Hydrogen Bond Length as a Key To Understanding Sweetness

Neutron diffraction experiments have been performed to investigate and compare the structure of the hydration shell of three monosaccharides, namely, fructose, glucose, and mannose. It is found that despite their differences with respect to many thermodynamical quantities, bioprotective properties against environmental stresses, and taste, the influence of these monosaccharides on the bulk water solvent structure is virtually identical. Conversely, these sugars interact with the neighboring water molecules by forming H bonds of different length and strength. Interestingly, the sweetness of these monosaccharides, along with that of the disaccharide trehalose, is correlated with the length of these H bonds. This suggests that the small differences in stereochemistry between the different sugars determine a relevant change in polarity, which has a fundamental impact on the behavior of these molecules in vivo.

Bind3P: Optimization of a Water Model Based on Host-Guest Binding Data

We report a water model, Bind3P (Version 0.1), which was obtained by using sensitivity analysis to readjust the Lennard-Jones parameters of the TIP3P model against experimental binding free energies for six host-guest systems, along with pure liquid properties. Tests of Bind3P against >100 experimental binding free energies and enthalpies for host-guest systems distinct from the training set show a consistent drop in the mean signed error, relative to matched calculations with TIP3P. Importantly, Bind3P also yields some improvement in the hydration free energies of small organic molecules and preserves the accuracy of bulk water properties, such as density and the heat of vaporization. The same approach can be applied to more sophisticated water models that can better represent pure water properties. These results lend further support to the concept of integrating host-guest binding data into force field parametrization.

Equilibration and analysis of first-principles molecular dynamics simulations of water

First-principles molecular dynamics (FPMD) simulations based on density functional theory are becoming increasingly popular for the description of liquids. In view of the high computational cost of these simulations, the choice of an appropriate equilibration protocol is critical. We assess two methods of estimation of equilibration times using a large dataset of first-principles molecular dynamics simulations of water. The Gelman-Rubin potential scale reduction factor [A. Gelman and D. B. Rubin, Stat. Sci. 7, 457 (1992)] and the marginal standard error rule heuristic proposed by White [Simulation 69, 323 (1997)] are evaluated on a set of 32 independent 64-molecule simulations of 58 ps each, amounting to a combined cumulative time of 1.85 ns. The availability of multiple independent simulations also allows for an estimation of the variance of averaged quantities, both within MD runs and between runs. We analyze atomic trajectories, focusing on correlations of the Kohn-Sham energy, pair correlation functions, number of hydrogen bonds, and diffusion coefficient. The observed variability across samples provides a measure of the uncertainty associated with these quantities, thus facilitating meaningful comparisons of different approximations used in the simulations. We find that the computed diffusion coefficient and average number of hydrogen bonds are affected by a significant uncertainty in spite of the large size of the dataset used. A comparison with classical simulations using the TIP4P/2005 model confirms that the variability of the diffusivity is also observed after long equilibration times. Complete atomic trajectories and simulation output files are available online for further analysis.

First-Principles Simulations of Liquid Water Using a Dielectric-Dependent Hybrid Functional

We carried out first-principles simulations of liquid water under ambient conditions using a dielectric-dependent hybrid functional, where the fraction of exact exchange is set equal to the inverse of the high-frequency dielectric constant of the liquid. We found excellent agreement with experiment for the oxygen-oxygen partial correlation function at the experimental equilibrium density and 311 ± 3 K. Other structural and dynamical properties, such as the diffusion coefficient, molecular dipole moments, and vibrational spectra, are also in good agreement with experiment. Our results, together with previous findings on electronic properties of the liquid with the same functional, show that the dielectric-dependent hybrid functional accurately describes both the structural and electronic properties of liquid water.

Magnetic properties and core electron binding energies of liquid water

The magnetic properties and the core and inner valence electron binding energies of liquid water are investigated. The adopted methodology relies on the combination of molecular dynamics and electronic structure calculations. Born-Oppenheimer molecular dynamics with the Becke and Lee-Yang-Parr functionals for exchange and correlation, respectively, and includes an empirical correction (BLYP-D3) functional and classical molecular dynamics with the TIP4P/2005-F model were carried out. The Keal-Tozer functional was applied for predicting magnetic shielding and spin-spin coupling constants. Core and inner valence electron binding energies in liquid water were calculated with symmetry adapted cluster-configuration interaction. The relationship between the magnetic shielding constant σ(¹⁷O), the role played by the oxygen atom as a proton acceptor and donor, and the tetrahedral organisation of liquid water are investigated. The results indicate that the deshielding of the oxygen atom in water is very dependent on the order parameter (q) describing the tetrahedral organisation of the hydrogen bond network. The strong sensitivity of magnetic properties on changes of the electronic density in the nuclei environment is illustrated by a correlation between σ(¹⁷O) and the energy gap between the 1a₁[O1s] (core) and the 2a₁ (inner valence) orbitals of water. Although several studies discussed the eventual connection between magnetic properties and core electron binding energies, such a correlation could not be clearly established. Here, we demonstrate that for liquid water this correlation exists although involving the gap between electron binding energies of core and inner valence orbitals.

Spin-state dependence of the structural and vibrational properties of solvated iron(ii) polypyridyl complexes from AIMD simulations: aqueous [Fe(bpy)3]Cl2, a case study

LS and HS IR spectra of aqueous [Fe(bpy)₃]²⁺ and corresponding HS–LS difference IR spectrum as obtained from state-of-the-art ab initio molecular dynamics simulations applied to the determination of the structural and vibrational properties of the solvated complex.

Dihydrogen vs. hydrogen bonding in the solvation of ammonia borane by tetrahydrofuran and liquid ammonia

The solvation structures of two systems rich in hydrogen and dihydrogen bonding interactions have been studied in detail experimentally through neutron diffraction with hydrogen/deuterium isotopic substitution.

The structures of liquid pyridine and naphthalene: the effects of heteroatoms and core size on aromatic interactions

Spatial and orientational structures of liquid naphthalene and pyridine revealed using neutron scattering combined with empirical potential structure refinement.

optPBE-vdW density functional theory study of liquid water and pressure-induced structural evolution in ice Ih

The accuracy of several local and non-local van der Waals (vdW) corrected exchange correlation functionals on the description of the effect of pressure on ice has been investigated. In a preliminary survey, the non-local vdW correction used in conjunction with the optPBE functional was shown to provide the best overall agreement on the structural parameters of ice Ih with experiments. More importantly, this combination reproduced correctly the recently observed crystal → crystal transformation in ice Ih at 80 K prior to amorphisation. The predicted transition pressure of 1.9 GPa is somewhat higher, showing that the current generation of vdW functionals are still not sufficiently accurate for the ice system. The existence of an intermediate crystalline state with a shear-hexagonal structure confirms the earlier prediction that the collapse of crystalline structure under compression originates from the softening of phonon modes in ice Ih’s basal plane.

Effect of heavy water on the conformational stability of globular proteins

It is well established from the experimental point of view that the native state of globular proteins is more stable in heavy water than in water. No robust explanation, however, has been provided up to now. The application of the theoretical approach, originally devised to rationalize the general occurrence of cold denaturation, indicates that the magnitude of the solvent-excluded volume effect is slightly smaller in heavy water than in water and cannot explain the observed protein stabilization. The latter has to be due to the strength of protein-water van der Waals attractions which are weaker in heavy water due to the smaller molecular polarizability of D₂ O compared with that of H₂ O molecules. Since protein-water van der Waals attractions occur more in the denatured than in the native state, this contribution leads to a stabilization of the latter through a destabilization of the former.

Highly compressed water structure observed in a perchlorate aqueous solution

The discovery by the Phoenix Lander of calcium and magnesium perchlorates in Martian soil samples has fueled much speculation that flows of perchlorate brines might be the cause of the observed channeling and weathering in the surface. Here, we study the structure of a mimetic of Martian water, magnesium perchlorate aqueous solution at its eutectic composition, using neutron diffraction in combination with hydrogen isotope labeling and empirical potential structure refinement. We find that the tetrahedral structure of water is heavily perturbed, the effect being equivalent to pressurizing pure water to pressures of order 2 GPa or more. The Mg²⁺ and ClO₄⁻ ions appear charge-ordered, confining the water on length scales of order 9 Å, preventing ice formation at low temperature. This may explain the low evaporation rates and high deliquescence of these salt solutions, which are essential for stability within the low relative humidity environment of the Martian atmosphere.

Significant amounts of different perchlorate salts have been discovered on the surface of Mars. Here, the authors show that magnesium perchlorate has a major impact on water structure in solution, providing insight into how an aqueous fluid might exist under the sub-freezing conditions present on Mars.

The Effect of Water upon Deep Eutectic Solvent Nanostructure: An Unusual Transition from Ionic Mixture to Aqueous Solution

The nanostructure of a series of choline chloride/urea/water deep eutectic solvent mixtures was characterized across a wide hydration range by neutron total scattering and empirical potential structure refinement (EPSR). As the structure is significantly altered, even at low hydration levels, reporting the DES water content is important. However, the DES nanostructure is retained to a remarkably high level of water (ca. 42 wt % H₂O) because of solvophobic sequestration of water into nanostructured domains around cholinium cations. At 51 wt %/83 mol % H₂O, this segregation becomes unfavorable, and the DES structure is disrupted; instead, water–water and DES–water interactions dominate. At and above this hydration level, the DES–water mixture is best described as an aqueous solution of DES components.

Ab initio molecular dynamics simulations of liquid water using high quality meta-GGA functionals

We have used ab initio molecular dynamics (AIMD) to characterize water properties using two meta-generalized gradient approximation (meta-GGA) functionals, M06-L-D3 and B97M-rV, and compared their performance against a standard GGA corrected for dispersion, revPBE-D3, at ambient conditions (298 K, and 1 g cm-3 or 1 atm). Simulations of the equilibrium density, radial distribution functions, self-diffusivity, the infrared spectrum, liquid dipole moments, and characterizations of the hydrogen bond network show that all three functionals have overcome the problem of the early AIMD simulations that erroneously found ambient water to be highly structured, but they differ substantially among themselves in agreement with experiment on this range of water properties. We show directly using water cluster data up through the pentamer that revPBE-D3 benefits from a cancellation of its intrinsic functional error by running classical trajectories, whereas the meta-GGA functionals are demonstrably more accurate and would require the simulation of nuclear quantum effects to realize better agreement with all cluster and condensed phase properties.

Coarse-grained empirical potential structure refinement: Application to a reverse aqueous micelle

Conventional atomistic computer simulations, involving perhaps up to 10⁶atoms, can achieve length-scales on the order of a few 10s of nm. Yet many heterogeneous systems, such as colloids, nano-structured materials, or biological systems, can involve correlations over distances up 100s of nm, perhaps even 1μm in some instances. For such systems it is necessary to invoke coarse-graining, where single atoms are replaced by agglomerations of atoms, usually represented as spheres, in order for the simulation to be performed within a practical computer memory and time scale. Small angle scattering and reflectivity measurements, both X-ray and neutron, are routinely used to investigate structure in these systems, and traditionally the data have been interpreted in terms of discrete objects, such as spheres, sheets, and cylinders, and combinations thereof. Here we combine the coarse-grained computer simulation approach with neutron small angle scattering to refine the structure of a heterogeneous system, in the present case a reverse aqueous micelle of sodium-dioctyl sulfosuccinate (AOT) and iso-octane. The method closely follows empirical potential structure refinement and involves deriving an empirical interaction potential from the scattering data. As in traditional coarse-grained methods, individual atoms are replaced by spherical density profiles, which, unlike real atoms, can inter-penetrate to a significant extent. The method works over an arbitrary range of length-scales, but is limited to around 2 orders of magnitude in distance above a specified dimension. The smallest value for this dimension is of order 1nm, but the largest dimension is arbitrary. This article is part of a Special Issue entitled "Recent Advances in Bionanomaterials" Guest Editor: Dr. Marie-Louise Saboungi and Dr. Samuel D. Bader.

Ionic diffusion and proton transfer in aqueous solutions of alkali metal salts

We report on a series of ab initio molecular dynamics investigations on LiCl, NaCl, and KCl aqueous solutions under the effect of static electric fields.

On the structure of prilocaine in aqueous and amphiphilic solutions

The solvation of prilocaine has been investigated in pure water and in amphiphilic solutions using a combination of neutron diffraction and simulations.

Probing the triplet correlation function in liquid water by experiments and molecular simulations

Three-body information of liquid water is extracted using X-ray diffraction experiment as well as in molecular simulations via isothermal pressure derivative of structure factor term.

Ab initio Electronic Structure of Liquid Water

Self-consistent GW calculations with efficient vertex corrections are employed to determine the electronic structure of liquid water. Nuclear quantum effects are taken into account through ab initio path-integral molecular dynamics simulations. We reveal a sizable band-gap renormalization of up to 0.7 eV due to hydrogen-bond quantum fluctuations. Our calculations lead to a band gap of 8.9 eV, in accord with the experimental estimate. We further resolve the ambiguities in the band-edge positions of liquid water. The valence-band maximum and the conduction-band minimum are found at -9.4 and -0.5  eV with respect to the vacuum level, respectively.

How van der Waals interactions determine the unique properties of water

Whereas the interactions between water molecules are dominated by strongly directional hydrogen bonds (HBs), it was recently proposed that relatively weak, isotropic van der Waals (vdW) forces are essential for understanding the properties of liquid water and ice. This insight was derived from ab initio computer simulations, which provide an unbiased description of water at the atomic level and yield information on the underlying molecular forces. However, the high computational cost of such simulations prevents the systematic investigation of the influence of vdW forces on the thermodynamic anomalies of water. Here, we develop efficient ab initio-quality neural network potentials and use them to demonstrate that vdW interactions are crucial for the formation of water's density maximum and its negative volume of melting. Both phenomena can be explained by the flexibility of the HB network, which is the result of a delicate balance of weak vdW forces, causing, e.g., a pronounced expansion of the second solvation shell upon cooling that induces the density maximum.

Neutron Scattering of Residual Hydrogen in 1,4-Dioxane-d8 Liquid: Understanding Measurements with Molecular Dynamics Simulations

That incoherent scattering from protiated molecular liquids adds a constant background to the measured scattering intensity is well-known, but less appreciated is the fact that coherent scattering is also induced by the presence of hydrogen in a deuterated liquid. In fact, the scattering intensity can be very sensitive, in the small-q region, with respect to the amounts and distribution of residual H in the system. We used 1,4-dioxane liquid to demonstrate that the partial structure factors of the HD and DD atom pairs contribute significantly to intermolecular scattering and that uncertainty in the extent of deuteration account for discrepancies between simulations and measurements. Both contributions to uncertainty have similar magnitudes: scattering interference of the hydrogen-deuterium pair, and complementary interference from the deuterium-deuterium pair by virtue of chemical inhomogeneity. This situation arises in practice since deuteration of liquids is often 99% or less. A combined experimental and extensive computational study of static thermal neutron scattering of 1,4-dioxane demonstrates the foregoing. We show, through simulations, that the reason for the differences is the content of protiated dioxane (vendors quote 1%). We estimate that up to 5% (at 298 K and at 343 K) protiated molar fraction may be involved in generating the scattering differences. Finally, we find that the particular distribution of hydrogen in the protiated molecules affects the results significantly; here, we considered molecules to be either fully protiated or fully deuterated. This scenario best reconciles the computational and experimental results, and leads us to speculate that the deuteration synthesis process tends to leave a molecule either fully deuterated or fully protiated. Although we have used 1,4-dioxane as a model liquid, the effects described in this study extend to similar liquids, and similar systematic experimental/computational studies can be performed to either understand measurements or calibrate/validate molecular dynamics models.

Multipolar Ewald methods, 2: applications using a quantum mechanical force field

A fully quantum mechanical force field (QMFF) based on a modified “divide-and-conquer” (mDC) framework is applied to a series of molecular simulation applications, using a generalized Particle Mesh Ewald method extended to multipolar charge densities. Simulation results are presented for three example applications: liquid water, p-nitrophenylphosphate reactivity in solution, and crystalline N,N-dimethylglycine. Simulations of liquid water using a parametrized mDC model are compared to TIP3P and TIP4P/Ew water models and experiment. The mDC model is shown to be superior for cluster binding energies and generally comparable for bulk properties. Examination of the dissociative pathway for dephosphorylation of p-nitrophenylphosphate shows that the mDC method evaluated with the DFTB3/3OB and DFTB3/OPhyd semiempirical models bracket the experimental barrier, whereas DFTB2 and AM1/d-PhoT QM/MM simulations exhibit deficiencies in the barriers, the latter for which is related, in part, to the anomalous underestimation of the p-nitrophenylate leaving group pKa. Simulations of crystalline N,N-dimethylglycine are performed and the overall structure and atomic fluctuations are compared with the experiment and the general AMBER force field (GAFF). The QMFF, which was not parametrized for this application, was shown to be in better agreement with crystallographic data than GAFF. Our simulations highlight some of the application areas that may benefit from using new QMFFs, and they demonstrate progress toward the development of accurate QMFFs using the recently developed mDC framework.

Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab initio molecular dynamics

We present a simple and accurate computational method which facilitates ab initio path-integral molecular dynamics simulations, where the quantum-mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions using density functional theory. This development will enable routine inclusion of nuclear quantum effects in ab initio molecular dynamics simulations of condensed-phase systems.

Segregated water observed in a putative fish embryo cryopreservative

Development of new cryopreservation strategies has major potential in medicine and agriculture and is critical to the conservation of endangered species that currently cannot be preserved. A critical property of any potential cryopreservative solution is its ability to prevent cell-damaging ice formation during cooling and subsequent heating. This study focuses on the freezing behaviour of promising model cryoprotective solutions. We perform neutron scattering analysis, combined with computer modelling, of the water structure after quench cooling these solutions. It is found that water in this solution forms nano-clusters encapsulated by the surrounding matrix of cryoprotectant solute molecules. We posit that these small volumes inhibit ice formation, because water does not have space for the structural relaxation required to crystallize on the timescale of the cooling process.

Atomic scale insights into urea–peptide interactions in solution

Investigations on the β-turn forming peptide, GPG, suggest that urea denatures proteins by replacing water molecules and subsequently weakening the peptide bonds as a possible mechanism of protein denaturation by urea.

Ab initio molecular dynamics study of an aqueous NaCl solution under an electric field

Ab initio molecular dynamics simulations of salty water under an electric field reveal two regimes of the relative mobilities of chlorine and sodium ions. When water dissociation and proton transfer are actived at strong field intensities, the presence of the ions hinders the efficiency of the proton transfer mechanism.

Neural network molecular dynamics simulations of solid–liquid interfaces: water at low-index copper surfaces

Molecular dynamics simulation of the water–copper interface have been carried out using high-dimensional neural network potential based on density functional theory.

On the atomic structure of cocaine in solution

A combination of neutron diffraction and computation has been used to investigate the atomic scale structure of cocaine in aqueous solutions.

Synthesis of heavy hydrocarbons at the core-mantle boundary

The synthesis of complex organic molecules with C-C bonds is possible under conditions of reduced activity of oxygen. We have found performing ab initio molecular dynamics simulations of the C-O-H-Fe system that such conditions exist at the core-mantle boundary (CMB). H₂O and CO₂ delivered to the CMB by subducting slabs provide a source for hydrogen and carbon. The mixture of H₂O and CO₂ subjected to high pressure (130 GPa) and temperature (4000 to 4500 K) does not lead to synthesis of complex hydrocarbons. However, when Fe is added to the system, C-C bonds emerge. It means that oil might be a more abundant mineral than previously thought.

Probing the structural and dynamical properties of liquid water with models including non-local electron correlation

Water is a ubiquitous liquid that displays a wide range of anomalous properties and has a delicate structure that challenges experiment and simulation alike. The various intermolecular interactions that play an important role, such as repulsion, polarization, hydrogen bonding, and van der Waals interactions, are often difficult to reproduce faithfully in atomistic models. Here, electronic structure theories including all these interactions at equal footing, which requires the inclusion of non-local electron correlation, are used to describe structure and dynamics of bulk liquid water. Isobaric-isothermal (NpT) ensemble simulations based on the Random Phase Approximation (RPA) yield excellent density (0.994 g/ml) and fair radial distribution functions, while various other density functional approximations produce scattered results (0.8-1.2 g/ml). Molecular dynamics simulation in the microcanonical (NVE) ensemble based on Møller-Plesset perturbation theory (MP2) yields dynamical properties in the condensed phase, namely, the infrared spectrum and diffusion constant. At the MP2 and RPA levels of theory, ice is correctly predicted to float on water, resolving one of the anomalies as resulting from a delicate balance between van der Waals and hydrogen bonding interactions. For several properties, obtaining quantitative agreement with experiment requires correction for nuclear quantum effects (NQEs), highlighting their importance, for structure, dynamics, and electronic properties. A computed NQE shift of 0.6 eV for the band gap and absorption spectrum illustrates the latter. Giving access to both structure and dynamics of condensed phase systems, non-local electron correlation will increasingly be used to study systems where weak interactions are of paramount importance.

Family of Oxygen-Oxygen Radial Distribution Functions for Water

In a typical X-ray diffraction experiment, the elastically scattered intensity, I(Q), is the experimental observable. I(Q) contains contributions from both intramolecular as well as intermolecular correlations embodied in the scattering factors, HOO(Q) and HOH(Q), with negligible contributions from HHH(Q). Thus, to accurately define the oxygen-oxygen radial distribution function, gOO(r), a model of the electron density is required to accurately weigh the HOO(Q) component relative to the intramolecular and oxygen-hydrogen correlations from the total intensity observable. In this work, we carefully define the electron density model and its underlying assumptions and more explicitly utilize two restraints on the allowable gOO(r) functions, which must conform to both very low experimental errors at high Q and the need to satisfy the isothermal compressibility at low Q. Although highly restrained by these conditions, the underdetermined nature of the problem is such that we present a family of gOO(r) values that provide equally good agreement with the high-Q intensity and compressibility restraints and with physically correct behavior at small r.

Ab initio molecular dynamics simulations of aqueous triflic acid confined in carbon nanotubes

Ab initio molecular dynamics simulations were performed to investigate the effects of nanoscale confinement on the structural and dynamical properties of aqueous triflic acid (CF3SO3H). Single-walled carbon nanotubes (CNTs) with diameters ranging from ∼11 to 14 Å were used as confinement vessels, and the inner surface of the CNT were either left bare or fluorinated to probe the influence of the confined environment on structural and dynamical properties of the water and triflic acidic. The systems were simulated at hydration levels of n = 1-3 H2O/CF3SO3H. Proton dissociation expectedly increased with increasing hydration. Along with the level of hydration, hydrogen bond connectivity between the triflic acid molecules, both directly and via a single water molecule, played a role on proton dissociation. Direct hydrogen bonding between the CF3SO3H molecules, most commonly found in the larger bare CNT, also promoted interactions between water molecules allowing for greater separation of the dissociated protons from the CF3SO3(-) as the hydration level was increased. However, this also resulted in a decrease in the overall proportion of dissociated protons. The confinement dimensions altered both the hydrogen bond network and the distribution of water molecules where the H2O in the fluorinated CNTs tended to form small clusters with less proton dissociation at n = 1 and 2 but the highest at n = 3. In the absence of nearby hydrogen bond accepting sites from H2O or triflic acid SO3H groups, the water molecules formed weak hydrogen bonds with the fluorine atoms. In the bare CNT systems, these involved the CF3 groups of triflic acid and were more frequently observed when direct hydrogen bonding between CF3SO3H hindered potential hydrogen bonding sites. In the fluorinated tubes, interactions with the covalently bound fluorine atoms of the CNT wall dominated which appear to stabilize the hydrogen bond network. Increasing the hydration level increased the frequency of the OH···F (CNT) hydrogen bonding which was highly pronounced in the smaller fluorinated CNT indicating an influence on the confinement dimensions on these interactions.