Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge

In the context of the SAMPL5 blinded challenge standard free energies of binding were predicted for a dataset of 22 small guest molecules and three different host molecules octa-acids (OAH and OAMe) and a cucurbituril (CBC). Three sets of predictions were submitted, each based on different variations of classical molecular dynamics alchemical free energy calculation protocols based on the double annihilation method. The first model (model A) yields a free energy of binding based on computed free energy changes in solvated and host-guest complex phases; the second (model B) adds long range dispersion corrections to the previous result; the third (model C) uses an additional standard state correction term to account for the use of distance restraints during the molecular dynamics simulations. Model C performs the best in terms of mean unsigned error for all guests (MUE \(3.2\,<\,3.4\,<\,3.6\,\text{kcal}\,\text{mol}^{-1}\)—95 % confidence interval) for the whole data set and in particular for the octa-acid systems (MUE \(1.7\,<\,1.9\,<\,2.1\,\text{kcal}\,\text{mol}^{-1}\)). The overall correlation with experimental data for all models is encouraging (\(R^2\, 0.65\,<\,0.70<0.75\)). The correlation between experimental and computational free energy of binding ranks as one of the highest with respect to other entries in the challenge. Nonetheless the large MUE for the best performing model highlights systematic errors, and submissions from other groups fared better with respect to this metric.     

Optimal transport and a bilevel location-allocation problem

In this paper a two-stage optimization model is studied to find the optimal location of new facilities and the optimal partition of the consumers (location-allocation problem). The social planner minimizes the social costs, i.e. the fixed costs plus the waiting time costs, taking into account that the citizens are partitioned in the region according to minimizing the capacity costs plus the distribution costs in the service regions. By using optimal transport tools, existence results of solutions to the location-allocation problem are presented together with some examples.     

Effect of initial conditions on decaying grid turbulence at low R λ

The transport equations for the second-order velocity structure functions 〈(δu)²〉 and 〈(δq)²〉 are used as a scale-by-scale budget to quantify the effect of initial conditions at low Reynolds numbers, typical of grid turbulence. The validity of these equations is first investigated via hot-wire measurements of velocity and transverse vorticity fluctuations. The transport equation for 〈(δq)²〉 is shown to be balanced at all scales, while anisotropy of the large scales leads to a significant imbalance in the equation for 〈(δu)²〉. The effect of using similarity to evaluate the transport equation is rigorously tested. This approach has the desirable benefit of requiring less extensive measurements to calculate the inhomogeneous term of the transport equation. The similarity form of the 〈(δq)²〉 equation produces nearly identical results as those obtained without the similarity assumption. In the case of the 〈(δu)²〉 equation, the similarity method forces a balance at large separation, although the imbalance due to large scale anisotropy remains. The initial conditions of the turbulence at constant R _M ≃ 10,400 (28≤ R _λ≤ 55) are changed by using three grids of different geometries. Initial conditions affect the shape and magnitude of the second- and third-order structure functions, as well as the anisotropy of the large scales. The effect of initial conditions on the scale-by-scale budget is restricted to the inhomogeneous term of the transport equations, while the dissipation term remains unaffected despite the low R _λ. Scales as small as λ are affected by the changes in initial conditions.     

Time-resolved optical emission spectroscopic measurements of He plasma induced by a high-power CO2 pulsed laser

Laser-induced breakdown spectroscopy of helium plasma, initially at room temperature and pressures ranging from 12 to 101 kPa was investigated using a transverse excitation atmospheric CO₂ pulsed laser (λ = 9.621 and 10.591 μm, a full width at half maximum of 64 ns, and an intensity from 1.5 to 5.36 GW cm⁻²). The helium breakdown spectrum is mainly due to electronic relaxation of excited He, He⁺ and H. Plasma characteristics were examined in detail on the emission lines of He and He⁺ by the time-integrated and time-resolved optical emission spectroscopy technique. Optical breakdown threshold intensities, ionization degree and plasma temperatures were obtained. An auxiliary metal mesh target was used to analyze the temporal evolution of the species in the plasma. The results show a faster decay of the continuum emission and He⁺ species than in the case of neutral He atoms. The velocity and kinetic energy distributions for He and He⁺ species were obtained from time-of-flight measurements. Electron density in the laser-induced plasma was estimated from the analysis of spectral data at various times from the laser pulse incidence. Temporal evolution of electron density has been used for the estimation of the three-body electron-ion recombination rate constant.     

Self-assembly of Acridine Orange into H-aggregates at the air/water interface: tuning of orientation of headgroup

The surface active derivative of the organic dye Acridine Orange (N-10-dodecyl-acridine orange (DAO)) has been included in mixed Langmuir monolayers with stearic acid (SA). The maximum relative content on DAO for a stable mixed monolayer is a molar ratio of X(DAO) = 0.5. Brewster angle microscopy (BAM) reveals a high homogeneity at the micrometer level for the mixed monolayer in equimolar proportion (X(DAO) = 0.5), whereas the appearance of domains occurs for lower content of DAO, i.e., X(DAO) = 0.2 and 0.1. The aggregation of the DAO headgroup leads to well-defined H-aggregates at the air/water interface for those mixed monolayers with a low content of DAO. However, for the mixed monolayers enriched in DAO, e.g., X(DAO) = 0.5, the molecular crowding prevents the formation of defined supramolecular structures. Molecular organization and tilting of the DAO headgroup is quantitatively analyzed by in situ UV-visible reflection spectroscopy. The formation of H-aggregates of the DAO headgroup can be reversibly tuned with the applied surface pressure. A molecular mechanism for the conformational rearrangement of the DAO molecule is proposed using RM1 quantum semiempirical calculations.     

Organization of bacteriochlorophylls in individual chlorosomes from Chlorobaculum tepidum studied by 2-dimensional polarization fluorescence microscopy

Chlorosomes are the largest and most efficient natural light-harvesting systems and contain supramolecular assemblies of bacteriochlorophylls that are organized without proteins. Despite a recent structure determination for chlorosomes from Chlorobaculum tepidum (Ganapathy Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 8525), the issue of a possible large structural disorder is still discussed controversially. We have studied individual chlorosomes prepared under very carefully controlled growth condition by a novel 2-dimensional polarization single molecule imaging technique giving polarization information for both fluorescence excitation and emission simultaneously. Contrary to the existing literature data, the polarization degree or modulation depth (M) for both excitation (absorption) and emission (fluorescence) showed extremely narrow distributions. The fluorescence was always highly polarized with M ≈ 0.77, independent of the excitation wavelength. Moreover, the fluorescence spectra of individual chlorosomes were identical within the error limits. These results lead us to conclude that all chlorosomes possess the same type of internal organization in terms of the arrangement of the bacteriochlorophyll c transition dipole moments and their total excitonic transition dipole possess a cylindrical symmetry in agreement with the previously suggested concentric multitubular chlorophyll aggregate organization (Ganapathy Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 8525).     

Comprehensive analysis of polycyclic aromatic hydrocarbons in wastewater using stir bar sorptive extraction and gas chromatography coupled to tandem mass spectrometry

The objective of this study was the optimization and comparison of two extraction methods for the determination of polycyclic aromatic hydrocarbons (PAHs) in wastewater (WW). A distribution study of the target compounds between the aqueous phase and the suspended particulate matter (SPM) has been performed in order to establish whether the analysis of both phases is necessary. In this sense, the feasibility of stir bar sorptive extraction (SBSE) and solid-phase extraction (SPE) for the determination of 24 PAHs in WW samples has been evaluated. The results demonstrated the suitability of SBSE to perform a comprehensive analysis of liquid samples containing high amounts of SPM, such as in the determination of PAHs in WWs. A gas chromatography triple quadrupole mass spectrometry (GC-QqQ-MS/MS) method has been also optimized for the separation and detection of the target compounds, avoiding the co-elution of some groups of isomers, such as benzo[b], [j] and [k] fluoranthenes and indene[1,2,3-cd]pyrene/dibenz[a,h]anthracene. For that purpose, a specific capillary column developed for PAH determination was used. The SBSE procedure was validated and adequate parameters (such as recovery, linearity, precision, limits of detection and quantification) were obtained. Finally, the validated method was applied to the analysis of real samples collected from an experimental WW treatment plant, detecting some PAHs at concentrations in the range 0.007-0.022 μg L(-1).     

Multi-component, regio-selective aldol addition of β-ketoesters to aldehydes: scope and applications

Simple and effective multi-component one-pot aldol addition/protection reactions of β-ketoesters to a series of aldehydes in the presence Me(3)SiCl and i-Pr(2)EtN have been described. The analysis of the scope of the reaction revealed a dramatic dependence of the reactivity on the substrates used. Thus the effect of a catalytic amount of DMF and different reaction conditions was widely investigated. Further transformations of the aldol adducts were particularly useful to give valuable diols and compounds with quaternary stereocenters, while X-ray structural analysis gave also important stereochemical information about this challenging reaction.     

Aldimines generated from aza-Wittig reaction between bis(iminophosphoranes) derived from 1,1'-diazidoferrocene and aromatic or heteroaromatic aldehydes: electrochemical and optical behaviour towards metal cations

Aldimine 4 bearing a 2-quinolyl group was prepared by aza-Wittig reaction between the triphenyliminophosphorane derived from the 1,1'-diazidoferrocene and 2-formylquinoline. However, aldimine 5, bearing a pyrene ring, was prepared using the most reactive tributyliminophosphorane derivative and the corresponding 1-formylpyrene. On the other hand, formation of aldimine 8 involves a tandem process, Staudinger reaction/intramolecular aza-Wittig reaction, by using directly 1,1'-diazidoferrocene and 2-(diphenylphosphonyl)benzaldehyde. Aldimine 4 behaves as chemosensor molecule for Ni(2+), Zn(2+), Cd(2+), Hg(2+) and Pb(2+) cations through two different channels: electrochemical (ΔE(1/2) = 222-361 mV) and chromogenic (Δλ = 122-153 nm), which can be used for the "naked eye" detection of these metal cations. Aldimine 5 behaves as a highly selective redox (in CH(3)CN) and fluorescent (in CH(3)Cl-DMF) probe for Hg(2+) metal cations even in the presence of a large excess of the other metal cations tested. Aldimine 8 displays electrochemical affinity (ΔE(1/2) = 60-288 mV) to Li(+), Ca(2+), Mg(2+), Zn(2+) and Pb(2+) metal cations, with the phosphorus oxide functionality as a binding site. From the (1)H NMR titration data as well as DFT calculations, different tentative binding modes have been established, for these structurally related ferrocenyl derivatives.