Ab Initio Molecular Dynamics Research Articles

Novel Two-dimensional Tellurophosphates: Visible Light Photocatalysts for Water Splitting and Carbon Dioxide Reduction

Exploring efficient two-dimensional (2D) photocatalysts for solar-driven water splitting into hydrogen and oxygen is crucial for sustainable hydrogen energy production. In this study, we investigated the suitability of novel 2D tellurophosphates M2P2Te6 (M=Mg, Ca, Sr, Ba, Ra) for photocatalytic overall water splitting using density functional theory (DFT) approach. The stability of tellurophosphates was assessed based on formation energies, phonon dispersions, ab initio molecular dynamics, and elastic modulus results. These monolayers have desirable direct bandgaps (∼1.6 – 2.2 eV) for efficient light absorption, and their valence and conduction bands ideally straddle both the oxidation and reduction potential of water along with the ability to reduce CO2 to hydrocarbons or carbonaceous products. Moreover, Gibbs free energies of Hydrogen Evolution Reaction (HER) and Oxygen Evolution Reaction (OER) of tellurophosphate monolayers are also computed and display that these monolayers are viable photocatalysts under the influence of applied external potential. The tellurophosphates monolayers show strong optical absorption, with an absorption coefficient reaching up to 105 cm-1, across both the visible and UV regions of the solar spectrum, accompanied by high carrier mobility (order of 103 cm2 V-1s-1). The predicted solar-to-hydrogen efficiency of all monolayers exceeds 12%, fulfilling the criteria for commercial and economic viability in solar hydrogen production. The theoretical findings of current study imply that novel 2D tellurophosphate monolayers are promising candidates for optoelectronics, especially as photocatalysts for overall water splitting and CO2 reduction.

Elastic properties of Fe95-yNb2Mo2Cu1Siy-xBx (x=5-8, y=20-26) at % amorphous alloys

Amorphous materials exhibit complex atomic structures characterized by the absence of long-range order, in contrast to the well-defined periodicity of crystalline materials. This structural complexity is further pronounced in compositions such as FeMCuSiB (M = Nb, Mo, W and Ta), which incorporate elements with varying atomic radii and valencies. The Young's modulus of structures generated using traditional methods, such as melt-quenching and random packing, shows poor agreement with experimental data. In this study, we employ hybrid methods for generating the structures, which involve randomly packing elements without overlap, followed by thermalization at room temperature using Ab-initio Molecular Dynamics simulations. The Young's modulus evaluated from these structures aligns well with values measured using Dynamic Mechanical Analysis. Additionally, we utilize these structures to determine other elastic moduli including the bulk modulus and tetragonal shear modulus and find that the obtained values are consistent with the expected range for these compounds. We attribute the improved accuracy to a more representative approximation of the amorphous structure and the direct application of energy-strain relationships, rather than stress-strain relationships, for elastic moduli determination. Our methodology facilitates reliable predictions of the physical properties of amorphous materials and contributes to the design of FeMCuSiB (M = Nb, Mo, W and Ta) alloys with enhanced mechanical properties.

Molten-salt-mediated Chemical Looping Oxidative Dehydrogenation of Ethane with In-situ Carbon Capture and Utilization.

The molten-salt-mediated oxidative dehydrogenation (MM-ODH) of ethane (C2H6) via a chemical looping scheme represents an effective carbon capture and utilization (CCU) method for the valorization of ethane-rich shale gas and concurrent mitigation of carbon dioxide (CO2) emissions. Here, stepwise experimentation with Li2CO3-Na2CO3-K2CO3 (LNK) ternary salts (i) assessed how each component of the LNK mixture impacted ethane MM-ODH performance and (ii) explored physicochemical and thermodynamic mechanisms behind melt-induced changes to ethylene (C2H4) and carbon monoxide (CO) yields. Of fifteen screened LNK compositions, nine exhibited ethylene yields greater than 50% at 800°C while maintaining C2H4 selectivities of 85% or higher. LNK salts rich in Li2CO3 content yielded more ethylene and CO on average than their counterparts, and net CO2 capture per cycle reached a maximum of ~75%. Extended MM-ODH cycling also demonstrated long-term stability of a high-performing LNK medium. Density functional theory (DFT) calculations and ab initio molecular dynamics (AIMD) simulations suggested that the molten salt does not directly activate C2H6. Meanwhile, an empirical model informed by experimental data and reaction thermodynamics adequately predicted overall MM-ODH performance from LNK composition and provided insights into the system's primary drivers.

Effect of Rare Earth Ce on Structure and Properties in 7CrSiMnMoV Die Steel Castings

In this study, rare earth (RE) Ce is used to modify the interaction between atoms in 7CrSiMnMoV die steel castings. The tensile properties are performed, and strengthening mechanism are analyzed by investigated fracture surface, and microstructure by optical microscopy (OM) and scanning electron microscope‐energy dispersive spectrometer (SEM‐EDS). And ab initio molecular dynamics (AIMD) is used to simulate the effect of the Ce element on the local atomic structure of the FeCeC system alloy steel. The results indicate the strength can increase from 722.55 to 1074.27 MPa, and the elongation can increase from 24.86% to 44.22% with a RE Ce concentration of 0.009%. It is attributed to that doping of Ce can inhibit the formation of network eutectic cementite, refine the lamellar spacing of pearlite, and even form granular cementite and martensite structures. AIMD simulation results show that C atoms tend to be surrounded by Fe, and the strong chemical bonds of FeC make the Fe‐centered C more stable with an increase in RE Ce concentration. And doping Ce can introduce new local topological and chemical orderings such that the FeCFe triplets predominantly form small and big angles shifting from near 75° and 136° to 47° and 81°, respectively.

Ab initio molecular dynamics simulation reveals the influence of entropy effect on Co@BEA zeolite-catalyzed dehydrogenation of ethane

The C–H bond activation in alkane dehydrogenation reactions is a key step in determining the reaction rate. To understand the impact of entropy, we performed ab initio static and molecular dynamics free energy simulations of ethane dehydrogenation over Co@BEA zeolite at different temperatures. AIMD simulations showed that a sharp decrease in free energy barrier as temperature increased. Our analysis of the temperature dependence of activation free energies uncovered an unusual entropic effect accompanying the reaction. The unique spatial structures around the Co active site at different temperatures influenced both the extent of charge transfer in the transition state and the arrangement of 3d orbital energy levels. We provided explanations consistent with the principles of thermodynamics and statistical physics. The insights gained at the atomic level have offered a fresh interpretation of the intricate long-range interplay between local chemical reactions and extensive chemical environments.

Exploring complete catalytic cycle of methane oxidation to methanol on Cu2O2 stabilized within MIL-53(Al) framework: A combined DFT and microkinetic study

Although inspiration from copper-based natural enzymes has shown promise in improving catalyst design for methane-to-methanol (MTM) oxidation, high productivity, and selectivity under mild conditions remain a significant challenge. This study constructs the dinuclear copper (Cu2) species stabilized within the metal-organic framework (MOF), MIL-53(Al), containing Cu as efficient catalytic sites and explores the ability of different oxidants (O2, N2O, and H2O2) to oxidize Cu2 into the dicopper-oxo (Cu2O2) species using density functional theory (DFT) calculations. Our results indicate the kinetic and thermodynamic favorability of Cu2O2 species formation using O2 as an oxidant within the MIL-53(Al) framework. Furthermore, the thermal stability of Cu2O2/MIL-53(Al) has been verified via ab initio molecular dynamics (AIMD) calculations. The kinetics of the complete MTM oxidation cycle over Cu2O2/MIL-53(Al) have been studied using both DFT and microkinetic simulation methods. The present study predicts that the C-H activation on the Cu2O2/MIL-53(Al) has a low free energy barrier (0.77 eV) and that the high stability of CH3 and its very low free energy barrier in the C-O coupling step favors the methanol formation over the formaldehyde. More importantly, Cu2O2/MIL-53(Al) exhibits high methanol selectivity owing to the inhibition of CH3 dehydrogenation and low methanol desorption energy (0.21 eV). Microkinetic simulations confirm the methanol production under relatively mild reaction conditions (200–280 K and 1 bar). This work provides insights into the feasibility of selective MTM oxidation over this family of MOF under mild conditions.

Acceleration of Diffusion in Ab Initio Nanoreactor Molecular Dynamics and Application to Hydrogen Sulfide Oxidation.

The computational description of chemical reactivity can become extremely complex when multiple different reaction products and intermediates come into play, forming a chemical reaction network. Therefore, computational methods for the automated construction of chemical reaction networks have been developed in the last decades. One of these methods, ab initio nanoreactor molecular dynamics (NMD), is based on external forces enhancing reactivity by e.g., periodically compressing the system and allowing it to relax. However, during the relaxation process, a significant simulation time is required to allow energy to dissipate and molecules to diffuse, making this part of the NMD simulation computationally intensive. This work aims to improve NMD by accelerating the diffusion process in the relaxation phase. We systematically investigate the speedup of reaction discovery gained by diffusion acceleration, leading to a factor of up to 28 in discovery frequency. Diffusion-accelerated nanoreactor molecular dynamics (DA-NMD) is then used to construct a reaction network of hydrogen sulfide oxidation under atmospheric conditions, where reactions are automatically detected by a change in the bond order and bond distance. A reaction network of 108 molecular species and 399 elementary reactions was constructed starting from hydrogen sulfide, hydroxy radicals, and molecular oxygen covering a broad variety of sulfur-oxygen chemistry and oxidation states of the sulfur atom ranging from -II to +VI.

Novel superhard orthorhombic O12 carbon: a first principle study

Abstract In this study, a new orthorhombic carbon structure with Ama2 symmetry, designated as O12 carbon, has been predicted on basis of the first-principles method. The thermal stability and dynamic stability of O12 carbon were evaluated and confirmed by combining ab initio molecular dynamics and phonon spectra analyses. Meanwhile, the mechanical properties of O12 carbon, compared with other superhard carbon allostrope like diamond, M-carbon, Bct-c4 and Cco-C8, have also been systematically investigated. With a bulk modulus of 351 GPa, a shear modulus of 333 GPa, and a Vickers hardness of 53 GPa, O12 carbon is identified as a superhard material of significantly technological and industrial applications. The existence of elastic anisotropy in O12 carbon has also been confirmed. The electronic band structure calculations have revealed that O12 carbon exhibits a semiconductor characteristic with a direct band gap of 2.5 eV, making it promising candidate in electronic applications. Additionally, the XRD spectra of O12 carbon were obtained to offer further insights for potential experimental observations. Our findings enrich the family of carbon structure and are expected to stimulate additional experimental interest.

Two-dimensional BiSbTeX2 (X = S, Se, Te) and their Janus monolayers as efficient thermoelectric materials.

Today, there is a huge need for highly efficient and sustainable energy resources to tackle environmental degradation and energy crisis. We have analyzed the electronic, mechanical and thermoelectric (TE) characteristics of two-dimensional (2D) BiSbTeX2 (X = S, Se and Te) and Janus BiSbTeXY (X/Y = S, Se and Te) monolayers by implementing first principles simulations. These monolayers' dynamic stability and thermal stability have been demonstrated through phonon dispersion spectra and ab initio molecular dynamics (AIMD) simulations, respectively. The band structure of these monolayers can be tuned by applying uniaxial and biaxial strains. The investigated lattice thermal conductivity (κl) for these monolayers lies between 0.23 and 0.37 W m-1 K-1 at 300 K. For a more precise calculation of the scattering rate, we implemented electron-phonon coupling (EPC) and spin-orbit coupling effects to calculate the transport properties. For p(n)-type carriers, the power factor of these monolayers is predicted to be as high as 2.08 × 10-3 W m-1 K-2 and (0.47 × 10-3 W m-1 K-2) at 300 K. The higher thermoelectric figure of merit (ZT) of p-type carriers at 300 K is obtained because of their very low value of κl and high power factor. Our theoretical investigation predicts that these monolayers can be potential candidates for fabricating highly efficient thermoelectric power generators.

Deciphering Spectroscopic Signatures of Competing Ca2+ - Peptide Interactions.

Calcium-protein interactions are of paramount importance in biochemistry. They are a key element in a number of biological processes, such as neuronal signaling. Therefore, an understanding of the interaction at the molecular level is highly desirable. Here, we study the zwitterionic model peptide l-alanyl-l-alanine (2Ala), which has two distinct and competing binding sites for Ca2+: The carbonyl of the peptide bond and the C-terminus, the carboxylate group. We perform linear and two-dimensional IR spectroscopy experiments and find that the spectroscopic signatures of both moieties in the IR spectra change in amplitude and peak position upon the addition of CaCl2: A blueshift of the asymmetric carboxylate band and a redshift for the amide I mode. Ab initio molecular dynamics simulations confirm the direct interaction of the Ca2+ ion at both the carboxylate and the amide CO site leading to different spectral responses. The blueshift of the asymmetric carboxylate band is caused by a localization of the charge, leading to a decoupling of the CO stretching modes of the carboxylate group. The slight redshift of the amide I mode of 2Ala upon the addition of CaCl2 contrasts the blueshift that has been observed for isolated amide motifs, such as N-methylacetamide (NMA). This difference is caused by the smaller number of water molecules being replaced by the Ca2+ ion for 2Ala's amide compared to less sterically hindered, isolated amide carbonyls, in conjunction with vibrational Stark effects. Our results highlight the importance of considering potential competing binding sites, such as the amide CO backbone, the termini and residues, as well as the nature of the hydration of both peptide and ion, when exploring ions' interacting with small peptides and larger proteins.

Efficient Parametrization of Transferable Atomic Cluster Expansion for Water.

We present a highly accurate and transferable parametrization of water using the atomic cluster expansion (ACE). To efficiently sample liquid water, we propose a novel approach that involves sampling static calculations of various ice phases and utilizing the active learning (AL) feature of the ACE-based D-optimality algorithm to select relevant liquid water configurations, bypassing computationally intensive ab initio molecular dynamics simulations. Our results demonstrate that the ACE descriptors enable a potential initially fitted solely on ice structures, which is later upfitted with few configurations of liquid, identified with AL to provide an excellent description of liquid water. The developed potential exhibits remarkable agreement with first-principles reference, accurately capturing various properties of liquid water, including structural characteristics such as pair correlation functions, covalent bonding profiles, and hydrogen bonding profiles, as well as dynamic properties like the vibrational density of states, diffusion coefficient, and thermodynamic properties such as the melting point of the ice Ih. Our research introduces a new and efficient sampling technique for machine learning potentials in water simulations while also presenting a transferable interatomic potential for water that reveals the accuracy of first-principles reference. This advancement not only enhances our understanding of the relationship between ice and liquid water at the atomic level but also opens up new avenues for studying complex aqueous systems.

Helium roaming in excess electrons in C60F60 as dynamic quasi-Matryoshka dolls.

Multi-guest clathrates exhibit lots of functional characteristics owing to their unique structures, which herald beautiful application prospects, but their fundamental information is still scarce. Herein, we explore a type of (helium, excess electrons/EEs)-C60F60 co-clathrates with quasi-Matryoshka-doll structures using abinitio molecular dynamics simulation and reveal the EEs-entangled He roaming dynamics in C60F60 and its effect on the characteristics of clathrates. Perfluorination ensures that C60F60 possesses an extremely electropositive interior cavity. Its unique confinement effect can stabilize He as an extremely inert entity by noticeably enlarging the 1s-2s orbital gap and can also trap 1-2 EEs in its s-type interior orbital with extremely large binding energies. Co-inclusion of He and EEs in C60F60 exhibits inter-repulsive He⋯EEs entangling dynamics featuring quasi-Matryoshka-doll structures (He@EEs@C60F60). In this structure, EEs screen the attraction of cage-shell Cδ+ to He 1s2 electrons, thus inhibiting their stabilization and orbital expansion, while He conversely decreases the stability of EEs and redshifts their transition absorption. He can roam in the cavity, but its trajectory is impacted by EEs serving as a medium, and thus, the structures exhibit anormal dynamic variation of internuclear He⋯C spin coupling JHeC, which is manipulated by the EEs-entangled He roaming dynamics. JHeC and JHeC' present opposite distance dependences for the colinearly aligned C⋅⋅⋅He⋅⋅⊗⋅⋅⋅⋅⋅C' (⊗, the cage center). This work provides insights into the Matryoshka-doll structured He@EEs@C60F60 with He-EEs entangling dynamics and its modulation on EEs absorption and reveals the dynamic role of EEs in manipulating He-roaming and JHeC coupling properties for promising applications.

Proton transport mechanisms in aqueous acids: Insights from abinitio molecular dynamics simulations.

The solvation and transport of protons in aqueous solutions of phosphoric acid (PA), sulfuric acid (SA), and nitric acid (NA) were studied using abinitio molecular dynamics simulations. Systems with acid-to-water ratios of 1:1 and 1:3 were examined to understand the similarities and differences in transport mechanisms. The solvation structure of H3O+ in these systems is similar to that in slightly acidic water, with variations in the strength of hydrogen bonds (H-bonds) accepted by acid molecules. In aqueous PA systems, strong H-bonds between PA molecules are slightly affected by water, leading to significantly greater H3O+ diffusion compared to aqueous SA and NA systems. This enhanced diffusion is attributed to the participation of PA molecules in H3O+ transport, where the PA molecule can shuttle a proton for H3O+, facilitating a large displacement via collective proton hopping. This shuttling mechanism is prominent in aqueous PA but rare in aqueous SA and absent in aqueous NA. Moreover, the decomposition of H3O+ diffusion into vehicular and structural components indicates that the higher diffusion in aqueous PA is primarily due to the structural mechanism with the aid of PA molecules. In the aqueous NA systems, the vehicular diffusion is dominant at low water contents and the increase in water content improves the structural diffusion by forming connected H-bonds within water molecules. Our findings elucidate the role of acid molecules in proton transport within their aqueous solutions, thereby advancing the fundamental understanding of proton transport mechanisms.

Robust Computation and Analysis of Vibrational Spectra of Layered Framework Materials Including Host-Guest Interactions.

Layered framework materials, a rapidly advancing class of porous materials, are composed of molecular components stitched together via covalent bonds and are usually synthesized through wet-chemical methods. Computational infrared (IR) and Raman spectra are among the most important characterization tools for this material class. Besides the a priori known spectra of the molecular building blocks and the solvent, they allow for in situ monitoring of the framework formation during synthesis. Therefore, they need to capture the additional peaks from host-guest interactions and the bands from emerging bonds between the molecular building blocks, verifying the successful synthesis of the desired material. In this work, we propose a robust computational framework based on ab initio molecular dynamics (AIMD), where we compute IR and Raman spectra from the time-correlation functions of dipole moments and polarizability tensors, respectively. As a case study, we apply our methodology to a covalent organic framework (COF) material, COF-1, and present its AIMD-computed IR and Raman spectra with and without 1,4-dioxane solvent molecules in its pores. To determine robust settings, we meticulously validate our model and explore how stacking disorder and different methods for computing dipole moments and polarizabilities affect IR and Raman intensities. Using our robust computational protocol, we achieve excellent agreement with experimental data. Furthermore, we illustrate how the computed spectra can be dissected into individual contributions from the solvent molecules, the molecular building blocks of COF-1, and the bonds connecting them.

DFT study of electronic and nonlinear optical properties of alkaline earth metals and superalkalis doped all-cis-1, 2, 3, 4, 5, 6-hexafluorocyclohexane as an efficient excess electron system

Continual advancements are being pursued to discover innovative strategies for developing materials with remarkable nonlinear optical (NLO) response. Herein, electronic, geometric, thermodynamic and NLO properties of excess electron systems based on stacked Janus dimer, all-cis-1,2,3,4,5,6-hexafluorocyclohexane (C6H6F6)2 are thoroughly investigated. The excess electron systems are designed by doping alkaline earth metals (AEMs) on fluorine face and superalkalis on hydrogen face of Janus dimer. The higher values of vertical ionization energies (VIE) and interaction energies (Eint), confirm the electronic and thermodynamic stabilities of the designed complexes, respectively. Natural bond orbital (NBO) analysis is performed, and the excess electron character of the complexes is confirmed through frontier molecular orbital (FMO) analysis by highest occupied molecular orbital (HOMO) iso-densities. FMO shows a significant decrease in energy gaps (Egap) of the complexes (i.e., Eg = 1.80–3.12 eV), compared to the stacked Janus dimer (i.e., Eg = 9.41 eV). The transparency of the complexes to UV region is confirmed through UV–vis analyses, revealing their maximum absorption in visible and near-IR regions. The higher NLO response of the designed excess electron systems is further proved by the greater values of first hyperpolarizability (β o ) i.e., up to 1.70 × 106 au. Moreover, the time dependent-density functional theory (TD-DFT) computations and two-level model are employed to investigate the controlling factors of hyperpolarizability, illustrating the contribution of transition energy (∆E3), change in dipole moment (∆μ) and oscillator strength (f o ) in controlling the β o . Ab-initio molecular dynamics (AIMD) simulation further confirm that the designed superalkalide complexes are kinetically and thermally stable. The thorough investigation of these excess electron systems proves them an appropriate candidate for NLO applications.

Modeling High Concentration Bisalt-in-Sulfolane Electrolytes and the Observation of Ligand-Bridged Cation-Pair Complexes.

Despite the abundance of sodium over lithium in Earth's crust and the copious amounts of expensive lithium salt required to make Li-ion high-concentration electrolytes (HCEs), studies of HCEs made from sodium salts remain sparse. A comparative molecular-level study of Li- and Na-ion HCEs and mixed cation or bisalt HCEs in an organic solvent is missing. To fill this gap, we studied model HCEs of pure and mixed Li and Na salts of bis(fluorosulfonyl)amide (FSI) in sulfolane using a confluence of classical molecular dynamics (MD), ab initio MD (AIMD) simulations, and quantum chemical cluster calculations. While Li-ion HCEs display transport properties superior to those of Na-ion HCEs, the latter's performance can be considerably improved by replacing even 25% of Na-ions with Li-ions. While the effects of doping are largely systemic, a larger sensitivity of the identity of solvation shells of Li-ions to the Li-content of the HCE is observed; in contrast, those of Na-ions are more oblivious to it. Fascinating ligand-bridged, short-distance cation pairs observed in the classical MD simulations are confirmed using density functional theory-based AIMD simulations. Quantum chemical calculations in the gas phase reveal the thermodynamic stability of such cation pairs complexed with multiple anions and solvent molecules.

Cellular Phosphate Sensing and Anion Binding by an Azacrown-Calixpyrrole Hybrid.

A hybrid receptor-sensor for anions originating from the merging of positively charged ammonium moieties for electrostatic attraction/stronger binding of azacrowns with directionality of calixpyrrole hydrogen bond donors for selectivity is investigated. As demonstrated this hybrid receptor-sensor shows a remarkable selectivity for orthophosphate even in the presence of other phosphates and anions found in cellular materials (Kassoc H2PO4 ->H2P2O7 2->AMP-≫ADP2- or ATP3- over halides, nitrate, or hydrogen sulfate; all Na+ salts in water) but also cellular polyphosphate or phospholipids. This selectivity is harnessed in a real-time monitoring of cell lysis by lysozyme, which releases orthophosphate and other phosphates and anions from the cells. This sensitive (LOD 0.4 μM) fluorescence-based microscale method compares favorably with the state-of-the-art techniques but can easily be practiced in a high-throughput screening (HTS) manner. The anion binding and selectivity in aqueous solutions were investigated by NMR and put in context with phosphate binding of the parent calix[4]pyrrole. The microscopic understanding of anion binding by the hybrid receptor was then obtained from a combination of density functional theory (DFT), classical molecular dynamics (MD) with explicit water solvation, and ab initio MD (AIMD) simulations. Correlating the NMR and fluorescence binding data with studies of solvation of the receptor, phosphate anion, and the resulting complex confirms the binding is largely driven by entropic component (TΔS) associated with receptor and anion desolvation.

Multiscale simulations of amorphous and crystalline AgSnSe2 alloy for reconfigurable nanophotonic applications

AbstractChalcogenide phase‐change materials (PCM) have been explored in novel nonvolatile memory and neuromorphic computing technologies. Upon fast crystallization process, the conventional PCM undergo a semiconductor–to–semiconductor transition. However, some PCM change from a semiconducting amorphous phase to a metallic crystalline phase with low conductivity (“bad metal”). In this work, we focus on new “bad metal” PCM, namely, AgSnSe2, and carry out multiscale simulations to evaluate its potential for reconfigurable nanophotonic devices. We study the structural features and optical properties of both crystalline and amorphous AgSnSe2 via density functional theory (DFT) calculations and DFT‐based ab initio molecular dynamic (AIMD) simulations. Then we use the calculated optical profiles as input parameters for finite difference time domain (FDTD) modeling of waveguide and metasurface devices. Our multiscale simulations predict AgSnSe2 to be a promising candidate for phase‐change photonic applications.

HexagonRingCalculator: A Handy Code for Hexagonal Ring Characterization in Atomistic Simulations.

Hexagonal rings are critical to the properties of many nanomaterials by determining their mechanical strength, thermal stability, and electrical conductivity, therefore this kind of structure has been intensively concerned in computational studies. However, existing molecular dynamics (MD) simulation tools lack specialized functions for identifying and characterizing them. To address this gap, we developed HexagonRingCalculator, a tool for identifying hexagonal rings and calculating their geometric properties, including bond lengths, ring area, and circularity, directly from MD simulation data. The code facilitates the analysis of ring deformation under varying conditions, such as temperature changes. We demonstrate its functionality and accuracy through classic and ab initio MD simulations of graphene and cellulose, highlighting its potential to advance computational studies in nanomaterials.

The Formation Criteria of LPSO Phase in Type I LPSO Mg-Y-X Alloy from the Perspective of Liquid-Solid Correlation.

The formation criteria of the LPSO phase are important for the design of long-period stacking-ordered (LPSO) Mg alloys. This work focuses on Type I LPSO Mg-Y-X alloys and attempts to explore the formation criteria of the LPSO phase from the perspective of liquid-solid correlation. With the aid of ab-initio molecular dynamics simulation, liquid Mg-Y-X alloys are investigated to obtain the common liquid characteristics from the reported Type I LPSO Mg-Y-X alloys. Following the liquid characteristics, a new Type I LPSO alloy, i.e., Mg-Y-Au, is experimentally confirmed. The discovery of a new Type I LPSO alloy supports liquid-solid correlation, and hence, the formation criteria of the LPSO phase in Type I LPSO alloys can be developed based on the common liquid characteristics of Type I LPSO Mg-Y-X alloys as follows: X should result in the reduction in equilibrium volume and cohesive energy; Y should repulse Y and be attracted by both Mg and X, and X should be repulsed by both Mg and X; X should enhance the threefold and fourfold symmetries and weaken the fivefold and sixfold ones so that the local structural symmetries are distributed close to liquid pure Mg.