Dimeric State Research Articles

Deciphering the Monomeric and Dimeric Conformational Landscapes of the Full-Length TDP-43 and the Impact of the C-Terminal Domain.

The aberrant aggregation of TAR DNA-binding protein 43 kDa (TDP-43) in cells leads to the pathogenesis of multiple fatal neurodegenerative diseases. Decoding the proposed initial transition between its functional dimeric and aggregation-prone monomeric states can potentially design a viable therapeutic strategy, which is presently limited by the lack of structural detail of the full-length TDP-43. To achieve a complete understanding of such a delicate phase space, we employed a multiscale simulation approach that unearths numerous crucial features, broadly summarized in two categories: (1) state-independent features that involve inherent chain collapsibility, rugged polymorphic landscape dictated by the terminal domains, high β-sheet propensity, structural integrity preserved by backbone-based intrachain hydrogen bonds and electrostatic forces, the prominence of the C-terminal domain in the intrachain cross-domain interfaces, and equal participation of hydrophobic and hydrophilic (charged and polar) residues in cross-domain interfaces; and (2) dimerization-modulated characteristics that encompass slower collapsing dynamics, restricted polymorphic landscape, the dominance of side chains in interchain hydrogen bonds, the appearance of the N-terminal domain in the dimer interface, and the prominence of hydrophilic (specifically polar) residues in interchain homo- and cross-domain interfaces. In our work, the ill-known C-terminal domain appears as the most crucial structure-dictating domain, which preferably populates a compact conformation with a high β-sheet propensity in its isolated state stabilized by intrabackbone hydrogen bonds, and these signatures are comparatively faded in its integrated form. Validation of our simulated observables by a complementary spectroscopic approach on multiple counts ensures the robustness of the computationally predicted features of the TDP-43 aggregation landscape.

HMGCS1 variants cause rigid spine syndrome amenable to mevalonic acid treatment in an animal model.

Rigid spine syndrome is a rare childhood-onset myopathy characterised by slowly progressive or non-progressive scoliosis, neck and spine contractures, hypotonia, and respiratory insufficiency. Biallelic variants in SELENON account for most cases of rigid spine syndrome, however, the underlying genetic cause in some patients remains unexplained. We used exome and genome sequencing to investigate the genetic basis of rigid spine syndrome in patients without a genetic diagnosis. In five patients from four unrelated families, we identified biallelic variants in HMGCS1 (3-hydroxy-3-methylglutaryl-coenzyme A synthase). These included six missense variants and one frameshift variant distributed throughout HMGCS1. All patients presented with spinal rigidity primarily affecting the cervical and dorsolumbar regions, scoliosis, and respiratory insufficiency. Creatine kinase levels were variably elevated. The clinical course worsened with intercurrent disease or certain drugs in some patients; one patient died from respiratory failure following infection. Muscle biopsies revealed irregularities in oxidative enzyme staining with occasional internal nuclei and rimmed vacuoles. HMGCS1 encodes a critical enzyme of the mevalonate pathway and has not yet been associated with disease. Notably, biallelic hypomorphic variants in downstream enzymes including HMGCR and GGPS1 are associated with muscular dystrophy resembling our cohort's presentation. Analyses of recombinant human HMGCS1 protein and four variants (p.S447P, p.Q29L, p.M70T, p.C268S) showed that all mutants maintained their dimerization state. Three of the four mutants exhibited reduced thermal stability, and two mutants showed subtle changes in enzymatic activity compared to the wildtype. Hmgcs1 mutant zebrafish displayed severe early defects, including immobility at 2 days and death by day 3 post-fertilisation and were rescued by HMGCS1 mRNA. We demonstrate that the four variants tested (S447P, Q29L M70T, and C268S) have reduced function compared to wildtype HMGCS1 in zebrafish rescue assays. Additionally, we demonstrate the potential for mevalonic acid supplementation to reduce phenotypic severity in mutant zebrafish. Overall, our analyses suggest that these missense variants in HMGCS1 act through a hypomorphic mechanism. Here, we report an additional component of the mevalonate pathway associated with disease and suggest biallelic variants in HMGCS1 should be considered in patients presenting with an unresolved rigid spine myopathy phenotype. Additionally, we highlight mevalonoic acid supplementation as a potential treatment for patients with HMGCS1-related disease.

Identification of a Hidden, Highly Aggregation-Prone Intermediate of Full-Length TDP-43 That Triggers its Misfolding and Amyloid Aggregation.

In cells, TDP-43 is a crucial protein that can form harmful amyloid aggregates linked to fatal and incurable human neurodegenerative disorders. Normally, TDP-43 exists in a smaller soluble native state that prevents aggregation. However, aging and stress can destabilize this native state, leading to the formation of disease-causing amyloid aggregates via the formation of partially unfolded, high-energy intermediates with a greater tendency to aggregate. These intermediates are crucial in the early stages of amyloid formation and are challenging to study due to their low stability. Understanding the structure of these early aggregation-prone states of TDP-43 is essential for designing effective treatments for TDP-43 proteinopathies. Targeting these initial intermediates could be more effective than focusing on fully formed amyloid aggregates. By disrupting the aggregation process at this early stage, we may be able to prevent the progression of diseases related to TDP-43 aggregation. Hence, we decided to uncover the hidden, high-energy intermediates in equilibrium with the native states of TDP-43 by modulating the thermodynamic stability of the soluble native dimer (N form) and monomeric molten globular state (MG form) of full-length TDP-43. The thermodynamic modulation performed in the current study successfully revealed the highly aggregation-prone intermediate of full-length TDP-43, i.e., PUF. Moreover, we observed that along with high aggregation propensity, the aggregation kinetics and mechanisms of PUF differ from previously identified intermediates of full-length TDP-43 (the MG and I forms). The information regarding the initial aggregation-prone state of full-length TDP-43 could lead to therapies for amyloid diseases by halting early protein aggregation.

Structural and catalytic properties of histidyl-tRNA synthetase: A potential drug target against leishmaniasis

Visceral leishmaniasis is caused by Leishmania donovani which affects the poorer sections of society, and despite the global spread, effective treatment is unavailable. The current study investigates the potential of leishmanial histidyl-tRNA synthetase (LdHisRS) as a drug target. LdHisRS delineated more closeness to other protozoan parasites than its mammalian counterparts and contained relevant differences in the active site residues. The important ATP-binding residues were mutated to alanine and all the proteins, including human HisRS, were purified to homogeneity. LdHisRS exhibited a dimeric state in solution and showed maximal amino acid activation activity in physiological conditions. It also demonstrated a greater affinity for substrate over cofactor, while magnesium and potassium enhanced its activity better than other tested metal ions. Comp-7m, a benzothiazolo-coumarin derivative, proved to be specific inhibitor of LdHisRS with competitive mode of inhibition for ATP whereas it displayed lower binding affinity towards mutants. LdHisRS majorly contained α-helices and most of the aromatic residues were present in its hydrophobic core. Additionally, Comp-7m superimposed on ATP adenine ring during docking analysis and LdHisRS-ligand complexes had comparable stability as well as rigidity in molecular dynamics simulation. We thus provide structural and functional insights of LdHisRS which can be useful for devising antileishmanials.

MAD2L2 Dimerization Is Not Essential for Mitotic Regulation.

MAD2L2 is a small HORMA domain protein that plays a crucial role in DNA repair and mitosis. In both TLS and shieldin, the dimerization of MAD2L2 via its HORMA domain is critical for the stability and function of these complexes. However, in mitosis, the dimerization state of MAD2L2 remains unknown. To assess the importance of MAD2L2's dimerization during mitosis, we utilized CRISPR/Cas9 to generate MAD2L2 knockout cells, which were subsequently complemented with MAD2L2 species carrying different dimer-disrupting point mutations. We assessed the ability of these MAD2L2 dimer-disrupting mutants to regulate mitosis by evaluating early mitotic events and mitotic fidelity. Our findings indicate that MAD2L2 can function in its monomeric form during mitosis, suggesting that MAD2L2 homodimerization is dispensable for early mitotic regulation. Furthermore, our results suggest that the binding of CDH1 to MAD2L2 is a key regulating factor in mitosis that may actively prevent the formation of MAD2L2 dimers, thereby shifting the cellular balance toward MAD2L2-CDH1 interaction. Thus, the equilibrium between the monomeric and dimeric forms of MAD2L2 is an important cellular factor regulating the MAD2L2-containing complexes.

In Silico Modeling of Myelin Oligodendrocyte Glycoprotein Disulfide Bond Reduction by Phosphine-Borane Complexes

Background: Neurodegenerative diseases can cause vision loss by damaging retinal ganglion cells in the optic nerve. Novel phosphine-borane compounds (PBs) can protect these cells from oxidative stress via the reduction of disulfide bonds. However, the specific targets of these compounds are unknown. Proteomic evidence suggests that myelin oligodendrocyte glycoprotein (MOG) is a potential target. MOG is of significant interest due to its role in anti-MOG optic neuritis syndrome. Methods: We used in silico modeling to explore the structural consequences of cleaving the extracellular domain MOG disulfide bond, both in isolation and in complex with anti-MOG antibodies. The potential binding of PBs to this bond was examined using molecular docking. Results: Cleaving the disulfide bond of MOG altered the structure of MOG dimers and reduced their energetic favorability by 46.13 kcal/mol. The energy profiles of anti-MOG antibody complexes were less favorable when the disulfide bond of MOG was reduced in the monomeric state by 55.21 kcal/mol, but the reverse was true in the dimeric state. PBs exhibited reducing capabilities with the MOG extracellular disulfide bond, with this best-scoring compound binding with an energy of −28.54 kcal/mol to the MOG monomer and −24.97 kcal/mol to the MOG dimer. Conclusions: These findings suggest that PBs can affect the structure of MOG dimers and the formation of antibody complexes by reducing the MOG disulfide bond. Structural changes in MOG could have implications for neurodegenerative diseases and anti-MOG syndrome.

Kinetics of Polyampholyte Dimerization: Influence of Charge Sequences

Polyampholytes (PAs) exhibit complex behaviors in various environments influenced by their charge distribution. This study focuses on the kinetics of dimerization of PAs, aiming to elucidate the underlying mechanisms and clarify relevant characteristics of the charge sequence. We focus on PAs with non-zero net charges, employing molecular dynamics simulations and theoretical analyses to examine how charge sequences influence the rates of dimer formation and dissociation. Our findings reveal that the charge sequence of tails and the blockiness of the minority charge group markedly influence the kinetics of dimerization: large blockiness and tails with a high number of majority-type charges slow down the dissociation of dimers. Additionally, the presence of an extended (central) block of the majority charge promotes structural diversity. Within dimer states, blocks alternate between intra- and inter-chain contacts. The duration times in the dimer states are significantly longer than the typical dwell times of block inter-contacts, with a notable extension when multiple blocks are engaged. Intrinsically disordered proteins (IDPs) play crucial roles in cellular functions, primarily due to their ability to undergo rapid conformational changes and form transient complexes. These properties largely depend on the sequence of charged residues. We provide insights into the fundamental principles governing the structural and dynamical properties of polyampholytic IDP, emphasizing the importance of sequence-specific effects on both aggregation and dissociation.

Cryo-electron microscopy structure of the di-domain core of Mycobacterium tuberculosis polyketide synthase 13, essential for mycobacterial mycolic acid synthesis.

Mycobacteria are known for their complex cell wall, which comprises layers of peptidoglycan, polysaccharides and unusual fatty acids known as mycolic acids that form their unique outer membrane. Polyketide synthase 13 (Pks13) of Mycobacterium tuberculosis, the bacterial organism causing tuberculosis, catalyses the last step of mycolic acid synthesis prior to export to and assembly in the cell wall. Due to its essentiality, Pks13 is a target for several novel anti-tubercular inhibitors, but its 3D structure and catalytic reaction mechanism remain to be fully elucidated. Here, we report the molecular structure of the catalytic core domains of M. tuberculosis Pks13 (Mt-Pks13), determined by transmission cryo-electron microscopy (cryoEM) to a resolution of 3.4 Å. We observed a homodimeric assembly comprising the ketoacyl synthase (KS) domain at the centre, mediating dimerization, and the acyltransferase (AT) domains protruding in opposite directions from the central KS domain dimer. In addition to the KS-AT di-domains, the cryoEM map includes features not covered by the di-domain structural model that we predicted to contain a dimeric domain similar to dehydratases, yet likely lacking catalytic function. Analytical ultracentrifugation data indicate a pH-dependent equilibrium between monomeric and dimeric assembly states, while comparison with the previously determined structures of M. smegmatis Pks13 indicates architectural flexibility. Combining the experimentally determined structure with modelling in AlphaFold2 suggests a structural scaffold with a relatively stable dimeric core, which combines with considerable conformational flexibility to facilitate the successive steps of the Claisen-type condensation reaction catalysed by Pks13.

Spontaneous Dimerization and Distinct Packing Modes of Transmembrane Domains in Receptor Tyrosine Kinases.

The insulin receptor (IR) and the insulin-like growth factor-1 receptor (IGF1R) are homodimeric transmembrane glycoproteins that transduce signals across the membrane on binding of extracellular peptide ligands. The structures of IR/IGF1R fragments in apo and liganded states have revealed that the extracellular subunits of these receptors adopt Λ-shaped configurations to which are connected the intracellular tyrosine kinase (TK) domains. The binding of peptide ligands induces structural transitions in the extracellular subunits leading to potential dimerization of transmembrane domains (TMDs) and autophosphorylation in TKs. However, the activation mechanisms of IR/IGF1R, especially the role of TMDs in coordinating signal-inducing structural transitions, remain poorly understood, in part due to the lack of structures of full-length receptors in apo or liganded states. While atomistic simulations of IR/IGF1R TMDs showed that these domains can dimerize in single component membranes, spontaneous unbiased dimerization in a plasma membrane having a physiologically representative lipid composition has not been observed. We address this limitation by employing coarse-grained (CG) molecular dynamics simulations to probe the dimerization propensity of IR/IGF1R TMDs. We observed that TMDs in both receptors spontaneously dimerized independent of their initial orientations in their dissociated states, signifying their natural propensity for dimerization. In the dimeric state, IR TMDs predominantly adopted X-shaped configurations with asymmetric helical packing and significant tilt relative to the membrane normal, while IGF1R TMDs adopted symmetric V-shaped or parallel configurations with either no tilt or a small tilt relative to the membrane normal. Our results suggest that IR/IGF1R TMDs spontaneously dimerize and adopt distinct dimerized configurations.

Analysis of the dynamics of a complex, multipathway reaction: Insulin dimer dissociation.

The protein hormone insulin forms a homodimer that must dissociate to bind to its receptor. Understanding the kinetics and mechanism of dissociation is essential for rational design of therapeutic analogs. In addition to its physiological importance, this dissociation process serves as a paradigm for coupled (un)folding and (un)binding. Based on previous free energy simulations, insulin dissociation is thought to involve multiple pathways with comparable free energy barriers. Here, we analyze the mechanism of insulin dimer dissociation using a recently developed computational framework for estimating kinetic statistics from short-trajectory data. These statistics indicate that the likelihood of dissociation (the committor) closely tracks the decrease in the number of (native and nonnative) intermonomer contacts and the increase in the number of water contacts at the dimer interface; the transition state with equal likelihood of association and dissociation corresponds to an encounter complex with relatively few native contacts and many nonnative contacts. We identify four pathways out of the dimer state and quantify their contributions to the rate, as well as their exchange, by computing reactive fluxes. We show that both the pathways and their extents of exchange can be understood in terms of rotations around three axes of the dimer structure. Our results provide insights into the kinetics of insulin analogues and, more generally, how to characterize complex, multipathway processes.

SAXS of murine amelogenin identifies a persistent dimeric species from pH 5.0 to 8.0

Amelogenin is an intrinsically disordered protein essential to tooth enamel formation in mammals. Using advanced small angle X-ray scattering (SAXS) capabilities at synchrotrons and computational models, we revisited measuring the quaternary structure of murine amelogenin as a function of pH and phosphorylation at serine-16. The SAXS data shows that at the pH extremes, amelogenin exists as an extended monomer at pH 3.0 (Rg = 38.4 Å) and nanospheres at pH 8.0 (Rg = 84.0 Å), consistent with multiple previous observations. At pH 5.0 and above there was no evidence for a significant population of monomeric species. Instead, at pH 5.0, ∼80 % of the population is a heterogenous dimeric species that increases to ∼100 % at pH 5.5. The dimer population was observed at all pH > 5 conditions in dynamic equilibrium with a species in the pentamer range at pH < 6.5 and nanospheres at pH 8.0. At pH 8.0, ∼40 % of the amelogenin remained in the dimeric state. In general, serine-16 phosphorylation of amelogenin appears to modestly stabilize the population of the dimeric species.

Aminolysis of five-membered cyclic carbonate catalyzed by guanidines: Solvent effects on the formation of guanidine dimers

This paper presents an experimental and computational investigation on the aminolysis reactions of five-membered cyclic carbonate (5CC) catalyzed by mono- or bi-cyclic guanidines in various solvents. For both liquid and solid 5CC substrate employed, higher polar solvent favors the monomeric active guanidine responsible for the catalytic aminolysis reactions. The formation of the dimeric state of the guanidine catalyst, which is seemingly inert to catalytic activity, is prevented by the bulkier substituents connecting to the guanidine moiety. Extensive DFT calculations further confirm that the relative stabilities of dimeric guanidine is depended on both the polarities of the solvents and the bulkiness of the substituents connected to the guanidine moiety, which is consistent with the experimental kinetic results.

Stabilization of dimeric PYR/PYL/RCAR family members relieves abscisic acid-induced inhibition of seed germination

Abscisic acid (ABA) is the primary preventing factor of seed germination, which is crucial to plant survival and propagation. ABA-induced seed germination inhibition is mainly mediated by the dimeric PYR/PYL/RCAR (PYLs) family members. However, little is known about the relevance between dimeric stability of PYLs and seed germination. Here, we reveal that stabilization of PYL dimer can relieve ABA-induced inhibition of seed germination using chemical genetic approaches. Di-nitrobensulfamide (DBSA), a computationally designed chemical probe, yields around ten-fold improvement in receptor affinity relative to ABA. DBSA reverses ABA-induced inhibition of seed germination mainly through dimeric receptors and recovers the expression of ABA-responsive genes. DBSA maintains PYR1 in dimeric state during protein oligomeric state experiment. X-ray crystallography shows that DBSA targets a pocket in PYL dimer interface and may stabilize PYL dimer by forming hydrogen networks. Our results illustrate the potential of PYL dimer stabilization in preventing ABA-induced seed germination inhibition.

Oligomeric State and Drug Binding of the SARS-CoV-2 Envelope Protein Are Sensitive to the Ectodomain.

The envelope (E) protein of SARS-CoV-2 is the smallest of the three structural membrane proteins of the virus. E mediates budding of the progeny virus in the endoplasmic reticulum Golgi intermediate compartment of the cell. It also conducts ions, and this channel activity is associated with the pathogenicity of SARS-CoV-2. The structural basis for these functions is still poorly understood. Biochemical studies of E in detergent micelles found a variety of oligomeric states, but recent 19F solid-state NMR data indicated that the transmembrane domain (ETM, residues 8-38) forms pentamers in lipid bilayers. Hexamethylene amiloride (HMA), an E inhibitor, binds the pentameric ETM at the lipid-exposed helix-helix interface. Here, we investigate the oligomeric structure and drug interaction of an ectodomain-containing E construct, ENTM (residues 1-41). Unexpectedly, 19F spin diffusion NMR data reveal that ENTM adopts an average oligomeric state of dimers instead of pentamers in lipid bilayers. A new amiloride inhibitor, AV-352, shows stronger inhibitory activity than HMA in virus-like particle assays. Distance measurements between 13C-labeled protein and a trifluoromethyl group of AV-352 indicate that the drug binds ENTM with a higher stoichiometry than ETM. We measured protein-drug contacts using a sensitivity-enhanced two-dimensional 13C-19F distance NMR technique. The results indicate that AV-352 binds the C-terminal half of the TM domain, similar to the binding region of HMA. These data provide evidence for the existence of multiple oligomeric states of E in lipid bilayers, which may carry out distinct functions and may be differentially targeted by antiviral drugs.

Grb2 Y160F mutant mimics the wild-type monomeric state dynamics and the monomer-dimer equilibrium

The Growth factor receptor-bound protein 2 (Grb2) participates in early signaling complexes and regulates tyrosine kinase-mediated signal transduction through a monomer-dimer equilibrium. Grb2 dimeric state inhibits signal transduction whereas the monomer promotes signaling downstream. Since Grb2 dimer KD is ∼0.8 μM, studies focused on the monomer are still challenging and require mutations or interaction with phosphotyrosine peptides. However, these mutants were never characterized considering their effects on protein structure and dynamics in solution. Here, we present the biophysical characterization of Grb2Y160F, the first Grb2 mutant to induce protein monomerization without disrupting its native behavior in solution due to net charge modifications or interaction with peptides. We also identified that Grb2Y160F exists in a monomer-dimer equilibrium. Grb2Y160F ability to dimerize implies that different dimerization interfaces might regulate signaling pathways in distinct ways and raises an important question about the role of the Y160 residue in other dimerization interfaces.

Spontaneous Dimerization and Distinct Packing Modes of Transmembrane Domains in Receptor Tyrosine Kinases.

The insulin receptor (IR) and the insulin-like growth factor-1 receptor (IGF1R) are homodimeric transmembrane glycoproteins that transduce signals across the membrane on binding of extracellular peptide ligands. The structures of IR/IGF1R fragments in apo and liganded states have revealed that the extracellular subunits of these receptors adopt Λ-shaped configurations to which are connected the intracellular tyrosine kinase (TK) domains. The binding of peptide ligands induces structural transitions in the extracellular subunits leading to potential dimerization of transmembrane domains (TMDs) and autophosphorylation in TKs. However, the activation mechanisms of IR/IGF1R, especially the role of TMDs in coordinating signal-inducing structural transitions, remain poorly understood, in part due to the lack of structures of full-length receptors in apo or liganded states. While atomistic simulations of IR/IGF1R TMDs showed that these domains can dimerize in single component membranes, spontaneous unbiased dimerization in a plasma membrane having physiologically representative lipid composition has not been observed. We address this limitation by employing coarse-grained (CG) molecular dynamics simulations to probe the dimerization propensity of IR/IGF1R TMDs. We observed that TMDs in both receptors spontaneously dimerized independent of their initial orientations in their dissociated states, signifying their natural propensity for dimerization. In the dimeric state, IR TMDs predominantly adopted X-shaped configurations with asymmetric helical packing and significant tilt relative to the membrane normal, while IGF1R TMDs adopted symmetric V-shaped or parallel configurations with either no tilt or a small tilt relative to the membrane normal. Our results suggest that IR/IGF1R TMDs spontaneously dimerize and adopt distinct dimerized configurations.

Triplon analysis of magnetic disorder and order in maple-leaf Heisenberg magnet

The nearest-neighbor spin-1/2 Heisenberg model on the maple-leaf lattice formed by hexagons (couplingJh), triangles (couplingJt), and dimers (couplingJd), is investigated in a parameter regime whereJh>0andJt,Jd<0. This investigation aims to identify regions hosting exotic valence-bond solid states. Two potential magnetically disordered ground states are identified, and their stability is assessed through plaquette-triplon mean-field analyses. The resulting quantum phase diagram reveals that at large|Jt|and|Jd|, the system adopts a magnetically disordered dimerized VBS state, while for small|Jd|, it stabilizes a Néel state. A second-order phase transition from the dimerized phase to a Néel phase is observed, which, being Landau-forbidden, suggests the potential presence of exotic phenomena such as a deconfined quantum critical point or the appearance of a quantum spin liquid. This work provides insights into the phase diagram of the nearest-neighbor spin-1/2 Heisenberg model on the maple-leaf lattice and lays the groundwork for further investigations into its intriguing physics.

(Invited) Computational Analysis of the Excited States in the Film States of Non-Fullerene Acceptors

Non-fullerene acceptors are currently widely used as the acceptors of organic thin film solar cells due to their high efficiency. However, the molecular mechanism is still unclear. We have studied the excited states in the film states of non-fullerene acceptors together with experimental collaborators by using theoretical methods. In this presentation, we will present recent progress of our research. For example, we will talk about the excited states in the film states of ITIC. ITIC is a popular acceptor-donor-acceptor-type non-fullerene acceptor. Recently, our collaborator, Prof. Yamakata at Okayama University, Japan, found that the charge separation can take place in ITIC acceptor film even without donor molecules. We investigated this phenomenon by using MD simulations and quantum chemical calculations. MD simulations of the ITIC film showed that the acceptor parts of ITIC are stacked with each other. The dominant angle between two stacked ITIC was found to be ~180 degrees, making J-type dimer. On the other hand, it was also found that there are quite a few V-type dimers with the angles less than 90 degrees. Quantum chemical calculations revealed that the dipole moment in the excited state of J-type dimer is almost zero whereas that of V-type dimer is quite large, indicating strong charge-transfer excited state. Therefore, it is considered that the charge separation of ITIC film can take place in the V-type dimers. We also investigated the excited states in the film states of ITIC analogs. Recently, our collaborator, Prof. Ie at Osaka University, Japan, synthesized several ITIC analogs with different sidechains and found the different efficiency of solar cells. We theoretically investigated the excited states in the film sates of ITIC analogs as in the case of ITIC. It is found that the modification of side chains can change the distributions of angles between two stacked molecules and excited-state properties. These findings highlight the importance of controlling stacking structures in the film state for the efficiency of organic thin film solar cells.

Bound impurities in a one-dimensional Bose lattice gas: Low-energy properties and quench-induced dynamics

We study two mobile bosonic impurities immersed in a one-dimensional optical lattice and interacting with a bosonic bath. We employ the exact diagonalization method for small periodic lattices to study stationary properties and dynamics. We consider the branch of repulsive interactions that induce the formation of bound impurities, akin to the bipolaron problem. A comprehensive study of ground-state and low-energy properties is presented, including an examination of the interaction strengths which induce the formation of a bound dimer of impurities. We also study the dynamics induced after an interaction quench to examine the stability of the bound dimers. We reveal that after large interaction quenches from strong to weak interactions the system can show large oscillations over time with revivals of the dimer states. We find that the oscillations are driven by selected eigenstates with phase-separated configurations.

Charge and Spin Transfer Dynamics in a Weakly Coupled Porphyrin Dimer.

The dynamics of electron and spin transfer in the radical cation and photogenerated triplet states of a tetramethylbiphenyl-linked zinc-porphyrin dimer were investigated, so as to test the relevant parameters for the design of a single-molecule spin valve and the creation of a novel platform for the photogeneration of high-multiplicity spin states. We used a combination of multiple techniques, including variable-temperature continuous wave EPR, pulsed proton electron-nuclear double resonance (ENDOR), transient EPR, and optical spectroscopy. The conclusions are further supported by density functional theory (DFT) calculations and comparison to reference compounds. The low-temperature cw-EPR and room-temperature near-IR spectra of the dimer monocation demonstrate that the radical cation is spatially localized on one side of the dimer at any point in time, not coherently delocalized over both porphyrin units. The EPR spectra at 298 K reveal rapid hopping of the radical spin density between both sites of the dimer via reversible intramolecular electron transfer. The hyperfine interactions are modulated by electron transfer and can be quantified using ENDOR spectroscopy. This allowed simulation of the variable-temperature cw-EPR spectra with a two-site exchange model and provided information on the temperature-dependence of the electron transfer rate. The electron transfer rates range from about 10.0 MHz at 200 K to about 53.9 MHz at 298 K. The activation enthalpies Δ‡H of the electron transfer were determined as Δ‡H = 9.55 kJ mol-1 and Δ‡H = 5.67 kJ mol-1 in a 1:1:1 solvent mixture of CD2Cl2/toluene-d8/THF-d8 and in 2-methyltetrahydrofuran, respectively, consistent with a Robin-Day class II mixed valence compound. These results indicate that the interporphyrin electronic coupling in a tetramethylbiphenyl-linked porphyrin dimer is suitable for the backbone of a single-molecule spin valve. Investigation of the spin density distribution of the photogenerated triplet state of the Zn-porphyrin dimer reveals localization of the triplet spin density on a nanosecond time scale on one-half of the dimer at 20 K in 2-methyltetrahydrofuran and at 250 K in a polyvinylcarbazole film. This establishes the porphyrin dimer as a molecular platform for the formation of a localized, photogenerated triplet state on one porphyrin unit that is coupled to a second redox-active, ground-state porphyrin unit, which can be explored for the formation of high-multiplicity spin states.