Exploring the dynamics of calix[4]pyrrole: effect of solvent and fluorine substitution

Molecular dynamics simulations show that calix[4]pyrrole (CP) and octafluorocalix[4]pyrrole (8F-CP) are extremely flexible molecules. CP mainly adopts the 1,3-alternate conformation in all the solvents, although the percentage of alternative conformations increases in polar solvents, especially those with good hydrogen-bonding acceptor properties. However, in the case of 8F-CP, the cone conformation is the most populated in some solvents. Transitions between conformers are common and fast, and both CP and 8F-CP can adopt the cone conformation needed for optimum interaction with anions more easily than would be predicted on the basis of previous gas-phase calculations. Furthermore, the present studies show that when a fluoride anion is specifically placed initially in close proximity to CP and 8F-CP in their respective 1,3-alternate conformations, an extremely fast change to the cone conformation is observed in both cases. The results suggest that preorganization does not represent a major impediment to anion-binding for either CP or 8F-CP, and that ion-induced conformational changes can follow different mechanisms depending on the solvent and the chemical substituents present on the calix[4]pyrrole beta-pyrrolic positions.     

Segregation of inorganic ions at surfaces of polar nonaqueous liquids.

We present a short review of recent computational and experimental studies on surfaces of solutions of inorganic salts in polar nonaqueous solvents. These investigations complement our knowledge of aqueous interfaces and show that liquids such as formamide, liquid ammonia, and ethylene glycol can also surface-segregate large polarizable anions like iodide, albeit less efficiently than water. For liquids whose surfaces are covered with hydrophobic groups (e.g. methanol), the surface-ion effect all but disappears. Based on the present data a general picture of inorganic-ion solvation at the solution-vapor interface of polar liquids is outlined.     

Ensemble‐Averaged QM/MM Kinetic Isotope Effects for the SN2 Reaction of Cyanide Anions with Chloroethane in DMSO Solution

The existence of solvent fluctuations leads to populations of reactant‐state (RS) and transition‐state (TS) configurations and implies that property calculations must include appropriate averaging over distributions of values for individual configurations. Average kinetic isotope effects 〈KIE〉 for NC^?+EtCl→NCEt+Cl^? in DMSO solution at 30 °C are best obtained as the ratio 〈f_RS〉/〈f_TS〉 of isotopic partition function ratios separately averaged over all RS and TS configurations. In this way the hybrid AM1/OPLS‐AA potential yields 〈KIE〉 values for all six isotopic substitutions (2° α‐²H₂, 2° β‐²H₃, α‐¹¹C/¹⁴C, leaving group ³⁷Cl, and nucleophile ¹³C and ¹⁵N) for this reaction in the correct direction as measured experimentally. These thermally‐averaged calculated KIEs may be compared meaningfully with experiment, and only one of them differs in magnitude from the experimental value by more than one standard deviation from the mean. This success contrasts with previous KIE calculations based upon traditional methods without averaging. The isotopic partition function ratios are best evaluated using all (internal) vibrational and (external) librational frequencies obtained from Hessians determined for subsets of atoms, relaxed to local minima or saddle points, within frozen solvent environments of structures sampled along molecular dynamics trajectories for RS and TS. The current method may perfectly well be implemented with other QM or QM/MM methods, and thus provides a useful tool for investigating KIEs in relation to studies of chemical reaction mechanisms in solution or catalyzed by enzymes.     

Self‐Propelled Polymer Nanomotors

Polymer conformations: The picture shows instantaneous conformations of product molecules produced in a catalytic reaction at the head of a polymer chain. The extended (left) and collapsed (right) polymers correspond to chains in good and poor solvent conditions, respectively. The product molecule concentration gradient leads to a directed force on the polymer, so that it functions as a self‐propelled nanomotor.

     

A Three‐Site Mechanism for Agonist/Antagonist Selective Binding to Vasopressin Receptors

Molecular‐dynamics simulations with metadynamics enhanced sampling reveal three distinct binding sites for arginine vasopressin (AVP) within its V₂‐receptor (V₂R). Two of these, the vestibule and intermediate sites, block (antagonize) the receptor, and the third is the orthosteric activation (agonist) site. The contacts found for the orthosteric site satisfy all the requirements deduced from mutagenesis experiments. Metadynamics simulations for V₂R and its V_1aR‐analog give an excellent correlation with experimental binding free energies by assuming that the most stable binding site in the simulations corresponds to the experimental binding free energy in each case. The resulting three‐site mechanism separates agonists from antagonists and explains subtype selectivity.     

A new QM/MM method oriented to the study of ionic liquids

The interest on room temperature ionic liquids has grown in the last decades because of their use as all‐purpose solvent and their low environmental impact. In the present work, a new theoretical procedure is developed to study pure ionic liquids within the framework of the quantum mechanics/molecular mechanics method. Each type of ion (cation or anion) is considered as an independent entity quantum mechanically described that follows a differentiated path in the liquid. The method permits, through an iterative procedure, the full coupling between the polarized charge distribution of the ions and the liquid structure around them. The procedure has been tested with 1‐ethyl‐3‐methylimidazolium tetrafluoroborate. It was found that, similar to non‐polar liquids and as a consequence of the low value of the reaction field, the cation and anion charge distributions are hardly polarized by the rest of molecules in the liquid. Their structure is characterized by an alternance between anion and cation shells as evidenced by the coincidence of the first maximum of the anion–anion and cation–cation radial distribution functions with the first minimum of the anion‐cation. Some degree of stacking between the cations is also found. © 2015 Wiley Periodicals, Inc.     

Tailoring of Polarizing Agents in the bTurea Series for Cross‐Effect Dynamic Nuclear Polarization in Aqueous Media

A series of 18 nitroxide biradicals derived from bTurea has been prepared, and their enhancement factors ? (¹H) in cross‐effect dynamic nuclear polarization (CE DNP) NMR experiments at 9.4 and 14.1 T and 100 K in a DNP‐optimized glycerol/water matrix (“DNP juice”) have been studied. We observe that ? (¹H) is strongly correlated with the substituents on the polarizing agents, and its trend is discussed in terms of different molecular parameters: solubility, average e–e distance, relative orientation of the nitroxide moieties, and electron spin relaxation times. We show that too short an e–e distance or too long a T_1e can dramatically limit ? (¹H). Our study also shows that the molecular structure of AMUPol is not optimal and its ? (¹H) could be further improved through stronger interaction with the glassy matrix and a better orientation of the TEMPO moieties. A new AMUPol derivative introduced here provides a better ? (¹H) than AMUPol itself (by a factor of ca. 1.2).