Shell Water Molecules Research Articles

Application of the flexible and polarisable hydration ion model to study Th(IV) aqueous solutions

Th(IV) hydration in aqueous solution is studied by means of molecular dynamics simulations based on a polarisable Th(IV)- H 2 O interaction potential developed in the framework of the hydrated ion concept. Molecular Dynamics (MD) simulations provide as the only in-solution representative motif the ennea-aqua ion, [ Th ( H 2 O ) 9 ] 4 + , with first shell water molecules at an average distance of 2.47 Å from the ion, in accordance with most of the experimental estimates. A well-defined second hydration shell is also identified, hosting ca. 19 solvent molecules at 4.65 Å. Non-structural aspects of the Th(IV) hydration phenomenon, such hydration enthalpy and ion diffusion are well reproduced by the simulation results. The analysis of the O-Th-O angle distribution suggests that the capped square antiprism arrangement prevails over the trigonal tricapped prism. The well-balanced definition of the ion–water and water–water interactions in such a demanding ion neighbourhood is confirmed by the EXAFS and XANES spectroscopies. The theoretical spectra, computed from the MD trajectory, are in fine agreement with some of the experimentally recorded. The sensitivity of the XAS spectroscopy to structural changes confirms how the presented potential manages in a proper way the response of the water molecules to the highly polarising electric field generated by the tetravalent ion.

Beyond the "spine of hydration": Chiral SFG spectroscopy detects DNA first hydration shell and base pair structures.

Experimental methods capable of selectively probing water at the DNA minor groove, major groove, and phosphate backbone are crucial for understanding how hydration influences DNA structure and function. Chiral-selective sum frequency generation spectroscopy (chiral SFG) is unique among vibrational spectroscopies because it can selectively probe water molecules that form chiral hydration structures around biomolecules. However, interpreting chiral SFG spectra is challenging since both water and the biomolecule can produce chiral SFG signals. Here, we combine experiment and computation to establish a theoretical framework for the rigorous interpretation of chiral SFG spectra of DNA. We demonstrate that chiral SFG detects the N-H stretch of DNA base pairs and the O-H stretch of water, exclusively probing water molecules in the DNA first hydration shell. Our analysis reveals that DNA transfers chirality to water molecules only within the first hydration shell, so they can be probed by chiral SFG spectroscopy. Beyond the first hydration shell, the electric field-induced water structure is symmetric and, therefore, precludes chiral SFG response. Furthermore, we find that chiral SFG can differentiate chiral subpopulations of first hydration shell water molecules at the minor groove, major groove, and phosphate backbone. Our findings challenge the scientific perspective dominant for more than 40 years that the minor groove "spine of hydration" is the only chiral water structure surrounding the DNA double helix. By identifying the molecular origins of the DNA chiral SFG spectrum, we lay a robust experimental and theoretical foundation for applying chiral SFG to explore the chemical and biological physics of DNA hydration.

Diverse Microstructures and Quasi-Ionic Liquid-like Transport Mechanisms in Concentrated "Water-in-Salt" Lithium Salt Electrolytes: A Molecular Dynamics Study.

"Water-in-salt"(WIS) electrolytes as potential green and nonflammable electrolytes are currently applied in various energy storage devices, such as lithium-ion batteries and supercapacitors. However, the microstructure at molecular scale and fast ion transport mechanism in such aqueous electrolytes are still under heavy debate due to the complex interactions among ions and water. Here, molecular dynamics simulations are used to study the microstructure and ion transport behaviors from the very dilute LiTFSI/water solution to the highly concentrated WIS electrolytes. It revealed that the diverse microstructures such as completely hydrated ions, ion complexes, and bridge-water molecules are jointly responsible for the electrochemical stability of WIS electrolytes. Diffusion model analysis showed that the Li+ ions exhibit a vehicular transport mechanism with first shell water molecules and structural diffusion mechanism with TFSI- anions. The lithium ion and its first hydration shell act as a single cationic entity. The entity forms a quasi-ionic liquid-like dynamic transport structure with associated anions. Our study challenges previous findings that the high transport dynamics of lithium ions arises from their transport in water-rich nanodomains in high-concentration WIS systems.

Hydration of N-Hydroxyurea from Ab Initio Molecular Dynamics Simulations.

N-Hydroxyurea (HU) is an important chemotherapeutic agent used as a first-line treatment in conditions such as sickle cell disease and β-thalassemia, among others. To date, its properties as a hydrated molecule in the blood plasma or cytoplasm are dramatically understudied, although they may be crucial to the binding of HU to the radical catalytic site of ribonucleotide reductase, its molecular target. The purpose of this work is the comprehensive exploration of HU hydration. The topic is studied using ab initio molecular dynamic (AIMD) simulations that apply a first principles representation of the electron density of the system. This allows for the calculation of infrared spectra, which may be decomposed spatially to better capture the spectral signatures of solute-solvent interactions. The studied molecule is found to be strongly hydrated and tightly bound to the first shell water molecules. The analysis of the distance-dependent spectra of HU shows that the E and Z conformers spectrally affect, on average, 3.4 and 2.5 of the closest H2O molecules, respectively, in spheres of radii of 3.7 Å and 3.5 Å, respectively. The distance-dependent spectra corresponding to these cutoff radii show increased absorbance in the red-shifted part of the water OH stretching vibration band, indicating local enhancement of the solvent's hydrogen bond network. The radially resolved IR spectra also demonstrate that HU effortlessly incorporates into the hydrogen bond network of water and has an enhancing effect on this network. Metadynamics simulations based on AIMD methodology provide a picture of the conformational equilibria of HU in solution. Contrary to previous investigations of an isolated HU molecule in the gas phase, the Z conformer of HU is found here to be more stable by 17.4 kJ·mol-1 than the E conformer, pointing at the crucial role that hydration plays in determining the conformational stability of solutes. The potential energy surface for the OH group rotation in HU indicates that there is no intramolecular hydrogen bond in Z-HU in water, in stark contrast to the isolated solute in the gas phase. Instead, the preferred orientation of the hydroxyl group is perpendicular to the molecular plane of the solute. In view of the known chaotropic effect of urea and its N-alkyl-substituted derivatives, N-hydroxyurea emerges as a unique urea derivative that exhibits a kosmotropic ordering of nearby water. This property may be of crucial importance for its binding to the catalytic site of ribonucleotide reductase with a concomitant displacement of a water molecule.

Going beyond Radial Hydration Models: The Hidden Structures of Chloride and Iodide Aqua Ions Revealed by the Use of Lone Pairs.

A novel model of hydration for the chloride and iodide ions in water is proposed, which overcomes the limitations of conventional radial models. A new approach, based on a representation of the halide lone pairs, highlighted a subset of first shell water molecules featuring preferential strong interactions with the ion lone pairs, giving rise to tetrahedral hydration structures in both Cl- and I- aqueous solutions. By adopting a novel descriptor correlated to the halide-water interaction energy, we were able to split the conventional first solvation shell into a tight first hydration shell, composed of water molecules strongly interacting with the ions via hydrogen bonds, and a loose first shell containing molecules that are only slightly perturbed by the halide electrostatic charge. The picture emerging from our findings indicates that lone pairs play an important role in the description of systems where hydrogen bonds are the main interactions taking place in the solvation process.

Designing Reaction Coordinate for Ion-Induced Pore-Assisted Mechanism of Halide Ions Permeation through Lipid Bilayer by Umbrella Sampling.

Ion permeation mechanism through lipid membranes helps to understand cellular processes. We propose new reaction coordinates that allow ions to permeate according to their water affinity and interaction with the hydrophilic layer. Simulations were done for three different halides (F-, Cl-, and I-) in two different lipid bilayers, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-dinervonoyl-sn-glycero-3-phosphocholine (DNPC). It is found that the involvement of the water molecules decreases the free energy barrier. The ions were found to follow different pathways for permeation. Formation of proper pores required a collaboration effort of the hydration shell water molecules and the hydrophilic lipid layer, which was favored in the case of Cl- ions. The optimum charge density and good water affinity of Cl- with respect to F- and I- ions helped to form the pore. The effect was prominently seen in the case of DNPC membrane because of its higher hydrophobic thickness. The umbrella sampling results were compared with other methods such as the Markov state model (MSM) and well-tempered metadynamics (WT-metaD).

Uncovering water effects in protein-ligand recognition: importance in the second hydration shell and binding kinetics.

Developing a ligand with high affinity for a specific protein target is essential for drug design, and water molecules are well known to play a key role in protein-drug recognition. However, predicting the role of particularly ordered water molecules in drug binding remains challenging. Furthermore, hydration free energy contributed from the water network, including the second shell of water molecules, is far from being well studied. In this research we focused on these aspects to accurately and efficiently evaluate water effects in protein-ligand binding affinity. We developed a new strategy using a free-energy calculation method, VM2. We successfully predicted the stable ordered water molecules in a number of protein systems: PDE 10a, HSP90, tryptophan synthase (TRPS), CDK2 and Factor Xa. In some of these, the second shell of water molecules appeared to be critical in protein-ligand binding. We also applied the strategy to largely improve binding free energy calculation using the MM/PBSA method. When applying MM/PBSA alone for two systems, CDK2 and Factor Xa, the computed binding free energy resulted in poor to moderate R2 values with experimental data. However, including water free energy correction greatly improved the free energy calculation. Furthermore, our work helped to explain how xk263 is a 1000 times faster binder to HIVp than ritonavir, a potentially useful tool for investigating binding kinetics. Our studies reveal the importance of fully considering water effects in therapeutic developments in pharmaceutical and biotechnology industries and for fundamental research in protein-ligand recognition.

Solvation Structure and Ion–Solvent Hydrogen Bonding of Hydrated Fluoride, Chloride and Bromide—A Comparative QM/MM MD Simulation Study

In this study, the correlated resolution-of-identity Møller–Plesset perturbation theory of second order (RIMP2) ab initio level of theory has been combined with the newly parameterised, flexible SPC-mTR2 water model to formulate an advanced QM/MM MD simulation protocol to study the solvation properties of the solutes F−, Cl− and Br− in aqueous solution. After the identification of suitable ion–water Lennard–Jones parameters for the QM/MM coupling, a total simulation period of 10 ps (equilibration) plus 25 ps (sampling) could be achieved for each target system at QM/MM conditions. The resulting simulation data enable an in-depth analysis of the respective hydration structure, the first shell ligand exchange characteristics and the impact of solute–solvent hydrogen bonding on the structural properties of first shell water molecules. While a rather unexpected tailing of the first shell ion–oxygen peak renders the identification of a suitable QM boundary region challenging, the presented simulation results provide a valuable primer for more advanced simulation approaches focused on the determination of single-ion thermodynamical properties.

Structure and rotational dynamics of water around hydrogen peroxide

The density functional theory-based molecular dynamics simulations were induced to study various properties of water around different solvation pockets around hydrogen peroxide(H2O2). Our study aims to understand water behavior in the vicinity of H2O2 molecule through analyzing structure, hydrogen bond statistics, orientational and non-diffusive jump profile. A water-like peroxide molecule can form four hydrogen bonds with nearby water molecules: two as a proton donor and two as a proton acceptor, which must disturb the local structure and dynamics of the surrounding water. The presence of two different peak maxima in radial distribution function (RDF) allows us to resolve the solvation environment into three solvation sites: solvation shell I, solvation shell II, and bulk. The probability distribution of the average distance of central water molecule from 4 nearest water molecules shows a shift in the peak for solvation shell I water molecules towards a ∼0.3Å higher value compared to two other solvation shells. This further affects tetrahedral order parameters as water molecules shift from the regular tetrahedron. For the first solvation layer, the water molecules lose their tetrahedrality to a significant extent as qtet probability distribution peaks at 0.5 and broaden in the higher values of qtet without any shoulder. For the second solvation layer, we find the qtet peak at 0.87 with a minor shoulder appearing at qtet = 0.55, a sign of slight loss of tetrahedrality in the unstructured water compared to undisturbed water. Loss of tetrahedrality hints at the change of orientation of H2O molecules in the vicinity of H2O2 and affects the water-water hydrogen bond (HB) formation. A noteworthy reduction in the HB donor/acceptor account and per water HB count shows interference of H2O2. The water molecules prefer H2O2 compared to neighboring water molecules for HB formation. The orientation autocorrelation function provides the rotational pace of water molecules in the different solvation layers. The reorientation time constant difference in the solvation shells I and II fluctuate by mere 0.20 ps, showcasing the trivial nature of hydrogen peroxide and water HBs. Using the HB descriptors, we also report the non-diffusive jump profile involving vicinal water molecules of H2O2. The jump angle profile of solvation shell water molecules is in line with bulk water.

Bridging the 12-6-4 Model and the Fluctuating Charge Model.

Metal ions play important roles in various biological systems. Molecular dynamics (MD) using classical force field has become a popular research tool to study biological systems at the atomic level. However, meaningful MD simulations require reliable models and parameters. Previously we showed that the 12-6 Lennard-Jones nonbonded model for ions could not reproduce the experimental hydration free energy (HFE) and ion-oxygen distance (IOD) values simultaneously when ion has a charge of +2 or higher. We discussed that this deficiency arises from the overlook of the ion-induced dipole interaction in the 12-6 model, and this term is proportional to 1/r 4 based on theory. Hence, we developed the 12-6-4 model and showed it could solve this deficiency in a physically meaningful way. However, our previous research also found that the 12-6-4 model overestimated the coordination numbers (CNs) for some highly charged metal ions. And we attributed this artifact to that the current 12-6-4 scheme lacks a correction for the interactions among the first solvation shell water molecules. In the present study, we considered the ion-included dipole interaction by using the 12-6 model with adjusting the atomic charges of the first solvation shell water molecules. This strategy not only considers the ion-induced dipole interaction between ion and the first solvation shell water molecules but also well accounts for the increased repulsion among these water molecules compared to the bulk water molecules. We showed this strategy could well reproduce the experimental HFE and IOD values for Mg2+, Zn2+, Al3+, Fe3+, and In3+ and solve the CN overestimation issue of the 12-6-4 model for Fe3+ and In3+. Moreover, our simulation results showed good agreement with previous ab initio MD simulations. In addition, we derived the physical relationship between the C 4 parameter and induced dipole moment, which agreed well with our simulation results. Finally, we discussed the implications of the present work for simulating metalloproteins. Due to the fluctuating charge model uses a similar concept to the 12-6 model with adjusting atomic charges, we believe the present study builds a bridge between the 12-6-4 model and the fluctuating charge model.

Peculiarities of the Physicochemical Properties of Hydrated C60 Fullerene Solutions in a Wide Range of Dilutions

Hydrated fullerene C60 (HyFn) is a supramolecular object in which the nanosized fullerene molecule is enclosed in a multilayer shell of water molecules. Despite the fact that fullerene C60 is chemically rather inert, aqueous solutions of HyFn exhibit a wide spectrum of biological activity in particular in low and ultra-low concentrations. Thus, physical and chemical properties of aqueous solutions of HyFn in a wide range of its dilutions are of interest. Here we compared some physical and chemical properties of aqueous systems prepared by successive 100-fold dilutions of HyFn (10–7 M) with deionized water, with their intensive shaking at each stage up to the calculated HyFn concentration of 10–31 M and of the corresponding “dilutions” of deionized water prepared in the same manner (controls). We studied the character of рН changes in dilutions when titrating them with HCl and NaOH. It turned out that HyFn dilutions had significantly higher buffering capacity against acidification with HCl than control water “dilutions.” At the highest acidity reached pH in all HyFn dilutions was almost 0.3 units higher than in the respective controls. Average buffering capacity of HyFn dilutions and water controls when titrated with NaOH did not differ. However, differences in buffering capacity could be seen between consecutive dilutions of HyFn at their titration either with NaOH or with HCl. Most prominent differences were observed between consecutive HyFn dilutions in the range of calculated concentrations 10–17–10–31 M titrated with NaOH while no significant differences in pH between equivalent “dilutions” of control water were observed. Similar though less prominent variations in buffering capacity between consecutive HyFn dilutions titrated with HCl were also noticed. Thus, titration with an acid and especially with an alkali made it possible to reveal differences between individual dilutions of HyFn, as well as differences between HyFn dilutions and corresponding dilutions of water. These features may be due to complexity in the structural properties of aqueous systems, which, supposedly, can arise due to the emergence of heterogenous aqueous regions (“clouds”) in the course of their dilutions with intensive mixing at each stage. In order to find out if such heterogeneity is a characteristic for HyFn dilutions we used the method of drying microsphere-containing droplets, whose aqueous base were either HyFn dilutions in the range of calculated HyFn concentration 10–7–10–31 M or respective water controls. It was found that a significant part of HyFn dilutions is characterized by mesoscopic heterogeneity. It showed up by the tendency of microspheres to concentrate in a specific way resembling ornaments once the droplets had dried. As the degree of HyFn dilution increased, the number of dried droplets with an ornament-like microsphere distribution increased. Same was also observed in water control drops. However, for the dilutions of HyFn equivalent to concentrations 10–19–10–31 M the percentage of complexly structured dried up droplets reached 60–80%, while for dried out drops of respective water controls it did not exceed 15–20%. Thus, the physicochemical properties of high dilutions of hydrated fullerene differ not only from each other dependently on the dilution level, but also from those of high dilutions of water, which can be explained by the structuredness and heterogeneity of these aqueous systems. Therefore, upon dilution process the properties of the solutions change according to complex and non-linear laws so that final dilutions cannot be identical in their properties and features to those of the initial solutions (before dilutions process) and to the untreated water. Dilution process, in view of the aforementioned, should not be underestimated when analyzing properties of the solutions, having shown to be able to affect dramatically properties of the solutions.

Transfer free energy of micro-hydrated ion clusters from water into acetonitrile solvent

The transfer free energies of micro-hydrated alkali ions (Li+, Na+, K+, and Cs+) and halide ions (F-, Cl-, Br-, and I-) clusters from bulk water to bulk acetonitrile are investigated within the framework of reaction density functional theory (RxDFT), in which the formation of micro-hydrated ion clusters containing one to four water molecules is treated as associated reaction. By analyzing the free energy of hydration and solvation, we show that the micro-hydrated ion clusters, [M(H2O)n]+, exist stably in both water and acetonitrile and a larger percentage of the total electrostatic interactions of ions is contributed by their first solvation shell water molecules. For the transfer free energy of bare ions, the calculated results agree well with the values of experimental observation. The transfer free energy significantly decreases as the size of bare ions and the number of water molecules in the cluster increase. This dependence is stronger for small ions than for large ions. Moreover, the lowest transfer free energy is correspond to the different coordinated number of water molecule (Nw). For Li+, Na+, F-, Cl-, Br-, and I- ion, the lowest transfer free energy are correspond to Nw = 4, while for K+ and Cs+ ion, Nw with the lowest transfer free energy are 3 and 2, respectively. Our findings provide not only the framework to predict transfer free energy but also theoretical guidance for solvent extraction, ion-selective electrodes, biological ion channels, and phase transfer catalysis.

GridSolvate: A Web Server for the Prediction of Biomolecular Hydration Properties.

We present a novel web server, named gridSolvate, dedicated to the prediction of biomolecular hydration properties. Given a solute in atomic representation, such as a protein or protein–ligand complex, the server determines positions and excess chemical potential of buried and first hydration shell water molecules. Calculations are based on our semiexplicit hydration model that provides computational efficiency close to implicit solvent approaches, yet captures a number of physical effects unique to explicit solvent representation. The model was introduced and validated before in the context of bulk hydration of drug-like solutes and determination of protein hydration sites. Current methodological developments merge those two avenues into a single, easily accessible tool. Here, we focus on the server’s ability to predict water distribution and affinity within protein–ligand interfaces. We demonstrate that with possibly minimal user intervention the server correctly predicts the locations of 77% of interface water molecules in an external set of test structures. The server is freely available at https://gsolvate.biomod.cent.uw.edu.pl.

Role of local order in anomalous ion diffusion: Interrogation through tetrahedral entropy of aqueous solvation shells

Small rigid ions perturb the water structure around them significantly. At constant viscosity, alkali cations (Li+, Na+, and so on) exhibit an anomalous non-monotonic dependence of diffusivity on ion-size, in stark violation of the Stokes-Einstein expression. Although this is a well-known problem, we find that an entropic view of the problem can be developed, which provides valuable insight. The local entropy experienced by the solute ion is relevant here, which leads to the connection with local viscosity, discussed earlier by many. Due to the strong interactions with ions, the translational and rotational entropy of solvation water decreases sharply; however, an opposite effect comes from the disruption of the tetrahedral network structure of water near the charges. We compute the tetrahedral order of water molecules (qtet) around the ion and suitably defined tetrahedral entropy [S(qtet)] that is a contribution to the excess entropy of the system. Our results reveal that although the structural properties of the second shell become nearly identical to the bulk, S(qtet) of the second shell is found to play an important role in giving rise to the non-monotonic ion-size dependence. The detailed study of the static and dynamic fluctuations in qtet and the number of hydration water molecules provides interesting insights into correlation between the structure and dynamics; the smallest static fluctuation of qtet for the first hydration shell water molecules of Li+ is indicative of the iceberg picture. The study of fluctuation properties of qtet and the coordination number also reveals the role of the second hydration layer and could explain the anomalous behavior of the Rb+ ion.

Molecular Dynamics Studies on the Effect of Surface Roughness and Surface Tension on the Thermodynamics and Dynamics of Hydronium Ion Transfer Across the Liquid/Liquid Interface

Molecular dynamics simulations are used to examine the effect of surface roughness and surface tension on the transfer of the classical hydronium ion (H3O+) across the water/1,2-dichloroethane interface. Free energy of transfer, hydration structure, and dynamics as a function of the ion location along the interface normal are calculated with six different values of a control parameter whose variation modifies the surface tension without impacting the bulk properties of the two solvents. Transfer of the classical hydronium ion across the water/1,2-dichloroethan interface involves the cotransfer of three hydration shell water molecules, independent of the surface tension. However, as the interaction between the two liquids weakens, a rise in interfacial tension and decrease in intrinsic water fingering and capillary fluctuations result in fewer water molecules cotransported with the ion in the second shell and a reduction in the length of the finger that the ion is attached to, consistent with the reduced size of the second hydration shell. First shell water residence time and lateral ion diffusion constants vary with the surface tension in a way that is consistent with the abovementioned structural insight.

Theoretical spectroscopy of isotopically dilute water and hydrophobicity.

Hydrophobic solutes significantly alter the water hydrogen bond network. The local alteration of solvation structures gets reflected in the vibrational spectroscopic signal. Although it is possible to detect this microscopic feature by modern infrared spectroscopy, bulk phase spectra often come with a formidable challenge of establishing the connection of experimental spectra to molecular structures. Theoretical spectroscopy can serve as a more powerful tool where spectroscopic data cannot provide the microscopic picture. In the present work, we build a theoretical spectroscopic map based on a hybrid quantum-classical molecular simulation approach using a methane-water system. The single oscillator O-H stretch frequency is well correlated with a collective variable solvation energy. We construct the spectroscopic maps for fundamental transition frequencies and also the transition dipoles. A bimodal frequency distribution with a blue-shifted population of transition frequency illustrates the presence of gas like water molecules in the hydration shell of methane. This observation is further complemented by a shell-wise decomposition of the O-H stretch frequencies. We observe a significant increase in the ordering of the first solvation water molecules, except those which are directly facing the methane molecule. This is manifested in the redshift of the observed transition frequencies. Temperature dependent simulations depict that the water molecules facing the methane molecule behave similarly to the high temperature water, and a few of the first shell water molecules behave more like cold water.

Aqueous hydroxyl group as the vibrational probe to access the hydrophobicity of amide derivatives

First principles molecular dynamics (FPMD) simulations of relatively dilute aqueous solutions of N-methylformamide (NMF), N, N-dimethylacetamide (DMA), N-methylacetamide (NMA) were carried out to elucidate the effects of variation of hydrophobicity of amide molecules on structure, dynamics and spectral properties of solvating water molecules. A quantitative analysis of dangling OH groups of water molecules, one of the consequences of hydrophobicity, around the amide molecules was performed to explore the structure of surrounding water molecules. We observe that DMA has the most hydrophobic character among the three amide molecules; the lifetime of dangling OH mode of water molecules and the number of such modes are found to be more inside the solvation shell of DMA as compared to NMA and NMF molecules. Overall this lifetime is more inside the solvation shell of amides compared to the bulk water molecules for all aqueous solutions of amides. Rotational dynamics calculation suggests significant retardation of OH bonds of water near the amide oxygen atom (O) due to the OwHw⋯O strong hydrogen bonds. A moderate slowdown of reorientational dynamics is also observed for OH modes that are close to the hydrophobic surface of DMA in its aqueous solution. Vibrational density of states (VDOS) and frequency distribution calculations point out the higher average stretching frequency (~3600–3850 cm−1) of free OH groups. Hydrogen bond lifetime calculations conceive that DMA, having three methyl groups, makes stronger hydrogen bonds through the CO moiety. Vibrational spectral diffusion of bulk water and solvation shell water molecules were also calculated in combination with wavelet transform and frequency-frequency autocorrelation functions. The CO group affected OH stretching frequency bands for aqueous solutions of NMF and NMA molecules are more pronounced than that of DMA. However, NH affected OH frequency bands are less pronounced for NMA and DMA due to the presence of more number of hydrophobic methyl groups. Going from NMF to DMA, the OH frequency bands inside the amide solvation shells shift towards the higher value due to the enhancement of hydrophobicity. The vibrational spectral diffusion of OH modes around CO and NH (N for DMA) groups, as well as for bulk water molecules, is also investigated. Three time scales were found for these calculations for all the cases. The fast time scales in the range ~50–100 fs are due to the amide-water intact hydrogen bonding, and two slower time scales in the range ~0.6–3.90 ps and ~10–20 ps were found. The time scales in the range of ~0.6 to 3.90 ps can be attributed to carbonyl-water and N-H-water hydrogen bonding, and the very long time scales are due to the escape dynamics water molecules from the solvation shell of CO and NH (N for DMA) groups.

Hydronium ion at the water/1,2-dichloroethane interface: Structure, thermodynamics, and dynamics of ion transfer.

Molecular dynamics simulations including umbrella sampling free energy calculations are used to examine the structure, thermodynamics, and dynamics that accompany the transfer of the classical hydronium ion (H3O+) across the water/1,2-dichloroethane interface. The calculated free energy of transfer (17 ± 1 kcal/mol) is somewhat larger than the experimental value (14 kcal/mol). A detailed examination of the hydration structure is provided, and several dynamical properties as a function of the distance along the interface normal are calculated. In particular, it is shown that the hydronium ion is transferred as an Eigen species, and while the three hydration shell water molecules' average structure is conserved during the transfer, they may be exchanged with nearby water molecules with a rate that decreases as the ion enters the organic phase.

Vibration Spectral Dynamics of Weakly Coordinating Water Molecules near an Anion: FPMD Simulations of an Aqueous Solution of Tetrafluoroborate.

The extent to which the ions affect the nearby water molecules will decide the structure-making or breaking nature of those ions in aqueous solutions. The effects of a weakly coordinating anion on the structure, dynamics, and vibrational properties of water molecules are not so significant as compared to an anion capable of making strong ion-water hydrogen bonds. The present work deals with the first-principles molecular dynamics study of an aqueous solution of such a weakly coordinating anion, tetrafluoroborate (BF4-), using dispersion-corrected DFT-based first-principles molecular dynamics (FPMD) simulations. Various structural, dynamical, and spectral properties, such as radial distribution functions (RDFs), rotational dynamics, vibrational density of states (VDOS), hydrogen bond as well as dangling OH autocorrelation functions, and residence dynamics, were calculated to investigate the effects of the anion on nearby water molecules. The process of spectral diffusion was assessed through a time series wavelet transformation of trajectories obtained from FPMD simulations. The first ion-water solvation shell extends up to 5.5 Å, containing around 20 water molecules. The lifetime of the ion-water hydrogen bond is found to be 1.19 ps, whereas the water-water hydrogen bond lifetime is found to be 1.13 ps. Inside the solvation shell, the persistence time of dangling OH chromophores and the average frequency of OH modes inside the solvation shell are found to be more compared to bulk. Three time scales are found for solvation shell OH modes from the frequency-frequency correlation function. A very short time scale is found for the intact ion-water interaction; the short time scale is for the ion-water hydrogen bond, and the long time scale is for escape dynamics of water molecules from the ion solvation shell. From the mean squared displacement, it is found that solvation water molecules diffuse slower than the bulk. However, solvation shell water molecules show faster relaxation from the analysis of rotational anisotropy. Within the longer time scale of spectral diffusion, this process (which is related to various dynamics of the molecules) is not yet complete, as compared to fast anisotropic decay. This fact is similar to the experimental finding of spectral diffusion and anisotropy time scales in the aqueous solution of borohydride anion. The calculated results are also compared with available experimental data wherever possible.

Thermoplastic Aluminoborophosphate-Aniline Polycomplexes

Products are obtained from interaction between oligomeric aluminoborophosphate (ABP) and aniline, both complexes based on hydrogen bonds, as confirmed with IR spectroscopy and quantum chemical calculations. Nitrogen and hydrogen atoms of an amino group in aniline form hydrogen bonds with hydrogen and oxygen atoms of a phosphate group in ABP, respectively, with a total energy of 14.2 kcal/mol. Aniline, when added to ABP surrounded with a shell of water molecules, displaces two water molecules from the surface of the chain. The energy gain is 9.1 kcal/mol. IR spectroscopy data show that there are strong donor-acceptor interactions between water molecules and aluminum and phosphorus atoms of ABP in the solid-state polycomplex sample. The thermoplastic oligomeric complexes leads to an increase in the softening temperature and fluidity with an increase in an amount of aniline. This means that polyoxide inorganic polymer (metal phosphate) is possible to be modified with a monofunctional amine under “mild” conditions. We showed that the water resistance of the polycomplex is greater than that of ABP.