Manipulation of an intramolecular NH...O hydrogen bond by photoswitching between stable E/Z isomers of the cinnamate framework

Novel carboxylic acid derivatives were synthesized, which allowed switching of the intramolecular distance between amide group and carboxylic oxygen atoms using E to Z photoisomerization of the cinnamate framework. An intramolecular NH...O hydrogen bond was formed in the Z carboxylate compound not only in solution but also in the solid state. The pK(a) value of the carboxylic acid was lowered as a consequence of the E/Z photoisomerization.     

Preparation of nano-sized Pt metal particles by photo-assisted deposition (PAD) on transparent Ti-containing mesoporous silica thin film

We have investigated a novel technique for the preparation of nano-sized Pt metals on Ti-containing mesoporous silica (TMS) thin film by photo-assisted deposition (PAD). The transparent TMS thin film was prepared on a quartz plate through sol—gel/spin coating. XRD, UV-Vis and Ti K-edge XAFS measurements revealed the formation of isolated Ti oxide species with a tetrahedral-coordination geometry in the silica framework. Deposition of Pt metal precursor on TMS thin film under UV-light irradiation, followed by reduction with molecular hydrogen, afforded a transparent thin film (Pt/TMS). The formation of highly dispersed nano-sized Pt metals having narrow size distributions was determined by Pd L_III-edge XANES and TEM analysis. The TMS and Pt/TMS thin films have been demonstrated to exhibit a strong hydrophilic property, even before UV irradiation, compared to the common mesoporous silica and TiO₂ thin films. After UV-light irradiation, the contact angle of water droplet on the TMS and Pt/TMS thin films became extremely lower, indicating the appearance of the photo-induced super-hydrophilic property.     

Synthesis of N-functionalized oleamide derivatives

Oleamide is an interesting compound, which shows various pharmacological activities including the inhibitory effect of gap junction formation. Recently, the studies of the gap junction have been some of the hot topics in biology and its inhibitors have become more useful tools [Cravatt, B. F.; Garcia, O. P.; Siuzdak, G.; Gilula, N. B.; Henriksen, S. J.; Boger, D. L.; Lerner, R. A. Science1995, 268, 1506-1509; Cravatt, B. F.; Lerner, R. A.; Boger, D. L. J. Am. Chem. Soc.1996, 118, 580-590; Guan, X; Cravatt, B. F.; Ehring, G. R.; Hall, J. E.; Boger, D. L.; Lerner, R. A.; Gilula, N. B. J. Cell Biol.1997, 139, 1785-1792; Boger, D. L.; Patterson, J. E.; Guan, X.; Cravatt, B. F.; Lerner, R. A.; Gilula, N. B. Proc. Natl. Acad. Sci. U.S.A.1998, 95, 4810-4815; Ito, A.; Morita, N.; Miura, D.; Koma, Y.; Kataoka, T. R.; Yamasaki, H.; Kitamura, Y.; Kita, Y.; Nojima, H. Carcinogenesis2004, 25, 2015-2022]. However, many reports suggest that the functionalizations of oleamide to retain its biological activity were difficult [Boger, D. L.; Patterson, J. E.; Guan, X.; Cravatt, B. F.; Lerner, R. A.; Gilula, N. B. Proc. Natl. Acad. Sci. U.S.A.1998, 95, 4810-4815; Ito, A.; Morita, N.; Miura, D.; Koma, Y.; Kataoka, T. R.; Yamasaki, H.; Kitamura, Y.; Kita, Y.; Nojima, H. Carcinogenesis2004, 25, 2015-2022]. The synthesis of the functionalized oleamide derivatives, whose biological activity is not blocked, has become attractive in both the biological and chemical fields.Herein, by linking the fluorophore to the oleamide by alkyl chains, we synthesized the fluorescently tagged oleamide whose biological feature is similar to that of oleamide. Moreover, we also synthesized other bioactive derivatives tagged by other groups such as the sugars and biotin via alkyl chain linkers.     

Estimation of dye configuration from conventional chiroptical spectra of porphyrin integrates: combination of exciton theory with Monte Carlo molecular structural simulation

Dye integrates (arrays and aggregates) are the subject of current interest in photochemical devices. However, they are in general not suitable for X-ray crystallography because of their poor crystallinity. Here, we improved a simple method of estimating dye configurations in porphyrin integrates from their visible absorption (AB) and circular dichroism (CD) spectra. For this purpose, we calculate the dipolar and optical rotatory strengths of an integrate on the basis of the exciton theory for a given porphyrin configuration, generate the theoretical AB and CD spectra of the dye integrate using a phenomenological line shape function, a Voigt function with an adjustable line width, and optimize the configuration by minimizing the square sum (S) of the difference between the observed and calculated spectra. We adopted two optimization methods to achieve a least-squares fit between the calculated and observed spectra: the Metropolis Monte Carlo (MC) method, which incorporates S into the molecular force-field energy as a constraint, and the quasi-Newton (QN) method, which numerically minimizes S and uses no molecular force field. To check the feasibility of these methods, we simulated the AB and CD spectra of Tr?ger's base and meso-meso-linked porphyrins using the QN program, then compared the dye configurations with their X-ray structures. The calculated dye configuration of Tr?ger's base porphyrin is sufficiently in agreement with that of the X-ray structure (RMSD=0.21 A for the ZnS4 center), whereas that of meso-meso-linked porphyrin was not. These results were discussed in terms of charge transfer between two porphyrins. Finally, we applied the QN and MC methods to the structural estimation of a newly prepared peptide-linked bis(porphyrin) Boc-(PorZn,S)2-OBut. The best configurations estimated by these two methods were sufficiently in agreement with each other.     

Specific isolation of N-terminal fragments from proteins and their high-fidelity de novo sequencing

A new method to determine N-terminal amino acid sequences of multiple proteins at low pmol level by a parallel processing has been developed. The method contains the following five steps: (1) reduction, S-alkylation and guanidination for targeted proteins; (2) coupling with sulfosucccimidyl-2-(biotinamido)ethyl-1,3-dithiopropionate(sulfo-NHS-SS-biotin) to N(alpha)-amino groups of proteins; (3) digestion of the modified proteins by an appropriate protease; (4) specific isolation of N-terminal fragments of proteins by affinity capture using the biotin-avidin system; (5) de novo sequence analysis of peptides by MALDI-TOF-/MALDI-TOF-PSD mass spectrometry with effective utilization of the CAF (chemically assisted fragmentation) method.1 This method is also effective for N-terminal sequencing of each protein in a mixture of several proteins, and for sequencing components of a multiprotein complex. It is expected to become an essential proteomics tool for identifying proteins, especially when used in combination with a C-terminal sequencing method.     

Simultaneous detection of N-terminal fragment ions in a protein mixture using a ruthenium(II) complex

Use of a bis(terpyridine)ruthenium(II) derivative as an N-terminal labeling reagent resulted in the simultaneous detection and individual determination of all the N-terminal fragments of the proteins in a mixture without requiring any separation. All of the N-termini of the guanidinated proteins were labeled selectively by the ruthenium complex (-CO-labeling). After chymotryptic digestion, the fragments were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and post-source decay (PSD). The -CO moiety exclusively enhanced N-terminal fragment ions in mass spectra and enabled easy N-terminal sequencing. In a mixture containing three different proteins (lysozyme, ubiquitin, and insulin), all of the N-terminal fragment ions labeled with the ruthenium complex were found to produce uniformly intense peaks without the detection of the other unlabeled fragments. The N-terminal sequences of these ions were determined individually by PSD analysis. Application to unknown proteins from Thermus thermophilus HB8 with two-dimensional electrophoretic separation resulted in the successful determination of the N-terminal sequence and easy identification of the target protein.     

Syntheses, structures, and photoluminescence properties of metal(II) halide complexes with pyridine-containing flexible tripodal ligands

Seven coordination compounds, [Zn(L3)Cl2] . MeOH . H2O (1), [Mn(L3)2Cl2] . 0.5EtOH . 0.5H2O (2), [Cu3(L2)2Cl6] . 2DMF (3), [Cu3(L2)2Br6] . 4MeOH (4), [Hg2(L4)Cl4] (5), [Hg2(L4)Br4] (6), and [Hg3(L4)2I6] . H2O (7), were synthesized by the reactions of ligands 1,3,5-tris(3-pyridylmethoxyl)benzene (L3), 1,3,5-tris(2-pyridylmethoxyl)benzene (L2), and 1,3,5-tris(4-pyridylmethoxyl)benzene (L4) with the corresponding metal halides. All the structures were established by single-crystal X-ray diffraction analysis. In complexes 1 and 2, L3 acts as a bidentate ligand using two of three pyridyl arms to link two metal atoms to result in two different 1D chain structures. In complexes 3 and 4, each L2 serves as tridentate ligand and connects three Cu(II) atoms to form a 2D network structure. Complexes 5 and 6 have the same framework structure, and L4 acts as a three-connecting ligand to connect Hg(II) atoms to generate a 3D 4-fold interpenetrated framework, while the structure of complex 7 is an infinite 1D chain. The results indicate that the flexible ligands can adopt different conformations and thus can form complexes with varied structures. In addition, the coordination geometry of the metal atom and the species of the halide were found to have great impact on the structure of the complexes. The photoluminescence properties of the complexes were investigated, and the Zn(II), Mn(II) and Hg(II) complexes showed blue emissions in solid state at room temperature.     

Crystal structures and 77Se NMR spectra of molybdenum(IV) areneselenolates having intramolecular NH...Se hydrogen bonds

Salts of the monooxomolybdenum(IV,V) areneselenolates having intramolecular NH...Se hydrogen bonds, [Mo(IV)O(Se-2-RCONHC6H4)4]2- (R = t-Bu, CH3, CF3) and [Mo(V)O(Se-2-t-BuCONHC6H4)4]-, were synthesized and characterized by 1H nuclear magnetic resonance (NMR), 77Se NMR, electron spin resonance (ESR), UV-visible spectra, X-ray analysis, and electrochemical measurements. 77Se-1H correlated spectroscopy (COSY) indicated a significant correlation between amide 1H and selenolate 77Se atoms through an NH...Se hydrogen bond with 1J(77Se-1H) = 5.4 Hz coupling. The hydrogen bonds contribute to the positive shift in the Mo(V)/Mo(IV) redox potential. In the crystal structure of (PPh4)2[Mo(IV)O(Se-2-CH3CONHC6H4)4], an NH...O=Mo hydrogen bond was found. Ab inito calculations support the presence of intramolecular NH...O=Mo and NH...Se hydrogen bonds.     

Syntheses, structures, near-infrared and visible luminescence, and magnetic properties of lanthanide-organic frameworks with an imidazole-containing flexible ligand

Reactions of tripodal ligand 1,3,5-tris(imidazole-1-ylmethyl)-2,4,6-trimethylbenzene (L) with lanthanide metal salts and triethyl orthoformate led to the formation of six bowl-like dinuclear compounds [Ln2(L)(HL)(NO3)6(HCOO)].3CH3OH (Ln = Gd 1, Tb 2, Dy 3, Er 4, Yb 5, and Eu 6). The single-crystal X-ray diffraction analysis revealed that six complexes are isomorphous and isostructural and that the dinuclear molecules are further connected by hydrogen bonds and pi-pi interactions, resulting in 3D channel-like structures. The luminescence properties have been studied, and the results showed that the Tb(III) (2) and Eu(III) (6) complexes exhibited sensitized luminescence in the visible region and their luminescence lifetimes in powder and DMSO-d6 solution are in the range of milliseconds. The Yb(III) complex (5) emits typical near-infrared luminescence in DMSO-d6 solution. Variable-temperature magnetic susceptibility measurements of 1-6 showed that complex 1 (Gd) is nearly a paramagnet and complexes 2 (Tb), 3 (Dy), and 4 (Er) show the ferromagnetic coupling between magnetic centers, whereas the depopulation of the Stark levels in complexes 5 (Yb) and 6 (Eu) leads to a continuous decrease in (chi M)T when the sample is cooled from 300 to 1.8 K.     

Apicidin选择性抑制ClassⅠ HDACs分子动力学研究

采用模拟方法研究组蛋白脱乙酰酶抑制剂(Apicidin)选择性抑制组蛋白去乙酰化酶(Histone deacetylases, HDACs)中的HDAC1和HDAC8. 通过HDAC8晶体结构同源模建HDAC1三维结构模型, 将Apicidin分别与HDAC1和HDAC8对接并进行分子动力学模拟, 结果表明, HDAC1活性口袋入口处的Arg270是Apicidin-HDAC1形成稳定结构的重要因素; HDAC1中Tyr303及His178与Apicidin形成2个持续存在的氢键, 而在HDAC8中未发现, 这是Apicidin选择性抑制HDAC1高于HDAC8的另一重要原因.