Techniques Used.
Building, Optimization,
Analysis of Bonding Parameters. Output Analysis
Abstract. One of the key features of modern molecular
recognition research is the use of complementary hydrogen bonding to produce
specific geometric relationships between molecules or between portions of
a larger molecule. While hydrogen bonding is not always treated effectively
by some computational methods, it can be very useful to model hydrogen bonds
in dimers and other aggregates, in order to get at least some idea of the
effects of hydrogen bonding on a system. In this exercise, you will build
and optimize some simple hydrogen bonded aggregates and compare their energies
to those of the isolated fragments, in order to evaluate the strength of
the interactions involved.
Procedure. Build and optimize monomer units of
each of the hydrogen bonded pairs of molecules shown above. Optimze them
using the OPLS or similarly bio-specific force field (generic force fields
typically do not handle hydrogen bonding in a quantitatively effective manner.
Record the enthalpies of formation of each molecule. Next, build appropriate
dimers of acetic acid and water. Record the enthalpy of formation of each
dimer or complex. The energy difference between the sum of the parts and
the aggregate gives the net stabilization in the latter due to the hydrogen
bonding. Comparison numbers are given below where available, all in kcal/mol.
Results.
Acetic Acid
Water
X
Exptl DH°
monomer
-103.3
-57.8
??
Computed DH°
monomer
Computed DH°
dimer
Exptl DH°
dimerization
13.8-17.0(a)
5.2 (b)
Estimated DH°
dimerization
(a) See L. Turi & J. J.
Dannenberg, J. Phys. Chem., 97, 12197 (1993).
(b) See L. A. Curtiss & M. Blander, Chem. Rev., 88, 827
(1988).
