Structure of 6,11-dichloro-9-dimethylthio-7,8-dicarba-nido-undecaborane [6,11-Cl2-9-SMe2-7,8-C2B9H9]

A technique is proposed for directed synthesis of 6,11-dichloro-9-dimethylthio-7,8-dicarba-nido-undecaborane [6,11-Cl₂-9-SMe₂-7,8-C₂B₉H₉]. Single-crystal X-ray diffraction is used to identify the molecular and crystal structure of the compound.     

Photochemical and thermal reactions of a kinetically stabilized 9-silaanthracene: the first spectroscopic observation of a 9,10-Dewar-9-silaanthracene isomer

A kinetically stabilized 9-silaanthracene (1) underwent unique photochemical and thermal reactions to afford 9,10-Dewar-9-silaanthracene 2a and the head-to-tail [4 + 4] dimer 3, respectively. The structure of 2a was confirmed by 1H, 13C, and 29Si NMR spectra, and the kinetic parameters for the thermal reversion of 2a to 1 were obtained by the measurement of UV/vis spectra. The dimer 3 was thermally stable, and the molecular structure of 3 was determined by X-ray crystallographic analysis. It was experimentally demonstrated for the first time that 9-silaanthracene, as well as anthracene, can afford either the Dewar isomer or [4 + 4] dimer, depending on the reaction conditions.     

9‐Phenyl‐3,4,4a,9a‐tetrahydrotri­ptycene and 9‐phenyl‐1,2,3,4,4a,9a‐hexa­hydro­triptycene

The structure of 9‐phenyl‐3,4,4a,9a‐tetra­hydro­triptycene, C₂₆H₂₂, (I), exhibits regiochemistry consistent with a stepwise mechanism for its formation from photo­cyclo­addition of 1,3‐cyclo­hexa­diene and 9‐phenyl­anthracene. Bond distances involving the bridgehead C atoms are similar in (I) and the hydrogenated derivative, 9‐phenyl‐1,2,3,4,4a,9a‐hexa­hydro­triptycene, C₂₆H₂₄, (II), with bonds to the quaternary‐C atoms exhibiting significant elongation [1.581 (2) Å in (I) and 1.585 (2) Å in (II)]. The molecular geometry precludes significant σ–π overlap between the phenyl groups and the interannular bonds in both compounds, indicating that the origin of the bond lengthening is steric in nature.     

9G DNAChip: microarray based on the multiple interactions of 9 consecutive guanines

We introduce the phenomenon of molecular recognition to immobilize oligonucleotides on AMCA slides for the production of 9G DNAChips. Facile and efficient method for the immobilization of the oligonucleotides appended with consecutive nine guanine bases is described. The 9G DNAChips shows more than 90% hybridization efficiency at 25 °C in 30 min.     

Intermolecular electronic coupling of 9-methyl-9H-dibenzo [a,c] carbazole for strong emission in aggregated state by substituent effect

Bright emission of organic luminogens at aggregated state has attracted increasing attention for their potential applications in opto-electronic devices and bio-/chemo-sensors. In this article, upon the introduction of different substituents(Br, Ph and TPh) to the large conjugated core of 9-methyl-9H-dibenzo[a,c]carbazole(DBC) moiety, the resultant luminogens demonstrated PL quantum yields in solid state ranging from 4.81% to 47.39%. Through the systematic investigation of molecular packing,together with theory calculation, the strong intermolecular electronic coupling in the dimers is proved as the main factor to the bright emission in the solid state. The results afforded a new avenue to investigate the intrinsic relationship among the molecular structures, packing modes and emission properties.     

Near-Enantiopure Trimerization of 9-Ethynylphenanthrene on a Chiral Metal Surface

Enantioselectivity in heterogeneous catalysis strongly depends on the chirality transfer between catalyst surface and all reactants, intermediates, and the product along the reaction pathway. Herein we report the first enantioselective on-surface synthesis of molecular structures from an initial racemic mixture and without the need of enantiopure modifier molecules. The reaction consists of a trimerization via an unidentified bonding motif of prochiral 9-ethynylphenanthrene (9-EP) upon annealing to 500 K on the chiral Pd₃-terminated PdGa{111} surfaces into essentially enantiopure, homochiral 9-EP propellers. The observed behavior strongly contrasts the reaction of 9-EP on the chiral Pd₁-terminated PdGa{111} surfaces, where 9-EP monomers that are in nearly enantiopure configuration, dimerize without enantiomeric excess. Our findings demonstrate strong chiral recognition and a significant ensemble effect in the PdGa system, hence highlighting the huge potential of chiral intermetallic compounds for enantioselective synthesis and underlining the importance to control the catalytically active sites at the atomic level.     

Towards the understanding of the activity of G9a inhibitors: an activity landscape and molecular modeling approach

In this work, we analyze the structure–activity relationships (SAR) of epigenetic inhibitors (lysine mimetics) against lysine methyltransferase (G9a or EHMT2) using a combined activity landscape, molecular docking and molecular dynamics approach. The study was based on a set of 251 G9a inhibitors with reported experimental activity. The activity landscape analysis rapidly led to the identification of activity cliffs, scaffolds hops and other active an inactive molecules with distinct SAR. Structure-based analysis of activity cliffs, scaffold hops and other selected active and inactive G9a inhibitors by means of docking followed by molecular dynamics simulations led to the identification of interactions with key residues involved in activity against G9a, for instance with ASP 1083, LEU 1086, ASP 1088, TYR 1154 and PHE 1158. The outcome of this work is expected to further advance the development of G9a inhibitors.

     

The 9-barbaralyl cation, 1,4-bishomotropylium ion and some related C9H9 carbocations : Electronic structures, stability and reactivity

The electronic structures of the 9-barbaralyl cation(1), the 1,4-bishomotropylium ion (5) and some related C₉H₉⁺ isomers have been studied byab initio STO-3G calculations. The stability of the cyclopropylcarbinyl cation 1 and the homoaromatic ion 5 as compared with their allylic counterparts is explained in terms of delocalization and MO interactions between molecular fragments. Both the symmetry of, and the distance between, molecular fragments are of importance for the electronic structure, and even symmetry-allowed interactions are negligible in the absence of favourable geometrical distortions. The non-classical ion 3 with D_3h symmetry presents special problems where other factors, such as strain, are important for the total energy. A choice between proposed mechanisms for the degenerate rearrangements of 1 can now be made with confidence.     

9—羟基—芴—9—羧酸的结构和性质的研究

运用IR、UV及NMR手段研究了9-羟基-芴-9-羧酸的结构,并用MNDO法计算出结构参数,计算结果与其甲基酯的X光晶体结构数据相符.该化合物为由共面性较好的芴环与羟基、羧基构成的不对称分子.     

Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9

Direct hydroxide attack on the scissile carbonyl of the substrate has been suggested as a likely mechanism for esterase antibodies elicited by phosphonate haptens, which mimic the transition states for the alkaline hydrolysis of esters.1 The unique amidase activity of esterase antibody 43C9 has been attributed to nucleophilic attack by an active-site histidine residue.2 Yet, the active site of 43C9 is strikingly similar to those of other esterase antibodies, particularly 17E8. We have carried out quantum mechanical calculations, molecular dynamics simulations, and free energy calculations to assess the mechanism involving direct hydroxide attack for 43C9. Results support this mechanism and suggest that the mechanism is plausible for other antiphosphonate antibodies that catalyze the hydrolysis of (p-nitro)phenyl esters.     

Insights into the Ligand Binding to Bromodomain-Containing Protein 9 (BRD9): A Guide to the Selection of Potential Binders by Computational Methods

The estimation of the binding of a set of molecules against BRD9 protein was carried out through an in silico molecular dynamics-driven exhaustive analysis to guide the identification of potential novel ligands. Starting from eight crystal structures of this protein co-complexed with known binders and one apo form, we conducted an exhaustive molecular docking/molecular dynamics (MD) investigation. To balance accuracy and an affordable calculation time, the systems were simulated for 100 ns in explicit solvent. Moreover, one complex was simulated for 1 µs to assess the influence of simulation time on the results. A set of MD-derived parameters was computed and compared with molecular docking-derived and experimental data. MM-GBSA and the per-residue interaction energy emerged as the main indicators for the good interaction between the specific binder and the protein counterpart. To assess the performance of the proposed analysis workflow, we tested six molecules featuring different binding affinities for BRD9, obtaining promising outcomes. Further insights were reported to highlight the influence of the starting structure on the molecular dynamics simulations evolution. The data confirmed that a ranking of BRD9 binders using key parameters arising from molecular dynamics is advisable to discard poor ligands before moving on with the synthesis and the biological tests.     

DFT and experimental studies on structure and spectroscopic parameters of 3,6-diiodo-9-ethyl-9H-carbazole

Structural Chemistry - The first report on crystal and molecular structure of 3,6-diiodo-9-ethyl-9H-carbazole is presented. Experimental room-temperature X-ray and 13C chemical shift studies were...     

Synthesis of Polymers by Using Fluorene. VI. Free-Radical and Anionic Polymerizations of 9-Fluorenyl and 9-Phenyl-9-fluorenyl Methacrylates

9-Fluorenyl (FMA) and 9-phenyl-9-fluorenyl methacrylates (PFMA) were prepared from methacryloyl chloride with 9-fluorenol and from silver methacrylate with 9-phenyl-9-fluorenyl chloride, respectively. The polymerizations of FMA and PFMA were studied by using α,α′-azobisisobutyronitrile (AIBN), n-butyllithium (n-BuLi), and n-BuLi-(?)-sparteine (Sp) complex in toluene and tetrahydrofuran (THF). Only PFMA polymers obtained with the n-BuLi-Sp complex showed a specific rotation ([α]_D ²¹ ?3 to ?16° in THF).

The number-average molecular weights of the FMA and PFMA polymers were 7 700-16 900 and 1 400-4 700, respectively.     

Characterization and Purification of the Mammalian COP9 Complex, a Conserved Nuclear Regulator Initially Identified as a Repressor of Photomorphogenesis in Higher Plants

The COP9 complex has been identified as a repressor of photomorphogenesis in Arabidopsis. Here we demonstrate that the COP9 complex is also present in mammals. Specific antibodies were generated against human counterparts of the Arabidopsis COP9 and COP11, the two known subunits of plant COP9 complex. Using these antibodies, we showed that indeed mammalian COP9 and COP11, also known as GPS1, could be coimmuno-precipitated using either of the two specific antibodies, definitively confirming that they are physically part of the same complex. Further, the mammalian COP9 and COP11/GPS1 were cofractionated in the same large molecular weight fractions of about 500 kDa and were absent from the monomeric fractions. The mammalian COP9 complex was present in all organs examined but abundances vary. Indirect immunofluorescence studies suggested that the mammalian COP9 complex is largely nuclear localized. Both conventional biochemical and affinity purifications of the COP9 complex from pig spleen indicated that the mammalian COP9 complex consists of eight distinct subunits. These findings indicate that mammals also have a COP9 complex with conserved molecular composition and biochemical and cellular properties similar to the higher plant counterpart.     

Waugh-型镍钼杂多酸的量子化学计算

采用半经验INDO法，完成了Waugh-型镍钼杂多酸（NH44）6〔NIMO9O32〕·6H2O的量子化学计算，得到146个成键轨道和78个反键轨道，轨道能级，电荷和键序等数据。通过对这些数据的分析，表明杂多酸分子中端氧和Ni都可能为化学活性中心，各原子轨道在分子轨道中都占有一定比例，其HOMO和LUMO能级皆为负值，其体系具有进一步接受电子的能力。这些结论与实验事实一致。     

含磷嘧啶类CDK9抑制剂的分子对接、3D-QSAR和分子动力学模拟

选取64个具有潜力的含磷嘧啶类细胞周期依赖性蛋白激酶(CDK9)小分子抑制剂,采用分子对接方法研究了该类小分子与CDK9的结合作用,结果表明,分子构象、氢键形成、疏水性和氨基酸残基Cys106在此类抑制剂与CDK9的结合过程中具有重要作用.在配体叠合的基础上,运用比较分子力场分析(Co MFA)、比较分子相似性指数分析(Co MSIA)和Topomer Co MFA(T-COMFA)研究了分子结构与抑制活性的关系,发现由训练集立体场、静电场和疏水场组合的Co MSIA模型为最优模型,其内部交叉验证相关系数(Q2=0.557)、非交叉验证相关系数(R2=0.959)和外部预测相关系数(r2=0.863)具有统计学意义,该模型的三维等值线图直观显示了化合物的活性与其三维结构的关系.根据这些结果设计了10个具有新结构的含磷嘧啶类化合物,分子对接和分子动力学模拟结果表明,新化合物和CDK9的结合模式与原化合物64相同,自由能分析从理论上证明了新化合物64d的CDK9抑制活性优于化合物64,并且显示含磷基团与残基Asp109的静电场能在化合物与CDK9作用过程中有重要作用.     

异质富勒烯C~5~9Si与C~6~9Si的理论研究

利用MNDO,AM1和PM3半经验量子化学计算方法对硅杂富勒烯C~5~9Si和C~6~9Si进行了系统的理论研究.计算了稳定构型、生成热、前沿轨道能级差、电离势、电子亲和势、绝对电负性和整体硬度.结果表明,硅杂富勒烯的稳定性虽然低于全碳富勒烯,但也具有相当的稳定性.C~5~9Si的稳定性比已经合成的C~5~8X~2(X=B,N)高,C~6~9Si与C~7~0的稳定性差异也很小,因此在适宜条件下文中所讨论的硅杂富勒烯是应该能够合成的.在C~6~9Si各异构体中,取代位置在赤道的异构体具有最低的能量和最大的前沿轨道能级差,也是最稳定的异构体.与全碳勒烯C~6~0和C~7~0相比,C~5~9Si和C~6~9Si具有较小的电离势和电子亲和势,表明硅杂富勒烯容易被氧化,而被还原的难度要些,但是仍容易发生还原反应而生成负离子.因此硅原子的掺杂能够使富勒烯的氧化还原性能得以改善.C~5~9Si和C~6~9Si更容易与亲电试剂反应,而发生亲核反应的活性要相对小一些.硅杂富勒烯C~5~9Si和C~6~9Si的绝对电负性和硬度都小于相对应的全碳富勒烯,对电子的束缚力要相对小一些。     

Synthesis and molecular structure of 4-nitro-9-phenyl-1H-and 9-hydroxy-3-oxo-9-phenyl-2,3-dihydro-9H-indeno-[2,1- c ]pyridines and 3,7-diphenyl-3a, 4,5,6-tetrahydroindeno[2,1- c ]isoxazolo[5,4- d ]pyridine

The 4-nitro derivatives and an oxidation by-product, 9-hydroxy-2-methyl-3-oxo-9-phenyl-2,3-dihydro-9H-indeno[2,1-c]pyridine were obtained by the nitration of N-alkyl-9-phenyl-2,3-dihydro-1H-indeno-[2,1-c]pyridines with sodium nitrite in acetic acid. Their molecular structures were studied by X-ray structural analysis. The product of [2+3] cycloaddition, 5-methyl-3,7-diphenyl-3a, 4,5,6-tetrahydroindeno[2,1-c]isoxazolo[5,4-d]pyridine, was obtained by the interaction of 2-chloro-1-hydroxy-2-phenylazomethine with 2-methyl-9-phenyl-2,3-dihydro-1H-indeno[2,1-c]pyridine. __________ Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1390–1399, September, 2007.     

Synthesis and crystal structures of fluorescent receptors for 9-butyladenine

Two pyrene containing fluorescent receptors, 2-(1-pyrenyl)benzoic acid (FR-1) and 8-(1-pyrenyl)-1-naphthoic acid (FR-2), have been designed and synthesized to mimic a pyrene dinucleotide for molecular recognition of 9-butyladenine (9-BuA). The X-ray crystal structures of the receptors FR-1 and FR-2 along with the binding substrate 9-BuA have been determined. FR-1 has the carboxyl group in the same plane as the phenyl group whereas the pyrenyl group is perpendicular to the phenyl group. However, both carboxyl and pyrenyl groups in FR-2 are parallel to each other but perpendicular to the naphthyl group. The binding constant for FR-2 to 9-BuA was found to be 7896±2187 M⁻¹, which is 8.3-fold greater than that for FR-1 (953±129 M⁻¹). The results indicate that the complex of 9-BuA with FR-2 is more stable than that with FR-1 by 1.2 kcal/mol. In addition, the molecular recognition of 9-BuA with the receptors can also be observed using fluorescence spectroscopy.     

9-羟基苯并萘酮分子内氢传递过程的理论计算

借助MNDO、AM 1、HF/ 3 2 1G、HF/ 6 31G 量子化学理论计算方法 ,对 9 羟基苯并萘酮 (9 HPO)的分子内氢传递过程进行了理论探讨 ,并与X射线衍射的结构数据作了比较。发现 :1 .A构型的 9 HPO比B构型的更稳定 ,两个等同的A可以通过分子内氢传递相互转化 ,反应的过渡态就是B .2 .B是一种严格对称的平面构型 ,它的H电荷和偶极矩都较A增大 ,所以分子内氢传递速率在极性溶剂中将加快。3.共轭在 9 HPO分子内氢传递反应中起了重要的作用。 4.对于类似分子IHT的计算 ,先用半经验方法或小基组的从头计算方法优化结构 ,再用大基组的从头计算方法计算单点能可以得到较好的结果。