Vibrational circular dichroism of a 2,5‐diketopiperazine (DKP) peptide: Evidence for dimer formation in cyclo LL or LD diphenylalanine in the solid state

Pérez‐Mellor, Ariel; Zehnacker‐Rentien, Anne

doi:10.1002/chir.22674

Cited by 40 publications

(55 citation statements)

References 80 publications

(137 reference statements)

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“…The former band would absorb at higher wavenumbers and have a higher IR intensity, and the latter would exhibit the opposite behavior. Moreover, for the racemic Ph substituted isoindolinone, a type I dimer (Figure ) was observed in the C 2 /c centrosymmetric crystal, and this kind of dimer has also been observed in similar systems . Thus, we first compared the DFT‐calculated IR spectra of 1 : 1 cyclic isoindolinone dimers with the experimental ones.…”

Section: Resultsmentioning

confidence: 93%

The Vibrational Circular Dichroism Pattern of the ν(C=O) Bands in Isoindolinones

et al. 2018

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The IR and vibrational circular dichroism (VCD) spectra of both enantiomers of Me-, iPr-, nBu-, Ph-, and CH Ph-substituted isoindolinones in solution and KBr pellets were measured and interpreted by DFT calculations. The spectra in solution revealed no important differences in the C=O stretching vibration region while the interpretation of very distinct spectra taken in pellets required determining the crystal structures. The studied compounds crystallized in the P2 2 2 (Me, iPr, CH Ph), P3 (nBu), and P2 (Ph) space groups. We found that the quality of simulated spectra strongly depends on the substituent, the structure of the molecular cluster assumed, basis set, and use of the dispersion correction. The IR spectra can be reproduced well based on the simplest linear arrangement of hydrogen-bonded chains mimicking the molecular arrangement in the crystals. We found no common approach to reproduce all the registered VCD spectra in the crystal phase. For the Me and nBu isoindolinones, the VCD pattern was the best reproduced by full optimization of the selected large molecular clusters. For iPr, Ph and CH Ph derivatives optimizing only the position of H-atoms in a fragment frozen as in the crystal provides the best results. Such an approach can reduce the computation time from months to one week.

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Section: Resultsmentioning

confidence: 93%

The Vibrational Circular Dichroism Pattern of the ν(C=O) Bands in Isoindolinones

et al. 2018

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“…The amide II region (δ (NH) bends) displays two broader bands, at 1537 cm −1 and 1520 cm −1 , which appear as a bisignate doublet in the VCD spectrum. The presence of a doublet may indicate either coupled modes or two noncoupled vibrations with opposite rotatory strengths . The intensity (difference in absorbance between left and right circular polarised light) of the bands is of the order of 10 −4 for the strongest features.…”

Section: Resultsmentioning

confidence: 99%

“…The 6‐31G++(d,p) level was chosen because it has been shown to give satisfactory results in calculating VCD spectra of flexible molecules . Moreover, using the smaller basis set 6‐31G(d,p) gives results similar to those at the B3LYP/6‐31G++(d,p) level for cyclic dipeptides and allows calculating large systems at a reasonable computational cost . Here also, similar results are obtained with the two levels of theory, as shown in Figure S1 on the example of the Mcis cis ‐ACBC monomer, extracted from the tetramer, and eventually used for the assignment (vide infra).…”

Section: Methodsmentioning

confidence: 99%

“…Vibrational circular dichroism (VCD) has proved to be a powerful tool for the study of secondary structures in peptides and proteins . The Amide I and II regions are especially informative as the coupling between modes localised on CO or NH of different residues has a strong signature in VCD . In contrast with electronic circular dichroism (ECD) signatures, which have been used for structural characterization of helices or strands, VCD has not been applied yet to ACBC‐based peptides, in particular to their solid state.…”

Section: Introductionmentioning

confidence: 99%

“…The unit can be thought of as a monomer, like in solution . In other cases, one has to take into account the crystal unit cell itself or a cluster of definite size like a dimer or a tetramer . Still, the intensity enhancement observed in the solid state has to be fully understood …”

Section: Introductionmentioning

confidence: 99%

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Vibrational circular dichroism as a probe of solid‐state organisation of derivatives of cyclic β‐amino acids: Cis‐ and trans‐2‐aminocyclobutane‐1‐carboxylic acid

et al. 2019

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Peptide models built from cis‐ and trans‐2‐aminocyclobutane‐1‐carboxylic acids (ACBCs) are studied in the solid phase by combining Fourier‐transform infrared spectroscopy (FTIR) absorption spectroscopy, vibrational circular dichroism (VCD), and quantum chemical calculations using density functional theory (DFT). The studied systems are N‐tert‐butyloxycarbonyl (Boc) derivatives of 2‐aminocyclobutanecarboxylic acid (ACBC) benzylamides, namely Boc−(cis‐ACBC)−NH−Bn and Boc−(trans‐ACBC)−NH−Bn. These two diastereomers show very different VCD signatures and intensities, which of the trans‐ACBC derivative being one order of magnitude larger in the region of the ν (CO) stretch. The spectral signature of the cis‐ACBC derivative is satisfactorily reproduced by that of the monomer extracted from the solid‐state geometry of related ACBC derivatives, which shows that no long‐range effects are implicated for this system. In terms of hydrogen bonds, the geometry of this monomer is intermediate between the C6 and C8 structures (exhibiting a 6‐ or 8‐membered cyclic NH⋯O hydrogen bond) previously evidenced in the gas phase. The benzyl group must be in an extended geometry to reproduce satisfactorily the shape of the VCD spectrum in the ν (CO) range, which qualifies VCD as a potential probe of dispersion interaction. In contrast, reproducing the IR and VCD spectrum of the trans‐ACBC derivative requires clusters larger than four units, exhibiting strong intermolecular H‐bonding patterns. A qualitative agreement is obtained for a tetramer, although the intensity enhancement is not reproduced. These results underline the sensitivity of VCD to the long‐range organisation in the crystal.

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How Crystal Symmetry Dictates Non‐Local Vibrational Circular Dichroism in the Solid State

et al. 2022

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Solid-State Vibrational Circular Dichroism (VCD) can be used to determine the absolute structure of chiral crystals, but its interpretation remains a challenge in modern spectroscopy. In this work, we investigate the effect of a twofold screw axis on the solid-state VCD spectrum in a combined experimental and theoretical analysis of P2 1 crystals of (S)-(+)-1-indanol. Even though the space group is achiral, a single proper symmetry operation has an important impact on the VCD spectrum, which reflects the supramolecular chirality of the crystal. Distinguishing between contributions originating from molecular chirality and from chiral crystal packing, we find that while IR absorption hardly depends on the symmetry of the space group, the situation is different for VCD, where completely new non-local patterns emerge. Understanding the two underlying mechanisms, namely gauge transport and direct coupling, will help to use VCD to distinguish polymorphic forms.

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Vibrational circular dichroism of a 2,5‐diketopiperazine (DKP) peptide: Evidence for dimer formation in cyclo LL or LD diphenylalanine in the solid state

Cited by 40 publications

References 80 publications

The Vibrational Circular Dichroism Pattern of the ν(C=O) Bands in Isoindolinones

The Vibrational Circular Dichroism Pattern of the ν(C=O) Bands in Isoindolinones

Vibrational circular dichroism as a probe of solid‐state organisation of derivatives of cyclic β‐amino acids: Cis‐ and trans‐2‐aminocyclobutane‐1‐carboxylic acid

How Crystal Symmetry Dictates Non‐Local Vibrational Circular Dichroism in the Solid State

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