Chemical Reactivity and Spectroscopy Explored From QM/MM Molecular Dynamics Simulations Using the LIO Code

Marcolongo, Juan P.; Zeida, Ari; Semelak, Jonathan A.; Foglia, Nicolás O.; Morzan, Uriel N.; Estrin, Darı́o A.; Lebrero, Mariano C. González; Scherlis, Damián A.

doi:10.3389/fchem.2018.00070

Cited by 32 publications

(42 citation statements)

References 61 publications

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“…Hence, the assessment of fluorescence lifetimes (τ ) of atomic species entails a stringent test of our development. To this end, equation 14 was implemented in a real time TDDFT code developed in our group based on Gaussian functions and pseudopotentials [48][49][50]. Details are given in the Supplemental Material.…”

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confidence: 99%

Dissipative Equation of Motion for Electromagnetic Radiation in Quantum Dynamics

et al. 2021

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The dynamical description of the radiative decay of an electronically excited state in realistic many-particle systems is an unresolved challenge. In the present investigation electromagnetic radiation of the charge density is approximated as the power dissipated by a classical dipole, to cast the emission in closed form as a unitary single-electron theory. This results in a formalism of unprecedented efficiency, critical for ab-initio modelling, which exhibits at the same time remarkable properties: it quantitatively predicts decay rates, natural broadening, and absorption intensities. Exquisitely accurate excitation lifetimes are obtained from time-dependent DFT simulations for C 2+ , B + and Be, of 0.565, 0.831 and 1.97 ns respectively, in accord with experimental values of 0.57±0.02, 0.86±0.07 and 1.77-2.5 ns. Hence, the present development expands the frontiers of quantum dynamics, bringing within reach first-principles simulations of a wealth of photophysical phenomena, from fluorescence to time-resolved spectroscopies.

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confidence: 99%

Dissipative Equation of Motion for Electromagnetic Radiation in Quantum Dynamics

et al. 2021

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“…MeSH/MeSand MeSSH/MeSSwere used as models of thiol and persulfide, respectively. Electronic structure calculations were performed with Gaussian09 (80) while QM/MM molecular dynamics (MD) simulations were performed using LIO (https://github.com/MALBECC/LIO), a software developed by the Group of Molecular Modeling in the Universidad de Buenos Aires, compiled with Amber14 (81,82). Dynamics visualizations and molecular drawings were performed with VMD 1.9.1 (83).…”

Section: Methodsmentioning

confidence: 99%

Acidity and nucleophilic reactivity of glutathione persulfide

Benchoam

Semelak

Cuevasanta

et al. 2020

Journal of Biological Chemistry

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Persulfides (RSSH/RSS-) participate in sulfur trafficking and metabolic processes, and are proposed to mediate the signaling effects of H2S. Despite their growing relevance, their chemical properties are poorly understood. Herein, we studied experimentally and computationally the formation, acidity, and nucleophilicity of glutathione persulfide (GSSH/GSS-), the derivative of the abundant cellular thiol, glutathione (GSH). We characterized the kinetics and equilibrium of GSSH formation from glutathione disulfide and H2S. A pKa of 5.45 for GSSH was determined, which is 3.49 units below that of GSH. The reactions of GSSH with the physiologically-relevant electrophiles peroxynitrite and hydrogen peroxide, as well as with the probe monobromobimane, were studied and compared with those of thiols. These reactions occurred through SN2 mechanisms. At neutral pH, GSSH reacted faster than GSH due to increased availability of the anion and, depending on the electrophile, increased reactivity. In addition, GSS- presented higher nucleophilicity with respect to a thiolate with similar basicity. This can be interpreted in terms of the so-called alpha effect, i.e. the increased reactivity of a nucleophile when the atom adjacent to the nucleophilic atom has high electron density. The magnitude of the alpha effect correlated with the Brønsted nucleophilic factor, βnuc, for the reactions with thiolates and with the ability of the leaving group. Our study constitutes the first determination of the pKa of a biological persulfide and the first examination of the alpha effect in sulfur nucleophiles, and sheds light on the chemical basis of the biological properties of persulfides.

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“…Nonadiabatic decay probabilities using excited-state molecular dynamics. Excitedstate AIMD was employed, as implemented in the LIO quantum-chemical package (https://github.com/MALBECC/lio) (31)(32)(33)(34), to analyze the influence of three key factors determining the optical properties of L-pyro-amm: 1) the formation of a SHB, 2) the presence of ammonium, and 3) the combination of ring deplanarization and carbonyl stretching. Our model system for this study was the L-pyro-amm dimer with a single SHB.…”

Section: Theoreticalmentioning

confidence: 99%

Short hydrogen bonds enhance nonaromatic protein-related fluorescence

Stephens

Qaisrani

Ruggiero

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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Fluorescence in biological systems is usually associated with the presence of aromatic groups. Here, by employing a combined experimental and computational approach, we show that specific hydrogen bond networks can significantly affect fluorescence. In particular, we reveal that the single amino acid L-glutamine, by undergoing a chemical transformation leading to the formation of a short hydrogen bond, displays optical properties that are significantly enhanced compared with L-glutamine itself. Ab initio molecular dynamics simulations highlight that these short hydrogen bonds prevent the appearance of a conical intersection between the excited and the ground states and thereby significantly decrease nonradiative transition probabilities. Our findings open the door to the design of new photoactive materials with biophotonic applications.

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Chemical Reactivity and Spectroscopy Explored From QM/MM Molecular Dynamics Simulations Using the LIO Code

Cited by 32 publications

References 61 publications

Dissipative Equation of Motion for Electromagnetic Radiation in Quantum Dynamics

Dissipative Equation of Motion for Electromagnetic Radiation in Quantum Dynamics

Acidity and nucleophilic reactivity of glutathione persulfide

Short hydrogen bonds enhance nonaromatic protein-related fluorescence

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