Side-chain effects on the structures of protonated amino acid dimers: A gas-phase infrared spectroscopy study

Seo, Jongcheol; Hoffmann, Waldemar; Malerz, Sebastian; Warnke, Stephan; Bowers, Michael T.; Pagel, Kevin; Helden, Gert von

doi:10.1016/j.ijms.2017.06.011

Cited by 21 publications

(38 citation statements)

References 45 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…It was previously reported by Seo et al that structures of Phe 2 H + are stabilized by the type A interaction, as well as cation‐π interaction between the aromatic side chain and the NH 3 group. Our conformational search performed for the LL and LD configurations has revealed two conformers of type A, which can essentially be populated in a broad range of temperatures.…”

Section: Resultsmentioning

confidence: 90%

“…Kong et al investigated the progressive stabilization of zwitterionic structures in serine clusters and found that Ser 2 H + favors charge‐solvated structures. Subsequent studies by Seo et al confirmed the type A structure to be the most stable species. Our conformational search, the results of which are presented in Figure , agrees with these findings and did not reveal any additional low‐energy conformers.…”

Section: Resultsmentioning

confidence: 93%

“…The relative populations and IR spectra obtained for individual conformers were used to create a composite spectrum. In order to take into account thermal broadening effects and resolution of IR sources, the absorption bands were then convoluted with Gaussian profile assuming full width at half maximum (FWHM) to be 10 cm −1 for individual conformers at 10 K and 20 cm −1 for combined spectra at room temperature . Noncovalent interaction (NCI) analysis was performed using the Multiwfn program, in order to establish the nature of the bonds that stabilize the complexes.…”

Section: Theoretical Approachmentioning

confidence: 99%

See 2 more Smart Citations

Theoretical studies of infrared signatures of proton‐bound amino acid dimers with homochiral and heterochiral moieties

et al. 2020

View full text Add to dashboard Cite

Proton‐bound homochiral and heterochiral dimers, X‐H+‐X, of five amino acids (X = Ser, Ala, Thr, Phe, and Arg) are investigated theoretically using quantum chemical density functional theory (DFT) calculations and molecular dynamics simulations with the aim to unveil diastereomer‐specific mid‐infrared (mid‐IR) absorption bands in the spectral range of 1000 to 1800 cm−1. The theoretical calculations performed in this work imply that all systems, except Ala2H+, have distinct mid‐IR absorption bands in homochiral and heterochiral configurations, which make them appropriate systems to be studied experimentally with mid‐IR spectroscopy. We show that intermolecular interaction with the side chain, in the form of hydrogen bonding or cation‐π interaction, is necessary for chiral effects to be present in the mid‐IR spectra of proton‐bound dimers of amino acids. We also report new conformers for Ala2H+, Thr2H+, Phe2H+, and Arg2H+, which were not found in earlier studies of these dimers.

show abstract

Section: Resultsmentioning

confidence: 90%

Section: Resultsmentioning

confidence: 93%

Section: Theoretical Approachmentioning

confidence: 99%

See 1 more Smart Citation

Theoretical studies of infrared signatures of proton‐bound amino acid dimers with homochiral and heterochiral moieties

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Mass spectra and collision cross-sections (W, DT CCS He )f or Leu and Arg. [20] Thus,toensure comparable datasets and to circumvent the influence of possible electrostatic interactions such as ion-dipole/induced dipole or Coulomb interactions on the packing efficiency in higher charge states,o nly charge states 1 + and 2 + were used to derive a. The most abundant clusters are labeled with their n/z ratio, where n represents the number of amino acid units in the cluster and z the charge.…”

mentioning

confidence: 99%

An Intrinsic Hydrophobicity Scale for Amino Acids and Its Application to Fluorinated Compounds

et al. 2019

Self Cite

View full text Add to dashboard Cite

More than 100 hydrophobicity scales have been introduced, with each being based on ad istinct condensedphase approach.However,acomparison of the hydrophobicity values gained from different techniques,a nd their relative ranking,isnot straightforward, as the interactions between the environment and the amino acid are unique to each method. Here,weovercome this limitation by studying the properties of amino acids in the clean-room environment of the gas phase.In the gas phase,e ntropic contributions from the hydrophobic effect are by default absent and only the polarity of the side chain dictates the self-assembly.This allows for the derivation of an ovel hydrophobicity scale,w hichi sb ased solely on the interaction between individual amino acid units within the cluster and thus more accurately reflects the intrinsic nature of as ide chain. This principle can be further applied to classify non-natural derivatives,a ss hown here for fluorinated amino acid variants.The accurate determination of the intrinsic hydrophobicity of amino acids is crucial for understanding the key aspects of biology and the application of noncanonical amino acids in the rational design of peptides and proteins.M any fundamental biological processes such as the folding, [1] stability, [2] and oligomerization [3] of proteins as well as protein-ligand interactions [4] are strongly influenced by the hydrophobic effect in solution, where the entropically unfavored solvent shell around nonpolar residues is released to the bulk water. To date,m ore than 100 hydrophobicity scales [5] have been established, with most of them being derived from condensedphase methods such as water/octanol partitioning, [6] calculations of the accessible surface area, [7] direct measurements of physical properties, [8] and chromatographic techniques. [9]

show abstract

“…[20] Um vergleichbare Datensätze zu ge-währleisten und den Einfluss mçglicher elektrostatischer Wechselwirkungen wie Ionen-Dipol/induzierter-Dipol-oder Coulomb-Wechselwirkungen auf die Packungseffizienz in hçheren Ladungszuständen zu minimieren, wurden deshalb nur die Ladungszustände 1 + und 2 + zur Bestimmung von a verwendet. Die untersuchten Aminosäuren unterscheiden sich zwar in ihrer Neigung,Cluster zu bilden, sie alle zeigen jedoch Cluster bis zum Ladungszustand 2 + .D arüber hinaus kçnnen Aminosäuren mit hçherem Ladungszustand einen zusätzlichen Einfluss auf die Anordnung der Cluster haben.…”

unclassified

Eine intrinsische Hydrophobieskala für Aminosäuren und ihre Anwendung auf fluorierte Verbindungen

et al. 2019

Self Cite

View full text Add to dashboard Cite

Es existieren über 100 Hydrophobieskalen für Aminosäuren, die auf unterschiedlichen Ansätzen basieren und einheitlich in kondensierter Phase ermittelt werden. Ein Vergleichder Hydrophobiewerte aus verschiedenen Methoden und die Ermittlung ihrer relativen Rangfolge sind jedoch anspruchsvoll, da die Wechselwirkungen zwischen der Umgebung und der Aminosäure in jeder Methode spezifischs ind. Hier überwinden wir diese Einschränkung, indem wir die Eigenschaften von Aminosäuren in der Reinraumumgebung der Gasphase untersuchen. In der Gasphase bleiben standardmäßig entropische Beiträge des hydrophoben Effektes aus,u nd nur die Polaritätd er Seitenkette ist fürd ie Selbstorganisation entscheidend. Dies ermçglicht die Ableitung einer neuartigen Hydrophobieskala, die ausschließlich auf der Interaktion einzelner Aminosäureeinheiten innerhalb des Clusters basiert und somit die Eigenschaften der Seitenketten besser abbildet. Dieses Prinzip kann fürdie Klassifizierung von nicht-natürlichen Derivaten angewendet werden, wie hier fürf luorierte Aminosäurevarianten gezeigt ist.

show abstract

Side-chain effects on the structures of protonated amino acid dimers: A gas-phase infrared spectroscopy study

Cited by 21 publications

References 45 publications

Theoretical studies of infrared signatures of proton‐bound amino acid dimers with homochiral and heterochiral moieties

Theoretical studies of infrared signatures of proton‐bound amino acid dimers with homochiral and heterochiral moieties

An Intrinsic Hydrophobicity Scale for Amino Acids and Its Application to Fluorinated Compounds

Eine intrinsische Hydrophobieskala für Aminosäuren und ihre Anwendung auf fluorierte Verbindungen

Contact Info

Product

Resources

About