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 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.
Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires (C1428EHA), Argentina.
Uriel N
UN
Morzan
Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires (C1428EHA), Argentina.
Francisco F
FF
Ramírez
Departamento de Matemática y Física, Facultad de Ciencias Químicas, INFIQC, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina.
M Belén
MB
Oviedo
Departamento de Matemática y Física, Facultad de Ciencias Químicas, INFIQC, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina.
Cristián G
CG
Sánchez
Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires (C1428EHA), Argentina.
Damián A
DA
Scherlis
Instituto de Química y Fisicoquímica Biológicas, IQUIFIB, CONICET, Argentina.
Mariano C González
MC
Lebrero
D001426:Bacterial Proteins / Q000737:chemistry*; D004583:Electrons; D005559:Formamides / Q000737:chemistry; D006418:Heme / Q000737:chemistry; D006420:Hemeproteins / Q000737:chemistry*; D007501:Iron / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D011789:Quantum Theory; D014867:Water / Q000737:chemistry
D001426:Bacterial Proteins; D005559:Formamides; D006420:Hemeproteins; C086193:flavohemoprotein, Bacteria; D014867:Water; D006418:Heme; C031066:formamide; D007501:Iron