应用分子图形学、分子力学、量子化学及静电势研究农药分子结构与性能关系(X)──磺酰脲分子内旋转通道的分子力学研究

磺酞豚分子是一类极其重要的低毒超高效除草剂，有着十分重要的用途．研究分子的空间结构对于了解分子的构效关系十分重要．最近，我们测定的一系列分子的晶体结构［‘－’1表明，分子1、2、3晶体结构的空间群分别为PZ；儿、Pz、Pz，说明晶体中分别有对称元素（对称面或者对称中心），分子以对映体的形式存在于晶体中．由于磺酸豚分子本身不存在手性原子，由此推断磺酷服分子在晶体中存在的对映异构体是由内旋转阻碍产生的，因而应是构象异构体．本项研究工作的目的是应用分子力学方法，计算阻碍内旋转的能垒，从而找出分子内旋转时的最低…     

Fractal phenomena in molecular mechanics calculation

It is proposed that in molecular mechanics calculation points belonging to various stable or meta-sta-ble conformtrs are mixed up and form fractal structures in conformation space.The calculation results show the following two phenomena:(i)Two levels of structure with fractal feature were observed.Around the conformer without mirror symmetry points belonging to the conformer and its enantiomer are mixed up and form the first level of fractal structure; on the boundary of the attractive basin o{ each atlractor,points belonging to different attractors form the second level of fractal structure.(ii) The variation of molecular mechanics parameters will influence the structure and area of each attractive basin significantly The above phenomena may become the basis of a new method for solving the troublesome multi-minimum-point problem in molecular mechanics calculation.     

Ab initio calculations and molecular mechanics (MM3) force field development for ammonium and protonated aliphatic amines

The geometries and vibrational frequencies of 11 training molecules containing the ammonium ion moiety were calculated at the MP2/6-31+G* level of theory. Various torsional energy profiles were also calculated using this basis set. From those ab initio calculations, a molecular mechanics (MM3) force field was developed using our Parameter Analysis and Refinement Toolkit System (PARTS). Using this set of parameters, the MM3 force field was found to well reproduce the molecular geometries and vibrational spectra for the all training molecules. CPU time was reduced from days to seconds. The availability of this new force field dramatically increases the feasibility of the computer-assisted drug design involving ammonium and protonated amino groups. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18 : 1371–1391, 1997     

Nuclear Magnetic Resonance Metabolomics with Double Pulsed-Field-Gradient Echo and Automatized Solvent Suppression Spectroscopy for Multivariate Data Matrix Applied in Novel Wine and Juice Discriminant Analysis

The quality of foods has led researchers to use various analytical methods to determine the amounts of principal food constituents; some of them are the NMR techniques with a multivariate statistical analysis (NMR-MSA). The present work introduces a set of NMR-MSA novelties. First, the use of a double pulsed-field-gradient echo (DPFGE) experiment with a refocusing band-selective uniform response pure-phase selective pulse for the selective excitation of a 5–10-ppm range of wine samples reveals novel broad ¹H resonances. Second, an NMR-MSA foodomics approach to discriminate between wine samples produced from the same Cabernet Sauvignon variety fermented with different yeast strains proposed for large-scale alcohol reductions. Third a comparative study between a nonsupervised Principal Component Analysis (PCA), supervised standard partial (PLS-DA), and sparse (sPLS-DA) least squares discriminant analysis, as well as orthogonal projections to a latent structures discriminant analysis (OPLS-DA), for obtaining holistic fingerprints. The MSA discriminated between different Cabernet Sauvignon fermentation schemes and juice varieties (apple, apricot, and orange) or juice authentications (puree, nectar, concentrated, and commercial juice fruit drinks). The new pulse sequence DPFGE demonstrated an enhanced sensitivity in the aromatic zone of wine samples, allowing a better application of different unsupervised and supervised multivariate statistical analysis approaches.     

化合物分子表面积计算方法的研究

化合物的分子表面积是重要的物理化学性质参数．根据不同的应用领域及数学方法,提出了多种分子表面积算法[1-10],由此产生了“分子表面积法”,各方法的有效性在各具体应用领域都已被验证．本文将统计方法中的随机变量引入计算化合物分子表面积体系,由分子模型化技术得到化合物分子的原子坐标,不考虑化合物分子中原子的相互作用及分子间近似,直接计算分子表面积．使用该方法可以计算“净”分子表面积、“溶剂可及表面积”、甚至分子结构片段,分子结构中有交叉重叠片段及存在“空洞”的各种分子表面积,该算法及程序较简捷,适应范围广,计算结果较为满意．     

NMR chemical shifts in the low–pH form of a-chymotrypsin. A QM/MM and ONIOM–NMR study

 The relationship between hydrogen bonding and NMR chemical shifts in the catalytic triad of low-pH α-chymotrypsin is investigated by combined use of the effective fragment potential [(2001) J Phys Chem A 105:293] and ONIOM–NMR [(2000) Chem Phys Lett 317:589] methods. Our study shows that while the His57 N^δ1−H bond is stretched by a relatively modest amount (to about 1.060 ?) this lengthening, combined with the polarization due to the molecular environment, is sufficient to explain the experimentally observed chemical shifts of 18.2 ppm. Furthermore, the unusual down-field shift of H^ɛ1 (9.2 ppm) observed experimentally is reproduced and shown to be induced by interactions with the C=O group of Ser214 as previously postulated. The free-energy cost of moving H^δ1 from His57 to Asp102 is predicted to be 5.5 kcal/mol. Received: 26 September 2001 / Accepted: 6 September 2002 / Published online: 21 January 2003 Contribution to the Proceedings of the Symposium on Combined QM/MM Methods at the 222nd National Meeting of the American Chemical Society, 2001 Correspondence to: J. H. Jensen e-mail: jan-jensen@uiowa.edu Acknowledgements. This work was supported by a Research Innovation Award from the Research Corporation and a type G starter grant from the Petroleum Research Fund. The calculations were performed on IBM RS/6000 workstations obtained through a CRIF grant from the NSF (CHE-9974502) and on supercomputers at the National Center for Supercomputer Applications at Urbana-Champaign. The authors are indebted to Visvaldas Kairys for help with the CHARMM program, and to Daniel Quinn for many helpful discussions.     

Dielectric-Barrier Discharges: Their History, Discharge Physics, and Industrial Applications

Dielectric-barrier discharges (silent discharges) are used on a large industrial scale. They combine the advantages of non-equilibrium plasma properties with the ease of atmospheric-pressure operation. A prominent feature is the simple scalability from small laboratory reactors to large industrial installations with megawatt input powers. Efficient and cost-effective all-solid-state power supplies are available. The preferred frequency range lies between 1 kHz and 10 MHz, the preferred pressure range between 10 kPa and 500 kPa. Industrial applications include ozone generation, pollution control, surface treatment, high power CO₂ lasers, ultraviolet excimer lamps, excimer based mercury-free fluorescent lamps, and flat large-area plasma displays. Depending on the application and the operating conditions the discharge can have pronounced filamentary structure or fairly diffuse appearance. History, discharge physics, and plasma chemistry of dielectric-barrier discharges and their applications are discussed in detail.     

Scaling Function Between the Exponential-6 and the Generalized Lennard-Jones Potential Functions

The van der Waals forces for non-bonded interaction can be expressed either by the Exponential-6 or by the Lennard-Jones(m-n) potential functions, whereby m > n. Hitherto a relationship exists between the Exponential-6 and the Lennard-Jones(12-6) potential functions, with a scaling factor = 13.772 at or near the equilibrium and = 12.0 for long range interaction. This paper attempts to develop relationships between Exponential-6 and a more generalized Lennard-Jones(m-n). Analysis reveals that the relationship exists only when n = 6 and that two sets of scaling factors (as functions of index m) applies for the relationship between Exponential-6 and the Lennard-Jones(m-6), whereby m > 6.     

Three new acid M+ arsenates and phosphates with multiply protonated As/PO4 groups

The crystal structures of caesium dihydrogen arsenate(V) bis[trihydrogen arsenate(V)], Cs(H₂AsO₄)(H₃AsO₄)₂, ammonium dihydrogen arsenate(V) trihydrogen arsenate(V), NH₄(H₂AsO₄)(H₃AsO₄), and dilithium bis(dihydrogen phosphate), Li₂(H₂PO₄)₂, were solved from single‐crystal X‐ray diffraction data. NH₄(H₂AsO₄)(H₃AsO₄), which was hydrothermally synthesized (T = 493 K), is homeotypic with Rb(H₂AsO₄)(H₃AsO₄), while Cs(H₂AsO₄)(H₃AsO₄)₂ crystallizes in a novel structure type and Li₂(H₂PO₄)₂ represents a new polymorph of this composition. The Cs and Li compounds grew at room temperature from highly acidic aqueous solutions. Li₂(H₂PO₄)₂ forms a three‐dimensional (3D) framework of PO₄ tetrahedra sharing corners with Li₂O₆ dimers built of edge‐sharing LiO₄ groups, which is reinforced by hydrogen bonds. The two arsenate compounds are characterized by a 3D network of AsO₄ groups that are connected solely via multiple strong hydrogen bonds. A statistical evaluation of the As—O bond lengths in singly, doubly and triply protonated AsO₄ groups gave average values of 1.70 (2) Å for 199 As—OH bonds, 1.728 (19) Å for As—OH bonds in HAsO₄ groups, 1.714 (12) Å for As—OH bonds in H₂AsO₄ groups and 1.694 (16) Å for As—OH bonds in H₃AsO₄ groups, and a grand mean value of 1.667 (18) Å for As—O bonds to nonprotonated O atoms.