A molecular mechanics force field implemented in the Sybyl program is described along with a statistical evaluation of its efficiency on a variety of compounds by analysis of internal coordinates and thermodynamic barriers. The goal of the force field is to provide good quality geometries and relative energies for a large variety of organic molecules by energy minimization. Performance in protein modeling was tested by minimizations starting from crystallographic coordinates for three cyclic hexapeptides in the crystal lattice with rms movements of 0.019 angstroms, 2.06 degrees, and 6.82 degrees for bond lengths, angles, and torsions, respectively, and an rms movement of 0.16 angstroms for heavy atoms. Isolated crambin was also analyzed with rms movements of 0.025 angstroms, 2.97 degrees, and 13.0 degrees for bond lengths, angles, and torsions respectively, and an rms movement of 0.42 angstroms for heavy atoms. Accuracy in calculating thermodynamic barriers was tested for 17 energy differences between conformers, 12 stereoisomers, and 15 torsional barriers. The rms errors were 0.8, 1.7, and 1.13 kcal/mol, respectively, for the three tests. Performance in general purpose applications was assessed by minimizing 76 diverse complex organic crystal structures, with and without randomization by coordinate truncation, with rms movements of 0.025 angstroms, 2.50 degrees, and 9.54 degrees for bond lengths, angles and torsions respectively, and an average rms movement of 0.192 angstroms for heavy atoms.
Eine Röntgenuntersuchung des Titelkomplexes, der ein saures H‐Atom enthält und als CH, C12 ‐Monosolvat vorliegt, zeigt, daß er Sandwichstruktur hat und in der Raumgruppe P212, 2, kristallisiert.
The structure of a synthetic bile pigment, 3,8,12,17-tetraethyl-4,5-dimethoxy-2,7,13,18-tetramethyl-4,5-dihydrobilin-l,19(21 H,24H) -dione, C33H44N404, has been determined using three-dimensional diffractometer data. It crystallizes in the triclinic space group P' T with a = 12.755 (2), b = 12.944(s), c = 12.61 5(2)A, o! = 11 2.27"(2), = 11 3.76"(2), y = 75.45"(2), Z = 2. There is one-half of an n-hexane molecule of crystallization present per formula unit. The structure was solved by direct methods and refined by full-matrix least squares to yield a final R factor of 0.1 05. The compound, which could be considered as a model for the far-red form ( Pfr) of the phytochrome chromphore, belongs to the class of bile pigments known trivially as bilipurpurins. Three of the four pyrrole rings form a conjugated system which is not strictly planar, but is quasi-helical in nature. The fourth ring which is joined to the others by an sp3 carbon atom, is considerably out of the plane of the other three. Bond lengths and angles show a large degree of bond fixation. There is intermolecular hydrogen bonding so that the molecules form hydrogen-bonded dimers.
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