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At least 19 records

Macromolecular phasing using diffraction from multiple crystal forms

A phasing algorithm for macromolecular crystallography is proposed that utilizes diffraction data from multiple crystal forms – crystals of the same molecule with different unit-cell packings (different unit-cell parameters or space-group symmetries). The approach is based on the method of iterated projections, starting with no initial phase information. The practicality of the method is demonstrated by simulation using known structures that exist in multiple crystal forms, assuming some information on the molecular envelope and positional relationships between the molecules in the different unit cells. With incorporation of new or existing methods for determination of these parameters, the approach has potential as a method for ab initio phasing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature

The nonstructural protein 3 (NSP3) macrodomain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Mac1) removes adenosine diphosphate (ADP) ribosylation posttranslational modifications, playing a key role in the immune evasion capabilities of the virus responsible for the coronavirus disease 2019 pandemic. Here, we determined neutron and x-ray crystal structures of the SARS-CoV-2 NSP3 macrodomain using multiple crystal forms, temperatures, and pHs, across the apo and ADP-ribose–bound states. We characterize extensive solvation in the Mac1 active site and visualize how water networks reorganize upon binding of ADP-ribose and non-native ligands, inspiring strategies for displacing waters to increase the potency of Mac1 inhibitors. Determining the precise orientations of active site water molecules and the protonation states of key catalytic site residues by neutron crystallography suggests a catalytic mechanism for coronavirus macrodomains distinct from the substrate-assisted mechanism proposed for human MacroD2. These data provoke a reevaluation of macrodomain catalytic mechanisms and will guide the optimization of Mac1 inhibitors.

60 APPLIED LIFE SCIENCES↗

Effects of Melt Processing on Evolution of Structure in PEEK

We report on the effects of melt processing temperature on structure formation in Poly(ether-ether-ketone), PEEK. Real time Small Angle X-ray Scattering, SAXS, and thermal analysis are used to follow the melting behavior after various stages of processing. Assignment of peaks to structural entities within the material, the relative perfection of the crystals, and the possibility of their reorganization, are all influenced by the melt processing history. With the advent of high intensity synchrotron sources of X-radiation, polymer scientists gain a research tool which, when used along with thermal analysis, provides additional structural information about the crystals during growth and subsequent melting. PEEK is an engineering thermoplastic polymer with a very high glass transition temperature (145 C) and crystal melting point (337 C). PEEK has been the subject of recent studies by X-ray scattering in which melt and cold crystallization were followed in real-time. X-ray scattering and thermal studies have been used to address the formation of dual endothermic response which has been variously ascribed to lamellar insertion, dual crystal populations, or melting followed by re-crystallization. Another important issue is whether all of the amorphous phase is located in interlamellar regions, or alternatively whether some is located in "pockets" away from the crystalline lamellar stacks. The interpretation of scattering from lamellar stacks varies depending upon whether such amorphous pockets are formed. Some groups believe all of the amorphous phase is interlamellar. This leads to selection of a smaller thickness for the crystals. Other groups suggest that most amorphous phase is not interlamellar, and this leads to the suggestion that the crystal thickness is larger than the amorphous layer within the stacks. To investigate these ideas, we used SAXS and Differential Scanning Calorimetry to compare results of single and dual stage melt crystallization of PEEK using a treatment scheme involving annealing/crystallization at T(sub a1) followed by annealing at T(sub a2) where either T(sub a1) < T(sub a2) or T(sub a1) > T(sub a2). We proposed a model to explain multiple melting endotherms in PPS, treated according to one or two-stage melt or cold crystallization. Key features of this model are that multiple endotherms: (1) are due to reorganization/recrystallization after cold crystallization; and, (2) are dominated by crystal morphology after melt crystallization at high T. In other words, multiple distinct crystal populations are formed by the latter treatment, leading to observation of multiple melting. PEEK 45OG pellets (ICI Americas) were the starting material for this study. Films were compression molded at 400 C, then quenched to ice water. Samples were heated to 375 C in a Mettler FP80 hot stage and held for three min. to erase crystal seeds before cooling them to T(sub a1) = 280 C . Samples were held at T(sub a2) for a period of time, then immediately heated to 360 C. In the second treatment samples were held at T(sub a1) = 31 C for different crystallization times t(sub c) then cooled to 295 C and held 15 min. In situ (SAXS) experiments were performed at the Brookhaven National Synchrotron Light Source with the sample located inside the Mettler hot stage. The system was equipped with a two-dimensional position sensitive detector. The sample to detector distance was 172.7 cm and the X-ray wavelength was 1.54 Angstroms. SAXS data were taken continuously during the isothermal periods and during the heating to 360 C at 5 C/min. Each SAXS scan was collected for 30 sec. Since the samples were isotropic, circular integration was used to increase the signal to noise ratio. After dual stage melt crystallization with T(sub a1) < T(sub a2) the lower melting endotherm arises from holding at T(sub a1). During cooling a broad distribution of crystals forms, and the low-melting tail is perfected during T(sub al). Heating to T(sub a2) melts these imperfect crystals and allows others with greater average long spacing to form in their place. After dual stage crystallization with T(sub a1) > T(sub a2), the amount of space remaining for additional growth at T(sub a2) depends upon the holding time at T(sub a1). The long period of crystals formed at T(sub a2) is smaller than that formed at T(sub a1) due to growth in a now-restricted geometry. Perfection of crystals is seen as an increase of the intensity of the population scattering at higher s, while the intensity of the population scattering at lower s stays constant. During heating from below to above the minor endotherm, we see rapid decrease of the intensity of the X-ray scattering corresponding to the population of crystals scattering in the shoulder. Another important observation is that after the sample is annealed at 295 C, the shoulder intensity is restored once again. The population scattering at higher s remains longer before it disappears in the sample treated to the second stage of melt crystallization, compared to the sample crystallized with a single stage. This could be interpreted as an effect of continued perfection of the less perfect population, which is also reflected in the increased melting temperature of the smaller endotherm as the holding time at 295 C increases. In the corresponding DSC scans we see a shift in the area and the peak temperature of the lower melting endotherm with an increase of the annealing time.

Georgiev, Georgi↗

Comparative Magma Oceanography

The question of whether the Earth ever passed through a magma ocean stage is of considerable interest. Geochemical evidence strongly suggests that the Moon had a magma ocean and the evidence is mounting that the same was true for Mars. Analyses of martian (SNC) meteorites have yielded insights into the differentiation history of Mars, and consequently, it is interesting to compare that planet to the Earth. Three primary features of Mars contrast strongly to those of the Earth: (i) the extremely ancient ages of the martian core, mantle, and crust (about 4.55 b.y.); (ii) the highly depleted nature of the martian mantle; and (iii) the extreme ranges of Nd isotopic compositions that arise within the crust and depleted mantle. The easiest way to explain the ages and diverse isotopic compositions of martian basalts is to postulate that Mars had an early magma ocean. Cumulates of this magma ocean were later remelted to form the SNC meteorite suite and some of these melts assimilated crustal materials enriched in incompatible elements. The REE pattern of the crust assimilated by these SNC magmas was LREE enriched. If this pattern is typical of the crust as a whole, the martian crust is probably similar in composition to melts generated by small degrees of partial melting (about 5%) of a primitive source. Higher degrees of partial melting would cause the crustal LREE pattern to be essentially flat. In the context of a magma ocean model, where large degrees of partial melting presumably prevailed, the crust would have to be dominated by late-stage, LREE-enriched residual liquids. Regardless of the exact physical setting, Nd and W isotopic evidence indicates that martian geochemical reservoirs must have formed early and that they have not been efficiently remixed since. The important point is that in both the Moon and Mars we see evidence of a magma ocean phase and that we recognize it as such. Several lines of theoretical inference point to an early Earth that was also hot and, perhaps, mostly molten. The Giant Impact hypothesis for the origin of the Moon offers a tremendous input of thermal energy and the same could be true for core formation. And current solar system models favor the formation of a limited number of large (about 1000 km) planetesimals that, upon accreting to Earth, would cause great heating, being lesser versions of the Giant Impact. Several lines of geochemical evidence do not favor this hot early Earth scenario. (i) Terrestrial man-tle xenoliths are sometimes nearly chondritic in their major element compositions, suggesting that these rocks have never been much molten. Large degrees of partial melting probably promote differentiation rather than homogenization. (ii) Unlike the case of Mars, the continental crust probably did not form as a highly fractionated residual liquid from a magma ocean (about 99% crystallization), but, rather, formed in multiple steps. [The simplest model for the formation of continental crust is complicated: (a) about 10% melting of a primitive mantle, making basalt; (b) hydrothermal alteration of that basalt, converting it to greenstone; and (c) 10% partial melting of that greenstone, producing tonalite.] This model is reinforced by the recent observation from old (about 4.1 b.y.) zircons that the early crust formed from an undepleted mantle having a chondritic Lu/Hf ratio. (iii) If the mantle were once differentiated by a magma ocean, the mantle xenolith suite requires that it subsequently be homogenized. The Os isotopic compositions of fertile spinel lherzolites place constraints on the timing of that homogenization. The Os isotopic composition of spinel lherzolites approaches that of chondrites and correlates with elements such as Lu and Al. As Lu and Al concentrations approach those of the primitive mantle, Os isotopic compositions approach chondritic. The Re and Os in these xenoliths were probably added as a late veneer. Thus, the mantle that received the late veneer must have been nearly chondritic in terms of its major elements (excluding Fe). If the mantle that the veneer was mixed into was not al-ready homogenized, then Os isotopes should not correlate with incompatible elements such as Al. Consequently, either early differentiation of the mantle did not occur or the homogenization of this differentiation must have occurred before the late veneer was added. The timing of the late veneer is itself uncertain but presumably postdated core formation at about 4.45 b.y. and did not postdate the 3.8-3.9 b.y. late bombardment of the Moon. This timing based on siderophile elements is consistent with the Hf isotopic evidence cited above. If the Earth, Moon and Mars had magma oceans, the Earth subsequently rehomogenized whereas the Moon and Mars did not. The simplest solution to this observation is that homogenization of igneous differentiates was never necessary on Earth, either because the hypothetical magma ocean never occurred or because this event did not produce mantle differentiation.

Jones, J. H.↗

Tunable coherent mixed-dimensional perovskite heterojunctions and quantum wells grown from solution

Coherent heterojunctions, quantum wells and multiple quantum wells are needed for high-performance devices; these are generally grown via a dedicated vapour phase epitaxy process. Here we demonstrate the growth of coherent perovskite heterojunctions and quantum wells made of mixed-dimensional perovskites using a solution process. By exploiting the solubility difference of methylammonium (MA + ) and 4-(aminomethyl)piperidinium (4AMP 2+ ), we assemble layered perovskites with different layer numbers. The resulting 4AMP-MA n–1 Pb n I 3n+1 materials each with different layer numbers or bandgaps form quantum wells. Heterojunctions and quantum wells made of 4AMP-MA 2 Pb 3 I 10 (n = 3) and 4AMP-MAPb 2 I 7 (n = 2) with various barrier thickness are tailored by the solution temperature profile during crystal growth. Multiple quantum wells have been formed by cycling temperature profiles. The planar heterojunction and quantum wells have lattice matching without interfacial defects, and exhibit strong thermal stability. Type I band alignment at the n = 2/n = 3 heterojunction is confirmed by both computation and optical studies. In conclusion, this study opens a new direction for the development of sophisticated perovskite heterojunction and quantum well devices.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Strain release by 3D atomic misfit in fivefold twinned icosahedral nanoparticles with amorphization and dislocations

Multiple twinning to form fivefold twinned nanoparticles in crystal growth is common and has attracted broad attention ranging from crystallography research to physical chemistry and materials science. Lattice-misfit strain and defects in multiple twinned nanoparticles (MTP) are key to understand and tailor their electronic properties. However, the structural defects and related strain distributions in MTPs are poorly understood in three dimensions (3D). Here, we show the 3D atomic misfit and strain relief mechanism in fivefold twinned icosahedral nanoparticles with amorphization and dislocations by using atomic resolution electron tomography. We discover a two-sided heterogeneity in variety of structural characteristics. A nearly ideal crystallographic fivefold face is always found opposite to a less ordered face, forming Janus-like icosahedral nanoparticles with two distinct hemispheres. The disordered amorphous domains release a large amount of strain. Molecular dynamics simulations further reveal the Janus-like icosahedral nanoparticles are prevalent in the MTPs formed in liquid-solid phase transition. This work provides insights on the atomistic models for the modelling of formation mechanisms of fivefold twinned structures and computational simulations of lattice distortions and defects. We anticipate it will inspire future studies on fundamental problems such as twin boundary migration and kinetics of structures in 3D at atomic level.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Desolvation Processes in Channel Solvates of Niclosamide

The antiparasitic drug niclosamide (NCL) is notable for its ability to crystallize in multiple 1:1 channel solvate forms, none of which are isostructural. Here, using a combination of time-resolved synchrotron powder X-ray diffraction and thermogravimetry, the process-induced desolvation mechanisms of methanol and acetonitrile solvates are investigated. Structural changes in both solvates follow a complicated molecular-level trajectory characterized by a sudden shift in lattice parameters several degrees below the temperature where the desolvated phase first appears. Model fitting of kinetic data obtained under isothermal heating conditions suggests that the desolvation is rate-limited by the nucleation of the solvent-free product. The desolvation pathways identified in these systems stand in contrast to previous investigations of the NCL channel hydrate, where water loss by diffusion initially yields an anhydrous isomorph that converts to the thermodynamic polymorph at significantly higher temperatures. Taking the view that each solvate lattice is a unique “pre-organized” precursor, a comparison of the pathways from different starting topologies to the same final product provides the opportunity to reevaluate assumptions of how various factors (e.g., solvent binding strength, density) influence solid-state desolvation processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Laning transitions in pattern-forming driven binary systems with competing interactions

A binary system of particles that move in opposite directions under an applied field can exhibit disordered states as well as laned states where the particles organize into oppositely moving high-mobility lanes to reduce collisions. Previous studies of laning transitions generally focused on particles with purely repulsive interactions. Here, in this study, we examine laning transitions for oppositely moving pattern-forming systems of particles with competing attractive and repulsive interactions, which in equilibrium form crystal, stripe, and bubble states. In addition to multiple types of laned states, we find jammed crystals, stripes, and bubbles, and generally observe a much richer variety of phases compared to the purely repulsive system. In the stripe-forming regime, the system can dynamically reorder into oppositely moving stripes that are aligned in the direction of the drive. The bubble phase can produce strongly polarized jammed states of elongated bubbles where particles in the individual bubbles segregate to opposite sides of the bubbles. We also find disordered states, segregated laned bubble states where the bubbles pass each other in lanes, and segregated bubbles that move through one another. In the compact bubble regime, we obtain a plastic bubble state in which the oppositely driven particles remain trapped in the bubbles but the bubbles move past each other at a slow velocity due to a net imbalance in the bubble population. At higher drives, individual particles begin to jump from bubble to bubble. We show that the different phases and the transitions between them produce signatures in the velocity-force and differential mobility curves. We demonstrate that the force for escaping from the jammed state is nonmonotonic, with stripes exhibiting the lowest unjamming force.

36 MATERIALS SCIENCE↗

Slip-free multiplication and complexity of dislocation networks in FCC metals

Abstract During plastic deformation of crystalline solids, intricate networks of dislocation lines form and evolve. To capture dislocation density evolution, prominent theories of crystal plasticity assume that 1) multiplication is driven by slip in active slip systems and 2) pair-wise slip system interactions dominate network evolution. In this work, we analyze a massive database of over 100 discrete dislocation dynamics simulations (with cross-slip suppressed), and our findings bring both of these assumptions into question. We demonstrate that dislocation multiplication is commonly observed on slip systems with no applied stress and no plastic strain rate, a phenomenon we refer to as slip-free multiplication. We show that while the formation of glissile junctions provides one mechanism for slip-free multiplication, additional mechanisms which account for the influence of coplanar interactions are needed to fully explain the observations. Unlike glissile junction formation which results from a binary reaction between a pair of slip systems, these new multiplication mechanisms require higher order reactions that lead to complex network configurations. While these complex configurations have not been given much attention previously, they account for about 50% of the line intersections in our database.

36 MATERIALS SCIENCE↗

Fluorescence Studies of Protein Crystal Nucleation

We have postulated that, in the case of tetragonal chicken egg white lysozyme, crystal growth occurs by the addition of pre-critical nuclei sized n-mers that form in the bulk solution, and that the n-mer growth units were multiples of the tetrameric 4(sub 3) helical structure. These have the strongest intermolecular bonds in the crystal and are therefore likely to be the first species formed. High resolution AFM studies provide strong supporting evidence for this model, but the data also suggest that the actual species in solution may not be identical in structure to that found in the crystal. We are using fluorescence resonance energy transfer (FRET) to study the initial solution phase self-assembly process, using covalent fluorescent derivatives which crystallize in the characteristic P4(sub 3)2(sub 1)2(sub 1) space group. FRET studies are being carried out between the cascade blue (CB-lys, donor, Ex(sub max) 366 nm, Em 420 nm) and lucifer yellow (LY-lys, acceptor, Ex(sub max) 430 nm, Em 528 nm) asp101 derivatives. The estimated R(sub 0) for this probe pair, the distance where 50% of the donor energy is transferred to the acceptor, is approx. 1.2 nm, compared to 2.2 nm between the side chain carboxyls of adjacent asp101's in the crystalline 4(sub 3) helix. The short donor lifetime of 2.80 ns (chi(sup 2) = 0.644), coupled with the large average distances between the molecules (greater than or equal to 50 nm) in solution, ensure that any energy transfer observed is not due to random diffusive interactions. Lifetime data show that CB-lys has a single lifetime when it is the only species in solution. Similarly, LY-lys also exhibits a single lifetime of 4.63 ns (chi(sup 2) = 0.42) when alone in solution. Addition of LY-lys to CB-lys results in the appearance of a third lifetime component of 0.348ns for the CB-lys. The fractional intensities of the different species present can be used to estimate the distribution of monomer and n-mers in solution. The self-association process is a function of the protein concentration relative to the saturation concentration, and observing it in dilute solution (conc. less than or equal to 10(exp -5)M) requires that the experiments be performed under low solubility conditions, i.e., low temperatures and high salt concentrations. Data from preliminary steady state FRET studies with N-terminal bound pyrene acetic acid (PAA-lys, donor, Ex 340 nm, Em 376 nm) and asp101 LY-lys as an acceptor showed a consistent trend of decreasing donor fluorescence intensity with increasing total protein concentration. The FRET data have been obtained at pH 4.6, 0.1M NaAc buffer, at 5 and 7% NaCl, 4 C. The corresponding C(sub sat) values are 0.471 and 0.362 mg/ml (approx. 3.3 and approx. 2.5 x 10(exp -5)M respectively). The donor fluorescence decrease is more pronounced at7% NaCl, consistent with the expected increased intermolecular interactions at higher salt concentrations as reflected in the lower solubility. Results from these and other ongoing studies will be discussed in conjunction with an emerging model for how tetragonal lysozyme crystals nucleate and the relevance of that model to other proteins.

Pusey, Marc↗

Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography

Since early 2020, COVID-19 has grown to affect the lives of billions globally. A worldwide investigation has been ongoing for characterizing the virus and also for finding an effective drug and developing vaccines. As time has been of the essence, a crucial part of this research has been drug repurposing; therefore, confirmation of in silico drug screening studies have been carried out for this purpose. Here we demonstrated the possibility of screening a variety of drugs efficiently by leveraging a high data collection rate of 120 images/second with the new low-noise, high dynamic range ePix10k2M Pixel Array Detector installed at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Linac Coherent Light Source (LCLS). The X-ray Free-Electron Laser (XFEL) is used for remote high-throughput data collection for drug repurposing of the main protease (Mpro) of SARS-CoV-2 at ambient temperature with mitigated X-ray radiation damage. We obtained multiple structures soaked with nine drug candidate molecules in two crystal forms. Although our drug binding attempts failed, we successfully established a high-throughput Serial Femtosecond X-ray crystallographic (SFX) data collection protocol.

60 APPLIED LIFE SCIENCES↗

A Proposed Pathway for the Nucleation and Crystal Growth of the Tetragonal Form of Lysozyme

A number of factors, the shape and charge distribution anisotropy, multiple components in the solution (buffer + counter ion, precipitant, protein, and water), conformational flexibility, and large numbers of intermolecular contacts, all serve as complicating variables in understanding the nucleation and growth mechanism for macromolecules. Intermolecular contacts include hydrogen bonds, van der Waals, hydrophobic, salt bridges, and ion-mediated contacts. The latter interactions are stronger and give specificity while the others are weaker, more prevalent, and more promiscuous, i.e., can lead to a range of possible molecular interactions. We propose that for tetragonal lysozyme, and by extension many other monomeric proteins, there is a solution-phase assembly process to form 4(sub 3) helix structures that are the basic unit for nucleation. The formation of these structures is continuous and concentration dependent. They subsequently also servc as growth units, with that process then being a recapitulation of the nucleation process. The advantages of solution phase assembly are the immediate burying of the strongest interactions, removing them from subsequent participation in the nucleation and growth process, and the introduction of symmetry into the system, which also assists in the assembly process.

Pusey, Marc L.↗

Nanostructure and compositional segregation of soft magnetic FeNi-based nanocomposites with multiple nanocrystalline phases

Soft magnetic metal amorphous nanocomposite alloys are produced through rapid solidification and thermal annealing yielding nanocrystals embedded within an amorphous precursor. Similar free energies in Co-rich and FeNi-based alloy systems result in multiple nanocrystalline phases being formed during devitrification. Studies of multi-phase crystallization processes have been reported for Co-rich alloys but relatively few have investigated FeNi-based systems. A detailed characterization of compositional partitioning and microstructure of an optimally annealed FeNi-based MANC (Fe 70 Ni 30 ) 80 Nb 4 Si 2 B 14 alloy is presented through complementary high-resolution transmission electron microscopy (HRTEM) and atom probe tomography (APT). HRTEM demonstrates orientation relationships between FCC and BCC nanocrystals, suggesting heterogeneous nucleation of nanocrystals in the amorphous matrix or a cooperative mechanism of nucleation between BCC and FCC nanocrystallites. APT results show evidence for (i) the segregation of Fe and Ni between nanocrystals of different phases, (ii) B partitioning to the amorphous phase, and (iii) an Nb-enriched shell surrounding nanocrystals.

36 MATERIALS SCIENCE↗

Nanostructure and compositional segregation of soft magnetic FeNi-based nanocomposites with multiple nanocrystalline phases

Soft magnetic metal amorphous nanocomposite alloys are produced through rapid solidification and thermal annealing yielding nanocrystals embedded within an amorphous precursor. Similar free energies in Co-rich and FeNi-based alloy systems result in multiple nanocrystalline phases being formed during devitrification. Studies of multi-phase crystallization processes have been reported for Co-rich alloys but relatively few have investigated FeNi-based systems. A detailed characterization of compositional partitioning and microstructure of an optimally annealed FeNi-based MANC (Fe70Ni30)80Nb4Si2B14 alloy is presented through complementary high-resolution transmission electron microscopy (HRTEM) and atom probe tomography (APT). HRTEM demonstrates orientation relationships between FCC and BCC nanocrystals, suggesting heterogeneous nucleation of nanocrystals in the amorphous matrix or a cooperative mechanism of nucleation between BCC and FCC nanocrystallites. APT results show evidence for (i) the segregation of Fe and Ni between nanocrystals of different phases, (ii) B partitioning to the amorphous phase, and (iii) an Nb-enriched shell surrounding nanocrystals.

soft magnetic materials↗

Mapping periplasmic binding protein oligosaccharide recognition with neutron crystallography

Numerous studies have shown how periplasmic binding proteins (PBPs) bind substrates with exquisite specificity, even distinguishing between sugar epimers and anomers, or structurally similar ions. Yet, marked substrate promiscuity is also a feature encoded in some PBPs. Except for three sub-Ångström crystal structures, there are no reports of hydrogen atom positions in the remaining (> 1000) PBP structures. The previous X-ray crystal structure of the maltodextrin periplasmic-binding protein from Thermotoga maritima (tmMBP) complexed with oligosaccharide showed a large network of interconnected water molecules stretching from one end of the substrate binding pocket to the other. These water molecules are positioned to form multiple hydrogen bonds, as well as forming interactions between the protein and substrate. Here we present the neutron crystal structure of tmMBP to a resolution of 2.1 Å. This is the first neutron crystal structure from the PBP superfamily and here we unambiguously identify the nature and orientation of the hydrogen bonding and water-mediated interactions involved in stabilizing a tetrasaccharide in the binding site. More broadly, these results demonstrate the conserved intricate mechanisms that underlie substrate-specificity and affinity in PBPs.

59 BASIC BIOLOGICAL SCIENCES↗

Enhanced polymorph metastability drives glycine nucleation in aqueous salt solutions

Crystal nucleation from aqueous solutions influences countless geological, biochemical, astrophysical, environmental, and materials science–related phenomena, including ice formation, the manufacturing of active pharmaceutical ingredients, development of diseases such as Alzheimer’s and the origin of life itself. Understanding and controlling nucleation is essential for designing materials with specific properties, developing strategies to inhibit or promote crystallization in various contexts and preventing pathological aggregation in neurodegenerative diseases. Similar to the protein structure prediction problem—where a single amino acid sequence can in theory adopt one most stable conformation but in practice may sample multiple competing conformations—crystal nucleation faces a parallel challenge: the same chemical species can form diverse polymorphs under different environmental conditions (e.g., temperature, pressure, solvent). Each polymorph presents its own set of physical and chemical properties, highlighting the importance of understanding and controlling polymorph selection in fields ranging from pharmaceuticals to materials design. Despite advances in experimental and computational methods for studying phase transitions and polymorph stability, nucleation remains challenging due to its nanoscale nature. Furthermore, in practical settings, salts and impurities can further influence crystal nucleation in diverse contexts, from scaling in pipelines and desalination plants to the durability of concrete and the efficiency of battery materials. This can lead to the formation of polymorphs that may differ from the most stable phase in pure solutions. Or, even though the final structure might appear same irrespective of whether the environment contained impurities or not, the mechanism through which it was formed might be completely different and not intuitive.

Wang, Ruiyu [University of Maryland, College Park,↗

Mixed-Domain Charge Transport in S-Se Alloys as a Li-S Battery Cathode Material

Lithium-sulfur batteries are emerging candidate systems for the next-generation long-range electric aircraft application owing to their potential to deliver high energy density per weight. Their cathodes are to be made primarily with sulfur, but sulfur by itself has much too low electron conductivity to serve as a useful cathode. An idea that has been suggested to overcome this bottleneck is to alloy sulfur with selenium in the hope that electron mobility, which is thought to improve charge transport at some expense of increased weight and reduced energy density. However, understanding of these alloy structures and their transport mechanism is insufficient, and electron mobility at varying degrees of selenium content is not well charted, which are critical for determining the optimum selenium content and testing whether this strategy is generally feasible. The difficulty of computationally characterizing these alloy systems is rooted in the structure. The structures of both sulfur and selenium exhibit eight-atom rings that pack together in various orientations to form their respective crystals. For one, because these crystals (and presumably their alloys as well) feature multiple polymorphs such that their structural coherence is rather unclear. Secondly, these are also relatively large systems (32 atoms per cell) with low-symmetry, which complicate computation both in terms of accuracy and efficiency. Thirdly, such semi-molecular, semi-crystalline structures lead to a combination of band-transport characteristics and hopping-transport characteristics, each of which is a domain with its own physics and set of computational, theoretical challenges. In addition, there is a general dearth of experimental transport data for sulfur-selenium alloys. In this study, we make a comprehensive attempt to tackle this problem using a wide array of first-principles methods. We generate special quasirandom structures to simulate alloy structures, and compute their first-principles Raman spectra for comparison with experimental data to ensure their structural soundness. We then proceed to use recently developed, state-of-the-art tool (AMSET) in order to efficiently compute electronic mobilities under band transport of pure sulfur, pure selenium, as well as their alloys of various compositions at a reasonable accuracy. We then sample numerous dimer configurations of nearest-neighbor eight-atom-ring-pairs and compute electronic hopping rates between them, which yields hopping mobility. A combination of these efforts lead to a general mapping of electron transport behaviors throughout the alloy range. Preliminary results show that introduction of selenium into sulfur initially damages electron mobility due to disorder but eventually improves it beyond that of pure sulfur with additional selenium content, ultimately peaking at the pure-selenium limit. Band transport dominates for holes in sulfur and electrons in selenium, but in all other cases, hopping transport is dominant. Ongoing efforts include determination of charge concentration and conductivity, as well as performing multiphysics modeling to determine the optimum selenium content for best tradeoff between conductivity and energy density for aircraft range.

Junsoo Park↗