Structure Optimization with HyperChem

Optimizing Molecular Structures

HyperChem combines optimization capabilities for quantum mechanics and molecular mechanics techniques with facilities for structure manipulation and visualization, molecular dynamics simulation and customization in an integrated, desk-top molecular-modeling system. With HyperChem, you can easily determine stable molecular structures. The added ability to handle restraints and selected parts of systems allows optimizers to become tools for investigation as well as refinement.

Straightforward Optimizing

Finding stable structures of molecules is probably the single most common computational task of molecular modeling programs. The relative energy of different optimized structures determines conformational stability, isomerization equilibria, heats of reaction, reaction products, and many other aspects of chemistry. HyperChem includes four optimizers:

A steepest descent optimizer, particularly useful for rapid removal of severe steric and strain problems in initial guess structures.
Two conjugate gradient optimizers (Fletcher-Reeves and Polak-Ribiere) for efficient convergence toward a minimum.
A block-diagonal Newton-Raphson optimizer (MM+ force field only), which moves one atom at a time using part of the second derivative information.

An Integrated Approach

HyperChem offers a truly integrated approach to structure optimization, providing efficiency, clarity and ease of use. This is feature of the overall design of the program provides several important benefits:

The same set of optimizers works with both molecular mechanics and semi-empirical quantum mechanics methods.
Optimization choices, such as termination conditions, frequency of screen update, and choice of algorithm, may be set in exactly the same way for all methods and all optimization algorithms.
The visual feedback on optimizations is provided in a consistent manner across methods.
The user retains full ability to rotate and translate the molecule while an optimization is in progress.

Selections

HyperChem makes extensive use of the ability to select a part of a system. Selections bring additional capabilities to the system in the context of optimizations.

Optimizing a Selection

If some atoms are selected when the optimization is started, only the selected atoms are allowed to move; the rest of the system remains fixed.
HyperChem treats the unselected portion as a potential to be included in the quantum calculation. In this way, HyperChem allows the user to carry out quantum calculations on parts of a large system while still retaining the influence of the rest of that system.

Using selections for restraining forces

Selections enable you to build in restraining forces for distances, angles and dihedral angles between atoms that need not be bonded. Atoms can also be tethered to points in space. These restraints have several applications:

To force a system towards a structure of interest.
To build structures from experimental data (such as distances or torsion angles deduced from NMR experiments).

Docking by Optimization

"Docking" a small molecule onto a site on a larger molecule is a common task in biochemical investigations. HyperChem's extensive structure optimizing capabilities provide an effective route for exploring the structure of docked systems.

Given the two molecules, and a hypothesis as to which pairs of atoms are adjacent, the docking calculation can be started by constructing a set of optimizer restraints specifying those distances. Once these restraints are in place, select the small molecule, and optimize its structure. The restraint forces pull it into place in the docking site. Once complete, the restraints can be removed and a final optimization completed to get an accurate structure.

Docking is just one example of the kind of chemically interesting tasks that can be addressed using HyperChem optimization features.

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