Quantitative Auger electron spectroscopy analysis with co-evaporated AuCu films

A method for the quantitative Auger electron spectroscopy (AES) analysis by using a co-evaporation technique is extended to the AuCu system following the previous work. The calibration curves for lower Auger energy have peaks at 60 eV for Cu and at 69 eV for Au, and for higher Auger energy peaks at 239 eV for Au and at 920 eV for Cu. It is found that a simple linear relation does not exist in the results for AES measurements and the bulk analysis by atomic absorption spectroscopy (AAS) because of the back-scattering effect and the overlap of the spectra at lower energies in the Au-Cu system. It is also found that the adsorption of oxygen caused by electron beam bombardment has a significant influence on the AES results. The calibration curves obtained after a correction for oxygen adsorption are successfully applied to the determination of the composition at the surface of a sputtered AuCu alloy.     

Evaluation of homology modeling of the severe acute respiratory syndrome (SARS) coronavirus main protease for structure based drug design

To accelerate the development of drugs against severe acute respiratory syndrome (SARS), we constructed a homology model of the SARS coronavirus main protease using our modeling software, FAMS Ligand&Complex, and released it before the X-ray structure was solved. The X-ray structure showed our model as accurately predicted and useful for structure based drug design.     

Photoisomerization of stilbene dendrimers: the need for a volume-conserving isomerization mechanisms

Highly branched stilbene dendrimers were synthesized and their photochemical behavior was studied. Even the stilbene dendrimer with molecular weight over 6500 underwent trans-cis isomerization in the excited singlet state within the lifetime of 10 ns. The photoisomerization of C=C double bond of stilbene dendrimers in the excited state may proceed by a volume-conserving novel mechanism such as hula-twist rather than conventional 180 degrees rotation around the C=C double bond based on fluorescence and isomerization experiments.     

Thionation of N‐(ω‐Halogenoalkyl)‐Substituted Amides with Lawesson's Reagent: Facile Synthesis of 4,5‐Dihydro‐1,3‐thiazoles and 5,6‐Dihydro‐4H‐1,3‐thiazines

The thionation and cyclization of N‐(ω‐halogenoalkyl)‐substituted amides (and related compounds) with Lawesson's reagent (LR=2,4‐bis(4‐methoxyphenyl)‐1,3,2,4‐dithiadiphosphetane 2,4‐disulfide) has been investigated. Treatment of the amides 1 with LR gave the corresponding thioamides 2 in moderate to good yields (Table). The latter, upon treatment with base, afforded, either in a separate step or in a one‐pot procedure, the cyclized title compounds, i.e., the 4,5‐dihydro‐1,3‐thiazoles 3 or the corresponding 5‐6‐dihydro‐4H‐thiazines 4 via dehydrohalogenation.     

Dynamic flexibility of a peptide-binding groove of human HLA-DR1 class II MHC molecules: normal mode analysis of the antigen peptide-class II MHC complex

Class II major histocompatibility complex (MHC) has tolerance for binding longer antigen peptides than those bound by class I MHC. In this paper, a normal mode analysis on HLA-DR1 class II MHC involving an antigen peptide indicated that the peptide-binding groove had some different dynamic characteristics from that of HLA-A2 class I MHC. The dynamic changes in the class I groove with removal of the bound peptide were limited primarily to the central region and the C-terminal side (corresponding to the C-terminal side of the bound peptide) of the groove, while the dynamic changes in the class II groove with removal of the bound peptide extended to the whole of the groove, and were especially remarkable around a strand located in the N-terminal side (corresponding to the N-terminal side of the bound peptide) of the groove. These results suggest that the N-terminal side of the class II groove is more flexible than the same side of the class I groove, and this flexibility may allow some N-terminal residues of the bound peptide to extend outside the class II groove. Definite anti-correlative motions with removal of the bound peptide appeared between two alpha-helical regions of class II MHC as in the case of class I MHC. These motions of the class II groove may play an important role in obtaining "a flexible dynamic fit" against diverse longer peptides both of whose terminals extend outside the groove.     

High-resolution analysis by nano-electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for the identification of molecular species of phospholipids and their oxidized metabolites

Nano-electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS) was applied to identify the molecular species of phosphatidylethanolamine of Caenorhabditis elegans, which has a high concentration of phospholipids with a fatty acyl chain having an odd number of carbon atoms. The molecular species of diacyl phosphatidylethanolamine with one fatty acyl chain having an odd number of carbon atoms and one fatty acyl chain having an even number of carbon atoms was identified separately from alkyl-acyl phosphatidylethanolamine with an alkyl chain having an even number of carbon atoms and a fatty acyl chain having an even number of carbon atoms. Furthermore, nano-ESI-FTICRMS was applied to the direct identification of oxidized phosphatidylcholine from soybean. The mass peaks of individual molecular species of oxidative phosphatidylcholine, such as 34:3 diacyl phosphatidylcholine with peroxide (+2O) (m/z 788.544) or 34:2 diacyl phosphatidylcholine with peroxide (+2O) (m/z 790.560), can be separated from the peaks of the molecular species of the non-oxidative phospholipids. This suggests that the mass peaks with a difference of less than 0.1 mass units in their molecular weight can be separated and that their individual exact molecular compositions can be obtained by the FTICRMS analysis. The high resolution and high accuracy of FTICRMS are very effective in the analysis of molecular species of phospholipids and their derivatives.     

Secondary ion emission processes of sputtered alkali ions from alkali/Si(100) and Si(111)

The secondary alkali ion yield vs. the work function change (Δφ) of Na, K and Cs/Si(100) and Si(111) was measured to discuss the details of secondary ion emission processes. In the case of alkali/metal systems, the secondary ion emission is explained by the electron tunneling model. In this model, the ionization of the ejected atom occurs as a result of electron resonant tunneling through the potential barrier separating an atom and a metal, and the secondary ion yield depends on exponentially the work function change of metal surface. For alkali/Si(100) systems, the secondary ion emission processes are explained in terms of the electron tunneling model since the secondary alkali ion yield vs. the work function change (Δφ) follows the exponential manner. However, it is not easy to apply the simple electron tunneling model to our experimental results for alkali/Si(111) systems. There is the essential difference in surface structures between Si(100) and Si(111). Therefore, it is suggested that the local electronic environment around the adsorbates might be taken into consideration for alkali/Si(111) systems.     

Influence of N-Substituents on Photovoltaic Properties of Singly Bay-Linked Dimeric Perylene Diimides

The influence of N-substituents on the photovoltaic properties of singly bay-linked perylene diimides (diPDIs) was systematically investigated to understand the aromatic-aliphatic balance, which is beneficial for achieving high device performance in organic photovoltaic (OPV) systems. The synthesis of various N-substituted diPDIs was successfully achieved using a newly developed one-step procedure, resulting in sufficiently high yields. Detailed investigations of seven variants of diPDIs demonstrated that the primary alkyl substituents, particularly the 2-ethylhexyl group, induce the self-organized growth of thin films with high crystallinity. This is beneficial for enhancing the device performance of bulk heterojunction (BHJ) systems. The results presented herein reveal the important roles of alkyl side chains as hydrophobic solubilizing auxiliaries or primary determinants in the control of the active layer nanomorphology. This offers a valuable guideline that is essential for developing high-performance organic semiconductor materials for future practical applications.