Structural determinations by circular dichroism spectra analysis using coupled oscillator methods: An update of the applications of the DeVoe polarizability model

Diagrammatic theory of magnetic and quadrupolar contributions to sum-frequency generation in composite systems

Second-order nonlinear processes like Sum-Frequency Generation (SFG) are essentially defined in the electric dipolar approximation. However, when dealing with the SFG responses of bulk, big nanoparticles, highly symmetric objects, or chiral species, magnetic and quadrupolar contributions play a significant role in the process too. We extend the diagrammatic theory for linear and nonlinear optics to include these terms for single objects as well as for multipartite systems in interaction. Magnetic and quadrupolar quantities are introduced in the formalism as incoming fields, interaction intermediates, and sources of optical nonlinearity. New response functions and complex nonlinear processes are defined, and their symmetry properties are analyzed. This leads to a focus on several kinds of applications involving nanoscale coupled objects, symmetric molecular systems, and chiral materials, both in line with the existing literature and opening new possibilities for original complex systems.

Revealing the nature of optical activity in carbon dots produced from different chiral precursor molecules

Carbon dots (CDs) are light-emitting nanoparticles that show great promise for applications in biology and medicine due to the ease of fabrication, biocompatibility, and attractive optical properties. Optical chirality, on the other hand, is an intrinsic feature inherent in many objects in nature, and it can play an important role in the formation of artificial complexes based on CDs that are implemented for enantiomer recognition, site-specific bonding, etc. We employed a one-step hydrothermal synthesis to produce chiral CDs from the commonly used precursors citric acid and ethylenediamine together with a set of different chiral precursors, namely, L-isomers of cysteine, glutathione, phenylglycine, and tryptophan. The resulting CDs consisted of O,N-doped (and also S-doped, in some cases) carbonized cores with surfaces rich in amide and hydroxyl groups; they exhibited high photoluminescence quantum yields reaching 57%, chiral optical signals in the UV and visible spectral regions, and two-photon absorption. Chiral signals of CDs were rather complex and originated from a combination of the chiral precursors attached to the CD surface, hybridization of lower-energy levels of chiral chromophores formed within CDs, and intrinsic chirality of the CD cores. Using DFT analysis, we showed how incorporation of the chiral precursors at the optical centers induced a strong response in their circular dichroism spectra. The optical characteristics of these CDs, which can easily be dispersed in solvents of different polarities, remained stable during pH changes in the environment and after UV exposure for more than 400 min, which opens a wide range of bio-applications.

Knowledge-Based Atomic Polarizabilities Used to Model Circular Dichroism Spectra of Proteins

We present a model of circular dichroism for proteins, which is mainly based on both the classical theory of optical activity and a series of effective atomic polarizabilities. Such polarizabilities are extracted from the analysis of a set of synchrotron radiation circular dichroism spectra and their corresponding three-dimensional structures from the Protein Data Bank. Each modeled spectrum is obtained from the protein atomic coordinates and the identification of its secondary structure elements. The resulting spectra are in good agreement with additional experimental data and also with the predictions of some other models. Among them, only our approach is able to describe the effect of d-amino acids. Moreover, our model is also utilized to evaluate protein reconstructions as well as structural changes.

ECD exciton chirality method today: a modern tool for determining absolute configurations

The application of the exciton chirality method (ECM) to interpret electronic circular dichroism (ECD) spectra is a well‐established and still popular approach to assign the absolute configuration (AC) of natural products, chiral organic compounds, and organometallic species. The method applies to compounds containing at least two chromophores with electric dipole allowed transitions (e.g., π–π* transitions). The exciton chirality rule correlates the sign of an exciton couplet (two ECD bands with opposite sign and similar intensity) with the overall molecular stereochemistry, including the AC. A correct application of the ECM requires three main prerequisites: (a) the knowledge of the molecular conformation, (b) the knowledge of the directions of the electric transition moments (TDMs), and (c) the assumption that the exciton coupling mechanism must be the major source of the observed ECD signals. All these prerequisites can be easily verified by means of quantum‐mechanical (QM) calculations. In the present review, we shortly introduce the general principles that underpin the use of the ECM for configurational assignments and survey its applications, both classic ones and some reported in the recent literature. Based on these examples, we will stress the advantages of the ECM but also the key requisites for its correct application. Additionally, we will discuss the dependence of the couplet sign on geometrical parameters (angles α,β,γ between TDMs), which can be helpful for discerning the sign of exciton chirality in ambiguous situations. Finally, we will present a molecular orbital (MO) description of the exciton coupling phenomenon.

Chirality Nanosensor with Direct Electric Readout by Coupling of Nanofloret Localized Plasmons with Electronic Transport

The detection of enantiopurity for small sample quantities is crucial, particularly in the pharmaceutical industry; however, existing methodologies rely on specific chiral recognition elements, or complex optical systems, limiting its utility. A nanoscale chirality sensor, for continuously monitoring molecular chirality using an electric circuit readout, is presented. This device design represents an alternative real-time scalable approach for chiral recognition of small quantity samples (less than 10³ adsorbed molecules). The active device component relies on a gold nanofloret hybrid structure, i.e., a high aspect ratio semiconductor-metal hybrid nanosystem in which a SiGe nanowire tip is selectively decorated with a gold metallic cap. The tip mechanically touches a counter electrode to generate a nanojunction, and upon exposure to molecules, a metal-molecule-metal junction is formed. Adsorption of chiral molecules at the gold tip induces chirality in the localized plasmonic resonance at the electrode-tip junction and manifests in an enantiospecific current response.

The role of chlorine position in the electronic circular dichroism of chlorophenyl-ethanol investigated by vibronic calculations

(R)-1-phenyl-ethanol (PhEtOH) and the different isomers of (R)-1-(chlorophenyl)ethanol (ClPhEtOH) exhibit very interesting electronic circular dichroism (ECD) in methanol. In all cases, the spectrum shows clear vibronic features, but it is monosignated and negative for PhEtOH and meta-ClPhEtOH, positive for the ortho isomer and bisignated for the para isomer. We used computational chemistry to rationalise this behaviour adopting CAM-B3LYP/def2-TZVP, describing the bulk solvent effects with polarizable continuum models and solute-solvent specific interactions with clusters comprising the solute and two solvent molecules. We adopted harmonic vibronic models to compute the ECD spectral shapes of all stable conformers, and we obtained the room-temperature spectra by Boltzmann average. Simulated spectra are in very good agreement with experiment and allow us to rationalise their difference in terms of the relevance of Franck-Condon (FC) and Herzberg-Teller (HT) intensity-borrowing contributions, modulated by the substituent effect. The bisignated shape of the spectrum of para-ClPhEtOH arises from the competition of opposite-sign FC and HT bands, promoted by different vibrational modes. Due to the challenges we document in computing its ECD spectrum, para-ClPhEtOH represents a good test case to help the development of novel methodologies for an improved description of weak vibronic ECD spectra of flexible systems in explicit solvents.

Dynamic Control of the Self-Assembling Properties of Cyclodextrins by the Interplay of Aromatic and Host-Guest Interactions

The presence of a doubly-linked naphthylene clip at the O-2^I and O-3^II positions in the secondary ring of β-cyclodextrin (βCD) derivatives promoted their self-assembly into head-to-head supramolecular dimers in which the aromatic modules act either as cavity extension walls (if the naphthalene moiety is 1,8-disubstituted) or as folding screens that separate the individual βCD units (if 2,3-disubstituted). Dimer architecture is governed by the conformational properties of the monomer constituents, as determined by NMR, fluorescence, circular dichroism, and computational techniques. In a second supramolecular organization level, the topology of the assembly directs host-guest interactions and, reciprocally, guest inclusion impacts the stability of the supramolecular edifice. Thus, inclusion of adamantane carboxylate, a well-known βCD cavity-fitting guest, was found to either preserve the dimeric arrangement, leading to multicomponent species, or elicit dimer disruption. The ensemble of results highlights the potential of the approach to program self-organization and external stimuli responsiveness of CD devices in a controlled manner while keeping full diastereomeric purity.

For a Correct Application of the CD Exciton Chirality Method: The Case of Laucysteinamide A

The circular dichroism (CD) exciton chirality method (ECM) is a very popular approach for assigning the absolute configuration (AC) of natural products, thanks to its immediacy and ease of application. The sign of an exciton couplet (two electronic CD bands with opposite sign and similar intensity) can be directly correlated with the molecular stereochemistry, including the AC. However, a correct application of the ECM necessitates several prerequisites: knowledge of the molecular conformation; knowledge of transition moment direction; and preeminence of the exciton coupling mechanism with respect to other sources of CD signals. In recent years, by using quantum-chemical CD calculations, we have demonstrated that some previous applications of ECM were wrong or based on incorrect assumptions. In a recent publication of this journal (Mar. Drugs, 2017, 15(4), 121), the ECM was employed to assign the AC of a marine metabolite, laucysteinamide A. This is a further case of incorrect application of the method, where none of the aforementioned prerequisites is fully met. Using this example, we will discuss the criteria required for a correct application of the ECM.

EXAT: EXcitonic analysis tool

We introduce EXcitonic Analysis Tool (EXAT), a program able to compute optical spectra of large excitonic systems directly from the output of quantum mechanical calculations performed with the popular Gaussian 16 package. The software is able to combine in an excitonic scheme the single-chromophore properties and exciton couplings to simulate energies, coefficients, and excitonic spectra (UV-vis, CD, and LD). The effect of the environment can also be included using a Polarizable Continuum Model. EXAT also presents a simple graphical user interface, which shows on-screen both site and exciton properties. To show the potential of the method, we report two applications on a a chiral perturbed BODIPY system and DNA G-quadruplexes, respectively. The program is available online at http://molecolab.dcci.unipi.it/tools/. © 2017 Wiley Periodicals, Inc.

Revision of the Absolute Configuration of Preussilides A-F Established by the Exciton Chirality Method

In a recent contribution to this Journal (J. Nat. Prod. 2017, 80, 1531-1540), Noumeur et al. reported the isolation and structure elucidation of six novel polyketides named preussilides A-F, endowed with remarkable antiproliferative activity. The absolute configuration of the new compounds was established mainly by analyzing exciton-coupled electronic circular dichroism (ECD) spectra. However, the application of the exciton chirality method (ECM) was incorrect, because the chirality defined by transition moments was assigned in a wrong way. A correct application of the ECM, substantiated by time-dependent density functional theory (TDDFT) calculations of ECD spectra, led us to revise the absolute configuration of Preussilides A-F. A brief discussion on the criteria required for a correct application of the ECM is also presented.

Enhancing and reducing chirality by opposite circularly-polarized light irradiation on crystalline chiral domains consisting of nonchiral photoresponsive W-shaped liquid crystal molecules

We found possible chirality enhancement and reduction in chiral domains formed by photoresponsive W-shaped molecules by irradiation with circularly polarized light (CPL). The W-shaped molecules exhibit a unique smectic phase with spontaneously segregated chiral domains, although the molecules are nonchiral. The chirality control was generated in the crystalline phase, which shows chiral segregation as in the upper smectic phase, and the result appeared to be as follows: for a certain chiral domain, right-CPL stimuli enhanced the chirality, while left-CPL stimuli reduced the chirality, and vice versa for another chiral domain. Interestingly, no domain-size change could be observed after CPL irradiation, suggesting some changes in the causes of chirality. In this way, the present system can recognize the handedness of the applied chiral stimuli. In other words, the present material can be used as a sensitive chiral-stimuli-recognizing material and should find invaluable applications, including in chiroptical switches, sensors, and memories as well as in chiral recognition.

Exciton circular dichroism in channelrhodopsin

Channelrhodopsins (ChRs) are of great interest currently because of their important applications in optogenetics, the photostimulation of neurons. The absorption and circular dichroism (CD) spectra of C1C2, a chimera of ChR1 and ChR2 of Chlamydomonas reinhardtii, have been studied experimentally and theoretically. The visible absorption spectrum of C1C2 shows vibronic fine structure in the 470 nm band, consistent with the relatively nonpolar binding site. The CD spectrum has a negative band at 492 nm (Δε(max) = -6.17 M(-1) cm(-1)) and a positive band at 434 nm (Δε(max) = +6.65 M(-1) cm(-1)), indicating exciton coupling within the C1C2 dimer. Time-dependent density functional theory (TDDFT) calculations are reported for three models of the C1C2 chromophore: (1) the isolated protonated retinal Schiff base (retPSB); (2) an ion pair, including the retPSB chromophore, two carboxylate side chains (Asp 292, Glu 162), modeled by acetate, and a water molecule; and (3) a hybrid quantum mechanical/molecular mechanical (QM/MM) model depicting the binding pocket, in which the QM part consists of the same ion pair as that in (2) and the MM part consists of the protein residues surrounding the ion pair within 10 Å. For each of these models, the CD of both the monomer and the dimer was calculated with TDDFT. For the dimer, DeVoe polarizability theory and exciton calculations were also performed. The exciton calculations were supplemented by calculations of the coupling of the retinal transition with aromatic and peptide group transitions. For the dimer, all three methods and three models give a long-wavelength C2-axis-polarized band, negative in CD, and a short-wavelength band polarized perpendicular to the C2 axis with positive CD, differing in wavelength by 1-5 nm. Only the retPSB model gives an exciton couplet that agrees qualitatively with experiment. The other two models give a predominantly or solely positive band. We further analyze an N-terminal truncated mutant because it was assumed that the N-terminal domain has a crucial role in the dimerization of ChRs. However, the CD spectrum of this mutant has an exciton couplet comparable to that of the wild-type, demonstrating that it is dimeric. Patch-clamp experiments suggest that the N-terminal domain is involved in protein stabilization and channel kinetics rather than dimerization or channel activity.

Chiral/ring closed vs. achiral/open chain triazine-based organogelators: induction and amplification of supramolecular chirality in organic gels

The purpose of this study is to compare the gelling behavior of two molecules: a chiral compound and its achiral counterpart. The chiral partner is characterized by a rigid, chiral pyrrolidine nucleus, while the achiral one contains a flexible diethanolamine moiety. The chiral compound is an already known good organogelator, but also the achiral compound shows remarkable gelling properties. Very interestingly, a small fraction of the chiral compound induces chirality and strong CD effects in its aggregates with the achiral one. The observed chirality amplification corresponds to a peculiar sergeant-and-soldier effect. Molecular modelling and CD calculations suggested a model for the supramolecular assembly of hetero-aggregates that fits the experimental data.

A TDDFT/MMPol/PCM model for the simulation of exciton-coupled circular dichroism spectra

A multiscale strategy is presented to simulate electronic CD spectra of multichromophoric systems using an excitonic approach in which all components are calculated self-consistently through a fully polarizable QM/MM/PCM method.

J- vs. H-type assembly: pentamethine cyanine (Cy5) as a near-IR chiroptical reporter

The DNA-enabled dimerization of pentamethine cyanine (Cy5) dyes was studied by optical methods. The value of cyanine as a chiroptical reporter using a monomer-to-dimer switch is demonstrated. The specific shape of the CD signal and its high intensity are a result of J-type assembly.

Advantages of electronic circular dichroism detection for the stereochemical analysis and characterization of drugs and natural products by liquid chromatography

The need for analytical methods for the determination of the enantiomeric excess of chiral compounds increased significantly in the last decades, and enantioselective separation techniques resulted particularly efficient to this purpose. Moreover, when detection systems based on chiroptical properties (optical rotation or circular dichroism) are employed in high-performance liquid chromatography (HPLC), the stereochemistry of a chiral analyte can be fully determined. Indeed, the coupling of HPLC with chiroptical detection systems allows the simultaneous assessment of the absolute configuration of stereoisomers and the evaluation of the enantiomeric/diastereomeric excess of samples. These features are particularly important in the study of drugs and natural products provided with biological activity, because the assignment of their absolute stereochemistry is essential to establish reliable structure-activity relationships. The following review aims to discuss the analytical advantages arising from the employment of electronic circular dichroism (ECD) detection systems in stereochemical analysis by HPLC upon chiral and non-chiral stationary phases and their use for the stereochemical characterization of chiral drugs and natural compounds. The different methods for the correlation between absolute stereochemistry and chiroptical properties are critically discussed. Relevant HPLC applications of ECD detection systems are then reported, and their analytical advantages are highlighted. For instance, the importance of the concentration-independent anisotropy factor (g-factor; g=Δɛ/ɛ) for the determination of the stereoisomeric composition of samples upon non-chiral stationary phases is underlined, since its sensitivity makes ECD detection very well suited for the enantioselective analysis of large libraries of chiral compounds in relatively short times.

Circular dichroism of quadruplex structures

Circular dichroism (CD) is a widespread technique for studying the polymorphism of G-quadruplexes. In this chapter the CD spectral features characteristic of different folding topologies of G4-DNA are analyzed in terms of the sequence of the syn or anti glycosidic bond angle (GBA) within a quadruplex stem. Depending on the GBA sequence, the chiral disposition of two stacked guanines, adjacent along a strand, is different and this leads to a predictable contribution to the overall CD spectrum. The CD spectra of a series of G-quadruplexes, chosen as prototypal of the most common strand folding, are illustrated. The validity and the prediction power of the approach is corroborated by the analysis of CD spectra of structurally modified G4-DNA either with chemically modified guanines or polarity inversion site (5'-5' or 3'-3') along the strands or additional nucleobases contributing to the stacking.

Conformational aspects in the studies of organic compounds by electronic circular dichroism

The electronic circular dichroism (ECD) spectra of flexible molecules include the contributions of all conformers populated at the working temperature. ECD spectra of chiral substrates depend on their stereochemistry in terms of both absolute configuration, as reflected in the sign of the spectrum, and molecular conformation, which dictates the overall spectral shape (possibly including the sign) in a very sensitive manner. The unique high sensitivity of ECD towards conformation, as well as of other chiroptical spectroscopies, renders these techniques a useful alternative or complement to standard spectroscopic tools for conformational investigations, such as NMR. This tutorial review provides first a brief discussion of the main principles of ECD spectroscopy and related methods for interpretation of spectra, with special reference to conformational aspects. The review focuses on the common problems encountered in the application of ECD for assignments of absolute configuration of flexible molecules. These problems can be handled either by taking into account the whole conformational ensemble or by considering rigid derivatives prepared ad hoc. Finally, the review presents the relatively less common but very interesting application of ECD spectroscopy for conformational analyses of organic compounds.

Axial chirality of donor-donor, donor-acceptor, and tethered 1,1'-binaphthyls: a theoretical revisit with dynamics trajectories

The circular dichroism (CD) spectra of (R)-2,2'-dimethoxy-1,1'-binaphthyl (DD) and its untethered and tethered donor-acceptor analogues (DA and DA7-DA9) were investigated experimentally and theoretically. The experimental CD spectra of DD and DA resembled each other in several aspects, displaying a positive-positive-negative Cotton effect pattern in the (1)L(b)-(1)L(a) region and a strong negative couplet at the (1)B(b) band, but significantly differed in transition energy and rotatory strength. The couplet amplitude (A) of the main band was 1.6 times larger in DA than in DD, despite the comparable extinction coefficients and seemingly analogous conformations. An additional positive Cotton effect was observed at the CT (CT) band for donor-acceptor binaphthyl DA. Our theoretical prediction of the CD spectra of binaphthyls involves three sequential first principle quantum mechanics (QM) calculations. Thus, the geometry optimizations of a series of conformers with varying dihedral angles were performed by the dispersion-corrected DFT-D method using the B97-D functional and the TZV2P basis set. The potential curve as a function of the dihedral angle (θ) was obtained by using the SCS-MP2/TZVPP single-point energy calculations with and without application of the solvent correction. The CD spectrum of each conformer was independently calculated by the second-order approximate coupled cluster calculation (CC2 method) using the TZVPP basis sets and the resolution of the identity (RI-J) approximation. The (net) theoretical CD spectrum was obtained by averaging over all possible conformers, where the dynamics trajectories based on the relative SCS-MP2 energies were taken into account. By using 17 possible conformers at θ varying from 50 to 130° by 5° intervals, the experimental CD spectra were successfully reproduced in a quantitative manner, enabling us to characterize properly almost all of the important spectral features and chiroptical properties. The two-state model, reported previously, turned out to have led to the right answer with wrong reasons. The couplet sign and amplitude A are critical functions of θ and can be used not only for (qualitatively) determining the absolute configuration but also for quantitatively analyzing the binaphthyl conformations. The angle dependence of A was already argued in the classical coupled oscillator and exciton chirality theories to provide reasonable structure elucidations but only in a qualitative or semiquantitative manner. Our method is able to predict the A value quantitatively as a function of θ. For tethered binaphthyls DA7-DA9, particular care should be exercised in the conformational assessment based on the classical treatment because the amplitude A was shown to be significantly affected by the existence of the tether itself. In the present method, the couplet amplitude A was nicely related to the dihedral angle θ of DA and DD by the state-of-the-art ab initio calculations, enabling us to gain the quantitative information about the conformation of axially chiral binaphthyls. The Cotton effect at the CT band also serves as a complementary clue for elucidating the conformation of donor-acceptor binaphthyls.

Determination of the absolute configurations of bicyclo[3.1.0]hexane derivatives via electronic circular dichroism, optical rotation dispersion and vibrational circular dichroism spectroscopy and density functional theory calculations

The electronic circular dichroism (ECD), optical rotation dispersion (ORD), and vibrational circular dichroism (VCD) spectra of a pair of enantiomers, i.e. 3 and 4, of a bicyclo[3.1.0]hexane derivative have been measured in acetonitrile and acetonitrile-d(3), respectively. Extensive conformational searches at the B3LYP/6-311++G** level have been carried out for 3, which has four OH and one N(3) functional groups. For the bicyclo[3.1.0]hexane ring of 3, the boat-like conformers have been found to be much more stable than the chair-like conformers, while the number and the strength of the intramolecular hydrogen bonds have been identified as the dominant factors in the relative stability among the boat-like and among the chair-like conformers. DFT simulations of the ECD, ORD and VCD spectra have been performed for all low energy conformers at the B3LYP/6-311++G** and B3LYP/aug-cc-pVDZ level. Implicit continuum polarization model has been used to account for solvent effects in all these chiroptical measurements. Comparison of the DFT simulations with the experimental data shows that all three chiroptical properties yield the same absolute configuration assignment for . This work demonstrates that using multiple chiroptical spectroscopic methods in combination with DFT calculations allows one to determine absolute configurations with high confidence for chiral carbohydrates and their analogues, which possess a large number of rotatable bonds.

On the chiroptical behavior of conjugated multichromophoric compounds of a new pseudoaromatic class: bicolchicides and biisocolchicides

BACKGROUND

It is well known that, stemming from the mutual interplay between chromophores, circular dichroism (CD) is a powerful technique to deal with structural problems for both the small organic molecule and the biopolymer. However, quantitative interpretations of the spectroscopic and structural terms that give rise to the exciton couplet are usually presented for ideal cases, or a few CD bands only are taken into account, overlooking the role of the solvent medium.

METHODOLOGY/PRINCIPAL FINDINGS

Circular dichroism and UV absorption spectra were carried out for colchicide (3) and isocolchicide (6), as well as their coupling products, 10,10'-bicolchicide (2) and 9,9'-biisocolchicide (5), in both hydrogen bonding and non hydrogen bonding solvents, as well as MeCN/H(2)O mixtures. A dramatic control by the solvent emerged, as even tiny changes in the composition of solvent mixtures, at ca 1 water molar fraction, induced a dramatic modification of their CD bands. A mutarotation phenomenon--long known for isocolchicine (8)--was also observed for 5, and can be attributed to the interconversion between atropisomers (R(a),7S),(R(a),7'S)-5a and (R(a),7S),(S(a),7'S)-5b.

CONCLUSIONS/SIGNIFICANCE

Our data show that with molecules built on two structurally identical moieties which embody both hydrophilic and hydrophobic groups, even tiny changes in the composition of solvent mixtures cause a dramatic modification of the CD bands. Their analysis arrives at a qualitative rationalization of the observed CD couplets from the coupling of high energy transitions, while attempts at a quantitative interpretation of these phenomena through time-dependent density functional theory allowed to reproduce satisfactorily the CD spectrum in the 300-450 nm region only. Failure with higher energies probably reflects currently inadequate specific theoretical treatments of the solvent medium.

A non-empirical chromophoric interpretation of CD spectra of DNA G-quadruplex structures

G-quadruplex DNA (G4-DNA) structures are four-stranded helical DNA (or RNA) structures, comprising stacks of G-tetrads, which are the outcome of planar association of four guanines in a cyclic Hoogsteen hydrogen-bonding arrangement. In the last decade the number of publications where CD spectroscopy has been used to study G4-DNAs, is extremely high. However, with very few exceptions, these investigations use an empirical interpretation of CD spectra. In this interpretation two basic types of CD spectra have been associated to a single specific difference in the features of the strand folding, i.e. the relative orientation of the strands, "parallel" (all strands have the same 5' to 3' orientation) or "antiparallel". Different examples taken from the literature where the empirical interpretation is not followed or is meaningless are presented and discussed. Furthermore, the case of quadruplexes formed by monomeric guanosine derivatives, where there is no strand connecting the adjacent quartets and the definition parallel/antiparallel strands cannot apply, will be discussed. The different spectral features observed for different G-quadruplexes is rationalised in terms of chromophores responsible for the electronic transitions. A simplified exciton coupling approach or more refined QM calculations allow to interpret the different CD features in terms of different stacking orientation (head-to-tail, head-to-head, tail-to-tail) between adjacent G-quartets irrespectively of the relative orientation of the stands (parallel/antiparallel).

Role of environmental factors on the structure and spectroscopic response of 5'-DNA-porphyrin conjugates caused by changes in the porphyrin-porphyrin interactions

We have explored the utility, strength, and limitation of through-space exciton-coupled circular dichroism in determination of the secondary structure of optically active chromophoric nanoarrays using the example of end-capped porphyrin- and metalloporphyrin-oligodeoxynucleotide conjugates. We put special emphasis on the explanation of the origin and significance of the distinctive multiple bands in the CD spectra (trisignate and tetrasignate CD bands). Such CD profiles are often observed in chiral aggregates or multichromophoric arrays but have never before been studied in detail. We found that variation of temperature and ionic strength has a profound effect on the geometry of the porphyrin-DNA conjugates and thus the nature of electronic interactions. At lower temperatures and in the absence of NaCl all three 5'-DNA-porphyrin conjugates display negative bisignate CD exciton couplets of variable intensity in the Soret region resulting from through-space interaction between the electric transition dipole moments of the two end-capped porphyrins. As the temperature is raised these exciton couplets are transformed into single positive bands originating from the porphyrin-single-strand DNA interactions. At higher ionic strengths and low temperatures, multisignate CD bands are observed in the porphyrin Soret region. These CD signature bands originate from a combination of intermolecular, end-to-end porphyrin-porphyrin stacking between duplexes and porphyrin-DNA interactions. The intermolecular aggregation was confirmed by fluorescence and absorption spectroscopy and resonance light scattering. DeVoe theoretical CD calculations, in conjunction with molecular dynamics simulations and Monte Carlo conformational searches, were used to mimic the observed bisignate exciton-coupled CD spectra as well as multiple CD bands. Calculations correctly predicted the sign and shape of the experimentally observed CD spectra. These studies reveal that the exciton-coupled circular dichroism is a very useful technique for the determination of the structure of optically active arrays.

Determination of absolute configuration--an overview related to this special issue

Rapid progress in asymmetric synthesis stimulated a further development of methods and techniques for the determination of absolute configuration of chiral molecules. In recent years the direct methods, i.e. X-ray diffraction analysis, circular dichroism (vibrational and electronic), Raman optical activity, optical rotation measurements, as well as indirect methods for relative configuration assignment with the use of NMR spectroscopy or enzymatic transformations, are receiving increasing attention not only by specialists in the field but also by synthetic and structural chemists alike. This paper provides a short overview of the methods currently used, as well as references to contributions collected in this Thematic Issue of Chirality.

Application of electronic circular dichroism in configurational and conformational analysis of organic compounds

This tutorial review is addressed to readers with a background in basic organic chemistry and spectroscopy, but without a specific knowledge of electronic circular dichroism. It describes the fundamental principles, instrumentation, data analysis, and different approaches for interpretation of ECD. The discussion focuses on the application of ECD, also in combination with other methods, in structural analysis of organic compounds, including host-guest complexes, and will emphasize the importance of the interplay between configurational and conformational factors. The tutorial also covers modern supramolecular aspects of ECD and recent developments in computational methods.

Application of chiral technology in a pharmaceutical company. Enantiomeric separation and spectroscopic studies of key asymmetric intermediates using a combination of techniques. Phenylglycidols

Phenylglycidols substituted in the 2-, 3-, and 4- positions with fluorine, chlorine, and trifluoromethyl, and with methoxy in the 3- position, were synthesized from the corresponding E-cinnamic acids and separated into their (R,R)- and (S,S)- enantiomers using subcritical fluid chromatography with mixtures of MeOH in CO(2), on either a Chiralpak AD or AS chiral stationary phase. These compounds and commercially-available (R,R)- and (S,S)-phenylglycidol were analyzed for their vibrational circular dichroism (VCD), electronic circular dichroism (ECD), and optical rotation (OR) properties to exemplify a strategy whereby the absolute stereochemistry of common and key chiral intermediates is established early in the structure-activity and structure-property relationship phase of a drug discovery program in a pharmaceutical company. From this study, substituents in the phenyl group of the synthesized molecules were found not to grossly alter spectroscopic features, and therefore, diagnostic absorption bands in the respective VCD spectra, and the sign and shape of the measured ECD curves could be used to determine and track the absolute stereochemistry of analogs without necessarily requiring time-consuming ab initio calculations of all low energy conformers for all compounds. VCD, OR, and ECD calculations for the determination of absolute configuration carried out at the DFT level with the hybrid B3PW91 functional and the TZVP basis set were found to be especially useful in this study.

Renaissance in chiroptical spectroscopic methods for molecular structure determination

Two of the chiroptical spectroscopic methods, namely optical rotatory dispersion (ORD) and electronic circular dichroism (ECD), have been around for several decades. But their use in determining the absolute configuration and predominant conformation is gaining renewed interest with the availability of quantum mechanical methods for predicting ORD and ECD. Two other methods, namely vibrational circular dichroism (VCD) and vibrational Raman optical activity (VROA), are relatively new and offer convenient approaches for deducing the structural information in chiral molecules. With the availability of quantum mechanical programs for predicting VCD and VROA, these methods have attracted numerous new researchers to this area. This review summarizes the latest developments in these four areas and provides examples where more than one method has been used to confirm the information obtained from individual methods.

Enantiomeric separation and determination of absolute stereochemistry of asymmetric molecules in drug discovery—Building chiral technology toolboxes

The application of Chiral Technology, or the (extensive) use of techniques or tools for the determination of absolute stereochemistry and the enantiomeric or chiral separation of racemic small molecule potential lead compounds, has been critical to successfully discovering and developing chiral drugs in the pharmaceutical industry. This has been due to the rapid increase over the past 10-15 years in potential drug candidates containing one or more asymmetric centers. Based on the experiences of one pharmaceutical company, a summary of the establishment of a Chiral Technology toolbox, including the implementation of known tools as well as the design, development, and implementation of new Chiral Technology tools, is provided.