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Abstract:

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.

Registro:

Documento: Artículo
Título:Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework
Autor:Morzan, U.N.; Ramírez, F.F.; Oviedo, M.B.; Sánchez, C.G.; Scherlis, D.A.; Lebrero, M.C.G.
Filiación:Departamento de Quimica Inorganica, Analitica y Quimica Fisica/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria, Pab. II, Buenos Aires (C1428EHA), Argentina
Departamento de Matemática y Física, Facultad de Ciencias Químicas, Ciudad Universitaria, X5000HUA Córdoba, Argentina
Instituto de Química y Fisicoquímica Biológicas, IQUIFIB, CONICET, Argentina
Palabras clave: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
Año:2014
Volumen:140
Número:16
DOI: http://dx.doi.org/10.1063/1.4871688
Título revista:Journal of Chemical Physics
Título revista abreviado:J Chem Phys
ISSN:00219606
CODEN:JCPSA
CAS:formamide, 75-12-7; heme, 14875-96-8; iron, 14093-02-8, 53858-86-9, 7439-89-6; water, 7732-18-5; Bacterial Proteins; flavohemoprotein, Bacteria; formamide; Formamides; Heme; Hemeproteins; Iron; Water
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00219606_v140_n16_p_Morzan

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Citas:

---------- APA ----------
Morzan, U.N., Ramírez, F.F., Oviedo, M.B., Sánchez, C.G., Scherlis, D.A. & Lebrero, M.C.G. (2014) . Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework. Journal of Chemical Physics, 140(16).
http://dx.doi.org/10.1063/1.4871688
---------- CHICAGO ----------
Morzan, U.N., Ramírez, F.F., Oviedo, M.B., Sánchez, C.G., Scherlis, D.A., Lebrero, M.C.G. "Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework" . Journal of Chemical Physics 140, no. 16 (2014).
http://dx.doi.org/10.1063/1.4871688
---------- MLA ----------
Morzan, U.N., Ramírez, F.F., Oviedo, M.B., Sánchez, C.G., Scherlis, D.A., Lebrero, M.C.G. "Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework" . Journal of Chemical Physics, vol. 140, no. 16, 2014.
http://dx.doi.org/10.1063/1.4871688
---------- VANCOUVER ----------
Morzan, U.N., Ramírez, F.F., Oviedo, M.B., Sánchez, C.G., Scherlis, D.A., Lebrero, M.C.G. Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework. J Chem Phys. 2014;140(16).
http://dx.doi.org/10.1063/1.4871688