Field programming

Molecular mechanics calculations with the molecular mechanics force field program were performed to compare thermodynamic stability among araguspongine B (17) (containing two cw-fused perhydropyrido[2,l-Z>] [l,3]oxazine bicycles), araguspongine D (18) (containing two tran -fused perhydropyrido[2,l-Z)][l,3]oxazine bicycles), and araguspongine E (19)... 

DFTB has been combined with various force field programs, including CHARMM [49], Amber [50, 51], SIGMA [52], TINKER [34] and GROMACS (to be published). All these combined methods have used the same strategy for the interface with respect to the treatment of bonding interactions at the interface and non-bonded Coulomb and van der Waals (vdW) terms. The concepts will not be reviewed in detail here, for this purpose we would like to refer to an excellent and extensive recent review [4],... 

Molecular mechanics methods achieve good structural accuracy for classical molecules, whereas their reliability for species with particular combinations of atoms may be questionable, particularly for molecules containing heteroatoms, which affect geometry and conformation via the position of their lone-pairs. Force-field programs, for example, often fail to calculate the geometry... 

An early attempt to resolve the discrepancy between the high values of Sugimura and Suzuki (1988) and more traditional analyses failed to reach a definitive conclusion (Williams, 1992). The start of the Joint Global Ocean Flux Study (JGOFS) field program with the North Atlantic Bloom Experiment in 1989 put additional pressure on the various groups to resolve this issue quickly. The National Science Foundation (NSF) and the National Oceanic and Atmospheric Administration (NOAA) funded a workshop held in Seattle in July 1991 to resolve the issue. 

CONFl. Simple force field program released by QCPE (35). MUB-2. Bartell s latest version of his modified Urey-Bradley force field model (36). 

MOLECULAR BUILDER. One of the earliest successful MM programs by Boyd (37) has been used as a prototype of several other force field programs. For example, a modified version is in-... 

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Monitoring sites were selected in northwestern Pennsylvania, central Ohio, western Maryland, and southern West Virginia. The field program was conducted between June and September 1973. Ozone was measured at each of the four sites, and precursor concentrations were measured at... 

Despite the above-mentioned features, ThFFF is not as widespread or popular as SEC. One possible reason is that calibration constants are only available for a very limited number of polymer-solvent systems. On the contrary, the SEC practitioner has available an extensive collection of Mark-Houwink constants for the different polymers, solvent types, and operating temperatures. In recent years, signihcant advances have been made in ThFFF calibration under isothermal conditions using a polydisperse standard as an alternative to a series of monodisperse standards. Recently, the calibration function was also made applicable to ThFFF field programming operation [32],... 

For many years, cosmochemistry depended on the chance discovery of meteorites - either witnessed falls and serendipitous finds, or the dogged determination of a few private collectors who systematically searched for them. That changed in 1969, when Japanese explorers in Antarctica led by Masaru Yoshida stumbled onto meteorites exposed on bare ice. American geologist William Cassidy immediately recognized an opportunity, and with support from the National Science Foundation he mounted a joint expedition with the Japanese to the Allan Hills region of Antarctica in 1977 to recover meteorites. This was the first of many expeditions, sponsored by the National Science Foundation and headed first by Cassidy and later by Ralph Harvey, that have returned to Antarctica every year to collect meteorites (Fig. 1.11). The Japanese have operated a parallel field program in... 

The molecular structures used in the calculations were optimized using a molecular force field program. The force field parameters were derived from various sources The bond length was taken into accound according to a model of Dewar and Llano (7). The VALBOND method of Root et al. (8) was used for the calculation of bond angels. The dihedral angles were parametrized according to the PIMM method (9). 

In principle, the force field does not have to be an integral part of the program, though most of the packages used include a basic force field. Programs that have been used in the area of inorganic chemistry and that have been shown to lead to reliable results... 

The MM2 program [52] is by faf the most widely used force field program in the area of hydrocarbon or moderately polar molecules and numerous publications have demonstrated its usefulness. Still the anomeric center had not until recently been properly defined by the force field parameters. Now there are parameters available which include the proper treatment of acetal fragments and hence reproduce the anomeric as well as the exo anomeric effect accurately [53]. Due to the full optimization of the geometry the MM2 program can treat only a limited number of atoms. 

A series of simplified force fields was created by Rasmussen et al. [56, 57]. The PEF400 [58] and PEF300 (potential energy function) and variants here of are used for the calculation of disaccharides and monosaccharides (cf. below). The parametri-sation of this force field program includes atomic charges which (in variant PEF422) differ for the anomeric carbon and the other carbon atoms. The parametrization is obtained from ab initio calculations. 

Cellobiose is also in the focus of interest with respect to its conformational features. Rasmussen et al. [87] used the PEF300 force field program and they calculated for P-D-cellobiose five conformers at the glycosidic bond within 3 kcal/mol, namely... 

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