The Conformation of Sterically Congested Seven-Membered Rings Containing Tetracoordinate Germanium(IV): A First X-Ray Crystallographic Structure Determination

The X-ray crystallographic analysis of 6,6-dimethyl-2,4,8,10-tetra-tert-octyl-dibenzo[d,f][1,3,2]dioxagermepin, 1 is reported. In the solid-state conformation of 1, the dihedral angle about the C─C sp²-sp ² σ bond connecting the two aryl rings is 50.1°. The observed C₂ symmetry in the solid-state conformation of 1 is consistent with the previously suggested solution conformation.     

测定核间距的不对称2D NOESY方法2.Cis-Pt(NH3)2(Guo)2Cl2的不对称2D NOESY实验研究

应用不对称2DNOESHY实验方法研究了顺铂配合物Cis-Pt (NH₃)₂(Guo)₂Cl₂的水溶液中的构象,表明鸟苷同铂配合后其糖环构象发生明显的变化。     

Some Properties for the Euclidean Distance Matrix and Positive Semidefinite Matrix Completion Problems

The Euclidean distance matrix (EDM) completion problem and the positive semidefinite (PSD) matrix completion problem are considered in this paper. Approaches to determine the location of a point in a linear manifold are studied, which are based on a referential coordinate set and a distance vector whose components indicate the distances from the point to other points in the set. For a given referential coordinate set and a corresponding distance vector, sufficient and necessary conditions are presented for the existence of such a point that the distance vector can be realized. The location of the point (if it exists) given by the approaches in a linear manifold is independent of the coordinate system, and is only related to the referential coordinate set and the corresponding distance vector. An interesting phenomenon about the complexity of the EDM completion problem is described. Some properties about the uniqueness and the rigidity of the conformation for solutions to the EDM and PSD completion problems are presented.     

Ultrasound irradiation alters the spatial structure and improves the antioxidant activity of the yellow tea polysaccharide

In this study, the impact of ultrasound irradiation on the structural characteristics and antioxidant properties of yellow tea polysaccharides with different molecular weights (Mw) were investigated. Native yellow tea polysaccharide containing YTPS-3N, YTPS-5N and YTPS-7N were prepared through precipitation with ethanol at various concentrations of 30%, 50%, and 70%, respectively, and irradiated with high intensity ultrasound (20 kHz) for 55 min to yield yellow tea polysaccharide including YTPS-3U, YTPS-5U and YTPS-7U. The molecular weight (Mw) of YTPS-3N (from 37.7 to 15.1 kDa) and YTPS-5N (from 14.6 to 5.2 kDa) sharply decreased upon ultrasound irradiation, coincidentally particle size (Zavg) was also significantly reduced for YTPS-3N (40%), YTPS-5N (48%) and YTPS-7N (54%). The high-performance liquid chromatography and Fourier transform-infrared spectroscopy analysis revealed a partial degradation of native yellow tea polysaccharide treated with ultrasound, though the monosaccharide composition was not altered. Furthermore, changes in morphology and the breakdown of native yellow tea polysaccharide upon irradiation was confirmed with the circular dichroism spectrum, atomic force and scanning electron microscopy. As a consequence, irradiation of yellow tea polysaccharide increased free radical scavenging activity with YTPS-7U exhibiting the highest levels of 2, 2-diphenyl-1-picrylhydrazyl free radical, superoxide and hydroxyl radicals scavenging activity. These results suggest that the alteration of the spatial structure of yellow tea polysaccharide can enhance its antioxidant activity which is an important property for functional foods or medicines.     

Prediction of Structure and Energy of Trans-1,4-Polybutadiene Glassy Surface by Atomistic Simulations of Free-Standing Ultrathin Films

Atomistic modeling of amorphous trans-1,4-polybutadiene (TPBD), using molecular mechanics and molecular dynamics (MD) simulations, is performed to generate three-dimensionally periodic bulk and two-dimensionally periodic thin film condensed phases. The condensed structures are constructed using multiple polymer chains. Structural and energetic relaxations and sampling of properties are performed using MD in the canonical ensemble (NVT) by a procedure that relieves local high-energy spots and brings the system to realistic thermodynamic states. The calculated surface energy for TPBD, 30.72 erg/cm², is in excellent agreement with the reported experimental value of 31 erg/cm². The structure of the surface layers is probed in terms of the atomic mass density variations, bond-bond orientation function profiles, and the distribution of the dihedral angles about the rotatable backbone bonds. The thickness of the surface layer over which the density varies smoothly but rapidly is found to be approximately 15 Å. The level of agreement of the calculated surface energy with the experimental value is superior in comparison to previous investigations in the literature using the atomistic approach for flexible polymers.     

亲水性两性离子聚合物刷的构象与结构

本文应用分子场理论,研究暴露于水蒸气中的亲水性两性离子聚合物(HP)刷的构象与结构.理论模型考虑HP-水(P-W)氢键和水-水(W-W)氢键效应,以及HP单体之间的偶极-偶极相互作用.研究发现,P-W与W-W氢键决定着HP的水合性,P-W氢键形成,会诱导HP刷溶胀.我们通过考察HP单体间的偶极-偶极相互作用发现,随着偶极-偶极相互作用增强,HP链在垂直培基表面沿着链方向,形成了结节状结构.这是由于HP单体之间的偶极-偶极静电吸引作用导致单体间汇聚结节,这种结节在刷内产生了较强的排斥体积作用,因此,这种HP刷具有抗污性能.在较高的接枝密度环境下,由于HP链间单体之间的偶极-偶极静电吸引作用,会形成链间单体-单体的结节,在刷内形成结节网络状凝胶结构,这种结构的出现,会使得HP刷呈现极强的抗污性.另外,当体系中水蒸气浓度增加、水合相互作用增强时,增加的P-W氢键将平衡HP单体之间的偶极-偶极相互作用,使得结节解开,聚合物链伸展.我们的理论结果符合实验观测,由此表明,P-W氢键效应,以及HP单体之间的偶极-偶极相互作用决定着HP刷的构象转变和结构特性,刷内出现的两性离子聚合物链内单体间的结节和链间单体结节状凝胶结构,是两性离子聚合物刷呈现较强抗污性的本质特性.     

Design considerations and computer modeling related to the development of molecular scaffolds and peptide mimetics for combinatorial chemistry

Summary A critical issue in drug discovery utilizing combinatorial chemistry as part of the discovery process is the choice of scaffolds to be used for a proper presentation, in a three-dimensional space, of the critical elements of structure necessary for molecular recognition (binding) and information transfer (agonist/ antagonist). In the case of polypeptide ligands, considerations related to the properties of various backbone structures (-helix, -sheets, etc.; , space) and those related to three-dimensional presentation of side-chain moieties (topography; (chi) space) must be addressed, although they often present quite different elements in the molecular recognition puzzle. We have addressed aspects of this problem by examining the three-dimensional structures of chemically different scaffolds at various distances from the scaffold to evaluate their putative diversity. We find that chemically diverse scaffolds can readily become topographically similar. We suggest a topographical approach involving design in chi space to deal with these problems.     

Ab initio investigation of boron nanodevices: conductances of the different geometric conformations

Conductances of different geometric conformations of boron ribbon devices are calculated by the ab initio method. The I-V characteristics of three devices are rather different due to the difference in structure. The current of the hexagonal boron device is the largest and increases nonlinearly. The current of the hybrid hexagon-triangle boron device displays a large low-bias current and saturates at a value of about 5.2 μA. The current of the flat triangular boron flake exhibits a voltage gap at low bias and rises sharply with increasing voltage. The flat triangular boron device can be either conducting or insulating, depending on the field.     

Discrete dihedral-angle modulation in porphyrin wheels adsorbed on Cu(1 0 0) observed by scanning tunneling microscopy

Conformations of two dodecameric porphyrin wheels adsorbed on a Cu(1 0 0) were probed by using scanning tunneling microscopy (STM). Whereas a wheel consisting of six meso-meso linked diporphyrins was detected as uniform ring structure, several different images with three discrete molecular heights were detected for a wheel consisting of six meso-meso, β-β,β-β triply-linked planar diporphyrins. These results indicate that the former has a conformation similar to that in a free space, while the latter has various conformations with respect to orientation of planar diporphyrin units toward the metal surface. Several discrete STM images of the latter have been interpreted in terms of possible eight conformations, which vary as to relative orientation of neighboring diporphyrin units.