PMID- 24784251
OWN - NLM
STAT- MEDLINE
DCOM- 20150416
LR  - 20140505
IS  - 1089-7690 (Electronic)
IS  - 0021-9606 (Linking)
VI  - 140
IP  - 16
DP  - 2014 Apr 28
TI  - Electron dynamics in complex environments with real-time time dependent density 
      functional theory in a QM-MM framework.
PG  - 164105
LID - 10.1063/1.4871688 [doi]
AB  - 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.
FAU - Morzan, Uriel N
AU  - Morzan UN
AD  - Departamento de Quimica Inorganica, Analitica y Quimica Fisica/INQUIMAE, Facultad 
      de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad 
      Universitaria, Pab. II, Buenos Aires (C1428EHA), Argentina.
FAU - Ramirez, Francisco F
AU  - Ramirez FF
AD  - Departamento de Quimica Inorganica, Analitica y Quimica Fisica/INQUIMAE, Facultad 
      de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad 
      Universitaria, Pab. II, Buenos Aires (C1428EHA), Argentina.
FAU - Oviedo, M Belen
AU  - Oviedo MB
AD  - Departamento de Matematica y Fisica, Facultad de Ciencias Quimicas, INFIQC, 
      Universidad Nacional de Cordoba, Ciudad Universitaria, X5000HUA Cordoba, 
      Argentina.
FAU - Sanchez, Cristian G
AU  - Sanchez CG
AD  - Departamento de Matematica y Fisica, Facultad de Ciencias Quimicas, INFIQC, 
      Universidad Nacional de Cordoba, Ciudad Universitaria, X5000HUA Cordoba, 
      Argentina.
FAU - Scherlis, Damian A
AU  - Scherlis DA
AD  - Departamento de Quimica Inorganica, Analitica y Quimica Fisica/INQUIMAE, Facultad 
      de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad 
      Universitaria, Pab. II, Buenos Aires (C1428EHA), Argentina.
FAU - Lebrero, Mariano C Gonzalez
AU  - Lebrero MC
AD  - Instituto de Quimica y Fisicoquimica Biologicas, IQUIFIB, CONICET, Argentina.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - J Chem Phys
JT  - The Journal of chemical physics
JID - 0375360
RN  - 0 (Bacterial Proteins)
RN  - 0 (Formamides)
RN  - 0 (Hemeproteins)
RN  - 0 (flavohemoprotein, Bacteria)
RN  - 059QF0KO0R (Water)
RN  - 42VZT0U6YR (Heme)
RN  - 4781T907ZS (formamide)
RN  - E1UOL152H7 (Iron)
SB  - IM
MH  - Bacterial Proteins/*chemistry
MH  - *Electrons
MH  - Formamides/chemistry
MH  - Heme/chemistry
MH  - Hemeproteins/*chemistry
MH  - Iron/chemistry
MH  - Molecular Dynamics Simulation
MH  - *Quantum Theory
MH  - Water/chemistry
EDAT- 2014/05/03 06:00
MHDA- 2015/04/17 06:00
CRDT- 2014/05/03 06:00
PHST- 2014/05/03 06:00 [entrez]
PHST- 2014/05/03 06:00 [pubmed]
PHST- 2015/04/17 06:00 [medline]
AID - 10.1063/1.4871688 [doi]
PST - ppublish
SO  - J Chem Phys. 2014 Apr 28;140(16):164105. doi: 10.1063/1.4871688.