Open Dimer Research Articles

Optimal polarization and susceptibility profiles of a half-filled open magnetoelectric Fermi-Hubbard optical dimer

Magnetoelectric materials, such as thin films and magnetoelectric antennae, exhibit tunable magnetic polarization using external electric field and electric polarization using external magnetic field at room temperature by introducing strain, for instance. A more straightforward method to optimize magnetoelectric effect is by adjusting the applied electromagnetic fields in systems modeled by the Fermi-Hubbard dimer. In this study, direct and converse magnetoelectric effects are theoretically observed in an open Fermi-Hubbard dimer by tuning the external electromagnetic fields. Results show that an external magnetic field can enhance the electric polarization and susceptibility of the dimer particles without the necessity of mechanical strain. Conversely, gradients in an external electric field modulate the magnetic polarization and susceptibility. This striking behavior in the Fermi-Hubbard dimer can serve as a physical model for developing quantum control of complex materials such as in biosensors, biomedical processes, and energy harvesting.

Self and hetero-association in Benzaldehyde/Quinoline − Formamide solutions: Time Domain Reflectometry studies

The complex permittivity spectra of binary solutions of Benzaldehyde (PhCHO)/Quinoline (QUI) with Formamide (FMD) have been obtained at different mole fractions of FMD in the frequency range from 10 MHz to 30 GHz using the Time Domain Reflectometry (TDR) technique. The complex permittivity spectra have been fitted with Debye function. Dielectric relaxation time values have been interpreted in terms of the nature and size of the self and hetero associates of the binary solutions. The effective Kirkwood correlation factor (geff) has been correlated with closed and open associates of the solutions. The geff∼0.51 is the characteristic value of closed dimers. It appears that geff∼0.75 signifies the presence of both closed and open dimers. The Excess static dielectric constant (εE) shows negative deviation. The corrective Kirkwood correlation factor (gf) and Bruggeman factor (fB) have been used to investigate the strength of the H-bond interactions. The Geometry optimization has been carried out using Density Functional Theory (DFT) with B3LYP/6–311++G (d, p) basis set. Population analysis on the optimized geometries shows that PhCHO has 53.61 and 46.39 % closed and open geometries, respectively, while FMD has 17.11 % open dimers and remaining are closed dimers.

Nanobodies counteract the toxicity of an amyloidogenic light chain by stabilizing a partially open dimeric conformation

Light chain amyloidosis (AL) is a systemic disease where fibrillar deposition of misfolded immunoglobulin light chains (LCs) severely affects organ function and results in poor prognosis for patients, especially when heart involvement is severe. Particularly relevant in this context is the cardiotoxicity exerted by still uncharacterized soluble LC species. Here, with the final goal of identifying alternative therapeutic strategies to tackle AL amyloidosis, we produced five llama-derived nanobodies (Nbs) specific against H3, a well-characterized amyloidogenic and cardiotoxic LC from an AL patient with severe cardiac involvement. We found that Nbs are specific and potent agents capable of abolishing H3 soluble toxicity in C. elegans in vivo model. Structural characterization of H3-Nb complexes revealed that the protective effect of Nbs is related to their ability to bind to the H3 VL domain and stabilise an unexpected partially open LC dimer in which the two VL domains no longer interact with each other. Thus, while identifying potent inhibitors of LC soluble toxicity, we also describe the first non-native structure of an amyloidogenic LC that may represent a crucial step in toxicity and aggregation mechanisms.

Magnetocaloric and electrocaloric heat engine and refrigeration cycles in the open Fermi-Hubbard optical dimer with attractive interactions

Quantum heat engines and refrigerators can be realized in a Fermi-Hubbard optical dimer through immersion in a mean-field Fermi gas bath using the magnetocaloric and electrocaloric effects. It is demonstrated that in the presence of onsite and heat bath-induced attractive interactions, singlet-to-triplet transitions are achieved with a finite external magnetic field. Similarly, triplet-to-singlet transitions occur in the presence of an applied finite electric field. Results show that to lift the degeneracies, considerable electric potential magnitudes are needed. These magnitudes are greater than the magnetic potential strengths where the degeneracies occur. Furthermore, in the attractive regime, combinations of direct and inverse caloric effects can be combined to operate quantum heat engines and refrigerators, like what happens in the repulsive regime.

Study on depolymerization kinetics of formic acid dimers in binary mixture.

In this study, polarization Raman spectra were collected for binary mixtures of formic acid/methanol and formic acid/acetonitrile with different volume fractions. The broad band of formic acid in the CO vibration region was divided into four vibration peaks, corresponding to CO symmetric and anti-symmetric stretching vibration from cyclic dimer, CO stretching from open dimer, and CO stretching from the free monomer. The experiments showed that as the volume fraction of formic acid in the binary mixture decreased, the cyclic dimer gradually converted to the open dimer, and at a volume fraction of 0.1, fully depolymerized into monomer form (free monomer, solvated monomer, and hydrogen bonding monomer clusters with solvent). The contribution percentage of the total CO stretching intensity of each structure at different concentrations was quantitatively calculated using high resolution infrared spectroscopy, and the results were consistent with the conclusions predicted by polarization Raman spectroscopy. Concentration-triggered 2D-COS synchronous and asynchronous spectra also confirmed the kinetics of formic acid diluted in acetonitrile. This work provides a spectroscopic method for studying the structure of organic compounds in solution and concentration-triggering kinetics in mixtures.

Propanol Clustering in Argon Matrix: 2D FTIR Correlation Spectroscopy

The dynamic FTIR spectra of propanol in the argon matrix have been measured using a thermal perturbation by heating the sample from T = 11 K to 30 K stepping by 1 K. The 2D Fourier-transform infrared (FTIR) absorption correlation analysis has been carried out, the main attention being concentrated to the region of propanol O–H stretching vibrations at 3000–3700 cm–1. The peaks of monomers, two conformers of open dimer, and the cyclic structures from a dimer to a pentamer have been resolved and studied in more details. Analyzing the dependences of the integral band intensities of various aggregates on the temperature, it has been deduced that monomers and dimers act in the initial clustering stage as the main "building units" whose diffusion sustains the formation of the higher H-bond structures in the matrix. The full width at half height (FWHH) for each band has been processed as afunction of the aggregation number (n). It is found that the FHWW is a perfectly linear function of n for all cyclic aggregates n ≥ 2. The resonance broadening has been proposed to be the most reliable mechanism for the formation of diffuse O–H stretching bands in the matrix isolated clusters.

Selective lithiation of 2,4-lutidine: Role of transition states of lithium dialkylamides

The lithiation of 2,4-lutidine (1) with non-nucleophilic bases, such as lithium diisopropylamide (LDA) and lithium diethylamide (LDEA) affords different regioisomers under similar reaction conditions. The mechanism of these reactions and the factors determining selectivity have not been well understood.The present endeavor explores experimental and quantum chemical approaches to investigate factors that determine regioselectivity of the reaction. It has been found that transition states of LDA/LDEA determine regioselectivity and the presence of acatalyst (LiCl) plays a vital role. The LDA mediated lithiation of 1 proceeds through a disolvated open dimer of LDA, leading to a 2-methyl lithiated product. LDEA mediated lithiation is dominated by a route involving interception of 1 with a trisolvated monomer-based transition state of LDEA resulting in a 4-methyl lithiated product. The mechanism is supported by LiCl catalyzed reactions. LiCl has also been found to effect a change in selectivity of the lithiation of BF3-complexed 2,4-lutidine.

Redox priming promotes Aurora A activation during mitosis.

Cell cycle-dependent redox changes can mediate transient covalent modifications of cysteine thiols to modulate the activities of regulatory kinases and phosphatases. Our previously reported finding that protein cysteine oxidation is increased during mitosis relative to other cell cycle phases suggests that redox modifications could play prominent roles in regulating mitotic processes. The Aurora family of kinases and their downstream targets are key components of the cellular machinery that ensures the proper execution of mitosis and the accurate segregation of chromosomes to daughter cells. In this study, x-ray crystal structures of the Aurora A kinase domain delineate redox-sensitive cysteine residues that, upon covalent modification, can allosterically regulate kinase activity and oligomerization state. We showed in both Xenopus laevis egg extracts and mammalian cells that a conserved cysteine residue within the Aurora A activation loop is crucial for Aurora A activation by autophosphorylation. We further showed that covalent disulfide adducts of this residue promote autophosphorylation of the Aurora A kinase domain. These findings reveal a potential mechanistic link between Aurora A activation and changes in the intracellular redox state during mitosis and provide insights into how novel small-molecule inhibitors may be developed to target specific subpopulations of Aurora A.

Spectroscopic and thermodynamic evidence of the auto-association of n-butylamine in open dimers and cyclic trimers

The type of n-mers present in butylamine was evaluated. With density functional theory (DFT) techniques using the B3LYP functional combined with the 6-31G (d,p) basis set was found that the energetically more favorable structures are the open dimers and cyclic trimers. FT-Raman and FT-infrared spectra of pure Butylamine and n-Hexane, as well as of the binary system, were recorded to investigate the type and nature of the intermolecular complexes. The recorded FTIR and Raman spectra confirm the existence of these types of hydrogen-bonded complexes, making it possible to calculate the association constants and the heats of formation of both structures. These values are in the same order of magnitude than the results of thermodynamic determinations of other authors. In this way it was possible to correlate macroscopic and microscopic studies.

Quantum Neimark-Sacker bifurcation

Recently, it has been demonstrated that asymptotic states of open quantum system can undergo qualitative changes resembling pitchfork, saddle-node, and period doubling classical bifurcations. Here, making use of the periodically modulated open quantum dimer model, we report and investigate a quantum Neimark-Sacker bifurcation. Its classical counterpart is the birth of a torus (an invariant curve in the Poincaré section) due to instability of a limit cycle (fixed point of the Poincaré map). The quantum system exhibits a transition from unimodal to bagel shaped stroboscopic distributions, as for Husimi representation, as for observables. The spectral properties of Floquet map experience changes reminiscent of the classical case, a pair of complex conjugated eigenvalues approaching a unit circle. Quantum Monte-Carlo wave function unraveling of the Lindblad master equation yields dynamics of single trajectories on “quantumtorus” and allows for quantifying it by rotation number. The bifurcation is sensitive to the number of quantum particles that can also be regarded as a control parameter.

Structural basis for virulence regulation in Vibrio cholerae by unsaturated fatty acid components of bile

The AraC/XylS-family transcriptional regulator ToxT is the master virulence activator of Vibrio cholerae, the gram-negative bacterial pathogen that causes the diarrheal disease cholera. Unsaturated fatty acids (UFAs) found in bile inhibit the activity of ToxT. Crystal structures of inhibited ToxT bound to UFA or synthetic inhibitors have been reported, but no structure of ToxT in an active conformation had been determined. Here we present the 2.5 Å structure of ToxT without an inhibitor. The structure suggests release of UFA or inhibitor leads to an increase in flexibility, allowing ToxT to adopt an active conformation that is able to dimerize and bind DNA. Small-angle X-ray scattering was used to validate a structural model of an open ToxT dimer bound to the cholera toxin promoter. The results presented here provide a detailed structural mechanism for virulence gene regulation in V. cholerae by the UFA components of bile and other synthetic ToxT inhibitors.

No magnesium is needed for binding of the stimulator of interferon genes to cyclic dinucleotides

Stimulator of interferon genes (STING) binds cyclic dinucleotides (CDNs), which induce a large conformational change of the protein. The structural basis of activation of STING by CDNs is rather well understood. Unliganded STING forms an open dimer that undergoes a large conformational change (∼10 Å) to a closed conformation upon the binding of a CDN molecule. This event activates downstream effectors of STING and subsequently leads to activation of the type 1 interferon response. However, a previously solved structure of STING with 3',3'-c-di-GMP shows Mg atoms mediating the interaction of STING with this CDN. Here, it is shown that no Mg atoms are needed for this interaction; in fact, magnesium can in some cases obstruct the binding of a CDN to STING.

Driven Bose-Hubbard dimer under nonlocal dissipation: A bistable time crystal

We investigate the critical behavior of the open coherently-driven Bose-Hubbard dimer under nonlocal dissipation. A conserved quantity arises from the nonlocal nature of the dissipation, rendering the dimer multistable. In the weak-coupling semiclassical limit, the displayed criticality takes the form of amplitude bistability and breaking of spatial and temporal symmetries. A period-bistable time crystal is formed, consisting of Josephson-like oscillations. Mean-field dynamics and quantum trajectories complement the spectral analysis of the Liouvillian in the approach to the semiclassical limit.

Quantum Lyapunov exponents beyond continuous measurements.

Quantum systems, when interacting with their environments, may exhibit nonequilibrium states that are tempting to be interpreted as quantum analogs of chaotic attractors. However, different from the Hamiltonian case, the toolbox for quantifying dissipative quantum chaos remains limited. In particular, quantum generalizations of Lyapunov exponents, the main quantifiers of classical chaos, are established only within the framework of continuous measurements. We propose an alternative generalization based on the unraveling of quantum master equation into an ensemble of "quantum trajectories," by using the so-called Monte Carlo wave-function method. We illustrate the idea with a periodically modulated open quantum dimer and demonstrate that the transition to quantum chaos matches the period-doubling route to chaos in the corresponding mean-field system.

Metal binding to the dynamic cytoplasmic domain of the cation diffusion facilitator (CDF) protein MamM induces a 'locked-in' configuration.

Cation diffusion facilitator (CDF) proteins are a conserved family of transmembrane transporters that ensure cellular homeostasis of divalent transition metal cations. Metal cations bind to CDF protein's cytoplasmic C-terminal domain (CTD), leading to closure from its apo open V-shaped dimer to a tighter packed structure, followed by a conformational change of the transmembrane domain, thus enabling transport of the metal cation. By implementing a comprehensive range of biochemical and biophysical methods, we studied the molecular mechanism of metal binding to the magnetotactic bacterial CDF protein MamM CTD. Our results reveal that the CTD is rather dynamic in its apo form, and that two dependent metal-binding sites, a single central binding site and two symmetrical, peripheral sites, are available for metal binding. However, only cation binding to the peripheral sites leads to conformational changes that lock the protein in a compact state. Thus, this work reveals how metal binding is regulating the sequential uptakes of metal cations by MamM, and extends our understanding of the complex regulation mechanism of CDF proteins. DATABASE: Structural data are available in RCSB Protein Data Bank under the accession numbers: 6G64, 6G55, 6G5E and 6G6I (for CS, C267S, CS-C267S and W247A, respectively).

CryoEM structures of open dimers of gyrase A in complex with DNA illuminate mechanism of strand passage

Gyrase is a unique type IIA topoisomerase that uses ATP hydrolysis to maintain the negatively supercoiled state of bacterial DNA. In order to perform its function, gyrase undergoes a sequence of conformational changes that consist of concerted gate openings, DNA cleavage, and DNA strand passage events. Structures where the transported DNA molecule (T-segment) is trapped by the A subunit have not been observed. Here we present the cryoEM structures of two oligomeric complexes of open gyrase A dimers and DNA. The protein subunits in these complexes were solved to 4 Å and 5.2 Å resolution. One of the complexes traps a linear DNA molecule, a putative T-segment, which interacts with the open gyrase A dimers in two states, representing steps either prior to or after passage through the DNA-gate. The structures locate the T-segment in important intermediate conformations of the catalytic cycle and provide insights into gyrase-DNA interactions and mechanism.

Hsp90 Mediates Membrane Deformation and Exosome Release

Hsp90 is an essential chaperone that guards proteome integrity and amounts to 2% of cellular protein. We now find that Hsp90 also has the ability to directly interact with and deform membranes via an evolutionarily conserved amphipathic helix. Using a new cell-free system and invivo measurements, we show this amphipathic helix allows exosome release by promoting the fusion of multivesicular bodies (MVBs) with the plasma membrane. We dissect the relationship between Hsp90 conformation and membrane-deforming function and show that mutations and drugs that stabilize the open Hsp90 dimer expose the helix and allow MVB fusion, while these effects are blocked by the closed state. Hence, we structurally separated the Hsp90 membrane-deforming function from its well-characterized chaperone activity, and we show that this previously unrecognized function is required for exosome release.

Dinitrogen as a Sensor for Metastable Carboxylic Acid Dimers and a Weak Hydrogen Bond Benchmarking Tool.

Molecular nitrogen as a weak hydrogen bond acceptor is added to formic and acetic acid and their monodeuterated isotopologues. FTIR spectroscopy of supersonic expansions in the O-H stretching region reveals the formation of the weakly bound N2-carboxylic acid complexes. Their respective spectral downshifts from the monomer fundamental vibration are used to benchmark electronic structure calculations and vibrational perturbation theory. The small size of the investigated systems allows for a wide range of electronic structure levels to be explored. The O-H stretching vibration of an open dimer of acetic acid can be discriminated from the cyclic dimer vibrations by its higher susceptibility to coexpanded nitrogen.

Thermodynamic investigations of excess heat capacities of ternary liquid mixtures containing [Bmmim][BF4] + [Bmim][BF4] or [Emim][BF4] + cyclopentanone or cyclohexanone

In this paper, molar heat capacities (C P)123 data of 1-butyl-2,3-dimethylimidazolium tetrafluoroborate, [Bmmim][BF4] (1) + 1-butyl-3-methylimidazolium tetrafluoroborate, [Bmim][BF4] or 1-ethyl-3-methylimidazolium tetrafluoroborate, [Emim][BF4] (2) + cyclopentanone or cyclohexanone (3) mixtures have been reported over the entire range of composition at (293.15, 298.15, 303.15, 308.15) K using micro-differential scanning calorimeter (Model—μDSC 7 Evo). The results have been utilized to calculate excess heat capacities $$ \left( {C_{\text{P}}^{\text{E}} } \right)_{123} $$ values of the studied mixtures. The $$ \left( {C_{\text{P}}^{\text{E}} } \right)_{123} $$ data have been fitted to Redlich–Kister equation to obtain ternary coefficients and standard deviations. The Moelwyn–Huggins concept of interaction between the surfaces of constituents of binary mixtures (Huggins in J Phys Chem 74:371–378, 1970) containing ionic liquid as one of the component has been extended to obtain expression (Graph theory) for $$ \left( {C_{\text{P}}^{\text{E}} } \right)_{123} $$ of ternary mixtures. The comparison between experimental and estimated values (Graph theory) suggests that while 1-butyl-2,3-dimethylimidazolium tetrafluoroborate or 1-butyl-3-methylimidazolium tetrafluoroborate or 1-ethyl-3-methylimidazolium tetrafluoroborate exists as monomer, cyclopentanone or cyclohexanone exists as mixture of open and cyclic dimer. The results further support the various processes involved in the formation of present mixtures. The $$ \left( {C_{\text{P}}^{\text{E}} } \right)_{123} $$ values have also been tested in term of modified Flory’s theory.

Thermodynamic properties of piperidine and cyclic alkanone mixtures

The excess molar enthalpies, $$H^{\text{E}}$$ , of piperidine (1) + cyclopentanone or cyclohexanone or cycloheptanone (2) at 308.15 K and densities, ρ, speeds of sound, u, and molar heat capacities, $$C_{\text{P}}^{{}}$$ , of the same set of the mixtures have been measured as a function of composition at temperatures from 293.15 to 308.15 K. The measured ρ, u, and $$C_{\text{P}}^{{}}$$ data have been employed to determine excess molar volumes, $$V^{\text{E}}$$ , excess isentropic compressibilities, $$\kappa_{\text{S}}^{\text{E}}$$ , and excess heat capacities, $$C_{\text{P}}^{\text{E}}$$ . The thermodynamic properties have been fitted to Redlich–Kister equation to compute binary adjustable parameters and their standard deviations. The results have been analyzed in terms of Graph theory (which deals with the topology of the molecule) to correctly predict (1) state of the components in pure and mixed states, (2) to understand the nature and extent of molecular interactions existing in their mixtures, (3) $$V^{\text{E}}$$ , $$\kappa_{\text{S}}^{\text{E}}$$ , $$H^{\text{E}}$$ , and $$C_{\text{P}}^{\text{E}}$$ values. The analysis of $$V^{\text{E}}$$ data in terms of Graph theory suggests that while piperidine is characterized by hydrogen bonding and exists as associated molecular entity, cyclopentanone, cyclohexanone, and cycloheptanone exist as mixture of open and cyclic dimers. The estimated inter-nuclear distances among the interacting atoms using quantum mechanical calculations also support the existence of proposed molecular entities in pure and mixed states. It has been found that $$V^{\text{E}}$$ , $$\kappa_{\text{S}}^{\text{E}}$$ , $$H^{\text{E}}$$ and $$C_{\text{P}}^{\text{E}}$$ data predicted by Graph theory compare well with the their experimental data. The IR studies also support this view point.