Characterization of the adsorption of oligonucleotides on mercaptopropionic acid-coated CdSe/ZnS quantum dots using fluorescence resonance energy transfer

Semiconductor quantum dots (QDs) coated with thioalkyl acid ligands are often used as probes and reporters for nucleic acid sensing, or protein sensing using aptamers, and are also potential vectors for gene delivery. In such applications, the interactions that potentially lead to the adsorption of oligonucleotides onto the surface of colloidal QDs are an important consideration. To explore such interactions, fluorescence resonance energy transfer (FRET) between QDs and oligonucleotides labeled with a fluorescent dye was used to identify and characterize a set of conditions that favor strong adsorption on 3-mercaptopropionic acid (MPA)-coated CdSe/ZnS QDs. Adsorption curves and competitive binding experiments were used to determine that the order of affinity for nucleobase adsorption was dC>dA≥dG?dT. The length of the oligonucleotide sequence was also important, with an 80-mer sequence adsorbing more strongly than its 20-mer analog. Adsorption decreased with increasing pH and corresponded to the ionization of the carboxylic acid groups of the MPA ligands. Increased ionic strength partially offsets ligand ionization and increased the extent of adsorption. The interaction between QDs and oligonucleotides was labile, with increases in adsorption at lower concentrations of oligonucleotide and with an increasing number of oligonucleotides per QD. The results were consistent with a hydrogen-bonding model for adsorption, where neutral thioalkyl acid ligands interact favorably with nucleobases and ionized ligands resist adsorption.     

Tuning of the spin distribution between ligand- and metal-based spin: electron paramagnetic resonance of mixed-ligand molybdenum tris(dithiolene) complex anions

Electron paramagnetic resonance spectra of homoleptic and mixed-ligand molybdenum tris(dithiolene) complex anions [Mo(tfd)(m)(bdt)(n)](-) (n + m = 3; bdt = S(2)C(6)H(4); tfd = S(2)C(2)(CF(3))(2)) reveal that the spin density has mixed metal-ligand character with more ligand-based spin for [Mo(tfd)(3)](-) and a higher degree of metal-based spin for [Mo(bdt)(3)](-): the magnitude of the isotropic (95,97)Mo hyperfine interaction increases continuously, by a factor of 2.5, on going from the former to the latter. The mixed complexes fall in between, and the metal character of the spin increases with the bdt content. The experiments were corroborated by density functional theory computations, which reproduce this steady increase in metal-based character.     

Atomic interactions in the p-type clathrate I Ba8Au5.3Ge40.7

Single crystals of Ba(8)Au(5.3)Ge(40.7) [space group Pm(3)n (No. 223), a = 10.79891(8) ?] were prepared by a Bridgman technique. The crystal structure refinement based on single-crystal X-ray diffraction data does not reveal any vacancies in the Au/Ge framework or in the cages. In addition to the ionic bonding between Ba and the anionic framework, a direct interaction between Ba and Au atoms was identified in Ba(8)Au(5.3)Ge(40.7) by applying the electron localizability indicator. As expected by the chemical-bonding picture, Ba(8)Au(5.3)Ge(40.7) is a diamagnet and shows p-type electrical conductivity with a hole carrier concentration of 7.14 × 10(19) cm(-3) at 300 K and very low lattice thermal conductivity of ≈0.6 W m(-1) K(-1) at 500 K. The thermoelectric figure of merit ZT of single crystals of Ba(8)Au(5.3)Ge(40.7) attains 0.3 at 511 K and reaches 0.9 at 680 K in a polycrystalline sample of closely similar composition. This opens up an opportunity for tuning of the thermoelectric properties of materials in the Ba-Au-Ge clathrate system by changing the chemical composition.     

Noble metals in polyoxometalate chemistry: palladium-containing derivatives of the monolacunary Keggin and Wells-Dawson tungstophosphates

We have prepared the three novel Pd(II)-containing tungstophosphates [Pd(2)(α-PW(11)O(39)H(0.5))(2)](9-) and two structural isomers of [Pd(2)(α(2)-P(2)W(17)O(61)H(n))(2)]((16-2n)-) via simple synthetic procedures and characterized their potassium salts by single-crystal X-ray diffraction, elemental analysis, and IR and multinuclear ((31)P and (183)W) NMR spectroscopy. This study sheds light on the long-standing question about the nature and structure of the actual products formed in the reaction of Pd(II) ions with monolacunary Keggin-type [α-XW(11)O(39)](n-) and Wells-Dawson-type [α(2)-P(2)W(17)O(61)](10-) heteropolytungstates.     

Anomalous diffusion of oligomerized transmembrane proteins

Transmembrane proteins frequently form (transient) oligomers on biomembranes, e.g., while participating in protein sorting and signaling events. Using coarse-grained membrane simulations we show here that transmembrane proteins show a subdiffusive motion on short time scales when being part of a linear oligomer, i.e., a flexible polymer, embedded in a two-dimensional membrane. Our results are in agreement with previous experimental observations. They further indicate that polymers of transmembrane proteins are well described by predictions from Rouse theory in two dimensions even in the presence of hydrodynamic interactions.     

PAs3S3 cage as a new building block in copper halide coordination polymers

First examples of the coordination chemistry of the PAs(3)S(3) cage were obtained from solutions of PAs(3)S(3)·W(CO)(5) (1) in CH(2)Cl(2) or CH(2)Cl(2)/toluene and CuX (X = Cl, Br, I) in MeCN through interdiffusion techniques. Crystals of [Cu(PAs(3)S(3))(4)]X (2, X = Cl; 3, X = Br) and [(Cu(2)I)(PAs(3)S(3))(3)]I (4) were obtained and characterized by Raman spectroscopy (2) and single-crystal X-ray crystallography. The solid-state structures reveal an unexpected coordination versatility of the PAs(3)S(3) ligand: apical phosphorus and bridging sulfur atoms interact with copper, while As···X interactions determine the dimensionality of the frameworks. The structures of 2 and 3 contain tetrahedral [(PAs(3)S(3))(4)Cu](+) cations as secondary building units (SBUs), which are arranged by interactions with Cl(-) or Br(-) anions into two- and three-dimensional substructures. These interpenetrate into a (2D + 3D) polycatenane. Compound 4 is built up by a one-dimensional [(Cu(2)I)(PAs(3)S(3))(3)](n)(n+) ribbon with PAs(3)S(3) cages as P,S-linkers. The As atoms of the exo PAs(3)S(4) linkers interact with iodide counterions (3.35 < d(As-I) < 3.59 ?). The resulting two-dimensional layer is organized by weak As···I interactions (d(As-I = 3.87 ?) into a 3D network.     

Effects of dynamical couplings in IR spectra of the hydrogen bond in N-phenylacrylamide crystals

This article presents the investigation results of the polarized IR spectra of the hydrogen bond in N-phenylacrylamide crystals measured in the frequency range of the proton and deuteron, ν(N-H) and ν(N-D), stretching vibration bands. The basic spectral properties of the crystals were interpreted quantitatively in terms of the "strong-coupling" theory. The proposed model of the centrosymmetric dimer of hydrogen bonds facilitated the explanation of the well-developed, two-branch structure of the ν(N-H) and ν(N-D) bands as well as the isotopic dilution effects in the spectra. The vibronic mechanism of the generation of the long-wave branch of the ν(N-H) band ascribed to the excitation of the totally symmetric proton vibration was elucidated. The complex fine structure pattern of ν(N-H) and ν(N-D) bands in N-phenylacrylamide spectra in comparison with the spectra of other secondary amide crystals (e.g., N-methylacetamide and acetanilide) can be accounted for in terms of the vibronic model for the forbidden transition breaking in the dimers. On the basis of the linear dichroic and temperature effects in the polarized IR spectra of N-phenylacrylamide crystals, the H/D isotopic "self-organization" effects were revealed.     

Spin exchange in solutions of TEMPOL in n-octanol and 1-methyl-3-octylimidazolium hexafluorophosphate in the temperature range from 300 to 500 K

Comprehensive examinations of the motional properties (rotational correlation time τ(R)) and the spin exchange ω(SS) of the spin probe TEMPOL have been carried out using ESR spectroscopy in two different solvents. For the first time, the dynamic parameters τ(R) and ω(SS) have been determined simultaneously by simulation of spectra measured at three different ESR frequencies (L-, X-, and Q-band) between 293 and 500 K using a dynamic model based on a stochastic fitting program and, for comparison, two alternative models involving the shift of the hyperfine lines and considering the line broadening due to spin exchange in a wide range of conditions. Possibilities and limits of the used models are shown upon comparing the obtained results of the spin exchange. Moreover, the analysis of the ESR spectra gave evidence for the existence of cage effects that produce re-encounters of the spin probes. This has been done for the activation energies, which have been calculated from the temperature dependence of the rate constants of the spin exchange. From the ratio of the activation energies and the influence of the viscosities on the dynamics of the examined systems in n-octanol and an ionic liquid, conclusions can be drawn for the re-encounter effects in solvent cages. However, in contrast to n-octanol, the dynamics of the spin probe in the ionic liquid depends on specific and anisotropic interactions. The temperature dependence of the Q-band measurements required the development of a novel Q-band cavity.     

Domain motion of individual F1-ATPase β-subunits during unbiased molecular dynamics simulations

F(1)-ATPase is the catalytic domain of F(1)F(o)-ATP synthase and consists of a hexameric arrangement of three noncatalytic α and three catalytic β subunits. We have used unbiased molecular dynamics simulations with a total simulation time of 900 ns to investigate the dynamic relaxation properties of isolated β-subunits as a step toward explaining the function of the integral F(1) unit. To this end, we simulated the open (β(E)) and the closed (β(TP)) conformations under unbiased conditions for up to 120 ns each using several samples. The simulations confirm that nucleotide-free β(E) retains its open configuration over the course of the simulations. The same is true when the neighboring α subunits are included. The nucleotide-depleted as well as the nucleotide-bound isolated β(TP) subunits show a significant trend toward the open conformation during our simulations, with one trajectory per case opening completely. Hence, our simulations suggest that the equilibrium conformation of a nucleotide-free β-subunit is the open conformation and that the transition from the closed to the open conformation can occur on a time scale of a few tens of nanoseconds.