Small-angle scattering and the structure of ambient liquid water

Solution and Surface Solvation of Nitrate Anions with Iron(III) and Aluminum(III) in Aqueous Environments: A Raman and Vibrational Sum Frequency Generation Study

Hydrated trivalent metal nitrate salts, Fe(NO3)3·9H2O and Al(NO3)3·9H2O, in both solid and aqueous phases are investigated. Raman and surface-selective vibrational sum frequency generation (SFG) spectroscopy, are used to shed light on ion-ion interactions and hydration in several spectral regions spanning low frequency (440-550 cm-1) to higher frequency modes of nitrate and water (720, 1050, 1250-1450, and 2800-3750 cm-1). These frequencies span the metal-water mode, nitrate in-plane deformation, nitrate symmetric and asymmetric modes, and the OH stretch of condensed phase water molecules. Comparison to NaNO3, and in some cases KNO3, is also shown, providing insight. Splitting and frequency shifts are observed and discussed for both the solid state and solution phase. The Lewis acidity of Fe3+ and Al3+ ions plays a significant role in the observed spectra, in particular for the nitrate asymmetric band splitting and frequency shift. The spectral response from water solvation for iron and aluminum nitrates is nonlinear as compared to linear for sodium nitrate, suggesting significantly different solvation environments that are limited by water hydration capacity at higher concentrations. Moreover, a non-hydrogen bonded OH, dangling OH, from hydrating water molecules is observed spectroscopically for Al and Fe nitrate solutions. Furthermore, aluminum nitrate perturbs the surface water structure more than iron nitrate despite aluminum being a weaker Lewis acid. The surface water structure is thus found to be unique for the Al(NO3)3 solutions as compared to both Fe(NO3)3 and NaNO3, such that surface solvation is more pronounced. This observation exemplifies the nature of the Fe(III) and Al(III) ions and their substantial influence on the surface water structure.

Biomolecular condensates form spatially inhomogeneous network fluids

The functions of biomolecular condensates are thought to be influenced by their material properties, and these will be determined by the internal organization of molecules within condensates. However, structural characterizations of condensates are challenging, and rarely reported. Here, we deploy a combination of small angle neutron scattering, fluorescence recovery after photobleaching, and coarse-grained molecular dynamics simulations to provide structural descriptions of model condensates that are formed by macromolecules from nucleolar granular components (GCs). We show that these minimal facsimiles of GCs form condensates that are network fluids featuring spatial inhomogeneities across different length scales that reflect the contributions of distinct protein and peptide domains. The network-like inhomogeneous organization is characterized by a coexistence of liquid- and gas-like macromolecular densities that engenders bimodality of internal molecular dynamics. These insights suggest that condensates formed by multivalent proteins share features with network fluids formed by systems such as patchy or hairy colloids.

Structure of liquid-vapor interfaces: Perspectives from liquid state theory, large-scale simulations, and potential grazing-incidence x-ray diffraction

Grazing-incidence x-ray diffraction (GIXRD) is a scattering technique that allows one to characterize the structure of fluid interfaces down to the molecular scale, including the measurement of surface tension and interface roughness. However, the corresponding standard data analysis at nonzero wave numbers has been criticized as to be inconclusive because the scattering intensity is polluted by the unavoidable scattering from the bulk. Here, we overcome this ambiguity by proposing a physically consistent model of the bulk contribution based on a minimal set of assumptions of experimental relevance. To this end, we derive an explicit integral expression for the background scattering, which can be determined numerically from the static structure factors of the coexisting bulk phases as independent input. Concerning the interpretation of GIXRD data inferred from computer simulations, we extend the model to account also for the finite sizes of the bulk phases, which are unavoidable in simulations. The corresponding leading-order correction beyond the dominant contribution to the scattered intensity is revealed by asymptotic analysis, which is characterized by the competition between the linear system size and the x-ray penetration depth in the case of simulations. Specifically, we have calculated the expected GIXRD intensity for scattering at the planar liquid-vapor interface of Lennard-Jones fluids with truncated pair interactions via extensive, high-precision computer simulations. The reported data cover interfacial and bulk properties of fluid states along the whole liquid-vapor coexistence line. A sensitivity analysis shows that our findings are robust with respect to the detailed definition of the mean interface position. We conclude that previous claims of an enhanced surface tension at mesoscopic scales are amenable to unambiguous tests via scattering experiments.

Deciphering Density Fluctuations in the Hydration Water of Brownian Nanoparticles via Upconversion Thermometry

We investigate the intricate relationship among temperature, pH, and Brownian velocity in a range of differently sized upconversion nanoparticles (UCNPs) dispersed in water. These UCNPs, acting as nanorulers, offer insights into assessing the relative proportion of high-density and low-density liquid in the surrounding hydration water. The study reveals a size-dependent reduction in the onset temperature of liquid-water fluctuations, indicating an augmented presence of high-density liquid domains at the nanoparticle surfaces. The observed upper-temperature threshold is consistent with a hypothetical phase diagram of water, validating the two-state model. Moreover, an increase in pH disrupts the organization of water molecules, similar to external pressure effects, allowing simulation of the effects of temperature and pressure on hydrogen bonding networks. The findings underscore the significance of the surface of suspended nanoparticles for understanding high- to low-density liquid fluctuations and water behavior at charged interfaces.

The structure of water: A historical perspective

Attempts to understand the molecular structure of water were first made well over a century ago. Looking back at the various attempts, it is illuminating to see how these were conditioned by the state of knowledge of chemistry and physics at the time and the experimental and theoretical tools then available. Progress in the intervening years has been facilitated by not only conceptual and theoretical advances in physics and chemistry but also the development of experimental techniques and instrumentation. Exploitation of powerful computational methods in interpreting what at first sight may seem impenetrable experimental data has led us to the consistent and detailed picture we have today of not only the structure of liquid water itself and how it changes with temperature and pressure but also its interactions with other molecules, in particular those relevant to water's role in important chemical and biological processes. Much remains to be done in the latter areas, but the experimental and computational techniques that now enable us to do what might reasonably be termed "liquid state crystallography" have opened the door to make possible further advances. Consequently, we now have the tools to explore further the role of water in those processes that underpin life itself-the very prospect that inspired Bernal to develop his ideas on the structure of liquids in general and of water in particular.

Biomolecular condensates form spatially inhomogeneous network fluids

The functions of biomolecular condensates are thought to be influenced by their material properties, and these will be determined by the internal organization of molecules within condensates. However, structural characterizations of condensates are challenging, and rarely reported. Here, we deploy a combination of small angle neutron scattering, fluorescence recovery after photobleaching, and coarse-grained molecular dynamics simulations to provide structural descriptions of model condensates that are formed by macromolecules from nucleolar granular components (GCs). We show that these minimal facsimiles of GCs form condensates that are network fluids featuring spatial inhomogeneities across different length scales that reflect the contributions of distinct protein and peptide domains. The network-like inhomogeneous organization is characterized by a coexistence of liquid- and gas-like macromolecular densities that engenders bimodality of internal molecular dynamics. These insights suggest that condensates formed by multivalent proteins share features with network fluids formed by systems such as patchy or hairy colloids.

Existence of Quantum Pharmacology in Sartans: Evidence in Isolated Rabbit Iliac Arteries

Quantum pharmacology introduces theoretical models to describe the possibility of ultra-high dilutions to produce biological effects, which may help to explain the placebo effect observed in hypertensive clinical trials. To determine this within physiology and to evaluate novel ARBs, we tested the ability of known angiotensin II receptor blockers (ARBs) (candesartan and telmisartan) used to treat hypertension and other cardiovascular diseases, as well as novel ARBs (benzimidazole-N-biphenyl tetrazole (ACC519T), benzimidazole-bis-N,N'-biphenyl tetrazole (ACC519T(2)) and 4-butyl-N,N0-bis[[20-2Htetrazol-5-yl)biphenyl-4-yl]methyl)imidazolium bromide (BV6(K+)2), and nirmatrelvir (the active ingredient in Paxlovid) to modulate vascular contraction in iliac rings from healthy male New Zealand White rabbits in responses to various vasopressors (angiotensin A, angiotensin II and phenylephrine). Additionally, the hemodynamic effect of ACC519T and telmisartan on mean arterial pressure in conscious rabbits was determined, while the ex vivo ability of BV6(K+)2 to activate angiotensin-converting enzyme-2 (ACE2) was also investigated. We show that commercially available and novel ARBs can modulate contraction responses at ultra-high dilutions to different vasopressors. ACC519T produced a dose-dependent reduction in rabbit mean arterial pressure while BV6(K+)2 significantly increased ACE2 metabolism. The ability of ARBs to inhibit contraction responses even at ultra-low concentrations provides evidence of the existence of quantum pharmacology. Furthermore, the ability of ACC519T and BV6(K+)2 to modulate blood pressure and ACE2 activity, respectively, indicates their therapeutic potential against hypertension.

Biomolecular condensates form spatially inhomogeneous network fluids

The functions of biomolecular condensates are thought to be influenced by their material properties, and these are in turn determined by the multiscale structural features within condensates. However, structural characterizations of condensates are challenging, and hence rarely reported. Here, we deploy a combination of small angle neutron scattering, fluorescence recovery after photobleaching, and bespoke coarse-grained molecular dynamics simulations to provide structural descriptions of model condensates that mimic nucleolar granular components (GCs). We show that facsimiles of GCs are network fluids featuring spatial inhomogeneities across hierarchies of length scales that reflect the contributions of distinct protein and peptide domains. The network-like inhomogeneous organization is characterized by a coexistence of liquid- and gas-like macromolecular densities that engenders bimodality of internal molecular dynamics. These insights, extracted from a combination of approaches, suggest that condensates formed by multivalent proteins share features with network fluids formed by associative systems such as patchy or hairy colloids.

Evidence for liquid-liquid phase separation during the early stages of Mg-struvite formation

The precipitation of struvite, a magnesium ammonium phosphate hexahydrate (MgNH4PO4 · 6H2O) mineral, from wastewater is a promising method for recovering phosphorous. While this process is commonly used in engineered environments, our understanding of the underlying mechanisms responsible for the formation of struvite crystals remains limited. Specifically, indirect evidence suggests the involvement of an amorphous precursor and the occurrence of multi-step processes in struvite formation, which would indicate non-classical paths of nucleation and crystallization. In this study, we use synchrotron-based in situ x-ray scattering complemented by cryogenic transmission electron microscopy to obtain new insights from the earliest stages of struvite formation. The holistic scattering data captured the structure of an entire assembly in a time-resolved manner. The structural features comprise the aqueous medium, the growing struvite crystals, and any potential heterogeneities or complex entities. By analysing the scattering data, we found that the onset of crystallization causes a perturbation in the structure of the surrounding aqueous medium. This perturbation is characterized by the occurrence and evolution of Ornstein-Zernike fluctuations on a scale of about 1 nm, suggesting a non-classical nature of the system. We interpret this phenomenon as a liquid-liquid phase separation, which gives rise to the formation of the amorphous precursor phase preceding actual crystal growth of struvite. Our microscopy results confirm that the formation of Mg-struvite includes a short-lived amorphous phase, lasting >10 s.

Eliminating finite-size effects on the calculation of x-ray scattering from molecular dynamics simulations

Structural studies using x-ray scattering methods for investigating molecules in solution are shifting focus toward describing the role and effects of the surrounding solvent. However, forward models based on molecular dynamics (MD) simulations to simulate structure factors and x-ray scattering from interatomic distributions such as radial distribution functions (RDFs) face limitations imposed by simulations, particularly at low values of the scattering vector q. In this work, we show how the value of the structure factor at q = 0 calculated from RDFs sampled from finite MD simulations is effectively dependent on the size of the simulation cell. To eliminate this error, we derive a new scheme to renormalize the sampled RDFs based on a model of the excluded volume of the particle-pairs they were sampled from, to emulate sampling from an infinite system. We compare this new correction method to two previous RDF-correction methods, developed for Kirkwood-Buff theory applications. We present a quantitative test to assess the reliability of the simulated low-q scattering signal and show that our RDF-correction successfully recovers the correct q = 0 limit for neat water. We investigate the effect of MD-sampling time on the RDF-corrections, before advancing to a molecular example system, comprised of a transition metal complex solvated in a series of water cells with varying densities. We show that our correction recovers the correct q = 0 behavior for all densities. Furthermore, we employ a simple continuum scattering model to dissect the total scattering signal from the solvent-solvent structural correlations in a solute-solvent model system to find two distinct contributions: a non-local density-contribution from the finite, fixed cell size in NVT simulations, and a local contribution from the solvent shell. We show how the second contribution can be approximated without also including the finite-size contribution. Finally, we provide a "best-practices"-checklist for experimentalists planning to incorporate explicit solvation MD simulations in future work, offering guidance for improving the accuracy and reliability of structural studies using x-ray scattering methods in solution.

Synthetic molecular motor activates drug delivery from polymersomes

The design of stimuli-responsive systems in nanomedicine arises from the challenges associated with the unsolved needs of current molecular drug delivery. Here, we present a delivery system with high spatiotemporal control and tunable release profiles. The design is based on the combination of an hydrophobic synthetic molecular rotary motor and a PDMS-b-PMOXA diblock copolymer to create a responsive self-assembled system. The successful incorporation and selective activation by low-power visible light (λ = 430 nm, 6.9 mW) allowed to trigger the delivery of a fluorescent dye with high efficiencies (up to 75%). Moreover, we proved the ability to turn on and off the responsive behavior on demand over sequential cycles. Low concentrations of photoresponsive units (down to 1 mol% of molecular motor) are shown to effectively promote release. Our system was also tested under relevant physiological conditions using a lung cancer cell line and the encapsulation of an Food and Drug Administration (FDA)-approved drug. Similar levels of cell viability are observed compared to the free given drug showing the potential of our platform to deliver functional drugs on request with high efficiency. This work provides an important step for the application of synthetic molecular machines in the next generation of smart delivery systems.

Understanding dynamics in coarse-grained models. II. Coarse-grained diffusion modeled using hard sphere theory

The first paper of this series [J. Chem. Phys. 158, 034103 (2023)] demonstrated that excess entropy scaling holds for both fine-grained and corresponding coarse-grained (CG) systems. Despite its universality, a more exact determination of the scaling relationship was not possible due to the semi-empirical nature. In this second paper, an analytical excess entropy scaling relation is derived for bottom-up CG systems. At the single-site CG resolution, effective hard sphere systems are constructed that yield near-identical dynamical properties as the target CG systems by taking advantage of how hard sphere dynamics and excess entropy can be analytically expressed in terms of the liquid packing fraction. Inspired by classical equilibrium perturbation theories and recent advances in constructing hard sphere models for predicting activated dynamics of supercooled liquids, we propose a new approach for understanding the diffusion of molecular liquids in the normal regime using hard sphere reference fluids. The proposed "fluctuation matching" is designed to have the same amplitude of long wavelength density fluctuations (dimensionless compressibility) as the CG system. Utilizing the Enskog theory to derive an expression for hard sphere diffusion coefficients, a bridge between the CG dynamics and excess entropy is then established. The CG diffusion coefficient can be roughly estimated using various equations of the state, and an accurate prediction of accelerated CG dynamics at different temperatures is also possible in advance of running any CG simulation. By introducing another layer of coarsening, these findings provide a more rigorous method to assess excess entropy scaling and understand the accelerated CG dynamics of molecular fluids.

Revealing the three-component structure of water with principal component analysis (PCA) of X-ray spectra

Combining principal component analysis (PCA) of X-ray spectra with MD simulations, we experimentally reveal the existence of three basic components in water. These components exhibit distinct structures, densities, and temperature dependencies. Among the three, the two major components correspond to the low-density liquid (LDL) and the high-density liquid (HDL) predicted by the two-component model, and the third component exhibits a unique 5-hydrogen-bond configuration with ultra-high local density. As the temperature increases, the LDL component decreases and the HDL component increases, while the third component varies non-monotonically with a peak around 20 °C to 30 °C. The 3D structure of the third component is further illustrated as the uniform distribution of five hydrogen-bonded neighbors on a spherical surface. Our study reveals experimental evidence for water's possible three-component structure, which provides a fundamental basis for understanding water's special properties and anomalies.

Modeling the temporal evolution and stability of thin evaporating films for wafer surface processing

The interaction of thin evaporating fluid films with solids is studied using the example of water on LiTaO3 (LTO). Adsorption energies are computed by ab initio density functional theory (DFT) and used to calculate the Gibbs free energy of adsorption of water on LTO. Integrating the disjoining pressure, consisting of molecular and structural components, with respect to film thickness gives an expression for the Gibbs free energy. In this way, parameters for the disjoining pressure can be calculated by fitting its integral to the Gibbs free energy computed by ab initio DFT. A combination of literature-known models for spin drying and evaporation is utilized to describe the temporal evolution of the water layer. The vapor above the water layer is modeled by diffusion and a mass balance is applied at the water-air interface. For thick initial layers, an analytical approximation is derived which only depends on fluid and ambient conditions but not on the substrate properties.

Charge Gradients around Dendritic Voids Cause Nanoscale Inhomogeneities in Liquid Water

Water is the matrix of life and serves as a solvent for numerous physical and chemical processes. The origins of the nature of inhomogeneities that exist in liquid water and the time scales over which they occur remains an open question. Here, we report femtosecond elastic second harmonic scattering (fs-ESHS) of liquid water in comparison to an isotropic liquid (CCl₄) and show that water is indeed a nonuniform liquid. The coherent fs-ESHS intensity was interpreted, using molecular dynamics simulations, as arising from charge density fluctuations with enhanced nanoscale polarizabilities around transient voids having an average lifetime of 300 fs. Although voids were also present in CCl₄, they were not characterized by hydrogen bond defects and did not show strong polarizability fluctuations, leading to fs-ESHS of an isotropic liquid. The voids increased in number at higher temperatures above room temperature, in agreement with the fs-ESHS results.

Molecular dynamics analysis of elastic properties and new phase formation during amorphous ices transformations

Unlike conventional first-order phase transitions, the kinetics of amorphous-amorphous transitions has been much less studied. The ultrasonic experiments on the transformations between low-density and high-density amorphous ice induced by pressure or heating provided the pressure and temperature dependencies of elastic moduli. In this article, we make an attempt to build a microscopic picture of these experimentally studied transformations using the molecular dynamics method with the TIP4P/Ice water model. We study carefully the dependence of the results of elastic constants calculations on the deformation rates. The system size effects are considered as well. The comparison with the experimental data enriches our understanding of the transitions observed. Our modeling gives new information about the formation mechanisms of new phase clusters during the transition between low-density and high-density amorphous ices. We analyse the applicability of the term "nucleation" for these processes.

Correlated Local Fluctuations in the Hydrogen Bond Network of Liquid Water

The hypothesis that liquid water can separate into two phases in the supercooled state has been supported by recent experimental and theoretical studies. However, whether such structural inhomogeneity extends to ambient conditions is under intense debate. Due to the dynamic nature of the hydrogen bond network of liquid water, exploring its structure requires detailed insight into the collective motion of neighboring water molecules, a missing link that has not been examined so far. Here, highly sensitive quantum mechanical calculations detect that the time evolution of nearby hydrogen bonds is strongly correlated, revealing a direct mechanism for the appearance of short-range structural fluctuations in the hydrogen bond network of liquid water for the first time. This correlated dynamics is found to be closely connected to the static structural picture. The distortions from the tetrahedral structure do not occur independently but are correlated due to the preference of nearby donors and acceptors to be in similar environments. The existence of such cooperative fluctuations is further supported by the temperature dependence of the local structural evolution and explained by conventional analysis of localized orbitals. It was found that such correlated structural fluctuations are only observed on a short length scale in simulations at ambient conditions. The correlations of the nearby hydrogen bond pairs of liquid water unveiled here are expected to offer a new insight into connecting the dynamics of individual water molecules and the local structure of the hydrogen bond network.

Ionic mobility driven by correlated van der Waals and electrostatic forces

Classical theories of dielectric friction make two critical assumptions: (i) friction due to van der Waals (vdW) forces is described by hydrodynamic drag and is independent of the ionic charge and (ii) vdW and electrostatic forces are statistically independent. Both assumptions turn out to be incorrect when tested against simulations of anions and cations with varying charge magnitude dissolved in water. Both the vdW and electrostatic components of the force variance scale linearly with the ionic charge squared. The two components are strongly anticorrelated producing simple relations for the total force variance in terms of self-variances. The inverse diffusion constant scales linearly with the charge squared. Solvation asymmetry between cations and anions extends to linear transport coefficients.

Quantifying Concentration Fluctuations in Binary Glass-Forming Systems by Small- and Wide-Angle X-ray Scattering

Functionality of amorphous multicomponent systems largely depends upon the miscibility among components, especially in systems such as amorphous drugs and electrolytes. An in-depth understanding of mixing behaviors of various constituents is necessitated. Here, we applied the small- and wide-angle X-ray scattering (SWAXS) technique to monitor the mixing behaviors in three typical glass-forming binary systems imposed by varied heat of mixing. It is found that the Porod invariant (Q) determined at the glass transition temperature is remarkably enhanced as the concentration fluctuation becomes intensified. Meanwhile, the deviation of Q from the ideal mixing law is markedly weaken at elevated temperatures. The results unambiguously suggest that the degree of concentration fluctuations in mixing systems can be accurately quantified by the structural property, allowing the link to mixing thermodynamics.

Understanding Relationships between Free Volume and Oxygen Absorption in Ionic Liquids

Understanding the factors that govern gas absorption in ionic liquids is critical to the development of high-capacity solvents for catalysis, electrochemistry, and gas separations. Here, we report experimental probes of liquid structure that provide insights into how free volume impacts the O₂ absorption properties of ionic liquids. Specifically, we establish that isothermal compressibility─measured rapidly and accurately through small-angle X-ray scattering─reports on the size distribution of transient voids within a representative series of ionic liquids and is correlated with O₂ absorption capacity. Additionally, O₂ absorption capacities are correlated with thermal expansion coefficients, reflecting the beneficial effect of weak intermolecular interactions in ionic liquids on free volume and gas absorption capacity. Molecular dynamics simulations show that the void size distribution─in particular, the probability of forming larger voids within an ionic liquid─has a greater impact on O₂ absorption than the total free volume. These results establish relationships between the ionic liquid structure and gas absorption properties that offer design strategies for ionic liquids with high gas solubilities.

The pervasive impact of critical fluctuations in liquid-liquid extraction organic phases

Liquid-liquid extraction is an essential chemical separation technique where polar solutes are extracted from an aqueous phase into a nonpolar organic solvent by amphiphilic extractant molecules. A fundamental limitation to the efficiency of this important technology is third phase formation, wherein the organic phase splits upon sufficient loading of polar solutes. The nanoscale drivers of phase splitting are challenging to understand in the complex hierarchically structured organic phases. In this study, we demonstrate that the organic phase structure and phase behavior are fundamentally connected in a way than can be understood with critical phenomena theory. For a series of binary mixtures of trialkyl phosphate extractants with linear alkane diluents, we combine small angle x-ray scattering and molecular dynamics simulations to demonstrate how the organic phase mesostructure over a wide range of compositions is dominated by critical concentration fluctuations associated with the critical point of the third phase formation phase transition. These findings reconcile many longstanding inconsistencies in the literature where small angle scattering features, also consistent with such critical fluctuations, were interpreted as reverse micellar-like particles. Overall, this study shows how the organic phase mesostructure and phase behavior are intrinsically linked, deepening our understanding of both and providing a new framework for using molecular structure and thermodynamic variables to control mesostructure and phase behavior in liquid-liquid extraction.

Bulk and interfacial nanostructure and properties in deep eutectic solvents: Current perspectives and future directions

Deep eutectic solvents (DESs) are a tailorable class of solvents that are rapidly gaining scientific and industrial interest. This is because they are distinct from conventional molecular solvents, inherently tuneable via careful selection of constituents, and possess many attractive properties for applications, including catalysis, chemical extraction, reaction media, novel lubricants, materials chemistry, and electrochemistry. DESs are a class of solvents composed solely of hydrogen bond donors and acceptors with a melting point lower than the individual components and are often fluidic at room temperature. A unique feature of DESs is that they possess distinct bulk liquid and interfacial nanostructure, which results from intra- and inter-molecular interactions, including coulomb forces, hydrogen bonding, van der Waals interactions, electrostatics, dispersion forces, and apolar-polar segregation. This nanostructure manifests as preferential spatial arrangements of the different species, and exists over several length scales, from molecular- to nano- and meso-scales. The physicochemical properties of DESs are dictated by structure-property relationships; however, there is a significant gap in our understanding of the underlying factors which govern their solvent properties. This is a major limitation of DES-based technologies, as nanostructure can significantly influence physical properties and thus potential applications. This perspective provides an overview of the current state of knowledge of DES nanostructure, both in the bulk liquid and at solid interfaces. We provide definitions which clearly distinguish DESs as a unique solvent class, rather than a subset of ILs. An appraisal of recent work provides hints towards trends in structure-property relationships, while also highlighting inconsistencies within the literature suggesting new research directions for the field. It is hoped that this review will provide insight into DES nanostructure, their potential applications, and development of a robust framework for systematic investigation moving forward.

Minimal Microscopic Model for Liquid Polyamorphism and Waterlike Anomalies

Liquid polyamorphism is the intriguing possibility for a single component substance to exist in multiple liquid phases. We propose a minimal model for this phenomenon. Starting with a binary lattice model with critical azeotropy and liquid-liquid demixing, we allow interconversion of the two species, turning the system into a single-component fluid with two states differing in energy and entropy. Unveiling the phase diagram of the noninterconverting binary mixture gives unprecedented insight on the phase behaviors accessible to the interconverting fluid, such as a liquid-liquid transition with a critical point, or a singularity-free scenario, exhibiting thermodynamic anomalies without polyamorphism. The model provides a unified theoretical framework to describe supercooled water and a variety of polyamorphic liquids with waterlike anomalies.

A SAXS-based approach to rationally evaluate radical scavengers - toward eliminating radiation damage in solution and crystallographic studies

X-ray-based techniques are a powerful tool in structural biology but the radiation-induced chemistry that results can be detrimental and may mask an accurate structural understanding. In the crystallographic case, cryocooling has been employed as a successful mitigation strategy but also has its limitations including the trapping of non-biological structural states. Crystallographic and solution studies performed at physiological temperatures can reveal otherwise hidden but relevant conformations, but are limited by their increased susceptibility to radiation damage. In this case, chemical additives that scavenge the species generated by radiation can mitigate damage but are not always successful and the mechanisms are often unclear. Using a protein designed to undergo a large-scale structural change from breakage of a disulfide bond, radiation damage can be monitored with small-angle X-ray scattering. Using this, we have quantitatively evaluated how three scavengers commonly used in crystallographic experiments - sodium nitrate, cysteine, and ascorbic acid - perform in solution at 10°C. Sodium nitrate was the most effective scavenger and completely inhibited fragmentation of the disulfide bond at a lower concentration (500 µM) compared with cysteine (∼5 mM) while ascorbic acid performed best at 5 mM but could only reduce fragmentation by ∼75% after a total accumulated dose of 792 Gy. The relative effectiveness of each scavenger matches their reported affinities for solvated electrons. Saturating concentrations of each scavenger shifted fragmentation from first order to a zeroth-order process, perhaps indicating the direct contribution of photoabsorption. The SAXS-based method can detect damage at X-ray doses far lower than those accessible crystallographically, thereby providing a detailed picture of scavenger processes. The solution results are also in close agreement with what is known about scavenger performance and mechanism in a crystallographic setting and suggest that a link can be made between the damage phenomenon in the two scenarios. Therefore, our engineered approach might provide a platform for more systematic and comprehensive screening of radioprotectants that can directly inform mitigation strategies for both solution and crystallographic experiments, while also clarifying fundamental radiation damage mechanisms.

On the existence of soliton-like collective modes in liquid water at the viscoelastic crossover

The problem of large-density variations in supercooled and ambient water has been widely discussed in the past years. Recent studies have indicated the possibility of nanometer-sized density variations on the subpicosecond and picosecond time scales. The nature of fluctuating density heterogeneities remains a highly debated issue. In the present work, we address the problem of possible association of such density variations with the dynamics of terahertz longitudinal acoustic-like modes in liquid water. Our study is based on the fact that the subpicosecond dynamics of liquid water are essentially governed by the structural relaxation. Using a mode coupling theory approach, we found that for typical values of parameters of liquid water, the dynamic mechanism coming from the combination of the structural relaxation process and the finiteness of the amplitude of terahertz longitudinal acoustic-like mode gives rise to a soliton-like collective mode on a temperature-dependent nanometer length scale. The characteristics of this mode are consistent with the estimates of the amplitudes and temperature-dependent correlation lengths of density fluctuations in liquid water obtained in experiments and simulations. Thus, the fully dynamic mechanism could contribute to the formation and dynamics of fluctuating density heterogeneities. The soliton-like collective excitations suggested by our analysis may be relevant to different phenomena connected with supercooled water and can be expected to be associated with some ultrafast biological processes.

Long-Range Orientational Organization of Dipolar and Steric Liquids

Long-range orientational correlations in liquids have received recent renewed interest, in particular for the neat water case. These long-range orientational correlations, exceeding several tens of nanometers, originate from the presence of the strong permanent water dipolar moment. However, the exact dependence with the dipolar moment and the role of other local forces like steric hindrance has never been addressed. In this work, we experimentally measure long-range correlations for a set of liquids differing by their molecular weight and dipolar moment, in order to reveal the origin of their long-range organization. Hence, we show that the dipolar moment of a solvent molecule is not the unique feature determining the orientational correlation. Steric hindrance significantly helps to structure the liquids as well. In order to quantify these long-range correlations, we also derive theoretically the polarization resolved second harmonic scattering intensity as a function of the rotational invariants describing the dipolar and octupolar interaction.

SAXS studies of X-ray induced disulfide bond damage: Engineering high-resolution insight from a low-resolution technique

A significant problem in biological X-ray crystallography is the radiation chemistry caused by the incident X-ray beam. This produces both global and site-specific damage. Site specific damage can misdirect the biological interpretation of the structural models produced. Cryo-cooling crystals has been successful in mitigating damage but not eliminating it altogether; however, cryo-cooling can be difficult in some cases and has also been shown to limit functionally relevant protein conformations. The doses used for X-ray crystallography are typically in the kilo-gray to mega-gray range. While disulfide bonds are among the most significantly affected species in proteins in the crystalline state at both cryogenic and higher temperatures, there is limited information on their response to low X-ray doses in solution, the details of which might inform biomedical applications of X-rays. In this work we engineered a protein that dimerizes through a susceptible disulfide bond to relate the radiation damage processes seen in cryo-cooled crystals to those closer to physiologic conditions. This approach enables a low-resolution technique, small angle X-ray scattering (SAXS), to detect and monitor a residue specific process. A dose dependent fragmentation of the engineered protein was seen that can be explained by a dimer to monomer transition through disulfide bond cleavage. This supports the crystallographically derived mechanism and demonstrates that results obtained crystallographically can be usefully extrapolated to physiologic conditions. Fragmentation was influenced by pH and the conformation of the dimer, providing information on mechanism and pointing to future routes for investigation and potential mitigation. The novel engineered protein approach to generate a large-scale change through a site-specific interaction represents a promising tool for advancing radiation damage studies under solution conditions.

Could Chemical Reaction at the Molecular Level Show Distinction between Two Liquid-Water States? Study of the Excited-State Water-Catalyzed Proton Transfer Reaction Provides a Clue

The two liquid-water states, which lead to some anomalies when temperature crosses over 50 ± 10 °C at the atmospheric pressure, have been continuously catching popular attention. In this study, using the excited-state proton transfer (ESPT) catalyzed by water molecules as a prototypical reaction, we demonstrate that the kinetics of ESPT indeed is influenced by the two liquid-water states. In the water-catalyzed ESPT of 3-cyano-7-azaindole (3CAI), a repetitive and comprehensive temperature-dependent study of ESPT in H₂O from 0 to 90 °C shows anomalous behavior. The plot of the logarithm of ESPT rate constant as a function of inverse of absolute temperature deviates from a straight line. The convex-Arrhenius behavior manifests the activation free energy for water-assisted ESPT being dependent on temperature and hence the liquid water structure. To simplify the discussion, the plot is well fitted by using two straight lines that are crossed over in the vicinity of 40 °C. The free energy difference between water-solvated 3CAI and the 1:1 H₂O:3CAI complex is deduced to be 2.29 ± 0.04 and 1.96 ± 0.04 kcal·mol^-1 in the regions of 0-40 and 40-90 °C water, respectively, which also results in different frequency factors, i.e., the proton transfer/tunneling rates of (5.83 ± 0.36) × 10¹⁰ and (3.48 ± 0.27) × 10¹⁰ s^-1, respectively. In a qualitative manner, the results are then rationalized by the different types of H-bonding configuration as proposed for two liquid-water phases, rendering experimental evidence to support the different water phases in ambient temperatures at 1 bar.

A Reactive Force Field with Coarse-Grained Electrons for Liquid Water

Nonreactive force fields are defined by perturbations of electron density that are relatively small, whereas chemical reactivity involves wholesale electronic rearrangements that make and break bonds. Thus, reactive force fields are incredibly difficult to develop compared to nonreactive force fields, yet at the same time, they fill a critical need when ab initio molecular dynamics methods are not affordable. We introduce a new reactive force field model for water that combines modified nonbonded terms of the ReaxFF model and its embedding in the electrostatic interactions described by our recently introduced coarse-grained electron model (C-GeM). The ReaxFF/C-GeM force field is characterized for many energetic and dissociative water properties for water clusters, structure, and dynamical properties under ambient conditions in the condensed phase, as well as the temperature dependence of density and water diffusion, with very good agreement with experiment. The ReaxFF/C-GeM force field should be more transferable and more broadly applicable to a range of reactive systems involving both proton and electron transfer in the condensed phase.

Beyond integration: modeling every pixel to obtain better structure factors from stills

Most crystallographic data processing methods use pixel integration. In serial femtosecond crystallography (SFX), the intricate interaction between the reciprocal lattice point and the Ewald sphere is integrated out by averaging symmetrically equivalent observations recorded across a large number (104-106) of exposures. Although sufficient for generating biological insights, this approach converges slowly, and using it to accurately measure anomalous differences has proved difficult. This report presents a novel approach for increasing the accuracy of structure factors obtained from SFX data. A physical model describing all observed pixels is defined to a degree of complexity such that it can decouple the various contributions to the pixel intensities. Model dependencies include lattice orientation, unit-cell dimensions, mosaic structure, incident photon spectra and structure factor amplitudes. Maximum likelihood estimation is used to optimize all model parameters. The application of prior knowledge that structure factor amplitudes are positive quantities is included in the form of a reparameterization. The method is tested using a synthesized SFX dataset of ytterbium(III) lysozyme, where each X-ray laser pulse energy is centered at 9034 eV. This energy is 100 eV above the Yb3+ L-III absorption edge, so the anomalous difference signal is stable at 10 electrons despite the inherent energy jitter of each femtosecond X-ray laser pulse. This work demonstrates that this approach allows the determination of anomalous structure factors with very high accuracy while requiring an order-of-magnitude fewer shots than conventional integration-based methods would require to achieve similar results.

Attosecond spectroscopy of liquid water

Electronic dynamics in liquids are of fundamental importance, but time-resolved experiments have so far remained limited to the femtosecond time scale. We report the extension of attosecond spectroscopy to the liquid phase. We measured time delays of 50 to 70 attoseconds between the photoemission from liquid water and that from gaseous water at photon energies of 21.7 to 31.0 electron volts. These photoemission delays can be decomposed into a photoionization delay sensitive to the local environment and a delay originating from electron transport. In our experiments, the latter contribution is shown to be negligible. By referencing liquid water to gaseous water, we isolated the effect of solvation on the attosecond photoionization dynamics of water molecules. Our methods define an approach to separating bound and unbound electron dynamics from the structural response of the solvent.

Experimental observation of density fluctuations in liquid metals associated with liquid-liquid, liquid-gas and metal-nonmetal transitions

We have developed a special technique and succeeded to carry out small-angle x-ray scattering measurements for some liquid metal systems. The purpose is to investigate effects of transitions such as liquid-liquid (LLT), liquid-gas (LGT) and metal-nonmetal (MNMT) transitions on mesoscopic density fluctuations in liquids. In liquid Te systems (Se-Te and Ge-Te mixtures), which show continuous LLT accompanying MNMT, parameters of density fluctuations show maxima almost in the middle of the transition, both in strength and spatial size. This work (and Kajihara et al 2012 Phys. Rev. B86 214202) was the first direct observation that density fluctuations exhibit maximum corresponding to LLT. However in this study, we could not clearly separate the effects of LLT and MNMT on the observed density fluctuations. Thus, we also investigated fluid Hg under high pressure and high temperature conditions, which shows MNMT near a critical point of LGT, to investigate how MNMT affects them. We observed distinct density fluctuations; a strength and a correlation length of them show maxima at around a critical isochore of LGT, and the former is basically consistent with a phase diagram (compressibility) of LGT; they do not show any peaks at MNMT region. Precise analysis revealed that MNMT only affects a shift of another parameter, a short-range correlation length. These results in fluid Hg indicate that the density fluctuations are mainly derived from a critical phenomena of LGT and MNMT does not play any critical role on them. We believe that the latter conclusion also holds true for liquid Te systems; MNMT plays no important role on the density fluctuations in liquid Te systems and LLT is the main origin of them.

The nano-structural inhomogeneity of dynamic hydrogen bond network of TIP4P/2005 water

A method for studying the time dependence of the short-range molecular order of water has been proposed. In the present study, water is considered as a dynamic network between molecules at distances not exceeding 3.2 Å. The instantaneous configurations obtained with the molecular dynamics method have been sequentially analyzed. The mutual orientation of each molecule with its neighboring molecules has been studied and the interaction energy of each pair of neighbor molecules has been calculated. The majority of mutual orientation angles between molecules lie in the interval [0°; 20°]. More than 85% of the molecular pairs in each instantaneous configuration form H-bonds and the H-bond network includes all water molecules in the temperature range 233-293 K. The number of H-bonds fluctuates near the mean value and increases with decreasing temperature, and the energy of the vast majority of such bonds is much higher than the thermal energy. The interaction energy of 80% of the H-bonding molecular pairs lies in the interval [-7; -4] kcal/mol. The interaction energy of pairs that do not satisfy the H-bond angle criterion lies in the interval [-5; 4] kcal/mol; the number of such bonds does not exceed 15% and decreases with decreasing temperature. For the first time it has been found that in each instantaneous configuration the H-bond network contains built-in nanometric structural heterogeneities formed by shorter H-bonds. The fraction of molecules involved in the structural heterogeneities increases from 40% to 60% with a temperature decrease from 293 K to 233 K. Each heterogeneity has a finite lifetime and changeable structure, but they are constantly present during the entire simulation time.

Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme

Correlated motions of proteins are critical to function, but these features are difficult to resolve using traditional structure determination techniques. Time-resolved X-ray methods hold promise for addressing this challenge, but have relied on the exploitation of exotic protein photoactivity, and are therefore not generalizable. Temperature jumps, through thermal excitation of the solvent, have been utilized to study protein dynamics using spectroscopic techniques, but their implementation in X-ray scattering experiments has been limited. Here, we perform temperature-jump small- and wide-angle X-ray scattering measurements on a dynamic enzyme, cyclophilin A, demonstrating that these experiments are able to capture functional intramolecular protein dynamics on the microsecond timescale. We show that cyclophilin A displays rich dynamics following a temperature jump, and use the resulting time-resolved signal to assess the kinetics of conformational changes. Two relaxation processes are resolved: a fast process is related to surface loop motions, and a slower process is related to motions in the core of the protein that are critical for catalytic turnover.

Hydrogen-Bonding in Liquid Water at Multikilobar Pressures

High-precision THz (30 to 360 cm^-1) spectra of bulk liquid water are presented from ambient conditions up to hydrostatic pressures of 10 kbar. In concert with ab initio simulations, this allows us to characterize the molecular-level changes of the H-bond network under solvent stress conditions. Both the experimental and theoretical THz spectra reveal a blue shift in the intermolecular translational mode at 180 cm^-1 by 40 cm^-1 at 10 kbar and a blue shift together with an intensity increase in the relaxation mode. These changes can be traced back to a pressure-induced increase of the population of so-called short H-bond double donor configurations at the expense of those with longer such intermolecular bonds. Distinct electronic polarization effects are critical to capture the characteristic intensity changes of the THz line shape function. These advances in high-pressure THz spectroscopy open the door to investigate the pressure response of solvation shells and solute-solvent couplings.

A proposal for the structure of high- and low-density fluctuations in liquid water

Based on recent experimental data that can be interpreted as indicating the presence of specific structures in liquid water, we build and optimize two structural models which we compare with the available experimental data. To represent the proposed high-density liquid structures, we use a model consisting of chains of water molecules, and for low-density liquid, we investigate fused dodecahedra as templates for tetrahedral fluctuations. The computed infrared spectra of the models are in very good agreement with the extracted experimental spectra for the two components, while the extracted structures from molecular dynamics (MD) simulations give spectra that are intermediate between the experimentally derived spectra. Computed x-ray absorption and emission spectra as well as the O-O radial distribution functions of the proposed structures are not contradicted by experiment. The stability of the proposed dodecahedral template structures is investigated in MD simulations by seeding the starting structure, and remnants found to persist on an ∼30 ps time scale. We discuss the possible significance of such seeds in simulations and whether they can be viable candidates as templates for structural fluctuations below the compressibility minimum of liquid water.

A dilute gold nanoparticle suspension as small-angle X-ray scattering standard for an absolute scale using an extended Guinier approximation

In this article, a practical procedure for absolute intensity calibration for small-angle scattering (SAXS) studies on liquid microjets is established. A gold nanoparticle suspension is used as standard so that the intercept at Q = 0 of the SAXS scattering curve provides a scaling reference. In order to obtain the most precise extrapolation at Q = 0, an extension of the Guinier approximation has been used, with a second-order term in the fit that adapts to a larger Q range.

Compatibility of quantitative X-ray spectroscopy with continuous distribution models of water at ambient conditions

The phase diagram of water harbors controversial views on underlying structural properties of its constituting molecular moieties, its fluctuating hydrogen-bonding network, as well as pair-correlation functions. In this work, long energy-range detection of the X-ray absorption allows us to unambiguously calibrate the spectra for water gas, liquid, and ice by the experimental atomic ionization cross-section. In liquid water, we extract the mean value of 1.74 ± 2.1% donated and accepted hydrogen bonds per molecule, pointing to a continuous-distribution model. In addition, resonant inelastic X-ray scattering with unprecedented energy resolution also supports continuous distribution of molecular neighborhoods within liquid water, as do X-ray emission spectra once the femtosecond scattering duration and proton dynamics in resonant X-ray-matter interaction are taken into account. Thus, X-ray spectra of liquid water in ambient conditions can be understood without a two-structure model, whereas the occurrence of nanoscale-length correlations within the continuous distribution remains open.