Wertheim’s thermodynamic perturbation theory with double-bond association and its application to colloid–linker mixtures

Megamolecule Self-Assembly Networks: A Combined Computational and Experimental Design Strategy

This work describes the use of computational strategies to design megamolecule building blocks for the self-assembly of lattice networks. The megamolecules are prepared by attaching four Cutinase-SnapTag fusion proteins (CS fusions) to a four-armed linker, followed by functionalizing each fusion with a terpyridine linker. This functionality is designed to participate in a metal-mediated self-assembly process to give networks. This article describes a simulation-guided strategy for the design of megamolecules to optimize the peptide linker in the fusion protein to give conformations that are best suited for self-assembly and therefore streamlines the typically time-consuming and labor-intensive experimental process. We designed 11 candidate megamolecules and identified the most promising linker, (EAAAK)2, along with the optimal experimental conditions through a combination of all-atom molecular dynamics, enhanced sampling, and larger-scale coarse-grained molecular dynamics simulations. Our simulation findings were validated and found to be consistent with the experimental results. Significantly, this study offers valuable insight into the self-assembly of megamolecule networks and provides a novel and general strategy for large biomolecular material designs by using systematic bottom-up coarse-grained simulations.

Phase Equilibrium Studies in the Geothermal Energy Development: The Effect of Hydrogen Bond on the Multi-Component Fluid

Geothermal energy has become an emerging resource with both large reserves and environmental friendliness and is playing an increasingly important role in the current energy transition progress. In this paper, a thermodynamically consistent NVT flash model is developed to consider the effect of hydrogen bond on the phase equilibrium states of multi-component fluid to resolve the challenges of the special thermodynamic characteristic of water as the main working fluid. In order to provide practical suggestions to the industry, a number of possible effects have been investigated on the phase equilibrium states, including the hydrogen bond, environmental temperature, and fluid compositions. The calculated phase stability and phase splitting results can provide thermodynamic foundations for the establishment of the multi-component multi-phase flow model and also help optimize the development process to control the phase transitions for a number of engineering purposes.

Effects of linker length on phase separation: lessons from the Rubisco-EPYC1 system of the algal pyrenoid

Biomolecular condensates are membraneless organelles formed via phase separation of macromolecules, typically consisting of bond-forming "stickers" connected by flexible "linkers". Linkers have diverse roles, such as occupying space and facilitating interactions. To understand how linker length relative to other lengths affects condensation, we focus on the pyrenoid, which enhances photosynthesis in green algae. Specifically, we apply coarse-grained simulations and analytical theory to the pyrenoid proteins of Chlamydomonas reinhardtii: the rigid holoenzyme Rubisco and its flexible partner EPYC1. Remarkably, halving EPYC1 linker lengths decreases critical concentrations by ten-fold. We attribute this difference to the molecular "fit" between EPYC1 and Rubisco. Varying Rubisco sticker locations reveals that the native sites yield the poorest fit, thus optimizing phase separation. Surprisingly, shorter linkers mediate a transition to a gas of rods as Rubisco stickers approach the poles. These findings illustrate how intrinsically disordered proteins affect phase separation through the interplay of molecular length scales.

Modular mixing in plasmonic metal oxide nanocrystal gels with thermoreversible links

Gelation offers a powerful strategy to assemble plasmonic nanocrystal networks incorporating both the distinctive optical properties of constituent building blocks and customizable collective properties. Beyond what a single-component assembly can offer, the characteristics of nanocrystal networks can be tuned in a broader range when two or more components are intimately combined. Here, we demonstrate mixed nanocrystal gel networks using thermoresponsive metal-terpyridine links that enable rapid gel assembly and disassembly with thermal cycling. Plasmonic indium oxide nanocrystals with different sizes, doping concentrations, and shapes are reliably intermixed in linked gel assemblies, exhibiting collective infrared absorption that reflects the contributions of each component while also deviating systematically from a linear combination of the spectra for single-component gels. We extend a many-bodied, mutual polarization method to simulate the optical response of mixed nanocrystal gels, reproducing the experimental trends with no free parameters and revealing that spectral deviations originate from cross-coupling between nanocrystals with distinct plasmonic properties. Our thermoreversible linking strategy directs the assembly of mixed nanocrystal gels with continuously tunable far- and near-field optical properties that are distinct from those of the building blocks or mixed close-packed structures.

Assembling Inorganic Nanocrystal Gels

Inorganic nanocrystal gels retain distinct properties of individual nanocrystals while offering tunable, network-structure-dependent characteristics. We review different mechanisms for assembling gels from colloidal nanocrystals including (1) controlled destabilization, (2) direct bridging, (3) depletion, as well as linking mediated by (4) coordination bonding or (5) dynamic covalent bonding, and we highlight how each impacts gel properties. These approaches use nanocrystal surface chemistry or the addition of small molecules to mediate inter-nanocrystal attractions. Each method offers advantages in terms of gel stability, reversibility, or tunability and presents new opportunities for the design of reconfigurable materials and fueled assemblies.

Colorimetric quantification of linking in thermoreversible nanocrystal gel assemblies

Nanocrystal gels can be responsive, tunable materials, but designing their structure and properties is challenging. By using reversibly bonded molecular linkers, gelation can be realized under conditions predicted by thermodynamics. However, simulations have offered the only microscopic insights, with no experimental means to monitor linking leading to gelation. We introduce a metal coordination linkage with a distinct optical signature allowing us to quantify linking in situ and establish structural and thermodynamic bases for assembly. Because of coupling between linked indium tin oxide nanocrystals, their infrared absorption shifts abruptly at a chemically tunable gelation temperature. We quantify bonding spectroscopically and use molecular simulation to understand temperature-dependent bonding motifs, revealing that gel formation is governed by reaching a critical number of effective links that extend the nanocrystal network. Microscopic insights from our colorimetric linking chemistry enable switchable gels based on thermodynamic principles, opening the door to rational design of programmable nanocrystal networks.

Colloidal Nanocrystal Gels from Thermodynamic Principles

Gels assembled from solvent-dispersed nanocrystals are of interest for functional materials because they promise the opportunity to retain distinctive properties of individual nanocrystals combined with tunable, structure-dependent collective behavior. By incorporating stimuli-responsive components, these materials could also be dynamically reconfigured between structurally distinct states. However, nanocrystal gels have so far been formed mostly through irreversible aggregation, which has limited the realization of these possibilities. Meanwhile, gelation strategies for larger colloidal microparticles have been developed using reversible physical or chemical interactions. These approaches have enabled the experimental navigation of theoretically predicted phase diagrams, helping to establish an understanding of how thermodynamic behavior can guide gel formation in these materials. However, the translation of these principles to the nanoscale poses both practical and fundamental challenges. The molecules guiding assembly can no longer be safely assumed to be vanishingly small compared to the particles nor large compared to the solvent.In this Account, we discuss recent progress toward the assembly of tunable nanocrystal gels using two strategies guided by equilibrium considerations: (1) reversible chemical bonding between functionalized nanocrystals and difunctional linker molecules and (2) nonspecific, polymer-induced depletion attractions. The effective nanocrystal attractions, mediated in both approaches by a secondary molecule, compete against stabilizing repulsions to promote reversible assembly. The structure and properties of the nanocrystal gels are controlled microscopically by the design of the secondary molecule and macroscopically by its concentration. This mode of control is compelling because it largely decouples nanocrystal synthesis and functionalization from the design of interactions that drive assembly. Statistical thermodynamic theory and computer simulation have been applied to simple models that describe the bonding motifs in these assembling systems, furnish predictions for conditions under which gelation is likely to occur, and suggest strategies for tuning and disassembling the gel networks. Insights from these models have guided experimental realizations of reversible gels with optical properties in the infrared range that are sensitive to the gel structure. This process avoids time-consuming and costly trial-and-error experimental investigations to accelerate the development of nanocrystal gel assemblies.These advances highlight the need to better understand interactions between nanocrystals, how interactions give rise to gel structure, and properties that emerge. Such an understanding could suggest new approaches for creating stimuli-responsive and dissipative assembled materials whose properties are tunable on demand through directed reconfiguration of the underlying gel microstructure. It may also make nanocrystal gels amenable to computationally guided design using inverse methods to rapidly optimize experimental parameters for targeted functionalities.