Dispersion interactions of carbohydrates with condensate aromatic moieties: theoretical study on the CH-π interaction additive properties

In this article we present the first systematic study of the additive properties (i.e. degree of additivity) of the carbohydrate-aromatic moiety CH-π dispersion interaction. The additive properties were studied on the β-D-glucopyranose, β-D-mannopyranose and α-L-fucopyranose complexes with the naphthalene molecule by comparing the monodentate (single CH-π) and bidentate (two CH-π) complexes. All model complexes were optimized using the DFT-D approach, at the BP/def2-TZVPP level of theory. The interaction energies were refined using single point calculations at highly correlated ab initio methods at the CCSD(T)/CBS level, calculated as E + (E(CCSD(T))-E(MP2))(Small Basis). Bidentate complexes show very strong interactions in the range from -10.79 up to -7.15 and -8.20 up to -6.14 kcal mol(-1) for the DFT-D and CCSD(T)/CBS level, respectively. These values were compared with the sum of interaction energies of the appropriate monodentate carbohydrate-naphthalene complexes. The comparison reveals that the bidentate complex interaction energy is higher (interaction is weaker) than the sum of monodentate complex interaction energies. Bidentate complex interaction energy corresponds to 2/3 of the sum of the appropriate monodentate complex interaction energies (averaging over all modeled carbohydrate complexes). The observed interaction energies were also compared with the sum of interaction energies of the corresponding previously published carbohydrate-benzene complexes. Also in this case the interaction energy of the bidentate complex was higher (i.e. weaker interaction) than the sum of interaction energies of the corresponding benzene complexes. However, the obtained difference is lower than before, while the bidentate complex interaction energy corresponds to 4/5 of the sum of interaction energy of the benzene complexes, averaged over all structures. The mentioned comparison might aid protein engineering efforts where amino acid residues phenylalanine or tyrosine are to be replaced by a tryptophan and can help to predict the changes in the interactions. The observed results also show that DFT-D correctly describes the CH-π interaction energy and their additive properties in comparison to CCSD(T)/CBS calculated interaction energies. Thus, the DFT-D approach might be used for calculation of larger complexes of biological interest, where dispersion interaction plays an important role.     

Density functional theory study of 10-atom germanium clusters: effect of electron count on cluster geometry

Density functional theory (DFT) at the hybrid B3LYP level has been applied to Ge10z germanium clusters (z = -6, -4, -2, 0, +2, +4, +6) starting from 12 different initial configurations. The D4d 4,4-bicapped square antiprism found experimentally in B10H102- and other 10-vertex clusters with 22 skeletal electrons is calculated for the isoelectronic Ge102- to be the global minimum by more than 15 kcal/mol. The global minima found for electron-rich clusters Ge104- and Ge106- are not those known experimentally. However, experimentally known structures for nido-B10H14 and the pentagonal antiprism of arachno-Pd@Bi104+ are found at higher but potentially accessible energies for Ge104- and Ge106-. The global minimum for Ge10 is the C3v 3,4,4,4-tetracapped trigonal prism predicted by the Wade-Mingos rules and found experimentally in isoelectronic Ni@Ga1010-. However, only slightly above this global minimum for Ge10 (+3.3 kcal/mol) is the likewise C3v isocloso 10-vertex deltahedron found in metallaboranes such as (eta6-arene)RuB9H9 derivatives. Structures found for more electron-poor clusters Ge102+ and Ge104+ include various capped octahedra and pentagonal bipyramids. This study predicts a number of 10-vertex cluster structures that have not yet been realized experimentally but would be interesting targets for future synthetic 10-vertex cluster chemistry using vertex units isolobal with the germanium vertices used in this work.     

Potent "clicked" MMP2 inhibitors: synthesis, molecular modeling and biological exploration

A new series of MMP2 inhibitors is described, following a fragment-based drug design approach. One fragment containing an azide group and a well known hydroxamate Zinc Binding Group in a α-sulfone, α-tetrahydropyrane scaffold, has been synthesized. Water-LOGSY, STD and competition-STD experiments indicate that this fragment binds to the active site of the enzyme. A click chemistry reaction was used to connect the azide to lipophilic alkynes selected to interact selectively with the S1' subunit of MMP2, as shown by docking and molecular dynamic experiments of the designed compounds. The most potent compounds 18 and 19 displayed an IC(50) of 1.4 and 0.3 nM against MMP2 respectively, and showed negligible activity towards MMP1 and MMP7, two metalloproteinases which have a shallow S1' subsite. Compound 18 also showed a promising selectivity profile against some antitarget metalloproteinases, such as MMP8, and considerably less activity against MMP14 (IC(50) = 65 nM), and MMP9 (IC(50) = 98 nM), other MMPs characterized by having a deep S1' pocket and, therefore, more similar to MMP2.     

Radical salts of bis(ethylenediseleno)tetrathiafulvalene with paramagnetic tris(oxalato)metalate anions

The synthesis, crystal structure, and physical characterization of five new radical salts formed by the organic donor bis(ethylenediseleno)tetrathiafulvalene (BEST) and the paramagnetic tris(oxalato)metalate anions [M(C2O4)3]3- (M = FeIII and CrIII) are reported. The salts isolated are (BEST)4[M(C2O4)3].PhCOOH.H2O with MIII = Cr (1) or Fe (2) (crystal data: 1, triclinic, space group P(-)1 with a = 14.0999(4) A, b = 15.3464(4) A, c =19.5000(4) A, alpha = 76.711(5) degrees, beta = 71.688(5) degrees, gamma = 88.545(5) degrees, V = 3893.5(2) A3, and Z = 2; 2, triclinic, space group P(-)1 with a = 14.0326(3) A, b =15.1981(4) A, c =19.4106(4) A, alpha = 76.739(5) degrees, beta = 71.938(5) degrees, gamma = 88.845(5) degrees, V = 3824.9(2) A3, and Z = 2), (BEST)4[M(C2O4)3].1.5H2O with MIII = Cr (3) or Fe (4) (crystal data: 3, monoclinic, space group C2/m with a = 33.7480(10) A, b =12.3151(7) A, c = 8.8218(5) A, beta = 99.674(5) degrees, V = 3614.3(3) A3, and Z = 2; 4, monoclinic, space group C2/m with a = 33.659(6) A, b =12.248(2) A, c = 8.759(2) A, beta = 99.74(3) degrees, V = 3558.9(12) A3, and Z = 2), and (BEST)9[Fe(C2O4)3]2.7H2O (5) (crystal data: triclinic, space group P(-)1 with a =12.6993(3) A, b =18.7564(4) A, c = 18.7675(4) A, alpha = 75.649(5) degrees, beta = 107.178(5) degrees, gamma = 79.527(5) degrees, V = 3977.5(3) A3, and Z = 1). The structures of all these salts consist of alternating layers of the organic donors and tris(oxalato)metalate anions. In 1 and 2 the anionic layers contain also benzoic acid molecules H-bonded to the terminal oxygen atoms of the anions. In all salts the organic layers adopt beta-type packings. Along the parallel stacks the donors form dimers in 3 and 4, trimers in 5, and tetramers in 1 and 2. All the compounds are paramagnetic semiconductors with high room-temperature conductivities and magnetic susceptibilities dominated by the Fe- or Cr-containing anions.     

Carboxylate anions binding and sensing by a novel tetraazamacrocycle containing ferrocene as receptor

A tetraazamacrocycle containing ferrocene moieties has been synthesized and characterized. The tetraprotonated form of this compound was evaluated as a receptor (R) for anion recognition of several substrates (S), Cl(-), PF(6)(-), HSO(4)(-), H(2)PO(4)(-) and carboxylates, such as p-nitrobenzoate (p-nbz(-)), phthalate (ph(2-)), isophthalate (iph(2-)) and dipicolinate (dipic(2-)). (1)H NMR titrations in CD(3)OD indicated that this receptor is not suitable for recognizing HSO(4)(-) and H(2)PO(4)(-), but weakly binds p-nbz(-), and strongly interacts with ph(2-), dipic(2-), and iph(2-) anions forming 1 : 2 assembled species. The largest beta(2) binding constant was determined for ph(2-), followed by dipic(2-) and finally iph(2-). The effect of the anionic substrates on the electron-transfer process of the ferrocene units of R was evaluated using cyclic voltammetry (CV) and square wave voltammetry (SWV) in methanol solution and 0.1 mol dm(-3)(CH(3))(4)NCl as the supporting electrolyte. Titrations of the receptor were undertaken by addition of anion solutions in their tetrabutylammonium or tetramethylammonium forms. The protonated ligand exhibits a reversible voltammogram, which shifts cathodically in the presence of the substrates. The data revealed kinetic constraints in the formation of the receptor/substrate entity for dipic(2-), ph(2-) and iph(2-) anions, but not for p-nbz(-). In spite of the slow kinetics of assembled species formation with the ph(2-) substrate, this anion provides the largest redox-response when the supramolecular entity is formed, followed by dipic(2-), iph(2-) and finally p-nbz(-) anions. This trend is in agreement with the (1)H NMR results and the values of the binding constants. Single crystal X-ray structures of the receptor with PF(6)(-), ph(2-), iph(2-) and p-nbz(-) were carried out and showed that supermolecules with a RS(2) stoichiometry are formed with the first three anions, but RS(4) with p-nbz(-). In all cases the binding occurs outside the macrocyclic cavity via N-H...O=C hydrogen bonds for carboxylate anions and N-H...F hydrogen bonds for the PF(6)(-) anion, which is in agreement with the solution results. The macrocyclic framework adopts different conformations in order to interact with each substrate having Fe...Fe intramolecular distances ranging from 10.125(14) to 12.783(15)A.     

Reactivity of 2-deoxy-2-iodoglycosyl isothiocyanates with O-, S-, and N-nucleophiles. Synthesis of glycopyranoso-fused thiazoles

The reactivity of 2-deoxy-2-iodoglycosyl isothiocyanates toward O- and S-nucleophiles gives an easy access to 2-deoxy-2-iodoglycopyranosyl thiocarbamates and dithiocarbamates. Internal nucleophilic displacement of the iodine by the sulfur atom in these compounds allows the preparation of glycopyranoso[1,2-d]-1,3-thiazoles and glycopyranoso[1,2-d]-1,3-thiazolidin-2-one or -2-thione. Reaction with amines or polyamines as N-nucleophiles led directly to 2-aminoglycopyranoso[1,2-d]-1,3-thiazoles without isolation of the intermediate thioureas. Methyl 2-deoxy-2-iodoglycopyranosyl thiocarbamates also allow the synthesis of 2-deoxyglycopyranosyl thiocarbamates or 2-deoxy-2-iodoglycopyranosyl carbamates.     

Preliminary characterization of anhydrous ethanol used in Brazil as automotive fuel

This work reports preliminary studies on the characterisation of anhydrous ethanol (AEA) used as an automotive fuel mixed with gasoline in Porto Alegre (South Brazil). Pre-concentration of the impurities contained in 1000 ml of AEA was carried on through solid-phase extraction using XAD4 resin. The main compounds in the extract were identified by means of spectral data from the library of the equipment. The concentrate was then fractionated using a preparative liquid chromatographic column filled with activated silica gel and the elution procedure was carried out with, n-hexane, n-hexane-benzene (1:1, v/v) and dichloromethane. Prior to analysis by GC-MS, each fraction was reduced to 1 ml with a gentle stream of nitrogen. Saturated linear hydrocarbons and aromatic hydrocarbons eluted in the first fraction and oxygenated compounds such as aldehydes. ketones and alcohols, eluted in the second one. were the main compounds detected in the sample.     

The role of steric and electronic interactions in the stereocontrol of the asymmetric 1,3-dipolar reactions of 5-ethoxy-3-p-(S)-tolylsulfinylfuran-2(5H)-ones with diazoalkanes: theoretical calculations and experimental evidences

The addition of diazomethane and diazoethane to (5S,SS)- and (5R,SS)-5-ethoxy-3-p-tolylsulfinylfuran-2(5H)-ones (1a and 1b) and their 4-methylderivatives (2a and 2b) proceeded in almost quantitative yields and complete regioselectivity. The observed pi-facial selectivity is determined by the configurations at both C-5 and the sulfinyl group, the later being the most important. The syn adducts were almost exclusively obtained from 1a and 2a in apolar solvents but the pi-facial selectivity was strongly decreased in more polar solvents. On the other hand, the major adducts from 1b and 2b were the anti ones and such predominance was slightly increased with solvent polarity. The exo-selectivity was complete in all the cases except for the anti approach to compounds 2a (in polar solvents) and 2b. The role of the sulfinyl group in this behavior was inferred by comparison of these results with those obtained in reactions of diazoalkanes with 5-methoxyfuran-2(5H)-one (3). Steric interactions seem to be the main ones responsible for the observed exo selectivity of reactions with diazoethane, but electronic factors, which can be modulated by the solvent, are also significant in the pi-facial selectivity control. DFT computational methods are able to correctly predict the reactivity, regioselectivity, and pi-facial selectivity exhibited by 5-alkoxyfuranones as well as their changes with the solvent polarity. A C-H.O hydrogen bond, involving the oxygen atom of the 5-alkoxy group at dipolarophiles and the endo-hydrogen atom at dipoles, seems to play a key role in the electronic interactions influencing the stereochemical course of these reactions.     

Electrokinetics of charged spherical colloidal particles taking into account the effect of ion size constraints

The electrokinetic properties of suspended spherical particles are examined using a modified standard electrokinetic model, which takes into account the finite ion size and considers that the minimum approach distance of ions to the particle surface need not be equal to their effective radius in the bulk solution. We calculate the conductivity increment and the electrophoretic mobility and present a detailed interpretation of the obtained results, based on the analysis of the equilibrium and field-induced ion concentrations, as well as the convective fluid flow in the neighborhood of the particle surface. We show that when charge reversal takes place, the sign of the concentration polarization remains unchanged while the sign of the electrophoretic mobility only changes under favorable circumstances.     

Cooperative effects in phospholipid monolayers induced by a peptide from HIV-1 capsid protein

The study of interactions between biological molecules and model membranes is essential for the understanding of a number of physiological mechanisms involved in viral infections and dissemination. In this paper, the analysis of the interaction between a peptide from the p24 protein of Human Immunodeficiency Virus type 1 (HIV-1) and a phospholipid monolayer has pointed to a cooperative response in which very small amounts of peptide p24-1 (e.g. 0.05 mol%) can lead to measurable effects. Monolayer surface pressure and surface potential isotherms were affected for peptide concentrations as low as 0.05 mol%, with saturation at 0.5 mol%. The expansion effect from p24-1 is confirmed by changes in morphology of the monolayers using Brewster angle microscopy. Even though p24-1 is disordered in aqueous solutions, the interaction with dipalmitoyl phosphatidylcholine (DPPC) causes it to adopt an alpha-helix structure, as shown by circular dichroism (CD) data for multilamellar vesicles (MLV). The expansion of the phospholipid monolayer in a cooperative way may imply that p24-1 has potential antiviral activity, by participating in the cell rupture, with no need of specific receptors in the membrane.