Measuring coexisting densities from a two-phase molecular dynamics simulation by voronoi tessellations

A new algorithm is presented that allows for the determination of bulk liquid and vapor densities from a two-phase Molecular Dynamics (2phiMD) simulation. This new method does not use any arbitrary cutoffs for phase definitions; rather it uses single-phase simulations as a self-consistency check. The method does not use any spatial bins for generating histograms of local properties, thereby avoiding the statistical issues associated with bins. Finally, it allows one to approach very close to the critical point. The new method utilizes Voronoi tessellations to determine the molecular volume of every point at every instance in a molecular dynamics simulation. Since the molecular volume is calculated throughout the simulation, statistical parameters such as the average molecular volume and average molecular variance are easy to obtain. To define the phases, the normalized variance of the molecular volume from 1phiMD and 2phiMD is used as a self-consistency check. The new method gives new insight into the nature of the near-subcritical fluid. The critical properties from this analysis are T(c) = 1.293 and rho(c) = 0.313. Direct simulation of the two-phase system was performed up to a temperature of 1.292. The results show excellent agreement to experimental results and Gibbs Ensemble Monte Carlo for coexisting densities. We see that well below the critical temperature, some particles are neither liquid nor vapor. These interfacial particles are primarily, but not exclusively, concentrated at the bulk interface. However, as we approach the critical point, some particles are considered both liquid and vapor. These interfacial particles are distributed through the system.     

Site-specific incorporation of a (19)F-amino acid into proteins as an NMR probe for characterizing protein structure and reactivity

19F NMR is a powerful tool for monitoring protein conformational changes and interactions; however, the inability to site-specifically introduce fluorine labels into proteins of biological interest severely limits its applicability. Using methods for genetically directing incorporation of unnatural amino acids, we have inserted trifluoromethyl-l-phenylalanine (tfm-Phe) into proteins in vivo at TAG nonsense codons with high translational efficiency and fidelity. The binding of substrates, inhibitors, and cofactors, as well as reactions in enzymes, were studied by selective introduction of tfm-Phe and subsequent monitoring of the 19F NMR chemical shifts. Subtle protein conformational changes were detected near the active site and at long distances (25 Angstrom). 19F signal sensitivity and resolution was also sufficient to differentiate protein environments in vivo. Since there has been interest in using 19F-labeled proteins in solid-state membrane protein studies, folding studies, and in vivo studies, this general method for genetically incorporating a 19F-label into proteins of any size in Escherichia coli should have broad application beyond that of monitoring protein conformational changes.     

The effects of dissolved halide anions on hydrogen bonding in liquid water

It is widely believed that the addition of salts to water engenders structural changes in the hydrogen-bond network well beyond the adjacent shell of solvating molecules. Classification of many ions as "structure makers" and "structure breakers" has been based in part on corresponding changes in the vibrational spectra (Raman and IR). Here we show that changes in O-H vibrational spectra induced by the alkali halides in liquid water result instead from the actions of ions' electric fields on adjacent water molecules. Computer simulations that accurately reproduce our experimental measurements suggest that the statistics of hydrogen-bond strengths are only weakly modified beyond this first solvation shell.     

Examination of analyte partitioning to monocationic and dicationic imidazolium-based ionic liquid aggregates using solid-phase microextraction-gas chromatography

Solid phase microextraction coupled to gas chromatography has been used to study the partitioning behaviour of several analytes to four monocationic and two dicationic imidazolium-based ionic liquid (IL) aggregates. The 14 different analytes studied consisted of aliphatic hydrocarbons, polycyclic aromatic hydrocarbons, phenols, and esters. The obtained partition coefficients for analytes that exhibited partitioning into the IL-aggregates ranged from 30 to 5200. Hydrophobic analytes (with octanol-water partition coefficients higher than 300) appear to be preferably extracted over more polar analytes revealing the possibility of carrying out selective extractions using these aggregate systems. Monocationic IL-aggregates generally exhibited higher partition coefficients compared to analogous dicationic ILs. The micellar shape of the IL-aggregates also influences the extent of analyte partitioning.     

The effect of two distinct fast time scales in the rotating,stratified Boussinesq equations: variations from quasi-geostrophy

Inspired by the use of fast singular limits in time-parallel numerical methods for a single fast frequency, we consider the limiting, nonlinear dynamics for a system of partial differential equations when two fast, distinct time scales are present. First-order slow equations are derived via the method of multiple time scales when the two small parameters are related by a rational power. We find that the resultant system depends only on the relationship of the two fast time scales, i.e. which fast time is fastest? Using the theory of cancellation of fast oscillations, we show that with the appropriate assumptions on the nonlinear operator of the full system, this reduced slow system is exactly that which the solution will converge to if each asymptotic limit is considered sequentially. The same result is also obtained via the method of renormalization. The specific example of the rotating, stratified Boussinesq equations is explored in detail, indicating that the most common distinguished limit of this system—quasi-geostrophy, is not the only limiting asymptotic system.     

Buffer Standards for pH Measurement of N-(2-Hydroxyethyl)piperazine-N′-2-ethanesulfonic Acid (HEPES) for I=0.16 mol⋅kg−1 from 5 to 55 °C

The values of the second dissociation constant, pK ₂, of N-(2-hydroxyethyl) piperazine-N′-2-ethanesulfonic acid (HEPES) have been reported at twelve temperatures over the temperature range 5 to 55 °C, including 37 °C. This paper reports the results for the pa _H of eight isotonic saline buffer solutions with an I=0.16 mol⋅kg⁻¹ including compositions: (a) HEPES (0.01 mol⋅kg⁻¹) + NaHEPES (0.01 mol⋅kg⁻¹) + NaCl (0.15 mol⋅kg⁻¹); (b) HEPES (0.02 mol⋅kg⁻¹) + NaHEPES (0.02 mol⋅kg⁻¹) + NaCl (0.14 mol⋅kg⁻¹); (c) HEPES (0.03 mol⋅kg⁻¹) + NaHEPES (0.03 mol⋅kg⁻¹) + NaCl (0.13 mol⋅kg⁻¹); (d) HEPES (0.04 mol⋅kg⁻¹) + NaHEPES (0.04 mol⋅kg⁻¹) + NaCl (0.12 mol⋅kg⁻¹); (e) HEPES (0.05 mol⋅kg⁻¹) + NaHEPES (0.05 mol⋅kg⁻¹) + NaCl (0.11 mol⋅kg⁻¹); (f) HEPES (0.06 mol⋅kg⁻¹) + NaHEPES (0.06 mol⋅kg⁻¹) + NaCl (0.10 mol⋅kg⁻¹); (g) HEPES (0.07 mol⋅kg⁻¹) + NaHEPES (0.07 mol⋅kg⁻¹) + NaCl (0.09 mol⋅kg⁻¹); and (h) HEPES (0.08 mol⋅kg⁻¹) + NaHEPES (0.08 mol⋅kg⁻¹) + NaCl (0.08 mol⋅kg⁻¹). Conventional pa _H values, for all eight buffer solutions from 5 to 55 °C, have been calculated. The operational pH values with liquid junction corrections, at 25 and 37 °C have been determined based on the NBS/NIST standard between the physiological phosphate standard and four buffer solutions. These are recommended as pH standards for physiological fluids in the range of pH = 7.3 to 7.5 at I=0.16 mol⋅kg⁻¹.     

Determining the stoichiometry and binding constants of inclusion complexes formed between aromatic compounds and β-cyclodextrin by solid-phase microextraction coupled to high-performance liquid chromatography

The complexation of native β-cyclodextrin (CD) and seven aromatic compounds, namely, phenetole, toluene, m-xylene, naphthalene, biphenyl, fluorene and phenanthrene, has been studied for first time utilizing a solid-phase microextraction (SPME)–high-performance liquid chromatography (HPLC) method. The stoichiometries of the analyte:β-CD complexes were found to be either 1:1 or 1:2. The formation of 1:2 complexes was confirmed for naphthalene, biphenyl, fluorene, and phenanthrene only when utilizing relatively high concentrations of β-CD (up to 6.6 mM). The 1:2 stoichiometries were confirmed using the classical modified Benesi–Hildebrand (BH) method. The calculated binding constants for 1:1 stoichiometries (K₁) using the SPME method varied from 115.3 M⁻¹ for toluene to 3510 M⁻¹ for phenanthrene, whereas the corresponding values to the 1:2 stoichiometries (K₃) varied from 7.30 × 10⁵ M⁻² for biphenyl to 9.03 × 10⁶ M⁻² for naphthalene.     

Utilization of solid-phase microextraction–high-performance liquid chromatography in the determination of aromatic analyte partitioning to imidazolium-based ionic liquid micelles

A solid-phase microextraction (SPME)–high-performance liquid chromatography (HPLC) approach is used, for the first time, to study the partitioning behavior of eight aromatic analytes to three imidazolium-based ionic liquid micelles, namely, 1-hexadecyl-3-methylimidazolium bromide (HDMIm-Br), 1-hexadecyl-3-butylimidazolium bromide (HDBIm-Br), and 1,3-didodecylimidazolium bromide (DDDDIm-Br). The model used to calculate the partition coefficients is improved by determining the accurate critical micelle concentration (CMC) value of the studied IL-micelles, which considers the nature and amount of organic modifier used in the experiments. Proper CMC values in the model improve the quality of the results and decrease the differences between theoretical and experimental intercepts. Surface tensiometry has been utilized to determine the CMC values for the micelles at different acetonitrile contents (1% and 1.5%, v/v). The calculated partition coefficient values for polycyclic aromatic hydrocarbons (PAHs) oscillate between 631 and 5980, whereas aromatic analytes with a lower number of fused rings in their structures suffer non-partitioning to any of the IL-micelles. The obtained partition coefficients to IL-micelles were highest with the DDDDIm-Br IL and were always higher than those obtained with the traditional surfactant cetyltrimethyl ammonium bromide (CTAB).     

Influence of buffer composition on the capillary electrophoretic separation of carbon nanoparticles

Carbon nanoparticles obtained from the flame of an oil lamp were examined by means of capillary electrophoresis. The influence of buffer composition on the separation of the mixture of negatively charged carbon nanoparticles was studied by varying buffer selection, pH, and concentration. The electrophoretic pattern was affected by both the co- and counter-ion in the buffer solution, influencing selectivity and peak shape. The capillary electrophoretic separations at different pH revealed species with large electrophoretic mobilities under a wide range of pH. The mobility of selected species in the mixture of nanoparticles showed a strong dependence upon the solution ionic strength. The mobility of these nanoparticles as a function of ionic strength was compared to classical electrokinetic theory, suggesting that under the experimental conditions utilized, the species are small, highly charged particles with appreciable zeta potentials, even at low pH.