Computational Approaches in the Design of Synthetic Receptors - Designing Receptors for the Next Generation of Biosensors - page 128

Computational Approaches in the Design
of Synthetic Receptors

Sreenath Subrahmanyam, Kal Karim, and Sergey A. Piletsky

Abstract Artificial receptors have been employed in molecular recognition for a
variety of biological applications. They have been used as materials for sensors,
affinity separation, solid-phase extraction, and for research into biomolecular
interaction. There have been a number of publications relating to the application
of molecular modeling in the characterization of their affinity and selectivity; there
are very few publications that discuss the application of molecular modeling to the
computational design of artificial receptors. This chapter discusses recent successes
in the use of computational design for the development of artificial receptors, and
touches upon possible future applications, further emphasizing an exciting group of
synthetic receptors—molecularly imprinted polymers.

Keywords Artificial receptors, Molecular dynamics, Molecular imprinting,

Molecular modeling, Sensors

Contents

1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
2 Computational Methods for Rational Design of MIPs .................................... 137
2.1 Rational Approaches That Involve Molecular Mechanics . . . . . . . . . . . . . . . . . . . . . . . . . 137

2.2 Examples of MM Methods Used in MIP Design .................................. 144

2.3 Rational Approaches to MIP Synthesis Involving Molecular Dynamics . ........ 146

2.4 Examples of MD Methods Used in MIP Design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146

2.5 Rational Approaches to MIP Design Involving Quantum Mechanics . . . . . . . . . . . . 151

2.6 Examples of QM Methods Used in MIP Design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152

2.7 Rational Approaches to MIP Design Involving Quantum Chemical Methods . . . 153

2.8 Examples of Quantum Chemical Methods Used in MIP Design . ................. 153

2.9 Rational Approaches to MIP Design Involving Chemometrics and Neural

Network Methods . . ................................................................. 154

S. Subrahmanyam ( * ), K. Karim, and S.A. Piletsky
Cranfield Biotechnology Centre, Cranfield University, Bedfordshire MK43 0AL, UK
e-mail: [e-mail]