Protein adsorption in fused-silica and polyacrylamide-coated capillaries

The model proteins cytochrome c, myoglobin, ovalbumin, and beta-lactoglobulin were investigated with regard to their adsorption properties on capillaries for electrophoresis. The model compounds were selected to cover a wide range of properties. Cytochrome c is a basic protein (isoelectric point (pI): 9.6; M(r): 11.7 kDa), beta-lactoglobulin is rather acidic (pI: 5.4, M(r): 18.4 kDa), myoglobin was chosen as a neutral reference protein (pI: 6.8-7.4, M(r): 17.8 kDa), and ovalbumin (pI: 5.1, M(r): 45.0 kDa) was selected as a relatively larger analyte. First, the pH dependence of adsorption was investigated for the bare fused silica. A clear correlation to the respective pIs was noted. For myoglobin and ovalbumin, none or negligible adsorption was found above the pI, whereas strong adsorption was noted just below this parameter. Cytochrome c and beta-lactoglobulin already showed distinct adsorption above their pIs. However, none of the proteins showed any significant adsorption more than one pH unit above the pIs. For linear polyacrylamide-coated capillaries, a decreased but not a complete lack of adsorption was observed. Here, pH-dependent adsorption was noted as well. Regeneration of the capillaries by rinsing with buffers containing 200 mM SDS was also investigated. This method was completely successful for myoglobin, but that too for only freshly-adsorbed protein. After a storage time of 24 h and due to the aging of the adsorbate, a sufficient regeneration was no longer possible.     

Kinetics studies of aqueous phase reactions of Cl atoms and Cl2(-) radicals with organic sulfur compounds of atmospheric interest

A laser flash photolysis-long path UV-visible absorption technique has been employed to investigate the kinetics of aqueous phase reactions of chlorine atoms (Cl) and dichloride radicals (Cl2(-)) with four organic sulfur compounds of atmospheric interest, dimethyl sulfoxide (DMSO; CH3S(O)CH3), dimethyl sulfone (DMSO2; CH3(O)S(O)CH3), methanesulfinate (MSI; CH3S(O)O-), and methanesulfonate (MS; CH3(O)S(O)O-). Measured rate coefficients at T = 295 +/- 1 K (in units of M(-1) s(-1)) are as follows: Cl + DMSO, (6.3 +/- 0.6) x 10(9); Cl2(-) + DMSO, (1.6 +/- 0.8) x 10(7); Cl + DMSO2, (8.2 +/- 1.6) x 10(5); Cl2(-) + DMSO2, (8.2 +/- 5.5) x 10(3); Cl2(-) + MSI, (8.0 +/- 1.0) x 10(8); Cl + MS, (4.9 +/- 0.6) x 10(5); Cl2(-) + MS, (3.9 +/- 0.7) x 10(3). Reported uncertainties are estimates of accuracy at the 95% confidence level and the rate coefficients for MSI and MS reactions with Cl2(-) are corrected to the zero ionic strength limit. The absorption spectrum of the DMSO-Cl adduct is reported; peak absorbance is observed at 390 nm and the peak extinction coefficient is found to be 5760 M(-1) cm(-1) with a 2sigma uncertainty of +/-30%. Some implications of the new kinetics results for understanding the atmospheric sulfur cycle are discussed.     

Zur Ermittlung der Äthylen-Sequenzlängenverteilung und der chemischen Uneinheitlichkeit in Copolymeren mit Propylen durch Pyrolyse-Gas-Chromatographie

Pyrolysis coupled with gas chromatography has been applied to investigate the sequence distribution in copolymers of ethylene and propylene. The copolymers analyzed have been prepared with soluble Ziegler-Natta-catalysts and show different degrees of crystallinity. In one series of samples the methyl group of the propylene units has been labeled with tritium. It was then possible to detect carbons by flame ionization detector and simultaneously the methyl groups by the radio-detector in parallel. Within the errors of these methods the results from both detectors are consistent with the calculations from kinetics. The accuracy of the data is best in copolymers with long ethylene sequences. By GPC fractionation a heterogeneity in the chemical composition can be observed. One component of the copolymers is of high molecular weight, while the other has a molecular weight of less than 1000 and is very rich in ethylene. The influence of chemical heterogeneity on sequence distribution derived from kinetics and pyrolysis has been discussed. A mechanism in which chains with different chemical composition are growing from different species of the catalyst has been proposed. The experimental results show that the heterogeneity is not critical for the sequence analysis by kinetics and pyrolysis.     

Initial applications of an exponential multi-reference wavefunction ansatz

Initial applications of a new exponential multi-reference wavefunction ansatz [M. Hanrath, J. Chem. Phys. 123 (2005) 084102] are reported. The proposed ansatz is based on the state universal ansatz of Jeziorski and Monkhorst [B. Jeziorski, H.J. Monkhorst, Phys. Rev. A 24 (1981) 1668] and uses a reference specific cluster operator with a determinant based indexing. The approach is Fermi vacuum invariant, size consistent, insensitive with respect to intruder states and converges to full CI with an increasing cluster operator excitation level. Applications on the H₄ and H₈ model systems are reported.     

Principles of rapid polymerase chain reactions: mathematical modeling and experimental verification

Polymerase chain reaction (PCR) is an important diagnostic tool for the amplification of DNA. The PCR process can be treated as a problem in biochemical engineering. This study focuses on the development of a mathematical model of the polymerase chain reaction. The PCR process consists of three steps: denaturation of target DNA, annealing of sequence-specific oligonucleotide primers and the enzyme-catalyzed elongation of the annealed complex (primer:DNA:polymerase). The denaturation step separates the double strands of DNA; this model assumes denaturation is complete. The annealing step describes the formation of a primer-fragment complex followed by the attachment of the polymerase to form a ternary complex. This step is complicated by competitive annealing between primers and incomplete fragments including primer-primer reactions. The elongation step is modeled by a stochastic method. Species that compete during the elongation step are deoxynucleotide triphosphates dCTP, dATP, dTTP, dGTP, dUTP, and pyrophosphate. Thermal deamination of dCTP to form dUTP is included in the model. The probability for a species to arrive at the active site is based on its molar fraction. The number of random insertion events depends on the average processing speed of the polymerase and the elongation time of the simulation. The numerical stochastic experiment is repeated a sufficient number of times to construct a probability density distribution (PDF). The moment of the PDF and the annealing step products provide the product distribution at the end of the elongation step. The overall yield is compared to six experimental values of the yield. In all cases the comparisons are very good.     

The absolute sign of J coupling constants determined using the order matrix calculation

A novel methodology using the order matrix calculation to determine the absolute sign of spin-spin couplings based on the structure of organic compounds is presented. The sign of the residual dipolar coupling (RDC) depends on the sign of corresponding scalar spin-spin coupling constant and the sign of the RDC has a dramatic influence on the order matrix calculation. Therefore, the sign of the spin-spin coupling constant can be obtained by an order matrix calculation through the corresponding RDC. Six types of spin-spin coupling constants, including 2J(H,H), 1J(C,F), 2J(C,F), 3J(C,F), 2J(F,H) and 3J(F,H), were obtained simultaneously. Except for 3J(C,F) where the measured RDCs have very small magnitudes, the signs were determined unambiguously.     

Location of type B carbonate ion in type A-B carbonate apatite synthesized at high pressure

The structure of a complex, disordered type A-B carbonate apatite (CAp) of approximate composition Ca₁₀(PO₄)_6−y(CO₃)_x+(3/2)y(OH)_2−2x, x-0.7, y-0.6, synthesized at 3 GPa, 1400°C has been determined using single-crystal X-ray diffraction and FTIR spectroscopy at room temperature and pressure. Crystal data are: hexagonal, space group P6₃/m, Z=1; a=9.5143(3), c=6.8821(2) Å, V=539.5 Å³, and R=0.025. There are three structural locations for the carbonate ion. The channel carbonate is mainly in the closed vertical configuration of the structure, with two of its oxygen atoms close to the c-axis (A1 carbonate; IR bands at 1541 and 1449 cm⁻¹), but subordinate amounts are also located in an open vertical configuration (A2 carbonate; IR bands at 1563 and 1506 cm⁻¹). The type B carbonate ion is located close to the sloping faces of the PO₄ tetrahedron (IR bands at 1474 and 1406 cm⁻¹), confirming earlier inferences from polarized IR spectra.     

On the Couette-Taylor instability in ferrohydrodynamics

A theory for the stabilizing influence of an axial external magnetic field on a magnetic colloid engaged in cylindrical Couette flow is presented. For the case of a narrow gap, analytical expressions which predict the magnetic field dependences of the critical wavelength and the critical Taylor number at the onset of cellular Taylor flow are obtained.     

The inclusion of electrostatic hydration energies in molecular mechanics calculations

Summary The problem of including solvent effects in molecular mechanics calculations is discussed. It is argued that the neglect of charge-solvent (solvation) interactions can introduce significant errors. The finite difference Poisson-Boltzmann (FDPB) method for calculating electrostatic interactions is summarized and is used as a basis for introducing a new pairwise energy term which accounts for charge-solvent interactions. This term acts between all pairs of atoms usually considered in molecular mechanics calculations and can be easily incorporated into existing force fields. As an example, a parameterization is developed for the CHARMm force field and the results compared to the predictions of the FDPB method. An approach to the realistic incorporation of solvent screening into force fields is also outlined.     

The Adamantane Rearrangement of 1,2endo-Trimethylenenorbornane. Preliminary communication

1,2endo-Trimethylenenorbornane (1) in the presence of aluminium bromide in carbon disulfide at ?60° isomerizes at a much higher rate than its 2exo-isomer 2 to 2endo, 6endo-trimethylenenorbornane (3) as the sole product. By consequence, the hydrocarbon 2 being the next intermediate in the sequence of the adamantane rearrangement of 1 seems to be very unlikely.