A new equation for the correlation of surface tension–composition data of solvent–solvent and solvent–fused salt mixtures

An attempt has been made to propose accurate equations for correlating the surface tension of binary liquid mixtures. The method is applicable to the systems comprising of components with widely different molecular sizes. Two adjustable parameters, δ_p and δ_m obtained from the least squares analyses of the surface tension–composition data are reported for a number of systems. Temperature dependence of δ_p and δ_m is demonstrated for a few systems. The framework of operational equations has later been applied to cover multi-component systems comprising of fused salts with a single liquid component in full mole fraction range. Excellent fits of the surface tension for binary, ternary and multi-component ionic systems in aqueous or non-aqueous media have been obtained from the proposed method. The surface tension–composition data of 59 different types of systems with about 400 data points can be correlated by the equation with an average percent deviation of about 0.61. In contrast to previous equations from literature to calculate surface tension data, the proposed correlation is noted to be more accurate in different situations.     

A novel and consistent method (TriPOD) to characterize an arbitrary porous solid for its accessible volume,accessible geometrical surface area and accessible pore size

We present an improved Monte Carlo integration method to calculate the accessible pore size distribution of a porous solid having known configuration of solid atoms. The pore size distribution obtained with the present method is consistent with the accessible volume and the accessible geometric surface area presented in previous publications (Do and Do, in J. Colloid Interface Sci. 316(2):317–330, 2007; Do et al. in Adsorpt. J., 2010). The accessible volume, accessible geometrical surface area and the pore size distribution method construct an unambiguous and robust single framework to characterize porous solids. This framework is based on the derivation of the space accessible to the center of mass of a probe molecule. The accessible pore size presented is an absolute quantity in the sense that a zero value is possible. We present the entire framework of this characterization method and compare the improved method with the one presented previously for a set of porous solids such as graphitic slit pores, defective slit pores, bundle of carbon nanotubes, zeolite and some metal organic frameworks.     

A targeted mass spectrometry-based approach for the identification and characterization of proteins containing α-aminoadipic and γ-glutamic semialdehyde residues

The site-specific identification of α-aminoadipic semialdehyde (AAS) and γ-glutamic semialdehyde (GGS) residues in proteins is reported. Semialdehydic protein modifications result from the metal-catalyzed oxidation of Lys or Arg and Pro residues, respectively. Most of the analytical methods for the analysis of protein carbonylation measure change to the global level of carbonylation and fail to provide details regarding protein identity, site, and chemical nature of the carbonylation. In this work, we used a targeted approach, which combines chemical labeling, enrichment, and tandem mass spectrometric analysis, for the site-specific identification of AAS and GGS sites in proteins. The approach is applied to in vitro oxidized glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and an untreated biological sample, namely cardiac mitochondrial proteins. The analysis of GAPDH resulted in the site-specific identification of two AAA and four GGS residues. Computational evaluation of the identified AAS and GGS sites in GAPDH indicated that these sites are located in flexible regions, show high solvent accessibility values, and are in proximity with possible metal ion binding sites. The targeted proteomic analysis of semialdehydic modifications in cardiac mitochondria yielded nine AAS modification sites which were unambiguously assigned to distinct lysine residues in the following proteins: ATP/ATP translocase isoforms 1 and 2, ubiquinol cytochrome-c reductase core protein 2, and ATP synthase α-subunit.     

Efficient method for the asymmetric reduction of α- and β-ketophosphonates

An efficient and versatile method for the asymmetric reduction of α- and β-ketophosphonates using chiral reactant derived from sodium borohydride and l-(+)- or d-(−)-tartaric acid is developed. The methodology was used for the preparation of a number of biologically interesting enantiomerically pure products: including 2,3-epoxypropylphosphonate 11, 2-hydroxy-3-aminopropylphosphonic acid 14 (phospho-GABOB), phospho-carnitine 19, and others in multigram scale.     

A facile method for the synthesis of enantiopure α-unsubstituted β-hydroxy esters

One-pot deacylation–debromination reactions involving the transesterification of the initial chiral α-bromo-β-hydroxy thioimide aldol adducts and subsequent Al–Hg mediated reductive cleavage of the C–Br bond allow for a facile synthesis of enantiopure β-hydroxy esters.     

Spectroscopic and computational studies of α-keto acid binding to Dke1: understanding the role of the facial triad and the reactivity of β-diketones

The O(2) activating mononuclear nonheme iron enzymes generally have a common facial triad (two histidine and one carboxylate (Asp or Glu) residue) ligating Fe(II) at the active site. Exceptions to this motif have recently been identified in nonheme enzymes, including a 3His triad in the diketone cleaving dioxygenase Dke1. This enzyme is used to explore the role of the facial triad in directing reactivity. A combination of spectroscopic studies (UV-vis absorption, MCD, and resonance Raman) and DFT calculations is used to define the nature of the binding of the α-keto acid, 4-hydroxyphenlpyruvate (HPP), to the active site in Dke1 and the origin of the atypical cleavage (C2-C3 instead of C1-C2) pattern exhibited by this enzyme in the reaction of α-keto acids with dioxygen. The reduced charge of the 3His triad induces α-keto acid binding as the enolate dianion, rather than the keto monoanion, found for α-keto acid binding to the 2His/1 carboxylate facial triad enzymes. The mechanistic insight from the reactivity of Dke1 with the α-keto acid substrate is then extended to understand the reaction mechanism of this enzyme with its native substrate, acac. This study defines a key role for the 2His/1 carboxylate facial triad in α-keto acid-dependent mononuclear nonheme iron enzymes in stabilizing the bound α-keto acid as a monoanion for its decarboxylation to provide the two additional electrons required for O(2) activation.     

A simplified method for the HPLC resolution of α-carotene and β-carotene (trans and cis) isomers

A new HPLC/DAD (Diode Array Detector) method is proposed for the identification of some carotene isomers. The operating conditions adopted permit the resolution of alpha-carotene, all-trans-beta-carotene, 9-cis-beta-carotene, 13-cis-beta-carotene and 15-cis-beta-carotene. Moreover, the chromatographic conditions reported are simplified in respect of those reported up to now. The method is applied to the determination of carotenoids in a dried Dunaliella salina extract, but it could be also applied to other organic matrices such as eggs.     

Effects of substituent and solvent on the Sonogashira coupling reaction of β-bromoporphyrin

A series of experiments were designed to understand the effects of substituent and solvent on the Sonogashira coupling reaction of β-bromoporphyrin using a Pd₂(dba)₃/AsPh₃ system as the catalyst. Electron-efficient groups and aprotic solvents are conducive to the reaction. A possible explanation was given. A new family of β-pyrrole substituted porphyrins was also synthesized during the study.     

Computational prediction of structure-activity relationships for the binding of aminocyclitols to β-glucocerebrosidase

Glucocerebrosidase (GCase, acid β-Glucosidase) hydrolyzes the sphingolipid glucosylceramide into glucose and ceramide. Mutations in this enzyme lead to a lipid metabolism disorder known as Gaucher disease. The design of competitive inhibitors of GCase is a promising field of research for the design of pharmacological chaperones as new therapeutic agents. Using a series of recently reported molecules with experimental binding affinities for GCase in the nanomolar to micromolar range, we here report an extensive theoretical analysis of their binding mode. On the basis of molecular docking, molecular dynamics, and binding free energy calculations using the linear interaction energy method (LIE), we provide details on the molecular interactions supporting ligand binding in the different families of compounds. The applicability of other computational approaches, such as the COMBINE methodology, is also investigated. The results show the robustness of the standard parametrization of the LIE method, which reproduces the experimental affinities with a mean unsigned error of 0.7 kcal/mol. Several structure-activity relationships are established using the computational models here provided, including the identification of hot spot residues in the binding site. The models derived are envisaged as important tools in ligand-design programs for GCase inhibitors.     

A Protocol for Accessing the β-Azidation of α,β-Unsaturated Carboxylic Acids

This contribution reports the preparation and use of a new immobilized catalyst, PS-DABCOF (9), which has been specifically designed to access for the first time the efficient β-azidation of α,β-unsaturated carboxylic acids.     

The balance between side-chain and backbone-driven association in folding of the α-helical influenza A transmembrane peptide

The correct balance between attractive, repulsive and peptide hydrogen bonding interactions must be attained for proteins to fold correctly. To investigate these important contributors, we sought a comparison of the folding between two 25-residues peptides, the influenza A M2 protein transmembrane domain (M2TM) and the 25-Ala (Ala₂₅). M2TM forms a stable α-helix as is shown by circular dichroism (CD) experiments. Molecular dynamics (MD) simulations with adaptive tempering show that M2TM monomer is more dynamic in nature and quickly interconverts between an ensemble of various α-helical structures, and less frequently turns and coils, compared to one α-helix for Ala₂₅. DFT calculations suggest that folding from the extended structure to the α-helical structure is favored for M2TM compared with Ala₂₅. This is due to CH⋯O attractive interactions which favor folding to the M2TM α-helix, and cannot be described accurately with a force field. Using natural bond orbital (NBO) analysis and quantum theory atoms in molecules (QTAIM) calculations, 26 CH⋯O interactions and 22 NH⋯O hydrogen bonds are calculated for M2TM. The calculations show that CH⋯O hydrogen bonds, although individually weaker, have a cumulative effect that cannot be ignored and may contribute as much as half of the total hydrogen bonding energy, when compared to NH⋯O, to the stabilization of the α-helix in M2TM. Further, a strengthening of NH⋯O hydrogen bonding interactions is calculated for M2TM compared to Ala₂₅. Additionally, these weak CH⋯O interactions can dissociate and associate easily leading to the ensemble of folded structures for M2TM observed in folding MD simulations.     

Revisiting the Corey-Chaykovsky reaction: the solvent effect and the formation of β-hydroxy methylthioethers

The classical Corey-Chaykovsky (CC) reaction of ketones in ethereal solvents (i.e., THF or Et₂O) resulted in the production of a significant amount of β-hydroxy methylthioether 2 along with normal epoxide product 1. Some interesting and synthetically useful transformations of the CC reaction product of cyclopropyl ketones were also described.     

Effects of solvent, pH and β-cyclodextrin on the fluorescent behaviour of lomustine

Fluorescent behaviour of lomustine, a DNA cross-linking agent, was investigated in different solvents, pH and in the presence of β-cyclodextrin (β-CD). The solvents in which fluorescence spectra were observed play a major role in determining the spectral intensity of fluorophore, since it was found to exhibit new fluorescent properties essentially influenced by intermolecular interactions, particularly by intermolecular H-bonding formed with solvents. The pH-dependence profile was typically U-shape with a maximum at pH between 3.51 and 6.58. It was corroborated that the fluorescence emission band of lomustine is significantly intensified in the presence of β-CD. From the changes in the fluorescence spectra, it was concluded that β-CD forms a 1:1 inclusion complex with lomustine and its association constant was calculated.     

What are the practical limits for the specific surface area and capacitance of bulk sp~2 carbon materials?

The possible practical limits for the specific surface area and capacitance performance of bulk sp~2 carbon materials were investigated experimentally and theoretically using a variety of carbon materials. We find the limit for the specific surface area to be 3500–3700 m~2 g~(-1), and based on this, the corresponding best capacitance was predicted for various electrolyte systems. A model using an effective ionic diameter for the electrolyte ions was proposed and used to calculate the theoretical capacitance. A linear dependence of experimental capacitance versus effective specific surface area of various sp~2 carbon materials was obtained for all studied ionic liquid, organic and aqueous electrolyte systems. Furthermore, excellent agreement between the theoretical and experimental capacitance was observed for all the tested sp~2 carbon materials in these electrolyte systems, indicating that this model can be applied widely in the evaluation of various carbon materials for supercapacitors.     

A,D-Oligomethylenic capping of α- and β-cyclodextrins

α- and β-cyclodextrins have easily been converted into basket molecules, the handle being an oligomethylenic chain bridging A and D positions on the primary rim. The size of the handle influences the complexing properties of these cyclodextrins. To cite this article: T. Lecourt et al., C. R. Chimie 6 (2003) 000–000.     

Thermodynamic scaling of α-relaxation time and viscosity stems from the Johari-Goldstein β-relaxation or the primitive relaxation of the coupling model

By now it is well established that the structural α-relaxation time, τ(α), of non-associated small molecular and polymeric glass-formers obey thermodynamic scaling. In other words, τ(α) is a function Φ of the product variable, ρ(γ)/T, where ρ is the density and T the temperature. The constant γ as well as the function, τ(α) = Φ(ρ(γ)/T), is material dependent. Actually this dependence of τ(α) on ρ(γ)/T originates from the dependence on the same product variable of the Johari-Goldstein β-relaxation time, τ(β), or the primitive relaxation time, τ(0), of the coupling model. To support this assertion, we give evidences from various sources itemized as follows. (1) The invariance of the relation between τ(α) and τ(β) or τ(0) to widely different combinations of pressure and temperature. (2) Experimental dielectric and viscosity data of glass-forming van der Waals liquids and polymer. (3) Molecular dynamics simulations of binary Lennard-Jones (LJ) models, the Lewis-Wahnstr?m model of ortho-terphenyl, 1,4 polybutadiene, a room temperature ionic liquid, 1-ethyl-3-methylimidazolium nitrate, and a molten salt 2Ca(NO(3))(2)·3KNO(3) (CKN). (4) Both diffusivity and structural relaxation time, as well as the breakdown of Stokes-Einstein relation in CKN obey thermodynamic scaling by ρ(γ)/T with the same γ. (5) In polymers, the chain normal mode relaxation time, τ(N), is another function of ρ(γ)/T with the same γ as segmental relaxation time τ(α). (6) While the data of τ(α) from simulations for the full LJ binary mixture obey very well the thermodynamic scaling, it is strongly violated when the LJ interaction potential is truncated beyond typical inter-particle distance, although in both cases the repulsive pair potentials coincide for some distances.