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Given the extensive use of fluorination in molecular design, it is imperative to understand the solvation properties of fluorinated compounds and the impact of the C–F bond on electrostatic interactions. Vibrational spectroscopy can provide direct insights into these interactions by using the C–F bond stretching [v(C–F)] as an electric field probe through the vibrational Stark effect (VSE). In this work, we explore the VSE of the three basic patterns of aliphatic fluorination, i.e., mono-, di-, and trifluorination in CF, CF2, and CF3 groups, respectively, and compare their response to the well-studied aromatic v(C–F). Magnitudes (i.e., Stark tuning rates) and orientations of the difference dipole vectors of the v(C–F)-containing normal modes were determined using density functional theory and a molecular dynamics (MD)-assisted solvatochromic analysis of model compounds in solvents of varying polarity. We obtain Stark tuning rates of 0.2–0.8 cm−1/(MV/cm), with smallest and largest electric field sensitivities for CFaliphatic and CF3,aliphatic, respectively. While average electric fields of solvation were oriented along the main symmetry axis of the CFn, and thus along its static dipole, the Stark tuning rate vectors were tilted by up to 87° potentially enabling to map electrostatics in multiple dimensions. We discuss the influence of conformational heterogeneity on spectral shifts and point out the importance of multipolar and/or polarizable MD force fields to describe the electrostatics of fluorinated molecules. The implications of this work are of direct relevance for studies of fluorinated molecules as found in pharmaceuticals, fluorinated peptides, and proteins. [ABSTRACT FROM AUTHOR]

In this article, we show that the collective light–matter strong coupling regime where N molecular emitters couple to the photon mode of an optical cavity can be mapped to a quantum impurity model where the photon is the impurity that is coupled to a bath of anharmonic transitions. In the thermodynamic limit where N ≫ 1, we argue that the bath can be replaced with an effective harmonic bath, leading to a dramatic simplification of the problem into one of the coupled harmonic oscillators. We derive simple analytical expressions for linear optical spectra (transmission, reflection, and absorption) where the only molecular input required is the molecular linear susceptibility. This formalism is applied to a series of illustrative examples, showing the role of temperature, disorder, vibronic coupling, and optical saturation of the molecular ensemble, explaining that it is useful even when describing an important class of nonlinear optical experiments. For completeness, we provide Appendixes A–C that include a self-contained derivation of the relevant spectroscopic observables for arbitrary anharmonic systems (for both large and small N) within the rotating-wave approximation. While some of the presented results herein have already been reported in the literature, we provide a unified presentation of the results as well as new interpretations that connect powerful concepts in open quantum systems and linear response theory with molecular polaritonics. [ABSTRACT FROM AUTHOR]

Molecular crystals are difficult to model with accurate first-principles methods due to large unit cells. On the other hand, accurate modeling is required as polymorphs often differ by only 1 kJ/mol. Machine learning interatomic potentials promise to provide accuracy of the baseline first-principles methods with a cost lower by orders of magnitude. Using the existing databases of the density functional theory calculations for molecular crystals and molecules, we train global machine learning interatomic potentials, usable for any molecular crystal. We test the performance of the potentials on experimental benchmarks and show that they perform better than classical force fields and, in some cases, are comparable to the density functional theory calculations. [ABSTRACT FROM AUTHOR]

We report a detailed density functional theory and molecular dynamics study of hydrogen bonding between trehalose and water, with a special emphasis on interactions in the amorphous solid state. For comparison, water–water interactions in water dimers and tetramers are evaluated using quantum calculations. The results show that the hydrogen bonding energy is dependent not only on the geometry (bond length and angle) but also on the local environment of the hydrogen bond. This is seen in quantum calculations of complexes in vacuum as well as in amorphous solid states with periodic boundary conditions. The temperature-induced glass transition in the trehalose–water system was studied using molecular dynamics simulations with varying cooling and heating rates. The obtained parameters of the glass transition are in good agreement with the experiments. Moreover, the dehydration of trehalose in the glassy state was investigated through a gradual dehydration with multiple small steps under isothermal conditions. From these simulations, the values of water sorption energy at different temperatures were obtained. The partial molar enthalpy of mixing of water value of −18 kJ/mol found in calorimetric experiments was accurately reproduced in these simulations. These findings are discussed in light of the hydrogen bonding data in the system. We conclude that the observed exothermic effect is due to different responses of liquid and glassy matrices to perturbations associated with the addition or removal of water molecules. [ABSTRACT FROM AUTHOR]

Traditional theories of the nuclear magnetic resonance (NMR) autocorrelation function for intra-molecular dipole pairs assume a single-exponential decay, yet the calculated autocorrelation of realistic systems displays a rich, multi-exponential behavior, resulting in anomalous NMR relaxation dispersion (i.e., frequency dependence). We develop an approach to model and interpret the multi-exponential intra-molecular autocorrelation using simple, physical models within a rigorous statistical mechanical development that encompasses both rotational diffusion and translational diffusion in the same framework. We recast the problem of evaluating the autocorrelation in terms of averaging over a diffusion propagator whose evolution is described by a Fokker–Planck equation. The time-independent part admits an eigenfunction expansion, allowing us to write the propagator as a sum over modes. Each mode has a spatial part that depends on the specified eigenfunction and a temporal part that depends on the corresponding eigenvalue (i.e., correlation time) with a simple, exponential decay. The spatial part is a probability distribution of the dipole pair, analogous to the stationary states of a quantum harmonic oscillator. Drawing inspiration from the idea of inherent structures in liquids, we interpret each of the spatial contributions as a specific molecular mode. These modes can be used to model and predict the NMR dipole–dipole relaxation dispersion of fluids by incorporating phenomena on the molecular level. We validate our statistical mechanical description of the distribution in molecular modes with molecular dynamics simulations interpreted without any relaxation models or adjustable parameters: the most important poles in the Padé–Laplace transform of the simulated autocorrelation agree with the eigenvalues predicted by the theory. [ABSTRACT FROM AUTHOR]

The significance of solvent effects in electronic structure calculations has long been noted, and various methods have been developed to consider this effect. The reference interaction site model self-consistent field with constrained spatial electron density (RISM-SCF-cSED) is a hybrid model that combines the integral equation theory of molecular liquids with quantum chemistry. This method can consider the statistically convergent solvent distribution at a significantly lower cost than molecular dynamics simulations. Because the RISM theory explicitly considers the solvent structure, it performs well for systems where hydrogen bonds are formed between the solute and solvent molecules, which is a challenge for continuum solvent models. Taking advantage of being founded on the variational principle, theoretical developments have been made in calculating various properties and incorporating electron correlation effects. In this review, we organize the theoretical aspects of RISM-SCF-cSED and its distinctions from other hybrid methods involving integral equation theories. Furthermore, we carefully present its progress in terms of theoretical developments and recent applications. [ABSTRACT FROM AUTHOR]

The significance of interfacial thermal resistance in the thermal conductivity of nanofluids is not well understood, in part because of the absence of measurements of this quantity. Here, we study the interfacial thermal resistance for metal–oil nanofluids of interest as heat transfer fluids for concentrating solar power, using density functional theory and molecular dynamics simulations. Insights on the role of chemical interactions in determining the interfacial thermal resistance are revealed. The results presented here showcase a general picture in which the stronger the chemical interactions between species at the interface, the lower the associated interfacial thermal resistance. The implications toward nanofluid design are discussed. We show that, for this important family of metal–oil nanofluids, the interfacial thermal resistance values are low enough so that it is possible to afford a reduction in particle size, minimizing stability and rheological issues while still offering enhancement in the effective thermal conductivity with respect to the base fluid. [ABSTRACT FROM AUTHOR]

Nuclear quantum effects play critical roles in a variety of molecular processes, especially in systems that contain hydrogen and other light nuclei, such as water. For water under ambient conditions, nuclear quantum effects are often interpreted as local effects resulting from a smearing of the hydrogen atom distribution. However, the orientational structure of water at interfaces determines long-range effects, such as electrostatics, through the O–H bond ordering that is impacted by nuclear quantum effects. In this work, I examine nuclear quantum effects on long-range electrostatics of water confined between hydrophobic walls using path integral simulations. To do so, I combine concepts from local molecular field theory with path integral methods at varying levels of approximation to develop efficient and physically intuitive approaches for describing long-range electrostatics in nonuniform quantum systems. Using these approaches, I show that quantum water requires larger electrostatic forces to achieve interfacial screening than the corresponding classical system. This work highlights the subtleties of electrostatics in nonuniform classical and quantum molecular systems, and the methods presented here are expected to be of use to efficiently model nuclear quantum effects in large systems. [ABSTRACT FROM AUTHOR]

In recent years, ionic microgels have garnered much attention due to their unique properties, especially their stimulus-sensitive swelling behavior. The tunable response of these soft, permeable, compressible, charged colloidal particles is increasingly attractive for applications in medicine and biotechnologies, such as controlled drug delivery, tissue engineering, and biosensing. The ability to model and predict variation of the osmotic pressure of a single microgel with respect to changes in particle properties and environmental conditions proves vital to such applications. In this work, we apply both nonlinear Poisson–Boltzmann theory and molecular dynamics simulation to ionic microgels (macroions) in the cell model to compute density profiles of microions (counterions, coions), single-microgel osmotic pressure, and equilibrium swelling ratios of spherical microgels whose fixed charge is confined to the macroion surface. The basis of our approach is an exact theorem that relates the electrostatic component of the osmotic pressure to the microion density profiles. Close agreement between theory and simulation serves as a consistency check to validate our approach. We predict that surface-charged microgels progressively deswell with increasing microgel concentration, starting well below close packing, and with increasing salt concentration, in qualitative agreement with experiments. Comparison with previous results for microgels with fixed charge uniformly distributed over their volume demonstrates that surface-charged microgels deswell more rapidly than volume-charged microgels. We conclude that swelling behavior of ionic microgels in solution is sensitive to the distribution of fixed charge within the polymer-network gel and strongly depends on bulk concentrations of both microgels and salt ions. [ABSTRACT FROM AUTHOR]

Delocalization error constrains the accuracy of density functional theory in describing molecular interactions in ion–water systems. Using Na+ and Cl− in water as model systems, we calculate the effects of delocalization error in the SCAN functional for describing ion–water and water–water interactions in hydrated ions, and demonstrate that density-corrected SCAN (DC-SCAN) predicts n-body and interaction energies with an accuracy approaching coupled cluster theory. The performance of DC-SCAN is size-consistent, maintaining an accurate description of molecular interactions well beyond the first solvation shell. Molecular dynamics simulations at ambient conditions with many-body MB-SCAN(DC) potentials, derived from the many-body expansion, predict the solvation structure of Na+ and Cl− in quantitative agreement with reference data, while simultaneously reproducing the structure of liquid water. Beyond rationalizing the accuracy of density-corrected models of ion hydration, our findings suggest that our unified density-corrected MB formalism holds great promise for efficient DFT-based simulations of condensed-phase systems with chemical accuracy. [ABSTRACT FROM AUTHOR]

The capacities of various interatomic potentials available for elemental germanium, with the scope to choose the potential suitable for the modeling of germanene (2D germanium) allotropes,f were investigated. Structural and mechanical properties of the flat, low-buckled, trigonal dumbbell, and large honeycomb dumbbell single-layer germanium (germanene) phases, were obtained using the density functional theory and molecular statics computations with Tersoff, modified embedded atom method, Stillinger–Weber, environment-dependent interatomic potential, ReaxFF, and machine-learning-based interatomic potentials. A systematic quantitative comparative study and discussion of the findings are given. [ABSTRACT FROM AUTHOR]

Effective "soft" interactions between macromolecules such as polymers, amphiphilic dendrimers, and suitably designed DNA based dendritic molecules have been shown to be purely repulsive and non-diverging. We report the structure and phase behavior of a mixture of hard colloids and soft coarse-grained macromolecules. Through the use of Reference Interaction Site Model theory and molecular dynamics simulations we find that hard colloids and soft macromolecules act as depletants toward each other, generating a medium-induced effective attraction. This effective attraction leads to the formation of non-dispersed phases at high densities. At low and high fractions of hard colloids the system macrophase separates into two disparate regions of hard colloids and soft macromolecules. However, this system microphase separates into a hard-rich and soft-rich self-assembled domains at intermediate compositions. The formation of microphase separated structure in this system of isotropic, disconnected, and purely repulsive colloids is surprising and quite novel. This behavior is likely due to a softening of the interface between hard-rich and soft-rich self-assembled domains. Molecular dynamics simulations have revealed that the microphase separated state has an overall disordered bicontinuous morphology. The hard-rich domain forms an ordered FCC structure and the soft-rich domain forms a disordered cluster-fluid, making the structure simultaneously ordered and disordered. [ABSTRACT FROM AUTHOR]

The velocity autocorrelation function (VACF) encapsulates extensive information about a fluid's molecular-structural and hydrodynamic properties. We address the following fundamental question: How well can a purely hydrodynamic description recover the molecular features of a fluid as exhibited by the VACF? To this end, we formulate a bona fide hydrodynamic theory of the tagged-particle VACF for simple fluids. Our approach is distinguished from previous efforts in two key ways: collective hydrodynamic modes and tagged-particle self-motion are modeled by linear hydrodynamic equations; the fluid's spatial velocity power spectrum is identified as a necessary initial condition for the momentum current correlation. This formulation leads to a natural physical interpretation of the VACF as a superposition of products of quasinormal hydrodynamic modes weighted commensurately with the spatial velocity power spectrum, the latter of which appears to physically bridge continuum hydrodynamical behavior and discrete-particle kinetics. The methodology yields VACF calculations quantitatively on par with existing approaches for liquid noble gases and alkali metals. Furthermore, we obtain a new, hydrodynamic form of the self-intermediate scattering function whose description has been extended to low densities where the Schmidt number is of order unity; various calculations are performed for gaseous and supercritical argon to support the general validity of the theory. Excellent quantitative agreement is obtained with recent MD calculations for a dense supercritical Lennard-Jones fluid. [ABSTRACT FROM AUTHOR]

A relatively recent approach in molecular graph theory for analyzing chemical networks and structures is called a modified polynomial. It emphasizes the characteristics of molecules through the use of a polynomial-based procedure and presents numerical descriptors in algebraic form. The Quantitative Structure-Property Relationship study makes use of Modified Polynomials (M-Polynomials) as a mathematical tool. M-Polynomials used to create connections between a material's various properties and its structural characteristics. In this study, we calculated several modified polynomials and gave a polynomial description of the magnesium iodide structure. Particularly, we computed first, second and modified Zagreb indices based M-polynomials. Randić index, and inverse Randić indices based M-polynomials are also computed in this work. [ABSTRACT FROM AUTHOR]

Preventing fluid penetration poses a challenging reliability concern in the context of power electronics, which is usually caused by unforeseen microfractures along the sealing joints. A better and more reliable product design heavily depends on the understanding of the dynamic wetting processes happening inside these complex microfractures, i.e. microchannels. A novel automated image processing procedure is proposed in this work for analyzing the moving interface and the dynamic contact angle in microchannels. In particular, the developed method is advantageous for experiments involving non-transparent samples, where extracting the fluid interface geometry poses a significant challenge. The developed method is validated with theoretical values and manual measurements and exhibits high accuracy. The implementation is made publicly available. The developed method is validated and applied to experimental investigations of forced wetting with two working fluids (water and 50 wt% glycerin/water mixture) in four distinct microchannels characterized by different dimensions and curvature. The comparison between the experimental results and molecular kinetic theory (MKT) reveals that the dynamic wetting behavior can be described well by MKT, even in highly curved microchannels. The dynamic wetting behavior shows a strong dependency on the channel geometry and curvature. [ABSTRACT FROM AUTHOR]

Liquid-liquid phase separation (LLPS) has increasingly been found to play pivotal roles in a number of intracellular events and reactions, and has introduced a new paradigm in cell biology to explain protein-protein and enzyme-ligand interactions beyond conventional molecular and biochemical theories. LLPS is driven by the cumulative effects of weak and promiscuous interactions, including electrostatic, hydrophobic and cation-π interactions, among polypeptides containing intrinsically disordered regions (IDRs) and describes the macroscopic behaviours of IDR-containing proteins in an intracellular milieu. Recent studies have revealed that interactions between 'charge blocks' - clusters of like charges along the polypeptide chain - strongly induce LLPS and play fundamental roles in its spatiotemporal regulation. Introducing a new parameter, termed 'charge blockiness', into physicochemical models of disordered polypeptides has yielded a better understanding of how the intrinsic amino acid sequence of a polypeptide determines the spatiotemporal occurrence of LLPS within a cell. Charge blockiness might also explain why some post-translational modifications segregate within IDRs and how they regulate LLPS. In this Review, we summarise recent progress towards understanding the mechanism and biological roles of charge block-driven LLPS and discuss how this new characteristic parameter of polypeptides offers new possibilities in the fields of structural biology and cell biology. [ABSTRACT FROM AUTHOR]

We propose that spontaneous folding and molecular evolution of biopolymers are two universal aspects that must concur for life to happen. These aspects are fundamentally related to the chemical composition of biopolymers and crucially depend on the solvent in which they are embedded. We show that molecular information theory and energy landscape theory allow us to explore the limits that solvents impose on biopolymer existence. We consider 54 solvents, including water, alcohols, hydrocarbons, halogenated solvents, aromatic solvents, and low molecular weight substances made up of elements abundant in the universe, which may potentially take part in alternative biochemistries. We find that along with water, there are many solvents for which the liquid regime is compatible with biopolymer folding and evolution. We present a ranking of the solvents in terms of biopolymer compatibility. Many of these solvents have been found in molecular clouds or may be expected to occur in extrasolar planets. [ABSTRACT FROM AUTHOR]

Recent studies have shown that active colloidal motors using enzymatic reactions for propulsion hold special promise for applications in fields ranging from biology to material science. It will be desirable to have active colloids with capability of computation so that they can act autonomously to sense their surroundings and alter their own dynamics. It is shown how small chemical networks that make use of enzymatic chemical reactions on the colloid surface can be used to construct motor‐based chemical logic gates. The basic features of coupled enzymatic reactions that are responsible for propulsion and underlie the construction and function of chemical gates are described using continuum theory and molecular simulation. Examples are given that show how colloids with specific chemical logic gates, can perform simple sensing tasks. Due to the diverse functions of different enzyme gates, operating alone or in circuits, the work presented here supports the suggestion that synthetic motors using such gates could be designed to operate in an autonomous way in order to complete complicated tasks. [ABSTRACT FROM AUTHOR]

A key challenge in flexible supercapacitor is balancing the trade‐off between high capacity and fast charging ability caused by dense structure‐induced sluggish ionic diffusion and storage dynamics. Herein, a hydrogen‐rich graphdiyne (GDY)–Ti3C2Tx electrode is reported with tunable interlayer spacing, abundant active sites, and extensive charge storage nanochannels. In particular, the GDY–Ti3C2Tx (12.6 wt.%) electrode has a remarkable volumetric capacitance (2296 F cm−3 at 1 A cm−3) and fast charging behavior (1262 F cm−3 at 50 A cm−3) resulting from the shortened transport pathways, enhanced ionic diffusion rate, and facilitated electrolyte mass transport. Moreover, an all‐solid‐state supercapacitor (ASSC) delivers a high volumetric energy density of 65.6 mWh cm−3, as well as long‐term deformable cyclic stability and high capacitance retention properties under harsh conditions. Density functional theory calculations and molecular dynamic simulation demonstrate the fast electronic responsiveness of the GDY–Ti3C2Tx heterostructure owning to the stronger H+ electrostatic attraction, lower migration resistance, and accelerated intercalation pseudocapacitance kinetics. In situ X‐ray diffraction reveals that a stable Ti─O─C bond bridged organic–inorganic heterostructure can tolerate the repeated high‐current charge/discharge cycling process. The state‐of‐the‐art ASSC delivers multiple functional outputs and shows great potential for efficient energy supply in practical applications. [ABSTRACT FROM AUTHOR]

Context: This study delves into the chemical nuances of thiophenols and their derivatives through a comprehensive computational analysis, moving beyond traditional energetic perspectives such as bond dissociation enthalpy and S−H dissociation dynamics. By employing the overlap model along with its topological descriptors (OP/TOP), quantum theory of atoms in molecules (QTAIM), and local vibrational mode (LVM) theories, the research provides a deeper understanding of the S−H and C−S bonding scenarios in substituted thiophenols. The investigation follows the electron-donating capacity of S−H substituent variation with the nature and positioning of other ring substituents. Energy profile analyses indicate distinct stability differences in the cis and trans conformations of meta- and para-PhSH systems, influenced by the electron-donating strength of these substituents. The study also uncovers significant variations in S−H bond distances and descriptor values, particularly in para-substituted PhSH, reflecting the influence of electron-donating or withdrawing substituents. In contrast, alterations at the meta-position show minimal effects on C−S bond descriptors, while para-substitutions markedly influence C−S bond characteristics, demonstrating a clear correlation with the electron-donating or withdrawing capabilities of the substituents. This research sheds light on the intricate bond dynamics in aromatic systems with diverse substituents, highlighting the complex interaction between electronic effects and molecular conformation. Methods: The study employs the ω B97X-D/Def2TZVP level of theory for molecular geometries, ensuring accurate characterization of structures as true minima via analytical harmonic frequency determination. The electronic properties of S−H and C−S bonds in variously substituted thiophenols were analyzed using OP/TOP, QTAIM, and LVM methodologies. Computational processes, including conformational scans, geometry optimizations, and vibrational frequency calculations, were conducted using Gaussian 09, with ultra-fine integration grids and tight convergence criteria for the SCF procedure. Bond descriptors were computed utilizing ChemBOS, Multiwfn, and LModeA software, providing a robust and detailed examination of bond properties. [ABSTRACT FROM AUTHOR]

As shown by W. H. Miller in a seminal article [J. Chem. Phys. 53, 3578 (1970)], the most convenient and accurate semiclassical (SC) theory of molecular scattering in action-angle coordinates is based on the initial value representation (IVR) and the use of shifted angles, which are different from the natural angles usually used in the quantum and classical treatments. Here, we show for an inelastic molecular collision that the initial and final shifted angles define three-segment classical paths that are exactly those involved in the classical-limit of Tannor–Weeks quantum scattering theory [J. Chem. Phys. 98, 3884 (1993)], provided that the translational wave packets |g+⟩ and |g−⟩ into play in this theory are both taken at |0⟩. Assuming this to be the case, using van Vleck propagators, and applying the stationary phase approximation, Miller's SCIVR expression of S-matrix elements is found, with an additional cut-off factor canceling the energetically forbidden transition probabilities. This factor, however, is close to unity in most practical cases. Furthermore, these developments show that the Møller operators underlie Miller's formulation, thus confirming, for molecular collisions, the results recently established in the simpler case of light-induced rotational transitions [L. Bonnet, J. Chem. Phys. 153, 174102 (2020)]. Last but not least, we show, based on the previous results, that for processes involving long-range anisotropic forces, implementing the Skinner–Miller method [Chem. Phys. Lett. 300, 20 (1999)] in shifted coordinates makes its predictions both easier and more accurate than in natural coordinates. [ABSTRACT FROM AUTHOR]

The generalized Langevin equation (GLE) formalism is a useful theoretical fundament for analyzing dynamical phenomena rigorously. Despite the systematic formulation of dynamics theories with practical approximations, however, the applicability of GLE-based methods is still limited to simple polyatomic liquids due to the approximate treatment of molecular orientations involved in the static molecular liquid theory. Here, we propose an exact framework of dynamics based on the GLE formalism incorporating the energy representation theory of solution, an alternative static molecular liquid theory. A fundamental idea is the projection of the relative positions and orientations of solvents around a solute onto the solute–solvent interaction, namely the energy coordinate, enabling us to describe the dynamics on a one-dimensional coordinate. Introducing systematic approximations, such as the overdamped limit, leads to the molecular diffusion equation in the energy representation that is described in terms of the distribution function of solvents on the energy coordinate and the diffusion coefficients. The present theory is applied to the solvation dynamics triggered by the photoexcitation of benzonitrile. The long-time behavior of the solvation time correlation function is in good agreement with that obtained by the molecular dynamics simulation. [ABSTRACT FROM AUTHOR]

Electrochemistry is central to many applications, ranging from biology to energy science. Studies now involve a wide range of techniques, both experimental and theoretical. Modeling and simulations methods, such as density functional theory or molecular dynamics, provide key information on the structural and dynamic properties of the systems. Of particular importance are polarization effects of the electrode/electrolyte interface, which are difficult to simulate accurately. Here, we show how these electrostatic interactions are taken into account in the framework of the Ewald summation method. We discuss, in particular, the formal setup for calculations that enforce periodic boundary conditions in two directions, a geometry that more closely reflects the characteristics of typical electrolyte/electrode systems and presents some differences with respect to the more common case of periodic boundary conditions in three dimensions. These formal developments are implemented and tested in MetalWalls, a molecular dynamics software that captures the polarization of the electrolyte and allows the simulation of electrodes maintained at a constant potential. We also discuss the technical aspects involved in the calculation of two sets of coupled degrees of freedom, namely the induced dipoles and the electrode charges. We validate the implementation, first on simple systems, then on the well-known interface between graphite electrodes and a room-temperature ionic liquid. We finally illustrate the capabilities of MetalWalls by studying the adsorption of a complex functionalized electrolyte on a graphite electrode. [ABSTRACT FROM AUTHOR]

A series of charge transfer cocrystals with fluorescence properties involving 1,2,4,5-tetracyanobenzene (TCNB, C10H2N4) as acceptor, fluorene (FR, C13H10) and its bromide 2-bromofluorene (2-BrFR, C13H9Br), carbazole (CZ, C12H9N) and its bromide 2-bromocarbazole (2-BrCZ, C12H8BrN) as donor were synthesized via cocrystal design strategies. The formation mechanism of the crystal structure was explored by density functional theory at the molecular level. The stacking structure of the cocrystal was formed by the combination of charge transfer interactions, π–π interactions and hydrogen bonding. The N atom of donors in TCNB–CZ and TCNB–2-BrCZ could enhance the charge transfer, appearing as a red shift of the fluorescence emission wavelength. Conversely, the Br atom in TCNB–2-BrFR and TCNB–2-BrCZ weakens the charge transfer, giving a blue shift in the fluorescence emission spectrum. The four new cocrystals exhibit tunable luminescence from green (529 nm) to yellow (552 nm) and to red (604 nm and 614 nm). It was found that the introduction of N and Br atoms in the assembly units can not only regulate the luminescence range of the cocrystals, but also adjust the luminescence efficiency, which provides a strategy for the development of promising organic luminescent materials. [ABSTRACT FROM AUTHOR]

Ostwald ripening (OR), a classic solution theory describing molecular transfer from metastable crystal to stable one, is applied to design time‐dependent crystal hydrogels that can automatically change their mechanical properties. Using a system made from crosslinked polyacrylamide (PAM) and sodium acetate (NaAc), we demonstrate that metastable fibrous crystal networks of NaAc preferably form in PAM hydrogels via a polymer‐involving mismatch nucleation. These fibrous crystals would undergo OR and evolve into isolated bulk crystals, leading to a significant reduction in material rigidity (179 folds) and interfacial adhesion (20 folds). This transformation can be applied to program time‐dependent self‐recovery in shape and self‐delamination. Since OR is a ubiquitous, robust feature of various crystals, the approach reported here represents a new direction for designing advanced transient soft materials. [ABSTRACT FROM AUTHOR]

Ostwald ripening (OR), a classic solution theory describing molecular transfer from metastable crystal to stable one, is applied to design time‐dependent crystal hydrogels that can automatically change their mechanical properties. Using a system made from crosslinked polyacrylamide (PAM) and sodium acetate (NaAc), we demonstrate that metastable fibrous crystal networks of NaAc preferably form in PAM hydrogels via a polymer‐involving mismatch nucleation. These fibrous crystals would undergo OR and evolve into isolated bulk crystals, leading to a significant reduction in material rigidity (179 folds) and interfacial adhesion (20 folds). This transformation can be applied to program time‐dependent self‐recovery in shape and self‐delamination. Since OR is a ubiquitous, robust feature of various crystals, the approach reported here represents a new direction for designing advanced transient soft materials. [ABSTRACT FROM AUTHOR]

In recent decades, peptide amphiphiles (PAs) have established themselves as promising self-assembling bioinspired materials in a wide range of medical fields. Herein, we report a dual-therapeutic system constituted by an antimicrobial PA and a cylindrical protease inhibitor (LJC) to achieve broad antimicrobial spectrum and to enhance therapeutic efficacy. We studied two strategies: PA-LJC nanostructures (Encapsulation) and PA nanostructures + free LJC (Combination). Computational modeling using a molecular theory for amphiphile self-assembly captures and explains the morphology of PA-LJC nanostructures and the location of encapsulated LJC in agreement with transmission electron microscopy and two-dimensional (2D) NMR observations. The morphology and release profile of PA-LJC assemblies are strongly correlated to the PA:LJC ratio: high LJC loading induces an initial burst release. We then evaluated the antimicrobial activity of our nanosystems toward gram-positive and gram-negative bacteria. We found that the Combination broadens the spectrum of LJC, reduces the therapeutic concentrations of both agents, and is not impacted by the inoculum effect. Further, the Encapsulation provides additional benefits including bypassing water solubility limitations of LJC and modulating the release of this molecule. The different properties of PA-LJC nanostructures results in different killing profiles, and reduced cytotoxicity and hemolytic activity. Meanwhile, details in membrane alterations caused by each strategy were revealed by various microscopy and fluorescent techniques. Last, in vivo studies in larvae treated by the Encapsulation strategy showed better antimicrobial efficacy than polymyxin B. Collectively, this study established a multifunctional platform using a versatile PA to act as an antibiotic, membrane-penetrating assistant, and slow-release delivery vehicle. [ABSTRACT FROM AUTHOR]

This work aims to give computational studies of Mn(II), Co(II), Ni(II) and Cu(II) complexes of gabapentin (Gpn), formulized as [M(Gpn)(H2O)3(Cl)].nH2O complexes (where n = 2-6), using DFT method. They were previously synthesized and characterized. DFT calculations are in good agreement with practical studies. Bond lengths of metal complexes reduced or increased rather than that of ligand due to complexation. Bond angles of complexes predict the octahedral environment around the central metal ions predicting sp3d2 or d2sp3hybridization. The calculated energy parameters are negative indicating stability of metal complexes. The small energy band gap of compounds predicts the higher biological activity and high tendency of electron transfer. The comparable frequencies of theoretical and experimental IR may be attributed to different phases of measurement. The induced fit docking SP G-score of the molecular interactions of drug (Gpn) and its metal(II) complexes show that all investigated compounds have a good interaction towards sertonine receptor 5-HT2C and D2 dopamine receptor proteins. Co(II)-Gpn interacts with active site residues of sertonine receptor 5-HT2C with an excellent dock score of -7.370 kcal/mol and RMSD = 1.581 Å. On the other hand, Ni(II)-Gpn has the best dock score of -6.638 kcal/mol and RMSD = 1.995 Å with D2 dopamine receptor. [ABSTRACT FROM AUTHOR]

To investigate the self-healing performance of multi-walled carbon nanotube-modified asphalt and its influencing mechanism, the asphalt molecular self-healing models were established by the molecular dynamics method. The results were analyzed based on molecular diffusion theory and surface energy repair theory. Based on the Arrhenius model, two theories were combined, and a new index healing factor was proposed to evaluate the self-healing performance by considering the diffusion characteristics and energy changes of asphalt molecules. The results show that multi-walled carbon nanotubes can accelerate the diffusion behavior of molecules in the temperature of 278--318 K to improve the self-healing properties of asphalt. Based on the proposed surface free energy equation, the self-healing properties are reasonably evaluated; the enthalpy change can be used as an index for judging the self-healing performance. The transformation model of the diffusion coefficient and cohesive work and the new index can reflect the self-healing performance more comprehensively. [ABSTRACT FROM AUTHOR]

In pursuit of developing novel cholinesterase (ChE) inhibitors through molecular hybridization theory, a novel series of isoindolin-1,3-dione-based acetohydrazides (compounds 8a–h) was designed, synthesized, and evaluated as possible acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) inhibitors. In vitro results revealed IC50 values ranging from 0.11 ± 0.05 to 0.86 ± 0.02 µM against AChE and 5.7 ± 0.2 to 30.2 ± 2.8 µM against BChE. A kinetic study was conducted on the most potent compound, 8a, to ascertain its mode of inhibition, revealing its competitive mode against AChE. Furthermore, the binding interaction modes of the most active compound within the AChE active site was elucidated. Molecular dynamics simulations of compound 8a were performed to assess the stability of the 8a-AChE complex. In silico pharmacokinetic predictions for the most potent compounds indicated their potential as promising lead structure for the development of new anti-Alzheimer's disease (anti-AD) agents. [ABSTRACT FROM AUTHOR]

In this paper, the quantum effects of fine scaling on the buckling behavior of carbon nanotubes (CNTs) under axial loading are investigated. Molecular mechanics and quantum mechanics are respectively utilized to study the buckling behavior and to obtain the molecular mechanics coefficients of fine-scale nanotubes. The results of buckling behavior of CNTs with different chiralities with finite and infinite dimensions are given, and a comparison study is presented on them. The differences between finite and infinite nanotubes reflect the quantum effects of fine scaling on the buckling behavior. In addition, the results show that the dimensional changes highly affect the mechanical properties and the buckling behavior of CNTs to certain dimensions. Moreover, dimensional changes have a significant effect on the critical buckling strain. Beside, in addition to the structure dimensions, the arrangement of structural and boundary atoms have a major influence on the buckling behavior. [ABSTRACT FROM AUTHOR]

The discovery of the 32-bp deletion allele of the chemokine receptor gene CCR5 showed that homozygous carriers display near-complete resistance to HIV infection, irrespective of exposure. Algorithms of molecular evolutionary theory suggested that the CCR5-Δ32 mutation occurred but once in the last millennium and rose by strong selective pressure relatively recently to a ~10% allele frequency in Europeans. Several lines of evidence support the hypothesis that CCR5-Δ32 was selected due to its protective influence to resist Yersinia pestis, the agent of the Black Death/bubonic plague of the 14th century. Powerful anti-AIDS entry inhibitors targeting CCR5 were developed as a treatment for HIV patients, particularly those whose systems had developed resistance to powerful anti-retroviral therapies. Homozygous CCR5-Δ32/Δ32 stem cell transplant donors were used to produce HIV-cleared AIDS patients in at least five "cures" of HIV infection. CCR5 has also been implicated in regulating infection with Staphylococcus aureus, in recovery from stroke, and in ablation of the fatal graft versus host disease (GVHD) in cancer transplant patients. While homozygous CCR5-Δ32/32 carriers block HIV infection, alternatively they display an increased risk for encephalomyelitis and death when infected with the West Nile virus. [ABSTRACT FROM AUTHOR]

The size dependence of the surface tension of critical bubbles in a superheated (stretched) Lennard–Jones solution with complete solubility of the components is considered. Two approaches are used to determine this dependence. The first one is based on the van der Waals gradient theory, and the second one is based on molecular dynamic simulation results of nucleation in a solution. It is established that, unlike in a one-component liquid, where the surface tension of the equilibrium bubble is less than that for the flat interface, in solution, it can exceed the flat limit. The ranges of temperatures, pressures, and mixture compositions, where this effect occurs, are determined. The asymptotic behavior of the surface tension of vapor phase nuclei within the limits of zero and infinitely large curvature of the dividing surface is analyzed. [ABSTRACT FROM AUTHOR]

This study comprehensively investigates Al2O3′s mechanical properties, focusing on fracture toughness, surface energy, Young's modulus, and crack propagation. The density functional theory (DFT) is employed to model the vacancies in Al2O3, providing essential insights into this material's structural stability and defect formation. The DFT simulations reveal a deep understanding of vacancy-related properties and their impact on mechanical behavior. In conjunction with molecular dynamics (MD) simulations, the fracture toughness and crack propagation in Al2O3 are explored, offering valuable information on material strength and durability. The surface energy of Al2O3 is also assessed using DFT, shedding light on its interactions with the surrounding environment. The results of this investigation highlight the significant impact of oxygen vacancies on mechanical characteristics such as ultimate strength and fracture toughness, drawing comparisons with the effects observed in the presence of aluminum vacancies. Additionally, the research underscores the validation of fracture toughness outcomes derived from both DFT and MD simulations, which align well with findings from established experimental studies. Additionally, the research underscores the validation of fracture toughness outcomes derived from DFT and MD simulations, aligning well with findings from established experimental studies. The combination of DFT and MD simulations provides a robust framework for a comprehensive understanding of Al2O3′s mechanical properties, with implications for material science and engineering applications. [ABSTRACT FROM AUTHOR]

For the last few years technical improvements of compositions and preparation procedures for perovskite-based solar cells have remarkably enhanced their energy conversion efficiency. Crystal and electronic structures together with ion diffusion in partially substituted cubic methylammonium (MA) perovskite based on lead halide MA0.5X0.5PbI3, where X is the cation, are theoretically investigated using density functional theory and molecular dynamics methods. The electronic structure of partially substituted perovskites studied is similar to the MAPbI3 structure, however, the band gap changes compared to their structures. Partial MA substitution distorts the lattice, which prevents MA or X diffusion between A sites in the perovskite crystal. The partial cation substitution affects the electronic structure and distorts the crystal lattice of perovskite, which makes it possible to control the optical properties of the material in different spectral regions and to influence the electronic composition of defects. [ABSTRACT FROM AUTHOR]

With the rapid increase in power conversion efficiency of organic photovoltaics due to the development of non‐fullerene acceptors (NFAs), prolonging the operational lifetime of devices becomes one of the critical prerequisites for commercial application. In this work, the degradation pathways of a wide range of state‐of‐the‐art NFA molecules via multiple spectroscopic techniques combined with density functional theory and molecular dynamics simulation are revealed. The structural confinement and molecular ordering are responsible for molecular conformational stability under illumination. More importantly, a very general trend is revealed that the origin of increased nonradiative decay under illumination is predominately in the aggregated states with strong intermolecular interactions while the intramolecular exciton dynamics are stable. The increased nonradiative decay correlates with reduced exciton diffusion length. This work provides vital information toward the design of intrinsically photo‐stable NFAs at the molecular level and the importance of aggregation control toward long‐term stable organic solar cells. [ABSTRACT FROM AUTHOR]

The novel macrocyclic ligands (N4MacL1-N4MacL3) and their Ru(II) complexes were synthesized by using 4-fulorobenzene-1,2-diamine, dicarboxylic acids (malonic acid, succinic acid, glutaric acid), and a 1:1 molar ratio of ligand to metal was used to create their metal complexes with the transition metals Ru (II). These metal complexes were identified using a variety of advanced methods, including, FTIR,1H-NMR, mass spectrophotometry, UV–Visible, PXRD, TGA and density functional theory (DFT) analysis. Kinetic and thermodynamic parameters were computed using the Coats-Redfern equations. Calculations based on molecular modelling (DFT) support the complexes' structural geometry. Synthesized macrocyclic compounds were tested for antimicrobial activity against bacterial strains B. subtilis, S. aureus, E. coli and K. pneumonia and fungal strains A. flavious and fusarium. When the ligands and their Ru(II) complexes were tested for their in vitro antimicrobial properties against some bacterial, fungal strains B. subtilis, S. aureus, E. coli, K. pneumonia and A. flavius, fusarium, respectively results revealed that the Ru(II) macrocyclic complexes were more effective against bacterial and fungal strains than tetraaza macrocyclic ligands (N4MacL1-N4MacL3). The antioxidant capacity of ligands and Ru(II) complexes were also assessed using the DPPH free radical test, with an IC50 range of 10.01–28.45 M. B. subtilis (PDB ID;5H67), S. aureus (PDB ID;3TY7), E. coli (PDB ID;3T88), K. pneumonia (PDB ID;6WII), and F. oxysporum (PDB ID;8EBB) proteins, were all subjected to docking studies using the AutoDock vina programme. Using the SRB test, the anticancer activity was assessed against four distinct cell lines HeLa, MCF-7, A549 and IMR-32. Comparing the ligands and complexes to the reference medication cis-platin revealed that it had far stronger cytotoxic effects. The research presented here proposes using these ligands in the creation of novel anticancer medications. [ABSTRACT FROM AUTHOR]

Half a century after its foundation, the neutral theory of molecular evolution continues to attract controversy. The debate has been hampered by the coexistence of different interpretations of the core proposition of the neutral theory, the 'neutral mutation–random drift' hypothesis. In this review, we trace the origins of these ambiguities and suggest potential solutions. We highlight the difference between the original, the revised and the nearly neutral hypothesis, and re‐emphasise that none of them equates to the null hypothesis of strict neutrality. We distinguish the neutral hypothesis of protein evolution, the main focus of the ongoing debate, from the neutral hypotheses of genomic and functional DNA evolution, which for many species are generally accepted. We advocate a further distinction between a narrow and an extended neutral hypothesis (of which the latter posits that random non‐conservative amino acid substitutions can cause non‐ecological phenotypic divergence), and we discuss the implications for evolutionary biology beyond the domain of molecular evolution. We furthermore point out that the debate has widened from its initial focus on point mutations, and also concerns the fitness effects of large‐scale mutations, which can alter the dosage of genes and regulatory sequences. We evaluate the validity of neutralist and selectionist arguments and find that the tested predictions, apart from being sensitive to violation of underlying assumptions, are often derived from the null hypothesis of strict neutrality, or equally consistent with the opposing selectionist hypothesis, except when assuming molecular panselectionism. Our review aims to facilitate a constructive neutralist–selectionist debate, and thereby to contribute to answering a key question of evolutionary biology: what proportions of amino acid and nucleotide substitutions and polymorphisms are adaptive? [ABSTRACT FROM AUTHOR]

Context: This article intends to show a new way to setup and solve chemical bonds which can be incorporated into molecules. The new approach is analytical and purely based on simple math and science. We need analytical methods in our molecular theory which can be used to obtain results with our eyes open to the process. The utilization of computer software is fine as long as the user understands what the software is exactly doing. An analytical molecular theory can be utilized in different areas of science including chemistry. It can be also an asset in classrooms to better train our future generations, making them better "thinkers" and ready to tackle the complicated issues in our changing world. This article first introduces a new analytical approach to study chemical bonds and then goes through several examples of chemical bonds to show the applicability of the suggested approach. Methods: All of the calculations and figures presented in this article are done by the use of Microsoft excel spreadsheet. The presented approach does not need any sophisticated software and/or heavy computations. [ABSTRACT FROM AUTHOR]

In this work, a field representation of the conservation law of linearmomentum is derived fromthe atomistic, using the theory of distributions as the mathematical tool, and expressed in terms of temperature field by defining temperature as a derived quantity as that in molecular kinetic theory and atomistic simulations. The formulation leads to a unified atomistic and continuum description of temperature and a new linear momentum equation that, supplemented by an interatomic potential, completely governs thermal and mechanical processes across scales from the atomic to the continuum. The conservation equation can be used to solve atomistic trajectories for systems at finite temperatures, as well as the evolution of field quantities in space and time, with atomic or multiscale resolution. Four sets of numerical examples are presented to demonstrate the efficacy of the formulation in capturing the effect of temperature and thermal fluctuations, including phonon density of states, thermally activated dislocation motion, dislocation formation during epitaxial processes, and attenuation of longitudinal acoustic waves as a result of their interaction with thermal phonons. [ABSTRACT FROM AUTHOR]

The Cassie–Baxter state of wetting explains a large equilibrium contact angle and the slippery dynamics of a water droplet on a superhydrophobic rough surface. It also causes a contact angle hysteresis (CAH) that cannot be fully described by dynamic wetting theories including the molecular kinetic theory (MKT). We analyze the contact line dynamics on a superhydrophobic surface in the framework of the MKT. Multi-body dissipative particle dynamics simulations of a capillary bridge confined between two rough surfaces under steady shear are performed. We find that, in addition to the contact line friction force from the MKT, an additional friction force contribution is needed on rough surfaces. It can be obtained by subtracting from the total friction force the force solely caused by the actual liquid–solid contact area. We find that the additional force is almost constant at all contact line velocities. Thus, it is directly related to the CAH. The CAH originates not only from contact line pinning but also from the shear flow due to the strong friction in the central region of the liquid–solid interface away from the contact line. The analysis of the particle flow inside the capillary bridge shows that liquid particles trapped in the grooves of the surface texture actually move with the same velocity as the surface and exert strong additional friction to other liquid particles. This work extends the MKT to rough surfaces, as well as to elucidate the origin of the CAH of a capillary bridge. The finding would help to better understand other situations of dynamic wetting on superhydrophobic surfaces. [ABSTRACT FROM AUTHOR]

Based on Schreiber's work on transfer entropy, a molecular theory of nonlinear information transfer between residue pairs in proteins is developed. The joint distribution function for residue fluctuations required by the theory is expressed in terms of tensor Hermite polynomials that conveniently separate harmonic and nonlinear contributions to information transfer. The harmonic part of information transfer is expressed as the difference between time dependent and independent mutual information. Third order nonlinearities are discussed in detail. The amount and speed of information transfer between residues, which are important for understanding allosteric activity in proteins, are discussed. Mutual information between two residues is commonly used for information transfer. While mutual information shows the maximum amount of information that may be transferred between two residues, it does not explain the actual amount of transfer nor the transfer rate of information. For this, dynamic equations of the system are needed. The solution of the Langevin equation and molecular dynamics trajectories are used in the present work for this purpose. Allosteric communication in human NAD-dependent isocitrate dehydrogenase is studied as an example. Calculations show that several paths contribute collectively to information transfer. Important residues on these paths are identified. Time resolved information transfer between these residues, their amplitudes, and transfer rates, which are in agreement with time resolved ultraviolet resonance Raman measurements in general, are estimated. Peak values of calculated information transfer, ∼0.01–0.04 bits, are about two orders of magnitude smaller than the information content of residues. They are comparable to mutual information values, however. Estimated transfer rates are in the order of 1–20 megabits per second, and sustained transfer during the activity time-span of proteins may be significant. Information transfer from third order contributions is one to two orders of magnitude smaller than the harmonic terms, showing that harmonic analysis is a good approximation to information transfer. [ABSTRACT FROM AUTHOR]

This study focuses on investigating the hydrogen adsorption-desorption properties and storage capacities of Li functionalized [1,1,1,1]paracyclophane (PCP1111) using dispersion-corrected density functional theory and molecular dynamics simulation. The Li atom is bound to the [1,1,1,1]paracyclophane's benzene ring via Dewar mechanism, with a binding energy of 0.32 eV without any clustering. Each Li atom is found to adsorb 5H 2 molecules, causing the host material PCP1111–4Li to adsorb up to 20H 2 molecules via charge polarization with an average adsorption energy of 0.156 eV/H 2 , indicating physisorption type adsorption. The charge polarization during hydrogen adsorption is studied using Hirshfeld charge analysis and electrostatic potential maps. PCP1111–4Li saturated with 20H 2 results in gravimetric densities as high as 9.4 wt%, which is considerably higher than the US-DOE target. During the H 2 adsorption process, the host material's geometry does not change significantly, indicating its chemical stability. When the temperature exceeds 180 K under 30–60 bar, the gravimetric density decreases, but it is still greater than 5.5 wt%, which is the target set by the US Department of Energy for 2025. The maximum H 2 desorption temperature estimated by the Vant-Hoff relation is found to be 216 K and 266 K at 1 atm and 5 atm, respectively. ADMP molecular dynamics shows the structural integrity and reversibility of host materials. [Display omitted] [ABSTRACT FROM AUTHOR]

We have explored the hydrogen storage capacity of zirconium doped psi-graphene employing Density Functional Theory. The Zr atom binds strongly on psi-graphene with a binding energy of −3.54 eV due to charge transfer from Zr 4d orbital to C 2p orbital. Zr atom adsorbs 9H 2 molecules with an average binding energy of −0.38eV/H 2 and an average desorption temperature 484.21 K. The gravimetric weight percent is 11.3 which meets the benchmark set by DoE. Zr and H 2 molecules bond by Kuba's interactions involving electron flow between metal d orbital and H 1s orbital. We have investigated the structural stability of the system at room temperature and at 400 K using ab-initio Molecular Dynamics (MD) simulations. Thus, we can attribute that our system is stable, recyclable and can be used as an excellent hydrogen storage medium. This work may inspire the experimentalist to synthesize psi-graphene based material for hydrogen storage. [Display omitted] • Using DFT, hydrogen storage is reported and analysed in Zr doped psi-graphene. • The Zr atom attached on the psi graphene system has a binding energy of −3.54eV. • The Zr atom could hold 9H 2 molecules with an average binding energy of −0.38eV. • Ab-initio MD simulations showed the system is stable till 400 K. • Metal-metal clustering is hindered by the diffusion energy barrier of 1.372eV. [ABSTRACT FROM AUTHOR]

In this work, we have studied the H2 adsorption‐desorption properties and storage capacities of [2,2,2]paracyclophane (PCP222) functionalized with Li atoms, using dispersion‐corrected density functional theory and molecular dynamic simulation. The Li atom was found to bond strongly with the benzene ring of PCP222 via Dewar interaction. Subsequently, the calculation of the diffusion energy barrier revealed a significantly high energy barrier of 1.38 eV, preventing the Li clustering on PCP222. The host material, PCP222‐3Li, adsorbed up to 15H2 molecules via charge polarization mechanism with an average adsorption energy of 0.145 eV/5H2, suggesting physisorption type of adsorption. The PCP222 functionalized with three Li atoms showed a maximum hydrogen uptake capacity of up to 8.32 wt%, which was fairly above the US‐DOE criterion. The practical H2 storage estimation revealed that the PCP222‐3Li desorbed 100% of adsorbed H2 molecules at the temperature range of 260 K to 300 K and pressure range of 1 bar to 10 bar. The maximum H2 desorption temperature estimated by the Vant‐Hoff relation was found to be 219 K and 266 K at 1 bar and 5 bar, respectively. The ADMP molecular dynamics simulations assured the reversibility of adsorbed H2 and the structural integrity of the host material at sufficiently above the desorption temperature (300 K and 500 K). Therefore, the Li‐functionalized PCP222 can be considered as a thermodynamically viable and potentially reversible H2 storage material below room temperature. [ABSTRACT FROM AUTHOR]

Context: Industrial production and humans cannot exist without energy, but the low efficiency of the heat transfer in the excessive use of energy is the most significant aspect of energy saving and emission reduction. Molecular dynamics simulation methods are devoted to simulate the heat transfer efficiency of a nanofluid system with different particle sizes, and the heat transfer enhancement mechanism of the nanofluid is simulated and studied from a microscopic perspective. The analysis showed that as nanoparticle size increases, the thermal conductivity of the Al–Ar nanofluid tends to decrease, but all of them are still higher than the thermal conductivity of the liquid argon system. According to the findings of the density and radial distribution function analyses, it can be seen that the microstructure of the system changes after putting solid nanoparticles to the original fluid. This alteration in the system's microstructure is the primary component responsible for the increased heat transfer efficiency of nanofluids. Methods: In this paper, based on the theory of molecular dynamics, the simulation calculations were mainly performed using LAMMPS software, which is a commonly used open source computational program in the field of MD simulation research. VMD is used for visualization and analysis. The Lennard–Jones potential function was used in the simulation to accurately describe the forces acting between the atoms. [ABSTRACT FROM AUTHOR]

Although line defects endow excellent catalytic performance by undercoordinated sites with compressive tensile strain, few studies have systematically unraveled the relationship between dislocation, strain, and electrochemical activity for formate oxidation reactions (FOR). Herein, a novel approach for synthesizing defect‐rich nanomaterials at room temperature is proposed for the first time. The heated and dealloyed AgPd nanoparticles (hd‐AgPd NPs) substantially improve the intrinsic electrocatalytic activity by introducing compressive strain to tune its electronic structure. Electrochemical experiments show that the mass activity of hd‐AgPd NPs for FOR is 5.3 times higher than that of pure Pd nanoparticle catalysts. Following a 3600 s chronoamperometric process, a portion of the dislocation vanishes, but the strain persists on the AgPd (111) facet. The mechanisms for activity enhancement are further explored through density functional theory and molecular dynamics calculations, which show that compressive strain effectively alters its electronic structure and decreases the energy of the rate‐determining step during the reaction, significantly enhancing the FOR performance and stability. The results of electrochemical performance and physical characterization show that lattice strain has a more significant impact on FOR performance than alloying and preoxidation. This study presents a new approach to produce high‐performance catalysts by inducing strain into nanoparticles. [ABSTRACT FROM AUTHOR]

An analysis of molecular single-phase distributions inside slitlike and cylindrical pores with homogeneous walls was carried out in a wide range of pressures and temperatures, when there is liquid or vapor in it. The pore walls are considered nondeformable; they form an external field for the fluid. The state of the "liquid in a pore" and "vapor in a pore" phases satisfies the equality of the chemical potential with the chemical potential of the bulk phase. The molecular distributions were calculated within the framework of the lattice gas model (LGM) with the simplest pair interaction potential of nearest neighbors. The distribution of molecular density in the inhomogeneous field of pore walls is associated with local distributions of two types of pressure: isothermal, associated with the chemical potential of the system, and internal mechanical pressure (or expansion pressure in terms of the LGM). The difference between each of the two types of pressure with the corresponding pressure in the bulk phase determines the disjoining pressure, which is actively used in the thermodynamic interpretation of the characteristics of thin layers depending on their width. It was found that both types of disjoining pressures in slitlike and cylindrical pores are proportional to each other. The proportionality coefficient depends on the parameter of the adsorbent–adsorbate interaction potential and its extent, pore geometry, and temperature, and also depends on the width of the cylindrical pores, but does not depend on the width of the slitlike pores. The dimensional derivatives of the two types of disjoining pressure from the pore width, through which the adsorbate flows are expressed, are also related to each other by the same proportionality coefficients. [ABSTRACT FROM AUTHOR]

Five stable tautomer and rotamers of the 2-(2-Mercaptophenyl)-1-azaazulene (thiol, thione, R1, R2, and R3) molecules were studied using density functional theory (DFT). The geometries of the studied tautomer and rotamers were fully optimized at the B3LYP/6-31G(d,p) level. Thermodynamic calculations were performed at M06-2X/6-311G++(2d,2p) and ωB97XD/6-311G++(2d,2p) in the gas phase and ethanol solution conditions modeled by the solvation model based on density (SMD). The kinetic constant of tautomer and rotamers conversion was calculated in the temperature range 270–320 K using variational transition state theory (VTST) accompanied by one-dimensional wigner tunneling correction. Energy refinement at CCSD(T)/6–311++G(2d,2p) in the gas phase has been calculated. All the studied DFT methods qualitatively give similar tautomer stability orders in the gas phase. The ethanol solvent causes some reordering of the relative stability of 2-(2-Mercaptophenyl)-1-azaazulene conformers. The transition states for the 2-(2-Mercaptophenyl)-1-azaazulene tautomerization and rotamerization processes were also determined. The reactivity, electric dipole moment, and spectroscopic properties of the studied tautomer and rotamers were computed. The hyper-Rayleigh scattering (βHRS), and depolarization ratio (DR) exhibited promising optical properties when nonlinear optical properties were calculated. [ABSTRACT FROM AUTHOR]

[Display omitted] As a common flexible sensing device, gels are widely used in electronic skin, personalized health monitoring, and smart manufacturing. However, gel suffers from temperature sensitivity, long polymerization times or thickness limitations. Deep eutectic solvents (DESs) have abundant hydrogen bond networks and low saturated vapor pressure, which can accelerate the frontal polymerization of ionic gels, and overcome the temperature sensitivity problem. Here, we showed how choline chloride (ChCl)-glycerol (Gly) DES can be used to create ionic gels with different properties and functions by combining them with different monomers (acrylamide (AM), acrylic acid (AA) and itaconic acid (IA)). Subsequently, we revealed the rapid gelation mechanism of PAM-ChCl-Gly ionic gel from multiple perspectives by density functional theory and molecular dynamics simulation, which was then applied to flexible sensing. The experimental results showed that the PAM-ChCl-Gly ionic gel had excellent tensile properties, high transparency, self-adhesion and stability. In addition, its gelation time was only 90 s without heating. ChCl-Gly DES offered a plentiful and stable hydrogen bonding network. PAM-ChCl-Gly ionic gels can detect tiny pressure and strain changes, making them suitable for flexible sensing. This greatly enriched the theoretical research foundation of DES-based ionic gels and broadened their application areas. [ABSTRACT FROM AUTHOR]