Dimer System Research Articles

Optimal power generation using dark states in dimers strongly coupled to their environment

Dark state protection has been proposed as a mechanism to increase the power output of light harvesting devices by reducing the rate of radiative recombination. Indeed many theoretical studies have reported increased power outputs in dimer systems which use quantum interference to generate dark states. These models have typically been restricted to particular geometries and to weakly coupled vibrational baths. Here we consider the experimentally-relevant strong vibrational coupling regime with no geometric restrictions on the dimer. We analyze how dark states can be formed in the dimer by numerically minimizing the emission rate of the lowest energy excited eigenstate, and then calculate the power output of the molecules with these dark states. We find that there are two distinct types of dark states depending on whether the monomers form homodimers, where energy splittings and dipole strengths are identical, or heterodimers, where there is some difference. Homodimers, which exploit destructive quantum interference, produce high power outputs but strong phonon couplings and perturbations from ideal geometries are extremely detrimental. Heterodimers, which are closer to the classical picture of a distinct donor and acceptor molecule, produce an intermediate power output that is relatively stable to these changes. The strong vibrational couplings typically found in organic molecules will suppress destructive interference and thus favor the dark-state enhancement offered by heterodimers.

Atomistic Characterization of Plasmonic Dimers in the Quantum Size Regime

Plasmonic dimer systems show great promise in a wide range of applications because of their unique optical and electronic properties that arise from the coupling of monomer plasmons. To determine t...

Energy transfer, correlations and decoherence in a dimer in terms of the two-level atomic distances

In this manuscript, we study the coherent single-excitation energy transfer for a dimer system consisting of a donor and an acceptor modeled by two-level systems (TLSs), which are immersed in common thermal environment. We illustrate the effects of the distance between TLSs and temperature of the thermal reservoir on the energy transfer process considering collective damping and dipole–dipole interaction. Concretely, the control and enhancement of the probability during the time evolution is performed by a suitable choice of the distance between TLSs with respect to the temperature of the reservoir. On the other hand, we study the time evolution of the quantum and classical correlations of the TLSs-state through calculating concurrence and quantum discord. We find that the dynamical behavior of quantum and classical correlations dynamics in thermal reservoir is similar to vacuum reservoir with slight decrease in the amount of correlations. These correlations are also very sensitive to the TLSs-distance and when the distance becomes significantly large, the amount of correlations exponentially decrease with the time. Finally, we explore the relationship between the probability and correlations during the evolution and shows that quantum and classical correlations can be created during the process of excitation energy transfer.

Optical Spectroscopy and Superconductivity of Cuprates (Review)

The optical properties of low-dimensional dielectric cuprates, including parent systems for high-temperature superconductors, such as La2CuO4, Sr2CuO2Cl2, and YBa2Cu3O6 are briefly reviewed. The main focus is on the d–d and p–d charge transfer transitions, which determine the fundamental absorption band. The analysis of optical properties shows the instability of parent cuprates against the d–d charge transfer with the formation of metastable electron–hole (EH) dimers of the Cu1+–Cu3+-type pairs coupled by the two-particle transfer and characterized by the giant electric polarizability. The formation of a system of stable EH dimers upon nonisovalent substitution determines the unconventional properties of the pseudogap and superconducting phases of doped cuprates.

C-N Bond Rotation Controls Photoinduced Electron Transfer in an Aminostyrene-Stilbene Donor-Acceptor System.

We investigate energy transfer and electron transfer in a dimethylsilylene-spaced aminostyrene-stilbene donor-acceptor dimer using time-dependent density functional theory calculations. Our results confirm that the vertical S3, S2, and S1 excited states are, respectively, a local excitation on the aminostyrene, local excitation on the stilbene, and the charge-transferred (CT) excited state with electron transfer from aminostyrene to stilbene. In addition, an energy minimum with the C-N bond of the amino group twisted at about 90° is also identified on the S1 potential energy surface. This S1 state exhibits a twisted intramolecular charge transfer (TICT) character. A potential energy scan along the C-N bond torsional angle reveals a conical intersection between the S2 stilbene local excitation and the S1 CT/TICT state at a torsional angle of ∼60°. We thus propose that the conical intersection dominates the electron transfer dynamics in the donor-acceptor dimer and copolymers alike, and the energy barrier along the C-N bond rotation controls the efficiency of such a process. Moreover, we show that despite the zero oscillator strength of the S1 excited states in the CT and TICT minima, an emissive S1 state with a V-shaped conformational structure can be located. The energy of this V-shape CT structure is thermally accessible; therefore, it is expected to be responsible for the CT emission band of the dimer observed in polar solvents. Our data provide a clear explanation of the complex solvent-dependent dual emission and photoinduced electron transfer properties observed experimentally in the dimer and copolymer systems. More importantly, the identifications of the conical intersection and energy barrier along the C-N bond rotation provide a novel synthetic route for controlling emissive properties and electron transfer dynamics in similar systems, which might be useful in the design of novel organic optoelectronic materials.

Model liquid crystalline dimers in a slit pore: Monte Carlo simulation study

ABSTRACTIn this work, we present results from (isobaric–isothermal) Monte Carlo Simulation studies of liquid crystalline dimer systems confined in a slit pore. Liquid crystalline dimer systems of various spacer numbers have been considered. Surface-induced conformational and alignment properties of these systems at different pressures under homeotropic anchoring condition have been investigated. We have used easily manageable coarse grained force fields to model both monomer–monomer and monomer–substrate interaction potentials. According to the simulated result, the anchoring of dimers to the surface and orientation of mesogenic units with respect to the surface normal seem to depend on the spacer number for messogen attractive confinement. Dimers with lower spacer number are able be adsorbed to the surface and most of their mesogens are oriented along the surface normal even at lower pressure. Those with larger spacer number are distributed throughout the volume at lower pressure. In the case of mesogen repulsive confinement, most of the dimers are adsorbed to the surface and most mesogens are randomly oriented at low pressure. As the pressure gets higher, the adsorption and orientability increase depending on the type of confinement and spacer number. As a result, clear submolecular partitioning and smectic A like structure have been identified.

Chromosome detachment from the nuclear envelope is required for genomic stability in closed mitosis.

Mitosis in metazoans involves detachment of chromosomes from the nuclear envelope (NE) and NE breakdown, whereas yeasts maintain the nuclear structure throughout mitosis. It remains unknown how chromosome attachment to the NE might affect chromosome movement in yeast. By using a rapamycin-induced dimerization system to tether a specific locus of the chromosome to the NE, I found that the tethering delays the separation and causes missegregation of the region distal to the tethered site. The phenotypes are exacerbated by mutations in kinetochore components and Aurora B kinase Ipl1. The chromosome region proximal to the centromere is less affected by the tether, but it exhibits excessive oscillation before segregation. Furthermore, the tether impacts full extension of the mitotic spindle, causing abrupt shrinkage or bending of the spindle in shortened anaphase. The study supports detachment of chromosomes from the NE being required for faithful chromosome segregation in yeast and segregation of tethered chromosomes being dependent on a fully functional mitotic apparatus.

Self-assembly of a dimer system.

In the self-assembly process which drives the formation of cellular membranes, micelles, and capsids, a collection of separated subunits spontaneously binds together to form functional and more ordered structures. In this work, we study the statistical physics of self-assembly in a simpler scenario: the formation of dimers from a system of monomers. The properties of the model allow us to frame the microstate counting as a combinatorial problem whose solution leads to an exact partition function. From the associated equilibrium conditions, we find that such dimer systems come in two types: "search-limited" and "combinatorics-limited," only the former of which has states where partial assembly can be dominated by correct contacts. Using estimates of biophysical quantities in systems of single-stranded DNA dimerization, transcription factor and DNA interactions, and protein-protein interactions, we find that all of these systems appear to be of the search-limited type, i.e., their fully correct dimerization regimes are more limited by the ability of monomers to find one another in the constituent volume than by the combinatorial disadvantage of correct dimers. We derive the parameter requirements for fully correct dimerization and find that rather than the ratio of particle number and volume (i.e., number density) being the relevant quantity, it is the product of particle diversity and volume that is constrained. Ultimately, this work contributes to an understanding of self-assembly by using the simple case of a system of dimers to analytically study the combinatorics of assembly.

ZMP-SAPT: DFT-SAPT using ab initio densities.

Symmetry Adapted Perturbation Theory (SAPT) has become an important tool when predicting and analyzing intermolecular interactions. Unfortunately, Density Functional Theory (DFT)-SAPT, which uses DFT for the underlying monomers, has some arbitrariness concerning the exchange-correlation potential and the exchange-correlation kernel involved. By using ab initio Brueckner Doubles densities and constructing Kohn-Sham orbitals via the Zhao-Morrison-Parr (ZMP) method, we are able to lift the dependence of DFT-SAPT on DFT exchange-correlation potential models in first order. This way, we can compute the monomers at the coupled-cluster level of theory and utilize SAPT for the intermolecular interaction energy. The resulting ZMP-SAPT approach is tested for small dimer systems involving rare gas atoms, cations, and anions and shown to compare well with the Tang-Toennies model and coupled cluster results.

Large dual spin-rectifying and high-efficiency dual spin-filtering in cyclooligomeric Mn-phthalocyanine dimer molecular junction

Abstract Based on density functional theory combined with nonequilibrium Green’s function technique, we investigate the spin-polarized transport properties of the cyclooligomeric Mn-phthalocyanine dimer and Fe-phthalocyanine dimer with carbon nanotube electrodes. The results show that the spin-polarized transport properties can be effectively tuned by changing the central transition metal atoms, and the Mn-phthalocyanine dimer system can exhibit large dual spin-rectifying and high-efficiency dual spin-filtering effects simultaneously under the [1, −1] magnetic configuration. The underlying mechanism is analyzed by spin-resolved transmission spectra, molecular projected self-consistent Hamiltonian orbitals and their spatial distribution.

Finite-Temperature Dimer Method for Finding Saddle Points on Free Energy Surfaces.

The dimer method and its variants have been shown to be efficient in finding saddle points on potential surfaces. In the dimer method, the most unstable direction is approximately obtained by minimizing the total potential energy of the dimer. Then, the force in this direction is reversed to move the dimer toward saddle points. When the finite-temperature effect is important for a high-dimensional system, one usually needs to describe the dynamics in a low-dimensional space of reaction coordinates. In this case, transition states are collected as saddle points on the free energy surface. The traditional dimer method cannot be directly employed to find saddle points on a free energy surface since the surface is not known a priori. Here, we develop a finite-temperature dimer method for searching saddle points on the free energy surface. In this method, a constrained rotation dynamics of the dimer system is used to sample dimer directions and an efficient average method is used to obtain a good approximation of the most unstable direction. This approximated direction is then used in reversing the force component and evolving the dimer toward saddle points. Our numerical results suggest that the new method is efficient in finding saddle points on free energy surfaces. © 2019 Wiley Periodicals, Inc.

Activated Niobium and Tantalum Imido Complexes: From Tuneable Polymerization to Selective Ethylene Dimerization Systems

AbstractThe niobium and tantalum imido complexes [CpMCl2(NDipp)], [MCl3(NR)(dme)] (R=tBu, Ph, 2,6‐iPr2C6H3 (Dipp), and Mes), and [TaCl3(NDipp)(tmeda)] were tested in combination with EtAlCl2 for the dimerization of ethylene. The niobium systems afforded dimers or polymers, depending on the nature of the imido ligand, with overall productivities in the range 720 to 13,720 (mol C2H4)(mol Nb)−1. The nature of the polyethylene produced (LDPE or HDPE) depended on the imido ligand and the niobium concentration at which catalysis was run. In contrast, the tantalum/dme systems all mediated ethylene dimerization with productivities of up to 4,503 (mol C2H4)(mol Ta)−1, with overall selectivities to butenes of between 73–81 wt %; selectivity within the dimer fraction to 1‐butene was in the range 72 to 100 %. The productivity of [TaCl3(NDipp)(tmeda)] was six times higher than that of its dme‐bearing counterpart, but at the cost of selectivity to 1‐butene. For the tantalum imido‐mediated ethylene dimerization the composition of the product slate formed is indicative of a metallacyclic mechanism being operative.

Structural basis for chemically-induced homodimerization of a single domain antibody

Chemically-induced dimerization (CID) systems are essential tools to interrogate and control biological systems. AcVHH is a single domain antibody homo-dimerizing upon caffeine binding. AcVHH has a strong potential for clinical applications through caffeine-mediated in vivo control of therapeutic gene networks. Here we provide the structural basis for caffeine-induced homo-dimerization of acVHH.

Оптическая спектроскопия и сверхпроводимость купратов (О б з о р)

AbstractThe optical properties of low-dimensional dielectric cuprates, including parent systems for high-temperature superconductors, such as La_2CuO_4, Sr_2CuO_2Cl_2, and YBa_2Cu_3O_6 are briefly reviewed. The main focus is on the d – d and p – d charge transfer transitions, which determine the fundamental absorption band. The analysis of optical properties shows the instability of parent cuprates against the d – d charge transfer with the formation of metastable electron–hole (EH) dimers of the Cu^1+–Cu^3+-type pairs coupled by the two-particle transfer and characterized by the giant electric polarizability. The formation of a system of stable EH dimers upon nonisovalent substitution determines the unconventional properties of the pseudogap and superconducting phases of doped cuprates.

A general approach for the site-selective modification of native proteins, enabling the generation of stable and functional antibody-drug conjugates.

Antibody-drug conjugates (ADCs) are a class of targeted therapeutics that utilize the specificity of antibodies to selectively deliver highly potent cytotoxins to target cells. Although recent years have witnessed significant interest in ADCs, problems remain with the standard linkage chemistries used for cytotoxin-antibody bioconjugation. These typically (1) generate unstable constructs, which may lead to premature cytotoxin release, (2) often give a wide variance in drug-antibody ratios (DAR) and (3) have poor control of attachment location on the antibody, resulting in a variable pharmacokinetic profile. Herein, we report a novel divinylpyrimidine (DVP) linker platform for selective bioconjugation via covalent re-bridging of reduced disulfide bonds on native antibodies. Model studies using the non-engineered trastuzumab antibody validate the utility of this linker platform for the generic generation of highly plasma-stable and functional antibody constructs that incorporate variable biologically relevant payloads (including cytotoxins) in an efficient and site-selective manner with precise control over DAR. DVP linkers were also used to efficiently re-bridge both monomeric and dimeric protein systems, demonstrating their potential utility for general protein modification, protein stabilisation or the development of other protein-conjugate therapeutics.

Molecular Dynamics Simulations with ab Initio Force Fields: A Review of Case Studies on CH4, CCl4, CHF3, and CHCl3 Dimers

Recent progress in our group on quantum chemistry calculated intermolecular interaction potential energy functions, or ab initio force fields, for use in molecular dynamics simulations is reviewed. These ab initio force fields have been calibrated by the current state-of-the-art computational techniques with respect to the correlation-method versus basis-set combinations. The case studies of CH4, CCl4, CHF3, and CHCl3 molecular dimeric systems are presented and compared. The simulation scheme can serve as a modern paradigm before a full-blown quantum mechanical molecular simulation can be achieved. It is our hope that this review can help stimulating interests among computational scientists in further exploring this important field of multiscale science and engineering.

Excited states and excitonic interactions in prototypic polycyclic aromatic hydrocarbon dimers as models for graphitic interactions in carbon dots.

The study of electronically excited states of stacked polycyclic aromatic hydrocarbons (PAHs) is of great interest due to promising applications of these compounds as luminescent carbon nanomaterials such as graphene quantum dots (GQDs) and carbon dots (CDs). In this study, the excited states and excitonic interactions are described in detail based on four CD model dimer systems of pyrene, coronene, circum-1-pyrene and circum-1-coronene. Two multi-reference methods, DFT/MRCI and SC-NEVPT2, and two single-reference methods, ADC(2) and CAM-B3LYP, have been used for excited state calculations. The DFT/MRCI method has been used as a benchmark method to evaluate the performance of the other ones. All methods produce useful lists of excited states. However, an overestimation of excitation energies and an inverted ordering of states, especially concerning the bright HOMO-LUMO excitation, are observed. In the pyrene-based systems, the first bright state appears among the first four states, whereas the number of dark states is significantly larger for the coronene-based systems. Fluorescence emission properties are addressed by means of geometry optimization in the S1 state. The inter sheet distances for the S1 state decrease in comparison to the corresponding ground-state values. These reductions are largest for the pyrene dimer and decrease significantly for the larger dimers. Several minima have been determined on the S1 energy surface for most of the dimers. The largest variability in emission energies is found for the pyrene dimer, whereas in the other cases a more regular behavior of the emission spectra is observed.

A 2-D π–π dimer model system to investigate structure-charge transfer relationships in rubrene

A two dimensional π–π model dimer system that will enable researchers to predict charge transport properties for rubrene-based materials using their single crystal π-stacking data.

Plaquette Singlet State of the Orthogonal Dimer System —Observation by High Pressure ESR Measurement in THz Region

Plaquette Singlet State of the Orthogonal Dimer System —Observation by High Pressure ESR Measurement in THz Region

Effect of an underdamped vibration with both diagonal and off-diagonal exciton-phonon interactions on excitation energy transfer.

A numerically exact approach, named as the hierarchical stochastic Schrödinger equation, is employed to investigate the resonant vibration-assisted excitation energy transfer in a dimer system, where an underdamped vibration with both diagonal and off-diagonal exciton-phonon interactions is incorporated. From a large parameter space over the site-energy difference, excitonic coupling, and reorganization energy, it is found that the promotion effect of the underdamped vibration is significant only when the excitonic coupling is smaller than the site-energy difference. Under the circumstance, there is an optimal strength ratio between diagonal and off-diagonal exciton-phonon interactions for the resonant vibration-assisted excitation energy transfer as the site-energy difference is greater than the reorganization energy, whereas in the opposite situation the most efficient energy transfer occurs as the exciton-phonon interaction is totally off-diagonal. © 2018 Wiley Periodicals, Inc.