Surrounding Water Molecules Research Articles

Theoretical Investigation of Racemization of Amino Acid using Organic Catalysts

Racemization of amino acid catalyzed by aldehyde and carboxylic acid has been proposed and widely used. Herein, we investigated the detailed racemization mechanism of alanine catalyzed by salicylaldehyde and acetic acid. Quantum chemistry calculations based on the density functional theory demonstrated that the dehydration reaction is the rate-determining step, and this dehydration step is enhanced by surrounding water molecules. We also discussed the dependence of the reaction rates on the type of amino acid.

Isotope Effects on the Vaporization of Organic Compounds from an Aqueous Solution-Insight from Experiment and Computations.

An isotope fractionation analysis of organic groundwater pollutants can assess the remediation at contaminated sites yet needs to consider physical processes as potentially confounding factors. This study explores the predictability of water–air partitioning isotope effects from experiments and computational predictions for benzene and trimethylamine (both H-bond acceptors) as well as chloroform (H-bond donor). A small, but significant, isotope fractionation of different direction and magnitude was measured with ε = −0.12‰ ± 0.07‰ (benzene), εC = 0.49‰ ± 0.23‰ (triethylamine), and εH = 1.79‰ ± 0.54‰ (chloroform) demonstrating that effects do not correlate with expected hydrogen-bond functionalities. Computations revealed that the overall isotope effect arises from contributions of different nature and extent: a weakening of intramolecular vibrations in the condensed phase plus additional vibrational modes from a complexation with surrounding water molecules. Subtle changes in benzene contrast with a stronger coupling between intra- and intermolecular modes in the chloroform–water system and a very local vibrational response with few atoms involved in a specific mode of triethylamine. An energy decomposition analysis revealed that each system was affected differently by electrostatics and dispersion, where dispersion was dominant for benzene and electrostatics dominated for chloroform and triethylamine. Interestingly, overall stabilization patterns in all studied systems originated from contributions of dispersion rather than other energy terms.

Understanding the Dissociation of Hydrogen Bond Based Cross-Links In Hydrogels Due to Hydration and Mechanical Forces

The submersion of a polymer network with a high density of hydrogen bond based cross-links in an aqueous bath results in the formation of a rubberlike hydrogel. The cross-links, which connect chains and maintain the structure of the network, can dissociate as a result of two main factors: (1) the interactions between the hydrogen bonds and the surrounding water molecules and (2) the forces that are exerted on the cross-link from the interconnected chains. We recall that these forces depend on the ratio between the end-to-end distance and the overall contour length of the chains. The application of an external loading translates into the stretching of chains in the network and, as a consequence, an increase in the forces that are exerted. Sufficiently large external loadings can break cross-links and alter the microstructure of the network. From a macroscopic viewpoint, the breaking of cross-links leads to significant microstructural changes such as a reduction in the chain density and an entropic gain. In this work, we derive a microscopically motivated and energy-based model that captures the effects of hydration and external loadings on the overall changes in properties and mechanical response of hydrogels. We provide a systematic method to estimate the percentage of cross-links that dissociate due to hydration and application of a force and provide representative examples to highlight the influence of the orientations of the interconnected chains with respect to a cross-link. To validate the model, we carry out uniaxial tension experiments on poly(methacrylic acid) hydrogels with five different water contents and fit the model parameters. We show that the model is capable of qualitatively and quantitatively capturing the experimental results. The model is also used to approximate the number of cross-links that dissociate due to the water and the externally applied uniaxial force. This work paves the way to the efficient design of multifunctional synthetic hydrogels with programmable properties and behaviors.

Size, interface and temperature effects on specific heat capacities of Cu-water nanofluid and Cu nanoparticle: A molecular analysis

Accurate estimation of specific heat capacity (Cp) is of essential importance for characterization of the heat transfer performance of nanofluids in many applications. In this study, the particle size, interface, and temperature effects on the Cp of Cu-water nanofluid and Cu nanoparticle are systematically studied. Also, the TIP4P rigid and the SPC/Fw flexible water models are compared to demonstrate their influence on the estimation of Cp. The investigation is performed by using the molecular dynamics simulation method, at the mean temperatures of 300 K, 350 K, and 400 K. The results show that the Cp increases with increasing nanoparticles size, but increases with decreasing temperature. The increase is attributed to the interface effect demonstrated by the vibrational density of state (VDOS). The VDOS mismatch is close to zero with the increase in the Cp of the Cu-water nanofluids. In contrast, there is a substantial divergence of the Cp of the nanoparticles from the theoretical values. The reason can be owing to the effect of particle size and the interaction with the surrounding water molecules. Compared to the TIP4P model, the SPC/Fw model shows an increase in the Cp. It is attributed to the intramolecular degrees of freedom that existed in the model, since they provide a small, but probably significant, contribution to intermolecular interactions. This work is helpful for understanding the enhancement mechanisms of specific heat capacity for nanofluids and the suspended nanoparticles used in, e.g., solar thermal applications.

Bridging Structure, Dynamics, and Thermodynamics: An Example Study on Aqueous Potassium Halides.

Aqueous salt systems are ubiquitous in all areas of life. The ions in these solutions impose important structural and dynamic perturbations to water. In this study, we employ a combined neutron scattering, nuclear magnetic resonance, and computational modeling approach to deconstruct ion-specific perturbations to water structure and dynamics and shed light on the molecular origins of bulk thermodynamic properties of the solutions. Our approach uses the atomistic scale resolution offered to us by neutron scattering and computational modeling to investigate how the properties of particular short-ranged microenvironments within aqueous systems can be related to bulk properties of the system. We find that by considering only the water molecules in the first hydration shell of the ions that the enthalpy of hydration can be determined. We also quantify the range over which ions perturb water structure by calculating the average enthalpic interaction between a central halide anion and the surrounding water molecules as a function of distance and find that the favorable anion-water enthalpic interactions only extend to ∼4 Å. We further validate this by showing that ions induce structure in their solvating water molecules by examining the distribution of dipole angles in the first hydration shell of the ions but that this perturbation does not extend into the bulk water. We then use these structural findings to justify mathematical models that allow us to examine perturbations to rotational and diffusive dynamics in the first hydration shell around the potassium halide ions from NMR measurements. This shows that as one moves down the halide series from fluorine to iodine, and ionic charge density is therefore reduced, that the enthalpy of hydration becomes less negative. The first hydration shell also becomes less well structured, and rotational and diffusive motions of the hydrating water molecules are increased. This reduction in structure and increase in dynamics are likely the origin of the previously observed increased entropy of hydration as one moves down the halide series. These results also suggest that simple monovalent potassium halide ions induce mostly local perturbations to water structure and dynamics.

QUAL È LA PIÙ PICCOLA GOCCIA D’ACQUA?

This presentation will bring the reader on a journey across the microscopic world of water clusters. After a brief introduction about molecular spectroscopy, I will show how the semiclassical approximation to quantum molecular dynamics allows for accurate full-dimensional quantum simulations of water cluster vibrational spectra, differently from classical molecular dynamics approaches. I will employ the semiclassical spectroscopy tool to determine the minimal network of surrounding water molecules needed to make the central one display the same vibrational features of liquid water. Remarkably, the minimal surrounding structure eventually responsible for proper solvation is made of just a few water molecules and includes two complete solvation shells.

Identification of difructose dianhydride I synthase/hydrolase from an oral bacterium establishes a novel glycoside hydrolase family

Fructooligosaccharides and their anhydrides are widely used as health-promoting foods and prebiotics. Various enzymes acting on β-D-fructofuranosyl linkages of natural fructan polymers have been used to produce functional compounds. However, enzymes that hydrolyze and form α-D-fructofuranosyl linkages have been less studied. Here, we identified the BBDE_2040 gene product from Bifidobacterium dentium (α-D-fructofuranosidase and difructose dianhydride I synthase/hydrolase from Bifidobacterium dentium [αFFase1]) as an enzyme with α-D-fructofuranosidase and α-D-arabinofuranosidase activities and an anomer-retaining manner. αFFase1 is not homologous with any known enzymes, suggesting that it is a member of a novel glycoside hydrolase family. When caramelized fructose sugar was incubated with αFFase1, conversions of β-D-Frup-(2→1)-α-D-Fruf to α-D-Fruf-1,2′:2,1′-β-D-Frup (diheterolevulosan II) and β-D-Fruf-(2→1)-α-D-Fruf (inulobiose) to α-D-Fruf-1,2′:2,1′-β-D-Fruf (difructose dianhydride I [DFA I]) were observed. The reaction equilibrium between inulobiose and DFA I was biased toward the latter (1:9) to promote the intramolecular dehydrating condensation reaction. Thus, we named this enzyme DFA I synthase/hydrolase. The crystal structures of αFFase1 in complex with β-D-Fruf and β-D-Araf were determined at the resolutions of up to 1.76 Å. Modeling of a DFA I molecule in the active site and mutational analysis also identified critical residues for catalysis and substrate binding. The hexameric structure of αFFase1 revealed the connection of the catalytic pocket to a large internal cavity via a channel. Molecular dynamics analysis implied stable binding of DFA I and inulobiose to the active site with surrounding water molecules. Taken together, these results establish DFA I synthase/hydrolase as a member of a new glycoside hydrolase family (GH172).

In Competition for Water: Hydrated Choline Chloride:Urea vs Choline Acetate:Urea Deep Eutectic Solvents

Unlike the archetypal deep eutectic solvent (DES) choline chloride:urea (ChCl:U), fundamental knowledge of the intermolecular network in choline acetate (ChOAc) DESs and how they change upon dilution is still missing. Here we jointly use UV resonance Raman (UVRR) and NMR spectroscopy to comparatively explore how the strength and distribution of hydrogen bonding and the solvation of the components are modified in ChOAc:U and ChCl:U with increasing hydration. Overall, Raman and NMR data indicate that ChOAc:U is continuously affected by hydration and, even at low water concentrations, undergoes a breakage of DES–DES interactions, with rapid solvation of the urea portion and full exchange of mobile protons. On the contrary, ChCl:U seems to maintain its structure as small interplays gradually occur between urea in the DES and the surrounding water molecules. The combined approach provides a multifaceted consistent description of the systems, outlining the crucial role of the anion in driving the structure and dynamics of the materials and then yielding valuable data toward the exploitation of DESs as tunable systems.

Photo-induced degradation of PFASs: Excited-state mechanisms from real-time time-dependent density functional theory

Per- and polyfluoroalkyl substances (PFASs) are hazardous, carcinogenic, and bioaccumulative contaminants found in drinking water sources. To mitigate and remove these persistent pollutants, recent experimental efforts have focused on photo-induced processes to accelerate their degradation; however, the mechanistic details of these promising degradation processes remain unclear. To shed crucial insight on these electronic-excited state processes, we present the first study of photo-induced degradation of explicitly-solvated PFASs using excited-state, real-time time-dependent density functional theory (RT-TDDFT) calculations. Furthermore, our large-scale RT-TDDFT calculations show that these photo-induced excitations can be highly selective by enabling a charge-transfer process that only dissociates the CF bond while keeping the surrounding water molecules intact. Collectively, the RT-TDDFT techniques used in this work (1) enable a new capability for probing photo-induced mechanisms that cannot be gleaned from conventional ground-state DFT calculations and (2) provide a rationale for understanding ongoing experiments that are actively exploring photo-induced degradation of PFASs and other environmental contaminants.

Molecular behavior of CO2 hydrate growth in the presence of dissolvable ionic organics

Hydration-based techniques involve hydrate formation in complicated systems containing ions and organics. Consequently, it is necessary to understand the molecular behavior of hydrate nucleation and growth in such solutions. This work shows that the hydrate-growth rate in a system containing methylene blue molecules does not necessarily accelerate on increasing the subcooling. Unexpected amorphous cage clusters were observed at a lower temperature of 240 K. To the best of our knowledge, this is the first study to propose that these amorphous clusters act as mass transfer barriers disturbing the agglomeration of solutes. Herein, hydrate growth was accompanied with the exclusion of methylene blue molecules. Although methylene blue can instantaneously reside in the cavity a half-cage structure, they were subsequently replaced by CO2 molecules. Notably, chloride ions were observed to participate in cage building (42510, 512, and 51262 cages) by bonding with the oxygen atoms of the surrounding water molecules. This phenomenon shows an interaction between the methylene blue molecules and hydrate cages during the exclusion process. These results support the current understanding on hydrate formation in the presence of ion-containing organics and could help improve kinetics-dependent applications in separation process.

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

The translational dynamics of water and cyclohexane in supercritical binary mixtures were investigated using molecular dynamics simulations. The effects of the local composition were examined through a decomposition scheme of the conditional time-correlation functions based on the solvation numbers for water and cyclohexane. The self-diffusion of water was found to be largely controlled by the continuous and collective attractive interactions with surrounding water molecules, while interactions with cyclohexane have minimal impact on water diffusion. On the other hand, the self-diffusion of cyclohexane is dominantly determined by uncorrelated collisional interactions with neighboring cyclohexane molecules. The results demonstrate the dynamic aspect of microscopic inhomogeneity and highlight the significance of interactions between molecules of the same species. An examination of the dependence of self-diffusion on the lifetime of the solvation shell indicated that the self-diffusion of water is confined within the solvation shell. This is attributed to the hydrogen bond interactions with neighboring water molecules, which create an energy barrier to the water molecules diffusing out of the hydration cage. In contrast, diffusing cyclohexane molecules migrate beyond the solvation shell, particularly at large water contents.

Origin and control of ionic hydration patterns in nanopores

In order to permeate a nanopore, an ion must overcome a dehydration energy barrier caused by the redistribution of surrounding water molecules. The redistribution is inhomogeneous, anisotropic and strongly position-dependent, resulting in complex patterns that are routinely observed in molecular dynamics simulations. Here, we study the physical origin of these patterns and of how they can be predicted and controlled. We introduce an analytic model able to predict the patterns in a graphene nanopore in terms of experimentally accessible radial distribution functions, giving results that agree well with molecular dynamics simulations. The patterns are attributable to a complex interplay of ionic hydration shells with water layers adjacent to the graphene membrane and with the hydration cloud of the nanopore rim atoms, and we discuss ways of controlling them. Our findings pave the way to designing required transport properties into nanoionic devices by optimising the structure of the hydration patterns.

Synergistic Enhancement of Fluorescence and Magnetic Resonance Signals Assisted by Albumin Aggregate for Dual-Modal Imaging.

Dual-modal fluorescence and magnetic resonance imaging (FLI/MRI) is important for the early diagnosis of malignant tumors. However, facile and opportune strategies to synergistically enhance fluorescence intensity and magnetic resonance (MR) contrast have rarely been reported. Herein, we present a facile strategy using albumin aggregates (AAs) to synergistically enhance the fluorescence intensity by aggregation-induced emission (AIE) and MR contrast with prolonged rotational correlation time (τR) of Gd(III) chelates and the diffusion correlation time (τD) of surrounding water molecules. The amphiphilic dual-modal FLI/MRI probe of NGd was facilely loaded into albumin pockets and then formed AAs to generate a supramolecular structure of NGd-albumin aggregates (NGd-AAs), which show excellent biocompatibility and biosafety, and exhibit superior fluorescence quantum yield and r1 over NGd with 6- and 8-fold enhancement, respectively. Moreover, compared with the clinical MRI contrast agent Gd-DOTA, r1 of NGd-AAs showed a 17-fold enhancement. Therefore, NGd-AAs successfully elicited high-performance dual-modal FLI/MRI in vitro and in vivo and high contrast MR signals were observed in the liver and tumor after intravenous injection of NGd-AAs at a dosage of 6 μmol Gd(III)/kg body weight. This generic and feasible strategy successfully realized a synergistic effect for dual-modal FLI/MRI.

Anomalous ion transport through angstrom-scale pores: Effect of hydration shell exchange on ion mobility

In this work, the ion transport of K+ and Li+ through angstrom-scale pores was thoroughly investigated using molecular dynamics (MD) simulation. Despite of their similar sizes, anomalously selective behaviors were observed. Our MD simulations found that the selectivities through two kinds of pores with diameters of 4 Å and 5 Å show an opposite preference on K+ or Li+ respectively under certain applied voltage. We demonstrated that the exchange of hydration shell with surrounding water molecules plays an important role in the ion mobility. Higher exchange rate equivalently reduces the apparent friction of the hydrated ion during its migration, thus increases the ion mobility. The interactions between ions and the pore edge also contribute to the ion mobility. Our results provide insights into the atomic scale details of ion transport process. Based on these findings, the applied voltage and pore size can be used to actively control the selectivity of K+/Li+ ions.

On the characterization of amine molecules behaviors in the nanochannels forming in calcium silicate hydrate gel

Determining the amine molecules behaviors in the nanochannels enables the interpretation of the microstructure and macroscopic properties of amines modified cement based materials. In this study, quantitative analysis were performed on the behaviors of amine molecules (TEPAs, PAMs and TEAs) by molecular dynamics (MD) simulation in the nanochannels of C–S–H gel. According to the interaction of amine molecules with C–S–H gel substrates or water molecules, research works revealed that amine molecules with special spatial structures illustrate different aggregation behaviors. TEPAs with linear structures tend to aggregate in a regular sequence at the center of the C–S–H gel nanochannels. Instead, PAMs and TEAs with branched structures prefer dispersing in the aqueous solution in the C–S–H gel nanochannels. Such different aggregation behaviors allow amine molecules to have various penetration depth and residence time in the interfacial regions. It was found that oxygen atoms and active hydrogen atoms in PAMs and TEAs can form stable interaction with calcium ions and oxygen atoms of C–S–H gel substrates, respectively. The oxygen involved bonds are stronger than nitrogen involved ones for all the molecules due to great electronegativity. There is no formation of hydrogen bonds in TEPAs, but polar atoms in PAMs and TEAs can interact through hydrogen bonding. Moreover, TEPAs cannot form strong hydrogen bonding with water molecules due to their aggregation behavior, whereas PAMs and TEAs formed strong hydrogen bonding with surrounding water molecules. In addition, formation of more hydrogen bonding with amine molecules leads to a lower diffusion coefficient of water molecules. Breakage of hydrogen bonds of water molecules causes the final failure of C–S–H/amine molecules nanocomposites subjected to tensile loads.

First-Principles Simulations of CuCl in High-Temperature Water Vapor.

Experimental data suggest that the solubility of copper in high-temperature water vapor is controlled by the formation of hydrated clusters of the form CuCl(H2O)n, where the average number of water molecules in the cluster generally increases with increasing density [Migdisov, A. A.; et al. Geochim. Cosmochim. Acta 2014, 129, 33-53]. However, the precise nature of these clusters is difficult to probe experimentally. Moreover, there are some discrepancies between experimental estimates of average cluster size and prior simulation work [Mei, Y. Geofluids 2018, 2018, 4279124]. We have performed first-principles Monte Carlo (MC) and molecular dynamics (MD) simulations to explore these clusters in finer detail. We find that molecular dynamics is not the most appropriate technique for studying aggregation in vapor phases, even at relatively high temperatures. Specifically, our MD simulations exhibit substantial problems in adequately sampling the equilibrium cluster size distribution. In contrast, MC simulations with specialized cluster moves are able to accurately sample the phase space of hydrogen-bonding vapors. At all densities, we find a stable, slightly distorted linear H2O-Cu-Cl structure, which is in agreement with the earlier simulations, surrounded by a variable number of water molecules. The surrounding water molecules do not form a well-defined second solvation shell but rather a loose network of hydrogen-bonded water with molecular CuCl on the outside edge of the water cluster. We also find a broad distribution of hydration numbers, especially at higher densities. In contrast to previous simulation work but in agreement with experimental data, we find that the average hydration number substantially increases with increasing density. Moreover, the value of the hydration number depends on the choice of cluster definition.

Elastic electron scattering with formamide-(H2O) n complexes (n = 1, 2): Influence of microsolvation on the π * and σ * resonances* *Project supported by the National Natural Science Foundation of China (Grant Nos. U1504109 and 11604085) and the Program for Science and Technology Innovation Talents in the Universities of Henan Province, China (Grant No. 19HASTIT018).

We report elastic cross sections for low-energy electron scattering with formamide-(H2O) n complexes (n = 1, 2) in the energy region of 0.01–8 eV. The scattering calculations are performed using the R-matrix method in the static-exchange (SE) approximation. We consider three structures of formamide–H2O and six structures of formamide–(H2O)2 in the present work. Our purpose is to investigate effects of water molecules hydrogen-bonding to formamide. We focus on the influence of microsolvation on the π * and σ * resonances of formamide. The scattering result for complexes shows that the position of π * resonance appears at lower or higher energies in the cluster than in the isolated formamide depending on the complex structure and the water role in the hydrogen bonding. We explain this behavior according to the net charge of the solute. It is found that the microsolvation environment has a substantial effect on the width of π * resonance. Our results indicate that surrounding water molecules may affect the lifetime of the resonances, and hence the process is driven by the anion state, such as the dissociative electron attachment.

Organics-Coated Nanoclays Further Promote Hydrate Formation Kinetics.

A deeper understanding of the kinetics of CO2 hydrate formation in the complicated natural environment is required for its enhanced sequestration. Here we found that the organics-coated nanoclays enriched in the natural sediments could contribute to a 92% decline of the induction time of hydrate formation. This can be ascribed to the negative charges carried by the organics and the resulting ordered arrangement of the surrounding water molecules. It was, for the first time, proposed that the abundant functional groups from the coating organics could function as a protecting crust enabling the system more resistant to the acidification potentially upon the CO2 sequestration; besides, the negative charges could help prevent the deposition of the nanoclays via interparticle repulsive forces. These would consequently secure their sustainable promoting effect on hydrate formation. The findings suggest the deposits of gas hydrate a kinetically promising geological setting for the CO2 sequestration via forming hydrates.

Chemical Energetics and Atomic Charges Distribution of Variably Sized Hydrated Sulfate Clusters in the light of Density Functional Theory

Among the ions classified in the Hofmeister series, the firstly ranked divalent sulfate anion has the strongest hydrating and water-structure making propensity. This unique characteristic actually makes it kosmotropic which causes water molecules to interact each other and contributes to gain structural stability of its hydrated clusters [SO42−(H2O)n]n = 1−40. In this study, few variably sized microhydrated sulfate clusters [SO42−(H2O)n]n = 1−4, 16 are considered separately, and inquired their chemical energetics and atomic charge distributions through ab initio based theoretical model. The main objective of this insight is to specify and interpret their thermodynamic stabilities, binding energies, and specific bonding and electronic interactions quantum mechanically. An in-depth analysis of their change in relative ground state electronic energy with respect to hydration number indicates stronger affinity of the sulfate ion towards water molecules while attaining structural stability in any aqueous type solutions. The mathematically determined values of their binding energy (DE) almost holds up the same with this structural stability order: [SO42−(H2O)16] > [SO42−(H2O)4] > [SO42−(H2O)3] > [SO42−(H2O)2] > [SO42−(H2O)], as reliable as experimentally and molecular dynamics simulation predicted trend. Moreover, the Mulliken derived partial atomic charges feature qualitative charge distribution in them which not only depicts electronic interactions between the specific atoms but also exemplifies the involvement of central sulfate units in hydrogen bond formation with surrounding water molecules.

Self-assembled H-bonded supramolecular interactions in monomeric complex [Mg(H2O)6].L2.2bipy.H2O; [LH = 2-amino-5-nitrobenzoic acid, bipy = 4,4′-bipyridine]]]]: Joint theoretical calculations and Hirshfeld surface analysis

The prepared monomeric H-bonded complex [Mg(H2O)6].L2.2bipy.H2O I [LH = 2-amino-5-nitrobenzoic acid, bipy = 4,4′-bipyridine], has been characterized by single-crystal X-ray crystallography, IR spectroscopy, elemental analysis, and thermal stability. This complex has been solved crystallographically in the monoclinic centrosymmetric space group (P21/n). In the molecular structure, the Mg2+ ion is connecting with six water molecules through coordination whereas L, bipy, and one lattice water are present as counter atoms. The L is behaving as a counter anion and the overall charge of this H-bonded complex is stabilized by [Mg(H2O)6]2+cationic unit. The stability of I is attained due to collective coordination and H-bonding interactions which are responsible for organizing it into a supramolecular 2D motif. Hirshfeld surface analysis has been applied to scrutinize supramolecular H-bonding interactions as well as short or weak contacts and then compared the results with single-crystal X-ray data. The fingerprint plots demonstrate that the huge number of weak non-bonding interactions as compare to strong contacts is important for stabilizing the crystal packing. DFT calculations demonstrated that the thermodynamic stabilization of I may be attributed to the existence of inter-and intramolecular hydrogen interaction. NBO–Second-order perturbation theory analysis, displayed detraction in positive charge on Mg2+ ion upon coordination with surrounding water molecules.