A QM/MM study on the reaction pathway leading to 2‐Aceto‐2‐hydroxybutyrate in the catalytic cycle of AHAS

The reaction between the intermediate 2‐hydroxyethyl‐thiamin diphosphate (HEThDP^?) and 2‐ketobutyrate, in the third step of the catalytic cycle of acetodydroxy acid synthase, is addressed from a theoretical point of view by means of hybrid quantum/molecular mechanical calculations. The QM region includes one molecule of 2‐ketobutyrate, the HEThDP^? intermediate, and the residues Arg 380 y Glu 139; whereas the MM region includes the rest of the protein. The study includes potential energy surface scans to identify and characterize critical points on it, transition state search and activation barrier calculations. The results show that the reaction occurs via a two‐step mechanism corresponding to the carboligation and proton transfer in the first stage; and the product release in the second step. © 2014 Wiley Periodicals, Inc.     

Unraveling σ and π Effects on Magnetic Anisotropy in cis‐NiA4B2 Complexes: Magnetization,HF‐HFEPR Studies,First‐Principles Calculations,and Orbital Modeling

By using complementary experimental techniques and first‐principles theoretical calculations, magnetic anisotropy in a series of five hexacoordinated nickel(II) complexes possessing a symmetry close to C_2v, has been investigated. Four complexes have the general formula [Ni(bpy)X₂]ⁿ⁺ (bpy=2,2′‐bipyridine; X₂=bpy ( 1 ), (NCS^?)₂ ( 2 ), C₂O₄^2? ( 3 ), NO₃^? ( 4 )). In the fifth complex, [Ni(HIM₂‐py)₂(NO₃)]⁺ ( 5 ; HIM₂‐py=2‐(2‐pyridyl)‐4,4,5,5‐tetramethyl‐4,5‐dihydro‐1H‐imidazolyl‐1‐hydroxy), which was reported previously, the two bpy bidentate ligands were replaced by HIM₂‐py. Analysis of the high‐field, high‐frequency electronic paramagnetic resonance (HF‐HFEPR) spectra and magnetization data leads to the determination of the spin Hamiltonian parameters. The D parameter, corresponding to the axial magnetic anisotropy, was negative (Ising type) for the five compounds and ranged from ?1 to ?10 cm^?1. First‐principles SO‐CASPT2 calculations have been performed to estimate these parameters and rationalize the experimental values. From calculations, the easy axis of magnetization is in two different directions for complexes 2 and 3 , on one hand, and 4 and 5 , on the other hand. A new method is proposed to calculate the g tensor for systems with S=1. The spin Hamiltonian parameters (D (axial), E (rhombic), and g_i) are rationalized in terms of ordering of the 3 d orbitals. According to this orbital model, it can be shown that 1) the large magnetic anisotropy of 4 and 5 arises from splitting of the e_g‐like orbitals and is due to the difference in the σ‐donor strength of NO₃^? and bpy or HIM₂‐py, whereas the difference in anisotropy between the two compounds is due to splitting of the t_2g‐like orbitals; and 2) the anisotropy of complexes 1 – 3 arises from the small splitting of the t_2g‐like orbitals. The direction of the anisotropy axis can be rationalized by the proposed orbital model.     

Salt effect on molecular orientation at air/liquid methanol interface

The salt effects on molecular orientation at air/liquid methanol interface were investigated by the polarization-dependent sum frequency generation vibrational spectroscopy(SFG-VS). We clarified that the average tilting angle of the methyl group to be u = 308 58 at the air/pure methanol surface assuming a d-function orientational distribution. Upon the addition of 3 mol/L Na I, the methyl group tilts further away from the surface normal with a new u = 418 38. This orientational change does not explain the enhancement of the SFG-VS intensities when adding Na I, implying the number density of the methanol molecules with a net polar ordering in the surface region also changed with the Na I concentrations. These spectroscopic findings shed new light on the salt effects on the surfaces structures of the polar organic solutions. It was also shown that the accurate determination of the bulk refractive indices and Raman depolarization ratios for different salt concentrations is crucial to quantitatively interpret the SFG-VS data.     

Stripping Voltammetric Determination of Uranium Traces in Sea Water Samples: Effect of Surfactants on the Measurements

The variables affecting determination of ultra trace levels of uranium (VI) in aqueous samples by differential pulse cathodic stripping voltammetry using chloranilic acid as the complexing agent have been examined in detail. Effect of organic surfactants on the voltammetric behavior has been studied. Electrochemical impedance measurements reveal the effect of adsorption of different surfactants on the adsorption pre-concentration step of uranium-chloranilic acid complex. Additionally, to better understand the analytical feature of the method, physicochemical aspects of the preconcentration process has been studied. Adsorption of uranium-chloranilic acid complex follows the Langmuir adsorption isotherm. Analysis results on sea water samples from India are reported.     

Triphenylphosphane Oxide Complexes of Lanthanide Nitrates: Polymorphs and Photophysics

A series of mer‐[Ln(NO₃)₃(Ph₃PO)₃] complexes were prepared from Ln(NO₃)₃ · xH₂O and Ph₃PO in chloroform (Ln = La, Nd, Sm, Eu, Gd, Tb, Dy, and Er). The La and Nd complexes were 0.25 CHCl₃ solvates, whereas the others were solvent‐free. The identical reaction using Yb(NO₃)₃ · xH₂O produced the unique salt trans‐[Yb(NO₃)₂(Ph₃PO)₄][Yb(NO₃)₄(Ph₃PO)] · Et₂O. All nitrate ions in all complexes are η²‐chelating. A comparison of the various [Ln(NO₃)₃(Ph₃PO)₃] structures, including those in the literature, reveals at least four common polymorphs, each of which is represented by isomorphic structures of multiple Ln ions. Luminescence of mer‐[Ln(NO₃)₃(Ph₃PO)₃] (Ln = Y, La, Nd, Sm, Eu, Gd, Tb, and Dy), trans‐[Yb(NO₃)₂(Ph₃PO)₄][Yb(NO₃)₄(Ph₃PO)] and Ph₃PO assignments are reported. Latva's empirical rule allows for the antenna effect, in which energy is transferred from the triplet state of the Ph₃PO ligand, to occur only for Tb³⁺. Excitation via Ph₃PO results in strong green luminescence for Tb³⁺ having twice the intensity as that which results from direct excitation of the f‐f transitions.     

Radiation enhanced P-diffusion in germanium

Abstract

Cascade size may affect phase stability under irradiation because of two distinct contributions: the replacement to displacement cross-section ratio depends on the deposited energy density; ballistic jumps which tend to disorder ordered compounds occur by bursts, while thermal jumps which restore long range order occur one by one.

The latter effect cannot be handled by standard rate theory. A stochastic treatment of the problem, based on a Fokker Planck approximation of the relevant master equation is summarized. It is shown that the possible values of the long range order parameter under irradiation are not affected by the size of the cascade but that the respective stability of the former is cascade size sensitive. As a consequence, the stability diagram of phases under irradiation varies with the size of the cascades. A numerical example of this is given for the B2 structure.     

Comparison of Force Fields on the Basis of Various Model Approaches—How To Design the Best Model for the [CnMIM][NTf2] Family of Ionic Liquids

In this contribution, we present two new united‐atom force fields (UA‐FFs) for 1‐alkyl‐3‐methylimidazolium bis(trifluoromethylsulfonyl)imide [C_nMIM][NTf₂] (n=1, 2, 4, 6, 8) ionic liquids (ILs). One is parametrized manually, and the other is developed with the gradient‐based optimization workflow (GROW). By doing so, we wanted to perform a hard test to determine how researchers could benefit from semiautomated optimization procedures. As with our already published all‐atom force field (AA‐FF) for [C_nMIM][NTf₂] (T. Köddermann, D. Paschek, R. Ludwig, ChemPhysChem­ 2007, 8, 2464 ), the new force fields were derived to fit experimental densities, self‐diffusion coefficients, and NMR rotational correlation times for the IL cation and for water molecules dissolved in [C₂MIM][NTf₂]. In the manual force field, the alkyl chains of the cation and the CF₃ groups of the anion were treated as united atoms. In the GROW force field, only the alkyl chains of the cation were united. All other parts of the structures of the ions remained unchanged to prevent any loss of physical information. Structural, dynamic, and thermodynamic properties such as viscosity, cation rotational correlation times, and heats of vaporization calculated with the new force fields were compared with values simulated with the previous AA‐FF and the experimental data. All simulated properties were in excellent agreement with the experimental values. Altogether, the UA‐FFs are slightly superior for speed‐up reasons. The UA‐FF speeds up the simulation by about 100 % and reduces the demanded disk space by about 78 %. More importantly, real time and efforts to generate force fields could be significantly reduced by utilizing GROW. The real time for the GROW parametrization in this work was 2 months. Manual parametrization, in contrast, may take up to 12 months, and this is, therefore, a significant increase in speed, though it is difficult to estimate the duration of manual parametrization.