Solvent effects on peroxynitrite structure and properties from QM/MM simulations
We have investigated the structure and the vibrational spectrum of peroxynitrite anion in aqueous solution by means of combined quantum-classical (QM/MM) molecular dynamics simulations. In our QM/MM scheme, the reactant was modeled using density functional theory with a Gaussian basis set and the so...
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2005
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| Acceso en línea: | https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_10895639_v109_n42_p9598_Lebrero http://hdl.handle.net/20.500.12110/paper_10895639_v109_n42_p9598_Lebrero |
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paper:paper_10895639_v109_n42_p9598_Lebrero2023-06-08T16:06:20Z Solvent effects on peroxynitrite structure and properties from QM/MM simulations Computer simulation Molecular dynamics Molecular structure Probability density function Quantum theory Solvents Anharmonicity Density functional theory Peroxynitrite structure Solvent effects Nitrogen compounds peroxynitrous acid water article chemical model chemical structure chemistry computer simulation solution and solubility Computer Simulation Models, Chemical Molecular Structure Peroxynitrous Acid Solutions Water We have investigated the structure and the vibrational spectrum of peroxynitrite anion in aqueous solution by means of combined quantum-classical (QM/MM) molecular dynamics simulations. In our QM/MM scheme, the reactant was modeled using density functional theory with a Gaussian basis set and the solvent was described using the mean-field TIP4P and the polarizable TIP4P-FQ force fields. The choice of basis sets, functionals and force field parameters has been validated by performing calculations on isolated peroxynitrite and on small peroxynitrite-water complexes. Poor values for isolated peroxynitrite structural properties and vibrational frequencies are found for most ab initio methods, particularly regarding the ON-OO- bond distance and the harmonic stretching frequency, probably due to the singlet-triplet instability found in the HF wave function. On the other hand, DFT methods yield results in better agreement with high level CCSD(T) ab initio calculations. We have computed the vibrational spectrum for aqueous peroxynitrite by calculating the Fourier transform of the velocity autocorrelation function extracted from the QM-MM molecular dynamics simulations. Our computational scheme, which allows for the inclusion of both anharmonicity and solvent effects, is able to clarify previous discrepancies regarding the experimental spectra assignments and to shed light on the subtle interplay between solvation and peroxynitrite structure and properties. © 2005 American Chemical Society. 2005 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_10895639_v109_n42_p9598_Lebrero http://hdl.handle.net/20.500.12110/paper_10895639_v109_n42_p9598_Lebrero |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
Computer simulation Molecular dynamics Molecular structure Probability density function Quantum theory Solvents Anharmonicity Density functional theory Peroxynitrite structure Solvent effects Nitrogen compounds peroxynitrous acid water article chemical model chemical structure chemistry computer simulation solution and solubility Computer Simulation Models, Chemical Molecular Structure Peroxynitrous Acid Solutions Water |
| spellingShingle |
Computer simulation Molecular dynamics Molecular structure Probability density function Quantum theory Solvents Anharmonicity Density functional theory Peroxynitrite structure Solvent effects Nitrogen compounds peroxynitrous acid water article chemical model chemical structure chemistry computer simulation solution and solubility Computer Simulation Models, Chemical Molecular Structure Peroxynitrous Acid Solutions Water Solvent effects on peroxynitrite structure and properties from QM/MM simulations |
| topic_facet |
Computer simulation Molecular dynamics Molecular structure Probability density function Quantum theory Solvents Anharmonicity Density functional theory Peroxynitrite structure Solvent effects Nitrogen compounds peroxynitrous acid water article chemical model chemical structure chemistry computer simulation solution and solubility Computer Simulation Models, Chemical Molecular Structure Peroxynitrous Acid Solutions Water |
| description |
We have investigated the structure and the vibrational spectrum of peroxynitrite anion in aqueous solution by means of combined quantum-classical (QM/MM) molecular dynamics simulations. In our QM/MM scheme, the reactant was modeled using density functional theory with a Gaussian basis set and the solvent was described using the mean-field TIP4P and the polarizable TIP4P-FQ force fields. The choice of basis sets, functionals and force field parameters has been validated by performing calculations on isolated peroxynitrite and on small peroxynitrite-water complexes. Poor values for isolated peroxynitrite structural properties and vibrational frequencies are found for most ab initio methods, particularly regarding the ON-OO- bond distance and the harmonic stretching frequency, probably due to the singlet-triplet instability found in the HF wave function. On the other hand, DFT methods yield results in better agreement with high level CCSD(T) ab initio calculations. We have computed the vibrational spectrum for aqueous peroxynitrite by calculating the Fourier transform of the velocity autocorrelation function extracted from the QM-MM molecular dynamics simulations. Our computational scheme, which allows for the inclusion of both anharmonicity and solvent effects, is able to clarify previous discrepancies regarding the experimental spectra assignments and to shed light on the subtle interplay between solvation and peroxynitrite structure and properties. © 2005 American Chemical Society. |
| title |
Solvent effects on peroxynitrite structure and properties from QM/MM simulations |
| title_short |
Solvent effects on peroxynitrite structure and properties from QM/MM simulations |
| title_full |
Solvent effects on peroxynitrite structure and properties from QM/MM simulations |
| title_fullStr |
Solvent effects on peroxynitrite structure and properties from QM/MM simulations |
| title_full_unstemmed |
Solvent effects on peroxynitrite structure and properties from QM/MM simulations |
| title_sort |
solvent effects on peroxynitrite structure and properties from qm/mm simulations |
| publishDate |
2005 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_10895639_v109_n42_p9598_Lebrero http://hdl.handle.net/20.500.12110/paper_10895639_v109_n42_p9598_Lebrero |
| _version_ |
1768542750849892352 |