Analysing traces of autoinducer-2 requires standardization of the <Emphasis Type="Italic">Vibrio harveyi</Emphasis> bioassay

Autoinducer-2 (furanosyl borate diester) is a biologically active compound whose role as a universal bacterial signalling molecule is currently under intense investigation. Because of its instability and the low concentrations of it found in biological samples, its detection relies at present on a bioassay that measures the difference in the timing of the luminescence of the Vibrio harveyi BB170 sensor strain with and without externally added AI-2. Here we systematically investigated which parameters affected the fold induction values of luminescence obtained in the bioassay and developed a modified protocol. Our experiments showed that growth and luminescence of V. harveyi BB170 are strongly influenced by trace elements. In particular, addition of Fe³⁺ within a certain concentration range to the growth medium of the preinoculum culture improved the reproducibility and reduced the variance of the bioassay. In contrast, trace elements and vitamins introduced directly into the bioassay caused inhibitory effects. The initial density and luminescence of the sensor strain are very important and the values required for these parameters were defined. Borate interferes with the detection of AI-2 by giving false positive results. The response of V. harveyi BB170 to chemically synthesized AI-2 in the bioassay is nonlinear except over a very small concentration range; it is maximum over three orders of magnitude and shows inhibition above 35 μM. Based on the modified protocol, we were able to detect AI-2 in the absence of inhibitors with maximum fold induction values for the positive control (chemically synthesized AI-2) of >120 with a standard deviation of ~30% in a reliable and reproducible way.     

Optimization of the Lennard-Jones parameters for a combined ab initio quantum mechanical and molecular mechanical potential using the 3-21G basis set

A combined ab initio quantum mechanical and molecular mechanical (AI-QM/MM) potential for use in molecular modeling and simulation has been described. In this article, we summarize a procedure for deriving the empirical parameters embedded in a combined QM/MM model and suggest a set of Lennard-Jones parameters for the combined ab initio 3-21G and MM OPLS-TIP3P (AI-3/MM) potential. Interaction energies and geometrical parameters predicted with the AI-3/MM model for over 80 hydrogen-bonded complexes of organic compounds with water were found to be in good accord with ab initio 6-31G(d) results. We anticipate that the AI-3/MM potential should be reasonable for use in condensed phase simulations. © 1996 by John Wiley & Sons, Inc.     

(Studies on AI-77s,microbial products with pharmacological activity) structures and the chemical nature of AI-77s

The structures of a novel gastroprotective substance AI-77-B and its analogues AI-77-C, D, F and G, which are produced by Bacillus pumilus, are described. Five of the asymmetric centers of AI-77-B have S absolute stereochemistry confirmed by X-ray in combination with chemical studies.     

An Efficient Synthesis of Optically Active [4-13C] Labelled Quorum Sensing Signal Autoinducer-2

A new synthetic route for the quorum sensing signal Autoinducer-2 (AI-2) is described and used for the preparation of [4-¹³C]-AI-2 starting from [1-¹³C]-bromoacetic acid. The key step in this process was the enantioselective reduction of an intermediate ketone. This synthesis provides, selectively, both enantiomers of the labelled or unlabelled parent compound, (R) or (S)-4,5-dihydroxypentane-2,3-dione (DPD) and was used for an improved synthesis of [1-¹³C]-AI-2.     

Total Synthesis of the Gastroprotective Substance AI-77-B and of Analogues

The Diels-Alder adducts 8 of furan to 1-cyanovinyl acetate were converted into (Methyl 3-chloro)-5-O-(3-chlorobenzoyl)-2, 3-dideoxy-α-dl-arabino-hexofuranosid)uronic acid ((α)- 18a ) and into (methyl 3-azido-5-O-(3-chlorobenzoyl_-2,3-dideoxy-α-dl-ribo-hexofuranosid)uronic acid ((α)- 41a ). These compounds were condensed to (3S)-3-[(1′S)-1′-amino-3′-methylbutyl]-3,4-dihydro-8-hydroxyisocoumarin hydrochloride ((?)- 2 ); the resulting mixtures of diastereoisomeric amides were transformed and separated to give the gastroprotective substance AI-77- B ((?)- 1 ) and analogues.     

Studies on AI-77s,microbial products with gastroprotective activity. Structures and the chemical nature of AI-77s

The structures and the chemical nature of a novel gastroprotective substance AI-77-B (1) and its analogues AI-77-C (2), D (3), F (4) and G (5), which are produced by Bacillus pumilus AI-77, are described. The structure of 1 was confirmed to be 6-[[1(S)-(3(S), 4-dihydro-8-hydroxy-1-oxo-1H-2-benzopyran-3-yl)-3-methylbutyl]amino]-4(S),5(S)-dihydroxy-6-oxo-3(S)-aminohexanoic acid by X-ray in combination with chemical studies and the structures of 2, 3, 4 and 5 were determined by chemical syntheses from 1 and spectral analyses.     

Quantitative 1H NMR spectroscopy (qNMR) in the early process development of a new quorum sensing inhibitor

2-methyl-5,6,7,8-tetrahydro-2H-chromen-4(3H)-one (called 6-oxo) is presented as a new AI-1 quorum sensing inhibitor for Vibrio harveyi. The development of a chemical process to afford traceable materials for new biological assays demands the development of analytical methods to ensure their purity and quality. This work describes the use of quantitative ¹H nuclear magnetic resonance (NMR) spectroscopy (qNMR) to assess the purity of a sample of 6-oxo (99.88%) and a sample of its major process impurity (E)-1-(2-hydroxycyclohex-2-en-1-yl)but-2-en-1-one (called HCB; 98.28%). To explore the scope of the use of qNMR to quantify the amount of low-content components in samples related to the chemical process for 6-oxo synthesis, this work also determined the amount of 6-oxo in two HCB samples: (a) the high-purity HCB sample described above and (b) a crude HCB sample collected during the chemical process. Despite the complexity of the crude sample, the amount of 6-oxo was readily assessed and could help to estimate the extent to which 6-oxo was already formed during the HCB synthesis. This information can help the understanding of how the process parameters can be modified to improve the performance of the whole process, by controlling the reaction mechanisms working at each step of this chemical process. In this context, our results reinforce qNMR as a complementary analytical tool for the quantification of the main component found in a sample, contributing to the standardization of reference materials and thus allowing the development of analytical methods for process control and traceability of the samples used for biological assays.     

Quorum sensing in <Emphasis Type="Italic">Erwinia</Emphasis> species

The term quorum sensing (QS) refers to the ability of bacteria to regulate gene expression according to the accumulation of signalling molecules that are made by every cell in the population. The erwiniae group of bacteria are often phytopathogens and the expression of a number of their important virulence determinants and secondary metabolites is under QS control. The erwiniae utilise two types of QS signalling molecules: N-acyl homoserine lactones and AI-2-type signalling molecules. Here, we review the regulatory networks involving QS in the soft rot erwiniae.     

The Antibacterial Activity Mode of Action of Plantaricin YKX against Staphylococcus aureus

We aimed to evaluate the inhibitory effect and mechanism of plantaricin YKX on S. aureus. The mode of action of plantaricin YKX against the cells of S. aureus indicated that plantaricin YKX was able to cause the leakage of cellular content and damage the structure of the cell membranes. Additionally, plantaricin YKX was also able to inhibit the formation of S. aureus biofilms. As the concentration of plantaricin YKX reached 3/4 MIC, the percentage of biofilm formation inhibition was over 50%. Fluorescent dye labeling combined with fluorescence microscopy confirmed the results. Finally, the effect of plantaricin YKX on the AI-2/LuxS QS system was investigated. Molecular docking predicted that the binding energy of AI-2 and plantaricin YKX was −4.7 kcal/mol and the binding energy of bacteriocin and luxS protein was −183.701 kcal/mol. The expression of the luxS gene increased significantly after being cocultured with plantaricin YKX, suggesting that plantaricin YKX can affect the QS system of S. aureus.     

Viscoelasticity and birefringence of polyisoprene

The complex Young's modulus, E^*(ω), and the complex strain-optical coefficient, O^*(ω), which is the ratio of the birefringence to the strain, were measured for polyisoprene (PIP) over a frequency range of 1 ～ 130 Hz and a temperature range of 22 ～ ?100°C. The imaginary part of O^*, O″, was positive at low frequencies and negative at high frequencies. The real part, O′, was always positive and showed a maximum. The complicated behavior of O^* could be understood by the assumption that E^* = E_R^* + E_G^* and O^* = C_RE_R^* + C_GE_G^*, where E_R^* and E_G^* were complex quantities and C_R and C_G were constants. The C_R value, equal to the ordinary stress-optical coefficient measured in the rubbery plateau zone, was 2.0 × 10^?9 Pa^?1. The C_G value, defined as the ratio O″/E″ in the glassy zone, was ?1.1 × 10^?11 Pa^?1. The E_G^*, which was the major component of E^* in the glassy zone, showed almost the same frequency dependence as that of polystyrene and polycarbonate. The E_R^*, which was dominant in the rubbery zone, was described well by the bead-spring theory. The temperature dependence of the E_G^* was stronger than that of the E_R^*. This difference caused the breakdown of the thermorheological simplicity for E^* and O^* around the glass-to-rubber transition zone. © 1995 John Wiley & Sons, Inc.     

Synthesis and Spectroscopic Characterization of Two Different Types of Heterobimetallic Glycolate Complexes of Niobium(V)

An entirely new class of heterobimetallic homoleptic glycolate complexes of the type Nb(OGO)₃{Ta(OGO)₂} [where G=CMe₂CH₂CH₂CMe₂ (G¹) (3); CMe₂CH₂ CHMe(G²) (4); CHMeCHMe (G³) (5); CH₂CMe₂CH₂ (G⁴) (6); CMe₂CMe₂(G⁵) (7); CH₂CHMeCH₂ (G⁶) (8); CH₂CEt₂CH₂ (G⁷) (9); CH₂CMe(Prⁿ)CH₂ (G⁸) (10)] have been prepared by the reactions of Nb(OGO)₂(OGOH) [G=G¹ (1a); G² (1b); G³ (1c); G⁴ (1d); G⁵ (1e); G⁶ (1f); G⁷ (1g); G⁸ (1h)] with Ta(OGO)₂ (OPrⁱ) (G=G¹ (2a); G² (2b); G³ (2c); G⁴ (2d); G⁵ (2e) G⁶ (2f); G⁷ (2g); G⁸ (2h). In addition to the novel derivatives (2)–(10), our earlier investigations on heterobimetallic glycolate-alkoxide derivatives have been extended to derivatives of the type Nb(OGO) [where M=A1 n=3, G=G³ (11);G⁴ (12); G⁶ (13) G⁷ (14); G^s (15); G⁹=CH₂CH₂CH₂ (16) and M=Ti (n=4, G=G⁴) (17), Zr(n=4,G=G⁴) (18)], which are conveniently prepared by the reactions of metalloligands Nb(OGO)₂(OGOH) [G=G³ (1c); G⁴ (1d); G⁶ (1f); G⁷ (1g); G⁸ (1h); G⁹ (1i)] with different metal alkoxides. All of these new complexes have been characterized by elemental analyses, molecular weight determinations, and spectroscopic (I.r. and ¹H, ²⁷Al-n.m.r.) studies. Structural features of the new derivatives have been elucidated on the basis of molecular weight and spectroscopic data.     

Elastic modulus of the crystalline phase of poly(cis 1,4-isoprene)

The crystalline elastic modulus of poly(cis 1,4-isoprene) has been measured by x rays and calculated by molecular mechanics. The experimental modulus is E = (2.3 ± 0.3) × 10⁹N m^?2. The calculated modulus is E = (8.8 ± 0.1) × 10⁹N m^?2 for chains in S⁺ cis S^?T conformation and E = (6.1 ± 0.1) × 10⁹N m^?2 for chains in S⁺ cis S+T conformation. The modulus calculated for a statistical structure including both conformation is E = (6.7 ± 0.1) × 10⁹N m^?2. The experimental modulus is thought to be a lower limit because of partial crystallinity of the sample. The chief mechanism of deformation is rotation around single bonds adjacent to the double bond.     

A Convenient Synthesis of New Macrocyclic Thioether-Esters and Ether-Esters: Extraction Properties of These Esters for Alkali,Alkaline Earth,and Transition Metal Cations

Macrocyclic thioether-esters and ether-esters have been prepared by treating 2,2′-dithiobenzoic acid dichloride and 1,2-benzendicarboxylic acid dichloride with appropriate glycols or dithiol. The complexing ability of these thioether-esters and ether-esters toward Li⁺, Na⁺, K⁺, Mg ^{2 +} , Ca ^{2 +} , Sr ²⁺ , Ba ^{2 +} , Co ^{2 +} , and Ni ^{2 +} has been measured by the solvent extraction method. The extraction data indicate that compound 2 exhibits stronger selectivity toward Li⁺, 3 toward Ba ^{2 +} , 4 toward K⁺, 5 toward Mg ^{2 +} , 6 toward Ba ^{2 +} and Sr ^{2 +} , and 7 toward Co ^{2 +} and Ni ^{2 +} when compared with other cations.     

INDO calculations of the solvent dependence of some spin–spin couplings of fluorocarbons

The results of some SCPT and SOS calculations of ¹J(CH), ¹J(FC), ²J(FH), ³J(FH), ³J(FF) and ¹J(CC) in a variety of solvents are reported. The calculations employ the solvaton model and INDO parameters. In almost all cases the coupling is predicted to increase as the dielectric constant of the solvent increases, the exception being ³J(FH)cis in trifluoroethylene which is supported by experimental results.     

Preparation and X-ray structures of complexes of 18-membered crown ethers with polyfunctional guests: Urea and (O-alkyliso)uronium salts

The preparation and X-ray structure determinations of six complexes of urea and (O-n-butyliso)uronium salts with crown ethers are presented. Urea forms isostructural 5:1 adducts with 18-crown-6 (1) and aza-18-crown-6 (2), in which two urea molecules are each hydrogen bonded to two neighbouring hetero atoms of the macroring. The remaining urea molecules form two-dimensional layers alternating with crown ether layers. In both complexes the macroring has theg ⁺ g ⁺ a ag ^– a ag ^– a g ^– g ^– a ag ⁺ a ag ⁺ a conformation withC _i symmetry. In the solid 1:1 complex of O-n-butylisouronium picrate with 18-crown-6 (3) two types of conformations of the macroring were observed: theg ⁺ g ⁺ a ag ^– a ag ⁺ a ag ^– g ^– ag ^– a ag ⁺ a conformation with approximateC _m symmetry and to a lesser extent theg ⁺ g ⁺ a ag ^– a ag ⁺ a g ⁺ g ⁺ a ag ^– a ag ⁺ a conformation with approximateC ₂ symmetry. Both conformations allow the guest to form three hydrogen bonds to the macrocyclic host. Three complexes of 18-crown-6 and uronium salts have been prepared and characterized by X-ray crystallography. The 1:1 complexes with uronium nitrate (4) and uronium picrate (5) both exhibit the sameC ₂ conformation and the same hydrogen bonding scheme as in the least occupied form of the previous complex. A 1:2 complex with uroniump-toluenesulphonate (6) has a different hydrogen bonding scheme (two hydrogen bonds per cation to neighbouring oxygen atoms of the macroring) and a different conformation of the host molecule (theag ⁺ a ag ^– a ag ⁺ a ag ^– a ag ⁺ a ag ^– a conformation with almostD _3d symmetry). An attempt to prepare a solid uronium nitrate complex with diaza-18-crown-6 in the same way as the 18-crown-6·uronium nitrate (1:1) complex did not yield the expected result. Instead X-ray analysis revealed that the uronium ion is dissociated, resulting in the nitrate salt of the diprotonated diaza crown ether (7). Supplementary Data relating to this article are deposited with the British Library as Supplementary Publication No. SUP 82058 (26 pages).     

Nuclear model calculation for cyclotron production of 61Cu as a PET imaging

⁶¹Cu is positron emitter and can be used as the PET and molecular imaging. In this study cyclotron production of ⁶¹Cu via ⁶¹Ni(p,n)⁶¹Cu, ^natNi(p,x)⁶¹Cu, ^natNi(d,x)⁶¹Cu, ^natNi(α,x)⁶¹Cu, ^natZn(p,x)⁶¹Cu and ⁵⁹Co(α,2n)⁶¹Cu reactions was investigated. The ALICE/ASH (hybrid and GDH models) and TALYS-1.2 codes were used to calculate excitation functions for proton, alpha and deuteron induced on ^natNi, proton on ⁶¹Ni and ^natZn and also alpha-particle on ⁵⁹Co targets that lead to the production of ⁶¹Cu radioisotopes using intermediate energy accelerators. In addition, we compared the data obtained from in this study with the reported measurement by experimental data. Moreover, optimal thickness of the targets and physical yield were obtained by stopping and range of ions in matter code for each reaction. Eventually ⁶¹Ni(p,n)⁶¹Cu and ⁵⁹Co(α,2n)⁶¹Cu reaction to produce ⁶¹Cu in no-carrier added state with high production yield was suggested. Finally the ^natNi(p,x)⁶¹Cu reaction was employed to test the target preparation using electroplating technique.     

Molecular dynamics simulation of brushes formed by star polyelectrolytes under theta solvent conditions

Using molecular dynamics simulations, we have studied polyelectrolyte brushes formed by partially or fully charged star polymers tethered on a planar surface under theta solvent conditions. The diagram of states for salt‐free solutions differs in the location of osmotic regime (OB) compared with the respective diagram reported by Borisov and Zhulina. In contrast, simulation results dictate that the OB regime appears for values of the ratio F /α ^?1/2 l_B ^?1 much larger than unity, which is the threshold of counterion localization, with F denoting the branch functionality, α the charged units fraction and l_B the Bjerrum length. The simulation results support that the brush height scaling laws H ～ α ² l_B F ^1.049S ³s ^?1 and H ～ α^0.302 F ^0.23S for the charged Pincus Brush (PB) and osmotic (OB) regimes, respectively, where S is the spacer length and s is the grafted area per star chain. The respective theoretical scaling laws are H ～ α ² l_B F ^1.88S ³s ^?1 and H ～ α ^1/2 F ^0.44S . © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55 , 1110–1117     

Thermodynamics of mixtures of hexane and heptane isomers with normal and branched hexadecane

Molar excess mixing enthalpies h ^E , Gibbs free energies g ^E and hence entropies s ^E have been obtained using calorimetry and the vapor sorption method at 25°C for hexane isomers+2,2,4,4,6,8,8-heptamethylnonane, a highly branched C ₁₆ . The h ^E and g ^E are negative while Ts ^E are positive, but small. The values are explained by the Prigogine-Flory theory through negative free volume contributions to h ^E and Ts ^E , counterbalanced in the case of Ts ^E by the positive combinatiorial Ts ^E for mixing molecules of different size. No contribution is seen from the interaction between methyl and methylene groups. The excess quantities are also obtained for hexane and heptane isomers mixed with n-hexadecane. Values of h ^E and Ts ^E are now strongly positive, while those of g ^E are only slightly less negative. The interpretation requires two recently advanced contributions in addition to those of the Prigogine-Flory theory: 1) a decrease of order when correlations of orientations between n-C ₁₆ molecules in the pure liquid are replaced in the solution by weaker correlations whose strengths depend on the shapes of the lower alkane isomers. For lower alkane isomers of the same shape, but highly sterically hindered, h ^E and Ts ^E are small, manifesting, 2) a negative contribution, ascribed to a rotational ordering of n-C ₁₆ segments on the sterically-hindered molecule. Enthalpy-entropy compensation is observed for these new contributions, arising from their rapid fall-off with increase of temperature.     

Kinetics of the reactions of OH with alkanes

The rate coefficients for the reactions of OH with ethane (k₁), propane (k₂), n-butane (k₃), iso-butane (k₄), and n-pentane (k₅) have been measured over the temperature range 212–380 K using the pulsed photolysis-laser induced fluorescence (PP-LIF) technique. The 298 K values are (2.43±0.20) × 10^?13, (1.11 ± 0.08) × 10^?12, (2.46 ± 0.15) × 10^?12, (2.06 ± 0.14) × 10^?12, and (4.10 ± 0.26) × 10^?12 cm³ molecule^?1 s^?1 for k₁, k₂, k₃, k₄, and k₅, respectively. The temperature dependence of k₁ and k₂ can be expressed in the Arrhenius form: k₁ = (1.03 ± 0.07) × 10^?11 exp[?(1110 ± 40)/T] and k₂ = (1.01 ± 0.08) × 10^?11 exp[?(660 ± 50)/T]. The Arrhenius plots for k₃ – k₅ were clearly curved and they were fit to three parameter expressions: k₃ = (2.04 ± 0.05) × 10^?17 T² exp[(85 ± 10)/T] k₄ = (9.32 ± 0.26) × 10^?18 T² exp[(275 ± 20)/T]; and k₅ = (3.13 ± 0.25) × 10^?17 T² exp[(115 ± 30)/T]. The units of all rate constants are cm³ molecule^?1 s^?1 and the quoted uncertainties are at the 95% confidence level and include estimated systematic errors. The present measurements are in excellent agreement with previous studies and the best values for atmospheric calculations are recommended. © 1994 John Wiley & Sons, Inc.     

A criterion for the confluence of two seams of conical intersection in triatomic molecules

It is shown that the cross product t ^{I J} (R _x )≡g ^{I J} (R _x )×h ^{I J} (R _x ), where g _τ ^{I J} (R)=(c ^I (R _x )−c ^J (c ^I (R _x )+c ^J (R _x )), h _τ ^{I J} (R)=c ^I (R _x )^† c ^J (R _x ), τ is an internal nuclear coordinate, the c ^I (R) satisfy [H(R)−E _I (R)]c ^I (R)=0 and H(R) is the electronic Hamiltonian matrix, is a unique property of a conical intersection at R _x . t ^{I J} (R _x )=0 when R _x is located at the intersection of two (or more) seams of conical intersection. This criterion for an intersection of two seams of conical intersection has important implications for algorithms that seek to locate such points. Here it␣is␣used to analyze the trifurcation of a generic C_2v ^2S+1 A−^2S+1 B seam of conical intersection, analogous to those recently found in AlH₂ and CH₂. Received: 31 July 1997 / Accepted: 27 August 1997