Computational Approaches in the Design of Synthetic Receptors - Designing Receptors for the Next Generation of Biosensors - page 148

Fig. 6 Snapshot of the interaction energy between SM 2 and monomers ( left ) and a schematic
diagram of surface imprinting and recognition mechanism ( right )[ 100 ]. Reproduced with
permission
Since MD simulations are numerical and generally include a large number of
particles, the simulation time required for modeling is very substantial. However,
contrary to MM, MD molecules and their complexes have the ability to adapt to
their environment, which provides a closer representation of reality.
2.5 Rational Approaches to MIP Design Involving Quantum
Mechanics
Quantum Mechanics (QM) is a field of quantum chemistry that uses a mathematical
basis to represent chemical phenomena at the molecular level. It uses a complex
mathematical expression called a wave function with which the energies and
properties of atoms and molecules can be computed. While for simple model systems
wave functions can be analytically determined, for complex systems such as those
that involve molecular modeling, approximations have to be made. One of the most
commonly employed approximation methods is that of Born and Oppenheimer [ 167 ].
This approximation is based on the idea that it is not necessary to develop a wave