Publications

The sequential ordering of different monomers within synthetic copolymers is remarkably difficult to control. Our understanding of the determinants of and variations within copolymer sequences, even in simple step-growth reactions, remains limited. In this work, we perform simulations on a generic model of irreversible step-growth copolymerization between two types of monomers, A and B, in solution. Our results demonstrate that relatively weak attractions among nascent oligomers can exert considerable influence over the sequential arrangement of monomers in the final set of copolymers, even when identical reaction barriers exist between all monomer pairs. The observed effects cannot be fully accounted for within conventional polymerization theories due to a breakdown in Flory’s principle of equal reactivity that occurred in some cases. Nonetheless, these anomalous results can be readily explained by the Flory–Huggins theory, as a phase separation between A-rich and B-rich segments can emerge from and also be limited by the copolymerization process itself. This observation suggests that new routes for the one-pot synthesis of sequence-biased copolymers may be available through the coupling of step-growth copolymerizations and emergent phase separations.

Nanoparticles (NPs) protected with a ligand monolayer hold promise for a wide variety of applications, from photonics and catalysis to drug delivery and biosensing. Monolayers that include a mixture of ligand types can have multiple chemical functionalities and may also self-assemble into advantageous patterns. Previous work has shown that both chemical and length mismatches among these surface ligands influence phase separation. In this work, we examine the interplay between these driving forces, first by using our previously-developed configurationally-biased Monte Carlo (CBMC) algorithm to predict, then by using our matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) technique to experimentally probe, the surface morphologies of a series of two-ligand mixtures on the surfaces of ultrasmall silver NPs. Specifically, we examine three such mixtures, each of which has the same chemical mismatch (consisting of a hydrophobic alkanethiol and a hydrophilic mercapto-alcohol), but varying degrees of chain-length mismatch. This delicate balance between chemical and length mismatches provides a challenging test for our CBMC prediction algorithm. Even so, the simulations are able to quantitatively predict the MALDI-MS results for all three ligand mixtures, while also providing atomic-scale details from the equilibrated ligand structures, such as patch sizes and co-crystallization patterns. The resulting monolayer morphologies range from randomly-mixed to Janus-like, demonstrating that chain-length modifications are an effective way to tune monolayer morphology without needing to alter chemical functionalities.

Detection of monolayer morphology on nanoparticles smaller than 10 nm has proven difficult with traditional visualization techniques. Here matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) is used in conjunction with atomistic simulations to detect the formation of Janus-like monolayers on noble metal nanoparticles. Silver metal nanoparticles were synthesized with a monolayer consisting of dodecanethiol (DDT) and mercaptoethanol (ME) at varying ratios. The nanoparticles were then analyzed using MALDI-MS, which gives information on the local ordering of ligands on the surface. The MALDI-MS analysis showed large deviations from random ordering, suggesting phase separation of the DDT/ME monolayers. Atomistic Monte Carlo (MC) calculations were then used to simulate the nanoscale morphology of the DDT/ME monolayers. In order to quantitatively compare the computational and experimental results, we developed a method for determining an expected MALDI-MS spectrum from the atomistic simulation. Experiments and simulations show quantitative agreement, and both indicate that the DDT/ME ligands undergo phase separation, resulting in Janus-like nanoparticle monolayers with large, patchy domains.

Optogenetics and photopharmacology are powerful approaches to investigating biochemical systems. While the former is based on genetically encoded photoreceptors that utilize abundant chromophores, the latter relies on synthetic photoswitches that are either freely diffusible or covalently attached to specific bioconjugation sites, which are often native or engineered cysteines. The identification of suitable cysteine sites and appropriate linkers for attachment is generally a lengthy and cumbersome process. Herein, we describe an in silico screening approach that is designed to propose a small number of optimal combinations. By applying this computational approach to human carbonic anhydrase and a set of three photochromic tethered ligands, the number of potential site-ligand combinations was narrowed from over 750 down to 6, which we then evaluated experimentally. Two of these six combinations resulted in light-responsive human Carbonic Anhydrases (LihCAs), which were characterized with enzymatic activity assays, mass spectrometry, and X-ray crystallography. Our study also provides insights into the reactivity of cysteines toward maleimides and the hydrolytic stability of the adducts obtained.

A one-step postpolymerization modification that converts three high bandgap poly(arylene ethynylene)s into low bandgap donor–acceptor copolymers is described. The strategy relies on a palladium-catalyzed cyclopentannulation reaction between the main-chain ethynylene functionality and a small molecule aryl bromide (6-bromo-1,2-dimethylaceanthrylene). The reaction installs new cyclopenta[hi]aceanthrylene electron-accepting groups between the electron rich arylenes along the polymer backbone. The modified polymers include poly(9,9-didodecyl-fluorene-2,7-ethynylene), poly(9-dodecyl-carbazole-2,7-ethynylene), and poly(2,5-dioctyloxyphenylene-1,4-ethynylene). The functionalization efficiency was evaluated via isotopic ¹³C labeling of the polymeric ethynylene carbons and then monitoring the chemical environment of those carbons via NMR spectroscopy. Near complete conversion of the sp carbon species to sp² carbon species was observed, which demonstrates the high efficiency of the modification strategy. Gel permeation chromatography shows that the hydrodynamic radius of the polymers is reduced considerably going from linear to kinked polymer morphology upon functionalization, and molecular dynamics simulations illustrate the underlying morphological change. The newly formed donor–acceptor polymers showed dramatically different optical and electrochemical properties from the precursor poly(arylene ethynylene) polymers. A new absorption band centered at ∼650 nm represents a red-shift of >300 nm for the onset of absorption compared with that of precursor polymers and cyclic voltammetry shows two new low-lying reduction peaks that coincide with the cyclopenta[hi]aceanthrylene moiety.

Conspectus

Folded protein structures are both stable and dynamic. Historically, our clearest window into these structures came from X-ray crystallography, which generally provided a static image of each protein’s singular “folded state”, highlighting its stability. Deviations away from that crystallographic structure were difficult to quantify, and as a result, their potential functional consequences were often neglected. However, several dynamical and statistical studies now highlight the structural variability that is present within the protein’s folded state. Here we review mounting evidence of the importance of these structural rearrangements; both experiment and computation indicate that folded proteins undergo substantial fluctuations that can greatly influence their function.

Crucially, recent studies have shown that structural elements of proteins, especially their side-chain degrees of freedom, fluctuate in ways that generate significant conformational heterogeneity. The entropy associated with these motions contributes to the folded structure’s thermodynamic stability. In addition, since these fluctuations can shift in response to perturbations such as ligand binding, they may play an important role in the protein’s capacity to respond to environmental cues. In one compelling example, the entropy associated with side-chain fluctuations contributes significantly to regulating the binding of calmodulin to a set of peptide ligands.

The neglect of fluctuations within proteins’ native states was often justified by the dense packing within folded proteins, which has inspired comparisons with crystalline solids. Many liquids, however, can achieve similarly dense packing yet fluidity is maintained through correlated molecular motions. Indeed, the studies we discuss favor comparison of folded proteins not with solids but instead with dense liquids, where the internal side chain fluidity is facilitated by collective motions that are correlated over long distances. These correlated rearrangements can enable allosteric communication between different parts of a protein, through subtle and varied channels. Such long-range correlations appear to be an innate feature of proteins in general, manifest even in molecules lacking known allosteric regulators and arising robustly from the physical nature of their internal environment. Given their ubiquity, it is only to be expected that, over time, nature has refined some subset of these correlated motions and put them to use.

Native state fluctuations increasingly appear to be vital for proteins’ natural functions. Understanding the diversity, origin, and range of these rearrangements may provide novel routes for rationally manipulating biomolecular activity.

Previous methods for determining whether a uniform region of a sample is crystalline or isotropic—what we call the “state of internal orientation” 𝒮S—require a priori knowledge of properties of the purely crystalline and purely isotropic states. In addition, these methods can be ambiguous in their determination of state 𝒮S for particular materials and, for a given material, the spectral methods can be ambiguous when using particular peaks. Using first-principles Raman theory, we have discovered a simple, non-resonance, polarized Raman method for determining the state 𝒮S that requires no information a priori and will work unambiguously for any material using any vibrational mode. Similar to the concept behind “magic angle spinning” in NMR, we have found that for a special set of incident/analyzed polarizations and scattering angle, the dependence of the Raman modulation depth M on the sample composition—and, for crystalline regions, the unit cell orientation—falls out completely, leaving dependence on only whether the region is crystalline (M = 1) or isotropic (M = 0). Further, upon scanning between homogeneous regions or domains within a heterogeneous sample, our signal M is a clear detector of the region boundaries, so that when combined with methods for determining the orientations of the crystalline domains, our method can be used to completely characterize the molecular structure of an entire heterogeneous sample to a very high certainty. Interestingly, our method can also be used to determine when a given mode is vibrationally degenerate. While simulations on realistic terthiophene systems are included to illustrate our findings, our method should apply to any type of material, including thin films, molecular crystals, and semiconductors. Finally, our discovery of these relationships required derivations of Raman intensity formulas that are at least as general as any we have found, and herein we present our comprehensive formulas for both the crystalline and isotropic states.

We have measured the single-molecule conductance of a family of bithiophene derivatives terminated with methyl sulfide gold-binding linkers using a scanning tunneling microscope based break-junction technique. We find a broad distribution in the single-molecule conductance of bithiophene compared with that of a methyl sulfide terminated biphenyl. Using a combination of experiments and calculations, we show that this increased breadth in the conductance distribution is explained by the difference in 5-fold symmetry of thiophene rings as compared to the 6-fold symmetry of benzene rings. The reduced symmetry of thiophene rings results in a restriction on the torsion angle space available to these molecules when bound between two metal electrodes in a junction, causing each molecular junction to sample a different set of conformers in the conductance measurements. In contrast, the rotations of biphenyl are essentially unimpeded by junction binding, allowing each molecular junction to sample similar conformers. This work demonstrates that the conductance of bithiophene displays a strong dependence on the conformational fluctuations accessible within a given junction configuration, and that the symmetry of such small molecules can significantly influence their conductance behaviors.

Single-molecule excitation polarization anisotropy and molecular dynamics simulations reveal that the folding of polymers composed of conjugated phenylene vinylene (PPV) oligomers joined by flexible linkers can be influenced by the length of the conjugated segments. By varying the number of PPV repeat units from three to five to seven, both the structure and the spectral properties of the polymer can be controlled at the synthetic level. The stronger interactions between longer conjugated units of the polymers lead to more ordered conformations. The mean modulation depth of a septamer containing PPV (M = 0.75) was found to be even higher than that of the traditional homopolymer MEH-PPV (M = 0.66), which suggests that these new polymers provide access to highly aligned nanostructures not typically found in homopolymer systems.

The modeling of the conformational properties of conjugated polymers entails a unique challenge for classical force fields. Conjugation imposes strong constraints upon bond rotation. Planar configurations are favored, but the concomitantly shortened bond lengths result in moieties being brought into closer proximity than usual. The ensuing steric repulsions are particularly severe in the presence of side chains, straining angles, and stretching bonds to a degree infrequently found in nonconjugated systems. We herein demonstrate the resulting inaccuracies by comparing the LMP2-calculated inter-ring torsion potentials for a series of substituted stilbenes and bithiophenes to those calculated using standard classical force fields. We then implement adjustments to the OPLS-2005 force field in order to improve its ability to model such systems. Finally, we show the impact of these changes on the dihedral angle distributions, persistence lengths, and conjugation length distributions observed during molecular dynamics simulations of poly[2-methoxy-5-(2′-ethylhexyloxy)-p-phenylene vinylene] (MEH-PPV) and poly 3-hexylthiophene (P3HT), two of the most widely used conjugated polymers.