Category Archives: Review

Current status of deMon2k for the investigation of the early stages of matter irradiation by time-dependent DFT approaches

Density Functional Theory, Electron dynamics simulations, Methodology, QM/MM, Radiation chemistry, Review

Karwan A Omar, Feven A Korsaye, Rika Tandiana, Damien Tolu, Jean Deviers, Xiaojing Wu, Angela Parise, Aurelio Alvarez-Ibarra, Felix Moncada, Jesus Nain Pedroza-Montero, Daniel Mejía-Rodriguez, Nguyen-Thi Van-Oanh, Fabien Cailliez, Carine Clavaguéra, Karim Hasnaoui, Aurélien de la Lande. Eur. J. Special Topics, 2023. doi.org/10.1140/epjs/s11734-023-00905-6. Full text in HAL.

Special collection: Ultrafast Phenomena from attosecond to picosecond timescales: theory and experiments

We summarize in this article the recent progress made in our laboratories in the development of numerical approaches dedicated to investigating ultrafast physicochemical responses of biological matter subjected to ionizing radiations. Our modules are integrated into the deMon2k software which is a readily available program with highly optimized algorithms for conducting Auxiliary Density Functional Theory (ADFT) calculations. We have developed a computational framework based on Real-Time Time-dependent ADFT to simulate the electronic responses of molecular systems to strong perturbations, while molecular dynamics simulations in the ground and excited states (Ehrenfest dynamics) are available to simulate irradiation-induced ultrafast bond breaking/formation. Constrained ADFT and Multi-component ADFT have also been incorporated to simulate charge transfer processes and nuclear quantum effects, respectively. Finally, a coupling to polarizable force fields further permits to realistically account for the electrostatic effects that the systems’ environment has on the perturbed electron density. The code runs on CPU or hybrid CPU/GPU architectures affording simulations of systems comprised up to 1000 atoms at the DFT level with controlled numerical accuracy. We illustrate the applications of these methodologies by taking results from our recent articles that aimed principally at understanding experimental data from pulse radiolysis experiments.

Heme ligation in the gas phase

hemes and chlorophylls, Review

N. Shafizadeh, M.E. Crestoni, A. de la Lande, B Soep. Intern. Rev. Phys. Chem. 2021, 40, 365-404 . doi.org/10.1080/0144235X.2021.1952006. Link to of full text in HAL.

This review summarizes the state-of-the-art knowledge of heme ligation in the gas phase. The unique aspect of the gas phase approach is to allow a step-by-step ligation of heme and thus enables the analysis of the properties of -four, -five and -six coordinate hemes in vacuo, under conditions directly comparable with quantum calculations. This approach also allows the characterization of situations uncommon in Nature, completing the coordination spectrum of hemes: four coordinate heme and protonated heme, an intermediate between ferrous and ferric heme. Therefore, a complete set of systems is described for the ferrous and ferric cases and there is no discontinuity between the two oxidation states of iron, so that the same mechanisms are at work, donation and back donation of different strengths depending upon the ligand. The similarity of ligation properties in ferrous and ferric hemes is consistent with calculations of the electron density at the Fe atom level, rather independent of the formal oxidation state in contrast with the porphyrin cycle. Hemes spin states have been reviewed, for they identify the electronic distribution of the metal. In ligated ferrous and ferric hemes, we find that binding energy measurements combined with spectroscopy describe their properties most effectively.

Molecular simulations with in-deMon2k QM/MM, a tutorial-review

Density Functional Theory, Methodology, QM/MM, Review

Aurélien de La Lande, Aurelio Alvarez-Ibarra, Karim Hasnaoui, Fabien Cailliez, Xiaojing Wu, Tzonka Mineva, Jérôme Cuny, Patrizia Calaminici, Luis López-Sosa, Gerald Geudtner, Isabelle Navizet, Cristina Garcia Iriepa, Dennis R Salahub, Andreas M Köster. Molecules, 2019, 24, 1653.doi.org/10.3390/molecules24091653. Full text from publisher.

Article from the special issue: Multiscale Chemical Modeling and Simulations Using Quantum Mechanics/Molecular Mechanics (QM/MM))

deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born–Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton.