Singlet Triplet-Pair Production and Possible Singlet-Fission in Carotenoids.

Internal conversion from the photoexcited state to a correlated singlet triplet-pair state is believed to be the precursor of singlet fission in carotenoids. We present numerical simulations of this process using a π-electron model that fully accounts for electron-electron interactions and electron-nuclear coupling. The time-evolution of the electrons is determined rigorously using the time-dependent density matrix renormalization group method, while the nuclei are evolved via the Ehrenfest equations of motion. We apply this to zeaxanthin, a carotenoid chain with 18 fully conjugated carbon atoms. We show that the internal conversion of the primary photoexcited state, S2, to the singlet triplet-pair state occurs adiabatically via an avoided crossing within ∼50 fs with a yield of ∼60%. We further discuss whether this singlet triplet-pair state will undergo exothermic versus endothermic intra- or interchain singlet fission.

Model-Independent Simulation Complexity of Complex Quantum Dynamics.

We present a model-independent measure of dynamical complexity based on simulation of complex quantum dynamics using stroboscopic Markovian dynamics. Tools from classical signal processing enable us to infer the Hilbert space dimension of the complex quantum system evolving under a time-independent Hamiltonian via pulsed interrogation. We illustrate this using simulated third-order pump-probe spectroscopy data for exciton transport in a toy model of a coupled dimer with vibrational levels, revealing the dimension of the singly excited manifold of the dimer. Finally, we probe the complexity of excitonic transport in light harvesting 2 (LH2) and Fenna-Matthews-Olson (FMO) complexes using data from two recent nonlinear ultrafast optical spectroscopy experiments. For the latter we make model-independent inferences that are commensurate with model-specific ones, including the estimation of the fewest number of parameters needed to fit the experimental data and identifying the spatial extent, i.e., delocalization size, of quantum states participating in this complex quantum dynamics.

Towards a spectroscopic protocol for unambiguous detection of quantum coherence in excitonic energy transport.

The role of quantum effects in excitonic energy transport (EET) has been scrutinised intensely and with increasingly sophisticated experimental techniques. This increased complexity requires invoking correspondingly elaborate models to fit spectroscopic data before molecular parameters can be extracted. Possible quantum effects in EET can then be studied, but the conclusions are strongly contingent on the efficacy of the fitting and the accuracy of the model. To circumvent this challenge, we propose a witness for quantum coherence in EET that can be extracted directly from two-pulse pump-probe spectroscopy experimental data. We provide simulations to judge the feasibility of our approach. Somewhat counterintuitively, our protocol does not probe quantum coherence directly, but only indirectly through its implicit deletion. It allows for classical models with no quantum coherence to be decisively ruled out.

Extracting structural information from MEH-PPV optical spectra.

The Frenkel-Holstein model in the Born-Oppenheimer regime is used to interpret temperature-dependent photoluminescence spectra of solutions made with the poly(p-phenylene vinylene) derivative MEH-PPV. Using our recently developed structural optimization method and assuming only intrachain electronic coupling, we predict the structure of emissive MEH-PPV chromophores in terms of a mean torsional angle ϕ0 and its static fluctuations σϕ, assuming no cis-trans defects. This allows us to fully account for the observed changes in spectra, and the chromophore structures obtained are consistent with the known phase transition at 180 K between a "red" and "blue" phase.

Structural Information for Conjugated Polymers from Optical Modeling.

We use a Frenkel-Holstein model of uncoupled chains in the adiabatic limit to simulate the optical spectra of the conjugated polymer ladder-type poly( p-phenylene) derivative (MeLPPP), which is a planar conjugated polymer with especially low interchain interactions. The theoretical calculations correctly reproduce the vibronic spectra and yield reasonable torsion angles between adjacent phenyl rings. The success of this approach indicates that, in contrast to interchain coupling, the strong electronic coupling along a polymer chain is more appropriately described in the adiabatic limit.

Perspective: Optical spectroscopy in π-conjugated polymers and how it can be used to determine multiscale polymer structures.

Exciton delocalization in conjugated polymer systems is determined by polymer conformations and packing. Since exciton delocalization determines the photoluminescent vibronic progression, optical spectroscopy provides an indirect link to polymer multiscale structures. This perspective describes our current theoretical understanding of how exciton delocalization in π-conjugated polymers determines their optical spectroscopy and further shows how exciton delocalization is related to conformational and environmental disorder. If the multiscale structures in conjugated polymer systems are known, then using first-principles modeling of excitonic processes it is possible to predict a wide-range of spectroscopic observables. We propose a reverse-engineering protocol of using these experimental observables in combination with theoretical and computational modeling to determine the multiscale polymers structures, thus establishing quantitative structure-function predictions.

Theory of optical transitions in curved chromophores.

Using first order perturbation theory in the Born-Oppenheimer regime of the Frenkel-Holstein model, we develop a theory for the optical transitions in curved chromophores of π-conjugated polymers. Our key results are that for absorption, A, and emission, I, polarized parallel to the 0-0 transition, I01/I00 ≃ A01/A00 = S(N), where S(N) = S(1)/IPR is the effective Huang-Rhys parameter for a chromophore of N monomers and IPR is the inverse participation ratio. In contrast, absorption and emission polarized perpendicular to the 0-0 transition acquires vibronic intensity via the Herzberg-Teller effect. This intensity generally increases as the curvature increases and consequently I01/I00 increases (where I01 is the total 0-1 emission intensity). This effect is enhanced for long chromophores and in the anti-adiabatic regime. We show via DMRG calculations that this theory works well in the adiabatic regime relevant to π-conjugated polymers, i.e., h ω/|J| ≲ 0.2.

Theory of optical transitions in π-conjugated macrocycles.

We describe a theoretical and computational investigation of the optical properties of π-conjugated macrocycles. Since the low-energy excitations of these systems are Frenkel excitons that couple to high-frequency dispersionless phonons, we employ the quantized Frenkel-Holstein model and solve it via the density matrix renormalization group (DMRG) method. First we consider optical emission from perfectly circular systems. Owing to optical selection rules, such systems radiate via two mechanisms: (i) within the Condon approximation, by thermally induced emission from the optically allowed j = ± 1 states and (ii) beyond the Condon approximation, by emission from the j = 0 state via coupling with a totally non-symmetric phonon (namely, the Herzberg-Teller effect). Using perturbation theory, we derive an expression for the Herzberg-Teller correction and show via DMRG calculations that this expression soon fails as h ω/J and the size of the macrocycle increase. Next, we consider the role of broken symmetry caused by torsional disorder. In this case the quantum number j no longer labels eigenstates of angular momentum, but instead labels localized local exciton groundstates (LEGSs) or quasi-extended states (QEESs). As for linear polymers, LEGSs define chromophores, with the higher energy QEESs being extended over numerous LEGSs. Within the Condon approximation (i.e., neglecting the Herzberg-Teller correction) we show that increased disorder increases the emissive optical intensity, because all the LEGSs are optically active. We next consider the combined role of broken symmetry and curvature, by explicitly evaluating the Herzberg-Teller correction in disordered systems via the DMRG method. The Herzberg-Teller correction is most evident in the emission intensity ratio, I00/I01. In the Condon approximation I00/I01 is a constant function of curvature, whereas in practice it vanishes for closed rings and only approaches a constant in the limit of vanishing curvature. We calculate the optical spectra of a model system, cyclo-poly(para-phenylene ethynylene), for different amounts of torsional disorder within and beyond the Condon approximation. We show how broken symmetry and the Herzberg-Teller effect explain the spectral features. The Herzberg-Teller correction to the 0-1 emission vibronic peak is always significant. Finally, we note the qualitative similarities between the optical properties of conformationally disordered linear polymers and macrocycles in the limit of sufficiently large disorder, because in both cases they are determined by the optical properties of curved chromophores.

Polarons in π-Conjugated Polymers: Anderson or Landau?

Using both analytical expressions and the density matrix renormalization group method, we study the fully quantized disordered Holstein model to investigate the localization of charges and excitons by vibrational or torsional modes-i.e., the formation of polarons-in conformationally disordered π-conjugated polymers. We identify two distinct mechanisms for polaron formation, namely Anderson localization via disorder (causing the formation of Anderson polarons) and self-localization by self-trapping via normal modes (causing the formation of Landau polarons). We identify the regimes where either description is more valid. The key distinction between Anderson and Landau polarons is that for the latter the particle wave function is a strong function of the normal coordinates, and hence the "vertical" and "relaxed" wave functions are different. This has theoretical and experimental consequences for Landau polarons. Theoretically, it means that the Condon approximation is not valid, and so care needs to be taken when evaluating transition rates. Experimentally, it means that the self-localization of the particle as a consequence of its coupling to the normal coordinates may lead to experimental observables, e.g., ultrafast fluorescence depolarization. We apply these ideas to poly(p-phenylenevinylene). We show that the high frequency C-C bond oscillation only causes Landau polarons for a very narrow parameter regime; generally we expect disorder to dominate and Anderson polarons to be a more applicable description. Similarly, for the low frequency torsional fluctuations we show that Anderson polarons are expected for realistic parameters.

Theory of optical transitions in conjugated polymers. I. Ideal systems.

We describe a theory of linear optical transitions in conjugated polymers. The theory is based on three assumptions. The first is that the low-lying excited states of conjugated polymers are Frenkel excitons coupled to local normal modes, described by the Frenkel-Holstein model. Second, we assume that the relevant parameter regime is ℏω ≪ J, i.e., the adiabatic regime, and thus the Born-Oppenheimer factorization of the electronic and nuclear degrees of freedom is generally applicable. Finally, we assume that the Condon approximation is valid, i.e., the exciton-polaron wavefunction is essentially independent of the normal modes. Using these assumptions we derive an expression for an effective Huang-Rhys parameter for a chain (or chromophore) of N monomers, given by S(N) = S(1)/IPR, where S(1) is the Huang-Rhys parameter for an isolated monomer. IPR is the inverse participation ratio, defined by IPR = (∑(n)|Ψ(n)|(4))(-1), where Ψ(n) is the exciton center-of-mass wavefunction. Since the IPR is proportional to the spread of the exciton center-of-mass wavefunction, this is a key result, as it shows that S(N) decreases with chain length. As in molecules, in a polymer S(N) has two interpretations. First, ℏωS(N) is the relaxation energy of an excited state caused by its coupling to the normal modes. Second, S(N) appears in the definition of an effective Franck-Condon factor, F(0v)(N) = S(N)(v)exp ( - S(N))/v! for the vth vibronic manifold. We show that the 0 - 0 and 0 - 1 optical intensities are proportional to F00(N) and F01(N), respectively, and thus the ratio of the 0 - 1 to 0 - 0 absorption and emission intensities are proportional to S(N). These analytical results are checked by extensive DMRG calculations and found to be generally valid, particularly for emission. However, for large chain lengths higher-lying quasimomentum exciton states become degenerate with the lowest vibrational excitation of the lowest exciton state. When this happens there is mixing of the electronic and nuclear states and a partial breakdown of the Born-Oppenheimer approximation, meaning that the ratio of the 0 - 0 to 0 - 1 absorption intensities no longer increases as fast as the IPR. When ℏω/J = 0.1, a value applicable to phenyl-based polymers, the critical value of N is ~20 monomers.

Theory of optical transitions in conjugated polymers. II. Real systems.

The theory of optical transitions developed in Barford and Marcus ["Theory of optical transitions in conjugated polymers. I. Ideal systems," J. Chem. Phys. 141, 164101 (2014)] for linear, ordered polymer chains is extended in this paper to model conformationally disordered systems. Our key result is that in the Born-Oppenheimer regime the emission intensities are proportional to S(1)/⟨IPR⟩, where S(1) is the Huang-Rhys parameter for a monomer. ⟨IPR⟩ is the average inverse participation ratio for the emitting species, i.e., local exciton ground states (LEGSs). Since the spatial coherence of LEGSs determines the spatial extent of chromophores, the significance of this result is that it directly relates experimental observables to chromophore sizes (where ⟨IPR⟩ is half the mean chromophore size in monomer units). This result is independent of the chromophore shape, because of the Born-Oppenheimer factorization of the many body wavefunction. We verify this prediction by density matrix renormalization group (DMRG) calculations of the Frenkel-Holstein model in the adiabatic limit for both linear, disordered chains and for coiled, ordered chains. We also model optical spectra for poly(p-phenylene) and poly(p-phenylene-vinylene) oligomers and polymers. For oligomers, we solve the fully quantized Frenkel-Holstein model via the DMRG method. For polymers, we use the much simpler method of solving the one-particle Frenkel model and employ the Born-Oppenheimer expressions relating the effective Franck-Condon factor of a chromophore to its inverse participation ratio. We show that increased disorder decreases chromophore sizes and increases the inhomogeneous broadening, but has a non-monotonic effect on transition energies. We also show that as planarizing the polymer chain increases the exciton band width, it causes the chromophore sizes to increase, the transition energies to decrease, and the broadening to decrease. Finally, we show that the absorption spectra are more broadened than the emission spectra and that the broadening of the absorption spectra increases as the chains become more coiled. This is primarily because absorption occurs to both LEGSs and quasi-extended exciton states (QEESs), and QEES acquire increased intensity as chromophores bend, while emission only occurs from LEGSs.

Comprehensively designed consensus of standalone secondary structure predictors improves Q3 by over 3%.

Protein fold is defined by a spatial arrangement of three types of secondary structures (SSs) including helices, sheets, and coils/loops. Current methods that predict SS from sequences rely on complex machine learning-derived models and provide the three-state accuracy (Q3) at about 82%. Further improvements in predictive quality could be obtained with a consensus-based approach, which so far received limited attention. We perform first-of-its-kind comprehensive design of a SS consensus predictor (SScon), in which we consider 12 modern standalone SS predictors and utilize Support Vector Machine (SVM) to combine their predictions. Using a large benchmark data-set with 10 random training-test splits, we show that a simple, voting-based consensus of carefully selected base methods improves Q3 by 1.9% when compared to the best single predictor. Use of SVM provides additional 1.4% improvement with the overall Q3 at 85.6% and segment overlap (SOV3) at 83.7%, when compared to 82.3 and 80.9%, respectively, obtained by the best individual methods. We also show strong improvements when the consensus is based on ab-initio methods, with Q3 = 82.3% and SOV3 = 80.7% that match the results from the best template-based approaches. Our consensus reduces the number of significant errors where helix is confused with a strand, provides particularly good results for short helices and strands, and gives the most accurate estimates of the content of individual SSs in the chain. Case studies are used to visualize the improvements offered by the consensus at the residue level. A web-server and a standalone implementation of SScon are available at http://biomine.ece.ualberta.ca/SSCon/ .

Long chain fatty Acyl-CoA synthetase 4 is a biomarker for and mediator of hormone resistance in human breast cancer.

The purpose of this study was to determine the role of long-chain fatty acyl-CoA synthetase 4 (ACSL4) in breast cancer. Public databases were utilized to analyze the relationship between ACSL4 mRNA expression and the presence of steroid hormone and human epidermal growth factor receptor 2 (HER2) in both breast cancer cell lines and tissue samples. In addition, cell lines were utilized to assess the consequences of either increased or decreased levels of ACSL4 expression. Proliferation, migration, anchorage-independent growth and apoptosis were used as biological end points. Effects on mRNA expression and signal transduction pathways were also monitored. A meta-analysis of public gene expression databases indicated that ACSL4 expression is positively correlated with a unique subtype of triple negative breast cancer (TNBC), characterized by the absence of androgen receptor (AR) and therefore referred to as quadruple negative breast cancer (QNBC). Results of experiments in breast cancer cell lines suggest that simultaneous expression of ACSL4 and a receptor is associated with hormone resistance. Forced expression of ACSL4 in ACSL4-negative, estrogen receptor α (ER)-positive MCF-7 cells resulted in increased growth, invasion and anchorage independent growth, as well as a loss of dependence on estrogen that was accompanied by a reduction in the levels of steroid hormone receptors. Sensitivity to tamoxifen, triacsin C and etoposide was also attenuated. Similarly, when HER2-positive, ACSL4-negative, SKBr3 breast cancer cells were induced to express ACSL4, the proliferation rate increased and the apoptotic effect of lapatinib was reduced. The growth stimulatory effect of ACSL4 expression was also observed in vivo in nude mice when MCF-7 control and ACSL4-expressing cells were utilized to induce tumors. Our data strongly suggest that ACSL4 can serve as both a biomarker for, and mediator of, an aggressive breast cancer phenotype.

Polytellurides of Mn, Fe, and Zn from mild solvothermal reactions in liquid ammonia.

The reaction of elemental Mn, Fe, and Zn with Te in liquid ammonia at 50 °C leads to the polytellurides [Mn(NH3)6]Te4 (1), [Fe(NH3)6]Te4·NH3 (2), and [Zn(NH3)4]2Te15 (3) in quantitative yield for 1 and 3, and in 30-50% yield for 2. The compounds form black crystals, which are air sensitive and easily lose ammonia without a protective atmosphere of NH3. Compound 3 is semiconducting with a thermal activation energy of 1.2 eV. In the crystal structures of 1 and 2, tetratelluride anions Te4(2-) in gauche conformation with dihedral angles around 90° are present, which are linked to form infinite spiral chains. Compound 3 contains an unusual Te15(4-) polyanion in the form of a bent chain Te7-Te-Te7. The connection between the Te4 groups in 1 and 2 and the two Te7 groups in 3 is achieved via linear Te3 entities, which are strongly asymmetric in 1, almost symmetric in 2, and symmetric in 3 (for 1, Te-Te···Te 174.0°, d1 = 2.87, d2 = 3.25 Å; for 2, Te-Te-Te 178.8°, d1 = 3.01, d2 = 3.09 Å; for 3, Te-Te-Te 180°, d1 = d2 = 3.06 Å). Periodic DFT calculations show that interaction between the Te4(2-) units is negligible in 1 and weak but undoubtedly present in 2. The overlap population amounts to 0.09 in the linear Te3 group of 3. The band structure calculation of 3 gives semiconducting behavior with a band gap of 1.5 eV in fair agreement with experimental data.