Department of NanoEngineering

This work introduces the Strategic Escape (SE) algorithm, an approach that systematically ensures effective exploration of the potential energy surface during global minimum searches for atomic clusters. The SE algorithm prioritizes the escape from local minima prior to geometry optimization, leveraging a combination of randomized direction vectors, distance-based uniqueness criteria, and covalent bonding heuristics. These principles enhance structural diversity and computational efficiency by reducing redundant geometry optimizations. Additionally, a symmetry-guided seed generation method based on an adaptive polygon is proposed to provide diverse and physically realistic initial configurations. Together, these methods achieve a 2.3-fold improvement in computational efficiency compared to conventional Basin-Hopping approaches. The effectiveness of the SE algorithm is demonstrated through its application to boron, metal clusters, and binary-composition clusters, achieving rapid convergence to global minimum structures with high reliability. These advancements establish the SE algorithm as a robust and scalable tool for exploring complex chemical systems.

Polarizable force fields advance our understanding of electrostatic interactions in molecular systems; however, their widespread application is limited by the complexity of required molecular modeling. We here present TinkerModeller (TKM), a versatile software package designed to streamline the construction of biological systems in the Tinker molecular simulation software. The core functionality of TKM lies in its capacity to generate input files for complex molecular systems and facilitate the conversion from classical to polarizable force fields. With a user-friendly, standalone script, TKM provides an intuitive interface that supports users from molecular modeling through to postanalysis, creating a comprehensive platform for molecular dynamics simulations within Tinker. Furthermore, TKM includes an electric field (EF) postanalysis module, introducing a novel approach that employs charge methods and point charge approximations for efficient internal EF estimation. This module offers a computationally low-demand solution for high-throughput EF estimation. Our work paves the way for broader, more accessible use of polarizable force fields within Tinker and introduces a new method for EF estimation, advancing our capacity to explore electrostatic effects in biological and materials science applications.

2D metal-chalcogenide nanoplatelets (NPLs) exhibit promising photocatalysis properties due to their ultrathin morphology, high surface-to-volume ratio, and enhanced in-plane electron transport mobility. However, NPLs, especially cadmium chalcogenides, encounter challenges in CO2 photoreduction due to insufficient solar energy utilization and fast recombination of photogenerated charge carriers. Defect engineering offers a potential solution but often encounters difficulties maintaining structural integrity, mechanical stability, and electrical conductivity. Herein, by taking two monolayers (2ML) CdSe NPLs as a model system, selenium (Se) vacancies confined in atomic layers can enhance charge separation and conductivity. A straightforward approach to create Se vacancies in various monolayers CdSe NPLs (2, 4, and 5ML) has been developed, enabling efficient CO2 photoreduction with a 4-fold increase in CO generation compared to their defect-free counterparts. Significantly, accounting for higher charge density and efficient carrier transport due to Se vacancies, defective 2ML CdSe NPLs (VSe-2ML CdSe) exhibit CO evolution performance up to 2557.5 µmol g-¹ h-¹ with no significant decay over 5 h, which is an order of magnitude higher than that of common semiconductor catalysts. This study establishes a practical way to design advanced 2D semiconductor photocatalysts to achieve efficient CO2 photoreduction via defect engineering.

Characterization of the structural and electron transport properties of single chiral molecules provides critical insights into the interplay between their electronic structure and electrochemical environments, providing broader implications given the significance of molecular chirality in chiroptical applications and pharmaceutical sciences. Here, we examined the topographic and electronic features of a recently developed chiral molecule, B,N-embedded double hetero[7]helicene, at the edge of Cu(100)-supported NaCl thin film with scanning tunneling microscopy and spectroscopy. An electron transport energy gap of 3.2 eV is measured, which is significantly larger than the energy difference between the highest occupied and the lowest unoccupied molecular orbitals given by theoretical calculations or optical measurements. Through first-principles calculations, we demonstrated that this energy discrepancy results from the Coulomb interaction between the tunneling electron and the molecule's electrons. This occurs in electron transport processes when the molecule is well decoupled from the electrodes by the insulating decoupling layers, leading to a temporary ionization of the molecule during electron tunneling. Beyond revealing properties concerning a specific molecule, our findings underscore the key role of Coulomb interactions in modulating electron transport in molecular junctions, providing insights into the interpretation of scanning tunneling spectroscopy features of molecules decoupled by insulating layers.

The structural and chemical properties of metal nanoparticles are often dictated by their interactions with molecular ligand shells. These interactions are highly material-specific and can vary significantly even among elements within the same group or materials with similar crystal structure. In this study, we surveyed the heterogeneous interactions between an m-terphenyl isocyanide ligand and Au and Ag nanoparticles (NPs) at the single-molecule limit. Specifically, we found that the ligation behavior with this molecule differs significantly between that of Au and AgNPs. Surface-enhanced Raman spectroscopy measurements revealed unique enhancement factors for two molecular vibrational modes between two metal surfaces, indicating different ligand binding geometries. Molecular-level characterization using scanning tunneling microscopy allowed us to directly visualize these variations between Ag and Au surfaces, which we assign as two distinct binding mechanisms. This molecular-scale visualization provides clear insights into the different ligand-metal interactions as well as the chemical behavior and spectroscopic characteristics of isocyanide-functionalized NPs.

Controlling molecular actions on demand is a critical step toward developing single-molecule functional devices. Such control can be achieved by manipulating the interactions between individual molecules and their nanoscale environment. In this study, we demonstrate the conformational transition of a single pyrrolidine molecule adsorbed on a Cu(100) surface, driven by vibrational excitation through tunneling electrons using scanning tunneling microscopy. We identify multiple transition pathways between two structural states, each governed by distinct vibrational modes. The nuclear motions corresponding to these modes are elucidated through density functional theory calculations. By leveraging fundamental forces, including van der Waals interactions, dipole-dipole interactions, and steric hindrance, we precisely tune the molecule-environment coupling. This tuning enables the modulation of vibrational energies, adjustment of transition probabilities, and selection of the lowest-energy transition pathway. Our findings highlight how tunable force fields in a nanoscale cavity can govern molecular conformational transitions, providing a pathway to engineer molecule-environment interactions for targeted molecular functionalities.

The structural and chemical properties of metal nanoparticles are often dictated by their interactions with molecular ligand shells. These interactions are highly material-specific and can vary significantly even among elements within the same group or materials with similar crystal structure. In this study, we surveyed the heterogeneous interactions between an m-terphenyl isocyanide ligand and Au and Ag nanoparticles (NPs) at the single-molecule limit. Specifically, we found that the ligation behavior with this molecule differs significantly between that of Au and AgNPs. Surface-enhanced Raman spectroscopy measurements revealed unique enhancement factors for two molecular vibrational modes between two metal surfaces, indicating different ligand binding geometries. Molecular-level characterization using scanning tunneling microscopy allowed us to directly visualize these variations between Ag and Au surfaces, which we assign as two distinct binding mechanisms. This molecular-scale visualization provides clear insights into the different ligand-metal interactions as well as the chemical behavior and spectroscopic characteristics of isocyanide-functionalized NPs.

Poisoning by organophosphate (OP) nerve agents remains a pressing global threat due to their extensive use in chemical warfare agents and pesticides, potentially causing high morbidity and mortality worldwide. This urgent need for effective countermeasures has driven considerable interest in innovative detoxification approaches. Among these, nanoparticle technology stands out for its multifunctional potential and wide-ranging applications. This review highlights recent advancements in nanoparticle platforms developed for OP detoxification, focusing on five main types: inorganic nanoparticles, lipid-based nanoparticles, polymer-based nanoparticles, metal-organic framework nanoparticles, and cellular nanoparticles. For each platform, we discuss representative examples that illustrate how structural and functional properties enhance their effectiveness as nanocarriers, nanocatalysts, or nanoscavengers, ultimately enabling safe and efficient OP detoxification. This review aims to stimulate further technological innovation in OP-detoxifying nanoparticles and encourage broader development of detoxification strategies.

Rechargeable Li-SO₂ batteries offer low-cost, high-energy density benefits and can leverage manufacturing processes for the existing primary version at a commercial scale. However, they have so far only been demonstrated in an "open-system" with continuous gas supply, preventing practical application. Here, the utilization and reversibility of SO₂ along with the lithium stability are addressed, all essential for long-life, high-energy batteries. The study discovers that high SO₂ utilization is achievable only from SO₂ dissolved in electrolytes between the lithium anode and carbon cathode. This results from a unique osmosis phenomenon where SO₂ consumption increases salt concentration, driving the influx of organic solvents rather than SO₂ from outside the current path. This insight leads to configure a bobbin-cell with all electrolytes between the electrodes, realizing nearly 70% of SO₂ utilization, > 12x greater than in conventional coin cells. To improve reaction rate and SO₂ reversibility, triphenylamine is employed to the electrolyte, creating an electron-rich environment that alleviates the disproportionation of discharge products. Incorporating this additive into a bobbin-cell with a lithium protective layer yields a cell with a projected energy density exceeding 183.2 Wh kg^-1. The work highlights the potential of Li-SO₂ batteries as affordable, sustainable energy storage options.

Ubiquitin-specific protease 18 (USP18) is a multifunctional cysteine protease primarily responsible for deconjugating the interferon-inducible ubiquitin-like modifier ISG15 from protein substrates. Here, we report the design and synthesis of activity-based probes (ABPs) that incorporate unnatural amino acids into the C-terminal tail of ISG15, enabling the selective detection of USP18 activity over other ISG15 cross-reactive deubiquitinases (DUBs) such as USP5 and USP14. Combined with a ubiquitin-based DUB ABP, the USP18 ABP is employed in a chemoproteomics screening platform to identify and assess inhibitors of DUBs including USP18. We further demonstrate that USP18 ABPs can be utilized to profile differential activities of USP18 in lung cancer cell lines, providing a strategy that will help define the activity-related landscape of USP18 in different disease states and unravel important (de)ISGylation-dependent biological processes.