Showing papers on "Dihedral angle published in 2022"

Amplified Circularly Polarized Electroluminescence Behavior Triggered by Helical Nanofibers from Chiral Co-assembly Polymers.

Abstract: Two chiral binaphthyl polymers ( R / S -P1 and R / S -P2 ) with different dihedral angles of binaphthyl moiety were chosen as chiral inducers to construct chiral co-assemblies with an achiral pyrene-naphthalimide dye ( NPy ) and then acted as the emitting layer (EML) of CP-EL devices. The anchored dihedral angle of R / S -P2 not only exhibited the enhanced chirality signal, but also had a strong chirality-inducing effect on the achiral NPy dye in the chiral co-assembly ( R / S -P2) 0.6 -(NPy) 0.4 . After annealing at 120 °C, the CPL signal (| g em |) of ordered helical nano-fibers ( R / S -P2) 0.6 -(NPy) 0.4 was amplified to 5.6×10 -2 , which was about 6-fold larger than that of ( R / S -P1) 0.6 -(NPy) 0.4 . The amplified g em value of ( R / S -P2) 0.6 -(NPy) 0.4 was due to the formation of a helical co-assembly through the strong π-π stacking interaction between the R / S -P2 and the achiral NPy . This kind of ordered helical nano-fibers ( R / S -P2) 0.6 -(NPy) 0.4 acted as the EML of CP-OLEDs, and achieved an excellent CP-EL performance (| g EL | = 4.8×10 -2 ).

Inverted Circularly Polarized Luminescence Behavior Induced by Helical Nanofibers through Chiral Co-Assembly from Achiral Liquid Crystal Polymers and Chiral Inducers.

Abstract: Chiral supramolecular assembly can provide a powerful strategy for developing circularly polarized luminescence (CPL)-active materials by forming helices or superhelices into single or multiple components. Herein, we chose three achiral liquid crystal polymers (LC-P1/P2/P3) and chiral binaphthyl-based inducers (R/S-M) with anchored dihedral angles to construct chiral co-assemblies and explore the induced CPL behavior from pyrenyl (Py) emitters in achiral LC polymers through the regulation of helical nanofibers during the supramolecular co-assembly process. Most interestingly, chiral co-assembly (R/S-M)0.1-(P3)0.9 emitted an inverted blue-colored CPL signal during thermal annealing treatment at the glass transition temperature due to the flexible main chain of the LC polymer (LC-P3). The strongest blue-colored CPL emission for the (R/S-M)0.1-(P3)0.9 spin-coated film (λem = 455 nm, |gem| = 6.47 × 10-2, ΦF = 48.5%) could be detected by using thermal annealing treatment at 105 °C.

Polymer Mechanochromism from Force-Tuned Excited-State Intramolecular Proton Transfer.

Abstract: Real-time monitoring of strain/stress in polymers is a big challenge to date. Herein, we for the first time report an ESIPT (excited-state intramolecular proton transfer)-based mechanochromic mechanophore (MM). The synthesis of target MM PhMz-4OH [(2-hydroxyphenyl)benzimidazole with four aliphatic hydroxyls] is quite facile. PhMz-4OH possesses characteristic dual emissions, and its ESIPT activity is greatly affected by steric hindrance. Then, PhMz-4OH was covalently linked into polyurethane chains (PhMz-4OH@PU). Upon stretching, the PhMz-4OH@PU films showed fluorescence color change and spectral variation with the increase in enol emission and blueshift of keto emission due to the force-induced torsion of the dihedral angle between the proton donor and the proton acceptor. The PhMz-4OH@PU films with high mechanophore concentrations (>0.36 mol %) might undergo a two-stage force-responsive process, including torsion of the dihedral angle via force-induced disaggregation and direct chain-transduced force-induced torsion of the dihedral angle. The intensity ratio of enol emission to keto emission (IE/IK) shows a quantitative correlation with elongation, and real-time strain sensing is achieved. PhMz-4OH is a successful type II MM (without covalent bond scission) and displays high sensitivity and excellent reversibility to stress. Two control structures PhMz-NH2 and PhMz-2OH were also embedded into PU but no spectral or color changes were detected, further confirming that mechanochromism of PhMz-4OH@PU films arises from the chain-transduced force. Density function theory (DFT) calculation was performed to study the force-tuned ESIPT process theoretically and rationalize the experimental results. This study might lay the foundation for real-time stress/strain sensing in practical applications.

Computational design of mechanically coupled axle-rotor protein assemblies

Abstract: Natural molecular machines contain protein components that undergo motion relative to each other. Designing such mechanically constrained nanoscale protein architectures with internal degrees of freedom is an outstanding challenge for computational protein design. Here we explore the de novo construction of protein machinery from designed axle and rotor components with internal cyclic or dihedral symmetry. We find that the axle-rotor systems assemble in vitro and in vivo as designed. Using cryo–electron microscopy, we find that these systems populate conformationally variable relative orientations reflecting the symmetry of the coupled components and the computationally designed interface energy landscape. These mechanical systems with internal degrees of freedom are a step toward the design of genetically encodable nanomachines. Description Steps toward a nanomachine Protein rotary machines such as ATP synthase contain axle-like and ring-like components and couple biochemical energy to the mechanical work of rotating the components relative to each other. Courbet et al. have taken a step toward designing such axel-rotor nanomachines. A structural requirement is that interactions between the components must be strong enough to allow assembly but still allow different rotational states to be populated. The authors met this design challenge and computationally designed ring-like protein topologies (rotors) with a range of inner diameters that accommodate designed axle-like binding partners. The systems assemble and populate the different rotational states anticipated by the designs. These rotational energy landscapes provide one of two needed elements for a directional motor. —VV Computationally designed self-assembling axle-rotor protein systems populate multiple rotational states.

Chain Stiffness of Donor–Acceptor Conjugated Polymers in Solution

Abstract: The optoelectronic properties of conjugated polymers are dictated by their chain conformations, which depend on the interplay of delocalization of electrons along the π-conjugated backbone and the intrachain interactions of pendant side chains. Here, we leverage small-angle neutron scattering to measure the chain shapes of several classes of commonly used, high mobility donor−acceptor conjugated polymers in dilute solution. We find that these model conjugated polymers are semiflexible with persistence lengths ranging from several to hundreds of nanometers, dependent on the molecular structure of the polymer, indicating the importance of repeat unit geometry, particularly side-chain size and branching, on the overall chain conformations. The measured persistence lengths show good agreement with those calculated according to dihedral distributions predicted from density functional theory. Larger persistence lengths are shown to correlate with increased charge-carrier mobility, signifying the importance of rational molecular design to obtain high persistence length organic semiconductors and thus advantageous optoelectronic properties.

Controlling the helicity of π-conjugated oligomers by tuning the aromatic backbone twist

Abstract: The properties of π-conjugated oligomers and polymers are commonly controlled by side group engineering, main chain engineering, or conformational engineering. The last approach is typically limited to controlling the dihedral angle around the interring single bonds to prevent loss of π-conjugation. Here we propose a different approach to conformational engineering that involves controlling the twist of the aromatic units comprising the backbone by using a tether of varying lengths. We demonstrate this approach by synthesizing an inherently twisted building unit comprised of helically locked tethered acenes, bearing acetylene end-groups to enable backbone extension, which was applied in a series of nine helical oligomers with varying backbone length and twist. We find that the optical and electronic properties of π-conjugated systems may be determined by the additive, antagonistic, or independent effects of backbone length and twist angle. The twisted oligomers display chiral amplification, arising from the formation of secondary helical structures.

Controlling the helicity of π-conjugated oligomers by tuning the aromatic backbone twist

Abstract: The properties of π-conjugated oligomers and polymers are commonly controlled by side group engineering, main chain engineering, or conformational engineering. The last approach is typically limited to controlling the dihedral angle around the interring single bonds to prevent loss of π-conjugation. Here we propose a different approach to conformational engineering that involves controlling the twist of the aromatic units comprising the backbone by using a tether of varying lengths. We demonstrate this approach by synthesizing an inherently twisted building unit comprised of helically locked tethered acenes, bearing acetylene end-groups to enable backbone extension, which was applied in a series of nine helical oligomers with varying backbone length and twist. We find that the optical and electronic properties of π-conjugated systems may be determined by the additive, antagonistic, or independent effects of backbone length and twist angle. The twisted oligomers display chiral amplification, arising from the formation of secondary helical structures.

Primitive quantum gates for dihedral gauge theories

Abstract: We describe the simulation of dihedral gauge theories on digital quantum computers. The nonabelian discrete gauge group $D_N$ -- the dihedral group -- serves as an approximation to $U(1)\times\mathbb{Z}_2$ lattice gauge theory. In order to carry out such a lattice simulation, we detail the construction of efficient quantum circuits to realize basic primitives including the nonabelian Fourier transform over $D_N$, the trace operation, and the group multiplication and inversion operations. For each case the required quantum resources scale linearly or as low-degree polynomials in $n=\log N$. We experimentally benchmark our gates on the Rigetti Aspen-9 quantum processor for the case of $D_4$. The fidelity of all $D_4$ gates was found to exceed $80\%$.

Singlet Fission and Triplet Pair Recombination in Bipentacenes with a Twist

Abstract: We investigate triplet pair dynamics in pentacene dimers that have varying degrees of coplanarity (pentacene-pentacene twist angle). The fine-tuning of the twist angle was achieved by alternating connectivity at the 1-position or 2-positions of pentacene. This mix-and-match connectivity leads to tunable twist angles between the two covalently linked pentacenes. These twisted dimers allow us to investigate the subtle effects that the dihedral angle between the covalently linked pentacenes imparts on singlet fission and triplet pair recombination dynamics. We observe that as the dihedral angle between the two bonded pentacenes is increased, the rates of singlet fission decrease, while the accompanying decrease in triplet recombination rates is stark. Temperature-dependent transient optical studies combined with theoretical calculations show that the triplet pair recombination proceeds primarily through a direct multiexciton internal conversion process. Calculations further show that the significant decrease in recombination rates can be directly attributed to a corresponding decrease in the magnitude of the nonadiabatic coupling between the singlet multiexcitonic state and the ground state. These results highlight the importance of the twist angle in designing systems that exhibit rapid singlet fission, while maintaining long triplet pair lifetimes in pentacene dimers.

Optimal Dihedral Angle in Twisted Donor-Acceptor Organic Emitters for Maximized Thermally Activated Delayed Fluorescence.

Abstract: The twisted donor-acceptor (D-A) organic formwork with a large dihedral angle (θDA) is usually adopted to narrow the singlet-triplet energy gap for obtaining excellent thermally activated delayed fluorescence (TADF) emitters. However, the dependence of overall TADF properties on θDA has not been systematically investigated to this day. Taking new designed CzBP, CzBP-1M and CzBP-2M via introducing methyl as investigated models, it is found that (i) with increasing θDA, the charge transfer component in S1 is larger than that in T1 in varying degrees, leading to non-monotonic spin-orbit couplings; (ii) the electron-vibration couplings between S1 and T1 states become the largest when θDA approaching 80o, facilitating phonon-driven up-conversion; (iii) the overall TADF rate reaches a peak at θDA near 80o. By this, the TADF on/off switching is realized via methyl moiety for regulating θDA from theoretical prediction to experimental confirmation. Importantly, the θDA near 80o would be a good descriptor for screening excellent D-A type TADF emitters.

Singlet fission and triplet pair recombination in bipentacenes with a twist

Abstract: We investigate triplet pair dynamics in pentacene dimers that have varying degrees of coplanarity (pentacene-pentacene twist angle). The fine-tuning of the twist angle was achieved by alternating connectivity at the 1-position or 2-positions of pentacene. This mix-and-match connectivity leads to tunable twist angles between the two covalently linked pentacenes. These twisted dimers allow us to investigate the subtle effects that the dihedral angle between the covalently linked pentacenes imparts on singlet fission and triplet pair recombination dynamics. We observe that as the dihedral angle between the two bonded pentacenes is increased, the rates of singlet fission decrease, while the accompanying decrease in triplet recombination rates is stark. Temperature-dependent transient optical studies combined with theoretical calculations show that the triplet pair recombination proceeds primarily through a direct multiexciton internal conversion process. Calculations further show that the significant decrease in recombination rates can be directly attributed to a corresponding decrease in the magnitude of the nonadiabatic coupling between the singlet multiexcitonic state and the ground state. These results highlight the importance of the twist angle in designing systems that exhibit rapid singlet fission, while maintaining long triplet pair lifetimes in pentacene dimers.

Geometrically programmed self-limited assembly of tubules using DNA origami colloids

Abstract: Significance Nature is replete with self-assembled materials that have one or more self-limited dimensions, including shells, tubules, and fibers. Despite significant advances in making nanometer- and micrometer-scale subunits, the programmable assembly of similar self-limiting architectures from synthetic components has remained largely out of reach. In this article, we create geometrically programmed subunits using DNA origami and study their assembly into tubules with a self-limited width. We show that the average self-limited dimension can be tuned by changing the local curvature encoded in a single subunit. Exploiting the programmability of our system, we further test the tradeoffs between fidelity and complexity embodied by two paradigms for self-limited assembly: self-closure through programmed curvature and addressable assembly through programmed specific interactions.

TorsionNet: A Deep Neural Network to Rapidly Predict Small-Molecule Torsional Energy Profiles with the Accuracy of Quantum Mechanics

Abstract: Fast and accurate assessment of small-molecule dihedral energetics is crucial for molecular design and optimization in medicinal chemistry. Yet, accurate prediction of torsion energy profiles remains challenging as the current molecular mechanics (MM) methods are limited by insufficient coverage of drug-like chemical space and accurate quantum mechanical (QM) methods are too expensive. To address this limitation, we introduce TorsionNet, a deep neural network (DNN) model specifically developed to predict small-molecule torsion energy profiles with QM-level accuracy. We applied active learning to identify nearly 50k fragments (with elements H, C, N, O, F, S, and Cl) that maximized the coverage of our corporate compound library and leveraged massively parallel cloud computing resources for density functional theory (DFT) torsion scans of these fragments, generating a training data set of 1.2 million DFT energies. After training TorsionNet on this data set, we obtain a model that can rapidly predict the torsion energy profile of typical drug-like fragments with DFT-level accuracy. Importantly, our method also provides an uncertainty estimate for the predicted profiles without any additional calculations. In this report, we show that TorsionNet can accurately identify the preferred dihedral geometries observed in crystal structures. Our TorsionNet-based analysis of a diverse set of protein-ligand complexes with measured binding affinity shows a strong association between high ligand strain and low potency. We also present practical applications of TorsionNet that demonstrate how consideration of DNN-based strain energy leads to substantial improvement in existing lead discovery and design workflows. TorsionNet500, a benchmark data set comprising 500 chemically diverse fragments with DFT torsion profiles (12k MM- and DFT-optimized geometries and energies), has been created and is made publicly available.

Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon

Abstract: Abstract Synonymous codons translate into chemically identical amino acids. Once considered inconsequential to the formation of the protein product, there is evidence to suggest that codon usage affects co-translational protein folding and the final structure of the expressed protein. Here we develop a method for computing and comparing codon-specific Ramachandran plots and demonstrate that the backbone dihedral angle distributions of some synonymous codons are distinguishable with statistical significance for some secondary structures. This shows that there exists a dependence between codon identity and backbone torsion of the translated amino acid. Although these findings cannot pinpoint the causal direction of this dependence, we discuss the vast biological implications should coding be shown to directly shape protein conformation and demonstrate the usefulness of this method as a tool for probing associations between codon usage and protein structure. Finally, we urge for the inclusion of exact genetic information into structural databases.

Laplace Transform Fitting as a Tool To Uncover Distributions of Reverse Intersystem Crossing Rates in TADF Systems

Abstract: Donor–acceptor (D–A) thermally activated delayed fluorescence (TADF) molecules are exquisitely sensitive to D–A dihedral angle. Although commonly simplified to an average value, these D–A angles nonetheless exist as distributions across the individual molecules embedded in films. The presence of these angle distributions translates to distributions in the rates of reverse intersystem crossing (krISC), observed as time dependent spectral shifts and multiexponential components in the emission decay, which are difficult to directly quantify. Here we apply inverse Laplace transform fitting of delayed fluorescence to directly reveal these distributions. Rather than a single average value, the crucial krISC rate is instead extracted as a density of rates. The modes and widths of these distributions vary with temperature, host environment, and intrinsic D–A torsional rigidity of different TADF molecules. This method gives new insights and deeper understanding of TADF host–guest interactions, as well as verifies future design strategies that target D–A bond rigidity.

Short-Range Backbone Dihedral Rotations Modulate Internal Friction in Intrinsically Disordered Proteins.

Abstract: Protein folding and dynamics are governed by an intricate interplay of thermal and viscosity-mediated effects. The solvent viscosity contributes to the frictional drag in protein dynamics. In addition to this viscosity-dependent effect, there is also an intriguing viscosity-independent component that represents the intrinsic resistance of the polypeptide chain to changing its conformation. This solvent-independent component is termed internal friction. A longstanding question is what is the fundamental molecular origin of internal friction in highly solvated and rapidly fluctuating intrinsically disordered proteins (IDPs) devoid of any persistent intrachain interactions? Here, we present a unique case to directly demonstrate that sequence-specific backbone dihedral barriers control local internal friction in an archetypal IDP, namely, α-synuclein. We performed site-directed fluorescence depolarization kinetics using picosecond time-resolved fluorescence anisotropy measurements to directly observe the directional decorrelation arising due to short-range backbone torsional fluctuations in the dihedral space. A linear viscosity-dependent model of the dihedral relaxation time yielded a finite zero-viscosity intercept that corresponds to internal friction. Our site-specific dynamic readouts were able to detect localized sequence-specific frictional components that are otherwise skewed in viscosity-dependent long-range chain fluctuations. Our results revealed the presence of low internal friction in nonproline sequence segments. In contrast, a proline introduces torsional stiffness in the segment exhibiting high internal friction that can be compensated by a conformationally flexible glycine. Such an intriguing interplay of local dihedral dynamics can modulate sequence-dependent internal friction in a wide range of IDPs involved in a myriad of important events including folding, binding, assembly, and phase transitions.

Synthesis, Characterization, and Properties of Three-Dimensional Analogues of 9-Borafluorenes.

Abstract: Three-dimensional (3D) analogues of 9-borafluorenes, (C2B10H10)2BR (R = Cl (1), Br (2), H (3, merely as ether or silane adduct), phenyl (4), mesityl (5)), were synthesized and fully characterized. Gutmann-Beckett and computational fluoride/hydride ion affinity (FIA/HIA) studies confirmed the Lewis superacidity of 1-4, with the Lewis acidity of 1-3 being higher than that of the corresponding 3D analogues of 9,10-diboraanthracenes (DBA). The phenyl group and the C4B borole unit are nearly coplanar in the solid state, while the rotation of the mesityl group of 5 is hindered, forcing 5 to adopt a large C4B/Mes dihedral angle, which leads to distinct properties: air-stable and bluish-violet fluorescence arising from the intramolecular charge-transfer (ICT) transition. The 29Si NMR spectra indicated a high silylium cation character of 3·Et3SiH. The reaction of 4 with Ph3CBr yielded (Ph3C)+[(C2B10H10)2B(Ph)Br]- (6). The 4/PPh3 Lewis pair was capable of splitting dihydrogen and Si-H bond of triethylsilane.

Crystal structure and Hirshfeld surface analysis of 5-amino-5′-bromo-2′-oxo-2,3-dihydro-1<i>H</i>-spiro[imidazo[1,2-<i>a</i>]pyridine-7,3′-indoline]-6,8-dicarbonitrile dimethyl sulfoxide disolvate

Abstract: In the title compound, C16H11BrN6O·2C2H6OS, the 1,2,3,7-tetra-hydro-imid-azo[1,2-a]pyridine ring system and the oxindole moiety are both nearly planar [maximum deviations = 0.042 (2) and 0.115 (2) Å, respectively] and their planes form a dihedral angle of 86.04 (5)° with each other. Inter-molecular N-H⋯O, C-H⋯O and C-H⋯N hydrogen bonds link mol-ecules in the crystal through the O atoms of the solvent mol-ecules, generating a three-dimensional network. A Hirshfeld surface analysis was performed to further analyse the inter-molecular inter-actions.

Atomistic structures of 〈0001〉 tilt grain boundaries in a textured Mg thin film.

Abstract: Nanocrystalline Mg was sputter deposited onto an Ar ion etched Si {100} substrate. Despite an ∼6 nm amorphous layer found at the interface, the Mg thin film exhibits a sharp basal-plane texture enabled by surface energy minimization. The columnar grains have abundant 〈0001〉 tilt grain boundaries in between, most of which are symmetric with various misorientation angles. Up to ∼20° tilt angle, they are composed of arrays of equally-spaced edge dislocations. Ga atoms were introduced from focused ion beam milling and found to segregate at grain boundaries and preferentially decorate the dislocation cores. Most symmetric grain boundaries are type-1, whose boundary planes have smaller dihedral angles with {21̄1̄0} rather than {101̄0}. Atomistic simulations further demonstrate that type-2 grain boundaries, having boundary planes at smaller dihedral angles with {101̄0}, are composed of denser dislocation arrays and hence have higher formation energy than their type-1 counterparts. The finding correlates well with the dominance of type-1 grain boundaries observed in the Mg thin film.

Optimizing reaction coordinate by flux maximization in the transition path ensemble.

Abstract: The transition path ensemble is a collection of reactive trajectories, all of which largely keep going forward along the transition channel from the reactant state to the product one, and is believed to possess the information necessary for the identification of reaction coordinates. Previously, the full coordinates (both position and momentum) of the snapshots in the transition path ensemble were utilized to obtain the reaction coordinate [W. Li and A. Ma, J. Chem. Phys. 144, 114103 (2016) and W. Li, J. Chem. Phys. 148, 084105 (2018)]. Here, with the conformational (or position) coordinates alone, it is suggested that a meaningful one-dimensional representation of the reaction coordinate can be obtained by maximizing the flux (the net number of transitions through the dividing surface) of a given coordinate in the transition path ensemble. In the application to alanine dipeptide in vacuum, dihedral angles ϕ and θ were identified to be the two best reaction coordinates, which was consistent with the results in the existing studies. A linear combination of these two coordinates gave a better reaction coordinate, which is highly correlated with the committor. Most importantly, the method obtained a linear combination of pairwise distances between heavy atoms, which was highly correlated with the committor as well. The standard deviation of the committor at the transition region defined by the optimized reaction coordinate is as small as 0.08. In addition, the effects of practical factors, such as the choice of transition path sub-ensembles and saving interval between frames in transition paths, on reaction coordinate optimization were also considered.

Non-commuting graph of the dihedral group determined by Hosoya parameters

Abstract: Hosoya introduced the concept of graph terminologies in chemistry and provide a modeling for molecules. This modeling leads to predict the chemical properties of molecules, easy classification of chemical compounds, computer simulations and computer-assisted design of new chemical compounds. In this article, we determine the non-commuting graph associated with the dihedral group by using three Hosoya parameters (Hosoya polynomial, reciprocal Hosoya polynomial and Hosoya index). These Hosoya parameters contain a pile of information about distance structure as well as the edge independent structure of the above-mentioned graph.

Efficient and interpretable graph network representation for angle-dependent properties applied to optical spectroscopy

Abstract: Abstract Graph neural networks are attractive for learning properties of atomic structures thanks to their intuitive graph encoding of atoms and bonds. However, conventional encoding does not include angular information, which is critical for describing atomic arrangements in disordered systems. In this work, we extend the recently proposed ALIGNN (Atomistic Line Graph Neural Network) encoding, which incorporates bond angles, to also include dihedral angles (ALIGNN-d). This simple extension leads to a memory-efficient graph representation that captures the complete geometry of atomic structures. ALIGNN-d is applied to predict the infrared optical response of dynamically disordered Cu(II) aqua complexes, leveraging the intrinsic interpretability to elucidate the relative contributions of individual structural components. Bond and dihedral angles are found to be critical contributors to the fine structure of the absorption response, with distortions that represent transitions between more common geometries exhibiting the strongest absorption intensity. Future directions for further development of ALIGNN-d are discussed.