Tetrahedral Order Research Articles

Topological Identification Criteria, Stability, and Relevance of Pentagonal Nanochannels in Amorphous Ice.

Considering the potential importance of pentagonal nanochannels (PNCs) in determining the structure of the amorphous ice, we introduce topological criteria to identify the PNCs with an optimal fivefold symmetric environment. The basic building block in our criteria, termed as a bicyclo octamer, is an axisymmetric cluster formed by combination of three 6-membered boat-shaped rings. This bicyclo octamer unit serves as a seamless interface of the PNCs with cubic-hexagonal stacking patterns of the amorphous ice. This interface results in a fivefold symmetric mesostructure of relatively high stability: a central PNC with extended five branches of two-dimensional (2-D) hexagonal (wurtzite) crystalline monolayers stacked with cubic (diamond) layers. We also unearth a hierarchy of symmetric structures in amorphous ice: the PNCs, together with dodecahedron cages, form a network consisting of (nearly) equilateral triangular patterns. At the next hierarchical level of symmetry, such triangular patterns combine to form triangular pyramids with dodecahedron cages as the vertices, PNCs as the edges, and confined 2-D hexagonal crystalline monolayers as the triangular faces of the pyramids. The central core of the pyramids consists of cubic (diamond) regions with a strong local tetrahedral order. The overall structure of the amorphous ice states is found to be profoundly affected by PNCs. Specifically, in states with a relatively large number of PNCs, the cubic-hexagonal stacking is primarily in the form of hexagonal crystalline monolayers stacked from both sides with cubic crystalline layers.

Understanding the Origin of the Breakdown of the Stokes-Einstein Relation in Supercooled Water at Different Temperature-Pressure Conditions.

A recent experiment has measured the viscosity of water down to approximately 244 K and up to 300 MPa. The correct viscosity and translational diffusivity data at various temperature-pressure (T-P) state points allowed for checking the validity of the Stokes-Einstein (SE) relation, which accounts for the coupling between translational self-diffusion and medium viscosity. The diffusion-viscosity decoupling increases with decreasing temperature, but the increasing pressure reduces the extent of the decoupling. Earlier simulation studies explained the breakdown of the SE relation in terms of the location of the Widom line, emanating from the liquid-liquid critical point (LLCP). Although these studies made a significant contribution to the current understanding of the above phenomena, a detailed molecular picture is still lacking. Recently, our group has explained the diffusion-viscosity decoupling from a jump-diffusion perspective. The jump-diffusion coefficient, emanating from the jump translation of water molecules, is calculated using a quantitative approach for different temperatures at ambient pressure. It has been observed that jump-diffusion is the key factor for diffusion-viscosity decoupling in supercooled water. The same method is adopted in the present work to estimate the jump-diffusion coefficient for different T-P state points and, thereby, explains the role of jump-diffusion for the different extents of the SE relation breakdown at different pressures. The residual diffusion coefficient, the other component of the total diffusion that originates from small step displacement and that is calculated by subtracting the jump-diffusion coefficient from the total diffusion, is seen to be fairly coupled to the viscosity at the entire range of temperature and pressure. Furthermore, we have calculated the average number of H-bonds per water molecule and the tetrahedral order for different T-P state points and investigated an approximate correlation between the average local structure and the contribution of the jump-diffusion to the total diffusion of water. This study, therefore, puts forward a new perspective for explaining the SE relation breakdown in supercooled water under different pressure conditions.

Structural origin of the anomalous density maximum in silica and alkali silicate glasses

AbstractSilica, sharing the same tetrahedral order and many structural, thermodynamic and dynamic anomalies with water, has been speculated to have a density increase upon melting similar to water. In this work, an increase in density upon melting cristobalite silica and a shallow density maximum followed by a density minimum during cooling of silica liquid are observed in classical molecular dynamics simulations. The density maximum gradually diminishes with the increase in alkali size/content in alkali silicate glasses. The structural origin of the anomalous density maximum in silica is revealed by detailed structural analysis. During the cooling process, a range of rings with different sizes form in liquid silica, with 6‐member rings being the most dominant, which cause the silica network to open up and compensate the regular volume shrinkage upon cooling. These two competing factors lead to a density maximum, but to a less extent than that observed in melting of cristobalite silica. With the increase in modifier size/content in the alkali silicate glasses, the connectivity of silica network gradually breaks down; the population of 6‐member rings decrease with the increase in smaller or larger rings, therefore the density maximum becomes less obvious and eventually disappears.

Effects of hexamethylenetetramine (HMTA) on the aqueous solution structure, dynamics and ion solvation scenario: A concentration and temperature dependent study with potential HMTA models

The local hydrogen bonding structure of water and its dynamics in hexamethylenetetramine (HMTA) solution is investigated by using classical molecular dynamics simulations. In this study, we have compared two potential HMTA models with different Lennard-Jones (L-J) combination rules. We have considered five different concentrations of HMTA, ranging from pure water to 6.181 m HMTA at 298 K, whereas to calculate the temperature dependence from 298 K to 353 K, we have used 4.187 m concentration of HMTA. From the radial distribution function, it is observed that the addition of HMTA facilitates structural making of water, whereas our calculated values of the tetrahedral order parameter and asphericity of water suggests disordered structure with increasing HMTA concentration. Also there is a significant development of self-aggregation among water and HMTA molecules at higher concentration of HMTA. The self-diffusion coefficient values of water and HMTA is found to be decreased with increasing HMTA concentration in the solution, whereas at concentrations below 1.0 m, it matches well with the experimental observations. Our calculated activation energy of diffusion for HMTA (4.10 ± 0.2 kcal/g mol for Model-II), is very close to the experimental observation (4.34–4.44 kcal/g mol). The structure of the hydration shell of ions of different charges and sizes is also investigated in the presence of HMTA. For all the models, it is observed that the structural and dynamical properties of water and the hydration shell of ion shows negligible difference with varying concentration and temperature. In contrast, the ion−HMTA correlations are model dependent. It is suggested that the HMTA model-I (AM) is the suitable model for representing ion-solvation structure and dynamics particularly at lower concentrations of aqueous-HMTA solution.

Effects of confinement on supercooled tetrahedral liquids.

We use molecular dynamics simulations to ascertain the effects of geometrical restriction on glass-forming tetrahedral liquids. Striving for a broad approach, we study families of waterlike and silicalike liquids, for which we systematically scale the partial charges and, hence, the relevance of the tetrahedral networks. The confined liquids and the confining matrices consist of the same type of particles to avoid disruptive interactions and distorted structures at the interfaces. Spatially resolved analyses show that these neutral confinements still impose static mobility gradients and density correlations on the liquids. We quantify the increasing degree and range of the altered properties upon cooling. For both families of models, common relations describe the confinement effects of all systems with tetrahedral order, while deviations occur for systems with lower polarities and different structures. The observations are rationalized by considering the fact that a pinned wall imprints a static energy landscape to a neighboring liquid. We explore the properties of this landscape based on changes in vibrational motion and structural relaxation and find that typical barrier heights amount to two to three times the activation energy of bulk dynamics. Combining the present and previous results, we predict the evolution of confinement effects down to the glass transition temperature for liquids without fragile-to-strong crossover. In addition, it is found for silicalike liquids that the temperature dependence of dynamic and static correlation lengths from confinement studies is not affected when cooling through fragile-to-strong transitions of the bulk materials, casting doubt on the relevance of these length scales for the glassy slowdown.

Hydration-Shell Vibrational Spectroscopy.

Hydration-shell vibrational spectroscopy provides an experimental window into solute-induced water structure changes that mediate aqueous folding, binding, and self-assembly. Decomposition of measured Raman and infrared (IR) spectra of aqueous solutions using multivariate curve resolution (MCR) and related methods may be used to obtain solute-correlated spectra revealing solute-induced perturbations of water structure, such as changes in water hydrogen-bond strength, tetrahedral order, and the presence of dangling (non-hydrogen-bonded) OH groups. More generally, vibrational-MCR may be applied to both aqueous and nonaqueous solutions, including multicomponent mixtures, to quantify solvent-mediated interactions between oily, polar, and ionic solutes, in both dilute and crowded fluids. Combining vibrational-MCR with emerging theoretical modeling strategies promises synergetic advances in the predictive understanding of multiscale self-assembly processes of both biological and technological interest.

The effect of polymorphism on the structural, dynamic and dielectric properties of plastic crystal water: A molecular dynamics simulation perspective.

We have employed molecular dynamics simulations based on the TIP4P/2005 water model to investigate the local structural, dynamical, and dielectric properties of the two recently reported body-centered-cubic and face-centered-cubic plastic crystal phases of water. Our results reveal significant differences in the local orientational structure and rotational dynamics of water molecules for the two polymorphs. The probability distributions of trigonal and tetrahedral order parameters exhibit a multi-modal structure, implying the existence of significant local orientational heterogeneities, particularly in the face-centered-cubic phase. The calculated hydrogen bond statistics and dynamics provide further indications of the existence of a strongly heterogeneous and rapidly interconverting local orientational structural network in both polymorphs. We have observed a hindered molecular rotation, much more pronounced in the body-centered-cubic phase, which is reflected by the decay of the fourth-order Legendre reorientational correlation functions and angular Van Hove functions. Molecular rotation, however, is additionally hindered in the high-pressure liquid compared to the plastic crystal phase. The results obtained also reveal significant differences in the dielectric properties of the polymorphs due to the different dipolar orientational correlation characterizing each phase.

High-throughput assessment of hypothetical zeolite materials for their synthesizeability and industrial deployability

Abstract Zeolites are important microporous framework materials, where 200+ structures are known to exist and many millions so-called hypothetical materials can be computationally created. Here, we screen the “Deem” database of hypothetical zeolite structures to find experimentally feasible and industrially relevant materials. We use established and existing criteria and structure descriptors (lattice energy, local interatomic distances, TTT angles), and we develop new criteria which are based on 5-th neighbor distances to T-atoms, tetrahedral order parameters (or, tetrahedrality), and porosity and channel dimensionality. Our filter funnel for screening the most attractive zeolite materials that we construct consists of nine different types of criteria and a total of 53 subcriteria. The funnel reduces the pool of candidate materials from initially >300,000 to 70 and 33, respectively, depending on the channel dimensionality constraint applied (2- and 3-dimensional vs. only 3-dimensional channels). We find that it is critically important to define longer range and more stringent criteria such as the new 5-th neighbor distances to T-atoms and the tetrahedrality descriptor in order to succeed in reducing the huge pool of candidates to a manageable number. Apart from four experimentally achieved structures (BEC, BOG, ISV, SSF), all other candidates are hypothetical frameworks, thus, representing most valuable targets for synthesis and application. Detailed analysis of the screening data allowed us to also propose an exciting future direction how such screening studies as ours could be improved and how framework generating algorithms could be competitively optimized.

DeepIce: A Deep Neural Network Approach To Identify Ice and Water Molecules.

Computer simulation studies of multiphase systems rely on the accurate identification of local molecular structures and arrangements in order to extract useful insights. Local order parameters, such as Steinhardt parameters, are widely used for this identification task; however, the parameters are often tailored to specific local structural geometries and generalize poorly to new structures and distorted or undercoordinated bonding environments. Motivated by the desire to simplify the process and improve the accuracy, we introduce DeepIce, a novel deep neural network designed to identify ice and water molecules, which can be generalized to new structures where multiple bonding environments are present. DeepIce demonstrates that the characteristics of a crystalline or liquid molecule can be classified using as input simply the Cartesian coordinates of the nearest neighbors without compromising the accuracy. The network is flexible and capable of inferring rotational invariance and produces a high predictive accuracy compared to the Steinhardt approach, the tetrahedral order parameter and polyhedral template matching in the detection of the phase of molecules in premelted ice surfaces.

Thermal expansion of the Al2SiO5 polymorphs, kyanite, andalusite and sillimanite, between 10 and 1573 K determined using time-of-flight neutron powder diffraction

Powder and single-crystal diffraction data measured from the three geologically important Al2SiO5 polymorphs, kyanite, andalusite and sillimanite, over the last six decades have given varying accounts of each polymorph’s thermal expansion, the scatter between and even within experimental datasets often being quite large. Furthermore, there are no lattice parameter determinations below 273 K, where the thermodynamic functions vary substantially, and few measurements above 1200 K. Accurate and precise lattice parameters of natural kyanite, andalusite and sillimanite have therefore been obtained in the range 10–1573 K using the high-resolution powder diffractometer (HRPD) at the ISIS neutron spallation source. Accuracy is ensured by the use of an internal standard (NIST silicon SRM640c) and use of a bulk probe (neutrons) to avoid the specimen-displacement corrections required by typical back-reflection X-ray diffraction methods. Precision is ensured by use of the time-of-flight method on one of the longest primary neutron flightpath instruments in the world. For kyanite, the improved precision reveals the true temperature dependence of the three inter-axial angles for the first time, permitting derivation of accurate thermal expansion tensor coefficients. For both andalusite and sillimanite, the measurements reveal hitherto unknown regions of substantial negative linear expansivity below room temperature, along the c-axis in andalusite and along the a-axis in sillimanite. Above 1200 K, sillimanite exhibits an anomalous increase in thermal expansion that may be due to a change in the Al/Si tetrahedral site ordering.

Influence of tetrahedral order on ferromagnetic gel phases

.We investigate the macroscopic dynamics of gels with tetrahedral/octupolar symmetry, which possess in addition a spontaneous permanent magnetization. We derive the corresponding static and dynamic macroscopic equations for a phase, where the magnetization is parallel to one of the improper fourfold tetrahedral symmetry axes. Apart from elastic strains, we take into account relative rotations between the magnetization and the elastic network. The influence of tetrahedral order on these degrees of freedom is investigated and some experiments are proposed that are specific for such a material and allow to indirectly detect tetrahedral order. We also consider the case of a transient network and predict that stationary elastic shear stresses arise when a temperature gradient is applied.Graphical abstract

Distinct signature of local tetrahedral ordering in the scattering function of covalent liquids and glasses.

Tetrahedral amorphous materials such as SiO2, GeO2, Si, Ge, C, and chalcogenides are extremely important in nature and technology. It is known that covalent bonding favors local tetrahedral order in these materials. However, how to extract information on this structural order from the scattering function has remained elusive. By analyzing the structure of simulated SiO2 and experimental data of various tetrahedral materials, we show that the lowest wave number peak, known as the first sharp diffraction peak (FSDP), and a few higher wave number ones in the scattering functions come from the characteristic density waves of a single tetrahedral unit. FSDP is thus a direct measure of the tetrahedrality. This finding opens the door for long-awaited experimental access to the characterization of disordered amorphous structures.

Bat biosonar echo analysis using spatial audio and wideband matched-filter techniques

Bats and dolphins show tremendous aptitude in hunting prey in difficult conditions. These conditions include large amounts of clutter, perhaps reverberation, and interfering signals/noisy backgrounds. Bats have been extensively studied to learn more about how they detect, track, and intercept prey. One important aspect of many of these studies is to understand the acoustics around the bat’s head. In this work, a new reproduction methodology using spatial audio and matched-filter techniques will be presented. A custom-built tetrahedral 1st order soundfield microphone that captures high-frequency sound up to 80 kHz from all directions was developed to measure bat echoes in B-format. The three-dimensional echoes that the bat received, now in Ambisonic B-format were further processed using a wideband matched-filter. The matched-filter produces a wideband cross-ambiguity function (WAF) of received data and the transmitted signal for every 1 deg in azimuth and elevation. The thresholded matched-filter output provides precise estimates of bearing, elevation, range, and normal velocity. This poster will present details of the hardware and software development along with experimental results that illustrate the capabilities of this new approach.

Does a pair of methane molecules aggregate in water?

Molecular dynamics (MD) simulations of methane-water mixtures were performed using ab initio force fields for the CH4-H2O, H2O-H2O, and CH4-CH4 interactions. Both methane and water molecules were polarizable. From these calculations, the potential of mean force (PMF) between two methane molecules was extracted. Our results are compared with PMFs from a density-functional-theory (DFT) based Born-Oppenheimer type MD (BOMD) simulation, from a Monte Carlo (MC) simulation with ab initio-based force fields, and from MD simulations with empirical force fields. Our PMF is qualitatively similar to that obtained from the simulations with empirical force fields but differs significantly from those resulting from the DFT-BOMD and MC simulations. The depth of the PMF global minimum obtained in the present work is in a much better agreement with the experimental estimate than the result of the DFT-BOMD simulation, possibly due to the inability of DFT to describe the dispersion interactions and the lack of extensive sampling in the BOMD simulations. Our work indicates that, for a pair of methane molecules, there are configurations where the solvent increases the attraction between the solutes, but there are also conformations in which the solvent causes a weak net repulsion. On average, the methane molecules are more likely to be in the configuration where they are separated by a water molecule than in the one in which they are in contact even though the minimum of the PMF at the latter configuration is deeper than that at the former. Finally, we found that the water structure around methane solutes does not show a greater tetrahedral ordering than in neat bulk water.

Tetrahedral chain ordering and low dimensional magnetic lattice in a new brownmillerite Sr2ScFeO5.

We report the synthesis, structure and physical properties of a hitherto unreported brownmillerite compound Sr2ScFeO5. We have shown a new ordering sequence of the interlayer iron tetrahedral chains. Reduced dimensionality of the magnetic lattice and the frustration in the two dimensional iron tetrahedral chains originate complex magnetic and magneto-dielectric effects. Our study highlights a novel approach to tailor the magnetic lattice in bulk oxides.

Influence of glycerol on the cooling effect of pair hydrophobicity in water: relevance to proteins' stabilization at low temperature.

Glycerol, as a cosolvent of water, stabilizes proteins under extreme conditions (both at high and low temperatures). However, the mechanism of stabilization of proteins by glycerol at low temperature is still elusive. Because the decrease of hydrophobic interactions at a lower temperature is one of the crucial factors for the cold denaturation, we ask here whether glycerol protects the hydrophobic interactions upon cooling and thereby acts against cold denaturation. Here, we have performed potential of mean force (PMF) calculations, using the umbrella sampling technique, between a pair of methane hydrophobic solute molecules either in pure water or in binary mixtures of water and glycerol for two different compositions and each of them at four different temperatures. We have found that glycerol increases the pair hydrophobic interaction at all the temperatures studied and that the enhancement is more prominent at the lower temperatures studied here. Decomposition of the PMF into the enthalpic and the entropic components and detailed molecular structural analyses give insight into the above observation. We have found that the enhancement of the hydrophobic interaction with increasing glycerol concentration occurs primarily due to the strengthening of the glycerol-water interaction near the associated methane solute molecule pair and the tetrahedral ordering of the H-bonding network being made uniform around the solute by the added glycerol molecules. These results indirectly justify the efficacy of glycerol for the preservation of proteins against cold denaturation at low temperature.

Bulk structural information from density functionals for patchy particles.

We investigate bulk structural properties of tetravalent associating particles within the framework of classical density functional theory, building upon Wertheim's thermodynamic perturbation theory. To this end, we calculate density profiles within an effective test-particle geometry and compare to radial distribution functions obtained from computer simulations. We demonstrate that a modified version of the functional proposed by Yu and Wu [J. Chem. Phys. 116, 7094 (2002)] based on fundamental measure theory for hard spheres produces accurate results, although the functional does not satisfy the exactly known low-density limit. In addition, at low temperatures where particles start to form an amorphous tetrahedral network, quantitative differences between simulations and theory emerge due to the absence of geometrical information regarding the patch arrangement in the latter. Indeed, here we find that the theory fits better to simulations of the floating-bond model [E. Zaccarelli et al., J. Chem. Phys. 127, 174501 (2007)], which exhibits a weaker tetrahedral order due to more flexible bonds between particles. We also demonstrate that another common density functional approach by Segura et al. [Mol. Phys. 90, 759 (1997)] fails to capture fundamental structural properties.

Dynamic interplay of nematic, magnetic, and tetrahedral order in ferromagnetic nematic phases

We consider the influence of tetrahedral (octupolar) order on ferromagnetic nematic liquid-crystalline phases. The presence of tetrahedral order leads to broken parity symmetry in an achiral liquid-crystalline system, in addition to broken time-reversal symmetry associated with the existence of a spontaneous magnetization. As a consequence, we find static as well as reversible and irreversible dynamic cross-coupling terms absent in usual ferromagnetic nematics. Several static and dynamic experiments are suggested to detect possible tetrahedral order. We predict that linear gradient terms in the generalized energy involving the ferromagnetic magnetization and the nematic director field lead to chiral domains of ambidextrous helicity. As a characteristic dissipative dynamic cross coupling we point out that the rotation of the magnetization can be driven by temperature and/or concentration gradients. Conversely, heat and concentration currents can be generated by rotations of the magnetization. As a characteristic example for reversible cross-coupling terms we analyze the consequences of the coupling between the molecular field of the nematic director and temperature and concentration gradients.

Increase in local crystalline order across the limit of stability leads to cubic-hexagonal stacking in supercooled monatomic (mW) water.

At the limit of stability of a supercooled tetrahedral liquid modeled by monatomic (mW) water potential, it was recently shown that relaxation occurs across a unique value of per particle potential energy (ϕmid ), which corresponds to a dynamical (non-stationary) condition of Gibbs free energy function G(T, P, N, ϕ): [∂2(G/N)/∂ϕ2 = 0] and [∂(G/N)/∂ϕ ≠ 0]. In this work, we explore the inherent structures responsible for the formation of the amorphous states through such a mechanism of relaxation of mW liquid. We first identify 6-member boat and chair shaped rings using a criterion based on the internal dihedral angles. We then consider the stacking of the cubic diamond (10-atom cluster with 4 chair shaped rings) and hexagonal wurtzite (12-atom cluster with 3 boat and 2 chair shaped rings) units through a shared chair ring. We find that the local crystalline (tetrahedral) order is exhibited by the eclipsed bond particles of the laterally connected wurtzite units which are stacked from both sides with the diamond units (DWD stacking). Increasingly longer range crystalline order is obtained as the number of stacked wurtzite layers increases: the particles shared by the stacked (laterally connected) wurtzite layers in DWWD show a longer range crystalline order. An even longer range crystalline order is exhibited by the eclipsed bond particles of the middle (laterally connected) wurtzite layer of DWWWD stacking. We find that cubic-hexagonal stacking occurs primarily in the form of DWD layers across the limit of stability. The local tetrahedral order of the purely cubic (diamond) network particles (which are not shared with wurtzite units) deviates significantly from that of the hexagonal crystal. Nonetheless, the average length of the bonds in the purely cubic network approaches that in the hexagonal crystal very closely. Thus a large increase in the purely cubic ice across the instability also leads to an increase in the local crystalline order in the form of bond-lengths. Our results are consistent with previous experimental and simulation studies which find a significant fraction of cubic ice along with cubic-hexagonal stacking layers in deeply supercooled water.

How Different Are the Characteristics of Aqueous Solutions of tert-Butyl Alcohol and Trimethylamine- N-Oxide? A Molecular Dynamics Simulation Study.

Atomistic molecular dynamics simulations have been used to investigate differences in the characteristics of the aqueous solutions of two structurally similar, biologically important molecules, namely, tert-butyl alcohol (TBA) and trimethylamine- N-oxide (TMAO). By analyzing radial distribution functions, preferential solvation factors, and the number of nearest neighbors, structural characteristics of the two aqueous solutions are found to be dramatically different. By examining the distribution of nearest neighbor solute and solvent molecules in these two solutions, it is found that the aqueous solution of TMAO is homogeneous, whereas that of TBA is not. Further scrutiny of TBA-TBA radial distribution function at a high concentration by splitting the surrounding TBA molecules into two hemispheres demonstrates that the TBA aggregation occurs not only from the side of methyl moieties of TBA as expected in hydrophobicity-induced aggregation, but also from the side of the polar C-OH group. To analyze the effect of concentration of the two solute molecules (TBA and TMAO) on the local structure of water, tetrahedral order parameter and distributions of tetrahedral angles and hydrogen-bonding angles have been calculated for both the solutions. It is surprising to see that at high concentrations, the local water structure in the TMAO solution is more disrupted compared to the same in the TBA solution. Finally, the action of these two solutes on the folding-unfolding behavior of Trp-cage miniprotein has been analyzed and their contrasting activities toward the protein stability are correlated to the strikingly different behavior of their aqueous solutions.