Comments on "Molecular Chirality in Classical Spacetime: Solving the Controversy about the Spinning Cone Model of Rotating Molecules".

A recent mathematical analysis by Michel Petijean aimed at solving the Barron/Mislow controversy concerning the chirality or otherwise of a non-translating spinning cone concluded that both are right: the controversy is a matter of an arbitrary choice of a conversion factor. This reassessment highlights the different physicochemical properties of a stationary spinning cone and a chiral molecule and concludes that Petitjean's analysis is misleading.

Solution Structure of Mannobioses Unravelled by Means of Raman Optical Activity.

Structural analysis of carbohydrates is a complicated endeavour, due to the complexity and diversity of the samples at hand. Herein, we apply a combined computational and experimental approach, employing molecular dynamics (MD) and density functional theory (DFT) calculations together with NMR and Raman optical activity (ROA) measurements, in the structural study of three mannobiose disaccharides, consisting of two mannoses with varying glycosidic linkages. The disaccharide structures make up the scaffold of high mannose glycans and are therefore important targets for structural analysis. Based on the MD population analysis and NMR, the major conformers of each mannobiose were identified and used as input for DFT analysis. By systematically varying the solvent models used to describe water interacting with the molecules and applying overlap integral analysis to the resulting calculational ROA spectra, we found that a full quantum mechanical/molecular mechanical approach is required for an optimal calculation of the ROA parameters. Subsequent normal mode analysis of the predicted vibrational modes was attempted in order to identify possible marker bands for glycosidic linkages. However, the normal mode vibrations of the mannobioses are completely delocalised, presumably due to conformational flexibility in these compounds, rendering the identification of isolated marker bands unfeasible.

Chiral Plasmonic Fields Probe Structural Order of Biointerfaces.

The structural order of biopolymers, such as proteins, at interfaces defines the physical and chemical interactions of biological systems with their surroundings and is hence a critical parameter in a range of biological problems. Known spectroscopic methods for routine rapid monitoring of structural order in biolayers are generally only applied to model single-component systems that possess a spectral fingerprint which is highly sensitive to orientation. This spectroscopic behavior is not a generic property and may require the addition of a label. Importantly, such techniques cannot readily be applied to real multicomponent biolayers, have ill-defined or unknown compositions, and have complex spectroscopic signatures with many overlapping bands. Here, we demonstrate the sensitivity of plasmonic fields with enhanced chirality, a property referred to as superchirality, to global orientational order within both simple model and "real" complex protein layers. The sensitivity to structural order is derived from the capability of superchiral fields to detect the anisotropic nature of electric dipole-magnetic dipole response of the layer; this is validated by numerical simulations. As a model study, the evolution of orientational order with increasing surface density in layers of the antibody immunoglobulin G was monitored. As an exemplar of greater complexity, superchiral fields are demonstrated, without knowledge of exact composition, to be able to monitor how qualitative changes in composition alter the structural order of protein layers formed from blood serum, thereby establishing the efficacy of the phenomenon as a tool for studying complex biological interfaces.

Biomacromolecular Stereostructure Mediates Mode Hybridization in Chiral Plasmonic Nanostructures.

The refractive index sensitivity of plasmonic fields has been exploited for over 20 years in analytical technologies. While this sensitivity can be used to achieve attomole detection levels, they are in essence binary measurements that sense the presence/absence of a predetermined analyte. Using plasmonic fields, not to sense effective refractive indices but to provide more "granular" information about the structural characteristics of a medium, provides a more information rich output, which affords opportunities to create new powerful and flexible sensing technologies not limited by the need to synthesize chemical recognition elements. Here we report a new plasmonic phenomenon that is sensitive to the biomacromolecular structure without relying on measuring effective refractive indices. Chiral biomaterials mediate the hybridization of electric and magnetic modes of a chiral solid-inverse plasmonic structure, resulting in a measurable change in both reflectivity and chiroptical properties. The phenomenon originates from the electric-dipole-magnetic-dipole response of the biomaterial and is hence sensitive to biomacromolecular secondary structure providing unique fingerprints of α-helical, ß-sheet, and disordered motifs. The phenomenon can be observed for subchiral plasmonic fields (i.e., fields with a lower chiral asymmetry than circularly polarized light) hence lifting constraints to engineer structures that produce fields with enhanced chirality, thus providing greater flexibility in nanostructure design. To demonstrate the efficacy of the phenomenon, we have detected and characterized picogram quantities of simple model helical biopolymers and more complex real proteins.

Ramachandran mapping of peptide conformation using a large database of computed Raman and Raman optical activity spectra.

In the past few decades, Raman optical activity (ROA) spectroscopy has been shown to be very sensitive to the solution structure of peptides and proteins. A major and urgent challenge remains the need to make detailed assignments of experimental ROA patterns and relate those to the solution structure adopted by the protein. In the past few years, theoretical developments and implementations of ROA theory have made it possible to use quantum chemical methods to compute the ROA spectra of peptides. In this work, a large database of ROA spectra of peptide model structures describing the allowed backbone conformations of proteins was systematically calculated and used to make unprecedented detailed assignments of experimental ROA patterns to the conformational elements of the peptide in solution. By using a similarity index to compare an experimental spectrum to the database spectra (2902 theoretical spectra), the conformational preference of the peptide in solution can be assigned to a very specific region in the Ramachandran space. For six (poly)peptides this approach was validated and gives excellent agreement between experiment and theory. Additionally, hydrogen/deuterium exchanged structures and the conformational dependence of the amide modes in Raman spectra can be analysed using the new database. The excellent agreement between experiment and theory demonstrates the power of the newly developed database as a tool to study Raman and ROA patterns of peptides and proteins. The interpretation of experimental ROA patterns of different proteins published in the scientific literature is discussed based on the spectral trends observed in the database.

"Superchiral" Spectroscopy: Detection of Protein Higher Order Hierarchical Structure with Chiral Plasmonic Nanostructures.

Optical spectroscopic methods do not routinely provide information on higher order hierarchical structure (tertiary/quaternary) of biological macromolecules and assemblies. This necessitates the use of time-consuming and material intensive techniques, such as protein crystallography, NMR, and electron microscopy. Here we demonstrate a spectroscopic phenomenon, superchiral polarimetry, which can rapidly characterize ligand-induced changes in protein higher order (tertiary/quaternary) structure at the picogram level, which is undetectable using conventional CD spectroscopy. This is achieved by utilizing the enhanced sensitivity of superchiral evanescent fields to mesoscale chiral structure.

'A careful disorderliness' in biomolecular structure revealed by Raman optical activity.

Following its first observation 50 years ago Raman optical activity (ROA), which refers to a circular polarization dependence of Raman scattering from chiral molecules, has evolved into a powerful chiroptical spectroscopy for studying a large range of biomolecules in aqueous solution. Among other things ROA provides information about motif and fold as well as secondary structure of proteins; structure of carbohydrates and nucleic acids; polypeptide and carbohydrate structure of intact glycoproteins; and protein and nucleic acid structure of intact viruses. Quantum chemical simulations of observed Raman optical activity spectra can provide complete three-dimensional structures of biomolecules, together with information about conformational dynamics. This article reviews how ROA has provided new insight into the structure of unfolded/disordered states and sequences, ranging from the complete disorder of the random coil to the more controlled type of disorder exemplified by poly L-proline II helix in proteins, high mannose glycan chains in glycoproteins and constrained dynamic states of nucleic acids. Possible roles for this 'careful disorderliness' in biomolecular function, misfunction and disease are discussed, especially amyloid fibril formation.

Cosmic chirality both true and false.

The discrete symmetries of parity P, time reversal T, and charge conjugation C may be used to characterize the properties of chiral systems. It is well known that parity violation infiltrates into ordinary matter via an interaction between the nucleons and electrons, mediated by the Z(0) particle, that lifts the degeneracy of the mirror-image enantiomers of a chiral molecule. Being odd under P but even under T, this P-violating interaction exhibits true chirality and so may induce absolute enantioselection under all circumstances. It has been suggested that CP violation may also infiltrate into ordinary matter via a P-odd, T-odd interaction mediated by the (as yet undetected) axion. This CP-violating interaction exhibits false chirality and so may induce absolute enantioselection in processes far from equilibrium. Both true and false cosmic chirality should be considered together as possible sources of homochirality in the molecules of life.

From cosmic chirality to protein structure: Lord Kelvin's legacy.

A selection of my work on chirality is sketched in two distinct parts of this lecture. Symmetry and Chirality explains how the discrete symmetries of parity P, time reversal T, and charge conjugation C may be used to characterize the properties of chiral systems. The concepts of true chirality (time-invariant enantiomorphism) and false chirality (time-noninvariant enantiomorphism) that emerge provide an extension of Lord Kelvin's original definition of chirality to situations where motion is an essential ingredient thereby clarifying, inter alia, the nature of physical influences able to induce absolute enantioselection. Consideration of symmetry violations reveals that strict enantiomers (exactly degenerate) are interconverted by the combined CP operation. Raman optical activity surveys work, from first observation to current applications, on a new chiroptical spectroscopy that measures vibrational optical activity via Raman scattering of circularly polarized light. Raman optical activity provides incisive information ranging from absolute configuration and complete solution structure of smaller chiral molecules and oligomers to protein and nucleic acid structure of intact viruses.

Determination of the helical screw sense and side-group chirality of a synthetic chiral polymer from Raman optical activity.

Splitting it up: excellent agreement between the experimental and the quantum-chemically simulated Raman optical activity (ROA) spectrum of (+)-poly(trityl methacrylate) shows that the polymer backbone adopts a left-handed helical conformation while the trityl side groups display a left-handed propeller conformation. Thus ROA can be used to determine the complete structure of synthetic chiral polymers in solution.

Superchiral near fields detect virus structure.

Optical spectroscopy can be used to quickly characterise the structural properties of individual molecules. However, it cannot be applied to biological assemblies because light is generally blind to the spatial distribution of the component molecules. This insensitivity arises from the mismatch in length scales between the assemblies (a few tens of nm) and the wavelength of light required to excite chromophores (≥150 nm). Consequently, with conventional spectroscopy, ordered assemblies, such as the icosahedral capsids of viruses, appear to be indistinguishable isotropic spherical objects. This limits potential routes to rapid high-throughput portable detection appropriate for point-of-care diagnostics. Here, we demonstrate that chiral electromagnetic (EM) near fields, which have both enhanced chiral asymmetry (referred to as superchirality) and subwavelength spatial localisation (∼10 nm), can detect the icosahedral structure of virus capsids. Thus, they can detect both the presence and relative orientation of a bound virus capsid. To illustrate the potential uses of the exquisite structural sensitivity of subwavelength superchiral fields, we have used them to successfully detect virus particles in the complex milieu of blood serum.

Controlling the symmetry of inorganic ionic nanofilms with optical chirality.

Manipulating symmetry environments of metal ions to control functional properties is a fundamental concept of chemistry. For example, lattice strain enables control of symmetry in solids through a change in the nuclear positions surrounding a metal centre. Light-matter interactions can also induce strain but providing dynamic symmetry control is restricted to specific materials under intense laser illumination. Here, we show how effective chemical symmetry can be tuned by creating a symmetry-breaking rotational bulk polarisation in the electronic charge distribution surrounding a metal centre, which we term a meta-crystal field. The effect arises from an interface-mediated transfer of optical spin from a chiral light beam to produce an electronic torque that replicates the effect of strain created by high pressures. Since the phenomenon does not rely on a physical rearrangement of nuclear positions, material constraints are lifted, thus providing a generic and fully reversible method of manipulating effective symmetry in solids.

Poly(L-proline) II helix propensities in poly(L-lysine) dendrigraft generations from vibrational Raman optical activity.

Vibrational Raman optical activity (ROA), measured as small circularly polarized components in Raman scattering from chiral molecules, was applied to study the backbone conformations of the first five generations of poly(L-lysine) dendrigrafts (DGLs) in water. Generation 1 was found to support predominantly the poly(L-proline) II (PPII) conformation, the amount of which steadily decreased with increasing generation, with a concomitant increase in other backbone conformations. This behavior may be due to increasing crowding of the lysine side chains, together with suppression of backbone hydration, with increasing branching. In contrast, the ROA spectra of a series of linear poly(L-lysine)s in water show little change with increasing molecular weight. Our results may have implications for the nonimmunogenic properties of DGLs.

Structure and behaviour of biomolecules from Raman optical activity.

Raman optical activity, which can be measured as a small circularly polarized component in Raman-scattered light from chiral molecules, holds much promise for studying a large range of biomolecules in aqueous solution. Among other things, it provides information about motif and fold, as well as secondary structure, of proteins; the solution structure of carbohydrates; and the structure of the polypeptide and carbohydrate components of intact glycoproteins. In addition, new insights into the structural elements present in unfolded protein sequences, and the structure of the protein and nucleic acid components of intact viruses can be obtained. Ab initio quantum-chemical simulations of observed Raman optical activity spectra provide the complete three-dimensional structure of small biomolecules. Raman optical activity measurements are now routine thanks to the availability of a commercial instrument based on a novel design.

Identification of a human estrogen receptor alpha-derived antiestrogenic peptide that adopts a polyproline II conformation.

Polyproline II (PPII) helix is an extended secondary structure present in a number of proteins. PPII-containing sequences mediate specific protein-protein interactions with partners containing appropriate cognate domains called PPII-recognizing domains (PRDs) and are involved in the activation of intracellular signaling pathways. Thus, the identification of PPII structures in proteins is of great interest, not only to explore molecular and physiological mechanisms, but also to elaborate new potential drugs. By revisiting X-ray crystal structures of liganded alpha-type human estrogen receptor (ERalpha), we have identified an 11-residue PPII-helical sequence (D(321)AEPPILYSEY(331)) in the ligand-binding domain of the receptor. The data recorded by far-ultraviolet circular dichroism (far-UV CD), vibrational Raman optical activity (ROA) and differential scanning calorimetry (DSC) show that the corresponding peptide (Ac-DAEPPILYSEY-NH(2)) is particularly well structured in PPII, with the same proportion of PPII as observed from X-ray structures (approximately 85%). In addition, studies carried out on ERalpha-negative Evsa-T breast cancer cells transiently co-transfected with a pcDNA3-ERalpha plasmid and a Vit-tk-Luc reporter gene revealed that the peptide antagonizes the estradiol-induced transcription providing perspectives for researching new molecules with antagonistic properties.

Vibrational Raman optical activity of 1-phenylethanol and 1-phenylethylamine: revisiting old friends.

The samples used for the first observations of vibrational Raman optical activity (ROA) in 1972, namely both enantiomers of 1-phenylethanol and 1-phenylethylamine, have been revisited using a modern commercial ROA instrument together with state-of-the-art ab initio calculations. The simulated ROA spectra reveal for the first time the vibrational origins of the first reported ROA signals, which comprised similar couplets in the alcohol and amine in the spectral range approximately 280-400 cm(-1). The results demonstrate how easy and routine ROA measurements have become, and how current ab initio quantum-chemical calculations are capable of simulating experimental ROA spectra quite closely provided sufficient averaging over accessible conformations is included. Assignment of absolute configuration is, inter alia, completely secure from results of this quality. Anharmonic corrections provided small improvements in the simulated Raman and ROA spectra. The importance of conformational averaging emphasized by this and previous related work provides the underlying theoretical background to ROA studies of dynamic aspects of chiral molecular and biomolecular structure and behavior.

Probing Specificity of Protein-Protein Interactions with Chiral Plasmonic Nanostructures.

Protein-protein interactions (PPIs) play a pivotal role in many biological processes. Discriminating functionally important well-defined protein-protein complexes formed by specific interactions from random aggregates produced by nonspecific interactions is therefore a critical capability. While there are many techniques which enable rapid screening of binding affinities in PPIs, there is no generic spectroscopic phenomenon which provides rapid characterization of the structure of protein-protein complexes. In this study we show that chiral plasmonic fields probe the structural order and hence the level of PPI specificity in a model antibody-antigen system. Using surface-immobilized Fab' fragments of polyclonal rabbit IgG antibodies with high specificity for bovine serum albumin (BSA), we show that chiral plasmonic fields can discriminate between a structurally anisotropic ensemble of BSA-Fab' complexes and random ovalbumin (OVA)-Fab' aggregates, demonstrating their potential as the basis of a useful proteomic technology for the initial rapid high-throughput screening of PPIs.

Residual structure in disordered peptides and unfolded proteins from multivariate analysis and ab initio simulation of Raman optical activity data.

Vibrational Raman optical activity (ROA), measured as a small difference in the intensity of Raman scattering from chiral molecules in right- and left-circularly polarized incident light, or as the intensity of a small circularly polarized component in the scattered light, is a powerful probe of the aqueous solution structure of proteins. The large number of structure-sensitive bands in protein ROA spectra makes multivariate analysis techniques such as nonlinear mapping (NLM) especially favorable for determining structural relationships between different proteins. We have previously used NLM to map a large dataset of peptide, protein, and virus ROA spectra into a readily visualizable two-dimensional space in which points close to or distant from each other, respectively, represent similar or dissimilar structures. As well as folded proteins, our dataset contains ROA spectra from many natively unfolded proteins, proteins containing both folded and unfolded domains, denatured partially structured molten globule and reduced protein states, together with folded proteins containing little or no alpha-helix or beta-sheet. In this article, the relative positions of these systems in the NLM plot are used to obtain information about any residual structure that they may contain. The striking differences between the structural propensities of proteins that are unfolded in their native states and those that are unfolded due to denaturation may be responsible for their often very different behavior, especially with regard to aggregation. An ab initio simulation of the Raman and ROA spectra of an alanine oligopeptide in the poly(L-proline) II-helical conformation confirms previous suggestions that this conformation is a significant structural element in disordered peptides and natively unfolded proteins. The use of ROA to identify and characterize proteins containing significant amounts of unfolded structure will, inter alia, be valuable in structural genomics/proteomics since unfolded sequences often inhibit crystallization.

Enantiomerically pure quaternary ammonium salts with a chiral alkyl chain N(CH3)(n-C3H7)2(sec-C4H9)I: synthesis and physical studies.

A pair of enantiomerically pure quaternary ammonium salts with a chiral side chain, methyl-(R)-(1-methylpropyl)di(n-propyl)ammonium iodide 1 and methyl-(S)-(1-methylpropyl)di(n-propyl)ammonium iodide 2, and the related racemate, methyl-(rac)-(1-methylpropyl)di(n-propyl)ammonium iodide 3, were synthesized through a reductive alkylation procedure, starting from enantiomerically pure and, also, racemic forms of (rac)-(1-methylpropyl)amine. A spectroscopic chiroptical signature in solution was provided by the Raman optical activity spectra of compounds 1 and 2. The crystallographic structures of 1, 2, and 3 were examined by single crystal X-ray diffraction. 1 crystallizes in the tetragonal space group P4(3)2(1)2 (no. 96), a = b = 12.826 (2) A, c = 17.730 (2) A, V = 2916.9 (5) A(3), Z = 8, Flack coefficient 0.04 (2). 2 crystallizes in the tetragonal space group P4(1)2(1)2 (no. 92), a = b = 12.842 (1) A, c = 17.749 (2) A, V = 2927.0 (5) A(3), Z = 8, Flack coefficient 0.05 (2). The crystal structures and space groups for 1 and 2 are enantiomorphs and the crystallographic investigation confirmed the absolute configuration of the stereocenter in both compounds. 3 crystallizes in the monoclinic space group P2(1)/n(no. 14), a = 8.178 (1) A, b = 14.309 (2) A, c = 12.328 (2) A, beta = 96.811 (6) degrees, V = 1432.4 (2) A(3), Z = 4.