Computational Approaches in the Design of Synthetic Receptors - Designing Receptors for the Next Generation of Biosensors - page 143

Table 2 Monomers with highest binding for nonylphenol [ 87 ]
Highest binding monomers for nonylphenol Binding energy (kcal/mol)

Itaconic acid 38.06

TFMAA 27.17

Urocanic acid 27.16

Methacrylic acid 21.63

Vinyl imidazole 16.00

DEAEM 12.66

2-Vinyl pyridine 6.60

Reproduced with permission

tests of the computationally designed MIP demonstrated higher affinity toward
nonylphenol, and both NIP and MIP were observed to be suitable for removal and
pre-concentration from contaminated water samples with 99% efficiency of the
recovery (231 mg/g for NIP and 228 mg/g for MIP). A comparative test under the
same conditions but using the commercial resins PH(EC) (Biotage) and C18 (Varian)
showed recovery rates 84%. The synthesized materials can be used for sample pre-

concentration and environmental analysis of this class of compounds [ 141 ].
The MM method is the fastest and least expensive method in computational
terms, and hence is an ideal choice for studies on analysis of structural parameters
and stable conformation for a variety of molecules. Optimization steps are often
carried out to confirm that the molecules are in their lowest energy state so that the
calculated results can be compared to those obtained experimentally. However,
since MM does not deal directly with electrons and orbitals, it cannot be used to
study, e.g., chemical reactivity of functional monomers.

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2.3 Rational Approaches to MIP Synthesis Involving Molecular
Dynamics

MD simulation provides better descriptions of interactions (generally electrostatic
and van der Waals) because they reflect the effect which the surrounding environ-
ment has on the properties of molecules. MD simulations in general are powerful
tools to investigate complex systems made of thousands of atoms. A good under-
standing of intermolecular interactions, mechanisms of imprinting, and properties
in molecular imprinting processes requires advanced state-of-the-art computational
tools which will help in investigations on the molecular clusters and prediction of
interaction energies (Table 1 ).

2.4 Examples of MD Methods Used in MIP Design

One of the successful approaches that are used for the computation of monomer
template ratio is simulated annealing. Simulated annealing is a Monte Carlo
approach for minimizing multivariate functions. The term simulated annealing