Raman Optical Activity (ROA) as a New Tool to Elucidate the Helical Structure of Poly(phenylacetylene)s

Poly(phenylacetylene)s are a family of helical polymers constituted by conjugated double bonds. Raman spectra of these polymers show a structural fingerprint of the polyene backbone which, in combination with its helical orientation, makes them good candidates to be studied by Raman optical activity (ROA). Four different well‐known poly(phenylacetylene)s adopting different scaffolds and ten different helical senses have been prepared. Raman and ROA spectra were recorded and allowed to establish ROA‐spectrum/helical‐sense relationships: a left/right‐handed orientation of the polyene backbone (M_helix/P_helix) produces a triplet of positive/negative ROA bands. Raman and ROA spectra of each polymer exhibited the same profile, and the sign of the ROA spectrum was opposite to the lowest‐energy electronic circular dichroism (ECD) band, indicating a resonance effect. Resonance ROA appears then as an indicator of the helical sense of poly(phenylacetylene)s, especially for those with an extra Cotton band in the ECD spectrum, where a wrong helical sense is assigned based on ECD, while ROA alerts of this misassignment.     

Large scale free energy calculations for blind predictions of protein–ligand binding: the D3R Grand Challenge 2015

We describe binding free energy calculations in the D3R Grand Challenge 2015 for blind prediction of the binding affinities of 180 ligands to Hsp90. The present D3R challenge was built around experimental datasets involving Heat shock protein (Hsp) 90, an ATP-dependent molecular chaperone which is an important anticancer drug target. The Hsp90 ATP binding site is known to be a challenging target for accurate calculations of ligand binding affinities because of the ligand-dependent conformational changes in the binding site, the presence of ordered waters and the broad chemical diversity of ligands that can bind at this site. Our primary focus here is to distinguish binders from nonbinders. Large scale absolute binding free energy calculations that cover over 3000 protein–ligand complexes were performed using the BEDAM method starting from docked structures generated by Glide docking. Although the ligand dataset in this study resembles an intermediate to late stage lead optimization project while the BEDAM method is mainly developed for early stage virtual screening of hit molecules, the BEDAM binding free energy scoring has resulted in a moderate enrichment of ligand screening against this challenging drug target. Results show that, using a statistical mechanics based free energy method like BEDAM starting from docked poses offers better enrichment than classical docking scoring functions and rescoring methods like Prime MM-GBSA for the Hsp90 data set in this blind challenge. Importantly, among the three methods tested here, only the mean value of the BEDAM binding free energy scores is able to separate the large group of binders from the small group of nonbinders with a gap of 2.4 kcal/mol. None of the three methods that we have tested provided accurate ranking of the affinities of the 147 active compounds. We discuss the possible sources of errors in the binding free energy calculations. The study suggests that BEDAM can be used strategically to discriminate binders from nonbinders in virtual screening and to more accurately predict the ligand binding modes prior to the more computationally expensive FEP calculations of binding affinity.     

Electric double layer for spherical particles in salt-free concentrated suspensions including ion size effects

The equilibrium electric double layer (EDL) that surrounds colloidal particles is essential for the response of a suspension under a variety of static or alternating external fields. An ideal salt-free suspension is composed of charged colloidal particles and ionic countercharges released by the charging mechanism. Existing macroscopic theoretical models can be improved by incorporating different ionic effects usually neglected in previous mean-field approaches, which are based on the Poisson-Boltzmann equation (PB). The influence of the finite size of the ions seems to be quite promising because it has been shown to predict phenomena like charge reversal, which has been out of the scope of classical PB approximations. In this work we numerically obtain the surface electric potential and the counterion concentration profiles around a charged particle in a concentrated salt-free suspension corrected by the finite size of the counterions. The results show the high importance of such corrections for moderate to high particle charges at every particle volume fraction, especially when a region of closest approach of the counterions to the particle surface is considered. We conclude that finite ion size considerations are obeyed for the development of new theoretical models to study non-equilibrium properties in concentrated colloidal suspensions, particularly salt-free ones with small and highly charged particles.     

Covalent-ionic nature of the potential energy surface of the Li-CO2 complex

Unrestricted Hartree-Fock calculations with large basis sets, including d-functions, and the estimation of the correlation energy, show that the potential energy surface for the Li-CO₂ complex is built from the crossing of two states, each of them corresponding to a different electron arrangement. One has a strong ionic character and the other is of van der Waals type. Each portion of the energy surface presents a minimum, which is stable in respect to the dissociation limit.     

Effect of pH on the Encapsulation of the Salicylic Acid / Salicylate System by Hydroxypropyl-β-Cyclodextrin at 25 °c. A Fluorescence Enhancement Study in Aqueous Solutions

The encapsulation of the acid/base conjugated system salicylic acid(HSA)/salicylate (SA^-) by hydroxypropyl--cyclodextrin (HPBCD) has beenstudied through fluorescence emission enhancement measurements in aqueoussolutions at 25 °C. With the aim of analyzing the crucial importance ofa proper and cautious choice of the pH of the medium (i.e. choice of thebuffer), the study has been carried out at pH = 1, 2, 4 and 7. Since the pK_a of the HSA/SA^- system is 2.95 at 25 °C, the presence of the protonated(HSA) and non-protonated (SA^-) forms suitable for inclusion by cyclodextrinvary appreciably within the different pH conditions: 99% HSA,1% SA^- at pH = 1, 90% HSA, 10% SA^- at pH = 2,10% HSA, 90% SA^- at pH = 4, and 0% HSA,100% SA- at pH =7. The association constants K CD : HSA and K _{CD: SA-} have been determined in all cases by using a nonlinear regressionanalysis of the experimental data at three different ^em. The effectof the pH of the medium on all the equilibria involved as well as in the Kvalues is fully discussed. The 8-anilino-1-naphthalene sulfonate (ANS) +-cyclodextrin (-CD) system, widely reported in literature, hasinitially been studied to check the experimental protocol and the numericalmethod.     

Nonstoichiometric spinel ferrites obtained from alpha-NaFeO2 via molten media reactions

Different solid/liquid "exchange" reactions involving divalent cations, protons, or ammonium ions have been performed at low/moderate temperatures (between 80 and 500 degrees C) on alpha-NaFeO2 dipped in molten salts (or acid) media. Several ferrites have been obtained which are nonstoichiometric with partially inverse spinel structures. When sodium is replaced by divalent cations (Mg2+, Co2+, Ni2+, and Zn2+), the obtained ferrites are hyperstoichiometric (cation/oxygen ratio higher than 3/4) whereas proton or ammonium reactions result in hypostoichiometric materials (cation/oxygen lower than 3/4). All these ferrites present a platelet-like morphology and show ferrimagnetic, soft magnet behavior.     

Stereochemical memory in the temperature-dependent photodenitrogenation of bridgehead-substituted DBH-type azoalkanes: inhibition of inverted-housane formation in the diazenyl diradical through the mass effect (inertia) and steric hindrance

The photochemical denitrogenation of the cyclopentene-annelated DBH-type azoalkanes 1 has been examined in solution as a function of bridgehead substitution and temperature. For all derivatives, namely, the unsubstituted 1a(H/H), monomethyl 1b(Me/H) dimethyl 1c(Me/Me), monophenyl 1d(Ph/H), and diphenyl 1e(Ph/Ph), the temperature-dependent ratio of syn and anti housanes 2 provides experimental support for a competition between the singlet (high temperature) and triplet (low temperature) reaction channels in the direct photolysis. The syn/anti ratio of the housanes 2 depends on the extent and type of bridgehead substitution; the amount of the anti diastereomer (retention) follows the order Ph > Me > H, and double substitution is more effective than single. This stereochemical memory is interpreted in terms of the mass effect (inertia) of the substituents and steric interaction (size) between the substituents at the bridgehead and the methylene bridge during the deazetation step of the transient diazenyl diradical conformations (1)DZ (exo-ax) and (1)DZ (exo-eq). These conformers are impulsively generated upon decay of the (1)(n,pi)-excited azoalkane, a trajectory assessed through computational work. The new mechanistic feature disclosed by the unprecedented anti stereoselectivity (retention) is the intervention of a puckered 1,3-cyclopentanediyl singlet diradical (1)DR as product bifurcation step, whose conformational relaxation to the planar species (loss of stereochemical memory) is encumbered by bridgehead substitution.