Dimer System Research Articles

Plasmon Hybridization Model for a Nanoparticle above a Dielectric Interface: Dielectric Effects, Comparison with the Dimer System, Range of Applicability, and Limits

In the presence of a nearby highly reflecting dielectric substrate, the optical response of a metal nanoparticle exhibits a rich multipolar plasmonic structure. For quantifying the multimodal plasmonic response of such hybrid particle/interface systems, the hydrodynamic plasmon hybridization (PH) method has been applied in the simple case of a solid metal sphere (PI-PH model). In this work I extend the formalism described in my previous paper (J. Phys. Chem. C 2014, 118, 28118−28133) to the more general case where underlying dielectric media are present in the whole space (polarizable ionic background and matrix). In the quasistatic limit the method of images allows the PI-PH model to be closely related to the two-sphere dimer PH model. However, because the dynamics of the electron fluid and of the polarization charges in the mirror particle are enslaved to those in the real metal particle, strong differences between both PH models result from the reduction by a factor of two of the number of dynamical variables describing the system. As compared to jellium spheres in vacuum, the PH formalism is much more complex because the induced surface polarization charges in the underlying media contribute to the energetics of the system. In this work a very detailed analytical description of both PH models, allowing a direct numerical implementation, is provided. In the frame of the original and physically transparent method developed in my previous paper, particular emphasis is given to modeling the coupling of the nanosystem with an external applied field. In the presence of underlying dielectric media, I show that the taking into account of the field created by the additional polarization charge distributions induced by the bare applied field is essential for defining the effective external field that is coupled to the nanosystem. The predictions of both PH models are also compared, through absorption and extinction cross-section spectra, to exact results computed in the frame of the multipole expansion method, allowing the range of applicability and limits of both models to be determined. Finally, the PH formalism is shown to be generalizable to deal with underlying dielectric media characterized by complex (that is, absorbing) frequency-dependent permittivities.

The Interplay of Disulfide Bonds, α-Helicity, and Hydrophobic Interactions Leads to Ultrahigh Proteolytic Stability of Peptides.

The contribution of noncovalent interactions to the stability of naturally occurring peptides and proteins has been generally acknowledged, though how these can be rationally manipulated to improve the proteolytic stability of synthetic peptides remains to be explored. In this study, a platform to enhance the proteolytic stability of peptides was developed by controllably dimerizing them into α-helical dimers, connected by two disulfide bonds. This platform not only directs peptides toward an α-helical conformation but permits control of the interfacial hydrophobic interactions between the peptides of the dimer. Using two model dimeric systems constructed from the N-terminal α-helix of RNase A and known inhibitors for the E3 ubiquitin ligase MDM2 (and its homologue MDMX), a deeper understanding into the interplay of disulfide bonds, α-helicity, and hydrophobic interactions on enhanced proteolytic stability was sought out. Results reveal that all three parameters play an important role on attaining ultrahigh proteolytic resistance, a concept that can be exploited for the development of future peptide therapeutics. The understanding gained through this study will enable this strategy to be tailored to new peptides because the proposed strategy displays substantial tolerance to sequence permutation. It thus appears promising for conveniently creating prodrugs composed entirely of the therapeutic peptide itself (i.e., in the form of a dimer).

Evidence of quantum dimer excitations inSr3Ir2O7

The magnetic excitation spectrum in the bilayer iridate Sr$_3$Ir$_2$O$_7$ has been investigated using high-resolution resonant inelastic x-ray scattering (RIXS) performed at the iridium L$_3$ edge and theoretical techniques. A study of the systematic dependence of the RIXS spectrum on the orientation of the wavevector transfer, $\mathbf{Q}$, with respect to the iridium-oxide bilayer has revealed that the magnon dispersion is comprised of two branches well separated in energy and gapped across the entire Brillouin zone. Our results contrast with those of an earlier study which reported the existence of a single dominant branch. While these earlier results were interpreted as two overlapping modes within a spin-wave model of weakly coupled iridium-oxide planes, our results are more reminiscent of those expected for a system of weakly coupled dimers. In this latter approach the lower and higher energy modes find a natural explanation as those corresponding to transverse and longitudinal fluctuations, respectively. We have therefore developed a bond-operator theory which describes the magnetic dispersion in Sr$_3$Ir$_2$O$_7$ in terms of quantum dimer excitations. In our model dimerisation is produced by the leading Heisenberg exchange, $J_c$, which couples iridium ions in adjacent planes of the bilayer. The Hamiltonian also includes in plane exchange, $J$, as well as further neighbour couplings and relevant anisotropies. The bond-operator theory provides an excellent account of the dispersion of both modes, while the measured $\mathbf{Q}$ dependence of the RIXS intensities is in reasonable qualitative accord with the spin-spin correlation function calculated from the theory. We discuss our results in the context of the quantum criticality of bilayer dimer systems in the presence of anisotropic interactions derived from strong spin-orbit coupling.

Computational studies of π–π interactions in dimers of heterosubstituted sumanenes

A computational study of dimers of heterosubstituted sumanenes has been carried out using a dispersion-corrected density functional theory method. In the heterosubstituted systems, the three bridging CH2 groups of sumanene have been replaced by O, NH, and S. For each dimer system, two motifs, staggered and eclipsed forms, were considered. The most stable geometry was the staggered stacked concave–convex motif where one monomer was rotated by 60° from the eclipsed configuration. The calculated binding energies and equilibrium distances of the staggered concave–convex dimers are predicted to be 20.1 kcal/mol and 3.7 A for the parent sumanene molecule, 17.4 kcal/mol and 3.8 A, 12.3 kcal/mol and 3.7 A, and 16.6 kcal/mol and 3.7 A for the NH-, O-, and S-substituted analogs, respectively. The binding energies of the dimers have been analyzed in terms of dipole–dipole contributions, dispersion contributions, and C–H···π interactions.

Effect of Asymmetric Dimeric Zwitterionic Surfactants on Micellization Behavior of Amphiphilic Drugs

The micellization process in mixtures of amphiphilic drugs and asymmetric dimeric zwitterionic surfactants have been investigated tensiometrically. The drugs used are from two families: imipramine hydrochloride (IMP)—a tricyclic antidepressant and ibuprofen (IBF)—a nonsteroidal antiinflammatory drug, whereas zwitterionic dimeric surfactants are heterogemini surfactants that contain quaternary ammonium and phosphate groups as heads. The results show that the cmc of drug-surfactant mixtures decreases with the increase in stoichiometric mole fraction of surfactants (α 1), suggesting attractive interaction among the two components. This is supported by the values of cmc id (critical micelle concentration values for ideal mixing) which are always greater than experimental cmc values. Also, the decrease in magnitude is more in IBF–dimeric surfactant mixed systems than in IMP–dimeric surfactant mixed systems. Micellar mole fraction values, obtained using Rubingh’s ( $$ X_{\text{1}}^{\text{m}} $$ ) and Motomura’s ( $$ X_{\text{1}}^{\text{m}} $$ ) models, are lower than the micellar mole fraction for ideal mixing ( $$ X_{\text{1}}^{{\text{id}}} $$ ). The micellar interaction parameter ( $$ \beta^{\text{m}} $$ ) follows the order: 8(−)−2−16(+) > 10(−)−2−16(+) > 10(−)−2−14(+) > 8(−)−2−14(+). The results are explained on the basis of difference in tail lengths. Interfacial mole fraction ( $$ X_{\text{1}}^{\upsigma} $$ ) values, evaluated using Rosen’s model, are higher than $$ X_{\text{1}}^{\text{m}} $$ values for IMP-10(−)−2−16(+) and IMP-10(−)−2−14(+) systems while for all other systems (except 8(−)−2−14(+)) the values are smaller than $$ X_{\text{1}}^{\text{m}} $$ . The interaction parameter at the interface ( $$ \beta^{\upsigma} $$ ) is negative and $$ \beta_{av}^{\text{m}} $$ values are greater than $$ \beta_{av}^{\upsigma} $$ in magnitude. All the results indicate that the dimeric surfactants are mostly in cationic form.

Modeling the high-energy electronic state manifold of adenine: Calibration for nonlinear electronic spectroscopy.

Pump-probe electronic spectroscopy using femtosecond laser pulses has evolved into a standard tool for tracking ultrafast excited state dynamics. Its two-dimensional (2D) counterpart is becoming an increasingly available and promising technique for resolving many of the limitations of pump-probe caused by spectral congestion. The ability to simulate pump-probe and 2D spectra from ab initio computations would allow one to link mechanistic observables like molecular motions and the making/breaking of chemical bonds to experimental observables like excited state lifetimes and quantum yields. From a theoretical standpoint, the characterization of the electronic transitions in the visible (Vis)/ultraviolet (UV), which are excited via the interaction of a molecular system with the incoming pump/probe pulses, translates into the determination of a computationally challenging number of excited states (going over 100) even for small/medium sized systems. A protocol is therefore required to evaluate the fluctuations of spectral properties like transition energies and dipole moments as a function of the computational parameters and to estimate the effect of these fluctuations on the transient spectral appearance. In the present contribution such a protocol is presented within the framework of complete and restricted active space self-consistent field theory and its second-order perturbation theory extensions. The electronic excited states of adenine have been carefully characterized through a previously presented computational recipe [Nenov et al., Comput. Theor. Chem. 1040-1041, 295-303 (2014)]. A wise reduction of the level of theory has then been performed in order to obtain a computationally less demanding approach that is still able to reproduce the characteristic features of the reference data. Foreseeing the potentiality of 2D electronic spectroscopy to track polynucleotide ground and excited state dynamics, and in particular its expected ability to provide conformational dependent fingerprints in dimeric systems, the performances of the selected reduced level of calculations have been tested in the construction of 2D electronic spectra for the in vacuo adenine monomer and the unstacked adenine homodimer, thereby exciting the Lb/La transitions with the pump pulse pair and probing in the Vis to near ultraviolet spectral window.

Effects of Different Quantum Coherence on the Pump-Probe Polarization Anisotropy of Photosynthetic Light-Harvesting Complexes: A Computational Study.

Observations of oscillatory features in the 2D spectra of several photosynthetic complexes have led to diverged opinions on their origins, including electronic coherence, vibrational coherence, and vibronic coherence. In this work, effects of these different types of quantum coherence on ultrafast pump-probe polarization anisotropy are investigated and distinguished. We first simulate the isotropic pump-probe signal and anisotropy decay of the Fenna-Matthews-Olson (FMO) complex using a model with only electronic coherence at low temperature and obtain the same coherence time as in the previous experiment. Then, three model dimer systems with different prespecified quantum coherence are simulated, and the results show that their different spectral characteristics can be used to determine the type of coherence during the spectral process. Finally, we simulate model systems with different electronic-vibrational couplings and reveal the condition in which long time vibronic coherence can be observed in systems like the FMO complex.

A single-cell model of PIP3 dynamics using chemical dimerization

Most cellular processes are driven by simple biochemical mechanisms such as protein and lipid phosphorylation, but the sum of all these conversions is exceedingly complex. Hence, intuition alone is not enough to discern the underlying mechanisms in the light of experimental data. Toward this end, mathematical models provide a conceptual and numerical framework to formally evaluate the plausibility of biochemical processes. To illustrate the use of these models, here we built a mechanistic computational model of PI3K (phosphatidylinositol 3-kinase) activity, to determine the kinetics of lipid metabolizing enzymes in single cells. The model is trained to data generated upon perturbation with a reversible small-molecule based chemical dimerization system that allows for the very rapid manipulation of the PIP3 (phosphatidylinositol 3,4,5-trisphosphate) signaling pathway, and monitored with live-cell microscopy. We find that the rapid relaxation system used in this work decreased the uncertainty of estimating kinetic parameters compared to methods based on in vitro assays. We also examined the use of Bayesian parameter inference and how the use of such a probabilistic method gives information on the kinetics of PI3K and PTEN activity.

Model Reconstruction for Moment-Based Stochastic Chemical Kinetics

Based on the theory of stochastic chemical kinetics, the inherent randomness of biochemical reaction networks can be described by discrete-state continuous-time Markov chains. However, the analysis of such processes is computationally expensive and sophisticated numerical methods are required. Here, we propose an analysis framework in which we integrate a number of moments of the process instead of the state probabilities. This results in a very efficient simulation of the time evolution of the process. To regain the state probabilities from the moment representation, we combine the fast moment-based simulation with a maximum entropy approach for the reconstruction of the underlying probability distribution. We investigate the usefulness of this combined approach in the setting of stochastic chemical kinetics and present numerical results for three reaction networks showing its efficiency and accuracy. Besides a simple dimerization system, we study a bistable switch system and a multiattractor network with complex dynamics.

Membrane Lipids in Migrating Cells Illuminated by Molecular Sensors and Chemical Actuators

Cell motility plays a vital role in both normal physiology and the pathogenesis of many diseases. We have recently shown that cell motility requires the signal transduction network serving as a pacemaker to drive cytoskeletal activities. This network features spontaneous firing that promotes the formation of sustained protrusions which govern random cell migration. However, a molecular identity of the signal excitability remains unknown. Phosphatidylinositol 4,5‐bisphosphate (PIP2) is one of the eight phosphoinositide species consisting of the cellular membrane structures, and well characterized as a substrate of PI3K that produces phosphatidylinositol 3,4,5‐trisphosphate (PIP3). PIP2 has long been viewed as a general source of negative charges, offering docking sites for cytosolic proteins through electrostatic interactions. Here, we examine the roles of PIP2 in this signal transduction network using a Dictyostelium cell as a model. To specifically manipulate PIP2 levels with high spatiotemporal precision, we rapidly recruited a yeast‐derived PIP2‐specific 5‐phosphotase, Inp54p, to the plasma membrane using the chemically‐induced dimerization (CID) system. Following the Inp54p recruitment, the cells went into a heterogeneous oscillation between a spreading and a crunching morphology. While a PIP3 phosphatase PTEN fell off the membrane when cells spread, it rebounded to the membrane as cells crunched. Other signaling events such as Ras activation, PIP3 production, and actin polymerization are largely induced along the periphery as cells spread. Together with a series of pharmacological experiments, our results indicate that PIP2 impedes protrusion events through multiple redundant pathways, providing a driving force for the excitable signaling network.

Reversible chemical dimerizer-induced recovery of PIP2 levels moves clathrin to the plasma membrane

Chemical dimerizers are powerful non-invasive tools for bringing molecules together inside intact cells. We recently introduced a rapidly reversible chemical dimerizer system which enables transient translocation of enzymes to and from the plasma membrane (PM). Here we have applied this system to transiently activate phosphatidylinositol 4,5-bisphosphate (PIP2) breakdown at the PM via translocation of phosphoinositide 5-phosphatase (5Ptase). We found that the PIP2 sensor phospholipase C-δ PH domain (PLCδ-PH) is released from the PM upon addition of the reversible chemical dimerizer rCD1. By outcompeting rCD1, rapid release of the 5Ptase from the PM is followed by PIP2 recovery. This permits the observation of the PIP2-dependent clathrin assembly at the PM.

Computational analysis of mutated AHAS in response to sulfonylurea herbicides

SummarySulfonylurea (SU) herbicides that target acetohydroxyacid synthase (AHAS, also called acetolactate synthase (ALS)) are regarded as one of the most important classes of herbicides, due to their extremely low toxicity towards mammals, ultra‐low dosage application and high selectivity. However, mutations of AHAS to a herbicide‐insensitive form appear to be a worldwide problem for acquired resistance. In this study, three mutated AHAS sequences were used. In the mutated AHASs, the proline (Pro) was replaced by one of threonine (Thr), alanine (Ala) or serine (Ser) in AHAS amino acid (AA) position 197Pro. To understand the herbicide resistance mechanism, we built dimeric AHAS complex models based on 1YBH of protein data bank (PDB) with SU herbicide, chlorimuron ethyl (CIE), using a homology. The three mutated AHASs in complex with CIE were analysed, and the resistance mechanism to SU herbicides was studied by molecular dynamics (MD) simulation performed using GROMACS 4.5.5. MD simulation analysis of wild‐type and the three mutated dimeric AHAS–CIE complex systems revealed the conformational stability and changes in herbicide binding to dimeric AHAS system due to the mutation. Additionally, it showed that conformational change of amino acid residue 200Met (methionine) was associated with the imidazolinone herbicide resistance mechanism. According to our computation, the detailed mechanism of herbicide resistance was variable, depending on the type of mutated amino acid, providing new insights for designing herbicides specific to each mutant AHAS.

In vivo regulation of erythropoiesis by chemically inducible dimerization of the erythropoietin receptor intracellular domain.

Erythropoietin (Epo) and its receptor (EpoR) are required for the regulation of erythropoiesis. Epo binds to the EpoR homodimer on the surface of erythroid progenitors and erythroblasts, and positions the intracellular domains of the homodimer to be in close proximity with each other. This conformational change is sufficient for the initiation of Epo-EpoR signal transduction. Here, we established a system of chemically regulated erythropoiesis in transgenic mice expressing a modified EpoR intracellular domain (amino acids 247–406) in which dimerization is induced using a specific compound (chemical inducer of dimerization, CID). Erythropoiesis is reversibly induced by oral administration of the CID to the transgenic mice. Because transgene expression is limited to hematopoietic cells by the Gata1 gene regulatory region, the effect of the CID is limited to erythropoiesis without adverse effects. Additionally, we show that the 160 amino acid sequence is the minimal essential domain of EpoR for intracellular signaling of chemically inducible erythropoiesis in vivo. We propose that the CID-dependent dimerization system combined with the EpoR intracellular domain and the Gata1 gene regulatory region generates a novel peroral strategy for the treatment of anemia.

Theoretical Study of Magnetic Excitation in Interacting Inequivalent Spin Dimer System NH4CuCl3

Magnetic excitation in the interacting spin dimer system NH4CuCl3 is investigated on the basis of an extended spin-wave theory, assuming a doubled unit cell with four dimer sublattices of inequivalent intradimer interactions as suggested by neutron scattering measurements. In the magnetically ordered phase, there are both transverse (Nambu–Goldstone) and longitudinal (Higgs) excitation modes as in the pressure-induced ordered phase of the isostructural spin dimer compounds TlCuCl3 and KCuCl3. The inequivalent dimer model is consistent with the magnon dispersion relation at zero magnetic field and with the field dependence of the excitation energies obtained by neutron scattering and ESR measurements. This supports the existence of four dimer sublattices with inequivalent dimers in NH4CuCl3.

Allosterically controlled threading of polymers through macrocyclic dimers.

As part of an ongoing study to construct a molecular Turing machine in which a polymer chain is encoded via allosteric information transfer between macrocyclic complexes, we describe the thermodynamic and kinetic characterization of a multicomponent self-assembled system based on a zinc porphyrin macrocyclic compound, a bidentate ligand (1,4-diazabicyclo[2.2.2]octane, DABCO), and a viologen-substituted polymer guest. Initial addition of DABCO to the porphyrin macrocycle in chloroform solution leads to the formation of a stable 2:1 (porphyrin:DABCO) dimeric complex, even under dilute conditions, by means of strong cooperative interactions involving hydrogen and metal-ligand bonds. Further titration of the porphyrin-DABCO mixtures with the polymer gives rise to a complex array of species in the solution. The system is analyzed in detail by a combination of spectroscopic measurements and computational modeling. Each association constant in the binding scheme and the fraction of each individual complex that is formed in solution are determined precisely using a mass-balance model. Kinetic studies revealed that the rates of the polymer threading and dethreading in and out of the dimeric system are remarkably slow, indicating that the polymer is locked inside the cavity of the stable 2:1 dimeric complex as a result of strong allosteric interactions.

Interaction between Nanoprisms with Different Coupling Strength

The aggregated noble metal system, consisting of two or more nanoparticles, possesses unique optical properties. The most important is the ability to generate larger local electric field enhancement than a single particle. In this work, we have modeled the system composed of silver nanoprisms with different geometries. For this purpose, the optical properties of the single silver nanoprism and the aggregated nanoprism dimer with adjacent and coplanar bases configuration have been studied by the finite integration technique. The relationship between the geometrical parameters, in particular the radius of the edges of curvature of a single nanoprism, and the position of the extinction peak has been described in a form of a mathematical equation. By moving and rotating one of the nanoprisms relative to the other in the dimer system, the coupling strength between them has been investigated by analyzing the near-field and far-field properties. On the basis of these results, a hybridization model of the nanopri...

Förster resonance energy transfer, absorption and emission spectra in multichromophoric systems. III. Exact stochastic path integral evaluation.

A numerically exact path integral treatment of the absorption and emission spectra of open quantum systems is presented that requires only the straightforward solution of a stochastic differential equation. The approach converges rapidly enabling the calculation of spectra of large excitonic systems across the complete range of system parameters and for arbitrary bath spectral densities. With the numerically exact absorption and emission operators, one can also immediately compute energy transfer rates using the multi-chromophoric Förster resonant energy transfer formalism. Benchmark calculations on the emission spectra of two level systems are presented demonstrating the efficacy of the stochastic approach. This is followed by calculations of the energy transfer rates between two weakly coupled dimer systems as a function of temperature and system-bath coupling strength. It is shown that the recently developed hybrid cumulant expansion (see Paper II) is the only perturbative method capable of generating uniformly reliable energy transfer rates and emission spectra across a broad range of system parameters.

Luttinger liquid behavior in the alternating spin-chain system copper nitrate

We determine the phase diagram of copper nitrate Cu(NO$_3$)$_2\cdot$2.5D$_2$O in the context of quantum phase transitions and novel states of matter. We establish this compound as an ideal candidate to study quasi-1D Luttinger liquids, 3D Bose-Einstein-Condensation of triplons, and the crossover between 1D and 3D physics. Magnetocaloric effect, magnetization, and neutron scattering data provide clear evidence for transitions into a Luttinger liquid regime and a 3D long-range ordered phase as function of field and temperature. Theoretical simulations of this model material allow us to fully establish the phase diagram and to discuss it in the context of dimerized spin systems.

Generalized mean-field description of entanglement in dimerized spin systems

We discuss a generalized self-consistent mean-field (MF) treatment, based on the selection of an arbitrary subset of operators for representing the system density matrix, and its application to the problem of entanglement evaluation in composite quantum systems. As a specific example, we examine in detail a pair MF approach to the ground state (GS) of dimerized spin-$1/2$ systems with anisotropic ferromagnetic-type $XY$ and $XYZ$ couplings in a transverse field, including chains and arrays with first neighbor and also longer range couplings. The approach is fully analytic and able to capture the main features of the GS of these systems, in contrast with the conventional single-spin MF. Its phase diagram differs significantly from that of the latter, exhibiting $({S}_{z})$ parity breaking just in a finite field window if the coupling between pairs is sufficiently weak, together with a fully dimerized phase below this window and a partially aligned phase above it. It is then shown that through symmetry restoration, the approach is able to correctly predict not only the concurrence of a pair, but also its entanglement with the rest of the chain, which shows a pronounced peak in the parity breaking window. Perturbative corrections allow to reproduce more subtle observables like the entanglement between weakly coupled spins and the low lying energy spectrum. All predictions are tested against exact results for finite systems.

Tuning Cytokine Receptor Signaling by Re-orienting Dimer Geometry with Surrogate Ligands

Most cell-surface receptors for cytokines and growth factors signal as dimers, but it is unclear whether remodeling receptor dimer topology is a viable strategy to "tune" signaling output. We utilized diabodies (DA) as surrogate ligands in a prototypical dimeric receptor-ligand system, the cytokine Erythropoietin (EPO) and its receptor (EpoR), to dimerize EpoR ectodomains in non-native architectures. Diabody-induced signaling amplitudes varied from full to minimal agonism, and structures of these DA/EpoR complexes differed in EpoR dimer orientation and proximity. Diabodies also elicited biased or differential activation of signaling pathways and gene expression profiles compared to EPO. Non-signaling diabodies inhibited proliferation of erythroid precursors from patients with a myeloproliferative neoplasm due to a constitutively active JAK2V617F mutation. Thus, intracellular oncogenic mutations causing ligand-independent receptor activation can be counteracted by extracellular ligands that re-orient receptors into inactive dimer topologies. This approach has broad applications for tuning signaling output for many dimeric receptor systems.