Investigations on isolated peptides by combined IR/UV spectroscopy in a molecular beam – structure, aggregation, solvation and molecular recognition

Three-dimensional docking of alcohols to ketones: an experimental benchmark based on acetophenone solvation energy balances

“…This can be tested by structural or vibrational spectroscopy of molecular complexes, by preference in the cold gas phase where error compensation from the environment and by thermal effects can be ruled out. 4,5 A model which successfully reproduces local structural and vibrational properties of hydrogen bonds to CQO groups may still predict the wrong energy sequence among different conformations, because the latter is a global quantity which heavily involves short and long range secondary contacts described by Pauli and London forces in addition to the primary hydrogen bond. Hence, it is important to develop experimental techniques which probe relative energies of different hydrogen bond arrangements, along with vibrational or rotational spectra.…”

Competition between folded and extended structures of alanylalanine (Ala-Ala) in a molecular beam

“…Gas-phase infrared (IR) spectroscopy is a powerful tool to derive structures of molecules, [5][6][7][8][9] especially when combined with quantum chemical calculations. A conventional method to measure IR spectra of neutral cold gas-phase molecules is IR-UV ion-dip action spectroscopy.…”

Molecular Recognition by a Short Partial Peptide of the Adrenergic Receptor: A Bottom‐Up Approach

“…Figures 2a and bs how IR spectra for the SIVSF-adrenalineH + complex as measured by fixing the frequency of the UV laser to the a-band (red) and the b-band (blue) in the UV spectrum, respectively.Asthese two IR spectra are completely different, the a-band and the bband must arise from different structural isomers (see also Figure S7), denoted as isomers a and b.T he NH stretching vibrations,t ypically observed below 3550 cm À1 ,r eflect the hydrogen-bonding pattern of the NH bonds in the peptide main chain, that is,t he secondary structure. [22,27] Thus,t hese two isomeric forms of SIVSF-adrenalineH + have significantly different secondary structures of SIVSF.…”

“…[20] The b 2 -adrenergic receptor has seven transmembrane helices,a nd the fifth ahelix (TM5) provides ab inding motif for adrenaline.T he sequence of this binding site is SIVSF (S:serine,I:isoleucine, V: valine,F :p henylalanine), wherein two serine residues form hydrogen bonds with adjoining phenolic OH groups (catechol OHs) of adrenaline. [21] We have synthesized apartial peptide,C H 3 CO-SIVSF-NHCH 3 (hereafter denoted by SIVSF peptide), whose termini were protected to mitigate hydrogen bonds [22] not present in the receptor. [9,23] By inclusion of such protecting groups,a na-turn structure (the unit structure of an a-helix) was observed in the gas phase (see the Supporting Information).…”