Force-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... 

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-... 

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... 

A vast amount of empirical molecular potential energy functions and a series of corresponding programs (molecular mechanics and consistent force field programs) are available (for recent reviews see 203 205)). Unfortunately these energy functions are always the result of optimization on a rather limited group of compounds. No... 

Constant force field provides for highest resolution of particles in the sample with resulting highest precision. However, characterization of samples with wide size distributions is difficult and time consuming. Force field programming [89,90] removes these limitations to ensure that the entire distribution can be analyzed in a convenient time. In time delayed exponential decay the initial force field is held constant for a time equal to r and after this the force field is decayed exponentially with a time constant r. In this mode, a log-linear relationship is obtained of particle mass against retention time. This simple relationship permits a convenient calculation of the quantitative information needed for the sample. Retention time is given by ... 

DMA models have also been incorporated into the molecular modeling force field program MOMO, ° which was used to study host-guest complexes, such as benzene in a hexaoxacyclophane host. The difficult problem of accurately modeling the intramolecular electrostatic energy of proteins has also used distributed-multipole-type models. ... 

Conversion Tools for Connection Between Different Force-Field Programs Using CPECM. ... 

J. J. Kirkland, C. H. Dilks, S. W. Rementer, and W. W. Yau. Asymmetric-channel flow fleld-flow fractionation with exponential force-field programming. J. Chromatogr. 593 339 (1992). 

Force-field programming commonly is used in the SdFFF characterization of many colloidal particles to ensure that the entire particle-size distribution can be described in a convenient analysis time (10, 15). Constant force-field operation provides for the highest resolution of particles in the sample, with resulting highest precision. However, this mode of operation does not permit the rapid optimization of operating parameters for analyzing many samples. Also, characterization of samples with wide particle-size distributions is difficult with constant force-field operation. Force-field programming removes these limitations and provides a convenient and practical compromise for most applications. 

Beck, H., Egert, E., 1988, Force-Field-Program MOMO, Univ. Gottingen... 

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