Search

Since the long-range structure of the Gd-doped system (Ce1−xGdxO2−x/2) remains in the fluorite structure in the x-range [0–0.3], it is of interest to study this system in the local range. Molecular dynamics simulations seem to be particularly suitable for this purpose. Among all the possible parameters used to describe the local order/disorder, we focus on the behavior of the bond lengths. Doping cations and oxygen vacancies are introduced inside the fluorite structure following two arrangements, the random (R) and the neighbor (N). We investigate the evolution of the bond lengths with the temperature and doping level and identify different trends depending on the bond type (cation–anion, cation–cation). The bond length thermal expansion can be drastically different from the long-range thermal expansion mainly for the bonds implying Gd3+ cation. The presence of C-type Gd2O3 clusters is discussed through the study of the double component of the Gd–Gd Radial Distribution Function. Comments are provided for evolution of distances beyond the first and second shells of the cations' environment. This study also demonstrates the impact of point defect distribution (R or N) on the evolution of the local structure, while maintaining the long-range fluorite structure. [ABSTRACT FROM AUTHOR]

We present an efficient first-principles based method geared toward reliably predicting the structures of solid materials across the Periodic Table. To this end, we use a density functional theory baseline with a compact, near-minimal min+s basis set, yielding low computational costs and memory demands. Since the use of such a small basis set leads to systematic errors in chemical bond lengths, we develop a linear pairwise correction, available for elements Z = 1–86 (excluding the lanthanide series), parameterized for use with the Perdew–Burke–Ernzerhof exchange–correlation functional. We demonstrate the reliability of this corrected approach for equilibrium volumes across the Periodic Table and the transferability to differently coordinated environments and multi-elemental crystals. We examine relative energies, forces, and stresses in geometry optimizations and molecular dynamics simulations. [ABSTRACT FROM AUTHOR]

This article investigates the relaxation dynamics of the ionized 2a1 state of a water molecule within a water dimer. The study was motivated by findings from two previous pieces of research that focused on the relaxation behaviors of the inner-valence ionized water dimer. The present study discloses an observation indicating that water dimers display specific fragmentation patterns following inner-valence ionization, depending on the position of the vacancy. Vacancies were created in the 2a1 state of the proton-donating water molecule (PDWM) and proton-accepting water molecule (PAWM). Utilizing Born–Oppenheimer molecular dynamics simulations, the propagation of the 2a1 ionized state was carried out for both scenarios. The results revealed proton transfer occurred when the vacancy resided in the PDWM, accompanied by the closing of decay channels for O–H bond distance (RO–H) > 1.187 Å (matching Richter et al.'s findings). Conversely, when vacancy was on PAWM, we observed no closing of decay channels (aligning with Jahnke et al.'s findings). This difference translates to distinct fragmentation pathways. In PDWM cases, 2a1 state ionization leads to H3O+ −OH• formation. In contrast, PAWM vacancies result in decay pathways leading to H2O+–H2O+ products. [ABSTRACT FROM AUTHOR]

We propose a novel implementation of the extended-dynamics equations for isothermal–isobaric ensemble in molecular dynamics, as the Martyna–Tobias–Klein thermostat and barostat. This method is suitable for systems with constraints and the Verlet-family integrators. Instead of iterations or the Trotter-expansion-based methods, both velocities and box sizes (scaling of bond lengths) are predicted. The algorithm begins with force calculation, requiring neither quarter nor half time steps, and necessitating iterations only inside SHAKE. Several tests demonstrate that the quality is comparable to other implementations. It is found that the formula relating the extended barostat mass to the characteristic time of volume fluctuations is inaccurate for condensed systems, which has consequences for the parameter setup. Emphasis is also put on the verification of the precise isothermal–isobaric ensemble and finite-size effects. [ABSTRACT FROM AUTHOR]

As the major hydration product of cement, hydrated calcium silicate (C‐S‐H) governs the overall performance of cement‐based materials. The molar ratio of CaO to SiO2 (Ca/Si ratio) significantly affects the structure and properties of C‐S‐H. This study analyzed the effect of Ca/Si ratios (0.83–2.0) on the structural morphology evolution, bond lengths and angles, polymerization process, and nanoporosity of amorphous C‐S‐H, with the help of the ReaxFF force field. The results showed that the reacted C‐S‐H tend to form a fibrous network‐like morphology at low Ca/Si ratios, while the silicate chains are prone to accumulating at high Ca/Si ratios, forming a dense granular ovoid structure. Meanwhile, the Ca/Si ratio has no effect on the bond lengths and angles. In addition, the Ca2+ ions can interrupt the silicate chains during hydration, which leads to a decrease in the average silicate chain length with increasing Ca/Si ratio. The porosity of C‐S‐H decreases from 59.3% to 54.3% when the Ca/Si ratio increases from 0.83 to 2.0. It can be deduced from these findings that the increase in the Ca/Si ratio decreases the compressive strength of cement‐based materials but increases their durability. [ABSTRACT FROM AUTHOR]

Topological constraint theory (TCT) and molecular dynamics simulations (MD) are utilized to study the effect of Y2O3/SiO2 substitution on the short‐ and medium‐range structures and properties in aluminosilicate glasses containing Y2O3. Experimental methods have been applied to characterize the structures of the as‐prepared glasses to verify the accuracy of MD simulations. It was found that the Y–O bond distance is around 2.38 Å and the Y average coordination number is around 5.78. The introduction of Y2O3 disrupts the Si–O and Al–O bonds in the network structure and elevates the proportion of non‐bridging oxygen. Meanwhile, the calculation results of Si–O and Al–O bond distances show Y shortens the distance between Si, Al cations and oxygen ions, improving the network structure tightness. Furthermore, the glass transition temperature (Tg), Vickers hardness (HV), and elastic modulus (E) of glass increase with the increase of Y2O3 content, while the viscosity decreases. TCT was used to analyze the relationship among glass compositions, structures, and properties, and the properties prediction models for Tg, HV, and E were established. The effectiveness of TCT prediction models was proved by the comparison between the results predicted by the models and the data reported in the literature. [ABSTRACT FROM AUTHOR]

In this study, we employ molecular dynamics simulations to develop a large model (19,998 atoms) of liquid SiO2 at 3500 K. We construct models at different pressures in the 0–100 GPa range using the Beest–Kramer–Santen (BKS) potential and periodic boundary conditions. The goal is to detail the structural transition from the polyamorphic liquid state of SiO2 to the crystalline stishovite form, which occurs between 45 and 60 GPa. We analyse the polyamorphic state of liquid SiO2 by examining the formation of SiOx clusters from 2 to 60 GPa. Beyond 60 GPa, the pair radial distribution functions (PRDFs) for Si–O, O–O and Si–Si display multiple peaks, indicating the crystalline phase. This observation is further supported by examining the bond angle distribution, the fraction of SiOx units and OSix linkages, Si–O bond lengths within SiOx units, structural visualisations and the analysis of ring statistics in the liquid SiO2 system, all of which underscore the comprehensive changes in the structure of the system. [ABSTRACT FROM AUTHOR]

SCAN/molecular mechanics molecular dynamics (SCAN/MM MD) simulations have been employed to investigate the structural and dynamical properties of La3+ in aqueous solution. These simulations revealed the presence of two distinct hydration shells, with the first shell exhibiting a La‐O bond distance of 2.56 Å. The water molecules in this initial hydration shell displayed a mean residence time (MRT) of 208 ps, suggesting a less rigid structure. Five successful ligand exchange events occurred within a simulation duration of 100 ps. The stretching frequency of La‐O was found to be 331 cm−1, with a force constant of 92 N/m. Notably, the data obtained from the SCAN/MM MD simulation demonstrated good agreement with experimental findings. [ABSTRACT FROM AUTHOR]

Various condensed phases of water, spanning from the liquid state to multiple ice phases, have been systematically investigated under extreme conditions of pressure and temperature to delineate their stability boundaries. This study focuses on probing the mechanical stability of liquid water through path-integral molecular dynamics simulations, employing the q-TIP4P/F potential to model interatomic interactions in flexible water molecules. Temperature and pressure conditions ranging from 250 to 375 K and $ {-}0.3 $ − 0.3 to 1 GPa, respectively, are considered. This comprehensive approach enables a thorough exploration of nuclear quantum effects on various physical properties of water through direct comparisons with classical molecular dynamics results employing the same potential model. Key properties such as molar volume, intramolecular bond length, H–O–H angle, internal and kinetic energy are analysed, with a specific focus on the effect of tensile stress. Particular attention is devoted to the liquid-gas spinodal pressure, representing the limit of mechanical stability for the liquid phase, at several temperatures. The quantum simulations reveal a spinodal pressure for water of $ {-}286 $ − 286 and $ {-}236 $ − 236 MPa at temperatures of 250 and 300 K, respectively. At these temperatures, the discernible shifts induced by nuclear quantum motion are quantified at 15 and 10 MPa, respectively. These findings contribute valuable insights into the interplay of quantum effects on the stability of liquid water under diverse thermodynamic conditions. [ABSTRACT FROM AUTHOR]

Experimental protein energy maps in the (φ, ψ) space for the dipeptides of 20 naturally occurring amino acids using the current collections of high-resolution entries in the protein data bank (PDB) are presented here. Data sets were generated for hydrogen bond distance cut-off values of 2.7 Å and 3.1 Å. Neighborhood effects of proline residues on the (φ, ψ) maps have been examined. The impact of disulphide bridges on these maps has been critically examined. The comparisons of experimental maps with those obtained using various molecular mechanics and molecular dynamics methods were published earlier. The comparison metrics are: (i) locations of global and secondary minima, (ii) percentage areas enclosed by isoenergy contours, (iii) energybased RMSD and (iv) barriers to conformational transitions. The experimental maps for individual amino acid dipeptide motifs show a higher degree of qualitative consistency with theoretical maps derived using molecular mechanics when compared to those from molecular dynamics methods. We also demonstrate that a majority of backbone conformations observed in the structures of small peptides in the Cambridge Crystallographic Database are within the allowed regions of the experimental Ramachandran maps. A few protein models obtained from NMR spectroscopy were evaluated in terms of the amino acid outlier energies using the experimental maps. [ABSTRACT FROM AUTHOR]

As conducting polymers become increasingly important in electronic devices, understanding their charge transport is essential for material and device development. Various semi-empirical approaches have been used to describe temporal charge carrier dynamics in these materials, but there have yet to be any theoretical approaches utilizing ab initio molecular dynamics. In this work, we develop a computational technique based on ab initio Car–Parrinello molecular dynamics to trace charge carrier temporal motion in archetypical conducting polymer poly(3,4-ethylenedioxythiophene) (PEDOT). Particularly, we analyze charge dynamics in a single PEDOT chain and in two coupled chains with different degrees of coupling and study the effect of temperature. In our model we first initiate a positively charged polaron (compensated by a negative counterion) at one end of the chain, and subsequently displace the counterion to the other end of the chain and trace polaron dynamics in the system by monitoring bond length alternation in the PEDOT backbone and charge density distribution. We find that at low temperature (T = 1 K) the polaron distortion gradually disappears from its initial location and reappears near the new position of the counterion. At the room temperature (T = 300 K), we find that the distortions induced by polaron, and atomic vibrations are of the same magnitude, which makes tracking the polaron distortion challenging because it is hidden behind the temperature-induced vibrations. The novel approach developed in this work can be used to study polaron mobility along and between the chains, investigate charge transport in highly doped polymers, and explore other flexible polymers, including n-doped ones. [ABSTRACT FROM AUTHOR]

We analyze the shear response of grafted polymer chains in shear flow via coarse-grained molecular dynamics simulations with an explicit solvent. We find that the solvent flow penetrates into almost the whole brush for "mushroom"-type brushes but only a few bond distances for dense brushes. In all cases, the external stress on the wall equals the entropic stress associated with the distorted polymer conformations. We find that the external stress increases linearly with shear rate at low rates and sublinearly at high rates. The transition from linear to sublinear scaling occurs where chains react to flow by reorienting. Sublinear scaling with shear rate disappears if the shear rate is nondimensionalized with the effective relaxation time of chain subsegments located in the outer part of the brush that experiences flow. [ABSTRACT FROM AUTHOR]

Iron phosphate glasses, known for their exceptional chemical durability and potential applicability in nuclear waste management, have gained significant attention over the years. The structures of these glasses are complicated by the coexistence of Fe3+ and Fe2+, which plays a crucial role in determining their structures and properties. This work uses molecular dynamics simulations to study the structural changes in Na2O–Fe2O3–P2O5 glasses with varying glass composition and Fe2+/Fe3+ redox ratio. It was found that the redox ratio and modifier contents significantly affected the short‐range and medium‐range orders in the glasses. Significant changes in the local environments around P5+ and Fe3+ were observed, as reflected by the bond distances and coordination numbers. Na+ cations are found to preferentially associate with Fe3+ (rather than Fe2+), whereas Fe2+ has stronger association with P5+ than Na+, confirming the structural role of Fe2+ as a glass modifier. The disruptions in P–O–P linkages upon increasing FeO suggest that FeO causes glass depolymerization. These glasses achieved higher connectivity with increasing Fe3+/(Fe3++Fe2+)${\mathrm{Fe}}^{3+}/({\mathrm{Fe}}^{3+}+{\mathrm{Fe}}^{2+})$ ratios, conerting phosphorous Q2 to Q3 units and iron Q5 units to Q4 units. The decrease of nonbridging oxygen fractions with increasing Fe3+/(Fe3++Fe2+)${\mathrm{Fe}}^{3+}/({\mathrm{Fe}}^{3+}+{\mathrm{Fe}}^{2+})$ ratios, through creating P–O–Fe linkages, is the main reason of enhanced network connectivity. Quantitative structure–property relationship analyses with different structural descriptors were used to correlate with measured properties. The analyses provided valuable insights into structure–property relationships, emphasizing the importance of choosing relevant energy parameters and defining glass network connectivity, particularly in Fnet descriptors. It was found the Fe–O–P linkage density exhibits strong correlations to measured dissolution rates, supporting the importance of these linkages in improving the chemical durability in iron phosphate glasses. [ABSTRACT FROM AUTHOR]

Solid-state electrolytes have garnered attention as potential replacements for liquid organic electrolytes in lithium-ion batteries due to their inherent nonflammability and mechanical stability. In this study, the effect of O doping on the transport properties of Li3PS4 solid electrolytes was investigated using ab initio molecular dynamics (AIMD) simulations. The P–O bond is shorter than the P–S bond after O doping, providing more space for Li-ion migration, and making it easier for Li ions to migrate between tetrahedral Li, which was originally somewhat restricted. The diffusion coefficients of Li ions increase in all XYZ directions after doping, with the most significant improvement observed in the Y direction. Radial distribution function and bond length tracking revealed fast Li ion migration, while the PS4 skeleton remained stable. Our results provide insights for the design of solid-state electrolytes through rational doping strategies. [ABSTRACT FROM AUTHOR]

Context: The DNAN/DNB eutectic is a high-energy explosive eutectic with superior safety and thermal stability compared to traditional melt-cast explosives. However, the addition of polymer binders can effectively enhance its mechanical properties, allowing for continued production demands without the need for changes to existing factory equipment. In this paper, a model of the DNAN/DNB eutectic explosive was established, and five different types of polymers—cis-1,4-polybutadiene (BR), ethylene–vinyl acetate copolymer (EVA), polyethylene glycol (PEG), fluorinated polymer (F2603), and polyvinylidene fluoride (PVDF)—were added to the (1 0 − 1), (1 0 1), and (0 1 1) cleavage planes, respectively, to form polymer-bonded explosives (PBXs). The stability, trigger bond length, mechanical properties, and detonation performance of the various polymer-bound PBXs were predicted retrogressively. Among the five PBX models, the DNAN/DNB/PEG model exhibited the highest binding energy and the shortest trigger bond length, indicating a significant improvement in stability, compatibility, and sensitivity compared to the original eutectic. Additionally, although the detonation performance of DNAN/DNB decreased after the addition of binders, the final results were still satisfactory. Overall, the DNAN/DNB/PEG model demonstrated excellent comprehensive performance, proving that among the many polymer binders, PEG is the optimal choice for DNAN/DNB. Methods: Within the Materials Studio software, molecular dynamics (MD) simulations were employed to predict the properties of the DNAN/DNB eutectic PBX. The MD simulation timestep was set to 1 fs, with a cumulative simulation duration of 2 ns. A 2 ns MD simulation was conducted using the isothermal-isobaric ensemble (NPT). The COMPASS force field was applied, and the temperature was fixed at 295 K. [ABSTRACT FROM AUTHOR]

A large-scale quantum chemical calculation program, Dcdftbmd, was integrated with a Python-based advanced atomistic simulation program, i-PI. The implementation of a client–server model enabled hierarchical parallelization with respect to replicas and force evaluations. The established framework demonstrated that quantum path integral molecular dynamics simulations can be executed with high efficiency for systems consisting of a few tens of replicas and containing thousands of atoms. The application of the framework to bulk water systems, with and without an excess proton, demonstrated that nuclear quantum effects are significant for intra- and inter-molecular structural properties, including oxygen–hydrogen bond distance and radial distribution function around the hydrated excess proton. [ABSTRACT FROM AUTHOR]

Experimental investigation and computational analysis with the DFT approach were done on 4-amino-3-hydroxy naphthalene-1-sulfonic acid (ANSA). Different spectroscopic analyses like NMR, FT-IR, and UV-Visible were performed. The molecular structure was optimized, and the wavenumbers of typical vibrational modes were calculated using the B3LYP method and the 6-311++G (d, p) basis set. After optimization, the calculated bond lengths and bond angles were compared with experimental ones and found well matched, described by RMSD values. Potential energy distribution (PED) obtained by VEDA. 13C and 1H NMR were calculated with the GIAO method which showed great resemblance with the experimental spectra. UV–Vis in different phases were calculated by the TD-DFT method and the CPCM solvent model and compared with the experimental. The HOMO-LUMO energy gap showed a great opportunity for charge transfer inside the molecule. The MEP surface analysis revealed the molecule's charge distribution. To investigate the degree of relative localization of electrons, the FLF diagram was used. Eight distinct receptors were used in biological investigations for molecular docking analysis and a molecular dynamic simulation of 15 ns was performed to determine the best ligand-protein interactions. The drug-likeness was also investigated to see the drug-like properties. [ABSTRACT FROM AUTHOR]

Ionic transport is a critical property for the glass industry, since emerging applications such as sensors, batteries, and electric melting are based on the phenomenon. Short-range interactions (anion-charge carrier) have not been able to explain the total activation barrier observed experimentally, and, as such, it is critical to understand the larger role of all ions in a glass, not just the carrier and the 'site' ions. This research focuses on the role of network formers and their impact on diffusion in glasses, something that current models lack an explicit explanation of. Atomistic simulations with randomly generated parameters for the cation potentials and classical simulations were used to determine the diffusion coefficients and activation energies for synthetic network formers. Using this database, explainable machine learning algorithms were employed to explore network former interactions and determine which parameters are the most influential for ion diffusion. Results suggest that the bond length of the cations changes the geometry of the structure contributing the greatest to cation-modifier interactions. [ABSTRACT FROM AUTHOR]

Methods: This study used molecular dynamics (MD) to simulate three materials (HMX, FOX-7, and TATB) under the NVT ensemble. Six temperatures (100 K, 200 K, 300 K, 400 K, 500 K, and 600 K) were simulated. In addition, the trigger bond lengths, energy bands, and density of states of three materials were obtained at different temperatures and compared with the calculated results at 0 K. Context: The results indicate that the trigger bond lengths of the three materials are very close to the experimental values. Overall, the maximum and average bond lengths of the trigger bonds increase with increasing temperature. The band gap value decreases with increasing temperature. The changes in trigger bond length and band gap value are consistent with the experimental fact that sensitivity increases with increasing temperature. And Eg > 1 eV is consistently found within the temperature range of 0–600 K, indicating that all three materials are non-metallic compounds. [ABSTRACT FROM AUTHOR]

Cytochrome c (Cyt c) is a key molecule involved in mitochondria-mediated apoptosis. Cyt c is released into the cytoplasm to bind to apoptotic enzyme activating factor 1 (Apaf-1) and then forms an apoptotic complex and activated Caspase-9 to further activate Caspase-3/6/7, thereby inducing apoptosis. Among them, the caspase-activated deoxyribonuclease causes DNA fragmentation. In this paper, the interactions between Cyt c and DNA are studied by UV, circular dichroism (CD), isothermal titration calorimetry (ITC), and molecular dynamics (MD) simulation methods. The results show that each 50 bp DNA fragment could bind about 8 Cyt c molecules on average, and the peroxidase activity of Cyt c is significantly enhanced when it interacts with DNA. The conformation around the alpha-helix (K13-C17) is slightly opened, the exposure of the active center (heme group) is slightly increased, and the average bond length of Fe-S (S in M80, Fe in heme group) is shortened, which may enhance the affinity between Cyt c and the substrate. The study also shows that lysine residues (especially K86, K87, and K88) may play a key role in the interaction between Cyt c and DNA. [ABSTRACT FROM AUTHOR]

Interface models of diamond-coated cemented carbide tool WC-Co / SiC/ Diamond with Co mass fraction of 6%, 8%, 10% and 12% were constructed. The influences of different deposition temperatures on the interface bonding strength were simulated with the molecular dynamics method, and the reasons were analyzed from perspectives of adhesion work and bond length distribution. The adhesion work analysis indicates that, compared with the other three Co content interface models, the two interfaces in WC-6% Co / SiC/ Diamond interface model have the highest adhesion work values at seven deposition temperatures. At different deposition temperatures, both interfaces of WC-6% Co / SiC and SiC/ Diamond in WC-6% Co / SiC/ Diamond have the highest adhesion work values of 2. 468 and 5. 394 J / m² at 1 123 and 1 173 K, respectively. The analysis results of bond length distribution indicate that, at any deposition temperature, compared with the other three Co content interface models, the maximum value of the bond length distribution range at each interface of WC-6% Co / SiC/ Diamond is smaller. The interface model obtained by sequentially depositing SiC layer on WC-6%Co substrate at 1 123 K and diamond coating on SiC layer at 1 173 K has the shortest interface bond length, the largest bond energy, and the best interface bonding property. Key words: diamond-coated cemented carbide; WC-Co / SiC/ Diamond; deposition temperature; Co content; interface [ABSTRACT FROM AUTHOR]

Ab initio molecular dynamics was used to estimate the response to constant imposed strain on a short polyethylene (PE) chain and a radical chain with a removed hydrogen atom. Two independent types of simulations were run. In the first case, the chains were strained by expanding a periodic cell, restraining the length but allowing the internal degrees of freedom to reach equilibrium. From these simulations, the average force on the chain was computed, and the resulting force was integrated to determine the Helmholtz free energy for chain stretching. In the second set of simulations, chains were constrained to various lengths, while a bond was restrained at various bond lengths using umbrella sampling. This provided free energy of bond scission for various chain strains. The sum of the two free energy functions results in an approximation of the free energy of chain scission under various strains and gives a realistic and new picture of the effect of chain strain on bond breaking. Unimolecular scission rates for each chain type were examined as a function of chain strain. The scission rate for the radical chain is several orders of magnitude larger than that of the pristine chain at smaller strains and at equilibrium. This highlights the importance of radical formation in PE rupture and is consistent with experiments. Constant strain results were used to derive a constant-force model for the radical chain that demonstrates a roll over in rate similar to the "catch-bond" behavior observed in protein membrane detachment experiments. [ABSTRACT FROM AUTHOR]

In this work, a first-principles systematic study of (Pt3Cu)n, n = 1–9, clusters was performed employing the linear combination of Gaussian-type orbital auxiliary density functional theory approach. The growth of the clusters has been achieved by increasing the previous cluster by one Pt3Cu unit at a time. To explore in detail the potential energy surface of these clusters, initial structures were obtained from Born–Oppenheimer molecular dynamics trajectories generated at different temperatures and spin multiplicities. For each cluster size, several dozens of structures were optimized without any constraints. The most stable structures were characterized by frequency analysis calculations. This study demonstrates that the obtained most stable structures prefer low spin multiplicities. To gain insight into the growing pattern of these systems, average bond lengths were calculated for the lowest stable structures. This work reveals that the Cu atoms prefer to be together and to localize inside the cluster structures. Moreover, these systems tend to form octahedra moieties in the size range of n going from 4 to 9 Pt3Cu units. Magnetic moment per atom and spin density plots were obtained for the neutral, cationic, and anionic ground state structures. Dissociation energies, ionization potential, and electron affinity were calculated, too. The dissociation energy and the electron affinity increase as the number of Pt3Cu units grows, whereas the ionization potential decreases. [ABSTRACT FROM AUTHOR]

In recent work, we have presented a new ReaxFF formulation with a superior conservation of energy in reactive molecular dynamics simulations. The key ingredient in the approach involved the tapering of bond order and bond distance discontinuities using Hermite polynomials. This Communication extends the previous formulation by alleviating additional sources of numerical instability in the original formalism. These "numerical pathologies" are rooted in the counting of lone-pair electrons, the sum of bond orders between atoms that form a valence angle, and the definition of a torsional potential. Based on a theoretical analysis, new functions that mitigate these limitations are designed and validated. The extent of their transferability with previous parameterizations is discussed. The new enhancements provide further gains in numerical stability to facilitate exploration of reactive energy landscapes. [ABSTRACT FROM AUTHOR]

Density‐modified structural features and mechanical properties of the amorphous Si2BC3N are studied by ab initio molecular dynamics simulations. The chemical bonds of Si2BC3N are insensitive to the density variation, which is reflected by the negligible changes in bond lengths, peak locations in density of states and Bader charge values under different densities. Instead, the composition of chemical bonds is altered. Meanwhile, high‐density condition induces the transition of polyhedral units from the sp2‐like trigonal configuration to the tetrahedral configuration, especially for B, C, and N. This variation is the main structural responding mechanism of Si2BC3N to increased density, which is different from the stretching and/or shrinkage of bonds as occurred in crystals. The increased tetrahedron content shall further benefit the amorphous structure stability of Si2BC3N by impeding the separation of turbostratic BN(C), and enhance the second‐order elastic constants, elastic moduli and tensile/shear strengths of Si2BC3N. The high density may decrease the debonding capability of the fiber/Si2BC3N interface but will not change the preference for crack deflection at interfaces. These results suggest the promising prospect of mechanical property optimization of SiBCN ceramics through density tailoring in experiments. [ABSTRACT FROM AUTHOR]

A theoretical study is conducted with three MX3$_{3}$ monolayer 2D materials (AlI3$_{3}$, AsI3$_{3}$, and IrBr3$_{3}$) on their electronic properties and how a halogen monovacancy affects their thermostability. Density functional theory (DFT) calculations are run to obtain the band structures and phonon dispersions for both pristine and defective structures. It is shown that AlI3$_{3}$ and AsI3$_{3}$ have indirect bandgaps of 2.40$2.40$ and 2.23$2.23$ eV, respectively. IrBr3$_{3}$ has a direct bandgap of 1.65$1.65$ eV. Phonon dispersions indicate that they are all thermodynamically stable in pristine state, but their defective counterparts are not. Ab‐initio molecular dynamics (AIMD) simulations are conducted for defective ones to further investigate their stability. It is found that AlI3 and AsI3 layers are decomposed while IrBr3 layer is bent. Further investigations are conducted by analyzing the bond energies and bond lengths of the three materials. It shows that AlI3$_{3}$ and AsI3$_{3}$ have lower bond energy and longer bond length, which makes them dissociated at the ambient temperature while higher bond energy and shorter bond length keep IrBr3$_{3}$ stabilized and enable its displacive phase transition in displacive limit. [ABSTRACT FROM AUTHOR]

A theoretical study is conducted with three MX3$_{3}$ monolayer 2D materials (AlI3$_{3}$, AsI3$_{3}$, and IrBr3$_{3}$) on their electronic properties and how a halogen monovacancy affects their thermostability. Density functional theory (DFT) calculations are run to obtain the band structures and phonon dispersions for both pristine and defective structures. It is shown that AlI3$_{3}$ and AsI3$_{3}$ have indirect bandgaps of 2.40$2.40$ and 2.23$2.23$ eV, respectively. IrBr3$_{3}$ has a direct bandgap of 1.65$1.65$ eV. Phonon dispersions indicate that they are all thermodynamically stable in pristine state, but their defective counterparts are not. Ab‐initio molecular dynamics (AIMD) simulations are conducted for defective ones to further investigate their stability. It is found that AlI3 and AsI3 layers are decomposed while IrBr3 layer is bent. Further investigations are conducted by analyzing the bond energies and bond lengths of the three materials. It shows that AlI3$_{3}$ and AsI3$_{3}$ have lower bond energy and longer bond length, which makes them dissociated at the ambient temperature while higher bond energy and shorter bond length keep IrBr3$_{3}$ stabilized and enable its displacive phase transition in displacive limit. [ABSTRACT FROM AUTHOR]

Copyright of Journal of China University of Petroleum is the property of China University of Petroleum and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Context: CL-20/DNDAP cocrystal is a promising new type of explosive with exceptional energy density and detonation parameters. However, compared to TATB, FOX-7 and other insensitive explosives, it still has higher sensitivity. In order to decrease the sensitivity of CL20/DNDAP cocrystal explosive, in this article, a CL20/DNDAP cocrystal model was established, and six different types of polymers, including butadiene rubber (BR), ethylene-vinyl acetate copolymer (EVA), polyethylene glycol (PEG), hydroxyl-terminated polybutadiene (HTPB), fluoropolymer (F2603), and polyvinylidene difluoride (PVDF), were added to the three cleaved surfaces of (1 0 0), (0 1 0) and (0 0 1) to obtain polymer-bonded explosives (PBXs). Predict the effects of different polymers on the stability, trigger bond length, mechanical properties, and detonation performance of PBXs. Among the six PBX models, CL-20/DNDAP/PEG model exhibited the highest binding energy and the lowest trigger bond length, indicating that CL-20/DNDAP/PEG model had the best stability, compatibility, and the least sensitivity. Furthermore, although the CL-20/DNDAP/F2603 model demonstrated superior detonation capabilities, it should be noted that this model displayed low levels of compatibility. Overall, CL-20/DNDAP/PEG model exhibited the superior comprehensive properties, thereby demonstrating that PEG is a more suitable binder option for PBXs based on the CL20/DNDAP cocrystal. Methods: The properties of CL-20/DNDAP cocrystal-based PBXs were predicted by molecular dynamics (MD) method under Materials Studio software. The MD simulation time step was set at 1fs and the total MD simulation time was 2ns. The Isothermal-isobaric (NPT) ensemble was used for the 2ns of MD simulation. The COMPASS force field was used, and the temperature was set at 295K. [ABSTRACT FROM AUTHOR]

The slow water dissociation process in alkaline electrolyte severely limits the kinetics of HER. The orientation of H2O is well known to affect the dissociation process, but H2O orientation is hard to control because of its random distribution. Herein, an atomically asymmetric local electric field was designed by IrRu dizygotic single‐atom sites (IrRu DSACs) to tune the H2O adsorption configuration and orientation, thus optimizing its dissociation process. The electric field intensity of IrRu DSACs is over 4.00×1010 N/C. The ab initio molecular dynamics simulations combined with in situ Raman spectroscopy analysis on the adsorption behavior of H2O show that the M−H bond length (M=active site) is shortened at the interface due to the strong local electric field gradient and the optimized water orientation promotes the dissociation process of interfacial water. This work provides a new way to explore the role of single atomic sites in alkaline hydrogen evolution reaction. [ABSTRACT FROM AUTHOR]

1,1′-Dihydroxy-5,5′-bi-tetrazolium dihydroxylamine salt (TKX-50) is a new type of high-energy low-sense explosive with great application value, but TKX-50 made directly from the reaction has problems such as irregular crystal morphology and relatively large length-diameter, and these factors seriously affect the sensitivity of TKX-50 and limit its large-scale application. The internal defects of TKX-50 crystals have a great influence on their weakness, and studying its related properties is of great theoretical significance and application value. To further investigate the microscopic properties of TKX-50 crystals and to explore the connection between microscopic parameters and macroscopic susceptibility, this paper reports the use of molecular dynamics simulations to construct TKX-50 crystal scaling models with three types of defects—vacancy, dislocation and doping—and conducts molecular dynamics simulations. The influence of TKX-50 crystal defects on the initiation bond length, density, bonding diatomic interaction energy, and cohesive energy density of the crystal was obtained. The simulation results show that the models with a higher bond length of the initiator bond and higher percentage activated the initiator's N-N bond and lowered the bond-linked diatomic energy, cohesive energy density, and density corresponding to higher crystal sensitivities. This led to a preliminary connection between TKX-50 microscopic model parameters and macroscopic susceptibility. The results of the study can provide a reference for the design of subsequent experiments, and the research method can be extended to the research work on other energy-containing materials. [ABSTRACT FROM AUTHOR]

The absence of adequate force field (FF) parameters to describe certain metallic complexes makes new and deeper analyses impossible. In this context, after a group of researchers developed and validated an AMBER FF for a platinum complex (PC) conjugated with AHBT, new possibilities emerged. Thus, in this work, we propose an improved path to obtain NMR spectroscopic parameters, starting from a specific FF for PC, allowing to obtain more reliable information and a longer simulation time. Initially, a docking study was carried out between a PC and PI3K enzyme, aiming to find the most favorable orientation and, from this pose, to carry out a simulation of classical molecular dynamics (MD) with an explicit solvent and simulation time of 50 ns. To explore a new PC environment, a second MD simulation was performed only between the complex and water molecules, under the same conditions as the first MD. After the results of the two MDs, we proposed strategies to select the best amino acid residues (first MD) and water molecules (second MD) through the analyses of hydrogen bonds and minimum distance distribution functions (MDDFs), respectively. In addition, we also selected the best frames from the two MDs through the OWSCA algorithm. From these resources, it was possible to reduce the amount and computational cost of subsequent quantum calculations. Thus, we performed NMR calculations in two chemical environments, enzymatic and aqueous, with theory level GIAO–PBEPBE/NMR-DKH. So, from a strategic path, we were able to obtain more reliable chemical shifts and, therefore, propose safer spectroscopic probes, showing a large difference between the values of chemical shifts in the enzymatic and aqueous environments. [ABSTRACT FROM AUTHOR]

The water dissolution mechanism in silicate melts under high pressures is not well understood. Here we present the first direct structure investigation of a water-saturated albite melt to monitor the interactions between water and the network structure of silicate melt at the molecular level. In situ high-energy X-ray diffraction was carried out on the NaAlSi3O8-H2O system at 800 °C and 300 MPa, at the Advanced Photon Source synchrotron facility. The analysis of the X-ray diffraction data was augmented with classical Molecular Dynamics simulations of a hydrous albite melt, incorporating accurate water-based interactions. The results show that metal–oxygen bond breaking at the bridging sites occurs overwhelmingly at the Si site upon reaction with H2O, with subsequent Si–OH bond formation and negligible Al–OH formation. Furthermore, we see no evidence for the dissociation of the Al3+ ion from the network structure upon breaking of the Si–O bond in the hydrous albite melt. The results also indicate that the Na+ ion is an active participant in the modifications of the silicate network structure of the albite melt upon water dissolution at high P–T conditions. We do not find evidence for the Na+ ion dissociating from the network structure upon depolymerization and subsequent formation of NaOH complexes. Instead, our results show that the Na+ ion persists as a structure modifier with a shift away from Na–BO bonding to an increase in the extent of Na-NBO bonding, in parallel with pronounced depolymerization of the network. Our MD simulations show that the Si–O and Al–O bond lengths are expanded by about 6% in the hydrous albite melt compared to those of the dry melt at high P–T conditions. The changes in the network silicate structure of a hydrous albite melt at high pressure and temperature, as revealed in this study, must be considered in the advancement of water dissolution models of hydrous granitic (or alkali aluminosilicate) melts. [ABSTRACT FROM AUTHOR]

[Display omitted] • BIA reaches 90.40 % efficiency in 1 M HCl on mild steel at 100 ppm and 303 K. • Inhibitor is mixed-type and adsorbs via physiochemical follows Langmuir isotherm. • SEM, EDX, and AFM confirm the inhibitor film formation on mild steel. • DFT reveals the inhibitor interacts with the mild steel surface. • MD simulations and RDF align with experimental results on chemisorption. Newly synthesized, cost-effective corrosion inhibitor, N-(4-(1,3-benzothiazol-2-ylcarbamoyl)phenyl)isonicotinamide (BIA) was evaluated for mild steel/1M HCl interface. BIA showed a maximum inhibition efficiency of 90.40 % at 100 ppm and 303 ± 1 K, with efficiency increasing with concentration but decreasing with temperature. Inhibitor's adsorption followed Langmuir isotherm via physicochemical interactions. Activation parameters revealed BIA retards both metal dissolution and hydrogen evolution held in unimolecular process. Potentiodynamic polarization (PDP) divulged BIA as a mixed-type, impeding charge-transfer. Electrochemical impedance spectra (EIS) confirmed BIA forms a protective double layer, blocking active sites at the interface. Surface analysis supported a protective film formation. Global and local reactivity descriptors using DFT/B3LYP/6-311G++(d,p) were calculated to relate inhibition efficiency with BIA's electronic properties. Molecular dynamics simulation (MDS) showed an interaction energy of −224.7 kJ/mol between BIA and Fe(1 1 0) at 303 K, with Radial Distribution Function (RDF) showing bond lengths under 3.5 Å, confirming a chemical interaction. Theoretical results align with experimental data. [ABSTRACT FROM AUTHOR]

• The phase transition boundary of the δ -AlOOH P2 1 nm to Pnnm structure was obtained from the bulk thermal expansion anomaly. • Hydrogen bonding symmetry points at different temperature and pressure were obtained by radial integrating the O-O distance. • The proton disorder and hydrogen bonding symmetrization phase diagrams of δ -AlOOH were constructed. Hydrogen bonding symmetrization of water-bearing minerals plays a key role in the water cycle of the deep Earth. The lower mantle is a high-temperature and high-pressure environment, and in this study a classical molecular dynamics simulation of the δ- AlOOH hydrogen bond symmetrization process is carried out using a deep learning potential model. Calculation the length of the H O bond reveals that AlOOH undergoes hydrogen bond symmetrization when the pressure reaches 9 GPa. The volume thermal expansion profile of AlOOH shows an anomalous phenomenon of negative correlation between phase transition pressure and temperature. The radial distribution functions g OH (r) and g HH (r) show the asymmetry of hydrogen bonding at 8 GPa and indicate the critical conditions for hydrogen bonding symmetry at 10 GPa. Calculations of the O 1 O 2 bond lengths show that the critical pressure required for hydrogen bond symmetry increases with temperature. Our simulation results provide some insight into the hydrogen bonding symmetry of water-bearing minerals in the deep Earth's. [ABSTRACT FROM AUTHOR]

[Display omitted] • Effects of DETA and NMP on CO 2 absorption via MD simulation were investigated. • C-N absorption bond formation and DEEA catalytic role were revealed. • Optimal Composition: 3:2.5:1 DETA: DEEA: NMP ratio found for efficient CO 2 capture. • Biphasic Variability: NMP ratios impact the solid or liquid rich-phase formation. • CN and PRDF parameters analyzed at the atomic scale; C-N bond length is 1.7–1.77 Å. In the context of solvent-based carbon capture, researchers and industries are often interested in improvements in the efficiency of CO 2 capture along with the reduction in the required energy. This study employs molecular dynamics (MD) simulation based on a reax force field and experimental investigation to study the effects and main mechanisms of a mutual amine absorbent including diethylenetriamine (DETA) and diethylethanolamine (DEEA), accompanied by NMP and water co-solvents, on the performance of CO 2 capture in a phase change system. The implementation of time-dependent partial radial distribution functions (TD-PRDF, g α β r t m) and coordination number (CN) analyses revealed the significant formation of C-N bonds between carbon (C) derived from CO 2 and nitrogen (N) within the solution. The direct relationship between changes in DETA molar ratios and CO 2 loading, coupled with examining the catalytic role of DEEA in facilitating CO 2 removal through protonation, has been thoroughly studied with MD. The experimental methodology was followed to validate the MD results. The optimum composition, DETA: DEEA: NMP with a molar ratio of 3:2.5:1, as determined through MD simulations exhibits g α β r | t m = 9.848, CN=0.403 at t m = 1 ns. The stable C-N absorption bond length is calculated to be between 1.7 and 1.77 Å. Experimental results confirm a CO 2 loading capacity of 0.93 mol/mol for this composition. [ABSTRACT FROM AUTHOR]

Ab initio molecular dynamics liquid-quench simulations and hybrid density functional calculations are performed to model the effects of room-temperature atomic fluctuations and photo-illumination on the structural and electronic properties of amorphous sub-stoichiometric In2O2.96. A large configurational ensemble is employed to reliably predict the distribution of localized defects as well as their response to the thermal and light activation. The results reveal that the illumination effects on the carrier concentration are greater in amorphous configurations with shorter In–O bond length and reduced polyhedral sharing as compared to the structures with a more uniform morphology. The obtained correlation between the photo-induced carrier density and the reduction in the number of fully coordinated In-atoms implies that metal oxides with a significant fraction of crystalline/amorphous interfaces would show a more pronounced response to illumination. Photo-excitation also produces In–O2–In defects that have not been previously found in sub-stoichiometric amorphous oxides; these defects are responsible for carrier instabilities due to overdoping. [ABSTRACT FROM AUTHOR]

FeO and Fe2O3 represent similar but different effects on the structure and properties of aluminosilicate system. Molecular dynamics was conducted to clarify the influences of FeO and Fe2O3 on the structure and properties of SiO2-CaO-Al2O3-FeO (Fe2O3) systems. The bond length and coordination number (CNs) of Si-O bond are almost not affected by FeO (Fe2O3), but FeO and Fe2O3 have opposite effects on the CNs of Al-O bond. The more the Fe3+ ion is, the closer the CN is to 4. The ability of Fe3+ ions to reduce bridging oxygen (BO) is greater than that of Fe2+ ions, while non-bridging oxygen (NBO) and free oxygen (FO) show an opposite trend. In the same way, the influence of Fe atomic numbers of different valence on BO, NBO and FO is similar to that of FeO (Fe2O3) on BO, NBO and FO. The total diffusion coefficient and viscosity of the system increase with the addition of iron oxide. [ABSTRACT FROM AUTHOR]

Polyphosphate-dependent glucomannokinase (PPGMK) is able to utilize inorganic polyphosphate to synthesize mannose-6-phosphate (M6P) instead of highly costly ATP. This enzyme was modified and designed by combining error-prone PCR (EP-PCR) and site-directed saturation mutagenesis. Two mutants, H92L/A138V and E119V, were screened out from the random mutation library, and we used site-specific saturation mutations to find the optimal amino acid at each site. Finally, we found the optimal combination mutant, H92K/E119R. The thermal stability of H92K/E119R increased by 5.4 times at 50 °C, and the half-life at 50 °C increased to 243 min. Moreover, the enzyme activity of H92K/E119R increased to 16.6 U/mg, and its enzyme activity is twice that of WT. We analyzed the structure of the mutant using molecular dynamics simulation. We found that the shortening of the hydrogen bond distance and the formation of salt bridges can firmly connect the α-helix and β-sheet and improve the stability of the PPGMK structure. [ABSTRACT FROM AUTHOR]

[Display omitted] • Quantify hydrogen bond strength between water and calcite or quartz by angle, length, and number. • Explained water's wedge-shaped diffusion pattern via hydrogen bonding. • Temperature has a dual effect on water diffusion. • Water distribution on aggregates is linked to hydrogen bond strength. In this study, molecular dynamics were employed to compare the angles, lengths, and numbers of hydrogen bonds between water molecules and different aggregates. Compared to quartz, calcite has shorter bond lengths, larger bond angles, and a greater number of bonds with water molecules. The differences in hydrogen bonds lead to the formation of a three-layer structure on the calcite surface by water molecules: ordered, relatively ordered, and disordered, while a two-layer structure—relatively ordered and disordered—is formed on the quartz surface. In the ordered layer, water molecules experience the strongest hydrogen bonding, are neatly arranged, and have low diffusion coefficients. In contrast, the disordered layer is characterized by weaker hydrogen bonding, random arrangement, and higher diffusion coefficients. The movement path of water molecules shows that the debonding of asphalt and aggregate is jointly influenced by the migration behavior of both the underlying and upper-layer water molecules. These findings reveal the microscopic mechanism of water molecules forming a wedge shape at the asphalt-aggregate interface from the perspective of hydrogen bonds, explaining why the constraint of water on the Calcite {214} and Calcite {018} surfaces is stronger compared to Calcite {1 0 4}, but the bonding energy with asphalt decays more rapidly. [ABSTRACT FROM AUTHOR]

Their great versatility makes polymer nanocomposites an important class of engineering materials. In order to gain detailed insights into the nanoscale mechanisms underlying their macroscopic mechanical properties, molecular dynamics (MD) simulations are a valuable tool to complement experimental studies. In this work, we modify the analytical potential functions of an efficient bead–spring model representing a generic polymer nanocomposite to account for the breaking of covalent bonds. We perform uniaxial tensile simulations of double-notched specimens and validate the model using experimental trends for overall stiffness, strength, and toughness. First, we study the effects of sample size, notch geometry, strain rate, temperature, and molar mass for the pure thermoplastic matrix material. Second, we analyze the influence of filler size and filler content on the mechanical behavior of the polymer nanocomposite. With this study, we show that in both the development of new materials and the optimization of established materials, it is possible to gain important preliminary insights into the effects of pertinent material characteristics with a simple MD setup, which can then be further refined by increasing the complexity of the material description and the boundary conditions. • Molecular dynamics simulations of double-notched polymer nanocomposite samples. • Physically sound implementation of bond scission in an efficient molecular model. • Qualitative reproduction of key experimental trends in polymer nanocomposites. • Toolbox for a rapid evaluation of the effects of various material parameters. • Major impact of the bond scission length on the bond, angle, and non-bonded energy. [ABSTRACT FROM AUTHOR]

Ab initio molecular dynamics (AIMD) simulations were performed to study the adsorption of the 1-hydroxyethane-1,1-diphosphonic acid (HEDP) molecule on the Fe (100) surface. Through molecular dynamics trajectory, changes in bond length and angle, density distribution, interaction region indicator (IRI) and electron localization function (ELF), the fundamental adsorption mechanism of HEDP on the iron surface was disclosed in detail. The oxygen atoms of four phosphonic acid groups of HEDP coordinated with the four Fe atoms form a stable adsorption on the iron (100) surface. The HEDP molecule is slightly distorted to bind with O atoms after adsorption. The bond length change tracking results show that the adsorption occurs very quickly. IRI analysis and Bader charges show that the electrostatic interaction between HEDP and the iron surface is strong and responsible for the stable adsorption state. The interaction between deprotonated O atoms and iron surface is stronger than that between protonated O atoms and iron surface. [ABSTRACT FROM AUTHOR]

Doping with a heteroatom is considered to be an effective tool in tuning the physico-chemical properties of metal clusters. Over a period of time, several experimental and theoretical investigations have been carried out to understand the effect of doping on structure, electronic properties and reactivity of main group clusters. However, issues pertaining to thermal stabilities of metal clusters, particularly in the context of heteroatom doping remain unexplored. Filling this lacuna, this report focuses on evaluating the finite temperature behaviour of the main group metal clusters which are doped with diagonally adjacent dopant atoms. Born-Oppenheimer Molecular Dynamical (BOMD) simulations are performed on diagonally doped Li m Mg, Be m Al and B m Si ( m = 1 − 5) clusters (doped diagonal pairs). The thermal response of these doped diagonal pairs is also compared with the corresponding pristine clusters such as Li n , Mg n , Be n , Al n , B n and Si n ( n = 2 − 6) clusters. The simulation trajectories and ionic motions are analysed and root mean square bond length fluctuations are calculated as a function of temperature. The results indicate that the diagonally doped B m Si ( m = 1 − 5) clusters are thermally more stable (1200 K) as compared to the other two doped clusters (Li m Mg, Be m Al). The enhanced thermal stability is attributed to the higher binding energies noted for B m Si ( m = 1 − 5) clusters. Moreover, it is found that for the B-Si cluster systems, diagonal doping always enhances the thermal stability, whereas both diagonal doping and the size of the cluster affect the thermal stabilities of the Li m Mg, and Be m Al cluster systems. An in-depth analysis of thermal-structural-electronic (frontier molecular orbitals) properties revealed that the strength of dopant-to-parent cluster interactions are playing a significant role in influencing the thermal stabilities of diagonally doped clusters. Overall this study also highlights how the heuristic chemical principle of 'diagonal relationship' widely used in main-group chemistry may be extended to cluster science to draw new insights regarding thermal stabilities of metal clusters. [ABSTRACT FROM AUTHOR]

Multiphase Al2O3 samples are simulated using molecular dynamics method. These samples consist of γ‐Al2O3 and α‐Al2O3 crystals embedded in a disordered phase matrix. The stress–strain curves of these samples show elastic and plastic deformation. Structural analysis indicates that the AlO bond lengths are stretched and the geometries of the AlOx (x = 4, 5, and 6) units are distorted during tensile deformation. AlO bond breakage causes the transformation of AlOx units; AlO4 increases while AlO6 decreases with increasing strain. The γ‐Al2O3 and α‐Al2O3 crystals transfer into the disordered phase, while a small number of atoms recrystallize under tensile loads. In plastic deformation, large simplexes with radii above 1.958 Å increase rapidly with increasing strains above 0.116, with the large simplexes coalescing to form the clusters in the disordered phase. The number of large simplexes in the largest cluster increases with increasing strain values above 0.127. The growth and coalescence of large simplexes in the disordered phase cause microscopic crack formation at high strains. [ABSTRACT FROM AUTHOR]

Hydrogen bonded liquids are associated liquids and tend to exhibit local inhomogeneity in the form of clusters and segregated sub-nano domains. It is an open question as to whether Hbonded clusters in pure water have common features with the water segregated pockets observed in various aqueous binary mixtures, such as water–alcohol mixtures, for example. In the present study, we demonstrate through classical molecular dynamics studies of the lifetime distributions of the hydrogen bonds in different types of binary mixtures, that these lifetimes exhibit the same universal features in the case of the pure liquids, independently of the species concentrations. The same types of three distinct lifetimes are observed, all of them in the sub picosecond regime. The primary lifetime concerns that of Hbonded dimers, and strongly depends on Hbonding criteria such as the bonding distance. The two others are independent of bonding criteria and appear as universal accross many liquids and mixtures. The secondary lifetime ( τ 1 ≈ 20 fs) concerns Hbonded cluster lifetimes, while the tertiary lifetime ( τ 2 ≈ 50 fs) concerns the topology of these clusters, such as chains or globules, for example. This surprizing separation in three distinct lifetimes suggests the existence of associated three distinct kinetic mechanisms in the very short sub-picosecond time scales, with, in addition, an appealing connection to the concepts of local energy and entropy. [ABSTRACT FROM AUTHOR]

A new force field for 1-propanol, in the united and all atom models, has been obtained by combining two different empirical methodologies. The first was developed by scaling atom charges and Lennard-Jones parameters to fit the dielectric constant, surface tension, and density; this methodology is named three steps systematic parameterization procedure (3SSPP), as reported by Pérez de la Luz et al. (J Chem Theory Comput 14:5949–5958, 2018). The second methodology consists of moving these parameters and together with the bond distance to obtain the liquid-vapor phase diagram of the CO2 molecule as discussed by Harris and Yung (J Phys Chem 99:12021–12024, 1995). The last methodology is used to obtain the self-diffusion coefficient, which was not consider in the 3SSPP. The 3SSPP/bond methodology is the 3SSPP plus the bond distance scaling. With this new methodology, the experimental density, dielectric constant, surface tension, and self-diffusion coefficient at ambient temperature could be achieved. Furthermore, we show the temperature dependence of the aforementioned properties. The static structure factors are in accordance with the experimental spectrum. Solubility is increased to the experimental value for the united atom (UA) model after applying this methodology and for all atom (AA) scheme, the experimental solubility value is maintained. [ABSTRACT FROM AUTHOR]

Copyright of Acta Materiae Compositae Sinica is the property of Acta Materiea Compositae Sinica Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Biphotochromic proteins simultaneously possess reversible photoswitching (on-to-off) and irreversible photoconversion (green-to-red). High photochemical reactivity of cysteine residues is one of the reasons for the development of "mox"-monomeric and oxidation resistant proteins. Based on site-saturated simultaneous two-point C105 and C117 mutagenesis, we chose C21N/C71G/C105G/C117T/C175A as the moxSAASoti variant. Since its on-to-off photoswitching rate is higher, off-to-on recovery is more complete and photoconversion rates are higher than those of mSAASoti. We analyzed the conformational behavior of the F177 side chain by classical MD simulations. The conformational flexibility of the F177 side chain is mainly responsible for the off-to-on conversion rate changes and can be further utilized as a measure of the conversion rate. Point mutations in mSAASoti mainly affect the pKa values of the red form and off-to-on switching. We demonstrate that the microscopic measure of the observed pKa value is the C–O bond length in the phenyl fragment of the neutral chromophore. According to molecular dynamics simulations with QM/MM potentials, larger C–O bond lengths are found for proteins with larger pKa. This feature can be utilized for prediction of the pKa values of red fluorescent proteins. [ABSTRACT FROM AUTHOR]