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Theoretical and Computational Photochemistry: Fundamentals, Methods, Applications and Synergy with Experimental Approaches
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Contents
Contributors
Preface
Part I. Fundamentals
1. Introduction to molecular photophysics
1.1. Interaction between electromagnetic radiation and molecules
1.1.1. Electromagnetic radiation
1.1.2. Time-dependent perturbation theory: A tool for describing the matter-radiation interaction
1.1.3. Electric dipole transitions
1.1.4. Spontaneous emission
1.2. Quantization of energy
1.3. The Franck-Condon principle
1.4. Electronic absorption spectra
1.4.1. Transition energy
1.4.2. Transition intensity: The oscillator strength and the transition dipole moment
1.4.3. Absorption band shape: The dynamic effect and the vibronic coupling
1.4.4. Multiphotonic absorption
1.5. Fluorescence and phosphorescence emission
1.5.1. Fluorescence
1.5.1.1. Fluorescence spectrum
1.5.1.2. Kashas rule
1.5.1.3. Fluorescence lifetime and quantum yield
1.5.1.4. Fluorescence quenching
1.5.1.5. Factors influencing fluorescence
1.5.1.6. Steady-state vs time-resolved fluorescence
1.5.1.7. Anti-Stokes photon emission
1.5.2. Phosphorescence
1.5.2.1. Phosphorescence from doublet and quartet states
References
2. Theoretical grounds in molecular photochemistry
2.1. The Jablonski diagram
2.2. Potential energy surfaces and reaction paths
2.3. The Born-Oppenheimer approximation in detail: Adiabatic and diabatic representations
2.3.1. Separation of nuclei and electrons motion
2.3.2. Adiabatic representation
2.3.3. Diabatic representation
2.4. When potential energy surfaces do cross: Avoided crossings and conical intersections
2.5. Excited state molecular dynamics
References
Part II. Methods
3. Density-functional theory for electronic excited states
3.1. Overview
3.2. Linear-response (time-dependentยดยด) DFT
3.2.1. Theoretical formalism
3.2.1.1. Linear-response theory
3.2.1.2. Adiabatic approximation
3.2.1.3. Tamm-Dancoff approximation
3.2.1.4. Analytic gradients
3.2.2. Performance and practice
3.2.2.1. Restriction of the excitation manifold
3.2.2.2. Exchange-correlation functionals
3.2.2.3. Accuracy for vertical excitation energies
3.2.2.4. Visualization
3.2.3. Systemic problems
3.2.3.1. Description of charge transfer
3.2.3.2. Conical intersections
3.3. Excited-state Kohn-Sham theory: The DeltaSCF approach
3.3.1. Theory
3.3.1.1. General considerations
3.3.1.2. Orbital-optimized non-aufbau SCF solutions
3.3.1.3. Transition potential methods
3.3.2. Examples
3.4. Time-dependent Kohn-Sham theory:Real-timeยดยด TDDFT
3.4.1. Theory
3.4.2. Examples
References
4. Algebraic diagrammatic construction schemes for the simulation of electronic spectroscopies
4.1. Introduction
4.2. Theoretical background
4.2.1. Intermediate-state representation
4.2.2. State properties and geometries
4.2.3. The physical meaning of ISR basis states and EE-ADC matrix elements
4.2.4. Relation of different ADC schemes
4.3. Comparison of ADC to configuration interaction and coupled cluster methods
4.4. ADC variants for excited states
4.4.1. Semiempirical EE-ADC schemes
4.4.2. EE-ADC schemes for multireference systems
4.4.3. EE-ADC methods for X-ray spectroscopies
4.5. Computational spectroscopy in complex environments with ADC
4.6. Computational photochemistry with ADC
4.7. Outlook and concluding remarks
References
5. Multiconfigurational quantum chemistry: The CASPT2 method
5.1. Introduction
5.2. Prelude: CASSCF
5.3. CASPT2 theory
5.3.1. CASPT2 fundamentals
5.3.1.1. The H0 operator
5.3.1.2. Defining the first-order interacting space
5.3.1.3. Computing the first-order interacting space and the second-order energy
5.3.2. The intruder state problem
5.3.3. Shift techniques
5.3.4. Alternative selection of the zeroth-order Hamiltonian
5.3.4.1. CASPT2 applied to an open-shell system
5.3.4.2. The gi family of corrections
5.3.4.3. The IPEA shift
5.3.4.4. Use of Koopmans matrices, CASPT2-K
5.3.4.5. The zeroth-order Hamiltonians of Dyall and Fink
5.3.4.6. Summary
5.4. Multistate CASPT2 theory
5.5. Performance
5.6. Future developments
5.7. Summary and conclusions
References
6. Machine learning methods in photochemistry and photophysics
6.1. Introduction
6.2. Machine learning models
6.2.1. Machine learning tasks
6.2.2. k-Nearest neighbor
6.2.3. Support vector machine
6.2.4. Kernel methods
6.2.5. Neural networks
6.3. Representations of molecules
6.3.1. Molecular strings and fingerprints
6.3.2. Molecular descriptors
6.3.3. Automatically generated descriptors
6.4. Training data for machine learning
6.4.1. Excited-state database across chemical space
6.4.2. Molecule-specific data generation
6.5. Applications of machine learning in photochemistry and photophysics
6.5.1. Machine learning-assisted high-throughput virtual screening
6.5.2. Machine learning-predicted electronic spectroscopy
6.5.3. Machine learning nonadiabatic molecular dynamics
6.5.4. Machine learning-extracted chemical insights from data
6.6. Summary
References
7. Polaritonic chemistry
7.1. Preliminary considerations on the electromagnetic field
7.2. Polaritonic eigenvalues and eigenstates
7.2.1. Cavity Born-Oppenheimer and vibrational strong coupling
7.2.2. Electronic strong coupling (ESC)
7.3. Polaritonic potential energy surfaces (PoPESs)
7.3.1. A didactical case: Azobenzene polaritonic potential energy surfaces (PoPESs)
7.3.2. Many molecules and dark states
7.4. Polariton dynamics and cavity losses
7.4.1. Nuclear dynamics in polaritonic systems: Full quantum vs semiclassical
7.5. Summary
References
Part III. Applications
8. First-principles modeling of dye-sensitized solar cells: From the optical properties of standalone dyes to the ...
8.1. Introduction
8.2. Computational modeling of DSSCs: Methods, limitations, and practical strategies
8.2.1. Generalities
8.2.2. Electronic structure and optical properties of dyes in solution
8.2.3. Electronic structure and optical properties of semiconductor materials and dye-sensitized interfaces
8.2.4. Machine learning and semiempirical methods applied to DSSCs
8.3. Design rules for Ru(II) sensitizers: The role of spin-orbit coupling (SOC)
8.4. Modeling the photophysics of Fe(II) metal complexes: Tools and findings
8.5. Interfacial properties of Fe-NHC-sensitized TiO2
8.6. Conclusions
References
9. Solar cells: Organic photovoltaic solar cells
9.1. Introduction
9.1.1. Organic photovoltaics
9.1.2. OPV materials
9.1.3. Models to describe charge generation in OSCs
9.2. Excitonic processes: Excited states at the donor/acceptor interfaces
9.2.1. Electronic structure methods to describe the excited states at D/A OPV interfaces
9.2.2. Analytical tools to characterize the excited-state wavefunction
9.2.3. Examples of polymer/fullerene OPV interfaces
9.3. Time-dependent processes: Excited-state dynamics in donor and donor/acceptor domains
9.3.1. Excited-state dynamics: Brief overview of nonadiabatic surface hopping and multiconfiguration time-dependent Hartr ...
9.3.2. Excited-state dynamics of oligothiophenes as prototypes for P3HT
9.3.3. Examples of polythiophene-/fullerene-based interfaces
9.4. Conclusions
References
10. Perovskite-based solar cells
10.1. Introduction
10.2. First-principles modeling of perovskites
10.3. Point defects in perovskites
10.3.1. First-principles modeling of point defects
10.3.2. Ion migration in perovskite
10.3.3. Photochemistry of iodine Frenkel defects
10.4. Interfaces in perovskite solar cells
10.4.1. Understanding charge extraction at the perovskite/ETL interface
10.4.2. Chemical tuning of the perovskite/HTL interface
10.5. Degradation and passivation of metal-halide perovskites
10.5.1. Water-induced degradation of lead-halide perovskites
10.5.2. Instability of lead-free perovskites in water environment
10.5.3. Perovskite surface passivation
10.6. Summary
References
11. Thermally activated delayed fluorescence
11.1. Introduction
11.2. Excited states calculations
11.3. Condensed phase effects
11.4. Role of charge transfer and local excited states
11.5. Vibronic effects and rate calculations
11.6. Synopsis
References
12. DNA photostability
12.1. Photophysics of canonical nucleobases in the gas phase. Photostability
12.1.1. Absorption properties in the gas phase
12.1.2. Photophysical paths for purine nucleobases
12.1.3. Excited-state dynamics of purine nucleobases
12.1.4. Photophysical paths for pyrimidine nucleobases
12.1.5. Excited-state dynamics of pyrimidine nucleobases
12.2. Photophysics of canonical nucleobases in solution. Impact of the solvent effects into the photostability
12.2.1. Purine nucleobases
12.2.1.1. Absorption spectra
12.2.1.2. Photophysical paths
12.2.1.3. Excited-state dynamics
12.2.2. Pyrimidine nucleobases
12.2.2.1. Absorption spectra
12.2.2.2. Photophysical paths
12.2.2.3. Excited-state dynamics
12.3. Photophysics of modified nucleobases. Impact of the substitution effects into the photostability
12.3.1. Addition of external groups into the pyrimidine/purine core
12.3.1.1. Methylation (CH3)
12.3.1.2. Amination (NH2)
12.3.1.3. Oxo incorporation (CO)
12.3.1.4. Other groups
12.3.2. Substitution of internal groups into the pyrimidine/purine core
12.3.2.1. Oxygen-by-sulfur or carbon-by-sulfur substitution
12.3.2.2. Carbon-by-nitrogen or nitrogen-by-carbon substitutions
12.4. Photophysics of canonical nucleobases in DNA/RNA environments. Photostability mechanisms
12.4.1. Single monomers embedded in a DNA/RNA environment
12.4.2. DNA/RNA light absorption and excited-state delocalization
12.4.3. Watson-Crick base pairing and interstrand charge transfer states. A doorway to proton transfer and photostability
12.5. Final remarks and future perspectives
References
13. Fluorescent proteins
13.1. Introduction
13.2. Modeling of absorption spectra
13.3. Frster resonance energy transfer
13.4. Photochemical reactions
13.5. Concluding remarks
References
14. Chemi- and bioluminescence: A practical tutorial on computational chemiluminescence
14.1. Introduction
14.2. Design of the methodology
14.3. Identification of the molecule responsible for chemiexcitation
14.3.1. Walsh correlation diagrams
14.3.2. Reaction paths for the chemiexcitation of small models
14.3.3. Activatorยดยด-chemiluminophoreยดยด configuration
14.4. Reaction paths of the isolated system
14.4.1. Formation of the chemiluminophore
14.4.2. Chemiexcitation
14.4.3. Light emission
14.4.4. Identification of relevant parameters in challenging systems
14.5. Solvent effects
14.6. Dynamical aspects
14.7. A perspective on future research directions
References
15. Chemi- and bioluminescence: Bioluminescence
15.1. Introduction
15.2. Bioluminescence, a reaction scheme of a chemiluminescent system catalyzed by a protein: Challenges for theoretical ...
15.2.1. Overview of a bioluminescent process
15.2.2. Generation of HEI
15.2.3. Decomposition of HEI to the light emitter
15.2.4. Emission of light
15.3. Tools and choices of the theoretical chemist: Divide to conquer
15.3.1. Performing calculation of a small chemiluminescent model in vacuum
15.3.2. Performing calculation of a chemiluminescent model in the solvent
15.3.3. Performing calculation of a bioluminescent model in the protein
15.3.3.1. Completing the protein
15.3.3.2. Docking the ligand in the protein
15.3.3.3. Getting the force field parameters for the substrate
15.3.3.4. Relaxing the structure
15.3.3.5. QM/MM calculations
15.3.4. Modeling spectral shape
15.4. Modeling formation of HEI: Case of firefly bioluminescent system
15.4.1. From d-luciferin substrate to d-luciferyl adenylate intermediate
15.4.2. Approach of dioxygen to the d-luciferyl adenylate intermediate
15.4.3. Deciphering between reaction schemes for the reaction of dioxygen with the d-luciferyl adenylate intermediate
15.4.4. Formation of the dioxetanone ring: Addition-elimination mechanism?
15.5. Modeling decomposition of HEI leading to the light emitter in firefly
15.5.1. Failure of small models
15.5.2. Model in vacuum
15.5.3. Model in proteins
15.6. Modeling light emission
15.6.1. Challenges in modeling and experiments
15.6.2. Nature of the light emitter of firefly: The oxyluciferin
15.6.3. Use of analogs of firefly oxyluciferin
15.6.4. Influence of the protein on the emitted light color
15.6.5. Example of one mutation in luciferase
15.6.6. Different colors in different luciferases
15.6.7. Modeling emission spectra for substrate analogs
15.7. Conclusion
References
16. Photocatalysis
16.1. Introduction and historical overview
16.2. Fundamental mechanism of heterogeneous photocatalysis
16.2.1. Light absorption and photoexcitation
16.2.2. Charge migration and recombination
16.2.3. Photoredox reactions
16.3. Brief overview of computational methodologies
16.3.1. Kohn-Sham density functional theory (KS-DFT)
16.3.2. Multireference and multiconfigurational methods
16.3.3. Combined quantum mechanical and molecular mechanical (QM/MM) methods
16.4. Computational studies
16.4.1. TiO2
16.4.2. ZnO
16.4.3. MoS2
16.4.4. UiO-66
16.4.5. PCN-601
16.4.6. g-C3N4
16.5. Outlook
References
17. Nonlinear spectroscopies
17.1. Introduction
17.2. Basic concepts
17.2.1. Introduction to the Liouville space
17.2.2. The displaced Brownian oscillator model
17.2.3. Including solvent effects through energy-gap correlation functions
17.3. Linear absorption
17.3.1. Linear spectroscopy in the Liouville space
17.3.1.1. Spectral lineshapes in linear absorption
17.3.2. The nuclear ensemble approach
17.3.2.1. Automated NEA broadenings with machine learning
17.4. Nonlinear spectroscopy
17.4.1. Nonlinear spectroscopy in the Liouville space
17.4.2. Nonlinear spectroscopies within a static approximation
17.4.2.1. The nuclear ensemble approach to nonlinear spectroscopy
17.4.3. Spectral broadenings in nonlinear spectroscopies
17.4.3.1. Time-resolved NEA approach to nonlinear spectroscopy
17.5. Overview
References
18. Mechano-photochemistry
18.1. Introduction
18.2. Mechanochemical models
18.3. Methodology and models in mechano-photochemistry
18.3.1. Absorption and emission tuning
18.3.2. Triplet energy transfer modulation
18.3.3. Mechanical effect on conical intersections/avoided crossings
18.3.4. Non-adiabatic molecular dynamics with explicit inclusion of mechanical external forces
18.3.5. Substituent effect as mechanical entity
18.4. Mechanical control of molecular photophysics and photoreactivity
18.4.1. Excitation energy
18.4.1.1. Complete mechanochemical control of the absorption spectrum
18.4.1.2. Mechanochemical control of absorption spectrum in photoswitches
18.4.2. Mechanochemical control of photochemical reactivity
18.4.2.1. Mechanical control of trans-cis photoisomerization quantum yield
18.4.2.2. Mechanical control of photoswitches in molecular solar thermal energy storage systems
18.4.2.3. Mechanical control of photoswitching of stilbenes with molecular force probes
18.4.2.4. Mechanical control of triplet-sensitized oxa-di-ฯ-methane rearrangement
18.5. Conclusions and perspectives
References
Part IV. Synergy with experimental approaches
19. Interplay between computations and experiments in photochemistry
19.1. Introduction
19.2. Correlation between the principal experimental techniques used in photochemistry and computational methods
19.2.1. UV-Vis spectroscopy
19.2.2. Photoluminescence spectroscopy, fluorescence, and phosphorescence
19.2.3. Time-resolved spectroscopy and transient absorption spectroscopy (TAS)
19.2.4. Other techniques
19.3. Different case studies combining theory and experiments
19.3.1. Design of new sunscreens by computational methods
19.3.2. Spectroscopic characterization of different families of photoswitches
19.3.3. Better understanding time-resolved spectroscopy
19.3.4. Two-photon absorption
19.4. Conclusions
References
Index
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