On the Validity of Clauser and Horne Factorizability

The Clauser–Horne approach used to derive experimentally measurable quantities for performing experiments on EPR paradox based on Type-I Spontaneous Parametric Down Conversion (SPDC) sources is discussed. It is proved that in this case the deduced Bell's type inequality does not correctly express separability and causality. A deeper analysis of the problem shows that the Clauser–Horne hypothesis of factorizability of joint detection probability cannot be considered so general as to describe this physical situation.     

A new rigidity result for holomorphic maps

In this paper we determine which vanishing order of a holomorphic map f at a point of the (non necessarily regular) boundary of a very generic domain of is required for f to be constant. In particular this vanishing order is 1 if the boundary is Dini-smooth whereas it is at least β/α if f locally maps a Dini-smooth corner of opening πα into a Dini-smooth corner of opening πβ. Finally an analogous result is stated for the case of a holomorphic map f which maps a cusp into a cusp.     

The rotational-conformational distribution of 2,2'-bithienyl in liquid crystals

We have investigated the distribution of conformations and orientations for a simple internal rotor molecule, 2,2'-bithienyl dissolved in liquid crystal solvents, by re-analysing published proton dipolar coupling data with the maximum entropy internal order method (MEIO). We show that detailed, model independent, conformational information can be obtained when data of sufficiently high quality are available. We also propose a novel and convenient representation method for the orientational-conformational coupling.     

Incorporating the effect of ionic strength in free energy calculations using explicit ions

The incorporation of explicit ions to mimic the effect of ionic strength or to neutralize the overall charge on a system in free energy calculations using molecular dynamics simulations is investigated. The difference in the free energy of hydration between two triosephosphate isomerase inhibitors calculated at five different ion concentrations is used as an example. We show that the free energy difference can be highly sensitive to the presence of explicit ions even in cases where the mutation itself does not involve a change in the overall charge. The effect is most significant if the molecule carries a net charge close to the site mutated. Furthermore, it is shown that the introduction of a small number of ions can lead to very severe sampling problems suggesting that in practical calculations convergence can best be achieved by incorporating either no counterions or by simulating at high ionic strength to ensure sufficient sampling of the ion distribution.     

Magnetic nanoparticle assemblies on denatured DNA show unusual magnetic relaxivity and potential applications for MRI

Denatured (substantially single-stranded) herring sperm DNA acts as a template for the preparation of magnetic nanowires, forming stable aqueous suspensions, which exhibit unprecedentedly high relaxivity at low field, suggesting that the material may be a potentially useful reagent for MRI.     

Regioselective epoxide ring opening. Steroselective synthesis of a tetrahydropyran ring

The stereoselective synthesis of a 2-substituted tetrahydropyran with adjacent alkoxy-bearing stereogenic centre is described. The key steps of this synthesis were the stereoselective epoxidation of an allylic alcohol and the regioselective epoxide ring opening by lithium aluminum hydride. The regio and stereoselective synthesis of a trihydroxyselenide and a trihydroxysulfide is also described. The latter compounds are not suitable for cyclization to tetrahydrofuran ring.     

Calculation of affinities of peptides for proteins

Several methodologies were employed to calculate the Gibbs standard free energy of binding for a collection of protein-ligand complexes, where the ligand is a peptide and the protein is representative for various protein families. Almost 40 protein-ligand complexes were employed for a continuum approach, which considers the protein and the peptide at the atomic level, but includes solvent as a polarizable continuum. Five protein-ligand complexes were employed for an all-atom approach that relies on a combination of the double decoupling method with thermodynamic integration and molecular dynamics. These affinities were also computed by means of the linear interaction energy method. Although it generally proved rather difficult to predict the absolute free energies correctly, for some protein families the experimental ranking order was correctly reproduced by the continuum and all-atom approach. Considerable attention has also been given to correctly analyze the affinities of charged peptides, where it is required to judge the effect of one or more ions that are being decoupled in an all-atom approach to preserve electroneutrality. The various methods are further judged upon their merits.     

Can the pi-facial selectivity of solvation be predicted by atomistic simulation?

This work is concerned with the rationalization and prediction of solvent and temperature effects in nucleophilic addition to alpha-chiral carbonyl compounds leading to facial diastereoselectivity. We study, using molecular dynamics simulations, the facial solvation of (R)-2-phenyl-propionaldehyde in n-pentane and n-octane at a number of temperatures and compare it with experimental selectivity data for the nBuLi addition leading to syn- and anti-(2R)-2-phenyl-3-heptanol, which give nonlinear Eyring plots with the presence of inversion temperatures. We have found from simulations that the facial solvation changes with temperature and alkane. Moreover, by introducing a suitable molecular chirality index we have been able to predict break temperatures (T(CI)) for the two solvents within less than 20 degrees of the inversion temperatures experimentally observed in the diastereoselective nBuLi addition. We believe this could lead to a viable approach for predicting inversion temperatures and other subtle solvent effects in a number of stereoselective reactions.