Solvation Shell Water Research Articles

On the Origins of Core−Electron Chemical Shifts of Small Biomolecules in Aqueous Solution: Insights from Photoemission and ab Initio Calculations of Glycineaq

The local electronic structure of glycine in neutral, basic, and acidic aqueous solution is studied experimentally by X-ray photoelectron spectroscopy and theoretically by molecular dynamics simulations accompanied by first-principle electronic structure and spectrum calculations. Measured and computed nitrogen and carbon 1s binding energies are assigned to different local atomic environments, which are shown to be sensitive to the protonation/deprotonation of the amino and carboxyl functional groups at different pH values. We report the first accurate computation of core-level chemical shifts of an aqueous solute in various protonation states and explicitly show how the distributions of photoelectron binding energies (core-level peak widths) are related to the details of the hydrogen bond configurations, i.e. the geometries of the water solvation shell and the associated electronic screening. The comparison between the experiments and calculations further enables the separation of protonation-induced (covalent) and solvent-induced (electrostatic) screening contributions to the chemical shifts in the aqueous phase. The present core-level line shape analysis facilitates an accurate interpretation of photoelectron spectra from larger biomolecular solutes than glycine.

Modeling aqueous solvation with semi-explicit assembly

We describe a computational solvation model called semi-explicit assembly (SEA). SEA water captures much of the physics of explicit-solvent models but with computational speeds approaching those of implicit-solvent models. We use an explicit-water model to precompute properties of water solvation shells around simple spheres, then assemble a solute's solvation shell by combining the shells of these spheres. SEA improves upon implicit-solvent models of solvation free energies by accounting for local solute curvature, accounting for near-neighbor nonadditivities, and treating water's dipole as being asymmetrical with respect to positive or negative solute charges. SEA does not involve parameter fitting, because parameters come from the given underlying explicit-solvation model. SEA is about as accurate as explicit simulations as shown by comparisons against four different homologous alkyl series, a set of 504 varied solutes, solutes taken retrospectively from two solvation-prediction events, and a hypothetical polar-solute series, and SEA is about 100-fold faster than Poisson-Boltzmann calculations.

Experimental and theoretical investigations into the counter-intuitive shift in the antisymmetric ν(Si–O) vibrational modes upon deuteration of solvated silicic acid (H4SiO4)

The IR and Raman spectra of fully deuterated silicic acid (D(4)SiO(4)) have been obtained for the first time in solution and contrasted with the analogous spectra of H(4)SiO(4). The IR spectra feature antisymmetric ν(SiO) stretching modes at 939 and 951 cm(-1) for H(4)SiO(4) and D(4)SiO(4) respectively. The observed increase in frequency of the ν(SiO) modes upon deuteration is contrary to the expected effect of increasing the reduced mass. Broader and weaker bands due to δ(SiOX), X = H or D, deformations occur in the IR spectra at ∼1100 and 800 cm(-1), respectively. The symmetric ν(SiO) modes in the Raman occur at 787 and 764 cm(-1) for H(4)SiO(4) and D(4)SiO(4), respectively, and exhibit the expected decrease in frequency upon deuteration. To analyse these phenomena, RB3LYP/6-31+G(d) calculations were initially performed on gaseous H(4)SiO(4) and D(4)SiO(4). Significant coupling between antisymmetric ν(SiO) and δ(SiOH) deformations, calculated to be of comparable frequency, is noted in gaseous H(4)SiO(4). The calculated frequencies of the δ(SiOD) modes in gaseous D(4)SiO(4) occur ∼200 cm(-1) lower than those of ν(SiO) vibrations and the modes are not coupled. However, the predicted gas phase frequencies of δ(SiOX) modes are ∼200 cm(-1) lower than those observed for the solvated H(D)(4)SiO(4), and the observed reverse isotope shift of the antisymmetric ν(SiO) is not reproduced. Inclusion of a highly disordered 28 water solvation shell is found to significantly stiffen δ(SiOX) modes, leading to a significant blue-shift of 200-300 cm(-1) relative to analogous gas-phase frequencies and providing an accurate description of the bending modes. This frequency shift decouples the ν(SiO) and δ(SiOH) modes in H(4)SiO(4) but leads to coupling in solvated D(4)SiO(4) which is responsible for the observed reverse isotope shift of the antisymmetric ν(SiO) modes.

Computational investigation of the speciation of uranyl gluconate complexes in aqueous solution

The geometries, relative energies and spectroscopic properties of a range of D-gluconate complexes of uranyl(VI) are studied computationally using density functional theory. The effect of pH is accommodated by varying the number of water and hydroxide ligands accompanying gluconate in the equatorial plane of the uranyl unit. For 1 : 1 complexes, the calculated uranyl ν(asym) stretching frequency decreases as pH increases, in agreement with previous experimental data. Three different gluconate chelating modes are studied. Their relative energies are found to be pH dependent, although the energetic differences between them are not sufficient to exclude the possibility of multiple speciation. (13)C NMR chemical shifts are calculated for the coordinated gluconate in the high pH mimics, and show good agreement with experimental data, supporting the experimental conclusion that the six-membered chelate ring is favoured at high pH. Attempts to improve the description of the aqueous environment via the addition of second solvation shell water molecules resulted in significantly worse agreement with experiment for ν(asym). The effect of increasing the gluconate concentration is modelled by calculating 1 : 2 and 1 : 3 uranyl : D-gluconate complexes.

Local Effects in the X-ray Absorption Spectrum of Salt Water

Both first-principles molecular dynamics and theoretical X-ray absorption spectroscopy have been used to investigate the aqueous solvation of cations in 0.5 M MgCl(2), CaCl(2), and NaCl solutions. We focus here on the species-specific effects that Mg(2+), Ca(2+), and Na(+) have on the X-ray absorption spectrum of the respective solutions. For the divalent cations, we find that the hydrogen-bonding characteristics of the more rigid magnesium first-shell water molecules differ from those in the more flexible solvation shell surrounding calcium. In particular, the first solvation shell water molecules of calcium are able to form acceptor hydrogen bonds, and this results in an enhancement of a post-edge peak near 540 eV. The absence of acceptor hydrogen bonds for magnesium first shell water molecules provides an explanation for the experimental and theoretical observation of a lack of enhancement at the post-main-edge peak. For the sodium monovalent cation we find that the broad tilt angle distribution results in a broadening of postedge features, despite populations in donor-and-acceptor configurations consistent with calcium. We also present the reaveraged spectra of the MgCl(2), CaCl(2), and NaCl solutions and show that trends apparent with increasing concentration (0.5, 2.0, 4.0 M) are consistent with experiment. Finally, we examine more closely both the effect that cation coordination number has on the hydrogen-bonding network and the relative perturbation strength of the cations on lone pair oxygen orbitals.

The solvent shell structure of aqueous iodide: X-ray absorption spectroscopy and classical, hybrid QM/MM and full quantum molecular dynamics simulations

The L 3 X-ray absorption spectrum of aqueous iodide is reported, and its EXAFS is compared to theoretical spectra reconstructed from the radial distribution function of the iodide hydration obtained from classical, hybrid Quantum Mechanics Molecular Mechanics, (QM/MM) and full quantum (density functional theory, DFT) molecular dynamics simulations. Since EXAFS is mainly sensitive to short distances around the iodide ion, it is a direct probe of the local solvation structure. The comparison shows that QM/MM simulations deliver a satisfactory description of the EXAFS signal, while nonpolarizable classical simulations are somewhat less satisfactory and DFT-based simulations perform poorly. We also identify a weak anisotropy of the water solvation shell around iodide, which may be of importance in electron photoejection experiments.

Ring polymer molecular dynamics beyond the linear response regime: Excess electron injection and trapping in liquids

Ring polymer molecular dynamics (RPMD) is used to directly simulate the injection and relaxation of excess electrons into supercritical helium fluid and ambient liquid water. A method for modulating the initial energy of the excess electron in the RPMD model is presented and used to study both low-energy (cold) and high-energy (hot) electron injections. For cold injection into both solvents, the RPMD model recovers electronically adiabatic dynamics with the excess electron in its ground state, whereas for hot electron injection, the model predicts slower relaxation dynamics associated with electronic transitions between solvent cavities. The analysis of solvent dynamics during electron localization reveals the formation of an outgoing solvent compression wave in helium that travels for over 2 nm and the delayed formation of water solvation shells on the timescale of 300 fs. Various system-size effects that are intrinsic to the simulation of excess electron injection are discussed. Comparison of the RPMD simulations with previous mixed quantum-classical dynamics simulations finds general agreement for both the mechanisms and timescales for electron localization, although the electron localization dynamics in the RPMD model is essentially completed within 400 fs in helium and 150 fs in water.

How to Replace the Residual Solvation Shell of Polar Active Site Residues to Achieve Nanomolar Inhibition of tRNA‐Guanine Transglycosylase

In a computational and structural study, we investigated a series of 4-substituted lin-benzoguanines that are potent inhibitors of tRNA-guanine transglycosylase (TGT), a putative target for the treatment of shigellosis. At first glance, it appears self-evident that the placement of a positively charged ligand functional group between the carboxylate groups of two adjacent aspartate residues in the glycosylase catalytic center leads to enhanced ligand binding. The concomitant displacement of water molecules that partially solvate the aspartates prior to ligand binding appears to result as a consequence of this. However, the case study presented herein shows that this premise is much too superficial. Placement of a likely positively charged amino group at such a pivotal position, interfering with the residual water solvation shell, is at best cost-neutral compared with the unsubstituted parent ligand not conflicting with the residual water shell. A ligand that orients a hydroxy group in this position shows even decreased binding. Based on the cost-neutral placement of the amino functionality, hydrophobic side chains can now be further attached to fill, with increasing potency, a small hydrophobic pocket remote to the aspartates. Any attempts to cross the pivotal position between both aspartates with nonpolar scaffolds reveals only decreased binding, even though the waters of the residual solvation shell are successfully repelled. This surprising observation fostered a detailed analysis of the role of water molecules involved in the residual solvation of polar active site residues. Their geometry and putative replacement in the binding pocket of TGT has been studied by a comparative database analysis, computational active site mapping, and a series of crystal structure analyses. Furthermore, conformational preferences of attached hydrophobic moieties explain their contribution to a gradual increase in binding affinity.

Hydrates of Copper Dichloride in Aqueous Solution: A Density Functional Theory and Polarized Continuum Model Investigation

In this work, the hydrates of copper dichloride in gas and aqueous phase have been investigated using the B3LYP method. Low-lying conformers of CuCl(2)(H(2)O)(n) clusters for n = 1-10 were obtained by an extensive conformation search. Contact ion pair (CIP) and solvent-shared ion pair (SSIP) with one dissociated chloride atom (SSIP/s) and SSIP with two dissociated chloride atoms (SSIP/d) all were considered. Our calculations present such a trend that a four-fold CIP conformer is more favorable for CuCl(2)(H(2)O)(n) cluster (n < or = 7) and four-fold SSIP/s for n = 8-10 in the gas phase, while in aqueous solution, more stable structures are five-fold SSIP/s conformer for n = 7-9 and four-fold CIP conformer for n = 2-6. Hydrogen bond (HB) plays an important role in the CuCl(2) solvation, especially HBs formed between the first and second solvation shell water molecules. Electronic absorption spectra of CuCl(2)(H(2)O)(n) clusters were obtained using long-range-corrected time-dependent density functional theory. The calculated electronic absorption peak around 270 nm of CIP conformers is coincident with the absorption of [CuCl(2)](0)(aq) species resolved from the spectra obtained in solutions of trace CuCl(2) (ca. 10(-5) mol/kg) + LiCl (0-18 m), while those of SSIP/s (approximately 250 nm) and SSIP/d (approximately 180 nm) conformers probably correspond to the absorption spectra of [CuCl](+)(aq) and [Cu](2+)(aq) species, respectively. Natural bond orbital charge population analyses show that charge transfer (CT) between a central copper(II) atom and ligands (Cl and H(2)O) increases as the hydrated cluster expands, especially CT from Cu(2+) to the first solvation shell, which enhances the strength of HBs. Such CT becomes more apparent for SSIP structure with the dissociation of chloride ion. OH stretching vibration frequencies of proton donor type water in CuCl(2)(H(2)O)(n) clusters are obviously red-shifted in comparison to those of water clusters, due to CT between the central atom Cu and ligands. SSIP conformers have apparent IR absorption peaks of OH stretching vibration at approximately 3000 cm(-1) for the effect of half-dissociated chloride atoms.

A new technique for determination of melting temperature of poly(ethylene glycol) by ultrasonic velocimetry

Ultrasonic velocity and density of poly(ethylene glycol) (PEG) (mol. wt. 2000 and 8000) solutions in water and benzene have been studied as a function of temperature from which respective isentropic compressibility has also been calculated. The velocity (as well as isentropic compressibility) undergoes a sudden change near melting temperature, T m, of the solute polymer. Normally, we expect only one peak in viscoelastic properties at the T m of PEG. However, we see two peaks (T m1 and T m2) in the case of the aqueous solution of PEG while there is only one peak for the case of benzene solution. This has been interpreted on the basis that one of the peaks (T m1) is for unsolvated PEG and the other peak (T m2) is that of PEG with water solvation shell. Such solvation shell is not formed with the aprotic solvent (benzene).

Fluorescence Dynamics of Coumarin C522 on Reduced-Charge Montmorillonite in Aqueous Dispersion

Solvation is an important phenomenon, especially in association with heterogeneous phase interactions. Coumarin C522, C(14)H(12)NO(2)F(3), is used as a fluorophore probe to study the interaction between coumarin and a reduced-charge montmorillonite (RCM) surface. Such hydrophilic and hydrophobic interactions are of interest for sorption processes in confined environments. The prepared RCM series with 0.00, 0.12, 0.26, 0.43, 0.66, and 0.97 Li(+) molar fractions provide different surface charges. The aqueous dispersion of the C522/water/RCM system is studied by using steady-state and time-resolved fluorescence spectroscopies. Both the Stokes shift and the dynamics of the solvation process varied as a function of surface charge. Steady-state fluorescence spectroscopy reveals that the C522 Stokes shift varies from 5,115 cm(-1) for the 0.00 Li(+) molar fraction to 3,988 cm(-1) for the 0.97 Li(+) molar fraction. Time-resolved fluorescence spectroscopy determines that the decay time T((1)) varies from 1.0 ps for the 0.00 Li(+) molar fraction to 3.6 ps for the 0.97 Li(+) molar fraction. Within the range of a few picoseconds, the dynamics of the water solvation shell may be described with H-bond rearrangement, modified with the different RCM surface charges. Two models illustrating the interactions between C522 and RCM in water are proposed which qualitatively describe the dynamics. To the best of our knowledge, this experiment is the first measurement of solvation dynamics on a montmorillonite structure surface using ultrafast laser fluorescence spectroscopy.

Single-Molecule Solvation-Shell Sensing

We present a new route to single-molecule sensing via solvation shells surrounding a current-carrying backbone molecule. As an example, we show that the presence of a water solvation shell "gates" the conductance of a family of oligothiophene-containing molecular wires, and that the longer the oligothiophene, the larger is the effect. For the longest example studied, the molecular conductance is over 2 orders of magnitude larger in the presence of a shell comprising just 10 water molecules. A first principles theoretical investigation of electron transport through the molecules, using the nonequilibrium Green's function method, shows that water molecules interact directly with the thiophene rings, significantly shifting transport resonances and greatly increasing the conductance. This reversible effect is confirmed experimentally through conductance measurements performed in the presence of moist air and dry argon.

Photoionization of Sodium Salt Solutions in a Liquid Jet

A liquid microjet was employed to examine the gas/liquid interface of aqueous sodium halide (Na+X−, X = Cl, Br, I) salt solutions. Laser excitation at 193 nm produced and removed cations of the form H+(H2O)n and Na+(H2O)m from liquid jet surfaces containing either NaCl, NaBr or NaI. The protonated water cluster yield varied inversely with increasing salt concentration, while the solvated sodium ion cluster yield varied by anion type. The distribution of H+(H2O)n at low salt concentration is identical to that observed from low-energy electron irradiated amorphous ice, and the production of these clusters can be accounted for using a localized ionization/Coulomb expulsion model. Production of Na+(H2O)m is not quantitatively accounted for by this model but requires ionization of solvation shell waters and a contact ion/Coulomb expulsion mechanism. The reduced yields of Na+(H2O)m from high concentration (10−2 and 10−1 M) NaBr and NaI solutions indicate a propensity for Br− and I− at the solution surfaces and interfaces. This is supported by the observation of multiphoton induced production and desorption of Br+ and I+ from the 10−2 and 10−1 M solution surfaces.

The effect of sequence on the conformational stability of a model heteropolymer in explicit water

We investigate the properties of a two-dimensional lattice heteropolymer model for a protein in which water is explicitly represented. The model protein distinguishes between hydrophobic and polar monomers through the effect of the hydrophobic monomers on the entropy and enthalpy of the hydrogen bonding of solvation shell water molecules. As experimentally observed, model heteropolymer sequences fold into stable native states characterized by a hydrophobic core to avoid unfavorable interactions with the solvent. These native states undergo cold, pressure, and thermal denaturation into distinct configurations for each type of unfolding transition. However, the heteropolymer sequence is an important element, since not all sequences will fold into stable native states at positive pressures. Simulation of a large collection of sequences indicates that these fall into two general groups, those exhibiting highly stable native structures and those that do not. Statistical analysis of important patterns in sequences shows a strong tendency for observing long blocks of hydrophobic or polar monomers in the most stable sequences. Statistical analysis also shows that alternation of hydrophobic and polar monomers appears infrequently among the most stable sequences. These observations are not absolute design rules and, in practice, these are not sufficient to rationally design very stable heteropolymers. We also study the effect of mutations on improving the stability of the model proteins, and demonstrate that it is possible to obtain a very stable heteropolymer from directed evolution of an initially unstable heteropolymer.

Charge Asymmetries in Hydration of Polar Solutes

We study the solvation of polar molecules in water. The center of water's dipole moment is offset from its steric center. In common water models, the Lennard-Jones center is closer to the negatively charged oxygen than to the positively charged hydrogens. This asymmetry of water's charge sites leads to different hydration free energies of positive versus negative ions of the same size. Here, we explore these hydration effects for some hypothetical neutral solutes, and two real solutes, with molecular dynamics simulations using several different water models. We find that, like ions, polar solutes are solvated differently in water depending on the sign of the partial charges. Solutes having a large negative charge balancing diffuse positive charges are preferentially solvated relative to those having a large positive charge balancing diffuse negative charges. Asymmetries in hydration free energies can be as large as 10 kcal/mol for neutral benzene-sized solutes. These asymmetries are mainly enthalpic, arising primarily from the first solvation shell water structure. Such effects are not readily captured by implicit solvent models, which respond symmetrically with respect to charge.

On the properties of aqueous amide solutions through classical molecular dynamics simulations

The structure and dynamics of infinitely diluted aqueous amide solutions is studied for 13 compounds in the NVT ensemble using classical molecular dynamics simulations. The aim of this work is to provide valuable insights into the effect of amides on liquid water properties in order to understand the amides role in the kinetic inhibition of clathrate hydrate formation in natural gas mixtures. The OPLS-AA forcefield is used to describe the amides, with parameters obtained through fitting of computed B3LYP/6-311++g* * data when not available in the literature, and the SPC-E model is applied for water molecules. Structural properties of the solutions are analyzed via calculated radial distribution functions and dynamic properties are studied with the computed mean square displacements and velocity autocorrelation functions. Most of the studied compounds show a remarkable structuring effect on the surrounding water with strong interactions resulting from hydrogen bonding between solute and solvent molecules. Hydrophobic and hydrophilic synergistic effects influence the amide–water interaction and the properties of the water solvation shells around amides.

Reaction intermediates and pathways in the photoreduction of oxygen molecules at the (1 0 1) TiO 2 (anatase) surface

Ab initio density functional calculations in the local spin density and Hubbard U approximations have been performed to investigate the formation of some important intermediates of the O 2 photoreduction at the (1 0 1) TiO 2 anatase surface as well as to compare with previous local density approximation results. A recently proposed approach has been used where molecules on the surface are treated like surface defects. Thus, by applying theoretical methods generally used in the physics of semiconductors, we successfully estimate the location and donor–acceptor character of the electronic levels induced by an adsorbed molecule in the TiO 2 energy gap, both crucial for the surface-molecule charge-transfer processes, and investigate the formation and the vibrational properties of charged intermediates. Present results confirm the key role played by charged intermediates in the O 2 photoreduction as well as a strong, deep acceptor character of an adsorbed O 2 molecule which gives a clear theoretical explanation of the O 2 electron scavenger behavior suggested by the experiment. Moreover, an investigation of the vibrational properties of some surface intermediates performed by ab initio molecular dynamics methods confirms an important role of H bonds forming between surface species and their water solvation shells.

Temperature Effect on the Absorption Spectrum of the Hydrated Electron Paired with a Lithium Cation in Deuterated Water

The absorption spectra of the hydrated electron in 1.0 to 4.0 M LiCl or LiClO4 deuterated water solutions were measured by pulse radiolysis techniques from room temperature to 300 degrees C at a constant pressure of 25 MPa. The results show that when the temperature is increased and the density is decreased, the absorption spectrum of the electron in the presence of a lithium cation is shifted to lower energies. Quantum classical molecular dynamics (QCMD) simulations of an excess electron in bulk water and in the presence of a lithium cation have been performed to compare with the experimental results. According to the QCMD simulations, the change in the shape of the spectrum is due to one of the three p-like excited states of the solvated electron destabilized by core repulsion. The study of s --> p transition energies for the three p-excited states reveals that for temperatures higher than room temperature, there is a broadening of each individual s --> p absorption band due to a less structured water solvation shell.

Dynamics of Water in Solvation Shells and Intersolute Regions of C60: A Molecular Dynamics Simulation Study

We present dynamical characteristics of the solvent in various solvation shells of a C60 molecule as well as intersolute region between two fullerene molecules. Results are obtained from extensive atomistic molecular dynamics simulations of aqueous solutions of C60 in the isothermal−isobaric ensemble. Information about translational mobilities of water in and around fullerene molecules are obtained from velocity auto correlation function and mean square displacements as calculated from simulation data. Reorientational behavior also is investigated by analyzing first and second rank dipole−dipole correlation functions as calculated from simulation trajectories. Both the translational and rotational mobilities of water in the first solvation shell around a C60 molecule are found to be much slower than the same in the second and third solvation shells. Slower decay of the occupation time correlation function for the water in the first hydration shell indicates slower exchange of these water molecules with th...

Predicting the Energy of the Water Exchange Reaction and Free Energy of Solvation for the Uranyl Ion in Aqueous Solution

The structures and vibrational frequencies of UO2(H2O)4(2+) and UO2(H2O)5(2+) have been calculated using density functional theory and are in reasonable agreement with experiment. The energies of various reactions were calculated at the density functional theory (DFT) and MP2 levels; the latter provides the best results. Self-consistent reaction field calculations in the PCM and SCIPCM approximations predicted the free energy of the water exchange reaction, UO2(H2O)4(2+) + H2O <--> UO2(H2O)5(2+). The calculated free energies of reaction are very sensitive to the choice of radii (O and H) and isodensity values in the PCM and SCIPCM models, respectively. Results consistent with the experimental HEXS value of -1.19 +/- 0.42 kcal/mol (within 1-3 kcal/mol) are obtained with small cavities. The structures and vibrational frequencies of the clusters with second solvation shell waters: UO2(H2O)4(H2O)8(2+), UO2(H2O)4(H2O)10(2+), UO2(H2O)4(H2O)11(2+), UO2(H2O)5(H2O)7(2+), and UO2(H2O)5(H2O)10(2+), were calculated and are in better agreement with experiment as compared to reactions involving only UO2(H2O)4(2+) and UO2(H2O)5(2+). The MP2 reaction energies for water exchange gave gas-phase results that agreed with experiment in the range -5.5 to +3.3 kcal/mol. The results were improved by inclusion of a standard PCM model with differences of -1.2 to +2.7 kcal/mol. Rearrangement reactions based on an intramolecular isomerization leading to a redistribution of water in the two shells provide good values in comparison to experiment with values of Delta G(exchange) from -2.2 to -0.5 kcal/mol so the inclusion of a second hydration sphere accounts for most solvation effects. Calculation of the free energy of solvation of the uranyl cation yielded an upper bound to the solvation energy of -410 +/- 5 kcal/mol, consistent with the best experimental value of -421 +/- 15 kcal/mol.