Chiral polymerisation and the RNA world

The purpose of this paper is to review two mathematical models: one for the formation of homochiral polymers from an originally chirally symmetric system; and the other, to show how, in an RNA-world scenario, RNA can simultaneously act both as information storage and a catalyst for its own production. We note the similarities and differences in chemical mechanisms present in the systems. We review these two systems, analysing steady-states, interesting kinetics and the stability of symmetric solutions. In both systems we show that there are ranges of parameter values where some chains increase their own concentrations faster than others.

Symmetry-breaking in chiral polymerisation

We propose a model for chiral polymerisation and investigate its symmetric and asymmetric solutions. The model has a source species which decays into left- and right-handed types of monomer, each of which can polymerise to form homochiral chains; these chains are susceptible to `poisoning' by the opposite handed monomer. Homochiral polymers are assumed to influence the proportion of each type of monomer formed from the precursor. We show that for certain parameter values a positive feedback mechanism makes the symmetric steady-state solution unstable. The kinetics of polymer formation are then analysed in the case where the system starts from zero concentrations of monomers and chains. We show that following a long induction time, extremely large concentrations of polymers are formed for a short time, during this time an asymmetry introduced into the system by a random external perturbation may be massively amplified. The system then approaches one of the steady-state solutions described above.

Chiral polymerisation and the RNA world

The purpose of this paper is to review two mathematical models: one for the formation of homochiral polymers from an originally chirally symmetric system; and the other, to show how, in an RNA-world scenario, RNA can simultaneously act both as information storage and a catalyst for its own production. We note the similarities and differences in chemical mechanisms present in the systems. We review these two systems, analysing steady-states, interesting kinetics and the stability of symmetric solutions. In both systems we show that there are ranges of parameter values where some chains increase their own concentrations faster than others.

Mapping chiral symmetry breaking in the excited baryon spectrum

We study the conjectured “insensitivity to chiral symmetry breaking” in the highly excited light baryon spectrum. While the experimental spectrum is being measured at JLab and CBELSA/TAPS, this insensitivity remains to be computed theoretically in detail. As the only existing option to have both confinement, highly excited states, and chiral symmetry, we adopt the truncated Coulomb-gauge formulation of QCD, considering a linearly confining Coulomb term. Adopting a systematic and numerically intensive variational treatment up to 12 harmonic oscillator shells we are able to access several angular and radial excitations. We compute both the excited spectra of I=1/2 and I=3/2 baryons, up to large spin J=13/2, and study in detail the proposed chiral multiplets. While the static-light and light-light spectra clearly show chiral symmetry restoration high in the spectrum, the realization of chiral symmetry is more complicated in the baryon spectrum than earlier expected.

PROLINE-BASED CHIRAL STATIONARY PHASES: INSIGHTS INTO THE MECHANISM OF CHIRAL SELECTIVITY

Proline (Pro) is a unique amino acid that has been examined previously as a potential chiral selector for high-performance liquid chromatography. In recent years, a new class of promising Pro based enantioselective stationary phases has been studied and the longer peptides were found to be competitive with commercial chiral stationary phases (CSPs). Here, we aim to perform a comprehensive examination of a t-butoxycarbonyl- (t-Boc-) terminated monoproline selector. This selector was grafted through an amide linkage to an aminopropyl siloxane-terminated Si (111) wafer and to a silicon atomic force microscopy tip. To ensure a flat, homogeneous overlayer of selectors suitable for force spectrometric measurements, the prepared surfaces were characterized using XPS, AFM and contact angle measurements. Chemical force spectrometry (CFS) has been used to examine the chiral discrimination in our monoproline CSP by measuring the interaction forces between two D- or L-monoproline monolayers in water and in the presence of a series of amino acids in solution to explore the degree to which binding of amino acids impacts self-selectivity. Chemical force titration (CFT) has been used to observe the influence of variations in pH on the binding interaction of proline modified chiral surfaces. Here we aim to explore the connection between side-chain hydrophobicity and differences in the nature of the binding between different ionic forms of amino acids and the t-Boc-Pro interface, and thereby to gain insight into the mechanism of chiral selectivity. The CFS results show several trends for different proline selector/amino acid combinations and indicate that the binding characteristics of amino acid to the proline surface is strongly dependent on the amino acid side chain where hydrophilic side chain amino acids exhibit a selectivity opposite to that seen for those with hydrophobic side chains. The CFT studies also provide valuable insights into interactions between the proline selector and the amino acids under a wide range of pH conditions, indicating that protonated amine groups of alanine and serine are closely involved in the binding mechanism to proline surfaces. On the other hand, the presence of the second carboxylic group in aspartic acid plays an important role while interacting with proline.

Chiroptical spectroscopy of biomolecules using chiral plasmonic nanostructures

This thesis explores the potential of chiral plasmonic nanostructures for the ultrasensitive detection of protein structure. These nanostructures support the generation of fields with enhanced chirality relative to circularly polarised light and are an extremely incisive probe of protein structure. In chapter 4 we introduce a nanopatterned Au film (Templated Plasmonic Substrate, TPS) fabricated using a high through-put injection moulding technique which is a viable alternative to expensive lithographically fabricated nanostructures. The optical and chiroptical properties of TPS nanostructures are found to be highly dependent on the coupling between the electric and magnetic modes of the constituent solid and inverse structures. Significantly, refractive index based measurements of strongly coupled TPSs display a similar sensitivity to protein structure as previous lithographic nanostructures. We subsequently endeavour to improve the sensing properties of TPS nanostructures by developing a high through-put nanoscale chemical functionalisation technique. This process involves a chemical protection/deprotection strategy. The protection step generates a self-assembled monolayer (SAM) of a thermally responsive polymer on the TPS surface which inhibits protein binding. The deprotection step exploits the presence of nanolocalised thermal gradients in the water surrounding the TPS upon irradiation with an 8ns pulsed laser to modify the SAM conformation on surfaces with high net chirality. This allows binding of biomaterial in these regions and subsequently enhances the TPS sensitivity levels. In chapter 6 an alternative method for the detection of protein structure using TPS nanostructures is introduced. This technique relies on mediation of the electric/magnetic coupling in the TPS by the adsorbed protein. This phenomenon is probed through both linear reflectance and nonlinear second harmonic generation (SHG) measurements. Detection of protein structure using this method does not require the presence of fields of enhanced chirality whilst it is also sensitive to a larger array of secondary structure motifs than the measurements in chapters 4 and 5. Finally, a preliminary investigation into the detection of mesoscale biological structure is presented. Sensitivity to the mesoscale helical pitch of insulin amyloid fibrils is displayed through the asymmetry in the circular dichroism (CD) of lithographic gammadions of varying thickness upon adsorption of insulin amyloid fibril spherulites and fragmented fibrils. The proposed model for this sensitivity to the helical pitch relies on the vertical height of the nanostructures relative to this structural property as well as the binding orientation of the fibrils.

Quark model with chiral-symmetry breaking and confinement in the Covariant Spectator Theory

We propose a model for the quark-antiquark interaction in Minkowski space using the Covariant Spectator Theory. We show that with an equal-weighted scalar-pseudoscalar structure for the confining part of our interaction kernel the axial-vector Ward-Takahashi identity is preserved and our model complies with the Adler-zero constraint for π-π-scattering imposed by chiral symmetry.

Chiral-symmetry Breaking and Pion Structure in the Covariant Spectator Theory

We introduce a covariant approach in Minkowski space for the description of quarks and mesons that exhibits both chiral-symmetry breaking and confinement. In a simple model for the interquark interaction, the quark mass function is obtained and used in the calculation of the pion form factor. We study the effects of the mass function and the different quark pole contributions on the pion form factor.

Hydrogen-bonding in cyclic imides and amide carboxylic acid derivatives from the facile reaction of cis-cyclohexane-1,2-carboxylic anhydride with o- and p-anisidine and m- and p-aminobenzoic acids

The structures of the open chain amide carboxylic acid rac-cis-[2-(2-methoxyphenyl)carbamoyl]cyclohexane-1-carboxylic acid, C15H19NO4, (I) and the cyclic imides rac-cis-2-(4-methoxyphenyl)-3a,4,5,6,7,7-hexahydroisoindole-1,3-dione,C15H17NO3, (II), chiral cis-2-(3-carboxyphenyl)-3a,4,5,6,7,7a-hexahydroisoindole-1,3-dione, C15H15NO4,(III) and rac-cis-2-(4-carboxyphenyl)- 3a,4,5,6,7,7a-hexahydroisoindole-1,3-dione monohydrate, C15H15NO4. H2O) (IV), are reported. In the amide acid (I), the phenylcarbamoyl group is essentially planar [maximum deviation from the least-squares plane = 0.060(1)Ang. for the amide O atom], the molecules form discrete centrosymmetric dimers through intermolecular cyclic carboxy-carboxy O-H...O hydrogen-bonding interactions [graph set notation R2/2(8)]. The cyclic imides (II)--(IV) are conformationally similar, with comparable phenyl ring rotations about the imide N-C(aromatic) bond [dihedral angles between the benzene and isoindole rings = 51.55(7)deg. in (II), 59.22(12)deg. in (III) and 51.99(14)deg. in (IV). Unlike (II) in which only weak intermolecular C-H...O(imide) hydrogen bonding is present, the crystal packing of imides (III) and (IV) shows strong intermolecular carboxylic acid O-H...O hydrogen-bonding associations. With (III), these involve imide O-atom acceptors, giving one-dimensional zigzag chains [graph set C(9)], while with the monohydrate (IV), the hydrogen bond involves the partially disordered water molecule which also bridges molecules through both imide and carboxyl O-atom acceptors in a cyclic R4/4(12) association, giving a two-dimensional sheet structure. The structures reported here expand the structural data base for compounds of this series formed from the facile reaction of cis-cyclohexane-1,2-dicarboxylic anhydride with substituted anilines, in which there is a much larger incidence of cyclic imides compared to amide carboxylic acids.

The acetal concept : regioselective access toortho,ortho-diphenols via dibenzo-1,3-dioxepines

Traditional methods are ill-suited for the synthesis of ortho,ortho-biphenols, a structural motif found in many polyphenolic natural products, as well as synthetically useful compounds such as the chiral ligands binol, vapol, and vanol. The new route consists of a radical-based reaction of an acetal-tethered biphenyl ether substrate and subsequent hydrolytic cleavage of the dibenzo-1,3-dioxepine intermediate.

Preparative deracemization of unnatural amino acids

Unnatural amino acids are a growing class of intermediates required for pharmaceuticals, agrochemicals and other industrial products. However, no single method has proven sufficiently versatile to prepare these compounds broadly at scale. To address this need, we have developed a general chemoenzymatic process to prepare enantiomerically pure L- and D-amino acids in high yield by deracemization of racemic starting materials. This method involves the concerted action of an enantioselective oxidase biocatalyst and a non-selective chemical reducing agent to effect the stereoinversion of one enantiomer and can result in an enantiomeric excess of >99% from the starting racemate, and product yields of over 90%. This approach compares very favourably with resolution processes, which have a maximum single-pass yield of 50%. We have developed efficient methods to adapt the process towards new target compounds and to optimize key factors that influence process efficiency and offer competitive economics at scale.

Electromagnetic propulsion and separation by chirality of nanoparticles in liquids

We introduce a new mechanism for the propulsion and separation by chirality of small ferromagnetic particles suspended in a liquid. Under the action of a uniform dc magnetic field H and an ac electric field E isomers with opposite chirality move in opposite directions. Such a mechanism could have a significant impact on a wide range of emerging technologies. The component of the chiral velocity that is odd in H is found to be proportional to the intrinsic orbital and spin angular momentum of the magnetized electrons. This effect arises because a ferromagnetic particle responds to the applied torque as a small gyroscope. © 2012 American Physical Society.

Single-walled carbon nanotube-based polymer monoliths for the enantioselective nano-liquid chromatographic separation of racemic pharmaceuticals

Many protocols have been used for extraction of DNA from Thraustochytrids. These generally involve the use of CTAB, phenol/chloroform and ethanol. They also feature mechanical grinding, sonication, N2 freezing or bead beating. However, the resulting chemical and physical damage to extracted DNA reduces its quality. The methods are also unsuitable for large numbers of samples. Commercially-available DNA extraction kits give better quality and yields but are expensive. Therefore, an optimized DNA extraction protocol was developed which is suitable for Thraustochytrids to both minimise expensive and time-consuming steps prior to DNA extraction and also to improve the yield. The most effective method is a combination of single bead in TissueLyser (Qiagen) and Proteinase K. Results were conclusive: both the quality and the yield of extracted DNA were higher than with any other method giving an average yield of 8.5 µg/100 mg biomass.

First donor-acceptor interaction promoted gelation of organic fluids

In recent years there has been considerable interest in developing new types of gelators of organic solvents.1 Despite the recent advances, a priori design of a gelator for gelling a given solvent has remained a challenging task. Various noncovalent interactions like hydrogen-bonding,2 metal coordination3 etc. have been used as the driving force for the gelation process. A special class of cholesterol-based gelators were reported by Weiss,4 and by Shinkai.5 Gels derived from these molecules have been used for chiral recognition/sensing,6 for studying photo- and metal-responsive functions,7 and as templates to make hollow fiber silica.8 Other types of organogels have been used for designing polymerized 9 and reverse aerogels,10 and in molecular imprinting.11 Hanabusa’s group has recently reported organogels with a bile acid derivative.12 This has prompted us to disclose our results on a novel electron donor–acceptor (EDA) interaction mediated two-component13 gelator system based on the bile acid14 backbone.