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Molecular Simulation of Nanoparticle-Nanopore Interactions: Adsorption Aggregation and Fracture.
Abstract not provided.
Molecular Dynamic Studies of Dye–Dye and Dye–DNA Interactions Governing Excitonic Coupling in Squaraine Aggregates Templated by DNA Holliday Junctions
Dye molecules, arranged in an aggregate, can display excitonic delocalization. The use of DNA scaffolding to control aggregate configurations and delocalization is of research interest. Here, we applied Molecular Dynamics (MD) to gain an insight on how dye–DNA interactions affect excitonic coupling between two squaraine (SQ) dyes covalently attached to a DNA Holliday junction (HJ). We studied two types of dimer configurations, i.e., adjacent and transverse, which differed in points of dye covalent attachments to DNA. Three structurally different SQ dyes with similar hydrophobicity were chosen to investigate the sensitivity of excitonic coupling to dye placement. Each dimer configuration was initialized in parallel and antiparallel arrangements in the DNA HJ. The MD results, validated by experimental measurements, suggested that the adjacent dimer promotes stronger excitonic coupling and less dye–DNA interaction than the transverse dimer. Additionally, we found that SQ dyes with specific functional groups (i.e., substituents) facilitate a closer degree of aggregate packing via hydrophobic effects, leading to a stronger excitonic coupling. This work advances a fundamental understanding of the impacts of dye–DNA interactions on aggregate orientation and excitonic coupling.
Anion chemical composition of poly(ethylene oxide)-based sulfonylimide and sulfonate lithium ionomers controls ion aggregation and conduction
Maximizing ion conduction in single-ion-conducting ionomers is essential for their application in energy-related technologies such as Li-ion batteries. Understanding the anion chemical composition impacts on ion conduction offers new perspectives to maximize ion transport, since the current approach of lowering T g has apparently reached a limit (lowest T g ~ 190 K, highest conductivity ~10 -5 –10 -4 S cm -1 ). Here, a series of random ionomers are synthesized by copolymerizing poly(ethylene glycol)methacrylate with either sulfonylimide lithium methacrylate (MTLi) or sulfonate lithium methacrylate (MSLi) using reversible addition–fragmentation chain transfer (RAFT) polymerization. Li-Ion conduction and self-diffusion coefficients (DLi+) of the ionomers are characterized with dielectric relaxation spectroscopy (DRS) and pulsed-field-gradient (PFG) NMR diffusometry, respectively. Increasing ion content decreases the Li-ion conductivity and D Li+ , as expected from the increased T g . Moreover, a considerably lower ionic conductivity and D Li+ are observed for MSLi compared to MTLi at constant ion content and T g /T. As revealed from X-ray scattering, strong ion aggregation in MSLi results in much lower conductivity and DLi+ compared with less aggregated MTLi based on the more delocalized sulfonylimide anion. These results emphasize the detrimental and molecularly specific role of ion aggregation in Li-ion conductivity, and highlight the necessity for minimizing ion aggregation via the rational choice of anion chemical composition.
Understanding the Aggregation of Model Island and Archipelago Asphaltene Molecules near Kaolinite Surfaces using Molecular Dynamics
Not Available
PhenoProfiling: Mapping phenotypic outcomes to molecular determinants of biochemical activity
The aggregate genomes of the trillions of microorganisms within soil, animal hosts, and aquatic systems encode for an extensive functional capacity for myriad biochemical activities. C, N, P, and S metabolism, synthesis of signaling molecules and vitamins, mineralization, and other activities are essential to microbe, community, and plant physiology, and more broadly to climate, water, animal, flora, and human health. The current understanding of the molecular basis for the function of microbial communities stems primarily from comparative metagenomic and metatranscriptomic studies. These same tools are employed to ascertain the impacts to the community resulting from perturbations, such as climate change, emerging pollutants, fires, and seawater infiltration for environmental communities, and dietary changes, xenobiotic exposure, and various disease states for the human gut microbiome. Such studies can identify the potential for a specific function, but they cannot determine that a particular cell is functionally active, nor can they determine the molecular architecture required for function. In short, genes and transcripts alone fail to reveal the complex subcellular arrangement of proteins and molecules that elicit a given phenotype in a microbial cell.
Simplification of the purification of heat stable recombinant low molecular weight proteins and peptides from GST-fusion products
The synthesis and purification of peptides of importance in the fields of research and medicine continue to be a challenging task. Chemical synthesis of oligopeptides, especially those greater than 25 amino acids, is cost prohibitive. On the other hand, several bottlenecks exist in the production of recombinant short peptides in heterologous expression hosts such as Escherichia coli (E. coli). In this paper, a rapid, cost-effective, and reliable method for the production and singlestep-purification of peptides and small proteins was developed. Five peptides and small proteins were overexpressed in E. coli as GST-fusion products in high yields. The recombinant peptides or proteins were successfully purified after enzymatic cleavage with selective heat-induced precipitation of the GST-affinity tag. Qualitative and quantitative analysis using SDS-PAGE and mass spectrometric methods suggest that the recombinant peptides/ proteins were purified to >95% homogeneity. Results of biophysical experiments, including multi-dimensional NMR spectroscopy, show that the purified proteins/ peptides retain their native conformation. Isothermal titration calorimetry studies indicate no significant change in the binding affinity of the heattreated purified product to their interacting partner(s) compared to the recombinant peptides purified by conventional chromatographic procedures without subjecting to heat treatment. In our opinion, the results reported render the purification of recombinant proteins/ peptides of biomedical relevance using our proposed method easy and reliable.
Amphiphile Organization in Organic Solutions: An Alternative Explanation for Small-Angle X-ray Scattering Features in Malonamide/Alkane Mixtures
In this work, the role of different intermolecular interactions in the aggregation of amphiphiles in an organic solvent is studied for systems of relevance to liquid-liquid extraction (LLE), a chemical process used to selectively recover metals from complex mixtures. Of specific interest is the role, or lack thereof, of hydrogen bonding, which is often assumed to be a main driver of the organic phase structural organization that has been linked to separation efficacy. Toward that end, a series of malonamide extractants in n-dodecane have been studied in the absence of any extracted aqueous solutes, including water. The series of extractants includes N,N'-dimethyl-N,N'-dibutyltetradecylmalonamide (DMDBTDMA), two of its homologs, and N,N'-dimethyl-N,N'-dioctylhexylethoxymalonamide (DMDOHEMA). This simplified model LLE system enables systematic investigation of the role of dipole-dipole and alkyl tail steric interactions in amphiphile aggregation. Small-angle X-ray scattering (SAXS) profiles computed from molecular dynamics trajectories are in good agreement with experimental SAXS data. Molecular dynamics simulations show that malonamide aggregation results from dipole-driven self-association and lacks characteristic aggregate sizes. Mid-q correlation peaks in the SAXS profiles emerge at high concentration for each malonamide. In those densely packed solutions, the correlation peaks are observed to result from alkyl tail-induced spacing between electron-rich polar head groups, with peak positions determined by the different alkyl tail lengths present in the malonamide molecule. This explanation of the SAXS correlation peaks contrasts with the prevailing literature, which attributes mesoscale features observed in small-angle scattering to the formation of microemulsions. Instead, this work finds that these features are present in the absence of water or any reverse micellar organization of the malonamides. As such, molecular-scale malonamide self-association and packing, rather than microemulsion-based colloidal-scale descriptions, is a more appropriate framework for these LLE systems.
Perspective on Lewis Acid‐Base Interactions in Emerging Batteries
Lewis acid-base interactions are common in chemical processes presented in diverse applications, such as synthesis, catalysis, batteries, semiconductors, and solar cells. The Lewis acid-base interactions allow precise tuning of material properties from the molecular level to more aggregated and organized structures. This review will focus on the origin, development, and prospects of applying Lewis acid-base interactions for the materials design and mechanism understanding in the advancement of battery materials and chemistries. The covered topics relate to aqueous batteries, lithium-ion batteries, solid-state batteries, alkali metal-sulfur batteries, and alkali metal-oxygen batteries. In this review, the Lewis acid-base theories will be first introduced. Thereafter the application strategies for Lewis acid-base interactions in solid-state and liquid-based batteries will be introduced from the aspects of liquid electrolyte, solid polymer electrolyte, metal anodes, and high-capacity cathodes. The underlying mechanism is highlighted in regard to ion transport, electrochemical stability, mechanical property, reaction kinetics, dendrite growth, corrosion, and so on. Last but not least, perspectives on the future directions related to Lewis acid-base interactions for next-generation batteries are like to be shared.
Polyphenols Weaken Pea Protein Gel by Formation of Large Aggregates with Diminished Noncovalent Interactions
Polyphenols are well-known native cross-linkers and gel strengthening agents for many animal proteins. However, their role in modifying plant protein gels remains unclear. In this study, multiple techniques were applied to unravel the influence of green tea polyphenols (GTP) on pea protein gels and the underlying mechanisms. We found that the elasticity and viscosity of pea protein gels decreased with increased GTP. The protein backbone became less rigid when GTP was present based on shortened T 1ρ H in relaxation solid-state NMR measurements. Electron microscopy and small-angle X-ray scattering showed that gels weakened by GTP possessed disrupted networks with the presence of large protein aggregates. Solvent extraction and molecular dynamic simulation revealed a reduction in hydrophobic interactions and hydrogen bonds among proteins in gels containing GTP. The current findings may be applicable to other plant proteins for greater control of gel structures in the presence of polyphenols, expanding their utilization in food and biomedical applications.
Intramolecular Charge Transfer and Ultrafast Nonradiative Decay in DNA-Tethered Asymmetric Nitro- and Dimethylamino-Substituted Squaraines
Not Available
Bulk Anion Recognition Kinetically Holds Back Interfacial Adsorption
The competition between bulk and interfacial phenomena underlies many key processes in complex chemical phenomena and transport. While competitive processes are often framed in a thermodynamic context, opportunities to leverage transient species found away from equilibrium can provide a kinetic handle to achieve unconventional reaction outcomes. In this work, we outfit an iminoguanidinium headgroup capable of selective SO 4 2– complexation with alkyl tails of varying complexity to probe competitive bulk and interfacial reaction pathways and tune kinetic pathways for selective chemical separations. Using sum frequency generation (SFG) vibrational spectroscopy we unexpectedly find that adsorption of ligands to the air–aqueous interface was dramatically slowed down for species with increasingly hydrophobic tails. Underlying this phenomenon, we show that the formation of bulk colloidal species with differing propensities for SO 4 2– inhibited surface adsorption via a kinetic bottleneck in the exchange of molecular extractants with colloidal aggregates. This kinetic effect could open up avenues to access unconventional selectivity via complexation of strongly coordinating species in the bulk phase, allowing for more weakly coordinating species to transport via interfacial mechanisms. Furthermore, this work broadly probes nonequilibrium phenomena in chemical separations that arise through unexpected interfacial events that are neglected in traditional equilibrium descriptions.
Amphiphile conformation impacts aggregate morphology and solution structure across multiple lengthscales
Although the self-assembly of amphiphiles is well-studied in aqueous solutions, much less is understood about the fundamental driving forces and structure property relationships in non-polar media. In recent work [Journal of Physical Chemistry B, 2020, 124, 10822.] the authors have studied a series of malonomide-based amphiphiles that are relevant to liquid-liquid extraction. That work demonstrated that aggregation is largely driven by local dipole-dipole interactions between molecules. Here, we build upon this observation to develop a more detailed understanding of how the balance of dipole-dipole interactions (controlled by conformation) and molecular architecture influences the morphology of the aggregates across lengthscales. Using constrained molecular dynamics about key degrees of freedom, we demonstrate that the conformation of N,N-dimethyl,N,N-dioctylhexylethoxy malonamide (DMDOHEMA) and N,N-dimethyl,N,N-dibutyltetradecyl malonamide (DMDBTDMA) has a significant impact upon self-association - where appropriate conformational sampling is essential. To quantify the aggregate morphology, several graph theoretic and persistent homology based properties are determined. The former examines the patterns of intermolecular interactions within clusters, while the latter examines the 3-dimensional spatial distribution. Based upon these analyses, we find that the morphology of aggregates, particularly at higher malonamide concentration, depends on a balance of dipole alignment and alkyl tail sterics. Dipole alignment encourages linear patterns of the intermolecular interactions within aggregates, while the alkyl tail steric interactions between the malonamide result in noticeably less linear aggregates for DMDOHEMA than DMDBTDMA. This is reflected in the spatial distribution, where more holes or voids exist between extractants within the DMDOHEMA that distribute within the solution in more of a "swiss cheese" arrangement as opposed to the more filamentous distribution of DMBDTDMA. This study links conformation and molecular structure to the morphology of amphiphile assemblies, and serves as a basis for ongoing study of multicomponent amphiphile solutions with polar and other solutes, and how these impact aggregation phenomena.
Fluorinated polythiophenes with ester side chains for boosting the V OC and efficiency in non-fullerene polymer solar cells
As the power conversion efficiency (PCE) of organic photovoltaics (OPVs) approximates the 19 % threshold, wide bandgap (WBG) polythiophenes (PTs) have gained increasing attention due to their simple chemical structures and ease of synthesis, making them promising candidates for large-scale production. However, the benchmark polymer poly(3-hexylthiophene) (P3HT) is limited by its high-lying HOMO energy level, which restricts the open-circuit voltage (V OC ) in solar cells. Here, in this study, we introduce a novel series of PT derivatives (PDC8-T, PDC8-3T, PDC16-3T, and PDC16-3T-2F) featuring ester side chains designed to fine-tune electronic properties through a streamlined three-step synthesis. Additionally, we incorporated a π-spacer to reduce steric hindrance and elongated alkyl side chains to improve solubility and processability. Compared to P3HT, these PT derivatives demonstrate a significant reduction in HOMO energy levels, lowering by approximately 0.3–0.4 eV. Among them, PDC16-3T-2F—with fluorine atom substitution—achieves the lowest HOMO energy level, induces a coplanar molecular conformation, and enhances polymer aggregation behavior. We evaluated these PT derivatives in inverted non-fullerene bulk-heterojunction (NFA BHJ) OPVs. The PDC8-3T device showed a relatively low PCE of 0.69 %, with a V OC of 0.76 V, a short-circuit current density (J SC ) of 3.32 mA/cm 2 , and a fill factor (FF) of 27.3 %. In contrast, the PDC16-3T-2F device achieved an impressive PCE of 7.21 %, with a V OC of 0.85 V, a J SC of 14.60 mA/cm 2 , and an FF of 58.4 %. This remarkable improvement is attributed to the fluorine substitution, which not only enhances molecular orientation but also downshifts the HOMO energy level and further boosts the V OC . Hence, these molecular design strategies have led to a fibrillar bicontinuous interpenetrating network with optimal nanoscale phase separation within the active layer.
Superoxide Dismutase 1 Folding Stability as a Target for Molecular Tweezers in SOD1-Related Amyotrophic Lateral Sclerosis
Protein misfolding and aggregation are hallmarks of many severe neurodegenerative diseases including Alzheimer's, Parkinson's and Huntington's disease. As a supramolecular ligand that binds to lysine and arginine residues, the molecular tweezer CLR01 was found to modify the aggregation pathway of disease-relevant proteins in vitro and in vivo with beneficial effects on toxicity. However, the molecular mechanisms of how tweezers exert these effects remain mainly unknown, hampering further drug development. Here, we investigate the modulation mechanism of unfolding and aggregation pathways of SOD1, which are involved in amyotrophic lateral sclerosis (ALS), by CLR01. Using a truncated version of the wildtype SOD1 protein, SOD1 bar , we show that CLR01 acts on the first step of the aggregation pathway, the unfolding of the SOD1 monomer. CLR01 increases, by ~10 °C, the melting temperatures of the A4V and G41D SOD1 mutants, which are commonly observed mutations in familial ALS. Molecular dynamics simulations and binding free energy calculations as well as native mass spectrometry and mutational studies allowed us to identify K61 and K92 as binding sites for the tweezers to mediate the stability increase. The data suggest that the modulation of SOD1 conformational stability is a promising target for future developments of supramolecular ligands against neurodegenerative diseases.
Magnesium ions mitigate metastable states in the regulatory landscape of mRNA elements
Residing in the 5' untranslated region of the mRNA, the 2'-deoxyguanosine (2'-dG) riboswitch mRNA element adopts an alternative structure upon binding of the 2'-dG molecule, which terminates transcription. RNA conformations are generally strongly affected by positively charged metal ions (especially Mg 2+ ). We have quantitatively explored the combined effect of ligand (2'-dG) and Mg 2+ binding on the energy landscape of the aptamer domain of the 2'-dG riboswitch with both explicit solvent all-atom molecular dynamics simulations (99 μsec aggregate sampling for the study) and selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) experiments. We show that both ligand and Mg 2+ are required for the stabilization of the aptamer domain; however, the two factors act with different modalities. The addition of Mg 2+ remodels the energy landscape and reduces its frustration by the formation of additional contacts. In contrast, the binding of 2'-dG eliminates the metastable states by nucleating a compact core for the aptamer domain. Mg 2+ ions and ligand binding are required to stabilize the least stable helix, P1 (which needs to unfold to activate the transcription platform), and the riboswitch core formed by the backbone of the P2 and P3 helices. Mg 2+ and ligand also facilitate a more compact structure in the three-way junction region.
Molecular dynamics studies of lattice defect effects on tritium diffusion in zirconium
Tritium diffusion in α-Zr containing point defects such as vacancies or self-interstitial atoms (SIAs) is simulated using molecular dynamics. Point defects rapidly aggregate to form extended defects, such as 3D nanoclusters and Frank loops. The geometry of extended defects is affected by the presence of tritium. At low temperature and in the absence of tritium, vacancies aggregate to form stacking fault pyramids. Addition of tritium at these temperatures promotes aggregation of vacancies to form 3D nanoclusters, within which the tritium concentration can be sufficiently high to suggest that these defects may serve as nucleation sites for hydride precipitation. Trapping of tritium in vacancy nanocluster reduces the calculated bulk diffusivity by an amount proportional to the vacancy concentration. At high temperature, vacancy clusters change shape to form planar basal dislocation loops, which bind tritium less strongly, leading to a sharp reduction in the fraction of trapped tritium and a corresponding increase in tritium diffusivity at high temperature. In contrast, SIAs increase tritium diffusion through α-Zr. Analysis of atomic trajectories shows that tritium does not interact directly with SIAs. In conclusion, diffusion enhancement is instead related to expansion of the lattice.
Superionic conduction in solid polymer electrolytes – decoupling ion transport from segmental relaxation
Solvent-free, solid polymer electrolytes (SPEs) are promising candidates for next-generation, electrochemical energy storage systems due to their potential to enhance safety and performance, enable flexible device architectures, and streamline manufacturing processes. Conventional SPEs suffer from limited ionic conductivity due to the strong coupling between ion transport and (generally slow) polymer segmental relaxation. The realization of superionic conduction in SPEs, in which ions move faster than the structural relaxation of the polymers, requires a shift in design principles to promote this type of decoupled ion motion. In this perspective, we discuss how polymer architecture, ion–ion correlations, and ion–polymer interactions can unlock superionic behavior. We highlight several key design features, such as crystallinity, bulky side groups, high molecular weight, and percolating ionic aggregation, with a focus on creating low-barrier transport pathways in various polymer systems. We also demonstrate opportunities to combine polymer chemistry and data science through high-throughput and automated screening approaches to reveal how phase behavior, ion dynamics, and ionic interactions govern transport, thereby potentially enabling data-driven discovery of superionic polymer electrolyte materials.