Computational Approaches in the Design of Synthetic Receptors

  • Sreenath SubrahmanyamEmail author
  • Kal Karim
  • Sergey A. Piletsky
Part of the Springer Series on Chemical Sensors and Biosensors book series (SSSENSORS, volume 12)


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.

Graphical Abstract


Artificial receptors Molecular dynamics Molecular imprinting Molecular modeling Sensors 

Acronyms and Further Descriptions

“ab initio”

Latin term meaning “from the beginning”


Binding energy


2-Vinyl pyridine


4-Vinyl pyridine


Acrylic acid

Accelrys DS viewer

Modeling and simulation tools for drug discovery

Agile molecule

A three-dimensional molecular viewer which shows molecular models and provides geometry editing capabilities


3-Oxo-C6-acyl-homoserine lactone




Assisted model building with energy refinement refers to a MM force field for the simulation of biomolecules and a package of molecular simulation programs


2-Acrylamido-2-methyl-1-propanesulfonic acid


Becke 3-parameter, Lee, Yang and Parr, a density functional method


“Bite-and-Switch” is defined in terms of polymer’s ability to bind the template (bite) and generate the signal (switch)


β-Lactam antibiotics


Biotin methyl ester


A general-purpose semiempirical molecular orbital package for the study of chemical structures and reactions


A software to visualize structures, predict the properties and behavior of chemical systems refine structural models (Molecular Simulations Inc.)

Chem 3D

A software that provides visualization and display of molecular surfaces, orbitals, electrostatic potentials, charge densities, and spin densities (


Density functional theory

Dielectric constant

A measure of the ability of a material to store a charge from an applied electromagnetic field and then transmit that energy


Dimethyl aminoethyl methacrylate


Program that addresses the problem of “docking” molecules to each other. It explores ways in which two molecules, such as a drug and an enzyme or protein receptor, might fit together




Ethylene glycol dimethacrylate


Enzyme-linked immunosorbent assay


General Atomic and Molecular Electronic Structure System: a general ab initio quantum chemistry package that can compute wave functions ranging from RHF, ROHF, UHF, GVB, and MCSCF

Gibbs free energy

The chemical potential that is minimized when a system reaches equilibrium at constant pressure and temperature


A computational procedure for detecting energetically favorable binding sites on molecules of known structure. The energies are calculated as the electrostatic, hydrogen bond and Lennard Jones interactions of a specific probe group with the target structure (Peter Goodford, Molecular Discovery Ltd)


“Ab initio” electronic structure program that originated in the research group of People at Carnegie-Melon. Calculate structures, reaction transition states, and molecular properties (


Graphical user interface (GUI) designed for use with Gaussian for easier computational analysis


Hydroxyethyl methacrylate




Linker search for fragments placed by MCSS


Hydroxy polychlorinated biphenyls


High performance liquid chromatography


Homovanillic acid


A molecular modeling package for windows


Itaconic acid


Retention factor


A component of the SYBYL™ software package (Tripos) and is a second-generation de novo drug discovery program that allows for the evaluation of potential ligand structures


Atom-based, stochastic search


General-purpose structure-based drug design program


Fragment-based, combinatorial search


Methacrylic acid

Materials Studio

Software for modeling/simulation of crystal structure, polymer properties, structure–activity relationships (




Molecular dynamics


Molecularly imprinted catalysis


Molecularly imprinted polymer


Molecular mechanics




A tool for conformational searching of highly flexible molecules


Molecular Operating Environment is a software system designed for computational chemistry

Monte Carlo

An algorithm which computes based on repeated random sampling to arrive at results


AM1 is used in the electronic part of the calculation to obtain molecular orbitals, the heat of formation and its derivative with respect to molecular geometry. MOPAC calculates the vibrational spectra, thermodynamic quantities, isotopic substitution effects and force constants for molecules, radicals, ions, and polymers


A scalable molecular dynamics code that can be run on the Beowulf parallel PC cluster for molecular dynamics simulations on selected molecular systems


Non-imprinted polymer


Molecular dynamics performed under constant number of atom, volume, and temperature ensemble


o-Phthalic dialdehyde


Molecular modeling software, National University of Ireland (


Ochratoxin A


Polymer consistent force field


Polarizable continuum model


Structure building, manipulation, and display program which uses molecular mechanics and semiempirical quantum mechanics to optimize geometry. Available on PC (DOS and Windows), Macintosh, SGI, Sun and IBM/RS computers (Kevin Gilbert, Serena Software)


Penicillin G


Ionization constant


Fragment-based search


Mean absolute atomic charge


Quantum mechanics


An algorithm for the rapid reconstruction of molecular charge densities and charge density-based electronic properties of molecules, using atomic charge density fragments precomputed from ab initio wave functions. The method is based on Bader’s quantum theory of atoms in molecules


Atomic partial charge assignment protocol




A molecular dynamics algorithm

Simulated annealing

A method that simulates the physical process of annealing, where a material is heated and then cooled leading to optimization






Fragment-based, sequential growth, combinatorial search


A molecular modeling and visualization package permitting construction, editing, and visualization tools for both large and small molecules (

T:M:X ratio

Template monomer cross-linker ratio


Transferable atom equivalent


2-(Trifluoromethyl) acrylic acid




ToxiQuant T1 System


United atom Hartree–Fock

van der Waals

Weak intermolecular forces that act between stable molecules




Visual molecular dynamics


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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Sreenath Subrahmanyam
    • 1
    Email author
  • Kal Karim
    • 1
  • Sergey A. Piletsky
    • 1
  1. 1.Cranfield Biotechnology CentreCranfield UniversityBedfordshireUK

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