Comparison of radii sets,entropy, QM methods,and sampling on MM‐PBSA,MM‐GBSA,and QM/MM‐GBSA ligand binding energies of F. tularensis enoyl‐ACP reductase (FabI)

To validate a method for predicting the binding affinities of FabI inhibitors, three implicit solvent methods, MM‐PBSA, MM‐GBSA, and QM/MM‐GBSA were carefully compared using 16 benzimidazole inhibitors in complex with Francisella tularensis FabI. The data suggests that the prediction results are sensitive to radii sets, GB methods, QM Hamiltonians, sampling protocols, and simulation length, if only one simulation trajectory is used for each ligand. In this case, QM/MM‐GBSA using 6 ns MD simulation trajectories together with GB^neck2, PM3, and the mbondi2 radii set, generate the closest agreement with experimental values (r² = 0.88). However, if the three implicit solvent methods are averaged from six 1 ns MD simulations for each ligand (called “multiple independent sampling”), the prediction results are relatively insensitive to all the tested parameters. Moreover, MM/GBSA together with GB^HCT and mbondi, using 600 frames extracted evenly from six 0.25 ns MD simulations, can also provide accurate prediction to experimental values (r² = 0.84). Therefore, the multiple independent sampling method can be more efficient than a single, long simulation method. Since future scaffold expansions may significantly change the benzimidazole's physiochemical properties (charges, etc.) and possibly binding modes, which may affect the sensitivities of various parameters, the relatively insensitive “multiple independent sampling method” may avoid the need of an entirely new validation study. Moreover, due to large fluctuating entropy values, (QM/)MM‐P(G)BSA were limited to inhibitors’ relative affinity prediction, but not the absolute affinity. The developed protocol will support an ongoing benzimidazole lead optimization program. © 2015 Wiley Periodicals, Inc.     

Development of a highly sensitive method for determining atmospheric carbonyl compounds by passive sampling and application of the method to a survey of indoor air

A simple, highly sensitive analytical method for measuring many kinds of carbonyls in air using a passive sampler containing a sorbent (silica gel) coated with 2,4-dinitrophenylhydrazine has been developed. The carbonyls collected by the sampler were extracted with a solvent, and the extracts were subjected to high-performance liquid chromatography (HPLC; UV detection) without first being concentrated. In this method, the volume injection is examined, and is found to have a sensitivity at least 20 times that of ordinary HPLC methods. The air concentrations of nine carbonyls collected by passive sampling over a period of 24?h were estimated by means of conversion equations derived from the results of active sampling;c?=?^{10[log ( y} )^{??? b ] a} , where c is the carbonyl concentration in air (µg/m³); y is the amount of carbonyl collected by the passive sampler (µg); and a and b are constants for each carbonyl compound. The calculated air concentrations were consistent with the concentrations measured by active sampling. This method may be useful in determining personal exposure to ambient carbonyls.     

The effect of solvents on the 13C NMR chemical shifts of the carbonyl carbon and the rotational barriers of N,N-dimethylbenzamide

The ¹³C solvent induced chemical shifts (SICS) of the carbonyl carbon and the thermodynamic barriers to rotation about the C? N bond of N,N-dimethylbenzamide are linearly related to the solvent parameter, E_T(30). A multi-parametric solvent parameter approach indicates that the SICS are influenced equally by polar effects and hydrogen-bond donor effects. Rotational barriers for N,N-dimethylbenzamide may, in principle, be determined by measurement of the ¹³C chemical shift of the carbonyl carbon in a particular solvent.     

Insecticidal volatiles from the marigold plant (genustagetes). Effect of species and sample manipulation

Summary Volatiles from three species of the genustagetes, commonly called marigold have been isolated and characterized. Simultaneous steam distillation extractions (SSDE) produced consistently extracts of higher insecticidal activity than Soxhlet extractions. Methylene chloride was the best solvent. Volatiles isolated from theminutae species showed higher activity than those frompatula anderecta. Comparison of extracts from the flower, foliage and roots of the plant showed that most of the activity is located in the flower. The volatiles are highly effective toward both larvae and adult mosquitoes.     

Thermodynamic Aspects of Metal–Ion Complexation in the Structured Solvent, <Emphasis Type="Italic">N</Emphasis>-Methylformamide

Chloride complexation of cobalt(II), nickel(II) and zinc(II) ions has been studied by calorimetry and spectrophotometry in N-methylformamide (NMF) containing 1.0 mol-dm^{− 3} (n-C₄H₉)₄NClO₄ as an ionic medium at 298 K. A series of mononuclear complexes, MCl_n^{(2 -n) +} (M=Co, Ni and Zn) with n = 1, 3 and 4 for cobalt(II), n = 1 for nickel(II), and n = 1–4 for zinc(II), are formed and their formation constants, enthalpies and entropies were obtained. It revealed that complexation is suppressed significantly in NMF relative to that in N,N-dimethylformamide (DMF) in all metal systems examined. The suppressed complexation in NMF is mainly ascribed to the smaller formation entropies in NMF reflecting that the solvent–solvent interaction or solvent structure in the bulk NMF is much stronger than that in the bulk DMF. Formation entropies, Δ S₁^o, of the monochloro complex in DMF, dimethyl sulfoxide and NMF are well correlated with the Marcus’ solvent parameter, Δ Δ_v S^o/R, according to Δ S₁^o/R = aΔ Δ_v S^o/R+b. The a value is negative and similar in all metal systems examined, whereas the b value depends on the metal system. When a gaseous ion is introduced into a solvent, the ionic process of solvation is divided into two stages: the ion destroys the bulk solvent structure to isolate solvent molecules at the first stage and the ion then coordinates a part of isolated solvent molecules around it at the second stage. We propose that the a and b values may reflect the changes in the freedom of motion of solvent molecules at the first and second stages, respectively, of the ionic process of solvation.     

A 13C-NMR spectral study of cellulose and glucopyranose dissolved in the NH3/NH4SCN solvent system

The ¹³C-NMR chemical shifts of a cellulose with a DP_w of 23 dissolved in the NH₃/NH₄SCN solvent system were found to be very similar to those of cellulose dissolved in DMSO (cellulose oligomers), in the LiCl/DMAC system and in the N-methylmorpholine N-oxide/DMSO system. It was concluded from this that cellulose does not react with the NH₃/NH₄SCN solvent. It was found, however, that glucose reacts with the solvent at C-1 to form β-D -glucopyranosy-lamine. Separation of this compound from the solvent resulted in another compound which was determined to be β,β-di-D -glucopyranosylamine. The compounds β-D -glucopyranosylamine, N-acetyl-2,3,4,6-tetra-O-acetyl-β-D -glucopyranosylamine, β,β-di-D -glucopyranosylamine, α,β-di-D -glucopyranosylamine, 2,3,4,6,2′,3′,4′,6′-octa-O-acetyl-α,β-di-D -glucopyranosylamine were all synthesized and the ¹³C-NMR chemical shifts of these compounds are reported. It was also found that for the low-DP cellulose sample which was used the reducing end group existed and had reacted with the solvent to form an amine at C-1.     

Orthogonal sampling in free‐energy calculations of residue mutations in a tripeptide: TI versus λ‐LEUS

In a recent article (Bieler et al., J. Chem. Theory Comput. 2014, 10, 3006), we introduced a combination of λ‐dynamics and local‐elevation umbrella‐sampling termed λ‐LEUS to calculate free‐energy changes associated with alchemical processes using molecular dynamics simulations. This method was suggested to be more efficient than thermodynamic integration (TI), because the dynamical variation of the alchemical variable λ opens up pathways to circumvent barriers in the orthogonal space (defined by the N – 1 degrees of freedom that are not subjected to the sampling enhancement), a feature λ‐LEUS shares with Hamiltonian replica‐exchange (HR) approaches. However, the mutation considered, hydroquinone to benzene in water, was no real challenge in terms of orthogonal‐space properties, which were restricted to solvent‐relaxation processes. In the present article, we revisit the comparison between TI and λ‐LEUS considering non‐trivial mutations of the central residue X of a KXK tripeptide in water (with X = G, E, K, S, F, or Y). Side‐chain interactions that may include salt bridges, hydrogen bonds or steric clashes lead to slow relaxation in the orthogonal space, mainly in the two‐dimensional subspace spanned by the central and ψ dihedral angles of the peptide. The efficiency enhancement afforded by λ‐LEUS is confirmed in this more complex test system and can be attributed explicitly to the improved sampling of the orthogonal space. The sensitivity of the results to the nontrivial choices of a mass parameter and of a thermostat coupling time for the alchemical variable is also investigated, resulting in recommended ranges of 50 to 100 u nm² and 0.2 to 0.5 ps, respectively. © 2015 Wiley Periodicals, Inc.     

Quantitative Determination of Escherichia Coli in Water Sources in the Environment Using a Surface Acoustic Wave Impedance System Modified with a Syringe Filter

A novel surface acoustic wave (SAW) sensor was developed in the study to measure the density of Escherichia coli in water sources in the environment. With a modified syringe filter sealed by a Teflon cover, the sensor system ensured that the CO₂ gas produced by bacteria flowed upward and accumulated at the headspace of the syringe filter. The measurements were obtained by immersing a pair of electrodes into a sealed syringe filter which contained a culture solution containing lauryl sulfate trytose (LST). The changes in frequency of the two electrodes were caused by generation of small CO₂ bubbles on the surface of the electrodes, which were connected in series to a SAW resonator. The signals obtained by the system were 10 times greater than those obtained by conventional SAW systems. The calibration curve of detection time versus density of E. coli showed a linear relationship with a correlation coefficient (R ² ) of 0.9434 over the range of 10² to 10⁷ cells/mL. Further integration of this sensing system with a suitable automated sampling device will enable this device to be used on-site for analysis and field studies.     

Synthetic Attempts towards ‘Aromatic’ Nonafulvenes

According to their spectroscopic behavior, four classes of nonafulvenes may be distinguished, but, so far, only three classes have been identified. Type-A nonafulvenes (including parent 1a ) are typically olefinic molecules with strongly alternating bond lengths and a nonplanar nine-membered ring. Type-B nonafulvenes are characterized by four pairs of equivalent ring H-atoms and ring C-atoms. Spectra of both Type-A and Type-B nonafulvenes are not dependent on temperature and solvent polarity. However, spectra of Type-C nonafulvenes (including prototype 1d with R¹ = R² = NMe₂) are strongly influenced by temperature and solvent polarity due to an equilibrium 1?1 ^± between the nonpolar olefinic 1 and dipolar planarized 1 ^±. So far, Type-D nonafulvenes occurring exclusively in the dipolar form 1 ^± were unknown. Synthetic attempts towards nonafulvenes of Type D are described and problems encountered in nonafulvene syntheses are discussed. Several new cyclononatetraenes and four new nonafulvenes (or nonafulvalenes) 31, 1n, 3 , and 5 have been synthesized. Spectroscopic evidence shows that 11,12-bis(diethylamino)nonatriafulvalene 5 is the first Type-D nonafulvene.     

The proton exchange reaction between indene and the indenyl anion

The proton exchange reaction between the indenyl carbanion and its parent compound indene has been studied by NMR as a function of temperature. The rate of this bimolecular reaction is very low and has been found to be strongly dependent on the polarity of the solvent. In solvents like dimethoxyethane (? = 7·2) and diglyme the reaction becomes manifest in the NMR spectrum only at elevated temperatures (T > 150°C). In hexamethylphosphortriamide (? = 30) the rate is much greater and line broadening may be observable at room temperature. The reaction in this solvent is characterised by a frequency factor f = 7 × 10⁷ 1 mol^?1 s^?1, an activation enthalpy ΔH ≠ = 9·5 kcal mol^?1 and an entropy of activation ΔS≠ = ?23 e.u. The low reaction rate and its solvent dependence are briefly discussed.     

The structuredness of solvents

The parameterization of the structuredness of a solvent as the difference between its molar heat of vaporization, Δ_vap H ^° and the sum of its internal donor-acceptor interactions (in terms of DN and AN) and its vdW interactions (in terms of Δ_vap H ^° of n-alkanes of the same molar volume) is criticized. As an alternative, the excess of the reduced Trouton constant, Δ_vapS^°/R over 12 and of Kirkwood's dipole correlation parameter g over 1.7 are suggested as criteria for the decision of whether a solvent is structured, both having to be met. Conversely, if either Δ_vapS^°/R is less than 11.6 or g is less than 1.3, then the solvent is to be considered unstructured. Exceptions are discussed.     

Tributyl phosphate degradation by immobilized cells of aCitrobacter sp.

Tributyl phosphate (TBP), a plasticizer and solvent, is used in nuclear fuel reprocessing, generating TBP wastes laden with residual uranium. ACitrobacter sp. accumulated heavy metals via a phosphohydrolase(s) that precipitated metals with inorganic phosphate liberated from an organic phosphate “donor” molecule (TBP). Mutant analysis suggested that TBP hydrolysis was not attributable to a previously documented acid phosphatase (monoesterase). Purified monoesterase had little activity against phospho di- and triesters, had no requirement for Mg²⁺ or Mn²⁺, and was EDTA-resistant. Conversely, TBP cleavage by immobilized cells was enhanced by Mg²⁺, and ininhibited by Mn²⁺ and EDTA. A separate phosphotri/diesterase was implicated.     

Disproportionation of 2,5-dichlorosemiquinone radicals in benzene according to unsteady-state kinetic data for the chain reaction between 2,5-dichlorohydroquinone and <Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>′-diphenyl-1,4-benzoquinone diimine

A method for determining the rate constant of disproportionation of 2,5-dichlorosemiquinone radicals (k ₆) from unsteady-state kinetic data for the initiated chain reaction of N,N′-diphenyl-1,4-benzoquinone diimine with 2,5-dichlorohydroquinone have been developed, and two variants of this method are presented. The method is based on the study of the unsteady-state disappearance kinetics of one of the initial reactants (quinone diimine) in its initiated chain reaction with hydroquinone. The unsteadiness of the reaction is due to the presence of semiquinone radicals or initiator radicals accumulated before the start of the reaction at a concentration exceeding the steady-state concentration of semiquinone radicals in the chain reaction. The variants of the method differ in the order of mixing the reactants and initiator, on which the nature and concentration of the radicals accumulated in the system before the reaction depend. In the first variant, a quinone diimine + initiator solution is initially prepared and initiator radicals are accumulated. Hydroquinone is added to this solution (start of the reaction). In the second variant, a hydroquinone + initiator solution is initially prepared and semiquinone radicals from hydroquinone are accumulated. Quinone imine is then added to the solution (start of the reaction). The disproportionation rate constant of semiquinone radicals (k ₆) is derived from the dependence of the decrease in the quinone imine concentration in a certain short time (∼20 s) after the start of the reaction on the initiation rate. The rate constant k ₆ in benzene is (7.3 ± 3.7) × 10⁶ l mol⁻¹ s⁻¹ according to the first variant of the method and (5.0 ± 2.2) × 10⁶ l mol⁻¹ s⁻¹ according to the second one.     

New methodologies in trace analysis of volatile organic compounds

Two methods for sampling and concentration of volatile organic compounds are reported. In the first method, traps coated with a very thick film (ca. 100 μm) of cross-linked silicone stationary phase are employed. Such thick films can be prepared with a modified dynamic coating procedure, which is briefly described. The low phase ratio traps can be utilized for enrichment of volatiles from gaseous as well as aqueous matrices. The second technique is based on chromatographic evaporation of a solvent in a capillary tube, where the process is sustained by a repeated sample injection and a cyclic flow reversal. In this way, large solvent volumes can be handled by a small volume system. Under optimal conditions, when using a solvent barrier, quantitative recovery is possible even for compounds of comparatively high volatility. Another important application of the technique is extraction of trace components from gases such as headspace samples, polluted air, etc.     

Applicability of the Levich Equation for a Two-Phase Solution in the Rotating Disk Electrode System

The mass-transter characteristics of a two-phase system formed by mixing a fixed quantity (20 v/v%) of organic solvent with an aqueous ferricyanide electrolyte solution in an RDE system were studied. The Levich eqution, I₁ = 0.62 nFAC_bD^2/3v^?1/6_ω^1/2, was found to be applicable to the two-phase system with only a minor modification in the angular velocity (ω) at Reynolds numbers between 3–5 × 10⁴. The experimental results indicate that the interfacial tension is the most important variable for the two-phase system. One group of organic solvents with smaller interfacial tension, such as benzene or toluene, needs a modification of the Levich equation by replacing the observed angular velocity (ω_o) with the true angular velocity (ω_t) which was observed to be 1.1 times the observed angular velocity. For the other group with larger interfacial tension, such as n-hexane or cyclohexane, there is no need to modify the observed angular velocity. In other words, the Levich equation may be expressed as I₁ = 0.65 nFAC_bD^2/3v^?1/6ω^1/2 for two-phase solution if the interfacial tension is smaller than 37.0 dyne/cm.     

Solvatochromism of the π* ← n transition of acetone by combined quantum mechanical—classical mechanical calculations

The solvent shift of the π* ← n transition of acetone in water, acetonitrile, and tetrachloromethane was calculated in a combined quantum mechanical—classical mechanical approach, using both dielectric continuum and explicit, polarizable molecular solvent models. The explicit modeling of solvent polarizability allows for a separate analysis of electrostatic, induction, and dispersion contributions to the shifts. The calculations confirm the qualitative theories about the mechanisms behind the blue shift in polar solvents and the red shift in nonpolar solvents, the solvation of the ground state due to electrostatic interactions being preferential in the former, and favorable dispersion interaction with the excited state, in the latter case. Good quantitative agreement for the solvent shift between experiment (+1,700, +400, and −350 cm⁻¹ in water, acetonitrile, and tetrachloromethane, respectively) and the explicit solvent model (+1,821, +922, and −381 cm⁻¹) was reached through a modest Monte Carlo sampling of the solvent degrees of freedom. A consistent treatment of the solvent could only be realized in the molecular solvent model. The dielectric-only model needs reparameterization for each solvent. © 1996 John Wiley & Sons, Inc.     

Lattice Monte Carlo investigations on copolymer systems, 3. Alternating and random copolymers

Alternating and random copolymers in dilute solution are investigated by means of Monte Carlo simulations on a cubic lattice. Each molecule consists of an equal number of A and B segments, either randomly distributed along the chain or forming an alternating sequence. The energy parameters chosen represent selective solvent conditions (the solvent is a good one for monomers of type A and a θ-solvent for B; between A and B repulsive interactions are operative). Comparison with di- and triblock copolymers of equal overall composition reveals that the behaviour of random or alternating copolymers (subject to the same selective solvent) is quite different. Their properties rather resemble those of homopolymers in a solvent of intermediate quality. The absolute chain dimensions (e.g. the mean square radius of gyration, 〈s²〉, and the mean square end-to-end distance, 〈h²〉) of random and alternating copolymers as well as their scaling exponents are significantly larger than those of block copolymers. The ratio between 〈h²〉 and 〈s²〉 as well as the shape of the polymer (expressed by the asphericity δ) are similar to those of athermal polymers indicating that there is no pronounced selectivity of the solvent. In contrast to block copolymers, these parameters exhibit no significant chain-length dependence. The number of the various types of polymer-polymer contacts (A-A, B-B and A-B) is almost independent of the type of contact at least for the solvent conditions investigated. This is in contrast to block copolymers where A-B contacts are widely suppressed and where the number of B-B contacts is approximately twice as high as that of A-A contacts.     

A simple and fast micromethod for the analysis of polychlorinated biphenyls in air by sorbent enrichment and ultrasound-assisted solvent extraction

A combination of sorbent enrichment and ultrasound-assisted solvent extraction has been used to determine polychlorinated biphenyls in air. Analytes were sampled by pumping a known volume of air through a porous polymer (Tenax TA). The enriched adsorbent was transferred into a glass vial, and ultrasound-assisted extraction of the analytes was then performed in n-hexane. Quantification was carried out by using gas chromatography coupled to tandem mass spectrometry. Breakthrough volume of the sampling step was studied, indicating that 10 m³ of air could be processed without losses of the most volatile compounds. Good recoveries (75–96%) were obtained, and limits of detection at the sub ng m^–3 were achieved for all the analytes. The proposed method is very simple and fast, avoiding the use of large solvent volumes and time-consuming preconcentration steps.     

Multivariate statistical treatment of solvent effects in the photoreduction of CoIII(En)2(Br)(RC6H4NH2)2+ complexes in aqua-organic solvent media

Ultraviolet photolysis (λ = 254 nm) studies were carried out for a series of cobalt(III) complexes, Co^III(En)₂(Br)(RC₆H₄NH₂)²⁺, where R = m-OMe, p-F, H, m-Me, p-Me, p-OEt, and p-OMe, in various compositions of water-methanol/1,4-dioxane mixtures (0, 5, 10, 15, 20, 25, and 30 vol % organic cosolvent) at two different temperatures (287 and 300 K). The ligand-to-metal charge-transfer excited state produced in the excitation of the complex initially generated a solvent-caged {Co^II; ligand radical} pair, which eventually undergoes recombination/separation into products. The quantum yield sharply increased from a mixture containing a lower mole fraction of organic cosolvent (x _org) to higher one. In other words, when x _org in the mixture increases, a steady increase in the quantum yield is observed. The quantum yield of Co^III(En)₂(Br)(RC₆H₄NH₂)²⁺ in various solvent mixtures is found to exhibit a linear (logΦ_Co(II) − 1/ε_r) dependence. This is consistent with solvation or solvent cage effect, which may be nonspecific, specific, or both. In order to throw light on these effects, a phenomenological model of solvent effects was applied. Therefore, the quantum yield values have been correlated statistically with some success containing different solvent parameters. The solvent parameters considered in this work are Grunwald-Winstein’s Y, Krygowski-Fawcett’s E _T ^N and DN ^N along with Kamlet-Taft’s α, β, π* parameters. The regression model proposed is Y _S = Y ₀ + Σ _{i = 1} ⁿ a _i X _i , where Y_S is the solvent-dependent property (here logΦ_Co(II)) in a given solvent; Y ₀ is the statistical quantity corresponding to the value of property in the reference solvent; X ₁, X ₂, X ₃ … are explanatory variables, the solvent parameters, which can explain the various solvation effects on reactants/{Co^II; ligand radical} pair, and a ₁, a ₂, a ₃… etc., are the regression coefficients. The coefficient values can be quantified to measure the relative importance of solvent effects on the physicochemical quantity, that is, the photoreduction yields in the present investigation. The text was submitted by the author in English.     

15N NMR spectroscopy 24—chemical shifts and coupling constants of α-amino acid N-carboxyanhydrides and related heterocycles

The chemical shifts of amino acid N-carboxyanhydrides (NCAs) and cyclic or linear urethanes are less sensitive to solvent effects than those of amides and lactams. The values of the one-bond ¹⁵N? ¹H coupling constants depend on the solvent and are 5-8 Hz larger than those of ureas and amides. The ¹⁵N? ¹³C coupling constant of the N? CO group is also unusually high, while that of the N—CH group lies within the range known for N-acylated aliphatic amines. The one-bond ¹⁵N? ¹³C coupling constant was found to be insensitive to conformational changes.