Circular Dichroism Spectra Research Articles

Celludinone C, a new dihydroisobenzofuran isolated from Talaromyces cellulolyticus BF-0307.

Celludinones A and B, isolated from the fungus Talaromyces cellulolyticus BF-0307, were inhibitors of sterol O-acyltransferase (SOAT). Further searches for their congeners in the culture broth of the fungus by LC/UV and LC/MS analysis resulted in the discovery of four structurally related compounds, including a new dihydroisobenzofuran named celludinone C (1). The structure of 1, including itsabsolute stereochemistry, was elucidated by 1D/2D NMR and electronic circular dichroism (ECD) spectra. All of these compounds inhibited both SOAT1 and 2, with IC50 values ranging from 8.5 to 30 µM.

Substitution of the axial Type 1 Cu Ligand Afford Binding of a Water Molecule in Axial Position Affecting Kinetics, Spectral, and Structural Properties of the Small Laccase Ssl1.

Multicopper oxidases use Cu ions as cofactors to oxidize various substrates. High reduction potential at Type 1 Cu is considered as crucial for effective catalysis. Previous studies have shown that replacing the axial methionine ligand of the Type 1 Cu with leucine or phenylalanine leads to an increased reduction potential, but not always to higher enzyme activity. Here we present a study of six variants of the small laccase Ssl1 from Streptomyces sviceus, where the axial methionine ligand was substituted and the effect of the axial ligand on reduction potential, activity, spectral properties and structure was investigated. Absorption, electronic circular dichroism and EPR spectra revealed the presence of a stronger coordinating axial ligand like oxygen, which influences the electronic and catalytic properties more than the nature of the amino acid side chain. The crystal structures of the Ssl1 variants were solved, which show that none of the amino acids side chains coordinates to the Cu. Instead, a water molecule is found in the axial coordination site, which support the spectroscopic data. Our findings highlight the importance of combining structural and spectroscopic methods to investigate the effect of amino acid exchange on multicopper oxidases.

Cycloartane-type triterpenoids from Combretum quadrangulare Kurz with PCSK9 secretion inhibitory activities.

Nine previously undescribed (1-9) and seven known (10-16) cycloartane-type triterpenoids were isolated and characterized from Combretum quadrangulare Kurz using physicochemical and spectroscopic methods. The absolute configurations of these compounds were determined through modified Mosher's method and quantum chemical calculation of electronic circular dichroism (ECD) and vibrational circular dichroism (VCD) spectra. Their inhibitory activities against PCSK9 secretion were assessed, and a plausible structure-activity relationship was delineated. Compounds 2, 14, and 15 exhibited notable inhibitory effects on PCSK9 mRNA and protein levels, and significant PCSK9 mRNA inhibition was observed when co-treated with atorvastatin. Compound 15 showed the most potent activity, markedly enhancing LDL uptake compared to the negative control. In vivo pharmacokinetic studies confirmed that compound 15 exhibited higher distribution in the liver than plasma, where PCSK9 is predominantly synthesized. These findings emphasize the potential significance of the cycloartane-type triterpenoid scaffold in discovering PCSK9 inhibitors.

Electronic Absorption and Circular Dichroism Spectra of One-Dimensional Bay-Substituted Chiral PDIs: Effects of Intermolecular Interactions, Vibronic Coupling, and Aggregate Size

Electronic Absorption and Circular Dichroism Spectra of One-Dimensional Bay-Substituted Chiral PDIs: Effects of Intermolecular Interactions, Vibronic Coupling, and Aggregate Size

Vibrational Mode-Dependent Circular Dichroism of Jet-Cooled Styrene Oxide.

Vibrational mode-dependent circular dichroism (CD) effects in vibrational CD spectra are often used to determine the handedness of molecules with multiple chiral centers. Here, we investigate vibrational mode-dependent CD effects in the electronic CD spectra of jet-cooled (R)-(+)- and (S)-(-)-styrene oxide obtained by using resonant two-photon ionization CD (R2PICD) spectroscopy. Although most fundamental vibronic bands demonstrated CD signatures consistent with that of the origin band, the overtone and combination bands exhibited opposite CD signatures. Theoretical calculations suggest that CD in fundamental bands are primarily governed by Franck-Condon contributions, whereas Herzberg-Teller contributions, which reflect the influences of vibrational modes on CD values, become more significant in overtone and combination bands. These results underscore the potential of mode-dependent vibronic CD signals in R2PICD spectra for determining the absolute configurations of molecules with multiple chiral centers.

Anti-inflammatory diterpenoids from the brown alga Dictyota coriacea.

A new xenicane diterpene named 4α-acetoxyisodictyohemiacetal (1) was isolated from the brown alga Dictyota coriacea, along with 11 known diterpenoids. The structure of 1 was established by spectroscopic analyses, and its absolute configuration was determined by comparing the experimental and theoretical electronic circular dichroism (ECD) spectra. Two dictyodiacetal diastereomers (5 and 6) were isolated and the full NMR assignments were performed. The anti-inflammatory activities of the isolated compounds were evaluated using the lipopolysaccharide-stimulated mouse macrophage cell line, RAW264. The hemiacetal-containing xenicanes and dictyol-type diterpene inhibited not only the production of nitric oxide, but also the expression of inducible nitric oxide synthase, interleukin-6, and cyclooxygenase-2 mRNA in RAW264 cells. This study demonstrated that diterpenes from Dictyota coriacea may be useful as natural anti-inflammatory agents.

Crystal structures and circular dichroism of {2,2′-[(1S,2S)-1,2-diphenylethane-1,2-diylbis(nitrilophenylmethanylylidene)]diphenolato}nickel(II) and its ethanol solvate

The title compound, [Ni(C40H30N2O2)] (1), with an optically active Schiff base ligand derived from 2-hydroxybenzophenone and (1S,2S)-1,2-diphenylethylenediamine, was crystallized as the solvent-free and ethanol solvate forms (1 and 1·2C2H5OH). In both structures, the two phenyl groups on the stereogenic centers of the O,N,N,O-tetradentate ligand are axially oriented, and the conformation of the central diamine chelate ring is λ. The circular dichroism (CD) spectra of 1 and the analogous nickel(II) complex [Ni(C30H26N2O2)] (2) in solution show partially similar patterns in the 350–450 nm range, but are mirror images in the longer wavelength region (450–650 nm). In the latter region, the sign of CD for these complexes is sensitive to the substituents on the C=N carbon atoms (phenyl for 1 and methyl for 2) rather than the diamine chelate ring conformation.

Synthesis, Chiroptical Properties, and Absolute Configuration Determination of Phenyl‐4‐pyridyl‐2,5‐dipyrimidinylmethane

Phenyl‐4‐pyridyl‐2,5‐dipyrimidinylmethane (1) has been synthesized in five steps from 5‐methylpyrimidine. The structural feature of 1 is the symmetry elements with respect to the 180º rotation of the aryl group along the central C‐C bonds. Due to this structural feature, the compound 1 is expected the good crystallinity despite of the asymmetric molecular structure. The optical resolution of 1 was achieved by high performance liquid chromatography using chiral stationary phase (chiral HPLC). The circular dichroism (CD) spectra of the two fractions showed opposite signs. As expected, the X‐ray crystallographic analysis was successfully performed for both the racemic and enantiomerically pure crystals of compound 1, with the nitrogen atoms being unambiguously assigned in both cases. It was concluded the first‐eluted fraction in chiral HPLC was determined to be S configuration both by the CD calculation for reproducing the experimental CD spectrum and by the anomalous diffraction of X‐ray crystallographic analysis of enantiomerically pure 1.

An Investigation of RNA Methylations with Biophysical Approaches in a Cervical Cancer Cell Model

RNA methylation adds a second layer of genetic information that dictates the post-transcriptional fate of RNAs. Although various methods exist that enable the analysis of RNA methylation in a site-specific or transcriptome-wide manner, whether biophysical approaches can be employed to such analyses is unexplored. In this study, Fourier-transform infrared (FT-IR) and circular dichroism (CD) spectroscopy are employed to examine the methylation status of both synthetic and cellular RNAs. The results show that FT-IR spectroscopy is perfectly capable of quantitatively distinguishing synthetic m6A-methylated RNAs from un-methylated ones. Subsequently, FT-IR spectroscopy is successfully employed to assess the changes in the extent of total RNA methylation upon the knockdown of the m6A writer, METTL3, in HeLa cells. In addition, the same approach is shown to accurately detect reduction in total RNA methylation upon the treatment of HeLa cells with tumor necrosis factor alpha (TNF-α). It is also demonstrated that m1A and m6A methylation induce quite a distinct secondary structure on RNAs, as evident from CD spectra. These results strongly suggest that both FT-IR and CD spectroscopy methods can be exploited to uncover biophysical properties impinged on RNAs by methyl moieties, providing a fast, convenient and cheap alternative to the existing methods.

Optimizing prolyl hydroxylation for functional recombinant collagen in Escherichia coli

Collagen, a key extracellular matrix component, is renowned for its biocompatibility, biodegradability, and bioactivity, finding wide applications in food, medicine, cosmetics, and industry. Recombinant collagen expression in Escherichia coli offers advantages such as shorter production cycles and lower costs compared to extraction from animal tissues, though it is known to lack essential post-translational modifications, such as proline hydroxylation, which are crucial for its stability and biological function. Studies have shown that certain prolyl hydroxylases, including BaP4H, DsP4H, and L593, exhibit relatively high modification efficiency in the E. coli expression system. However, structures and functions of recombinant human type III collagen after modification by three prolyl hydroxylases remain uncertain. In this study, we investigated the percentage of proline hydroxylation, hydroxylation sites, circular dichroism spectra, and biological functions of recombinant human type III collagen modified by various prolyl hydroxylases. The results indicated that the L593 exhibited the highest percentage of proline hydroxylation, and the percentage of proline hydroxylation was closely associated with the formation of the collagen triple helix, while the hydroxylation ratio of prolines is not positively correlated with the stability of the collagen triple helix structure. The biological function results showed that the cell adhesion of recombinant collagen 3-3(BaP4H) and 3-3(L593) was significantly enhanced, which was closely related to the triple helix structure of recombinant human type III collagen. Our study provides valuable insights into the industrial production and biological applications of collagen, enhancing its functional research and scalability.

Investigation on the interaction mechanism of trilobatin with pepsin and trypsin by multi-spectroscopic and molecular docking methods

Pepsin and trypsin are noteworthy for the digestion of proteins in the human body. Trilobatin is a dihydrochalone that has anti-obesity, antioxidant, and anti-diabetes functions. The interaction of trilobatin and pepsin or trypsin is not currently being explored. Therefore, in this research multiple methods involving fluorescence spectroscopy, synchronous fluorescence spectroscopy, ultraviolet–visible (UV–Vis) spectroscopy, Fourier transform infrared (FT-IR) spectroscopy, circular dichroism (CD) and molecular docking were employed for studying the interaction between trilobatin and pepsin or trypsin. During the interaction between trilobatin and pepsin or trypsin, the quenching type was static quenching and a single binding site existed. The binding constants (Ka) values were 2.177 and 3.028 × 104 L/mol in trilobatin-pepsin and trilobatin-trypsin system at 298 K, respectively. However, the presense of metal ions (Zn2+, Ca2+ and K+) decreased the binding of trilobatin to pepsin and trypsin. The complex between trilobatin and pepsin was generated typically through hydrogen bonding and van der Waals force (ΔH° < 0 and ΔS° < 0), in comparison the complex between trilobatin and trypsin was established chiefly through hydrogen bond and hydrophobic force (ΔH° > 0 and ΔS° > 0). The data from UV–Vis, synchronous fluorescence, FT-IR and CD spectra indicated that trilobatin reduced the hydrophobicity of Tyrosine (Tyr) residues of pepsin and trypsin. Furthermore, trilobatin altered the secondary structures of pepsin and trypsin. Meanwhile, trilobatin changed the conformation of pepsin and trypsin so that the viscosity of the interaction systems decreased with increased of trilobatin concentration. The molecular docking modeling identified that the trilobatin interacted with amino acid residues around pepsin and trypsin. This work consistently showed the interaction between trilobatin and pepsin or trypsin, in addition to offering valuable information for the application of trilobatin.

The biologically and ecologically important natural products from the Chinese sea hare Bursatella leachii: structures, stereochemistry and beyond

A novel amide alkaloid, bursatamide A (1), featuring an unprecedented propyl-hexahydronaphthalene carbon framework, was isolated from the infrequently studied sea hare Bursatella leachi, alongside a new 3-phenoxypropanenitrile alkaloid, bursatellin B (2), and twelve known compounds. The structures of 1 and 2 were elucidated through comprehensive spectroscopic data analyses, while their relative and absolute configurations (ACs) were established through total synthesis and a series of quantum chemical calculations, including calculated electronic circular dichroism (ECD) spectra, optical rotatory dispersion (ORD) methods, and DP4+ probability analyses. Bursatamide A (1) demonstrated inhibitory effects against the human pathogenic bacteria Listeria monocytogenes and Vibrio cholerae. Erythro-bursatellin B (21), a diastereoisomer of 2, exhibited notable antibacterial activity against the fish pathogenic bacterium Streptococcus parauberis FP KSP28, with an MIC90 value of 0.0472 μg·mL−1.

Unveiling molecular mechanism underlying inhibition of human islet amyloid polypeptide fibrillation by benzene carboxylic acid-peptide conjugate

Type 2 diabetes (T2D) is linked to the apoptosis of insulin-producing β-cells due to the aberrant fibrillation of the human islet amyloid polypeptide (hIAPP or amylin) to cytotoxic aggregates. Profit et al. generated conjugates (C1–C7) by appending benzene carboxylic acids of varying charges to the N-terminal of hIAPP22-29 fragment peptide NFGAILSS to modulate hIAPP fibrillation and cytotoxicity. C5 (4 µM) derived by conjugating low-cost, commercially available benzene-1,2,4,5-tetracarboxylic acid known as pyromellitic acid to NFGAILSS completely abolishes the hIAPP (40 µM) self-assembly as noted in the thioflavin T (ThT) fluorescence assay. The circular dichroism (CD) spectra highlighted that C5 stabilized hIAPP in a distinctive conformation and blocked its conformational switching to amyloidogenic β-sheet structure. C5 possessing a charge-dense pyromellitic acid moiety appended on the N-terminal region of self-recognition hIAPP fragment sequence NFGAILSS created significant interest as it effectively inhibited hIAPP fibrillation and possessed lower molecular mass, smaller size, and charge as compared to hIAPP aggregation inhibitor EEEENFGAILSS (P10). However, it remains unclear how C5 traps hIAPP into a unique conformation that abolishes its self-aggregation propensity. Thus, molecular dynamics (MD) simulations have been employed to illuminate the conformational transitions and structural changes in hIAPP on the inclusion of C5. C5 displayed high-affinity binding interactions to hIAPP (ΔGbinding = −37.11 ± 3.72 kcal/mol) with major contributions from the van der Waals and electrostatic interactions. Furthermore, residue-specific binding free energy analysis depicted high-affinity binding interactions of C5 with Phe15, His18, Asp21, and Tyr37 of hIAPP that play a crucial role in hIAPP fibrillation. The negatively charged carboxylate groups of pyromellitic acid moiety of C5 displayed interactions with the key residues of hIAPP as noted in the conformational clustering analysis. Notably higher sampling of helix from 24.00 ± 0.84 % in hIAPP to 34.20 ± 1.92 % in hIAPP–C5 is consistent with the CD studies, which depicted that C5 trapped hIAPP monomer in a conformation that blocked its self-association. MD simulations illuminated the molecular mechanism and atomistic details of the C5 interactions with hIAPP, which are responsible for its inhibitory activity against hIAPP fibrillation and alleviating hIAPP aggregates-induced cytotoxicity.

Emergence of Optical Activity and Surface Morphology Changes in Racemic Amino Acid Films Under Circularly Polarized Lyman-α Light Irradiation.

The homochirality of life remains one of the most enigmatic issues in the study of the origin of life. A proposed mechanism for symmetry breaking involves irradiation by circularly polarized light (CPL). To investigate the photoreaction of amino acids under CPL irradiation, a vacuum ultraviolet (VUV) CPL irradiation system was developed at the synchrotron light source UVSOR-III. Hydrogen Lyman-α CPL (121.6 nm) is considered a potential asymmetric source in space. Therefore, racemic alanine film samples were irradiated with Lyman-α CPL to explore the photoreaction of biomolecules. Circular dichroism (CD) spectra measurements revealed that irradiation with right- (left-) handed CPL induced a positive (negative) anisotropy factor g in the wavelength range of 180-240 nm. However, the spectra differed from those of enantiopure alanine, exhibiting broad wavelength ranges and no sign change. Liquid chromatography-mass spectrometry (LC-MS) measurements indicate formation of larger molecules, such as oligomeric alanine adducts or modified oligomers after the Lyman-α CPL irradiation. Additionally, CPL irradiation considerably changes the microstructure of the alanine film surface, leading to the formation of circular network aggregates on the scale of 100 nm. The morphology changes in the alanine film and/or the formation of the larger molecules could be possible causes of the modified anisotropy factor spectra compared to those of enantiopure alanine. These findings highlight the need for further research on the photoreaction of biomolecules in solid states under VUV CPL irradiation, particularly in the photoionization energy range, to validate the cosmic scenario of homochirality.

Nanoscale chirality generated in zinc(II) orthophosphate clusters: evidence by vibrational circular dichroism.

Layered zinc(II) hydroxides (LZH) intercalating the deprotonated forms of R-(-) or S-(+)-1,1'-binaphthyl-2,2'-diyl hydrogenphosphate (denoted as R- or S-BNDHPH, respectively) were prepared from Zn(NO3)2 at pH 5 and 60 °C by the mixing method. The obtained hybrid compounds (denoted as R- or S-BNDHP-/LZH, respectively) were heated from room temperature up to 800 °C under nitrogen atmosphere. According to the thermal gravimetric/differential thermal analysis measurements, hydroxyl groups were dehydrated at 270-400 °C, followed by the decomposition of organic components at 420-600 °C. X-ray diffraction patterns and scanning electron microscopy images indicated that the final products were a mixture of α-Zn3(PO4)2, ZnO crystals and non-crystalline zinc(II) orthophosphates. Vibrational circular dichroism (VCD) spectra were recorded before and after calcination. Before calcination, R- or S-BNDHP-/LZH exhibited VCD peaks assigned to intercalated R- or S-BNDHP-. The calcined products exhibited several VCD peaks in the range of 900-1200 cm-1, maintaining the mirror-image relationship between R-BNDHP-/LZH and S-BNDHP-/LZH used as starting materials. The observed peaks were assigned to the PO (symmetric), -POO-, and PO (asymmetric) stretching vibrations of the PO43- groups. According to theoretical simulations, the observed VCD activity can be rationalised in terms of vibrational coupling between two PO43- groups in a generated chiral zinc(II) orthophosphate cluster.

Chiral Homodinuclear Dysprosium Macrocyclic Complexes with Single‐Molecule Magnetic Behaviours

AbstractA pair of enantiomerically chiral dysprosium homodinuclear complexes: [(acac)4Dy2(R,R,R,R‐L)] (R‐Dy) and [(acac)4Dy2(S,S,S,S‐L)] (S‐Dy) (Hacac=acetylacetone) have been synthesized based on macrocyclic chiral ligands (R,R,R,R‐H2L or S,S,S,S‐H2L), derived from the [2+2] template condensation of 4‐tert‐butyl‐2,6‐diformylphenol, dysprosium acetylacetonate and (1R,2R)‐/(1S,2S)‐1,2‐cyclohexanediamine, respectively. Circular dichroism spectra confirms their enantiomeric chirality. Single‐crystal structures show two crystallographic independent dysprosium(III) ions have square antiprismatic coordination with different D4d local symmetry. Furthermore, the selected R‐Dy complex owns the slow magnetic relaxation behaviour with the ferromagnetic Dy3+⋅⋅⋅Dy3+ coupling.

Biflavonoids and bi- and tricoumarins from Daphne mezereum and inhibition of TNF-α secretion

Daphne mezereum L. (Thymelaeaceae) was an important medicinal plant in Norway during the 18th and 19th centuries and used against diseases such as diarrhea, swelling, stomach pain, and tuberculosis. Five previously undescribed phenolic compounds, including two biflavonoids with a catechin core structure, two tricoumarins, and one bicoumarin, together with ten known compounds were isolated from a 50% EtOH extract of the bark of D. mezereum. Using NMR, HRESIMS, acid hydrolysis, and circular dichroism spectra, the biflavonoids were identified as 3′-hydroxygenkwanol A and 3′-hydroxydihydrodaphnodorin B, and the coumarins were identified as 3‴-O-acetyltriumbellin, triumbellin 4‴-O-β-d-glucopyranoside, and daphnogitin-7-O-β-d-glucopyranoside. The absolute configuration of dihydrodaphnodorin B was for the first time established as 2R, 3S, 2″S, 3″S. Daphnin, syringin, 3′-hydroxydihydrodaphnodorin B, dihydrodaphnodorin B, and neochamaejasmin A and B were identified as the major secondary metabolites in the extract. Neochamaejasmin A and B showed the most potent inhibition of TNF-α secretion in Con A stimulated peripheral blood mononuclear cells (PBMCs) with 71.3 ± 3.4 and 83.5 ± 11.5% inhibition, respectively, at 50 μM.

Impact of Loss Mechanisms on Linear Spectra of Excitonic and Polaritonic Aggregates.

The presence of loss mechanisms governed by empirical timescales can profoundly affect the dynamics in molecular systems, leading to changes in their spectra. However, incorporation of these effects along with the system's interaction with the thermal dissipative environments proves to be challenging. In this work, we demonstrate the possibility of utilizing the recently developed path integral Lindblad dynamics (PILD) method to study the linear spectra of molecular aggregates. PILD presents a uniquely powerful simulation technique for retaining the effects of the vibrations in a numerically exact manner through the Feynman-Vernon influence functional while incorporating the effects of losses in an empirical manner using the Lindbald master equation. As illustrations of this technique, we provide examples taken from chiral excitonic and polaritonic aggregates for which we simulate both the absorption spectra and circular dichroism (CD) spectra. We demonstrate that the effect of loss on particular states can differ not just on the basis of the symmetries of the state but also on the basis of complicated "interactions" of the structured dissipative environments with the system and its loss mechanisms. Due to the different selection rules between the absorption and CD spectra and the relative intensities and broadening of the peaks, the two linear spectra together give an interesting insight into the contributions of the various eigenstates to the correlation functions. While the focus here is on linear spectroscopy, it should be possible in the future to use PILD to study multidimensional spectra under loss mechanisms as well.

Elucidating the effects of hofmeister salts on the formation mechanism and biocompatibility of lysozyme-hyaluronic acid complexes

This study aimed to investigate the morphologies, biocompatibility, and formation mechanism of lysozyme-hyaluronic acid complexes in the presence of various Hofmeister salts. During the complexation of lysozyme (Lys) and hyaluronic acid (HA), salts can control the formation of colloidal nanoparticles, amyloid-like aggregates, and amorphous aggregates. Circular dichroism spectra revealed that the α-helix content of Lys involved in complexation significantly increased from 21.40 % to 34.19 %, whereas the β-sheet content significantly decreased from 38.65 % to 24.42 % with increasing salt concentration. The fluorescence spectra indicated that the number of binding sites for HA and Lys decreased from 2.19 to 0.63 as the salt concentration increased from 0 to 300 mM, which was consistent with the different anion-specific effects (NaCl < NaBr < NaI). Interestingly, in vitro experiment results demonstrated that colloidal nanoparticles and amorphous aggregates have good biocompatibility, with NCM460 cell viability exceeding 85.92 %, whereas amyloid like aggregates exhibit certain cytotoxicity, with cell viability significantly reduced to 50.47 %. Overall, these findings provide a better understanding of the conformational changes of Lys involved in complexation with HA in the presence of salts, expanding its application in the food and pharmaceutical industries.

Acremochlorin S and other prenylated chlorophenol antimicrobial metabolites from the fungus Acremonium sp. Strain MNA-F-1

Chemical prospection for the mycelial extract of the fungus Acremonium sp. Strain MNA-F-1, derived from the inner tissue of anise roots (Pimpnella anisum L., family Apiaceae), led to the isolation and characterization of one previously undescribed natural product, acremochlorin S (1), together with five related derivatives (2–6) and an alkaloidal metabolite, ilicicolin H (7). Structure elucidation of the isolated compounds was determined through comprehensive 1D/2D NMR spectroscopic analyses and HR-ESI-MS measurements. The absolute configuration of acremochlorin S (1) was concluded based on the comparison of its experimental and calculated electronic circular dichroism (ECD) spectra implementing Time-dependent density functional theory (TDDFT). All isolated compounds were assessed for their antibacterial activity against Staphylococcus aureus, Escherichia coli and Mycobacterium tuberculosis, where several compounds revealed potent activities against tested Gram-positive strains.