Preface
Chapter I - The structure of proteins
1.1 Introduction
1.2 The primary structure
1.3 The secondary structure 1.4 The tertiary structure
1.5 The quaternary structure
1.6 Driving forces in protein folding 1.7 Structural flexibility in proteins
1.8 Thermodynamics of protein-ligand complexes
1.9 Characterization of protein structures 1.10 Summary
References
Chapter II - Enzymes and their function (with Andrés Illanes)
2.1 Introduction 2.2 The structure of enzymes
2.3 The enzymatic process
2.4 Enzyme kinetics
2.4.1 Single-substrate reactions
2.4.1.1 Michaelis-Menten kinetics
2.4.2 Multi-substrate reactions
2.4.3 Non-Micheaelis-Menten kinetics
2.5 Factors influencing enzyme activity 2.5.1 Environmental conditions: Temperature and pH
2.5.2 Activators and inhibitors
2.5.2.1 Reversible inhibition
2.5.2.2 Irreversible inhibition
2.5.2.3 Allosteric activation and inhibition
2.5.2.4 Biogenic regulation
2.6 Summary
References
Chapter III - Introduction to molecular catalysis (with Andrés Illanes)
3.1 The science of catalysis
3.1.1 Homogeneous, heterogeneous and enzymatic catalysis
3.1.2 Catalytic activity, selectivity and yield
3.2 Kinetics of catalytic reactions
3.2.1 Reaction rates
3.2.2 Transition state theory
3.2.3 The Arrhenius equation
3.3 Fundamental concepts in heterogeneous catalysis
3.3.1 Steps in heterogeneous catalysis
3.3.2 The Sabatier principle
3.3.3 The Bell-Evans-Polanyi principle
3.3.4 Chemisorption and physisorption
3.3.5 Langmuir-Hinshelwood versus Eley-Rideal mechanism
3.3.6 Mars and van Krevelen mechanism
3.4 Summary
References
Chapter IV - The complex nature of active sites
4.1 Dynamic behavior of active sites 4.2 Active sites in heterogeneous catalysis: Historical background
4.2.1 Single-site heterogeneous catalysts
4.2.2 Small metal particles
4.2.3 Zeolites
4.2.4 Oxide catalysts
4.3 Active sites in enzymatic catalysis
4.3.1 Allosterically regulated enzymes: the case of ATCase
4.3.2 Active sites and electric fields
4.4 Active sites in homogeneous catalysis
4.4.1 Catalytic cycles and flexibility
4.5 Summary References
Chapter V - Complexity in catalysis (with Nik Lygeros)
5.1 Self-organizing systems
5.2 Complexity of catalytic processes
5.2.1 Thermodynamic considerations
5.2.2 Topological aspects and real surfaces
5.3 Well and ill-conditioned systems
5.4 Cooperations and synergies
5.5 New modelling approaches for decoding complexity in catalysis
5.5.1 The theory of hyperstructures
5.5.1.1 Cooperation and synergistic hyperstructures
5.5.1.2 Strategic relevance
5.5.2 Application of the game theory to catalytic systems
5.6 Artificial intelligence faces catalytic complexity
5.7 Summary
References
