The conformations of protonated PheGlyGly and GlyGlyPhe tripeptides, generated at temperatures approximately 300-350 K through a photochemical mechanism, were investigated in the gas phase using ...R-IRMPD spectroscopy in the OH and NH stretch region in combination with quantum chemistry calculations. The results aid characterisation of their conformational landscapes and specifically, help identify the intramolecular interactions that control the peptide conformations. The dominant intramolecular interaction in protonated PheGlyGly operates between the N-and C-termini but in protonated GlyGlyPhe there is a strong cation-pi interaction. The observation of a cation-pi interaction in the warm ions highlights its strong, stable nature.
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► Ph-β-d-xylose-H2O has four low energy minima, separated by low barriers. ► The four minima are stable at 40K, but rapidly interconvert at 300K. ► Two isomers give very good ...agreement with the spectrum in the beam experiment.
Structure optimization, ab initio molecular dynamics (AIMD) simulation of transitions between structures, vibrational self-consistent field (VSCF) calculations of vibrational spectra and infrared ion dip (IRID) experiments have been used to explore the potential energy landscape of isomeric xylose·H2O (and D2O). The VSCF predictions are in close correspondence with the experimental data but the spectra associated with their two low energy isomers are too similar to permit an unequivocal structural assignment. At cryogenic temperatures several low energy isomers could be ‘frozen in’ but at 300K the AIMD simulations predict rapid transitions between them and in consequence, a highly fluxional system.
Consider a sequence of numbers x_n \in \mathbb{Z_+} defined by x_{n+1}= \frac{x_n}{2} if x_n is even, and x_{n+1}= \frac{x_n+2x_{n-1}+q}{2} if x_n is odd. A 1-cycle is a periodic sequence with one ...transition from odd to even numbers. We prove theoretical and computational results for the existence of 1-cycles, and discuss a generalization to more complex cycles.
A novel photochemical technique combined with mass spectrometry and resonant infrared multiphoton dissociation spectroscopy (R-IRMPD) has been used to record infrared vibrational spectra of the free ...protonated noradrenaline analogue, 2-amino-1-phenylethanol (APE-H(+)), the amino acid, lysine (Lys-H(+)), and the dipeptide, alanyl alanine (Ala-Ala-H(+)) in the gas phase. Coupling their spectra, obtained in the OH, NH and CH stretch regions, with ab initio calculations has allowed assignment of their preferred protonation sites and conformations. This simple technique will have wide applicability in future investigations of protonated biomolecular structure and conformation.
The excited-state dynamics of porphyrins, and related compounds, impact on their applications as photosensitizers for tumor-targeting drugs and solar cells. Many researchers have examined the ...influence of non-planar distortions in the ground-state geometry on the properties of photoexcited states. We have identified the added importance of conformational changes in the excited state, relative to the initial geometry, on the resulting decay pathways. The ground-state structure and photodynamics of free-base and Cu(ii) complexes of protoporphyrin IX, laser desorbed into a cold supersonic expansion, have been investigated using infrared ion-dip spectroscopy combined with density-functional theory calculations. The vibrational bands associated with the N-H stretching mode of the free base are broader in the first electronically excited state, accessed via the Q band of protoporphyrin IX, than the corresponding bands in the ground-electronic state. This is attributed to rapid intersystem crossing in the excited state promoted by extension of the N-H bonds. Our calculations show that the stretching modes are highly anharmonic, which suggests the likelihood that other conformational changes are also taking place in the excited state.
The intrinsic conformational preferences and structures of the branched trimannoside, α-phenyl 3,6-di-O-(α-d-mannopyranosyl)-α-d-mannopyranoside (which contains the same carbohydrates found in a key ...subunit of the core pentasaccharide in N-glycans) and its singly hydrated complex, have been investigated in the gas phase isolated at low temperature in a molecular beam expansion. Conformational assignments of their infrared ion dip spectra, based on comparisons between experiment and ONIOM (B3LYP/6-31+G(d):HF/6-31G(d)) and single-point MP2 calculations have identified their preferred structures and relative energies. The unhydrated trimannoside populates a unique structure supported by two strong, central hydrogen bonds linking the central mannose unit (CM), and its two branches (3M and 6M) closely together, through a cooperative hydrogen-bonding network: OH4(CM)→OH6(3M)→OH6(6M). A closely bound structure is also retained in the singly hydrated oligosaccharide, with the water molecule bridging across the 3M and 6M branches to provide additional bonding. This structure contrasts sharply with the more open, entropically favored trimannoside structure determined in aqueous solution at 298 K. In principle this structure can be accessed from the isolated trimannoside structure by a simple conformational change, a twist about the α(1,3) glycosidic linkage, increasing the dihedral angle ψC1(3M)−O3(3M)−C3(CM)−C2(CM) from ∼74° to ∼146° to enable accommodation of a water molecule at the centrally bound site occupied by the hydroxymethyl group on the 3M ring and mediation of the water-linked hydrogen-bonded network: OH4(CM) →OHW→OH6(6M). The creation of a “water pocket” motif localized at the bisecting axis of the trimannoside is strikingly similar to the structure of more complex N-glycans in water, suggesting perhaps a general role for the “bisecting” OH4 group in the central (CM) mannose unit.
A computational (ab initio and molecular dynamics) and experimental exploration of the relative importance of molecular conformation and explicit solvent effects on the electronic circular dichroism ...(ECD) of chiral molecules, is presented. The exploration includes an assessment of the validity of angular correlation (sector) rules linking ECD to molecular conformation. It is based upon studies of 1-(R) phenylethanol (including its Raman optical activity spectrum), the corresponding 'benchmark' base, 1-(R)-phenylethylamine and its protonated cation; their hydrated clusters in the gas phase; and their non-polar and aqueous solutions. Emphasis is placed on the influence of specific, hydrogen bonded interactions with the aqueous solvent. The theoretical validity of the (otherwise empirical) sector rule in the neutral molecules and in their specifically hydrated clusters has been established--but with a reversal of the 'historical' sign convention. Protonation of the amine leads to a breakdown of the conventional sector rule but the change in its ECD intensity can still be related to the side chain dihedral angular dependence of its rotatory strength, computed ab initio for its explicitly hydrated clusters. Comparisons between ECD spectra measured in aqueous and in hydrocarbon solutions and the results of molecular dynamics calculations for aqueous solutions at 300 K, identify solvent induced structural change as the principal determinant of their relative ECD spectral intensities. Further links connecting the structures and conformations of chiral molecules and their explicitly solvated clusters in the gas phase, to their structures and conformational populations in solution can be expected through measurement, ab initio computation and analysis of their vibrational, ROA spectra.
This article describes a technique to manage dislocations of mobile bearing lateral unicompartmental knee replacements. When dislocations occur, the bearing usually subluxes medially over the medial ...wall of the tibial component into the intercondylar notch. By positioning small fragment screws with their heads above the vertical wall, thereby increasing the height of the wall, subsequent dislocations can be prevented. Seven cases treated in this manner are reported, of which one of the seven has redislocated. In the remaining six, their clinical outcomes are comparable to the outcomes of those without dislocations.
Level of evidence
Retrospective case series, Level IV.
The β(1→4) glycosidic linkage found in lactose is a prevalent structural motif in many carbohydrates and glycoconjugates. Using UV and IR ion-dip spectroscopies to probe benzyl lactoside isolated in ...the gas phase, we find that the disaccharide unit adopts only a single, rigid structure. Its fully resolved infrared ion-dip spectrum is in excellent agreement with that of the global minimum structure computed ab initio. This has glycosidic torsion angles of φH (H1−C1−O−C4‘) ≈ 180° and ψH (C1−O−C4‘−H4‘) ≈ 0° which correspond to a rotation of ∼150° about the glycosidic bond compared to the accepted solution-phase conformation. We discuss the biological implications of this discovery and the generality of the strategies employed in making it.
The structures of benzyl alcohol, its 1:1 water complex, and its dimer have been investigated by R2PI spectroscopy and IR−UV ion dip spectroscopy, combined with ab initio computation. The sole ...molecular conformer observed in the jet has a gauche arrangement of the gauche arrangement of the OH group relative to the C1−Cα bond, but the extent of π-type intramolecular H-bonding is small. Analysis of its rotational band contours suggests the incidence of vibronic coupling involving motion of the side chain and also leads to an estimate for the dihedral angle τ1(OCCC) lying in the range 35°−60°, in good agreement with the values (50°−60°) indicated by high-level ab initio calculations. The 1:1 water complex is assigned to a structure in which water binds as a proton acceptor to the alcohol group, and as a weak proton donor to the π-system of the aromatic ring. The arrangement of H-bonds is similar within the dimer: the OH of one molecule acts as both acceptor to the alcohol group and as donor to the π-system of the other molecule. Reexamination of published UV band contour and IR/UV ion dip spectroscopic data on 3-phenylpropanol provides unambiguous assignments for the two conformers most heavily populated in the jet expansion: they have AGt and GGt conformations about their Cα−Cβ (anti/gauche), Cβ−Cγ (anti/gauche), and Cγ−O (trans/gauche) bonds that do not involve any OH···π bond. The consequences of increasing chain length for the formation of OH···π bonds is discussed with reference to benzyl alcohol, 2-phenylethanol, and 3-phenylpropanol. The short side-chain of benzyl alcohol permits only a very weak OH···π interaction. The extra methylene units of 2-phenylethanol and 3-phenylpropanol provide enough flexibility for significant OH···π interactions to be possible, but only in 2-phenylethanol does this lead to a strong energetic preference for the H-bonded conformer: the interaction energy gained via the intramolecular H-bond in 3-phenylpropanol is negated by the strain induced in the aliphatic chain.
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