Rotational spectra of the deuterated carbon chain molecules: C3D, C4D, C3HD, and C4HD

The rotational spectra of the deuterated carbon chain molecules, C₃D, C₄D, C₃HD, and C₄HD, have been measured with the Fourier transform microwave (FTMW) spectrometer. The C₃D and C₄D radicals are produced by discharging the DCCD gas diluted in Ar. On the other hand, the gaseous mixture of HCCH, DCCD, and HCCD diluted in Ar is used for producing C₃HD and C₄HD. For C₃D, the molecular constants are determined from a joint least-squares analysis with the previously published millimeter- and submillimeter-wave data by considering the vibronic interaction between the ²Π ground state and the low-lying ²Σ vibronic state. The molecular constants of C₄D are determined by use of the conventional Hamiltonian of the ²Σ radical, while the effective rotational constant and centrifugal distortion constant are derived for C₃HD and C₄HD. In the present study, the hyperfine interaction constants of the deuterium nuclei in C₃D and C₄D are determined accurately. In particular, the nuclear quadrupole interaction constant, eQq, of the C₃D radical is found to be significantly smaller than those of C₂D and C₄D, indicating that C₃D has a floppy motion of the CCD bending mode due to the large Renner-Teller effect.     

Mesoscopic biology

In this paper we present a qualitative outlook of mesoscopic biology where the typical length scale is of the order of nanometers and the energy scales comparable to thermal energy. Novel biomolecular machines, governed by coded information at the level of DNA and proteins, operate at these length scales in biological systems. In recent years advances in technology have led to the study of some of the design principles of these machines; in particular at the level of an individual molecule. For example, the forces that operate in molecular interactions, the stochasticity involved in these interactions and their spatio-temporal dynamics are beginning to be explored. Understanding such design principles is opening new possibilities in mesoscopic physics with potential applications.     

Theoretical study of two C50H40 isomers with three dodecahedrane cages sharing two pentagons

Structures, energies, and vibrational frequencies have been calculated for two C₅₀H₄₀ isomers with three dodecahedrane cages sharing two pentagons at the B3LYP/6‐31G* level of theory. Thus, two C₅₀H₄₀ isomers have the form of coplanar tri‐dodecahedrane‐cage molecules. The symmetry of one isomer is D_5d and that of another is C_2V. Heats of formation and vertical ionization energies for two C₅₀H₄₀ isomers have been estimated in this study. Heats of formation as well as vibrational analysis indicate that two C₅₀H₄₀ isomers enjoy sufficient stability to allow for its experimental preparation. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Single‐molecule Spectroscopy: Exploring Heterogeneity in Chemical and Biological Systems

Many chemical and biological systems are heterogeneous in the molecular length scale (～ 1 nm). Heterogeneity in many chemical systems and organized assemblies may be monitored using single‐molecule spectroscopy (SMS). In SMS, the size of the focal spot (i.e., the smallest region to be probed) is nearly half of the excitation wavelength (λ/2, i.e., 200–375 nm) for visible light (400–750 nm). We discuss how one can get spatial resolutions better than 200 nm using molecules as nanometric probes. We show that polymer hydrogels, lipid vesicles, room temperature ionic liquids (RTILs), and binary liquid mixtures exhibit such heterogeneity. Another important observation is solute‐dependent friction in RTILs. In an RTIL, diffusion of an ionic solute is slower than that of a neutral solute.     

Attracting cavities for docking. Replacing the rough energy landscape of the protein by a smooth attracting landscape

Molecular docking is a computational approach for predicting the most probable position of ligands in the binding sites of macromolecules and constitutes the cornerstone of structure‐based computer‐aided drug design. Here, we present a new algorithm called Attracting Cavities that allows molecular docking to be performed by simple energy minimizations only. The approach consists in transiently replacing the rough potential energy hypersurface of the protein by a smooth attracting potential driving the ligands into protein cavities. The actual protein energy landscape is reintroduced in a second step to refine the ligand position. The scoring function of Attracting Cavities is based on the CHARMM force field and the FACTS solvation model. The approach was tested on the 85 experimental ligand–protein structures included in the Astex diverse set and achieved a success rate of 80% in reproducing the experimental binding mode starting from a completely randomized ligand conformer. The algorithm thus compares favorably with current state‐of‐the‐art docking programs. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Functionalized carbon nanotubes and nanofibers for biosensing applications

This review summarizes recent advances in electrochemical biosensors based on carbon nanotubes (CNTs) and carbon nanofibers (CNFs) with an emphasis on applications of CNTs. CNTs and CNFs have unique electric, electrocatalytic and mechanical properties, which make them efficient materials for developing electrochemical biosensors.We discuss functionalizing CNTs for biosensors. We review electrochemical biosensors based on CNTs and their various applications (e.g., measurement of small biological molecules and environmental pollutants, detection of DNA, and immunosensing of disease biomarkers). Moreover, we outline the development of electrochemical biosensors based on CNFs and their applications. Finally, we discuss some future applications of CNTs.     

Measurement of the differences in electrophoretic mobilities of individual molecules of E. coli beta-galactosidase provides insight into structural differences which underlie enzyme microheterogeneity

The electrophoretic mobility and catalytic activity of individual molecules of Escherichia coli beta-galactosidase were measured using CE-LIF detection. Both the mobility and activity were reproducible for each molecule but differed between individual molecules. Assays were performed using uncoated capillaries and capillaries coated with different polymers, using enzymes from different sources and by three different experimental protocols. In all cases the observed ranges in electrophoretic mobilities were similar. The observed range in the electrophoretic mobility may be explained by structural microheterogeneity resulting in a gain or loss of up to 1.6 suppressed charge units. There was no observed relationship between the observed activities and electrophoretic mobilities. If the finding that individual beta-galactosidase molecules have heterogeneous electrophoretic mobility can be extended to other proteins, this may limit the resolution possible for capillary zone electrophoresis protein separations.     

2-酰胺-6-乙酰基吡啶类化合物的微波合成及其晶体结构

2,6-二甲基吡啶经氧化、酯化、Claisen酯缩合后制得新型化合物2-乙酯基-6-乙酰基吡啶(4), 用其作为前驱体, 与一系列小分子脂肪胺: 甲胺、乙胺、乙二胺在微波条件下生成3个吡啶酰胺化合物5, 6, 7. 通过元素分析, ¹H NMR, IR和MS对这些化合物进行了表征. 对6-乙酰基-N-甲基吡啶-2-甲酰胺(5)的X射线晶体衍射研究表明: 其属于正交晶系, Pca2(1)空间群, 晶胞参数a＝2.2784(2) nm, b＝0.4350(4) nm, c＝0.9267(3) nm; α＝β＝γ＝90°; D_c＝1.288 Mg•m^－3, V＝0.91856(14) nm³. 实验还发现: 2-乙酯基-6-乙酰基吡啶与脂肪胺及芳香胺缩合时会发生两类不同的反应, 小分子脂肪胺选择与酯基发生胺解反应, 而芳香胺则率先在乙酰基上发生席夫碱缩合. 对这两类有趣的反应机理进行了深入探讨.     

Molecular modeling on pyruvate phosphate dikinase of Entamoeba histolytica and in silico virtual screening for novel inhibitors

Pyruvate phosphate dikinase (PPDK) is the key enzyme essential for the glycolytic pathway in most common and perilous parasite Entamoeba histolytica. Inhibiting the function of this enzyme could control the wide spread of intestinal infections caused by Entamoeba histolytica in humans. With this objective, we modeled the three dimensional structure of the PPDK protein. We used templates with 51% identity and 67% similarity to employ homology-modeling approach. Stereo chemical quality of protein structure was validated by protein structure validation program PROCHECK and VERIFY3D. Experimental proof available in literature along with the in silico studies indicated Lys21, Arg91, Asp323, Glu325 and Gln337 to be the probable active sites in the target protein. Virtual screening was carried out using the genetic docking algorithm GOLD and a consensus scoring function X-Score to substantiate the prediction. The small molecule libraries (ChemDivision database, Diversity dataset, Kinase inhibitor database) were used for screening process. Along with the high scoring results, the interaction studies provided promising ligands for future experimental screening to inhibit the function of PPDK in Entamoeba histolytica. Further, the phylogeny study was carried out to assess the possibility of using the proposed ligands as inhibitors in related pathogens.     

Synthesis and characterization of lower generation broom molecules

Dendritic molecules with dodecyl groups as the hyperbranchs were synthesized in methanol by Michael addition with dodecylamine and methyl acrylate as raw materials. This new-type dendritic molecules were called vividly ＂broom molecules＂ in this report. The surface tension of the aqueous solution of broom molecule terminated amino group was measured by using the dropvolume method. The demulsification performance of the broom molecules for the oil/water （O/W） simulated crude oil emulsion was examined. The experimental results revealed that, as a new-type of surfactants, the broom molecules terminated amino groups showed demulsification for the O/W simulated crude oil emulsion. 2007 Jun Wang. Published by Elsevier B.V. on behalf of Chinese Chemical Society. All fights reserved.