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1. Ab Initio Simulations of Poorly- and Well-Equilibrated (CH3CN)n¯ Cluster Anions: Assigning Experimental Photoelectron Peaks to Surface-Bound Electrons and Solvated Monomer and Dimer Anions

   https://doi.org/10.1021/acs.jpca.1c05855  

   Narvaez, W. A.; Schwartz, B. J. (January 2021, The journal of physical chemistry)

   Excess electrons in liquid acetonitrile are of particular interest because they exist in two different forms in equilibrium: they can be present as traditional solvated electrons in a cavity, and they can form some type of solvated molecular anion. Studies of small acetonitrile cluster anions in the gas phase show two isomers with distinct vertical detachment energies, and it is tempting to presume that the two gas-phase cluster anion isomers are precursors of the two excess electron species present in bulk solution. In this paper, we perform DFT-based ab initio molecular dynamics simulations of acetonitrile cluster anions to understand the electronic species that are present and why they have different binding energies. Using a long-range-corrected density functional that was optimally tuned to describe acetonitrile cluster anion structures, we have theoretically explored the chemistry of (CH3CN)n¯ cluster anions with sizes n=5,7 and 10. Since the temperature of the experimental cluster anions is not known, we performed two sets of simulations that investigated how the way in which the cluster anions are prepared affects the excess electron binding motif: one set of simulations simply attached excess electrons to neutral (CH3CN)n clusters, providing little opportunity for the clusters to relax in the presence of the excess electron, while the other set allowed the cluster anions to thermally equilibrate near room temperature. We find that both sets of simulations show three distinct electron binding motifs: electrons can attach to the surface of the cluster (dipole-bound) or be present as either solvated monomer anions, CH3CN¯, or as solvated molecular dimer anions, (CH3CN)2¯. All three species have higher binding energies at larger cluster sizes. Thermal equilibration strongly favors the formation of the valence-bound molecular anions relative to surface-bound excess electrons, and the dimer anion becomes more stable than the monomer anion and surface-bound species as the cluster size increases. The calculated photoelectron spectra from our simulations in which there was poor thermal equilibration are in good agreement with experiment, suggesting assignment of the two experimental cluster anion isomers as the surface-bound electron and the solvated molecular dimer anion. The simulations also suggest that the shoulder seen experimentally on the low-energy isomer's detachment peak is not part of a vibronic progression but instead results from molecular monomer anions. Nowhere in the size range that we explore do we see evidence for a non-valence, cavity-bound interior-solvated electron, indicating that this species is likely only accessible at larger sizes with good thermal equilibration. 

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2. Modeling molecular ensembles with gradient-domain machine learning force fields

   https://doi.org/10.1039/d3dd00011g  

   Maldonado, Alex M; Poltavsky, Igor; Vassilev-Galindo, Valentin; Tkatchenko, Alexandre; Keith, John A (June 2023, Digital Discovery)

   Gradient-domain machine learning (GDML) force fields have shown excellent accuracy, data efficiency, and applicability for molecules with hundreds of atoms, but the employed global descriptor limits transferability to ensembles of molecules. Many-body expansions (MBEs) should provide a rigorous procedure for size-transferable GDML by training models on fundamental n-body interactions. We developed many-body GDML (mbGDML) force fields for water, acetonitrile, and methanol by training 1-, 2-, and 3-body models on only 1000 MP2/def2-TZVP calculations each. Our mbGDML force field includes intramolecular flexibility and intermolecular interactions, providing that the reference data adequately describe these effects. Energy and force predictions of clusters containing up to 20 molecules are within 0.38 kcal/mol per monomer and 0.06 kcal/(mol Å) per atom of reference supersystem calculations. This deviation partially arises from the restriction of the mbGDML model to 3-body interactions. GAP and SchNet in this MBE framework achieved similar accuracies but occasionally had abnormally high errors up to 17 kcal/mol. NequIP trained on total energies and forces of trimers experienced much larger energy errors (at least 15 kcal/mol) as the number of monomers increased—demonstrating the effectiveness of size transferability with MBEs. Given these approximations, our automated mbGDML training schemes also resulted in fair agreement with reference radial distribution functions (RDFs) of bulk solvents. These results highlight mbGDML as valuable for modeling explicitly solvated systems with quantum-mechanical accuracy. 

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3. Protein sensing using deep subwavelength-engineered photonic crystals

   https://doi.org/10.1364/OL.510541  

   Zhang, Yanrong; Whittington, Christopher_S; Layouni, Rabeb; Cotto, Andres_M; Arnold, Kellen_P; Halimi, Sami_I; Weiss, Sharon_M (January 2024, Optics Letters)

   We demonstrate a higher sensitivity detection of proteins in a photonic crystal platform by including a deep subwavelength feature in the unit cell that locally increases the energy density of light. Through both simulations and experiments, the sensing capability of a deep subwavelength-engineered silicon antislot photonic crystal nanobeam (PhCNB) cavity is compared to that of a traditional PhCNB cavity. The redistribution and local enhancement of the energy density by the 50 nm antislot enable stronger light–molecule interaction at the surface of the antislot and lead to a larger resonance shift upon protein binding. This surface-based energy enhancement is confirmed by experiments demonstrating a nearly 50% larger resonance shift upon attachment of streptavidin molecules to biotin-functionalized antislot PhCNB cavities. 

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4. The effects of methanol clustering on methanol–water nucleation

   https://doi.org/10.1063/5.0120876  

   Sun, Tong; Wilemski, Gerald; Hale, Barbara N.; Wyslouzil, Barbara E. (November 2022, The Journal of Chemical Physics)

   The formation of subcritical methanol clusters in the vapor phase is known to complicate the analysis of nucleation measurements. Here, we investigate how this process affects the onset of binary nucleation as dilute water–methanol mixtures in nitrogen carrier gas expand in a supersonic nozzle. These are the first reported data for water–methanol nucleation in an expansion device. We start by extending an older monomer–dimer–tetramer equilibrium model to include larger clusters, relying on Helmholtz free energy differences derived from Monte Carlo simulations. The model is validated against the pressure/temperature measurements of Laksmono et al. [Phys. Chem. Chem. Phys. 13, 5855 (2011)] for dilute methanol–nitrogen mixtures expanding in a supersonic flow prior to the appearance of liquid droplets. These data are well fit when the maximum cluster size imax is 6–12. The extended equilibrium model is then used to analyze the current data. On the addition of small amounts of water, heat release prior to particle formation is essentially unchanged from that for pure methanol, but liquid formation proceeds at much higher temperatures. Once water comprises more than ∼24 mol % of the condensable vapor, droplet formation begins at temperatures too high for heat release from subcritical cluster formation to perturb the flow. Comparing the experimental results to binary nucleation theory is challenged by the need to extrapolate data to the subcooled region and by the inapplicability of explicit cluster models that require a minimum of 12 molecules in the critical cluster. 

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5. Textile Functionalization by Porous Protein Crystal Conjugation and Guest Molecule Loading

   https://doi.org/10.3390/cryst13020352  

   Hartje, Luke F; Andales, David A; Gintner, Lucas P; Johnson, Lucas B; Li, Yan V; Snow, Christopher D (February 2023, Crystals)

   Protein crystals are versatile nanostructured materials that can be readily engineered for applications in nanomedicine and nanobiotechnology. Despite their versatility, the small size of typical individual protein crystals (less than one cubic mm) presents challenges for macroscale applications. One way to overcome this limitation is by immobilizing protein crystals onto larger substrates. Cotton is composed primarily of cellulose, the most common natural fiber in the world, and is routinely used in numerous material applications including textiles, explosives, paper, and bookbinding. Here, two types of protein crystals were conjugated to the cellulosic substrate of cotton fabric using a 1,1′-carbonyldiimidazole/aldehyde mediated coupling protocol. The efficacy of this attachment was assessed via accelerated laundering and quantified by fluorescence imaging. The ability to load guest molecules of varying sizes into the scaffold structure of the conjugated protein crystals was also assessed. This work demonstrates the potential to create multifunctional textiles by incorporating diverse protein crystal scaffolds that can be infused with a multiplicity of useful guest molecules. Cargo molecule loading and release kinetics will depend on the size of the guest molecules as well as the protein crystal solvent channel geometry. Here, we demonstrate the loading of a small molecule dye into the small pores of hen egg white lysozyme crystals and a model enzyme into the 13-nm pores delimited by “CJ” crystals composed of an isoprenoid-binding protein from Campylerbacter jejuni. 

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