Multicanonical parallel simulations of proteins with continuous potentials

The determination of the three‐dimensional (3D) structure of a protein or peptide is a very important research problem in biological and medical sciences. Anfinsen's experiments (Science 1973, 181, 223) on renaturation of denatured proteins have shown that the native 3D structure of a (small) protein at low (room) temperatures is uniquely determined by its amino acid sequence, which suggests that it might be possible to determine the 3D structure of a protein from its amino acid sequence by pure computations. As a step toward that goal, in this article we present a simple approach for parallelization of multicanonical Monte Carlo simulations of proteins with continuous potentials. Our method is based on the parallel calculation of the protein energy function. The algorithm is tested by simulated annealing and multicanonical simulations of two small peptides, and known results are reproduced accurately. An acceptable degree of parallelization can be achieved in the simulation of Protein L using up to 30 PCs. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1287–1296, 2001     

Study on new typical ionic clusters K+ (KNO3)n and NO3‐(KNO3)m

The sample solution of KNO₃ is ejected into the gas phase and the ionic dusters of K⁺(KNO₃)_n and NO₃ (KNO₃)_m are formed and observed by electrospray ionization mass spectrometry (ESIMS). Hie full mass spectra of both the positive ion and the negative ion show that the differences between each peak nearby are all about 101 (m/z), which correspond to the molecular weight of KNO₃. The general formula of the ionic clusters can be assigned as K⁺(KNO₃)_n and NO₃′‐(KNO₃)_m..     

Synthesis,characterization of diorganotin (IV) schiff base complexes and their in vitro antitumor activity

Six novel diorganotin(IV) complexes have been synthesized in good yields by the reaction of R₂SnCl₂ (R= methyl, phenyl) with the Schiff base derived from salicylaldehyde and substituted thiosemicarbazide. The complexes were characterized by elemental analysis, IR, ¹H NMR and MS spectra. The structure of 2f was confirmed by single crystal X‐ray diffraction. The crystal of 2f is triclinic, space group P‐1 with a = 0.84996(12), b = 1.1204(2), c = 1.27597(12) nm, β = 81.908(9)°, V=1.0904(2) nm³, Z = 2, D_c= 1.551 g/cm³. The final discrepancy factors are R = 0.0211 and R_w = 0.0536 for 3710 independent reflections. Tests of antitumor activities in vitro showed that the obtained complexes had relative inhibition interaction to the KB, HCT‐8 and BEL‐7402 tumor cell lines.     

Molecular mechanics calculations on carbonyl compounds. II. Open‐chain ketones

Open‐chain aliphatic ketones were studied with the molecular mechanics (MM4) force field. A total of seven compounds were examined. Structures were well fit, including moments of inertia. Rotational barriers, vibrational spectra, and dipole moments were also well fit. The overall root mean square errors for MM3 and MM4 were 0.27 and 0.18%, respectively, for the six moments of inertia (known experimentally for two compounds) and 31 and 20 cm^?1, respectively, for the vibrational frequencies (over 99 weighted modes). © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1426–1450, 2001     

Molecular mechanics calculations on carbonyl compounds. III. Cycloketones

Molecular mechanics (MM4) calculations were carried out on cycloketones for ring sizes ranging from 4 to 11 carbon atoms. The MM4 relative energies for the various conformations of the cycloketones were compared to density functional theory (DFT) calculations (B3LYP/6‐31G*), which were also carried out in this work. For small ring sizes (n=4–6), calculated molecular geometries, dipole moments, moments of inertia, and vibrational spectra were compared to experimental data. The axial–equatorial energy differences in methyl‐substituted cyclohexanones were also calculated by MM4 and compared to ab initio, DFT, and experimental results. The results of the MM4 studies on cycloketones showed significant improvement from those of MM3 calculations performed in parallel with the MM4 calculations. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1451–1475, 2001     

Molecular mechanics calculations on carbonyl compounds. IV. Heats of formation

Molecular mechanics (MM4) calculations on the heats of formation of aldehydes and ketones were carried out for a total of 59 compounds (10 aldehydes and 49 ketones). Optimization of the heat of formation parameters was obtained by a least squares fit to the experimentally known heats of formation. With the optimized MM4 heat of formation parameters, the MM4 calculated heats of formation showed significant improvement over those of MM3. The standard and weighted root mean square deviations for the MM4 values were 0.35 and 0.31 kcal mol^?1, respectively, whereas for the MM3 values they were 0.42 and 0.39 kcal mol^?1, respectively. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1476–1483, 2001     

Studies on chemistry and immuno‐ modulating mechanism of a glycoconjugate from Lycium barbarum L.

The detailed structure of an O‐glycan derived from the fruit of Lycium barbarum L. was elucidated based on glycosidic linkage analysis, complete and partial acid hydrolysis, ¹H‐NMR and ¹³C NMR spectroscopy. According to the experiments, the carbohydrate was in the form of polysacchride (arabinogalactan) chains with highly branched 3, 4‐galactans and terminal arabinofuranosyl substituents. The immuno‐modulating mechanism of glycoconjugate and its glycan were investigated using tritium thymidine incorporation assay, flow cytometry assay and electrophoretical mobility shift assay (EMSA). The results suggested that the immunoactive components of the fruit of Lycium barbarum L. could enhance the splenocyte proliferation in normal mice and the effects of glycan chain were stronger than those of glycoconjugate. The target cell was most likely to be B‐lymphocyte, on which existed receptor binding site acting with the glycan. In addition, the immuno‐stimulatory effect of glycoconjugate (LbGp4) and its glycan (LbGp4‐OL) was associated with activating the expression of nuclear factor KB (NF‐KB) and activator protein 1 (AP‐1).     

A phase separation fluoroimmunoassay of estradiol

A competitive indirect fluoroimmunoassay of free estradiol (E₂) was established based on the thermal sensitivity of hydrogel–‐poly‐N‐isopropylacrylamide. Free estradiol was covalently bound to bovine serum albumin (BSA) to form complete antigen (E₂‐BSA), which was in turn labeled by fluorescein isothiocyanate (FTTC) as the fluorescence probe. The anti‐ E₂ monoclonal antibody (McAb) was prepared by an in vivo method, and coupled with N‐isopropylacrylamide (NIPA) to make an immune copolymer, poly‐N‐isopropylacylamidemonoclonal antibody (pNIPA‐McAb), for the determination of free E₂. The immunoassay method was based on the competitive binding of free E₂ and fluoresceinated antigen (E₂‐BSA‐FTTC) with limited amount of pNIPA‐McAb. When the immunological reaction was over, precipitation and centrifugal procedures were carried out to separate pNIPA‐McAb‐E₂‐BSA‐FTTC from other constituents in solution. The precipitate pNIPA‐McAb‐E₂‐BSA‐FTTC was dissolved in solution and then the fluorescence intensity was measured. The calibration curve covered a range of 78–500 ng/mL for free E₂. The recoveries were 91.2–107.2%.     

Reaction of HCFC‐133a (CF3CH2C1) or HFC‐134a (CF3CH2F) with alcohols or phenols in DMSO in the presence of KOH

In an open glassware, heating a gas HCFC‐133a (CF₃CH₂C1) or HFC‐134a (CF₃CH₂F), KOH and a phenol (or an alcohol) in DMSO at 80°C gave ethers ROCF₂CH₂X and (E/Z)‐ROCF = CHX (X = Cl, F) in moderate yields.     

Synthesis of 4‐halo‐2 (5H)‐furanones and their suzuki‐coupling reactions with organoboronic acids. A general route to 4‐aryl‐2 (5 H) ‐furanones

4‐Halo‐2(5H)‐furanones were prepared by the halolactonization of 2,3‐allenoic acids. The subsequent Suzuki coupling reaction of 4‐halo 2(5H)‐furanones with aryl boronic acids was carried out to produce 4‐aryl‐2(5H)‐furanones in excellent yields.