Model builders

This section describes briefly some of the basic concepts and methods of automatic 3D model builders. However, interested readers are referred to Chapter II, Section 7.1 in the Handbook, where a more detailed description of the approaches to automatic 3D structure generation and the developed program systems is given. 

The first task was the aeation of large 3D chemical structure databases. By devising so-called fast Automatic 3D model builder, software such as the CORINA [27, 28] and CONCORD [29, 30] programs resulted in a boom in 3D database development (see Section 2.9 in this book and Chapter II, Section 7.1 in the Handbook). A subsequent step was the development of fast... 

Model Builder lo get a reasonable starting geometry, with the possibility of refilling the geometry by sem i-empirical calculations before submitting it to ah initio computation. 

ZIXDO/S is parameteri/ed to reproduce spectroscopic transitions, therefore we do not recommend using this method for geometry optim i/ation. You can obtain better results by performing a single-point calculation wuth ZIXDO/S on a geometry obtained from the Model Builder, an optim Ization iisln g one of IlyperChem s oth er methods, or an external source. 

A restrain t (not to be confused with a Model Builder constraint) is a nser-specified one-atom tether, two-atom stretch, three-atom bend, or four-atom torsional interaction to add to the list ol molec-11 lar mechanics m teraction s computed for a molecule. These added iiueraciious are treated no differently IVoin any other stretch, bend, or torsion, except that they employ a quadratic functional form. They replace no in teraction, on ly add to the computed in teraction s. 

Use the HyperChem Model Builder to construct an approximate geometry. If you want to look at the relative energies of a set of molecules, you may want to carry out the calculations using fully optimized molecular geometries. These geometry optimization calculations can use either molecular mechanics or quantum mechanics to further refine the molecular geometry beyond that given by the Model Builder. 

Nickel and its alloys form another important class of non-ferrous metals (Table 1.3). The superb creep resistance of the nickel-based superalloys is a key factor in designing the modern gas-turbine aero-engine. But nickel alloys even appear in a model steam engine. The flat plates in the firebox must be stayed together to resist the internal steam pressure (see Fig. 1.3). Some model-builders make these stays from pieces of monel rod because it is much stronger than copper, takes threads much better and is very corrosion resistant. 

The missing link between the constitution of a molecule and its 3D structure in computahonal chemistry is a technique capable of automatically generating 3D models starhng from the connectivity information of a given molecule. Due to its basic role, 3D structure generation is one of the fundamental problems in computahonal chemistry. As a consequence, in recent years a number of automahc 3D model builders and conformer generators have become available. For two comprehensive reviews, see Refs. [3, 4]. 

Numerical methods. Computer-intensive numerical methods like quantum mechanics, molecular mechanics, or distance geometry [8] do not normally fall into the scope of automatic model builders. However, some model builders have built-in fast geometry optimization procedures or make use of distance geometry in order to generate fragment conformations. 

Clearly, there is no sharp border between all of the concepts discussed above. Most model builders try to use at least some of them in an efficient mixture in order to achieve the best compromise between computation times and quality. 

Sadowski,., Gasteiger,. From atoms and bonds to three-dimensional atomic coordinates automatic model builders. Chm. Rev. 1993, 7, 2567-2581. 

Sadowski, J., Gasteiger, J., Klebe, G. Comparison of automatic three-dimensional model builders using 639 X-ray structures. J. Chem. Inf. Comput. Sci. 1994, 34,1000-1008. 

It is not possible to extract in a direct way theoretical information on the model. It is to be considered as an empirical model builder such as a spline or polynomial fitting procedure. 

This paper describes a new approach to building molecular models using methods of expert systems. We are applying symbolic reasoning to a problem previously only approached numerically. The goals of this project were to develop a rapid model builder that mimicked the manual process used by chemists. A further aim was to provide a justification for the model as a chemist would justify a particular conformation. The AIMS algorithm reported here is extremely fast and has a complexity that increases linearly with the number of atoms in the model. 

A significant goal is to have our model builder explain and... 

Sadowski, J., Gasteiger, J. and Klebe, G. (1994) Comparison of Automatic 3-Dimensional Model Builders Using 639 X-Ray Structures. Journal of Chemical Information and Computer Sciences, 34. 1000-1008. 

Sadowski, J. and Gasteiger, J. (1993) From atoms and bonds to 3-dimensional atomic coordinates — Automatic model builders. Chemical Reviews, 93, 2567—2581. 

Michael Schrage Right. It may be not be appropriate for certain kinds of model builders to focus on user interfaces because that is not how modelers are trained. There are two things going on. There is designing for the better model versus better access. An experimentalist might get useful information from what the modeler would consider to be junk. 

Figure 14.11. Construction of biopolymer with HyperChem. Two menus are available for creating 3D structure models in HyperChem. The Build menu provides tools for creating organic molecules. Use the Drawing tool to sketch atoms in a molecule and connect them with covalent bonds. Invoke the Model builder to create a 3D structure from the 2D sketch. The Databases menu offers tools for creating biopolymers from residues with user specified linkages and conformations—that is, polysaccharides from monosaccharides, polypeptides form amino acids, and polynucleotides from nucleotides. A double-stranded DNA chain, for example, is constructed from nucleotide residues in a desired conformation (the inset).

Comparison of Automatic Three-Dimensional Model Builders Using 639 X-Ray Structures. 

Use only high-grade nickel chrome wire employed by model builders to home-turn smalt springs. Generally, diameters of between. 015- and. 02G-inch are best, but if one has a less sensitive primer, more powerful batteries must be used with heavier wire. Anything over. 025-inch diameter will probably blow fuzes in a residential electrical system. This is definitely the upper size limit for bridge wires. 

Sadowski J, Gasteiger J, Klebe G (1994) Comparison of automatic three-dimensional model builders using 639 X-ray structures. J Chem Inf Comp Sci 34 1000-1008 Stenberg P, Luthman K, Artursson P (1999) Prediction of membrane permeability to peptides from calculated dynamic molecular surface properties. Pharm Res 16 205-212 Stenberg P, Luthman K, Ellens H et al. (1999) Prediction of the intestinal absorption of endothelin receptor antagonists using three theoretical methods of increasing complexity. Pharm Res 16 1520-1526... 

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