Infrared spectroscopy of SO2 aqueous solutions

The chemistry of SO2 solutions was studied with infrared transmission and total internal reflection (ATR) spectroscopy. The cross-sections of the SO2 stretching vibrations v1, v3 and the combination band of v1 + v3 were obtained and found to be slightly different from their gas phase values. Six features we associate with sulfur-containing ions were observed. We present the first infrared evidence for the bisulfite ion HOSO2- through detection of its OH stretching vibration. Other features may be associated with HSO3-, another isomer of the bisulfite ion, and a new compound we propose to be H2S2O6(2-). We found no evidence for sulfurous acid H2SO3.     

On the structure of water—alcohol and ammonia—alcohol protonated clusters

Collision-induced dissociation (CID) of protonated ammonia-alcohol and water-alcohol heteroclusters was studied using a triple quadrupole mass spectrometer with a corona discharge atmospheric pressure ionization source. CID results suggested that the ammonia-alcohol clusters had NH: at the core of the cluster and that hydrogen-bonded alcohol molecules solvated this central ion. In contrast, CID results in water-alcohol clusters showed that water loss was strongly favored over alcohol loss and that there was a preference for the charge to reside on an alcohol molecule. The results also indicated that a loose chain of hydrogen-bonded molecules was formed in the water-alcohol clusters and that there appeared to be no rigid protonation site or a fixed central ion. (J Am Soc Mass     

Structures and properties of linear Cn molecules

Total energies, bond lengths, charge distributions, electronic configurations, and cohesive energies are calculated for linear C_n clusters, n = 2–6. The calculations are done at the single determinant Hartree-Fock level using both double-zeta and double-zeta plus polarization basis sets.     

DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases

In this paper we describe the search strategies developed for docking flexible molecules to macomolecular sites that are incorporated into the widely distributed DOCK software, version 4.0. The search strategies include incremental construction and random conformation search and utilize the existing Coulombic and Lennard-Jones grid-based scoring function. The incremental construction strategy is tested with a panel of 15 crystallographic testcases, created from 12 unique complexes whose ligands vary in size and flexibility. For all testcases, at least one docked position is generated within 2 Å of the crystallographic position. For 7 of 15 testcases, the top scoring position is also within 2 Å of the crystallographic position. The algorithm is fast enough to successfully dock a few testcases within seconds and most within 100 s. The incremental construction and the random search strategy are evaluated as database docking techniques with a database of 51 molecules docked to two of the crystallographic testcases. Incremental construction outperforms random search and is fast enough to reliably rank the database of compounds within 15 s per molecule on an SGI R10000 cpu.     

A modular model of the crystal structure of the pyrochlore-murataite polysomatic series

This paper reports on the results of a structural investigation of an important group of synthetic compounds with derivative structures of the mineral murataite, a potential matrix for immobilization of radioactive wastes. A model describing the structure of the entire group of compounds is proposed on the basis of analyzing the results obtained using chemical (electron microprobe) analysis methods, high-resolution transmission electron microscopy (high-resolution electron images and microdiffraction patterns), and X-ray diffractometry of a large array of artificial murataite ceramics. In essence, the proposed structural model is as follows: in the structure, layers of two (pyrochlore and murataite) packing types alternate along the [111] direction of the cubic supercell, so that the resulting structures can undergo substitutional and displacive modulations. Experiments on irradiation of different murataite modifications with heavy ions demonstrate that these modifications have close values of the radiation resistance, which is higher than that of the pyrochlore coexisting with them.     

Eulerian–Lagrangian localized adjoint methods for reactive transport with biodegradation

The microbial degradation of organic contaminants in the subsurface holds significant potential as a mechanism for in-situ remediation strategies. The mathematical models that describe contaminant transport with biodegradation involve a set of advective–diffusive–reactive transport equations. These equations are coupled through the nonlinear reaction terms, which may involve reactions with all of the species and are themselves coupled to growth equations for the subsurface bacterial populations. In this article, we develop Eulerian–Lagrangian localized adjoint methods (ELLAM) to solve these transport equations. ELLAM are formulated to systematically adapt to the changing features of governing partial differential equations. The relative importance of retardation, advection, diffusion, and reaction is directly incorporated into the numerical method by judicious choice of the test functions that appear in the weak form of the governing equation. Different ELLAM schemes for linear variable–coefficient advective–diffusive–reactive transport equations are developed based on different operator splittings. Specific linearization techniques are discussed and are combined with the ELLAM schemes to solve the nonlinear, multispecies transport equations. © 1995 John Wiley & Sons, Inc.