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Polymer-Assisted Polymorph Transition in Melt-Processed Molecular Semiconductor Crystals
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Directing Polymorphism of Colloid Crystals Using Conformational Entropy of Polymer Chains
Controlling the polytypes of close-packed structures of spherical colloids is still a challenging problem despite their wide occurrence. Here, in this work, we show that systematic engineering of the polytype structures of close-packed colloids is possible by using the conformational entropy of polymer chains confined in the interstitial space of colloid crystals. Our interstitial space analysis shows that the hexagonal close-packed (HCP) structures offer larger local interstitial space domains, and the structure director chains in favor of HCP counteract the entropic advantages of the face-centered cubic (FCC) lattices. Using model block copolymer colloids and the known lattice entropy of FCC, a proportionality parameter, β CP = 1.91 × 10 –3 ± 3.67 × 10 –4 , for quantifying the conformational entropy contribution toward HCP structures is extracted. This work demonstrates that the interstitial space of colloid crystals serves as a new structure engineering tool for the self-assembly of colloids.
Polymorphism of Magnesium Chloride Decahydrate under High Pressures and Low Temperatures Found in Icy Moons
Magnesium chloride hydrates show a rich diversity of structural forms, with different hydration numbers ranging from 1 to 12. Here, we show that this structural versatility is also present within the same hydration numbers, with the formation of a new phase of magnesium chloride decahydrate (MgCl 2 ·10H 2 O-II) stable at the conditions of 0.03–0.40(14) GPa at 234(11) K and up to 2.11(3) GPa at 220(2) K, as determined by in situ single-crystal X-ray diffraction. The hydrogen bonding interactions of MgCl 2 ·10H 2 O-II are identified and the bulk modulus determined at B 0 = 18.9(12) GPa at 220(2) K. We discuss the implication of this high-pressure MgCl 2 hydrate for icy moon compositional investigations and showcase the structural and density changes between the various hydrates in MgCl 2 ·nH 2 O.
Planar Defect Layers Template a High-Pressure InBi Polymorph
The short- and long-range order of III–V materials under high pressure has long been the subject of debate, with advancements in structural characterization leading to significant revisions to the accepted structural models. Despite these revisions, previous high-pressure structural assignments in the In–Bi system include the site-disordered β-Sn structure type, a structure type demonstrated to be nonexistent in analogous III–V systems. While X-ray diffraction is consistent with site disordering in InBi at high pressure, cluster expansion calculations indicate that disordering requires temperatures above 3000 K. Here, we propose InBi as a model material for studying unique high-pressure planar defects due to its highly anisotropic stress-dependent properties and structure. Specifically, we identify two sets of planar defects that mimic the diffraction pattern of a site disordered β-Sn structure type and are compatible with the calculated disorder barrier. We derive these defects by symmetry relations over crystallographic transitions. Density functional theory calculations of the proposed defects suggest that these defects are stabilized by diminishing interlayer separations with pressure. Further, we find that one of the proposed defects closely resembles a bulk high-pressure phase of InBi, InBi-ϵ, and we assert that the proposed defects order upon heating, acting as a template for InBi-ϵ growth. The proposed defects and their electronic structure provide a basis for the trend of superconducting critical temperature with increasing pressure. These methods for identifying defects are generalizable to other materials with reports of site disorder at high pressure, prompting a broader search for related high-pressure defects.
Testing the evolutionary theory of inversion polymorphisms in the yellow monkeyflower (Mimulus guttatus)
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Kinetic analyses for solid-state phase transition of metastable amorphous-AlO x (2.5 < x ≤ 3.0) nanostructures into crystalline alumina polymorphs
Solid-solid phase change materials (SS-PCMs) hold promise for energy storage/dissipation in batteries and energetic materials. Yet, phase change kinetics for SS-PCMs undergoing metastable to semi-stable/stable phase transformations remain relatively ill-studied because trapping metastable phases remain challenging. Recently, we demonstrated the kinetic entrapment and stabilization of a highly disordered and amorphous Al-oxide phase m-AlO x @C (x~2.5-3.0) via laser ablation synthesis in solution (LASiS). We report here, to our knowledge, the first chemical kinetics analysis for S-S phase transition of the m-AlO 3 @C nanocomposites (< 5–8 nm sizes) into semi-stable equilibrium alumina phases (θ/γ-Al 2 O 3 ) via disproportionation reaction, while releasing excess trapped gases. Our results indicate the atomic density of the AlO 3 structures to be ~5–10 times less than that of the final Al 2 O 3 phases, which led to the hypothesis of a volume shrinkage process during their phase transition. Temperature-dependent X-ray diffraction studies reveal the high-temperature phase transition for m-AlO 3 → θ/γ-Al 2 O 3 to follow contracting volume kinetics model, thereby validating our earlier hypothesis. Using the geometric volume contraction model, reaction kinetics analyses from Arrhenius plots reveal the activation energy barrier for the phase transition to be ~270±11 kJ/mol. This makes the activation energy barrier nearly identical to the oxidation of micron-sized Al particles.
Resolving intermediates during the growth of aluminum deuteroxide (Hydroxide) polymorphs in high chemical potential solutions
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Polymorphism of Pb 5 (PO 4 ) 3 OH δ within the LK-99 mixture
During the synthetic exploration targeting the polycrystalline compound LK-99, an unexpected phase, Pb 5 (PO 4 ) 3 OH δ , was identified as a byproduct. We elucidated the composition of this compound through single-crystal X-ray diffraction analysis. Subsequent synthesis of the target compounds was achieved via high-temperature solid-state pellet reactions. The newly identified Pb 5 (PO 4 ) 3 OH δ has an orthorhombic crystal structure with space group Pnma , representing a unique structure differing from the hexagonal apatite phases of Pb 10 (PO 4 ) 6 O and Pb 5 (PO 4 ) 3 OH. Comprehensive temperature- and magnetic-field-dependent magnetization studies unveiled a temperature-independent magnetic characteristic of Pb 5 (PO 4 ) 3 OH δ . Solid-state nuclear magnetic resonance spectroscopy was employed to decipher the origins of the phase stability and confirm the presence of hydrogen atoms in Pb 5 (PO 4 ) 3 OH δ . These investigations revealed the presence of protonated oxygen sites, in addition to the interstitial water molecules within the structure, which may play critical roles in stabilizing the orthorhombic phase.
Atomic-scale structure of ZrO 2 : Formation of metastable polymorphs
Metastable phases can exist within local minima in the potential energy landscape when they are kinetically “trapped” by various processing routes, such as thermal treatment, grain size reduction, chemical doping, interfacial stress, or irradiation. Despite the importance of metastable materials for many technological applications, little is known about the underlying structural mechanisms of the stabilization process and atomic-scale nature of the resulting defective metastable phase. Investigating ion-irradiated and nanocrystalline zirconia with neutron total scattering experiments, we show that metastable tetragonal ZrO 2 consists of an underlying structure of ferroelastic, orthorhombic nanoscale domains stabilized by a network of domain walls. The apparent long-range tetragonal structure that can be recovered to ambient conditions is only the configurational ensemble average of the underlying orthorhombic domains. This structural heterogeneity with a distinct short-range order is more broadly applicable to other nonequilibrium materials and provides insight into the synthesis and recovery of functional metastable phases with unique physical and chemical properties.
From Nonclassical to Classical: Crystallization Seeds Reshape Nucleation Mechanisms
Crystalline seeds are widely employed in crystallization to accelerate nucleation and control product polymorphs; yet, their impact on nucleation mechanisms remains poorly understood. While homogeneous nucleation of crystals from solution often proceeds through nonclassical pathways involving amorphous intermediates, it is unclear how seeds that promote heterogeneous nucleation reshape these mechanisms and govern polymorph selection. Here, in this study, we provide the first direct evidence that crystalline seeds can bypass the need for amorphous intermediates as nucleation sites, converting nonclassical nucleation mechanisms into classical, monomer-by-monomer crystallization pathways. Using molecular dynamics simulations of zeolite synthesis, we uncover a complex reaction network of competing nucleation processes mediated by intermediate interfacial polymorphs. The interplay between thermodynamic stability and kinetic favorability of these interfacial polymorphs dictates nucleation outcomes, creating a dynamic balance between the interfacial polymorph stability and crystallization rates. Furthermore, we show that the synthesis environment-whether monomers or aggregates serve as reactants-profoundly impacts these pathways. At moderate supersaturation, seeds eliminate amorphous intermediates and promote classical nucleation, whereas high supersaturation or aggregate-based reactants favor nonclassical pathways, even in the presence of seeds. These findings establish a general framework for understanding how seeds govern crystallization mechanisms, with broad implications for controlling nucleation kinetics, polymorph selection, and material properties. While focused on zeolites, this work reveals insights that may be applicable to biominerals, pharmaceuticals, functional materials, and catalysts, providing a basis for engineering crystallization pathways in diverse applications.
Machine Learning a Simple Interpretable Short-Range Potential for Silica
A wide array of models, spanning from computationally expensive ab initio methods to a spectrum of force-field approaches, have been developed and employed to probe silica polymorphs and understand growth processes and atomic-level dynamical transitions in silica. However, the quest for a model capable of making accurate predictions with high computational efficiency for various silica polymorphs is still ongoing. Recent developments in short-range machine-learned models, such as GAP and NNPScan, have shown promise in providing reasonable descriptions of silica, but their computational cost remains high compared to force fields such as BKS which are based on simple interpretable functional forms. Here, in this study, we build on the recent success of our reinforcement learning (RL) workflow to derive a new set of optimal parameters for a promising short-range BKS-based model proposed by Soules. We use RL to navigate the eight-dimensional parameter space of the Soules potential using an experimental training data set that includes both local and global structural features from approximately 21 experimentally realized silica polymorphs, including high density phases and porous zeolites. We compare the performance of our machine-learned ML-Soules model with other high quality models including our recent machine-learned parametrization of BKS (ML-BKS), a machine-learned potential (GAP), as well as predictions of ab initio calculations with the highly fidelity SCAN functional. The ML-Soules accurately captures the relative energetic ordering of various polymorphs as well as their structural features at a significantly reduced computational expense. The ML-Soules model also reasonably captures the structure, density, and elastic constants of quartz, as well as metastable silica polymorphs. We further discuss the limitations of the Soules functional form and propose potential enhancements, including the incorporation of additional three-body terms and/or the utilization of different short-ranged functional forms to achieve greater accuracy for both global and local features in the modeling of silica while retaining low computational cost.
Hub stability in the calcium calmodulin-dependent protein kinase II
The calcium calmodulin protein kinase II (CaMKII) is a multi-subunit ring assembly with a central hub formed by the association domains. There is evidence for hub polymorphism between and within CaMKII isoforms, but the link between polymorphism and subunit exchange has not been resolved. Here, we present near-atomic resolution cryogenic electron microscopy (cryo-EM) structures revealing that hubs from the α and β isoforms, either standalone or within an β holoenzyme, coexist as 12 and 14 subunit assemblies. Single-molecule fluorescence microscopy of Venus-tagged holoenzymes detects intermediate assemblies and progressive dimer loss due to intrinsic holoenzyme lability, and holoenzyme disassembly into dimers upon mutagenesis of a conserved inter-domain contact. Molecular dynamics (MD) simulations show the flexibility of 4-subunit precursors, extracted in-silico from the β hub polymorphs, encompassing the curvature of both polymorphs. The MD explains how an open hub structure also obtained from the β holoenzyme sample could be created by dimer loss and analysis of its cryo-EM dataset reveals how the gap could open further. An assembly model, considering dimer concentration dependence and strain differences between polymorphs, proposes a mechanism for intrinsic hub lability to fine-tune the stoichiometry of αβ heterooligomers for their dynamic localization within synapses in neurons.
Alkali triel chalcogenide nanocrystals: a molecular reactivity approach to ternary phase selectivity
Alkali-metal-based materials are promising building blocks for energy conversion and storage technologies. Here, we use a molecular reactivity-based solution-phase approach to selectively synthesize multiple phases and specific polymorphs of lithium- and sodium-containing triel chalcogenide nanocrystals, LiTrCh 2 , NaTrCh 2 , and NaTr 3 Ch 5 , where Tr = Ga and In and Ch = S, Se, and Te. Analogous to the case of binary II–VI and III–V tetrahedral semiconductors, where the two commonly isolated zinc blende and wurtzite polymorphs are separated by only 1–50 meV f.u. −1 , we find that LiTrCh 2 nanocrystals easily adopt tetragonal (chalcopyrite) and orthorhombic polymorphs separated by only 2.7–6.2 meV f.u. −1 Because of this small energy difference, soft colloidal synthesis succeeds in accessing either one of these polymorphs, depending on the specific dichalcogenide precursor used. Highly reactive diethyl diselenide favors the thermodynamically more stable tetragonal I$\bar{4}2$d phase, whereas mildly reactive diphenyl diselenide favors the kinetic, metastable orthorhombic Pna2 1 phase. Density functional theory calculations confirm the relative energies among multiple LiTrCh 2 polymorphs and also model the observed powder X-ray diffraction pattern of a new C2 NaIn 3 Te 5 phase. 7 Li, 69 Ga, and 77 Se solid-state NMR spectra are consistent with phase-pure ternary LiGaSe 2 nanocrystals. A majority of the nanocrystal compositions are visible-light emitters. This work opens the door to new Li/Na-based ternary triel chalcogenide nanostructures for energy storage and conversion applications.
Hydrogen bonding to the formate ligand: Structural characterization of 2,2′:6′,2″-terpyridine zinc formate·H 2 O
Here, two polymorphs of the 2,2’:6’,2”-terpyridine zinc formate compound (terpy)Zn(O 2 CH) 2 •H 2 O have been structurally characterized by X-ray diffraction. In each case, the formate ligands coordinate via a K 1 -monodentate coordination mode and participate in hydrogen bonding interactions with water molecules. Despite this similarity, however, the polymorphs exhibit different hydrogen bonding motifs. Specifically, while one polymorph forms chains in which water molecules link adjacent (terpy)Zn(O 2 CH) 2 molecules, the other polymorph consists of discrete tetranuclear [(terpy)Zn(O 2 CH) 2 •H 2 O] 4 moieties.
Populus VariantDB v3.2 facilitates CRISPR and functional genomics research
The success of CRISPR genome editing studies depends critically on the precision of guide RNA (gRNA) design. Sequence polymorphisms in outcrossing tree species pose design hazards that can render CRISPR genome editing ineffective. Despite recent advances in tree genome sequencing with haplotype resolution, sequence polymorphism information remains largely inaccessible to various functional genomics research efforts. The Populus VariantDB v3.2 addresses these challenges by providing a user-friendly search engine to query sequence polymorphisms of heterozygous genomes. The database accepts short sequences, such as gRNAs and primers, as input for searching against multiple poplar genomes, including hybrids, with customizable parameters. We provide examples to showcase the utilities of VariantDB in improving the precision of gRNA or primer design. The platform-agnostic nature of the probe search design makes Populus VariantDB v3.2 a versatile tool for the rapidly evolving CRISPR field and other sequence-sensitive functional genomics applications. The database schema is expandable and can accommodate additional tree genomes to broaden its user base.