Crystalline inclusion compounds of new hydroxy hosts featuring a pentaaryl substituted cyclopentadienol framework

The new host compounds 2 and 3 containing a biphenyl or terphenyl moiety attached to the 1-position of a bulky 2,3,4,5-tetraphenylcyclopentadiene-1-ol building unit have been synthesized. Crystal structures of corresponding inclusion complexes with n-hexane (2a), DMSO (2b) and THF (3a) are reported and comparatively discussed involving known inclusion structures of 1, being the parent of this particular class of host molecules. The structural modification from 1 via 2?C3 gives rise to distinct changes of the inclusion property concerning molecular assembly and stoichiometric ratio of the crystal components.     

3D-QSAR and molecular modeling of HIV-1 integrase inhibitors

Three-dimensional quantitative structure-activity relationship (3D QSAR) methods were applied on a series of inhibitors of HIV-1 integrase with respect to their inhibition of 3-processing and 3-end joining steps in vitro.The training set consisted of 27 compounds belonging to the class of thiazolothiazepines. The predictive ability of each model was evaluated using test set I consisting of four thiazolothiazepines and test set II comprised of seven compounds belonging to an entirely different structural class of coumarins. Maximum Common Substructure (MCS) based method was used to align the molecules and this was compared with other known methods of alignment. Two methods of 3D QSAR: comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were analyzed in terms of their predictive abilities. CoMSIA produced significantly better results for all correlations. The results indicate a strong correlation between the inhibitory activity of these compounds and the steric and electrostatic fields around them. CoMSIA models with considerable internal as well as external predictive ability were obtained. A poor correlation obtained with hydrophobic field indicates that the binding of thiazolothiazepines to HIV-1 integrase is mainly enthalpic in nature. Further the most active compound of the series was docked into the active site using the crystal structure of integrase. The binding site was formed by the amino acid residues 64-67, 116, 148, 151-152, 155-156, and 159. The comparison of coefficient contour maps with the steric and electrostatic properties of the receptor shows high level of compatibility.     

Hybrid molecular nanostructures with donor-acceptor chains

We have fabricated hybrid molecular chain structures formed by electron acceptor compound 1 and electron donor molecules 2 and 3 at the liquid/solid interface of graphite surface.The structural details of the mono-component and the binary assemblies are revealed by high resolution scanning tunneling microscopy (STM).Compound 1 can form two well-ordered lamellar patterns at different concentrations.In the co-adsorption structures,compounds 2 and 3 can insert into the space between molecular chains of compound 1 and form large area well-ordered nanoscale phase separated lamellar structures.The unit cell parameters for the coassemblies can be "flexibly" adjusted to make the electron donors and acceptors perfectly match along the molecular chains.Scanning tunneling spectroscopy (STS) results indicate that the electronic properties of individual molecular donors and acceptors are preserved in the binary self-assembly.These results provide molecular insight into the nanoscale phase separation of organic electron acceptors and donors on surfaces and are helpful for the fabrication of surface supramolecular structures and molecular devices.     

Probing the physicochemical interactions of 3-hydroxy-benzo[a]pyrene with different monoclonal and recombinant antibodies by use of fluorescence line-narrowing spectroscopy

Characterization of interactions between antigens and antibodies is of utmost importance both for fundamental understanding of the binding and for development of advanced clinical diagnostics. Here, fluorescence line-narrowing (FLN) spectroscopy was used to study physicochemical interactions between 3-hydroxybenzo[a]pyrene (3OH-BaP, as antigen) and a variety of solvent matrices (as model systems) or anti-polycyclic aromatic hydrocarbon antibodies (anti-PAH). We focused the studies on the specific physicochemical interactions between 3OH-BaP and different, previously obtained, monoclonal and recombinant anti-PAH antibodies. Control experiments performed with non-binding monoclonal antibodies and bovine serum albumin (BSA) indicated that nonspecific interactions did not affect the FLN spectrum of 3OH-BaP. The spectral positions and relative intensities of the bands in the FLN spectra are highly dependent on the molecular environment of the 3OH-BaP. The FLN bands correlate with different vibrational modes of 3OH-BaP which are affected by interactions with the molecular environment (π–π interactions, H-bonding, or van-der-Waals forces). Although the analyte (3OH-BaP) was the same for all the antibodies investigated, different binding interactions could be identified from the FLN spectra on the basis of structural flexibility and conformational multiplicity of the antibodies’ paratopes.

Switchable dielectric permittivity with temperature and Dc-bias in a semifluorinated azobenzene derivative

The thermodynamic, optical, structural, and dynamic properties of the semifluorinated (E)-1-(4-octylphenyl)-2-(4-(perfluorooctyl)phenyl)diazene (4) and the corresponding (E)-1,2-bis(4-octylphenyl)diazene (5) have been studied with differential scanning calorimetry, polarizing optical microscopy, X-ray diffraction, and dielectric spectroscopy. 4 combines the azobenzene properties with the fluorophobic effect and gives rise to a responsive material with a temperature and dc-bias-driven switchable dielectric permittivity within the narrower nematic phase. This is caused by the nematic potential that inevitably brings some fluorocarbon chains in proximity to the hydrocarbon chains from adjacent molecules. Frustration is alleviated by reducing the nematic-to-isotropic transition temperature and by increasing the crystalline-to-nematic transition temperature, thus limiting the stability of the nematic phase. Unlike the normal isotropic phase of compound 5, the isotropic phase of compound 4 contains dipoles with short-range orientation correlations. Optimizing the type of interactions may result in materials with applications as molecular switches and electrooptic devices.     

Molecular electrostatic potentials as input for the alignment of HIV-1 integrase inhibitors in 3D QSAR

Comparative molecular similarity indices analysis (CoMSIA), a three-dimensional quantitative structure activity relationship (3D QSAR) paradigm, was used to examine the correlations between the calculated physicochemical properties and the in vitro activities (3'-processing and 3'-strand transfer inhibition) of a series of human immunodeficiency virus type 1 (HIV-1) integrase inhibitors. The training set consisted of 34 molecules from five structurally diverse classes: salicylpyrazolinones, dioxepinones, coumarins, quinones, and benzoic hydrazides. The data set was aligned using extrema of molecular electrostatic potentials (MEPs). The predictive ability of the resultant model was evaluated using a test set comprised of 7 molecules belonging to a different structural class of thiazepinediones. A CoMSIA model using an MEP-based alignment showed considerable internal as well external predictive ability (r2(cv) = 0.821, r2(pred) = 0.608 for 3'-processing; and r2(cv) = 0.759, r2(pred.) = 0.660 for 3'-strand transfer).     

Role of CH�C�� interaction energy in self-assembled gear-shaped amphiphile molecules: correlated ab initio molecular orbital and density functional theory study

Ab initio molecular orbital and density functional theory calculations with inclusion of dispersion interaction effect are employed to reveal the characteristic features of intermolecular interactions for the molecular capsule (1 ₆) consisting of six gear-shaped amphiphile molecules (1) discovered by Hiraoka et al. (J Am Chem Soc 130:14368?C14369, 2008). The contributions of CH?C?? and ?ШC?? type dispersion energies are found to be indispensable for the formation of hexameric capsule 1 ₆ by the analysis of decomposed interaction energies between fragmented-model species in the 1 molecule. We have also calculated the hexameric capsule (2 ₆) from demethylated 1 molecule (2). Such subtle structural difference induces the different characters of intermolecular interactions, in which the stabilization energy of hexameric 2 ₆ capsule is about 40?kcal/mol smaller than that of the original 1 ₆ capsule, due to the lack of three methyl groups for the CH?C?? interactions in 2 molecules.     

3D QSAR Modeling and Molecular Docking Studies on a Series of Triazole Analogues as Antibacterial Agents

The 3D QSAR analysis using the comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) techniques is performed on novel nalidixic acid based 1,2,4-triazole derivatives suggested earlier as antibacterial agents. The CoMFA and CoMSIA models employed for a training set of 28 compounds gives reliable values of Q² (0.53 and 0.52, respectively) and R² (0.79 and 0.85, respectively). The contour maps produced by the CoMFA and CoMSIA models are used to determine a three-dimensional quantitative structure-activity relationship. Based on the 3D QSAR contours new molecules with high predicted activities are designed. In addition, surflex-docking is performed to confirm the stability of predicted molecules in the receptor.     

Global QSAR models of skin sensitisers for regulatory purposes

Background

The new European Regulation on chemical safety, REACH, (Registration, Evaluation, Authorisation and Restriction of CHemical substances), is in the process of being implemented. Many chemicals used in industry require additional testing to comply with the REACH regulations. At the same time EU member states are attempting to reduce the number of animals used in experiments under the 3 Rs policy, (refining, reducing, and replacing the use of animals in laboratory procedures). Computational techniques such as QSAR have the potential to offer an alternative for generating REACH data. The FP6 project CAESAR was aimed at developing QSAR models for 5 key toxicological endpoints of which skin sensitisation was one.

Results

This paper reports the development of two global QSAR models using two different computational approaches, which contribute to the hybrid model freely available online.

Conclusions

The QSAR models for assessing skin sensitisation have been developed and tested under stringent quality criteria to fulfil the principles laid down by the OECD. The final models, accessible from CAESAR website, offer a robust and reliable method of assessing skin sensitisation for regulatory use.

     

Host-guest supramolecular complexes of the composition [M{NH(CH2)4O}{S2CN(C2H5)2}2] · CHCl3 (M = Zn, 63Cu(II)): Synthesis, structure, spectral properties, and thermal behavior

Solvated forms of adducts [M{NH(CH₂)₄O}{S₂CN(C₂H₅)₂}₂] · CHCl₃ (M = Zn (I), ⁶³Cu (II)) are preparatively isolated. Nonequivalence of the dithiocarbamate groups in structure I is revealed by the ¹³C MAS NMR method. According to the X-ray analysis data, adduct I is a supramolecular compound, whose structure includes a system of ordered channels occupied by outer-sphere solvating guest molecules of CHCl₃ (structural type of lattice clathrates). The solvation of the initial adduct is accompanied by the structural unification of its isomeric forms and an increase in the strength of binding of the morpholine molecules and in the contribution of the trigonal-bipyramidal component to the geometry of the zinc polyhedron. The character of triaxial anisotropy of the EPR parameters of isotopically substituted compound II in the magnetically dilute state is due to the geometry of the copper polyhedron, which is intermediate between a tetragonal pyramid and a trigonal bipyramid with the ground state of an unpaired electron formed by mixing of the $3d_{x^2 - y^2 } $ - and $3d_{z^2 } $ -atomic orbitals (AO) of copper(II). The thermal destruction of compound I studied by simultaneous thermal analysis includes stages of desorption of solvating chloroform molecules and coordinated morpholine molecules and thermolysis of the ??dithiocarbamate part?? of the adduct.     

Insight into the acidic behavior of oxazolidin-2-one,its thione and selone analogs through computational techniques

Deprotonation thermochemistry of Oxazolidin-2-one (OXA), Oxazolidine-2-thione (OXA-S), and Oxazolidine-2-selone (OXA-Se) has been studied in order to find the most acidic site and relative acidities of these heterocyclics at various sites. The deprotonation enthalpies at MP2/6-311++G**//MP2/6-31+G* and B3LYP/6-31+G* levels, while the free energies for deprotonation process and pKa values at B3LYP/6-31+G* level both in gas and aqueous phase (using PCM continuum model) of the anions of the three heterocyclics have been computed at 298 K. Calculated aqueous phase pKa values of OXA vary by ~6–7 units from the experimental aqueous phase pKa values of OXA and its derivatives. The deprotonation at the nitrogen is favored in OXA over the carbon atoms in contrast to the OXA-S and OXA-Se where in the deprotonation at the carbon attached to the nitrogen is most preferred. Deprotonation at this carbon induces an important C–O bond rupture in OXA-S and OXA-Se promoting an energetically favored ring-opening process. The finding offers a rare case when C–H acidity is able to dominate over the N–H acidity. In order to explain the relative stabilities, relative acidities and deprotonation enthalpies various characteristics of these molecules as well as their anions such as molecular electrostatic potential surface (MEP), frontier molecular orbital (FMO) features, chemical hardness, softness have been governed. The three dimensional MEP maps and HOMO–LUMO orbitals encompassing these molecules yield a reliable relative stability and reactivity (in terms of acidity) map displaying the most probable regions for deprotonation. The differential distribution of the electrostatic potential over the neutral and anionic species of OXA, OXA-S, and OXA-Se molecules is authentically reflected by HOMO–LUMO orbitals and NBO charge distribution analysis. The lone pair occupancies, second order delocalization energies for orbital interactions and the distribution of atomic charges over the entire molecular framework as obtained from natural bond orbital (NBO) analysis are found to faithfully replicate the predictions from the MEP maps and HOMO–LUMO band gaps in respect of explaining the relative stabilities and acidities in most of the cases. Good linear correlations have been obtained between HOMO–LUMO gap and pKa values in the aqueous phase for OXA and OXA-S molecules.     

CAESAR models for developmental toxicity

Background

The new REACH legislation requires assessment of a large number of chemicals in the European market for several endpoints. Developmental toxicity is one of the most difficult endpoints to assess, on account of the complexity, length and costs of experiments. Following the encouragement of QSAR (in silico) methods provided in the REACH itself, the CAESAR project has developed several models.

Results

Two QSAR models for developmental toxicity have been developed, using different statistical/mathematical methods. Both models performed well. The first makes a classification based on a random forest algorithm, while the second is based on an adaptive fuzzy partition algorithm. The first model has been implemented and inserted into the CAESAR on-line application, which is java-based software that allows everyone to freely use the models.

Conclusions

The CAESAR QSAR models have been developed with the aim to minimize false negatives in order to make them more usable for REACH. The CAESAR on-line application ensures that both industry and regulators can easily access and use the developmental toxicity model (as well as the models for the other four endpoints).

     

Arg188 in rice sucrose transporter OsSUT1 is crucial for substrate transport

Background

Epitope tags and fluorescent fusion proteins have become indispensable molecular tools for studies in the fields of biochemistry and cell biology. The knowledge collected on the subdomain organization of the two subunits of the adhesion complex dystroglycan (DG) enabled us to insert the 10 amino acids myc-tag at different locations along the ??-subunit, in order to better visualize and investigate the DG complex in eukaryotic cells.

Results

We have generated two forms of DG polypeptides via the insertion of the myc-tag 1) within a flexible loop (between a.a. 170 and 171) that separates two autonomous subdomains, and 2) within the C-terminal domain in position 500. Their analysis showed that double-tagging (the ??-subunit is linked to GFP) does not significantly interfere with the correct processing of the DG precursor (pre-DG) and confirmed that the ??-DG N-terminal domain is processed in the cell before ??-DG reaches its plasma membrane localization. In addition, myc insertion in position 500, right before the second Ig-like domain of ??-DG, proved to be an efficient tool for the detection and pulling-down of glycosylated ??-DG molecules targeted at the membrane.

Conclusions

Further characterization of these and other myc-permissive site(s) will represent a valid support for the study of the maturation process of pre-DG and could result in the creation of a new class of intrinsic doubly-fluorescent DG molecules that would allow the monitoring of the two DG subunits, or of pre-DG, in cells without the need of antibodies.