Interdimer Interactions Research Articles

Emergent Berezinskii-Kosterlitz-Thouless and Kugel-Khomskii Physics in the Triangular Lattice Bilayer Colbaltate.

Motivated by the experiments on the triangular lattice bilayer colbaltate K_{2}Co_{2}(SeO_{3})_{3}, we consider an extended XXZ model to explore the underlying physics. The model is composed of interacting Co^{2+} dimers on the triangular lattice, where the Co^{2+} ion provides an effective spin-1/2 local moment via the spin-orbit coupling and the crystal field effect. The intradimer interaction is dominant and would simply favor the local spin singlet, and the interdimer interactions compete with the interdimer interaction, leading to rich behaviors. With the easy-axis anisotropy, it is shown that, in the ground state manifold of the intradimer Ising interaction, the system realizes an effective quantum Ising model, where the ground state is either a three-sublattice order with a mixture of antiferromagnetic Ising order and a valence-bond spin singlet or Ising disordered. The finite temperature regime realizes the Berezinskii-Kosterlitz-Thouless physics. To explore the full excitations, we incorporate the excited state manifold of the intradimer Ising interaction and establish the emergent Kugel-Khomskii physics. Thus, the triangular lattice bilayer colbaltate is an excellent platform to explore the interplay between geometrical frustration and anisotropic interactions as well as the emergent effective models and the resulting physics.

Magnetic field-induced phase transitions in Cu(en)2SO4 – A dimerized S = 1/2 quantum antiferromagnet

Magnetic susceptibility, magnetization and specific heat of powder and single crystal of Cu(en)2SO4 were investigated. The analysis of the data confirmed that Cu(en)2SO4 can be treated as a quasi-two-dimensional array of magnetic dimers with singlet-ground state persisting up to about 6.5 T. Magnetization and susceptibility studies were performed in the singlet phase and the analysis revealed that g-factor anisotropy is the main mechanism responsible for the different behavior in the magnetic field applied along the b and c axis. The investigation of powder and single crystal specific heat in magnetic fields applied along all three crystallographic directions revealed only small anisotropy associated with the g-factor anisotropy. All mentioned data sets resemble main features of the spin 1/2 HAF dimer model with J/kB = -5.52 K. The observed deviations can be ascribed to the presence of inter-dimer interactions with the effective strength z’J’/kB = -2.7 K. In fields above 6.5 T the system passes from the singlet phase to the ordered state stable up to about 11 T. The expectation of a dome shape magnetic phase diagram is based on the strong dimerization of the magnetic lattice. Future experiments and calculations are discussed to identify the origin of the quantum phase transition associated with the gap closing.

A copper(II) coordination polymer of formate-bridged dimers: an alternating S = ½ antiferromagnetic chain

Reaction of 1,3-propanediamine with copper(II) perchlorate hexahydrate in basic solution in the presence of trimethyl orthoformate and o-iodophenol serendipitously formed sodium [triformato-diperchlorato-di-1,3-propanediaminodicopper(II)], Na[Cu2(HCO2)3(1,3-pn)2](ClO4)2 (1). Single-crystal X-ray diffraction measurements show the compound to be a coordination polymer with the Cu(II) ions alternately bridged in μ1,1- and μ1,3-fashion by the formate ions. The sodium ions are coordinated to both formate ions and perchlorate ions in the lattice. Magnetic measurements were made over the range 1.8-310 K and show the presence of a singlet ground state at low temperature, the µ1,1-bridged copper ions being strongly antiferromagnetically coupled. The data were modeled equally well, within experimental error, by the alternating chain model and the dimer model with a Curie-Weiss correction for weak inter-dimer interactions, yielding C = 0.432(2) emu-K/mol-Oe, J/kB = −94.3(9) K and J’ = −2.4(1.5) K ().

Charge glass in an extended dimer Hubbard model

The charge degrees of freedom in several different organic charge transfer salts display slow or glassy dynamics. In order to gain insight into this behaviour, we obtain the low energy theory for an extended dimer Hubbard model, taking into account the occupations of sites on neighbouring dimers. We take a classical limit of the resulting effective model of coupled spins and dimers and study it using classical Monte Carlo simulations. We find that frustration induced by intra- and inter-dimer interactions leads to glassiness in the charge degress of freedom in the absence of ordering of the spin degrees of freedom. Our results may have relevance to experimental observations of relaxor ferroelectric behaviour in the dynamics of organic charge transfer salts.

The tuning of oxalato-bridge on magnetic interaction and field-induced phase transition in Ba2Co2Cl2(C2O4)3·4H2O

The crystal structure of the oxalato-bridged compound Ba2Co2Cl2(C2O4)3·4H2O has C2/c symmetry and contains two types of oxalate-bridged modes. We have investigated the magnetization behavior of the Ba2Co2Cl2(C2O4)3·4H2O sample with both the static and pulsed magnetic fields. The Bleaney-Bowers fitting for the temperature dependence of magnetization shows that there are two different spin-dimers with the different intra- and inter-dimer interactions. Using the high field sweep rate of the pulsed magnetic field, magnetization measurements show four continuous phase transitions (with four different critical magnetic fields) in a smaller magnetic field range from 5.5 to 7 T, which also confirms there are two different dimers. Based on the structure analysis, the four phase transitions might result from four different magnetic exchange interactions (J1, J'1, J2 and J'2) in the two different dimers. Thus, in the design of the molecular-based magnetic materials, the oxalato-bridged and its various bridging modes can be used to mediate the magnetic interaction of the intra- and inter-dimers, the electronic effect between the metal ions and induce new phases.

In silico insights into the dimer structure and deiodinase activity of type III iodothyronine deiodinase from bioinformatics, molecular dynamics simulations, and QM/MM calculations

The homodimeric family of iodothyronine deiodinases (Dios) regioselectively remove iodine from thyroid hormones. Currently, structural data has only been reported for the monomer of the mus type III thioredoxin (Trx) fold catalytic domain (Dio3Trx), but the mode of dimerization has not yet been determined. Various groups have proposed dimer structures that are similar to the A-type and B-type dimerization modes of peroxiredoxins. Computational methods are used to compare the sequence of Dio3Trx to related proteins known to form A-type and B-type dimers. Sequence analysis and in silico protein-protein docking methods suggest that Dio3Trx is more consistent with proteins that adopt B-type dimerization. Molecular dynamics (MD) simulations of the refined Dio3Trx dimer constructed using the SymmDock and GalaxyRefineComplex databases indicate stable dimer formation along the β4α3 interface consistent with other Trx fold B-type dimers. Free energy calculations show that the dimer is stabilized by interdimer interactions between the β-sheets and α-helices. A comparison of MD simulations of the apo and thyroxine-bound dimers suggests that the active site binding pocket is not affected by dimerization. Determination of the transition state for deiodination of thyroxine from the monomer structure using QM/MM methods provides an activation barrier consistent with previous small model DFT studies. Communicated by Ramaswamy H. Sarma

Activation of STING by targeting a pocket in the transmembrane domain.

Stimulator of interferon genes (STING) is an adaptor protein in innate immunity against DNA viruses or bacteria1-5. STING-mediated immunity could be exploited in the development of vaccines or cancer immunotherapies. STING is a transmembrane dimeric protein that is located in the endoplasmic reticulum or in the Golgi apparatus. STING is activated by the binding of its cytoplasmic ligand-binding domain to cyclic dinucleotides that are produced by the DNA sensor cyclic GMP-AMP (cGAMP) synthase or by invading bacteria1,6,7. Cyclic dinucleotides induce a conformational change in the STING ligand-binding domain, which leads to a high-order oligomerization of STING that is essential for triggering the downstream signalling pathways8,9. However, the cGAMP-induced STING oligomers tend to dissociate in solution and have not been resolved to high resolution, which limits our understanding of the activation mechanism. Here we show that a small-molecule agonist, compound 53 (C53)10, promotes the oligomerization and activation of human STING through a mechanism orthogonal to that of cGAMP. We determined a cryo-electron microscopy structure of STING bound to both C53 and cGAMP, revealing a stable oligomer that is formed by side-by-side packing and has a curled overall shape. Notably, C53 binds to a cryptic pocket in the STING transmembrane domain, between the two subunits of the STING dimer. This binding triggers outward shifts of transmembrane helices in the dimer, and induces inter-dimer interactions between these helices to mediate the formation of the high-order oligomer. Our functional analyses show that cGAMP and C53 together induce stronger activation of STINGthan either ligand alone.

Fractional magnetization plateaux of a spin-1/2 Heisenberg model on the Shastry-Sutherland lattice: effect of quantum XY interdimer coupling

Spin-1/2 Heisenberg model on the Shastry-Sutherland lattice is considered within the many-body perturbation theory developed from the exactly solved spin-1/2 Ising-Heisenberg model with the Heisenberg intradimer and Ising interdimer interactions. The former model is widely used for a description of magnetic properties of the layered compound SrCu_22(BO_33)_22, which exhibits a series of fractional magnetization plateaux at sufficiently low temperatures. Using the novel type of many-body perturbation theory we have found the effective model of interacting triplet excitations with the extended hard-core repulsion, which accurately recovers 1/8, 1/6 and 1/4 magnetization plateaux for moderate values of the interdimer coupling. A possible existence of a striking quantum phase of bound triplons is also revealed at low enough magnetic fields.

Crystal structure of histone chaperone Vps75 from Candida albicans

Vps75 is a histone chaperone that interacts with the fungal-specific histone acetyltransferase Rtt109 and stimulates its acetylation activity on histone H3. Here we report the crystal structure of Vps75 of Candida albicans, one of the most common fungal pathogens. CaVps75 exists as a headphone-like dimer that forms a large negatively charged region on its concave side, showing the potential to bind positively charged regions of histones. The distal ends of the concave side of the CaVps75 dimer are positively charged and each has one more α helix than yeast Vps75. CaVps75 exhibits ionic strength- and concentration-dependent higher oligomerization in solution. In the crystal, two dimers are bound through electrostatic interactions between charged regions on the concave side of their earmuff domains, and this inter-dimer interaction differs from the currently known inter-dimer interactions of Vps75s. Our results will help to understand the role of Vps75 in C. albicans.

Phase-Amplitude Coupling Analysis of EEG and EMG After Stroke

Vps75 is a histone chaperone that interacts with the fungal-specific histone acetyltransferase Rtt109 and stimulates its acetylation activity on histone H3. Here we report the crystal structure of Vps75 of Candida albicans, one of the most common fungal pathogens. CaVps75 exists as a headphone-like dimer that forms a large negatively charged region on its concave side, showing the potential to bind positively charged regions of histones. The distal ends of the concave side of the CaVps75 dimer are positively charged and each has one more α helix than yeast Vps75. CaVps75 exhibits ionic strength- and concentration-dependent higher oligomerization in solution. In the crystal, two dimers are bound through electrostatic interactions between charged regions on the concave side of their earmuff domains, and this inter-dimer interaction differs from the currently known inter-dimer interactions of Vps75s. Our results will help to understand the role of Vps75 in C. albicans.

Reliability of the Phonon Density of States Determined by Real-Coded Genetic Algorithm from Heat Capacities of Benzoic Acid Crystals.

Constant-pressure heat capacities (CPs) of crystalline benzoic acid (BAh) and its deuterated analogue (C6H5COOD, BAd) were measured by adiabatic calorimetry, and the phonon density (g(ω)) of states was determined from their CP data using a real-coded genetic algorithm (RCGA) with just generation gap + real-coded ensemble cross-over. The distribution of g(ω) was in reasonable agreement with the spectroscopic one observed for molecular vibration modes, indicating sufficient reliability of g(ω) determined by the RCGA. Based on the fact that CPs reveals an inverse-isotope effect in the temperature range 30-130 K, the determined g(ω)s were used to investigate the molecular mechanism of the effect: g(ω) of BAd revealed blue shifts in the ranges of ω = 80-100 and 150-230 K, as referred to that of BAh. It was suggested from the combined considerations on g(ω) and spectroscopic results that an anticooperative correlation exists between O-H···O hydrogen bonds and interdimer interactions in BA.

Orbital effects and Affleck-Haldane-type spin dimerization in Ba4Ru3O10

${\mathrm{Ba}}_{4}{\mathrm{Ru}}_{3}{\mathrm{O}}_{10}$, the quasi-one-dimensional spin-1 ($S$ = 1) compound, has rather intricate magnetic properties. The compound consists of structural Ru trimers, which together form the zig-zag chains where the Ru has two inequivalent crystallographic sites. While at high temperature both the inequivalent Ru ions stay in the $4+$ state with effective $S=$ 1 spin state, upon lowering the temperature, the magnetic moment of the central Ru atom is completely quenched accompanied by a change in the octahedral environment. This effectively gives rise to a bond-alternating chain and provides an opportunity to study the excitation of such a spin network in a real material. We have used microscopic tools such as neutron scattering and muon spin relaxation along with the density functional theory based calculations to address the spin state of the two inequivalent Ru ions in this material. From our neutron powder diffraction, on lowering of temperature, we find a large tetragonal distortion of the central ${\mathrm{RuO}}_{6}$ octahedra of the trimer. The splitting of the ${t}_{2g}$ level of the central Ru due to this distortion is found to be significant leading to the quenching of the moment underscoring the Hund's exchange. The nonmagnetic central Ru promotes a strong antiferromagnetic superexchange between the other two Ru ions in the trimer, which gives rise to a dimeric state. The presence of spin dimers is reflected by the manifestation of a gap in the spin excitation spectra. The spin-dimer formation in ${\mathrm{Ba}}_{4}{\mathrm{Ru}}_{3}{\mathrm{O}}_{10}$ is at par with the effective model proposed by Affleck and Haldane for the $S$ = 1 bond alternating chains in the light of valence bond solid formalism. Eventually, at a lower temperature, a long-range ordered antiferromagnetic state emerges from the gapped dimer state due to the significant interdimer interactions.

Field-induced successive phase transitions in the J1−J2 buckled honeycomb antiferromagnet Cs3Fe2Cl9

The magnetic properties of ${\mathrm{Cs}}_{3}{\mathrm{Fe}}_{2}{\mathrm{Cl}}_{9}$ single crystals were investigated by magnetic and thermal measurements. The crystal structure of ${\mathrm{Cs}}_{3}{\mathrm{Fe}}_{2}{\mathrm{Cl}}_{9}$ consists of a bilayer triangular lattice of ${\mathrm{Fe}}^{3+}$ ions. The analysis of magnetic susceptibility clarified that the intra- and interdimer interactions are comparable with each other, and ${\mathrm{Cs}}_{3}{\mathrm{Fe}}_{2}{\mathrm{Cl}}_{9}$ is regarded as a spin-5/2 ${J}_{1}\text{\ensuremath{-}}{J}_{2}$ buckled honeycomb antiferromagnet with the ferromagnetic interlayer interaction ${J}_{3}$. The susceptibility for the magnetic field $H||c$ axis exhibits a sudden drop at the N\'eel temperature ${T}_{\mathrm{N}}=5.4\phantom{\rule{0.16em}{0ex}}\mathrm{K}$, indicating a first-order magnetic phase transition. One of the characteristic features is the linear temperature dependence below ${T}_{\mathrm{N}}$. Furthermore, ${\mathrm{Cs}}_{3}{\mathrm{Fe}}_{2}{\mathrm{Cl}}_{9}$ undergoes successive magnetic phase transitions in high magnetic fields along the $c$ axis. We obtained a rich H-T phase diagram in which the ${M}_{\mathrm{s}}/2$ magnetization-plateau phase is included. These unique magnetic behaviors probably originate from the competition of magnetic interactions and the easy-axis anisotropy in the antiferromagnetic ${J}_{1}\text{\ensuremath{-}}{J}_{2}$ buckled honeycomb network.

Particle-Hole Symmetry Breaking in a Spin-Dimer System TlCuCl_{3} Observed at 100T.

The entire magnetization process of TlCuCl_{3} has been experimentally investigated up to 100T employing the single-turn technique. The upper critical field H_{c2} is observed to be 86.1T at 2K. A convex slope of the M-H curve between the lower and upper critical fields (H_{c1} and H_{c2}) is clearly observed, which indicates that a particle-hole symmetry is broken in TlCuCl_{3}. By quantum MonteCarlo simulation and the bond-operator theory method, we find that the particle-hole symmetry breaking results from strong interdimer interactions.

Type III ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization

Mitochondrial ATP synthases form functional homodimers to induce cristae curvature that is a universal property of mitochondria. To expand on the understanding of this fundamental phenomenon, we characterized the unique type III mitochondrial ATP synthase in its dimeric and tetrameric form. The cryo-EM structure of a ciliate ATP synthase dimer reveals an unusual U-shaped assembly of 81 proteins, including a substoichiometrically bound ATPTT2, 40 lipids, and co-factors NAD and CoQ. A single copy of subunit ATPTT2 functions as a membrane anchor for the dimeric inhibitor IF1. Type III specific linker proteins stably tie the ATP synthase monomers in parallel to each other. The intricate dimer architecture is scaffolded by an extended subunit-a that provides a template for both intra- and inter-dimer interactions. The latter results in the formation of tetramer assemblies, the membrane part of which we determined to 3.1 Å resolution. The structure of the type III ATP synthase tetramer and its associated lipids suggests that it is the intact unit propagating the membrane curvature.

Microtubule instability driven by longitudinal and lateral strain propagation.

Tubulin dimers associate longitudinally and laterally to form metastable microtubules (MTs). MT disassembly is preceded by subtle structural changes in tubulin fueled by GTP hydrolysis. These changes render the MT lattice unstable, but it is unclear exactly how they affect lattice energetics and strain. We performed long-time atomistic simulations to interrogate the impacts of GTP hydrolysis on tubulin lattice conformation, lateral inter-dimer interactions, and (non-)local lateral coordination of dimer motions. The simulations suggest that most of the hydrolysis energy is stored in the lattice in the form of longitudinal strain. While not significantly affecting lateral bond stability, the stored elastic energy results in more strongly confined and correlated dynamics of GDP-tubulins, thereby entropically destabilizing the MT lattice.

Ground-state properties of the K−Γ model on a honeycomb lattice

We investigate the ground-state properies of the $K-\Gamma$ model on a honeycomb lattice using series expansions and numerical exact diagonalizations, where the model includes Kitaev ($K$) and symmetric off-diagonal ($\Gamma$) interactions. Starting from the weakly interacting dimers on the specific bond, we strengthen the interdimer interactions to the isotropically interacting system. We show that depending on $\Gamma$ and $K$, the dimer state survives up to the isotropically interacting system, where the phase transition occurs, or obeys a phase transition to a magnetically ordered state at an anisotropic interaction. The results are summarized in the phase diagram. We also show that the Kekul\'{e} dimerized state is unstable in the isotropic $K-\Gamma$ model.

Structural Modulation of Electrically Conducting TCNQ Salts Using Na+(crown ether) Supramolecular Cations

The single crystals of Na+([12]crown-4)2(TCNQ)2 (1), Na+([15]crown-5)(TCNQ)2 (2), Na+([18]crown-6)(TCNQ)2.5 (3), and Na+([24]crown-8)(TCNQ)2 (4) (TCNQ = 7,7,8,8-tetracyano-p-quinodimethane) were prepared and defined by single-crystal X-ray structural analyses. Of these, salts 1 and 2 showed structural phase transitions at 320 and 185 K, respectively, upon heating. According to differential scanning calorimetry, temperature (T)-dependent crystal structures, and dielectric measurements, the motional freedom and orientation change of the spherical sandwich-type Na+([12]crown-4)2 supramolecular cation activated the phase transition. Furthermore, a symmetry change in salt 2 from the low-T Pc to the high-T P21/c was observed and a symmetry change in the Na+···NC– coordination environment is the origin of the structural phase transition at 185.4 K. Conversely, no distinct structural phase transitions were observed for salts 3 and 4. In all of the crystals, the π dimer of the partially reduced TCNQ formed a segregated π-stacking structure that interacted further by interdimer interactions to form electrically conducting TCNQ layers. Nonuniform and one-dimensional (1D) π-stacking columns of TCNQ were observed in salts 1, 3, and 4, while two-dimensional (2D) spanning-overlap interdimer interactions were confirmed in salt 2. The electrical resistivity and activation energy of 2D salt 2 were 10–10000 and 2 times lower, respectively, than those of the 1D electronic systems of salts 1, 3, and 4.

Effects of staggered Dzyaloshinskii-Moriya interactions in a quasi-two-dimensional Shastry-Sutherland model

Frustrated quantum spin systems exhibit exotic physics induced by external magnetic field with anisotropic interactions. Here, we study the effect of non-uniform Dzyaloshinskii-Moriya (DM) interactions on a quasi-two-dimensional Shastry-Sutherland lattice using a matrix product states (MPS) algorithm. We first recover the magnetization plateau structure present in this geometry and then we show that both interdimer and intradimer DM interactions significantly modify the plateaux. The non-number-conserving intradimer interaction smoothens the shape of the magnetization curve, while the number-conserving interdimer interaction induces different small plateaux, which are signatures of the finite size of the system. Interestingly, the interdimer DM interaction induces chirality in the system. We thus characterize these chiral phases with particular emphasis to their robustness against intradimer DM interactions.

Competition between intermediate plaquette phases in SrCu2 ( BO3)2 under pressure

Building on the growing evidence based on NMR, magnetization, neutron scattering, ESR, and specific heat that, under pressure, SrCu$_2$(BO$_3$)$_2$ has an intermediate phase between the dimer and the N\'eel phase, we study the competition between two candidate phases in the context of a minimal model that includes two types of intra- and inter-dimer interactions without enlarging the unit cell. We show that the empty plaquette phase of the Shastry-Sutherland model is quickly replaced by a quasi-1D full plaquette phase when intra- and/or inter-dimer couplings take different values, and that this full plaquette phase is in much better agreement with available experimental data than the empty plaquette one.