Design of a flexible organometallic tecton: host–guest chemistry with picric acid and self-assembly of platinum macrocycles

A new “flexible” and ditopic Pt(ii) organometallic compound is a tecton for the self-assembly of neutral metallacycles. It also exhibits significant binding affinity for picric acid.

Probing the triplet correlation function in liquid water by experiments and molecular simulations

Three-body information of liquid water is extracted using X-ray diffraction experiment as well as in molecular simulations via isothermal pressure derivative of structure factor term.

Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes

The architecture of a biological membrane hinges upon the fundamental fact that its properties are determined by more than the sum of its individual components. Studies on model membranes have shown the need to characterize in molecular detail how properties such as thickness, fluidity, and macroscopic bending rigidity are regulated by the interactions between individual molecules in a non-trivial fashion. Simulation-based approaches are invaluable to this purpose but are typically limited to short sampling times and model systems that are often smaller than the required properties. To alleviate both limitations, the use of coarse-grained (CG) models is nowadays an established computational strategy. We here present a new CG force field for cholesterol, which was developed by using measured properties of small molecules, and can be used in combination with our previously developed force field for phospholipids. The new model performs with precision comparable to atomistic force fields in predicting the properties of cholesterol-rich phospholipid bilayers, including area per lipid, bilayer thickness, tail order parameter, increase in bending rigidity, and propensity to form liquid-ordered domains in ternary mixtures. We suggest the use of this model to quantify the impact of cholesterol on macroscopic properties and on microscopic phenomena involving localization and trafficking of lipids and proteins on cellular membranes.

The role of Glu41 in the binding of dimannose to P51G-m4-CVN

The carbohydrate binding protein, Cyanovirin-N, obtained from cyanobacteria, consists of high-affinity and low-affinity binding domains. To avoid the formation of a domain swapped structure in solution and also to better focus on the binding of carbohydrates at the high-affinity site, the Ghirlanda group (Biochemistry, 46, 2007, 9199-9207) engineered the P51G-m4-CVN mutant which does not dimerize nor binds at the low-affinity site. This mutant provides an excellent starting point for the experimental and computational study of further transformations to enhance binding at the high-affinity site as well as to retool this site for the possible binding of different sugars. However, before such endeavors are pursued, detailed understanding of apparently key interactions both present in wild-type and P51G-m4-CVN at the high-affinity site must be derived and controversies about the importance of certain residues must be resolved. One such interaction is that of Glu41, a charged residue in intimate contact with 2'OH of dimannose at the nonreducing end. We do so computationally by performing two mutations using the thermodynamic integration formalism in explicit solvent. Mutations of P51G-m4-CVN Glu41 to Ala41 and Gly41 reveal that whereas the loss of Coulomb interactions result in a free energy penalty of about 2.1 kcal/mol, this is significantly compensated by favorable contributions to the Lennard-Jones portion of the transformation, resulting in almost no change in the free energy of binding. At least in terms of free energetics, and in the case of this particular CVN mutant, Glu41 does not appear to be as important as previously thought. This is not because of lack of extensive hydrogen bonding with the ligand but instead because of other compensating factors.

Anions, the Reporters of Structure in Ionic Liquids

In this work we compare the role that different anions play in the structure function S(q) for a set of liquids with the same cation. It is well established that because of their amphiphilic nature and their often larger size, cations play a fundamental role in the structural landscape of ionic liquids. On the other hand, it is often atoms in the anions that display the largest X-ray form factors and therefore play a very significant role as reporters of structure in small- and wide-angle X-ray scattering (SAXS/WAXS)-type experiments. For a set of liquids with similar topological landscape, how does S(q) change when the anionic scattering is deemphasized? Also, how do we computationally recover the typical length scale of important and perhaps universal ionic liquid structural features such as charge alternation when these are experimentally inaccessible from S(q) because of interference cancellations? We answer these questions by studying three different tetrapentylammonium-based liquids with the I(-), PF6(-) and N(CN)2(-) anions.

Limiting ionic conductivity and solvation dynamics in formamide

A self-consistent microscopic theory has been used to calculate the limiting ionic conductivity of unipositive rigid ions in formamide at different temperatures. The calculated results are found to be in good agreement with the experimental data. The above theory can also predict successfully the experimentally observed temperature dependence of total ionic conductivity of a given uniunivalent electrolyte in formamide. The effects of dynamic polar solvent response on ionic conductivity have been investigated by studying the time dependent progress of solvation of a polarity probe dissolved in formamide. The intermolecular vibration (libration) band that is often detected in the range of 100-200 cm(-1) in formamide is found to play an important role in determining both the conductivity and the ultrafast polar solvent response in formamide. The time dependent decay of polar solvation energy in formamide has been studied at three different temperatures, namely, at 283.15, 298.15, and 328.15 K. While the predicted decay at 298.15 K is in good agreement with the available experimental data, the calculated results at the other two temperatures should be tested against experiments.