Synthesis of N-labeled 4-oxo-2,2,6,6-tetraethylpiperidine nitroxide for EPR brain imaging

A scalable synthetic route for ¹⁵N-labeled 4-oxo-2,2,6,6-tetraethylpiperidine nitroxide (¹⁵N-TEEPONE) is described. This ¹⁵N-labeled nitroxide is suitable for electron paramagnetic resonance imaging of brain, and its higher sensitivity compared with that of its ¹⁴N-counterpart is an important advantage of the labeled derivative.     

A mesoporous silica/fluorinated alcohol adduct: an efficient metal-free,three-component synthesis of indazolophthalazinetrione heterocycles using a reusable nanoporous/trifluoroethanol adduct (SBA-15/TFE)

The channels of mesoporous (SBA-15) represent a straightforward reactor for the rapid synthesis of indazolophthalazinetrione skeletons via three-component coupling reactions in 2,2,2-trifluoroethanol. The solid SBA-15 and TFE could be recovered and reused. The present method carries the advantage of being performed under neutral conditions and requires no activation or modification of the substrates.     

Substituent effects on 15N and 13C NMR chemical shifts of 3-phenylisoxazoles: a theoretical and spectroscopic study

The synthesis and assignment of 15N and 13C NMR signals of the isoxazole ring in a series of para-substituted 3-phenyl derivatives are reported. DFT calculations of 15N and 13C chemical shifts are presented and compared to observed values. Substituent effects are interpreted in terms of the Hammett correlation and calculated bond orders.     

Complete 1H, 13C and 15N NMR assignment of tirapazamine and related 1,2,4-benzotriazine N-oxides

1H, 13C and 15N NMR measurements (1D and 2D including 1H--15N gs-HMBC) have been carried out on 3-amino-1, 2,4-benzotriazine and a series of N-oxides and complete assignments established. N-Oxidation at any position resulted in large upfield shifts of the corresponding N-1 and N-2 resonances and downfield shifts for N-4 with the exception of the 3-amino-1,2,4-benzotriazine 1-oxide in which a small upfield shift of N-4 was observed. Density functional GIAO calculations of the 15N and 13C chemical shifts [B3LYP/6-31G(d)//B3LYP/6-311+G(2d,p)] gave good agreement with experimental values confirming the assignments. The combination of 13C and 15N NMR provides an unambiguous method for assigning the 1H and 13C resonances of N-oxides of 1,2,4-benzotriazines.     

beta-Barrel transmembrane proteins: Geometric modelling, detection of transmembrane region, and structural properties

The location of the membrane lipid bilayer relative to a transmembrane protein structure is important in protein engineering. Since it is not present on the determined structures, it is essential to automatically define the membrane embedded protein region in order to test mutation effects or to design potential drugs. beta-Barrel transmembrane proteins, present in nature as outer membrane proteins (OMPs), comprise one of the two transmembrane protein fold classes. Lately, the number of their determined structures has increased and this enables the implementation and evaluation of structure-based annotation methods and their more comprehensive study. In this paper, we propose two new algorithms for (i) the geometric modelling of beta-barrels and (ii) the detection of the transmembrane region of a beta-barrel transmembrane protein. The geometric modelling algorithm combines a non-linear least square minimization method and a genetic algorithm in order to find the characteristics (axis, radius) of a shape with axial symmetry which best models a beta-barrel. The transmembrane region is detected by profiling the external residues of the beta-barrel along its axis in terms of hydrophobicity and existence of aromatic and charged residues. TbB-Tool implements these algorithms and is available in . A non-redundant set of 22 OMPs is used in order to evaluate the algorithms implemented and the results are very satisfying. In addition, we quantify the abundance of all amino acids and the average hydrophobicity for external and internal beta-stranded residues along the axis of beta-barrel, thus confirming and extending other researchers' results.     

New Steroidal Saponins from the Leaves of Yucca elephantipes

Two new spirostanol saponins, namely elephanosides G and H ( 1 and 2 , resp.) were isolated from the leaves of Yucca elephantipes (Agavaceae), together with the two known furostanol saponins 3 and 4 and the six known flavonoid O‐ and C‐glycosides 5 – 10 . The new structures were elucidated as (3β,25S)‐spirost‐5‐en‐3‐yl O‐β‐D ‐glucopyranosyl‐(1→3)‐O‐β‐D ‐glucopyranosyl‐(1→4)‐β‐D ‐galactopyranoside ( 1 ) and (3β,5β,25R)‐3‐[(2‐O‐β‐D ‐glucopyranosyl‐β‐D ‐galactopyranosyl)oxy]spirostan‐12‐one ( 2 ) on the basis of detailed spectroscopic analysis and acidic hydrolysis.     

CHARMM36 all‐atom additive protein force field: Validation based on comparison to NMR data

Protein structure and dynamics can be characterized on the atomistic level with both nuclear magnetic resonance (NMR) experiments and molecular dynamics (MD) simulations. Here, we quantify the ability of the recently presented CHARMM36 (C36) force field (FF) to reproduce various NMR observables using MD simulations. The studied NMR properties include backbone scalar couplings across hydrogen bonds, residual dipolar couplings (RDCs) and relaxation order parameter, as well as scalar couplings, RDCs, and order parameters for side‐chain amino‐ and methyl‐containing groups. It is shown that the C36 FF leads to better correlation with experimental data compared to the CHARMM22/CMAP FF and suggest using C36 in protein simulations. Although both CHARMM FFs contains the same nonbond parameters, our results show how the changes in the internal parameters associated with the peptide backbone via CMAP and the χ₁ and χ₂ dihedral parameters leads to improved treatment of the analyzed nonbond interactions. This highlights the importance of proper treatment of the internal covalent components in modeling nonbond interactions with molecular mechanics FFs. © 2013 Wiley Periodicals, Inc.     

MnOx/Al-SBA-15的结构性质及低温NH3选择性催化还原NOx

采用后合成法制备MnO_x/Al-SBA-15催化剂, 考察了催化剂的低温NH₃选择性催化还原(SCR)NO_x的性能. 利用傅里叶透射红外变换(FTIR)光谱、N₂吸附-脱附、X射线衍射(XRD)、扫描电镜(SEM)、拉曼光谱(Raman)、X射线光电子能谱(XPS)及NH₃程序升温脱附(NH₃-TPD)的表征手段, 对催化剂的结构性质和SCR性能进行了系统分析. 结果表明, 适量Al的掺杂能提高MnO_x/SBA-15催化剂的SCR活性, 当硅铝摩尔比为50时, 催化剂活性最佳. 表征结果显示, Al掺杂后, 催化剂仍保持良好的骨架结构, 较大比表面、孔容和孔径, 并且Mn在催化剂表面富集, 由低价态转化为高价态, MnO₂为催化剂的主要活性相. 此外, Al的掺杂使MnO_x在催化剂表面高度分散, 表面酸性增强, 从而提高了催化剂的SCR活性.     

An efficient,mild and selective Ullmann‐type N‐arylation of indoles catalysed by Pd immobilized on amidoxime‐functionalized mesoporous SBA‐15 as heterogeneous and recyclable nanocatalyst

A wide range of N‐arylated indoles were selectively synthesized through intermolecular C(aryl)? N bond formation from the corresponding aryl iodides and indoles through Ullmann‐type coupling reactions in the presence of a catalytic amount of Pd immobilized on amidoxime‐functionalized mesoporous SBA‐15 (SBA‐15/AO/Pd(0)) under mild reaction conditions. These cross‐coupled products were obtained in excellent yields under mild conditions at extremely low palladium loading (ca 0.3 mol%), and the heterogeneous catalyst can be readily recovered by simple filtration and reused seven times with loss in its activity. Copyright © 2015 John Wiley & Sons, Ltd.     

Reduced dimensionality (3,2)D NMR experiments and their automated analysis: implications to high‐throughput structural studies on proteins

Protein NMR spectroscopy has expanded dramatically over the last decade into a powerful tool for the study of their structure, dynamics, and interactions. The primary requirement for all such investigations is sequence‐specific resonance assignment. The demand now is to obtain this information as rapidly as possible and in all types of protein systems, stable/unstable, soluble/insoluble, small/big, structured/unstructured, and so on. In this context, we introduce here two reduced dimensionality experiments – (3,2)D‐hNCO canH and (3,2)D‐hN coCA nH – which enhance the previously described 2D NMR‐based assignment methods quite significantly. Both the experiments can be recorded in just about 2–3 h each and hence would be of immense value for high‐throughput structural proteomics and drug discovery research. The applicability of the method has been demonstrated using alpha‐helical bovine apo calbindin‐D9k P43M mutant (75 aa) protein. Automated assignment of this data using AUTOBA has been presented, which enhances the utility of these experiments. The backbone resonance assignments so derived are utilized to estimate secondary structures and the backbone fold using Web‐based algorithms. Taken together, we believe that the method and the protocol proposed here can be used for routine high‐throughput structural studies of proteins. Copyright © 2014 John Wiley & Sons, Ltd.