VCD Spectra Research Articles

Insights into chromatographic enantiomeric separation of allenes on cellulose carbamate stationary phase

Allenes are cumulenes with three contiguous carbons linked together through double bonds. 1,3-disubstituted allenes are not superimposable on their mirror image; as a consequence they are chiral. Chiral allenes are increasingly important in organic synthesis due to their interesting reactivity. Because of their applications in the field of asymmetric catalysis and in the pharmaceutical industry their optical purity is always a parameter which needs to be determined. In this article, we report the enantiomeric separation of hexa-3,4-diene-3-ylbenzene, an aromatic allene, on a cellulose carbamate (Chiralcel OD-3) stationary phase, using heptane as the mobile phase. Spectroscopic studies using infrared (IR) and vibrational circular dichroism revealed that, in the presence of heptane, the stationary phase undergoes a conformational change due to intermolecular H-bonding between the CO and NH of the neighboring polymer chains. Van’t Hoff plots for the retention factor, k, showed that the retention of the two enantiomers is dominated by the enthalpy, while the plot for the selectivity, α, is entropy driven. This suggests that the enantioselectivity is a result of inclusion of the enantiomers in the cavities of the chrial stationary phase. VCD spectra, along with density functional theory calculation (DFT) of the interaction between each enantiomer and the chiral stationary phase, supported the chromatographic elution order findings.

Tribenzotriquinacene receptors for C60 fullerene rotors: towards C3 symmetrical chiral stators for unidirectionally operating nanoratchets.

The synthesis of a stereochemically pure concave tribenzotriquinacene receptor (7) for C60 fullerene, possessing C3 point group symmetry, by threefold condensation of C2 -symmetric 1,2-diketone synthons (5) and a hexaaminotribenzotriquinacene core (6) is described. The chiral diketone was synthesized in a five-step reaction sequence starting from C2h -symmetric 2,6-di-tert-butylanthracene. The highly diastereo-discriminating Diels-Alder reaction of 2,6-di-tert-butylanthracene with fumaric acid di(-)menthyl ester, catalyzed by aluminium chloride, is the relevant stereochemistry introducing step. The structure of the fullerene receptor was verified by (1)H and (13)C NMR spectroscopy, mass spectrometry and single crystal X-ray diffraction. VCD and ECD spectra were recorded, which were corroborated by ab initio DFT calculations, establishing the chiral nature of 7 with about 99.7 % ee, based on the ee (99.9 %) of the chiral synthon (1). The absolute configuration of 7 could thus be established as all-S [(2S,7S,16S,21S,30S,35S)-(7)]. Spectroscopic titration experiments reveal that the host forms 1:1 complexes with either pure fullerene (C60) or fullerene derivatives, such as rotor 1'-(4-nitrophenyl)-3'-(4-N,N-dimethylaminophenyl)-pyrazolino[4',5':1,2][60]fullerene (R). The complex stability constants of the complexes dissolved in CHCl3/CS2 (1:1 vol. %) are K([C60 ⊂7]) = 319(±156) M(-1) and K([R⊂7]) = 110(±50) M(-1). With molecular dynamics simulations using a first-principles parameterized force field the asymmetry of the rotational potential for [R⊂7] was shown, demonstrating the potential suitability of receptor 7 to act as a stator in a unidirectionally operating nanoratchet.

Interaction of Beta-Sheets to Form Aggregates and Fibrils. Theoretical and Experimental Spectroscopic Studies of Peptide Ir and Vcd Spectra

Many peptides form aggregates and some develop fibrillar morphologies. Vibrational spectroscopic methods have been used to establish β-sheet structures underlying many of these and isotope labeling has been used to indicate parallel vs. antiparallel forms. We have developed a DFT-based calculational model of β-sheet vibrational spectra based on Ala-oligopeptides, that initially focused on IR, VCD, and Raman spectra for isolated ideal sheet structures, and have since explored its variation with structure, alignment of strands, isotope labeling, twisting of single sheets and stacking and relative rotation of multiple sheets. We have computationally simulated spectra reported in the literature for several peptides forming fibrillar structures based on our static stacked β-sheet models. With isotopic labeling we can identify the nature of the sheet formed, parallel or antiparallel, and in many cases can determine the registry between sheets. In particular, for model peptides we have prepared, our analyses of the spectra of Glu10 based peptides that form both regular, β1, and bifurcated H-bond , β2 sheets are analyzed in this way to show both are antiparallel in nature but the β2 is out of register by one residue, most likely in a step-wise pattern, while the β1 structure is different, but less well organized. We have extended these calculations by computing IR and VCD for structures obtained as snapshots along MD trajectories that show contributions of sidechains and other modes in qualitative agreement with experiment.

Identification of the specific, shutter-like conformational reorientation in a chiroptical switching polycarbodiimide by VCD spectroscopy.

The specific conformational states responsible for the unique, reversible temperature- and solvent-driven chiroptical switching process experienced by poly(N-1-naphthyl-N'-octadecyl-carbodiimide) (PNOC) have been identified using VCD spectroscopy and DFT calculations. The distinct VCD spectra of PNOC corresponding to the two specific conformations were obtained for the polymer dissolved in DCM-d2 (state A) and CDCl3 (predominantly state B). To specifically assign the structures of both conformations, two simplified 7mer models were constructed and optimized using DFT calculations. The theoretical spectra associated with these model conformations show a high level of agreement when compared to the experimental VCD spectra. The two states consist of the naphthyl pendant groups aligned directionally opposing the helical rotation (model A) and aligned with the helicity of the backbone (model B). This pendant reorientation causes very large OR and ECD Cotton effect inversions upon modification to the temperature or solvent composition of dilute (+)-PNOC solutions in specific solvents. In addition, the pendant group equilibrium from state A to B causes a contraction of the helical pitch from the more expanded 5/1 pitch to the more contracted 7/2 pitch resulting in increased disorder of the solvation sphere surrounding the polymer chain.

Substituent effect in theoretical VCD spectra

A correlational study shows for the first time a quantitative substituent effect on Vibrational Circular Dichroism intensity.

Conformational landscape of l-threonine in neutral, acid and basic solutions from vibrational circular dichroism spectroscopy and quantum chemical calculations

The biological relevance of amino acids is well known. They can be used as zwitterionic, cationic or anionic forms according to the pH of the medium where they are. Thus, our aim herein was to study the conformational preference of the polar amino acid l-threonine [C4H9NO3, (2S,3R)-2-amino-3-hydroxybutyric acid] under different pH conditions. A conformational study in an aqueous solution of the dissociation equilibrium of the amino acid l-threonine was carried out for this purpose. We recorded, at room temperature, the Mid-IR, Far-IR, Raman and VCD spectra of l-threonine from the aqueous solutions at pH values 5.70 (zwitterionic species), 1.00 (protonated species) and 13.00 (deprotonated species). The number of conformers found with the conformational search was 9 zwitterions, 27 anions and 52 cations. Both the study of the conformational landscape and the theoretical analysis of the vibrational features were accomplished by using DFT and ab initio calculations, that is, B3LYP/6-311++G(d,p) level of theory for all the conformers obtained from the conformational search, M062X/6-311++G(d,p) and MP2/6-311++G(d,p) levels of theory for the most stable conformers. The presence of water was included with the IEF-PCM implicit hydration model. With regard to the zwitterion, the importance of the analysis of the low frequency region (700–30cm–1) in the Far-IR spectra should be noted, because it provides relevant information that can be used to determine the presence of the most stable structures.

Prediction of l-Methionine VCD Spectra in the Gas Phase and Water Solution

In this paper we provide a computational study of the l-methionine conformational landscape and VCD spectra in the gas phase and a water environment simulated by implicit PCM and the hybrid model, i.e., a combination of explicit "microsolvation" and implicit models. In the gas phase, two groups of conformers differing in H-bonding, i.e., OH···NH2 and NH···O═C, could be distinguished based solely on the IR ν(OH) and ν(NH) stretching vibrations range. On the other hand, VCD better reflected chain differences. The most stable OH···NH2 conformer was predicted to be easily detected, and the presence of two out of four NH···O═C conformers could be confirmed. Three zwitterionic methionine conformers were shown to dominate in water. Their VCD spectra, simulated within the hybrid model at the B3LYP-IEF-PCM/aug-cc-pVDZ level of theory, indicated that they could be recognized in the mixture. Use of the hybrid model is crucial for good reproduction of the hydrogen bonding pattern in the VCD spectra of methionine in water solution. However, the 1300-800 cm(-1) region of the skeleton vibrations of methionine appeared to be relatively insensitive to the model of the solvent.

Insight into the Packing Pattern of β2 Fibrils: A Model Study of Glutamic Acid Rich Oligomers with 13C Isotopic Edited Vibrational Spectroscopy

Polyglutamic acid at low pH forms aggregates and self-assembles into a spiral, fibril-like superstructure formed as a β2-type sheet conformation that has a more compact intersheet packing than commonly found. This is stabilized by three-centered bifurcated hydrogen bonding of the amide carbonyl involving the protonated glutamic acid side chain. We report vibrational spectroscopic results and analyses for oligopeptides rich in glutamic acid enhanced with (13)C isotope labeling in a study modeling low pH poly-Glu self-assembly. Our results indicate bifurcated H-bonding and β2 aggregation can be attained in these model decamers, confirming they have the same conformations as poly-Glu. We also prepared conventional β1-sheet aggregates by rapid precipitation from the residual peptides in the higher pH supernatant. By comparing the isotope-enhanced IR and VCD spectra with theoretical predictions, we deduced that the oligo-Glu β2 structure is based on stacked, twisted, antiparallel β-sheets. The best fit to theoretical predictions was obtained for the strands being out of register, sequentially stepped by one residue, in a ladder-like fashion. The alternate β1 conformer for this oligopeptide was similarly shown to be antiparallel but was less ordered and apparently had a different registry in its aggregate structure.

Absolute configuration assignment made easier by the VCD of coupled oscillating carbonyls: the case of (−)-propanedioic acids, 2-(2,3)-dihydro-3-oxo-1H-isoindol-1-yl)-1,3-dimethyl ester

Depending on their relative orientation, coupled oscillating carbonyl groups provide a VCD spectrum with a characteristic CO bond stretching region showing a strong bisignate VCD feature, which can be readily predicted adopting long available semiempirical methods. The extended coupled oscillator (ECO) formalism has been used to assign the absolute configuration of a recently synthesized chiral 3-substituted isoindolinone. The prediction of (S) configuration for the (−) enantiomer has been confirmed by quantum mechanical calculations.

Structural Analyses of Experimental 13C Edited Amide I′ IR and VCD for Peptide β-Sheet Aggregates and Fibrils Using DFT-Based Spectral Simulations

In the preceding paper, computational models based on density functional theory (DFT) were presented to characterize the sensitivity of vibrational spectroscopic methods (IR, VCD, and Raman) to structural features of β-sheets. Isotopically edited amide I' IR for peptides labeled with (13)C in multiple different sites provides the most structurally distinct signatures of strand alignment, while VCD is sensitive to the sheet twist and intersheet stacking. In this report, we simulate the IR and VCD spectra for models approximating structures of four β-sheet forming peptides previously experimentally studied using these methods with (13)C isotopic editing. Various register alignments are tested. Agreement with experiment is evaluated based on frequency shifts of both the (12)C and (13)C IR amide I' signals, relative intensity patterns, and VCD spectra where available. While for the simulation of IR spectra canonical planar sheets provide a sufficient model system, for VCD simulation twisted, stacked sheets are required in order to reproduce strong couplet-like amide I' VCD. Effects of the solvent (water) and amino acid side chains are also tested by using a simplified, electrostatic solvent model and atomic partial charges for the side chains. Very good agreement with experimental spectra is obtained, particularly for the relative (12)C and (13)C band frequencies. All four peptide models are shown to be antiparallel as had previously been assumed. However, in some cases our simulations are consistent with different register alignment of strands than originally proposed.

Chiral Recognition of Amino Acid Enantiomers by a Crown Ether: Chiroptical IR-VCD Response and Computational Study

We report on a combined experimental and computational study of the chiral recognition of the amino acid serine in protonated form (L/D-SerH(+)), by the crown ether (all-S)-(18-crown-6)-2,3,11,12-tetracarboxylic acid (S-18c6H4). Infrared and vibrational circular dichroism spectroscopies (IR-VCD) are employed to characterize the chiroptical response of the complexes formed by S-18c6H4 with the L-SerH(+) and D-SerH(+) enantiomers in dried thin films obtained from aqueous solutions. The study focuses on vibrational modes directly related to the intermolecular hydrogen bonds between the crown ether derivative and serine, responsible for crown-serine binding, namely, the C═O and C-O stretching modes, and on the C-O-H bending mode, which yield intense IR and VCD signals in the range of wavenumbers 900-2000 cm(-1). The experimental spectra are analyzed in combination with a computational structural survey and optimization at different levels of density functional theory. The conformational landscape of the complexes is found to be primarily governed by a bowl-like structure of the crown ether host and a tripodal coordination of the protonated R-NH3(+) group of serine with the oxygen atoms of the central ether ring. Additionally, one or two of the carboxylic side groups of the crown ether interact with the -COH and -COOH groups of serine. Chiral selectivity is probed by recording the IR and VCD spectra of dried thin films obtained from aqueous solutions with equimolar concentrations of the two serine enantiomers and the macrocycle. The results demonstrate a marked chiral recognition of L-SerH(+) relative to D-SerH(+) by the S-18c6H4 substrate, which arises from the favorable host-guest coordination through H-bonds at optimum distances and collinear orientations, also involving a limited distortion of the crown ether backbone.

Circular Dichroism Spectroscopy Study of Crystalline‐to‐Amorphous Transformation in Chiral Platinum(II) Complexes

Two couples of enantiomeric platinum(II) complexes: Pt(L1a )Cl (1a), Pt(L1b )Cl (1b) and Pt(L1a )(C ≡ C - Ph) (2a), Pt(L1b )(C ≡ C - Ph) (2b) (L1a = (+)-1,3-di-(2-(4,5-pinene)pyridyl)benzene, L1b = (-)-1,3-di-(2-(4,5-pinene)pyridyl)benzene) were synthesized and characterized. Their absolute configurations were determined by single crystal X-ray diffraction and further verified by circular dichroism (CD) spectra (including electronic circular dichroism [ECD] and vibrational circular dichroism [VCD]). These complexes show interesting mechanoluminescence and/or vapoluminescence due to crystalline-to-amorphous transformation. The crystalline solids, grinding-induced amorphous powders, and vapor-induced amorphous powders of complexes 2a and 2b were comparatively investigated by solid-state ECD and VCD spectra. The transformation from crystalline solids to amorphous powders was accompanied by significant variances of the spectral feature in both ECD and VCD spectra.

Determination of Absolute Configuration and Conformation of a Cyclic Dipeptide by NMR and Chiral Spectroscopic Methods

Increasing precision of contemporary computational methods makes spectroscopies such as vibrational (VCD) and electronic (ECD) circular dichroism attractive for determination of absolute configurations (AC) of organic compounds. This is, however, difficult for polar, flexible molecules with multiple chiral centers. Typically, a combination of several methods provides the best picture of molecular behavior. As a test case, all possible stereoisomers with known AC (RS, SR, SS, and RR) of the cyclic dipeptide cyclo(Arg-Trp) (CAT) were synthesized, and the performances of the ECD, infrared (IR), VCD, Raman, Raman optical activity (ROA), and nuclear magnetic resonance (NMR) techniques for AC determination were investigated. The spectra were interpreted with the aid of density functional theory (DFT) calculations. Folded geometries stabilized by van der Waals and electrostatic interactions between the diketopiperazine (DKP) ring and the indole group are predicted to be preferred for CAT, with more pronounced folding due to Arg-Trp stacking in the case of SS/RR-CAT. The RS/SR isomers prefer a twist-boat puckering of the DKP ring, which is relatively independent of the orientation of the side chains. Calculated conformer-averaged VCD and ECD spectra explain most of the experimentally observed bands and allow for AC determination of the tryptophan side-chain, whereas the stereochemical configuration of the arginine side-chain is visible only in VCD. NMR studies provide characteristic long-range (2)J(C,H) and (3)J(C,H) coupling constants, and nuclear Overhauser effect (NOE) correlations, which in combination with either ECD or VCD also allow for complete AC determination of CAT.

DFT-Level Calculations of IR, VCD and Raman Spectra for 13C-Labeled Beta Sheets

With the aid of theoretical models, optical spectroscopy has proven valuable for elucidating secondary structural features in protein systems including β-sheets, which form a large portion of protein assemblies in amyloid systems. For such large systems, computational methods must be both efficient and robust in order to achieve accurate predictions in a timely manner. Quantum chemical methods are in principle the most robust methods available, but suffer from high computational cost that usually makes them impractical for large bimolecular assemblies. In this study optical spectra for β-sheets composed of five strands, ten-amides each, 5x10, were obtained by transferring parameters calculated using DFT for smaller 3x3 sheet segments. Sensitivity of spectra to variations in conformations was examined for parallel, anti-parallel, twisted and flat sheets. Some effects of having strands shifted out of register were also explored. Predicted amide I IR spectra show classic features for parallel and anti-parallel sheets and some new possibilities for discerning between the two are observed, primarily in IR and VCD spectra, while Raman amide I spectra was predicted to be less useful for structural discrimination. Predictions for particular isotopic labeling schemes show clear IR patterns that might be used in elucidating shifts in register for anti-parallel sheets.

Implementation in the Pyvib2 program of the localized mode method and application to a helicene

In this paper, after reviewing key elements for simulating and interpreting IR, Raman, VCD, and ROA spectra, as well as after describing the localized mode procedure, we present a graphical user interface to carry out the normal mode localizations and we illustrate its application on the ROA spectra of the [19]helicene molecule. The overall procedure consists of four steps, and therefore, a specific interface has been designed for each of them. The first and most important part of the procedure is the selection of the mode ensemble under which the localization procedure is performed. Then, during our step-by-step guided tour of the localized mode procedure in Pyvib2, we highlight the importance of the ordering of the localized modes and the importance to set correctly the phase factor between the localized modes. Finally, the vibrational coupling matrix (\(\tilde{\varvec{\Upomega}}\)), the intensity coupling matrix (\({\tilde{\user2{I}}}\)), and the unitary transformation matrix (U) can be analyzed from their representation in the different panels. The ROA spectrum of the [19]helicene molecule is dominated by the positive peaks associated with two normal modes. From the localized mode procedure, we have identified the atomic displacements of these modes as a few-node combination of localized modes characterized by atomic displacements that look like the motion of a “claw”.

VCD spectroscopy probing of weak intermolecular interactions between copper coordination compounds and N-blocked amino acids

Vibrational and electronic circular dichroism (VCD and ECD) spectroscopic investigations of chiral molecular interactions between copper coordination compounds and N-blocked amino acids were reported. VCD and IR spectra in the region of 1700–1500cm−1 exhibit abundant information of intermolecular interactions which were insensitive in ECD studies. These signals can be further interpreted by complexation-induced interactions between the copper coordination compounds and amino acids through ion coordination, hydrogen bonding and van der Waals interactions. The results testify the superiority of VCD spectroscopy for detecting weak intermolecular interactions such as in biologically active systems concerning copper ion.

Organocatalytic asymmetric addition of malonates to unsaturated 1,4-diketones

The organocatalytic Michael addition of malonates to symmetric unsaturated 1,4-diketones catalyzed by thiourea and squaramide derivatives with Cinchona alkaloids afforded the formation of a new C–C bond in high yields (up to 98%) and enantiomeric purities (up to 93%). The absolute configuration of the product was suggested from comparison of the experimental and calculated VCD spectra of the reaction product 3a.

Further monoterpene chromane esters from Peperomia obtusifolia: VCD determination of the absolute configuration of a new diastereomeric mixture

A reinvestigation of the monoterpene chromane ester enriched fraction from Peperomia obtusifolia using chiral chromatography led to the identification of a minor peak, which was elucidated by NMR and HRMS as fenchyl-3,4-dihydro-5-hydroxy-2,7-dimethyl-8-(3″-methyl-2″-butenyl)-2-(4′-methyl-1′,3′-pentadienyl)-2H-1-benzopyran-6-carboxylate, the same structure assigned to two other fenchyl esters described previously, pointing out a stereoisomeric relationship among them. Further NMR analysis revealed that it was actually a mixture of two compounds, whose absolute configurations were determined by VCD measurements. Although, almost no vibrational transitions could be assigned to the chiral chromane, the experimental VCD spectrum was largely opposite to that obtained for the average experimental VCD [(2S,1‴R,2‴R,4‴S+2R,1‴R,2‴R,4‴S)/2] for fenchol derivatives. These results allowed us to assign the putative compounds as a racemic mixture of the chiral chromane esterified with the monoterpene (1S,2S,4R)-fenchol, which had not been identified in our early work.

Vibrational Circular Dichroism Shows Reversible Helical Handedness Switching in Peptidomimetic l-Valine Fibrils.

We elucidate the supramolecular organization in the form of microsize fibrils of gels formed by a l-Valine peptidomimetic compound. Analysis was based on circular dichroism spectroscopies, vibrational (VCD) and electronic (CD), supported by microscopy (atomic force and scanning electron). We show how the VCD spectra give account of the micrometric structure of the fibrils formed by the helicoidal arrangement of simpler proto-fibrils, which are organized in a lower hierarchical level. This ability is used to monitorize a fully reversible change in the handedness of the helix by modulating different external stimuli as pH or ionic strength, thus providing the first observation by VCD of such a phenomenon in a short peptide.

Revisiting Vibrational Circular Dichroism Spectra of (S)-(+)-Carvone and (1S,2R,5S)-(+)-Menthol Using SimIR/VCD Method.

The VCD spectra of (S)-(+)-carvone and (1S,2R,5S)-(+)-menthol are recalculated using the DFT method with extended conformation and configuration spaces. The calculated individual and averaged spectra are compared against observed ones using the previously reported similarity index, SV. It is found that the SV population forms approximately two normal distributions, depending on whether a spectrum matches the observed one or not. This statistical character can be used to estimate the error in absolute configuration (AC) assessments. To avoid erroneous AC assignments and incomplete conformation searching, it is advisible to employ a minimum |SV| of 0.2 and maximize it using conformation averaging. It is demonstrated that this approach is suitable and robust for flexible chiral molecules.