Separation,determination and antifungal activity test of the products from a new Bacillus amyloliquefaciens

A new Bacillus amyloliquefaciens named ZJU-2011 was discovered, and the culture supernatant showed a strong inhibitory effect against Candida albicans. In this study, a novel method was developed to purify the antifungal compounds in high purity. The obtained products were analysed by high performance liquid chromatography and proven to be of high purity. Mass spectrometry showed that the molecular weights of the two bioactive components were 270 and 288, respectively, and their structures were determined to be bacilysin and chlorotetaine by using ¹H and ¹³C nuclear magnetic resonance spectroscopy. To the best of our knowledge, this is the first time that B. amyloliquefaciens has been reported to produce bacilysin and chlorotetaine simultaneously. The minimum inhibitory concentration of chlorotetaine against six common fungal pathogens were determined to be in the range of 1.8–7.8 μg/mL.     

Sensitive Detection of Trypsin using Liquid‐Crystal Droplet Patterns Modulated by Interactions between Poly‐L‐Lysine and a Phospholipid Monolayer

Liquid‐crystal (LC) droplet patterns are formed on a glass slide by evaporating a solution of nematic LC dissolved in heptane. In the presence of an anionic phospholipid, 1,2‐dioleoyl‐sn‐glycero‐3‐phospho‐rac‐(1‐glycerol) (DOPG), the LCs display a dark cross pattern, indicating a homeotropic orientation. When LC patterns are incubated with an aqueous mixture of DOPG and poly‐L ‐lysine (PLL), there is a transition in the LC pattern from a dark cross to a bright fan shape due to the electrostatic interaction between DOPG and PLL. Known to catalyze the hydrolysis of PLL into oligopeptide fragments, trypsin is preincubated with PLL, significantly decreasing the interactions between PLL and DOPG. LCs adopt a perpendicular orientation at the water–LC droplet interface, which gives rise to a dark cross pattern. This optical response of LC droplets is the basis for a quick and sensitive biosensor for trypsin.     

In silico study directed towards identification of the key structural features of GyrB inhibitors targeting MTB DNA gyrase: HQSAR,CoMSIA and molecular dynamics simulations

ABSTRACT

Mycobacterium tuberculosis DNA gyrase subunit B (GyrB) has been identified as a promising target for rational drug design against fluoroquinolone drug-resistant tuberculosis. In this study, we attempted to identify the key structural feature for highly potent GyrB inhibitors through 2D-QSAR using HQSAR, 3D-QSAR using CoMSIA and molecular dynamics (MD) simulations approaches on a series of thiazole urea core derivatives. The best HQSAR and CoMSIA models based on IC₅₀ and MIC displayed the structural basis required for good activity against both GyrB enzyme and mycobacterial cell. MD simulations and binding free energy analysis using MM-GBSA and waterswap calculations revealed that the urea core of inhibitors has the strongest interaction with Asp79 via hydrogen bond interactions. In addition, cation-pi interaction and hydrophobic interactions of the R₂ substituent with Arg82 and Arg141 help to enhance the binding affinity in the GyrB ATPase binding site. Thus, the present study provides crucial structural features and a structural concept for rational design of novel DNA gyrase inhibitors with improved biological activities against both enzyme and mycobacterial cell, and with good pharmacokinetic properties and drug safety profiles.     

Photo-controllable electro-optic response of liquid crystalline cells using photo-isomeric molecules

A photo-controllable liquid crystal (LC) material was evaluated using a nematic LC mixture with azobenzene. This study aimed to determine the mechanisms that result in variations of material parameters specifically caused by the morphological change of guest molecules. The transition from rod-shaped trans isomers to bent-shaped cis isomers weakened the intermolecular ordering interactions and the decreasing order parameter caused variations of material parameters. The shift of dielectric response cannot be solely explained by the weakened intermolecular interactions but is also significantly influenced by the properties of the guest cis isomer itself. The bend elastic constant was more affected than the splay elastic constant, which implies that the shift of the elastic properties is due to the morphological shape of the cis isomer as well as the decreased molecular ordering. Thus, three different mechanisms are involved in the variations of the material properties: (i) weakened intermolecular ordering interactions, (ii) direct contribution of cis isomers, and (iii) molecular morphological interactions of the cis isomer with the host LCs. It was also demonstrated that the optical properties of twisted nematic (TN) cells can be controlled, and that the stability of the bend state in the optically compensated birefringence (OCB) mode cell can be improved.     

Tunable self-organization in n-type liquid crystalline dibenzocoronene tetracarboxdiimides for high photoconductivity

ABSTRACT

A comprehensive study on the self-organised mesomorphism and charge-transport properties of three n-type liquid crystalline (LC) dibenzocoronene tetracarboxdiimide derivatives (Dibenzo-CDI 1, 2, 3) bearing branched alkyl chains with varied side-chain length and branching point (α or β site) has been carried out. All three Dibenzo-CDI compounds possessed high solubility in common organic solvents and low-lying lowest unoccupied molecular orbital energy levels below ?4.0 eV indicating their air-stable electron-transport capacity under ambient conditions. It is discovered that the side-chain length has a moderate influence on the molecular arrangement and thus leads to only limited variation of electron-transport properties. In contrast, the branching position plays a critical role on tuning molecular packing and orientation in the bulk mesophases, thereby resulting in dramatic differences in electron mobilities. Remarkably, Dibenzo-CDI 3 demonstrates good photoconductivity by time-of-flight method with high electron mobility up to 0.075 cm²/Vs, close to the highest value reported in certain n-type LC derivatives. All these results reveal that LC Dibenzo-CDI derivatives are potential candidates for high-performance solution-processable electronics, such as air-stable n-type organic field-effect transistors (OFETs) and solar cells.     

Applications of liquid crystals in biosensing and organic light-emitting devices: future aspects

ABSTRACT

This article summarises recent advances made in our laboratory towards the development of new technological applications, such as biosensors and organic light-emitting diodes (OLEDs) based on liquid crystals (LCs) other than LC displays. The study of biomolecular interaction using LC material relies on the specific interaction between the LC and the biomolecule of interest at interfaces that permit the biomolecular events to be amplified into easily measured signals for various sensing applications. In the first part, we emphases recent studies in the design and modulation of LC-based interfaces based on robust colloidal LC gels for biological amplification, qualitative and quantitative understanding of important biomolecular interactions at LC–aqueous interfaces for diagnostic and laboratory applications and design of LC droplets that hold promise to act as a marker for cells and cell-based interactions. In the second part, we described design of organic materials for application in OLEDs on various discotic monomers, dimers and oligomers. These molecules have the ability to transport charges, holes and electrons. In addition, because of the high conductivity and π–π stacking, they are considered as the advanced materials for practical applications. The technological advances in our laboratory using discotic LCs will be briefly presented in this article.     

A Comparison of Polymer Separation Efficiency and Resolution by Gradient LC,GPC and TLC

Abstract

The specific resolution of gradient LC and reversed phase TLC methods for the separation of different molecular weight standards of poly(isoprene), poly(ethylene glycol), poly(ethylene oxide), poly(styrene) and poly(α-methylstyrene) were determined. It was found that gradient LC has an order of magnitude greater resolving power (for high polymers) than gel permeation chromatography (GPC) while TLC had from two to five times the resolving power of GPC in the molecular weight range investigated. This is a direct result of the greater selectivity of gradient LC and TLC techniques. The specific resolution is also dependent on the type of gradient used to achieve fractionation for the LC technique.     

Synthesis,characterization, thermal behavior,and DFT aspects of some oxovanadium(IV) complexes involving ONO-donor sugar Schiff bases

Seven new Schiff base complexes of oxovanadium(IV), [VO(L)(H₂O)], where H₂L = H₂bmpph-gls, H₂bumpph-gls, H₂iso-vmpph-gls, H₂pmpph-gls, H₂iso-bumpph-gls, H₂ampph-gls, and H₂vmpph-gls, have been synthesized by the reaction of VOSO₄·5H₂O and the said ligands in aqueous ethanol. The resulting complexes have been characterized on the basis of elemental analysis, vanadium determination, molar conductance, magnetic measurements, thermogravimetric (TG) analysis, infrared, electronic mass, and electron spin resonance studies. The thermal decomposition processes of one representative complex is discussed, and the order of reaction (n) and the activation energies (E_a) have been calculated from TG and differential TG curves. Molecular geometry optimizations, molecular surface electrostatic potentials, vibrational frequency calculations, bond lengths, bond angles and dihedral angles, and natural atomic charges obtained by natural bond orbital and Mulliken population analysis and calculations of molecular energies, highest occupied molecular orbital and lowest unoccupied molecular orbital were performed with the Gaussian 09 software package using density functional theory methods with Becke3–Lee–Yang–Parr (B3LYP) hybrid exchange–correlation functional and the standard 6-311G(+) basis set for (ampph-glsH₂) and LANL2DZ basis set for one of its complexes, [VO(ampph-gls)(H₂O)]. No imaginary frequency was found in the optimized model compounds, and hence it ensures that the molecule is in the lowest point of the potential energy surface, that is, an energy minimum. Finally calculated results were applied to simulate infrared spectra which show good agreement with observed spectra. Based on experimental and theoretical data, suitable square pyramidal structures have been proposed for these complexes.     

Optical resolution of racemic amino acid derivatives with molecularly imprinted membranes bearing oligopeptide tweezers

Molecularly imprinted polymeric membranes were prepared from various oligopeptide tweezers by the adoption of N‐α‐tert‐butoxycarbonyl‐D ‐tryptophan (Boc‐D ‐Trp) or N‐α‐tert‐butoxycarbonyl‐L ‐tryptophan (Boc‐L ‐Trp) as a print molecule. The chiral recognition ability of the formed molecular recognition sites was dependent on the absolute configuration of the print molecule adopted in the membrane preparation (molecular imprinting) process, whereas the candidate oligopeptide tweezers consisted of the L ‐amino acid residues. In other words, the membranes imprinted by the D ‐isomer recognized the D ‐isomer in preference to the corresponding L ‐isomer, and vice versa. The affinity constant between the target molecule and the chiral recognition site from the oligopeptide tweezers was higher than that from a single‐strand oligopeptide derivative. Those membranes selectively transported the enantiomer, which was preferentially incorporated into the membrane by dialysis. The permselectivities for these membranes exceeded their adsorption selectivities. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 385–396, 2005     

Free Energy Peturbation and Molecular Dynamics Simulation Studies on the Enantiomeric Discrimination of Amines by Dimethyldiketopyridino-18-Crown-6

Abstract

Discrimination of chiral amines by dimethyldiketopyridino-18-crown-6 (1) is studied by free energy peturbation (FEP) and molecular dynamics (MD) methods. 1 has two (S)-chiral centers and discriminates chiral amines through host-guest interactions. The optically active amines in this study are α-(1-naphthyl)ethylamine, methylbenzylamine, cyclohexylethylamine, and sec-butylamine. The trends in binding free energy differences obtained from FEP calculations were in excellent agreement with experimental results obtained in the gas phase. In order to explain the enantioselectivity of the host in terms of the host-guest interactions at the molecular level, we analyzed the structures generated by 10-ns MD simulations of host-guest complexes. The suggested chiral discrimination mechanism, the π-π interaction and the steric repulsion between the guest and the host, was verified by our MD simulation analysis.     

An examination of intermolecular and intramolecular hydrogen bonding in biomolecules by AM1 and MNDO/M semiempirical molecular orbital studies

The recent NMDO/M modification and parameterization of the MNDO molecular orbital method has been used to analyze intermolecular hydrogen bonding between amino acids and water, and intramolecular hydrogen bonding in monosaccharides. The results have been compared to AM1 calculations on the same systems. The MNDO/M calculations gave values which were similar to ab initio calculations with respect to the intermolecular interactions, but yielded significantly poorer results for the intramolecular interactions. The AM1 procedure performed better on the intramolecular interactions than the MNDO/M procedure, but frequently provided unfavorable three-centered hydrogen bonding geometries for the intermolecular interactions.     

Interpretation of interactions of halogenated hydrocarbons with modified silica adsorbent coated with 3-benzylketoimine group silane

The paper reports a new group of adsorbents obtained by modification of silica surface with silane containing 3-benzylketoimine groups with bonded Cu(II) and Ni(II) chlorides. The adsorbents obtained were subjected to a chromatographic study to establish the type of adsorbate-adsorbent interactions for aliphatic and aromatic halogenated hydrocarbons used as adsorbates. The following retention parameters were determined: retention factor (k), Kovats retention index (I), specific retention volume (V _g), and molecular retention index (ΔM _e). Values of the molecular retention index were subjected to complex statistical analysis providing qualitative relations between the adsorbates’ properties and spatial structure and their retention. It was observed that bonding of chlorides of Cu(II) and Ni(II) with the ketoimine groups resulted in an increase of the retention index and the molecular retention index indicating an increase of the adsorbate-adsorbent interaction in comparison with the reference column coated with silane including a 3-benzylketoimine group without transition metal chlorides. Along with the observed increase of the adsorbate-adsorbent interaction, larger difference between the retention indices was observed for both halogenated compounds. This indicates a positive influence of the introduced transition metals on the selectivity of the adsorbate-adsorbent interactions of the examined columns.     

Syntheses,crystal structures,and fluorescence properties of two isomorphic binuclear compounds incorporating N-acetyl-N-phenylglycinate with N-donor co-ligands

In this study, two new isomorphic binuclear compounds, [Ln(µ-NAP)₄(NAP)₂(phen)₂]?·?H₂O (1) and (2) (Ln?=?Eu, Tb, NAP?=?N-acetyl-N-phenylglycinate; phen?=?1,10-phenanthroline), have been synthesized and characterized by infrared spectroscopy, elemental analysis, and X-ray crystallography. These compounds crystallize in a triclinic form with space group Pī with a?=?11.7519(11), b?=?13.4293(12), c?=?14.0686(13)?Å, V?=?1992.7(3)?ų, and Z?=?1. Single-crystal X-ray structural analysis reveals that 1 is binuclear, assembled into a 3-D supramolecular network with self-complementary double hydrogen-bonding interactions and aromatic π–π interactions. Fluorescence properties of 1 and 2 are also discussed.     

Using ONIOM calculations to investigate the abilities of simple and nitrogen,boron, sulfur-doped carbon nanotubes in sensing of carbon monoxide

In this work, geometries, stabilities, and electronic properties of the carbon monoxide (CO) molecule as an adsorbent in a simple carbon nanotube (CNT) and nitrogen (N), boron (B), sulfur (S)-doped CNTs (NCNT, BCNT, and SCNT) with parallel and perpendicular configurations are fully considered using ONIOM, natural bond orbital, and quantum theory of atom in molecule (QTAIM) calculations. The adsorption energies (E_ad) demonstrate that a CO molecule could be adsorbed on the surface of the simple CNT with parallel configuration and N-doped CNT with perpendicular configuration in an exothermic process. QTAIM calculations showed the close-shell (noncovalent) interactions between the CO molecule and CNT or N, B, S-doped CNTs. In addition, the energy gap (E_g) values between the highest occupied molecular orbital and the lowest unoccupied molecular orbital are calculated. In accordance with the results of energy gap, simple and N-doped CNTs could be used as CO sensors.     

Identifying ligand-binding specificity of the oligopeptide receptor OppA from Bifidobacterium longum KACC91563 by structure-based molecular modeling

As a ATP-binding cassette (ABC) transporter the OppA receptor plays key roles in protecting the host organism and transporting nutrients across the intestine by the oligopeptide transporter from symbiotic bacteria and directs maturation of the host immune system. Among lactic acid bacteria, Bifidobacterium longum KACC91563, isolated from fecal samples of healthy Korean neonates, has the capability to alleviate food allergy effects. Operating as a peptide importer, the extracellular OppA receptor from gram-positive B. longum KACC91563 translocates nutrients, specifically peptides, from the outside environment of the intestinal tract to the inside of symbiotic cells. In the present study we attempt to explicate the relationship between the substrate’s specificity from the OppA importer and the probiotic effects of B. longum KACC91563 in the host intestine. It was first identified in this study the specialized structure–function relationship from the OppA importer of B. longum KACC91563 with its structural and functional determinants. This could provide insights into substrate specificity of unique immunological properties and a key switch for the substrate’s metabolism to reprogramming immune responses in the host intestine by structure-based molecular modeling. The probiotic effects of oligopeptide substrate (such as a proline-rich peptide containing at least one branched residue of leucine, isoleucine, and valine) and its metabolism for the OppA from B. longum KACC91563 are attributed to enhancement of the epithelial barrier by several different strain specific pathways to prevent the strong adhesion of pathogens.     

Tuning the Product Spectrum of a Glycoside Hydrolase Enzyme by a Combination of Site-Directed Mutagenesis and Tyrosine-Specific Chemical Modification

Selective chemical modification of proteins plays a pivotal role for the rational design of enzymes with novel and specific functionalities. In this study, a strategic combination of genetic and chemical engineering paves the way for systematic construction of biocatalysts by tuning the product spectrum of a levansucrase from Bacillus megaterium (Bm-LS), which typically produces small levan-like oligosaccharides. The implementation of site-directed mutagenesis followed by a tyrosine-specific modification enabled control of the product synthesis: depending on the position, the modification provoked either enrichment of short oligosaccharides (up to 800 % in some cases) or triggered the formation of high molecular weight polymer. The chemical modification can recover polymerization ability in variants with defective oligosaccharide binding motifs. Molecular dynamic (MD) simulations provided insights into the effect of modifying non-native tyrosine residues on product specificity.     

Syntheses,crystal structures,and properties of two molecular double-supporting polyoxotungstates

Two molecular double-supporting polyoxotungstates [SiW₁₂O₄₀{M(phen)₂H₂O}₂] · nH₂O (phen = 1,10′-phenanthroline, M = Mn 1, n = 2; M = Co 2, n = 3) were synthesized hydrothermally and characterized by elemental analyses, IR, TG, and X-ray single-crystal diffraction. The variable-temperature magnetic susceptibilities were measured at 2–300 K. The double-supporting polyoxotungstate molecule consists of a Keggin-type dodecatungstosilicate anion and a pair of transition metal complex fragments which are covalently linked to opposite sides of the Keggin anion. The transition metal ion locates in the center of a distorted octahedron. Multiple H-bonding interactions are observed between the coordinated waters of the transition metal complex fragments and terminal oxygen atoms of Keggin units and also between the bridging oxygen atoms of Keggin units and the lattice waters, which creates one-dimensional chains or two-dimensional layers. Between the layers or chains there are weak CH···O hydrogen bonding interactions and van der Waals forces. The molecular double-supporting polyoxotungstosilicate begins to decompose at ca. 500 °C. The variable-temperature magnetic behavior of 1 shows weak antiferromagnetic characteristics with a small value of θ = −0.289 K.