Kinetic relationship in parallel autocatalytic amplifications of pyridyl alkanol and chiral trigger pyrimidyl alkanol

Experimental and kinetic analysis of a chemical system combines autocatalytic amplification of 2-alkynyl-5-pyrimidyl alkanol 2 and 6-alkynyl-3-pyridyl akanol 4 in which 2 acts as a chiral trigger and 4 being the subsequent autocatalyst. Starting from a very low initial ee, both alkanols are produced with high enantiopurity in one single cycle. This provides insight into a dual nonlinear amplification of chirality observed with amplifying trigger 2 and accelerated amplification of autocatalyst 4 . These kinetic studies reveal a five-fold magnitude superior amplification rates of 4 associated with trigger's enantiopurity at the outset.     

Organocatalytic aza-Michael/retro-aza-Michael reaction: pronounced chirality amplification in aza-Michael reaction and racemization via retro-aza-Michael reaction

A detailed experimental investigation of an aza-Michael reaction of aniline and chalcone is presented. A series of Cinchona alkaloid-derived organocatalysts with different functional groups were prepared and used in the aza-Michael and retro-aza-Michael reaction. There was an interesting finding that a complete reversal of stereoselectivity when a benzoyl group was introduced to the cinchonine and cinchonidine. The chirality amplification vs. time proceeds in the quinine-derived organocatalyst containing silicon-based bulky group, QN-TBS, -catalyzed aza-Michael reaction under solvent-free conditions. In addition, we have demonstrated for the first time that racemization was occurred in suitable solvents under mild conditions due to retro-aza-Michael reaction of the Michael adduct of aniline with chalcone. These indicate the equilibrium of retro-aza-Michael reaction and aza-Michael reaction produce the happening of chirality amplification in aza-Michael reaction and racemization via retro-aza-Michael reaction under different conditions, which would be beneficial to the development of novel chiral catalysts for the aza-Michael reactions.     

Supramolecular exciton chirality of carotenoid aggregates

The conventional organic chemistry concept of chirality relates to single molecules. This article deals with cases in which exciton chirality is generated by the interaction of associated carotenoids. The handed property responsible for exciton signals in these systems is due to the alignment of neighboring molecules held together by secondary chemical forces. Their mutual positions are characterized by the overlay angle. Experimental manifestation is obtained by spectroscopic studies on carotenoid aggregates. Compared to molecular spectra, both UV/visible and circular dichroism spectroscopic observations reveal modified absorption bands and induced Cotton effects of opposite sign (exciton couplets), respectively. A new term, "supramolecular exciton chirality," is suggested for these phenomena, allowing the detection of weak chemical interactions not readily accessible for experimental studies, although highly important in the mechanism of biological processes.     

Chirality: A Relational Geometric‐Physical Property

The definition of the term chirality by Lord Kelvin in 1893 and 1904 is analyzed by taking crystallography at that time into account. This shows clearly that chirality is a relational geometric‐physical property, i.e., two relations between isometric objects are possible: homochiral or heterochiral. In scientific articles the relational term chirality is often mistaken for the two valued measure for the individual (absolute) sense of chirality, an arbitrary attributive term. Chirality 25:684–685, 2013. © 2013 Wiley Periodicals Inc.     

Topological chirality of iron-sulfur proteins

An examination of x-ray structures of single-cluster [4Fe-4S] proteins in the Protein Data Bank has revealed that all redox proteins and the glutamine 5-phosphoribosyl-1-pyrophosphate amidotransferase from Bacillus subtilis have a topological configuration arbitrarily designated as D, whereas the DNA repair enzyme endonuclease III from Escherichia coli has the opposite topological configuration, L. This is the first example in which both senses of topological chirality have been observed in a class of proteins. © 1997 John Wiley & Sons, Inc. Biopoly 42: 411–414, 1997     

Astrobiology and Biological Chirality

The emerging discipline of astrobiology could gain valuable support from research dealing with the problems of biological chirality. The most profitable fields of common interest are: (a) living organisms under extraterrestrial conditions, (b) extraterrestrial signatures of life and (c) origin(s) of biological chirality. These areas of complementary and overlapping fields are analysed on the basis of selected references. Presented at: National Workshop on Astrobiology: Search for Life in the Solar System, Capri, Italy, 26 to 28 October, 2005.     

Molecular mechanisms of production of symmetrical and asymmetrical chromosome exchanges

The formation of a heteroduplex is probably the first step leading to chromosome exchanges. Heteroduplexes occur by complementary association of two single DNA strands from different chromosomes. Therefore, repetitive DNA is the most common region involved in heteroduplex formation. DNA repeats are defined as polarized when they run the same, and antipolarized when they run opposite from centromere to telomere in two different chromosomes or chromosome arms. Paracentric inversions may easily account for the origin of antipolarized repeats. Palindromes are a special type of reversed repeats which always run the same from centromere to telomere independently of the existence or not of chromosomal rearrangements. Heteroduplexes leading to symmetrical exchanges can only occur by association of DNA strands with polarized repeats. On the other hand, antipolarized repeats are essential for the occurrence of asymmetrical rearrangements. Accordingly, the frequency of induced symmetrical and asymmetrical exchanges in a cell population may partially depend on the frequency of polarized and antipolarized repeats in the genome.     

Measurement of circular birefringence and circular dichroism of the single crystals of lambda-(+)589- and delta-(-)589-tris(ethylenediamine)cobalt(III) triiodide monohydrate by the extended HAUP method

We have achieved measuring four optical parameters simultaneously, namely, linear birefringence (LB), circular birefringence (CB), linear dichroism (LD), and circular dichroism (CD), of single crystals of Lambda-(+)(589)- and Delta-(-)(589)-tris(ethylenediamine) cobalt(III) triiodide monohydrate (1) along the <001> plane at the fixed wavelength (514.5 nm). Such measurements are possible only when the High Accuracy Universal Polarimeter (HAUP) is employed; it is called the extended HAUP method. Our experimental results showed that both LB and LD of the Lambda-(+)(589)-(1) crystal have the same magnitude as those of the Delta-(-)(589)-(1) crystal. It was also revealed for the first time that the CB data of crystals of Lambda-(+)(589)-(1) and Delta-(-)(589)-(1) are almost of the same magnitude, but are of opposite sign, reflecting their opposite absolute configurations. On the other hand, although the CD data obtained for Lambda-(+)(589)-(1) is almost three times larger than that for Delta-(-)(589)-(1,) these CD data are also opposite in sign, as expected from the opposite chirality of crystals. .     

The origin of chirality in protein amino acids

We discuss the origin of the chirality of protein amino acids from the point of view of a phase transition from a racemic mixture into an optically pure state. We assume that Bose–Einstein condensation may act as an amplification mechanism. The original theory is due to Salam. We suggest a new role for the phase transition. Following Quack we distinguish parity violation of two kinds (de facto and de lege symmetry breaking). While the Salam phase transition corresponds to parity violation of the second kind (de lege), the phase transition we discuss in this work corresponds to parity violation of what we may call a third kind. This is suggested by recent experimental phenomena which correlate chiral symmetry breaking and pattern formation (spontaneous symmetry breaking that separates an initial racemic mixture into right- and left-handed space domains by means of a substrate). Tentative comments are given on the eventual design of possible experiments that may test this new hypothesis. © 1994 Wiley-Liss, Inc.     

Helical stereochemistry and chiral apple halves. 2. La coupe du roi via double helical complexation using oligo(bipyridine) strands and Cu(I)/Ag(I)

Oligo(bipyridine) strands and Cu(I)/Ag(I) form duplexes having a 2₁-screw coincidental with a C₂-axis. A segment containing a complete turn of the duplex can be considered to be a coupe du roi ensemble of two homochiral strands. Moreover, for D_2d symmetry monocationic Cu(I) complexes of bipyridine trimers and pentamers, addition of the requisite Cu(I) cations is a true chemical example of la coupe du roi. In this reaction, an achiral monocationic complex is converted into a multiple-cationic duplex of two homochiral and homotopic 2₁-helical halves. The chirality of the resulting duplex is a function of the particular set of bipyridine enantiotopic faces which are used for binding the additional cations. © 1993 Wiley-Liss, Inc.     

γ-Radiation Induced Polymerization of a Chiral Monomer: A New Way to Produce Chiral Amplification

The treatment of the terpene β(−)pinene with γ radiation (at dose level: 150, 300 and 600 kGy) causes its polymerization into a resin and into a dimer. The yield of the resin and of the dimer appears to be linearly dependent to the radiation dose. The structure of the products was studied by FT–IR spectroscopy also in comparison to a reference β(−)pinene resin prepared by cationic polymerization. A highly ordered structure was found in the case of the radiopolymer in comparison to the resin from cationic polymerization. Polarimetric measurements have shown astonishing enhancement in the optical activity of the radiopolymer and radiodimer in comparison to the starting optical activity of the β(−)pinene monomer. Also DSC (differential scanning calorimetry) data supports the unexpected highly ordered structure for the β(−)pinene radiopolymer in comparison to the resin prepared by cationic polymerization. The results have been discussed in terms of amplification of chirality caused by γ radiation and the implications of this fact on the mechanism of chiral amplification on prebiotic molecules. Presented at: National Workshop on Astrobiology: Search for Life in the Solar System, Capri, Italy, 26 to 28 October, 2005.     

Chirality and chemical processes: a few afterthoughts

Chirality and chiral have become terms that pervade a wide range of disciplines in physical and life sciences. Although such terms are precisely defined, their use often engenders confusion and ambiguity. Perhaps, the most improper use of chirality, yet widely accepted, is related to its association with stereodynamics and physico-chemical transformations, such as chiral discrimination, chiral resolution, chiral recognition, chiral synthesis, and so on. Even though this conceptual perversion has been highlighted by renowned stereochemists, it has become a recurring keyword and a hot message in modern literature. It is timely to renew the correct use and context in forums such as the present journal, adding further reflections that may help both beginners and practitioners. This short article is not intended to criticize or highlight errors, but rather to encourage a level of rigor and the use of statements, which should be universally correct.     

Exploring the role of chirality in nucleic acid recognition

The study of the base-pairing properties of nucleic acids with sugar moieties in the backbone belonging to the L-series (β-L-DNA, β-L-RNA, and their analogs) are reviewed. The major structural factors underlying the formation of stable heterochiral complexes obtained by incorporation of modified nucleotides into natural duplexes, or by hybridization between homochiral strands of opposite sense of chirality are highlighted. In addition, the perspective use of L-nucleic acids as candidates for various therapeutic applications, or as tools for both synthetic biology and etiology-oriented investigations on the structure and stereochemistry of natural nucleic acids is discussed.     

Structure and chiroptical properties of supramolecular flower pigments

Research over the last 30 years has shown that at physiological concentrations of ca. 5 x 10(-3) M, flower pigments composed of anthocyanins, either alone or complexed with flavone copigments, and frequently with metals, are self-assembled into non-covalent, chiral supramolecular complexes. This serves several biological functions including color stability, protection against UV radiation and provision for specific colors to attract insects for pollination. Self-association of the monomers takes place under conditions of molecular crowding by precise matching of the pi-pi stacking interactions of the aromatic chromophores and intermolecular hydrogen bonding between the attached sugars. The resulting handedness is controlled by the chiral information provided by the sugars joined glycosidically at certain positions around the periphery of the aromatic nuclei. This review gives an overview of (i) the physicochemical evidence including circular dichroism, (1)H NMR, and X-ray analysis for the structure and supramolecular chirality of these amphiphilic complexes, (ii) the role of the sugars on directing the chirality of the resulting supramolecules, (iii) the energetics of monomer association, and (iv) the possible influence of stacking chirality on insect pollination.     

The enduring legacy of Koji Nakanishi's research on natural products and bioorganic chemistry. Part 2. Inception and establishment of the ECD exciton chirality method in 1960s to 1970s: A marvel of Nakanishi's Japanese team

The electronic circular dichroism (ECD) exciton chirality method is very useful for determining the absolute configuration (AC) of chiral compounds. In the ECD spectroscopy, the chromophore-chromophore interaction, ie, exciton coupling, is very important. For example, Harada and Nakanishi first discovered in 1969 that chiral dibenzoates exhibit exciton split bisignate Cotton effects, from the sign of which the screw sense between two long axes of benzoate chromophores, ie, the AC of dibenzoate, can be determined. This method was named the dibenzoate chirality rule and has been successfully applied to various natural products to determine their ACs. During these studies, it was also found that this CD method was expanded to encompass other aromatic and olefin chromophores like naphthalene, diene, enone, etc. Therefore, the name of the dibenzaote chirality rule was changed to the CD exciton chirality method. In 1970s, there were heated controversies about the inconsistency between X-ray Bijvoet and CD exciton chirality methods, which was a shocking and serious problem in the community of molecular chirality research. Harada and coworkers synthesized the most ideal cage compound with two anthracene chromophores to connect X-ray Bijvoet and CD exciton chitality methods and proved that these two methods are consistent with each other.     

Terrestrial and extraterrestrial sources of molecular homochirality

The unique chirality of biomolecules is reviewed, and the prebiotic requirement for the absolute chiral homogeneity of such molecules prior to their capability of self-replication is emphasized. Biotic and abiotic theories embracing both chance and determinate mechanisms which have been proposed for the origin of terrestrial chiral molecules are briefly summarized and evaluated, as are abiotic mechanisms for the subsequent amplification of the small enantiomeric excesses (e.e.s) in the chiral molecules which might be formed by such processes. While amplification mechanisms are readily validated experimentally and are potentially viable on the primitive Earth, it is concluded that all terrestrial mechanisms proposed for the origin of chirality have one or more limitations which make them either intrinsically invalid or highly improbable in the chaotic and turbulent environment of the prebiotic Earth. To circumvent these difficulties we have proposed an extraterrestrial scenario for the production of terrestrial chirality in which circularly polarized synchrotron radiation from the neutron star remnant of a supernova interacts with the organic mantles on interstellar grains, producing chiral molecules by the partial asymmetric photolysis of racemic constituent in the mantles, after which the interstellar grains with their enantiomerically enriched mantles are transported to Earth either by direct accretion or through cometary impact. At this point one of the known terrestrial e.e. enrichment mechanisms could promote the small extraterrestrially produced e.e.s. into the state of chiral homogeneity required for self-replicating biomolecules.     

Sexual selection maintains whole-body chiral dimorphism in snails

Although the vast majority of higher animals are fixed for one chiral morph or another, the cause for this directionality is known in only a few cases. In snails, for example, rare individuals of the opposite coil are unable to mate with individuals of normal coil, so directionality is maintained by frequency-dependent selection. The snail subgenus Amphidromus presents an unexplained exception, because dextral (D) and sinistral (S) individuals occur sympatrically in roughly equal proportions (so-called 'antisymmetry') in most species. Here we show that in Amphidromus there is sexual selection for dimorphism, rather than selection for monomorphism. We found that matings between D and S individuals occur more frequently than expected by chance. Anatomical investigations showed that the chirality of the spermatophore and the female reproductive tract probably allow a greater fecundity in such inter-chiral matings. Computer simulation confirms that under these circumstances, sustained dimorphism is the expected outcome.     

Crystallization and solid-state reaction as a route to asymmetric synthesis from achiral starting materials

Many molecules which are achiral can crystallize in chiral (enantiomorphic) crystals and, under suitable conditions, crystals of only one chirality may be obtained. The formation of right- or left-handed crystals in excess is equally probable. Lattice-controlled (topochemical) photochemical or thermal solid-state reactions may then afford stable, optically active products. In the presence of the chiral products, achiral reactants may preferentially produce crystals of one chirality, leading to a feedback mechanism for the generation and amplification of optical activity. Amplification of optical activity can also be achieved by solid-state reactions. The optical synthesis of biologically relevant compounds by such routes may be envisaged.     

Chirality of peridinin and dinoxanthin

Details are reported for the configurational assignment of peridinin as 3S, 5R, 6R, 3′S, 5′R, 6′S including ozonolytic degradation of its p-bromobenzoate to derivatives of known chirality obtained from fucoxanthin and violaxanthin. Details regarding derivatization and CD correlations in favour of the same chirality for dinoxanthin = neoxanthin 3-acetate are given.