MOLECULAR MODELING AND MOLECULAR MECHANICS 161
software in an entirely new kind of experimental methodology. Computational
chemists, for example, don ’ t study matter directly. In the past, chemists who
wanted to determine molecular properties chose their instrumentation, pre-
pared a sample, observed the reactions of the sample, and deduced the mole-
cule ’ s properties. Computational chemists now choose their computer and
software packages and get their information by modeling and mathematical
analyses. ” This portion of Chapter 4 will provide and introduction to this fast -
growing and changing area of chemistry.
Theoretical models include those based on classical (Newtonian) mechani-
cal methods — force fi eld methods known as molecular mechanical methods.
These include MM2, MM3, Amber, Sybyl, UFF, and others described in the
following paragraphs. These methods are based on Hook ’ s law describing
the parabolic potential for the stretching of a chemical bond, van der Waal ’ s
interactions, electrostatics, and other forces described more fully below. The
combination assembled into the force fi eld is parameterized based on fi tting
to experimental data. One can treat 1500 – 2500 atom systems by molecular
mechanical methods. Only this method is treated in detail in this text. Other
theoretical models are based on quantum mechanical methods. These
include:
- H ü ckel and extended H ü ckel treatments that consider many fundamen-
tal ideas of orbitals and bonding but neglect electron repulsions in mol-
ecules. These methods treat systems up to 200 atoms. - Semiempirical (CNDO, MNDO, ZINDO, AM1, PM3, PM3(tm), and
other) methods based on the Hartree – Fock self - consistent fi eld (HF -
SCF) model, which treats valence electrons only and contains approxi-
mations to simplify (and shorten the time of) calculations. Semiempirical
methods are parameterized to fi t experimental results, and the PM3(tm)
method treats transition metals. These methods treat systems of up to
200 atoms. - Ab initio (nonempirical, from “ fi rst principles ” ) methods also use the
HF - SCF model but include all electrons and use minimal approximation.
Basis sets of functions based on linear combinations of atomic orbitals
(LCAO) increase in complexity from the simplest (STO - 3G) to more
complex (3 - 21G( )) to extended basis sets (6 - 311+G * ) for the most
accurate (and most time - consuming) results. Ab initio methods treat
systems up to 50 atoms. - Density functional methods treat larger molecules more successfully
than ab initio methods and make use of explicit atomic basis sets as
described for ab initio methods.
4.3.2 Molecular Modeling, Molecular Mechanics, and Molecular Dynamics
Molecular modeling seeks to answer questions about molecular properties —
stabilities, reactivities, electronic properties — as they are related to molecular