Effects of ionic strength on SAXS data for proteins revealed by molecular dynamics simulations

The combination of small-angle X-ray solution scattering (SAXS) experiments and molecular dynamics (MD) simulations is now becoming a powerful tool to study protein conformations in solution at an atomic resolution. In this study, we investigated effects of ionic strength on SAXS data theoretically by using MD simulations of hen egg white lysozyme at various NaCl concentrations from 0 to 1 M. The calculated SAXS excess intensities showed a significant dependence on ion concentration, which originates from the different solvent density distributions in the presence and absence of ions. The addition of ions induced a slow convergence of the SAXS data, and a ～20 ns simulation is required to obtain convergence of the SAXS data with the presence of ions whereas only a 0.2 ns simulation is sufficient in the absence of ions. To circumvent the problem of the slow convergence in the presence of ions, we developed a novel method that reproduces the SAXS excess intensities with the presence of ions from short MD trajectories in pure water. By applying this method to SAXS data for the open and closed forms of transferrin at 1 M ion concentration, the correct form could be identified by simply using short MD simulations of the protein in pure water for 0.2 ns.     

Superspherical-shape approximation to describe the morphology of small crystalline particles having near-polyhedral shapes with round edges

Small crystalline particles are often formed comprising near-polyhedral shapes with round edges. When near-polyhedral shapes are analyzed and discussed, it is convenient if these shapes can be expressed by equations with simple parameters. Superspheres are solids expressing various shapes between those of polyhedra and spheres. The superspherical-shape approximation is used in this study to consider the morphology of cubic crystal structure particles. Various near-polyhedral shapes composed of {100}, {111} and {110} planes are described using a simple equation with three shape-related parameters. It is shown that the superspherical-shape approximation is a useful geometrical tool for evaluating the morphology of small crystalline particles.     

Pd-catalyzed asymmetric allylic alkylation of glycine imino ester using a chiral phase-transfer catalyst

Pd-catalyzed asymmetric allylic alkylation of the glycine imino ester 1a has been developed using a chiral quaternary ammonium salt 3d without chiral phosphine ligands. The proper choice of the achiral Pd ligand, P(OPh)3, is important to achieve high enantioselectivity. By this method with the dual catalysts, numerous enantiomerically enriched alpha-allylic amino acids 4a-h could be prepared with comparable to higher enantioselectivity than that of the conventional asymmetric alkylation of 1a. In addition, the Pd-catalyzed reaction of 1a with 1-phenyl-2-propenyl acetate 2i afforded the branch product 6 with high enantio- and diastereoselectivity (>95% de, 85% ee).     

NH/pi interaction in a spin-crossover complex [FeII(HLMe)2](BPh4)2.2CH3CN (BPh4-=Tetraphenylborate; HLMe=2-Methylimidazol-4-yl-methylideneamino-2-ethylpyridine)

Three FeII complexes, [Fe(HLR)2](BPh4)2.solvent (R=H, Me, Ph), were synthesized, where BPh4-=tetraphenylborate and HLR=2-substituted-imidazol-4-yl-methylideneamino-2-ethylpyridine. The magnetic susceptibility measurements in 5-300 K revealed that [Fe(HLH)2](BPh4)2.H2O, [Fe(HLMe)2](BPh4)2.2CH3CN, and [Fe(HLPh)2](BPh4)2.CH3CN are low-spin (LS), spin-crossover (SC), and high-spin (HS) FeII complexes, respectively, indicating that the spin state can be effectively tuned by the bulkiness of the substituent. Complex shows a steep SC around 250 K, where it assumes a cyclic structure of {[Fe(HLMe)2]BPh4}2 constructed by four NH/pi bonds between the imidazole group and the phenyl ring of BPh4- in the HS state and a deformed structure with NH/pi bonds and linear CH3CN...HN hydrogen bonds at the terminals in the LS state.     

Bifunctional-thiourea-catalyzed diastereo- and enantioselective aza-Henry reaction

Bifunctional thiourea 1a catalyzes aza-Henry reaction of nitroalkanes with N-Boc-imines to give syn-beta-nitroamines with good to high diastereo- and enantioselectivity. Apart from the catalyst, the reaction requires no additional reagents such as a Lewis acid or a Lewis base. The N-protecting groups of the imines have a determining effect on the chirality of the products, that is, the reaction of N-Boc-imines gives R adducts as major products, whereas the same reaction of N-phosphonoylimines furnishes the corresponding S adducts. Various types of nitroalkanes bearing aryl, alcohol, ether, and ester groups can be used as nucleophiles, providing access to a wide range of useful chiral building blocks in good yield and high enantiomeric excess. Synthetic versatility of the addition products is demonstrated by the transformation to chiral piperidine derivatives such as CP-99,994.     

Enantioselective aza-Henry reaction catalyzed by a bifunctional organocatalyst

[reaction: see text] The aza-Henry reaction of imines with nitroalkanes was promoted by chiral thiourea with an N,N-dimethylamino group to give beta-nitroamines with good enantioselectivity. Various N-protected imines were examined as substrates. N-Phosphinoylimine gave the best result in terms of chemical yield and enantioselectivity (up to 91% yield, up to 76% ee).     

Characteristics of all-optical 3R regenerators using cascaded second-order nonlinear effect in quasi-phase matched lithium niobate devices

We numerically show that quasi-phase matched (QPM) lithium niobate (LN) devices employing the cascaded second-order nonlinear effect of second harmonic generation (SHG) and difference frequency mixing (DFM) have all-optical decision gate characteristics. The decision gate function is realized by a parabolic transmittance for a low-power region and a limiting characteristic for a high-power region. The limiter function is attributed to the large group-velocity mismatch between the fundamental and second harmonic pulses. This operation principle differs from those of other all-optical 2R (reamplification and reshaping) or 3R (2R and retiming) regenerators that have been proposed in the past. Furthermore, we show that an initial time offset between the signal and clock pulses can improve the output signal power or the switching efficiency of the device. Based on the numerical results, we propose a method for designing all-optical 3R regenerators using the cascade of SHG and DFM in the QPM-LN devices. Following the design method, all-optical 3R operation at the bit rate of 200 Gbps can be achieved using a 1-cm-long waveguide device.     

Bifunctional thiourea-catalyzed enantioselective double Michael reaction of γ,δ-unsaturated β-ketoester to nitroalkene: asymmetric synthesis of (−)-epibatidine

The asymmetric synthesis of 4-nitrocyclohexanone derivatives has been accomplished by enantioselective double Michael additions of γ,δ-unsaturated β-ketoesters to nitroalkenes using a catalytic amount of bifunctional thiourea and TMG. The three contiguous stereogenic centers of the obtained products were constructed with good to high diastereoselectivity and up to 92% ee. The biologically active natural product, (−)-epibatidine, has been synthesized from the intermediate 11a in seven steps in 30% overall yield.