A computational stochastic approach is applied to the description of flexible molecules. By combining (i) molecular dynamics simulations, (ii) hydrodynamics approaches, and (iii) a multidimensional diffusive description for internal and global dynamics, it is possible to build an efficient integrated approach to the interpretation of relaxation processes in flexible systems. In particular, the model is applied to the interpretation of nuclear magnetic relaxation measurements of linear oligosaccharides, namely a mannose-containing trisaccharide and the pentasaccharide LNF-1. Experimental data are reproduced with sufficient accuracy without free model parameters.

Cryptophane-C is composed of two nonequivalent cyclotribenzylene caps, one of which contains methoxy group substituents on the phenyl rings. The two caps are connected by three OCH2CH2O linkers in an anti arrangement. Host–guest complexes of cryptophane-C with dichloromethane and chloroform in solution were investigated in detail by nuclear magnetic resonance techniques and density functional theory (DFT) calculations. Variable temperature proton and carbon-13 spectra show a variety of dynamic processes, such as guest exchange and host conformational transitions. The guest exchange was studied quantitatively by exchange spectroscopy measurements or by line-shape analysis. The conformational preferences of the guest-containing host were interpreted through cross-relaxation measurements, providing evidence of the gauche+2 and gauche−2 conformations of the linkers. In addition, the mobility of the chloroform guest inside the cavity was studied by carbon-13 relaxation experiments. Combining different types of evidence led to a detailed picture of molecular recognition, interpreted in terms of conformational selection. Copyright © 2012 John Wiley & Sons, Ltd.

Reactions catalyzed by palladium(II) acetate and trifluoroacetic acid (TFA) have a clear preactivation phase.However, the structure of real catalytic species remains unclear. We show that the key species are cyclic trinuclear complexes of composition [Pd 3 (OAc) 6−x (OTFA) x ] (x = 1-6) formed by a sequential ligand exchange from [Pd 3 (OAc) 6 ]. Furthermore, we prove that the trinuclear palladium backbone of the precatalyst remains preserved during the first phase of the C-H activation reaction of acetanilides. In other words, the reaction pathway including the trinuclear species should be taken into account in discussion about mechanisms of the reactions catalyzed by palladium acetates.

Guest-host complex between cryptophane C, possessing two non-equivalent caps, and chloroform is investigated by NMR spectroscopy. The kinetics of the chloroform exchange between the bound and free sites is determined by (1)H exchange spectroscopy. Moreover, the preferential orientation of chloroform molecule with respect to the cryptophane C frame is examined by the NOESY and ROESY experiments. The experimental findings are compared to the results of quantum chemical calculations.

Standard spectral density mapping protocols, well suited for the analysis of (15)N relaxation rates, introduce significant systematic errors when applied to (13)C relaxation data, especially if the dynamics is dominated by motions with short correlation times (small molecules, dynamic residues of macromolecules). A possibility to improve the accuracy by employing cross-correlated relaxation rates and on measurements taken at several magnetic fields has been examined. A suite of protocols for analyzing such data has been developed and their performance tested. Applicability of the proposed protocols is documented in two case studies, spectral density mapping of a uniformly labeled RNA hairpin and of a selectively labeled disaccharide exhibiting highly anisotropic tumbling. Combination of auto- and cross-correlated relaxation data acquired at three magnetic fields was applied in the former case in order to separate effects of fast motions and conformational or chemical exchange. An approach using auto-correlated relaxation rates acquired at five magnetic fields, applicable to anisotropically moving molecules, was used in the latter case. The results were compared with a more advanced analysis of data obtained by interpolation of auto-correlated relaxation rates measured at seven magnetic fields, and with the spectral density mapping of cross-correlated relaxation rates. The results showed that sufficiently accurate values of auto- and cross-correlated spectral density functions at zero and (13)C frequencies can be obtained from data acquired at three magnetic fields for uniformly (13)C-labeled molecules with a moderate anisotropy of the rotational diffusion tensor. Analysis of auto-correlated relaxation rates at five magnetic fields represents an alternative for molecules undergoing highly anisotropic motions.

Dynamics of exocyclic groups in the Escherichia coli O91 O-antigen polysaccharide in solution studied by carbon-13 NMR relaxation. Journal of Biomolecular NMR,

The microscopic structure of ethanol in the liquid state is characterized as a dynamic equilibrium of hydrogen-bonded clusters of different sizes and topologies. We have developed a novel method for determination of the average size of the clusters that combines the measurement of diffusion coefficient by means of NMR diffusometry technique and hydrodynamic simulations. The approach includes the use of HydroNMR [J. Garcı̀a de la Torre, M. L. Huertas, and B. Carrasco, J. Magn. Reson. 147, 2000, 138] for small molecules, which is attained here by the calibration procedure using a dilute solution of tetramethylsilane. It is thus possible to correlate the experimentally determined diffusion coefficient of ethanol with calculated diffusion coefficients of the modeled clusters of different sizes. We found that average size of the clusters in 0.16 M solution of ethanol in n-hexane corresponds to the monomer above 300 K and to the pentamer/hexamer below 240 K. The clusters in the case of 0.44 M solution are generally slightly larger, from the average size corresponding to the dimer at 320 K and the hexamer at 210 K.

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