Theoretical Investigation into Polymorphic Transformation between β-HMX and δ-HMX by Finite Temperature String

Polymorphic transformation is important in chemical industries, in particular, in those involving explosive molecular crystals. However, due to simulating challenges in the rare event method and collective variables, understanding the transformation mechanism of molecular crystals with a complex structure at the molecular level is poor. In this work, with the constructed order parameters (OPs) and K-means clustering algorithm, the potential of mean force (PMF) along the minimum free-energy path connecting β-HMX and δ-HMX was calculated by the finite temperature string method in the collective variables (SMCV), the free-energy profile and nucleation kinetics were obtained by Markovian milestoning with Voronoi tessellations, and the temperature effect on nucleation was also clarified. The barriers of transformation were affected by the finite-size effects. The configuration with the lower potential barrier in the PMF corresponded to the critical nucleus. The time and free-energy barrier of the polymorphic transformation were reduced as the temperature increased, which was explained by the pre-exponential factor and nucleation rate. Thus, the polymorphic transformation of HMX could be controlled by the temperatures, as is consistent with previous experimental results. Finally, the HMX polymorph dependency of the impact sensitivity was discussed. This work provides an effective way to reveal the polymorphic transformation of the molecular crystal with a cyclic molecular structure, and further to prepare the desired explosive by controlling the transformation temperature.

Finite Temperature String with Order Parameter as Collective Variables for Molecular Crystal: A Case of Polymorphic Transformation of TNT under External Electric Field

An external electric field is an effective tool to induce the polymorphic transformation of molecular crystals, which is important practically in the chemical, material, and energy storage industries. However, the understanding of this mechanism is poor at the molecular level. In this work, two types of order parameters (OPs) were constructed for the molecular crystal based on the intermolecular distance, bond orientation, and molecular orientation. Using the K-means clustering algorithm for the sampling of OPs based on the Euclidean distance and density weight, the polymorphic transformation of TNT was investigated using a finite temperature string (FTS) under external electric fields. The potential of mean force (PMF) was obtained, and the essence of the polymorphic transformation between o-TNT and m-TNT was revealed, which verified the effectiveness of the FTS method based on K-means clustering to OPs. The differences in PMFs between the o-TNT and transition state were decreased under external electric fields in comparison with those in no field. The fields parallel to the c-axis obviously affected the difference in PMF, and the relationship between the changes in PMFs and field strengths was found. Although the external electric field did not promote the convergence, the time of the polymorphic transformation was reduced under the external electric field in comparison to its absence. Moreover, under the external electric field, the polymorphic transformation from o-TNT to m-TNT occurred while that from m-TNT to o-TNT was prevented, which was explained by the dipole moment of molecule, relative permittivity, chemical potential difference, nucleation work and nucleation rate. This confirmed that the polymorphic transformation orientation of the molecular crystal could be controlled by the external electric field. This work provides an effective way to explore the polymorphic transformation of the molecular crystals at a molecular level, and it is useful to control the production process and improve the performance of energetic materials by using the external electric fields.

How the Support Defines Properties of 2D Metal-Organic Frameworks: Fe-TCNQ on Graphene versus Au(111)

The functionality of 2D metal-organic frameworks (MOFs) is crucially dependent on the local environment of the embedded metal atoms. These atomic-scale details are best ascertained on MOFs supported on well-defined surfaces, but the interaction with the support often changes the MOF properties. We elucidate the extent of this effect by comparing the Fe-TCNQ 2D MOF on two weakly interacting supports: graphene and Au(111). We show that the Fe-TCNQ on graphene is nonplanar with iron in quasi-tetrahedral sites, but on Au(111) it is planarized by stronger van der Waals interaction. The differences in physical and electronic structures result in distinct properties of the supported 2D MOFs. The dz2 center position is shifted by 1.4 eV between Fe sites on the two supports, and dramatic differences in chemical reactivity are experimentally identified using a TCNQ probe molecule. These results outline the limitations of common on-surface approaches using metal supports and show that the intrinsic MOF properties can be partially retained on graphene.

Finite temperature string by K-means clustering sampling with order parameters as collective variables for molecular crystals: application to polymorphic transformation between β-CL-20 and ε-CL-20

Polymorphic transformation of molecular crystals is a fundamental phase transition process, and it is important practically in the chemical, material, biopharmaceutical, and energy storage industries. However, understanding of the transformation mechanism at the molecular level is poor due to the extreme simulating challenges in enhanced sampling and formulating order parameters (OPs) as the collective variables that can distinguish polymorphs with quite similar and complicated structures so as to describe the reaction coordinate. In this work, two kinds of OPs for CL-20 were constructed by the bond distances, bond orientations and relative orientations. A K-means clustering algorithm based on the Euclidean distance and sample weight was used to smooth the initial finite temperature string (FTS), and the minimum free energy path connecting β-CL-20 and ε-CL-20 was sketched by the string method in collective variables, and the free energy profile along the path and the nucleation kinetics were obtained by Markovian milestoning with Voronoi tessellations. In comparison with the average-based sampling, the K-means clustering algorithm provided an improved convergence rate of FTS. The simulation of transformation was independent of OP types but was affected greatly by finite-size effects. A surface-mediated local nucleation mechanism was confirmed and the configuration located at the shoulder of potential of mean force, rather than overall maximum, was confirmed to be the critical nucleus formed by the cooperative effect of the intermolecular interactions. This work provides an effective way to explore the polymorphic transformation of caged molecular crystals at the molecular level.

Structural Transformation of Surface-Confined Porphyrin Networks by Addition of Co Atoms

The self-assembly of a nickel-porphyrin derivative (Ni-DPPyP) containing two pyridyl coordinating sites and two pentyl chains at trans meso positions was studied with scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS) and low energy electron diffraction (LEED) on Au(111). Deposition of Ni-DPPyP onto Au(111) gave rise to a close-packed network for coverages smaller or equal to one monolayer as revealed by STM and LEED. The molecular arrangement of this two-dimensional network is stabilized via hydrogen bonds formed between the pyridyl's nitrogen and hydrogen atoms from the pyrrole groups of neighboring molecules. Subsequent deposition of cobalt atoms onto the close-packed network and post-deposition annealing at 423 K led to the formation of a Co-coordinated hexagonal porous network. As confirmed by XPS measurements, the porous network is stabilized by metal-ligand interactions between one cobalt atom and three pyridyl ligands, each pyridyl ligand coming from a different Ni-DPPyP molecule.

Synthesis and photophysics of new pyridyl end-capped 3D-dithia[3.3]paracyclophane-based Janus tectons: surface-confined self-assembly of their model pedestal on HOPG

Once synthesized, these new tectons demonstrated both ionic and coordination bonding. Surprisingly, P forms a quasi-square self-assembly independently of the underlying HOPG lattice.

Adsorption of Nile Red Self-Assembled Monolayers on Au(111)

The ability of Nile Red to self-assemble into supramolecular packings on Au(111) was studied using scanning tunneling microscopy and modeled through theoretical semiempirical calculations. At both submonolayer (sub-ML) and ML coverages, two distinct molecular packings, that is, four-leaf clover and dense chain, were observed, both weakly interacting with the underlying metal surface. Theoretical calculations suggested that the dipole moment plays a subtle role in both molecular assemblies, held together by hydrogen bonds between the Nile Red molecules. Furthermore, although both molecular assemblies were observed in as-deposited samples, a mild thermal annealing caused the transition from the four-leaf clover to the dense-chain packing, pointing out the greater stability of the dense-chain configuration. The study further emphasized how the established interactions between the Nile Red molecules are strongly influenced by the surrounding environment.

Gold adatoms modulate sulfur adsorption on gold

Sulfur adsorption on Au(111) at high coverage has been studied by density functional calculations. In this case S species organize into rectangular structures containing 8 S atoms irrespective of the S source, which have been alternatively assigned to adsorbed monomeric S, adsorbed S₂, adsorbed monomeric plus S₂ species, and gold sulfide. We found that monomeric S at the high coverage organizes into S₂ species that are stabilized into the 8-S structures by Au adatoms, forming gold disulfide complexes (Au-(S₂)₄). The Au atoms could be provided by decomposition of more diluted AuS₃ containing phases, as recently proposed, and direct removal from terraces and step edges, both explaining the surface coverage of vacancy islands coexisting with the 8-S structures. The gold-disulfide complexes capture the disorder shown in the experimental STM images, explain the intrigued features of XPS, and also, give a smooth pathway to gold sulfide formation at higher temperatures. More importantly, the gold-disulfide complexes allow a unified picture of the gold-sulfur surface chemistry at high coverage for thiols and adsorbed sulfur species where the surface chemistry remains under discussion.