Electronic Circular Dichroism Spectroscopy Research Articles

Controlling Chirogenic Effects in Porphyrin Based Supramolecular Systems: Theoretical Analysis Versus Experimental Observations.

Electronic circular dichroism (ECD) spectroscopy is a widely employed method for studying chiral analysis, requiring the presence of a chromophore close to a chiral centre. Porphyrinoids are found to be one of the best chromophoric systems serving for this purpose and enabling the application of ECD spectroscopy for chirality determination across diverse classes of organic compounds. Consequently, it is crucial to understand the induction mechanisms of ECD in the porphyrin-based complexes. The present study explores systematically the influence of secondary chromophores, bonded to an achiral zinc porphyrin or to chiral guest molecules, on the B-region of ECD spectra using the time-dependent density functional theory (TD-DFT) calculations. The study analyses the impact of change in both the conformation of achiral porphyrin (host) and change in position and conformation of chiral organic molecule (guest) on the B-band of ECD spectra (energy, intensity, sign of Cotton effect). Finally, conclusions made on model complexes are applied to published experimental data, contributing to a deeper understanding of various factors influencing ECD spectra in chiral systems. In addition, a computer program aimed to help rationalise ECD spectra by visualizing corresponding orbital energies, rotatory strengths, electric and magnetic transition moments, and angles between them, is presented.

Caffeoylquinic acid esters, lignans and flavones from Yua thomsonii with cytotoxic and nitric oxide inhibitory activities

Phytochemical study on the aerial parts of Yua thomsonii resulted in the isolation of 11 secondary metabolites, including a new caffeoyl quinic acid derivative, 3-O-trans-caffeoyl-4-O-acetylquinic acid methyl ester (1), a new dihydrobenzofuran neolignan, 3,5-dimethoxy-4-(1″,3″-dihydroxy-2″-propyloxyl)-4′,7-epoxy-8,5′-neolignan-4,9,9′-triol (3) and nine known compounds, methyl 4-O-coumaroylquinate (2), (7S*,8S*)-3-methoxy-3′,7-epoxy-8,4′-oxyneolignan-4,9,9′-triol (4), kompasinol A (5), lyoniresinol (6), schizandriside (7), (−)-isolariciresinol 3a-O-β-D-xylopyranoside (8), lyoniside (9), vitexin (10) and luteolin 4′-O-β-glucopyranoside (11). Their structures were elucidated using comprehensive spectroscopic methods, including 1D and 2D NMR and HRESI mass spectra. The absolute configurations of 1 and 3 were deduced by electronic circular dichroism spectroscopy. Compounds 1, 3, 5 and 6 exhibited nitric oxide (NO) inhibitory effects, with IC50 values ranging from 12.18 to 29.45 µM. However, compounds 1, 3, 6 and 8 were non-cytotoxic towards HepG2 and MCF-7 carcinoma cells.

Three new constituents from the stems of Knema globularia and their α-glucosidase inhibitory activity

Three new metabolites (1−3) were isolated from the stems of Knema globularia, along with five known compounds, including kaempferol (4), quercetin (5), isovanillic acid (6), protocatechuic acid (7), and gallic acid (8). Their structures were deduced using NMR spectroscopic, mass spectrometric analyses, and literature data. The absolute configurations of 1−3 were established by electronic circular dichroism (ECD) spectroscopy. α-Glucosidase inhibitory activities of those compounds were evaluated using a spectrophotometric method, compounds 1−3 showed very strong effects towards α-glucosidase with IC50 values 1.59, 0.58 and 1.37 µM, respectively (the positive control, acarbose, IC50 93.63 µM). Simultaneously, enzyme kinetics study indicated that 2 was a mix-type inhibitor. 2 interacted well in the active site of α-glucosidase enzyme, primarily through hydrogen bonds and hydrophobic interactions.

Synthesis, Resolution, and Absolute Configuration of a Phosphine-Based Hemicryptophane Cage with an Endo Phosphorus Lone Pair and Formation of the Corresponding Gold Complex.

The synthesis, characterization, and chiroptical properties of a new class of hemicryptophanes combining a phosphine moiety and a cyclotriveratrylene unit are reported. The synthesis was short and efficient. The racemic mixture of the cage was resolved by chiral high-performance liquid chromatography (HPLC), giving access to enantiopure molecular cages, whose absolute configurations could be assigned by electronic circular dichroism (ECD) spectroscopy. These new phosphines were then reacted with gold in order to make the corresponding enantiopure gold complexes. The X-ray structure reveals an endohedral functionalization of the cage with the gold metal entrapped in the heart of the cavity, leading to a Vbur of 58%. Moreover, the chirality of the cyclotriveratrylene unit was found to control the chiral arrangement of the aryl group linked to the phosphorus atom, located at the opposite side of the cavity.

Temperature-dependent chlorosomal self-aggregation of bacteriochlorophyll-d analogs with a branched alkyl chain in a single 1-chlorooctane solvent

Abstract Recently, the supramolecular polymerization of chlorophyll pigments mimicking a natural light-harvesting apparatus (chlorosome) was demonstrated in low-polar organic solvents or aqueous solutions. To obtain the most aggregation models, a concentrated solution of the pigments in a polar organic solvent was diluted with a large amount of a nonpolar organic solvent or water. Here, bacteriochlorophyll-d analogs possessing branched alkyl chains of different lengths at the peripheral 17-propionate residue on the core chlorin π-system were prepared and their highly soluble chlorosomal supramolecules were produced in single 1-chlorooctane as a low-polar solvent. Temperature-dependent electronic absorption and circular dichroism spectroscopies were employed to analyze their self-aggregation and disaggregation mechanisms. The synthetic analogs were monomeric at high temperatures and self-aggregated during cooling of the hot solution through a non-sigmoidal pathway. The obtained chlorosomal self-aggregates were reversibly monomerized by heating the homogeneous solution. The disaggregation pathway was fitted to an isodesmic model whose melting points depended on the alkyl-chain lengths.

Physical insight into optical spectroscopy of chiral covalent organic pillars as molecular nanotubes

In this paper, we theoretically investigate chiral covalent organic pillars synthesized by connecting rim-desymmetrized macrocycle, stimulated by recent experimental synthesis [Nat. Synth. 2023, 2, 395–402]. Transition densities reveal physical mechanism of spectral intensity in one-photon absorption (OPA) and two-photon absorption (TPA), and solvent effect strongly influence the spectral profile and intensity in TPA, but little influence the spectrum in OPA. The intra-unit and inter-unit charge transfer are visualized in five phenylenediamine linkers. The chirality of covalent organic pillars is revealed by electronic circular dichroism (ECD) spectroscopy, and interpreted by the visualized transition electric and magnetic dipole moments. Molecular vibrational information is demonstrated by normal and resonance Raman spectra and vibrational modes. The visualization of static and dynamic (hyper) polarization can reveal the physical mechanisms of polarization dependent normal and resonance Raman scattering. Our results provide deeper understanding on the physical mechanism of chiral covalent organic pillars as molecular nanotubes.

Four Undescribed compounds Isolated from the Aerial Parts of Phyllanthus cochinchinensis with Antimicrobial Activity and NO Production Inhibitory Activity in LPS Activated RAW 264.7 Cells.

Four previously undescribed compounds named phyllancosides A and B (1 and 2), and phyllancochines A and B (3 and 4) together with ten known compounds (5-14) were isolated from the aerial parts of Phyllanthus cochinchinensis Spreng. Their chemical structures were elucidated on the basis of comprehensive analysis of IR, HR-ESI-MS, 1D and 2D NMR spectra. The absolute configurations of 1 and 2 were determined by electronic circular dichroism (ECD) spectra. Compounds 3, 4, and 10 showed antimicrobial activity against E. faecalis, S. aureus, and B. cereus with the MIC values in range of 32-256 μg/mL. Compound 11 inhibited E. faecalis and B. cereus, and 7 inhibited S. aureus with the MIC values in range of 64-128 μg/mL. In addition, compounds 1, 3, 4, 8, and 9 showed significantly NO production inhibitory activity in LPS activated RAW 264.7 cells with IC50 values ranging from 36.57 to 56.34 μM.

Chimgin from Ferula haussknechtii as AChE inhibitor and confirmation of the absolute configuration

Alzheimer’s disease (AD) is the most common cause of dementia worldwide and is classified as a neurodegenerative disorder. From a drug design perspective, natural products (NPs) are more drug-like and are highly compatible with biological systems compared to most synthetic libraries. NPs provide a more efficient and cost-effective approach to new drug discovery. However, the complexity of NPs makes their identification a challenging task. Chimgin, a bicyclic monoterpene with three chiral centers, exhibits a wide range of biological activity. Despite this, the exact structure of chimgin has remained unclear until now. In this study, we quantified the amount of chimgin in Ferula haussknechtii using analytical Reversed-phase high-pressure liquid chromatography equipped with photodiode array detector (RP-HPLC-PDA). Furthermore, we determined the absolute configuration of chimgin through electronic circular dichroism (ECD) spectroscopy and time-dependent density functional theory (TDDFT) calculations. Finally, we evaluated its inhibitory effect on AChE through in vitro and in silico studies. The extraction process yielded an output of 2.82 ± 0.10% with an exact amount of 0.62 ± 0.04 mg of chimgin per 100 g of plant. Based on the results of ECD and TDDFT calculation, the absolute configuration of chimgin was determined to be 1S, 2S, 4S. Chimgin exhibited an inhibitory effect on AChE with an IC50 of 37.43 µM and its mechanism of action was found to be competitive. Highlights Chimgin was isolated from the roots of Ferula haussknechtii. The amount of chimgin in the plant was determined by RP-HPLC-PDA. Its absolute configuration of chimgin was determined using ECD. In vitro acetylcholinesterase activity of the chimgin was evaluated. The docking and molecular dynamic simulation of chimgin was done. Communicated by Ramaswamy H. Sarma

Spectroscopic Validation of Crystallographic Structures of a Protein Active Site by Chiroptical Spectroscopy.

Out-of-plane distortions of a cofactor molecule in a protein active site are functionally important, and in photoreceptors, it has been proposed that they are crucial for spectral tuning and energy storage in photocycle intermediates. However, these subtle structural features are often beyond the grasp of structural biology. This issue is strikingly exemplified by photoactive yellow protein: its 14 independently determined crystal structures exhibit considerable differences in the dihedral angles defining the chromophore geometry, even though most of these are at excellent resolution. Here we developed a strategy to verify cofactor distortions in crystal structures by using quantum chemical calculations and chiroptical spectroscopy, particularly Raman optical activity and electronic circular dichroism spectroscopies. Based on this approach, we identify seven crystal structures with the chromophore geometries inconsistent with the experimentally observed data. The strategy implemented here promises to be widely applicable to uncovering cofactor distortions at active sites and to studies of reaction intermediates.

Inhibitory effect of γ-ray-modified hydroxymethylated baicalins on NO production

Baicalin, a glucuronic flavone, is the major active component in the medicinal plant Scutellaria baicalensis. Herein, baicalin was irradiated by γ-rays to afford four unusual flavanones, baicalinols A (2), B (3), and C (4) and peroxybaicaleinol (5), and two known flavones, oroxylin A (6) and baicalein (7). The structures of the hydroxymethylated products were elucidated using nuclear magnetic resonance spectroscopy and mass spectrometry, and their absolute configuration was established using electronic circular dichroism spectroscopy. Novel hydroxymethylated flavanones 2 and 3 suppressed both nitric oxide (NO) production and the expression of inducible NO synthase and showed significantly higher anti-inflammatory activities in lipopolysaccharide-stimulated macrophages than the parent compound. These newly generated hydroxymethylated flavanones can be potentially used for treating inflammatory diseases.

Peroxisome Proliferator Activated Receptor-γ Agonistic Compounds from the Jellyfish-Derived Fungus Cladosporium oxysporum.

In our search for peroxisome proliferator-activated receptor (PPAR) agonists, five undescribed compounds, namely two acyclic diterpenes (1 and 2; cladopsol A and cladopsol B), two sesquiterpenes (3 and 4; cladopsol C and cladopsol D), and one C21-ecdysteroid (5; cladopsol E), and 15 known compounds were isolated from the jellyfish-derived fungus - Cladosporium oxysporum. The structures of the undescribed compounds were defined using UV, NMR, HR-ESI-MS, and electronic circular dichroism (ECD) spectroscopy and a modified Mosher's method. Luciferase reporter assay and docking analysis suggested that cladopsol B may function as a PPAR-γ partial agonist with a potential antidiabetic lead which may evade the side effects of full agonists. Moreover, cladopsol B stimulated glucose uptake in HepG2 cells with an efficacy comparable to that of rosiglitazone, but with less side effect induced by lipid accumulation in 3T3-L1 cells. Therefore, cladopsol B could serve as a molecular skeleton in a study of advanced antidiabetic lead with less side effect.

Absolute configuration reassignment of nectamazin A: Implications to related neolignans

The ability of nature to produce structurally complex molecules makes the determination of the absolute configuration of natural products a challenging task. Although extensive NMR analysis generally allows for the reliable assignment of relative configurations, the assignments of absolute stereochemistry are commonly performed by empirical comparisons of optical rotation (OR) and/or electronic circular dichroism (ECD) data obtained for related molecules. Such an approach, however, may lead to misassignments and consequent error propagations. Herein, we present the case of the bicyclo(3.2.1)octane neolignan named (+)-nectamazin A. This compound was first reported in 2009 from Nectandra amazonum Nees. (Lauraceae) and had its absolute configuration determined as 7R,8S,3′S,4′R,5′S by means of experimental ECD spectroscopy. Our chemical studies on Ocotea aciphylla (Lauraceae) led to the isolation of (+)-nectamazin A. The extensive analysis of OR, ECD, and vibrational CD data aided by quantum chemical calculations, however, indicated (+)-nectamazin A to have the 7S,8R,3′R,4′S,5′R absolute configuration, in conflict with the configuration reported in the literature. The cause of the original incorrect assignment of (+)-nectamazin A derives from the direct comparison of experimental OR and ECD data obtained for structurally related molecules with different chromophoric systems. As an alternative, VCD spectroscopy is presented as a more reliable and sensitive technique to stereochemical investigations of bicyclo(3.2.1)octane neolignans.

Inhibitor Design Strategy for Myostatin: Dynamics and Interaction Networks Define the Affinity and Release Mechanisms of the Inhibited Complexes.

Myostatin, an important negative regulator of muscle mass, is a therapeutic target for muscle atrophic disorders such as muscular dystrophy. Thus, the inhibition of myostatin presents a strategy to treat these disorders. It has long been established that the myostatin prodomain is a strong inhibitor of the mature myostatin, and the minimum peptide of the prodomain-corresponding to the α1-helix of its lasso-region-responsible for the inhibitory efficiency was defined and characterized as well. Here we show that the minimum peptide segment based on the growth differentiation factor 11 (GDF11), which we found to be more helical in its stand-alone solvated stfate than the similar segment of myostatin, is a promising new base scaffold for inhibitor design. The proposed inhibitory peptides in their solvated state and in complex with the mature myostatin were analyzed by in silico molecule modeling supplemented with the electronic circular dichroism spectroscopy measurements. We defined the Gaussian-Mahalanobis mean score to measure the fraction of dihedral angle-pairs close to the desired helical region of the Ramachandran-plot, carried out RING analysis of the peptide-protein interaction networks and characterized the internal motions of the complexes using our rigid-body segmentation protocol. We identified a variant-11m2-that is sufficiently ordered both in solvent and within the inhibitory complex, forms a high number of contacts with the binding-pocket and induces such changes in its internal dynamics that lead to a rigidified, permanently locked conformation that traps this peptide in the binding site. We also showed that the naturally evolved α1-helix has been optimized to simultaneously fulfill two very different roles: to function as a strong binder as well as a good leaving group. It forms an outstanding number of non-covalent interactions with the mature core of myostatin and maintains the most ordered conformation within the complex, while it induces independent movement of the gate-keeper β-hairpin segment assisting the dissociation and also results in the least-ordered solvated form which provides extra stability for the dissociated state and discourages rebinding.

Supramolecular Chirogenesis in a Sterically Hindered Porphyrin: A Critical Theoretical Analysis.

The determination of molecular stereochemistry and absolute configuration is an important part of modern chemistry, pharmacology, and biology. Electronic circular dichroism (ECD) spectroscopy is a widely used tool for chirality assignment, especially with porphyrin macrocycles employed as reporter chromophores. However, the mechanisms of induced ECD in porphyrin complexes are yet to be comprehensively rationalized. In this work, the ECD spectra of a sterically hindered hexa-cationic porphyrin with two camphorsulfonic acids in dichloromethane and chloroform were experimentally measured and computationally analyzed. The influence of geometric factors such as the position of chiral guest molecules, distortion of the porphyrin macrocycle, and orientation of aromatic and non-aromatic peripheral substituents on the ECD spectra was theoretically studied. Various potential pitfalls, such as a lack of significant conformations and accidental agreement of experimental and simulated spectra, are considered and discussed.

Hard nut to crack: Solving the disulfide linkage pattern of the Neosartorya (Aspergillus) fischeri antifungal protein 2.

As a consequence of the fast resistance spreading, a limited number of drugs are available to treat fungal infections. Therefore, there is an urgent need to develop new antifungal treatment strategies. The features of a disulfide bond-stabilized antifungal protein, NFAP2 secreted by the mold Neosartorya (Aspergillus) fischeri render it to be a promising template for future protein-based antifungal drug design, which requires knowledge about the native disulfide linkage pattern as it is one of the prerequisites for biological activity. However; in the lack of tryptic and chymotryptic proteolytic sites in the ACNCPNNCK sequence, the determination of the disulfide linkage pattern of NFAP2 is not easy with traditional mass spectrometry-based methods. According to in silico predictions working with a preliminary nuclear magnetic resonance (NMR) solution structure, two disulfide isomers of NFAP2 (abbacc and abbcac) were possible. Both were chemically synthesized; and comparative reversed-phase high-performance liquid chromatography, electronic circular dichroism and NMR spectroscopy analyses, and antifungal susceptibility and efficacy tests indicated that the abbcac is the native pattern. This knowledge allowed rational modification of NAFP2 to improve the antifungal efficacy and spectrum through the modulation of the evolutionarily conserved γ-core region, which is responsible for the activity of several antimicrobial peptides. Disruption of the steric structure of NFAP2 upon γ-core modification led to the conclusions that this motif may affect the formation of the biologically active three-dimensional structure, and that the γ-core modulation is not an efficient tool to improve the antifungal efficacy or to change the antifungal spectrum of NFAP2. This article is protected by copyright. All rights reserved.

Chirality of Alanine Molecules in Water Solvent: A Theoretical Perspective

Sequential quantum mechanics/molecular mechanics (QM/MM) calculations combining the average solvent electrostatic configuration (ASEC) and the free energy gradient method are employed to locate minimum structures of α- and β-alanine in a water environment. Herein, we study the solvation effects in the nuclear magnetic resonance (NMR) spectroscopy, vibrational circular dichroism (VCD) spectroscopy, and electronic circular dichroism (ECD) spectroscopy of dl-α-alanine and β-alanine molecules. Our results point out that the ASEC-FEG (average solvent electrostatic configuration with the free energy gradient) method is a suitable approach for finding equilibrium structures of the alanine molecules in aqueous solution. Its accuracy is checked by comparing the optimized structures with those reached by the polarizable continuum model (PCM) and via experimental data. NMR parameters and vibrational and electronic UV-vis spectra are computed with a remarkable agreement with their corresponding experimental values.

The effect of pH and nitrite on the haem pocket of GLB-33, a globin-coupled neuronal transmembrane receptor of Caenorhabditis elegans

Out of the 34 globins in Caenorhabditis elegans, GLB-33 is a putative globin-coupled transmembrane receptor with a yet unknown function. The globin domain (GD) contains a particularly hydrophobic haem pocket, that rapidly oxidizes to a low-spin hydroxide-ligated haem state at physiological pH. Moreover, the GD has one of the fastest nitrite reductase activity ever reported for globins. Here, we use a combination of electronic circular dichroism, resonance Raman and electron paramagnetic resonance (EPR) spectroscopy with mass spectrometry to study the pH dependence of the ferric form of the recombinantly over-expressed GD in the presence and absence of nitrite. The competitive binding of nitrite and hydroxide is examined as well as nitrite-induced haem modifications at acidic pH. Comparison of the spectroscopic results with data from other haem proteins allows to deduce the important effect of Arg at position E10 in stabilization of exogenous ligands. Furthermore, continuous-wave and pulsed EPR indicate that ligation of nitrite occurs in a nitrito mode at pH 5.0 and above. At pH 4.0, an additional formation of a nitro-bound haem form is observed along with fast formation of a nitri-globin.

Jozibrevine D from Ancistrocladus ileboensis, the fifth alkaloid in a series of six possible atropo-diastereomeric naphthylisoquinoline dimers, showing antiparasitic and antileukemic activities

A new dimeric naphthylisoquinoline alkaloid, jozibrevine D (4e), was isolated from the Central-African liana Ancistrocladus ileboensis. It is a Dioncophyllaceae-type metabolite, being R-configured at C-3 and lacking an oxygen function at C-6 in both isoquinoline moieties. The two identical monomers of jozibrevine D are symmetrically linked via the sterically constrained 3′,3′'-positions of the naphthalene units so that the central biaryl linkage is rotationally hindered and the alkaloid is, thus, C2-symmetric. With the two outer biaryl bonds being chiral, too, 4e possesses three consecutive stereogenic axes. The absolute stereostructure of the new compound was assigned by 1D and 2D NMR, ruthenium-mediated oxidative degradation, and electronic circular dichroism (ECD) spectroscopy. Jozibrevine D (4e) is the fifth discovered isomer in a series of six possible natural atropo-diastereomeric dimers. It shows potent, and selective, antiprotozoal activity against P. falciparum (IC50 = 0.14 μM), and it also exhibits good cytotoxic activities against drug-sensitive acute lymphoblastic CCRF-CEM leukemia cells (IC50 = 11.47 μM) and their multidrug-resistant CEM/ADR5000 subline (IC50 = 16.61 μM).

Theoretical and experimental study of the diastereoisomers (2S) and (2R)-naringenin-6-C-β-D-glucopyranoside obtained from Clitoria guianensis

In this work the diastereoisomers (2S) and (2R)-naringenin-6-C-β-D-glucopyroside, isolated for the first time from Clitoria guianensis, were studied using the density functional theory. The frontier molecular orbitals and structural properties showed that the diastereoisomers exhibit the same energy gap 166.61kcalmol-1 and structural properties different, where in the S diastereoisomer, the bond length between the chiral carbon and the phenolic group is greater (difference of 0.0126Å). The HPLC data showed that the retention time of the S-diastereoisomer (16.7min) is shorter than that of R, suggesting that the S compound is more polar than R. The HPLC results corroborates with the molecular electrostatic potential which showed that in the S configuration, the electronegative density was more intense overall, particularly in the glucose molecule. The reactivity indices showed that the diastereoisomers are good electrophiles and reactive species. Finally, the absolute configuration of the diastereoisomers were determined using electronic circular dichroism (ECD) spectroscopy and the theoretical spectra were similar to the experimental. METHODS : All calculations of Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TDDFT) were performed using the program Gaussian 09 and the structures of the diastereoisomers were generated and analyzed using the GaussView program. The optimization and vibrational frequency calculations were performed using the functional CAM-B3LYP and 6-311 + + G(2d,2p) basis set. Conformational searches were performed for R configuration, by molecular mechanics using the MM + , MMFF, and OPLS05 force fields; the entire molecular mechanics simulation was performed using the Maestro/MacroModel software. The calculations for the simulations of the ECD spectra were performed for the eight lowest energy conformers obtained in the geometric optimization step, and the TDDFT at the CAM-B3LYP/6-311 + + G(2d,2p) theory level used. The effects of methanol and chloroform were calculated using the SMD implicit solvent model.

Cystodytin L, a Pyridoacridine Alkaloid from the Senegalese Tunicate Cystodytes sp.

Chemical investigation of the brown-colored tunicate Cystodytes sp. yielded six pyridoacridine alkaloids, including the known metabolites arnoamine C (1), styelsamine C (2), cystodytin B (3), E (4) and G (5) and the new compound, cystodytin L (6). Their chemical structures were established on the basis of combination of [α]D, physical and spectroscopic methods 1D and 2D NMR, in addition to mass spectrometry and comparison with literature data. The absolute configuration of C-12 in compounds 4-6 was identified as R by electronic circular dichroism (ECD) spectroscopy coupled with time-dependent density functional theory calculations.