Monomer Dimer Research Articles

Spectroscopy and dynamics of double proton transfer in formic acid dimer.

We present the isolated gas phase infrared spectra of formic acid dimer, (HCOOH)2, and its deuterated counterpart formic-d acid, (DCOOH)2, at room temperature. The formic acid dimer spectrum was obtained by spectral subtraction of a spectrum of formic acid vapor recorded at low pressure from that recorded at a higher pressure. The spectra of formic acid vapor contain features from both formic acid monomer and formic acid dimer, but at low and high pressures of formic acid, the equilibrium is pushed towards the monomer and dimer, respectively. A similar approach was used for the formic-d acid dimer. Building on the previous development of the Molecular Mechanics with Proton Transfer (MMPT) force field for simulating proton transfer reactions, molecular dynamics (MD) simulations were carried out to interpret the experimental spectra in the OH-stretching region. Within the framework of MMPT, a combination of symmetric single and double minimum potential energy surfaces (PESs) provides a good description of the double proton transfer PES. In a next step, potential morphing together with electronic structure calculations at the B3LYP and MP2 level of theory was used to align the computed and experimentally observed spectral features in the OH-stretching region. From this analysis, a barrier for double proton transfer between 5 and 7 kcal mol(-1) was derived, which compares with a CCSD(T)/aug-cc-pVTZ calculated barrier of 7.9 kcal mol(-1). Such a combination of experimental and computational techniques for estimating barriers for proton transfer in gas phase systems is generic and holds promise for further improved PESs and energetics of these important systems. Additional MD simulations at the semi-empirical DFTB level of theory agree quite well for the center band position but underestimate the width of the OH-stretching band.

Specific Optical Rotations and the Horeau Effect.

The observation of nonequivalence of optical and enantiomeric purities, referred to as the Horeau effect, is thought to arise from molecular aggregation in liquid solutions. Although this effect was first observed in 1969, the conditions under which this effect may, or may not, be observable are not established. Considering the formation of dimers as the simplest form of aggregation, the expressions for specific optical rotations in the presence of homochiral and heterochiral monomer-dimer equilibria are presented. Analysis of these equations indicates that the Horeau effect will not be observable even in the presence of aggregation under either of the following two situations: 1) The specific optical rotation of the monomeric species is equal to that of the dimeric species; 2) The heterochiral equilibrium constant is twice that of the homochiral equilibrium constant.

Topochemical effect in thermalE–Zisomerization of azodioxides in solid state

The thermally inducedE–Zisomerization of the benzeneazodioxide derivatives is studied in the solid polycrystalline state. The reactions are studied from the kinetic and mechanistic aspects. In contrast to the solution, where isomerizations of azodioxides occur through the formation of corresponding nitroso monomers, the topochemical effect in solid state lead to the mechanism that includes formation of the “torsional” transition state, as it is the case in other known cis–trans isomerizations. It is proposed that both the reactions in solid state, the nitroso monomer–dimer equilibrium, and isomerization about the azodioxide NN bond tentatively involve similar transition states. Copyright © 2015 John Wiley & Sons, Ltd.

The Synthesis, Characterization and Dehydrogenation of Sigma-Complexes of BN-Cyclohexanes.

The coordination chemistry of the 1,2‐BN‐cyclohexanes 2,2‐R2‐1,2‐B,N‐C4H10 (R2=HH, MeH, Me2) with Ir and Rh metal fragments has been studied. This led to the solution (NMR spectroscopy) and solid‐state (X‐ray diffraction) characterization of [Ir(PCy3)2(H)2(η2η2‐H2BNR2C4H8)][BArF 4] (NR2=NH2, NMeH) and [Rh(iPr2PCH2CH2CH2PiPr2)(η2η2‐H2BNR2C4H8)][BArF 4] (NR2=NH2, NMeH, NMe2). For NR2=NH2 subsequent metal‐promoted, dehydrocoupling shows the eventual formation of the cyclic tricyclic borazine [BNC4H8]3, via amino‐borane and, tentatively characterized using DFT/GIAO chemical shift calculations, cycloborazane intermediates. For NR2=NMeH the final product is the cyclic amino‐borane HBNMeC4H8. The mechanism of dehydrogenation of 2,2‐H,Me‐1,2‐B,N‐C4H10 using the {Rh(iPr2PCH2CH2CH2PiPr2)}+ catalyst has been probed. Catalytic experiments indicate the rapid formation of a dimeric species, [Rh2(iPr2PCH2CH2CH2PiPr2)2H5][BArF 4]. Using the initial rate method starting from this dimer, a first‐order relationship to [amine‐borane], but half‐order to [Rh] is established, which is suggested to be due to a rapid dimer–monomer equilibrium operating.

Unbiased charge oscillations in B-DNA: monomer polymers and dimer polymers.

We call monomer a B-DNA base pair and examine, analytically and numerically, electron or hole oscillations in monomer and dimer polymers, i.e., periodic sequences with repetition unit made of one or two monomers. We employ a tight-binding (TB) approach at the base-pair level to readily determine the spatiotemporal evolution of a single extra carrier along a N base-pair B-DNA segment. We study highest occupied molecular orbital and lowest unoccupied molecular orbital eigenspectra as well as the mean over time probabilities to find the carrier at a particular monomer. We use the pure mean transfer rate k to evaluate the easiness of charge transfer. The inverse decay length β for exponential fits k(d), where d is the charge transfer distance, and the exponent η for power-law fits k(N) are computed; generally power-law fits are better. We illustrate that increasing the number of different parameters involved in the TB description, the fall of k(d) or k(N) becomes steeper and show the range covered by β and η. Finally, for both the time-independent and the time-dependent problems, we analyze the palindromicity and the degree of eigenspectrum dependence of the probabilities to find the carrier at a particular monomer.

STIM1 dimers undergo unimolecular coupling to activate Orai1 channels.

The endoplasmic reticulum (ER) Ca2+ sensor, STIM1, becomes activated when ER-stored Ca2+ is depleted and translocates into ER–plasma membrane junctions where it tethers and activates Orai1 Ca2+ entry channels. The dimeric STIM1 protein contains a small STIM-Orai-activating region (SOAR)—the minimal sequence sufficient to activate Orai1 channels. Since SOAR itself is a dimer, we constructed SOAR concatemer–dimers and introduced mutations at F394, which is critical for Orai1 coupling and activation. The F394H mutation in both SOAR monomers completely blocks dimer function, but F394H introduced in only one of the dimeric SOAR monomers has no effect on Orai1 binding or activation. This reveals an unexpected unimolecular coupling between STIM1 and Orai1 and argues against recent evidence suggesting dimeric interaction between STIM1 and two adjacent Orai1 channel subunits. The model predicts that STIM1 dimers may be involved in crosslinking between Orai1 channels with implications for the kinetics and localization of Orai1 channel opening.

Dimer–monomer model on the Towers of Hanoi graphs

The number of dimer–monomers (matchings) of a graph [Formula: see text] is an important graph parameter in statistical physics. Following recent research, we study the asymptotic behavior of the number of dimer–monomers [Formula: see text] on the Towers of Hanoi graphs and another variation of the Sierpiński graphs which is similar to the Towers of Hanoi graphs, and derive the recursion relations for the numbers of dimer–monomers. Upper and lower bounds for the entropy per site, defined as [Formula: see text], where [Formula: see text] is the number of vertices in a graph [Formula: see text], on these Sierpiński graphs are derived in terms of the numbers at a certain stage. As the difference between these bounds converges quickly to zero as the calculated stage increases, the numerical value of the entropy can be evaluated with more than a hundred significant figures accuracy.

Structure and capacitance of an electric double layer formed by fused dimer cations and monomer anions: a Monte Carlo simulation study

ABSTRACTCanonical Monte Carlo simulation results are obtained for the structure and differential capacitance of a planar electric double layer consisting of fused dimer cations and monomer anions in a dielectric continuum (solvent). The physical double layer model is mimicked by a uniformly charged, non-polarisable, planar electrode next to an electrolyte consisting of positively charged fused dimers and negatively charged monomer rigid spheres in a continuum dielectric. The fused dimer comprises two same sized hard spheres that are fused into one another, one of the hard spheres being charged and the other neutral. The various electrode-particle species singlet distribution functions and the mean electrostatic potential profiles are obtained for 1:1, 2:2, 2:1, and 1:2 valency systems for different degrees of fusion. The differential capacitance as a function of the electrode surface charge density is evaluated for a 1:1 system. Comparison of these results are made with those corresponding to the situation when the dimer spheres are simply tangentially tethered. It is seen that the fused dimer influences the double layer structure and capacitance substantially for a negatively charged electrode but less so for a positively charged electrode.

Terahertz Absorption Spectra Simulation of Glutamine Based on Quantum-Chemical Calculation

With simulation of absorption spectra in THz region based on quantum-chemical calculation, the THz absorption features of target materials can be assigned with theoretical normal vibration modes. This is necessary for deeply understanding the origin of THz absorption spectra. The reliabilities of simulation results mainly depend on the initial structures and theoretical methods used throughout the calculation. In our study, we utilized THz-TDS to obtain the THz absorption spectrum of solid-state L-glutamine. Then three quantum-chemical calculation schemes with different initial structures commonly used in previous studies were proposed to study the inter-molecular interactions' contribution to the THz absorption of glutamine, containing monomer structure, dimer structure and crystal unit cell structure. After structure optimization and vibration modes' calculation based on density functional theory, the calculation results were converted to absorption spectra by Lorentzian line shape function for visual comparison with experimental spectra. The result of dimmer structure is better than monomer structure in number of absorption features while worse than crystal unit cell structure in position of absorption peaks. With the most reliable simulation result from crystal unit cell calculation, we successfully assigned all three experimental absorption peaks of glutamine ranged from 0.3 to 2.6 THz with overall vibration modes. Our study reveals that the crystal unit cell should be used as initial structure during theoretical simulation of solid-state samples' THz absorption spectrum which comprehensively considers not only the intra-molecular interactions but also inter-molecular interactions.

Metal ion sensing soluble α or β tetrasubstituted gallium and indium phthalocyanines: Synthesis, characterization, photochemistry and aggregation behaviors

This paper reports on the synthesis and characterization of peripherally and non-peripherally tetra-substituted gallium and indium phthalocyanines (3, 4, 5 and 6) containing 6-hydroxyhexylthio group. Synthesized compounds have been characterized by elemental analysis, FT-IR, 1H NMR, 13C NMR, MALDI-TOF and UV–Vis spectral data. Atomic force microscopy was also used as complementary techniques to investigate the morphology. Absorption spectral changes of the functional MPcs during addition of Ag(I) and Pd(II) soft-metal ions were evaluated by UV–Vis spectroscopy with monomer–dimer formation. All the same, photochemical properties and photophysical properties (Fluorescence quantum yields and flouresans behavior) of these phthalocyanines were performed. General trends focus on fluorescence, photodegradation and singlet oxygen quantum yields of these compounds in dimethylformamide. The nature of the substituent and solvent effect on the photophysical and photochemical parameters of the substituted phthalocyanines (3, 4, 5 and 6) are also reported.

α-Synuclein dimer structures found from computational simulations.

Dimer formation is likely the first step in the oligomerization of α-synuclein in Lewy bodies. In order to prevent α-synuclein aggregation, knowledge of the atomistic structures of possible α-synuclein dimers and the interaction affinity between the dimer domains is a necessary prerequisite in the process of rational design of dimerization inhibitors. Using computational methodology, we have investigated several possible α-synuclein dimer structures, focusing on dimers formed from α-helical forms of the protein found when it is membrane-bound, and dimers formed from β-sheet conformations predicted by simulations. Structures and corresponding binding affinities for the interacting monomers in possible α-synuclein dimers, along with properties including the contributions from different interaction energies and the radii of gyration, were found through molecular docking followed by MD simulations and binding-energy calculations. We found that even though α-synuclein is highly charged, hydrophobic contributions play a significant role in stabilizing dimers.

Regulation of excitation energy transfer in diatom PSII dimer: How does it change the destination of excitation energy?

Energy transfer dynamics in dimeric photosystem II (PSII) complexes isolated from four diatoms, Chaetoceros gracilis, Cyclotella meneghiniana, Thalassiosira pseudonana, and Phaeodactylum tricornutum, are examined. Time-resolved fluorescence measurements were conducted in the range of 0–80ns. Delayed fluorescence spectra showed a clear difference between PSII monomer and PSII dimer isolated from the four diatoms. The difference can be interpreted as reflecting suppressed energy transfer between PSII monomers in the PSII dimer for efficient energy trapping at the reaction center. The observation was especially prominent in C. gracilis and T. pseudonana. The pathways seem to be suppressed under a low pH condition in isolated PSII complexes from C. gracilis, and excitation energy may be quenched with fucoxanthin chlorophyll a/c-binding protein (FCP) that was closely associated with PSII in C. gracilis. The energy transfer between PSII monomers in the PSII dimer may play a role in excitation energy regulation in diatoms.

Spin-Liquid Ground State in the Spin 1/2 Distorted Diamond Chain Compound K3Cu3AlO2(SO4)4

The new compound K3Cu3AlO2(SO4)4, representing a spin 1/2 distorted diamond chain system, was synthesized and its magnetic properties were studied by magnetic susceptibility, specific heat, and high-field magnetization measurements. Magnetic Cu2+ ions were found to form a highly one-dimensional distorted diamond chain with strong intrachain interactions. Short-range magnetic correlations were observed to develop in a two-stage process without magnetic long-range ordering by magnetic susceptibility and specific heat measurements. The exchange constant ratio J2/J1, where J2 is the magnetic interaction of the diamond backbone and J1 is the magnetic interaction of the monomers along the chain, was estimated to be 2.5, demonstrating that the magnetic ground state is composed of an alternating dimer–monomer spin-liquid phase. The absence of an M = 0 plateau in the high-field magnetization curve is also consistent with an alternating dimer–monomer model. These results strongly suggest that K3Cu3AlO2(SO4)4 is the first material exhibiting an alternating dimer–monomer spin-liquid ground state.

Homodimerization of glucocorticoid receptor from single cells investigated using fluorescence correlation spectroscopy and microwells

Glucocorticoid receptor α (GR) binds to the promoter regions of target genes as a homodimer and activates its transcriptional process. Though the homodimerization is thought to be the initial and essential process, the dissociation constant for homodimerization of GR remains controversial. To quantify homodimerization of (enhanced green fluorescence protein) EGFP–(glucocorticoid receptor) GR, the particle brightness in lysates from single cell was estimated for the fraction of homodimeric EGFP–GR using fluorescence correlation spectroscopy and microwells. Fitting the data with a bimolecular reaction model, the dissociation constant was determined. Moreover slow-diffusion complex was observed. These results suggest that EGFP–GR forms not only a monomer–dimer equivalent state but also a large-molecular-weight complex.

Matching Measure, Benjamini–Schramm Convergence and the Monomer–Dimer Free Energy

We define the matching measure of a lattice L as the spectral measure of the tree of self-avoiding walks in L. We connect this invariant to the monomer–dimer partition function of a sequence of finite graphs converging to L. This allows us to express the monomer–dimer free energy of L in terms of the matching measure. Exploiting an analytic advantage of the matching measure over the Mayer series then leads to new, rigorous bounds on the monomer–dimer free energies of various Euclidean lattices. While our estimates use only the computational data given in previous papers, they improve the known bounds significantly.

A Mean-Field Monomer–Dimer Model with Randomness: Exact Solution and Rigorous Results

Independent random monomer activities are considered on a mean-field monomer–dimer model. Under very general conditions on the randomness the model is shown to have a self-averaging pressure density that obeys an exactly solvable variational principle. The dimer density is exactly computed in the thermodynamic limit and shown to be a smooth function.

Misfolding caused by the pathogenic mutation G47R on the minor allele of alanine:glyoxylate aminotransferase and chaperoning activity of pyridoxine

Liver peroxisomal alanine:glyoxylate aminotransferase (AGT), a pyridoxal 5′-phosphate (PLP) enzyme, exists as two polymorphic forms, the major (AGT-Ma) and the minor (AGT-Mi) haplotype. Deficit of AGT causes Primary Hyperoxaluria Type 1 (PH1), an autosomal recessive rare disease. Although ~one-third of the 79 disease-causing missense mutations segregates on AGT-Mi, only few of them are well characterized. Here for the first time the molecular and cellular defects of G47R-Mi are reported. When expressed in Escherichia coli, the recombinant purified G47R-Mi variant exhibits only a 2.5-fold reduction of its kcat, and its apo form displays a remarkably decreased PLP binding affinity, increased dimer–monomer equilibrium dissociation constant value, susceptibility to thermal denaturation and to N-terminal region proteolytic cleavage, and aggregation propensity. When stably expressed in a mammalian cell line, we found ~95% of the intact form of the variant in the insoluble fraction, and proteolyzed (within the N-terminal region) and aggregated forms both in the soluble and insoluble fractions. Moreover, the intact and nicked forms have a peroxisomal and a mitochondrial localization, respectively. Unlike what already seen for G41R-Mi, exposure of G47R-Mi expressing cells to pyridoxine (PN) remarkably increases the expression level and the specific activity in a dose-dependent manner, reroutes all the protein to peroxisomes, and rescues its functionality. Although the mechanism of the different effect of PN on the variants G47R-Mi and G41R-Mi remains elusive, the chaperoning activity of PN may be of value in the therapy of patients bearing the G47R mutation.

Positivity of the virial coefficients in lattice dimer models and upper bounds on the number of matchings on graphs

Using a simple relation between the virial expansion coefficients of the pressure and the entropy expansion coefficients in the case of the monomer–dimer model on infinite regular lattices, we have shown that, on hypercubic lattices of any dimension, the virial coefficients are positive through the 20th order. We have observed that all virial coefficients so far known for this system are positive also on infinite regular lattices with different structure. We are thus led to conjecture that the virial expansion coefficients mk are always positive.These considerations can be extended to the study of related bounds on finite graphs generalizing the infinite regular lattices, namely the finite grids and the regular biconnected graphs. The validity of the bounds Δkln(i!N(i))≤0 for k≥2, where N(i) is the number of configurations of i dimers on the graph and Δ is the forward difference operator, is shown to correspond to the positivity of the virial coefficients.Our tests on many finite lattice graphs indicate that on large lattices these bounds are satisfied, giving support to the conjecture on the positivity of the virial coefficients. Moreover, in an exhaustive survey of some classes of regular biconnected graphs with a not too large number v of vertices, we observe only few violations of these bounds. We conjecture that the frequency of the violations vanishes as v→∞.Using an inequality by Heilmann and Lieb, we find rigorous upper bounds on N(i) valid for arbitrary graphs and for regular graphs. The similarity between this inequality and the one conjectured above suggests that one study the stricter inequality mk≥12k for the virial coefficients, which is valid for all the known coefficients of the infinite regular lattice models.

Structure and Mechanism of Dimer–Monomer Transition of a Plant Poly(A)-Binding Protein upon RNA Interaction: Insights into Its Poly(A) Tail Assembly

Poly(A)-binding proteins (PABPs) play crucial roles in mRNA biogenesis, stability, transport and translational control in most eukaryotic cells. Although animal PABPs are well-studied proteins, the biological role, three-dimensional structure and RNA-binding mode of plant PABPs remain largely uncharacterized. Here, we report the structural features and RNA-binding mode of a Citrus sinensis PABP (CsPABPN1). CsPABPN1 has a domain architecture of nuclear PABPs (PABPNs) with a single RNA recognition motif (RRM) flanked by an acidic N-terminus and a GRPF-rich C-terminus. The RRM domain of CsPABPN1 displays virtually the same three-dimensional structure and poly(A)-binding mode of animal PABPNs. However, while the CsPABPN1 RRM domain specifically binds poly(A), the full-length protein also binds poly(U). CsPABPN1 localizes to the nucleus of plant cells and undergoes a dimer–monomer transition upon poly(A) interaction. We show that poly(A) binding by CsPABPN1 begins with the recognition of the RNA-binding sites RNP1 and RNP2, followed by interactions with residues of the β2 strands, which stabilize the dimer, thus leading to dimer dissociation. Like human PABPN1, CsPABPN1 also seems to form filaments in the presence of poly(A). Based on these data, we propose a structural model in which contiguous CsPABPN1 RRM monomers wrap around the RNA molecule creating a superhelical structure that could not only shield the poly(A) tail but also serve as a scaffold for the assembly of additional mRNA processing factors.

Adsorption equilibrium and kinetics of monomer–dimer monoclonal antibody mixtures on a cation exchange resin

Adsorption equilibrium and kinetics are determined for a monoclonal antibody (mAb) monomer and dimer species, individually and in mixtures, on a macroporous cation exchange resin both under the dilute limit of salt gradient elution chromatography and at high protein loads and low salt based on batch adsorption equilibrium and confocal laser scanning microscopy (CLSM) experiments. In the dilute limit and weak binding conditions, the dimer/monomer selectivity in 10mM phosphate at pH 7 varies between 8.7 and 2.3 decreasing with salt concentration in the range of 170–230mM NaCl. At high protein loads and strong binding conditions (0–60mM NaCl), the selectivity in the same buffer is near unity with no NaCl added, but increases gradually with salt concentration reaching high values between 2 and 15 with 60mM added NaCl. For these conditions, the two-component adsorption kinetics is controlled by pore diffusion and is predicted approximately by a dual shrinking core model using parameters based on single component equilibrium and kinetics measurements.