Toshimichi Shibue

Gas-phase stability of double-stranded oligodeoxynucleotides and their noncovalent complexes with DNA-binding drugs as revealed by collisional activation in an ion trap

The intrinsic (gas-phase) stabilities of duplex, self-complementary oligonucleotides were measured in a relative way by subjecting the duplex precursor ions to increasing amounts of collision energy during the collisional-activated decomposition (CAD) events in an ion-trap mass spectrometer. The results are displayed as a dissociation profile, an s-shaped curve that shows the dependence of the relative abundance of the duplex on the applied collision energy. The total number of charges, the total number of base pairs, and the location of the high proton-affinity bases (i.e., G and C) are the main factors that affect the intrinsic stability of the duplex oligonucleotides. If the charge state is the same, the stability, as measured as a half-wave collision energy, E1/2, correlates well with the total number of H bonds for the duplex. The intrinsic stabilities of noncovalent complexes between duplex oligonucleotide and some DNA-binding drugs were also measured by using the newly developed method. Although duplexes are stabilized in the gas phase when they bind to drug molecules, correlations between gas-phase stabilities and the solution-binding affinities have not yet been obtained. Complexes in which the drug is bound in the minor groove must be joined tightly because they tend to dissociate in the gas phase by breaking covalent bonds of the oligonucleotide to give base loss and small sequence-ion formation. Complexes in which the drug is known to favor intercalation dissociate by breaking weak, noncovalent bonds to form single-stranded oligonucleotides although cleavage of covalent bonds of the oligonucleotide also occurs.

Topotactic conversion of β-helix-layered silicate into AST-type zeolite through successive interlayer modifications.

AST-type zeolite with a plate morphology can be synthesized by topotactic conversion of a layered silicate (β-helix-layered silicate; HLS) by using N,N-dimethylpropionamide (DPA) to control the layer stacking of silicate layers and the subsequent interlayer condensation. Treatment of HLS twice with 1) hydrochloric acid/ethanol and 2) dimethylsulfoxide (DMSO) are needed to remove interlayer hydrated Na ions and tetramethylammonium (TMA) ions in intralayer cup-like cavities (intracavity TMA ions), both of which are introduced during the preparation of HLS. The utilization of an amide molecule is effective for the control of the stacking sequence of silicate layers. This method could be applicable to various layered silicates that cannot be topotactically converted into three-dimensional networks by simple interlayer condensation by judicious choice of amide molecules.

Crystalline calcium phosphate and magnetic mineral content of Daphnia resting eggs.

Abstract Daphnia is a key crustacean zooplankton of freshwater food chains. One factor that ensures successful propagation is the Daphnia resting eggs, which are able to retain structural integrity under extreme conditions. Until recently little was known about the chemical composition, microanatomy, and physical properties of the egg itself. The current study demonstrates that the resting eggs: (1) have shells that are made up of crystalline calcium phosphate and include a honeycombed structure, and (2) contain magnetic material having properties consistent with magnetite. These properties of the resting eggs may ensure Daphnia survival in harsh environments.

Photochromic Solid Materials Based on Poly(decylviologen) Complexed with Alginate and Poly(sodium 4-styrenesulfonate)

Photochromic solid materials based on the cationic polymer poly(decylviologen) are reported. The solids were obtained by freeze-drying colloidal suspensions of nanocomplexes obtained by mixing aqueous solutions of the polycation with different solutions of polyanions such as poly(sodium 4-styrenesulfonate) or sodium alginate, at a cationic/anionic polymeric charge ratio of 0.7. The photochromic responses of the solid materials fabricated with alginate as complementary charged polyelectrolyte of the cationic polyviologen are faster than those of the solid materials fabricated with poly(sodium 4-styrenesulfonate), achieving coloration kinetics in the order of minutes, and discoloration kinetics in the order of hours for the former. Aromatic-aromatic interactions between the latter polyanion and the polyviologen may stabilize the dicationic form of the viologen derivative, increasing the necessary energy to undergo photoreduction, thus decreasing the reduction kinetics.

Comparison of the applicability of mass spectrometer ion sources using a polarity-molecular weight scattergram with a 600 sample in-house chemical library

To provide a practical guideline for the selection of a mass spectrometer ion source, we compared the applicability of three types of ion source: direct analysis in real time (DART), electrospray ionization (ESI) and fast atom bombardment (FAB), using an in-house high-resolution mass spectrometry sample library consisting of approximately 600 compounds. The great majority of the compounds (92%), whose molecular weights (MWs) were broadly distributed between 150 and 1000, were detected using all the ion sources. Nevertheless, some compounds were not detected using specific ion sources. The use of FAB resulted in the highest sample detection rate (>98%), whereas the detection rates obtained using DART and ESI were slightly lower (>96%). A scattergram constructed using MW and topological polar surface area (tPSA) as a substitute for molecular polarity showed that the performance of ESI was weak in the low-MW (<400), low-polarity (tPSA < 60) area, whereas the performance of DART was weak in the high-MW (>800) area. These results might provide guidelines for the selection of ion sources for inexperienced mass spectrometry users.

Structural characterization of "tailed picket-fence porphyrins" by high-energy fast atom bombardment collision-induced dissociation mass spectrometry/mass spectrometry

The applicability of high-energy fast atom bombardment (FAB) collision-induced dissociation mass spectrometry/mass spectrometry (CID-MS/MS) to the structural characterization of side-chains of porphyrin derivatives with a “tailed picketfence” structure was examined. These porphyrins showed a molecular ion [M]+• as well as a protonated molecule [M + H]+ and another at [M + 2]+ in the positive ion mode. Doubly-charged ions were observed when the “tail” has an imidazole ring. The linked-scan spectrometry indicated that the “tail” of the porphyrin is eliminated first as a neutral species from the pyrrole-2-position as a β-type cleavage, after which each of the four pivaloyl “picket-fences” are cleaved off in series from the remainder of the molecule-related ions. The spectrum also clearly showed charge-remote product ions in the low mass region, in addition to charge-mediated product ions representing the precise side chain structure of the “tailed picket-fence” porphyrin. FAB CID-MS/MS spectra of [M]+•, [M + 1]+ and [M + 2]+, using the EBEB-type four-sector tandem mass spectrometer, show similar fragmentation patterns to each other with 1 u difference in parallel. The CID-MS/MS of [M + 1]+ and [M + 2]+ showed higher product ion intensities than the corresponding product ion intensities of [M]+•. CID-MS/MS, using an EBEB-type four-sector tandem mass spectrometer, showed charge-remote product ions much more clearly than those observed in B/E-constant linked-scan spectra.

Water-Induced Phase Transition in Cyclohexane/n-Hexanol/Triton X-100 Mixtures at a Molar Composition of 1/16/74 Studied by NMR

Molecular aggregation in a mixture of Triton X-100/n-hexanol/cyclohexane at a molar ratio of 1/16/74 is studied upon addition of small amounts of water. The composition of organic components has been chosen at a ratio n-hexanol/cyclohexane where a well-formed hydrogen bond network has been described. The ratio Triton X-100/n-hexanol has been chosen to afford a stoichiometry of ethylene oxide (EO) residues/n-hexanol of 1/2. At these conditions the addition of water consecutively produces the appearance of three defined phases: a clear solution, a lamellar phase, and a microemulsion. The two corresponding transitions occur at water/EO/n-hexanol molar ratios of 2/1/2 (clear to lamella), and 3/1/2 (lamella to microemulsion), while phase separation occurs at a molar ratio of 4/1/2, highlighting the important role of stoichiometry. Molecular dynamics measured by 1H NMR techniques, such as DOSY, and calculations of T1 and T2 relaxation times allow distinguishing the transition between the different phases and justifying their structure. Molecular assembly in the three phases is organized around hydrogen bond networks in which the hydroxyl groups of both TX-100 and n-hexanol, ethylene oxide groups of TX-100, and water participate. 1D 1H NMR spectral changes correlate with the different characteristics of the different phases. As the main characteristics of the lamellar phase we find a very restricted mobility of the molecules involved, and water chemical shifts in 1D 1H NMR spectra of around 5.0 ppm, higher than that of bulk water appearing at 4.7 ppm.

Stability of Water/Poly(ethylene oxide)43-b-poly(ε-caprolactone)14/Cyclohexanone Emulsions Involves Water Exchange between the Core and the Bulk

The formation of emulsions upon reverse self-association of the monodisperse amphiphilic block copolymer poly(ethylene oxide)43-b-poly(ε-caprolactone)14 in cyclohexanone is reported. Such emulsions are not formed in toluene, chloroform, or dichloromethane. We demonstrate by magnetic resonance spectroscopy the active role of the solvent on the stabilization of the emulsions. Cyclohexanone shows high affinity for both blocks, as predicted by the Hansen solubility parameters, so that the copolymer chains are fully dissolved as monomeric chains. In addition, the solvent is able to produce hydrogen bonding with water molecules. Water undergoes molecular exchange between water molecules associated with the polymer and water molecules associated with the solvent, dynamics of major importance for the stabilization of the emulsions. Association of polymeric chains forming reverse aggregates is induced by water over a concentration threshold of 5 wt %. Reverse copolymer aggregates show submicron average hydrodynamic diameters, as seen by dynamic light scattering, depending on the polymer and water concentration.

Prediction of adducts on positive mode electrospray ionization mass spectrometry: proton/sodium selectivity in methanol solutions.

We used positive mode electrospray ionization (ESI) mass spectrometry to examine 540 in-house high-resolution mass spectrometry (HRMS) samples that formed an adducted positive ion. Of the 540 samples, the sodium adduct ([M + Na]+) was detected in 480 samples, and the protonated molecule ([M + H]+) was detected in 92 samples; both [M + Na]+ and [M + H]+ were detected in 32 samples. No other adduct ions were predominant. The selectivities of these adducts were evaluated by a two-dimensional plot using topological polar surface area (tPSA) and molecular weight. Two predominant trends were observed: [M + H]+ converged around tPSA (Å2) = 20 and molecular weight = 250, and the selectivity for [M + Na]+ correlated with the tPSA value. These observations were found to be related to the elemental composition of the sample compounds. From the results obtained by positive mode ESI mass spectroscopy under our experimental conditions, predominant trends were observed with respect to adduct selectivity: compounds containing oxygen atom(s) form [M + Na]+, and compounds containing nitrogen but not oxygen atom(s) form [M + H]+. Based on these trends, we developed the “Nitrogen–Oxygen rule” (NO rule) to predict the adduct formed by a given compound on positive mode ESI. This NO rule provides a guideline to estimate elemental composition using ESI-HRMS with methanol as mobile phase.

Structural Insights into a Hemoglobin–Albumin Cluster in Aqueous Medium

A hemoglobin (Hb) wrapped covalently by three human serum albumins (HSAs) is a triangular protein cluster designed as an artificial O2-carrier and red blood cell substitute. We report the structural insights into this Hb-HSA3 cluster in aqueous medium revealed by 3D reconstruction based on cryogenic transmission electron microscopy (cryo-TEM) data and small-angle X-ray scattering (SAXS) measurements. Cryo-TEM observations showed individual particles with approximately 15 nm diameter in the vitrified ice layer. Subsequent image processing and 3D reconstruction proved the expected spatial arrangements of an Hb in the center and three HSAs at the periphery. SAXS measurements demonstrated the monodispersity of the Hb-HSA3 cluster having a molecular mass of 270 kDa. The pair-distance distribution function suggested the existence of oblate-like particles with a maximum dimeter of ∼17 nm. The supramolecular 3D structure reconstructed from the SAXS intensity using an ab initio procedure was similar to that obtained from cryo-TEM data.