Dependency of ligand free energy landscapes on charge parameters and solvent models

We performed replica-exchange molecular dynamics (REMD) simulations of six ligands to examine the dependency of their free energy landscapes on charge parameters and solvent models. Six different charge parameter sets for each ligand were first generated by RESP and AM1-BCC methods using three different conformations independently. RESP charges showed some conformational dependency. On the other hand, AM1-BCC charges did not show conformational dependency and well reproduced the overall trend of RESP charges. The free energy landscapes obtained from the REMD simulations of ligands in vacuum, Generalized-Born (GB), and TIP3P solutions were then analyzed. We found that even small charge differences can produce qualitatively different landscapes in vacuum condition, but the differences tend to be much smaller under GB and TIP3P conditions. The simulations in the GB model well reproduced the landscapes in the TIP3P model using only a fraction of the computational cost. The protein-bound ligand conformations were rarely the global minimum states, but similar conformations were found to exist in aqueous solution without proteins in regions close to the global minimum, local minimum or intermediate states.     

2D FT-ICR MS of Calmodulin: A Top-Down and Bottom-Up Approach

Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry (2D FT-ICR MS) allows data-independent fragmentation of all ions in a sample and correlation of fragment ions to their precursors through the modulation of precursor ion cyclotron radii prior to fragmentation. Previous results show that implementation of 2D FT-ICR MS with infrared multi-photon dissociation (IRMPD) and electron capture dissociation (ECD) has turned this method into a useful analytical tool. In this work, IRMPD tandem mass spectrometry of calmodulin (CaM) has been performed both in one-dimensional and two-dimensional FT-ICR MS using a top-down and bottom-up approach. 2D IRMPD FT-ICR MS is used to achieve extensive inter-residue bond cleavage and assignment for CaM, using its unique features for fragment identification in a less time- and sample-consuming experiment than doing the same thing using sequential MS/MS experiments.

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Inclusion Complex Formation of Thiacalix[4]arene and Xe in Aqueous Solution Studied by Hyperpolarized 129Xe NMR

The inclusion complex formation of 4-sulfothiacalix[4]arene sodium salt (STCAS) and Xe has been investigated by using hyperpolarized ¹²⁹Xe NMR spectroscopy. Our new continuous-flow type hyperpolarizing system has advantageous capabilities that can supply hyperpolarized gases continuously and directly to a sample solution in a NMR tube. Consequently saturated Xe concentration in the aqueous solution of STCAS is maintained during the NMR experiment, and ¹²⁹Xe NMR spectra can be obtained in remarkably short time. STCAS concentration dependence of ¹²⁹Xe chemical shift has been analyzed in an elaborated way by a computer method as well as a simple graphic method that we have proposed. The association constant K:13.6±0.8 M⁻¹ at 25 °C was obtained, and further analysis of the temperature dependence has successfully given thermodynamic parameters of enthalpy (ΔH) and entropy (ΔS) for the inclusion complex formation: ΔH = −11.9±1.9 kJ mol⁻¹ and ΔS = −17.4±5.8 JK⁻¹ mol⁻¹. The energetic aspects of complex formation are discussed from the size effect and from the molecular theory of standard entropy, and a release of definite number of water molecules from STCAS cavity is suggested in the inclusion complex formation with Xe.     

Synthesis of a Stimuli‐Responsive P‐Chiral Polymer with Chiral Phosphorus Atoms and Azobenzene Moieties in the Main Chain

A reaction of the P‐chiral compound (S,S)‐1,2‐bis(boranato(tert‐butyl)methylphosphino)ethane with an azobenzene derivative gave stimuli‐responsive polymers with P‐chiral phosphines in the main chain. This is the first example of a stimuli‐responsive P‐chiral polymer. The polymer isomerized from the trans to the cis form upon UV irradiation and reverted to the trans form reversibly. The polymer was able to coordinate to platinum, and the resulting polymer complex exhibited the Cotton effect owing to the chirality of the phosphorus atoms. The structure of the P‐chiral polymer obtained could be changed reversibly by light and thermal stimuli, and the polymer chain was induced to rotate helically when complexed with transition metals through the chiral phosphorus atoms.     

Synthesis of Optically Active P‐Chiral and Optically Inactive Oligophosphines

A series of optically active P‐chiral oligophosphines (S,R,R,S)‐ 2 , (S,R,S,S,R,S)‐ 3 , (S,R,S,R,R,S,R,S)‐ 4 , and (S,R,S,R,S,R,R,S,R,S,R,S)‐ 5 with four, six, eight, and 12 chiral phosphorus atoms, respectively, were successfully synthesized by a step‐by‐step oxidative‐coupling reaction from (S,S)‐ 1 . The corresponding optically inactive oligophosphines 1′ – 5′ were also prepared. Their properties were characterized by DSC, XRD, and optical‐rotation analyses. While optically active bisphosphine (S,S)‐ 1 and tetraphosphine (S,R,R,S)‐ 2 behaved as small molecules, octaphosphine (S,R,S,R,R,S,R,S)‐ 4 and dodecaphosphine (S,R,S,R,S,R,R,S,R,S,R,S)‐ 5 exhibited the features of a polymer. Furthermore, DSC and XRD analyses showed that hexaphosphine (S,R,S,S,R,S)‐ 3 is an intermediate between a small molecule and a polymer. Comparison of optically active oligophosphines 1 – 5 with the corresponding optically inactive oligophosphines 1′ – 5′ revealed that the optically active phosphines have higher crystallinity than the optically inactive counterparts. It is considered that the properties of oligophosphines depend on the enantiomeric purity as well as the oligomer chain length.     

Size distribution and characteristics of chemical components in ambient particulate matter.

Ambient particulate matter and gas in Kyoto were investigated by gravimetric analysis, X-ray fluorescence spectrometry, and ion chromatography in order to clarify their behavior and origin. The size distribution and characteristics of the chemical components in ambient particulates collected on PTFE membrane filters using an Andersen air sampler were examined from August 2001 to April 2004. A four-stage filter pack method was used to sample the atmosphere for the determination of gas (SO2, HNO3, HCl, NH3) and particulate matter (SO42, NO3, Cl-, Na+, K+, Ca2+, Mg2+, NH4+) concentrations from October 2002 to April 2004. The concentration of SPM mass was in the range of 6.7 - 80.2 microg/m3. The size distributions of SPM mass were bimodal, peaking at around 0.65 - 1.1 and 3.3 - 4.7 microm, and 40 - 85% of SPM mass was fine particles (< 2.1 microm). Na, Mg, Al, Si, Ca, Cl, and Fe were mainly present in coarse particles (2.1 to 11.0 microm), while S was present in fine particles. The concentrations of Al, Si, Ca, Mg, and Fe in fine particles increased from March to April in 2002, and those in coarse particulates increased in November 2002 and from March to April in 2004. This may be the effect of the continental yellow sand "Kosa." The differences in the size distributions of Al, Si, Ca, Mg, and Fe in particles may depend on differences in their place of occurrence and course of transport from China to Japan. The concentration of HCl gas was higher than that of particulate chloride ion in summer. Nitric acid gas existed at higher concentrations in summer, but fine particulate nitrate ion was observed in winter. The gaseous-to-fine aerosol nitrate fraction became higher at warmer temperatures. Coarse sulfate was below 10%, and SO2 gas and fine particulate sulfate were above 90%.     

Synthesis of 2-, 4- and 5-(2-alkylcarbamoyl-1-methylvinyl)-7-alkyloxybenzo[b]furans and their leukotriene B4 receptor antagonistic activity

Variable benzo[b]furan derivatives having (E)- and (Z)-2-alkylcarbamoyl-1-methylvinyl groups at the 2-, 4- and 5-positions and a carboxylpropoxy or (1-phenyl)ethoxy group at the 7-position were prepared to find novel and selective leukotriene B4(LTB4) receptor antagonists. (E)-2-(2-diethylcarbamoyl-1-methylvinyl)-7-(1-phenylethoxy)benzo[b]furan (4v) showed selective inhibition to the human BLT2 receptor (hBLT2). On the other hand, (E)-2-acetyl-4-(2-diethylcarbamoyl-1-methylvinyl)-7-(1-phenylethoxy)benzo[b]furan (7v) inhibited both human BLT(1) receptor (hBLT1) and hBLT2. The (E)-2-(2-diethylcarbamoyl-1-methylvinyl) group lay on approximately the same plane as the benzo[b]furan ring, whereas the (E)-4-(2-diethylcarbamoyl-1-methylvinyl) group had the torsion angle (45.7 degree) from the benzo[b]furan ring plane. However, the (Z)-(2-alkylcarbamoyl-1-methylvinyl)benzo[b]furans were inactive. The inhibitory activity depended on the conformation of the 2-diethylcarbamoyl-1-methylvinyl group.     

Stereoselective synthesis of (Z)-fluoroalkenes directed to peptide isosteres: copper mediated reaction of trialkylaluminum with 4,4-difluoro-5-hydroxyallylic alcohol derivatives

Copper mediated alkyl-transfer reaction of trialkylaluminum (R₃Al) with (E)-4,4-difluoro-5-hydroxyallylic alcohol derivative smoothly proceeded to give the corresponding 2-alkylated 4-fluoro-5-hydroxyhomoallylic alcohol derivative with completely Z and 2,5-syn selective manner. Regio- and stereoselective conversion of the C5-hydroxyl group of the fluoroolefin thus obtained to amino group could be achieved through one-pot mesylation and azidation reaction.