Computational Design of Molecularly Imprinted Polymers

  • Sreenath SubrahmanyamEmail author
  • Sergey A. Piletsky
Part of the Integrated Analytical Systems book series (ANASYS)


Artificial receptors have been in use for several decades as sensor elements, in affinity separation, and as models for investigation of molecular recognition. Although there have been numerous publications on the use of molecular modeling in characterization of their affinity and selectivity, very few attempts have been made on the application of molecular modeling in computational design of synthetic receptors. This chapter discusses recent successes in the use of computational design for the development of one particular branch of synthetic receptors – molecularly imprinted polymers.


Molecular Dynamics Simulation Molecularly Imprint Polymer Functional Monomer Imprint Polymer Template Molecule 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Acronyms and Further Descriptions


Binding energy


2-Vinyl pyridine


4-Vinyl pyridine


Latin term meaning ‘from the beginning’


Acrylic acid

Acceryls DS Viewer

Modeling and simulation tools for drug discovery

Agile molecule

Is a 3 Dimensional molecular viewer which shows molecular models and provides geometry editing capabilities




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

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




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, (Molecu lar Simulations Inc.)

Chem 3D

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


Density functional theory

Dielectric constant

Is 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 immuno sorbent assay


General Atomic and Molecular Electronic Structure System; a general ab initio quantum chemistry package that can computewave 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


Is a computational procedure for detecting energetically favorablebinding sites on molecules of known structure. The energiesare 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


Is 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


A general purpose program for structure-based drug design


Fragment-based, combinatorial search


Methacrylic acid

Materials Studio

A software for modeling and simulation of crystal structure, polymer properties, and 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 specifically for computational chemistry

Monte Carlo

An algorithm that computes based on repeated random samplingto 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 substitutioneffects and force constants for molecules, radicals, ions, and polymers


A scal able molecular dynamics code that can be run on the Beowulf parallel PC cluster used to run molecular dynamics simulations on selected molecular systems


Nonimprinted polymer


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


o-phthalic dialdehyde


A molecular modeling software from National University of Ireland. (


Ochratoxin A


Polymer consistent force field


Polarizable continuum model


Is a structure building, manipulation and display program which uses molecular mechanics and semiempirical quantum mechan ics 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 precomputedfrom 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


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 crosslinker ratio


Transferable atom equivalent


2-(trifluoromethyl) acrylic acid




United Atom Hartree-Fock

Van-der Waals

Weak intermolecular forces that act between stable molecules




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© Springer Science + Business Media, LLC 2009

Authors and Affiliations

  1. 1.Cranfield Biotechnology CenterCranfield University at SilsoeBedfordshireUK

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