Coverage-dependent adsorption of small gas molecules on black phosphorene: a DFT study
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Chemistry↗
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Phase segregation mechanisms of small molecule-polymer blends unraveled by varying polymer chain architecture
As phase separation between the small-molecule semiconductor and the polymer binder is the key enabler of blend-based organic field-effect transistors (OFETs) fabricated by low-cost solution processing, it is crucial to understand the underlying phase separation mechanisms that determine the phase morphology, which significantly impacts device performance. Beyond the parameter space investigated in previous work, here we investigate the formation of blends by varying the branch architecture of the polymer binder and by shortening the solvent dry time using ultrasonic spray casting. The phase morphologies of the resulting blend films have been thoroughly characterized with a variety of techniques in three dimensions over multiple length scales, including AFM, energy-filtered transmission electron microscope, and neutron reflectivity, and have been correlated with electrical transport performance. From the results, we have inferred that the phase morphology is kinetically determined, limited by the inherent slow movement of polymer macromolecules. The kinetic picture, supported by molecular dynamics modeling, not only consistently explains our observations but also resolves inconsistencies in previous works. The achieved mechanistic understanding will guide further optimization of blend-based organic electronics, such as OFETs and organic photovoltaics.
36 MATERIALS SCIENCE↗
Quantifying Membrane Structure and Dynamics during Bioproduct Production in Zymomonas mobilis by Molecular Simulation
The conversion of lignocellulosic biomass into biofuels and bioproducts by microbial biorefineries is central to a sustainable chemical industry. Zymomonas mobilis is one such biorefinery chassis and is resistant to ethanol stress, leading to its use in biomass conversion to biofuels and bioproducts. However, Z. mobilis growth is often inhibited by organic acids, aldehydes, alcohols, ketones, and amides found in biomass hydrolysate. The resulting slow growth inhibits production and as a result drives up the price for the resulting products. One hypothesis is that these molecules interact with or disrupt the bacterial membrane, triggering stress responses and hindering growth. To test this hypothesis at the molecular level, we employ all-atom molecular dynamics (MD) simulations to investigate lignocellulose-derived small molecules and their impact on a biologically relevant Z. mobilis membrane model. Simulations were conducted across a range of inhibitor concentrations from 0 to 2.5 mol %, analyzing key membrane properties such as area per lipid (APL), membrane thickness, lipid-order parameter (−S CH ), lateral diffusion coefficient (D xy ), and permeability coefficient (Pm). From simulation, we observed altered membrane structure and dynamics at these modest small molecule concentrations commonly found in hydrolysates. Generally, the membranes become thinner, with a higher area per lipid and lower-order parameter as the small molecule concentration increases. These trends are stronger for more hydrophobic molecules with greater hydrophobic bulk, as isobutanol, propanol, and propanoic acid showed greater membrane perturbations as the concentration increased compared to other small molecules. Tracking small molecule distributions directly in our equilibrium simulations allows us to determine concentration-dependent free energy profiles for these molecules. While the trends are noisy, generally the barriers to crossing the membrane decrease as the concentration increases, indicating that the membranes become leakier as small molecule concentrations rise. Comparing between native Z. mobilis membranes with hopanoids and membranes sharing the same phospholipid composition but without hopanoids, hopanoids stabilize and order the membrane for smaller molecules to maintain membrane structure but appear insufficient for larger hydrophobic molecules like isobutanol. These findings provide a mechanistic understanding of how small molecules found in biomass degradation streams interact with the Z. mobilis membrane, offering valuable insights for future strain engineering efforts to optimize biofuel and bioproduct synthesis from biomass feedstocks by highlighting limits to small molecule tolerance. This knowledge can guide the modification of membrane composition to develop more robust microbes, thereby improving microbial survival and yields in industrial contexts.
Singh, Nitin Kumar [Michigan State Univ., East Lan↗
Spectroscopic and Dynamical Studies of Highly Energized Small Polyatomic Molecules (End-of-Grant Report)
The aim of this research program has been to develop models for qualitative and quantitative understanding of complex processes in small molecules, such as vibronic coupling, predissociation, photodissociation, and isomerization. Simple models capture physical insights and lead to intuitive ideas that can enlighten a broad array of problems. Numerical fits can provide predictive power, but rarely impart insights into the underlying mechanisms responsible for the observed phenomena. This DOE supported program has prioritized a quantum mechanical understanding over a perfect numerical fit of spectra. Finding few-parameter models, when those parameters have physical meaning, allows the insights gained from one problem to be easily applied to related problems in other systems. The systems that have been under investigation include atmospherically relevant sulfur-containing compounds, various unimolecular dynamical processes of electronically excited acetylene, and the rovibrational dynamics of formaldehyde and SO 2 .
74 ATOMIC AND MOLECULAR PHYSICS↗
Probing Molecular Assembly of Small Organic Molecules during Meniscus-Guided Coating Using Experimental and Molecular Dynamics Approaches
Evaporation-based thin-film coating processes are ubiquitous in fields such as organic electronics, dye coatings, and the pharmaceutical industry. Based on experimental observations of enhanced thin-film alignment during meniscus-guided coating (MGC), a molecular dynamics simulation was developed to describe the thin-film formation that occurs due to the interplay between evaporation and fluid dynamics. The process of solvent evaporation from solution is first examined, which leads to the formation of a solid thin film after evaporation is complete. Next, an MGC process was simulated by introducing a flow profile coupled with the evaporative system. In this work, we gain insights into how molecules respond and reorient in the presence of a flow profile. These results indicate that both the evaporation and the flow profile have an impact on orienting small molecules in a thin film during the MCG process. Combining experimental techniques with simulations helps enhance the understanding of the forces that are significant in directing molecular aggregation during coating processes.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Catalytic Upcycling of Polyolefins
The large production volumes of commodity polyolefins (specifically, polyethylene, polypropylene, polystyrene, and poly(vinyl chloride)), in conjunction with their low unit values and multitude of short-term uses, have resulted in a significant and pressing waste management challenge. Only a small fraction of these polyolefins is currently mechanically recycled, with the rest being incinerated, accumulating in landfills, or leaking into the natural environment. Since polyolefins are energy-rich materials, there is considerable interest in recouping some of their chemical value while simultaneously motivating more responsible end-of-life management. An emerging strategy is catalytic depolymerization, in which a portion of the C–C bonds in the polyolefin backbone is broken with the assistance of a catalyst and, in some cases, additional small molecule reagents. When the products are small molecules or materials with higher value in their own right, or as chemical feedstocks, the process is called upcycling. This review summarizes recent progress for four major catalytic upcycling strategies: hydrogenolysis, (hydro)cracking, tandem processes involving metathesis, and selective oxidation. Key considerations include macromolecular reaction mechanisms relative to small molecule mechanisms, catalyst design for macromolecular transformations, and the effect of process conditions on product selectivity. Metrics for describing polyolefin upcycling are critically evaluated, and an outlook for future advances is described.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
How KRAS Mutations Impair Intrinsic GTP Hydrolysis: Experimental and Computational Investigations
Oncogenic KRAS mutations impair GTP hydrolysis and increase the active GTP-bound KRAS population, which leads to growth-factor-independent cell proliferation and survival of cancer cells. Despite notable successes of small-molecule inhibitors in the treatment of KRASG12C cancer, many of these small-molecule inhibitors preferentially bind to inactive (GDP-bound) mutant KRAS, whose availability is limited by the slow rate of intrinsic GTP hydrolysis. A better understanding of how KRAS mutations impair intrinsic hydrolysis is important for designing more effective small-molecule therapeutics. In this work, experimental and computational approaches were utilized to investigate how the most important oncogenic mutations affect the intrinsic hydrolysis of GTP. Here, we found that Q61H, G12V, and G12R mutations impair intrinsic hydrolysis by around 7-fold, 9-fold, and more than 20-fold, respectively, whereas G12A, G12C, G12D, and G13D have less effect. Based on mechanistic investigations, we propose that KRAS mutations impair intrinsic hydrolysis by disrupting the interactions needed to align the nucleophilic water molecule with GTP for nucleophilic attack. These results can assist small-molecule inhibitor design and also benefit the development of other therapeutic strategies, such as rescuing hydrolysis.
Ab Initio↗
A small heterocyclic molecule as a multistate transistor: a quantum many-body approach
Weakly coupled molecular junctions are an active and important field of research due to their non-linear charge carrier transport. In this study, we investigate transport properties in a weakly coupled molecule, B 2 C 2 N 2 H 6 , using a combined quantum many-body approach and kinetic (master) equations. Various non-linear current–voltage characteristics such as negative differential conductance (NDC), rectifications, and Coulomb staircase, which are the hallmarks of multistate transport devices, have been obtained. We further explore the effect of different perturbations such as gate voltage and perpendicular magnetic field on molecular transport. Depending on the strength of the applied perturbing field, several phenomena such as current switching, and suppression of NDC, have been realized in the device. This study demonstrates small molecules as promising components in next-generation nano-devices.
36 MATERIALS SCIENCE↗
Molecular Vision - Multimodal, multitask retrieval of molecular structure from measured signatures for reference-free compound identification
We are currently at risk of generating false conclusions based on limited methods to identify small molecules in biological systems and in chemical forensics. By definition, the chemical structures of novel small molecules have not been determined, let alone measured or synthesized. Currently, unambiguous structure determination of small molecules is constrained by the time and effort needed to isolate compounds and perform de novo structure elucidation using laboratory-based methods, significantly extending the time to inform mitigation strategies. To address this gap, we have developed a deep learning approach to directly map molecular structure to experimental signatures. We aim to unify measurement technologies employed in untargeted small molecule identification studies—such as infrared (IR) spectrometry, tandem mass spectrometry (MS/MS), ion mobility spectrometry-derived collision cross section (CCS)—through use of a multimodal, multitask deep learning architecture. Where existing methods require direct generation of information-rich spectra and/or properties, an inherently difficult task, we will simplify molecular signature-based identification by posing the problem as a recognition or retrieval task. The model is thus presented with relevant endpoints – structure and one or more molecular signatures – and need only determine whether they are semantically related. Thus, our approach offers the following advantages over existing techniques: (i) circumvents difficulties associated with direct generation of molecular signatures from structure and structure from signatures; (ii) incorporates multiple molecular signatures simultaneously, as available, to support identification; and (iii) enables rapid computation of structural embeddings toward broad coverage of known chemical space. Taken together, the approach removes the need to explicitly obtain or compute reference spectra, representing a powerful method for compound identification that requires only experimentally observed signatures.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Precise synthesis and photovoltaic properties of giant molecule acceptors
Series of giant molecule acceptors DY, TY and QY with two, three and four small molecule acceptor subunits are synthesized by a stepwise synthetic method and used for systematically investigating the influence of subunit numbers on the structure-property relationship from small molecule acceptor YDT to giant molecule acceptors and to polymerized small molecule acceptor PY-IT. Among these acceptors-based devices, the TY-based film shows proper donor/acceptor phase separation, higher charge transfer state yield and longer charge transfer state lifetime. Combining with the highest electron mobility, more efficient exciton dissociation and lower charge carrier recombination properties, the TY-based device exhibits the highest power conversion efficiency of 16.32%. These results indicate that the subunit number in these acceptors has significant influence on their photovoltaic properties. This stepwise synthetic method of giant molecule acceptors will be beneficial to diversify their structures and promote their applications in high-efficiency and stable organic solar cells.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
De novo design of a homo-trimeric amantadine-binding protein
The computational design of a symmetric protein homo-oligomer that binds a symmetry-matched small molecule larger than a metal ion has not yet been achieved. We used de novo protein design to create a homo-trimeric protein that binds the C 3 symmetric small molecule drug amantadine with each protein monomer making identical interactions with each face of the small molecule. Solution NMR data show that the protein has regular three-fold symmetry and undergoes localized structural changes upon ligand binding. A high-resolution X-ray structure reveals a close overall match to the design model with the exception of water molecules in the amantadine binding site not included in the Rosetta design calculations, and a neutron structure provides experimental validation of the computationally designed hydrogen-bond networks. Exploration of approaches to generate a small molecule inducible homo-trimerization system based on the design highlight challenges that must be overcome to computationally design such systems.
59 BASIC BIOLOGICAL SCIENCES↗
Anomalous Self-Optimizing Microporous Graphene-Based Lithium-ion Battery Anode from Laser Activation
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Zhang, Binghao↗
Design of Diverse Asymmetric Pockets in De Novo Homo-oligomeric Proteins
A challenge for design of protein–small-molecule recognition is that incorporation of cavities with size, shape, and composition suitable for specific recognition can considerably destabilize protein monomers. This challenge can be overcome through binding pockets formed at homo-oligomeric interfaces between folded monomers. Interfaces surrounding the central homo-oligomer symmetry axes necessarily have the same symmetry and so may not be well suited to binding asymmetric molecules. To enable general recognition of arbitrary asymmetric substrates and small molecules, we developed an approach to designing asymmetric interfaces at off-axis sites on homo-oligomers, analogous to those found in native homo-oligomeric proteins such as glutamine synthetase. We symmetrically dock curved helical repeat proteins such that they form pockets at the asymmetric interface of the oligomer with sizes ranging from several angstroms, appropriate for binding a single ion, to up to more than 20 Å across. Of the 133 proteins tested, 84 had soluble expression in E. coli, 47 had correct oligomeric states in solution, 35 had small-angle X-ray scattering (SAXS) data largely consistent with design models, and 8 had negative-stain electron microscopy (nsEM) 2D class averages showing the structures coming together as designed. Both an X-ray crystal structure and a cryogenic electron microscopy (cryoEM) structure are close to the computational design models. The nature of these proteins as homo-oligomers allows them to be readily built into higher-order structures such as nanocages, and the asymmetric pockets of these structures open rich possibilities for small-molecule binder design free from the constraints associated with monomer destabilization.
59 BASIC BIOLOGICAL SCIENCES↗
Microbe-iron interactions control lignin decomposition in soil
Lignin decomposition is critically linked to terrestrial carbon (C) cycle due to the enormous C mass of lignin and its importance in controlling overall rates of litter decomposition. Interactions between lignin and iron (Fe) minerals have been increasingly recognized as key mediators of lignin decomposition in experimental studies. However, we still lack a quantitative understanding of how Fe minerals interact with microbes to control lignin decomposition. Here, we leveraged experimental results from an incubation of Fe-rich soil, in which lignin decomposition rates were measured at aerobic conditions after four levels of pre-treated O2 availability, to examine microbe-Fe (MiFe) interactions in lignin decomposition with a MiFe model. We quantified how Fe redox cycling interacted with microbial activities to control lignin decomposition via data-model integration. Our results showed that the MiFe model with time-dependent growth and mortality functions better represented CO2 release from lignin decomposition (R2 ranging from 0.96 to 0.97) than models assuming either first-order or Michaelis-Menten kinetics. Reduction of Fe(III) to Fe(II) after pre-treatments with lower O2 availability stimu-lated the Fenton reaction to break down macro-molecular lignin into small molecules available to microbes. The small molecules of lignin and necromass bounded with oxidized Fe and were protected from decomposition. After 1-year incubation, the model implied that most of C stabilized with Fe minerals was derived from small molecular lignin C. Our quantitative analysis of microbe-Fe interactions sheds new light on lignin decomposition and preservation and helps improve model prediction of soil C persistence under global change.
Liao, Cuijuan↗
CFM-ID 4.0 – a web server for accurate MS-based metabolite identification
The CFM-ID 4.0 web server (https://cfmid.wishartlab.com) is an online tool for predicting, annotating and interpreting tandem mass (MS/MS) spectra of small molecules. It is specifically designed to assist researchers pursuing studies in metabolomics, exposomics and analytical chemistry. More specifically, CFM-ID 4.0 supports the: 1) prediction of electrospray ionization quadrupole time-of-flight tandem mass spectra (ESI-QTOF-MS/MS) for small molecules over multiple collision energies (10 eV, 20 eV, and 40 eV); 2) annotation of ESI-QTOF-MS/MS spectra given the structure of the compound; and 3) identification of a small molecule that generated a given ESI-QTOF-MS/MS spectrum at one or more collision energies. The CFM-ID 4.0 web server makes use of a substantially improved MS fragmentation algorithm, a much larger database of experimental and in silico predicted MS/MS spectra and improved scoring methods to offer more accurate MS/MS spectral prediction and MS/MS-based compound identification. Compared to earlier versions of CFM-ID, this new version has an MS/MS spectral prediction performance that is ~22% better and a compound identification accuracy that is ~35% better on a standard (CASMI 2016) testing dataset. CFM-ID 4.0 also features a neutral loss function that allows users to identify similar or substituent compounds where no match can be found using CFM-ID’s regular MS/MS-to-compound identification utility. Finally, the CFM-ID 4.0 web server now offers a much more refined user interface that is easier to use, supports molecular formula identification (from MS/MS data), provides more interactively viewable data (including proposed fragment ion structures) and displays MS mirror plots for comparing predicted with observed MS/MS spectra. These improvements should make CFM-ID 4.0 much more useful to the community and should make small molecule identification much easier, faster, and more accurate.
59 BASIC BIOLOGICAL SCIENCES↗
Efficient and mechanically-robust organic solar cells based on vertical stratification modulation through sequential blade-coating
Mechanically durable organic solar cells (OSCs) with high efficiency are deemed as the ideal candidate for the power source of the next generation wearable electronic devices. However, the brittle nature of small molecules in most high-efficiency OSCs consisting of polymer and small molecule encourages easy formation of cracks in the photoactive film under deformation. Here, the vertical composition distribution of the active layer has been well optimized through sequential blade coating to realize highly deformable while efficient OSC. The optimized morphology exhibits distinct donor-rich and homogenous region distributed along the vertical direction in the bulk. The donor-rich region provides sufficient chain entanglements and strong interfaces beneficial for mechanical robustness of film, while homogeneously mixed region offers continuous interpenetrating network to maintain high device through-put, resulting in superior efficiency of 14.4% with high crack-onset strain (COS) of 30.5%. This efficiency versus COS combination is much higher than the best combination reported in all polymer systems (COS of 15.9% and efficiency of 11.1%). To the best of our knowledge, it is the highest COS value achieved in polymer-small molecule systems. As a result, the rational control over vertical stratification demonstrated here would guide researchers in the development of innovative wearable electronics.
36 MATERIALS SCIENCE↗
Clathrate hydrates in the solar system
Clathrate hydrates are crystalline compounds in which an expanded ice lattice forms cages that contain gas molecules. There are two principal hydrate structures. Structure I, with a 12 A cubic unit cell, contains 46 water molecules and 8 cages of two types, giving an ideal formula (for CH4) of CH4.5.75H2O. The actual formula contains somewhat more water as the cages are not completely filled. Other examples that form Structure I hydrates are C2H6, C2H4, C2H2, CO2, SO2, OCS, Xe, H2S. Structure II, with a 17 A cubic unit cell, contains 136 water molecules, and 8 large and 16 small cages. The ideal formula for CHCl3 is CHCL3.17H2O. Other examples of Structure II hydrates include C3H8, C2H5Cl, acetone, and tetrahydrofuran. Small molecules such as Ar, Kr and probably N2 and O2 also form a Structure II hydrate. The small molecules occupy both the large and small cages, giving an ideal formula of Ar.5.67H2O. The conditions of pressure and temperature for hydrate formation are discussed.
Miller, S. L.↗
QM7-X, a comprehensive dataset of quantum-mechanical properties spanning the chemical space of small organic molecules
We introduce QM7-X, a comprehensive dataset of 42 physicochemical properties for ≈4.2 million equilibrium and non-equilibrium structures of small organic molecules with up to seven non-hydrogen (C, N, O, S, Cl) atoms. To span this fundamentally important region of chemical compound space (CCS), QM7-X includes an exhaustive sampling of (meta-)stable equilibrium structures—comprised of constitutional/structural isomers and stereoisomers, e.g., enantiomers and diastereomers (including cis-/trans- and conformational isomers)—as well as 100 non-equilibrium structural variations thereof to reach a total of ≈4.2 million molecular structures. Computed at the tightly converged quantum-mechanical PBE0+MBD level of theory, QM7-X contains global (molecular) and local (atom-in-a-molecule) properties ranging from ground state quantities (such as atomization energies and dipole moments) to response quantities (such as polarizability tensors and dispersion coefficients). By providing a systematic, extensive, and tightly-converged dataset of quantum-mechanically computed physicochemical properties, we expect that QM7-X will play a critical role in the development of next-generation machine-learning based models for exploring greater swaths of CCS and performing in silico design of molecules with targeted properties.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗