Synthesis, Characterization, and Density Functional Theory Investigation of the Solid-State [UO 2 Cl 4 (H 2 O)] 2– Complex
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Results for “Noncovalent interactions”
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Uranyl Naphthylsalophen and Pyrasal Complexes: Oxo Ligands Acting as Hydrogen Bond Acceptors in the Solid State
Uranium is most stable when it is exposed to oxygen or water in its +6 oxidation state as the uranyl (UO 2 2+ ) ion. This ion is subsequently particularly stable and very resistant to functionalization due to the inverse trans effect. Uranyl oxo ligands are typically not considered good hydrogen bond acceptors due to their weak Lewis basicity; however, the ligands bound in the equatorial plane greatly affect the strength of the oxo ligands’ hydrogen bonding. Here, in this work, new naphthylsalophen and pyrasal complexes of uranium were synthesized and crystallized for characterization in the solid state. The bond lengths and angles of the uranyl ion and the ligand conformation are compared. In the solid state, one of the pyrasal complexes showed a hydrogen bond directly from a water molecule to the uranyl oxo ligand, which resulted in an asymmetric lengthening of the U–O yl bonds from 1.789 to 1.862 Å and 1.784 to 1.844 Å.
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Linear Free Energy Relationships Associated with Hydride Transfer From [(6,6'-R 2 -bpy)Re(CO) 3 H]: A Cautionary Tale in Identifying Hydrogen Bonding Effects in the Secondary Coordination Sphere
Here, six rhenium hydride complexes, [(6,6'-R 2 -bpy)Re(CO) 3 H] (bpy = 2,2'-bipyridine, R = OEt, OMe, NHMe, Me, F, Br), were synthesized. These complexes insert CO 2 to form rhenium formate complexes of the type [(6,6'-R 2 -bpy)Re(CO) 3 {OC(O)H}]. All the rhenium formate species were characterized using X-ray crystallography, which revealed that the bpy ligand is not coplanar with the metal coordination plane containing the two nitrogen donors of the bpy ligand but tilted. A solid-state structure of [(6,6'-Me 2 -bpy)Re(CO) 3 H] determined using MicroED also featured a tilted bpy ligand. The kinetics of CO 2 insertion into complexes of the type [(6,6'-R 2 -bpy)Re(CO) 3 H] were measured experimentally and the thermodynamic hydricities of [(6,6'-R 2 -bpy)Re(CO) 3 H] species were determined using theoretical calculations. A Brønsted plot constructed using the experimentally determined rate constants for CO 2 insertion and the calculated thermodynamic hydricities for [(6,6'-R 2 -bpy)Re(CO) 3 H] revealed a linear free energy relationship (LFER) between thermodynamic and kinetic hydricity. This LFER is different to the previously determined relationship for CO 2 insertion into complexes of the type [(4,4'-R 2 -bpy)Re(CO) 3 H]. At a given thermodynamic hydricity, CO 2 insertion is faster for complexes containing a 6,6'-substituted bpy ligand. This is likely in part due to the tilting observed for systems with 6,6'-substituted bpy ligands. Notably, the 6,6'-(NHMe) 2 -bpy ligand could in principle stabilize the transition state for CO 2 insertion via hydrogen bonding. This work shows that if only the rate of CO 2 insertion into [(6,6'-(NHMe) 2 -bpy)Re(CO) 3 H] is compared to [(4,4'-R 2 -bpy)Re(CO) 3 H] systems, the increase in rate could be easily attributed to hydrogen bonding, but in fact all 6,6'-substituted systems lead to faster than expected rates.
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Minimal Experimental Bias on the Hydrogen Bond Greatly Improves Ab Initio Molecular Dynamics Simulations of Water
Experiment Directed Simulations (EDS) is a method within a class of techniques seeking to improve molecular simulations by minimally biasing the system Hamiltonian to reproduce certain experimental observables. In a previous application of EDS to ab initio molecular dynamics (AIMD) simulation based on electronic density functional theory (DFT), the AIMD simulations of water were biased to reproduce its experimentally derived solvation structure. In particular, by solely biasing the O-O pair correlation functions, other structural and dynamical properties that were not biased were improved. In this work, the hypothesis is tested that directly biasing the OH pair correlation (and hence the H-O∙∙∙H hydrogen bonding), will provide an even better improvement of DFT-based water properties in AIMD simulations. The logic behind this hypothesis is that for most electronic DFT descriptions of water the hydrogen bonding is known to be deficient due to anomalous charge transfer and over polarization in the DFT. Using recent advances to the EDS learning algorithm, we thus train a minimal bias on AIMD water that reproduces the O-H radial distribution function derived from the highly accurate MB-pol model of water. Finally, it is then confirmed that biasing the O-H pair correlation alone can lead to improved AIMD water properties, with structural and dynamical properties in even closer to experiment than the previous EDS-AIMD model.
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Investigating the Accuracy of Water Models through the Van Hove Correlation Function
In this study, we present molecular-simulation-based calculations of the Van Hove correlation function (VHF) of water using multiple modeling approaches: classical molecular dynamics with simple three-site nonpolarizable models, with a polarizable model, and with a reactive force field; density functional tight-binding molecular dynamics; and ab initio molecular dynamics. Due to the many orders of magnitude difference in the computational cost of these approaches, we investigate how small and short the simulations can be while still yielding sufficiently accurate and interpretable results for the VHF. We investigate the accuracy of the different models by comparing them to recently published inelastic X-ray scattering measurements of the VHF. We find that all of the models exhibit qualitative agreement with the experiments, and in some models and for some properties, the agreement is quantitative. This work lays the foundation for future simulation approaches to calculating the VHF for aqueous solutions in bulk and under nanoconfinement.
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Direct Observation of Protonation State Modulation in SARS-CoV-2 Main Protease upon Inhibitor Binding with Neutron Crystallography
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The Aqueous and Acetonitrile Bond Dissociation Free Energies of N -Hydroxyphthalimide
Widely cited values of 89 and 90.9 kcal/mol for the bond-dissociation free energy of N-hydroxyphthalimide (NHPI) in water and acetonitrile, respectively, are in error. The sources of the errors leading to these values have been explored and corrected. Here, the corrected values are confirmed through new experiments in aqueous and acetonitrile media and are found to be 84.4 ± 0.1 and 80.04 ± 0.06 kcal/mol, respectively.
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Effect of Oxidation Level on the Interfacial Water at the Graphene Oxide–Water Interface: From Spectroscopic Signatures to Hydrogen-Bonding Environment
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Modeling of Peptides with Classical and Novel Machine Learning Force Fields: A Comparison
The replacement of classical force fields (FFs) with novel neural-network-based frameworks is an emergent topic in molecular dynamics (MD) simulations. In contrast to classical FFs, which have proven their capability to provide insights into complex soft matter systems at an atomistic resolution, the machine learning (ML) potentials have yet to demonstrate their applicability for soft materials. However, the underlying philosophy, which is learning the energy of an atom in its surrounding chemical environment, makes this approach a promising tool. In particular for the exploration of novel chemical compounds, which have not been considered in the original parametrization of classical FFs. In this article, we study the performance of the ANI-2x ML model and compare the results with those of two classical FFs, namely, CHARMM27 and the GROMOS96 43a1 FF. We explore the performance of these FFs for bulk water and two model peptides, trialanine and a 9-mer of the α-aminoisobutyric acid, in vacuum and water. The results for water describe a highly ordered water structure, with a structure similar to those using ab initio molecular dynamics simulations. The energy landscape of the peptides described by Ramachandran maps show secondary structure basins similar to those of the classical FFs but differ in the position and relative stability of the basins. Details of the sampled structures show a divergent performance of the different models, which can be related either to the short-ranged nature of the ML potentials or to shortcomings of the underlying data set used for training. These findings highlight the current state of the applicability of ANI-2x ML potential for MD simulations of soft matter systems. Simultaneously, they provide insights for future improvements of current ML potentials.
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Side-Chain and Ring-Size Effects on Permeability in Artificial Water Channels
Artificial water channels (AWCs) have emerged as a promising framework for stable water permeation, with water transport rates comparable to aquaporins (3.4–40.3 × 10 8 H 2 O/channel/s). In this study, we probe the influence of ring-size and side-chain length on the water permeability observed within a class of AWCs termed ligand-appended pillar[n]arenes (LAPs) that have an adjustable ring-size (m) and side-chain length (n). Through all-atom molecular dynamics simulations, we calculate the permeability of these channels using the collective diffusion model and find their permeabilities. We characterize the mechanistic influence of pillar[n]arene ring-size and side-chain length on the channel water permeability by analyzing the characteristics of the internal permeating water-wire and the surrounding channel structure. We observe that water permeability decreases as a function of increasing ring-size due to increases in hydrophilic contacts between the permeating water-wire and the oxygen groups on the channel wall. Further, we observe an increase in water permeability as a function of side-chain length due to increased partitioning of the channel terminal groups into the hydrophilic blocks of the surrounding bilayer. For the LAP6 channel, with increase in side-chain length, the distance between terminal groups increases and leads to an increase in pore size, thereby enhancing water permeability. In the case of LAP5, as side-chain length increases, the channel displays a compensatory effect between tilt and bend angle due to the flexible side-chains. Such flexibility leads to higher terminal group partitioning in the hydrophilic blocks of the bilayer and extends the permeating water-wire. Furthermore, this increase in water-wire length and hydrophilic block access overcomes the nonmonotonic pore size trend in pillar[5]arene channels.
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Computational Investigations of the Water Structure at the α-Al 2 O 3 (0001)–Water Interface
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Influence of Kosmotrope and Chaotrope Salts on Water Structural Relaxation
The structural relaxation in water solutions of kosmotrope (structure maker) and chaotrope (structure breaker) salts, namely sodium chloride, potassium chloride, and cesium chloride, were studied through quasielastic neutron scattering measurements. We found that the collective dynamics relaxation time at the structure factor peak obtained using heavy water solutions shows a distinctively different behavior in the kosmotrope as opposed to the chaotrope solutions, increasing with the salt concentration in the former and decreasing in the latter. In both cases the trends are proportional to the concentration dependence of the relative viscosity of the solutions. Furthermore, these results indicate that kosmotropes and chaotropes influence the solution’s viscosity by impacting in opposite ways the hydrogen bond network of water, strengthening it in one case and softening it in the other.
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Nuclear Quantum Effects on the Electronic Structure of Water and Ice
The electronic properties and optical response of ice and water are intricately shaped by their molecular structure, including the quantum mechanical nature of the hydrogen atoms. Despite numerous previous studies, a comprehensive understanding of the nuclear quantum effects (NQEs) on the electronic structure of water and ice at finite temperatures remains elusive. Here, we utilize molecular simulations that harness efficient machine-learning potentials and many-body perturbation theory to assess how NQEs impact the electronic bands of water and hexagonal ice. By comparing path-integral and classical simulations, we find that NQEs lead to a larger renormalization of the fundamental gap of ice, compared to that of water, ultimately yielding similar bandgaps in the two systems, consistent with experimental estimates. Our calculations suggest that the increased quantum mechanical delocalization of protons in ice, relative to water, is a key factor leading to the enhancement of NQEs on the electronic structure of ice.
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Quasielastic and Inelastic Neutron Scattering Study of Ultraconfined Water in Natural Mordenite ((Ca,Na 2 ,K 2 )Al 2 Si 10 O 24 ·7H 2 O)
Mordenite ((Ca,Na 2 ,K 2 )Al 2 Si 10 O 24 ·7H 2 O) is a natural and synthetic nanoporous zeolite containing several channels of different sizes in its structure. Because of this, its structure provides an important opportunity to study the relationship between confined and ultraconfined water as these channels have sizes between those typical of these water environments. In this study, the properties of water molecules in these environments were analyzed using inelastic and quasielastic neutron spectroscopy of a natural mordenite. The quasielastic spectra showed the presence of nonfreezing, mobile water molecules through the entire temperature range of the measurements, but very little anisotropy of the dynamics measured along and perpendicular to the channels. Faster and slower quasi-elastic neutron scattering (QENS) components may be consistent with the presence of two separate classes of water molecules in mordenite. Inelastic neutron spectroscopy also found no evidence of directional anisotropy. In conclusion, the strong intensity characteristic of neutron recoil on protons from highly mobile water molecules at low temperature (5 K), along with a significant shift of water librational band to lower energies and the O–H stretching modes to high energies, indicate that the hydrogen bonds acting on these water molecules in mordenite resemble those in liquid water rather than ice.
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Hydrogen Bonding and Its Effect on the Orientational Dynamics of Water Molecules inside Polyelectrolyte Brush-Induced Soft and Active Nanoconfinement
Despite being the most ubiquitous compound on Earth, the fundamental properties of water are not fully understood, especially in nanoconfinement. Densely grafted polyelectrolyte (PE) molecules attain the configuration of a “brush”: these PE brushes, due to their ability to form hydrogen bonds (HBs) with water via the PE functional groups, act as a source of soft and active nanoconfinement for the brush-trapped water molecules. In this paper, we study the effects of PE brush-induced confinement on the structure, dynamics and energetics of the water-water and water-PE HBs. Our results indicate a significant weakening of the HBs from bulk to sparsely grafted to densely grafted brushes. i.e., by increasing the degree of brush-induced nanoconfinement. We explain that this weakening of water-water HBs is caused by the disruption of the extended network of water molecules within the brush-induced nanoconfinement. This is confirmed by performing a ring structure analysis of the water molecules, which yields a reduction in the average ring size at higher degrees of brush-induced nanoconfinement (i.e., at higher brush grafting densities). Furthermore, we investigate the role of HB on the orientational dynamics of the water molecules. Here, we observe that the rotational motion of the water molecules becomes sluggish inside the PE brushes. Recent findings have indicated that the water and counterions trapped in brush-induced nanoconfinement demonstrate structures (in combination with the PE functional group) analogous to that in “water-in-salt” electrolytes that have seen extensive recent uses for Li-ion battery applications. However, the rotational dynamics of water molecules inside the brush-induced nanoconfinement is found to be distinctly different from that of conventional “water-in-salt” electrolytes in absence of any confinement; therefore, the present study will provide the necessary platform towards conceptualizing polymer-based nanoconfinement for battery applications.
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Simulations of Glass Transition and Mechanical Behavior of Off-Stoichiometric Crosslinked Polymers
Here, this work explores the influence of blend composition, network architecture, and hydrogen bonding on the material properties of crosslinked epoxy networks, focusing on the glass transition temperature (T g ) and Young’s modulus (Y). We used coarse-grained molecular dynamics simulations to simulate varying compositions of stiff and flexible components in epoxy monomer blends with varying excess of curative. We find that, without hydrogen bonding, networks of any composition show a monotonically increasing T g with decreasing excess curative, consistent with theory. In contrast, we find that when hydrogen bonding is introduced, the binary blend networks show significant enhancement in T g for lightly crosslinked systems. This result contributes to an explanation of the anomalous T g behavior observed experimentally in these systems. We further find that Y is generally enhanced by hydrogen bonds, especially below T g , demonstrating that hydrogen bonding has a significant influence on mechanical properties and can allow access to other desirable dynamic behavior, especially self-healing.
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How Silica Surface Chemistry Modulates Interfacial Water: Insights from Machine Learning Molecular Dynamics
Controlling water structure and dynamics at silica interfaces are central to a wide range of technologies, including protective oxide layers for solar water splitting and nanoporous membranes. In this work, we develop a machine learning interatomic potential, trained via active learning, to achieve ab initio accuracy for water confined between hydroxylated silica surfaces over a range of silanol coverages and slit widths. We find that partially hydroxylated surfaces (50 and 75% OH) support stronger water−surface hydrogen bonding and more extended interfacial density profiles than fully hydroxylated (100% OH) surfaces, indicating that increasing OH coverage does not necessarily strengthen interfacial hydrogenbond networks. Translational diffusion decreases approximately linearly with slit width and OH coverage, whereas rotational dynamics respond nonlinearly. In particular, at the smallest slit width of 5 Å, 75% OH coverage produces an enhanced local tetrahedral ordered interfacial network that strongly suppresses reorientation, while 100% coverage yields a crowded, disordered interfacial layer that also hinders rotation. In contrast, the 50% OH coverage is sufficiently sparse that it does not markedly alter water structure or dynamics under confinement. These results show that coupled control of pore size and surface chemistry enables nonlinear tuning of interfacial water structure and transport, providing a design strategy for optimizing porous silica for either enhanced interfacial stability and controlled reactivity or rapid and selective transport.
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