Biomedical Engineering Reference
In-Depth Information
Table. 1 Computational procedures for the rational design of MIPs
Process
Application
Targets and references
Molecular mechanics (MM)
LEAPFROG algorithm used to
screen virtual library of
functional monomers;
simulation of complex
formation done using
simulated annealing
(SYBYL)
Optimization of polymer
composition; selection of
best monomers leading to
MIPs with high binding
capacity for the template
leading to synthesis of MIP
Creatinine [
63
]; microcystin-
LR [
64
]; ochratoxin-A [
64
,
77
]; abacavir [
78
]; biotin
[
79
]; carbaryl [
80
]; cocaine,
deoxyephedrine,
methadone, morphine [
81
];
triazines [
82
,
83
]; tylosin
[
84
]; acyl-homoserine
lactone [
85
]; aflatoxin-B1
[
86
]; nonylphenol [
87
];
cholic acid [
88
];
deoxynivalenol [
89
];
amiodarone [
90
]
MM calculations with AMBER
7 Docking software to map
the energetic interactions
Prediction of binding affinity
and selectivity
Theophylline and its derivative
[
91
]
MM and MD calculations
performed for the
template-monomer
complex using HyperChem
Analysis of the complex
formation between
template and monomer and
possible structure of
imprinting sites
L
-or
D
-tryptophan methyl ester
[
92
];
N
-
a
-
t
-boc-
L
-histidine
[
93
]
Interactions between template
and monomer in MIPs
analyzed using Amber MM
method
Prediction of the ratios of
template, functional
monomer and solvent
Caffeine and theophylline [
68
];
ibuprofen [
94
]
3D chemical structures of the
labeled BLAs mechanics
using MOPAC, AM1 force
field, and Chem3D Ultra
7.0 software
Analysis of recognition of the
fluorescent analogues of
template by the MIPs
Penicillin G [
72
]
Energy minimization by MM/
QM to estimate enthalpies
of formation, bond orders,
intermolecular distances
and ionization potentials
using PCModel for
windows
Analysis of enthalpies of
complex formation between
functional monomer and
template
Dibenzothiophene sulfone
[
185
]
Calculations of interaction
energies using PCMODEL
8.0, MMFF94 and force
field
Selection of monomers for
synthesis of MIPs based on
the interaction energies
Paracetamol [
95
]
p
K
a
calculations of template by
Gaussian03W in vacuum
Correlation between molecular
volumes, p
K
a
of templates
and the retention factors
Hydroxy polychlorinated
biphenyls [
96
]
Molecular dynamics (MD)
Molecular models of template
and monomers optimized
by HyperChem 501
Selection of best monomers for
MIPs with high binding
capacity for the template
N
,
O
-dibenzylcarbamate [
97
]
(continued)
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