Unraveling non-covalent interactions within flexible biomolecules: from electron density topology to gas phase spectroscopy.

The NCI (Non-Covalent Interactions) method, a recently-developed theoretical strategy to visualize weak non-covalent interactions from the topological analysis of the electron density and of its reduced gradient, is applied in the present paper to document intra- and inter-molecular interactions in flexible molecules and systems of biological interest in combination with IR spectroscopy. We first describe the conditions of application of the NCI method to the specific case of intramolecular interactions. Then we apply it to a series of stable conformations of isolated molecules as an interpretative technique to decipher the different physical interactions at play in these systems. Examples are chosen among neutral molecular systems exhibiting a large diversity of interactions, for which an extensive spectroscopic characterization under gas-phase isolation conditions has been obtained using state-of-the-art conformer-specific experimental techniques. The interactions presently documented range from weak intra-molecular H-bonds in simple amino-alcohols, to more complex patterns, with interactions of various strengths in model peptides, as well as in chiral bimolecular systems, where invaluable hints for the understanding of chiral recognition are revealed. We also provide a detailed technical appendix, which discusses the choices of cut-offs as well as the applicability of the NCI analysis to specific constrained systems, where local effects require attention. Finally, the NCI technique provides IR spectroscopists with an elegant visualization of the interactions that potentially impact their vibrational probes, namely the OH and NH stretching motions. This contribution illustrates the power and the conditions of use of the NCI technique, with the aim of providing an easy tool for all chemists, experimentalists and theoreticians, for the visualization and characterization of the interactions shaping complex molecular systems.

Conformational analysis of quinine and its pseudo enantiomer quinidine: a combined jet-cooled spectroscopy and vibrational circular dichroism study.

Laser-desorbed quinine and quinidine have been studied in the gas phase by combining supersonic expansion with laser spectroscopy, namely, laser-induced fluorescence (LIF), resonance-enhanced multiphoton ionization (REMPI), and IR-UV double resonance experiments. Density funtional theory (DFT) calculations have been done in conjunction with the experimental work. The first electronic transition of quinine and quinidine is of π-π* nature, and the studied molecules weakly fluoresce in the gas phase, in contrast to what was observed in solution (Qin, W. W.; et al. J. Phys. Chem. C2009, 113, 11790). The two pseudo enantiomers quinine and quinidine show limited differences in the gas phase; their main conformation is of open type as it is in solution. However, vibrational circular dichroism (VCD) experiments in solution show that additional conformers exist in condensed phase for quinidine, which are not observed for quinine. This difference in behavior between the two pseudo enantiomers is discussed.

Excited-state intramolecular proton transfer reaction modulated by low-frequency vibrations: an effect of an electron-donating substituent on the dually fluorescent bis-benzoxazole.

Excited-state intramolecular proton transfer (ESIPT) reaction has been studied in a molecule showing dual fluorescence, the 2,5-bis(2-benzoxazolyl)-4-methoxyphenol (BBMP), and its isotopomers, where the methoxy, and alternatively, the OH group has been deuterated. Attention is focused on the influence of electron donating OCH(3) substituent on fast excited state reaction. Comparison between the resonance-enhanced multiphoton ionization spectrum and the laser-induced excitation of the primary and phototautomeric emissions has been done. The geometry, electron density distribution, vibrational structure as well as the potential energy profiles in the S(0) and S(1) states of four possible rotameric forms of BBMP were calculated with application of the density functional theory (DFT). It allowed identifying the most probable conformer and assessing the role of low-frequency motions for the ESIPT efficiency.

Chiral recognition in cinchona alkaloid protonated dimers: mass spectrometry and UV photodissociation studies.

Chiral recognition in protonated cinchona alkaloid dimers has been studied in mass spectrometry experiments. The experimental setups involved a modified 7T FT-ICR (Fourier transform-ion cyclotron resonance) mass spectrometer (MS) and a modified Paul ion trap both equipped with an electrospray ionization source (ESI). The Paul ion trap has been coupled to a frequency-doubled dye laser. The fragmentation of protonated dimers made from cinchonidine (Cd) and the two pseudoenantiomers of quinine, namely, quinine (Qn) and quinidine (Qd), has been assessed by means of collision-induced dissociation (CID) as well as UV photodissociation (UVPD). Whereas CID fragmentation of the dimers only leads to the evaporation of the monomers, UVPD results in the additional loss of a neutral radical fragment corresponding to the quinuclidinyl radical. The effect of the excitation wavelength and of complexation with H(2)SO(4) has been studied to cast light on the reaction mechanism. Complexation with H(2)SO(4) modifies the photoreactivity of the dimers; only evaporation of the monomeric fragments, quinine, and cinchonidine is observed. Comparison between the mass spectra of the cinchona alkaloid (CdQnH(+)) or (CdQdH(+)) dimers resulting from the UVPD of (CdQnH(2)SO(4)H(+)) and that of bare (CdQnH(+)) helps propose a fragmentation mechanism, which is thought to involve fast proton transfer from the quinuclidine part of a molecular subunit to the quinoline ring. CID and UV fragmentation experiments show that the homochiral dimer is more strongly bound than the heterochiral adduct.

Chiral recognition in jet-cooled complexes of (1R,2S)-(+)-cis-1-amino-2-indanol and methyl lactate: on the importance of the CH...pi interaction.

Complexation between (1R,2S)-(+)-cis-1-amino-2-indanol (AI) and the two enantiomers of methyl lactate has been studied by means of laser-induced fluorescence, resonance-enhanced two-photon ionisation, and IR-UV double resonance spectroscopy, in the region of 3 microm. Two isomeric complexes have been spectroscopically characterised for each diastereoisomer. Comparison with ab initio calculations shows that the most stable form is an insertion structure, common to the two diastereoisomers, in which the OH group of methyl lactate inserts into the intramolecular bond of AI. This structure shows almost no chiral discrimination. A secondary structure has been observed, which is specific to each enantiomer. It involves a main hydrogen bond from the OH group of methyl lactate to AI together with weaker hydrogen bonds, which depend on chirality. The enantioselectivity in the hydrogen bond topology is due to a weak stabilizing CH...pi interaction, involving the CH located on the asymmetric carbon of methyl lactate, which can be obtained for one of the enantiomers only.