Experimental Circular Dichroism Spectra Research Articles

KCD: A prediction web server of knowledge-based circular dichroism.

We present a web server that predicts the far-UV circular dichroism (CD) spectra of proteins by utilizing their three-dimensional (3D) structures from the Protein Data Bank (PDB). The main algorithm is based on the classical theory of optical activity together with a set of atomic complex polarizabilities, which are obtained from the analysis of a series of synchrotron radiation CD spectra and their related 3D structures from the PDB. The results of our knowledge-based CD method (KCD) are in good agreement with measured spectra that could include the effect of D-amino acids. Our method also delivers some of the most accurate predictions, in comparison with the calculated spectra from well-established models. Specifically, using a metric of closeness based on normalized absolute deviations between experimental and calculated spectra, the mean values for a series of 57 test proteins give the following figures for such models: 0.26 KCD, 0.27 PDBMD2CD, 0.30 SESCA, and 0.47 DichroCalc. From another point of view, it is worth mentioning the remarkable capabilities of the recent approaches based on artificial intelligence, which can precisely predict the native structure of proteins. The structure of proteins, however, is flexible and can be modified by a diversity of environmental factors such as interactions with other molecules, mechanical stresses, variations of temperature, pH, or ionic strength. Experimental CD spectra together with reliable predictions can be utilized to assess eventual secondary structural changes. A similar kind of evaluation can be done for the case of an incomplete protein structure that has been reconstructed by using different approaches. The KCD method can be freely accessed from: https://kcd.cinvestav.mx/.

Anti-inflammatory activity of phenolics from Hypericum japonicum

Two new phenolics, one xanthonoid (1) and one phloroglucinol derivative (2), together with eighteen known phenolics (3–20), were isolated from the aerial parts of Hypericum japonicum. Their structures were established by extensive spectral analysis, and the absolute configuration of compound 1 was determined by comparison of the calculated and experimental circular dichroism spectra. An anti-inflammatory activity assay revealed that compound 1 exhibited effective inhibitory effects on NO generation in LPS-stimulated RAW 264.7 macrophages, with an IC50 value of 6.34 μg/mL.

(+)-/(−)-Rutabenzofuran A and (+)-/(−)- Rutabenzofuran B: Two unprecedented pairs of Z/E isomeric benzofuran enantiomers from the aerial part of Ruta graveolens L

Two pairs of Z/E isomeric benzofuran enantiomers possessing unprecedented carbon skeletons featuring ring cleavage and addition reactions in the α-pyrone ring of furocoumarin, named rutabenzofuran A [(+)-1 and (−)-1], and rutabenzofuran B [(+)-2 and (−)-2], respectively, were isolated as minor compounds from the water extract of the aerial part of Ruta graveolens L. Their structures were determined by extensive spectroscopic data analysis. The absolute configurations were assigned by comparing the optical rotation with previous research and the experimental circular dichroism (CD) spectra with the calculated electronic CD (ECD) spectra. (−)-1, (+)-2, and (−)-2 were evaluated for antibacterial, anticoagulant, anticancer, and acetylcholinesterase (AChE) inhibitory activities. No anticancer or anticoagulant activities were observed, yet (−)-2 exhibited weak antibacterial activity against Salmonella enterica subsp. Enterica. At the same time, (−)-1, (+)-2, and (−)-2 displayed weak inhibitory activity on AChE.

Anisotropic Circular Dichroism in Aligned Chiral Tellurium Nanorods

AbstractThe anisotropic chiroptical activity of chiral tellurium nanorods (Te NRs) is studied experimentally via circular dichroism (CD) measurements of macroscopically aligned samples. Te NRs with chiral, twisted prismatic shapes, and aspect ratio of ~4 are synthesized using the chiral ligand D‐penicillamine and the surfactant sodium dodecyl sulfate. The anisotropy of their optical activity is studied at two different configurations with the long axis of the NRs oriented parallel and perpendicular to the CD probe beam. The parallel alignment is achieved in aqueous suspension using an alternating electric field that acts on their polarizability anisotropy, estimated to be 3.8 × 10−30 F m2. The perpendicular orientation is measured in a film of the NRs, prepared at a liquid water–organic interface such that the NRs are deposited on a substrate with their long‐axis in‐plane. Finite‐element electromagnetic simulations reproduce well the experimental CD spectra, demonstrating that the optical activity is dominated by the chiral shape‐related Mie‐type resonances. Both the experimental results and simulations show that the CD spectrum is practically inverted between the two light incidence orientations, a phenomenon that appears general to twisted anisotropic nano‐objects.

New Phenylspirodrimanes from the Sponge-Associated Fungus Stachybotrys chartarum MUT 3308

Two phenylspirodrimanes, never isolated before, stachybotrin J (1) and new stachybocin G (epi-stachybocin A) (2), along with the already reported stachybotrin I (3), stachybotrin H (4), stachybotrylactam (5), stachybotrylactam acetate (6), 2α-acetoxystachybotrylactam acetate (7), stachybotramide (8), chartarlactam B (9), and F1839-J (10) were isolated from the sponge-associated fungus Stachybotrys chartarum MUT 3308. Their structures were established based on extensive spectrometric (HRMS) and spectroscopic (1D and 2D NMR) analyses. Absolute configurations of the stereogenic centers of stachybotrin J (1), stachybocin G (2), and stachybotrin I (3), were determined by comparison of their experimental circular dichroism (CD) spectra with their time-dependent density functional theory (TD-DFT) circular dichroism (ECD) spectra. The putative structures of seventeen additional phenylspirodrimanes were proposed by analysis of their respective MS/MS spectra through a Feature-Based Molecular Networking approach. All the isolated compounds were evaluated for their cytotoxicity against five aggressive cancer cell lines (MP41, 786, 786R, CAL33, and CAL33RR), notably including two resistant human cancer cell lines (786R, CAL33RR), and compounds 5, 6, and 7 exhibited cytotoxicity with IC50 values in the range of 0.3-2.2 µM.

Kadsindutalignans A–C: three new dibenzocyclooctadiene lignans from Kasura induta A.C.Sm. and their nitric oxide production inhibitory activities

Phytochemical study on the methanol extract of the stems and leaves of Kadsura induta led to the isolation of six dibenzocyclooctadiene lignans, including three new compounds named kadsindutalignans A–C (1–3), and three known ones, heteroclitalignan B (4), kadsuphilin C (5) and kadsulignan E (6). Their structures were elucidated based on extensive spectroscopic analyses, including HRESIMS, 1D- (1H NMR and 13C NMR), 2D-NMR (HSQC, HMBC, 1H-1H COSY and NOESY), and experimental circular dichroism (CD) spectra. All the isolates inhibited NO production in LPS-activated RAW264.7 cells with IC50 values in the range from 5.67 ± 0.54 µM to 38.19 ± 2.03 µM, compared to that of the positive control of N G-monomethyl-L-arginine acetate (L-NMMA) with an IC50 value of 8.90 ± 0.48 µM. Interestingly, the new compound 2 showed potential inhibition of NO production with an IC50 value of 5.67 ± 0.54 µM, which was higher than that of the positive control.

Two dimers generated by lithospermic decarboxylation coupling from Danshen

To further reveal the active ingredients of Danshen, we systematically studied its chemical components and obtained two new lithospermic acid derivatives (compounds 1 and 2) together with five known phenylpropionic acids (compounds 3–7) from the dried rhizomes of Salvia miltiorrhiza. The structures of the two new compounds were determined by multiple spectral analyses (UV, IR, HR-ESI-MS, NMR, and ECD). In addition, the absolute configurations were established by chiral analysis and calculated and experimental circular dichroism spectra. Biological research indicated that compound 1 could significantly inhibit the proliferation of isoproterenol (ISO)-treated cardiac fibroblasts (AC16 cells), and MMP9 was found to be the most likely target of compound 1. The protein expression and mRNA levels of MMP9 were increased in ISO-induced AC16 cells, which could be reversed by treatment with compound 1. Furthermore, this treatment could alleviate the migration and activation of ISO-induced cardiac fibroblasts.

Strychnovanosides A - C, Three New Lignan Glycosides from Strychnos vanprukii

Phytochemical study of the methanolic extract of the stems and leaves of Strychnos vanprukii led to the isolation of three new (1-3) and four known (4-7) compounds. Their chemical structures were elucidated to be (+)-lyoniresinol 3 α-O- β-D-allopyranoside (1), (-)-lyoniresinol 3 α-O- β-D-allopyranoside (2), 2 α-[(3,5-dimethoxy-4-hydroxy)-benzoyl]-(-)-lyoniresinol-3 α-O- β-D-glucopyranoside (3), (+)-lyoniresinol 3 α-O- β-D-glucopyranoside (4), (-)-lyoniresinol 3 α-O- β-D-glucopyranoside (5), palicoside (6), and rutin (7) by means of detailed HR-ESI-MS, 1D and 2D NMR spectroscopic analysis. In addition, the absolute configurations of 1–3 were determined by experimental Circular Dichroism (CD) spectra. This is the first report of compounds 5 and 7 from S. vanprukii. Compounds 1 - 7 showed inhibitory effects on NO production in LPS stimulated RAW 264.7 cells with IC50 values of 58.50 ± 2.30, 67.70 ± 2.23, 54.44 ± 1.26, 71.58 ± 3.59, 74.47 ± 2.61, 83.62 ± 2.25, and 47.57 ± 4.01 µM, respectively, compared to a value of 43.24 ± 2.41 µM for the positive control compound, NG-monomethyl-L-arginine (L-NMMA).

Theory of Apparent Circular Dichroism Reveals the Origin of Inverted and Noninverted Chiroptical Response under Sample Flipping.

Circular dichroism (CD) finds widespread application as an optical probe for the structure of molecules and supramolecular assemblies. Its underlying chiral light-matter interactions effectively couple between photonic spin states and select quantum-mechanical degrees of freedom in a sample, implying an intricate connection with photon-to-matter quantum transduction. However, effective transduction implementations likely require interactions that are antisymmetric with respect to the direction of light propagation through the sample, yielding an inversion of the chiroptical response upon sample flipping, which is uncommon for CD. Recent experiments on organic thin films have demonstrated such chiroptical behavior, which was attributed to "apparent CD" resulting from an interference between the sample's linear birefringence and linear dichroism. However, a theory connecting the underlying optical selection rules to the microscopic electronic structure of the constituent molecules remains to be formulated. Here, we present such a theory based on a combination of Mueller calculus and a Lorentz oscillator model. The theory reaches good agreement with experimental CD spectra and allows for establishing the (supra)molecular design rules for maximizing or minimizing this chiroptical effect. It furthermore highlights that, in addition to antisymmetrically, it can manifest symmetrically such that no chiroptical response inversion occurs, which is a consequence of a helical stacking of molecules in the light propagation direction.

Chiroptical properties of anionic and neutral nickel(II) bis(dithiolene) complexes based on methyl and dimethyl-dddt ligands.

Racemic and enantiopure nickel(II) bis(dithiolene) anionic and neutral complexes based on the methyl-5,6-dihydro-1,4-dithiin-2,3-dithiolate (me-dddt) and dimethyl-5,6-dihydro-1,4-dithiin-2,3-dithiolate (dm-dddt) ligands have been experimentally and theoretically investigated with a special focus on their chiroptical properties. According to the time-dependent density-functional theory (TD-DFT) calculations, the strong near-infrared absorption bands typical for such complexes are only weakly active in circular dichroism (CD), and moreover, they have opposite signs for the axial and equatorial conformations, due to the variation of the angle between the transition electric and magnetic dipole moments, thus leading to the mutual cancellation of their contributions and the absence of these bands in the experimental CD spectra. The influence of the number of stereogenic centers and of the oxidation state of the complexes on their chiroptical properties is highlighted. The solid-state structure of the complex (TMA)[Ni(rac-me-dddt)2 ] (TMA = tetramethylammonium), determined by single-crystal X-ray diffraction analysis, shows a rather unusual cis arrangement of the two dithiolene ligands, with the methyl substituents adopting an axial conformation, which is not the most stable one in the gas phase.

Structure and Dynamics of RNA Guanine Quadruplexes in SARS-CoV-2 Genome. Original Strategies against Emerging Viruses.

Guanine quadruplex (G4) structures in the viral genome have a key role in modulating viruses’ biological activity. While several DNA G4 structures have been experimentally resolved, RNA G4s are definitely less explored. We report the first calculated G4 structure of the RG-1 RNA sequence of SARS-CoV-2 genome, obtained by using a multiscale approach combining quantum and classical molecular modeling and corroborated by the excellent agreement between the corresponding calculated and experimental circular dichroism spectra. We prove the stability of the RG-1 G4 arrangement as well as its interaction with G4 ligands potentially inhibiting viral protein translation.

Effect of the Metal–Ligand Interface on the Chiroptical Activity of Cysteine‐Protected Nanoparticles

Gold, silver, and copper small nanoparticles (NPs), with average size ≈2 nm, are synthesized and afterward protected with l- and d-cysteine, demonstrating emergence of chiroptical activity in the wavelength range of 250-400 nm for all three metals with respect to the bare nanoparticles and ligands alone. Silver-cysteine (Ag-Cys) NPs display the higher anisotropy factor, whereas gold-cysteine (Au-Cys) NPs show optical and chiroptical signatures slightly more displaced to the visible range. A larger number of circular dichroism (CD) bands with smaller intensity, as compared to gold and silver, is observed for the first time for copper-cysteine (Cu-Cys) NPs. The manifestation of optical and chiroptical responses upon cysteine adsorption and the differences between the spectra corresponding to each metal are mainly dictated by the metal-ligand interface, as supported by a comparison with calculations of the oscillatory and rotatory strengths based on time-dependent density functional theory, using a metal-ligand interface motif model, which closely resembles the experimental absorption and CD spectra. These results are useful to demonstrate the relevance of the interface between chiral ligands and the metal surfaces of Au, Ag, and Cu NPs, and provide evidence and further insights into the origin of the transfer mechanisms and induction of extrinsic chirality.

Concise synthesis and confirmation of the absolute configurations of naturally occurring bioactive 2,7′-cyclolignans

A concise asymmetric synthesis of naturally occurring bioactive 2,7′-cyclolignans, namely 4,4′-dihydroxy-3′,5,5′-trimethoxy-2,7′-cyclolignan and 4,4′-dihydroxy-3,3′,5-trimethoxy-2,7′-cyclolignan, possessing the uncommon 8,8′-syn dimethyl stereochemistry and unsymmetrical C-6 units with 7′,8′-anti-orientation is described using a substrate-controlled stereoselective Friedel-Crafts cyclization as the key step. The products were obtained in good yields with high stereoselectivity. The absolute configurations of natural 4,4′-dihydroxy-3′,5,5′-trimethoxy-2,7′-cyclolignan and those of natural 4,4′-dihydroxy-3,3′,5-trimethoxy-2,7′-cyclolignan were assigned as (7′S,8S,8′S) and (7′R,8R,8′R), respectively, based on the experimental circular dichroism (CD) spectra of the corresponding synthesized compounds.

Chirality analysis of helical polymers

Abstract Optically active macromolecules, having a preferred- or single-handed helical conformation, play important roles in polymeric materials and in life. This article presents how helical polymers can be assessed from a view of chirality. These assessments, based on optical rotation (OR) and circular dichroism (CD) spectral measurements with associated information, include theoretical spectral calculations as well as chromatographic resolution. Specific applied examples are discussed for poly(9,9-dioctylfluorene-2,7-diyl) and derivatives, stereoregular polyolefins bearing centers of chirality in the side chain, isotactic poly(triphenylmethyl methacrylate), and π-stacked poly(dibenzofulvene). For more convincing establishment of a helix, it is important to correlate chiroptical properties with related information such as molar-mass effects, temperature effects, and chemical transformation effects on the properties. Helices of the polyolefins and poly(TrMA) were confirmed considering these aspects. In addition, comparison of chiroptical properties between the polymer in question and a monomeric unit model compound generally helps to confirm a helix. There are no general, reliable methods to quantify helical sense excess. On the other hand, absolute helical sense can be determined by comparing experimental and theoretical CD spectra as well as considering exciton coupling effects in CD spectra. The former method can be more generally applied for a wide range of polymers as far as a good model for calculations is designed, while the latter can be more conveniently and empirically applied for a certain class of polymer structures that are suited to exhibit exciton coupling without using computers.

Exciton Delocalization in Indolenine Squaraine Aggregates Templated by DNA Holliday Junction Scaffolds.

Exciton delocalization plays a prominent role in the photophysics of molecular aggregates, ultimately governing their particular function or application. Deoxyribonucleic acid (DNA) is a compelling scaffold in which to template molecular aggregates and promote exciton delocalization. As individual dye molecules are the basis of exciton delocalization in molecular aggregates, their judicious selection is important. Motivated by their excellent photostability and spectral properties, here, we examine the ability of squaraine dyes to undergo exciton delocalization when aggregated via a DNA Holliday junction (HJ) template. A commercially available indolenine squaraine dye was chosen for the study given its strong structural resemblance to Cy5, a commercially available cyanine dye previously shown to undergo exciton delocalization in DNA HJs. Three types of DNA-dye aggregate configurations-transverse dimer, adjacent dimer, and tetramer-were investigated. Signatures of exciton delocalization were observed in all squaraine-DNA aggregates. Specifically, strong blue shift and Davydov splitting were observed in steady-state absorption spectroscopy and exciton-induced features were evident in circular dichroism (CD) spectroscopy. Strongly suppressed fluorescence emission provided additional, indirect evidence for exciton delocalization in the DNA-templated squaraine dye aggregates. To quantitatively evaluate and directly compare the excitonic Coulombic coupling responsible for exciton delocalization, the strength of excitonic hopping interactions between the dyes was obtained by simultaneously fitting the experimental steady-state absorption and CD spectra via a Holstein-like Hamiltonian, in which, following the theoretical approach of Kühn, Renger, and May, the dominant vibrational mode is explicitly considered. The excitonic hopping strength within indolenine squaraines was found to be comparable to that of the analogous Cy5 DNA-templated aggregate. The squaraine aggregates adopted primarily an H-type (dyes oriented parallel to each other) spatial arrangement. Extracted geometric details of the dye mutual orientation in the aggregates enabled a close comparison of aggregate configurations and the elucidation of the influence of dye angular relationship on excitonic hopping interactions in squaraine aggregates. These results encourage the application of squaraine-based aggregates in next-generation systems driven by molecular excitons.

Excitonic coupling effect on the circular dichroism spectrum of sodium-pumping rhodopsin KR2.

We investigate the role of excitonic coupling between retinal chromophores of Krokinobacter eikastus rhodopsin 2 (KR2) in the circular dichroism (CD) spectrum using an exciton model combined with the transition density fragment interaction (TDFI) method. Although the multimer formation of retinal protein commonly induces biphasic negative and positive CD bands, the KR2 pentamer shows only a single positive CD band. The TDFI calculation reveals the dominant contribution of the Coulomb interaction and negligible contributions of exchange and charge-transfer interactions to the excitonic coupling energy. The exciton model with TDFI successfully reproduces the main features of the experimental absorption and CD spectra of KR2, which allow us to investigate the mechanism of the CD spectral shape observed in the KR2 pentamer. The results clearly show that the red shift of the CD band is attributed to the excitonic coupling between retinal chromophores. Further analysis reveals that the weak excitonic coupling plays a crucial role in the shape of the CD spectrum. The present approach provides a basis for understanding the origin of the KR2 CD spectrum and is useful for analyzing the mechanism of chromophore-chromophore interactions in biological systems.

PDBMD2CD: providing predicted protein circular dichroism spectra from multiple molecular dynamics-generated protein structures.

PDBMD2CD is a new web server capable of predicting circular dichroism (CD) spectra for multiple protein structures derived from molecular dynamics (MD) simulations, enabling predictions from thousands of protein atomic coordinate files (e.g. MD trajectories) and generating spectra for each of these structures provided by the user. Using MD enables exploration of systems that cannot be monitored by direct experimentation. Validation of MD-derived data from these types of trajectories can be difficult via conventional structure-determining techniques such as crystallography or nuclear magnetic resonance spectroscopy. CD is an experimental technique that can provide protein structure information from such conditions. The website utilizes a much faster (minimum ∼1000×) and more accurate approach for calculating CD spectra than its predecessor, PDB2CD (1). As well as improving on the speed and accuracy of current methods, new analysis tools are provided to cluster predictions or compare them against experimental CD spectra. By identifying a subset of the closest predicted CD spectra derived from PDBMD2CD to an experimental spectrum, the associated cluster of structures could be representative of those found under the conditions in which the MD studies were undertaken, thereby offering an analytical insight into the results. PDBMD2CD is freely available at: https://pdbmd2cd.cryst.bbk.ac.uk.

Combined Experimental and Theoretical Studies on Planar Chirality of Partially Overlapped C2-Symmetric [3.3](3,9)Dicarbazolophanes.

Partially overlapped dicarbazolophanes exhibit a planar chirality. In this study, C2-symmetrical [3.3](3,9)dicarbazolophane derivatives (CZ1-CZ3) have been optically resolved by preparative chiral high-performance liquid chromatography for the first time. In their circular dichroism (CD) spectra, moderate Cotton effects (CEs) were observed for their 1Lb and 1La transitions (|Δε| = 10-12 and 51-57 M-1 cm-1, respectively), while intense CEs were notified in their 1B transitions (|Δε| = 156-216 M-1 cm-1), absorption dissymmetry (gabs) factors being in orders of 10-2. Circularly polarized luminescence spectrum was also obtained for cyanamide derivative CZ1, with a comparative luminescence dissymmetry (glum) factor of 0.013. A computational investigation was applied to address the factors for such remarkable chiroptical responses in these dicarbazolophanes of planar chirality. Absolute configurations were unambiguously determined by the comparison of experimental and theoretical CD spectra, which was affirmed by the X-ray crystal structural analysis of enantiomerically pure sulfonamide derivative CZ2.

Structures and exciton dynamics of aggregated lutein and zeaxanthin in aqueous media

We carried out comprehensively experimental and theoretical studies of the aggregates of lutein and zeaxanthin. The experimental absorption, Circular Dichroism (CD) spectra of these aggregates are measured in aqueous ethanol media with different concentrations of water at temperature range of 20–65 °C. Comparing with the broad absorption of monomers around 450 nm, the sharp peaks of absorption band ca. at 369 and 384 nm of lutein evidence two tightly packed H–aggregates, exhibiting non-vibrational bands of monomer. Zeaxanthin tends to form H–type at 20 °C and J–type at 65 °C, based on the absorption spectral shifts. The helical structures of these aggregates are proved by CD spectra with classic excitonic bisignate line-shape due to Cotton effect. Combining with Frenkel exciton model and line-shape spectral theory, the theoretical simulations of experimental absorption and CD spectra are carried out to investigate the helical details of these aggregates. The calculated distance ranges from 0.57 to 0.66 nm with the overlay angle of 10° for all H–types of helical aggregates, which is coherent to the value of nearest distance (~0.65 nm) of lutein and zeaxanthin dimers optimized by Gaussian program. Furthermore, with the help of Pauli master equation, we studied theoretically the dynamics and diffusion of Frenkel exciton in the one-dimensional carotenoid aggregates, using the parameters obtained from the fit of the absorption spectra. As compared with loosely packed J–aggregate, the exciton of tightly structured H–aggregate experiences a faster relaxation within 10 ps from highest excited state to lowest one along with the exciton traveling on the aggregate chain to be trapped. We propose a pattern of gradient diagonal disorder that can localize the exciton at the segment of certain molecules on the aggregate chain. The study involved would be helpful and valuable to understand energy absorption, transfer and trapping in antenna system.

Targeting G-quadruplexes with Organic Dyes: Chelerythrine-DNA Binding Elucidated by Combining Molecular Modeling and Optical Spectroscopy.

The DNA-binding of the natural benzophenanthridine alkaloid chelerythrine (CHE) has been assessed by combining molecular modeling and optical absorption spectroscopy. Specifically, both double-helical (B-DNA) and G-quadruplex sequences—representative of different topologies and possessing biological relevance, such as telomeric or regulatory sequences—have been considered. An original multiscale protocol, making use of molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations, allowed us to compare the theoretical and experimental circular dichroism spectra of the different DNA topologies, readily providing atomic-level details of the CHE–DNA binding modes. The binding selectivity towards G-quadruplexes is confirmed by both experimental and theoretical determination of the binding free energies. Overall, our mixed computational and experimental approach is able to shed light on the interaction of small molecules with different DNA conformations. In particular, CHE may be seen as the building block of promising drug candidates specifically targeting G-quadruplexes for both antitumoral and antiviral purposes.