Ab initio calculations and molecular mechanics (MM3) force field development for ammonium and protonated aliphatic amines

The geometries and vibrational frequencies of 11 training molecules containing the ammonium ion moiety were calculated at the MP2/6-31+G* level of theory. Various torsional energy profiles were also calculated using this basis set. From those ab initio calculations, a molecular mechanics (MM3) force field was developed using our Parameter Analysis and Refinement Toolkit System (PARTS). Using this set of parameters, the MM3 force field was found to well reproduce the molecular geometries and vibrational spectra for the all training molecules. CPU time was reduced from days to seconds. The availability of this new force field dramatically increases the feasibility of the computer-assisted drug design involving ammonium and protonated amino groups. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18 : 1371–1391, 1997     

Comparison of rigid and flexible simple point charge water models at supercritical conditions

This study investigates the differences between the predictions of various properties of rigid and flexible simple point charge water models at supercritical conditions. Molecular dynamics simulations were conducted for supercritical water in a temperature range of 773–1073 K and densities in the range 115–659 kg/m³. We present thermodynamic data, pair correlation functions, self-diffusivity, power spectra, dielectric constants, and variaous measures of hydrogen bonding at different state conditions. The flexible water model performs better in predicting the pressures along the supercritical isotherms simulated. Agreement between experimental and calculated dielectric constants is superior for the flexible water model, particularly at high densities. The flexible model exhibits a greater degree of hydrogen bonding and more persistent hydrogen bonds than does the rigid model. The structural features of supercritical water at high densities are identical for the two water models. At low densities, however, the flexible potential exhibits pair correlation functions with enhanced peaks. Inclusion of flexibility in the potential model does not result in a significant shift in the position of the rotational/librational peak in the power spectrum. The self-diffusivities obtained from the simulations are within the accuracy of the experimental values for both the rigid and flexible models. On balance the inclusion of flexibility improves agreement with the properties of real supercritical water while incurring little or no additional computational burden. © 1996 by John Wiley & Sons, Inc.     

Electrophysiological Responses of Bactrocera kraussi (Hardy) (Tephritidae) to Rectal Gland Secretions and Headspace Volatiles Emitted by Conspecific Males and Females

Pheromones are biologically important in fruit fly mating systems, and also have potential applications as attractants or mating disrupters for pest management. Bactrocera kraussi (Hardy) (Diptera: Tephritidae) is a polyphagous pest fruit fly for which the chemical profile of rectal glands is available for males but not for females. There have been no studies of the volatile emissions of either sex or of electrophysiological responses to these compounds. The present study (i) establishes the chemical profiles of rectal gland contents and volatiles emitted by both sexes of B. kraussi by gas chromatography–mass spectrometry (GC–MS) and (ii) evaluates the detection of the identified compounds by gas chromatography–electroantennogram detection (GC–EAD) and –electropalpogram detection (GC–EPD). Sixteen compounds are identified in the rectal glands of male B. kraussi and 29 compounds are identified in the rectal glands of females. Of these compounds, 5 were detected in the headspace of males and 13 were detected in the headspace of females. GC–EPD assays recorded strong signals in both sexes against (E,E)-2,8-dimethyl-1,7-dioxaspiro[5.5]undecane, 2-ethyl-7-mehtyl-1,6-dioxaspiro[4.5]decane isomer 2, (E,Z)/(Z,E)-2,8-dimethyl-1,7-dioxaspiro[5.5]undecane, and (Z,Z)-2,8-dimethyl-1,7-dioxaspiro[5.5]undecane. Male antennae responded to (E,E)-2,8-dimethyl-1,7-dioxaspiro[5.5]undecane, 2-methyl-6-pentyl-3,4-dihydro-2H-pyran, 6-hexyl-2-methyl-3,4-dihydro-2H-pyran, 6-oxononan-1-ol, ethyl dodecanoate, ethyl tetradecanoate and ethyl (Z)-hexadec-9-enoate, whereas female antennae responded to (E,E)-2,8-dimethyl-1,7-dioxaspiro[5.5]undecane and 2-methyl-6-pentyl-3,4-dihydro-2H-pyran only. These compounds are candidates as pheromones mediating sexual interactions in B. kraussi.     

Unprecedented examples of double-addition of aromatic amines across a ruthenium(II)-coordinated nitrile function: Isolation and X-ray structures of ruthenium complexes of amidinate and cyclometalated amidine

The present report examplifies a novel type of aromatic amine addition reactions at a ruthenium(II) complexed acetonitrile. The electrophilic cationic complex, cis-[L₂Ru(CH₃CN)₂](ClO₄)₂ (1) [L = 2-(phenylazo)pyridine] reacts with aromatic primary amines only in neat to produce a violet amidinate complex, [L₂Ru-N(Ar)-C(CH₃)-N(Ar)]⁺ (2) of ruthenium(II). Along with it a blue ortho-metalated ruthenium(II) amidine complex, [L₂Ru-N(H)C(CH₃)-N(H)Ar]⁺ (3) is also formed. X-ray structures of the two representative complexes are reported. The transformation 1 → 2 is unprecedented, involves multiple steps and occurs with addition of two equivalents of ArNH₂ across a coordinated nitrile function. In this complex, amidinate ligand binds to ruthenium(II) center as a σ,σ symmetrical bidentate chelate. The formation of 3 is a combination of nucleophilic amine addition and cyclometalation. ¹H and ¹³C NMR spectra of the products are examined, which are consistent with their formulations and structures. Optical spectra and redox properties of the newly synthesized complexes are reported. Visible range spectra of 2 and 3 are dominated by moderately intense metal-to-ligand charge transfer transitions. The complexes show multiple redox responses. The anodic potential response occurs at a high positive potential, which is attributed to a Ru(II)/Ru(III) couple. The cathodic potential responses are due to reductions of the coordinated diazo ligands.     

Kinetics and mechanism of tetrahydrofuran synthesis via 1,4-butanediol dehydration in high-temperature water

We conducted an experimental investigation into the kinetics and mechanism of tetrahydrofuran synthesis from 1,4-butanediol via dehydration in high-temperature liquid water (HTW) without added catalyst at 200-350 degrees C. The reaction was reversible, with tetrahydrofuran being produced at an equilibrium yield of 84% (at 200 degrees C) to 94% (at 350 degrees C). The addition of CO2 to the reaction mixture increased the reaction rate by a factor of 1.9-2.9, because of the increase in acidity resulting from the formation and dissociation of carbonic acid. This increase was much less than that expected (factor of 37-60) from a previously suggested acid-catalyzed mechanism. This disagreement prompted experiments with added acid (HCl) and base (NaOH) to investigate the influence of pH on the reaction rate. These experiments revealed three distinct regions of pH dependence. At high and low pH, the dehydration rate increased with increasing acidity. At near-neutral pH, however, the rate was essentially insensitive to changes in pH. This behavior is consistent with a mechanism where H2O, in addition to H+, serves as a proton donor. This work indicates that the relatively high native concentration of + (large KW), which has commonly been thought to lead to the occurrence of acid-catalyzed reactions in HTW without added catalyst, does not explain the dehydration of 1,4-butanediol in HTW without catalyst. Rather, H2O serves directly as the proton donor for the reaction.     

The response of a spherical tissue-equivalent proportional counter to different heavy ions having similar velocities

A tissue-equivalent proportional counter (TEPC) has been used as a dosimeter in mixed radiation fields. Since it does not measure LET directly, the response function must be characterized in order to estimate quality factor and thus equivalent dose for the incident radiation. The objectives of this study were to measure the response of a spherical TEPC for different high-energy heavy ions (HZE) having similar velocity and to determine how quality factors can be determined. Data were obtained at the HIMAC heavy ion accelerator for ⁴He and ¹²C at (β=0.59) and ¹²C, ¹⁶O, ²⁸Si and ⁵⁶Fe at (β=0.70). A particle spectrometer recorded the charge and position of each incident beam particle. Events with low energy deposition were observed for particles that passed through the wall of the TEPC but not through the sensitive volume. The frequency averaged lineal energy, , was always less than the LET of the incident particles. The dose averaged lineal energy, , was approximately equal to LET for particles with LET greater than 10 keV/μm, whereas was larger than LET for the lighter particles with lower LET. Part of this effect is due to detector resolution and energy straggling that increases the variance of the response function. Although the TEPC is not a LET spectrometer, it can provide real time measurements of dose and provide estimates of quality factors for HZE particles using averaged values of lineal energy.     

A Bioinspired Polymeric Template for 1D Assembly of Metallic Nanoparticles,Semiconductor Quantum Dots,and Magnetic Nanoparticles

A precise control of metallic‐nanoparticle assembly is highly critical for the realization of tangible, high‐performance devices or materials. Until recently, nanoparticle assembly using 1D templates had been limited to a narrow spectrum of nanoparticles as it was mostly dependent on the surface chemistry of the nanoparticles used. Inspired by the universal adhesive properties of mussels, we demonstrate a universal polymeric template for 1D assembly of various nanoparticles including, gold nanoparticles, iron oxide nanoparticles, and quantum dots. We find that the length of the 1D assembly is tunable using hyaluronic acid‐graft‐catechol templates with various contour lengths.

     

The relative isotopic abundance (δ13C, δ15N) during composting of agricultural wastes in relation to compost quality and feedstock

Variations in the relative isotopic abundance of C and N (δ¹³C and δ¹⁵N) were measured during the composting of different agricultural wastes using bench-scale bioreactors. Different mixtures of agricultural wastes (horse bedding manure?+?legume residues; dairy manure?+?jatropha mill cake; dairy manure?+?sugarcane residues; dairy manure alone) were used for aerobic–thermophilic composting. No significant differences were found between the δ¹³C values of the feedstock and the final compost, except for dairy manure?+?sugarcane residues (from initial ratio of ?13.6?±?0.2?‰ to final ratio of ?14.4?±?0.2?‰). δ¹⁵N values increased significantly in composts of horse bedding manure?+?legumes residues (from initial ratio of +5.9?±?0.1?‰ to final ratio of +8.2?±?0.5?‰) and dairy manure?+?jatropha mill cake (from initial ratio of +9.5?±?0.2?‰ to final ratio of +12.8?±?0.7?‰) and was related to the total N loss (mass balance). δ¹³C can be used to differentiate composts from different feedstock (e.g. C₃ or C₄ sources). The quantitative relationship between N loss and δ¹⁵N variation should be determined.