Protein adsorption onto silica nanoparticles: conformational changes depend on the particles' curvature and the protein stability

We have analyzed the adsorption of protein to the surfaces of silica nanoparticles with diameters of 6, 9, and 15 nm. The effects upon adsorption on variants of human carbonic anhydrase with differing conformational stabilities have been monitored using methods that give complementary information, i.e., circular dichroism (CD), nuclear magnetic resonance (NMR), analytical ultracentrifugation (AUC), and gel permeation chromatography. Human carbonic anhydrase I (HCAI), which is the most stable of the protein variants, establishes a dynamic equilibrium between bound and unbound protein following mixture with silica particles. Gel permeation and AUC experiments indicate that the residence time of HCAI is on the order of approximately 10 min and slowly increases with time, which allows us to study the effects of the interaction with the solid surface on the protein structure in more detail than would be possible for a process with faster kinetics. The effects on the protein conformation from the interaction have been characterized using CD and NMR measurements. This study shows that differences in particle curvature strongly influence the amount of the protein's secondary structure that is perturbed. Particles with a longer diameter allow formation of larger particle-protein interaction surfaces and cause larger perturbations of the protein's secondary structure upon interaction. In contrast, the effects on the tertiary structure seem to be independent of the particles' curvature.     

Structure and bonding in solution of dioxouranium(VI) oxalate complexes: isomers and intramolecular ligand exchange

Structural isomers of [UO(2)(oxalate)(3)](4-), [UO(2)(oxalate)F(3)](3-), [UO(2)(oxalate)(2)F](3-), and [UO(2)(oxalate)(2)(H(2)O)](2-) have been studied by using EXAFS and quantum chemical ab initio methods. Theoretical structures and their relative energies were determined in the gas phase and in water using the CPCM model. The most stable isomers according to the quantum chemical calculations have geometries consistent with the EXAFS data, and the difference between measured and calculated bond distances is generally less than 0.05 A. The complex [UO(2)(oxalate)(3)](4-) contains two oxalate ligands forming five-membered chelate rings, while the third is bonded end-on to a single carboxylate oxygen. The most stable isomer of the other two complexes also contains the same type of chelate-bonded oxalate ligands. The activation energy for ring opening in [UO(2)(oxalate)F(3)](3-), deltaU++ = 63 kJ/mol, is in fair agreement with the experimental activation enthalpy, deltaH++ = 45 +/- 5 kJ/mol, for different [UO(2)(picolinate)F(3)](2-) complexes, indicating similar ring-opening mechanisms. No direct experimental information is available on intramolecular exchange in [UO(3)(oxalate)(3)](4-). The theoretical results indicate that it takes place via the tris-chelated intermediate with an activation energy of deltaU++ = 38 kJ/mol; the other pathways involve multiple steps and have much higher activation energies. The geometries and energies of dioxouranium(VI) complexes in the gas phase and solvent models differ slightly, with differences in bond distance and energy of typically less than 0.06 A and 10 kJ/mol, respectively. However, there might be a significant difference in the distance between uranium and the leaving/entering group in the transition state, resulting in a systematic error when the gas-phase geometry is used to estimate the activation energy in solution. This systematic error is about 10 kJ/mol and tends to cancel when comparing different pathways.     

Controlling qubit arrays with anisotropic XXZ Heisenberg interaction by acting on a single qubit

We investigate anisotropic XXZ Heisenberg spin-1 / 2 chains with control fields acting on one of the end spins, with the aim of exploring local quantum control in arrays of interacting qubits. In this work, which uses a recent Lie-algebraic result on the local controllability of spin chains with “always-on” interactions, we determine piecewise-constant control pulses corresponding to optimal fidelities for quantum gates such as spin-flip (NOT), controlled-NOT (CNOT), and square-root-of-SWAP (). We find the minimal times for realizing different gates depending on the anisotropy parameter Δ of the model, showing that the shortest among these gate times are achieved for particular values of Δ larger than unity. To study the influence of possible imperfections in anticipated experimental realizations of qubit arrays, we analyze the robustness of the obtained results for the gate fidelities to random variations in the control-field amplitudes and finite rise time of the pulses. Finally, we discuss the implications of our study for superconducting charge-qubit arrays.     

Classical and Sobolev orthogonality of the nonclassical Jacobi polynomials with parameters \alpha =\beta =-1

In this paper, we consider the second-order differential expression $$\begin{aligned} \ell [y](x)=(1-x^{2})(-(y^{\prime }(x))^{\prime }+k(1-x^{2})^{-1} y(x))\quad (x\in (-1,1)). \end{aligned}$$ This is the Jacobi differential expression with nonclassical parameters $\alpha =\beta =-1$ in contrast to the classical case when $\alpha ,\beta >-1$ . For fixed $k\ge 0$ and appropriate values of the spectral parameter $\lambda ,$ the equation $\ell [y]=\lambda y$ has, as in the classical case, a sequence of (Jacobi) polynomial solutions $\{P_{n}^{(-1,-1)} \}_{n=0}^{\infty }.$ These Jacobi polynomial solutions of degree $\ge 2$ form a complete orthogonal set in the Hilbert space $L^{2}((-1,1);(1-x^{2})^{-1})$ . Unlike the classical situation, every polynomial of degree one is a solution of this eigenvalue equation. Kwon and Littlejohn showed that, by careful selection of this first-degree solution, the set of polynomial solutions of degree $\ge 0$ are orthogonal with respect to a Sobolev inner product. Our main result in this paper is to construct a self-adjoint operator $T$ , generated by $\ell [\cdot ],$ in this Sobolev space that has these Jacobi polynomials as a complete orthogonal set of eigenfunctions. The classical Glazman–Krein–Naimark theory is essential in helping to construct $T$ in this Sobolev space as is the left-definite theory developed by Littlejohn and Wellman.     

Spectroscopy of Dibenzorubicene: Experimental Data for a Search in Interstellar Spectra

We report on the characterization of dibenzo[cde,opq]rubicene (C₃₀H₁₄). The molecule was studied in solution at room temperature with absorption spectroscopy in the visible (vis) and ultraviolet (UV) wavelength ranges, and with emission spectroscopy. The infrared (IR), visible, ultraviolet, and vacuum ultraviolet (VUV) absorption spectra of a thin film were measured also at room temperature. In addition, the UV/vis absorption spectrum was measured at cryogenic temperatures using the matrix isolation spectroscopy technique. The interpretation of spectra was supported by theoretical calculations based on semiempirical and ab initio models, as well as on density functional theory. Finally, the results of the laboratory study were compared with interstellar spectra.     

The DMAP-catalyzed acetylation of alcohols--a mechanistic study (DMAP = 4-(dimethylamino)pyridine)

The acetylation of tert-butanol with acetic anhydride catalyzed by 4-(dimethylamino)pyridine (DMAP) has been studied at the Becke3 LYP/6-311 + G(d,p)//Becke3 LYP/6-31G(d) level of theory. Solvent effects have been estimated through single-point calculations with the PCM/UAHF solvation model. The energetically most favorable pathway proceeds through nucleophilic attack of DMAP at the anhydride carbonyl group and subsequent formation of the corresponding acetylpyridinium/acetate ion pair. Reaction of this ion pair with the alcohol substrate yields the final product, tert-butylacetate. The competing base-catalyzed reaction pathway can either proceed in a concerted or in a stepwise manner. In both cases the reaction barrier far exceeds that of the nucleophilic catalysis mechanism. The reaction mechanism has also been studied experimentally in dichloromethane through analysis of the reaction kinetics for the acetylation of cyclohexanol with acetic anhydride, in the presence of DMAP as catalyst and triethylamine as the auxiliary base. The reaction is found to be first-order with respect to acetic anhydride, cyclohexanol, and DMAP, and zero-order with respect to triethyl amine. Both the theoretical as well as the experimental studies strongly support the nucleophilic catalysis pathway.     

In Situ Structural Determination of a Homogeneous Ruthenium Racemization Catalyst and Its Activated Intermediates Using X-Ray Absorption Spectroscopy

The activation process of a known Ru-catalyst, dicarbonyl(pentaphenylcyclopentadienyl)ruthenium chloride, has been studied in detail using time resolved in situ X-ray absorption spectroscopy. The data provide bond lengths of the species involved in the process as well as information about bond formation and bond breaking. On addition of potassium tert-butoxide, the catalyst is activated and an alkoxide complex is formed. The catalyst activation proceeds via a key acyl intermediate, which gives rise to a complete structural change in the coordination environment around the Ru atom. The rate of activation for the different catalysts was found to be highly dependent on the electronic properties of the cyclopentadienyl ligand. During catalytic racemization of 1-phenylethanol a fast-dynamic equilibrium was observed.