Improving the quality of 3D-QSAR by using flexible-ligand receptor models

To address the problems associated with molecular conformations and alignments in the 3D-QSAR studies, we have developed the Flexible Ligand - Atomic Receptor Model (FLARM) 2.0 method. The FLARM 2.0 method has three unique features as compared to other pseudoreceptor model methods: (1) the training ligands are flexibly optimized inside the receptors to achieve minimal docking energies; (2) the receptor atoms are spatially moveable in the process of genetic evolving in order to avoid improper initial receptor shapes; and (3) void receptor sites are specially favored in order to obtain open receptor models that allow large gaps. Advantages of an open model include less noise information, a smaller risk of overfitting, and ease of locating the key interaction sites. The latter two features, inherited from the previous FLARM 1.0 method, can improve the predictive ability of the 3D-QSAR models, while the first feature is newly implemented to relieve the uncertainty caused by improper conformation and alignment. Three FLARM 2.0 case studies were performed, and the results show that FLARM 2.0 models are highly predictive and robust. FLARM 2.0 pseudoreceptor models can correspond well with the pharmacophore models and/or the binding sites of the real protein receptors.     

酸碱软硬度的电势原子势标度

软硬酸碱原则在化学的各个领域都得到了广泛的应用。在其定量化标度方面也做了不少工作,例如Yingst等的酸度量|α/β|,Klopman的E_n~≠和E_m~≠值,parr和pearson的绝对硬度以及Yatsimirski的ΔA_(FH)等。但是,他们的工作在理论性和应用上都无法统一起来。本文提出一种具有广泛应用性的酸碱软硬度的键参数标度。Mulliken在研究一类弱lewis加合物的光谱时,首先用量子力学原理阐述了lewis     

羧基膦－钯－酸体系催化烯烃氢酯基化反应

以钯－膦－酸体系催化烯烃氢酯基化的反应日显重要，而膦配体是决定此反应的重要因素，用二苯基膦乙酸（ＤＰＡ）为配体的钯催化剂体系，对烯烃的氢酯基化反应作了研究。对影响反应的各种因素如反应温度、反应压力、不同的溶剂、膦配体及酸助剂的量等作了考察，发现此配体对烯烃的区域选择性有改善。并用此催化体系对不同结构的烯烃进行了研究，发现有如下的活性顺序：环烯烃＞直链端烯＞直链内烯。     

Triterpenoid Saponins from Schefflera arboricola

Four new triterpenoid saponins, named scheffarboside A – D ( 1 – 4 ), along with five known saponins were isolated from the stems of Schefflera arboricola. The structures of the four new saponins were determined as 3‐O‐(O‐β‐glucuronopyranosyl‐(1 → 3)‐O‐α‐rhamnopyranosyl‐(1 → 2)‐α‐arabinopyranosyl)oleanolic acid ( 1 ), 3‐O‐(O‐α‐arabinopyranosyl‐(1 → 4)‐O‐α‐arabinopyranosyl‐(1 → 3)‐O‐α‐rhamnopyranosyl‐(1 → 2)‐α‐arabinopyranosyl)oleanolic acid ( 2 ), 3‐O‐(O‐α‐arabinopyranosyl‐(1 → 4)‐O‐α‐arabinopyranosyl‐(1 → 3)‐O‐α‐rhamnopyranosyl‐(1 → 2)‐α‐arabinopyranosyl)hederagenin ( 3 ), 3‐O‐(O‐α‐arabinopyranosyl‐(1 → 4)‐O‐α‐arabinopyranosyl‐(1 → 3)‐O‐α‐rhamnopyranosyl‐(1 → 2)‐α‐arabinopyranosyl)oleanolic acid O‐α‐rhamnopyranosyl‐(1 → 4)‐O‐β‐glucopyranosyl‐(1 → 6)‐β‐glucopyranosylester ( 4 ), respectively, on the basis of spectroscopic and chemical degradation methods.     

CRYSTALLIZATION AND MELTING OF POLY（ETHYLENE OXIDE） CONFINED IN NANOSTRUCTURED PARTICLES WITH CROSS-LINKED SHELLS OF POLYBUTADIENE

Small fixed aggregates of a poly(ethylene oxide)-block-polybutadiene diblock copolymer(PEO-b-PB)in THFsolution were obtained by adding a selective solvent for PB blocks,followed by cross-linking the PB shells.Themorphologies of the nanostructured particles with a cross-linked shell were investigated by atomic force microscopy andtransmission electron microscopy.The average behaviors of the PEO crystallization and melting confined within thenanostructured particles were studied by using differential scanning calorimetry experiments.For the deeply cross-linkedsample(SCL-1),the crystallization of the PEO blocks was fully confined.The individual nanoparticles only crystallized atvery low crystallization temperatures(T_cs),wherein the homogenous primary nucleation determined the overallcrystallization rate.For the lightly cross-linked sample(SCL-2),the confinement effect was T_c dependent.At T_c(?)42℃,thecrystallization and melting behaviors of SCL-2 were similar to those of the pure PEO-b-PB diblock copolymer.At T_c>42℃,SCL-2 could form PEO lamellae thicker than those of the pure PEO-b-PB crystallized at the same T_c.     

Magic-angle spinning solid-state NMR spectroscopy of the beta1 immunoglobulin binding domain of protein G (GB1): 15N and 13C chemical shift assignments and conformational analysis

Magic-angle spinning solid-state NMR (SSNMR) studies of the beta1 immunoglobulin binding domain of protein G (GB1) are presented. Chemical shift correlation spectra at 11.7 T (500 MHz 1H frequency) were employed to identify signals specific to each amino acid residue type and to establish backbone connectivities. High sensitivity and resolution facilitated the detection and assignment of every 15N and 13C site, including the N-terminal (M1) 15NH3, the C-terminal (E56) 13C', and side-chain resonances from residues exhibiting fast-limit conformational exchange near room temperature. The assigned spectra lend novel insight into the structure and dynamics of microcrystalline GB1. Secondary isotropic chemical shifts report on conformation, enabling a detailed comparison of the microcrystalline state with the conformation of single crystals and the protein in solution; the consistency of backbone conformation in these three preparations is the best among proteins studied so far. Signal intensities and line widths vary as a function of amino acid position and temperature. High-resolution spectra are observed near room temperature (280 K) and at <180 K, whereas resolution and sensitivity greatly degrade substantially near 210 K; the magnitude of this effect is greatest among the side chains of residues at the intermolecular interface of the microcrystal lattice, which we attribute to intermediate-rate translational diffusion of solvent molecules near the glass transition. These features of GB1 will enable its use as an excellent model protein not only for SSNMR methods development but also for fundamental studies of protein thermodynamics in the solid state.     

Synthesis, crystal structure and in vitro antitumor activity of di-n-butyltin 4′-(7-oxabicyclo [2,2,1]-5-heptane-2,3-dicarboximide) benzoates

Dibutyltin(IV) oxide reacts with the cantharidin analogue, 4′-(7-oxabicyclo [2,2,1]-5-heptane-2,3-dicarboximide) benzoic acid, A, to give the complexes [(p-C₈H₈NO₃-C₆H₄-COOBu₂Sn)₂O]₂ (1) and (p-C₈H₈NO₃-C₆H₄-COO)₂SnBu₂ (2) which had been characterized by IR and ¹H, ¹³C, ¹¹⁹Sn NMR. Single X-ray crystal structure analysis has been determined for compound (1), which was analogue to most other [(RCOOBu₂Sn)₂O]₂. The dimer features central of Bu₄Sn₂O₂ unit with the two Bu₂Sn groups being linked via bridging oxygen atom. Each tin atom adopts distorted trigonal bipyramidal structures via two carbons from a dibutyl moiety and three oxygen atoms from cantharidin derivative and bridging oxygen atom. In vitro tests show compounds 1 and 2 exhibit high cytotoxicity against P388 and HL-60.     

Self-assembly of a novel series of hetero-duplexes driven by donor-acceptor interaction

The self-assembly of a novel series of donor-acceptor interaction-driven artificial hetero-duplexes in organic media has been described. Four linear compounds 1a-1d, bearing two to five electron rich 1,5-dioxynaphthalene units connected by the tetra(ethylene glycol) linker, respectively, have been prepared and used as donors, while eight compounds 2a-2d, 13-16, bearing one to four electron deficient pyromellitic diimide, 1,4,5,8-naphthalene-tetracarboxydiimide, or perylene-3,4,9,10-tetracarboxydiimide units, respectively, have been used as acceptors. The structure of the hetero-duplexes has been characterized by the ¹H NMR, UV-vis spectroscopy and vapor pressure osmometry. It is revealed that the binding stability of the duplexes vary greatly, depending on the length and structure of the monomers and also the solvent, and hetero-duplex 1d·2d displays a maximum association constant of ca. 1.0×10⁴ M⁻¹ in chloroform.     

Calculations on the octupolar molecules with enhanced two-photon absorption cross sections based on the Zn (II) and Cu (I) as centers

The equilibrium geometries, electronic structures, as well as one- and two-photon absorption cross sections of a series of octupolar chromophores with Zn(2+) or Cu(+) as coordinate centers and 4,4'-bis(dibutylaminostyryl)-[2,2']-bis(bipyridyl) as ligands have been determined by using B3LYP/6-31G and ZINDO methods. These molecules are designed by controlled combination of two or three bipyridyl ligands with the metal centers. The results show that Zn(2+) is an effective template for the design of octupolar structures which enable it to form tetrahedral and octahedral coordinated complexes; while Cu(+) only exists in a tetrahedral coordinated complex, comparing the tetrahedral complex with Zn(2+) as the center with that of Cu(+) as the center, it is found that the complex with the Cu(+) center is a better two-photon absorption material than the former as far as the transparency/nonlinearity is concerned. Furthermore, for the same metal center of Zn(2+), both one- and two-photon absorptions of the tetrahedral complex are redshifted relative to those of the octahedral complex, is attributed to the spiroconjugation effect in the tetrahedral complex. Our theoretical findings are consistent with recent experimental observations and provide an important foundation for the design of improved transparency-nonlinearity two-photon absorption materials.     

Electrocatalysis of the SiC Particle‐Modified Glassy Carbon Electrode for the Oxidation of Adrenaline

The electrocatalytic properties of the SiC particle‐modified glassy carbon electrode (MGC) for adrenaline oxidation were studied by cyclic voltammetry (CV), double‐potential step chronocoulometry (DPSCC), and electrochemical impedance spectroscopy (EIS) techniques in McIlvaine buffer solution. It was shown that the electrode modified with SiC particles markedly displayed an electrocatalytic effect on the process of the electrochemical reaction of adrenaline, i.e., the activity and the reversibility of the MGC electrode has been significantly improved. This was attributed to the adsorption effect of the electroactive adrenaline molecules on the MGC electrode surface.