Chem3D Users Manual - CambridgeSoft

Chapter 8: Computation Concepts
Computational
Chemistry Overview
Computational chemistry extends beyond the
traditional boundaries separating chemistry from
physics, biology, and computer science. It allows
the exploration of molecules by using a computer
when an actual laboratory investigation may be
inappropriate, impractical, or impossible. As an
adjunct to experimental chemistry, its significance
continues to be enhanced by increases in computer
speed and power.
Aspects of computational chemistry include:
• Molecular modeling.
• Computational methods.
• Computer-Aided Molecular Design (CAMD).
• Chemical databases.
• Organic synthesis design.
While a number of different definitions have been
proposed, the definition offered by Lipkowitz and
Boyd of computational chemistry as “those aspects
of chemical research that are expedited or rendered
practical by computers” is perhaps the most
inclusive.
Molecular modeling, while often taken to include
computational methods, can be thought of as the
rendering of a 2D or 3D model of a molecule’s
structure and properties. Computational methods,
on the other hand, calculate the structure and
property data necessary to render the model. Within
a modeling program, such as Chem3D,
computational methods are referred to as
computation engines, while geometry engines and
graphics engines render the model.
Chem3D supports a number of powerful
computational chemistry methods and extensive
visualization options.
Computational
Methods Overview
Computational chemistry encompasses a variety of
mathematical methods which fall into two broad
categories:
• Molecular mechanics—applies the laws of
classical physics to the atoms in a molecule
without explicit consideration of electrons.
• Quantum mechanics—relies on the
Schrödinger equation to describe a molecule
with explicit treatment of electronic structure.
Quantum mechanical methods can be
subdivided into two classes: ab initio and
semiempirical.
The generally accepted method classes are shown in
the following chart.
Computational Chemistry Methods
Molecular
Mechanical Methods
Semiempirical
Methods
Quantum
Mechanical Methods
Chem3D provides the following methods:
Ab Initio
Methods
• Molecular mechanical MM2 and MM3
method.
ChemOffice 2005/Chem3D Computation Concepts • 129
Computational Methods Overview