Dimer Coupling Research Articles

Exciton Coherence and Energy Transport in the Light-Harvesting Dimers of Allophycocyanin

Femtosecond transient grating and photon echo spectroscopies with a sub-20 fs time resolution are applied to allophycocyanin (APC), a protein located at the base of the phycobilisome antenna of cyanobacteria. Coupling between pairs of phycocyanobilin pigments with nondegenerate energy levels gives rise to the four-level exciton electronic structure of APC. Spectroscopic signals obtained in multiple experiments (e.g., linear absorption, fluorescence, transient grating, 2D Fourier transform photon echo) are used to constrain the parameters of a Frenkel exciton Hamiltonian. Comparison between experiment and theory yields a robust microscopic understanding of the electronic and nuclear relaxation dynamics. In agreement with previous work, transient absorption anisotropy establishes that internal conversion between the exciton states of the dimer occurs with time constants of 35, 220, and 280 fs. The sub-100 fs dynamics are decomposed into three distinct relaxation processes: electronic population transfer, intramolecular vibrational energy redistribution, and the dephasing of electronic and nuclear coherences. Model calculations show that the sub-100 fs red-shift in the transient absorption signal spectrum reflects interference between stimulated emission (ESE) and excited state absorption (ESA) signal components. It is also established that the pigment fluctuations in the dimer are not well-correlated, although further experiments will be required to precisely quantify the amount of correlation. The findings of this paper suggest that the light harvesting function of APC is enhanced by nondegeneracy of the pigments comprising the dimer and strong vibronic coupling of intramolecular modes on the phycocyanobilins. We find that the exciton states are 96% localized to the individual molecular sites within a particular dimer. Localization of the transition densities, in turn, is suggested to promote significant vibronic coupling which serves to both broaden the absorption line shape and open channels for fast internal conversion. The dominant internal conversion channel is assigned to a promoting mode near 800 cm(-1) involving hydrogen out-of-plane (HOOP) wagging motion similar to that observed in phytochrome and retinal. This rate enhancement ensures that all photoexcitations quickly and efficiently relax to the electronic origin of the lower energy exciton state from which energy transfer to the reaction center occurs.

Steady-state Function of the Ubiquitous Mammalian Na/H Exchanger (NHE1) in Relation to Dimer Coupling Models with 2Na/2H Stoichiometry

Steady-state Function of the Ubiquitous Mammalian Na/H Exchanger (NHE1) in Relation to Dimer Coupling Models with 2Na/2H Stoichiometry

Steady-state Function of the Ubiquitous Mammalian Na/H Exchanger (NHE1) in Relation to Dimer Coupling Models with 2Na/2H Stoichiometry

We describe the steady-state function of the ubiquitous mammalian Na/H exchanger (NHE)1 isoform in voltage-clamped Chinese hamster ovary cells, as well as other cells, using oscillating pH-sensitive microelectrodes to quantify proton fluxes via extracellular pH gradients. Giant excised patches could not be used as gigaseal formation disrupts NHE activity within the patch. We first analyzed forward transport at an extracellular pH of 8.2 with no cytoplasmic Na (i.e., nearly zero-trans). The extracellular Na concentration dependence is sigmoidal at a cytoplasmic pH of 6.8 with a Hill coefficient of 1.8. In contrast, at a cytoplasmic pH of 6.0, the Hill coefficient is <1, and Na dependence often appears biphasic. Results are similar for mouse skin fibroblasts and for an opossum kidney cell line that expresses the NHE3 isoform, whereas NHE1−/− skin fibroblasts generate no proton fluxes in equivalent experiments. As proton flux is decreased by increasing cytoplasmic pH, the half-maximal concentration (K1/2) of extracellular Na decreases less than expected for simple consecutive ion exchange models. The K1/2 for cytoplasmic protons decreases with increasing extracellular Na, opposite to predictions of consecutive exchange models. For reverse transport, which is robust at a cytoplasmic pH of 7.6, the K1/2 for extracellular protons decreases only a factor of 0.4 when maximal activity is decreased fivefold by reducing cytoplasmic Na. With 140 mM of extracellular Na and no cytoplasmic Na, the K1/2 for cytoplasmic protons is 50 nM (pH 7.3; Hill coefficient, 1.5), and activity decreases only 25% with extracellular acidification from 8.5 to 7.2. Most data can be reconstructed with two very different coupled dimer models. In one model, monomers operate independently at low cytoplasmic pH but couple to translocate two ions in “parallel” at alkaline pH. In the second “serial” model, each monomer transports two ions, and translocation by one monomer allosterically promotes translocation by the paired monomer in opposite direction. We conclude that a large fraction of mammalian Na/H activity may occur with a 2Na/2H stoichiometry.

5,6-Dihydroxyindole Tetramers with “Anomalous” Interunit Bonding Patterns by Oxidative Coupling of 5,5‘,6,6‘-Tetrahydroxy-2,7‘-biindolyl: Emerging Complexities on the Way toward an Improved Model of Eumelanin Buildup

Chemical or enzymatic oxidation of 5,6-dihydroxyindole (1) leads to the rapid deposition of a black solid resembling eumelanin pigments by way of a complex oligomerization/polymerization process that proceeds in the early stages via dimers 2-3 and trimers 5-6 characterized by 2,4'- and 2,7'-couplings. Despite extensive efforts, the structures of the higher oligomers, which define the structural architecture and physicochemical properties of the eumelanin particles, have so far defied elucidation. Using a dimer-dimer coupling strategy that has recently allowed the first successful entry to a tetramer of 1, we report now three additional tetramers obtained by oxidation of 5,5',6,6'-tetrahydroxy-2,7'-biindolyl (3) with the peroxidase/H2O2 system. On the basis of extensive 2D NMR and mass spectrometric analysis, the products were identified as 5,5',5'',5''',6,6',6'',6'''-octaacetoxy-7,2':3',3'':2'',7'''-tetraindolyl (acetylated 8, 3%), 5,5',5'',5''',6,6',6'',6' ''-octaacetoxy-2,7':4',4'':7'',2'''-tetraindolyl (acetylated 9, 4%), and 5,5',5'',5''',6,6',6'',6'''-octaacetoxy-2,7':2',3'':2'',7'''-tetraindolyl (acetylated 10, 5%), in which the inner units are linked through unexpected 3,3'-, 4,4'-, and 2,3'-linkages. If verified in further studies, the newly uncovered coupling patterns would entail important consequences for current models of eumelanin structure based on one-dimensional structural chains with extended pi-electron conjugation or pi-stacked flat oligomer aggregates.

Antiferromagnetic coupling through cyano-bridge and H-bonds in [Mn III(3-OMesalophen)(H 2O) 2] 2[Mn III(3-OMesalophen)(H 2O)] [W V(CN) 8] · 2H 2O

The synthesis, X-ray structure and magnetic properties of a new octacyanotungstate(V) based zero-dimensional [Mn III(3-OMesalophen)(H 2O) 2] 2[Mn III(3-OMesalophen)(H 2O)] [W V(CN) 8] · 2H 2O ( 1) system are reported. Compound 1 crystallizes in the triclinic system, has space group P 1 ¯ and unit cell dimensions a = 13.494(2) Å, b = 17.080(4) Å, c = 18.739(5) Å with Z = 2. The structure of 1 consists of the dimeric Mn–NC–W cyano-bridged {[Mn(3-OMesalophen)(H 2O)][W(CN) 8]} 2− anions and bis-μ-aqua-bridged dimers of [Mn(3-OMesalophen)(H 2O) 2] + cations linked by H-bonds and π–π stacking into Mn 6 III W 2 V distinguishable structural and magnetic units. The magnetic behavior of 1 correspond to a dominant antiferromagnetic coupling within the cyano-bridged {Mn IIIW V} 2− dimer ( J 1 = −20 cm −1) and weaker AF coupling between hydrogen bonded moieties ( J 2 = −0.46 cm −1) with zero-field splitting D parameter of Mn(III) centre in axially distorted surroundings of −4.0 cm −1.

The Soft Mode Transition Induced by Magnetic Field and Pressure in TlCuCl3and Related Dimer Compounds

TlCuCl 3 is an example of a quantum spin liquid of S = 1/2 Cu 2+ dimers. Strong inter-dimer superexchange interactions give rise to a three-dimensional dispersion of the triplet magnon. The minimum excitation energy determines the spin gap which is significantly smaller than the dimer coupling. It can be closed by an applied hydrostatic pressure of the order of 1 kbar or by a magnetic field of 5.6 T, offering a unique opportunity to study the evolution of the magnon modes through the pressure- and field-induced quantum phase transitions.

Pressure- and field-induced magnetic quantum phase transitions inTlCuCl3

TlCuCl3 is a quantumspin liquid of S = 1/2 Cu2+ dimers. Interdimer superexchange interactions give a three-dimensional magnon dispersionand a spin gap significantly smaller than the dimer coupling, which is closed by an appliedhydrostatic pressure of approximately 2.5 kbar or by a magnetic field of 5.6 T, offering aunique opportunity to explore both the pressure- and field-induced quantum phasetransitions and their associated critical phenomena.

Field- and pressure-induced magnetic quantum phase transitions inTlCuCl3

Thallium copper chloride is a quantum spin liquid of S = 1/2 Cu^2+ dimers. Interdimer superexchange interactions give a three-dimensional magnon dispersion and a spin gap significantly smaller than the dimer coupling. This gap is closed by an applied hydrostatic pressure of approximately 2kbar or by a magnetic field of 5.6T, offering a unique opportunity to explore the both types of quantum phase transition and their associated critical phenomena. We use a bond-operator formulation to obtain a continuous description of all disordered and ordered phases, and thus of the transitions separating these. Both pressure- and field-induced transitions may be considered as the Bose-Einstein condensation of triplet magnon excitations, and the respective phases of staggered magnetic order as linear combinations of dimer singlet and triplet modes. We focus on the evolution with applied pressure and field of the magnetic excitations in each phase, and in particular on the gapless (Goldstone) modes in the ordered regimes which correspond to phase fluctuations of the ordered moment. The bond-operator description yields a good account of the magnetization curves and of magnon dispersion relations observed by inelastic neutron scattering under applied fields, and a variety of experimental predictions for pressure-dependent measurements.

Quantitative analysis of dinuclear manganese(II) EPR spectra

A quantitative method for the analysis of EPR spectra from dinuclear Mn(II) complexes is presented. The complex [(Me 3TACN) 2Mn(II) 2(μ-OAc) 3]BPh 4 ( 1) (Me 3TACN= N, N ′, N ′′-trimethyl-1,4,7-triazacyclononane; OAc=acetate 1−; BPh 4=tetraphenylborate 1−) was studied with EPR spectroscopy at X- and Q-band frequencies, for both perpendicular and parallel polarizations of the microwave field, and with variable temperature (2–50 K). Complex 1 is an antiferromagnetically coupled dimer which shows signals from all excited spin manifolds, S=1 to 5. The spectra were simulated with diagonalization of the full spin Hamiltonian which includes the Zeeman and zero-field splittings of the individual manganese sites within the dimer, the exchange and dipolar coupling between the two manganese sites of the dimer, and the nuclear hyperfine coupling for each manganese ion. All possible transitions for all spin manifolds were simulated, with the intensities determined from the calculated probability of each transition. In addition, the non-uniform broadening of all resonances was quantitatively predicted using a lineshape model based on D- and r-strain. As the temperature is increased from 2 K, an 11-line hyperfine pattern characteristic of dinuclear Mn(II) is first observed from the S=3 manifold. D- and r-strain are the dominate broadening effects that determine where the hyperfine pattern will be resolved. A single unique parameter set was found to simulate all spectra arising for all temperatures, microwave frequencies, and microwave modes. The simulations are quantitative, allowing for the first time the determination of species concentrations directly from EPR spectra. Thus, this work describes the first method for the quantitative characterization of EPR spectra of dinuclear manganese centers in model complexes and proteins. The exchange coupling parameter J for complex 1 was determined ( J=−1.5±0.3 cm −1 ; H ex =−2J S 1· S 2) and found to be in agreement with a previous determination from magnetization. The phenomenon of exchange striction was found to be insignificant for 1.

A coherent relation between structure and conduction of infinite atomicwires

We demonstrate a theoretical analysis concerning the geometrical structures andelectrical conduction of infinite monatomic gold and aluminium wires in theprocess of their elongation, based on first-principles molecular-dynamicssimulations using the real-space finite-difference method. Our study predicts thatthe single-row gold wire ruptures up to form a dimer coupling structure when theaverage interatomic distance increases up to more than 3.0 Å, and that the wire isconductive before breaking but changes to an insulator at the rupturing point. Inthe case of the aluminium wire, it exhibits a magnetic ordering due to the spinpolarization, and even when stretched up to the average interatomic distance of3.5 Å, a dimerization does not occur and the wire keeps a metallic nature.

Magnetic properties of phosphate-bridged copper(ii) organic–inorganic hybrid compounds

Hydrothermal synthesis has allowed us to isolate and characterize three new inorganic–organic hybrid materials, the compounds [Cu2(phen)2(H2O)2(H2PO4)2](NO3)2·2H2O (1), [(Cu2bipy2)2(V4O9)(PO4)2(HPO4)(H2P2O7)]n·nH2O (2) and [Cu2(dpa)2(V2P2O12)]n, (4), which have been magneto-structurally characterized. In addition, the magnetic behaviour of the related compound [Cu2(bipy)2(VO2)2(PO4)2]n (3), has been measured. Compound 1 has a dimeric structure, while compound 2 and 4 have dimer chain structures. The dependence of the magnetic susceptibility on temperature suggests antiferromagnetic coupling for 1, 2 and 3, while compound 4 can be well understood in terms of the Curie–Weiss law with θ = −23 K. The fitting of the magnetic behaviour to the Bleaney–Bowers spin–dimer coupling expression leads to J = −8.0 cm−1 for 1, J = −28.8 cm−1 for 2 and J = −29.0 cm−1 for 3. The use of alternating chain expressions leads to J = −28.8 cm−1, α = −0.03 for 2 and J = −29.4 cm−1, α = −0.027 for 3. Although a variety of coordination geometries are exhibited by the compounds in the series, all of them have O–P–O bridges connecting the cupric centres. It was possible to identify the role of the vanadyl groups of the phosphovanadate framework as an important factor affecting the ability of the phosphate groups to transmit magnetic interactions.

A High-Pressure Spectral Hole Burning Study of Correlation between Energy Disorder and Excitonic Couplings in the LH 2 Complex from Rhodopseudomonas Acidophila

Low-temperature (5 K) nonphotochemical hole burning and absorption spectroscopies were used to study the effects of high pressure (up to 1015 MPa) on excitonic coupling energies and energy disorder in the light-harvesting complex 2 (LH 2) from Rhodopseudomonas Acidophila (strain 10050). The pressure dependences of the widths and positions of the B850 and B870 (lowest exciton level of the B850 ring) bands were determined. The results show, for the first time, that these parameters are linearly correlated (common scaling law), consistent with recent theoretical predictions (Jang; et al. J. Phys. Chem. B 2001, 105, 6655). Excitonic calculations for the B850 ring of bacteriochlorophyll a molecules were performed in the nearest dimer−dimer coupling approximation (Wu; et al. J. Phys. Chem. B 1997, 101, 7654) with E1+ diagonal energy disorder. Such a symmetry is known to dictate the response of the B870 level (absorption bandwidth, displacement (ΔE) from the B850 band maximum) to either diagonal or off-diagonal energy disorder. The results reveal that the pressure dependences of nearest neighbor coupling energies and the width of the distribution function for energy disorder are positively correlated, both increasing with pressure. Importantly, an effective pressure dependent excitonic Hamiltonian for the B850 ring was obtained. This Hamiltonian was used to show that mixing of the upper excitonic levels of the B850 ring in close proximity to the B800 levels is too weak to account for the additional (other than B800 → B850 energy transfer) decay channel of the B800 band. A simple combinatorial model for intra-B800 band downward energy transfer is presented that qualitatively explains all available low-temperature data on the additional decay channel.

Quantum-mechanical coherence in cell microtubules: a realistic possibility?

We discuss the possibility of quantum-mechanical coherence in Cell MicroTubules (MT), based on recent developments in quantum physics. We focus on potential mechanisms for `energy-loss-free' transport along the microtubules, which could be considered as realizations of Fröhlich's ideas on the role of solitons for superconductivity and/or biological matter. In particular, by representing the MT arrangements as cavities, we review a novel scenario, suggested in collaboration with D.V. Nanopoulos, concerning the formation of macroscopic (or mesoscopic) quantum-coherent states, as a result of the (quantum-electromagnetic) interactions of the MT dimers with the surrounding molecules of the ordered water in the interior of the MT cylinders. We suggest specific experiments to test the above-conjectured quantum nature of the microtubular arrangements inside the cell. These experiments are similar in nature to those in atomic physics, used in the detection of the Rabi-Vacuum coupling between coherent cavity modes and atoms. Our conjecture is that a similar Rabi-Vacuum-splitting phenomenon occurs in the absorption (or emission) spectra of the MT dimers, which would constitute a manifestation of the dimer coupling with the coherent modes in the ordered-water environment (dipole quanta), which emerge due to the phenomenon of `super-radiance'.

Effect of La substitution on the CuO2 chain spin gap in Sr14Cu24O41

The compound Sr14Cu24O41 has a unique structure. It consists of an alternating stack of the plane containing edge-sharing CuO2 chains, and the plane containing two-leg Cu2O3 ladders sandwiched by Sr layers. The CuO2 chain also has a singlet ground state originating from a dimerization. The dimerized state in the chain depends critically on the number of holes. The effect of La substitution for Sr on the CuO2 chain spin gap is investigated by measuring the magnetic susceptibility of Sr14−xLaxCu24O41 with x⩽1. Due to the large spin gap, the Cu2O3 plane is magnetically inert below room temperature. For x=0, the susceptibility shows a characteristic decrease below 80 K, followed by an upturn below 20 K due to a Curie contribution. After subtracting the Curie term, the susceptibility is fitted by a dimer description. The dimer number ND=1.45 and the dimer coupling constant JD=139 K are obtained. With increasing La content, both ND and JD decrease gradually, indicating the weakening of the antiferromagnetic interaction between Cu2+ spins in the CuO2 chain. The Curie contribution enhances at the same time, and the gap feature becomes gradually smeared. It is difficult to fit the data when x=1.0.

On Quantum Mechanical Aspects of Microtubules

We discuss possible quantum mechanical aspects of MicroTubules (MT), based on recent developments in quantum physics. We focus on potential mechanisms for "energy-loss-free" transport along the microtubules, which could be considered as realizations of Fröhlich's ideas on the rôle of solitons for superconductivity and/or biological matter. In particular, by representing the MT arrangements as cavities, we present a novel scenario on the formation of macroscopic (or mesoscopic) quantum-coherent states, as a result of the (quantum-electromagnetic) interactions of the MT dimers with the surrounding molecules of the ordered water in the interior of the MT cylinders. Such states decohere due to dissipation through the walls of the MT. Transfer of energy without dissipation, due to such coherent modes, could occur only if the decoherence time is larger than the average time scale required for energy transfer across the cells. We present some generic order of magnitude estimates or the decoherence time in a typical model for MT dynamics. Our conclusion is that the quantum coherent states play a rôle in energy transfer if the dissipation through the walls of the MT cavities is fairly suppressed, corresponding to damping time scales Tr≥10-4-10-5 sec, for moderately large MT networks. We suggest specific experiments to test the above-conjectured quantum nature of the microtubular arrangements inside the cell. These experiments are similar in nature to those in atomic physics, used in the detection of the Rabi-Vacuum coupling between coherent cavity modes and atoms. Our conjecture is that a similar Rabi-Vacuum-splitting phenomenon occurs in the absorption (or emission) spectra of the MT dimers, which would constitute a manifestation of the dimer coupling with the coherent modes in the ordered-water environment (dipole quanta), which emerge due to "super-radiance".