Closed-loop transfer enables artificial intelligence to yield chemical knowledge.

Artificial intelligence-guided closed-loop experimentation has emerged as a promising method for optimization of objective functions1,2, but the substantial potential of this traditionally black-box approach to uncovering new chemical knowledge has remained largely untapped. Here we report the integration of closed-loop experiments with physics-based feature selection and supervised learning, denoted as closed-loop transfer (CLT), to yield chemical insights in parallel with optimization of objective functions. CLT was used to examine the factors dictating the photostability in solution of light-harvesting donor-acceptor molecules used in a variety of organic electronics applications, and showed fundamental insights including the importance of high-energy regions of the triplet state manifold. This was possible following automated modular synthesis and experimental characterization of only around 1.5% of the theoretical chemical space. This physics-informed model for photostability was strengthened using multiple experimental test sets and validated by tuning the triplet excited-state energy of the solvent to break out of the observed plateau in the closed-loop photostability optimization process. Further applications of CLT to additional materials systems support the generalizability of this strategy for augmenting closed-loop strategies. Broadly, these findings show that combining interpretable supervised learning models and physics-based features with closed-loop discovery processes can rapidly provide fundamental chemical insights.

Secondary structure determines electron transport in peptides.

Proteins play a key role in biological electron transport, but the structure-function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green's function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 310 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.

Enhanced Electron Transport in Nonconjugated Radical Oligomers Occurs by Tunneling.

Incorporating temperature- and air-stable organic radical species into molecular designs is a potentially advantageous means of controlling the properties of electronic materials. However, we still lack a complete understanding of the structure-property relationships of organic radical species at the molecular level. In this work, the charge transport properties of (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO) radical-containing nonconjugated molecules are studied using single-molecule charge transport experiments and molecular modeling. Importantly, the TEMPO pendant groups promote temperature-independent molecular charge transport in the tunneling region relative to the quenched and closed-shell phenyl pendant groups. Results from molecular modeling show that the TEMPO radicals interact with the gold metal electrodes near the interface to facilitate a high-conductance conformation. Overall, the large enhancement of charge transport by incorporation of open-shell species into a single nonconjugated molecular component opens exciting avenues for implementing molecular engineering in the development of next-generation electronic devices based on novel nonconjugated radical materials.

Electron Tomography and Machine Learning for Understanding the Highly Ordered Structure of Leafhopper Brochosomes.

Insects known as leafhoppers (Hemiptera: Cicadellidae) produce hierarchically structured nanoparticles known as brochosomes that are exuded and applied to the insect cuticle, thereby providing camouflage and anti-wetting properties to aid insect survival. Although the physical properties of brochosomes are thought to depend on the leafhopper species, the structure-function relationships governing brochosome behavior are not fully understood. Brochosomes have complex hierarchical structures and morphological heterogeneity across species, due to which a multimodal characterization approach is required to effectively elucidate their nanoscale structure and properties. In this work, we study the structural and mechanical properties of brochosomes using a combination of atomic force microscopy (AFM), electron microscopy (EM), electron tomography, and machine learning (ML)-based quantification of large and complex scanning electron microscopy (SEM) image data sets. This suite of techniques allows for the characterization of internal and external brochosome structures, and ML-based image analysis methods of large data sets reveal correlations in the structure across several leafhopper species. Our results show that brochosomes are relatively rigid hollow spheres with characteristic dimensions and morphologies that depend on leafhopper species. Nanomechanical mapping AFM is used to determine a characteristic compression modulus for brochosomes on the order of 1-3 GPa, which is consistent with crystalline proteins. Overall, this work provides an improved understanding of the structural and mechanical properties of leafhopper brochosomes using a new set of ML-based image classification tools that can be broadly applied to nanostructured biological materials.

Expanding the Molecular Alphabet of DNA-Based Data Storage Systems with Neural Network Nanopore Readout Processing.

DNA is a promising next-generation data storage medium, but challenges remain with synthesis costs and recording latency. Here, we describe a prototype of a DNA data storage system that uses an extended molecular alphabet combining natural and chemically modified nucleotides. Our results show that MspA nanopores can discriminate different combinations and ordered sequences of natural and chemically modified nucleotides in custom-designed oligomers. We further demonstrate single-molecule sequencing of the extended alphabet using a neural network architecture that classifies raw current signals generated by Oxford Nanopore sequencers with an average accuracy exceeding 60% (39× larger than random guessing). Molecular dynamics simulations show that the majority of modified nucleotides lead to only minor perturbations of the DNA double helix. Overall, the extended molecular alphabet may potentially offer a nearly 2-fold increase in storage density and potentially the same order of reduction in the recording latency, thereby enabling new implementations of molecular recorders.

Efficient Intermolecular Charge Transport in π-Stacked Pyridinium Dimers Using Cucurbit[8]uril Supramolecular Complexes.

Intermolecular charge transport through π-conjugated molecules plays an essential role in biochemical redox processes and energy storage applications. In this work, we observe highly efficient intermolecular charge transport upon dimerization of pyridinium molecules in the cavity of a synthetic host (cucurbit[8]uril, CB[8]). Stable, homoternary complexes are formed between pyridinium molecules and CB[8] with high binding affinity, resulting in an offset stacked geometry of two pyridiniums inside the host cavity. The charge transport properties of free and dimerized pyridiniums are characterized using a scanning tunneling microscope-break junction (STM-BJ) technique. Our results show that π-stacked pyridinium dimers exhibit comparable molecular conductance to isolated, single pyridinium molecules, despite a longer transport pathway and a switch from intra- to intermolecular charge transport. Control experiments using a CB[8] homologue (cucurbit[7]uril, CB[7]) show that the synthetic host primarily serves to facilitate dimer formation and plays a minimal role on molecular conductance. Molecular modeling using density functional theory (DFT) reveals that pyridinium molecules are planarized upon dimerization inside the host cavity, which facilitates charge transport. In addition, the π-stacked pyridinium dimers possess large intermolecular LUMO-LUMO couplings, leading to enhanced intermolecular charge transport. Overall, this work demonstrates that supramolecular assembly can be used to control intermolecular charge transport in π-stacked molecules.

Designing Multicomponent Polymer Colloids for Self-Stratifying Films.

Aqueous polymer colloids known as latexes are widely used in coating applications. Multicomponent latexes comprised of two incompatible polymeric species organized into a core-shell particle morphology are a promising system for self-stratifying coatings that spontaneously partition into multiple layers, thereby yielding complex structured coatings requiring only a single application step. Developing new materials for self-stratifying coatings requires a clear understanding of the thermodynamic and kinetic properties governing phase separation and polymeric species transport. In this work, we study phase separation and self-stratification in polymer films based on multicomponent acrylic (shell) and acrylic-silicone (core) latex particles. Our results show that the molecular weight of the shell polymer and heat aging conditions of the film critically determine the underlying transport phenomena, which ultimately controls phase separation in the film. Unentangled shell polymers result in efficient phase separation within hours with heat aging at reasonable temperatures, whereas entangled shell polymers effectively inhibit phase separation even under extensive heat aging conditions over a period of months due to kinetic limitations. Transmission electron microscopy is used to track morphological changes as a function of thermal aging. Interestingly, our results show that the rheological properties of the latex films are highly sensitive to morphology, and linear shear rheology is used to understand morphological changes. Overall, these results highlight the importance of bulk rheology as a simple and effective tool for understanding changes in morphology in multicomponent latex films.

Role of Interfacial Interactions in the Graphene-Directed Assembly of Monolayer Conjugated Polymers.

Development of graphene-organic hybrid electronics is one of the most promising directions for next-generation electronic materials. However, it remains challenging to understand the graphene-organic semiconductor interactions right at the interface, which is key to designing hybrid electronics. Herein, we study the influence of graphene on the multiscale morphology of solution-processed monolayers of conjugated polymers (PII-2T, DPP-BTz, DPP2T-TT, and DPP-T-TMS). The strong interaction between graphene and PII-2T was manifested in the high fiber density and high film coverage of monolayer films deposited on graphene compared to plasma SiO2 substrates. The monolayer films on graphene also exhibited a higher relative degree of crystallinity and dichroic ratio or polymer alignment, i.e., higher degree of order. Raman spectroscopy revealed the increased backbone planarity of the conjugated polymers upon deposition on graphene as well as the existence of electronic interaction across the interface. This speculation was further substantiated by the results of photoelectron spectroscopy (XPS and UPS) of PII-2T, which showed a decrease in binding energy of several atomic energy levels, movement of the Fermi level toward HOMO, and an increase in work function, all of which indicate p-doping of the polymer. Our results provide a new level of understanding on graphene-polymer interactions at nanoscopic interfaces and the consequent impact on multiscale morphology, which will aid in the design of efficient graphene-organic hybrid electronics.

Divalent cations promote TALE DNA-binding specificity.

Recent advances in gene editing have been enabled by programmable nucleases such as transcription activator-like effector nucleases (TALENs) and CRISPR-Cas9. However, several open questions remain regarding the molecular machinery in these systems, including fundamental search and binding behavior as well as role of off-target binding and specificity. In order to achieve efficient and specific cleavage at target sites, a high degree of target site discrimination must be demonstrated for gene editing applications. In this work, we studied the binding affinity and specificity for a series of TALE proteins under a variety of solution conditions using in vitro fluorescence methods and molecular dynamics (MD) simulations. Remarkably, we identified that TALEs demonstrate high sequence specificity only upon addition of small amounts of certain divalent cations (Mg2+, Ca2+). However, under purely monovalent salt conditions (K+, Na+), TALEs bind to specific and non-specific DNA with nearly equal affinity. Divalent cations preferentially bind to DNA over monovalent cations, which attenuates non-specific interactions between TALEs and DNA and further stabilizes specific interactions. Overall, these results uncover new mechanistic insights into the binding action of TALEs and further provide potential avenues for engineering and application of TALE- or TALEN-based systems for genome editing and regulation.

Transition between Nonresonant and Resonant Charge Transport in Molecular Junctions.

Efficient long-range charge transport is required for high-performance molecular electronic devices. Resonant transport is thought to occur in single molecule junctions when molecular frontier orbital energy levels align with electrode Fermi levels, thereby enabling efficient transport without molecular or environmental relaxation. Despite recent progress, we lack a systematic understanding of the transition between nonresonant and resonant transport for molecular junctions with different chemical compositions. In this work, we show that molecular junctions undergo a reversible transition from nonresonant tunneling to resonant transport as a function of applied bias. Transient bias-switching experiments show that the nonresonant to resonant transition is reversible with the applied bias. We determine a general quantitative relationship that describes the transition voltage as a function of the molecular frontier orbital energies and electrode Fermi levels. Overall, this work highlights the importance of frontier orbital energy alignment in achieving efficient charge transport in molecular devices.

Nonlinear Transient and Steady State Stretching of Deflated Vesicles in Flow.

Membrane-bound vesicles and organelles exhibit a wide array of nonspherical shapes at equilibrium, including biconcave and tubular morphologies. Despite recent progress, the stretching dynamics of deflated vesicles is not fully understood, particularly far from equilibrium where complex nonspherical shapes undergo large deformations in flow. Here, we directly observe the transient and steady-state nonlinear stretching dynamics of deflated vesicles in extensional flow using a Stokes trap. Automated flow control is used to observe vesicle dynamics over a wide range of flow rates, shape anisotropy, and viscosity contrast. Our results show that deflated vesicle membranes stretch into highly deformed shapes in flow above a critical capillary number Cac1. We further identify a second critical capillary number Cac2, above which vesicle stretch diverges in flow. Vesicles are robust to multiple nonlinear stretch-relax cycles, evidenced by relaxation of dumbbell-shaped vesicles containing thin lipid tethers following flow cessation. An analytical model is developed for vesicle deformation in flow, which enables comparison of nonlinear steady-state stretching results with theories for different reduced volumes. Our results show that the model captures the steady-state stretching of moderately deflated vesicles; however, it underpredicts the steady-state nonlinear stretching of highly deflated vesicles. Overall, these results provide a new understanding of the nonlinear stretching dynamics and membrane mechanics of deflated vesicles in flow.

Understanding How Coacervates Drive Reversible Small Molecule Reactions to Promote Molecular Complexity.

Liquid-liquid phase-separated coacervate droplets give rise to membraneless compartments that play an important role in the spatial organization and reactivity in cells. Due to their molecularly crowded nature and ability to sequester biomolecules, coacervate droplets create distinct environments for enzymatic reaction kinetics and reaction mechanisms that markedly differ from bulk solution. In this work, we use a combination of experiments and quantitative modeling to understand how coacervate droplets promote reversible small molecule reaction chemistry. In particular, we study a model condensation reaction generating an unstable fluorescent imine in polyacrylic acid-polyethylene glycol coacervate droplets over a range of conditions. At equilibrium, the concentration of the imine product in coacervate droplets is approximately 140-fold larger than that in bulk solution, which arises due to preferential partitioning of reactants and products into coacervate droplets and a reaction equilibrium constant that is roughly threefold larger in coacervate droplets than in solution. A reaction-diffusion model is developed to quantitatively describe how competing reaction and partitioning equilibria govern the spatial distribution of the imine product inside coacervate droplets. Overall, our results show that compartmentalization stabilizes kinetically labile reaction products, which enables larger reactant concentrations in coacervate droplets compared to bulk solution. Broadly, these results provide an improved understanding of how biomolecular condensates promote multistep reaction pathways involving unstable reaction intermediates and suggest how coacervates provide a potential abiotic mechanism to promote molecular complexity.

Covalent Ag-C Bonding Contacts from Unprotected Terminal Acetylenes for Molecular Junctions.

Robust molecule-metal linkages are essential for developing high-performance and air-stable devices for molecular and organic electronics. In this work, we report a facile method for forming robust and covalent bonding contacts between unprotected terminal acetylenes and metal (Ag) interfaces. Using this approach, we study the charge transport properties of conjugated oligophenylenes with covalent metal-carbon contacts to silver electrodes formed from unprotected terminal acetylene anchors. We performed single molecule charge transport experiments and molecular simulations on a series of arylacetylenes using gold and silver electrodes. Our results show that molecular junctions on silver electrodes spontaneously form silver-carbynyl carbon (Ag-C) contacts, resulting in a nearly 10-fold increase in conductance compared to the same molecules on gold electrodes. Overall, this work presents a simple, new electrode-anchor pair that reliably forms molecular junctions with stable and robust contacts for molecular electronics.

Crooks Fluctuation Theorem for Single Polymer Dynamics in Time-Dependent Flows: Understanding Viscoelastic Hysteresis.

Nonequilibrium work relations have fundamentally advanced our understanding of molecular processes. In recent years, fluctuation theorems have been extensively applied to understand transitions between equilibrium steady-states, commonly described by simple control parameters such as molecular extension of a protein or polymer chain stretched by an external force in a quiescent fluid. Despite recent progress, far less is understood regarding the application of fluctuation theorems to processes involving nonequilibrium steady-states such as those described by polymer stretching dynamics in nonequilibrium fluid flows. In this work, we apply the Crooks fluctuation theorem to understand the nonequilibrium thermodynamics of dilute polymer solutions in flow. We directly determine the nonequilibrium free energy for single polymer molecules in flow using a combination of single molecule experiments and Brownian dynamics simulations. We further develop a time-dependent extensional flow protocol that allows for probing viscoelastic hysteresis over a wide range of flow strengths. Using this framework, we define quantities that uniquely characterize the coil-stretch transition for polymer chains in flow. Overall, generalized fluctuation theorems provide a powerful framework to understand polymer dynamics under far-from-equilibrium conditions.

Charge Transport in Sequence-Defined Conjugated Oligomers.

A major challenge in synthetic polymers lies in understanding how primary monomer sequence affects materials properties. In this work, we show that charge transport in single molecule junctions of conjugated oligomers critically depends on the primary sequence of monomers. A series of sequence-defined oligomers ranging from two to seven units was synthesized by an iterative approach based on the van Leusen reaction, providing conjugated oligomers with backbones consisting of para-linked phenylenes connected to oxazole, imidazole, or nitro-substituted pyrrole. The charge transport properties of these materials were characterized using a scanning tunneling microscope-break junction (STM-BJ) technique, thereby enabling direct measurement of molecular conductance for sequence-defined dimers, trimers, pentamers, and a heptamer. Our results show that oligomers with specific monomer sequences exhibit unexpected and distinct charge transport pathways that enhance molecular conductance more than 10-fold. A systematic analysis using monomer substitution patterns established that sequence-defined pentamers containing imidazole or pyrrole groups in specific locations provide molecular attachment points on the backbone to the gold electrodes, thereby giving rise to multiple conductance pathways. These findings reveal the subtle but important role of molecular structure including steric hindrance and directionality of heterocycles in determining charge transport in these molecular junctions. This work brings new understanding for designing molecular electronic components.

Conformational dynamics and phase behavior of lipid vesicles in a precisely controlled extensional flow.

Lipid vesicles play a key role in fundamental biological processes. Despite recent progress, we lack a complete understanding of the non-equilibrium dynamics of vesicles due to challenges associated with long-time observation of shape fluctuations in strong flows. In this work, we present a flow-phase diagram for vesicle shape and conformational transitions in planar extensional flow using a Stokes trap, which enables control over the center-of-mass position of single or multiple vesicles in precisely defined flows [A. Shenoy, C. V. Rao and C. M. Schroeder, Proc. Natl. Acad. Sci. U. S. A., 2016, 113(15), 3976-3981]. In this way, we directly observe the non-equilibrium conformations of lipid vesicles as a function of reduced volume ν, capillary number Ca, and viscosity contrast λ. Our results show that vesicle dynamics in extensional flow are characterized by the emergence of three distinct shape transitions, including a tubular to symmetric dumbbell transition, a spheroid to asymmetric dumbbell transition, and quasi-spherical to ellipsoid transition. The experimental phase diagram is in good agreement with recent predictions from simulations [V. Narsimhan, A. P. Spann and E. S. Shaqfeh, J. Fluid Mech., 2014, 750, 144]. We further show that the phase boundary of vesicle shape transitions is independent of the viscosity contrast. Taken together, our results demonstrate the utility of the Stokes trap for the precise quantification of vesicle stretching dynamics in precisely defined flows.

Unexpected entanglement dynamics in semidilute blends of supercoiled and ring DNA.

Blends of polymers of different topologies, such as ring and supercoiled, naturally occur in biology and often exhibit emergent viscoelastic properties coveted in industry. However, due to their complexity, along with the difficulty of producing polymers of different topologies, the dynamics of topological polymer blends remains poorly understood. We address this void by using both passive and active microrheology to characterize the linear and nonlinear rheological properties of blends of relaxed circular and supercoiled DNA. We characterize the dynamics as we vary the concentration from below the overlap concentration c* to above (0.5c* to 2c*). Surprisingly, despite working at the dilute-semidilute crossover, entanglement dynamics, such as elastic plateaus and multiple relaxation modes, emerge. Finally, blends exhibit an unexpected sustained elastic response to nonlinear strains not previously observed even in well-entangled linear polymer solutions.

Charge Transport and Quantum Interference Effects in Oxazole-Terminated Conjugated Oligomers.

Charge transport in single molecule junctions critically depends on the chemical identity of anchor groups used to connect molecular wires to electrodes. In this work, we report the charge transport properties of conjugated oligomers with oxazole anchors, focusing on the role of the heteroatom substitution position in terminal oxazole groups. Our results show that oxazole serves as an efficient anchor group to form stable gold-molecule-gold junctions. We further observe quantum interference (QI) effects in oxazole-terminated phenylene molecular junctions, including destructive QI in meta-substituted phenyl rings and constructive QI in para-substituted phenyl rings containing terminal oxazole groups with the same chemical constitution on both termini (i.e., O5O5 (5-oxazolyl) or O4O4 (4-oxazolyl) linkages on both termini). Surprisingly, meta-substituted phenyl rings with nonequivalent constitutions (i.e., O4O5 oxazole terminal linkages) show unexpectedly higher conductance as compared to para-substituted analogues. These results suggest that charge transport in oxazole-terminated molecules is determined by the heteroatom substitution position of the oxazole anchor in addition to the aryl substitution pattern of the π-conjugated core. Our results further show that conjugated molecules with homogeneous oxazole linkages obey a quantum circuit rule such that GO4-p-O4/GO4-m-O4 = GO5-p-O5/GO5-m-O5, where G is molecular conductance. Overall, our work provides key insight into the development of new chemistries for molecular circuitry in the rapidly advancing field of single molecule electronics.

In Situ Photophysical Characterization of π-Conjugated Oligopeptides Assembled via Continuous Flow Processing.

Bioinspired materials have been developed with the aim of harnessing natural self-assembly for precisely engineered functionality. Microfluidics is poised to play a key role in the directed assembly of advanced materials with ordered nano and mesoscale features. More importantly, there is a strong need for understanding the kinetics of continuous assembly processes. In this work, we describe a continuous microfluidic system for the assembly and alignment of synthetic oligopeptides with π-conjugated cores using a three-dimensional (3D) flow focusing of inlet reactant streams. This system facilitates in situ confocal fluorescence microscopy and in situ fluorescence lifetime imaging microscopy (FLIM), which can be used in unprecedented capacity to characterize the integrity of peptides during the assembly process. To achieve continuous assembly, we integrate chevron patterns in the ceiling and floor of the microdevice to generate a 3D-focused sheath flow of the reactant peptide. Consequently, the peptide stream is directed toward an acidic triggering stream in a cross-slot geometry which mediates assembly into higher-order fiber-like structures. Using this approach, the focused peptide stream is assembled using a planar extensional flow, which ensures high degrees of microstructural alignment within the assembled material. We demonstrate the efficacy of this approach using three different synthetic oligopeptides, and in all cases, we observe the efficient and continuous assembly of oligopeptides. In addition, finite element simulations are used to guide device design and to validate 3D focusing. Overall, this approach presents an efficient and effective method for the continuous assembly and alignment of ordered materials using microfluidics.

Stokes trap for multiplexed particle manipulation and assembly using fluidics.

The ability to confine and manipulate single particles and molecules has revolutionized several fields of science. Hydrodynamic trapping offers an attractive method for particle manipulation in free solution without the need for optical, electric, acoustic, or magnetic fields. Here, we develop and demonstrate the Stokes trap, which is a new method for trapping multiple particles using only fluid flow. We demonstrate simultaneous manipulation of two particles in a simple microfluidic device using model predictive control. We further show that this approach can be used for fluidic-directed assembly of multiple particles in solution. Overall, this technique opens new vistas for fundamental studies of particle-particle interactions and provides a new method for the directed assembly of colloidal particles.