On the mechanisms of spatial electron relaxation in nonisothermal plasmas

The impact of different collision processes of the electrons with the gas atoms on their spatial relaxation under the action of space-independent electric fields is analyzed in a weakly ionized, collision-dominated helium plasma. Based on the numerical solution of the one-dimensional inhomogeneous electron Boltzmann equation, the spatial evolution of the electron velocity distribution function and of the related macroscopic quantities is investigated for different models concerning the treatment of the elastic, exciting, and ionizing collision processes. The spatial relaxation into homogeneous states is initiated by a disturbance which is directly imposed on the electron velocity distribution as a boundary condition. At moderate and higher electric fields this disturbance excites spatially periodic structures in the distribution function which are damped out by special mechanisms inherent in the exciting and ionizing collision processes. With decreasing field strength the damping due to the energy loss in elastic collisions becomes more effective and causes at lower fields an aperiodic establishment into homogeneous states.     

局域平衡假设和反应-扩散过程

局域平衡假设作为不可逆过程热力学理论的基础通常被认为适用于一般条件下的物理化学过程。本文从玻耳兹曼方程和涨落的随机理论出发重新研究了局域平衡假设对反应—扩散过程的适用性。表明对于涉及非线性化学动力学的反应—扩散过程, 从随机理论得到的结果和局域平衡假设是不一致的。     

Nonuniform charge scaling (NUCS): a practical approximation of solvent electrostatic screening in proteins

In molecular mechanics calculations, electrostatic interactions between chemical groups are usually represented by a Coulomb potential between the partial atomic charges of the groups. In aqueous solution these interactions are modified by the polarizable solvent. Although the electrostatic effects of the polarized solvent on the protein are well described by the Poisson--Boltzmann equation, its numerical solution is computationally expensive for large molecules such as proteins. The procedure of nonuniform charge scaling (NUCS) is a pragmatic approach to implicit solvation that approximates the solvent screening effect by individually scaling the partial charges on the explicit atoms of the macromolecule so as to reproduce electrostatic interaction energies obtained from an initial Poisson--Boltzmann analysis. Once the screening factors have been determined for a protein the scaled charges can be easily used in any molecular mechanics program that implements a Coulomb term. The approach is particularly suitable for minimization-based simulations, such as normal mode analysis, certain conformational reaction path or ligand binding techniques for which bulk solvent cannot be included explicitly, and for combined quantum mechanical/molecular mechanical calculations when the interface to more elaborate continuum solvent models is lacking. The method is illustrated using reaction path calculations of the Tyr 35 ring flip in the bovine pancreatic trypsin inhibitor.     

Hybrid boundary element and finite difference method for solving the nonlinear Poisson-Boltzmann equation

A hybrid approach for solving the nonlinear Poisson-Boltzmann equation (PBE) is presented. Under this approach, the electrostatic potential is separated into (1) a linear component satisfying the linear PBE and solved using a fast boundary element method and (2) a correction term accounting for nonlinear effects and optionally, the presence of an ion-exclusion layer. Because the correction potential contains no singularities (in particular, it is smooth at charge sites) it can be accurately and efficiently solved using a finite difference method. The motivation for and formulation of such a decomposition are presented together with the numerical method for calculating the linear and correction potentials. For comparison, we also develop an integral equation representation of the solution to the nonlinear PBE. When implemented upon regular lattice grids, the hybrid scheme is found to outperform the integral equation method when treating nonlinear PBE problems. Results are presented for a spherical cavity containing a central charge, where the objective is to compare computed 1D nonlinear PBE solutions against ones obtained with alternate numerical solution methods. This is followed by examination of the electrostatic properties of nucleic acid structures.     

Quinoxalines XIV. Synthesis, H, C, N NMR spectroscopic, and quantum chemical study of 1H-pyrazolo[3,4-b]quinoxalines (flavazoles)

The synthesis of a series of 1H-pyrazolo[3,4-b]quinoxalines (flavazoles) by acylation, alkylation, halogenation, and aminomethylation of the parent compound is reported and their structure is investigated by ¹H, ¹³C, and ¹⁵N NMR spectroscopy. The restricted rotation about the partial C, N double bond of the N-acyl derivatives 7-10 is studied by dynamic NMR spectroscopy and the barriers to rotation are determined. In order to assign unequivocally the ¹⁵N chemical shifts of N-4 and N-9, in case of 3-substituted flavazoles, exemplary the ¹H, ¹³C, and ¹⁵N NMR chemical shifts of 34, 35, and 39 are also theoretically calculated by quantum chemical methods [ab initio at different levels of theory (HF/6-31G* and B3LYP/6-31G*)].     

Quantification of cephalexin as residue levels in bovine milk by high-performance liquid chromatography with on-line sample cleanup

A multidimensional, selective and precise high performance liquid chromatography (HPLC) method based on direct injection of biological samples has been developed for the determination of cephalexin in skimmed and whole bovine milk. The cephalosporin antibiotic was extracted from bovine milk using an octyl restricted access medium bovine serum albumin column (C₈-RAM-BSA) and analyzed on an octadecyl column using phosphate buffer (pH 7.5, 0.01 M): ACN (92:8, v/v) and ultraviolet detection at 260 nm. The calibration graph was linear in the concentration range of 25-1600 ng/mL and this is in accordance with the tolerance level of 100 ng/mL set by the FDA (Food and Drug Administration) and EU (European Union) for cephalexin as residue in bovine milk. The intra- and inter-day coefficients of variation for the replicate analysis at the quality control levels were less than 15% while the transfer efficiency was in the range of 90.2-92.3%. The limits of detection and quantification were 10 and 20 ng/mL, respectively.     

A restricted active space (RAS) SCF study of the lifetime of theA 3Π state of OH+

Summary Restricted Active Space (RAS) SCF calculations have been performed of the potential curves for theX ^3– andA ³ states of the OH⁺ ion and on the lifetime of thev=0–2 vibrational levels of theA state. The convergence of the transition moment integral as a function of the size of the active orbital space was used to select the active orbitals. The calculated value of thev=0 lifetime is 2.4 µs. An estimate of the errors remaining in the calculation leads to a final theoretical value of 2.7±0.1 µs. Computed bond distances and bond energies are 1.031 (1.029) Å and 5.05 (5.01) eV, respectively, for theX state, and 1.137 (1.135) Å and 1.57 eV, respectively, for theA state (experimental values within parenthesis).On leave from Departamento de Quimica Fisica, Universitat de València, Dr. Moliner 50, Burjassot, 46 100 València, Spain     

Support Vector Machines for predicting HIV protease cleavage sites in protein

Knowledge of the polyprotein cleavage sites by HIV protease will refine our understanding of its specificity, and the information thus acquired is useful for designing specific and efficient HIV protease inhibitors. The pace in searching for the proper inhibitors of HIV protease will be greatly expedited if one can find an accurate, robust, and rapid method for predicting the cleavage sites in proteins by HIV protease. In this article, a Support Vector Machine is applied to predict the cleavability of oligopeptides by proteases with multiple and extended specificity subsites. We selected HIV-1 protease as the subject of the study. Two hundred ninety-nine oligopeptides were chosen for the training set, while the other 63 oligopeptides were taken as a test set. Because of its high rate of self-consistency (299/299 = 100%), a good result in the jackknife test (286/299 = 95%) and correct prediction rate (55/63 = 87%), it is expected that the Support Vector Machine method can be referred to as a useful assistant technique for finding effective inhibitors of HIV protease, which is one of the targets in designing potential drugs against AIDS. The principle of the Support Vector Machine method can also be applied to analyzing the specificity of other multisubsite enzymes.     

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations

In a recent article (Lee, M. S.; Salsbury, F. R. Jr.; Brooks, C. L., III. J Chem Phys 2002, 116, 10606), we demonstrated that generalized Born (GB) theory provides a good approximation to Poisson electrostatic solvation energy calculations if one uses the same definitions of molecular volume for each. In this work, we present a new and improved analytic method for reproducing the Lee-Richards molecular volume, which is the most common volume definition for Poisson calculations. Overall, 1% errors are achieved for absolute solvation energies of a large set of proteins and relative solvation energies of protein conformations. We also introduce an accurate SASA approximation that uses the same machinery employed by our GB method and requires a small addition of computational cost. The combined methodology is shown to yield an efficient and accurate implicit solvent representation for simulations of biopolymers.     

Combining restricted access material (RAM) and turbulent flow for the rapid on-line extraction of the cyclooxygenase-2 inhibitor rofecoxib in plasma samples

Restricted access material (RAM) has been used in the packing of a solid-phase extraction (SPE) column for on-line extractions under turbulent flow conditions. The bio-compatible RAM material works by the principle of size exclusion in addition to conventional reversed-phase chromatography, thereby allowing the extraction and preconcentration of small analyte molecules from biological samples such as plasma. Using small column dimensions (0.76 mm x 50 mm) and a consequently high linear velocity, turbulent flow was achieved during online sample extractions. The improved mass-transfer rate characteristic of turbulent flow allows fast sample cleanup without decreased extraction efficiency. The novel use of the RAM column, connected upstream to a C18 monolithic column, allowed the direct injection, extraction, separation, and MS/MS detection of plasma samples spiked with rofecoxib in a span of 5 min. Calibration curves obtained using this RAM turbulent flow coupled column method showed good linearity (R2 > 0.99) and reproducibility (%RSD < or = 7%). The lower limit of quantitation of rofecoxib in plasma samples was found to be 40 ng/ml. The extraction method showed good recovery of rofecoxib from a plasma matrix with minimal signal loss and robustness after more than 200 plasma injections.