Alkali metal ion binding to glutamine and glutamine derivatives investigated by infrared action spectroscopy and theory

The gas-phase structures of alkali-metal cationized glutamine are investigated by using both infrared multiple photon dissociation (IRMPD) action spectroscopy, utilizing light generated by a free electron laser, and theory. The IRMPD spectra contain many similarities that are most consistent with glutamine adopting nonzwitterionic forms in all ions, but differences in the spectra indicate that the specific nonzwitterionic forms adopted depend on metal-ion identity. For ions containing small alkali metals, the metal ion is solvated predominantly by the amino group, the carbonyl oxygen of the carboxylic acid group, and the carbonyl oxygen of the amide group. With increasing alkali-metal-ion size, additional structures are present in which the carboxylic acid group donates a hydrogen bond to the amino group and the metal ion is solvated only by the amide and carboxylic acid groups. The effects of alkylation of the amino and amide groups on the proton affinity of isolated glutamine and the relative zwitterion stability of sodiated glutamine were examined computationally. Methylation of the amino group increases the proton affinity of isolated glutamine and preferentially stabilizes the zwitterionic form of sodiated glutamine by roughly 20 kJ/mol. Ethylation and isopropylation of the amide group each increase the proton affinity of isolated glutamine by roughly 13 kJ/mol but preferentially stabilize the zwitterionic form of sodiated glutamine by less than 3 kJ/mol. These results indicate that effects of proton affinity on relative zwitterion stability compete with effects of metal-ion solvation.     

Sample-distance partial least squares: PLS optimized for many variables,with application to CoMFA

Summary Three-dimensional molecular modeling can provide an unlimited number m of structural properties. Comparative Molecular Field Analysis (CoMFA), for example, may calculate thousands of field values for each model structure. When m is large, partial least squares (PLS) is the statistical method of choice for fitting and predicting biological responses. Yet PLS is usually implemented in a property-based fashion which is optimal only for small m. We describe here a sample-based formulation of PLS which can be used to fit any single response (bioactivity). SAMPLS reduces all explanatory data to the pairwise distances among n sample (molecules), or equivalently to an n-by-n covariance matrix C. This matrix, unmodified, can be used to fit all PLS components. Furthermore, SAMPLS will validate the model by modern resampling techniques, at a cost independent of m. We have implemented SAMPLS as a Fortran program and have reproduced conventional and cross-validated PLS analyses of data from two published studies. Full (leaveach-out) cross-validation of a typical CoMFA takes 0.2 CPU s. SAMPLS is thus ideally suited to structure-activity analysis based on CoMFA fields or bonded topology. The sample-distance formulation also relates PLS to methods like cluster analysis and nonlinear mapping, and shows how drastically PLS simplifies the information in CoMFA fields.Abbreviations PLS partial least squares - SAMPLS sample-distance partial least squares - CoMFA comparative molecular field analysis.     

New high-temperature superconductor Bi4Sr4CaCu3O14+x . Crystal structure and defectiveness of cationic sublattice

Crystal structure of a new high-temperature superconductor Bi₄Sr₄CaCu₃O_14+x is determined (AgK_α, a=5.411(2), b=5.417(3), c=27.75(1) Å, space group Pbmm, R=8.80%, R_w=11.92%, 248 F(hkl)). The structure has two types of copper-oxygen layers with diverse coordination of oxygen to Cu. The separate BiO layers of the (BiO)₂ double layer differ in structure. Percolation methods are used to relate superconductive properties of the new superconductor to defectiveness of its cationic sublattice.     

C64H6的结构和光谱的理论研究

本文用INDO系列方法研究了C64H6的结构与光谱, 表明C64H6有C2v和Cs两种稳定构型, 其中C2v构型能量较低, 讨论其加成及环加成产物对称性的规律并与13C NMR谱的实验结果相结合。计算了两种构型的电子光谱, 对电子跃迁进行了理论指认,并讨论了C64H6谱带红移的原因, 理论计算结果与实验事实基本吻合。     

A direct-to-biology high-throughput chemistry approach to reactive fragment screening

Methods for rapid identification of chemical tools are essential for the validation of emerging targets and to provide medicinal chemistry starting points for the development of new medicines. Here, we report a screening platform that combines ‘direct-to-biology’ high-throughput chemistry (D2B-HTC) with photoreactive fragments. The platform enabled the rapid synthesis of >1000 PhotoAffinity Bits (HTC-PhABits) in 384-well plates in 24 h and their subsequent screening as crude reaction products with a protein target without purification. Screening the HTC-PhABit library with carbonic anhydrase I (CAI) afforded 7 hits (0.7% hit rate), which were found to covalently crosslink in the Zn²⁺ binding pocket. A powerful advantage of the D2B-HTC screening platform is the ability to rapidly perform iterative design–make–test cycles, accelerating the development and optimisation of chemical tools and medicinal chemistry starting points with little investment of resource.

A photoreactive fragment screening platform employing direct-to-biology high-throughput chemistry (D2B-HTC) for the rapid iterative synthesis and screening of libraries of photoaffinity bits.     

氢原子在Ru(0001)和Ru(1010)面上吸附扩散势能面的结构

本文构造了H-Ru相互作用的五参数Morse势,用经典的对势方法研究了氢原子在Ru(0001)和Ru(1010)面上的吸附和扩散,得到了氢原子在两个表面上的吸附位、吸附几何、结合能及本征振动等数据与实验结果符合得很好;同时研究了两个体系的吸附扩散势能面结构。     

Neuromelanins Isolated from Different Regions of the Human Brain Exhibit a Common Surface Photoionization Threshold

Neuromelanin isolated from the premotor cortex, cerebellum, putamen, globus pallidus and corpus callosum of the human brain is studied by scanning probe and photoelectron emission microscopies and the results are compared with previously published work on neuromelanin from the substantia nigra. Scanning electron microscopy reveals common structure for all neuromelanins. All exhibit spherical entities of diameters between 200 and 400 nm, composed of smaller spherical substructures, ∼30 nm in diameter. These features are similar to that observed for many melanin systems including Sepia cuttlefish, bovine eye, and human eye and hair melanosomes. Photoelectron microscopy images were collected for all neuromelanins at specific wavelengths of ultraviolet light between 248 and 413 nm, using the spontaneous emission output from the Duke free electron laser. Analysis of the data establishes a common threshold photoionization potential for neuromelanins of 4.7 ± 0.2 eV, corresponding to an oxidation potential of −0.3 ± 0.2 V vs the normal hydrogen electrode (NHE). These results are consistent with previously reported potentials for neuromelanin from the substantia nigra of 4.5 ± 0.2 eV (−0.1 ± 0.2 V vs NHE). All neuromelanins exhibit a common low surface oxidation potential, reflecting their eumelanic component and their inability to trigger redox processes with neurotoxic effect.     

Infrared spectroscopy of hydrated amino acids in the gas phase: protonated and lithiated valine

We report here infrared spectra of protonated and lithiated valine with varying degrees of hydration in the gas phase and interpret them with the help of DFT calculations at the B3LYP/6-31++G** level. In both the protonated and lithiated species our results clearly indicate that the solvation process is driven first by solvation of the charge site and subsequently by formation of a second solvation shell. The infrared spectra of Val x Li+ (H2O)4 and Val x H+ (H2O)4 are strikingly similar in the region of the spectrum corresponding to hydrogen-bonded stretches of donor water molecules, suggesting that in both cases similar extended water structures are formed once the charge site is solvated. In the case of the lithiated species, our spectra are consistent with a conformation change of the amino acid backbone from syn to anti accompanied by a change in the lithium binding from a NO coordination to OO coordination configuration upon addition of the third water molecule. This change in the mode of metal ion binding was also observed previously by Williams and Lemoff [J. Am. Soc. Mass Spectrom. 2004, 15, 1014-1024] using blackbody infrared radiative dissociation (BIRD). In contrast to the zwitterion formation inferred from results of the BIRD experiments upon addition of a third water molecule, our spectra, which are a more direct probe of structure, show no evidence for zwitterion formation with the addition of up to four water molecules.