MD simulation of self-diffusion and structure in some n-alkanes over a wide temperature range at high pressures

Self-diffusion and structural properties of n-alkanes have been studied by molecular dynamics simulation in the temperature range between the melting pressure curve and 600 K at pressures up to 300 MPa. The simulated results of lower n-alkanes are in good agreement with the existing experimental data, and support the reliability of results of the simulations of self-diffusion coefficients obtained at the extreme conditions. We predict the self-diffusion coefficients for methane, ethane, propane and n-butane at the similar reduced temperatures and pressures to draw a comparison between them. Then the correlation between self-diffusion and structural properties are further investigated by calculating the coordination numbers. Moreover, we define four distances and their corresponding relative deviations to characterize the flexibility of long-chain n-alkanes. The simulated results show that the self-diffusion of n-alkane molecules is mainly affected by the close packing, and the flexibility has a strong impact on the self-diffusion of longer n-alkane molecules.

Molecular dynamics simulation of the reciprocal fused LiF–KBr mixture: local structure and self-diffusion coefficients

This paper describes the molecular dynamics simulation of the reciprocal fused LiF–KBr mixture, which is located above the critical mixing point, in the temperature range 1280–1450 K. The first coordination sphere is found to form as follows: a smaller ion is formed around a smaller counter-ion, and a larger ion is formed around a larger counter-ion. The calculated concentration dependence of the self-diffusion coefficients and the radial distribution functions of all ion pairs indicate that the degree of association of the Li–F pair increases as the lithium fluoride fraction in the mixture decreases.     

Volatile compounds detected in blood of drunk drivers by headspace/capillary gas chromatography/ion trap mass spectrometry.

As shown by others, ethanol and methanol appear in the breath of normals, and endogenous methanol becomes detectable also in the blood after intake of ethanol. In this study I have investigated whether low-molecular-weight volatile organics, other than methanol, arise in the blood of drunk drivers who had imbibed alcoholic beverages. To this end a method for searching for such compounds in the blood is described. It was based on headspace extraction, gas chromatographic separation on a DB-WAX capillary, and ion trap detection in the mass range 29-99 u. Detection limits, as defined by the analyte concentration that gives a signal equal to three times the standard deviation of the baseline noise, were estimated for the different mass numbers used in the substance search. Given the detection limits, presented as mmoles per litre (numbers within parentheses), in every drunk driver's blood with more than 10 mmol l-1 of ethanol between seven and nine different volatile substances were spotted. These were ethanol (0.15), 2-propanone (0.015), ethyl acetate (0.0005), 2-butanone (0.006), methanol (1.5), 2-propanol (0.06), ethanol (0.7), 2-butanol (0.03), and 1-propanol (0.03).     

A molecular dynamics study of liquid aliphatic alcohols: simulation of density and self-diffusion coefficient using a modified OPLS force field

A set of 13 aliphatic alcohols was modelled by molecular dynamics simulations at temperatures from 288 to 338 K using the optimised potential for liquid simulations (OPLS) united-atom force field, the OPLS all-atom force field and the OPLS all-atom force field with modified partial charges of the hydroxyl group. The set includes primary and secondary alcohols, and mono-, di- and trialcohols, and covers a broad range of polarities from log P = ? 0.74 (methanol) to log P = 2.9 (octanol). The density, the radial distribution function, the self-diffusion coefficient and the dielectric constant were evaluated. A long equilibration time of at least 50 ns and a large size of the molecular system of more than 75,000 atoms were used. Except for glycerol, the OPLS all-atom force field reliably reproduced the experimentally determined density with deviations of less than 4% over the whole temperature range. In contrast, the modelled self-diffusion coefficient deviated from its experimental value by up to 55%. To modify the force field, the partial charges of the hydroxyl group were varied by up to 3%. Using the modified OPLS force field, the deviation of the self-diffusion coefficients from their experimental values decreased to less than 19%, while the densities changed by less than 1%.     

Analysis of dissociation process for gas hydrates by molecular dynamics simulation

The dissociation processes of methane and carbon dioxide hydrates were investigated by molecular dynamics simulation. The simulations were performed with 368 water molecules and 64 gas molecules using NPT ensembles. The TraPPE (single-site) and 5-site models were adopted for methane molecules. The EPM2 (3-site) and SPC/E models were used for carbon dioxide and water molecules, respectively. The simulations were carried out at 270 K and 5.0 MPa for hydrate stabilisation. Then, temperature was increased up to 370 K. The temperature increasing rates were 0.1–20 TK/s. The gas hydrates dissociated during increasing temperature or at 370 K. The potential models of methane molecule did not much influence the dissociation process of methane hydrate. The mechanisms of dissociation process were analysed with the coordination numbers and mean square displacements. It was found that the water cages break down first, then the gas molecules escape from the water cages. The methane hydrate was more stable than the carbon dioxide hydrate at the calculated conditions.     

Studies on the effect of alcohols on the chiral discrimination mechanisms of amylose stationary phase on the enantioseparation of nebivolol by HPLC

The chiral recognition mechanism of amylose CSPs has been described by achieving the enantiomeric resolution of (+/-)-nebivolol on Chiralpak AD and Chiralpak AD-RH columns with methanol, ethanol, 1-propanol, 2-propanol, 1-butanol as mobile phases at different flow rates. The energies of interactions of methanol, ethanol, 1-propanol, 2-propanol and 1-butanol with both phases were calculated. The (+)-RRRS enantiomer eluted first when using methanol, ethanol and 1-propanol, while the elution order was reversed when using 2-propanol and 1-butanol as the mobile phases. It has been concluded that the reversal elution order observed was due in part to the chiral cavities on the amylose CSP which were responsible for the bondings of different magnitude between chiral stationary phase and enantiomers, which are influenced with the type of alcohol used as mobile phase on the conformation of the 3,5-dimethyl phenyl carbamate moiety on the pyranose ring system of the amylose.     

Continuous lipase-catalyzed esterification of soybean fatty acids under ultrasound irradiation

This work investigates the continuous production of alkyl esters from soybean fatty acid (FA) charges using immobilized Novozym 435 as catalyst. The experiments were performed in a packed-bed bioreactor evaluating the effects of FA charge to alcohol (methanol and ethanol) molar ratio, from 1:1 to 1:6, substrate flow rate in the range of 0.5–2.5 mL/min and output irradiation power up to 154 W, at fixed temperature of 65 °C, on the reaction conversion. Results showed that almost complete conversions to fatty acids ethyl esters were achieved at mild ultrasonic power (61.6 W), FA to ethanol molar ratio of 1:6, operating temperature (65 °C) and remained nearly constant for long-term reactions without negligible enzyme activity losses.     

Eutectic formation analysis of amino acid mixtures using molecular dynamics simulations

The mechanism of eutectic formation was investigated via computer-aided molecular dynamics techniques based on experimental results. The CBZ group mixtures CBZ-l-Asp/d-AlaNH2 x HCl/methanol, CBZ-l-Asp/l-PheOMe x HCl/methanol, and CBZ-l-Tyr/l-ArgNH2 x 2HCl/methanol formed transparent eutectic melts. The non-CBZ group mixtures l-Asp/d-AlaNH2 x HCl/methanol, l-Asp/l-PheOMe x HCl/methanol, and l-Tyr/l-ArgNH2 x 2HCl/methanol did not form eutectic melts. According to molecular dynamics simulation results, increase in the kinetic energy values of eutectic forming mixtures was much larger than the increase in potential energy over a temperature shift from 298 to 333 K. However, the results for non-eutectic forming mixtures were reversed. The Coulomb interaction energies of eutectic forming mixtures significantly decreased, because eutectic melting can increase the mobility of molecules in the mixtures. The enhancement of molecular mobility was confirmed by increased self-diffusion constant values, and the change of solid-to-liquid phase was detected by radial distribution function results. The periodic boundary conditions for calculation of molecular dynamics were found to be reliable.     

Effect of Biomass Pre-Treatment and Solvent Extraction on β-Carotene and Lycopene Recovery from Blakeslea trispora Cells

Abstract

The production of carotenoids from Blakeslea trispora cells in a synthetic medium has been reported, with the main products being β-carotene, lycopene, and γ-carotene. The effect of biomass pretreatment and solvent extraction on their selective recovery is reported here. Eight solvents of class II and III of the International Conference of Harmonization: ethanol, methanol, acetone, 2-propanol, pentane, hexane, ethyl acetate, and ethyl ether, and HPLC analysis were used for the evaluation of their selectivities towards the three main carotenoids with regard to different biomass pre-treatment. The average C_max values (maximum concentration of caronoids in a specific solvent) were estimated to 16 mg/L with the five out of eight solvents investigated, whereas methanol, pentane, and hexane gave lower values of 10, 11, and 9 mg/L, respectively. The highest carotenoid yield was obtained in the case of wet biomass, where 44–56% is recovered with one solvent and three extractions and the rest is recovered only after subsequent treatment with acetone; thus, four extractions of 2.5 h are needed. Two extractions of 54 min are enough to recover carotenoids from dehydrated biomass, with the disadvantage of a high degree of degradation. Our results showed that, for maximum carotenoid recovery, ethyl ether, 2-propanol, and ethanol could be successfully used with biomass without prior treatment, whereas fractions enriched in β-carotene or lycopene can be obtained by extraction with the proper solvent, thus avoiding degradation due to time-consuming processes.     

Molecular dynamics simulations of hydrogen storage capacity of few-layer graphene

The adsorption of molecular hydrogen on few-layer graphene (FLG) structures is studied using molecular dynamics simulations. The interaction between graphene and hydrogen molecules is described by the Lennard-Jones potential. The effects of pressure, temperature, number of layers in a FLG, and FLG interlayer spacing are evaluated in terms of molecular trajectories, binding energy, binding force, and gravimetric hydrogen storage capacity (HSC). The simulation results show that the effects of temperature and pressure can offset each other to improve HSC. An insufficient interlayer spacing (0.35 nm) largely limits the HSC of FLG because hydrogen adsorbed at the edges of the graphene prevents more hydrogen from entering the structure. A low temperature (77 K), a high pressure, a large number of layers in a FLG, and a large FLG interlayer spacing maximize the HSC.     

Predicted melt curve and liquid-state transport properties of TATB from molecular dynamics simulations

The melt curve and the liquid-state transport properties shear viscosity, self-diffusion coefficient and thermal conductivity of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) were predicted using all-atom molecular dynamics simulations. The TATB melt curve was obtained using solid–liquid coexistence simulations and is in good accord with the Simon–Glatzel equation. The temperature dependencies of the shear viscosity and self-diffusion coefficient are predicted to obey Arrhenius behaviour for pressures up to P = 20 kbar. The thermal conductivity has a linear temperature dependence for P < 15 kbar and a linear density (ρ) dependence for ρ > 1200 kg m^?3. At similar densities the shear viscosity of liquid TATB is close to the predictions for liquid nitromethane [58] but lower than the predictions for liquid HMX [24] and RDX [59]. The self-diffusion coefficient for TATB is predicted to be higher than predictions for nitromethane, HMX and RDX at similar densities. The conductivity of TATB is ≈20% greater than the conductivity of liquid HMX at a given density.     

Stress testing the ELBA water model

The ELBA coarse-grained model describes a water molecule as a single-site Lennard-Jones particle embedded with a point dipole. ELBA was previously reported to capture several properties of real water with relatively high accuracy, while being up to two orders of magnitude more computationally efficient than atomistic models. Here, we ‘stress test’ the ELBA model by investigating the temperature and pressure dependences of two most important water properties, the liquid density and the self-diffusion coefficient. In particular, molecular dynamics simulations are performed spanning temperatures from 268 K up to 378 K and pressures from 1 atm up to 4000 atm. Comparisons are made with literature data from experiments and from simulations of traditional three-site atomistic models. Remarkably, the ELBA results show an overall similar (and sometimes higher) accuracy with respect to the atomistic data. We also calculate a number of additional thermodynamic properties at ambient conditions, namely isothermal compressibility, shear viscosity, isobaric heat capacity, thermal expansion coefficient and melting point. The accuracy of ELBA is relatively good compared to atomistic and other coarse-grained models.     

Investigation of rubidium(I) ion solvation in liquid ammonia using QMCF-MD simulation and NBO analysis of first solvation shell structure

Rb(I) ion solvation in liquid ammonia has been studied by an ab initio quantum mechanical charge field molecular dynamics simulation, and the first solvation shell structure has been analyzed using natural bond orbital. The simulation was performed for an ion and 593 ammonia molecules in a box with a length of 29.03 Å corresponding to a liquid ammonia density of 0.69 g/mL at 235.16 K. The quantum mechanical calculation was carried out for atomic interactions in the radius of 6.4 Å from the ion using LANL2DZ ECP and DZP (Dunning) basis sets for Rb(I) ion and ammonia respectively. The trajectories of the simulation were analyzed in terms of radial, angular, and coordination number distribution functions, vibration, and mean residence time (MRT). Two solvation shell regions are observed for the Rb(I)-N as well as the Rb(I)-H. The maximum distance of Rb(I)-N in the first solvation shell is in accordance with experimental data where a coordination number of 8 is favorable. A non-single coordination number of the first and second shell indicates dynamic solvation structure. It is confirmed by frequent exchange ligand processes observed within a simulation time of 15 ps. The low stabilization energy of donor acceptor ion-ligand interaction with a small Wiberg bond index affirms that the Rb(I)-NH₃ interaction is weak electrostatically.     

Oxidation of ABTS by silicate-immobilized cytochrome c in nonaqueous solutions

Cytochrome c can be readily adsorbed onto mesoporous silicates at high loadings of up to 10 mmol g(-)(1) of silicate. The adsorbed protein retains its peroxidative activity, with no diffusional limitations being observed. The protein can be adsorbed onto the external surface of the silicate or, provided that the pore diameter is sufficiently large, into the channels. In aqueous buffer, the catalytic activity of the adsorbed protein (for the oxidation of ABTS) decreased with increasing temperature, with the decrease being less marked for cytochrome c held within the silicate channels. Similar results were obtained in 95% methanol. Analysis of kinetic data showed that significant increases in k(cat)/K(M) occurred in methanol, ethanol, and formamide, with slight decreases occurring in 1-methoxy-2-propanol. The observed increases were primarily a result of substantial increases in k(cat), while the results in 1-methoxy-2-propanol can be ascribed to increases in K(M). Resonance Raman spectroscopy indicated that the structure of the heme environment of the adsorbed protein was essentially unchanged, in aqueous buffer and in the nonaqueous solvents, methanol, 1-methoxy-2-propanol, and ethanol. In addition, Raman spectra of the lyophilized protein indicated that there were no apparent changes in the heme structure.     

Vapor–liquid equilibria and thermophysical behavior of the SPC-HW model for heavy water

The vapor–liquid coexistence curve of the simple point charge heavy-water model (SPC-HW), [J. Chem. Phys., 114, 8064–8067 (2001)] is determined by Gibbs Ensemble Monte-Carlo (GEMC) simulation. The estimated critical conditions of the model based on the Wegner-type expansion for the order parameters and the rectilinear diameter are ρ_c = 0.300 g/cc, T _c = 661 K and P _c = 156 bars. The dielectric constant determined by isothermal–isochoric molecular dynamics is underpredicted along the coexistence curve by 29–44% in comparison with the experimental values. The analysis of the orthobaric temperature dependence of the system microstructure, in terms of the three site–site radial distribution functions, indicates that the first coordination numbers for the oxygen–oxygen and the oxygen–deuterium interactions are ～4.3 ± 0.1 and ～1.9 ± 0.1 at T = 300 K, and decrease by 15 and 55%, respectively, at criticality. The dipole–dipole correlation functions show that the orientational order in heavy water is quickly lost beyond the first oxygen–oxygen coordination shell. The model's second virial coefficient is determined by Monte-Carlo integration and used to aid the interpretation of the predicted phase equilibrium results.     

Calculation of diffusion coefficient for supercritical carbon dioxide and carbon dioxide+naphthalene system by molecular dynamics simulation using EPM2 model

NVT ensemble molecular dynamics (MD) simulation has been applied to calculate the self-diffusion coefficients of carbon dioxide and the tracer diffusion coefficients of naphthalene in supercritical carbon dioxide. The simulation was carried out in the pressure range from 8 to 40 MPa. The elementary physical model proposed by Harris and Yung was adopted for carbon dioxide and some approximation models were used for naphthalene. The systems of MD simulation for carbon dioxide consist of 256 particles. One naphthalene molecule was added for carbon dioxide+naphthalene system. The system can be assumed to be an infinite dilution condition for carbon dioxide+naphthalene system and the mutual diffusion coefficients are equal to the tracer diffusion coefficients of naphthalene. The self-diffusion coefficients of carbon dioxide and the tracer diffusion coefficients of naphthalene in supercritical carbon dioxide can be calculated by mean square displacement. The calculated results of diffusion coefficients showed good agreement with the experimental data without adjustable parameters.     

Senescence regulation by alcohols in cut flowers of Calendula officinalis L.

This study was conducted to investigate the effect of alcohols viz., ethanol, methanol and n-butanol at different concentrations not only on the vase life of Calendula officinalis L. cut flowers but also to record changes in metabolites like starch content and amount of sugars, and activities of α-amylase, and antioxidant enzymes like peroxidase and superoxide dismutase as well as lipid peroxidation. Ethanol as holding solution significantly increased the vase life as compared to other treatments or the control. n-Butanol shortened vase life and caused the flower stem to fold, whereas ethanol and methanol individually delayed drying up and petals dried slowly from their tips. Significant increments in solution uptake, moisture content and flower diameter were noticed with 2 % ethanol followed by 2 % methanol. Cut scapes having 2 % ethanol exhibited maximum amount of starch and considerably lower amount of reducing and non-reducing sugars. This treatment not only brings down the specific activities of α-amylase and peroxidase but also decreases the process of lipid peroxidation. Effectiveness of methanol (2 %) is evident just after ethanol application (2 %). Lowest concentrations of ethanol and methanol also show relatively higher level of SOD activity in cut flowers of Calendula officinalis.     

Investigating the effects of vacancies on self-diffusion in silicon clusters using classical molecular dynamics

Due to recent advances in the field of microelectronics, the growth in microelectronics applications, and the exponentially increasing demand for microelectronic devices in the power sector, it is important to study the behavior of silicon at the nanoscale, given that nanoclusters of silicon could be used to design a new kind of lithium-ion batteries with strongly enhanced performance. Here, molecular dynamics was employed to calculate the self-diffusion coefficients of silicon clusters at room temperature and at a temperature approaching the melting point of silicon, complementing experimental efforts in this field. Silicon clusters of the same spherical geometry and size but with different vacancy fractions were studied using molecular dynamics using the Tersoff potential in order to estimate phase changes and self-diffusion coefficients. At 300 K, the self-diffusion coefficient was found to vary non-monotonically: the self-diffusion coefficient at a vacancy fraction of 7.5% is half than the vacancy at a fraction of 0%, while the self-diffusion coefficient at a vacancy fraction of 20% is two orders of magnitude larger than that at a vacancy fraction of 0%. However, there is only a marginal monotonic increase in the self-diffusion coefficient values with vacancy fraction at 2000 K. The results of this investigation of vacancy-mediated self-diffusion could aid attempts to improve diffusion control, which is crucial to nanocluster applications in various devices, and the results also provide insight into how the temperature, energy, pressure, and phase changes of the silicon clusters depend on vacancy fraction. This may ultimately allow the design and selection of materials for thermoelectric and optoelectronic devices and thermal transducers to be optimized. Our results also indicated that the findings we obtained for the clusters are independent of the particular random vacancy distribution considered and the heating rate applied to the clusters.

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Graphical Abstract Silicon nanoparticles (SNP) are among the best options to choose from for the design of devices for renewable energies; SNP based material performance can be effectively tailored by controling the vacancy, temperature and other properties of the SNP.

     

Association of methanol and ethanol with heme proteins.

The behavior of ferrihemoglobin and ferrimyoglobin in widely varying concentrations of the lowest four alcohols has been studied by optical and electron paramagnetic resonance absorption spectroscopy. Methanol and ethanol, at concentrations too low to cause general conformational destabilization of the protein, produce both optical and electron paramagnetic resonance absorption spectral changes in ferrihemoglobin. These changes arise from equilibrium associations, characterized by dissociation constants at 25 degrees C of about 40 and 200 mM, respectively, for the methanol-ferrihemoglobin and ethanol-ferrihemoglobin complexes so formed. Other optical spectral changes appear when the methanol concentration exceeds 3.5 M and the ethanol, 1.0 M. At concentrations lower than 0.5 M, 1- and 2-propanol produce spectral changes of this second kind. At room temperature no optical evidence has been found that the propanols associate with ferrihemoglobin in the manner of methanol and ethanol. Methanol and ethanol at low concentration have specific effects, characterized by electron paramagnetic resonance spectral differences, upon ferric alphaSH chains. All four alcohols, over a wide range of concentrations, reduce the symmetry of electron paramagnetic resonance spectra from frozen solutions of ferrihemoglobin; even at the high end of this concentration range, none of the alcohols reduces the symmetry of electron paramagnetic resonance spectra from frozen ferrimyoglobin. Ferrimyoglobin and catalase association with methanol is measurable optically; the binding is about five and sixty times weaker, respectively, for these two proteins as compared with ferrihemoglobin.     

Characterization of a solvent resistant and thermostable aminopeptidase from the hyperthermophillic bacterium, Aquifex aeolicus

A leucine aminopeptidase gene of Aquifex aeolicus, a hyperthermophilic bacterium, was cloned and expressed in Escherichia coli, and its expression product was purified and characterized. The expressed protein was purified to homogeneity by using heat to denature contaminating proteins followed by ion-exchange chromatography to purify the heat-stable product. The purified enzyme gave a single band on SDS-PAGE with a molecular weight of 54 kDa. Kinetic studies on the purified enzyme confirmed that it was a leucine aminopeptidase. The optimum temperature for its activity was around 80 degrees C and the optimum pH was in the range from 8.0 to 8.5. It was stable at high temperatures and 27% of its activity was retained after heating at 115 degrees C for 30 min. The purified enzyme had a pH stability range between 4.0 and 11.0. This aminopeptidase was highly resistant to organic solvents such as methanol, ethanol, tetrahydrofuran, dimethyl sulfoxide, acetone, acetonitrile, dimethyl formamide, 1-propanol, 2-propanol, and dioxane.