A doubly deprotonated form of calix[6]arene: Crystal and molecular structure of (calix[6]arene-2H)2−·(HNEt 3 + )2

The doubly deprotonated form of calix[6]arene, with two protonated triethylamines as counter-ions, crystallizes in the monoclinic system: space groupP2₁/n,a=8.465(4),b=17.822(8),c=15.182(6) Å,=90.18(4)°,V=2291(2) ų,Z=2. Refinement led to a final conventionalR value of 0.063 for 1046 reflections. The macrocycle conformation is not apinched cone, usual for freeR-calix[6]arene, but a distorted 1,2,3-alternate cone, since the molecule lies on a symmetry center. Furthermore, one of the torsion angles defined by the methylene bridges is near to zero, which is unusual in calixarene structures. Supplementary Data relating to this article (atomic coordinates for hydrogen atoms, anisotropic displacement parameters for oxygen and nitrogen atoms, and observed and calculated structure factors) are deposited with the British Library as Supplementary Publication No. SUP 82182 (7 pages).     

Dendritic encapsulation-roles of cores and branches

Examples of new dendrimers are presented. In the first, the effect on electron transfer rate attenuation is investigated for two dendrimer isomers that differ only in the linkage (ortho- versus meta-linked) of the phenyl ether units within one generation of the structure. Second, the effect of encapsulation on electrochemical and luminescence behavior of a new type of rhenium selenide cluster core dendrimer is illustrated.     

Structure elucidation and 3D solution conformation of the antibiotic enduracidin determined by NMR spectroscopy and molecular dynamics

Enduracidin and ramoplanin belong to the large family of cyclodepsipeptide antibiotics, highly effective against Gram-positive bacteria. The primary and 3D solution structure of ramoplanin is already well known, and the primary structure of enduracidin has been determined by a combination of chemical and NMR spectroscopic methods. Both antibiotics share a similar peptide core of 17 amino acids and differ mainly in the length of the acyl chain and the presence of two D-mannose moieties in ramoplanin. Based on the high sequence homology with ramoplanin, the structure in solution of enduracidin is modeled as a cyclic peptide. The tertiary structure thus obtained was refined through molecular dynamics (MD) simulation, in which the interatomic NOE-derived distance restraints were imposed. MD simulations yielded a family of representative 3D structures (RMSD = 0.89), which highlighted a backbone geometry similar to that of ramoplanin in its beta-hairpin arrangement. In contrast, enduracidin displays a different arrangement of the side-chain and of the residues forming the hydrophobic core.     

双氮桥联1,10-菲咯啉大环化合物分子构型的从头算研究

应用规范不变原子轨道法(GIAO)在RHF/6-31G**和B3LYP/6-31G**水平上计算了质子化双氮桥联1,10-菲咯啉大环化合物(H4HAPP2+)C2h和C2h构型的1HNMR,并用TDDFT法计算了H4HAPP2+电子光谱.结果表明,B3LYP/6-31G*优化的C2h构型为较优构型,经谐振频率验证无虚频,C2h构型是H4HAPP2+合理的对称性构型.     

Applications of homemade kit in mutation detection of genes

With the accomplishment of Human Genome Project (HGP), single nucleotide polymorphism (SNP) and mutation detection in human genome are becom-ing a new researching focus. These researches can help us to understand the phenotype diversity of indi-vidual, disease susceptibility and drug resistance of different colonies. Traditional method used for muta-tion detection is slab gel electrophoresis, which re-mains labor-intensive and time-consuming because of the requirement of radioactivity or te…     

Study on the Binding Effect between Cordycepin and Calf Thymus DNA by Circular Dichroism

DNA works as hereditary material and plays vital role in life science. The study of the binding of small molecules complex to DNA has been the focus of intense investigation, owning to their stereo and sequence specific interaction with the double helix1-…     

A molecular mechanics study of the effect of substitution in position 1 on the conformational space of the oxytocin/vasopressin ring

Summary The effect of the substitution in position 1 on the low-energy conformations of the oxytocin/vasopressin 20-membered ring was investigated by means of molecular mechanics. Three representative substitutions were considered: -mercapto-,-dimethyl)propionic acid (Dmp), (-mercapto-,-cyclopentamethylene)propionic acid (Cpp), both forming strong antagonists, and (,-dimethyl--mercapto)propionic acid (-Dmp), forming analogs of strongly reduced biological activity, with the -mercaptopropionic (Mpa) residue taken as reference. Both ECEPP/2 (rigid valence geometry) and AMBER (flexible valence geometry) force fields were employed in the calculations. Three basic types of backbone conformations were taken into account which are distinguished by the type of -turn at residues 3 and 4: 1/III, II, and I/III, all types containing one or two intra-annular hydrogen bonds. The allowed (ring-closed) disulfide-bridge conformations were searched by an algorithm formulated in terms of scanning the disulfide-bridge torsional angle C-S-S-C. The ECEPP/2 and AMBER energies of the obtained conformations were found to be in reasonable agreement. Two of the low-energy conformers of the [Mpa¹]-compound agreed very well with the cyclic part of the two conformers found in the crystal structure of [Mpa¹]-oxytocin. An analysis of the effect of -substitution on relative energies showed that the conformations with the N-C-CH₂-CH₂ (₁) and C-CH₂-CH₂-S (₁) angles of the first residue around (–100°, 60°) and (100°, –60°) are not affected; this in most cases implies a left-handed disulfide bridge. In the case of -substitution the allowed values of ₁ are close to ± 60°. This requirement, being in contradiction to the one concerning -substitution, could explain the very low biological activity of the -substituted analogs. The conformational preferences of substituted compounds can largely be explained by the analysis of local interactions within the first residue. Based on the selection of the conformations which are low in energy for both the reference and -substituted compounds, two distinct types of possible binding conformations were proposed, the first one being similar to the crystal conformer with a left-handed disulfide bridge, the second one having a right-handed bridge, but a geometry different from that of the crystal conformer with the right-handed bridge. The first type of disulfide-bridge arrangement is equally favorable for both I/III and II types of backbone structure, while the second one is allowed only for the II type of backbone. No conformation of the I/III type has a low enough energy to be considered as a possible binding conformation for all of the active compounds studied in this work.     

Conformational state of benzilidene aniline derivatives from ab initio calculation and NMR spectroscopy data

Quantum chemical calculations of the structure and conformational state of a number of Shiff bases have been performed. ¹³C NMR spectra of investigated molecules were calculated and compared with experimental data to test verification of the used calculation model. The effect of terminal substituents on the conformation of azomethines and a relation between the conformation and ¹³C NMR chemical shift were examined.     

Synthesis and Crystal Structure of Lithium Tetrametaphosphimate Tetrahydrate Li4(PO2NH)4 · 4 H2O

Single crystals of Li₄(PO₂NH)₄ · 4 H₂O were obtained by dissolving LiOH and H₄(PO₂NH)₄ · 2 H₂O in water and subsequent precipitation with acetone and ethanol followed by slow evaporation of the solvents. The structure of Li₄(PO₂NH)₄ · 4 H₂O was solved by single‐crystal X‐ray methods ( (No. 2), a = 489.2(2), b = 853.2(2), c = 880.5(2) pm, α = 101.71(3), β = 102.39(3), γ = 94.88(3)°, Z = 1). The structure is composed of LiO₄ tetrahedra and (PO₂NH)₄^4? ions. The P₄N₄ rings of the anions exhibit a slightly distorted chair–1 conformation, which is supported by IR data and has been described by torsion angles, displacement asymmetry parameters and puckering parameters. Via Li⁺ ions and hydrogen bonds, the tetrametaphosphimate anions are connected forming a three‐dimensional network.