Infrared Photodissociation Spectroscopy of C2n+1N− Anions with n = 1 – 5

The gas phase vibrational spectroscopy of cryogenically cooled C2n + 1N− anions with n = 1 − 5 is investigated in the spectral range of the C≡C and C≡N stretching modes (1850–2400 cm–1) by way of infrared photodissociation (IRPD) spectroscopy of messenger-tagged C2n+1N–· mD2 complexes. The IRPD spectra are assigned based on a comparison to previously reported anharmonic and harmonic CCSD(T) vibrational frequencies and intensities. Experimentally determined and predicted anharmonic vibrational transition energies lie within ± 21 cm–1. For the harmonic CCSD(T)/vqz+ vibrational frequencies a scaling factor of 0.9808 is determined, resulting in comparable absolute deviations. The influence of the D2-messenger molecules on the structure and the IRPD spectrum is found to be small. Compared to the results of previous IR matrix isolation studies additional, in particular weaker, IR-active transitions are identified

gas phase vibrational spectroscopy of V3O6-8+

We present gas phase vibrational spectra of the trinuclear vanadium oxide cations V3O6+·He1–4, V3O7+·Ar0,1, and V3O8+·Ar0,2 between 350 and 1200 cm−1. Cluster structures are assigned based on a comparison of the experimental and simulated IR spectra. The latter are derived from B3LYP/TZVP calculations on energetically low-lying isomers identified in a rigorous search of the respective configurational space, using higher level calculations when necessary. V3O7+ has a cage-like structure of C3v symmetry. Removal or addition of an O-atom results in a substantial increase in the number of energetically low-lying structural isomers. V3O8+ also exhibits the cage motif, but with an O2 unit replacing one of the vanadyl oxygen atoms. A chain isomer is found to be most stable for V3O6+. The binding of the rare gas atoms to V3O6–8+ clusters is found to be strong, up to 55 kJ/mol for Ar, and markedly isomer-dependent, resulting in two interesting effects. First, for V3O7+·Ar and V3O8+·Ar an energetic reordering of the isomers compared to the bare ion is observed, making the ring motif the most stable one. Second, different isomers bind different number of rare gas atoms. We demonstrate how both effects can be exploited to isolate and assign the contributions from multiple isomers to the vibrational spectrum. The present results exemplify the structural variability of vanadium oxide clusters, in particular, the sensitivity of their structure on small perturbations in their environment

Carbohydrate-aromatic interactions: a computational and IR spectroscopic investigation of the complex, methyl alpha-L-fucopyranoside·toluene, isolated in the gas phase

a b s t r a c t A carbohydrate-aromatic complex, methyl a-L-fucopyranoside Á toluene, which provides a model for probing the physical basis of carbohydrate-protein 'stacking' interactions, has been created in a molecular beam and probed through IR ion dip spectroscopy in the CH and OH regions. The results are interpreted in the light of DFT calculations using the MO5-2X functional. They indicate the creation of stacked structures with the aromatic molecule bonded either to the upper or to the lower face of the pyranoside ring, through CH 3,4 -p (upper) or CH 1 -p (lower) interactions leading to binding energies 618 kJ mol À1

White-Light Optimal Control of Photoinduced Processes

The photofragmentation of Cu₃ and Al₄ clusters during charge reversal with white-light pulses is optimized by using an evolutionary algorithm and a pulse shaping setup. By controlling the spectral phase over the full spectral range of the supercontinuum, tailored pulses are generated with the aim of adapting the energetic and temporal structure of the pulse to the characteristic dynamics and electronic manifold of the investigated systems. In this context, maximizing the ratio of the cationic yield of a selected fragment (Cu₂⁺ and Al⁺) and the parent ion is chosen as an optimization target. Significant enhancement factors are achieved, demonstrating a high selectivity in populating specific points on the potential energy surface, which facilitates the targeted photofragmentation of the investigated systems. The optimal pulse shapes indicate that both vibronic as well as electronic wave packets are probed. Additional laser-induced dissociation experiments suggest that fragmentation of the Cu₃ clusters occurs in an excited state of the neutral species. Further photofragmentation studies of the Cu₃^– anions present a strong wavelength dependence, with the formation of Cu^– occurring only when irradiated with wavelengths shorter than 528 nm. No photodissociation is observed for the Al₄^– anions

Identification of preferred carbohydrate binding modes in xenoreactive antibodies by combining conformational filters and binding site maps

Carbohydrates are notoriously flexible molecules. However, they have an important role in many biochemical processes as specific ligands. Understanding how carbohydrates are recognized by other biological macromolecules (usually proteins) is therefore of considerable scientific value. Interfering with carbohydrate-protein interactions is a potentially useful strategy in combating a range of disease states, as well as being of critical importance in facilitating allo- and xenotransplantation. We have devised an in silico protocol for analyzing carbohydrate-protein interactions. In this study, we have applied the protocol to determine the structures of aGal-terminating carbohydrate antigens in complex with a panel of xenoreactive antibodies. The most important feature of the binding modes is the fixed conformation of the Galß(1,4)Glc/GlcNAc linkage across all of the binding modes. The preferred conformation of the terminal Gala(1,3)Gal linkage varies depending on the antibody binding site topography, although it is possible that some of the antibodies studied recognize more than one Gala(1,3)Gal conformation. The binding modes obtained indicate that each antibody uses distinct mechanisms in recognizing the target antigens. © The Author 2010. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: [email protected]

Molecular bases of cyclodextrin adapter interactions with engineered protein nanopores

Engineered protein pores have several potential applications in biotechnology: as sensor elements in stochastic detection and ultrarapid DNA sequencing, as nanoreactors to observe single-molecule chemistry, and in the construction of nano- and micro-devices. One important class of pores contains molecular adapters, which provide internal binding sites for small molecules. Mutants of the α-hemolysin (αHL) pore that bind the adapter β-cyclodextrin (βCD) ∼104 times more tightly than the wild type have been obtained. We now use single-channel electrical recording, protein engineering including unnatural amino acid mutagenesis, and high-resolution x-ray crystallography to provide definitive structural information on these engineered protein nanopores in unparalleled detail