Computational Approaches in the Design of Synthetic Receptors - Designing Receptors for the Next Generation of Biosensors - page 146

Fig. 5 Structures of a typically simulated equilibrated conformation of dimethoate interacting
with poly(BMA) (NPT at 300 K, 1 atm) [ 101 ]. Reproduced with permission

In another example of MD simulation, Benito-Pe˜a et al. [ 72 ] analyzed binding
of seven novel fluorescent labeled -lactam antibiotics (BLAs) with a library of six

polymers imprinted with penicillin G (PenG). The 3D chemical structures of the
labeled BLAs have been modeled followed by energy minimization by molecular
dynamics (MOPAC, AM1 force field) using Chem3D Ultra 7.0 software
(Cambridge-Soft, MA). The results of molecular modeling showed that recognition
of the fluorescent analogues of PenG by the molecularly imprinted material is due
to a combination of size and shape selectivity.
Yoshida et al. [ 92 ] employed HyperChem and performed MD calculations to
verify the recognition mechanism of the MIP they synthesized for the separation of
optically active tryptophan methyl ester. The computational modeling proved that
the enantiomeric selectivity is conferred by electrostatic and hydrogen-bonding
interactions between the functional molecule and the target tryptophan methyl
ester, along with the chiral space formed on the polymer surface.
Li et al. [ 100 ] demonstrated a detection method for veterinary drugs, wherein
they employed MD simulations and screening to identify functional monomers
capable of interacting with sulfadimidine (SM 2 ). The authors prepared a library
comprising monomers and calculated their interactions with SM 2 in acetonitrile
using GROMACS 3.3 (Fig. 6 ). The GROMOS-96 force fields of the functional
monomers, SM 2 and acetonitrile molecule were presented and computationally
evaluated the PRODRG SEVER 2.5. The NVT-MD simulations were performed
at 300 K, and the functional monomer and template with ratio 1:1 were immersed in
acetonitrile. Molecular dynamics simulations in explicit solvent were performed for
1 ns with time steps of 0.002 ps. The authors performed energy calculations of the
simulated system using GROMACS software package and visual MD (VMD). The
surface molecularly imprinted silica with SM 2 as template was prepared by a
surface-imprinting technique prepared using MAA and DVB in acetonitrile. The
molecular recognition of SM 2 was analyzed in detail using Gaussian 03. The
experimental validation reported in this work is in conjunction with the theoretical
calculations.

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