Polar Water Molecules Research Articles

Entropy-Enthalpy Compensations Fold Proteins in Precise Ways.

Exploring the protein-folding problem has been a longstanding challenge in molecular biology and biophysics. Intramolecular hydrogen (H)-bonds play an extremely important role in stabilizing protein structures. To form these intramolecular H-bonds, nascent unfolded polypeptide chains need to escape from hydrogen bonding with surrounding polar water molecules under the solution conditions that require entropy-enthalpy compensations, according to the Gibbs free energy equation and the change in enthalpy. Here, by analyzing the spatial layout of the side-chains of amino acid residues in experimentally determined protein structures, we reveal a protein-folding mechanism based on the entropy-enthalpy compensations that initially driven by laterally hydrophobic collapse among the side-chains of adjacent residues in the sequences of unfolded protein chains. This hydrophobic collapse promotes the formation of the H-bonds within the polypeptide backbone structures through the entropy-enthalpy compensation mechanism, enabling secondary structures and tertiary structures to fold reproducibly following explicit physical folding codes and forces. The temperature dependence of protein folding is thus attributed to the environment dependence of the conformational Gibbs free energy equation. The folding codes and forces in the amino acid sequence that dictate the formation of β-strands and α-helices can be deciphered with great accuracy through evaluation of the hydrophobic interactions among neighboring side-chains of an unfolded polypeptide from a β-strand-like thermodynamic metastable state. The folding of protein quaternary structures is found to be guided by the entropy-enthalpy compensations in between the docking sites of protein subunits according to the Gibbs free energy equation that is verified by bioinformatics analyses of a dozen structures of dimers. Protein folding is therefore guided by multistage entropy-enthalpy compensations of the system of polypeptide chains and water molecules under the solution conditions.

Effective and Rapid Removal of Polar Organic Micropollutants from Water by Amide Naphthotube‐Crosslinked Polymers

AbstractIt is challenging to remove polar organic micropollutants from water through adsorption‐mediated processes. Macrocycle‐crosslinked polymers were recently shown to be effective adsorbents for nonpolar or charged organic micropollutants through specific host–guest binding, but are rarely used for the treatment of neutral and polar organic micropollutants. This is due to the challenge of recognizing polar molecules in water by macrocyclic hosts. In this research, we report two amide naphthotube‐crosslinked polymers which can effectively and rapidly adsorb a wide scope of polar organic micropollutants from water through biomimetic molecular recognition. Amide naphthotubes possess hydrogen bonding sites in their deep hydrophobic cavities and can effectively bind polar organic micropollutants in water through the hydrophobic effects and shielded hydrogen bonds. The cross‐linked polymers containing amide naphthotubes are even able to remove a complex mixture of organic micropollutants from water and the used materials can be easily regenerated through washing with MeOH or EtOH. This research provides a solution for the treatment of polar organic micropollutants by using biomimetic molecular recognition in water.

Effective and Rapid Removal of Polar Organic Micropollutants from Water by Amide Naphthotube-Crosslinked Polymers.

It is challenging to remove polar organic micropollutants from water through adsorption-mediated processes. Macrocycle-crosslinked polymers were recently shown to be effective adsorbents for nonpolar or charged organic micropollutants through specific host-guest binding, but are rarely used for the treatment of neutral and polar organic micropollutants. This is due to the challenge of recognizing polar molecules in water by macrocyclic hosts. In this research, we report two amide naphthotube-crosslinked polymers which can effectively and rapidly adsorb a wide scope of polar organic micropollutants from water through biomimetic molecular recognition. Amide naphthotubes possess hydrogen bonding sites in their deep hydrophobic cavities and can effectively bind polar organic micropollutants in water through the hydrophobic effects and shielded hydrogen bonds. The cross-linked polymers containing amide naphthotubes are even able to remove a complex mixture of organic micropollutants from water and the used materials can be easily regenerated through washing with MeOH or EtOH. This research provides a solution for the treatment of polar organic micropollutants by using biomimetic molecular recognition in water.

Influence of additives on rheological and textural properties of cellulose based fat mimetic

Cellulose based fat mimetics play important role in substitution of fat in reduced fat food products. Production of food often includes application of additives. This work examines the influence of additives on the obtaining stable fat mimetic based on fibers of microcrystalline cellulose. Applied additives affect to the durability of food products and increase their shelf life. The influence of added additives was observed trough the rheological and textural properties of MCG fat mimetic, thus its further functional characteristics. Increasing concentration of fibers positively influenced to crosslinking during hydration and increased strength and consistency of obtained gel. But, application of small hydrophilic molecules of additives disturbed rheological and textural properties of fat mimetics. Obtained gels were still with the thixotropic behavior, but with significantly reduced viscoelastic properties, consistency, firmness and cohesiveness. Based on results, in the aim to ensure obtaining of stable, cross–linked gel of fat mimetic with adequate rheological, textural and functional properties, the mixture of additives is added after the hydration of fat mimetic gels, because of competition for polar water molecules between small additives molecules and available hydroxyl groups of cellulose chains.

The influence of cations on the dipole moments of neighboring polar molecules

AbstractIn this article we show how the dipole moment of a single molecule in a cluster can be calculated and used for describing the polarization effect. Additionally, we review the accuracy of the calculation of the dipole moment of several simple protic and aprotic molecules. It is shown that the dipole moment of polar (water, methanol, formamide, acetone and acetonitrile) molecules in the neighborhood of a cation is increased primarily by polarization from the bare electrostatic charge of the cation, although the effective value of the latter is somewhat reduced by “back donation” of electrons from neighboring polar molecules. In other words, the classical picture may be viewed as if a point charge slightly smaller than the nominal charge of the cation would be placed at the cation site. It was found that the geometrical arrangement of the polar molecules in the first solvation shell is such that their mutual polarization reduces the dipole moments of individual molecules, so that in some cases they become smaller than the dipole moment of the free protic or aprotic molecule. We conjecture, for the first time, that this behavior, namely the about 10%–20% decrease of the dipole moment of water in the first shell of cations, with the cation itself removed, is essentially a manifestation of the Le Chatelier–Braun principle. We also remark that if the cation‐molecule bond order is too large then the calculated dipole moment for these complexes can be questionable, due to the questionable definition of a single molecule within the “supermolecule”‐like cluster.

Understanding supercooling mechanism in sodium sulfate decahydrate phase-change material

Salt hydrate-based phase-change materials are considered promising for future heat storage applications in residential heating/cooling systems. Smooth phase transition from the liquid to solid phase and vice versa is essential for effective heat exchanger; however, supercooling in salt hydrates delays the onset of liquid–solid phase transition. We investigate the molecular level mechanism of supercooling in sodium sulfate decahydrate (SSD). SSD is a complex salt hydrate whose properties are governed by electrostatic forces that include pure Coulombic interactions as well as hydrogen bonds. Experimentally, we examine the importance of a nucleator in reducing supercooling temperatures. We investigated the effect of various mass concentrations of a borax nucleator on a decrease of supercooling temperatures. Molecular dynamics simulation techniques are used to obtain a basic understanding of supercooling in SSD. We observe that by introducing borax as a nucleator, there is a decrease in the supercooling temperature before nucleation. Our molecular dynamics simulations show that long-range electrostatics between sodium and sulfate ion pairs and that with polar water molecules is responsible for delayed nucleation in SSD that results in supercooling, and also, dynamics of charged molecules slows down. The lack of crystallization leads to amorphous structures in supercooled SSD.

Robust cleaning mechanism permanently detaches hydrocarbon species from silicate surfaces by amphiphiles

This paper studies the role of 1-methyl-2-pyrrolidone (NMP) additive to enhance the desorption power of toluene to detach the bitumen from siliceous surfaces. The latter desorption is critical for successful recycling of old asphalt roads where aged bitumen is expected to come off the stones and blend with virgin bitumen used in construction of new roads. Toluene, a documented neurotoxin, has been commonly used to separate aged bitumen from siliceous surface; increasing toluene desorption power and dosage efficiency allows reduced application rate leading to significant environmental and economic benefits. Here, we used the laboratory experiments and computational modeling to understand mechanism of desorption afforded by a hybrid solvent made from blends of toluene and NMP. Our results showed the hybrid solvent interacts with both bitumen and siliceous surfaces; this in turn allows the solvent not only dissolve the asphaltene agglomerates in aged bitumen, but also supersede bitumen compounds for adsorption to silica. Our modeling revealed the hybrid solvent creates an amphiphile that is both able to attach to the asphaltene molecules and interact with polar water molecules, thus making a monolithic cluster that is easy to detach from the siliceous surface under hydraulic pressure. This was further evidenced in a high reduction in the shear-thinning rate of bitumen-silica matrix when hybrid solvent was introduced; for instance, in the case of severely aged bitumen bonded to silica, shear-thinning rate reduced by 60% when hybrid solvent was introduced. Study outcomes provide insights into the merits of using hybrid solvent for desorption as well as its working mechanism. Such insights set a path for future efforts in pavement recycling and promote resource conservation and sustainable development.

Effect of Relative Humidity on Micropitting Behavior in Rolling–Sliding Contacts with Zinc Dialkyldithiophosphate-Containing Lubricants

Two different lubricants containing zinc dialkyldithiophosphate (ZDDP) additive were tested in a rolling–sliding contact test rig (micropitting rig) at different relative humidities. The effect of relative humidity on the bulk properties (e.g., viscosity, water concentration, water saturation level) of the lubricants and their tribological performance (e.g., friction, wear, micropitting level) as well as the related tribochemistry was extensively explored. Relative humidity had a limited effect on the viscosity of the tested lubricants. However, the friction and micropitting level decreased, while the wear increased at higher relative humidity. This increased wear was attributed to a thinner tribofilm and shorter chain length of the polyphosphates derived from the ZDDP additive. Hydrolysis of the ZDDP additive occurred, and the polar water molecules limited the access of the ZDDP additive to the substrate. The different polarities of the two base oils (Ester, polyalphaolefin) also led to different tribological and tribochemical performance.

Kinesin ATP Hydrolysis Requires Proton Tunneling within the Zundel Cation and a Second Proton Transfer

Occurring between hydrogen-bonded networks of polar residues and water molecules, proton transfer reactions are essential in energy conversion, transduction, and storage in biological systems. Here, we determine the contribution of proton transfer to the biological acceleration of ATP hydrolysis in kinesins. A novel two-water cluster, or a Zundel cation, was observed to be hydrogen-bonded to a salt bridge in the kinesin motor protein active site. Solvent kinetic isotope experiments showed proton abstraction from the two-water cluster commits kinesin to catalysis.

Production of green electricity from strained BaTiO3 and TiO2 ceramics based hydroelectric cells

Electricity generation from water molecules dissociation instantly without use of any chemical/light by invented hydroelectric cell (HEC) has emerged a new field of green energy generation without disturbing the environment. Specially engineered nanoporous and oxygen deficient metal oxides have already shown drastic capability of water dissociation at room temperature. In this direction we have heat treated TiO2 (TO) and synthesized BaTiO3 (BTO) in which oxygen defect induced strain through processing has been obtained. Oxygen vacancies produced in TO and BTO have been confirmed by Photoluminescence spectroscopy (PL). The cation-oxygen vacancy pairs (Ti+3-Vo) on the BTO surface provide acid-base pair to attract polar water molecules to get chemidissociated into OH− and H3O+ ions. Further chemisorbed surface hydroxyl ions provide high surface charge potential to physisorbed multilayer of water molecules dissociation and some of H3O+ ions get trapped inside the nanopores. The trapped ions inside nanopores generate enough charge potential to further physi-dissociate adsorbed water molecules. Titanium dioxide samples exhibit increase in strain that has been estimated from the X-ray diffraction results. Bond length and bond angle in both of TiO2 (TO) and BaTiO3 (BTO) decrease while strain increases in their lattice structure. A circular disc of 2 cm diameter and 1 mm thickness of TiO2 and BaTiO3 have been fabricated as hydroelectric cell. BTO based HEC of area 3.14 cm2 generated maximum current 3.66 mA and voltage 0.975 V. Varying the synthesis parameters to produce more defects in the compound may further increase electricity generation. Perovskite based HEC is very stable, repetitive and eco-friendly technique for portable green electricity generation.

Energy of adsorption of polar molecules on NaLSX zeolite

The article presents precision data of isotherms and total thermodynamic characteristics, i.e. ΔH, ΔF and ΔS of H2O adsorption on NaLSX zeolite. The stepwise nature of the change in the heat of adsorption on the studied systems with surface filling is revealed, and the molecular mechanism of water adsorption on NaLSX zeolite in the entire filling area is revealed. It was found that the polar water molecule is adsorbed in the NaLSX zeolite in an amount of 31.8 H2O/1/8 e.u., of which 25.3 are in super cavities, and 6.5 are in β-cavities.

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

Abstract A 14N and 1H NMR spectroscopic study was carried out to shed light on microscopic aspects of the reaction of model alkylamines at a supercritical temperature of 400 °C. It is disclosed that NH3 and ROH (R = CH3CH2 and CH3 (CH2)3) are initially produced from the hydrolysis of ethylamine and butylamine, respectively. When the water density is doubled from 0.2 g cm−3, the pseudo-first-order reaction rate is markedly enhanced beyond the linear response. It suggests that the transition state of the C-N bond cleavage is in a dipolar (ionic) state that can be more stabilized due to the many-body solvation by highly polar water molecules at a higher density.

C−S−H gel structure and water molecules behaviors under different chemical environments in a range of temperatures

Cement based materials are especially vulnerable to serious temperature changes in saline land or marine environments, resulting in the degradation of structures and properties. As the main binding components in cement based materials, the investigation of the C−S−H gel structure and water molecules behaviors enabled the detail damage mechanism of cement-based material under different temperatures. In this study, C−S−H gel models were successfully constructed with the final chemical formula of (CaO)1.65(SiO2)(H2O)1.79. Systematical research works were performed on the structures and properties of both C−S−H gel and water molecules in different local environments by molecular dynamics (MD) under temperatures ranging from 100 K to 500 K. Subsequently, the time correlation function (TCF) and mean square displacement (MSD) methods were introduced to explore the dynamic properties of various chemical bonds. The volume expansion of C−S−H gel under higher temperatures resulted from stretched bond length between silicon atoms and oxygen atoms, and variation of corresponding bond angles. In addition, higher temperatures promoted the prolonged hydrogen bond length, thus reduced the number of hydrogen bond. Moreover, the polarization of water molecules was weakened gradually under higher temperatures, but water molecules’ orientation fluctuated obviously along the out of plane directions of interlayer region. Additionally, MSD results revealed that water molecules showed temperature dependent diffusion behaviors in different chemical environments.

Accurate Crystal Structure Refinement of Natrolite and Localization of Free Water

Crystals that contain water molecules spaced by distances excluding their chemical interaction are model systems for studying the so-called “water ferroelectricity”: ordering of polar water molecules, interacting via electric dipole bonds. Natrolite crystal Na2(Al2Si3O10)(H2O)2, which contains water molecules localized in cages (isolated cavities) formed by framework ions, has been investigated by X-ray diffraction (XRD) analysis at 93 K (sp. gr. Fdd2, Z = 8, a = 18.24822(6) A, b = 18.59561(8) A, c = 6.57868(4) A, R1(|F|)/wR2(|F|) = 1.149/1.294%, and Δρmin/Δρmax = –0.19/0.17 e/A3 for 11 145 independent reflections). Hydrogen atomic parameters have been refined in the anisotropic approximation of atomic displacements, which made it possible to determine the orientation of water molecules. The mineral under investigation is a model object for spectroscopic analysis of water ferroelectricity.

Water splitting on the mesoporous surface and oxygen vacancies of iron oxide generates electricity by hydroelectric cell

The impact of water splitting by specially processed maghemite/iron oxide for generating ecologically sustainable, low-cost green electricity is a vital step. In the present work, a facile and a low-cost chemical synthesis technique has been adopted to produce versatile, oxygen deficient, mesoporous maghemite (iron oxide) nanostructure. The maghemite nanoparticles have been synthesized by the oxidation of magnetite nanoparticles, using a coprecipitation technique followed by heat treatment at elevated temperature 350 °C for 2 h. In the modified process, oxygen (VO) and iron vacancies (VFe) in maghemite have been systematically created. The VFe sites generated at octahedral sites due to Fe2+ ion oxidation has been estimated by Raman and X-ray photoelectron spectroscopy (XPS). Water splitting is prominently occurring at VO sites. Splitting of polar water molecules on the surface oxygen vacancies of nanoporous ferrite and metal oxide pellets has been translated into a primary hydroelectric cell by attaching two dissimilar electrodes to the pellets to generate an electric current. However, preferable associative water adsorption on VFe sites have been confirmed by unique XPS bands with multilayered physisorbed water adsorption modes. The role of VFe, VO sites in water molecule dissociation, and further dissociated ions diffusion kinetics through respective maghemite and magnetite pellets has been thoroughly explored by dielectric measurements. Maghemite based hydroelectric cell (HEC) has delivered a maximum current of 19 mA and emf 0.85 V by using only 200 μL water. The maximum electrical power 16.15 mW delivered by maghemite HEC is 0.58, 0.42 times lower than the respective magnetite, hematite HECs. The magnitude of dielectric relaxation is reduced in maghemite due to preferable associative water adsorption on VFes compared to other iron oxides. Hence, lesser VO concentration, larger average pore size along with the presence of hydrophobic VFe sites are responsible for the lower performance of maghemite based HEC. Variation in spinel magnetite, maghemite HEC performance has been analysed by simulating its V–I characteristic curve. The electricity generation by maghemite HEC is reduced due to lower VO concentration along with the presence of hydrophobic VFe sites reducing the overall number of dissociated ions. Hydroelectric cell from earth- abundant iron oxide is an eco-friendly, bio-compatible, and cost-effective green energy source by water splitting at room temperature.

Electrical double layer interactions between soil colloidal particles: Polarization of water molecule and counterion

The electrical double layer (EDL) interactions strongly affect aggregation and dispersion of soil colloidal particles. In this research a modified model taking the polarization of water molecule and counterion into account was proposed based on nonlinear Poisson-Boltzmann theory to describe electrostatic interaction. The polarizations of both the counterion and the water molecule can increase the interaction between ion/water and soil particle surface, and then decrease the surface potential. Particle surface potential also depends on the surface separation when the EDL overlaps. The midpoint potential between colloidal particles decreases with increase of ion polarization but increases in the presence of water polarization through the change of the double layer thickness. Both the electrostatic repulsive pressure between soil particles and its force range increase markedly in the presence of the polarization of water molecules, but decrease with increase of counterion polarization. The water molecule polarization, rather than the counterion polarization, contributes more to EDL interactions. The counterion polarization is the origin of Hofmeister effects of the EDL interactions, which is affected by water polarization. The theoretical predicted force curve between clay particles by the modified model was verified by the experimental determination of surface force. In addition, the hydration force, fitted to a double exponential decay function, can be estimated by subtraction of the electrostatic interaction force based on DLVO theory from that based on the present model.

Probing the Proton-Loading Site of Cytochrome C Oxidase Using Time-Resolved Fourier Transform Infrared Spectroscopy.

Crystal structure analyses at atomic resolution and FTIR spectroscopic studies of cytochrome c oxidase have yet not revealed protonation or deprotonation of key sites of proton transfer in a time-resolved mode. Here, a sensitive technique to detect protolytic transitions is employed. In this work, probing a proton-loading site of cytochrome c oxidase from Paracoccus denitrificans with time-resolved Fourier transform infrared spectroscopy is presented for the first time. For this purpose, variants with single-site mutations of N131V, D124N, and E278Q, the key residues in the D-channel, were studied. The reaction of mutated CcO enzymes with oxygen was monitored and analyzed. Seven infrared bands in the “fast” kinetic spectra were found based on the following three requirements: (1) they are present in the “fast” phases of N131V and D124N mutants, (2) they have reciprocal counterparts in the “slow” kinetic spectra in these mutants, and (3) they are absent in “fast” kinetic spectra of the E278Q mutant. Moreover, the double-difference spectra between the first two mutants and E278Q revealed more IR bands that may belong to the proton-loading site protolytic transitions. From these results, it is assumed that several polar residues and/or water molecule cluster(s) share a proton as a proton-loading site. This site can be propionate itself (holding only a fraction of H+), His403, and/or water cluster(s).

Competitive adsorption of benzene and water vapor on lignite-based activated carbon: Experiment and molecular simulation study

Exploring the effect of water vapor on the benzene adsorptive behavior is of practical importance and scientific interest. The presence of water vapor in the gas stream altered the breakthrough curves of benzene, as well as the selectivity of carbon materials towards adsorbates. The work herein elucidated the competitive adsorption mechanism based on experimental observation and molecular simulation. At relative humidity (RH) 10%, water molecules showed less effect on the benzene adsorption that benzene entered the micropores and mesopores while water molecules were primarily adsorbed in the mesopores. Since the polar water molecules presented higher affinity towards the surface functionalities, these molecules preferentially occupied the adsorption site via hydrogen bonding with increased RH. Water cluster was gradually formed through water-water interactions which were characteristics of pore filling. A two-layer stacking of adsorbates was observed for co-adsorption. The first layer was primarily composed of water molecules with the average distance of 2.99 ~ 3.19 Å to the surface functionalities. The second layer was primarily benzene molecules which were aggregated in T-shaped, displaced T-shaped and parallel configurations. These molecules were separated at 4.67 ~ 6.17 Å from the functional groups, and mainly adsorbed by water-benzene interaction (via hydrogen bonding).

Molecular Mean-Field Theory of Ionic Solutions: A Poisson-Nernst-Planck-Bikerman Model.

We have developed a molecular mean-field theory—fourth-order Poisson–Nernst–Planck–Bikerman theory—for modeling ionic and water flows in biological ion channels by treating ions and water molecules of any volume and shape with interstitial voids, polarization of water, and ion-ion and ion-water correlations. The theory can also be used to study thermodynamic and electrokinetic properties of electrolyte solutions in batteries, fuel cells, nanopores, porous media including cement, geothermal brines, the oceanic system, etc. The theory can compute electric and steric energies from all atoms in a protein and all ions and water molecules in a channel pore while keeping electrolyte solutions in the extra- and intracellular baths as a continuum dielectric medium with complex properties that mimic experimental data. The theory has been verified with experiments and molecular dynamics data from the gramicidin A channel, L-type calcium channel, potassium channel, and sodium/calcium exchanger with real structures from the Protein Data Bank. It was also verified with the experimental or Monte Carlo data of electric double-layer differential capacitance and ion activities in aqueous electrolyte solutions. We give an in-depth review of the literature about the most novel properties of the theory, namely Fermi distributions of water and ions as classical particles with excluded volumes and dynamic correlations that depend on salt concentration, composition, temperature, pressure, far-field boundary conditions etc. in a complex and complicated way as reported in a wide range of experiments. The dynamic correlations are self-consistent output functions from a fourth-order differential operator that describes ion-ion and ion-water correlations, the dielectric response (permittivity) of ionic solutions, and the polarization of water molecules with a single correlation length parameter.

Tailor-Made Zeolitic Water Nanochannels for Liquid Fuel Production

Conversion of CO2 into valuable liquid fuels or other chemicals has been one of the attractive ways for effective utilization of CO2 produced by burning fossil fuels. However, this task is challenging due to the difficulties associated with the chemical inertness of CO2. In addition to research efforts devoted to the development of more active and selective catalysts for CO2 hydrogenation reaction, removing the by-product water from the system is proven beneficial for improving the reaction thermodynamics and kinetics toward desirable products. Therefore, highly water-selective membranes able to operate under reaction conditions like high temperature and pressure have long been pursued. In a recent study, Yu et al. reported a zeolite membrane with gas-impeding water-conduction nanochannels that selectively remove by-product water from CO2 dehydrogenation process, greatly enhancing CO2 conversion and methanol yield.