Thermally Induced Self-Assembly and Cyclization of l-Leucyl-l-Leucine in Solid State

Cyclization of alanyl-valine dipeptides in the solid state. The effects of molecular radiator and heat capacity

Heating of linear dipeptides above a critical temperature initiates their cyclization even in the solid state. This method of obtaining cyclic dipeptides meets the requirements of "green chemistry", provides a high yield of the main product and releases only water as a by-product of the reaction, and does not require solvents. However, to date, the cyclization of only a small number of dipeptides in the solid state has been studied, and some correlations of the process were discovered. The influence of the structure of dipeptide molecules and their crystal packing on the kinetics of solid-state cyclization is still not fully understood. In this work, the cyclization of L-alanyl-L-valine in the solid state upon heating was studied. Using non-isothermal kinetic approaches, the kinetic parameters of this reaction and the optimal kinetic model describing this process were determined. The effect of the features of the crystal packing of dipeptides and their heat capacity on the temperature of the cyclization in the solid state was analyzed. This study expands our knowledge about solid-state reactions involving dipeptides and the ability to control such reactions.

How do cultivar origin and stepwise industrial processing impact Sesamum indicum seeds' metabolome and its paste and in relation to their antioxidant effects? A case study from the sesame industry

Sesame is a valuable crop recognized for its rich composition and myriad of health benefits. The current study attempts to characterize sesame seeds' metabolome in relation to geographical origins i.e., Egypt, Sudan, Nigeria, in addition to samples from paste production lines along its different steps. UPLC-PDA-ESI-qTOF-MS was employed for untargeted profiling and in correlation to antioxidant capacity using DPPH, FRAP and β-carotene-lineolate assays. 139 Peaks were identified, including novel phospholipids and catechol lignan in sesame. Furthermore, discriminatory markers belonging to coumarins, lignans, phenolic and organic acids were revealed among raw accessions, whereas roasted and unroasted seeds were distinguished by sugar, peptide/amino acid, and organic acid contents. Negative processing impact was observed in the loss of lignans during dehulling and decreased antioxidant capacity in sesame paste. However, malic acid in roasted seeds and verbascoside in Nigerian sesame could account for their improved antioxidant effects as revealed using chemometrics.

Identification of heterochirality-mediated stereochemical interactions in peptide architectures

In this work, we illustrate a strategy for constructing heterochiral peptide architectures with distinct structural, mechanical and thermal characteristics. A series of nanotube structures based on diphenylalanine (FF) and its chiral derivatives were examined. Pronounced effects relating to heterochirality on mechanostability and thermal stability can be identified. The homochiral peptide FF and its enantiomer ff formed nanotubes with high thermal and mechanical stabilities (Young's modulus: 20.3 ± 5.9 GPa for FF and 21.2 ± 4.7 GPa for ff). In contrast, heterochiral nanotubes formed by Ff and fF manifest superstructures along the axial direction with differed thermal and mechanical strength (Young's modulus: 7.3 ± 2.4 GPa for Ff and 8.3 ± 2.1 GPa for fF). Combining their single-crystal XRD structure and in silico results, it was demonstrated that the spatial orientations of aromatic moieties were subtly changed by heterochirality of peptide building blocks, which led to intramolecular face-to-face interactions. As the result, both intermolecular axial and interchannel interactions in heterochiral nanotubes were weakened as reflected in the strikingly deteriorated mechanical and thermal stabilities. Conversely, two aromatic side chains of the homochiral peptides were staggered and formed interdigitated steric zippers, which served as strong glues that secured the robustness of nanotubes in both axial and radial orientation. Furthermore, the generality of the heterochiral-mediated stereochemical effects was demonstrated in other "FF class" dipeptides, including fluorinated Ff, FW and FL. Our results unequivocally revealed the relationship between amino acid chirality, peptide molecule packing, and physical stabilities of "FF class" dipeptide self-assembled materials and provide valuable molecular insights into chirality-mediated stereochemical interactions in determining the properties of peptide architectures.

Insights into the Thermally Activated Cyclization Mechanism in a Linear Phenylalanine-Alanine Dipeptide

Dipeptides, the prototype peptides, exist in both linear (l-) and cyclo (c-) structures. Since the first mass spectrometry experiments, it has been observed that some l-structures may turn into the cyclo ones, likely via a temperature-induced process. In this work, combining several different experimental techniques (mass spectrometry, infrared and Raman spectroscopy, and thermogravimetric analysis) with tight-binding and ab initio simulations, we provide evidence that, in the case of l-phenylalanyl-l-alanine, an irreversible cyclization mechanism, catalyzed by water and driven by temperature, occurs in the condensed phase. This process can be considered as a very efficient strategy to improve dipeptide stability by turning the comparatively fragile linear structure into the robust and more stable cyclic one. This mechanism may have played a role in prebiotic chemistry and can be further exploited in the preparation of nanomaterials and drugs.

Diketopiperazine Gels: New Horizons from the Self-Assembly of Cyclic Dipeptides

Cyclodipeptides (CDPs) or 2,5-diketopiperazines (DKPs) can exert a variety of biological activities and display pronounced resistance against enzymatic hydrolysis as well as a propensity towards self-assembly into gels, relative to the linear-dipeptide counterparts. They have attracted great interest in a variety of fields spanning from functional materials to drug discovery. This concise review will analyze the latest advancements in their synthesis, self-assembly into gels, and their more innovative applications.

Exploring the polymorphism, conformational dynamics and function of amyloidogenic peptides and proteins by temperature and pressure modulation

Our understanding of amyloid structures and the mechanisms by which disease-associated peptides and proteins self-assemble into these fibrillar aggregates, has advanced considerably in recent years. It is also established that amyloid fibrils are generally polymorphic. The molecular structures of the aggregation intermediates and the causes of molecular and structural polymorphism are less understood, however. Such information is mandatory to explain the pathological diversity of amyloid diseases. What is also clear is that not only protein mutations, but also the physiological milieu, i.e. pH, cosolutes, crowding and surface interactions, have an impact on fibril formation. In this minireview, we focus on the effect of the less explored physical parameters temperature and pressure on the fibrillization propensity of proteins and how these variables can be used to reveal additional mechanistic information about intermediate states of fibril formation and molecular and structural polymorphism. Generally, amyloids are very stable and can resist harsh environmental conditions, such as extreme pH, high temperature and high pressure, and can hence serve as valuable functional amyloid. As an example, we discuss the effect of temperature and pressure on the catalytic activity of peptide amyloid fibrils that exhibit enzymatic activity.

High-pressure studies on l,l-dileucine crystals by Raman spectroscopy and synchrotron X-ray diffraction combined with DFT calculations

The vibrational properties of the dipeptide l-leucyl-l-leucine hydrate were investigated through Raman and infrared spectroscopy. With the aid of first principle calculations using the density functional theory, the assignment of the vibrational modes from the material was furnished. In addition, the behavior of the crystal under high pressure was investigated using Raman spectroscopy (~8 GPa) and synchrotron X-ray diffraction (~26 GPa). The results show significant changes in both the X-ray diffractogram and the Raman spectra, suggesting that l-leucyl-l-leucine hydrate undergoes a phase transition between 2.3 and 2.9 GPa. Finally, for pressures above 16 GPa the broadening of X-ray peaks suggests a disorder in the crystal lattice induced by high-pressure effects.

Solid-state synthesis of cyclo LD-diphenylalanine: A chiral phase built from achiral subunits

The solid-state structure of LL/DD or LD/DL diphenylalanine diluted in KBr pellets is studied by infrared (IR) absorption and vibrational circular dichroism (VCD) spectroscopy. The structure depends on the absolute configuration of the residues. The natural LL diphenylalanine exists as a mixture of neutral and zwitterionic structures, depending on the humidity of the sample, while mostly the zwitterion is observed for LD diphenylalanine whatever the experimental conditions. The system undergoes spontaneous cyclization upon heating at 125°C, resulting to the formation of a diketopiperazine (DKP) dipeptide as the only product. The reaction is faster for LD than for LL diphenylalanine. As expected, LL and DD diphenylalanine react to form the LL and DD enantiomers of cyclo diphenylalanine. Interestingly, the DKP dipeptides formed from the LD or DL diphenylalanine show unexpected optical activity, with opposite VCD spectra for the products formed from the LD and DL reagents. This is explained in terms of chirality synchronization between the monomers within the crystal, which retain the symmetry of the reagent, resulting to the formation of a new chiral phase made from transiently chiral molecules.

Solid-state polymerization of a novel cyanate ester based on 4-tert-butylcalix[6]arene

Solid-state polymerization of a cyclic cyanate ester shows zero-order kinetics and proceeds through cooperative breaking of CN bonds.

Self-Assembly of Cyclic Dipeptides: Platforms for Functional Materials

Supramolecular self-assembled functional materials comprised of cyclic dipeptide building blocks have excellent prospects for biotechnology applications due to their exceptional structural rigidity, morphological flexibility, ease of preparation and modification. Although the pharmacological uses of many natural cyclic dipeptides have been studied in detail, relatively little is reported on the engineering of these supramolecular architectures for the fabrication of functional materials. In this review, we discuss the progress in the design, synthesis, and characterization of cyclic dipeptide supramolecular nanomaterials over the past few decades, highlighting applications in biotechnology and optoelectronics engineering.

Thermally induced cyclization of L -isoleucyl-L -alanine in solid state: Effect of dipeptide structure on reaction temperature and self-assembly

Thermal treatment of short-chain oligopeptides is able to initiate the process of their self-assembly with the formation of organic nanostructures with unique properties. On the other hand, heating can lead to a chemical reaction with the formation of new substances with specific properties and ability to form structures with different morphology. Therefore, in order to have a desired process, researcher needs to find its temperature range. In the present work, cyclization of _L -isoleucyl-_L -alanine dipeptide in the solid state upon heating was studied. Kinetic parameters of this reaction were estimated within the approaches of the nonisothermal kinetics. The correlation between side chain structure of dipeptides and temperature of their cyclization in the solid state was found for the first time. This correlation may be used to predict the temperature, at which dipeptide self-assembly changes to chemical reaction. The differences in self-assembly of linear and cyclic dipeptides were demonstrated using atomic force microscopy. The effect of dipeptide concentration in a source solution and an organic solvent used on self-assembly of dipeptides was shown. The new information obtained on the thermal properties and self-assembly of linear and cyclic forms of _L -isoleucyl-_L -alanine may be useful for the design of new nanomaterials based on oligopeptides, as well as for the synthesis of cyclic oligopeptides.

Hierarchically oriented organization in supramolecular peptide crystals

Hierarchical self-assembly and crystallization with long-range ordered spatial arrangement is ubiquitous in nature and plays an essential role in the regulation of structures and biological functions. Inspired by the multiscale hierarchical structures in biology, tremendous efforts have been devoted to the understanding of hierarchical self-assembly and crystallization of biomolecules such as peptides and amino acids. Understanding the fundamental mechanisms underlying the construction and organization of multiscale architectures is crucial for the design and fabrication of complex functional systems with long-range alignment of molecules. This Review summarizes the typical examples for hierarchically oriented organization of peptide self-assembly and discusses the thermodynamic and kinetic mechanisms that are responsible for this specific hierarchical organization. Most importantly, we propose the concept of hierarchically oriented organization for self-assembling peptide crystals, distinct from the traditional growth mechanism of supramolecular polymerization and crystallization based on the Ostwald ripening rule. Finally, we assess critical challenges and highlight future directions towards the mechanistic understanding and versatile application of the hierarchically oriented organization mechanism.

Role of water in the formation of unusual organogels with cyclo(leucyl-leucyl)

The key role of water in the formation of cyclo(leucyl-leucyl) organogels was demonstrated. The conditions required for preparation of previously unknown gels with aliphatic hydrocarbons at room temperature were determined. Cyclo(leucyl-leucyl) self-assembles to form different structures depending on the medium used. The molecular organization of gels was studied by the methods of microscopy, spectroscopy and X-ray powder diffractometry. The organogel of cyclo(leucyl-leucyl) can reversibly change volume during the heating/cooling cycle. We showed the possibility of practical application of cyclo(leucyl-leucyl) for water purification. The results obtained give a new insight into the mechanism of gelation with cyclo(dipeptide)-based low-molecular-weight gelators and may be useful for the preparation of new physical gels.

One Step up the Ladder of Prebiotic Complexity: Formation of Nonrandom Linear Polypeptides from Binary Systems of Amino Acids on Silica

Evidence for the formation of linear oligopeptides with nonrandom sequences from mixtures of amino acids coadsorbed on silica and submitted to a simple thermal activation is presented. The amino acid couples (glutamic acid+leucine) and (aspartic acid+valine) were deposited on a fumed silica and submitted to a single heating step at moderate temperature. The evolution of the systems was characterized by X-ray diffraction, infrared spectroscopy, thermosgravimetric analysis, HPLC, and electrospray ionization mass spectrometry (ESI-MS). Evidence for the formation of amide bonds was found in all systems studied. While the products of single amino acids activation on silica could be considered as evolutionary dead ends, (glutamic acid+leucine) and, at to some extent, (aspartic acid+valine) gave rise to the high yield formation of linear peptides up to the hexamers. Oligopeptides of such length have not been observed before in surface polymerization scenarios (unless the amino acids had been deposited by chemical vapor deposition, which is not realistic in a prebiotic environment). Furthermore, not all possible amino acid sequences were present in the activation products, which is indicative of polymerization selectivity. These results are promising for origins of life studies because they suggest the emergence of nonrandom biopolymers in a simple prebiotic scenario.

Melting properties of peptides and their solubility in water. Part 1: dipeptides based on glycine or alanine

Melting properties (melting temperature, melting enthalpy and heat capacity difference between liquid and solid phase) of biomolecules are indispensable for natural and engineering sciences. The direct determination of these melting properties by using conventional calorimeters for biological compounds is often not possible due to decomposition during slow heating. In the current study this drawback is overcome by using fast scanning calorimetry (FSC) to directly measure the melting properties of five dipeptides (glycyl-glycine, glycyl-l-alanine, l-alanyl-glycine, l-alanyl-l-alanine and cyclo(l-alanyl-glycine)). The experimental melting properties were used as inputs into a thermodynamic solid–liquid equilibrium relation to predict solubility of the dipeptides in water. The required activity coefficients were predicted with PC-SAFT using solubility-independent model parameters. PC-SAFT predicted different solubility profiles (solubility vs. temperature) of isomers. The predictions were validated by new experimental solubility data, and the crystal structure of the dipeptides in saturated solution was verified by X-ray diffraction. The different water solubility profiles of isomers (glycyl-l-alanine and l-alanyl-glycine) were found to be caused by the big difference in the melting enthalpy of the two dipeptides. To conclude, combining the PC-SAFT and FSC methods allows for accurate prediction of dipeptide solubility in water in a wide temperature range without the need to fit any model parameters to experimental solubility data.

Combination of the PC-SAFT and FSC methods allows for accurate prediction of dipeptide solubility in water in a wide temperature range without the need to fit any model parameters to experimental solubility data.

Reversibly Thermochromic Cyclic Dipeptide Nanotubes

Owing to their capability of forming extensive hydrogen bondings and the facile introduction of chirality, cyclic dipeptides (CDPs) have gained great attention as scaffolds for functional supramolecules. Surprisingly, introduction of a photopolymerizable diacetylene (DA) moiety to the CDP afforded nanotubular structures with enhanced stability and reversible thermochromism. A series of CDP-containing DAs (CDP-DAs) are prepared by coupling 10,12-pentacosadiynoic acid with CDPs, cyclo(-Gly-Ser) and cis/trans cyclo(-Ser-Ser). Fabrication of CDP-DA self-assemblies in a polar chloroform and methanol solvent mixture affords nanotubes comprising single-wall and multiwall structures. The self-assembly behavior and morphology characteristic are examined by scanning electron microscopy and transmission electron microscopy. Next, X-ray diffraction analysis confirms well-ordered lamellar structures with a perfect agreement with the bilayer formation leading to the tubular structure via lamellar scrolling behavior. Upon UV irradiation, monomeric CDP-DA tubular assemblies result in the blue-colored CDP/polydiacetylene (PDA) nanotubes. Interestingly, CDP/PDA nanotubes exhibit a reversible blue-to-red color change for over 10 consecutive thermal cycles. The CDP-DA/PDA supramolecular system demonstrates potential applications in developing stimulus-responsive functional materials.

Thermal decomposition of the amino acids glycine, cysteine, aspartic acid, asparagine, glutamic acid, glutamine, arginine and histidine

Background

The pathways of thermal instability of amino acids have been unknown. New mass spectrometric data allow unequivocal quantitative identification of the decomposition products.

Results

Calorimetry, thermogravimetry and mass spectrometry were used to follow the thermal decomposition of the eight amino acids G, C, D, N, E, Q, R and H between 185 °C and 280 °C. Endothermic heats of decomposition between 72 and 151 kJ/mol are needed to form 12 to 70% volatile products. This process is neither melting nor sublimation. With exception of cysteine they emit mainly H₂O, some NH₃ and no CO₂. Cysteine produces CO₂ and little else. The reactions are described by polynomials, AA→a NH₃+b H₂O+c CO₂+d H₂S+e residue, with integer or half integer coefficients. The solid monomolecular residues are rich in peptide bonds.

Conclusions

Eight of the 20 standard amino acids decompose at well-defined, characteristic temperatures, in contrast to commonly accepted knowledge. Products of decomposition are simple. The novel quantitative results emphasize the impact of water and cyclic condensates with peptide bonds and put constraints on hypotheses of the origin, state and stability of amino acids in the range between 200 °C and 300 °C.