DeePMD-kit v2: A software package for Deep Potential models

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, Deep Potential - Range Correction (DPRc), Deep Potential Long Range (DPLR), GPU support for customized operators, model compression, non-von Neumann molecular dynamics (NVNMD), and improved usability, including documentation, compiled binary packages, graphical user interfaces (GUI), and application programming interfaces (API). This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, the article benchmarks the accuracy and efficiency of different models and discusses ongoing developments.Comment: 51 pages, 2 figure

Multi-Objective De Novo Molecular Design of Organic Structure-Directing Agents for Zeolites Using Nature-Inspired Ant Colony Optimization

Organic structure-directing agents (OSDAs) are often employed for synthesis of zeolites with desired frameworks. A priori prediction of such OSDAs has mainly relied on the interaction energies between OSDAs and zeolite frameworks, without cost considerations. For practical purposes, the cost of OSDAs becomes a critical issue. Therefore, the development of a computational de novo prediction methodology that can speed up the trial-and-error cycle in search for less expensive OSDAs is desired. This study utilized a nature-inspired ant colony optimization method to predict physicochemically and/or economically preferable OSDAs, while also taking molecular similarity and heuristics of zeolite synthesis into consideration. The prediction results included experimentally known OSDAs, candidates having structures closely related to known OSDAs, and novel ones, suggesting the applicability of this approach.</div

Mesoporous architectures with highly crystallized frameworks

Porous materials have played an increasingly critical role in materials sciences and chemistry. From the viewpoint of applications, highly crystallized mesoporous architectures are very promising mainly due to their unique properties arising from the crystallized frameworks and many exciting applications in diverse fields. In this Highlight article, we summarize recent innovative researches in the creation of mesoporous architectures possessing crystalline pore walls. In particular, new strategies to synthesize highly crystallized mesoporous metals and metal oxides, metal-organic frameworks with large-sized mesopores, and zeolites with hierarchical mesoporosity are described. These mesoporous architectures show a lot of promise in energy and environment-related areas

Tracking Rearrangement of Atomic Configurations During the Conversion from FAU Zeolite to CHA Zeolite

In order to realize designed synthesis, understanding the formation mechanism of zeolites at an atomic level has long been aspired, but remains challenging due to the fact that knowledge of atomic configurations of the species formed during the process is limited. We focus on a synthesis system that crystallizes CHA zeolite from FAU zeolite as the sole source of tetrahedral atoms of Si and Al, so that end-to-end characterization can be conducted. Solid-state 29Si MAS NMR is followed by high-throughput computational modeling to under-stand how atomic configurations changed during the interzeolite conversion. This reveals that the structural motif commonly found in FAU and CHA is not preserved during the conversion; rather, there is a specific rearrangement of silicates and aluminates within the motif. The atomic configuration of CHA seems to be influenced by that of the starting FAU, considering that CHA synthesized without using FAU results in a random Al distribution. A Metropolis Monte-Carlo simulation combined with a lattice minimization technique reveals that CHA derived from FAU has energetically favorable, biased atomic locations, which could be a result of atomic configurations of the starting FAU. These results suggest that by choosing the proper reactant, Al placement could be designed, to enhance targeted properties of zeolites for catalysis and adsorption

Energy Analysis of Aluminosilicate Zeolites with Comprehensive Ranges of Framework Topologies, Chemical Compositions, and Aluminum Distributions

The contents and locations of Al in the zeolite frameworks are one of the key factors determining the physicochemical properties of zeolites. Systematic evaluation of the characteristics of zeolites with a wide variety of framework topologies, a wide range of Si/Al ratios, and various locations of Al is of great significance, but very challenging due to the limitation of the realizable ranges of Al contents in zeolites as well as the limited information on the Al locations obtained from the current analytical techniques. Here, we report the systematic analysis of the energetics of aluminosilicate zeolites with 209 existing framework topologies at different Si/Al ratios using molecular mechanics. More than 43 000 initial structures were generated to give comprehensive views of the energetics of zeolites. The results coincide well with the structural knowledge obtained experimentally. It was revealed that the relation between the relative framework energies versus the Al contents varies in accordance with the topologies, suggesting that the relative stability of zeolites depends not only on the topologies, but also on the substituting contents of Al. For particular topologies with the same Al contents, in addition, comparisons between random and specific distributions of Al showed that zeolite with Al at a particular T site is energetically more stable than those with random distributions, suggesting the inherent influences of the Al locations. The contents and locations of Al in zeolites likely have a certain preference that may reflect the range of chemical compositions, the Al distributions, and consequently the physicochemical properties of realizable aluminosilicate zeolites

Density Functional Theory Study of Deoxydehydration Reaction by TiO₂‑Supported Monomeric and Dimeric Molybdenum Oxide Catalysts

The development of efficient heterogeneous catalysts for converting biomass into value-added chemical compounds remains at the forefront of catalysis research. Deoxydehydration (DODH) reaction that can transform vicinal hydroxy groups with the cis-configuration to the corresponding CC bond in a single step is one of the promising techniques, and molybdenum oxide catalysts supported on TiO2 have been reported as an effective catalyst using hydrogen as a reducing agent. Here, using density functional theory calculations, structures of monomeric and dimeric molybdenum oxide catalysts supported on anatase TiO2(101) have been determined, and we decipher the reaction mechanisms of the conversion of 1,4-anhydroerythritol to 2,5-dihydrofuran over these catalysts as a model reaction. We have found that MoO3 and Mo2O5 are the most stable structures for monomeric and dimeric species that exhibit the oxidation states of MoVI and MoV–MoVI, respectively, under the experimental conditions. For monomeric species, it is rather difficult to catalyze DODH reaction due to the instability for MoIV species and also the higher barrier for the C–O bond scission for MoV or MoVI species. For dimeric species, structures with the oxidation state of MoIV–MoV or MoV–MoV that is found in the form of Mo2O4 exhibit promising energy profiles in terms of stability and energy barrier (∼1.0 eV) for the C–O bond dissociation. Considering the experimental facts that MoIV species is responsible for the DODH reaction and Mo–Mo bond is present, the MoIV–MoV structure could be the plausible active species. Our findings would provide useful information for the catalyst design using earth-abundant and less-expensive metal-based catalysts for the DODH reaction