Resolving the Framework Position of Organic Structure-Directing Agents in Hierarchical Zeolites via Polarized Stimulated Raman Scattering.

The direct synthesis of hierarchically intergrown silicalite-1 can be achieved using a specific diquaternary ammonium agent. However, the location of these molecules in the zeolite framework, which is critical to understand the formation of the material, remains unclear. Where traditional characterization tools have previously failed, herein we use polarized stimulated Raman scattering (SRS) microscopy to resolve molecular organization inside few-micron-sized crystals. Through a combination of experiment and first-principles calculations, our investigation reveals the preferential location of the templating agent inside the linear pores of the MFI framework. Besides illustrating the attractiveness of SRS microscopy in the field of material science to study and spatially resolve local molecular distribution as well as orientation, these results can be exploited in the design of new templating agents for the preparation of hierarchical zeolites.

Correction: Weak backbone CHO[double bond, length as m-dash]C and side chain tButBu London interactions help promote helix folding of achiral NtBu peptoids.

Correction for 'Weak backbone CHO[double bond, length as m-dash]C and side chain tButBu London interactions help promote helix folding of achiral NtBu peptoids' by G. Angelici et al., Chem. Commun., 2016, 52, 4573-4576.

Weak backbone CH···O=C and side chain tBu···tBu London interactions help promote helix folding of achiral NtBu peptoids.

The synthesis of all-cis amide (NtBu)-glycine oligomers up to 15 residues long by a blockwise coupling approach is reported. The structure and dynamical behavior of these peptoids have been studied by X-ray crystallography, NMR and molecular modeling. Analyses reveal that the folding of these oligomers is driven by weak CH···O=C hydrogen bonding along the peptoid backbone and London interaction between tBu···tBu side-chains.

Ligand effect on the NMR, vibrational and structural properties of tetra- and hexanuclear ruthenium hydrido clusters: a theoretical investigation.

Structural and spectroscopic properties of tetranuclear ruthenium hydrido clusters, and to a less extent, of hexanuclear ruthenium hydrido clusters, are investigated theoretically. Some of these (H)(n)Ru(k)(L)(m) (k = 4, 6) clusters were experimentally synthesized and characterized. Non-existing structures are also considered in order to examine the role of ligands on their structure, vibrational spectra and (1)H NMR chemical shifts. The calculated properties are found in very good agreement with experimental data, when available. Beyond the intrinsic interest elicited by transition metal clusters, these compounds are also considered in this paper as relevant to diamagnetic ruthenium nanoparticles as well as building blocks of hcp surfaces, which is the ruthenium nanoparticle lattice. On the basis of the very good agreement between experiments and theory, the structural and spectroscopic properties of several model clusters are also predicted in order to bring additional data which may help to analyze the spectral signature of ruthenium nanoparticles. A particular emphasis is put on (1)H NMR, which is of high practical importance for characterizing the presence of hydrides in ruthenium clusters and nanoparticles. Several topics are discussed: the structural preference of surface hydrides for terminal-, edge-bridging or face-capping coordination modes, hydrides adsorption energies, the possible presence of interstitial hydrogen atoms, the dependence of (1)H chemical shifts on ligands and on electron counting.

DFT calculations of 1H and 13C NMR chemical shifts in transition metal hydrides.

Transition metal hydrides are of great interest in chemistry because of their reactivity and their potential use as catalysts for hydrogenation. Among other available techniques, structural properties in transition metal (TM) complexes are often probed by NMR spectroscopy. In this paper we will show that it is possible to establish a viable methodological strategy in the context of density functional theory, that allows the determination of 1H NMR chemical shifts of hydride ligands attached to transition metal atoms in mononuclear systems and clusters with good accuracy with respect to experiment. 13C chemical shifts have also been considered in some cases. We have studied mononuclear ruthenium complexes such as Ru(L)(H)(dppm)2 with L = H or Cl, cationic complex [Ru(H)(H2O)(dppm)2]+ and Ru(H)2(dppm)(PPh3)2, in which hydride ligands are characterized by a negative 1H NMR chemical shift. For these complexes all calculations are in relatively good agreement compared to experimental data with errors not exceeding 20% except for the hydrogen atom in Ru(H)2(dppm)(PPh3)2. For this last complex, the relative error increases to 30%, probably owing to the necessity to take into account dynamical effects of phenyl groups. Carbonyl ligands are often encountered in coordination chemistry. Specific issues arise when calculating 1H or 13C NMR chemical shifts in TM carbonyl complexes. Indeed, while errors of 10 to 20% with respect to experiment are often considered good in the framework of density functional theory, this difference in the case of mononuclear carbonyl complexes culminates to 80%: results obtained with all-electron calculations are overall in very satisfactory agreement with experiment, the error in this case does not exceed 11% contrary to effective core potentials (ECPs) calculations which yield errors always larger than 20%. We conclude that for carbonyl groups the use of ECPs is not recommended, although their use could save time for very large systems, for instance in cluster chemistry. The reliance of NMR chemical shielding on dynamical effects, such as intramolecular rearrangements or trigonal twists, is also examined for H2Fe(CO)4, K+[HFe(CO)](-), HMn(CO)5 and HRe(CO)5. The accuracy of the theory is also examined for complexes with two dihydrogen ligands (Tp*RuH(H2)2 and [FeH(H2)(DMPE)2]+) and a ruthenium cluster, [H3Ru4(C6H6)4(CO)]+. It is shown that for all complexes studied in this work, the effect of the ligands on the chemical shielding of hydrogen coordinated to metal is suitably calculated, thus yielding a very good correlation between experimental chemical shifts and theoretical chemical shielding.

Determination of the orientation and dynamics of ergosterol in model membranes using uniform 13C labeling and dynamically averaged 13C chemical shift anisotropies as experimental restraints.

A new strategy was established to determine the average orientation and dynamics of ergosterol in dimyristoylphosphatidylcholine model membranes. It is based on the analysis of chemical shift anisotropies (CSAs) averaged by the molecular dynamics. Static (13)C CSA tensors were computed by quantum chemistry, using the gauge-including atomic-orbital approach within Hartree-Fock theory. Uniformly (13)C-labeled ergosterol was purified from Pichia pastoris cells grown on labeled methanol. After reconstitution into dimyristoylphosphatidylcholine lipids, the complete (1)H and (13)C assignment of ergosterol's resonances was performed using a combination of magic-angle spinning two-dimensional experiments. Dynamically averaged CSAs were determined by standard side-band intensity analysis for isolated (13)C resonances (C(3) and ethylenic carbons) and by off-magic-angle spinning experiments for other carbons. A set of 18 constraints was thus obtained, from which the sterol's molecular order parameter and average orientation could be precisely defined. The validity of using computed CSAs in this strategy was verified on cholesterol model systems. This new method allowed us to quantify ergosterol's dynamics at three molar ratios: 16 mol % (Ld phase), 30 mol % (Lo phase), and 23 mol % (mixed phases). Contrary to cholesterol, ergosterol's molecular diffusion axis makes an important angle (14 degrees) with the inertial axis of the rigid four-ring system.

Potential energy surface crossings and the mechanistic spectrum for intramolecular electron transfer in organic radical cations.

The structure of the potential energy surface for the intramolecular electron transfer (IET) of four different model radical cations has been determined by using reaction path mapping and conical intersection optimization at the ab initio CASSCF level of theory. We show that, remarkably, the calculated paths reside in regions of the ground-state energy surface whose structure can be understood in terms of the position and properties of a surface crossing between the ground and the first excited state of the reactant. Thus, in the norbornadiene radical cation and in an analogue compound formed by two cyclopentene units linked by a norbornyl bridge, IET proceeds along direct-overlap and super-exchange concerted paths, respectively, that are located far from a sloped conical intersection point and in a region where the excited-state and ground-state surfaces are well separated. A second potential energy surface structure has been documented for 1,2-diamino ethane radical cation and features two parallel concerted (direct) and stepwise (chemical) paths. In this case a peaked conical intersection is located between the two paths. Finally, a third type of energy surface is documented for the bismethyleneadamantane radical cation and occurs when there is, effectively, a seam of intersection points (not a conical intersection) which separates the reactant and product regions. Since the reaction path cannot avoid the intersection, IET can only occur nonadiabatically. These IET paths indicate that quite different IET mechanisms may operate in radical cations, revealing an unexpectedly enriched and flexible mechanistic spectrum. We show that the origin of each path can be analyzed and understood in terms of the one-dimensional Marcus-Hush model.

Conformational and electronic properties of the two cis (5S,6R) and (5R,6S) diastereoisomers of 5,6-dihydroxy-5,6-dihydrothymidine: X-ray and theoretical studies.

The structure of (+)-cis-(5S,6R)-5,6-dihydroxy-5,6-dihydrothymidine was obtained using X-ray crystallography [space group P2(1) with a = 10.130(3) angstroms, b = 6.434(9) angstroms, c = 11.02(5) angstroms, and beta = 112.646(2) angstroms]. The comparison of the two cis diastereoisomers of thymidine glycol (I, II) showed several structural and conformational differences. The solid state structures appear to be in agreement with the results of 1H NMR studies which were carried out in aqueous solution. Conformational and electronic properties of the ground state of the molecules I and II were obtained using ab initio LSD-DFT theory. Only slight differences between the crystal structure and the optimized geometry are observed for each of the two oxidized nucleosides. On the other hand, molecules I and II exhibit significant differences in their electronic properties. In particular, the dipole moment of (5S,6R)-thymidine glycol (I) is twice smaller than that of the (5R,6S) diastereoisomer (II). It is noteworthy that these differences in the electronic properties between the two compounds may be related to changes in the rotameric population around the C4'-C5' bond. The repartition of the electrostatic potential is different in the two compounds. These observations lead to a better understanding of the structural changes when the above lesions are included within a DNA molecule.