Secondary structure of Ac-Alan_n-LysH+^+ polyalanine peptides (nn=5,10,15) in vacuo: Helical or not?

The polyalanine-based peptide series Ac-Ala_n-LysH+ (n=5-20) is a prime example that a secondary structure motif which is well-known from the solution phase (here: helices) can be formed in vacuo. We here revisit this conclusion for n=5,10,15, using density-functional theory (van der Waals corrected generalized gradient approximation), and gas-phase infrared vibrational spectroscopy. For the longer molecules (n=10,15) \alpha-helical models provide good qualitative agreement (theory vs. experiment) already in the harmonic approximation. For n=5, the lowest energy conformer is not a simple helix, but competes closely with \alpha-helical motifs at 300K. Close agreement between infrared spectra from experiment and ab initio molecular dynamics (including anharmonic effects) supports our findings.Comment: 4 pages, 4 figures, Submitted to JPC Letter

Infrarotspektroskopie zur Charakterisierung von Sekundärstrukturelementen von Biomolekülen in der Gasphase

Vibrational spectroscopy is a commonly used method in structural investigations of biomolecules in the condensed phase. Vibrational modes, such as C−O stretching vibrations (amide-I) in the range of 1700 cm−1 or N−H bending vibrations (amide-II) at around 1500 cm−1 , are sensitive to the three-dimensional arrangement of the atoms in the proteins. Knowledge of the band positions makes it possible to obtain a global picture of the fundamental conformation of the molecule. Investigations on gas-phase biomolecules allow for an insight into the intrinsic intra-molecular interactions, which determine the molecular structure. Many proteins possess secondary structural elements, including for instance α-helix and β-sheet, and these motifs often determine the structure of the entire protein. For this thesis biomolecules in the gas phase were investigated using infrared spectroscopy, the goal being to define band positions of significant structural characteristics in the infrared spectrum. The amide-I band position for the various secondary structural elements was an area of particular research interest. In the pursuit of these research aims mass spectrometry, infrared spectroscopy, and density functional theory methodologies were employed.Schwingungsspektroskopie ist eine gebräuchliche Methode zur Strukturaufklärung von Biomolekülen in der kondensierten Phase. Schwingungsmoden, wie zum Beispiel die C−O Streckschwingung (Amid-I Bande) im Bereich von 1700 cm−1 oder die N−H Biegeschwingung (Amid-II Bande) bei 1500 cm−1 sind empfindlich auf die dreidimensionale Anordnung der Atome in Proteinen. Die Kenntnis der Bandenposition kann es ermöglichen, ein umfassendes Bild der zugrundeliegenden Konformation des Moleküls zu erhalten. Untersuchungen an Biomolekülen in der Gasphase können einen Einblick in die intrinsischen strukturbestimmenden Wechselwirkungen des Moleküls liefern. Vielen Proteinen sind Sekundärstrukturelemente, wie zum Beispiel die α-Helix oder das β-Faltblatt gemein und deren Motive bestimmen häufig die Struktur des ganzen Proteins. Im Rahmen dieser Arbeit wurden Biomoleküle in der Gasphase mittels Infrarotspektroskopie untersucht. Das Ziel war es, strukturcharakteristische Bandenpositionen im Infrarotspektrum, insbesondere die der Amid-I Bande, von verschiedenen Sekundärstrukturelementen zu finden. Hierzu wurden Methoden der Massenspektrometrie mit denen der Infrarotspektroskopie sowie der Dichtefunktionaltheorie verbunden

Catching proteins in liquid helium droplets

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Amide-I and -II Vibrations of the Cyclic β-Sheet Model Peptide Gramicidin S in the Gas Phase

In the condensed phase, the peptide gramicidin S is often considered as a model system for a β-sheet structure. Here, we investigate gramicidin S free of any influences of the environment by measuring the mid-IR spectra of doubly protonated (deuterated) gramicidin S in the gas phase. In the amide I (i.e., CO stretch) region, the spectra show a broad split peak between 1580 and 1720 cm⁻¹. To deduce structural information, the conformational space has been searched using molecular dynamics methods and several structural candidates have been further investigated at the density functional level. The calculations show the importance of the interactions of the charged side-chains with the backbone, which is responsible for the lower frequency part of the amide I peak. When this interaction is inhibited via complexation with two 18-crown-6 molecules, the amide I peak narrows and shows two maxima at 1653 and 1680 cm⁻¹. A comparison to calculations shows that for this complexed ion, four CO groups are in an antiparallel β-sheet arrangement. Surprisingly, an analysis of the calculated spectra shows that these β-sheet CO groups give rise to the vibrations near 1680 cm⁻¹. This is in sharp contrast to expectations based on values for the condensed phase, where resonances of β-sheet sections are thought to occur near 1630 cm⁻¹. The difference between those values might be caused by interactions with the environment, as the condensed phase value is mostly deduced for β-sheet sections that are embedded in larger proteins, that interact strongly with solvent or that are part of partially aggregated species

Secondary Structure of Ac-Ala_<i>n</i>-LysH⁺ Polyalanine Peptides (<i>n</i> = 5,10,15) in Vacuo: Helical or Not?

The polyalanine-based peptide series Ac-Ala_<i>n</i>-LysH⁺ (<i>n</i> = 5−20) is a prime example that a secondary structure motif that is well-known from the solution phase (here: helices) can be formed in vacuo. Here we revisit the series members <i>n</i> = 5,10,15, using density functional theory (van der Waals corrected generalized gradient approximation) for structure predictions, which are then corroborated by room temperature gas-phase infrared vibrational spectroscopy. We employ a <i>quantitative</i> comparison based on Pendry’s reliability factor (popular in surface crystallography). In particular, including <i>anharmonic</i> effects into calculated spectra by way of ab initio molecular dynamics produces remarkably good experiment−theory agreement. We find the longer molecules (<i>n</i> = 10,15) to be firmly α-helical in character. For <i>n</i> = 5, calculated free-energy differences show different H-bond networks to still compete closely. Vibrational spectroscopy indicates a predominance of α-helical motifs at 300 K, but the lowest-energy conformer is not a simple helix

Ir spectroscopy of gas-phase c(60)(-)

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