Competition between compaction of single chains and bundling of multiple chains in giant DNA molecules

It has been established that in a dilute solution individual giant DNA molecules undergo a large discrete transition between an elongated coil state and a folded compact state. On the other hand, in concentrated solutions, DNA molecules assemble into various characteristic states, including multichain aggregate, liquid crystalline, ionic crystal, etc. In this study, we compared single-chain and multiple-chain events by observing individual chains using fluorescence microscopy. We used spermidine, SPD(3+), as a condensing agent for giant DNA. When the concentration of DNA is below 1 microM in base-pair units, individual DNA molecules exhibit a transition from an elongated state to a compact state. When the concentration of DNA is increased to 10 microM, a thick fiberlike assembly of multiple chains appears. AFM measurements of this thick fiber revealed that more than tens of DNA molecules form a bundle structure with parallel ordering of the chains. The transition between single-chain compaction and bundle formation with multiple-chain assemblies was reproduced by a theoretical calculation.     

Thermodynamics in folding transition of DNA

Recently, it has been found that individual giant DNA molecules exhibit a discrete transition, or first order phase‐transition, between the compact folded state and the elongated coiled state, i.e., the folding transition. In order to clarify the thermodynamics in the folding transition of single DNA molecules, we have studied the temperature effect on the bimodal distribution of conformation for the ensemble of T4DNA chains (166 kbps) in both poly(ethylene glycol) (PEG) and spermidine (SPD), using single‐chain observation with fluorescence microscopy. From the van't Hoff relationship, the entropy change in the transition from the compact state to the unfolded state is deduced as, ΔS = +11, +38 k/molecule in the aqueous solution of PEG with sodium chloride and potassium chloride, respectively, where k is Boltzmann's constant, whereas, ΔS with SPD is estimated to be −32 k/molecule. The values of ΔS with the transition are discussed in term of the translational entropy of counterions together with the hydration effect.     

Specific formation of beads-on-a-chain structures on giant DNA using a designed polyamine derivative

Fluorescence microscopy was used to study the folding transition of giant DNAs, T4 DNA (ca. 166 kbp), and lambda DNA (ca. 48 kbp), which proceeds through intermediates with intramolecular segregation induced by pteridine-polyamine conjugates, i.e., 2-amino-6,7-dimethyl-4-(4,9,13-triazatridecylamino)pteridine and -4-(3-(aminopropyl)amino)pteridine. According to the results of DNA denaturation, UV and fluorescent spectroscopy, and transmission electron microscopic observations, it became clear that DNA folding induced by the polyamine derivative is not a continuous shrinking process but a combination of discontinuous processes.     

Marked differences in volume phase transitions between gel and single molecule in DNA

Volume phase transitions of a DNA gel and a single giant DNA chain caused by spermidine(3+) (SPD(3+)) were investigated. The change in volume for the single DNA (VV(0) approximately 10(-5)) was four orders of magnitude greater than that for the DNA gel ( approximately 10(-1)), while the critical SPD(3+) concentration for the gel (1.8 mM) was one order of magnitude greater than that of the single DNA (0.12-0.25 mM) at the same pH 6.86. We tried to describe mean-field theories with virial expansion, which is valid for the coil-globule transition of a single polymer chain, for the volume phase transitions to explain the reason why such marked differences appeared. Considering the degree of the ordering of Kuhn segments arising from the gel network structure together with the chain length of cross-linked polymer chains, the volume phase transitions were described and then the significant differences were reproduced quantitatively. We concluded that the network structure plays a significant role in the volume phase transition of the gel.     

Manganese(II) and copper(II) hexafluoroacetylacetonate 1:1 complexes with 5-(4-[N-tert-butyl-N-aminoxyl]phenyl)pyrimidine: regiochemical parity analysis for exchange behavior of complexes between radicals and paramagnetic cations

Mn(hfac)(2) and Cu(hfac)(2) form coordination complexes with 5-(4-[N-tert-butyl-N-aminoxyl]phenyl)pyrimidine, PyrimPh-NIT. (Mn[PyrimPh-NIT](hfac)(2))(2) and (Cu[PyrimPh-NIT](hfac)(2))(2), 1 and 2, respectively, are cyclic M(2)L(2) dimers that exhibit strong exchange coupling between the coordinated paramagnetic dication (M) and nitroxide (NIT) unit. The M-NIT exchange is strongly antiferromagnetic (AFM) in 1 and strongly ferromagnetic (FM) in 2. Magnetic susceptibility measurements for 1 were fitted to an AFM spin pairing model with J/k = -0.25 K between Mn-NIT spin sites units. Complex 2 also exhibits AFM spin pairing between S = 1 Cu-NIT spin units that is somewhat field dependent at low temperature. The fit of corrected paramagnetic susceptibility chi(T) to an AFM spin pairing model at 200 Oe yields J/k = (-)3.8 K, quite similar to earlier measurements at 1000 Oe yielding J/k = (-)5.0 K. At 1.40 K, the magnetization of 2 does not approach saturation until somewhat above 170 kOe, giving an S-shaped curve; at 0.55 K, the magnetization curve shows steps characteristic of field-induced crossover between the S = 0 ground state and excited spin states. From the steps in the 0.55 K data, we estimate J/k = (-)3.8-4.0 K for 2, in good agreement with the analysis of chi(T).     

Density functional analysis of the magnetic structure of Li3RuO4: importance of the Ru-O···O-Ru spin-exchange interactions and substitutional Ru defects at the Li sites

We evaluated the spin-exchange interactions of Li(3)RuO(4) by performing energy-mapping analysis based on density functional calculations and examined the nature of its magnetic transition at T(1) = 66 K and the divergence of the field-cooled and zero-field-cooled susceptibilities below T(2) = 32 K. Our study shows that T(1) is associated with a three-dimensional antiferromagnetic ordering, in which the two-dimensional antiferromagnetic lattices parallel to the ab plane are antiferromagnetically coupled along the c direction. We examined how the substitutional defects, Ru atoms residing in the Li sites, affect the antiferromagnetic coupling along the c direction to explain why the expected c-axis doubling is not detected from powder neutron diffraction measurements. The susceptibility divergence below T(2) is attributed to a slight spin canting out of the ab plane.     

Synthesis and characterization of single-layer silver-decanethiolate lamellar crystals

We report the synthesis of silver-decanethiolate (AgSC10) lamellar crystals. Nanometer-sized Ag clusters grown on inert substrates react with decanethiol vapor to form multilayer AgSC10 lamellar crystals with both layer-by-layer and in-plane ordering. The crystals have strong (010) texture with the layers parallel to the substrates. The synthesis method allows for a precise control of the number of layers. The thickness of the lamellae can be manipulated and systematically reduced to a single layer by decreasing the amount of Ag and lowering the annealing temperature. The single-layer AgSC10 lamellae are two-dimensional crystals and have uniform thickness and in-plane ordering. These samples were characterized with nanocalorimetry, atomic force microscopy (AFM), transmission electron microscopy (TEM), X-ray diffraction (XRD), X-ray reflectivity (XRR), Fourier transform infrared spectroscopy (FTIR), and Rutherford backscattering spectroscopy (RBS).     

Peculiar field-dependent magnetic behavior of cyano-bridged coordination polymer Er(H2O)4[W(CN)8

The two-dimensional cyano-bridged coordination polymer Er(H(2)O)(4)[W(CN)(8)] exhibits a magnetic transition at 12 K and an unusual field-dependent transition from short-range to ferromagnetic ordering.     

Nonspecificity induces chiral specificity in the folding transition of giant DNA

The all-or-none type DNA folding transition from a coil to globule can be differentiated by the chirality of the triamines. The fluorescent microscope observation on single DNA molecules makes it clear that the tripeptides obtained from naturally occurring basic amino acids (l-lysine or l-arginine) can compact DNA molecules at concentrations lower than those from d-isomers. Nanometer-sized beads are found in the AFM images on the folded DNA molecule.     

Multiscale self-organization of the organic semiconductor alpha-quinquethiophene

We show that thin films grown by vacuum sublimation, or formed by melted powders, of semiconductor alpha-quinquethiophene (T5) exhibit a hierarchical self-affinity organization that spans scales from tens of nanometers to hundreds of micrometers. T5 organization was investigated by X-ray diffraction (XRD), atomic force microscopy (AFM), and optical microscopy. XRD showed that vacuum-evaporated T5 films were characterized by a preferred orientation of the h00 planes parallel to the glass substrate. Melting of the films followed by rapid quenching to room temperature led to the formation of micrometer-sized, single-crystal-like structures, characterized by uniaxially aligned stripes. XRD proved that the melting-quenching process enhanced molecular ordering and increased the size of domains with the molecule's long axes tilted by about 65 degrees with respect to the substrate plane and piled up side-by-side along parallel columns. AFM measurements on the melt-quenched structures showed that a hierarchical architecture was built by reiteration across multiple length scales of the same recurring motif. Because of the tendency of T5 to form highly crystalline vacuum-evaporated thin films, a field-effect hole mobility comparable to state-of-the-art FET mobility of alpha-sexithiophene films was reached, without any attempt to optimize deposition conditions.     

Ground state properties of perovskite and post-perovskite CaRuO3: Ferromagnetism reduction

Aiming at the disputed ground state properties of perovskite (Pv) CaRuO₃, we have investigated the variations of electronic structures and magnetism between Pv and post-perovskite (PPv) phases of CaRuO₃, based on the generalized gradient approximation (GGA) plus on-site Coulomb interaction U and spin-orbital coupling (SOC) effect correction, namely GGA + U + SOC method. Both Pv and PPv phases have Mott-Hubbard insulating characteristics. Under Pnma symmetry, the 4d electrons have the stronger SOC effect and the weaker electronic correlation. Under Cmcm symmetry, however, the situation is just reversed. The G-type antiferromagnetic (AFM) superexchange interaction of Ru–Ru is perfected in Pv phase, antiferromagnetically mediated by O atoms. PPv phase exhibits the AFM ground state along c direction, but the FM–AFM fluctuation exists in a–b plane of PPv phase. The strong magnetic anisotropy and big exchange constants are the inexistent evidences of spin-glass behavior in Pv and PPv phases. Ru⁴⁺ is in low-spin state, S ～ 1. Pv–PPv phase transition changed the electronic and magnetic structures, but the magnetism is not sensitive to pressure in each phase. The suppression of ferromagnetism in Pv and PPv phases arises from the AFM interaction induced by the SOC effect and the FM–AFM fluctuation, respectively.     

Ordering evolution of block copolymer thin films upon solvent-annealing process

Morphologies of polystyrene-block-poly(2-vinylpyridine) copolymer (S2VP) thin films, which are forming poly(2-vinylpyridine) cylinders in bulk phase, were investigated by atomic force microscopy (AFM) and transmission electron microscopy (TEM) to account for their ordering behavior induced by solvent annealing. Initially, when the copolymer was dissolved in toluene, which is selective solvent for majority polystyrene (PS) blocks, and was spin-coated on Si substrates, dimple-type micellar structures of S2VP were formed. After the film was placed in a solvent-annealing chamber covered with a lid under the existence of chloroform, surface morphologies of S2VP were measured as a function of annealing time. In this study, it was found that the morphologies of S2VP thin film repeated the cycle of the creation and extinction of various morphologies on ordering process. Namely, S2VP exhibited the various transformations between different morphologies, including highly disordered state, cylinders normal to the plane, and cylinders parallel to the plane. Each of the morphologies observed here was employed as a template to synthesize gold (Au) nanoparticles or nanowires. The arrays of Au nano-objects were used to tune a surface plasmon resonance.     

Field-induced ferrimagnetic state in a molecule-based magnet consisting of a Co(II) ion and a chiral triplet Bis(nitroxide) radical

We present the synthesis, crystal structure, and temperature and field dependence of the magnetic properties of a new molecule-based magnet, [Co(hfac)2].BNO* (1), where hfac = 1,1,1,5,5,5-hexafluoroacetylacetonato and BNO* is the chiral triplet bis(nitroxide), 1,3-bis(N-tert-butyl-N-oxylamino)-5-{1'-methyl-1'-[2' '-(S)-methylbutoxy]ethyl}benzene. The presence of enantiomer-pure BNO induces the formation of chiral one-dimensional chains that are packed parallel to each other in the noncentrosymmetric P1 space group. 1 exhibits four magnetic ground states: paramagnetic; antiferromagnetic; forced ferrimagnetic; field-induced metastable ferrimagnetic. In the paramagnetic state (T > 20 K), it presents short-range antiferromagnetic interaction between Co ion and nitroxide radical and has a minimum of chimT value at 220 K. The Weiss temperature estimated in the temperature range 220-300 K is found to be -89.9 K. At 20 K (TN), an antiferromagnetic long-range ordering is established. In the temperature range 4 K < T < 20 K, the isothermal magnetization curve show a spin-flip transition to the forced ferrimagnetic state at around 850 Oe. Below 4 K, this compound enters into a field-induced ferrimagnetic state, which is metastable and stabilized by the Ising character of the Co ion. In the low-temperature phase, the material becomes a very hard magnet with wide hysteresis loop whose coercive field reaches 25 kOe at 2 K. The magnetic phase diagram based on these magnetic data is presented.     

Characterization and biocompatibility of chitosan nanocomposites

Chitosan nanocomposites were prepared from chitosan and gold nanoparticles (AuNPs) or silver nanoparticles (AgNPs) of ～5 nm size. Transmission electron microscopy (TEM) showed the NPs in chitosan did not aggregate until higher concentrations (120-240 ppm). Atomic force microscopy (AFM) demonstrated that the nanocrystalline domains on chitosan surface were more evident upon addition of AuNPs (60 ppm) or AgNPs (120 ppm). Both nanocomposites showed greater elastic modulus, higher glass transition temperature (T(g)) and better cell proliferation than the pristine chitosan. Additionally, chitosan-Ag nanocomposites had antibacterial ability against Staphylococcus aureus. The potential of chitosan-Au nanocomposites as hemostatic wound dressings was evaluated in animal (rat) studies. Chitosan-Au was found to promote the repair of skin wound and hemostasis of severed hepatic portal vein. This study indicated that a small amount of NPs could induce significant changes in the physicochemical properties of chitosan, which may increase its biocompatibility and potential in wound management.     

Metallic behavior and periodical valence ordering in a MMX chain compound, Pt(2)(EtCS(2))(4)I.

A new one-dimensional (1-D) halogen-bridged mixed-valence diplatinum(II,III) compound, Pt(2)(EtCS(2))(4)I (3), has been successfully synthesized from [Pt(2)(EtCS(2))(4)] (1) and [Pt(2)(EtCS(2))(4)I(2)] (2). These three compounds have been examined using UV-visible-near-IR, IR, polarized Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), and X-ray crystal structure analyses (except for 1). Compound 3 was further characterized through electrical transport measurements, determination of the temperature dependence of lattice parameters, X-ray diffuse scattering, and SQUID magnetometry. 3 crystallizes in the monoclinic space group C2/c and exhibits a crystal structure consisting of neutral 1-D chains with a repeating -Pt-Pt-I- unit lying on the crystallographic 2-fold axis parallel to the b axis. The Pt-Pt distance at 293 K is 2.684 (1) A in the dinuclear unit, while the Pt-I distances are essentially equal (2.982 (1) and 2.978 (1) A). 3 shows relatively high electrical conductivity (5-30 S cm(-1)) at room temperature and undergoes a metal-semiconductor transition at T(M-S) = 205 K. The XPS spectrum in the metallic state reveals a Pt(2+) and Pt(3+) mixed-valence state on the time scale of XPS spectroscopy ( approximately 10(-17) s). In accordance with the metal-semiconductor transition, anomalies are observed in the temperature dependence of the crystal structure, lattice parameters, X-ray diffuse scattering, and polarized Raman spectra near T(M-S). In variable-temperature crystal structure analyses, a sudden and drastic increase in the Pt-I distance near the transition temperature is observed. Furthermore, a steep increase in U(22) of iodine atoms in the 1-D chain direction has been observed. The lattice parameters exhibit significant temperature dependence with drastic change in slope at about 205-240 K. This was especially evident in the unit cell parameter b (1-D chain direction) as it was found to lengthen rapidly with increasing temperature. X-ray diffraction photographs taken utilizing the fixed-film and fixed-crystal method for the metallic state revealed the presence of diffuse scattering with line shapes parallel to the a* axis indexed as (-, n + 0.5, l) (n; integer). Diffuse scattering with k = n + 0.5 is considered to originate from the 2-fold periodical ordering corresponding to -Pt(2+)-Pt(2+)-I-Pt(3+)-Pt(3+)-I- or -Pt(2+)-Pt(3+)-I-Pt(3+)-Pt(2+)-I- in an extremely short time scale. Diffuse lines corresponding to 2-D ordering progressively decrease in intensity below 252 K and are converted to the diffuse planes corresponding to 1-D ordering near T(M-S). Furthermore, diffuse planes condensed into superlattice reflections below T(M-S). Polarized Raman spectra show temperature dependence through a drastic low-energy shift of the Pt-I stretching mode and also through broadening of bands above T(M-S).     

Stable metallic behavior and antiferromagnetic ordering of Fe(III) d spins in (EDO-TTFVO)2.FeCl4

We report the crystal structure and physical properties of the 2:1 FeCl4- salt of a new donor molecule, EDO-TTFVO. Crystal structure analysis of this salt revealed that the donor molecules formed a beta' '-type two-dimensional conducting layer, and there is a short S...Cl contact between the donor molecules and the FeCl4- ions, which is expected to mediate a strong pi-d interaction. This salt showed a stable metallic conducting behavior down to 0.3 K and an antiferromagnetic ordering at TN approximately 3.0 K, indicating that this salt becomes a new antiferromagnetic molecular metal at ambient pressure. The appearance of the magnetic ordering is considered to originate from the strong pi-d interactions between the donor molecules and the FeCl4- ions because the field dependence of magnetoresistances was remarkably affected below the antiferromagnetic transition temperature.     

Macromolecular crowding tunes folding landscape of parallel α/β protein, apoflavodoxin

Proteins normally fold in crowded cellular environments. Here we use a set of Desulfovibrio desulfuricans apoflavodoxin variants to assess--with residue-specific resolution--how apoflavodoxin's folding landscape is tuned by macromolecular crowding. We find that, under crowded conditions, initial topological frustration is reduced, subsequent folding requires less ordering in the transition state, and β-strand 1 becomes more important in guiding the process. We propose that conditions more closely mimicking the cellular environment make the ensemble of unfolded conformations less expanded, resulting in a folding funnel that is smoother and narrower.     

Ordered self-assembled locked nucleic acid (LNA) structures on gold(111) surface with enhanced single base mismatch recognition capability

Locked nucleic acid (LNA) is a conformationally restricted nucleic acid analogue, which is potentially a better alternative than DNA for application in the nucleic acid based biosensor technologies, due to its efficient and sequence-specific DNA/RNA detection capability and lack of molecule-surface interaction on solid surfaces, compared to DNA. We report, for the first time, a straightforward way (based on simple immersion method) of generating an ordered self-assembled LNA monolayer, which is bioactive, onto a gold(111) surface. This layer is capable of giving rise to a stronger DNA recognition signal (4-4.5 times) than its DNA counterpart, and importantly, it can differentiate between a fully complementary DNA target and that having a single base mismatch, where the mismatch discrimination ratio is almost two times compared to the ratio relevant in case of DNA-based detection. We have presented high-resolution atomic force microscopy (AFM) topographs of the well-defined one-dimensional LNA molecular ordering (few hundred nanometers long) and of the two-dimensional ordered assembly formed over a large area (7 μm × 7 μm) due to parallel positioning of the one-dimensional ordered arrangements. The effects of different parameters such as LNA concentration and incubation time on LNA self-assembly have been investigated. Further, reflection absorption infrared (RAIR) spectroscopy has been applied to obtain information about the orientation of the surface-immobilized LNA molecules for the first time. It has been found that the LNA molecules undergo an orientational transition from the "lying down" to the "upright" configuration in a time scale of few hours.     

Mode of interaction of ganglioside Langmuir monolayer originated from echinoderms: three binary systems of ganglioside/DPPC, ganglioside/DMPE, and ganglioside/cholesterol

The surface pressure (pi)-area (A), the surface potential (DeltaV)-A, and the dipole moment (mu( perpendicular))-A isotherms were obtained for monolayers made from a ganglioside originated from echinoderms [Diadema setosum ganglioside (DSG-1)], dipalmitoylphosphatidylcholine (DPPC), dimyristoylphosphatidylethanolamine (DMPE), cholesterol (Ch), and their combinations. Monolayers spread on several different substrates were investigated at the air/water interface by the Wilhelmy method, ionizing electrode method, fluorescence microscopy (FM) and atomic force microscopy (AFM). Surface potentials (DeltaV) of pure components were analyzed using the three-layer model proposed by Demchak and Fort [R.J. Demchak, T. Fort, J. Colloid Interface Sci. 46 (1974) 191-202]. The new finding was that DSG-1 was stable and showed a liquid-expanded film and that its monolayer behavior of DeltaV was sensitive for the change of the NaCl concentration in the subphase. Moreover, the miscibility of DSG-1 and three major lipids in the two-component monolayers was examined by plotting the variation of the molecular area and the surface potential as a function of the DSG-1 molar fraction (X(DSG-1)), using the additivity rule. From the A-X(DSG-1) and DeltaV(m)-X(DSG-1) plots, partial molecular surface area (PMA) and apparent partial molecular surface potential (APSP) were determined at the discrete surface pressure. The PMA and APSP with the mole fraction were extensively discussed for the miscible system. The miscibility was also investigated from the two-dimensional phase diagrams. Furthermore, a regular surface mixture, for which the Joos equation was used for the analysis of the collapse pressure of two-component monolayers, allowed calculation of the interaction parameter (xi) and the interaction energy (-Deltavarepsilon) between them. The observations using fluorescence microscopy and AFM image also provide us the miscibility in the monolayer state.     

A two transition state model for radical-molecule reactions: a case study of the addition of OH to C2H4

A two transition state model is applied to the study of the addition of hydroxyl radical to ethylene. This reaction serves as a prototypical example of a radical-molecule reaction with a negative activation energy in the high-pressure limit. The model incorporates variational treatments of both inner and outer transition states. The outer transition state is treated with a recently derived long-range transition state theory approach focusing on the longest-ranged term in the potential. High-level quantum chemical estimates are incorporated in a variational transition state theory treatment of the inner transition state. Anharmonic effects in the inner transition state region are explored with direct phase space integration. A two-dimensional master equation is employed in treating the pressure dependence of the addition process. An accurate treatment of the two separate transition state regions at the energy and angular momentum resolved level is essential to the prediction of the temperature dependence of the addition rate. The transition from a dominant outer transition state to a dominant inner transition state is predicted to occur at about 130 K, with significant effects from both transition states over the 10 to 400 K temperature range. Modest adjustment in the ab initio predicted inner saddle point energy yields theoretical predictions which are in quantitative agreement with the available experimental observations. The theoretically predicted capture rate is reproduced to within 10% by the expression [4.93 x 10(-12) (T/298)(-2.488) exp(-107.9/RT) + 3.33 x 10(-12) (T/298)(0.451) exp(117.6/RT); with R = 1.987 and T in K] cm3 molecules(-1) s(-1) over the 10-600 K range.