Regioselective Arylation and Alkynylation of 2,3‐Dibromo‐1H‐inden‐1‐one by Suzuki?Miyaura and Sonogashira Cross‐Coupling Reactions

Suzuki? Miyaura reactions of 2,3‐dibromo‐1H‐inden‐1‐one afforded a wide range of arylated 1H‐inden‐1‐ones. Sonogashira cross‐coupling reactions gave alkynylated indenones. The reactions proceeded with very good regioselectivity in the less sterically hindered and more electron‐deficient position 3.     

Piperazine Functionalization of C70 for Incorporation into Supramolecular Assemblies

The photochemical reaction of piperazine with C₇₀ produces a mono‐adduct (N(CH₂CH₂)₂NC₇₀) in high yield (67 %) along with three bis‐adducts. These piperazine adducts can combine with various Lewis acids to form crystalline supramolecular aggregates suitable for X‐ray diffraction. The structure of the mono‐adduct was determined from examination of the adduct I₂N(CH₂CH₂)₂NI₂C₇₀ that was formed by reaction of N(CH₂CH₂)₂NC₇₀ with I₂. Crystals of polymeric {Rh₂(O₂CCF₃)₄N(CH₂CH₂)₂NC₇₀}_n?nC₆H₆ that formed from reaction of the mono‐adduct with Rh₂(O₂CCF₃)₄ contain a sinusoidal strand of alternating molecules of N(CH₂CH₂)₂NC₇₀ and Rh₂(O₂CCF₃)₄ connected through Rh?N bonds. Silver nitrate reacts with N(CH₂CH₂)₂NC₇₀ to form black crystals of {(Ag(NO₃))₄(N(CH₂CH₂)₂NC₇₀)₄}_n?7nCH₂Cl₂ that contain parallel, nearly linear chains of alternating (N(CH₂CH₂)₂NC₇₀ molecules and silver ions. Four of these {Ag(NO₃)N(CH₂CH₂)₂NC₇₀}_n chains adopt a structure that resembles a columnar micelle with the ionic silver nitrate portion in the center and the nearly non‐polar C₇₀ cages encircling that core. Of the three bis‐adducts, one was definitively identified through crystallization in the presence of I₂ as ¹²{N(CH₂CH₂)₂N}₂C₇₀ with addends on opposite poles of the C₇₀ cage and a structure with C_2v symmetry. In ¹²{I₂N(CH₂CH₂)₂N}₂C₇₀, individual ¹²{I₂N(CH₂CH₂)₂N}₂C₇₀ units are further connected by secondary I2???N2 interactions to form chains that occur in layers within the crystal. Halogen bond formation between a Lewis base such as a tertiary amine and I₂ is suggested as a method to produce ordered crystals with complex supramolecular structures from substances that are otherwise difficult to crystallize.     

Synthesis and X-ray crystallographic studies of novel proton-ionizable nitro- and halogen-substituted acridono-18-crown-6 chromo- and fluorogenic ionophores

Starting from acridono-18-crown-6 ligand 1 (Fig. 1) seven new proton-ionizable chromogenic and fluorogenic ionophores 2-8 (Fig. 1) containing NO₂ group(s) and/or Br or Cl atom(s) in the aromatic rings were prepared by electrophilic substitution. The precursor macrocycle 1 was obtained by a modification of the reported procedure which made chromatography unnecessary in purification and gave higher yield. X-ray crystallographic studies of the complexes of acridono-18-crown-6 type ligands 1, 2, 3, 6 and 8 show that the proton-ionizable units are in the acridone tautomeric form and that the ligands invariably bind a water molecule in their cavities by multipodal hydrogen bonding. In two cases (6 and 8) an additional DMF solvent molecule is also bound at the crown perimeter in the solid state.     

New Microporous and Mesoporous Materials: Elucidation of Their Structures by Electron Microscopy

We have recently published three papers (P. Wagner et al., Phys. Chem. 103 (1999) 8245; S. Inagaki et al., J. Am. Chem. Soc. 121 (1999) 9611; A. Carlsson et al., J. Electron Microscopy 48 (1999) 795) that herald a new approach to structural solutions in micro- and mesoporous solid state materials. Among these materials are the first hybrid inorganic–organic mesoporous materials, synthesized using the organosilane compound 1,2-bis(trimethoxysilyl) ethane (BTME). Both organic and inorganic fragments are distributed completely uniformly at the molecular scale in the mesoporous walls. Two distinct phases with two- and three-dimensional (2d- and 3d-) hexagonal periodic pore-arrangements have been detected. We have also recently reported another new cubic hybrid phase with a decaoctahedral crystal morphology. Two new approaches for solving the structures of porous materials from either electron diffraction (ED) or high-resolution electron microscope (HREM) observations have also been developed. The former was successfully applied by combining direct methods for structural analysis of the new microporous crystal SSZ-48, which crystallizes only in very small crystals. The latter technique was applied to 3d-structural analysis of the mesoporous material MCM-48. The structure solutions, in the latter case, are obtained uniquely without preassumed models or parameterization, unlike previous reports.     

Studies on the conformation of α-arylcinnamic acids and their esters: Crystal structures of methyl (E)-2,3-bis(3,4-dimethoxyphenyl)propenoate and methyl (Z)-2,3-bis(3,4-dimethoxyphenyl)propenoate

The conformations of stereoisomers of -arylcinnamic acids and their esters are discussed based on crystal structures of the E and Z forms of 2,3-bis(3,4-dimethoxyphenyl)propenoic acid and its methyl ester. In the E forms of the cinnamic acid and the cinnamic acid ester, the plane of the -aryl substituent is approximately perpendicular to that of the rest of the molecule. In the Z forms the plane of the carboxyl or methoxycarbonyl group is approximately perpendicular to that of the ethylenic group, and both the aromatic group planes are significantly twisted out of the ethylenic group plane. Crystal structures of methyl (E)-2,3-bis(3,4-dimethoxyphenyl)propenoate (space group P2₁/n with a = 8.1697(5), b = 11.3882(9), c = 19.7766(9) Å, = 90.058(4)°, V = 1840.0(2) ų, and Z = 4), monoclinic methyl (Z)-2,3-bis(3,4-dimethoxyphenyl)propenoate (space group P2₁/n with a = 11.183(2), b = 5.640(2), c = 29.737(7) Å, = 99.19(2)°, V = 1851.4(9) ų, and Z = 4), and orthorhombic methyl (Z)-2,3-bis(3,4-dimethoxyphenyl)propenoate (space group P2₁2₁2₁ with a = 8.849(4), b = 24.288(9), c = 8.734(3) Å, V = 1877(1) ų, and Z = 4) are reported.     

蛋白质空间结构的实验技术和理论方法

文章主要介绍几种蛋白质空间结构的实验测定方法，在现代生物学研究中，最常用的方法包括X射线晶体学、二维核磁共振（2D-NMR）和低温冷冻电镜，近几年发展起来的单分子技术在生物大分子动态结构的研究中应用越来越多，这些方法都有它们特定的时间和空间分辨率，所测定的结构及其动力学受环境热运动涨落的影响也非常不同，文章对这些问题作了较详细的分析，在蛋白质结构的理论方法方面，介绍了一个新的折叠理论及其与现有折叠模型的关系．讨论了模拟计算在研究蛋白质构象变化和动力学方面的应用，同时强调了分子动力学和蒙特卡罗方法．指出粗粒化模型是研究的热点之一，对生物学中经常遇到的多长度多时问尺度问题提供了一个可行的解决方案。     

Radiation damage to protein specimens from electron beam imaging and diffraction: a mini‐review of anti‐damage approaches,with special reference to synchrotron X‐ray crystallography

Recent research progress using X‐ray cryo‐crystallography with the photon beams from third‐generation synchrotron sources has resulted in recognition that this intense radiation commonly damages protein samples even when they are held at 100 K. Other structural biologists examining thin protein crystals or single particle specimens encounter similar radiation damage problems during electron diffraction and imaging, but have developed some effective countermeasures. The aim of this concise review is to examine whether analogous approaches can be utilized to alleviate the X‐ray radiation damage problem in synchrotron macromolecular crystallography. The critical discussion of this question is preceded by presentation of background material on modern technical procedures with electron beam instruments using 300–400 kV accelerating voltage, low‐dose exposures for data recording, and protection of protein specimens by cryogenic cooling; these practical approaches to dealing with electron radiation damage currently permit best resolution levels of 6 Å (0.6 nm) for single particle specimens, and of 1.9 Å for two‐dimensional membrane protein crystals. Final determination of the potential effectiveness and practical value of using such new or unconventional ideas will necessitate showing, by experimental testing, that these produce significantly improved protection of three‐dimensional protein crystals during synchrotron X‐ray diffraction.     

Oleanane‐Type Triterpenoids from the Endophytic Fungus Pestalotiopsis clavispora Isolated from the Chinese Mangrove Plant Bruguiera sexangula

Three new triterpenoid derivatives, named (15α)‐15‐hydroxysoyasapogenol B ( 1 ), (7β,15α)‐7,15‐dihydroxysoyasapogenol B ( 2 ), and (7β)‐7,29‐dihydroxysoyasapogenol B ( 3 ), were isolated from cultures of the plant endophytic fungus Pestalotiopsis clavispora. Their structures and relative configurations were elucidated by extensive spectroscopic analysis and X‐ray crystallography.     

Structures of the Reactive Intermediates in Organocatalysis with Diarylprolinol Ethers

Structures of the reactive intermediates (enamines and iminium ions) of organocatalysis with diarylprolinol derivatives have been determined. To this end, diarylprolinol methyl and silyl ethers, 1 , and aldehydes, Ph? CH₂? CHO, ^tBu? CH₂? CHO, Ph? CH=CH? CHO, are condensed to the corresponding enamines, A and 3 (Scheme 2), and cinnamoylidene iminium salts, B and 4 (Scheme 3). These are isolated and fully characterized by melting/decomposition points, [α]_D, elemental analysis, IR and NMR spectroscopy, and high‐resolution mass spectrometry (HR‐MS). Salts with BF₄, PF₆, SbF₆, and the weakly coordinating Al[OC(CF₃)₃]₄ anion were prepared. X‐Ray crystal structures of an enamine and of six iminium salts have been obtained and are described herein (Figs. 2 and 4–8, and Tables 2 and 7) and in a previous preliminary communication (Helv. Chim. Acta 2008 , 91, 1999). According to the NMR spectra (in CDCl₃, (D₆)DMSO, (D₆)acetone, or CD₃OD; Table 1), the major isomers 4 of the iminium salts have (E)‐configuration of the exocyclic N?C(1′) bond, but there are up to 11% of the (Z)‐isomer present in these solutions (Fig. 1). In all crystal structures, the iminium ions have (E)‐configuration, and the conformation around the exocyclic N‐C? C‐O bond is synclinal‐exo (cf. C and L ), with one of the phenyl groups over the pyrrolidine ring, and the RO group over the π‐system. One of the meta‐substituents (Me in 4b , CF₃ in 4c and 4e ) on a 3,5‐disubstituted phenyl group is also located in the space above the π‐system. DFT Calculations at various levels of theory (Tables 3–6) confirm that the experimentally determined structures (cf. Fig. 10) are by far (up to 8.3 kcal/mol) the most stable ones. Implications of the results with respect to the mechanism of organocatalysis by diarylprolinol derivatives are discussed.     

Multifarious injection chamber for molecular structure study (MICOSS) system: development and application for serial femtosecond crystallography at Pohang Accelerator Laboratory X‐ray Free‐Electron Laser

The multifarious injection chamber for molecular structure study (MICOSS) experimental system has been developed at the Pohang Accelerator Laboratory X‐ray Free‐Electron Laser for conducting serial femtosecond crystallography. This system comprises several instruments such as a dedicated sample chamber, sample injectors, sample environment diagnostic system and detector stage for convenient distance manipulation. Serial femtosecond crystallography experiments of lysozyme crystals have been conducted successfully. The diffraction peaks have reached to ～1.8 Å resolution at the photon energy of 9.785 keV.