Search for: All records

Not AvailableCarbon dots have received considerable attention due to their tunable emission. Single-particle techniques revealed that individual top-down and bottom-up green carbon dots can support several chromophores. In particular, several studies demonstrated that bottom-up synthesized carbon dots are typically made of amorphous carbon and are multichromophoric but may also just be chemically impure, with free dye in solution or polymerized in a carbon matrix. Carbon dots made by top-down precursors, however, are highly graphitic and more often single-chromophoric, begging the question if carbon dots made from bottom-up precursors could have similar optical properties compared to their top-down counterparts, if properly purified. Here, we compare green-emitting carbon dots made by two methods: top-down by chemical oxidation and bottom-up from small-molecule precursors in a solvothermal synthesis followed by rigorous purification. Such dots have cores of different crystallinity, but both types have oxidized surfaces. Just as ensemble absorption and emission spectra show only subtle differences, we find based on single-particle emission imaging that both types of carbon dots contain similar weights of carbon dots with single and multiple chromophores. Surprisingly, the carbon dots are optically similar, despite coming from opposing synthetic approaches. Although the majority of all carbon dots are single-chromophoric, top-down carbon dots are found to more likely have only one emitting chromophore, whereas bottom-up carbon dots are comparatively more multichromophoric. In the multichromophoric case, bottom-up carbon dots have on average a greater number of chromophores than top-down carbon dots. Our results showing that very differently made carbon dots with different structural properties exhibit strikingly similar emission properties reveal the important insight that out of structural heterogeneity emerges spectroscopic homogeneity. 

Hybridization between semiconductor surfaces and covalently bound organic molecules offers a pathway to engineer surface-specific electronic states. However, due to the nanoscale nature of molecular functionalization, resolving such hybrid orbitals spatially and energetically is experimentally challenging. Here, we investigate a model system comprised of a silicon(111) substrate functionalized with anthracene (Si–Anth) to elucidate semiconductor-molecule hybrid electronic structure. Si–Anth was functionalized with a surface coverage ≲ 7% anthracene sites and backfilled with methyl groups. Anthracene was selected due to the relative energetic proximity of its frontier molecular orbitals to the silicon band edges, rendering it amenable to near band-edge spectroscopic investigation. STM imaging of the Si–Anth surface revealed molecular structures consistent with anthracene molecules oriented as expected from the covalent attachment procedure, compared with a lack of such anthracene-like structures on methyl-only samples. Ultrahigh vacuum techniques of ultraviolet photoelectron spectroscopy (UPS), low-energy inverse photoemission spectroscopy (LEIPS), and scanning tunneling spectroscopy (STS) were performed to compare both ensemble and local (single-molecule specific) electronic structure near the semiconductor band edges. Intriguingly, the UPS/LEIPS measurements resulted in a wider experimentally observed band gap for Si–Anth (Eg ≈ 1.5 eV) relative to the methylated Si–CH3 control (Eg ≈ 1.1 eV) on both p- and n-type samples. STS supported the Eg trends and revealed HOMO-like and LUMO-like features corresponding to hybridized Si–Anth states. These results demonstrate experimentally detectable features that quantitatively confirm semiconductor-molecule hybridization and provide spectroscopic signatures for future studies of hybrid semiconductor-molecule states. 

Enzyme–enzyme interactions are fundamental to the function of cells. Their atomistic mechanisms remain elusive mainly due to limitations of in-cell measurements. We address this challenge by atomistically modeling, for a total of ≈80 μs, a slice of the human cell cytoplasm that includes three successive enzymes along the glycolytic pathway: glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycerate kinase (PGK), and phosphoglycerate mutase (PGM). We tested the model for nonspecific protein stickiness, an artifact of current atomistic force fields in crowded environments. The simulations reveal that the human enzymes co-organize in-cell into transient submetabolon complexes, consistent with previous experimental results. Our data both reiterate known specificity between GAPDH and PGK and reveal extensive direct interactions between GAPDH and PGM. Our simulations further reveal, through force field benchmarking, the critical role of protein solvation in facilitating these enzyme–enzyme interactions. Transient interenzyme interactions with μs lifetime occur repeatedly in our simulations via specific sticky protein surface patches, with interactions often mediated by charged patch residues. Some of the residues that interact frequently with one another lie in or near the active site of the enzymes. We show that some of these patches correspond to a general mode to interact with several partners for promiscuous enzymes like GAPDH. We further show that the non-native yeast PGK is stickier than human PGK in our human cytoplasm model, supporting the idea of evolutionary pressure to reduce sticking. Our cytoplasm modeling paves the way toward capturing the atomistic dynamics of an entire enzymatic pathway in-cell. 

For carbon dots, careful purification and electronic structure calculations facilitate learning about the origin of optical properties. 

Nanomaterials acquire a biomolecular corona upon introduction to biological media, leading to biological transformations such as changes in protein function, unmasking of epitopes, and protein fibrilization. Ex vivo studies to investigate the effect of nanoparticles on protein–protein interactions are typically performed in buffer and are rarely measured quantitatively in live cells. Here, we measure the differential effect of silica nanoparticles on protein association in vitro vs. in mammalian cells. BtubA and BtubB are a pair of bacterial tubulin proteins identified inProsthecobacterstrains that self-assemble like eukaryotic tubulin, first into dimers and then into microtubules in vitro or in vivo. Förster resonance energy transfer labeling of each of the Btub monomers with a donor (mEGFP) and acceptor (mRuby3) fluorescent protein provides a quantitative tool to measure their binding interactions in the presence of unfunctionalized silica nanoparticles in buffer and in cells using fluorescence spectroscopy and microscopy. We show that silica nanoparticles enhance BtubAB dimerization in buffer due to protein corona formation. However, these nanoparticles have little effect on bacterial tubulin self-assembly in the complex mammalian cellular environment. Thus, the effect of nanomaterials on protein–protein interactions may not be readily translated from the test tube to the cell in the absence of particle surface functionalization that can enable targeted protein–nanoparticle interactions to withstand competitive binding in the nanoparticle corona from other biomolecules. 

Intrinsically disordered proteins (IDPs) that lie close to the empirical boundary separating IDPs and folded proteins in Uversky’s charge–hydropathy plot may behave as “marginal IDPs” and sensitively switch conformation upon changes in environment (temperature, crowding, and charge screening), sequence, or both. In our search for such a marginal IDP, we selected Huntingtin-interacting protein K (HYPK) near that boundary as a candidate; PKIα, also near that boundary, has lower secondary structure propensity; and Crk1, just across the boundary on the folded side, has higher secondary structure propensity. We used a qualitative Förster resonance energy transfer-based assay together with circular dichroism to simultaneously probe global and local conformation. HYPK shows several unique features indicating marginality: a cooperative transition in end-to-end distance with temperature, like Crk1 and folded proteins, but unlike PKIα; enhanced secondary structure upon crowding, in contrast to Crk1 and PKIα; and a cross-over from salt-induced expansion to compaction at high temperature, likely due to a structure-to-disorder transition not seen in Crk1 and PKIα. We then tested HYPK’s sensitivity to charge patterning by designing charge-flipped variants including two specific sequences with identical amino acid composition that markedly differ in their predicted size and response to salt. The experimentally observed trends, also including mutants of PKIα, verify the predictions from sequence charge decoration metrics. Marginal proteins like HYPK show features of both folded and disordered proteins that make them sensitive to physicochemical perturbations and structural control by charge patterning. 

The ultimate regularity of quantum mechanics creates a tension with the assumption of classical chaos used in many of our pictures of chemical reaction dynamics. Out-of-time-order correlators (OTOCs) provide a quantum analog to the Lyapunov exponents that characterize classical chaotic motion. Maldacena, Shenker, and Stanford have suggested a fundamental quantum bound for the rate of information scrambling, which resembles a limit suggested by Herzfeld for chemical reaction rates. Here, we use OTOCs to study model reactions based on a double-well reaction coordinate coupled to anharmonic oscillators or to a continuum oscillator bath. Upon cooling, as one enters the tunneling regime where the reaction rate does not strongly depend on temperature, the quantum Lyapunov exponent can approach the scrambling bound and the effective reaction rate obtained from a population correlation function can approach the Herzfeld limit on reaction rates: Tunneling increases scrambling by expanding the state space available to the system. The coupling of a dissipative continuum bath to the reaction coordinate reduces the scrambling rate obtained from the early-time OTOC, thus making the scrambling bound harder to reach, in the same way that friction is known to lower the temperature at which thermally activated barrier crossing goes over to the low-temperature activationless tunneling regime. Thus, chemical reactions entering the tunneling regime can be information scramblers as powerful as the black holes to which the quantum Lyapunov exponent bound has usually been applied.