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In this work, we report an energy upconversion system based on triplet-triplet annihilation comprised of rose bengal dye as the sensitizer and a highly fluorescent 9-(triphenyl)ethynyl-10-phenylanthracene (TPE-PAn) as the triplet annihilator. The energy upconversion can be observed with a low-power laser excitation at 532 nm or noncoherent Xe arc lamp excitaion at 540 nm. A delayed fluorescence from (TPE-PAn) at 418 nm was observed with an energy upconversion up to 0.64 eV and quantum yield of 0.8 %. A white-light emission was achieved as a result of combination of delayed fluorescence from TPE-PAn and residual fluorescence from rose bengal dye.

Gene expression is prone to burst production, making it a highly noisy process that requires additional controls. Upstream open reading frames (uORFs) are widely present in the 5′ leader sequences of 30–50% of eukaryotic messenger RNAs1–3. The translation of uORFs can repress the translation efficiency of the downstream main coding sequences. Whether the low translation efficiency leads to a different variation, or noise, in gene expression has not been investigated, nor has the direct biological impact of uORF-repressed translation. Here we show that uORFs achieve low but precise protein production in plant cells, possibly by reducing the protein production rate. We also demonstrate that, by buffering a stable TIMING OF CAB EXPRESSION 1 (TOC1) protein production level, uORFs contribute to the robust operation of the plant circadian clock. Our results provide both an action model and the biological impact of uORFs in translational control to mitigate transcriptional noise for precise protein production.

A series of NIR-II fluorescent TADF-incorporated polymer dots were successfully synthesized. The function of the TADF moiety was fully studied and the bio-applications of these polymer dots including bone imaging were also demonstrated.

We reformulate the thermally assisted-occupation density functional theory (TAO-DFT) into the Kohn–Sham single-determinant framework and construct two new post-self-consistent field (post-SCF) static correlation correction schemes, named rTAO and rTAO-1. In contrast to the original TAO-DFT with the density in an ensemble form, in which each orbital density is weighted with a fractional occupation number, the ground-state density is given by a single-determinant wavefunction, a regular Kohn–Sham (KS) density, and total ground state energy is expressed in the normal KS form with a static correlation energy formulated in terms of the KS orbitals. In post-SCF calculations with rTAO functionals, an efficient energy scanning to quantitatively determine θ is also proposed. The rTAOs provide a promising method to simulate systems with strong static correlation as original TAO, but simpler and more efficient. We show that both rTAO and rTAO-1 is capable of reproducing most results from TAO-DFT without the additional functional Eθ used in TAO-DFT. Furthermore, our numerical results support that, without the functional Eθ, both rTAO and rTAO-1 can capture correct static correlation profiles in various systems.

In this study we investigated the synergistic effects of the chirality (molecular structure) and surface morphology (nanostructure) of a newly designed sensing platform for the stereoselective recognition of biomolecules. We synthesized 3,4-ethylenedioxythiophene monomers presenting an OH functional group on the side chain (EDOT-OH) with either R or S chirality and then electropolymerized them in a template-free manner to engineer poly(EDOT-OH) nanotubes and smooth films with R or S chirality. We used a quartz crystal microbalance (QCM) to examine the differential binding of fetal bovine serum, RGD peptide, insulin, and (R)- and (S)-mandelic acid (MA) on these chiral polymeric platforms. All of these biomolecules bound stereoselectively and with greater affinity toward the nanotubes than to the smooth films. The sensitive chiral recognition of (S)- and (R)-MA on the (R)-poly(EDOT-OH) nanotube surface occurred with the highest chiral discrepancy ratio of 1.80. In vitro experiments revealed a greater degree of protein deposition from MCF-7 cells on the chiral nanotube surfaces. We employed ab initio molecular dynamics simulations and density functional theory calculations to investigate the mechanism underlying the sensitive chiral recognition between the chiral sensing platforms and the chiral analyte molecules.

Singlet fission (SF) is a process where a singlet exciton is split into a pair of triplet excitons. The increase in the excitonic generation can be exploited to enhance the efficiency of solar cells. Molecules with conjugated π bonds are commonly developed for optoelectronic applications including SF, due to their low energy gaps. The electronic coupling for SF in such well-stacked π-conjugated molecule pairs can be rather limited due to the orthogonal π and π* orbital overlaps that are involved in the coupling elements, leading to a large cancellation in the coupling. In the present work, we show that such limits can be removed by involving triplet states of different origins, such as those with nonbonding n orbitals. We demonstrate such an effect for formaldehyde and methylenimine dimers, with a low-lying n-π* triplet state (T

In this study we investigated the synergistic effects of the chirality (molecular structure) and surface morphology (nanostructure) of a newly designed sensing platform for the stereoselective recognition of biomolecules. We synthesized 3,4-ethylenedioxythiophene monomers presenting an OH functional group on the side chain (EDOT-OH) with either

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange–correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear–electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an “open teamware” model and an increasingly modular design. This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.

Two hole-transporting materials (HTMs) based on carbohelicene cores, CH1 and CH2, are developed and used in fabricating efficient and stable perovskite solar cells (PSCs). Owing to the rigid conformation of the helicene core, both compounds possess unique CH-π interactions in the crystalline packing pattern and good phase stability, which are distinct from the π-π intermolecular interactions of conventional planar and spiro-type molecules. PSCs based on CH1 and CH2 as HTMs deliver excellent device efficiencies of 19.36 and 18.71%, respectively, outperforming the control device fabricated with spiro-OMeTAD (18.45%). Furthermore, both PSCs exhibit better ambient stability, with 90% of initial performance retained after aging with a 50-60% relative humidity at 25 °C for 500 h. Due to the low production cost of both compounds, these newly designed carbohelicene-type HTMs have the potential for the future commercialization of PSCs.

Electron transfer coupling is a critical factor in determining electron transfer rates. This coupling strength can be sensitive to details in molecular geometries, especially intermolecular configurations. Thus, studying charge transporting behavior with a full first-principle approach demands a large amount of computation resources in quantum chemistry (QC) calculation. To address this issue, we developed a machine learning (ML) approach to evaluate electronic coupling. A prototypical ML model for an ethylene system was built by kernel ridge regression with Coulomb matrix representation. Since the performance of the ML models highly dependent on their building strategies, we systematically investigated the generality of the ML models, the choice of features and target labels. The best ML model trained with 40 000 samples achieved a mean absolute error of 3.5 meV and greater than 98% accuracy in predicting phases. The distance and orientation dependence of electronic coupling was successfully captured. Bypassing QC calculation, the ML model saved 10-10

Semiconducting polymer dots (Pdots) have recently emerged as a new type of ultrabright fluorescent probe that has been proved to be very useful for biomedical imaging. However, Pdots often suffer from serious fluorescence aggregation-caused quenching (ACQ) especially for near-infrared (NIR) fluorescent Pdots. This article compared two strategies to overcome the ACQ effect in near-infrared emissive Pdot systems: aggregation-induced emission (AIE) and anti-aggregation-caused quenching (anti-ACQ). The results show that the anti-ACQ platform outperforms the AIE system. The fluorescence quantum yield of anti-ACQ-based Pdots can be over 50% and the average per-particle brightness of the Pdots is about 5 times higher than that of the commercially available quantum dots. To help understand why the monomer conformations could greatly affect the optical properties of Pdots, molecular dynamics simulations were performed for the first time in such complicated Pdot systems. To demonstrate applications for in vivo fluorescence imaging, both microangiography imaging on living zebrafish embryos and specific tumor targeting on mice were performed. We anticipate that these studies will pave the way for the design of new highly fluorescent Pdot systems.

Modeling biochemical systems can provide insights into behaviors that are difficult to observe or understand. It requires software, programming, and understanding of the system to build a model and study it. Softwares exist for systems biology modeling, but most support only certain types of modeling tasks. Desirable features including ease in preparing input, symbolic or analytical computation, parameter estimation, graphical user interface, and systems biology markup language (SBML) support are not seen concurrently in one software package. In this study, we developed a python-based software that supports these features, with both deterministic and stochastic propagations. The software can be used by graphical user interface, command line, or as a python import. We also developed a semi-programmable and intuitively easy topology input method for the biochemical reactions. We tested the software with semantic and stochastic SBML test cases. Tests on symbolic solution and parameter estimation were also included. The software we developed is reliable, well performing, convenient to use, and compliant with most of the SBML tests. So far it is the only systems biology software that supports symbolic, deterministic, and stochastic modeling in one package that also features parameter estimation and SBML support. This work offers a comprehensive set of tools and allows for better availability and accessibility for studying kinetics and dynamics in biochemical systems.

A series of twisted N,N-linked benzo[ghi]-perylenetriimide dimers (t-BPTI) with various lengths of the α-branched alkyl side chain at the six-membered imide ring position was designed, synthesized, and characterized. These compounds showed the low-lying LUMO energy level of -3.78 eV, which was similar to that of PC61 BM (-3.71 eV), but with intensive optical absorption in the range 350-500 nm. The twisted molecular geometry with two nearly perpendicular BPTI planes achieved a favorable nanoscale phase separation by relieving the self-aggregation of rigid BPTI units in blend films. The acceptor t-BPTI-3 unit with the longest alkyl side chains has been demonstrated to be an efficient electron acceptor in solution-processed bulk heterojunction organic photovoltaics (OPV), giving a power conversion efficiency of 3.68 % when using conjugated polymer PTB7-Th as the donor and without additional treatments.

In higher plants (e.g., Arabidopsis thaliana), the core structure of the circadian clock is mostly governed by a repression process with very few direct activators. With a series of simplified models, we studied the underlying mechanism and found that the Arabidopsis clock consists of type-2 incoherent feed-forward loops (IFFLs), one of them creating a pulse-like expression in PRR9/7. The double-negative feedback loop between CCA1/LHY and PRR5/TOC1 generates a bistable, hysteretic behavior in the Arabidopsis circadian clock. We found that the IFFL involving PRR9/7 breaks the bistability and moves the system forward with a rapid pulse in the daytime, and the evening complex (EC) breaks it in the evening. With this illustration, we can intuitively explain the behavior of the clock under mutant conditions. Thus, our results provide new insights into the underlying network structures of the Arabidopsis core oscillator.

The design principle of establishing an intracellular protein gradient for asymmetric cell division is a long-standing fundamental question. While the major molecular players and their interactions have been elucidated via genetic approaches, the diversity and redundancy of natural systems complicate the extraction of critical underlying features. Here, we take a synthetic cell biology approach to construct intracellular asymmetry and asymmetric division in Escherichia coli, in which division is normally symmetric. We demonstrate that the oligomeric PopZ from Caulobacter crescentus can serve as a robust polarized scaffold to functionalize RNA polymerase. Furthermore, by using another oligomeric pole-targeting DivIVA from Bacillus subtilis, the newly synthesized protein can be constrained to further establish intracellular asymmetry, leading to asymmetric division and differentiation. Our findings suggest that the coupled oligomerization and restriction in diffusion may be a strategy for generating a spatial gradient for asymmetric cell division., Establishing protein gradients for asymmetric cell division is fundamental across all kingdoms of life. Here the authors construct asymmetric cell division in E. coli by localizing the expression of RNA polymerase using an orthogonal unipolar scaffold, and restricting diffusion of its products.

The concept of an exciton as a quasiparticle that represents collective excited states was originally adapted from solid-state physics and has been successfully applied to molecular aggregates by relying on the well-established limits of the Wannier exciton and the Frenkel exciton. However, the study of excitons in more complex chemical systems and solid materials over the past two decades has made it clear that simple concepts based on Wannier or Frenkel excitons are not sufficient to describe detailed excitonic behavior, especially in nano-structured solid materials, multichromophoric macromolecules, and complex molecular aggregates. In addition, important effects such as vibronic coupling, the influence of charge-transfer (CT) components, spin-state interconversion, and electronic correlation, which had long been studied but not fully understood, have turned out to play a central role in many systems. This has motivated new experimental approaches and theoretical studies of increasing sophistication. This article provides an overview of works addressing these issues that were published for A Special Topic of the Journal of Chemical Physics on "Excitons: Energetics and spatio-temporal dynamics" and discusses their implications., Comment: 6 pages, no figure

As an animal's surface area expands during development, skin cell populations must quickly respond to maintain sufficient epithelial coverage. Despite much progress in understanding of skin cell behaviours in vivo

Stereotypic dendrite arborizations are key morphological features of neuronal identity, as the size, shape and location of dendritic trees determine the synaptic input fields and how information is integrated within developed neural circuits. In this review, we focus on the actions of extrinsic intercellular communication factors and their effects on intrinsic developmental processes that lead to dendrite patterning. Surrounding neurons or supporting cells express adhesion receptors and secreted proteins that respectively, act via direct contact or over short distances to shape, size, and localize dendrites during specific developmental stages. The different ligand-receptor interactions and downstream signaling events appear to direct dendrite morphogenesis by converging on two categorical mechanisms: local cytoskeletal and adhesion modulation and global transcriptional regulation of key dendritic growth components, such as lipid synthesis enzymes. Recent work has begun to uncover how the coordinated signaling of multiple extrinsic factors promotes complexity in dendritic trees and ensures robust dendritic patterning.

In describing the dynamics of electron transfer or charge transport, the reorganization energy and the spectral density function describe the influence of nuclei motion to the transporting electron. The spectral density can be obtained using various theoretical approaches: from a model of dielectric response, or calculated with various computational means. With the vast advancement of modern computational techniques, many details in vibronic coupling can be obtained, including those described in the early literature. In this work, we provide a comprehensive understanding of the nature of vibronic coupling in light of some early literature. The theoretical connection among different quantities for vibronic coupling is discussed, followed by a brief review of the spectral density function. Various approaches and some of the results for the spectral density function are also reviewed. The importance of low-frequency bands in nonpolar systems that can be overlooked is also discussed, for both Holstein and Peierls types of electron–phonon couplings.

The circadian clock is a complex system that plays many important roles in most organisms. Previously, many mathematical models have been used to sharpen our understanding of the Arabidopsis clock, which brought to light the roles of each transcriptional and post-translational regulations. However, the presence of both regulations, instead of either transcription or post-translation, raised curiosity of whether the combination of these two regulations is important for the clock’s system. In this study, we built a series of simplified oscillators with different regulations to study the importance of post-translational regulation (specifically, 26S proteasome degradation) in the clock system. We found that a simple transcriptional-based oscillator can already generate sustained oscillation, but the oscillation can be easily destroyed in the presence of transcriptional leakage. Coupling post-translational control with transcriptional-based oscillator in a feed-forward loop will greatly improve the robustness of the oscillator in the presence of basal leakage. Using these general models, we were able to replicate the increased variability observed in the E3 ligase mutant for both plant and mammalian clocks. With this insight, we also predict a plausible regulator of several E3 ligase genes in the plant’s clock. Thus, our results provide insights into and the plausible importance in coupling transcription and post-translation controls in the clock system., Author summary For circadian clocks, several current models had successfully captured the essential dynamic behavior of the clock system mainly with transcriptional regulation. Previous studies have shown that the 26S proteasome degradation controls are important in maintaining the stability of circadian rhythms. However, how the loss-of-function or over-expression mutant of this targeted degradations lead to unstable oscillation is still unclear. In this work, we investigate the importance of coupled transcriptional and post-translational feedback loop in the circadian oscillator. With general models our study indicate that the unstable behavior of degradation mutants could be caused by the increase in the basal level of the clock genes. We found that coupling a non-linear degradation control into this transcriptional based oscillator using feed-forward loop improves the robustness of the oscillator. Using this finding, we further predict some plausible regulators of Arabidopsis’s E3 ligase protein such as COP1 and SINAT5. Hence, our results provide insights on the importance of coupling transcription and post-translation controls in the clock system.

Reactions with post-transition-state bifurcations (PTSBs) involve initial ambimodal transition-state structures followed by an unstable region leading to two possible products. PTSBs are seen in many organic, organometallic, and biosynthetic reactions, but analyzing the origins of selectivity for these reactions is challenging, in large part due to the complex nature of the potential energy surfaces involved, which precludes analyses based on single intrinsic reaction coordinate (IRC; steepest-descent path in mass-weighted coordinate). While selectivity can be predicted using molecular dynamics simulation, connecting results from such calculations to the topography of potential energy surfaces is difficult. In the present work, a method for generating two-dimensional potential energy surfaces for PTSBs is described. The first dimension starts with the IRC for the first transition-state structure, followed by a modified reaction coordinate that reaches the second transition-state structure, which interconverts the two products of a bifurcating reaction path. The IRC for the second transition-state structure constitutes the second dimension. In addition, a method for mapping trajectories from Born-Oppenheimer molecular dynamics simulations onto these surfaces is described. Both approaches are illustrated with representative examples from the field of organic chemistry. The 2D-PESs for five asymmetric cases tested have clear tilted topography after the first transition-state structure, and the tilted direction correlates well with the selectivity observed from previous dynamic simulation. Instead of selecting reaction coordinates by chemical intuition, our method provides a general means to construct two-dimensional potential energy surfaces for reactions with post-transition-state bifurcations.

Establishing appropriate sizes and shapes of dendritic arbors is critical for proper wiring of the central nervous system. Here we report that Insulin-like Peptide 2 (DILP2) locally activates transiently expressed insulin receptors in the central dendrites of Drosophila Dm8 amacrine neurons to positively regulate dendritic field elaboration. We found DILP2 was expressed in L5 lamina neurons, which have axonal terminals abutting Dm8 dendrites. Proper Dm8 dendrite morphogenesis and synapse formation required insulin signaling through TOR (target of rapamycin) and SREBP (sterol regulatory element-binding protein), acting in parallel with previously identified negative regulation by Activin signaling to provide robust control of Dm8 dendrite elaboration. A simulation of dendritic growth revealed trade-offs between dendritic field size and robustness when branching and terminating kinetic parameters were constant, but dynamic modulation of the parameters could mitigate these trade-offs. We suggest that antagonistic DILP2 and Activin signals from different afferents appropriately size Dm8 dendritic fields.

The mobility in molecular crystals exhibits anisotropy and power-law temperature dependence. In this work, we developed an analytic expression to account for the anisotropic mobility observed in molecular crystals. The charge mobility is related to the friction coefficient in the Drude model, and the latter is expressed in terms of force–force correlation function through the fluctuation–dissipation theorem, calculated with a polaron model Hamiltonian under the Merrifield transformation. With electronic couplings and reorganization energies derived from first-principle calculation, and both acoustic and optical phonons considered, the temperature dependence of mobility calculated follows the power law, μ ∝ T−2.06 (90–210 K), close to the observed T−2. The anisotropy of mobility calculated as the ratio of mobility of the fast-axis over slow-axis, μa/μb, was 2.9 (300 K). With most parameters determined by first-principle calculation, our model offers a way to predict and understand the behavior of charge mobilities of molecular crystals.

Fluorescence probes emitting in the second near-infrared (NIR-II, 1000-1700 nm) window with the ability for deep-tissue imaging in mammals herald a new era in surgical methodology. However, the brightness of these NIR-II probes is still far from satisfactory due to their low fluorescence quantum yields (QYs), preventing the observation of high-resolution images such as whole-organ vascular networks in real time. Described here is the molecular engineering of a series of semiconducting polymer dots (Pdots) incorporated with aggregation-induced emission moieties to exhibit the QYs as high as 14% in the NIR-II window. Benefiting from the ultrahigh brightness, a 1400 nm long-pass filter is utilized to realize in vivo 3D tumor mapping in mice. To further understand how the geometrical and electron structures of the semiconducting polymers affect their optical properties, the in-depth and thorough density-functional theory calculations are performed to interpret the experimental results. This study lays the groundwork for further molecular design of highly bright NIR-II Pdots.

Two series of trinuclear diimine Re(I) tricarbonyl complexes bridged by 2,4,6-tri(pyridin-4-yl)-1,3,5-triazine (L1) or 2,4,6-tri(pyridin-3-yl)-1,3,5-triazine (L2) have been synthesized and characterized. These two series of trinuclear complexes show distinctly different photophysical and electrochemical properties. The L2-bridged complexes exhibit strong luminescence and relatively long emission lifetimes in room-temperature solution, which are typical of decay from 3MLCT excited states, whereas L1-bridged complexes show only very weak luminescence and short lifetimes under the same experimental conditions. The prominent differences in the photophysical behaviors between these two groups of trinuclear complexes has been rationalized by energy gap law, which has been supported by detailed analysis of the steady state and time-resolved luminescence of these complexes. Moreover, computational results indicated that a low-lying excited state locates below 3MLCT states in the series of L1-bridged complexes.

A series of contorted and polyfused aromatic tetrabenzoacene derivatives differing in conjugation length were synthesized and characterized. X-ray diffraction revealed the contorted molecular shape, as well as the packing arrangement of these molecules. Thus unsubstituted tetrabenzoacenes showed a shifted or perfect face-to-face π-stacking depending on their conjugation length. The single crystals of these tetrabenzoacenes were used as conducting channels in fabricating field-effect transistors (SCFETs). Tetrabenzotetracene (TBT) exhibited the highest measured mobility, approaching 0.81 cm2 V−1 s−1 (average 0.64 cm2 V−1 s−1) among these molecules. In contrast, theoretical calculation showed that the tetrabenzooctacene (TBO) crystal has large-area, face-to-face π-packing, with the highest intermolecular coupling in the series. The lower charge mobility (average 0.32 cm2 V−1 s−1, highest 0.55 cm2 V−1 s−1) observed was rationalized as a result of possible involvement of delocalized polaron formation due to comparable electronic coupling and reorganization energy in TBO, as supported by the Monte Carlo simulation with this delocalized effect taken into account.

The synthesis of an exceptionally thermally stable, chemically stable, guest-free low-κ dielectric metal–organic coordination framework [Zn2(Hbbim)2(bbim)]n (1, H2bbim = bisbenzimidazole) was achieved under hydrothermal conditions. Structural analysis showed that compound 1 crystallizes in a triclinic space group P1 and possesses a guest-free structure. Compound 1 was found to be a low-κ dielectric material (3.05 at 1 MHz) that was extremely robust towards various solvents. The compound was exceptionally thermally stable and retained its structure at temperatures of up to 450 °C. Temperature-dependent dielectric studies revealed that 1 has a low-dielectric constant that remains stable upon increasing the temperature. This low-dielectric constant was further supported by density functional theory calculations, which showed that the dielectric property can be mainly attributed to electronic polarizability.