States Of Oligomers Research Articles

Investigating Excited States and Absorption Spectra of the Poly-cyclopenta-dithiophene-benzothiadiazole Oligomers (Poly-CPDTBT)-A Theoretical Study.

Poly-CPDTBT, as typical low-band gap copolymers, have potential applications in organic bulk heterojunction solar cells. To have a clear picture of its excited-state processes, the first task is to understand their excited states, in particular, electronic character and relevant optical absorption. Herein, the low-lying singlet excited states of Poly-CPDTBT oligomers were investigated via Algebraic Diagrammatic Construction Second Order (ADC(2)) and time-dependent density functional theory (TDDFT) method with several functionals. Six CPDTBTN (N = 1-6) oligomers were taken as prototypes to study their excited states in detail. The results provide interesting clues to extrapolate the photophysical properties of such polymers with potential applications in photovoltaic materials. The result provided by ωB97XD functional gives good agreement with the experiment result. The vertical excitation energies of the four lowest excited states decrease almost linearly with increasing polymerization degree (N) for CPDTBTN (N = 1-6). The transition density analysis indicates that the local excitations (LE) and the short-distance charge transfer (CT) excitations between two adjacent CPDT and BT units are dominant for low-lying excited states for short oligomers. For the long-chain oligomers (trimer to hexamer), the transition density shows a ladder (or zigzag) pattern along the diagonal blocks at the planar geometry. For long oligomers, the whole chain is involved in the transitions, and the CT excitations only exist between two adjacent CPDT and BT units. The present work provides a valuable basis for understanding the excited-state processes of Poly-CPDTBT and other conjugated polymers that conduct solar energy conversions, which has great significance for the development of new solar cells.

High-Throughput Single-Particle Characterization of Aggregation Pathways and the Effects of Inhibitors for Large (Megadalton) Protein Oligomers.

Protein aggregation is involved in many human diseases, but characterizing the sizes and shapes of intermediate oligomers (∼10-100 nm) that are important to the formation of macroscale aggregates like amyloid fibrils is a significant analytical challenge. Here, charge detection mass spectrometry (CDMS) is used to characterize individual conformational states of bovine serum albumin oligomers with up to ∼225 molecules (15 MDa). Elongated, partially folded, and globular conformational families for each oligomer can be readily distinguished based on the extent of charging. The abundances of individual conformers vary with changes in the monomer concentration or by adding aggregation inhibitors, such as SDS, heparin, or MgCl2. These results show the potential of CDMS for investigating intermediate oligomers in protein aggregation processes that are important for understanding aggregate formation and inhibition mechanisms and could accelerate formulation buffer development to prevent the aggregation of biotherapeutics.

Single-molecule digital sizing of proteins in solution

The physical characterization of proteins in terms of their sizes, interactions, and assembly states is key to understanding their biological function and dysfunction. However, this has remained a difficult task because proteins are often highly polydisperse and present as multicomponent mixtures. Here, we address this challenge by introducing single-molecule microfluidic diffusional sizing (smMDS). This approach measures the hydrodynamic radius of single proteins and protein assemblies in microchannels using single-molecule fluorescence detection. smMDS allows for ultrasensitive sizing of proteins down to femtomolar concentrations and enables affinity profiling of protein interactions at the single-molecule level. We show that smMDS is effective in resolving the assembly states of protein oligomers and in characterizing the size of protein species within complex mixtures, including fibrillar protein aggregates and nanoscale condensate clusters. Overall, smMDS is a highly sensitive method for the analysis of proteins in solution, with wide-ranging applications in drug discovery, diagnostics, and nanobiotechnology.

The efficient triplet states formation of Se-modified PDI dimers and tetramers in solvents.

The triplet excited states of molecules play an important role in photophysical processes, which has attracted great research interest. Perylene diimide (PDI) is a widely studied material closely associated with the generation of triplet states, and it is highly anticipated to become an electron acceptor material for improving photovoltaic conversion efficiency. In this work, we prepared dimers and tetramers composed of selenium-modified PDI-C5 (N,N'-bis(6-undecyl) perylene-3,4,9,10-bis(dicarboximide)) units. We investigated the photophysical processes of these dimers and tetramers in chloroform and toluene using UV-visible absorption spectroscopy, fluorescence spectroscopy, and femtosecond transient absorption spectroscopy. Both the dimers and tetramers undergo efficient triplet state formation processes in the solvents. Solvents with higher polarity facilitate charge transfer thereby promote the triplet states formation. The differences in the configurations of the dimer and tetramer molecules lead to variations in triplet states generation. The twisted angles in the tetramer restricted the intramolecular electronic coupling, posing certain hindrances to exciton coupling and lowering the intramolecular CT characteristics. The emission of excimer in tetramers also competes with the triplet states formation. The research demonstrates the influence of various factors on the generation of triplet states of PDI oligomers.

Determining the Functional Oligomeric State of Membrane-Associated Protein Oligomers Forming Membrane Pores on Giant Lipid Vesicles.

Several peripheral membrane proteins are known to form membrane pores through multimerization. In many cases, in biochemical reconstitution experiments, a complex distribution of oligomeric states has been observed that may, in part, be irrelevant to their physiological functions. This phenomenon makes it difficult to identify the functional oligomeric states of membrane lipid interacting proteins, for example, during the formation of transient membrane pores. Using fibroblast growth factor 2 (FGF2) as an example, we present a methodology applicable to giant lipid vesicles by which functional oligomers can be distinguished from nonspecifically aggregated proteins without functionality. Two distinct populations of fibroblast growth factor 2 were identified with (i) dimers to hexamers and (ii) a broad population of higher oligomeric states of membrane-associated FGF2 oligomers significantly distorting the original unfiltered histogram of all detectable oligomeric species of FGF2. The presented statistical approach is relevant for various techniques for characterizing membrane-dependent protein oligomerization.

Alphafold Predictions Provide Insights into the Structural Features of the Functional Oligomers of All Members of the KCTD Family.

Oligomerization endows proteins with some key properties such as extra-stabilization, long-range allosteric regulation(s), and partnerships not accessible to their monomeric counterparts. How oligomerization is achieved and preserved during evolution is a subject of remarkable scientific relevance. By exploiting the abilities of the machine-learning algorithms implemented in AlphaFold (AF) in predicting protein structures, herein, we report a comprehensive analysis of the structural states of functional oligomers of all members of the KCTD protein family. Interestingly, our approach led to the identification of reliable three-dimensional models for the pentameric states of KCNRG, KCTD6, KCTD4, KCTD7, KCTD9, and KCTD14 and possibly for KCTD11 and KCTD21 that are involved in key biological processes and that were previously uncharacterized from a structural point of view. Although for most of these proteins, the CTD domains lack any sequence similarity, they share some important structural features, such as a propeller-like structure with a central cavity delimited by five exposed and regular β-strands. Moreover, the structure of the related proteins KCTD7 and KCTD14, although pentameric, appears to be characterized by a different organization of the CTD region, with the five chains forming a circle-like structure with a large cavity. Our predictions also suggest that other members of the family, such as KCTD10, KCTD13, and TNFAIP1, present a strong propensity to assume dimeric states. Although the structures of the functional oligomers reported herein represent models that require additional validations, they provide a consistent and global view of KCTD protein oligomerization.

Oligomeric State Transitions of Pore Forming Toxins Induce Non-Monotonic Lipid Dynamics in Biomembranes

Membrane-bound protein complexes involving PFTs, released by virulent bacteria are known to form pores leading to host cell lysis. However, membrane remodelling and related repair processes during attack by PFTs remain largely unexplored. in our recent experiments [1] with GUVs exposed to prototypical cholesterol dependent cytolysin, Listeriolysin O (LLO), we were able to correlate changes in lipid dynamics to membrane bound conformational states of LLO oligomers. We now report non-monotonic variations in lipid diffusion due to interplay of lipid ejection and crowding by membrane bound oligomers of LLO. Our experiments monitor lipid dynamics and membrane micro-rheology over a broad range of protein-to-lipid ratios encompassing the dilute, intermediate as well as the crowded regime. This systematic variation of protein concentration reveals for the first time a unique non-monotonic behaviour of lipid diffusivity as a function of PFT concentration which falls outside the purview of existing membrane dynamics models. by monitoring the fluorescent intensity of lipids using confocal microscopy and number of lipids in FCS we provide direct evidence of lipid loss during pore formation. Not only do we observe the anticipated crowding induced decreasing lipid diffusivities at high protein concentration, but our results reveal a counter-intuitive increase in lipid diffusivity at intermediate LLO concentrations. We quantitatively capture these trends using an established model based on the dependence of membrane lipidxdiffusion on the available free area. We correlate changes in observed lipid diffusivity to the free area contributions from different PFT oligomeric states, thus providing unique insights connecting lipid dynamics to bound protein distributions. 1. Ilanila IP, Ramesh Cheerla, K Ganapathy Ayappa and Jaydeep K Basu, “Correlated protein conformational states and membrane dynamics during attack by pore-forming toxins”, Proc Nat Acad Sci. 116, 12839 (2019).

Supramolecular nanochannels self-assembled by helical pyridine-pyridazine oligomers.

Herein, we demonstrate a supramolecular nanochannel formed by intermolecular π stacking of pyridine-pyridazine helical oligomers, wherein alkali ions could be easily recognized and transported. Importantly, this nanochannel also revealed reversible collection and triggered-release behaviors via modulating the folded and unfolded states of helical pyridine-pyridazine oligomers.

Comparing the Aggregation Free Energy Landscapes of Amyloid Beta(1-42) and Amyloid Beta(1-40).

Using a predictive coarse-grained protein force field, we compute and compare the free energy landscapes and relative stabilities of amyloid-β protein (1-42) and amyloid-β protein (1-40) in their monomeric and oligomeric forms up to the octamer. At the same concentration, the aggregation free energy profile of Aβ42 is more downhill, with a computed solubility that is about 10 times smaller than that of Aβ40. At a concentration of 40 μM, the clear free energy barrier between the pre-fibrillar tetramer form and the fibrillar pentamer in the Aβ40 aggregation landscape disappears for Aβ42, suggesting that the Aβ42 tetramer has a more diverse structural range. To further compare the landscapes, we develop a cluster analysis based on the structural similarity between configurations and use it to construct an oligomerization map that captures the paths of easy interconversion between different but structurally similar states of oligomers for both species. A taxonomy of the oligomer species based on β-sheet stacking topologies is proposed. The comparison of the two oligomerization maps highlights several key differences in the landscapes that can be attributed to the two additional C-terminal residues that Aβ40 lacks. In general, the two terminal residues strongly stabilize the oligomeric structures for Aβ42 relative to Aβ40, and greatly facilitate the conversion from pre-fibrillar trimers to fibrillar tetramers.

Sequence analysis of cyclic polyester copolymers using ion mobility tandem mass spectrometry

Tandem mass spectrometry (MS2) via collisionally activated dissociation (CAD), coupled with ion mobility (IM) separation, has been employed to determine the sequence of macrocyclic polyester copolymers with thermoresponsive properties. The polyesters were synthesized by polyesterification of succinic acid with two diols functionalized with different, bioinspired amide pendants. MS analysis confirmed the formation of cyclic and linear chains composed of two different polyester repeat units, N and P. MS2 experiments on the sodiated macrocyclic trimer P3 showed that fragmentation encompasses ring opening by 1,5-H rearrangement over an ester group and consecutive dissociation of the ring-opened species via the same mechanism. Investigation of the macrocyclic trimers N1P2 and N2P3 revealed that ring opening occurs randomly at any of the ester groups of the macrocycle. Armed with these data, the sequence of the macrocyclic tetramer N2P2 was elucidated based on the dimeric NN, NP (or PN), and PP fragments generated by CAD of the sodiated ion. The observed fragment distribution provided evidence that the tetramer had predominantly a block architecture, viz. cyclo-NNPP. Preference for the block arrangement of the monomers was also found for a linear oligomer with four diol units. The IM dimension enabled the examination of singly sodiated cyclic or linear chains that overlapped with higher charge states of larger oligomers. The described sequencing strategy should be generally applicable to polymers with ester groups in the backbone. The architectural information deduced by such sequencing would significantly facilitate structure/property correlations and the design of copolymers with the desired physical properties.

Deciphering Molecular Mechanisms of Interface Buildup and Stability in Porous Si/Eumelanin Hybrids.

Porous Si/eumelanin hybrids are a novel class of organic–inorganic hybrid materials that hold considerable promise for photovoltaic applications. Current progress toward device setup is, however, hindered by photocurrent stability issues, which require a detailed understanding of the mechanisms underlying the buildup and consolidation of the eumelanin–silicon interface. Herein we report an integrated experimental and computational study aimed at probing interface stability via surface modification and eumelanin manipulation, and at modeling the organic–inorganic interface via formation of a 5,6-dihydroxyindole (DHI) tetramer and its adhesion to silicon. The results indicated that mild silicon oxidation increases photocurrent stability via enhancement of the DHI–surface interaction, and that higher oxidation states in DHI oligomers create more favorable conditions for the efficient adhesion of growing eumelanin.

Effect of Conjugation Length on Photoinduced Charge Transfer in π-Conjugated Oligomer-Acceptor Dyads.

A series of π-conjugated oligomer-acceptor dyads were synthesized that feature oligo(phenylene ethynylene) (OPE) conjugated backbones end-capped with a naphthalene diimide (NDI) acceptor. The OPE segments vary in length from 4 to 8 phenylene ethynene units (PEn-NDI, where n = 4, 6 and 8). Fluorescence and transient absorption spectroscopy reveals that intramolecular OPE → NDI charge transfer dominates the deactivation of excited states of the PEn-NDI oligomers. Both charge separation (CS) and charge recombination (CR) are strongly exothermic (ΔG0CS ∼ -1.1 and ΔG0CR ∼ -2.0 eV), and the driving forces do not vary much across the series because the oxidation and reduction potentials and singlet energies of the OPEs do not vary much with their length. Bimolecular photoinduced charge transfer between model OPEs that do not contain the NDI acceptors with methyl viologen was studied, and the results reveal that the absorption of the cation radical state (OPE+•) remains approximately constant (λ ∼ 575 nm) regardless of oligomer length. This finding suggests that the cation radical (polaron) of the OPE is relatively localized, effectively occupying a confined segment of n ≤ 4 repeat units in the longer oligomers. Photoinduced intramolecular electron transfer dynamics in the PEn-NDI series was investigated by UV-visible femtosecond transient absorption spectroscopy with visible and mid-infrared probes. Charge separation occurs on the 1-10 ps time scale with the rates decreasing slightly with increased oligomer length (βCS ∼ 0.15 Å-1). The rate for charge-recombination decreases in the sequence PE4-NDI > PE6-NDI ∼ PE8-NDI. The discontinuous distance dependence in the rate for charge recombination may be related to the spatial localization of the positive polaron state in the longer oligomers.

ChemInform Abstract: Structural Insights into the Polymorphism of Self‐Assembled Amylin Oligomers

AbstractReview: 43 refs.

Excitonic Coupling and Femtosecond Relaxation of Zinc Porphyrin Oligomers Linked with Triazole Bridge: Dynamics and Modeling.

The synthesis of new zinc porphyrin oligomers linked by a triazole bridge was carried out via "click" reaction. A split in the porphyrin oligomer B-band was observed. It was considered as evidence of exciton-excitonic coupling. The relaxation of excited states in Q-band porphyrin oligomers was studied by the femtosecond laser spectroscopy technique with a 20 fs pump pulse. The transient oscillations of two B-band excitonic peaks have a π-radian shift. For explanation of the coherent oscillation, a theoretical model was developed. The model considered the combination of the exciton-excitonic coupling between porphyrin rings in dimer and weak exciton-vibronic coupling in one porphyrin ring. By varying the values of the structural parameters of porphyrins (the strength values of this couplings and measure of symmetry breaking), we obtained correspondence between the experimental data (phase shift and amplitudes of the spectrum oscillations) and the predictions of the model developed here.

Theoretical insights into the photo-protective mechanisms of natural biological sunscreens: building blocks of eumelanin and pheomelanin.

Eumelanin (EM) and pheomelanin (PM) are ubiquitous in mammalian skin and hair--protecting against harmful radiation from the sun. Their primary roles are to absorb solar radiation and efficiently dissipate the excess excited state energy in the form of heat without detriment to the polymeric structure. EU and PM exist as polymeric chains consisting of exotic arrangements of functionalised heteroaromatic molecules. Here we have used state-of-the-art electronic structure calculations and on-the-fly surface hopping molecular dynamics simulations to study the intrinsic deactivation paths of various building blocks of EU and PM. Ultrafast excited state decay, via electron-driven proton transfer (in EU and PM) and proton-transfer coupled ring-opening (in PM) reactions, have been identified to proceed along hitherto unknown charge-separated states in EU and PM oligomers. These results shed light on the possible relaxation pathways that dominate the photochemistry of natural skin melanins. Extrapolation of such findings could provide a gateway into engineering more effective molecular constituents in commercial sunscreens--with reduced phototoxicity.

Photogenerated triplet states in supramolecular porphyrin ladder assemblies: an EPR study.

Introducing bridging ligands such as DABCO to solutions of linear zinc porphyrin oligomers has previously been shown to lead to the formation of ladder-type assemblies in which the single porphyrin units in each strand adopt a predominantly co-planar conformation. Here, we employ transient Electron Paramagnetic Resonance (EPR) to study photogenerated triplet states of these complexes in frozen solution with a particular focus on the extent of spin delocalisation. We make use of two different techniques: (i) the zero-field splitting parameters D and E are determined using transient continuous wave (cw) EPR spectroscopy and (ii) the hyperfine coupling constants, which directly reveal the extent of spin delocalisation, are quantified by orientation-selective proton Electron Nuclear DOuble Resonance (ENDOR) spectroscopy. It is found that ladder formation does not encourage triplet state delocalisation either across the bridging ligand DABCO or along the individual porphyrin strands despite their co-planar conformation, which was previously shown to allow increased electronic delocalisation.

Low-lying electronic excited states of pentacene oligomers: a comparative electronic structure study in the context of singlet fission.

The lowest-lying electronic excited states of pentacene and its oligomers are investigated using accurate multireference wave function methods (CASPT2/CASSCF) and the many-body Greens's function approach (GW/BSE). The results obtained for dimers and trimers of different geometry reveal a complex electronic structure, which includes locally excited, charge transfer, and multiexciton states. For singlets of single-excitation character, both approaches yield excitation energies that are in good overall quantitative agreement. While the multiexciton states are located relatively high in energy in all systems investigated, charge transfer states exist in close proximity to the lowest-lying absorbing states. The implications of the results for the mechanisms of singlet fission in pentacene are discussed.

Electronic Excitations in Push–Pull Oligomers and Their Complexes with Fullerene from Many-Body Green’s Functions Theory with Polarizable Embedding

We present a comparative study of excited states in push-pull oligomers of PCPDTBT and PSBTBT and prototypical complexes with a C60 acceptor using many-body Green's functions theory within the GW approximation and the Bethe-Salpeter equation. We analyze excitations in oligomers up to a length of 5 nm and find that for both materials the absorption energy practically saturates for structures larger than two repeat units due to the localized nature of the excitation. In the bimolecular complexes with C60, the transition from Frenkel to charge transfer excitons is generally exothermic and strongly influenced by the acceptor's position and orientation. The high CT binding energy of the order of 2 eV results from the lack of an explicit molecular environment. External polarization effects are then modeled in a GW-BSE based QM/MM approach by embedding the donor-acceptor complex into a polarizable lattice. The lowest charge transfer exciton is energetically stabilized by about 0.5 eV, while its binding energy is reduced to about 0.3 eV. We also identify a globally unbound charge transfer state with a more delocalized hole at higher energy while still within the absorption spectrum, which opens another potential pathway for charge separation. For both PCPDTBT and PSBTBT, the energetics are largely similar with respect to absorption and the driving force to form intermediate charge transfer excitations for free charge generation. These results support that the higher power conversion efficiency observed for solar cells using PSBTBT as donor material is a result of molecular packing rather than of the electronic structure of the polymer.

Electronic structure of conducting organic polymers: insights from time‐dependent density functional theory

Conducting organic polymers (COPs) became an active field of research after it was discovered how thin films rather than insoluble infusible powders can be produced. The combination of the properties of plastics with those of semiconductors opened the research field of organic electronics. COPs share many electronic properties with inorganic semiconductors, but there are also major differences, e.g., the nature of the charge carriers and the amount of the exciton binding energy. Theoretical analysis has been used to interpret experimental observations early on. The polaron model that was developed from one‐electron theories is still the most widely used concept. In the 1990s, time‐dependent density functional theory (TDDFT) became available for routine calculations. Using TDDFT, electronic states of long oligomers can be calculated. Now UV spectra of neutral and oxidized or reduced species can be compared with in situ UV spectra recorded during doping. Likewise states of cations can be used to model photoelectron spectra. Analysis of states has resolved several puzzles which cannot be understood with the polaron model, e.g., the origin of the dual absorption band of green polymers and the origin of a ‘vestigial neutral band’ upon doping of long oligomers. DFT calculations also established that defect localization is not crucial for spectral changes observed during doping and that there are no bound bipolarons in COPs. WIREs Comput Mol Sci 2014, 4:601–622. doi: 10.1002/wcms.1194This article is categorized under: Structure and Mechanism > Computational Materials Science Electronic Structure Theory > Density Functional Theory Theoretical and Physical Chemistry > Spectroscopy

Quantum dynamics of ultrafast exciton relaxation on a minimal lattice

A combined electronic structure and quantum dynamical study is presented that addresses the nature of the low-lying excitonic states in thiophene oligomers, and the evolution of such states in the presence of a torsional defect. Electronic structure calculations for a thiophene hexamer are carried out using the Second-Order Approximate Coupled-Cluster (CC2) method in conjunction with a transition density analysis. The latter analysis connects to an electron–hole quasi-particle representation that is subsequently used in the quantum dynamical description. Quantum dynamical propagation using the Multi-Configuration Time-Dependent Hartree (MCTDH) method is carried out on a minimal six-site lattice, yielding a basis of 36 electron–hole states in accordance with a Merrifield exciton model. The analysis accounts for vibronic coupling to site-correlated inter-ring stretch modes and a central ring torsional mode that in turn interacts with a dissipative harmonic-oscillator bath, similarly to our recent study of oligo-(p-phenylene vinylene) systems (Binder et al., Faraday Discuss. 163, 205, 2013). The dynamical description illustrates how a partially delocalized initial exciton coherently expands across a torsional defect and converges to a local exciton ground state on a larger fragment within about 300 femtoseconds. Exciton relaxation is found to occur as an intrinsic property of the finite-dimensional lattice structure featuring vibronic couplings.