Toward direct determination of conformations of protein building units from multidimensional NMR experiments. V. NMR chemical shielding analysis of N-formyl-serinamide,a model for polar side-chain containing peptides

Knowledge of chemical shift-structure relationships could greatly facilitate the NMR chemical shift assignment and structure refinement processes that occur during peptide/protein structure determination via NMR spectroscopy. To determine whether such correlations exist for polar side chain containing amino acid residues the serine dipeptide model, For-L-Ser-NH(2), was studied. Using the GIAO-RHF/6-31+G(d) and GIAO-RHF/TZ2P levels of theory the NMR chemical shifts of all hydrogen ((1)H(N), (1)H(alpha), (1)H(beta1), (1)H(beta2)), carbon ((13)C(alpha), (13)C(beta), (13)C') and nitrogen ((15)N) atoms have been computed for all 44 stable conformers of For-L-Ser-NH(2). An attempt was made to establish correlation between chemical shift of each nucleus and the major conformational variables (omega(0), phi, psi, omega(1), chi,(1) and chi(2)). At both levels of theory a linear correlation can be observed between (1)H(alpha)/phi, (13)C(alpha)/phi, and (13)C(alpha)/psi. These results indicate that the backbone and side-chain structures of For-L-Ser-NH(2) have a strong influence on its chemical shifts.     

Relative stability of major types of beta-turns as a function of amino acid composition: a study based on Ab initio energetic and natural abundance data

Folding properties of small globular proteins are determined by their amino acid sequence (primary structure). This holds both for local (secondary structure) and for global conformational features of linear polypeptides and proteins composed from natural amino acid derivatives. It thus provides the rational basis of structure prediction algorithms. The shortest secondary structure element, the beta-turn, most typically adopts either a type I or a type II form, depending on the amino acid composition. Herein we investigate the sequence-dependent folding stability of both major types of beta-turns using simple dipeptide models (-Xxx-Yyy-). Gas-phase ab initio properties of 16 carefully selected and suitably protected dipeptide models (for example Val-Ser, Ala-Gly, Ser-Ser) were studied. For each backbone fold most probable side-chain conformers were considered. Fully optimized 321G RHF molecular structures were employed in medium level [B3LYP/6-311++G(d,p)//RHF/3-21G] energy calculations to estimate relative populations of the different backbone conformers. Our results show that the preference for beta-turn forms as calculated by quantum mechanics and observed in Xray determined proteins correlates significantly.     

[2.2.2.2](2,7)‐1‐Bromonaphthalenophane from a Desymmetrized Building Block Bearing Electrophilic and Masked Nucleophilic Functionalities

In search of 2,7‐ethylene‐bridged naphthalenophanes with desymmetrized naphthalene cores as inherently chiral cyclophanes, nucleophilic substitution of 1‐bromo‐7‐(bromomethyl)‐2‐[(trimethylsilyl)methyl]naphthalene, a desymmetrized building block bearing an electrophilic group (CH₂Br) and a masked nucleophilic functionality (CH₂TMS) which can be activated by fluoride anion, was examined. As a result, in contrast to the case of parent naphthalenophanes wherein the smallest [2.2]naphthalenophane was obtained as the major product, only [2.2.2.2](2,7)‐1‐bromonaphthalenophane was obtained albeit in low yields, whereas the corresponding [2.2]‐ or [2.2.2]naphthalenophanes were not obtained. Though the [2.2.2.2]‐1‐bromonaphthalenophane can adopt four idealized geometries of different symmetry, among which three are inherently chiral, theoretical calculations predict that three conformers have almost equal energy and may equilibrate in solution. The X‐ray crystallographic study shows that it adopts a C₂ conformation with anti,anti,anti orientation of the C?Br bonds at least as a major component in crystal.     

AIEgens/Nucleic Acid Nanostructures for Bioanalytical Applications

DNA occupies significant roles in life processes, which include encoding the sequences of proteins and accurately transferring genetic information from generation to generation. Recent discoveries have demonstrated that a variety of biological functions are correlated with DNA′s conformational transitions. The non‐B form has attained great attention among the diverse forms of DNA over the past several years. The main reason for this is that a large number of studies have shown that the non‐B form of DNA is associated with gross deletions, inversions, duplications, translocations as well as simple repeating sequences, which therefore causes human diseases. Consequently, the conformational transition of DNA between the B‐form and the non‐B form is important for biology. Conventional fluorescence probes based on the conformational transitions of DNA usually need a fluorophore and a quencher group, which suffers from the complex design of the structure and tedious synthetic procedures. Moreover, conventional fluorescence probes are subject to the aggregation‐caused quenching (ACQ) effect, which limits their application toward imaging and analyte detection. Fluorogens exhibiting aggregation‐induced emission (AIE) have attracted tremendous attention over the past decade. By taking advantage of this unique behavior, plenty of fluorescent switch‐on probes without the incorporation of fluorescent quenchers/fluorophore pairs have been widely developed as biosensors for imaging a variety of analytes. Herein, the recent progress in bioanalytical applications on the basis of aggregation‐induced emission luminogens (AIEgens)/nucleic acid nanostructures are presented and discussed.     

The stable planar conformation of the γ-butyrolactone ring in solution

<正>The conformations ofγ-butyrolactone ring in solution were deduced on the basis of ~1H NMR spectra of geminal protons of the butyrolactone ring.A series of optically pure(Z)-(-)-4-(1'-alkoxyl-1'-carbalkoxy-methylene)-5(R)[(1R)-menthyloxy]-γ-butyr-olactones with a stable planar conformation of γ-butyrolactone ring were found.     

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…     

Novel Hydrogen‐bond Three Dimensional Networks Generated from the Reaction of Metal Nitrate Hydrate (M = Co,Ni) with Ammonium Thiocynate and Bidentate Ligand Piperazine

The reaction of Co(NO₃)₂·6H₂O with two equivalents of PPz (PPz = piperazine hexahydrate) and two equivalents of NH₄SCN in CH₃OH afforded the complex [Co(NCS)₂(PPz)₂(CH₃OH)₂]. The reaction of Ni(NO₃)₂·6H₂O with two equivalents of PPz and four equivalents of NH₄SCN in CH₃OH afforded the complex [Ni(NCS)₄(PPz)₂]. Their IR spectra have been recorded and the structures have been determined. Crystal data for 1 : space group P&1bar;, a = 6.7208(6) Å, b = 8.4310(8) Å, c = 8.5923(8) Å, a = 77.881(2)°, β = 76.342(2)°, γ = 83.936(2)°, V = 461.75(1) ų, Z = 1 with final residuals R1 = 0.0650 and wR2 = 0.1725. Crystal data for 2 : space group P2(1)/n, a = 7.4209(6) Å, b = 11.0231(9) Å, c = 12.317(1) Å, β = 96.642(9)°, V = 1000.9(2) ų, Z = 2 with final residuals R1 = 0.0378 and wR2 = 0.0809. Important NCS—H‐N and O‐H—N(PPz) hydrogen‐bonding interactions in compound 1 and NCS···H‐N hydrogen‐bonding interactions and NCS—SCN interactions in compound 2 play a significant role in aligning the polymer strands in crystalline solids.     

Chains in Critical Fluids and Nanopores

Summary: The conformational behavior of a polymer in a critical binary solvent confined in a porous medium is studied. The size of the polymer in bulk, which is mainly governed by the correlation length of the solvent density fluctuations, depends on the proximity to the critical point of the binary mixture. We find that in contrast to the bulk behavior, the conformational properties of the polymer in a porous medium depends strongly on the pore size. The latter controls the correlation length of the solvent density fluctuations and thus determines the polymer size.     

X-Ray Investigation of Chiral β-Hydroxyketone Derived From (+)-Isomenthone

X-ray analysis was carried out to study the molecular structure of β-hydroxyketone, which is one of the minor products of selective aldol condensation of (−)-menthone with 4-carbomethoxybenzaldehyde. The cyclohexanone ring of the compound has a practically undistorted chair conformation with an axial orientation of the 1-methyl group and the bulkiest 2-[1′-hydroxy-1′ -(4-carbomethoxyphenyl)]methyl substituent and the equatorial orientation of the isopropyl group in the 4 position. The stereochemical configuration was found to be (1R,2R,4 R, 1′ S), supporting that the compound belongs to the group of (+)-isomenthones; i.e., the starting (-)-menthone undergoes (to a certain extent) epimerization under the reaction conditions used. In crystal, there is intermolecular hydrogen bonding >C=O...HO- (the -O...H- bond length is 2.15 Å). The molecular conformation in hydroxyketone crystals differs from the one which prevails in solutions (according to previous NMR data) and which is characterized by an inverted cyclohexanone ring and intramolecular hydrogen bonding >C=O...HO.Original Russian Text Copyright © 2004 by S. V. Shishkina, T. G. Drushlyak, L. A. Kutulya, N. S. Pivnenko, and O. V. Shishkin__________Translated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 5, pp. 933–940, September–October, 2004.