Chem3D Users Manual - CambridgeSoft

Administrator
• Semiempirical Extended Hückel, MINDO/3,
MNDO, MNDO-d, AM1 and PM3 methods
through Chem3D and CS MOPAC.
• Ab initio methods through the Chem3D
Gaussian or GAMESS interface.
Uses of Computational
Methods
Computational methods calculate the potential
energy surfaces (PES) of molecules. The potential
energy surface is the embodiment of the forces of
interaction among atoms in a molecule. From the
PES, structural and chemical information about a
molecule can be derived. The methods differ in the
way the surface is calculated and in the molecular
properties derived from the energy surface.
The methods perform the following basic types of
calculations:
• Single point energy calculation—The
energy of a given spacial arrangement of the
atoms in a model or the value of the PES for a
given set of atomic coordinates.
• Geometry optimization—A systematic
modification of the atomic coordinates of a
model resulting in a geometry where the net
forces on the structure sum to zero. A
3-dimensional arrangement of atoms in the
model representing a local energy minimum (a
stable molecular geometry to be found without
crossing a conformational energy barrier).
• Property calculation—Predicts certain
physical and chemical properties, such as
charge, dipole moment, and heat of formation.
Computational methods can perform more
specialized functions, such as conformational
searches and molecular dynamics simulations.
Choosing the Best Method
Not all types of calculations are possible for all
methods and no one method is best for all
purposes. For any given application, each method
poses advantages and disadvantages. The choice of
method depend on a number of factors, including:
• The nature of the molecule
• The type of information sought
• The availability of applicable experimentally
determined parameters (as required by some
methods)
• Computer resources
The three most important of the these criteria are:
• Model size—The size of a model can be a
limiting factor for a particular method. The
limiting number of atoms in a molecule
increases by approximately one order of
magnitude between method classes from ab
initio to molecular mechanics. Ab initio is limited
to tens of atoms, semiempirical to hundreds,
and molecular mechanics to thousands.
• Parameter Availability—Some methods
depend on experimentally determined
parameters to perform computations. If the
model contains atoms for which the
parameters of a particular method have not
been derived, that method may produce invalid
predictions. Molecular mechanics, for example,
relies on parameters to define a force-field.
Any particular force-field is only applicable to
the limited class of molecules for which it is
parametrized.
• Computer resources—Requirements
increase relative to the size of the model for
each of the methods.
Ab initio: The time required for performing
computations increases on the order of N 4 ,
where N is the number of atoms in the model.
130•Computation Concepts
CambridgeSoft
Computational Methods Overview