Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework

This article presents a time dependent density functional theory (TDDFT) implementation to propagate the Kohn-Sham equations in real time, including the effects of a molecular environment through a Quantum-Mechanics Molecular-Mechanics (QM-MM) hamiltonian. The code delivers an all-electron descripti...

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Autor principal:	Morzan, Uriel Nicolas
Publicado:	2014
Materias:	Computer graphics Density functional theory Dynamics Molecules Program processors Quantum theory Chemical environment Complex environments Exchange correlation energy Gaussian basis functions Graphics Processing Unit Kohn Sham equations Molecular environment Time dependent density functional theory Hamiltonians bacterial protein flavohemoprotein, Bacteria formamide formamide derivative heme hemoprotein iron water chemistry electron molecular dynamics quantum theory Bacterial Proteins Electrons Formamides Heme Hemeproteins Iron Molecular Dynamics Simulation Quantum Theory Water
Acceso en línea:	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00219606_v140_n16_p_Morzan http://hdl.handle.net/20.500.12110/paper_00219606_v140_n16_p_Morzan
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

id	paper:paper_00219606_v140_n16_p_Morzan
record_format	dspace
spelling	paper:paper_00219606_v140_n16_p_Morzan2023-06-08T14:44:25Z Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework Morzan, Uriel Nicolas Computer graphics Density functional theory Dynamics Molecules Program processors Quantum theory Chemical environment Complex environments Exchange correlation energy Gaussian basis functions Graphics Processing Unit Kohn Sham equations Molecular environment Time dependent density functional theory Hamiltonians bacterial protein flavohemoprotein, Bacteria formamide formamide derivative heme hemoprotein iron water chemistry electron molecular dynamics quantum theory Bacterial Proteins Electrons Formamides Heme Hemeproteins Iron Molecular Dynamics Simulation Quantum Theory Water This article presents a time dependent density functional theory (TDDFT) implementation to propagate the Kohn-Sham equations in real time, including the effects of a molecular environment through a Quantum-Mechanics Molecular-Mechanics (QM-MM) hamiltonian. The code delivers an all-electron description employing Gaussian basis functions, and incorporates the Amber force-field in the QM-MM treatment. The most expensive parts of the computation, comprising the commutators between the hamiltonian and the density matrix - required to propagate the electron dynamics -, and the evaluation of the exchange-correlation energy, were migrated to the CUDA platform to run on graphics processing units, which remarkably accelerates the performance of the code. The method was validated by reproducing linear-response TDDFT results for the absorption spectra of several molecular species. Two different schemes were tested to propagate the quantum dynamics: (i) a leap-frog Verlet algorithm, and (ii) the Magnus expansion to first-order. These two approaches were confronted, to find that the Magnus scheme is more efficient by a factor of six in small molecules. Interestingly, the presence of iron was found to seriously limitate the length of the integration time step, due to the high frequencies associated with the core-electrons. This highlights the importance of pseudopotentials to alleviate the cost of the propagation of the inner states when heavy nuclei are present. Finally, the methodology was applied to investigate the shifts induced by the chemical environment on the most intense UV absorption bands of two model systems of general relevance: the formamide molecule in water solution, and the carboxy-heme group in Flavohemoglobin. In both cases, shifts of several nanometers are observed, consistently with the available experimental data. © 2014 AIP Publishing LLC. Fil:Morzan, U.N. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 2014 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00219606_v140_n16_p_Morzan http://hdl.handle.net/20.500.12110/paper_00219606_v140_n16_p_Morzan
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	Computer graphics Density functional theory Dynamics Molecules Program processors Quantum theory Chemical environment Complex environments Exchange correlation energy Gaussian basis functions Graphics Processing Unit Kohn Sham equations Molecular environment Time dependent density functional theory Hamiltonians bacterial protein flavohemoprotein, Bacteria formamide formamide derivative heme hemoprotein iron water chemistry electron molecular dynamics quantum theory Bacterial Proteins Electrons Formamides Heme Hemeproteins Iron Molecular Dynamics Simulation Quantum Theory Water
spellingShingle	Computer graphics Density functional theory Dynamics Molecules Program processors Quantum theory Chemical environment Complex environments Exchange correlation energy Gaussian basis functions Graphics Processing Unit Kohn Sham equations Molecular environment Time dependent density functional theory Hamiltonians bacterial protein flavohemoprotein, Bacteria formamide formamide derivative heme hemoprotein iron water chemistry electron molecular dynamics quantum theory Bacterial Proteins Electrons Formamides Heme Hemeproteins Iron Molecular Dynamics Simulation Quantum Theory Water Morzan, Uriel Nicolas Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework
topic_facet	Computer graphics Density functional theory Dynamics Molecules Program processors Quantum theory Chemical environment Complex environments Exchange correlation energy Gaussian basis functions Graphics Processing Unit Kohn Sham equations Molecular environment Time dependent density functional theory Hamiltonians bacterial protein flavohemoprotein, Bacteria formamide formamide derivative heme hemoprotein iron water chemistry electron molecular dynamics quantum theory Bacterial Proteins Electrons Formamides Heme Hemeproteins Iron Molecular Dynamics Simulation Quantum Theory Water
description	This article presents a time dependent density functional theory (TDDFT) implementation to propagate the Kohn-Sham equations in real time, including the effects of a molecular environment through a Quantum-Mechanics Molecular-Mechanics (QM-MM) hamiltonian. The code delivers an all-electron description employing Gaussian basis functions, and incorporates the Amber force-field in the QM-MM treatment. The most expensive parts of the computation, comprising the commutators between the hamiltonian and the density matrix - required to propagate the electron dynamics -, and the evaluation of the exchange-correlation energy, were migrated to the CUDA platform to run on graphics processing units, which remarkably accelerates the performance of the code. The method was validated by reproducing linear-response TDDFT results for the absorption spectra of several molecular species. Two different schemes were tested to propagate the quantum dynamics: (i) a leap-frog Verlet algorithm, and (ii) the Magnus expansion to first-order. These two approaches were confronted, to find that the Magnus scheme is more efficient by a factor of six in small molecules. Interestingly, the presence of iron was found to seriously limitate the length of the integration time step, due to the high frequencies associated with the core-electrons. This highlights the importance of pseudopotentials to alleviate the cost of the propagation of the inner states when heavy nuclei are present. Finally, the methodology was applied to investigate the shifts induced by the chemical environment on the most intense UV absorption bands of two model systems of general relevance: the formamide molecule in water solution, and the carboxy-heme group in Flavohemoglobin. In both cases, shifts of several nanometers are observed, consistently with the available experimental data. © 2014 AIP Publishing LLC.
author	Morzan, Uriel Nicolas
author_facet	Morzan, Uriel Nicolas
author_sort	Morzan, Uriel Nicolas
title	Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework
title_short	Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework
title_full	Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework
title_fullStr	Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework
title_full_unstemmed	Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework
title_sort	electron dynamics in complex environments with real-time time dependent density functional theory in a qm-mm framework
publishDate	2014
url	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00219606_v140_n16_p_Morzan http://hdl.handle.net/20.500.12110/paper_00219606_v140_n16_p_Morzan
work_keys_str_mv	AT morzanurielnicolas electrondynamicsincomplexenvironmentswithrealtimetimedependentdensityfunctionaltheoryinaqmmmframework
_version_	1768543453633839104

Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework

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