184 molecular rearrangement
been optimized to better reproduce structures for a spe-
cific class of compounds, such as peptides (for proteins
and enzymes) or carbohydrates (for sugars, polysaccha-
rides, and cellulose), thereby sacrificing some degree of
general utility. Force fields have also been parameterized
using QM results, a technique useful to extend MM capa-
bilities when little or no experimental data are available
for specific atom or bond types.
MM is inherently limited to studying systems com-
posed of well characterized atom and bond types. It pro-
vides molecular geometries in good agreement with
experimental values and reliable comparative energies,
but it can not model chemical reactions. The biggest
advantage of MM is its speed. MM studies can consist of
multiple molecules including thousands of atoms. MM
force fields can also be used in molecular dynamics and
Monte Carlo calculations, which are used to investigate
time-dependent phenomena (e.g., protein folding), and in
free-energy calculations that are not feasible with QM.
Molecular mechanics has been used in a wide range of
applications, including simulation of ice crystal growthinhibition by fish antifreeze peptides, comparison of
enzyme inhibitors to design improved drugs, investigation
of surfactant aggregation in micelles, and studying poly-
mer conformations in solution.
A fundamental postulate of quantum mechanics is
that atoms consist of a nucleus surrounded by electrons in
discrete atomic orbitals. When atoms bond, their atomic
orbitals combine to form molecular orbitals. The redistri-
bution of electrons in the molecular orbitals determines
the molecule’s physical and chemical properties. QM
methods do not employ atom or bond types but derive
approximate solutions to the Schrödinger equation to opti-
mize molecular structures and electronic properties. QM
calculations demand significantly more computational
resources than MM calculations for the same system. In
part to address computer-resource constraints, QM calcu-Molecular Modeling
(continued)Molecular model of carbon dioxide, CO 2. The black sphere
represents an atom of carbon. Gray spheres represent oxy-
gen. The atoms in this linear molecule are held together by
two double bonds, each involving a shared pair of elec-
trons. Carbon dioxide is a colorless gas at room tempera-
ture. It occurs naturally in the atmosphere and is a waste
product of animal and plant respiration.(Courtesy of Adam
Hart-Davis/Science Photo Library)Molecular model of hydrogen gas. The two white spheres
represent individual hydrogen atoms, and the gray bar
represents the single bond between them. Two forms of
hydrogen exist: orthohydogen (75 percent) and parahydro-
gen (25 percent). The former’s two nuclei spin in parallel;
the latter’s spin antiparallel. They have slightly different
boiling and melting points. Hydrogen is the lightest ele-
ment and is a widespread constituent of water, minerals,
and organic matter. It is produced by electrolysis of water
or reactions between acids and metals. Hydrogen is used
industrially in hydrogenation of fats and oils and in hydro-
carbon synthesis.(Courtesy of Adam Hart-Davis/Science
Photo Library)