Effect of Cage Occupancies on Molecular Vibrations of Methane in Structure H Clathrate Hydrate: Ab Initio Molecular Dynamics Simulation

The structure H (sH) of methane hydrate, which has a distinctive structure with large (LL) cages capable of encapsulating multiple methane molecules, has been suggested as a methane reservoir in large icy bodies such as Titan, making it important in planetary science. This high-pressure phase, which exists in the GPa range, lends itself to the study of methane states and dynamics using powerful experimental techniques such as IR and Raman spectroscopy. However, the interpretation of the vibrational spectra of methane in the sH structure has been challenging because of the spectral complexities. The signals attributed to the methane molecules in the LL cage, as well as those of the other two cage types, overlap in the spectra. In this study, we investigated the microscopic origins of the shape of the C-H stretching vibration spectrum of methane in the LL cage using ab initio molecular dynamics (AIMD) simulations. For a single methane molecule in the LL cage, the ν band of the C-H stretching mode was observed at a higher frequency typical of isolated molecules in vacuum due to the large size of the LL cage. As the number of methane molecules in the LL cage increased beyond one, a tendency to blue-shift with increasing methane occupancy was observed, consistent with a loose-cage-tight-cage model. By characterizing the time correlation function of methane stretching vibrations based on the solvation number of methane and water molecules proximal to methane within the LL cage, we showed that the complicated spectral line shape observed in cases of higher methane occupancy in the LL cage resulted from the wider variation of the solvation shell states. Analysis of the solvation structures of the AIMD trajectories provided interpretations of the experimental spectral line shape, demonstrating the complementary nature of AIMD to the experiment and its effectiveness in analysis.


Nuclear Magnetic Resonance Analysis of Hydrothermal Reactions of Ethyl- and Octylamine in Sub- and Supercritical Water

Hydrothermal reactions of aliphatic amines have recently gained importance in relation to the application of amines as film-forming corrosion inhibitors for steam-water cycles. The kinetics and mechanism of the hydrothermal reactions of ethylammomiun cation (EtAH) and -octylammonium cation (OctAH) were studied for comparison with the corresponding neutral amines to elucidate their reaction products and pathways at sub- and supercritical temperatures of 300-400 °C as model reactions of aliphatic ammonium cations. We analyzed the reaction of C-N-labeled EtAH using NMR spectroscopy and revealed that the initial hydrolysis to ethanol, known as the main path, is followed by the elimination reaction producing ethene and the disproportionation reaction giving diethylammonium cation. The OctAH yields octene and octanol, each of which isomerizes to thermodynamically more stable species as the major products. Comparisons were made between the reactions of the neutral amines and ammonium cations to highlight their different reactivity. The hydrolysis, alkene formation, and dehydration of alcohols to alkenes were all found to be accelerated at low pH. The formation of low-molecular-weight organic acids such as acetic acid and formic acid was not observed. These results indicate that the corrosion protection effect of film-forming amines will be maintained under practical conditions with pH values as high as around 9 to 10, and hence side reactions involving byproducts will be suppressed.


Significant role of counterion for lead(II) ion adsorption on carbon pore surface


Microscopic Structure and Binding Mechanism of the Corrosion-Protective Film of Oleylpropanediamine on Copper in Hot Water


Solvation shell dynamics of supercritical water-cyclohexane mixtures in relation to the translational and rotational dynamics as studied by molecular dynamics simulation


Temperature Dependence of Water Cluster on Functionalized Graphite


14N NMR Evidence for Initial Production of NH3 Accompanied by Alcohol from the Hydrolysis of Ethylamine and Butylamine in Supercritical Water


Self-diffusion of water-cyclohexane mixtures in supercritical conditions as studied by NMR and molecular dynamics simulation

The self-diffusion coefficients of water (D) and cyclohexane (D) in their binary mixtures were determined using the proton pulsed field gradient spin-echo method from medium to low densities in subcritical and supercritical conditions. The density (ϱ), temperature (T), and water mole fraction (x) are studied in the ranges 0.62-6.35 M (M = mol dm), 250-400 °C, and 0.109-0.994, respectively. A polynomial fitting function was developed for a scaled value of Ξ = ϱDT with ϱ, T, and x as variables in combination with a comprehensive molecular dynamics (MD) simulation. The NMR and MD results agree within 5% for water and 6% for cyclohexane, on average. The differences between D and D in the dependence on ϱ, T, and x are characterized by the activation energy E and the activation volume ΔV expressed by the scaled fitting function. The decrease in the ratio D/D and the increase in the E of water with increasing x are related to the increase in the number of hydrogen bonds (HBs). The D value for a solitary water molecule at a low x is controlled by the solvation shell, most of which is occupied by nonpolar cyclohexane molecules that provide less friction as a result of weaker interactions with water. A microscopic diffusion mechanism is discussed based on an analysis of the HB number as well as the first-peak height of the radial distribution functions that are taken as measures of the potential of the mean field controlling self-diffusion.


High-Pressure and High-Temperature NMR Observation of Synthetic Polymers: High-Resolution Measurement Taking Advantage of Motional Narrowing in Sub-Critical Fluids

合成高分子の高圧高温NMR観測:亜臨界流体中の高い分子運動性を利用した高分解能測定

The Review of High Pressure Science and Technology


Hydrogen-bond-assisted isotactic-specific radical polymerization of N-vinyl-2-pyrrolidone with tartrate additives in toluene at low temperatures: high-resolution 1H NMR analysis

A diethyl L-tartrate (L-EtTar)-assisted radical polymerization of N-vinyl-2-pyrrolidone has been developed as the first reported example of the synthesis of isotactic-rich poly(N-vinyl-2-pyrrolidone) (PVP). The addition of L-EtTar in toluene at temperatures of -40 °C and lower led to a significant increase in the polymer yield by one order of magnitude compared with the reaction in the absence of L-EtTar. Decreasing the polymerization temperature led to increases in the isotacticity of the PVP, with the mm triad reaching 66.4% at -93 °C. 1H NMR measurement at 920 MHz was conducted to establish a reliable strategy for quantifying the triad tacticities. High-temperature NMR measurements at 250 °C were performed using a specially-designed NMR probe, which led to dramatic narrowing of the 1H line width.

N-ビニル-2-ピロリドンの低温ラジカル重合系に酒石酸ジエチルを添加すると，収率や分子量が増加するとともにイソタクチシチーも増加することを見出した．また，1H NMRの測定条件を最適化することで，3連子立体規則性を定量することに成功した．


Effect of Rotational Couplings on Vibrational Spectrum Line Shape of Bending Mode in Low-Density Supercritical Water: Density and Hydrogen Isotopes Dependencies


Effect of Water on Hydrolytic Cleavage of Non-Terminal α-Glycosidic Bonds in Cyclodextrins To Generate Monosaccharides and Their Derivatives in a Dimethyl SulfoxideWater Mixture

Hydrolytic cleavage of the non-terminal α-1,4-glycosidic bonds in α-, β-, and γ-cyclodextrins and the anomeric-terminal one in d-maltose was investigated to examine how the cleavage rate for α-, β-, and γ-cyclodextrins is slower than that for d-maltose. Effects of water and temperature were studied by applying in situ (13)C NMR spectroscopy and using a dimethyl sulfoxide (DMSO)-water mixture over a wide range of water mole fraction, xw = 0.004-1, at temperatures of 120-180 °C. The cleavage rate constant for the non-anomeric glycosidic bond was smaller by a factor of 6-10 than that of the anomeric-terminal one. The glycosidic-bond cleavage is significantly accelerated through the keto-enol tautomerization of the anomeric-terminal d-glucose unit into the d-fructose one. The smaller the size of the cyclodextrin, the easier the bond cleavage due to the ring strain. The remarkable enhancement in the cleavage rate with decreasing water content was observed for the cyclodextrins and d-maltose as well as d-cellobiose. This shows the important effect of the solitary water whose hydrogen bonding to other water molecules is prohibited by the presence of the organic dipolar aprotic solvent, DMSO, and which has more naked partial charges and higher reactivity. A high 5-hydroxymethyl-2-furaldehyde (5-HMF) yield of 64% was attained in a non-catalytic conversion by tuning the water content to xw = 0.30, at which the undesired polymerization by-paths can be most effectively suppressed. This study provides a step toward designing a new optimal, earth-benign generation process of 5-HMF starting from biomass.


Effect of Water Content on Conversion of D-Cellobiose into 5-Hydroxymethyl-2-furaldehyde in DimethylsulfoxideWater Mixture

Noncatalytic conversion of D-cellobiose (at 0.5 M) into 5-hydroxymethyl-2-furaldehyde (5-HMF), a platform chemical for fuels and synthetic materials, was analyzed at 120-200 °C over a wide range of water mole fraction, xw = 0.007-1 in a binary dimethyl sulfoxide (DMSO)-water mixture by means of the in situ (13)C NMR spectroscopy. Effects of the water content were revealed as follows: (i) The tautomerization of the anomeric residue of D-cellobiose from D-glucose to D-fructose type was not initially observed at a lower water content, in contrast to the significant tautomerization into the D-fructose type in a higher water content and pure water. (ii) The lower the water content, the faster the glycosidic-bond cleavage by hydrolysis, because of the high reactivity of solitary water molecules with the large partial charges more naked as in supercritical water clusters due to the isolation by the organic solvent DMSO. (iii) The amount of D-fructose as the intermediate product was larger at the higher xw; despite the increase of D-fructose, the production of 5-HMF from D-fructose was slowed down. (iv) A high 5-HMF yield of 71% was reached at xw = 0.20-0.30 that was 6-10 times the initial D-cellobiose concentration. The best yield of 5-HMF was attained in the low xw region when the polymerization paths into NMR-undetectable species via 5-HMF and anhydromonosaccharides were effectively suppressed. This study provides a new framework to design optimal, noncatalytic reaction process to produce 5-HMF from cellulosic biomass by tuning the water content as well as the temperature and the reaction time.


Effect of heavy hydrogen isotopes on the vibrational line shape for supercritical water through rotational couplings

The rotational couplings, which determine the infrared spectral line shape in the low-density supercritical water, were analyzed as functions of the density and the temperature by applying molecular dynamics simulation to a flexible water model, SPCFw and by varying the moment of inertia of the water through substitution for the H atom in H2O by heavy hydrogen isotopes. The differences in the frequency and the relative intensity between the sharp center peak and the rotational broad side-bands were analyzed for the O-H, O-D, and O-T stretch spectra. The frequency differences between the sharp center peak and the rotational broad side-bands are linearly correlated with the inverse of the moment of inertia of the isotope-substituted water species. The intensity of the sharp peak is associated with the long-time component of the reorientational time correlation function for the stretching bond vector. At 400 °C, where a substantial amount of hydrogen bonds are dynamically persisting, an intensity decrease in the rotational broad side-bands was observed with increasing density from 0.01 to 0.40 g cm(-3), respectively, corresponding to 0.56 and 22.2 M (=mol dm(-3)), orders of magnitude higher than the ideal gas densities. This arises from the decrease in the correlation time of the angular velocity and the rotational couplings due to an increase in the hydrogen-bonding perturbation. The intensity decrease of the rotational side-bands with increasing density is more significant for the water isotopes with heavier hydrogens. At a high temperature of 1200 °C, the rotational side-bands at 0.01 to 0.05 g cm(-3) were more distinct than those at 400 °C, and even at a medium density of 0.40 g cm(-3) a significant signal broadening due to the rotational couplings was clearly observed because of the accelerated rotational momentum. The vibrational spectrum cannot be decomposed into definite chemical clusters for the thermodynamic and kinetic analysis because of the dynamic origin.


Density effect on infrared spectrum for supercritical water in the low- and medium-density region studied by molecular dynamics simulation

The origin of the line shape of the O-H stretch vibrational spectrum is analyzed for supercritical water in the low- and medium-density region by using classical molecular dynamics simulation for the flexible point-charge model, SPC/Fw. The spectrum calculated for the water model is in good agreement with the experimental one in the low-density region. The spectral origins in the low-density region of 0.01-0.04 g cm(-3) are assigned to a sharp peak due to the bond oscillation along the O-H vector and two broad bands due to the rotational coupling, by taking an isolated single molecule as a reference in the low-density limit. The bands due to the rotational coupling reduce in intensity with increasing density as the rotations are more hindered by the hydrogen-bonding interactions, and their intensities increase with increasing temperature due to the accelerated rotational motion. The O-H stretch oscillation in the time correlation function attenuates in a timescale comparable with the lifetime of the hydrogen bonds, and the spectra conditioned by the number of hydrogen bonds are dominantly controlled by the local solvation structure.


Structure of the pentameric ligand-gated ion channel ELIC cocrystallized with its competitive antagonist acetylcholine

ELIC, the pentameric ligand-gated ion channel from Erwinia chrysanthemi, is a prototype for Cys-loop receptors. Here we show that acetylcholine is a competitive antagonist for ELIC. We determine the acetylcholine-ELIC cocrystal structure to a 2.9-Å resolution and find that acetylcholine binding to an aromatic cage at the subunit interface induces a significant contraction of loop C and other structural rearrangements in the extracellular domain. The side chain of the pore-lining residue F247 reorients and the pore size consequently enlarges, but the channel remains closed. We attribute the inability of acetylcholine to activate ELIC primarily to weak cation-ϖ and electrostatic interactions in the pocket, because an acetylcholine derivative with a simple quaternary-to-tertiary ammonium substitution activates the channel. This study presents a compelling case for understanding the structural underpinning of the functional relationship between agonism and competitive antagonism in the Cys-loop receptors, providing a new framework for developing novel therapeutic drugs.


NMR-NOE and MD Simulation Study on Phospholipid Membranes: Dependence on Membrane Diameter and Multiple Time Scale Dynamics

Motional correlation times between the hydrophilic and hydrophobic terminal groups in lipid membranes are studied over a wide range of curvatures using the solution-state (1)H NMR-nuclear Overhauser effect (NOE) and molecular dynamics (MD) simulation. To enable (1)H NMR-NOE measurements for large vesicles, the transient NOE method is combined with the spin-echo method, and is successfully applied to a micelle of 1-palmitoyl-lysophosphatidylcholine (PaLPC) with diameter of 5 nm and to vesicles of dipalmitoylphosphatidylcholine (DPPC) with diameters ranging from 30 to 800 nm. It is found that the NOE intensity increases with the diameter up to ∼100 nm, and the model membrane is considered planar on the molecular level beyond ∼100 nm. While the NOE between the hydrophilic terminal and hydrophobic terminal methyl groups is absent for the micelle, its intensity is comparable to that for the neighboring group for vesicles with larger diameters. The origin of NOE signals between distant sites is analyzed by MD simulations of PaLPC micelles and DPPC planar bilayers. The slow relaxation is shown to yield an observable NOE signal even for the hydrophilic and hydrophobic terminal sites. Since the information on distance and dynamics cannot be separated in the experimental NOE alone, the correlation time in large vesicles is determined by combining the experimental NOE intensity and MD-based distance distribution. For large vesicles, the correlation time is found to vary by 2 orders of magnitude over the proton sites. This study shows that NOE provides dynamic information on large vesicles when combined with MD, which provides structural information.


Scaled Polynomial Expression for Self-Diffusion Coefficients for Water, Benzene, and Cyclohexane over a Wide Range of Temperatures and Densities

Journal of Chemical and Engineering Data


Self-diffusion in supercritical water and benzene in high-temperature high-pressure conditions studied by NMR and dynamic solvation-shell model


Self-diffusion coefficients for water and organic solvents at high-temperatures along the coexistence curve

The self-diffusion coefficients D for water, benzene, and cyclohexane are determined by using the pulsed-field-gradient spin echo method in high-temperature conditions along the liquid branch of the coexistence curve: 30-350 degrees C (1.0-0.58 g cm(-3)), 30-250 degrees C (0.87-0.56 g cm(-3)), and 30-250 degrees C (0.77-0.48 g cm(-3)) for water, benzene, and cyclohexane, respectively. The temperature and density effects are separated and their origins are discussed by examining the diffusion data over a wide range of thermodynamic states. The temperature dependence of the self-diffusion coefficient for water is larger than that for organic solvents due to the large contribution of the attractive hydrogen-bonding interaction in water. The density dependence is larger for organic solvents than for water. The difference is explained in terms of the van der Waals picture that the structure of nonpolar organic solvents is determined by the packing effect due to the repulsion or exclusion volumes. The dynamic solvation shell scheme [K. Yoshida et al., J. Chem. Phys. 127, 174509 (2007)] is applied for the molecular interpretation of the translational dynamics with the aid of molecular dynamics simulation. In water at high temperatures, the velocity relaxation is not completed before the relaxation of the solvation shell (mobile-shell type) as a result of the breakdown of the hydrogen-bonding network. In contrast, the velocity relaxation of benzene is rather confined within the solvation shell (in-shell type).


Self-diffusion coefficients for water and organic solvents in extremely low-density supercritical states


Cholesterol Location and Orientation in Aqueous Suspension of Large Unilamellar Vesicles of Phospholipid Revealed by Intermolecular Nuclear Overhauser Effect

The locational and orientational structure and the dynamics of cholesterol in the bilayer membrane were studied by using the solution-state NMR. The intermolecular nuclear Overhauser effect (NOE) was analyzed for large unilamellar vesicles (100 nm in diameter) composed of dimyristoylphosphatidylcholine (DMPC) and cholesterol at cholesterol concentrations of 9-33 mol %. The DMPC headgroups show (1)H-{(1)H}-NOEs with the methyl groups at the hydrophobic terminals of both cholesterol and DMPC, illustrating the significant fluctuation of the bilayer membrane in the vertical (bilayer normal) direction. Cholesterol was found to keep the hydroxyl (OH) group toward the outer water pool on the basis of the following observations: (1) the cross correlation between the DMPC headgroup and the cholesterol terminal methyl group is weaker than those between the DMPC headgroups and (2) the methyl group at the hydrophobic terminal of cholesterol shows strong correlation with the terminal group of the DMPC chain portion. The OH group plays a crucial role in orienting cholesterol with its OH group outward, since cholestane, which has a molecular structure similar to that of cholesterol except for the absence of the OH group, was found to have no orientational preference in the bilayer membrane. The dynamic slowdown at high cholesterol concentrations is demonstrated on the basis of the correlation times for NOE as well as the broadening of the proton linewidths.


Solvation shell dynamics studied by molecular dynamics simulation in relation to the translational and rotational dynamics of supercritical water and benzene

The solvation shell dynamics of supercritical water is analyzed by molecular dynamics simulation with emphasis on its relationship to the translational and rotational dynamics. The relaxation times of the solvation number (tau S), the velocity autocorrelation function (tau D), the angular momentum correlation function (tau J), and the second-order reorientational correlation function (tau 2R) are studied at a supercritical temperature of 400 degrees C over a wide density region of 0.01-1.5 g cm(-3). The relaxation times are decomposed into those conditioned by the solvation number n, and the effect of the short-ranged structure is examined in terms of its probability Pn of occurrence. In the low to medium-density range of 0.01-0.4 g cm(-3), the time scales of water dynamics are in the following sequence: tau D>tau S approximately or > tau J approximately or > tau 2R. This means that the rotation in supercritical water is of the "in-shell" type while the translational diffusion is not. The comparison to supercritical benzene is also performed and the effect of hydrogen bonding is examined. The water diffusion is not of the in-shell type up to the ambient density of 1.0 g cm(-3), which corresponds to the absence of the transition from the collision to the Brownian picture, whereas such transition is present in the case of benzene. The absence of the transition in water comes from the fast reorganization of the hydrogen bonds and the enhanced mobility of the solvation shell in supercritical conditions.


Kinetic and Equilibrium Study on Formic Acid Decomposition in Relation to the Water-Gas-Shift Reaction

Kinetics and equilibrium are studied on the hydrothermal decarbonylation and decarboxylation of formic acid, the intermediate of the water-gas-shift (WGS) reaction, in hot water at temperatures of 170-330 degrees C, to understand and control the hydrothermal WGS reaction. (1)H and (13)C NMR spectroscopy is applied to analyze as a function of time the quenched reaction mixtures in both the liquid and gas phases. Only the decarbonylation is catalyzed by HCl, and the reaction is first-order with respect to both [H(+)] and [HCOOH]. Consequently, the reaction without HCl is first and a half (1.5) order due to the unsuppressed ionization of formic acid. The HCl-accelerated decarbonylation path can thus be separated in time from the decarboxylation. The rate and equilibrium constants for the decarbonylation are determined separately by using the Henry constant (gas solubility data) for carbon monoxide in hot water. The rate constant for the decarbonylation is 1.5 x 10(-5), 2.0 x 10(-4), 3.7 x 10(-3), and 6.3 x 10(-2) mol(-1) kg s(-1), respectively, at 170, 200, 240, and 280 degrees C on the liquid branch of the saturation curve. The Arrhenius plot of the decarbonylation is linear and gives the activation energy as 146 +/- 3 kJ mol(-1). The equilibrium constant K(CO) = [CO]/[HCOOH] is 0.15, 0.33, 0.80, and 4.2, respectively, at 170, 200, 240, and 280 degrees C. The van't Hoff plot results in the enthalpy change of DeltaH = 58 +/- 6 kJ mol(-1). The decarboxylation rate is also measured at 240-330 degrees C in both acidic and basic conditions. The rate is weakly dependent on the solution pH and is of the order of 10(-4) mol kg(-1) s(-1) at 330 degrees C. Furthermore, the equilibrium constant K(CO2) = [CO(2)][H(2)]/[HCOOH] is estimated to be 1.0 x10(2) mol kg(-1) at 330 degrees C.


Self-diffusion of supercritical water in extremely low-density region

The self-diffusion coefficient D for super- and subcritical water is determined by using the proton pulsed-field-gradient spin echo method at high temperatures and low densities. The density of water is ranged in the steamlike region from 0.0041 to 0.0564 g [corrected] cm(-3) at a supercritical temperature of 400 degrees C, also at 0.0041-0.0079 and 0.0041-0.0462 g [corrected] cm(-3) (the steam-branch densities on the coexistence curve and lower) at 200 and 300 degrees C, respectively. The density is precisely determined on the basis of the PVT dependence of the proton chemical shift. The density-diffusivity products in the zero-density limit divided by the square root of the temperature, (rho D)0/square root of T, are 0.94, 1.17, and 1.35 mg m(-1) s(-1) K(-1/2) (mg=10(-3)g) [corrected] at 200, 300, and 400 degrees C, respectively. The (rhoD)0/square root of T obtained decreases with decreasing temperature and is significantly smaller than the temperature-independent value from the hard sphere model, 1.95 mg [corrected] m(-1) s(-1) K(-1/2). The marked temperature dependence reflects the presence of the strong attractive interaction between a pair of water molecules. The magnitude of the experimental D values and the temperature dependence are well reproduced by the molecular dynamics simulation using TIP4P-FQ model. The initial slope of the product rhoD/square root of T against rho is slightly negative at 300 and 400 [corrected] degrees C.


Synthesis of Bis(germacyclopropa)benzenes and Structures of Their Annelated Benzene Rings


A new high-temperature multinuclear-magnetic-resonance probe and the self-diffusion of light and heavy water in sub- and supercritical conditions

A high-resolution nuclear-magnetic-resonance probe (500 MHz for 1H) has been developed for multinuclear pulsed-field-gradient spin-echo diffusion measurements at high temperatures up to 400 degrees C. The convection effect on the self-diffusion measurement is minimized by achieving the homogeneous temperature distributions of +/-1 and +/-2 degrees C, respectively, at 250 and 400 degrees C. The high temperature homogeneity is attained by using the solid-state heating system composed of a ceramic (AlN) with high thermal conductivity comparable with that of metal aluminium. The self-diffusion coefficients D for light (1H2O) and heavy (2H2O) water are distinguishably measured at subcritical temperatures of 30-350 degrees C with intervals of 10-25 degrees C on the liquid-vapor coexisting curve and at a supercritical temperature of 400 degrees C as a function of water density between 0.071 and 0.251 gcm3. The D value obtained for 1H2O is 10%-20% smaller than those previously reported because of the absence of the convection effect. At 400 degrees C, the D value for 1H2O is increased by a factor of 3.7 as the water density is reduced from 0.251 to 0.071 gcm3. The isotope ratio D(1H2O)D(2H2O) decreases from 1.23 to approximately 1.0 as the temperature increases from 30 to 400 degrees C. The linear hydrodynamic relationship between the self-diffusion coefficient divided by the temperature and the inverse viscosity does not hold. The effective hydrodynamic radius of water is not constant but increases with the temperature elevation in subcritical water.


NMR Spectroscopic Evidence for an Intermediate of Formic Acid in the Water-Gas-Shift Reaction


Effect of Concentration, Acid, Temperature, and Metal on Competitive Reaction Pathways for Decarbonylation of Formic Acid in Hot Water