Molecular Dynamics Simulation Studies of the Limiting Conductances of MgCl2 and CaCl2 in Supercritical Water Using SPC/E Model for Water

We report results of molecular dynamics (MD) simulations of the limiting conductances of MgCl² and CaCl² in supercritical water as a function of water density using the SPC/E model for water. The limiting conductances of Mg²⁺, Ca²⁺ and Cl^- over the whole range of water density considered exhibits a linear dependence of the limiting conductance on the water density. In the cases of Mg²⁺ and Ca²⁺, a solventberg picture for the behavior of small divalent cation emerges from our studies. From the view of the solventberg picture, the ion and its shell moving together as an entity interacts with the second hydration shell water molecules, and its mobility is restricted mostly by the number of the second hydration shell water which is proportional to the water density of the whole system. In the case of Cl^-, the range of water density considered in this study belongs to the higher-density region (above 0.45?g/cm³) in which the effect of the number of hydration water molecules around ions dominated. As the water density increases, the water molecules of the first hydration shell restrict the mobility of Cl^- and the limiting conductance of Cl^- decreases nearly linearly. Significant different dependence on the water density is observed between the calculated limiting conductances of MgCl² and CaCl² at 673?K and the experimental results over the water density of 0.60–0.90?g/cm³. Possible limitation of the extended simple point charge (SPC/E) model with regard to this difference should be pointed out and the use of a more precise model like the revised polarizable (RPOL) model is indispensable for a further MD study to gain a complete picture of the chemical circumstance around the ions.     

Molecular Dynamics Simulation Studies of the Limiting Conductances of CaCl2 using Extended Simple Point Charge and Revised Polarizable Models

We have carried out molecular dynamics (MD) simulations of the limiting conductances of CaCl₂ in ambient and supercritical states as a function of water density using extended simple point charge (SPC/E) and revised polarizable (RPOL) models for ions and water molecules. Both models predict the limiting conductances of CaCl₂ in supercritical water that are a linear dependence on water density. The effect of the electronic polarization on the limiting conductances is too small to cause a deduction in the lower water density of 0.6?～?0.7?g/cc in this study. The most significant effect of the electronic polarization is appeared in a decrease in the ion–water potential energy and, as a result, an increase in the limiting conductances for both ions. Different charge distributions of water molecules in the first hydration shell around the ions lead the opposite behavior of the induced dipole moment with water density for a positive and a negative ion in supercritical water; the induced dipole moment of Ca²⁺ decreases with increasing water density but for Cl^-, the opposite is observed. The same kind of opposite behavior due to the structure of water molecules around the ions is also found in hydrogen-bond correlations of water around the ions and of bulk water; hydrogen bonding around Ca²⁺ persists longer than in bulk water whereas the opposite is observed for Cl^-.     

Molecular Dynamics Simulation of Limiting Conductance for Na2+, Cl2−, Na°, and Cl° in Supercritical Water

Abstract

We report results of molecular dynamics simulations of the limiting conductance of Na²⁺, Cl^2?, Na°, and Cl° in supercritical water using the SPC/E model for water in conjuction with our previous study (Lee et al., Chem. Phys. Lett. 293, 289 (1998)). The behavior of the limiting conductances of Na²⁺ and Cl^2? in the whole range of water density shows almost the same trend as those of Na⁺ and Cl^?, but the deviation from the assumed linear dependence of limiting conductances of Na²⁺ and Cl^2? on the water density is smaller than that of Na⁺ and Cl^?. The ratio of the limiting conductance of the divalentions to that of the corresponding monovalentions over the whole range of water density is almost constant. In the cases of Na²⁺ and Cl^2?, the dominating factor of the number of hydration water molecules around ions in the higher-density region and the dominating factor of the interaction strength between the ions and the hydration water molecules in the lower-density region are also found as was the cases for Na⁺ and Cl^?. These factors, however, are not so strong as for the corresponding monovalent ions because the change in the energetics, structure, and dynamics are very small mainly due to the strong Coulomb interaction of the divalent ions with the hydration water molecules. The diffusion coefficient of Na° and Cl° monotonically increases with decreasing water density over the whole range of water density. The increase of the diffusion coefficient with decreasing water density is attributed only to the dramatic decrease of the hydration number of water in the first solvation shell around the uncharged species. Among the two important competing factors in the limiting conductance of Na⁺ and Cl^?, the effect of the number of hydration water molecules around the uncharged species is the only existing factor over the whole range of water density since the interaction strength between the uncharged species and the hydration water molecules very small through the LJ interaction. This result has confirmed the dominating factor of the number of hydration water molecules around ions in the higher-density region in the explanation of the limiting conductance of Na⁺ and Cl^? in supercritical water at 673 K.     

Global Potential Energy Minima of SPC/E Water Clusters without and with Induced Polarization Using a Genetic Algorithm

The global minimum potential energy structures of water clusters, (H₂O) _n , n = 2-14, have been calculated for the SPC/E (Simple Point Charge/Extended) model and a recent fluctuating charge version of the latter using a simple genetic algorithm. The SPC/E cluster geometries are in good agreement with previous TIP3P (Transferable Intermolecular Potential-3 Point) and TIP4P (Transferable Intermolecular Potential-4 Point) calculations as well as the interpretation of experimental measurements. In contrast to this, the polarizable version of the SPC/E model, which is based on the fluctuating charge approach, deviates rather strongly for n=6 with few exceptions. However, comparing the polarizable model to ab initio results for identical cluster geometries we find reasonable agreement for the magnitude of the average molecular dipole moment, the corresponding energy per molecule, and the average oxygen-oxygen distance as functions of n.Electronic Supplementary Material available.     

Molecular dynamics simulation of the graphene–water interface: comparing water models

In this work, different water models (i.e. SPC/E, TIP3P, TIP4P/2005, TIP5P, SPC/Fw, TIP4P/2005f and SWM4_DP) are implemented to simulate water on neutral, negatively charged and positively charged graphene. In all cases ambient conditions are considered. Structural and dynamical properties for water are calculated to quantify the differences among various water models. The results show that SPC/E, TIP4P/2005, SPC/Fw, TIP4P/2005f and SWM4_DP water models yield a similar structure for interfacial water on graphene, whether it is neutral, negatively charged or positively charged. TIP5P is the model whose predictions for the structure of the interface deviate the most from those of the other models. Although qualitatively the results are for the most part similar, a large quantitative variation is observed among the dynamical properties predicted when various water models are implemented. Although experimental data are not available to discriminate the most/least accurate of the model predictions, our results could be useful for comparing results for interfacial water obtained implementing different models. Such critical comparison will benefit practical applications such as the development of energy-storage and water-desalination devices (e.g. electric double-layer capacitors), among others.     

Molecular dynamics simulation of cation motion in water-filled gramicidinlike pores.

A model calculation is carried out to study the potential energy profile of a sodium ion with several water molecules inside a simplified model of the gramicidin ion channel. The sodium ion is treated as a Lennard-Jones sphere with a point charge at its center. The Barnes polarizable water model is used to mimic the water molecules. A polarizable and deformable gramicidinlike channel is constructed based on the model obtained by Koeppe and Kimura. Potential minima and saddle points are located and the static energy barriers are computed. The potential minima at the two mouths of the channel exhibit an aqueous solvation structure very different from that at any of the interior minima. These sites are approximately 23.6 and 24.4 A apart for binding of a sodium ion and a cesium ion, respectively. Ionic motion from these exterior sites to the first interior minimum requires substantial rearrangement of the waters of solvation; this rearrangement may be the hydration/dehydration step in ionic permeation through the channel. Based on these results, a mechanism by which the sodium ion moves from the exterior binding site to the interior of the channel is proposed. Our model channel accommodates about eight water molecules and the transport of the ion and water within the channel is found to be single file. Results of less extensive calculations for Cs+ and Li+ ions in a channel with or without water are also reported.     

The equivalent conductivity of aqueous solutions of alkali metal salts of a number of ionic polysaccharides

Measurements of the equivalent conductivity of aqueous solutions of alkalimetal salts of a number of ionic polysaccharides at 25 degrees C are reported. The polysaccharides studied are: (1) three carboxymethylcelluloses of various degrees of substitution (Li+, Na+, Cs+ salts) in the concentration range 4 X 10(-4) - 6 X 10(-2) equivalents alkali ion per liter, (2) Polypectate (Li+, Na+, K+, Cs+ salts) in the range 1.5 X 10(-4) - 2 X 10(-2) equivalent alkali ion per liter, and (3) Dextransulfate (Li+, Na+, K+ salts) in the range 3 X 10(-4) - 10(-1) equivalent alkali ion per liter. The results are compared to some earlier data and to a limiting law for conductance of rod-like polyions derived by Manning. It is concluded that although qualitative agreement is obtained between observed data and the limiting law when various polyions of different charge densities are compared at a given concentration, the concentration dependence predicted by the limiting law is in agreement with the observed curves only for polyions of a relatively low charge density. At higher charge densities appreciable deviations occur, and dextransulfate which does not have the rod-like polyion structure required by theory does not conform to the predicted concentration dependence at all.     

Molecular dynamics simulation of a decasaccharide fragment of heparin in aqueous solution

Molecular dynamics (MD) simulations on heparin-water-sodium systems were carried out in order to establish a simulation protocol able to represent heparin solution conformation under physiological conditions. Atomic charges suitable for heparin oligosaccharides were obtained from ab initio quantum-mechanical computations, at the 6-31G(**) level. The GROMACS forcefield, the SPC, and SPC/E water models were employed. Also heparin was simulated with IdoA residues in 1C(4) or 2S(0) conformational states. The results of the performed MD simulations are in agreement with the available experimental data, suggesting that this approach can be applied for the study of heparin interactions with its target proteins and thus play a role in the development of new antithrombotic agents.     

Activation of the cisplatin and transplatin complexes in solution with constant pH and concentration of chloride anions; quantum chemical study

The thermodynamics of cisplatin and transplatin hydration is studied within the model of constant pH solution. Several implicit solvation models were chosen for the determination of pK_a and pK constants of the hydration reactions. The polarizable dielectric model (DPCM), integral equation formalism polarizable model (IEFPCM), and polarizable conductor model (CPCM) were combined with the ‘united atom model for Hartree-Fock’ (UAHF) method for cavity construction and the B3LYP/6-31++G(2dp,2pd) level of calculations for the determination of electronic energies. The results were compared with the COSMO-RS and SM8 model developed by Truhlar (with M06 and MPWX functionals and the charge model CM4). The RMS difference between experimental and calculated pK_a values of cis/transplatin, water, HCl, and NH₄⁺ was used to evaluate accuracy of calculations. The DPCM model was confirmed to perform the best. The predicted pK_a constants were used in Legendre transformation for the estimation of the ΔG’ energies in the constant-pH model. The dependence of the pK constant on pH is plotted and compared with experimental value at pH=7.4. The influence of various chloride concentrations on the molar fractions of dissolved forms of cisplatin is examined for the DPCM model. The increased ratio of cisplatin active aqua-forms is clearly visible for 4 mM chloride solution in comparison with 104 mM Cl^- concentration.     

A study of the quadrupolar NMR splittings of 7Li+, 23Na+, and 133Cs+ counterions in macroscopically oriented DNA fibers.

The hydration and temperature dependencies of the 23Na+, 133Cs+, and 7Li+ quadrupolar splitting have been determined in hydrated, macroscopically oriented DNA fibers. At low water contents the quadrupolar splitting is found to decrease as the water content increases, regardless of counterion, while at high water contents the hydration dependence is reversed. The 23Na+ and 133Cs+ quadrupolar splittings decrease as the temperature increases, while the 7Li+ splitting shows the opposite behavior. At high water contents the 23Na+ and 133Cs+ splittings decrease, and then, after passing zero splitting, increase as the temperature increases. The interpretation of the temperature dependence is discussed in terms of a two-site model (free and bound ions) and a three-site model (free ions and specifically or nonspecifically bound ions). It is suggested that a three-site model is more consistent with the data for the present system. At high water contents, the temperature dependence of the 7Li+ splitting vanishes, indicating counterion condensation. The behavior of the 7Li+ splitting is confirmed by measurements on DNA fibers in equilibrium with a C2H5OD-D2O-LiCl solution. The salt dependence in this system is weak. The counterion quadrupolar splitting is seen to be very sensitive to structural transitions in double-helical DNA.     

Polarizability rescaling and atom-based Thole scaling in the CHARMM Drude polarizable force field for ethers

Within the CHARMM polarizable force field based on the classical Drude oscillator, atomic polarizabilities are derived via fitting to ab initio calculated data on isolated gas phase molecules, with an empirical scaling factor applied to account for differences between the gas and condensed phases. In the development of polarizable models for the ethers, a polarizability scaling factor of 0.7 was previously applied [Vorobyov et al. J Comput Chem 3:1120–1133, 2007]. While the resulting force field models gave good agreement with a variety of experimental data, they systematically underestimated the liquid phase dielectric constants. Here, a new CHARMM polarizable model is developed for the ethers, employing a polarizability scaling factor of 0.85 and including atom-based Thole scale factors recently introduced into the CHARMM Drude polarizable force field [Harder et al. J Phys Chem B 112:3509-3521, 2008]. The new model offers a significant improvement in the reproduction of liquid phase dielectric constants, while maintaining the good agreement of the previous model with all other experimental and quantum mechanical data, highlighting the sensitivity of liquid phase properties to the choice of atomic polarizability parameters.     

H-bonding in protein hydration revisited

H-bonding between protein surface polar/charged groups and water is one of the key factors of protein hydration. Here, we introduce an Accessible Surface Area (ASA) model for computationally efficient estimation of a free energy of water-protein H-bonding at any given protein conformation. The free energy of water-protein H-bonds is estimated using empirical formulas describing probabilities of hydrogen bond formation that were derived from molecular dynamics simulations of water molecules at the surface of a small protein, Crambin, from the Abyssinian cabbage (Crambe abyssinica) seed. The results suggest that atomic solvation parameters (ASP) widely used in continuum hydration models might be dependent on ASA for polar/charged atoms under consideration. The predictions of the model are found to be in qualitative agreement with the available experimental data on model compounds. This model combines the computational speed of ASA potential, with the high resolution of more sophisticated solvation methods.     

A 210-min solid phase cytometry test for the enumeration of Escherichia coli in drinking water

A 210-min-test for the enumeration of Escherichia coli in drinking water is described, based on solid phase cytometry (SPC) and a two-step enzymatic procedure for fluorescence labelling of single cells and small microcolonies. The test involves membrane filtration through a 25-mm black polyester filter, induction of beta-glucuronidase in the retained target cells, fluorescence labelling with fluorescein-di-beta-Dglucuronide as an enzyme substrate and laser scanning of the membrane filter. Scan results can be confirmed on-line by epifluorescence microscopy. Application to 149 naturally contaminated and uncontaminated well, tap, out-of-pump centre (distribution), surface and sewage-spiked water samples indicated > or =90% agreement and equivalence with plate count methods, including Chromocult Coliform agar and m FC agar. In 5.4% of all samples examined, SPC detected between 1 and 11 E. coli per 100 ml, while the two plate methods yielded negative results. Cases of a negative SPC result but a positive E. coli count on both reference media were not observed. This test would primarily be useful for 'emergency' monitoring of drinking water when rapid results are crucial.     

Infrared studies of fully hydrated unsaturated phosphatidylserine bilayers. Effect of Li+ and Ca2+

Infrared spectroscopy has been used to characterize the thermal-phase behavior of fully hydrated 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine (POPS) and 1,2-dioleoyl-sn-glycero-3-phospho-L-serine (DOPS) as well as their interaction with Li+ and Ca2+. The order-disorder transition of POPS-NH4+ is at 17 degrees C; in the presence of Li+ a POPS-Li+ complex is formed, and the transition temperature of this complex is 40 degrees C. DOPS-NH4+ has an order-disorder transition at -11 degrees C, and unlike POPS the addition of Li+ has no effect on the thermal behavior of DOPS-NH4+. This indicates that the binding of Li+ to DOPS is negligible or very weak. Li+ binds to the phosphate and carboxylate groups of POPS, and as a result these groups lose their water of hydration. Li+ binding induces a conformational change, probably in the glycerol backbone of POPS; however, the conformation of the two P-O ester bonds remains gauche-gauche as in POPS-NH4+. Both POPS and DOPS form crystalline complexes with Ca2+. As a result of Ca2+ binding to the phosphate, this group loses its water of hydration and there is a conformational change in the P-O ester bonds from gauche-gauche to antiplanar-antiplanar. In contrast to the POPS-Li+ complex, the carboxylate group remains hydrated in the Ca2+ complexes. Furthermore, in these PS-Ca2+ complexes a new hydrogen bond is formed between one of the ester C=O groups and probably water. Such a situation is not found in the NH4+ and Li+ salts of phosphatidylserine.     

Responses of stomatal conductance to light, humidity and temperature in winter wheat and barley grown at three concentrations of carbon dioxide in the field

Responses of leaf stomatal conductance to light, humidity and temperature were characterized for winter wheat and barely grown at ambient (about 350 μmol mol^?1 in the daytime), ambient + 175 and ambient + 350 μmol mol^?1 concentrations of carbon dioxide in open‐topped chambers in field plots over a three year period. Stomatal responses to environment were determined by direct manipulation of single environmental factors, and those results were compared with responses derived from natural day to day variation in mid‐day stomatal conductance. The purpose of these experiments was to determine the magnitude of reduction in stomatal conductance at elevated [CO₂], and to assess whether the relative response of conductance to elevated [CO₂] was constant across light, humidity and temperature conditions. The results indicated that light, humidity and temperature all significantly affected the relative decrease in stomatal conductance at elevated [CO₂]. The relative decrease in conductance with elevated [CO₂] was greater at low light, low water vapour pressure difference, and high temperature in both species. For measurements made at saturating light near mid‐day, the ratio of mid‐day stomatal conductances at doubled [CO₂] to that at ambient [CO₂] ranged from 0.42 to 0.86, with a mean of 0.66 in barley, and from 0.33 to 0.80, with a mean of 0.56 in wheat. Day‐to‐day variation in the relative effect of elevated [CO₂] on conductance was correlated with the relative stimulation of [CO₂] assimilation rate and with temperature. Some limitations of multiple linear regression, multiplicative, and ‘Ball–Berry' models as summaries of the data are discussed. In barley, a better fit to the models occurred in individual years than for the combined data, and in wheat a better fit to the models occurred when data from near the end of the season were removed.     

Stomatal regulation in a changing climate: a field study using Free Air Temperature Increase (FATI) and Free Air CO2 Enrichment (FACE)

This study investigates effects of climate warming (+ 2.5°C ubove ambient) and elevated CO₂ concentration (600 μmol mol^?1) on the stomatal functioning and the water relations of Lolium perenne, using Free Air Temperature Increase (FATI) and Free Air CO₂ Enrichment (FACE). Compared to growth at ambient temperature, whole-season temperature increase reduced leaf stomatal conductance, but only at the top of the canopy (-14.6 and -8.8% at ambient and elevated CO₂, respectively). However, because higher canopy temperature raised the leaf-to-air vapour pressure difference, leaf transpiration rate increased (+28% at ambient and +48% at elevated CO₂) and instantaneous leaf water use efficiency, derived from short-term measurements of assimilation and transpiration rate, declined (-11% at ambient and -13% at elevated CO₂). Nevertheless, at the stand level, growth at + 2.5°C reduced transpiration due to fewer tillers per plant and a smaller leaf area per tiller. This sparser vegetation was also more closely coupled to the atmosphere and maintained a drier internal microclimate. To assess whether the stomatal behaviour observed in this experiment could be explained by prevailing concepts of stomatal functioning, three models were applied (Cowan 1977; Ball, Woodrow & Berry 1987; Leuning 1995). The latter model accounted for the highest proportion of variability in the data (58%) and was insensitive to CO₂ and temperature regime, which suggests that the principles of stomatal regulation are not affected by changes in CO₂ or climate.     

Simulation of protein diffusion: a sensitive probe of protein–solvent interactions

Aqueous solutions of Candida antarctica lipase B (CALB) were simulated considering three different water models (SPC/E, TIP3P, TIP4P) by a series of molecular dynamics (MD) simulations of three different box sizes (L = 9, 14, and 19 nm) to determine the diffusion coefficient, the water viscosity and the protein density. The protein–water systems were equilibrated for 500 ns, followed by 100 ns production runs which were analysed. The diffusional properties of CALB were characterized by the Stokes radius (R_S), which was derived from the diffusion coefficient and the viscosity. R_S was compared to the geometric radius (R_G) of CALB, which was derived from the protein density. R_S and R_G differed by 0.27 nm for SPC/E and by 0.40 and 0.39 nm for TIP3P and TIP4P, respectively, which characterizes the thickness of the diffusive hydration layer on the protein surface. The simulated hydration layer of CALB resulted in agreement with those experimentally determined for other seven different proteins of comparable size. By avoiding the most common pitfalls, protein diffusion can be reliably simulated: simulating different box sizes to account for the finite size effect, equilibrating the protein–water system sufficiently, and using the complete production run for the determination of the diffusion coefficient.     

Molecular Dynamics Simulation of a Micellar System

We present the results of an atomistic molecular dynamics simulation based on the AMBER/OPLS force field applied to segments of isolated one-dimensional micelles, 2,3,6,7,10,11-Hexa-(1,4,7-Trioxaoctyl)-Triphenylene, in aqueous solution using the SPC/E water model. The quantities which we study include the intra-micellar monomer structure, e.g., the equilibrium monomer-monomer separation along the micelle, the micelle-water interface, which yields the effective micellar diameter, and the flexibility of the micelle in terms of its persistence length as a function of temperature. In addition, we determine the micelle size distribution at low concentration via the free enthalpy gain per monomer-monomer contact using a hydration shell model in combination with thermodynamic integration. Finally, we locate the isotropic-to-nematic transition by using our results as input for an analytical model.