Introduction of a new scale into reversed-phase high-performance liquid chromatography of pyridylamino sugar chains for structural assignment

Addition of a monosaccharide residue to a pyridylaminated (PA)-N-linked sugar chain results in an increment or decrement in the elution time on reversed-phase HPLC, the difference being defined as the partial elution time of the residue. Based on this principle, an empirical rule was deduced, which states that the elution time is roughly equal to the sum of the partial elution times of the component sugar residues [Anal. Biochem., 167 (1987) 321–326]. In practice, however, some partial elution times obtained from different pairs of mother PA-sugar chains are found to deviate, and consequently the closeness of the elution times of PA-sugar chains calculated therefrom to the observed times is reduced in such cases. To improve the reliability of the additivity rule and to generalize elution times so that they are less dependent on minor alterations in the elution conditions, we have devised a new scale for elution time, which we have named a reversed-phase scale. The elution times on the reversed-phase scale (the R values) are read from a conversion curve constructed using the elution times of eight selected standard PA-sugar chains. The partial elution times on the reversed-phase scale of 22 monosaccharide residues were calculated from the R values of 93 PA-sugar chains. The R values obtained by summing the partial elution times of all the component monosaccharide residues became much closer to the R values obtained from the reversed-phase scale, compared to the results obtained using the previous method. In addition, the R values were less influenced by minor change in the elution conditions. These features of the new scale allow more accurate structural assignment of sugar chains.     

Inelastic scattering dynamics of Ar from a perfluorinated self-assembled monolayer surface

Dynamics of Ar atom collisions with a perfluorinated alkanethiol self-assembled monolayer (F-SAM) surface on gold were investigated by classical trajectory simulations and atomic beam scattering techniques. Both explicit-atom (EA) and united-atom (UA) models were used to represent the F-SAM surface; in the UA model, the CF3 and CF2 units are represented as single pseudoatoms. Additionally the nonbonded interactions in both models are different. The simulations show the three limiting mechanisms expected for collisions of rare gas atoms (or small molecules) with SAMs, that is, direct scattering, physisorption, and penetration. Surface penetration results in a translational energy distribution, P(Ef), that can be approximately fit to the Boltzmann for thermal desorption, suggesting that surface accommodation is attained to a large extent. Fluorination of the alkanethiol monolayer leads to less energy transfer in Ar collisions. This results from a denser and stiffer surface structure in comparison with that of the alkanethiol SAM, which introduces constraints for conformational changes which play a significant role in the energy-transfer process. The trajectory simulations predict P(Ef) distributions in quite good agreement with those observed in the experiments. The results obtained with the EA and UA models are in reasonably good agreement, although there are some differences.     

Theoretical study of the molecular structure and normal coordinate analysis of hydrogen cyanide addition compound with boron trifluoride, HCN-BF(3)

An extensive HF, MP2, B3LYP and CCSD study of the molecular structure and normal vibrations have been performed for the HCN-BF(3) molecule. Calculations with a wide range of basis sets were classified into two groups based on the optimized N-B bond distance. The results for Group A are compared with the experimental structure of the solid phase molecules. The N-B lengths of Group A are approximately linear related to the N-B-F valence angles and also to the N-B stretching frequencies. HF/DZV calculation was used to represent the solid phase model. The N-B lengths of Group B are close to those of the gas phase molecule and both N-B-F angles and N-B sensitive frequencies have roughly the same values. Differences in the chemical bond between gaseous and solid phase HCN-BF(3) are discussed based on the calculated force constants, vibrational frequencies and potential energy distributions. Vibration mode analysis indicates that the nu(4) mode in the 600-700 cm(-1) region can be assigned to the BF(3) symmetric deformation, which shifts upon (10)B/(11)B isotopic substitution. The nu(5) mode which is insensitive to isotope substitution and changes band position with the N-B distance is assigned to the N-B bond stretching vibration.     

Manipulation of cell-sized phospholipid-coated microdroplets and their use as biochemical microreactors

Cell-sized water droplets coated by a phospholipid layer mimicking the inner surface of living cells were manipulated by laser tweezers and used as biochemical microreactors. The cell-sized phospholipid-coated microdroplets (CPMDs) consisted of a water droplet in mineral oil with a diameter of 1-100 microm and coated by 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine. We monitored the time development of biochemical reactions in a single CPMD obtained after the controlled fusion of two CPMDs containing a substrate and an enzyme, respectively. We present results on two enzymatic reactions: calcein production in the presence of esterase and green fluorescence protein expression.     

Rapid geometrical equilibrium of palladium(II) complexes with tris[2-(diphenylphosphino)ethyl]phosphine disulfide and diselenide and their catalytic activity for Suzuki coupling reaction

Palladium(II) complexes with a tetradentate pseudo-tripodal ligand having two phosphino groups and two phosphine sulfide or selenide groups, pp₃X₂ (pp₃ = tris[2-(diphenylphosphino)ethyl]phosphine, X = S (1) or Se (2)), were prepared from [PdCl(pp₃)]Cl. Both of these phosphine chalcogenide complexes 1 and 2 showed rapid equilibrium between the five-coordinate [PdCl(pp₃X₂)]Cl with two bound phosphine chalcogenide groups and four-coordinate [PdCl₂(pp₃X₂)] with two dissociated pendant ones in chloroform. The thermodynamic parameters for the reaction, [PdCl(pp₃X₂)]⁺ + Cl⁻?[PdCl₂(pp₃X₂)], were obtained by low-temperature ³¹P NMR as follows: K²⁹⁸ = 3.7 × 10³ and 5.4 × 10² mol⁻¹, ΔH^° = 11.3 ± 0.3 and 13.4 ± 0.4 kJ mol⁻¹, and ΔS^° = 106 ± 2 and 97 ± 2 J mol⁻¹ K⁻¹ for 1 and 2, respectively. The rate for the geometrical change at 246.7 K for 1 was appreciably faster than that for 2. These thermodynamic and kinetic results indicate that the phosphine selenide Se atoms can stabilize the five-coordinate structure by effective π-back donation from Pd(II) compared with the phosphine sulfide S atoms. Difference in retention of the catalytic activity for Suzuki coupling, 2 > 1 > [PdCl(pp₃ or p₃)]Cl, was explained by difference in the π-accepting ability that stabilizes the catalytically active Pd(0) species. Considering the rapid dissociation-coordination equilibrium of the phosphine chalcogenide groups on Pd(II), it is probable that the oxidative addition and the subsequent transmetallation of the Pd(II) species are hardly blocked by the phosphine chalcogenide groups.     

The clinical usefulness of preoperative dynamic MRI to select decompression levels for cervical spondylotic myelopathy

The study subjects included 54 patients with cervical spondylotic myelopathy who underwent a selective laminoplasty. The patients were divided into three groups according to the number of decompressed levels: two levels, three levels and four or five levels. The number of cord compressions at every intervertebral level was determined in the flexion, neutral, and extension position using a dynamic magnetic resonance imaging (MRI) scan in consideration of both static and dynamic compressions. For each group, the clinical outcomes were evaluated. Moreover, the patients were divided into two groups according to their age. Then, the appearance ratios of cord compression between the neutral and extension position were compared at each intervertebral level. The clinical outcomes were satisfactory. There were no statistical differences among the three groups, except for the age and operation time. The position of the neck influenced the number of cord compressions. The appearance ratios of cord compression, which were especially prominent at C2/3, C3/4 and C4/5, showed high scores in the aged. The preoperative dynamic MRI scan was clinically useful. In the aged, attention should be given to C2/3, C3/4 and C4/5.     

The infrared fundamental intensities and polar tensor of allene.

The polar tensor of allene was calculated from the infrared fundamental band intensities of C3H4 and C3D4. The ambiguities in the signs of the dipole moment derivatives with respect to their normal coordinates were resolved by comparison of tensor elements with ab initio calculations at the B3LYP, MP2(FC) and CCD(FC) levels with a 6/311 + + G(3d,3p) basis set. The results are similar to those previously obtained by Koga and co-workers except for the choice of an average of two sign combinations for the E symmetry elements. The values of the mean dipole moment derivatives for the sp and sp2 carbon atoms obtained in this work, 0.032 and -0.133 e, respectively, are in good agreement with the CCD(FC)/6-311 + + G(3d,3p), 0.061 and -0.128 e, and MP2(FC)/6-311 + + G(3d,3p), 0.072 and -0.153 e, theoretical results. The mean dipole moment derivatives are shown to be consistent with potential models relating 1s electron ionization energies and atomic charges.     

Vectorization of the general Monte Carlo classical trajectory program VENUS

The general chemical dynamics computer program VENUS is used to perform classical trajectory simulations for large polyatomic systems, with many atoms and complicated potential energy functions. To simulate an ensemble of many trajectories requires a large amount of CPU time. Since each trajectory is independent, it is possible to parallel process a large set of trajectories instead of processing the trajectories by the conventional sequential approach. This enhances the vectorizability of the VENUS program, since the integration of Hamilton's equations of motion and the gradient evaluation, which comprise 97.8% of the CPU, can each be parallel processed. In this article, the vectorization and ensuing optimization of VENUS on the CRAY-YMP and IBM-3090 are presented in terms of both global strategies and technical details. A switching algorithm is designed to enhance the vector performance and to minimize the memory storage. A performance of 140 MFLOPS and a vector/scalar execution rate ratio of 10.6 are observed when this new version of VENUS is used to study the association of CH₃ with the H(Ar)₁₂ cluster on the CRAY-YMP.