Molecular dynamics study of hydration in ethanol-water mixtures using a polarizable force field

The abnormal physicochemical characteristics of ethanol solvation in water are commonly attributed to the phenomenon of hydrophobic hydration. To investigate the structural organization of hydrophobic hydration in water-ethanol mixtures, we use molecular dynamics simulations based on detailed atomic models. Induced polarization is incorporated into the potential function on the basis of the classical Drude oscillator model. Water-ethanol mixtures are simulated at 11 ethanol molar fractions, from 0.05 to 0.9. Although the water and ethanol models are parametrized separately to reproduce the vaporization enthalpy, static dielectric constant, and self-diffusion constant of neat liquids at ambient conditions, they also reproduce the energetic and dynamical properties of the mixtures accurately. Furthermore, the calculated dielectric constant for the various water-alcohol mixtures is in excellent agreement with experimental data. The simulations provide a detailed structural characterization of the mixtures. A depletion of water-water hydrogen bonding in the first hydration shell of ethanol is compensated by an enhancement in the second hydration shell. The structuring effect from the second solvation shell gives rise to a net positive hydrogen-bonding excess for ethanol molar fractions up to approximately 0.5. For larger molar fractions, the second hydration shell is not sufficiently populated to overcome the net H-bond depletion from the first shell.     

A theoretical study of aqueous solvation of K comparing ab initio, polarizable, and fixed-charge models

The hydration of K(+) is studied using a hierarchy of theoretical approaches, including ab initio Born-Oppenheimer molecular dynamics and Car-Parrinello molecular dynamics, a polarizable force field model based on classical Drude oscillators, and a nonpolarizable fixed-charge potential based on the TIP3P water model. While models based more directly on quantum mechanics offer the possibility to account for complex electronic effects, polarizable and fixed-charges force fields allow for simulations of large systems and the calculation of thermodynamic observables with relatively modest computational costs. A particular emphasis is placed on investigating the sensitivity of the polarizable model to reproduce key aspects of aqueous K(+), such as the coordination structure, the bulk hydration free energy, and the self diffusion of K(+). It is generally found that, while the simple functional form of the polarizable Drude model imposes some restrictions on the range of properties that can simultaneously be fitted, the resulting hydration structure for aqueous K(+) agrees well with experiment and with more sophisticated computational models. A counterintuitive result, seen in Car-Parrinello molecular dynamics and in simulations with the Drude polarizable force field, is that the average induced molecular dipole of the water molecules within the first hydration shell around K(+) is slightly smaller than the corresponding value in the bulk. In final analysis, the perspective of K(+) hydration emerging from the various computational models is broadly consistent with experimental data, though at a finer level there remain a number of issues that should be resolved to further our ability in modeling ion hydration accurately.     

Letter to the Editor: Stockwell and Wavelet Transforms

Recent applied literature introduces the Stockwell transform (S-transform) as a new approach to time-frequency analysis. It is the purpose of this letter to encourage the interaction between the wavelet and the Stockwell communities by demonstrating that—up to minor modifications—the S-transform is a special case of the well-known continuous wavelet transform via a Morlet-type mother wavelet, with the features of a linear frequency scale, and an amplitude and modulation adjustment in phase space. The extensive research and applications obtained for the continuous wavelet transform can therefore be directly applied to the Stockwell domain.     

NCO quantitative measurement in premixed low pressure flames by combining LIF and CRDS techniques

NCO is a short-lived species involved in NO(x) formation. It has never been quantitatively measured in flame conditions. In the present study, laser-induced fluorescence (LIF) and cavity ring-down spectroscopy (CRDS) were combined to measure NCO radical concentrations in premixed low-pressure flames (p = 5.3 kPa). NCO LIF excitation spectrum and absorption spectrum (using CRDS) measured in a stoichiometric CH(4)/O(2)/N(2)O/N(2) flame were found in good agreement with a simulated spectrum using PGOPHER program that was used to calculate the high-temperature absorption cross section of NCO in the A(2)Σ(+)-X(2)Π transition around 440.479 nm. The relative NCO-LIF profiles were measured in stoichiometric CH(4)/O(2)/N(2)O/N(2) flames where the ratio N(2)O/O(2) was progressively decreased from 0.50 to 0.01 and in rich CH(4)/O(2)/N(2) premixed flames. Then, the LIF profiles were converted into NCO mole fraction profiles from the absorption measurements using CRDS in a N(2)O-doped flame.     

Laser-induced incandescence technique to identify soot nucleation and very small particles in low-pressure methane flames

This paper presents the study we carried out on the formation of soot particles in low-pressure premixed CH₄/O₂/N₂ flames by using Laser-Induced Incandescence (LII). Flames were stabilised at 26.6 kPa (200 torr). Four different equivalence ratios were tested (Φ = 1.95, 205, 2.15 and 2.32), Φ = 1.95 corresponding to the equivalence ratio for which LII signals begin to be measurable along the flame. The evolution of the LII signals with laser fluence (fluence curve), time (temporal decay) and emission wavelength is reported at different heights above the burner. We specifically took advantage of the low-pressure conditions to probe with a good spatial resolution the soot inception zone of the flames. Significant different behaviours of the fluence curves are observed according to the probed region of the flames and Φ. In addition, while the surface growth process is accompanied by an increase in the LII decay-times (indicator of the primary particle diameter) at higher Φ, decay-times become increasingly short at lower Φ reaching a constant value along the flame at Φ = 1.95. These behaviours are consistent with the detection of the smallest incandescent particles in the investigated flames, these particles having experienced very weak surface growth. Flame modelling including soot formation has been implemented in flames Φ = 2.05 and 2.32. Experimental quantitative soot volume fraction profiles were satisfactorily reproduced by adjusting the fraction of reactive soot surface available for reactions. The qualitative variation of the computed soot particle diameter and the relative weight of surface growth versus nucleation were consistent with the experimental observations.     

Synthesis of 2-hydroxy-3-substituted naphthoquinones using the Heck reaction

An efficient Heck coupling of 2-hydroxy-3-iodo-naphthoquinone with a series of electron-deficient alkenes in aqueous solution has been accomplished. The method is characterized by simple conditions and facile work-up to isolate the products in good to excellent yields. The products contain the motif present in several naphthoquinone pigments but with enhanced polarity.     

Reflections on the almost Mathieu operator

An explicit derivation of a tridiagonal matrix form for the almost Mathieu operator (Harper's equation) is obtained via conjugation with a reflection operator, valid for all rational values of the rotation parameter. The difference between even and odd values of the denominator is highlighted. This tridiagonal form is useful for numerical eigenvalue computations; some Matlab code is included.This research was supported in part by an NSERC individual research grant.     

Spectroscopic and structural impact of a stem base-pair change in DNA hairpins: GTTC-ACA-GAAC versus GTAC-ACA-GTAC

Successive investigations over the last decade have revealed and confirmed a stable loop closure in a family of d-[GTAC-5Pur6N7N-GTAC] hairpins, where 5Pur6N7N is a AAA, GAG and AXC loop (X being any nucleotide). The trinucleotide loop is characterized by a well defined 5Pur-7N mispairing mode, and by upfield chemical shifts for three sugar protons of the apical nucleotide 6N. The GTTC-ACA-GAAC DNA hairpin, of interest for its likely involvement in Vibrio cholerae genome mutations, has now been investigated. The GTAC-ACA-GTAC DNA hairpin has also been studied because it is intermediate between the other structures, as it contains the loop of the hairpin under consideration and the stem of the above family. The two hairpins with the ACA loop are stable. They show the same mispairing mode and similar upfield shifts as the previous family, but GTTC-ACA-GAAC seems to be slightly less compact than any other. GTTC-ACA-GAAC is remarkable in that it exhibits a B(II) character for the phosphate-ester conformation at 8Gp9A, together with a swing of the upper hairpin into the major groove that, in particular, brings 6CH1' roughly as close to 7AH2 as to 6CH6. These unexpected structural features are qualitatively deduced from (1)H and (31)P NMR spectra, and confirmed by Raman spectroscopy. This comparative study shows that not only the loop sequence but also the stem sequence may control hairpin structures.