Structural analyses of isolated cyclic tetrapeptides with varying amino acid residues

Stamm, Anke; Maué, Dominique; Schaly, Astrid; Schlicher, S.; Bartl, Julia; Kubik, Stefan; Gerhards, Markus

doi:10.1039/c6cp08696a

Cited by 10 publications

(25 citation statements)

References 71 publications

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“…In comparison to the N-H and O-H stretching modes, the C=O stretching vibrations (with their mainly double bonding character) are also quite localized modes. However, they exhibit a slightly less anharmonic character than the amide A modes, which is also revealed in the higher scaling factor used in the amide I region 74,79,135,157,160,250,284,335,383,394 .…”

Section: Some General Aspectsmentioning

confidence: 97%

“…The backbone of the inverse -turn is constrained by hyperconjugative interactions, which tend to align the CO and NH covalent bonds of the residue and therefore oppose to the formation of a strong 7 H-bond. a) H-bonds shifting the NH stretches below 3300 cm -1 are observed in some cyclic (tetra)peptides 335,391…”

Section: Spectroscopic Probe Of Backbone-backbone Interactions Specific To Uncapped Peptides (Cooh/nh 2 ): Oh/nh/nh 2 Hydride Stretchesmentioning

confidence: 99%

“…This is why two-step strategies were developed and are still in use today. 31,79,257,319,[333][334][335][336] In the first step, the exploration of the minima of the potential energy surface (PES) can be carried out using either Monte-Carlo or molecular dynamics (MD) simulations, where peptides are usually described by a force field. This force field is expected to depict the PES well enough to select a reasonable number of lowest-energy structures, which will be considered in the second step where heavier quantitative calculations are targeted.…”

Section: Introduction To Theorymentioning

confidence: 99%

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Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues

et al. 2020

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Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes by successively adding aggregation partners and thus an environment to a molecule. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottomup approach was successfully applied to neutral amino acids starting around the 1990s. Ever since experimental and theoretical methods developed further and investigations could be extended to larger peptide systems. Beyond, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behaviour are presented. Beyond the linear α-peptides the main results of structural analysis on cyclic systems as well as on β-and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance. 45) , non-protected (cf. e.g. 46-48) and protected amino acids (cf. e.g. 49) up to dipeptide models (cf. e.g. 50).In this context, laser spectroscopic techniques combining IR and UV excitations, that one can consider as belonging to the so-called 'action spectroscopies', provide an isomer-selective method of choice to tackle the 87 ) or immunoglobulins (cf. e.g. 88), but they are also found in context with neurodegenerative diseases (cf. e.g. [89][90][91][92][93][94][95] and Section 12). A further structure associated with these diseases (cf. e.g. 96 ) is the β-helix, which presents a protein structure of several parallel β-strands in a helical arrangement with a frequently repetitive amino acid sequence. The structure is stabilized by H-bonds, sometimes ionic interactions or so called protein-protein interactions, which e.g. include electrostatic and hydrophobic effects. Further aspects of peptide structure in gas phase The role of protection groupsWith the unmodified N-and C-terminus amino acids and peptides can exhibit strong preferences for intramolecular H-bonds involving the N-and C-terminus, and can also form intermolecular H-bonds leading to polymer chains. Nevertheless, in a context where the description of the properties of a protein or a long peptide (with respect to its backbone) by smaller peptides is targeted, the introduction of protecting groups at the N-and...

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Section: Some General Aspectsmentioning

confidence: 97%

Section: Spectroscopic Probe Of Backbone-backbone Interactions Specific To Uncapped Peptides (Cooh/nh 2 ): Oh/nh/nh 2 Hydride Stretchesmentioning

confidence: 99%

Section: Introduction To Theorymentioning

confidence: 99%

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Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues

et al. 2020

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“…Fort he DPE-H 2 Oc omplexes,I R/R2PI spectra [5] were recorded at different UV excitation wavenumbers obtained from an R2PI spectrum (see Figure S6 in the Supporting Information). This leads to partly isomer-selective IR spectra as shown in Figure 1.…”

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confidence: 99%

The Effect of Dispersion on the Structure of Diphenyl Ether Aggregates

et al. 2018

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Dispersion interactions can play an important role in understanding unusual binding behaviors. This is illustrated by a systematic study of the structural preferences of diphenyl ether (DPE)-alcohol aggregates, for which OH⋅⋅⋅O-bound or OH⋅⋅⋅π-bound isomers can be formed. The investigation was performed through a multi-spectroscopic approach including IR/UV and microwave methods, combined with a detailed theoretical analysis. The resulting solvent-size-dependent trend for the structural preference turns out to be counter-intuitive: the hydrogen-bonded OH⋅⋅⋅O structures become more stable for larger alcohols, which are expected to be stronger dispersion energy donors and thus should prefer an OH⋅⋅⋅π arrangement. Dispersion interactions in combination with the twisting of the ether upon solvent aggregation are key for understanding this preference.

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“…The dimerization via the carboxyl moieties is considered as well as chelation of one ruthenium by the second molecule. For all structures vibrational spectra are calculated, scaled with the factor 0.9608 and convolved with a Gaussian (FWHM = 15 cm –1 ). Characterization of C1–N bicarbazole product: see ref .…”

Section: Methodsmentioning

confidence: 99%