Total Number Of Water Molecules Research Articles

Deciphering the mechanism of γ-cyclodextrin's hydrophobic cavity hydration: an integrated experimental and theoretical study.

Cyclodextrins (CDs) are host systems with inherent capability for inclusion complex formation with various molecular entities, mostly hydrophobic substances. Host CDs are highly accommodative to water molecules as well and usually contain water in the native state. There is still an ongoing discussion on both the total number of water molecules and their preferred binding position inside the cavities of the CDs. To understand the hydration/dehydration properties of γ-CD (the largest of the three most abundant native CDs), the main experimental methods applied in this study were differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). By coupling these techniques with density functional theory (DFT) calculations we try to shed some light on the mechanism of the γ-CD hydration and to address some unanswered questions: (i) what are the preferable locations for water molecules in the macrocyclic cavity ("hot spots"); (ii) what are the major factors contributing to the stability of the water cluster in the CD interior; (iii) what type of interactions (i.e., water-water and/or water-CD walls) contribute to the stability of the water assemble; (iv) how does the mechanism of the γ-CD hydration compare with those of its α-CD and β-CD counterparts.

Next generation multimodal chromatography resins via an iterative mapping approach: Chemical diversity, high-throughput screening, and chromatographic modelling

Multimodal chromatography resins are becoming a key tool in the purification of biomolecules. The main objective of this research was the establishment of an iterative framework for the rapid development of new multimodal resins to provide novel selectivity for the future purification challenges. A large chemically diverse virtual library of 100 multimodal Capto™ MMC ligand analogues was created, and a broad array of chemical descriptors were calculated for each ligand in silico. Principal component analysis (PCA) was used to map the chemical diversity and guide selection of ligands for synthesis and coupling to the Capto ImpRes agarose base matrix. Twelve new ligands were prepared in two groups: ‘group one’ consist of L00-L07 and ‘group two’ consist of L08-L12. These ligands are diverse in the influence of varied secondary interactions such as hydrophobic interactions, H-bonding, etc. Additional resin prototypes were also prepared to look at the chromatographic impact of ligand density variation. High-throughput plate-based studies were performed for parallel resin screening for batch-binding of six model proteins at different chromatographic binding pH and sodium chloride concentration conditions. Principal component analysis of the binding data provided a chromatographic diversity map leading to the identification of ligands with improved binding. Further, the new ligands have improved separation resolution between a monoclonal antibody (mAb1) and product related impurities, a Fab fragment and high molecular weight (HMW) aggregates, using linear salt gradient elutions. To quantify the importance of secondary interactions, analysis of the retention factor of mAb1 on the ligands at various isocratic conditions lead to estimations of (a) the total number of water molecules and counter salt ions released during adsorption, and (b) hydrophobic contact area (HCA). The iterative mapping approach of chemical and chromatography diversity maps described in the paper proves to be a promising method for identifying new chromatography ligands for biopharmaceutical purification challenges.

Molecular dynamics study of water confined in MIL-101 metal–organic frameworks

Molecular dynamics simulations of water adsorbed in Material Institute Lavoisier MIL-101(Cr) metal-organic frameworks are performed to analyze the kinetic properties of water molecules confined in the framework at 298.15 K and under different vapor pressures and clarify the water adsorption mechanism in MIL-101(Cr). The terahertz frequency-domain spectra (THz-FDS) of water are calculated by applying fast Fourier transform to the configurational data of water molecules. According to the characteristic frequencies in the THz-FDS, the dominant motions of water molecules in MIL-101(Cr) can be categorized into three types: (1) low-frequency translational motion (0-0.5 THz), (2) medium-frequency vibrational motion (2-2.5 THz), and (3) high-frequency vibrational motion (>6 THz). Each type of water motion is confirmed by visualizing the water configuration in MIL-101(Cr). The ratio of the number of water molecules with low-frequency translational motion to the total number of water molecules increases with the increase in vapor pressure. In contrast, that with medium-frequency vibrational motion is found to decrease with vapor pressure, exhibiting a pronounced decrease after water condensation has started in the cavities. That with the high-frequency vibrational motion is almost independent of the vapor pressure. The interactions between different types of water molecules affect the THz-FDS. Furthermore, the self-diffusion coefficient and the velocity auto-correlation function are calculated to clarify the adsorption state of the water confined in MIL-101(Cr). To confirm that the general trend of the THz-FDS does not depend on the water model, the simulations are performed using three water models, namely, rigid SPC/E, flexible SPC/E, and rigid TIP5PEw.

Constraining spatial pattern of early activity of comet 67P/C–G with 3D modelling of the MIRO observations

ABSTRACT Our aim is to investigate early activity (2014 July) of 67P/C–G with 3D coma and radiative transfer modeling of Microwave Instrument on the Rosetta Orbiter (MIRO) measurements, accounting for nucleus shape, illumination, and orientation of the comet. We investigate MIRO line shape information for spatial distribution of water activity on the nucleus during the onset of activity. During this period we show that MIRO line shape have enough information to clearly isolate contribution from ‘neck’ (Hapi) and bottom of large lobe (Imhotep), and compare it to the nominal case of activity from the entire illuminated surface. We also demonstrate that spectral line shapes differ from the 1D model for different viewing geometries and coma conditions relevant to this study. Specifically, line shapes are sensitive to the location of the terminator in the coma. At last, fitting the MIRO observations we show that the Imhotep region (possible distributed source of H2O sublimating from the icy grains in the coma lifted due to CO2 activities) contributes negligible fraction of the total number of water molecules into MIRO beam in the early activity. On the other hand, a strong enhancement of water activity from the ‘neck’ region seems required to fit the MIRO line shapes. This is consistent with earlier analysis of Rosetta results. Nevertheless, within the assumption of our coma and surface boundary conditions we cannot get a reasonable fit to all MIRO mapping observations in 2014 July. We provide discussion on how to enhance these results and resolve the found issues in the future.

Thermodynamic modeling of protein retention in mixed-mode chromatography: An extended model for isocratic and dual gradient elution chromatography

An extended model is developed to describe protein retention in mixed-mode chromatography based on thermodynamic principles. Special features are the incorporation of pH dependence of the ionic interaction on a mixed-mode resin and the addition of a water term into the model which enables one to describe the total number of water molecules released at the hydrophobic interfaces upon protein-ligand binding. Examples are presented on how to determine the model parameters using isocratic elution chromatography. Four mixed-mode anion-exchanger prototype resins with different surface chemistries and ligand densities were tested using isocratic elution of two monoclonal antibodies at different pH values (7–10) and encompassed a wide range of NaCl concentrations (0–5M). U-shape mixed-mode retention curves were observed for all four resins. By taking into account of the deprotonation and protonation of the weak cationic functional groups in these mixed-mode anion-exchanger prototype resins, conditions which favor protein-ligand binding via mixed-mode strong cationic ligands as well as conditions which favor protein-ligand binding via both mixed-mode strong cationic ligands and non-hydrophobic weak cationic ligands were identified. The changes in the retention curves with pH, salt, protein, and ligand can be described very well by the extended model using meaningful thermodynamic parameters like Gibbs energy, number of ionic and hydrophobic interactions, total number of released water molecules as well as modulator interaction constant. Furthermore, the fitted model parameters based on isocratic elution data can also be used to predict protein retention in dual salt-pH gradient elution chromatography.

Proton transfer through hydrogen bonds in two-dimensional water layers: A theoretical study based on ab initio and quantum-classical simulations

The dynamics of proton transfer (PT) through hydrogen bonds in a two-dimensional water layer confined between two graphene sheets at room temperature are investigated through ab initio and quantum-classical simulations. The excess proton is found to be mostly solvated as an Eigen cation where the hydronium ion donates three hydrogen bonds to the neighboring water molecules. In the solvation shell of the hydronium ion, the three coordinated water molecules with two donor hydrogen bonds are found to be properly presolvated to accept a proton. Although no hydrogen bond needs to be broken for transfer of a proton to such presolvated water molecules from the hydronium ion, the PT rate is still found to be not as fast as it is for one-dimensional chains. Here, the PT is slowed down as the probability of finding a water with two donor hydrogen bonds in the solvation shell of the hydronium ion is found to be only 25%-30%. The hydroxide ion is found to be solvated mainly as a complex anion where it accepts four H-bonds through its oxygen atom and the hydrogen atom of the hydroxide ion remains free all the time. Here, the presolvation of the hydroxide ion to accept a proton requires that one of its hydrogen bonds is broken and the proton comes from a neighboring water molecule with two acceptor and one donor hydrogen bonds. The coordination number reduction by breaking of a hydrogen bond is a slow process, and also the population of water molecules with two acceptor and one donor hydrogen bonds is only 20%-25% of the total number of water molecules. All these factors together tend to slow down the hydroxide ion migration rate in two-dimensional water layers compared to that in three-dimensional bulk water.

Unfolding Action of Alcohols on a Highly Negatively Charged State of Cytochrome c

It is well-known that hydrophobic effect play a major role in alcohol-protein interactions leading to structure unfolding. Studies with extremely alkaline cytochrome c (U(B) state, pH 13) in the presence of the first four alkyl alcohols suggests that the hydrophobic effect persistently overrides even though the protein carries a net charge of -17 under these conditions. Equilibrium unfolding of the U(B) state is accompanied by an unusual expansion of the chain involving an intermediate, I(alc), from which water is preferentially excluded, the extent of water exclusion being greater with the hydrocarbon content of the alcohol. The mobility and environmental averaging of side chains in the I(alc) state are generally constrained relative to those in the U(B) state. A few nuclear magnetic resonance-detected tertiary interactions are also found in the I(alc) state. The fact that the I(alc) state populates at low concentrations of methanol and ethanol and the fact that the extent of chain expansion in this state approaches that of the U(B) state indicate a definite influence of electrostatic repulsion severed by the low dielectric of the water/alcohol mixture. Interestingly, the U(B) ⇌ I(alc) segment of the U(B) ⇌ I(alc) ⇌ U equilibrium, where U is the unfolded state, accounts for roughly 85% of the total number of water molecules preferentially excluded in unfolding. Stopped-flow refolding results report on a submillisecond hydrophobic collapse during which almost the entire buried surface area associated with the U(B) state is recovered, suggesting the overwhelming influence of hydrophobic interaction over electrostatic repulsions.

A complete volume profile for the reversible binding of camphor to cytochrome P450cam

The effect of pressure on the kinetics and thermodynamics of the reversible binding of camphor to cytochrome P450(cam) was studied as a function of the K(+) concentration. The determination of the reaction and activation volumes enabled the construction of the first complete volume profile for the reversible binding of camphor to P450(cam). Although the volume profiles constructed for the reactions conducted at low and high K(+) concentrations are rather similar, and both show a drastic volume increase on going from the reactant to the transition state and a relatively small volume change on going from the transition to the product state, the position of the transition state is largely affected by the K(+) concentration in solution. Similarly, the activation volume determined for the dissociation of camphor is influenced by the presence of K(+), which reflects changes in the ease of water entering the active site of camphor-bound P450(cam) that depends on the K(+) concentration. Careful analysis of the components that contribute to the observed volume changes allowed the estimation of the total number of water molecules expelled to the bulk solvent during the binding of camphor to P450(cam) and the subsequent spin transition. The results are discussed in reference to other studies reported in the literature that deal with the kinetics and thermodynamics of the binding of camphor to P450(cam) under various reaction conditions.

Cation disorder in NaW 2O 6+ δ· nH 2− zO post-ion exchange with K, Rb, Sr, and Cs

The structure of the defect pyrochlore NaW 2O 6+ δ · nH 2− z O after ion exchange with K, Rb, Sr or Cs for Na has been investigated using thermal analysis, solid-state nuclear magnetic resonance, laboratory X-ray and neutron diffraction methods. Neutron diffraction studies show that both the A-type cations (Na +, K +, Rb +, and/or Cs +) and the water molecules reside within the channels that form in the 111 direction of the W 2O 6 framework and that these strongly interact. The analytical results suggest that the water and A-type cations compete for space in the tunnels within the W 2O 6 pyrochlore framework, with the total number of water molecules and cations being approximately constant in the six samples investigated. The interplay between the cations and water explains the non-linear dependence of the a lattice parameter on the choice of cation. It appears that the ion-exchange capacity of the material will be controlled by the amount of water initially present in the sample.

Computational analysis of water residence on ceramide and sphingomyelin bilayer membranes

Many physical chemical properties of lipid membranes, for example, the thickness, phase state, order parameter, and fluidity, can be understood straightforwardly. Water residence on a membrane is, however, an exception. To tackle this problem, we have performed molecular dynamics simulations of the distribution of water normal to the surface of several lipid membranes and from this deduced the associated water residence time. Our analysis of the results clearly indicates that lipid membranes have hydration shells on their surface, just as a solute in an aqueous solution does, and that the water residence time can be estimated from the potential for the mean force field derived from the distribution function of the water. We have done this atomic-scale analysis for ceramide bilayers and contrasted the calculation results with those for sphigomyelin bilayers, revealing that sphingomyelin bilayers can retain water molecules longer than ceramide bilayers and that the total number of water molecules retained on the membrane surface of sphingomyelin is larger than that for ceramide. In addition, we find that not only polar atoms of lipid molecules, such as oxygen, but also non-polar atoms, such as carbon, influence the motion of water on the membranes.

Effect of hydrogen bonds on polarizability of a water molecule in (H2O)N (N = 6, 10, 20) isomers

Polarizabilities of the low-lying isomers of (H(2)O)(N) (N = 6, 10, 20) clusters were computed by using Density Functional Theory. The global polarizabilities of the water isomers were found to depend mainly on the total number of water molecules rather than their cluster structures. We show that this result hides in fact a strong heterogeneity of the molecular polarizability within the different isomers. The global polarizability of a cluster was divided into a sum of molecular contributions by using the Hirshfeld partitioning scheme. We reveal that the value of the local polarizability of a molecule in the cluster is correlated with the number and type of the hydrogen bonds (HB) the molecule forms. Consequently, the molecules located in the interior of the cluster, which usually form more HBs, have smaller molecular polarizabilities than the molecules at the surface, which form less HBs. The contribution of intermolecular interaction to the global polarizability was analyzed by decomposing the cluster polarizability into intra- and inter-molecular contributions. The former measures the polarization within the molecular basin against the external electric field, while the latter is described as the sum of polarizability caused by charge flow through the HBs. These two contributions vary with the cluster size: the intermolecular contribution decreases with the cluster size on the contrary of the intramolecular contribution which increases.

Solvation of Propylene Oxide in Water: Vibrational Circular Dichroism, Optical Rotation, and Computer Simulation Studies

The solvation of propylene oxide (PO) in water has been studied using vibrational circular dichroism (VCD) spectroscopy, optical rotation dispersion (ORD) spectroscopy, molecular dynamics simulations, and ab initio calculations. VCD and ORD measurements were carried out for PO as neat liquid, in CCl4, and in water solutions. The classical molecular dynamics simulations were carried out for the PO + water binary mixtures at different concentrations, and the solvation information was derived from the radial distribution functions obtained in the simulations. The total number of water molecules within the closest vicinity of PO was predicted to be about 3. The geometry optimizations, vibrational frequencies, and VCD intensities were evaluated for the PO monomer and the PO-(H2O)n clusters with n = 1-3 , using density functional theory calculations at the B3LYP/aug-cc-pVTZ level of theory. The chirality transfer VCD feature, which is a direct result of the explicit H-bonding between water and the chiral PO solute, was detected experimentally at the water bending band region. This feature exhibits high sensitivity to the solvation structure around PO. Comparison of the calculated and experimental chirality transfer features leads to the conclusion that the PO-water binary complex is the dominating species in aqueous solution at room temperature and the anti conformation, where water is on the opposite side of the oxirane ring of the PO methyl group, is preferred over the syn one. This conclusion is also supported by the complementary ORD studies. Possible contributions from the ternary and quaternary PO-water complexes are also discussed.

Quantification of Redox-Induced Thickness Changes of 11-Ferrocenylundecanethiol Self-Assembled Monolayers by Electrochemical Surface Plasmon Resonance

Redox-induced orientation changes (or monolayer thickness changes) of self-assembled monolayers (SAMs) of 11-ferrocenylundecanethiol (FcC11SH) were quantified by the electrochemical surface plasmon resonance (EC-SPR). EC-SPR enables one to determine the collective effect of the monolayer thickness and refractive index changes resulted from the oxidation of ferrocene (Fc) to ferrocenium. To measure the monolayer volume variation associated with the molecular orientation change, an electrochemical quartz crystal microbalance (EQCM) was used to determine the total number of water molecules accompanying with the ion-pairing between the ferrocenium cation and the counteranion in the solution. With the maximum void space within the SAM for water incorporation known, the Lorentz-Lorenz equation was used to correlate the SPR dip shift to the maximum monolayer thickness variation. In the presence of 0.1 M HClO4 and 0.1 M HNO3, the monolayer thickness changes were deduced to be 0.09 and 0.08 nm, respectively. Thus, upon electrochemical oxidation of the FcC11SH SAM, the swinging of the alkyl chain farther away from the electrode (Ye et al., Langmuir, 1997, 13, 3157) or the rotation or flipping of the Fc cyclopentyldiene ring around the bond between the Fc group and the alkyl chain (Viana et al., J. Electroanal. Chem. 2001, 500, 290) can both lead to the observed film thickness changes, with the former probably being the more important process.

Validation of the doubly labeled water method under low and high humidity to estimate metabolic rate and water flux in a tropical snake (Boiga irregularis).

This study uses indirect calorimetry to assess the effects of humidity on the accuracy of the doubly labeled water (DLW) technique to predict metabolic rate and water flux in brown treesnakes (Boiga irregularis). The DLW technique accurately predicted total water efflux in brown treesnakes under low-humidity conditions and found that the total number of water molecules exchanged with the environment under humid conditions was not significantly different than maximum net total evaporative water loss under low humidity conditions plus fecal water loss. Because of changes of total body water of >12%, the DLW technique overestimated metabolic rate by a factor of 2.2 under low-humidity conditions. Under high-humidity conditions, the DLW technique overestimated metabolic rate in brown treesnakes by a factor of 4.6. Researchers using the DLW technique in humid or moist environments should be cautious because this study indicates that DLW estimates of metabolic rate may be inflated when large amounts of water vapor are exchanged through the skin or respiratory passages.

Competitive charge transfer reactions in small [Mg(H2O)N]2+ clusters

Production of stable hydrated magnesium complexes of the general form [Mg(H2O)N]2+ (where 2⩽N⩽24) has been possible using the pick-up technique. Observations of ion intensities as a function of N together with data from collision induced dissociation processes (for ions in the range 3⩽N⩽10), indicates the existence of a closed solvation shell for N=6 to which additional water molecules are strongly bound. Collision-induced charge transfer in ions of all sizes yields solvated magnesium hydroxide ions Mg+OH(H2O)N−M−2 accompanied by the loss of a hydronium ion, H3O+, and M water molecules. For N=3, 4, and 5, the above process is seen to be in competition with charge transfer to unprotonated water, and clusters of the general form Mg(H2O)N−M+ are detected, where M now represents the total number of water molecules lost. These two separate loss channels are interpreted as being due to the presence of different structural (or transient) forms of those cluster ions where N⩽6. One structure corresponds to a highly symmetrical arrangement of the water molecules bonded directly to the magnesium dication, and is responsible for the formation of Mg(H2O)N−M+ ions by charge transfer. In the second type of structure, at least one water molecule moves to an outer solvation shell, but remains hydrogen bonded to a molecule in the first shell. In this latter configuration, it is suggested that the formation of a salt-bridge structure may lower the barrier to proton transfer and lead to the loss of a hydronium ion.

Thermodynamic properties of alkali halides. III. Volumes and heat capacities of transfer from H2O to D2O at 25�C

The volumetric specific heats and densities of alkali fluorides, alkali bromides, and soduum halides were measured in D2O at 25°C in the concentration range 0.05 to 1 aquamolal. The results can be combined with data in H2O to give the corresponding standard and excess transfer functions from H2O to D2O. The volumes and heat capacities of transfer are both negative but, contrary to the hydration functions, show little dependence on ionic size and sign. Also, while heats, entropies, and volumes of transfer are usually small compared with the hydration functions, the heat capacity of transfer is of comparable magnitude. These observations, when interpreted with the Frank and Wen model, suggest that the total number of water molecules in the hydration cosphere is approximately constant for all alkali halides and that heat capacities are more sensitive to structural interactions than volumes and enthalpies. The sign of the excess transfer functions is consistent with the presence of structural ion-ion interactions, but no systematic trend with ionic size can be detected in view of the large experimental uncertainty.