SAMPL6: calculation of macroscopic p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> values from ab initio quantum mechanical free energies

Macroscopic pK_a values were calculated for all compounds in the SAMPL6 blind prediction challenge, based on quantum chemical calculations with a continuum solvation model and a linear correction derived from a small training set. Microscopic pK_a values were derived from the gas-phase free energy difference between protonated and deprotonated forms together with the Conductor-like Polarizable Continuum Solvation Model and the experimental solvation free energy of the proton. pH-dependent microstate free energies were obtained from the microscopic pK_as with a maximum likelihood estimator and appropriately summed to yield macroscopic pK_a values or microstate populations as function of pH. We assessed the accuracy of three approaches to calculate the microscopic pK_as: direct use of the quantum mechanical free energy differences and correction of the direct values for short-comings in the QM solvation model with two different linear models that we independently derived from a small training set of 38 compounds with known pK_a. The predictions that were corrected with the linear models had much better accuracy [root-mean-square error (RMSE) 2.04 and 1.95 pK_a units] than the direct calculation (RMSE 3.74). Statistical measures indicate that some systematic errors remain, likely due to differences in the SAMPL6 data set and the small training set with respect to their interactions with water. Overall, the current approach provides a viable physics-based route to estimate macroscopic pK_a values for novel compounds with reasonable accuracy.     

Synthesis and structural characterization of amino-functionalized polysaccharides

A variety of carbohydrates, in particular polysaccharides can be subjected to chemical modification to obtain derivatives with amphiphilic properties, which enable biochemical or biological reactions at the polymer surface. In the present work, a polydisperse maltodextrin mixture of average molecular weight 3000 was coupled with 1,6-hexamethylenediamine (HMD) via reductive amination reaction. Resulting products were characterized by thermal analysis and positive nanoelectrospray quadrupole time-of-flight (Q-TOF) mass spectrometry (MS) and tandem mass spectrometry (MS/MS). Both thermal analysis and MS screening confirmed the formation of the HMD-polysaccharide coupling products. Moreover, HMD-linked polysaccharide chains containing 2 to 26 glucose building blocks were identified by nanoESI Q-TOF MS. MS/MS fragmentation using collision-induced dissociation (CID) at low ion acceleration energies provided strong evidence for HMD-maltodextrin linkage formation and the set of sequence ions diagnostic for the composition and structure of a HMD-linked chain containing 18 glucose residues.      

Feynman-Kac Formula for Left Continuous Additive Functionals and Extended Kato Class Measures

The perturbation of the generator of a Borel right process by a signed measure is investigated, using probabilistic and analytic potential theoretical methods. We establish a Feynman-Kac formula associated with measures charging no polar set and belonging to an extended Kato class. A main tool of this approach is the validity of a Khas’minskii Lemma for Stieltjes exponentials of positive left continuous additive functionals.      

A new bridge in [2.2]cyclophanes: The addition of Se2Cl2 to pseudogeminally substituted bispropargylic alcohols

The regio‐ and stereo‐specific addition of monoselenium monochloride to pseudogeminally substituted bispropargylic alcohols has been performed under high dilution conditions. The disproportionation reaction of selenium monochloride to selenium dichloride and triselenium dichloride leads to the corresponding divinylic mono‐ and tri‐selenides. The stereochemistry of the newly generated double bond was assigned as Z by 2D NMR experiments. © 2010 Wiley Periodicals, Inc. Heteroatom Chem 21:126–130, 2010; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20586     

Studies regarding the formation from metal nitrates and diol of NiM 2 III O4 spinels, inside a silica matrix

The present study deals with preparation and characterization of spinel mixed oxide systems NiM ₂ ^III O₄, where M^III?=?Fe^III, Cr^III. In order to obtain 50% NiFe₂O₄/50% SiO₂ and 50% NiCr₂O₄/50% SiO₂ nanocomposite, we have used a versatile route based on the thermal decomposition inside the SiO₂ matrix, of some particular precursors, coordination compounds of the involved M^II and M^III cations with dicarboxylate ligands. The ligands form in the redox reaction between metal nitrates mixture and 1,3-propanediol at the heating around 140?°C of the gels (tetraethylorthosilicate?Cmetal nitrates?C1,3-propanediol?Cwater). The as-obtained precursors, embedded in silica gels, have been characterized by FT-IR spectrometry and thermal analysis. Both precursors thermally decompose up to 350?°C leading to the formation of the corresponding metal oxides inside the silica matrix. X-ray diffraction of the annealed powders have evidenced the formation of NiFe₂O₄ starting with 600?°C, and NiCr₂O₄ starting with 400?°C. This behavior can be explained by the fact that, by thermal decomposition of the Fe(III) carboxylate at 300?°C, the spinelic phase ??-Fe₂O₃ is formed, which interacts with the NiO, forming the ferrite nuclei. By thermal decomposition of chromium carboxylate, a nonstoichiometric chromium oxide (Cr₂O_3+x ) is formed. In the range 380?C400?°C, Cr₂O_3+x turns into Cr₂O₃ which immediately interacts with NiO leading to the formation of nickel chromites nuclei inside the pores of silica matrix. Both spinels have been obtained as nanocrystalites homogenously dispersed as resulted from XRD and TEM data.     

Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the OPLS-AA force field

All-atom molecular dynamics computer simulations were used to blindly predict the hydration free energies of a range of chloro-organic compounds as part of the SAMPL3 challenge. All compounds were parameterized within the framework of the OPLS-AA force field, using an established protocol to compute the absolute hydration free energy via a windowed free energy perturbation approach and thermodynamic integration. Three different approaches to deriving partial charge parameters were pursued: (1) using existing OPLS-AA atom types and charges with minor adjustments of partial charges on equivalent connecting atoms; (2) calculation of quantum mechanical charges via geometry optimization, followed by electrostatic potential (ESP) fitting, using Jaguar at the LMP2/cc-pVTZ(-F) level; and (3) via geometry optimization and CHelpG charges (Gaussian03 at the HF/6-31G* level), followed by two-stage RESP fitting. Protocol 3 generated the most accurate predictions with a root mean square (RMS) error of 1.2 kcal mol(-1) for the entire data set. It was found that the deficiency of the standard OPLS-AA parameters, protocol 1 (RMS error 2.4 kcal mol(-1) overall), was mostly due to compounds with more than three chlorine substituents on an aromatic ring. For this latter subset, the RMS errors were 1.4 kcal mol(-1) (protocol 3) and 4.3 kcal mol(-1) (protocol 1), respectively. We propose new OPLS-AA atom types for aromatic carbon and chlorine atoms in rings with ≥4 Cl-substituents that perform better than the best QM-based approach, resulting in an RMS error of 1.2 kcal mol(-1) for these difficult compounds.     

Capillary flooding of wood with microemulsions from Winsor I systems

A new approach based on microemulsions formulated with at least 85% water and minority components consisting of oil (limonene) and surfactant (anionic and nonionic) is demonstrated for the first time to be effective for flooding wood's complex capillary structure. The formulation of the microemulsion was based on phase behavior scans of Surfactant-Oil-Water systems (SOWs) and the construction of pseudo-ternary diagrams to localize thermodynamically stable one-phase emulsion systems with different composition, salinity and water-to-oil ratios. Wicking and fluid penetration isotherms followed different kinetic regimes and indicated enhanced performance relative to that of the base fluids (water, oil or surfactant solutions). The key properties of microemulsions to effectively penetrate the solid structure are discussed; microemulsion formulation and resultant viscosity are found to have a determining effect in the extent of fluid uptake. The solubilization of cell wall components is observed after microemulsion impregnation. Thus, the microemulsion can be tuned not only to effectively penetrate the void spaces but also to solubilize hydrophobic and hydrophilic components. The concept proposed in this research is expected to open opportunities in fluid sorption in fiber systems for biomass pretreatment, and delivery of hydrophilic or lipophilic moieties in porous, lignocellulosics.     

Biomolecules from Plant Wastes Potentially Relevant in the Management of Irritable Bowel Syndrome and Co-Occurring Symptomatology

During and following the processing of a plant’s raw material, considerable amounts are wasted, composted, or redistributed in non-alimentary sectors for further use (for example, some forms of plant waste contribute to biofuel, bioethanol, or biomass production). However, many of these forms of waste still consist of critical bioactive compounds used in the food industry or medicine. Irritable bowel syndrome (IBS) is one of the most common functional gastrointestinal disorders. The primary treatment is based on symptomatology alleviation and controlled dietary management. Thus, this review aimed to describe the possible relevance of molecules residing in plant waste that can be used to manage IBS and co-occurring symptoms. Significant evidence was found that many forms of fruit, vegetable, and medicinal plant waste could be the source of some molecules that could be used to treat or prevent stool consistency and frequency impairments and abdominal pain, these being the main IBS symptoms. While many of these molecules could be recovered from plant waste during or following primary processing, the studies suggested that enriched food could offer efficient valorization and prevent further changes in properties or stability. In this way, root, stem, straw, leaf, fruit, and vegetable pomaces were found to consist of biomolecules that could modulate intestinal permeability, pain perception, and overall gastrointestinal digestive processes.