Molecular models building

This paper describes the first application of analogy and intelligence to molecular model building. It represents a departure from previous methods, a new approach aimed at rapid, automatic, accurate molecular model building. 

Structure Refinement. The refinement of the structure was based on an energy function approach (Brunger etal., 1987) arbitrary combinations of empirical and effective energy terms describing crystallographic data as implemented in XPLOR. Molecular model building was done on an IRIS Workstation (Silicon Graphics) with the software TOM, a version of FRODO (Jones, 1978). 

Ball-and-stick molecular-model building kit protractor drawing paper colored... 

Pencil tracing paper magazines reproductions of two-dimensional artwork using positive and negative space ruler ball-and-stick molecular-model building kit. (Comment Don t use Styrofoam balls—correct bond angle holes are needed for tetrahedral shape.)... 

Use the molecular-model building kit constructed in Activity 1.1 to make ball-and-stick models of the molecules listed on the chalkboard. The balls represent atoms and the sticks represent bonds. 

With the existence of this new cyclodextrin lock, it was again important to select a key to fit it and to serve as substrate. For this we wanted a cyclic phosphate ester that this cyclodextrin bisimidazole could hydrolyze. The enzyme ribonuclease hydrolyzes cyclic phosphates as the second step in the hydrolysis of RNA, and cyclic phosphates are used as assay substrates for the enzyme. The advantage to us of such a substrate was that the geometry of the transition state would be relatively well-defined, so that it should be possible to design congruence between the catalyst and the transition state. Molecular model building indicated that a possible substrate was the cyclic phosphate derived from 4-f-butylcatechol (VIII). Indeed, the cyclodextrin bisimidazole (VII) is a catalyst for the cleavage of cyclic phosphate (VIII) (14). 

Computer-based approaches to molecular model-building offer promise as potentially facile methods of gaining structural information about complex molecules of biological Interest. 

Molecular model-building (conformational search) methods fall into two general classes systematic and random. - Systematic methods search all possible combinations of torsional angles, whereas random methods usually involve a Monte Carlo (with Metropolis sampling ) or molecular dynamics trajectory. Both approaches attempt to search large areas of conformational space and eventually converge on the desired conformation or structure. Dis-... 

The fourth area in which we have introduced students to computational chemistry at the first year level is in the field of molecular model building and molecular mechanics. We provide exercises in which the student is required to build and optimize the molecular structure of water and of dimethyl ether using the MM2 force field. Students compare the bond angles around the O atom in the two cases and examine wire frame, ball and stick, and CPK models of the molecules. They also explore the stereoisomers of carvone. One of these stereoisomers has dill scent and the other spearmint. Samples of the two isomers are available in the laboratory where the students do the molecular modeling. 

Wipke, W. T. Hahn, M. A. Analogy and Intelligence in Molecular Model Building . In Applications Artificial Intelligence in Chemistry, Pierce, T. Hohne, B. American Chemical Society, Symposium Series No. 306, 1986, pp. 136-146. 

Stereochemically acceptable extended-chain (so-called yS-sheet) structures were first described by Pauling and Corey from molecular model building [78, 79]. In some cases, specific structures of synthetic polypeptides have been deteraiined from X-ray diffraction studies. These have provided the bases for the vibrational analyses of this class of polypeptide chain conformations. 

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