Assignment of Vibrational Circular Dichroism Cross-Referenced Electronic Circular Dichroism Spectra of Flexible Foldamer Building Blocks: Towards Assigning Pure Chiroptical Properties of Foldamers

Assignment of the most established electronic circular dichroism (ECD) spectra of polypeptides and foldamers is either “evidence based” or relies on the 3D structures of longer oligomers of limited internal dynamics, which are derived from NMR spectroscopy (or X-ray) data. Critics warn that the use of NMR spectroscopy and ECD side by side has severe limitations for flexible molecules because explicit knowledge of conformational ensembles is a challenge. Herein, an old–new method of comparing ab initio computed and measured vibrational circular dichroism (VCD) data is presented to validate both the structures (conf(i)) and their relative weights (c(i)) that make up the conformational ensemble. Based on the array of {conf(i), c(i)}, the pure ECD spectra, g(i)^conf(i), can be ab initio calculated. The reconstructed spectrum Σc(i)g(i)^conf(i) can thus help to assign any experimental ECD counterparts. Herein, such a protocol is successfully applied to flexible foldamer building blocks of sugar β-amino acid diamides. The epimeric pair of the model system was selected because these molecules were conformationally tunable by simple chemical modification, and thus, the robustness of the current approach could be probed. The initial hydrogen bond (NH⋅⋅⋅O) eliminated by N-methylation reorients the amide plain, which influences the chiroptical properties of the foldamer building block; this structural change is successfully monitored by changes to the VCD and ECD transitions, which are now assigned to pure conformers. The current method seems to be general and effective without requiring extensive CPU and spectroscopic resources.     

Induced Chiroptical Changes of a Water‐Soluble Cryptophane by Encapsulation of Guest Molecules and Counterion Effects

We report the synthesis of the water‐soluble cryptophanol derivative 1 and the study of the chiroptical properties of its two enantiomers (>99 % ee) by polarimetry, electronic circular dichroism (ECD), and vibrational circular dichroism (VCD). We show that cryptophanol 1 exhibits unusual chiroptical properties in water under basic conditions (pH>12). For instance, the shapes of the ECD and VCD spectra of 1 in water were strongly dependent on the nature of the alkali metal ions (Li⁺, Na⁺, K⁺, Cs⁺) surrounding the cryptophane and whether or not a guest molecule is present inside the cavity of the host. To the best of our knowledge, this is the first example in which the nature of these counterions governs the chiroptical properties of a host molecule. Moreover, specific ECD spectra were obtained depending on the size of the guest molecules. This makes 1 a good sensor for small neutral molecules in aqueous solvent. Finally, VCD experiments associated with DFT calculations show that the chiroptical changes can be directly correlated to the presence of charges close to the aromatic rings and with a conformational change of the alkyl chains upon encapsulation.     

Determination of the Absolute Configuration of Perylene Quinone‐Derived Mycotoxins by Measurement and Calculation of Electronic Circular Dichroism Spectra and Specific Rotations

Altertoxins I–III, alterlosins I and II, alteichin (alterperylenol), stemphyltoxins I–IV, stemphyperylenol, stemphytriol, 7‐epi‐8‐hydroxyaltertoxin I, and 6‐epi‐stemphytriol are mycotoxins derived from perylene quinone, for which the absolute configuration was not known. Electronic circular dichroism (ECD) spectra were calculated for these compounds and compared with measured spectra of altertoxins I–III, alteichin, and stemphyltoxin III and with reported Cotton effects. Specific rotations were calculated and compared with reported specific rotations. The absolute configuration of all the toxins, except for stemphyltoxin IV, could thus be determined. The validity of the assignment was high whenever reported ECD data were available for comparison, and the validity was lower when the assignment was based only on the comparison of calculated and reported specific rotations. ECD spectra are intrinsically different for toxins with a biphenyl substructure and for toxins derived from dihydroanthracene.     

Xanthones and Oxepino[2, 3‐b]chromones from Three Endophytic Fungi

Three new metabolites, microsphaeropsones A–C ( 1 – 3 ) with a unique oxepino[2,3‐b]chromen‐6‐one (ring‐enlarged xanthone) skeleton, were isolated from the endophytic fungus Microsphaeropsis species, co‐occurring with their putative biogenetic anthraquinoide precursors citreorosein ( 4 ) and emodin ( 5 ). From another Microsphaeropsis species, large amounts of fusidienol A ( 8 a ), smaller amounts of emodin ( 5 ), the known aromatic xanthones 9 a and 9 b , the new 3,4‐dihydrofusidienol A ( 8 b ), and the new aromatic xanthone 9 c were isolated. The endophyte Seimatosporium species produced a new aromatic xanthone, seimatoxanthone A ( 10 ), and 3,4‐dihydroglobosuxanthone A ( 12 ), closely related to α‐diversolonic ester ( 13 ) from Microdiplodia sp.. The structures were determined mainly by extensive 1D and 2D NMR experiments and supported by X‐ray single‐crystal analysis of 1 and the oxidation product 7 . The absolute configurations of the microsphaeropsones A–C ( 1 – 3 ) were established by comparison of the electronic and vibrational circular dichroism (ECD and VCD) spectra of 1 with time‐dependent DFT (TDDFT) and DFT calculations by using either the solid‐state structures or DFT‐optimized geometries as inputs. Preliminary studies indicated that 1 , 2 , and enone 7 showed antibacterial, fungicidal, and algicidal properties.     

Optical Activity in the Near‐IR Region: The λ=980 nm Multiplet of Chiral Yb3+ Complexes

We used a very simplified electrostatic model based on charge and polarizability of atoms and groups on an organic ligand around a lanthanide ion to predict the near‐infrared electronic circular dichroism (NIR ECD) spectra of Yb³⁺ (a monoelectronic ion). We tuned our method by using two widely different complexes. The first was the heterobimetallic species CsYb(hfbc)₄ [hfbc=(?)‐3‐heptafluorobutyrylcamphorate], in which the ligand is a diketonate and, as such, is endowed with a chromophore with strong UV absorption (π–π^*). Its oxygen atoms define a square antiprism, which provides a symmetric coordination polyhedron. The second system was Yb DOTMA [DOTMA=(1R,4R,7R,10R)‐α,α′,α′′,α′′′‐tetramethyl‐1,4,7,10‐tetraazacyclododecane‐1,4,7,10‐tetraacetic acid], a chiral Yb analogue of Gd DOTA (DOTA=1,4,7,10‐tetraazacyclododecane‐1,4,7,10‐tetraacetic acid), in which the ligand lacks relevant electronic transitions and provides a dissymmetric cage. The relative weights of dynamic (ligand polarization) and static contributions to Yb NIR ECD were evaluated, and the spectra appear to have been well predicted by theory through the introduction of a heuristic weight factor. To validate the approach and to confirm the value of the weight factor, we applied it to two other compounds, namely, Na₃Yb(BINOLate)₃ and Yb(BINOLAM)₃ [BINOLate=2,2′‐dihydroxy‐1,1′‐binaphthyl; BINOLAM=3,3′‐bis(diethylaminomethyl)‐1‐1′‐bi‐2‐naphthol].     

Aromatic Cluster Sensor of Protein Folding: Near‐UV Electronic Circular Dichroism Bands Assigned to Fold Compactness

Both far‐ and near‐UV electronic circular dichroism (ECD) spectra have bands sensitive to thermal unfolding of Trp and Tyr residues containing proteins. Beside spectral changes at 222 nm reporting secondary structural variations (far‐UV range), L_b bands (near‐UV range) are applicable as 3D‐fold sensors of protein's core structure. In this study we show that both L_b(Tyr) and L_b(Trp) ECD bands could be used as sensors of fold compactness. ECD is a relative method and thus requires NMR referencing and cross‐validation, also provided here. The ensemble of 204 ECD spectra of Trp‐cage miniproteins is analysed as a training set for “calibrating” Trp?Tyr folded systems of known NMR structure. While in the far‐UV ECD spectra changes are linear as a function of the temperature, near‐UV ECD data indicate a non‐linear and thus, cooperative unfolding mechanism of these proteins. Ensemble of ECD spectra deconvoluted gives both conformational weights and insight to a protein folding?unfolding mechanism. We found that the L_b²⁹³ band is reporting on the 3D‐structure compactness. In addition, the pure near‐UV ECD spectrum of the unfolded state is described here for the first time. Thus, ECD folding information now validated can be applied with confidence in a large thermal window (5≤T≤85 °C) compared to NMR for studying the unfolding of Trp?Tyr residue pairs. In conclusion, folding propensities of important proteins (RNA polymerase II, ubiquitin protein ligase, tryptase‐inhibitor etc.) can now be analysed with higher confidence.     

Outstanding Chiroptical Properties: A Signature of Enantiomerically Pure Alleno–Acetylenic Macrocycles and Monodisperse Acyclic Oligomers

A second series of shape‐persistent alleno–acetylenic macrocycles and monodisperse acyclic oligomers with conformationally less flexible backbones were synthesized in enantiomerically pure form by short, high‐yielding routes starting from optically active 1,3‐diethynylallenes. All seven stereoisomers—two pairs of enantiomers and three achiral stereoisomers—in the macrocyclic series were separated and configurationally assigned. The electronic circular dichroism (ECD) spectra of the D₂‐symmetric, (P,P,P,P)‐ and (M,M,M,M)‐configured macrocycles display remarkably intense chiroptical responses. A strong amplification of chirality is observed in the acyclic oligomeric series. Their preference for helical secondary structures of one handedness was supported by X‐ray analysis and computational studies. This new set of data provides proof that outstanding ECD responses are a hallmark of alleno–acetylenic macrocyclic and acyclic oligomeric chromophores.     

Three Types of Induced Tryptophan Optical Activity Compared in Model Dipeptides: Theory and Experiment

The tryptophan (Trp) aromatic residue in chiral matrices often exhibits a large optical activity and thus provides valuable structural information. However, it can also obscure spectral contributions from other peptide parts. To better understand the induced chirality, electronic circular dichroism (ECD), vibrational circular dichroism (VCD), and Raman optical activity (ROA) spectra of Trp‐containing cyclic dipeptides c‐(Trp‐X) (where X=Gly, Ala, Trp, Leu, nLeu, and Pro) are analyzed on the basis of experimental spectra and density functional theory (DFT) computations. The results provide valuable insight into the molecular conformational and spectroscopic behavior of Trp. Whereas the ECD is dominated by Trp π–π* transitions, VCD is dominated by the amide modes, well separated from minor Trp contributions. The ROA signal is the most complex. However, an ROA marker band at 1554 cm^?1 indicates the local χ₂ angle value in this residue, in accordance with previous theoretical predictions. The spectra and computations also indicate that the peptide ring is nonplanar, with a shallow potential so that the nonplanarity is primarily induced by the side chains. Dispersion‐corrected DFT calculations provide better results than plain DFT, but comparison with experiment suggests that they overestimate the stability of the folded conformers. Molecular dynamics simulations and NMR results also confirm a limited accuracy of the dispersion‐DFT model in nonaqueous solvents. Combination of chiral spectroscopies with theoretical analysis thus significantly enhances the information that can be obtained from the induced chirality of the Trp aromatic residue.     

Three New Chromone Derivatives Produced by Phomopsis sp. HNY29‐2B from Acanthus ilicifolius Linn.

Three new chromone derivatives, phomochromenones A‐C ( 1–3 ), and one known chaetocyclinone B ( 4 ) were obtained from the cultures of Phomopsis sp. HNY29‐2B isolated from the mangrove Acanthus ilicifolius Linn., which was collected from the South China Sea. Their structures were determined by the analysis of ¹D NMR and ²D NMR as well as mass spectroscopic data. The absolute configurations of 1 and 2 were assigned by quantum chemical calculations of the electronic circular dichroism (ECD ) spectra. Compound 3 is the third example of alkaloids possessing the unique chromeno [3,2‐c ] pyridine nucleus. In the bioactivity assay, compound 4 showed cytotoxicity against human prostate cancer cell lines (PC ‐3 and DU145 cells) with the IC₅₀ values of 8.13 and 3.59 µmol/L, respectively.     

A new pregnane steroid from cultures of Aspergillus versicolor

A new pregnane steroid, named aspergillon A (1), together with two known compounds, (22E,24R)-ergosta-5,7,22-trien-3β-ol (2) and (22E, 24R)-ergosta-4,6,8(14),22-tetraen-3-one (3) were isolated from cultures of the tin mine tailings-associated fungus Aspergillus versicolor. The new structure and absolute configuration were determined with the help of extensive spectroscopic analyses and quantum chemical calculations of the electronic circular dichroism (ECD) spectra.     

Synthesis,Structure and Photophysical Properties of a New Class of Inherently Chiral Boron(III) Chelates—The tert-Leucine Complexes

A new family of boron(III) chelates is introduced whereby molecular chirality, confirmed by circular dichroism, is imported during synthesis such that isolation of the diastereoisomers does not require separation procedures. The photophysical properties of two members of the family have been examined: the N,O,O-salicylaldehyde-based derivative shows pronounced intramolecular charge-transfer character in fluid solution and is weakly fluorescent, with a large Stokes shift. The corresponding 2-methylamino-benzaldehyde-derived N,N,O-chelate absorbs and fluoresces in the visible region with a much smaller Stokes shift. Orange fluorescence is also observed for this compound as a cast film. Temperature-dependence studies show that decay of the fluorescent state is weakly activated but emission is less than quantitative at 77 K. Quite rare for boron(III)-based chelates, this derivative undergoes intersystem crossing to form a meta-stable triplet-excited state. X-ray crystal structures are reported for both compounds, along with simulated ECD spectra.     

Helicene Monomers and Dimers: Chiral Chromophores Featuring Strong Circularly Polarized Luminescence

The synthesis and chiroptical properties of a series of enantiomerically pure, C₂-symmetrical carbo[6]helicene dimers are reported. Two helicene cores are connected through a buta-1,3-diyne-1,4-diyl linker or a heteroaromatic bridge and bear arylethynyl substituents at their 15-positions. This ensures the possibility of extended electronic communication throughout the whole molecule. The new chromophores exhibit intense ECD spectra with strong bands in the UV/Vis region well above 400 nm. The anisotropy factor g_abs (defined as Δϵ/ϵ) reaches values up to 0.047, which are unusually large for single organic molecules. They also display blue fluorescence, with good quantum yields (Φ_f∼0.25). The emitted light is circularly polarized to an outstanding extent: in some cases, the luminescence dissymmetry factor g_lum=2(I_L−I_R)/(I_L+I_R) attains values of |0.025|. To the best of our knowledge, such values are among the highest ever reported for non-aggregated organic fluorophores.     

Synthesis of the Natural Product Building Block 5‐(3‐Bromophenyl)‐4‐hydroxy‐5‐methylhexan‐2‐one and its Chiral Characterization by Using Chiroptical Spectroscopy

The absolute configuration of 5‐(3‐bromophenyl)‐4‐hydroxy‐5‐methylhexan‐2‐one, an intermediate in the synthesis of various natural products, is assigned by using vibrational circular dichroism (VCD), electronic circular dichroism (ECD), and optical rotatory dispersion (ORD). Experimental spectra were compared to density functional theory (DFT) calculations of the molecule with known configuration. These three techniques independently confirm that the absolute configuration is (S)‐5‐(3‐bromophenyl)‐4‐hydroxy‐5‐methylhexan‐2‐one, thus enabling us to assign the absolute configuration with high reliability. The reliability of the VCD analysis was assessed quantitatively by using the CompareVOA program. We found that, in cases in which the agreement between theory and experiment was very good, a value of 10 cm^?1 for the triangular weighting function gave a more‐realistic discriminative power between enantiomers than the default value of 20 cm^?1.     

Aplysiasecosterol A: A 9,11‐Secosteroid with an Unprecedented Tricyclic γ‐Diketone Structure from the Sea Hare Aplysia kurodai

A new 9,11‐secosteroid having an unprecedented tricyclic γ‐diketone structure, aplysiasecosterol A ( 1 ), was isolated from the sea hare Aplysia kurodai. The structure was determined by one‐ and two‐dimensional NMR spectroscopic analysis, molecular modeling studies, a comparison of experimental and calculated ECD spectra, and a modified Mosher′s method. Aplysiasecosterol A ( 1 ) exhibited cytotoxicity against human myelocytic leukemia HL‐60 cells. A biosynthetic pathway for 1 from a known cholesterol was proposed and includes twice α‐ketol rearrangements and an intramolecular acetalization.     

Electronic Circular Dichroism-Circularly Polarized Raman (eCP-Raman): A New Form of Chiral Raman Spectroscopy

This Concept article summarizes recent work on the development of a new form of chiral Raman spectroscopy, e CP-Raman, which combines two spectroscopies: electronic circular dichroism (ECD) and circularly polarized Raman (CP-Raman). First, some puzzling observations while carrying out Raman optical activity (ROA) measurements of several transition metal complexes under resonance are described, as well as the search for the mechanisms responsible. Then an equation for quantifying the e CP-Raman contribution is presented, followed by several examples of how e CP-Raman influences the I_R−I_L spectra of achiral and chiral solvent molecules and of a number of chiral solutes under resonance. The conditions to extract resonance ROA, when the e CP-Raman contribution is minimized, are also discussed. Finally, we comment on the potential applications of e CP-Raman.     

Enantioselective complexation of carbamoylated quinine and quinidine with <Emphasis Type="Italic">N</Emphasis>-blocked amino acids: vibrational and electronic circular dichroism study

Infrared absorption (IR) and vibrational and electronic circular dichroism (VCD and ECD, respectively) spectra of tert-butylcarbamoylquinine (t-BuCQN) and pseudoenantiomeric tert-butylcarbamoylquinidine (t-BuCQD), denoted as selectors (SO), complexed with chiral (S) and (R)-3,5-dinitrobenzoylleucine (DNB-Leu) and achiral 3,5-dinitrobenzoylglycine (DNB-Gly), denoted as selectands (SA), in methanol and acetonitrile, with the spectra of pure SA and SO are reported. H–D exchange of exchangeable hydrogen atoms of SA and SO in deuterated methanol which occurs in IR and VCD experiments is exploited to identify Amide II and Amide III vibrational modes. The formation of preferentially bound complexes composed of sterically compatible combinations of DNB-Leu and SO are manifested by increased intensity of VCD bands assigned to vibrations of amide, carbamate, quinoline, and dissociated carboxylate group and also by increased ECD signals. The VCD technique revealed similarities between the strongly bound diastereomeric complex of chiral DNB-Leu and SO and the complex of achiral DNB-Gly and SO, highlighting the leading role of SO in the formation of SA–SO complex. Figure Vibrational circular dichroism study: Interaction markers typical of the binding between the quinine selector and the derivatized amino acid selectand     

Ruthenium‐Grafted Vinylhelicenes: Chiroptical Properties and Redox Switching

The properties of mono‐ and bis‐Ru–vinyl[6]helicene complexes ( 2 a and 2 b , respectively), recently synthesized by using molecular engineering of helicenes based on the grafting of lateral organometallic substituents on the π‐helical backbone through a vinyl bridge, are presented. These helicene derivatives are thoroughly characterized, with special attention given to their chiroptical properties and redox switching activity. The UV/Vis and electronic circular dichroism (ECD) spectra of P and M enantiopure species, both in the neutral and oxidized states ([ 2 a ] ^{. +}, [ 2 b ] ^{. +}, and [ 2 b ]²⁺), are analyzed with the aid of quantum‐chemical calculations. The extended π‐conjugation facilitated by the vinyl moiety, clearly visible in the electronic structures of 2 a , b , introduces new active bands in the ECD spectra that consequently lead to a significant increase in optical rotation of Ru–vinylhelicenes compared with the organic precursors. The vibrational circular dichroism (VCD) spectra were measured and calculated for both the organic and organometallic species and constitute the first examples of VCD for metal‐based helicene derivatives. Finally, the redox‐triggered chiroptical switching activity of 2 a , b is examined in detail by using ECD spectroscopy. The modifications of the ECD spectra in the UV/Vis and NIR region are well reproduced and rationalized by calculations.     

Origin‐independent sum over states simulations of magnetic and electronic circular dichroism spectra via the localized orbital/local origin method

Although electronic and magnetic circular dichroism (ECD, MCD) spectra reveal valuable details about molecular geometry and electronic structure, quantum‐chemical simulations significantly facilitate their interpretation. However, the simulated results may depend on the choice of coordinate origin. Previously (?těpánek and Bou?, J. Comput. Chem. 2013, 34, 1531), the sum‐over‐states (SOS) methodology was found useful for efficient MCD computations. Approximate wave functions were “resolved” using time‐dependent density functional theory, and the origin‐dependence was avoided by placing the origin to the center of mass of the investigated molecule. In this study, a more elegant way is proposed, based on the localized orbital/local origin (LORG) formalism, and a similar approach is also applied to generate ECD intensities. The LORG‐like approach yields fully origin‐independent ECD and MCD spectra. The results thus indicate that the computationally relatively cheap SOS simulations open a new way of modeling molecular properties, including those involving the origin‐dependent magnetic dipole moment operator. © 2015 Wiley Periodicals, Inc.     

Pseudopotential-fragment spectroscopy for organic molecules and carbon allotropes

Following on from a previous work (Punter et al., IJQC 2019, 119, 23), pseudopotential sets are developed and tested for a variety of sp² and sp³ carbon fragments. These fragments contain only one or two explicit protons and electrons, and make use of non-atom-centered potentials. They are tested with density functional theory calculations in a selection of chemical environments in which several physical characteristics, including orbital and first ionization energies, are found to be well reproduced. They are then employed in the reproduction of molecular absorption spectra for large organic molecules and carbon allotropes, and are found to recreate both absorption and electronic circular dichroism spectra to a high accuracy. They are also found significantly to increase the computational efficiency of time dependent density functional theory (TDDFT) calculations in which they are used.