-21G] energy calculations to estimate relative populations of the different backbone conformers. Our results show that the preference for beta-turn forms as calculated by quantum mechanics and observed in Xray determined proteins correlates significantly.     

Chiral electrokinetic chromatography using dipeptide polymeric surfactants: present state of the art

Polymeric amino acid based surfactants have been recently employed as pseudostationary phases in capillary electrophoresis. These phases are effective for chiral separation of analytes in different charge states and hydrophobicities. This review paper focuses on polymeric dipeptide surfactants. The benefits of dipeptide over single amino acid micelle polymers are shown. Some aspects of dipeptide surfactants that are presented here includes the amino acid order, effect of number and position of chiral centers, and steric factors on enantiomeric separation of chiral compounds in different charge states. In addition, the preferential site of interaction of the chiral analyte using diastereomers of polymeric dipeptide surfactants is discussed.     

Chiral ferrocene amines derived from amino acids and peptides: synthesis, solution and X-ray crystal structures and electrochemical investigations

For the recognition of all but the simplest naturally occurring molecules, electrochemical sensors based on ferrocene will certainly require chiral centers. To advance the necessary chemistry, this work describes the synthesis and properties of ferrocene derivatives of enantiomerically pure amino acids, peptides, and other chiral amines. Ferrocene aldehyde is condensed with amino acid esters to yield the corresponding Schiff bases 2, which are reduced by NaBH4 in methanol to the ferrocene methyl amino acids 3. An X-ray single-crystal analysis was carried out on the phenylalanine derivative 3a (monoclinic space group P2(1), a = 10.301(1) A, b = 9.647(1) A, c = 18.479(2) A, beta = 102.98(2) degrees, Z = 4). Further peptide chemistry at the C terminus proceeds smoothly as demonstrated by the synthesis of the ferrocene labeled dipeptide Fc-CH2-Phe-Gly-OCH3 5 (Fc = ferrocenyl ((eta-C5H4)Fe(eta-C5H5))). We also report the synthesis of the C,N-bis-ferrocene labeled tripeptide Phe-Ala-Leu and its electrochemical characterization. Starting from the enantiomerically pure ferrocene derivative 9, which was synthesized from ferrocene aldehyde and L-1-amino-ethylbenzene, two diastereomers 10 were obtained by peptide coupling with N-Boc protected D- and L-alanine. There was, however, only very little diastereomeric induction if 0.5 equiv of a racemic mixture of alanine were used. This suggests that amino acid activation rather than coupling is the rate-determining step. A combination of NOESY (nuclear Overhauser effect spectroscopy) spectra and molecular modeling furnished detailed insights into the solution structures of 3, 9, and 10 and was used to rationalize their different reactivity.     

Thermoanalytical study of acid-treated clay containing amino acid immobilized on its surface

The aim of this study is to investigate the incorporation of amino acid molecules in an acid-activated montmorillonite by means of solid characterization after the incorporation of these biomolecules. The acid activation procedure was carried out for the purpose of increasing the acid sites in the clay as well as the impurity elimination in the mineral. Cysteine, aspartic, and glutamic acids were adsorbed on montmorillonite K10 which was previously treated with a hydrochloric acid solution. The clay was put in contact with amino acid solutions at two different concentrations. Each amino acid was adsorbed at identical conditions, with the pH fixed to ensure the charge of molecules and surface clay. The solid was characterized by means of X-ray diffraction, infrared spectroscopy, thermogravimetric analysis, and nitrogen adsorption at 77 K. After the amino acid adsorption, the powders showed changes in their characteristics as well as in their thermal behavior, which depended on both the concentration and the nature of the adsorbed amino acid. The thermal decomposition and elimination of cysteine occurred at a higher temperature than the aspartic and glutamic acid; the complete removal of glutamic acid molecules was not observed at 850 °C. The differences observed in the solid characteristic after the adsorption of each amino acid were discussed. Both the thermoanalytical study and characterization of materials after the interaction with amino acid molecules can be useful to understand the adsorption mechanism of biomolecules on solid surfaces.     

Adsorption of chiral aromatic amino acids onto carboxymethyl-β-cyclodextrin bonded Fe(3)O(4)/SiO(2) core-shell nanoparticles

Surface of magnetic silica nanoparticles is modified by grafting with carboxymethyl-β-cyclodextrin (CM-β-CD) via carbodiimide activation. The functionalized magnetic core-shell nanoparticles (MNPs) are characterized by Transmission Electron Microscopy (TEM), Fourier Transform Infra Red (FTIR) spectroscopy, X-ray Diffraction (XRD), X-ray Photoelectron Spectroscopy (XPS) and Vibrating Sample Magnetometer (VSM). These nano-sized particles are scrutinized for adsorption of certain chiral aromatic amino acid enantiomers namely, d- and l-tryptophan (Trp), d- and l-phenylalanine (Phe) and d- and l-tyrosine (Tyr) from phosphate buffer solutions. Adsorption capacities of the coated magnetic nanoparticles toward amino acid enantiomers are in the order: l-Trp>l-Phe>l-Tyr and under the same condition, adsorption capacities are higher for l-enantiomers than the corresponding d-enantiomers. All the equilibrium adsorption isotherms are fitted well to Freundlich model. FTIR studies depict significant changes after adsorption of amino acids onto nanoparticles. The stretching vibration frequencies of NH bonds of the amino acid molecules are changed with complex formation through host-guest interaction. The structure and hydrophobicity of amino acid molecules emphasize the interactions between amino acid molecules and the nano-adsorbents bearing cyclodextrin, thus play important roles in the difference of their adsorption behaviors.     

Highly Cytotoxic Bioconjugated Gold(I) Complexes with Cysteine‐Containing Dipeptides

Several gold(I) complexes with cysteine‐containing dipeptides have been prepared starting from cystine by coupling different amino acids and using several orthogonal protections. The first step is the reaction of cystine, where the sulfur centre is protected as disulfide, with Boc₂O in order to protect the amino group, followed by coupling of an amino acid ester; finally the disulfide bridge is broken with mercaptoethanol to afford the dipeptide derivative. Further reaction with [AuCl(PPh₃)] gives the gold‐dipeptide‐phosphine species. Starting from these formally gold(I) thiolate–dipeptide phosphine complexes with the general formula [Au(SR)(PR₃)] different structural modifications, such as change in the type of the amino protecting group, the type of phosphine, the number of gold(I) atoms per molecule, or the use of a non‐proteinogenic conformationally restricted amino acid ester, were introduced in order to evaluate their influence in the biological activity of the final complexes. The cytotoxic activity, in vitro, of these complexes was evaluated against different tumour human cell lines (A549, MiaPaca2 and Jurkat). The complexes show an outstanding cytotoxic activity with IC₅₀ values in the very low micromolar range. Structure–activity relationship studies from the complexes open the possibility of designing more potent and promising gold(I) anticancer agents.     

Synthesis and Characterization of Some Amino Acid Derived Schiff Bases Bearing Nonionic Species as Corrosion Inhibitors for Carbon Steel in 2N HCl

A novel series of nonionic amino acid Schiff-Bases were synthesized and characterized using different spectroscopic tools to elucidate their chemical structures. The surface and thermodynamic properties of these compounds were studied using classical measurements including surface and interfacial tension and emulsification tendency. The surface parameters of these compounds including surface tension, critical micelle concentration (CMC), effectiveness (π_cmc), efficiency (Pc₂₀), maximum surface excess (Γ_max), and minimum surface area (A_min) showed their good surface activity. Their thermodynamic parameters of adsorption and micellization including free energy change of micellization and adsorption showed their tendency toward adsorption at the interfaces and also micelle formation at lower concentrations. The synthesized compounds were also evaluated as corrosion inhibitors for carbon steel at different doses (400, 200, 100, 50, and 25 ppm) in 2 N HCl using gravimetric technique (weight loss). The results showed that these inhibitors are characterized by very high corrosion inhibition efficiency ranged between 99.93% and 97.98% and low corrosion rates varied between 0.09 mpy and 0.17 mpy for higher doses (400 ppm). The efficiency of inhibition was decreased by increasing the exposure time. The most efficient corrosion inhibitor of the synthesized compounds was the inhibitor which contains polyethylene oxide chain length of 23 EO units and alkyl chain length of 12 methylene groups. The effect of the hydrophobic and hydrophilic chain length in the inhibitor molecules was discussed and rationalized with their inhibition efficiency. The tendency of these inhibitors toward complexation with the transition metals was also discussed in order to explain their higher efficiency.     

Total synthesis of chlorofusin, its seven chromophore diastereomers, and key partial structures

Chlorofusin is a recently isolated, naturally occurring inhibitor of p53-MDM2 complex formation whose structure is composed of a densely functionalized azaphilone-derived chromophore linked through the terminal amine of ornithine to a nine residue cyclic peptide. Herein we report the full details of the total synthesis of chlorofusin, resulting in the assignment of the absolute stereochemistry and reassignment of the relative stereochemistry of the complex chromophore. Condensation of each enantiomer of an azaphilone chromophore precursor with the N(delta)-amine of a protected ornithine-threonine dipeptide, followed by a one-step oxidation/spirocyclization of the most reactive olefin provided all eight diastereomers of the fully elaborated chromophore-dipeptide conjugate. Comparison of the spectroscopic properties for these eight compounds and those of simpler models with that reported for the natural product allowed the full assignment of the (4R,8S,9R)-stereochemistry of the chlorofusin chromophore. The natural, but stereochemically reassigned, diastereomer of the dipeptide conjugate was incorporated in a convergent total synthesis of chlorofusin confirming the stereochemical reassignment and establishing its absolute stereochemistry. Similarly and enlisting the late stage convergent point in the total synthesis, the remaining seven diastereomers of the chromophore-dipeptide conjugates were individually incorporated into the nine-residue cyclic peptide of chlorofusin (4 steps each) providing all seven remaining possible chromophore diastereomers of the natural product.     

Amino acids and peptides—IV: Novel peptide bond formation catalysed by metal ions—II Formation of optically active peptide esters

The novel peptide bond formation previously reported in the reaction of glycine ester with Cu(II) ion in an anhydrous solvent, was examined using several kinds of optically active amino acid esters. Various reaction conditions were studied in detail for Phe-OEt. From Phe-OEt, Ala-OMe, Leu-OMe, Trp-OMe, Ser-OMe, and Met-OMe, the expected dipeptide esters with the same amino acid components were obtained without racemization. Asp(OEt)-OEt, and Glu(OMe)-OMe gave only optically active α-dipeptide esters. No formation of dipeptide esters was observed with Ile-OMe, Cys-OMe, His-OMe, and Pro-OEt. However, Lys-OMe, and Orn-OMe afforded optically active lactam derivatives. Some explanations of these abnormal observations have been given.Attempts to prepare di- and tri-peptide esters carrying different kinds of amino acid units were also studied.     

Single-Crystal-to-Single-Crystal Topochemical Synthesis of a Collagen-inspired Covalent Helical Polymer

There is much demand for crystalline covalent helical polymers. Inspired by the helical structure of collagen, we synthesized a covalent helical polymer wherein the repeating dipeptide Gly-Pro units are connected by triazole linkages. We synthesized an azide and alkyne-modified dipeptide monomer made up of the repeating amino acid sequence of collagen. In its crystals, the monomer molecules aligned in head-to-tail fashion with proximally placed azide and alkyne forming supramolecular helices. At 60 °C, the monomer underwent single-crystal-to-single-crystal (SCSC) topochemical azide-alkyne cycloaddition polymerization, yielding a covalent helical polymer as confirmed by single-crystal X-ray diffraction (SCXRD) analysis. Compared to the monomer crystals, the polymer single-crystals were very strong and showed three-fold increase in Young's modulus, which is higher than collagen, many synthetic polymers and other materials. The crystals of this covalent helical polymer could bear loads as high as 1.5 million times of their own weight without deformation. These crystals could also withstand high compression force and did not disintegrate even at an applied force of 98 kN. Such light-weight strong materials are in demand for various technological applications.     

The effect of solvation processes on amino acid‐ and peptide‐silica stationary phases

The surface excess adsorption isotherms of water, acetonitrile, and methanol from binary hydro‐organic mobile phases were investigated on nine home‐made stationary phases with chemically bonded amino acids, dipeptides, and tripeptides using the dynamic minor disturbance method. The stationary phases were modified by the following amino acids: glycine, alanine, phenylalanine, leucine, and aspartic acid. We investigated the influence of the type of immobilized amino acids, in particular their different side chains, on the solvent adsorption. The interpretation of solvation phenomena shows significant accumulation of investigated solvents on the adsorbent surface according to their hydrophilic or hydrophobic properties. Moreover, the accumulated amount was dependent on the length and type of amino acid sequences bonded to the silica surface. Stationary phases with bonded amino acids and peptides show stronger water and acetonitrile adsorption in contrast to the stationary phase modified with aminopropyl groups—a support for the synthesis. The comparison of water and acetonitrile adsorption as well as a data obtained with the two‐site adsorption model reveal and confirm the heterogeneity of chemically bonded phases. As a consequence of performed investigations, the classification of tested stationary phases for the potential usage in particular high‐performance liquid chromatography mode was also accomplished.     

Structure and electronic properties of amino acid ionic liquids

The interactions between eight amino acid based anions and four imidazolium-based cations have been investigated by density functional theory. The electronic and structural properties of the resulting amino acid ionic liquids (AAILs) have been unveiled by means of the atoms in molecules framework. The calculated interaction energy was found to increase in magnitude with decreasing alkyl chain length at imidazolium ring. Moreover, AAILs composed of an amino acid with some functional group such as aromatic ring had decreased interaction energy. Finally, several correlative relationships between glass transition temperature and interaction energy as well as density at bond critical point have been checked for 1-ethyl-3-methylimidazolium based ILs. Although the obtained correlations do not show excellent fits, a preliminary estimation of the glass transition temperature of different AAILs can be achieved by use of their electronic properties.     

Hydrophobic contribution of amino acids in peptides measured by hydrophobic interaction chromatography

The adsorption behaviors of amino acids in short chain peptides were examined. Each amino acid, aliphatic or charged, was inserted between the two tryptophans of a peptide, GWWG. The capacity factors of these peptides on an Ocytl-Sepharose column were measured. The adsorption enthalpies, entropies, and the number of repelled water molecules after adsorption were estimated to analyze the contribution of each different amino acid to its hydrophobic adsorption. The peptides inserted with aliphatic amino acids owned the highest capacity factors but released the least amount of adsorption heat among all the peptides under examination. It was found that the hydrophobic contribution of aliphatic amino acids was derived from the entropy gain by repelling the ordered water surrounding them. The insertion of negatively charged amino acids greatly reduced the capacity factors but still repelled a significant number of water molecules after adsorption. This indicated that the water molecules surrounding ionic amino acids were not orderly aligned. The dehydration cost energy but the water repelling did not offer enough entropy to drive the adsorption. Subsequently, lower retention was obtained from the peptides inserted with negatively charged ionic amino acids. The insertion of lysine increased the adsorption enthalpy but repelled no water molecules after adsorption. It was speculated that the inserted lysine still interacted with hydrophobic ligands but disturbed the interaction between ligands and adjacent tryptophans. Therefore, the adsorption enthalpy increased and the capacity factors decreased. Different amino acids contributed to hydrophobic interaction in different ways. The simultaneous analysis of capacity factor, adsorption enthalpy, adsorption entropy, and the number of repelled water molecules facilitated the understanding of the adsorption processes.     

The competitive adsorption of water and toluene on KU-2-8 ion exchanger in the presence of aromatic amino acids

The Weitkamp procedure was used to calculate hydrophobicity indices for several ion exchange systems, including adsorbed aromatic amino acids. The determination of hydrophobicity indices was based on the competitive adsorption of water and toluene from their mixture. Strongly acid KU-2 ion exchanger with hydrophilic properties predominantly sorbed water molecules in the competitive adsorption from their mixture with toluene vapor. The saturation of the ion exchanger with aromatic amino acids substantially decreased its sorption ability because of amino acid structuring and a decrease in permeability. The conclusion was drawn that the saturation of the ion exchanger with amino acids caused not only a decrease in the sorption of water but also a decrease in the sorption of hydrophobic toluene. This contradicted the assertion of an increase in hydrophobicity as a whole.     

Engineering Homochiral Metal–Organic Frameworks by Spatially Separating 1D Chiral Metal–Peptide Ladders: Tuning the Pore Size for Enantioselective Adsorption

The reaction of the chiral dipeptide glycyl‐L(S)‐glutamate with Co^II ions produces chiral ladders that can be used as rigid 1D building units. Spatial separation of these building units with linkers of different lengths allows the engineering of homochiral porous MOFs with enhanced pore sizes, pore volumes, and surface areas. This strategy enables the synthesis of a family of isoreticular MOFs, in which the pore size dictates the enantioselective adsorption of chiral molecules (in terms of their size and enantiomeric excess).     

Reversed-phase high-performance liquid chromatographic separation of diastereomers of (R,S)-mexiletine prepared by microwave irradiation with four new chiral derivatizing reagents based on trichloro-s-triazine having amino acids as chiral auxiliaries and 10 others having amino acid amides

A new series of chiral derivatizing reagents (CDRs) consisting of four dichloro-s-triazine reagents was synthesized by nucleophilic substitution of one chlorine atom in trichloro-s-triazine with amino acids, namely L-Leu, D-Phg, L-Val and L-Ala as chiral auxiliaries. Two other sets of CDRs consisting of four dichloro-s-triazine (DCT) and six monochloro-s-triazine (MCT) reagents were also prepared by nucleophilic substitution of chlorine atom(s) with different amino acid amides as chiral auxiliaries in trichloro-s-triazine and its 6-methoxy derivative, respectively. These 14 CDRs were used for the synthesis of diastereomers of (R,S)-mexiletine under microwave irradiation (i.e. 60s and 90 s at 85% power (of 800 W) using DCT and MCT reagents, respectively), which were resolved by reversed-phase high-performance liquid chromatography using C18 column and gradient eluting mixtures of methanol with aqueous trifluoroacetic acid (TFA) with UV detection at 230 nm. The resolution (R(s)), difference between retention times of resolved diastereomers (Δt) and retention factors (k) obtained for the three sets of diastereomers were compared among themselves and among the three groups. Explanations have been offered for longer retention times and better resolution of diastereomers prepared with DCT reagents in comparison of their MCT counterparts and, for the influence of hydrophobicity of the side chain R of the amino acid in the CDRs on retention times and resolution. The newly synthesized CDRs were observed to be superior as compared to their amide counterparts in terms of providing better resolution and cost effectiveness. The method was validated for limit of detection, linearity, accuracy and precision.     

Peptide mesocrystals as templates to create an Au surface with stronger surface-enhanced Raman spectroscopic properties

The design and fabrication of various nanostructures with predefined geometry and composition is a big challenge of nanotechnology. Here we demonstrate an Au nanoflake film replicated from a self-assembled, well-ordered, dipeptide flower-like hierarchical architecture. Such morphology can give rise to useful and remarkable surface-enhanced Raman spectroscopy (SERS) properties. We obtained these nanostructures by using a scaffold of flake-built spherical dipeptide aggregations. Gold nanoparticles were sputtered on the surface of as-assembled dipeptide by an etching system. After removing the dipeptide templates by ethanol, a metal crust was left with a morphology similar to that of the dipeptide hierarchical structure. The different steps within the process were monitored by using electron microscopy, energy-dispersive spectrum (EDS) analysis and atomic force microscopy (AFM). Cyclic voltammetry and Raman spectra were employed to prove the SERS effect of the obtained Au substrates. The enhancement factor is estimated to be about 10(4) for 4-mercaptobenzoic acid (4-MBA) molecules on the Au nanoflake surfaces.     

Synthesis and chiral discrimination of cyclic aromatic amides and the determination of their absolute configuration by TD-DFT calculations

Novel chiral cyclic molecules composed of aromatic triamides were constructed in modest yield from 4-N-(4′-methoxybenzyl)amino-3-decyloxybenzoic acid using dichlorotriphenylphosphorane, because of the preorganized component of the tertiary benzanilide moieties. A racemic mixture of two diastereomers, syn and anti conformers of cyclic aromatic triamides, was resolved into enantiomers by HPLC using a preparative chiral column. The absolute configuration of each enantiomer in both diastereomers was determined by comparison of the time-dependent density functional theory (TD-DFT) calculated circular dichroic (CD) spectra with the experimentally derived CD spectra recorded on each sample.     

A molecular dynamics study of the dielectric properties of aqueous solutions of alanine and alanine dipeptide

Molecular dynamics simulations were used to compute the frequency-dependent dielectric susceptibility of aqueous solutions of alanine and alanine dipeptide. We studied four alanine solutions, ranging in concentration from 0.13-0.55 mol/liter, and two solutions of alanine dipeptide (0.13 and 0.27 mol/liter). In accord with experiment we find a strong dielectric increment for both solutes, whose molecular origin is shown to be the zwitterionic nature of the solutes. The dynamic properties were analyzed based on a dielectric component analysis into solute, a first hydration shell, and all remaining (bulk) waters. The results of this three component decomposition were interpreted directly, as well as by uniting the solute and hydration shell component to a "suprasolute" component. In both approaches three contributions to the frequency-dependent dielectric properties can be discerned. The quantitatively largest and fastest component arises from bulk water [i.e., water not influenced by the solute(s)]. The interaction between waters surrounding the solute(s) (the hydration shell) and bulk water molecules leads to a relaxation process occurring on an intermediate time scale. The slowest relaxation process originates from the solute(s) and the interaction of the solute(s) with the first hydration shell and bulk water. The primary importance of the hydration shell is the exchange of shell and bulk waters; the self-contribution from bound water molecules is comparatively small. While in the alanine solutions the solute-water cross-terms are more important than the solute self-term, the solute contribution is larger in the dipeptide solutions. In the latter systems a much clearer separation of time scales between water and alanine dipeptide related properties is observed. The similarities and differences of the dielectric properties of the amino acid/peptide solutions studied in this work and of solutions of mono- and disaccharides and of the protein ubiquitin are discussed.     

Reversed-phase high performance liquid chromatographic separation of diastereomers of β-amino alcohols and microwave assisted synthesis of Marfey's reagent,its chiral variants and diastereomers

Ten chiral derivatizing reagents (CDRs) were synthesized by replacing the l-Ala–NH₂ moiety in Marfey's reagent (MR) by seven l-amino acid amides and three l-amino acids employing microwave irradiation (MW) and were characterized. Ten racemic amino alcohols were derivatized with these CDRs under MW. The diastereomers were separated on a reversed-phase C₁₈ column using binary mixtures of acetonitrile with aqueous trifluoroacetic acid (TFA) and triethylammonium phosphate buffer (TEAP). In general, amino acid variants of MR provided better separation of diastereomers in comparison to amino acid amide variants. The method was also found successful for the separation of 20 diastereomers from a mixture.