Polarizable Embedding For The Algebraic-diagrammatic Construction Scheme: Investigating Photoexcitations In Large Biomolecular Systems (bestmasters)

Maximilian Scheurer presents a method for modeling excited states in atomistic, heterogeneous environments. The method utilizes the polarizable embedding (PE) model to mimic electrostatic and polarization interactions of a molecule with its environment. For high-level modeling of the molecules excited states, the algebraic-diagrammatic construction scheme for the polarization propagator (ADC) is employed. The presented work outlines the theoretical foundations of PE and ADC and the combination of both methods, termed PE-ADC. The accuracy of PE-ADC is tested, and the charge-transfer (CT) excitation in the dodecin protein is studied. This book presents a comprehensive elaboration on the new PE-ADC method and a state-of-the-art application of PE-ADC to a photo-biochemical process. Contents Comprehensive Introduction to Polarizable Embedding Models Derivation of the Perturbative PE-ADC Approach and Benchmark Case Study of a Flavoprotein Quenching Mechanism Target Groups Lecturers and students in computational photochemistry Computational chemists in the field of solvent modeling The Author Maximilian Scheurer studied Biochemistry and is now a PhD student in the Theoretical and Computational Chemistry group of Prof. Dr. Andreas Dreuw at the Interdisciplinary for Scientific Computing at Heidelberg University, Germany. His main research focus is the development of ab-initio methods for excited states, molecular properties, and application of such methods to photochemical processes in biomolecular systems Abstract 6 Abbreviations 8 Contents 10 1 Introduction 12 2 Theoretical Aspects 16 2.1 Second Quantization 16 2.1.1 Fock Space 16 2.1.2 Elementary Operators 17 2.1.3 Operators in Second Quantization 18 2.2 Hartree-Fock Theory 20 2.3 Algebraic-Diagrammatic Construction 25 2.4 Polarizable Embedding 26 2.4.1 Prerequisites 27 2.4.2 Interaction Hamiltonian 29 2.4.3 The Effective PE Operator 34 3 Combination of PE and ADC 39 4 Implementation 42 4.1 Motivation and Design Goals 42 4.2 Pilot Version of the CPPE Library 45 4.2.1 Implementation of CPPE-internal PE Routines 47 4.3 Code Availability 50 5 Computational Methodology 51 5.1 Para-Nitroaniline with Water Clusters 51 5.2 Lumiflavin in Bulk Solvent 52 5.3 Lumiflavin Embedded in Dodecin Environment 55 6 Results and Discussion 58 6.1 para-Nitroaniline in Presence of Water Clusters 58 6.2 Lumiflavin in Bulk Solvent 62 6.3 Protein Environment Effects on the Charge-Transfer Excitation in Dodecin 68 7 Conclusions and Outlook 74 Notes 76 Bibliography 77 A Original Implementation of PE in Q-Chem 95 A.1 The PeCalcHandler Class 95 A.2 Interface to PElib 96 A.3 Interface to CPPE-internal Back-End 97 B Recasting the Interaction Hamiltonian 99 Publication List 102 Front Matter ....Pages I-X Introduction (Maximilian Scheurer)....Pages 1-4 Theoretical Aspects (Maximilian Scheurer)....Pages 5-27 Combination of PE and ADC (Maximilian Scheurer)....Pages 29-31 Implementation (Maximilian Scheurer)....Pages 33-41 Computational Methodology (Maximilian Scheurer)....Pages 43-49 Results and Discussion (Maximilian Scheurer)....Pages 51-66 Conclusions and Outlook (Maximilian Scheurer)....Pages 67-68 Back Matter ....Pages 69-97