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Since the inception of this volume, the world's nancial climate has
radically changed.
Theemphasishasshiftedfromboomingeconomiesandeconomicgrowth
totherealityofrecessionanddiminishingoutlook.
Witheconomicdownturncomes
opportunity,inallareasofchemistryfromresearchanddevelopmentthroughto
productregistrationandriskassessment,replacementsarebeingsoughtforcostly
time-consumingprocesses.
Leadingamongstthereplacementsaremodelswithtrue
predictivecapability. Ofthesecomputationalmodelsarepreferred. This
volume addresses a broad need within various areas of the "chemical
industries", from pharmaceuticals and pesticides to personal
products to provide
computationalmethodstopredicttheeffects,activitiesandpropertiesofmolecules.
Itaddressestheuseofmodelstodesignnewmoleculesandassesstheirfateand
effectsbothtotheenvironmentandtohumanhealth.
Thereisanemphasisrunning
throughoutthisvolumetoproducerobustmodelssuitableforpurpose.
Thevolume aimstoallowthereaderto
nddataanddescriptorsanddevelop,discoverandutilise validmodels.
Gdansk, ' Poland TomaszPuzyn Jackson,MS,USA JerzyLeszczynski
Liverpool,UK MarkT. D. Cronin May2009 CONTENTS Part I Theory of
QSAR 1 QuantitativeStructure-ActivityRelationships(QSARs)-
ApplicationsandMethodology...3 Mark T. D. Cronin 1. 1.
Introduction...3 1. 2. PurposeofQSAR...4 1. 3.
ApplicationsofQSAR...4 1. 4. Methods...5 1. 5.
TheCornerstonesofSuccessfulPredictiveModels ...7 1. 6.
AValidated(Q)SARoraValidPrediction? ...9 1. 7.
UsinginSilicoTechniques ...9 1. 8. NewAreasforinSilicoModels...11
1. 9. Conclusions...11 References ...11 2
TheUseofQuantumMechanicsDerivedDescriptorsin
ComputationalToxicology...13 Steven J. Enoch 2. 1.
Introduction...13 2. 2. TheSchrodingerEquation...15 2. 3.
Hartree-FockTheory...17 2. 4. Semi-EmpiricalMethods:AM1andRM1...18
2. 5. ABInitio:DensityFunctionalTheory...19 2. 6.
QSARforNon-ReactiveMechanismsofAcute(Aquatic) Toxicity...19 2. 7.
QSARsforReactiveToxicityMechanisms...21 2. 7. 1.
AquaticToxicityandSkinSensitisation...21 2. 7. 2.
QSARsforMutagenicity ...24 2. 8. FutureDirectionsandOutlook...25 2.
9. Conclusions...26 References ...26 vii viii Contents 3
MolecularDescriptors...29 Viviana Consonni and Roberto Todeschini
3. 1. Introduction...29 3. 1. 1. De nitions...29 3. 1. 2.
History...31 3. 1. 3. Theoreticalvs. ExperimentalDescriptors...33
3. 2. MolecularRepresentation ...35 3. 3. TopologicalIndexes...38
3. 3. 1. MolecularGraphs...38 3. 3. 2. De
nitionandCalculationofTopologicalIndexes(TIs) 39 3. 3. 3.
Graph-TheoreticalMatrixes...42 3. 3. 4. ConnectivityIndexes ...48
3. 3. 5. CharacteristicPolynomial ...50 3. 3. 6. SpectralIndexes
...53 3. 4. AutocorrelationDescriptors ...
Since the inception of this volume, the world's nancial climate has
radically changed.
Theemphasishasshiftedfromboomingeconomiesandeconomicgrowth
totherealityofrecessionanddiminishingoutlook.
Witheconomicdownturncomes
opportunity,inallareasofchemistryfromresearchanddevelopmentthroughto
productregistrationandriskassessment,replacementsarebeingsoughtforcostly
time-consumingprocesses.
Leadingamongstthereplacementsaremodelswithtrue
predictivecapability. Ofthesecomputationalmodelsarepreferred. This
volume addresses a broad need within various areas of the "chemical
industries", from pharmaceuticals and pesticides to personal
products to provide
computationalmethodstopredicttheeffects,activitiesandpropertiesofmolecules.
Itaddressestheuseofmodelstodesignnewmoleculesandassesstheirfateand
effectsbothtotheenvironmentandtohumanhealth.
Thereisanemphasisrunning
throughoutthisvolumetoproducerobustmodelssuitableforpurpose.
Thevolume aimstoallowthereaderto
nddataanddescriptorsanddevelop,discoverandutilise validmodels.
Gdansk, ' Poland TomaszPuzyn Jackson,MS,USA JerzyLeszczynski
Liverpool,UK MarkT. D. Cronin May2009 CONTENTS Part I Theory of
QSAR 1 QuantitativeStructure-ActivityRelationships(QSARs)-
ApplicationsandMethodology...3 Mark T. D. Cronin 1. 1.
Introduction...3 1. 2. PurposeofQSAR...4 1. 3.
ApplicationsofQSAR...4 1. 4. Methods...5 1. 5.
TheCornerstonesofSuccessfulPredictiveModels ...7 1. 6.
AValidated(Q)SARoraValidPrediction? ...9 1. 7.
UsinginSilicoTechniques ...9 1. 8. NewAreasforinSilicoModels...11
1. 9. Conclusions...11 References ...11 2
TheUseofQuantumMechanicsDerivedDescriptorsin
ComputationalToxicology...13 Steven J. Enoch 2. 1.
Introduction...13 2. 2. TheSchrodingerEquation...15 2. 3.
Hartree-FockTheory...17 2. 4. Semi-EmpiricalMethods:AM1andRM1...18
2. 5. ABInitio:DensityFunctionalTheory...19 2. 6.
QSARforNon-ReactiveMechanismsofAcute(Aquatic) Toxicity...19 2. 7.
QSARsforReactiveToxicityMechanisms...21 2. 7. 1.
AquaticToxicityandSkinSensitisation...21 2. 7. 2.
QSARsforMutagenicity ...24 2. 8. FutureDirectionsandOutlook...25 2.
9. Conclusions...26 References ...26 vii viii Contents 3
MolecularDescriptors...29 Viviana Consonni and Roberto Todeschini
3. 1. Introduction...29 3. 1. 1. De nitions...29 3. 1. 2.
History...31 3. 1. 3. Theoreticalvs. ExperimentalDescriptors...33
3. 2. MolecularRepresentation ...35 3. 3. TopologicalIndexes...38
3. 3. 1. MolecularGraphs...38 3. 3. 2. De
nitionandCalculationofTopologicalIndexes(TIs) 39 3. 3. 3.
Graph-TheoreticalMatrixes...42 3. 3. 4. ConnectivityIndexes ...48
3. 3. 5. CharacteristicPolynomial ...50 3. 3. 6. SpectralIndexes
...53 3. 4. AutocorrelationDescriptors ...
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