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Computational Design of Molecularly Imprinted Polymers

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

Abstract

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.

Keywords

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

ΔE

Binding energy

2-VP

2-Vinyl pyridine

4-VP

4-Vinyl pyridine

“ab-initio”

Latin term meaning ‘from the beginning’

AA

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

ALM

Allylamine

AMBER

Assisted Model Building with Energy Refinement refers to a MM force field for the simulation of biomolecules and a package of molecular simulation programs.

AMPSA

2-acrylamido-2-methyl-1-propanesulfonic acid

B3LYP

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)

BLAs

β-lactams

B-Me

Biotin methyl ester

CAChe MOPAC

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

Cerius

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 (http://www.cambridgesoft.com/)

DFT

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

DMAEM

Dimethyl aminoethyl methacrylate

DOCK

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

EGDMA

Ethylene glycol dimethacrylate

ELISA

Enzyme linked immuno sorbent assay

GAMESS

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

GRID

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)

Guassian

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

Guassview

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

HEM

Hydroxyethyl methacrylate

His

Histidine

HOOK

Linker search for fragments placed by MCSS

HO-PCBs

Hydroxy polychlorinated biphenyls

HPLC

High performance liquid chromatography

HVA

Homovanillic acid

HyperChem

A molecular modeling package for windows

IA

Itaconic acid

k′

Retention factor

Leapfrog™

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

LEGEND

Atom-based, stochastic search

Ligbuilder

A general purpose program for structure-based drug design

LUDI

Fragment-based, combinatorial search

MAA

Methacrylic acid

Materials Studio

A software for modeling and simulation of crystal structure, polymer properties, and structure-activity relationships (http://www.accelrys.com/products/mstudio)

MBAA

N,N′-methylenebisacrylamide

MD

Molecular dynamics

MIC

Molecularly imprinted catalysis

MIP

Molecularly imprinted polymer

MM

Molecular mechanics

MMA

Methylmethacrylate

MMFF94

A tool for conformational searching of highly flexible molecules

MOE

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

MOPAC AM1

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

NAM

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

NIP

Nonimprinted polymer

NVT-MD

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

OPA

o-phthalic dialdehyde

OscailX

A molecular modeling software from National University of Ireland. (http://www.ucg.ie/cryst/software.htm)

OTA

Ochratoxin A

PCFF

Polymer consistent force field

PCM

Polarizable continuum model

PCModel

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)

PenG

Penicillin G

pKa

Ionization constant

PRO-LIGAND

Fragment-based search

Qm

Mean absolute atomic charge

QM

Quantum mechanics

RECON

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.

RESP

Atomic partial charge assignment protocol

SDIM

Sulfadimethoxine

SHAKE

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.

SMZ

Sulfamethazine

SPROUT

Fragment-based, sequential growth, combinatorial search

SYBYL™

A molecular modeling and visualization package permitting construction, editing, and visualization tools for both large and small molecules (http://www.tripos.com)

T:M:X ratio

Template monomer crosslinker ratio

TAE

Transferable atom equivalent

TFMAA

2-(trifluoromethyl) acrylic acid

THO

Theophylline

UAHF

United Atom Hartree-Fock

Van-der Waals

Weak intermolecular forces that act between stable molecules

VI

1-vinylimidazole

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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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