Conformational analysis systems

MAECIS also contains a molecular conformation analysis system (4). This system allows the user to generate all possible conformations of the current molecule over a series of single bond rotations. Energy contour maps can be obtained for the various conformations and this allows for the selection of low energy conformations for further manipulation or calculations. 

CAMSEQ/M A Microprocessor-Based Conformational Analysis System... 

MICROPROCESSOR-BASED CONFORMATIONAL ANALYSIS SYSTEM DO YOU MAUE A JOYSTICK (Y/N)... 

Tsujishita H, Hirono S (1997) Camdas an automated conformational analysis system using molecular dynamics. J Comput Aided Mol Des 11 305-315... 

There is a lot of confusion over the meaning of the terms theoretical chemistry, computational chemistry and molecular modelling. Indeed, many practitioners use all three labels to describe aspects of their research, as the occasion demands "Theoretical chemistry is often considered synonymous with quantum mechanics, whereas computational chemistry encompasses not only quantum mechanics but also molecular mechaiucs, minimisation, simulations, conformational analysis and other computer-based methods for understanding and predicting the behaviour of molecular systems. Molecular modellers use all of these methods and so we shall not concern ourselves with semantics but rather shall consider any theoretical or computational tecluiique that provides insight into the behaviour of molecular systems to be an example of molecular modelling. If a distinction has to be... 

Gilson M K and B Honig 1988. Calculation of the Total Electrostatic Energy of a Macromoleculai System Solvation Energies, Binding Energies and Conformational Analysis. Proteins Structure Function and Genetics 4 7-18. 

Careful conformational analysis of acyclic systems is needed. Hornoallylie Systems... 

Sample test data are either manually entered into the system or captured from analytical instmments coimected to the LIMS. The system performs any necessary calculations and compares the result to the appropriate specification stored in the database. If the comparison indicates the material is in conformance, the system can automatically provide an approval. Otherwise, the LIMS can alert lab supervision to the nonconforming sample analysis. 

Application of NMR spectroscopy to heterocyclic chemistry has developed very rapidly during the past 15 years, and the technique is now used almost as routinely as H NMR spectroscopy. There are four main areas of application of interest to the heterocyclic chemist (i) elucidation of structure, where the method can be particularly valuable for complex natural products such as alkaloids and carbohydrate antibiotics (ii) stereochemical studies, especially conformational analysis of saturated heterocyclic systems (iii) the correlation of various theoretical aspects of structure and electronic distribution with chemical shifts, coupling constants and other NMR derived parameters and (iv) the unravelling of biosynthetic pathways to natural products, where, in contrast to related studies with " C-labelled precursors, stepwise degradation of the secondary metabolite is usually unnecessary. 

In a different context, conformational analysis is essential for the analysis of molecular dynamics simulations. As discussed in Chapter 3, the direct output of a molecular dynamics simulation is a set of confonnations ( snapshots ) that were saved along the trajectory. These conformations are subsequently analyzed in order to extract information about the system. However, if, during a long simulation, the molecule moves from one... 

MK Gilson, B Homg. Calculation of the total electrostatic energy of a macromolecular system Solution energies, binding energies, and conformational analysis. Proteins 4 7-18, 1988. 

Conformation analysis methods. In many cases in the process of building a 3D structure from scratch, decisions have to be made between multiple alternatives with similar energy. A typical example is an sp -sp torsion angle with similar energies for the alternatives of -i-60°, -60° and 180°. In many cases, rules are used to decide (e.g. stretch an open chain portion as much as possible to avoid clashes). Sometimes, the best result cannot be determined without a conformation analysis (e.g. complex ring systems with exocycHc substituents). Despite conformation analysis being a topic of its own covered in the next chapter, many automatic 3D structure generators have to fall back in certain situations to a limited conformation search in order so solve a specific problem and to come up with a reasonable solution. 

Dolata, D. P., Carter, R. E. WIZARD applications of expert system techniques to conformational analysis. 1. The basic algorithms exemplified on simple hydrocarbons. J. Chem. Inf. Comp. Sci. 1987, 27, 36-47. 

Conformational analysis of orthoamides has been previously discussed <1996CHEC-II(8)967> and calculations of reactivity for systems containing a bridgehead nitrogen are generally consistent with experimental observations <1984CHEC(4)443>. 

Conformational analysis of the novel bicyclo[3.3.0]octasilane and bicyclo[4.2.0]octasilane systems was carried out by X-ray crystallography (Figs. 19-21). The bicyclo[3.3.0]octasilane framework of trans-17 has a trans-fused structure of cyclopentasilane rings. The trans-fused structure is... 

Corey et al.39 introduced a chiral controller system, chiral auxiliary 55, which has shown excellent practical potential because of its availability, recoverability, and high enantioselectivity. Furthermore, using conformation analysis,... 

The currently available quantum chemical computational methods and computer programs have not been utilized to their potential in elucidating the electronic origin of zeolite properties. As more and more physico-chemical methods are used successfully for the description and characterization of zeolites, (e.g. (42-45)), more questions will also arise where computational quantum chemistry may have a useful contribution towards the answer, e.g. in connection with combined approaches where zeolites and metal-metal bonded systems (e.g. (46,47)) are used in combination. The spectacular recent and projected future improvements in computer technology are bound to enlarge the scope of quantum chemical studies on zeolites. Detailed studies on optimum intercavity locations for a variety of molecules, and calculations on conformation analysis and reaction mechanism in zeolite cavities are among the promises what an extrapolation of current developments in computational quantum chemistry and computer technology holds out for zeolite chemistry. 

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