Synthetic Phenolic Glycolipids for Application in Diagnostic Tests for Leprosy.

Point-of-care (POC) diagnostic tests for the rapid detection of individuals infected with Mycobacterium leprae, the causative pathogen of leprosy, represent efficient tools to guide therapeutic and prophylactic treatment strategies in leprosy control programs, thus positively contributing to clinical outcome and reducing transmission of this infectious disease. Levels of antibodies directed against the M. leprae-specific phenolic glycolipid I (PGL-I) closely correlate with an individual's bacterial load and a higher risk of developing leprosy. We describe herein the assembly of a set of PGL glycans carrying the characteristic phenol aglycon and featuring different methylation patterns. The PGL trisaccharides were applied to construct neoglycoproteins that were used to detect anti-PGL IgM antibodies in leprosy patients. ELISAs and quantitative lateral-flow assays based on up-converting nanoparticles (UCP-LFAs) showed that the generated PGL-I and PGL-II trisaccharide neoglycoconjugates can be applied for the detection of anti M. leprae IgM antibodies in POC tests.

Evaluation of different solvents and solubility parameters on the morphology and diameter of electrospun pullulan nanofibers for curcumin entrapment.

In this work, the effect of different solvents and solvent binary mixtures on the morphology of electrospun pullulan (Pull) nanofibers was evaluated. The solution viscosities, interactions between solvent and polymer, as well as, solvent vapor pressure, were correlated to the morphology and diameters of the nanofibers. Water, dimethylformamide (DMF) and dimethyl sulfoxide (DMSO) and Teas graphs that rely on the use of Hildebrand solubility parameters were used to identify the most suitable mixtures of solvents. The best binary mixture of solvents to produce Pull nanofibers without defects and with small diameters (203±32 nm) was DMF/DMSO in the ratio of 70/30 wt.%. Pull nanofibers containing 3 and 5 wt. % of curcumin (Curc) in a mixture of DMF/DMSO (70/30 wt.%) were then obtained, and the entrapment efficiency was evaluated using 1H NMR and a UV--vis spectrophotometer. The results obtained in this work create a new approach for the production of Pull nanofibers for drug delivery systems.

Systematic modifications of amino acid-based organogelators for the investigation of structure-property correlations in drug delivery system.

Thermogels, used as multi-functional drug-loading materials, have properties that mainly rely on their gelator structure. Although a large variety of organogel systems are used as drug delivery carriers, relatively few have been investigated in terms of their structure-property correlations based on amino acid derivative gelators. Here, a series of amino acid based gelators were synthesized to explore the role of the gelator structure on functional properties, with the aim of establishing a connection between the molecular parameters and gel properties. By varying the three substitutions of the gelator backbone, it was found that a comprehensive interaction, consisting of hydrophobic forces, H-bonding interactions, conformational flexibility and steric repulsion, play a crucial role in determining the gelation properties. Hansen solubility parameters were employed to explore the solvent effect on the network forming and gel properties. From an analysis of the morphologies obtained from polarized optical microscope (POM), atomic force microscopic images (AFM) and scanning electron microscopy (SEM), the gelator structure was found to have an impact on the self-assembly. According to the X-ray diffraction (XRD), the possible conformations adopted by the gelators were revealed through molecular modelling. The ability to form intermolecular H-bonding is vital in molecular packing and, thus, gelation. A structure-property relationship was developed and proposed to provide a theoretical basis for controllable drug delivery implants.

Application of Solvent Parameters for Predicting Organogel Formation.

Solvents, accounting the majority of the organogel system, have a tremendous impact on the characteristics of gels. To date, there is a large variety of organogel systems; relatively few have been investigated in the field of structure-solvent correlation. Here, a series of solvent parameters were applied to explore the role of solvent effect on network forming and gel property, intending to build the connection between the precise solvent parameter and gel property. Among the solvent parameters, Kamlet-Taft Parameters and Hansen solubility parameters can distinguish specific types of intermolecular interactions, which could correlate solvent parameter with the gel property. From an analysis of the morphologies obtained from POM and SEM, the gelator structure has an impact on its self-assembly. For possible conformations, the gelators were investigated through XRD. The investigation of solvent-property relationship will provide a theoretical basis for controllable drug delivery implants.

Double differential cross sections for proton induced electron emission from molecular analogues of DNA constituents for energies in the Bragg peak region.

For track structure simulations in the Bragg peak region, measured electron emission cross sections of DNA constituents are required as input for developing parameterized model functions representing the scattering probabilities. In the present work, double differential cross sections were measured for the electron emission from vapor-phase pyrimidine, tetrahydrofuran, and trimethyl phosphate that are structural analogues to the base, the sugar, and the phosphate residue of the DNA, respectively. The range of proton energies was from 75 keV to 135 keV, the angles ranged from 15° to 135°, and the electron energies were measured from 10 eV to 200 eV. Single differential and total electron emission cross sections are derived by integration over angle and electron energy and compared to the semi-empirical Hansen-Kocbach-Stolterfoht (HKS) model and a quantum mechanical calculation employing the first Born approximation with corrected boundary conditions (CB1). The CB1 provides the best prediction of double and single differential cross section, while total cross sections can be fitted with semi-empirical models. The cross sections of the three samples are proportional to their total number of valence electrons.

Bio-Based Solvents for Green Extraction of Lipids from Oleaginous Yeast Biomass for Sustainable Aviation Biofuel.

Lipid-based oleaginous microorganisms are potential candidates and resources for the sustainable production of biofuels. This study was designed to evaluate the performance of several alternative bio-based solvents for extracting lipids from yeasts. We used experimental design and simulation with Hansen solubility simulations and the conductor-like screening model for realistic solvation (COSMO-RS) to simulate the solubilization of lipids in each of these solvents. Lipid extracts were analyzed by high performance thin-layer chromatography (HPTLC) to obtain the distribution of lipids classes and gas chromatography coupled with a flame ionization detector (GC/FID) to obtain fatty acid profiles. Our aim was to correlate simulation with experimentation for extraction and solvation of lipids with bio-based solvents in order to make a preliminary evaluation for the replacement of hexane to extract lipids from microorganisms. Differences between theory and practice were noted for several solvents, such as CPME, MeTHF and ethyl acetate, which appeared to be good candidates to replace hexane.

Molecular structure and vibrational spectroscopic studies of prothionamide by density functional theory.

Prothionamide (PTH) is the secondary drug used against Mycobacterium tuberculosis bacteria and leprosy. The aim of this work was to investigate the potential energy surface map, anharmonic and harmonic vibrational spectra, NBO analysis and ELF (Electron Localization Function) of the title compound using DFT approach with the B3LYP (Becke, three-parameter, Lee-Yang-Parr) exchange-correlation functional with the 6-31G++(d,p) and the Z3POLX basis sets were employed. In the experimental part of this study, FT-Mid IR, FT-Far IR and FT-Raman spectra of the molecule were recorded in the regions 4000-450cm(-1), 700-30cm(-1) and 4000-100cm(-1) respectively in the solid phase. The comparison between calculated and experimental vibrational spectra (infrared and Raman spectra) and assignments of fundamental vibrational modes were characterized by total energy distribution (TED). Theoretical spectra were seen to be in good agreement with those of the experimental ones.

Theoretical and experimental electrostatic potential around the m-nitrophenol molecule.

This work concerns a comparison of experimental and theoretical results of the electron charge density distribution and the electrostatic potential around the m-nitrophenol molecule (m-NPH) known for its interesting physical characteristics. The molecular experimental results have been obtained from a high-resolution X-ray diffraction study. Theoretical investigations were performed using the Density Functional Theory at B3LYP level of theory at 6-31G* in the Gaussian program. The multipolar model of Hansen and Coppens was used for the experimental electron charge density distribution around the molecule, while we used the DFT methods for the theoretical calculations. The electron charge density obtained in both methods allowed us to find out different molecular properties such us the electrostatic potential and the dipole moment, which were finally subject to a comparison leading to a good match obtained between both methods. The intramolecular charge transfer has also been confirmed by an HOMO-LUMO analysis.

Intermolecular interactions, charge-density distribution and the electrostatic properties of pyrazinamide anti-TB drug molecule: an experimental and theoretical charge-density study.

An experimental charge-density analysis of pyrazinamide (a first line antitubercular drug) was performed using high-resolution X-ray diffraction data [(sin θ/λ)max = 1.1 Å(-1)] measured at 100 (2) K. The structure was solved by direct methods using SHELXS97 and refined by SHELXL97. The total electron density of the pyrazinamide molecule was modeled using the Hansen-Coppens multipole formalism implemented in the XD software. The topological properties of electron density determined from the experiment were compared with the theoretical results obtained from CRYSTAL09 at the B3LYP/6-31G** level of theory. The crystal structure was stabilized by N-H...N and N-H...O hydrogen bonds, in which the N3-H3B...N1 and N3-H3A...O1 interactions form two types of dimers in the crystal. Hirshfeld surface analysis was carried out to analyze the intermolecular interactions. The fingerprint plot reveals that the N...H and O...H hydrogen-bonding interactions contribute 26.1 and 18.4%, respectively, of the total Hirshfeld surface. The lattice energy of the molecule was calculated using density functional theory (B3LYP) methods with the 6-31G** basis set. The molecular electrostatic potential of the pyrazinamide molecule exhibits extended electronegative regions around O1, N1 and N2. The existence of a negative electrostatic potential (ESP) region just above the upper and lower surfaces of the pyrazine ring confirm the π-electron cloud.

Mycolic acids: structures, biosynthesis, and beyond.

Mycolic acids are major and specific lipid components of the mycobacterial cell envelope and are essential for the survival of members of the genus Mycobacterium that contains the causative agents of both tuberculosis and leprosy. In the alarming context of the emergence of multidrug-resistant, extremely drug-resistant, and totally drug-resistant tuberculosis, understanding the biosynthesis of these critical determinants of the mycobacterial physiology is an important goal to achieve, because it may open an avenue for the development of novel antimycobacterial agents. This review focuses on the chemistry, structures, and known inhibitors of mycolic acids and describes progress in deciphering the mycolic acid biosynthetic pathway. The functional and key biological roles of these molecules are also discussed, providing a historical perspective in this dynamic area.

Solvent based hydrogen bonding: impact on poly(3-hexylthiophene) nanoscale morphology and charge transport characteristics.

We demonstrate that supramolecular assembly and subsequent enhancement of charge transport characteristics of conjugated polymers can be facilitated simply by adding small amounts of a more volatile poor solvent, which can hydrogen bond with the majority solvent. Addition of up to 2 vol % acetone to a precursor solution of poly(3-hexylthiophene) (P3HT) in chloroform leads to approximately a 4-fold increase in P3HT field-effect mobility. The improvement is associated with hydrogen bonding interactions between acetone and chloroform which decrease the evaporation rate of the mixed solvent. P3HT is less soluble in the binary solvent than in the more readily vaporized chloroform component, and this characteristic enables the supramolecular assembly of P3HT chains at the nanoscale. Two-dimensional molecular ordering of the polymer film was controlled by varying the quantity of poor solvent added to the precursor solution, and the correlation between field-effect mobility and molecular ordering was investigated. Hansen solubility parameters were used to systematically understand how the solvent mixture enhances the alignment and assembly of polymer chains and influences subsequent thin film properties. The value of the relative energy difference (RED) of the solvent with respect to P3HT increased from less than 1 to more than 1 during film formation, which indicates that the solvent characteristics are initially those of a good solvent but transform into those of a poor dissolution medium. A mechanistic illustration of the molecular ordering process during film formation is postulated.

Solid-state tautomeric structure and invariom refinement of a novel and potent HIV integrase inhibitor.

The conformation and tautomeric structure of (Z)-4-[5-(2,6-difluorobenzyl)-1-(2-fluorobenzyl)-2-oxo-1,2-dihydropyridin-3-yl]-4-hydroxy-2-oxo-N-(2-oxopyrrolidin-1-yl)but-3-enamide, C27H22F3N3O5, in the solid state has been resolved by single-crystal X-ray crystallography. The electron distribution in the molecule was evaluated by refinements with invarioms, aspherical scattering factors by the method of Dittrich et al. [Acta Cryst. (2005), A61, 314-320] that are based on the Hansen-Coppens multipole model [Hansen & Coppens (1978). Acta Cryst. A34, 909-921]. The ß-diketo portion of the molecule exists in the enol form. The enol -OH hydrogen forms a strong asymmetric hydrogen bond with the carbonyl O atom on the ß-C atom of the chain. Weak intramolecular hydrogen bonds exist between the weakly acidic α-CH hydrogen of the keto-enol group and the pyridinone carbonyl O atom, and also between the hydrazine N-H group and the carbonyl group in the ß-position from the hydrazine N-H group. The electrostatic properties of the molecule were derived from the molecular charge density. The molecule is in a lengthened conformation and the rings of the two benzyl groups are nearly orthogonal. Results from a high-field (1)H and (13)C NMR correlation spectroscopy study confirm that the same tautomer exists in solution as in the solid state.

Efficient and accurate local single reference correlation methods for high-spin open-shell molecules using pair natural orbitals.

A production level implementation of the high-spin open-shell (spin unrestricted) single reference coupled pair, quadratic configuration interaction and coupled cluster methods with up to doubly excited determinants in the framework of the local pair natural orbital (LPNO) concept is reported. This work is an extension of the closed-shell LPNO methods developed earlier [F. Neese, F. Wennmohs, and A. Hansen, J. Chem. Phys. 130, 114108 (2009); F. Neese, A. Hansen, and D. G. Liakos, J. Chem. Phys. 131, 064103 (2009)]. The internal space is spanned by localized orbitals, while the external space for each electron pair is represented by a truncated PNO expansion. The laborious integral transformation associated with the large number of PNOs becomes feasible through the extensive use of density fitting (resolution of the identity (RI)) techniques. Technical complications arising for the open-shell case and the use of quasi-restricted orbitals for the construction of the reference determinant are discussed in detail. As in the closed-shell case, only three cutoff parameters control the average number of PNOs per electron pair, the size of the significant pair list, and the number of contributing auxiliary basis functions per PNO. The chosen threshold default values ensure robustness and the results of the parent canonical methods are reproduced to high accuracy. Comprehensive numerical tests on absolute and relative energies as well as timings consistently show that the outstanding performance of the LPNO methods carries over to the open-shell case with minor modifications. Finally, hyperfine couplings calculated with the variational LPNO-CEPA∕1 method, for which a well-defined expectation value type density exists, indicate the great potential of the LPNO approach for the efficient calculation of molecular properties.

An experimental charge density of HEPES.

We report the experimental charge density of HEPES [4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid], which is a common buffering agent. The structure was refined using the Hansen-Coppens formalism. The ability of the HEPES molecule to form stable intermolecular interactions and intermolecular hydrogen bonds in the crystal structure is discussed in terms of its buffering properties. The protonation mode observed in the crystal structure is different from that expected in solution, suggesting that additional factors must be taken into consideration in order to explain the solution properties of the compound. As ordered HEPES molecules are found in the active sites of proteins in several protein crystal structures, our results will allow for quantitative analysis of the electrostatic potential of the interacting surfaces of those proteins.

The influence of oxygen-containing functional groups on the dispersion of single-walled carbon nanotubes in amide solvents.

Surface composition plays an important role in carbon nanotube dispersibility in different environments. Indeed, it determines the choice of dispersion medium. In this paper the effect of oxidation on the dispersion of HiPCO single-walled carbon nanotubes (SWNTs) in N-methyl-pyrrolidinone (NMP), N,N-dimethylformamide (DMF), N,N-dimethylacetamide (DMA), N-dodecyl-pyrrolidinone (N12P) and cyclohexyl-pyrrolidinone (CHP) was systematically studied. During the oxidation process, similar amounts of carboxylic acid and phenolic groups were introduced to mostly already existing defects. For each solvent the dispersion limits and the absorption coefficients were estimated by optical absorption analysis over a range of SWNT concentrations. The presence of acid oxygenated groups increased SWNT dispersibility in NMP, DMF and DMA, but decreased in N12P and CHP. The absorption coefficients, however, decreased for all solvents after oxidation, reflecting the weakening of the effective transition dipole of the π-π transition with even limited extension functionalization and solvent interaction. The analysis of the results in terms of Hansen and Flory-Huggins solubility parameters evidenced the influence of dipolar interactions and hydrogen bonding on the dispersibility of oxidized SWNTs.

The crystal structures of yeast Get3 suggest a mechanism for tail-anchored protein membrane insertion.

Tail-anchored (TA) proteins represent a unique class of membrane proteins that contain a single C-terminal transmembrane helix. The post-translational insertion of the yeast TA proteins into the ER membrane requires the Golgi ER trafficking (GET) complex which contains Get1, Get2 and Get3. Get3 is an ATPase that recognizes and binds the C-terminal transmembrane domain (TMD) of the TA proteins. We have determined the crystal structures of Get3 from two yeast species, S. cerevisiae and D. hansenii, respectively. These high resolution crystal structures show that Get3 contains a nucleotide-binding domain and a "finger" domain for binding the TA protein TMD. A large hydrophobic groove on the finger domain of S. cerevisiae Get3 structure might represent the binding site for TMD of TA proteins. A hydrophobic helix from a symmetry-related Get3 molecule sits in the TMD-binding groove and mimics the TA binding scenario. Interestingly, the crystal structures of the Get3 dimers from S. cerevisiae and D. hansenii exhibit distinct conformations. The S. cerevisiae Get3 dimer structure does not contain nucleotides and maintains an "open" conformation, while the D. hansenii Get3 dimer structure binds ADP and stays in a "closed" conformation. We propose that the conformational changes to switch the Get3 between the open and closed conformations may facilitate the membrane insertions for TA proteins.

Application of the Hansen solubility Parameters theory to carbon nanotubes.

Carbon nanotubes (CNT) are very promising nano-objects due to their exceptional properties. However, their tendency to form bundles as well as their insolubility in common solvents makes them difficult to handle. The main way to solve the problem is chemical or physical CNTs functionalisations, with all the problems inherent to the methods. In this contribution, we present a new approach that allows predicting the solubility of carbon nanotubes in many solvents but also predicting the most appropriate solvents to use for given samples of CNTs. Solubilisation and dispersion being directly connected, the present approach of solubilisation proves also to be efficient in dispersing the CNTs bundles. This contribution is a first step toward the control of carbon nanotube's dispersion in polymers and their homogenous functionalisation. Moreover, we also report here a new method, based on solvents, to separate carbon nanotubes by size, the use of mixture of non-solvents in order to obtain good solvents and the use of mixture of good solvents to obtain higher solubility. The use of mixture of good solvents allowed us to obtain high solubility, up to three times higher then that reported in literature. We have also measured and analysed the solubility of some functionalised carbon nanotubes.

Invarioms for improved absolute structure determination of light-atom crystal structures.

The determination of molecular absolute configuration from an X-ray analysis for structures that contain only light elements is challenging owing to the weak anomalous dispersion signal. The achievable precision of the Flack x parameter for such structures is therefore limited, especially when the independent-atom model is employed. Invariom modelling can improve this situation. Invarioms are theoretically predicted pseudoatoms within the Hansen & Coppens multipole formalism. They are transferable from one molecule to another and provide generalized aspherical atomic form factors. It is shown that, by application of the invariom approach, the precision and standard uncertainty of the Flack x parameter and therefore the reliability of deducing molecular chirality in an absolute structure determination can be improved.

Chiral inversion of drugs: coincidence or principle?

2-arylpropionic acid derivatives are probably the most frequently cited drugs exhibiting the phenomenon that is best known as chiral inversion. One enantiomer of drug is converted into its antipode either in the presence of a solvent or more often in inner environment of an organism. Mechanistic studies of the metabolic chiral inversion were carried out for several drugs from NSAIDs, and a model of this inversion was suggested and subsequently confirmed. The chiral inversion of NSAIDs has been intensively studied in the context of the pharmacological and toxicological consequences. However, the group of NSAIDs is not the sole group of drugs in which the inversion phenomenon can be observed. There exist several other drugs that also display chiral inversion of one or even both of their enantiomers. These drugs belong to different pharmacotherapeutic groups as monoamine oxidase inhibitors, antiepileptic drugs, drugs used in the treatment of hyperlipoproteinemia or drugs that are effective in the treatment of leprosy. Moreover, some chiral or prochiral drugs are metabolized to give chiral metabolites that undergo chiral inversion too, which can have direct impact on pharmacological properties or toxicity of the drug. As the process of chiral inversion is affected by several factors, so the intensity of chiral inversion of individual substances and at different conditions can differ considerably. Interspecies differences and types of tissue are reported to be the main factors that were recognized to play the key role in the process of chiral inversion. Some of more recent studies have revealed that several other factors, such as the route of administration or interaction with other xenobiotics, can influence the enantiomeric conversion, too. Chiral inversion does not seem to be a phenomenon connected with only several drugs from some unique group of 2-arylpropionic acid derivatives: it is also observed in drugs with rather different chemical structures and is much more frequent than it can be realized.

Structural features of MHC class I molecules that might facilitate alternative pathways of presentation.

Comparisons of the structures of different mouse MHC class I molecules define how polymorphic residues determine the unique structural motif and atomic anchoring of their bound peptides. Here, Ted Hansen and colleagues speculate that quantitative differences in how class I molecules interact with peptide, beta2-microglobulin and molecular chaperones that facilitate peptide loading might determine their relative participation in different pathways of antigen presentation.