Hyperfine Coupling Tensors of the Benzosemiquinone Radical Anion from Car–Parrinello Molecular Dynamics

Asher, James R.; Kaupp, Martin

doi:10.1002/cphc.200600325

Cited by 22 publications

(23 citation statements)

References 50 publications

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“…However, it was demonstrated that the cusp problem can be overcome by adding very tight s functions to the Gaussian‐type basis sets . The verification of Gaussian‐type bases demonstrated that the double‐ζ sets are definitely too small for A iso calculations on isolated atoms, whereas they were successful in the case of polyatomic main‐group radicals including iminoxyls, nitroxides, and semiquinones . Surprisingly, inspection of Table shows that the isotropic HFCCs ( A iso ) due to the phosphorus nucleus in •PR 2 , when calculated at the DFT level, are rather sensitive to the size of the basis set.…”

Section: Resultsmentioning

confidence: 99%

Density functional theory and ab initio studies on hyperfine coupling constants of phosphinyl radicals

Witwicki

2018

Int J of Quantum Chemistry

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The 31P hyperfine coupling constants for various phosphinyl radicals were calculated using density functional theory (DFT) as well as the ab initio orbital‐optimized spin‐component‐scaled MP2 (OO‐SCS‐MP2) and coupled cluster methods (with relaxed and unrelaxed density). However before that, electron correlation in phosphinyl radicals was investigated by means of the fractional occupation number weighted electron density (FOD). The isotropic hyperfine coupling constants for phosphinyl radicals posed a considerable challenge to DFT; among other issues, the well‐known functional B3LYP substantially underperformed, but TPSS0 provided highly accurate results. Two tested double hybrid functionals, namely B2PLYP and mPW2PLYP, and OO‐SCS‐MP2 were found to be reasonably accurate. The unbalanced description of spin polarization in the valance region was identified as the root of the problems of DFT methods with correct prediction of the isotropic hyperfine coupling constants. In calculations at the coupled cluster level, relaxed and unrelaxed density matrices were tested and both were proved to provide highly satisfactory results for phosphinyl radicals. This was confirmed for a set of small paramagnetic species.

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Section: Resultsmentioning

confidence: 99%

Density functional theory and ab initio studies on hyperfine coupling constants of phosphinyl radicals

Witwicki

2018

Int J of Quantum Chemistry

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“…The mechanism of solvent effect on A F was compared to the reasons for EPR parameters changes reported for semiquinones [23][24][25][26][27][28][29][30][31] and nitroxides [32][33][34][35][36] . For these two types of radicals the solvent was shown to significantly alter their molecular and electronic structures, which brought about changes in the EPR parameters.…”

Section: Discussionmentioning

confidence: 99%

Toward an Understanding of the Ambiguous Electron Paramagnetic Resonance Spectra of the Iminoxy Radical from o-Fluorobenzaldehyde Oxime: Density Functional Theory and ab Initio Studies

Witwicki

Jezierska

2015

J. Phys. Chem. A

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Iminoxy radicals (R1R2C═N—O•) possess an inherent ability to exist as E and Z isomers. Although isotropic hyperfine couplings for the species with R1 = H allow one to distinguish between E and Z, unequivocal assignment of the parameters observed in the EPR spectra of the radicals without the hydrogen atom at the azomethine carbon to the right isomer is not a simple task. The iminoxyl derived from o-fluoroacetophenone oxime (R1 = CH3 and R2 = o-FC6H5) appears to be a case in point. Moreover, for its two isomers the rotation of the o-FC6H5 group brings into existence the syn and anti conformers, depending on the mutual orientation of the F atom and C═N—O• group, making a description of hyperfine couplings to structure even more challenging. To accomplish this, a vast array of theoretical methods (DFT, OO-SCS-MP2, QCISD) was used to calculate the isotropic hyperfine couplings. The comparison between experimental and theoretical values revealed that the E isomer is the dominant radical form, for which a fast interconversion between anti and syn conformers is expected. In addition, the origin of the significant AF increase with solvent polarity was analyzed.

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“…The inclusion of the HFC term is highly considerable, specifically for the phosphorus atoms, which active spin nuclei show a 100% natural abundance [24] and strongly affect the behavior of unpaired electrons in the PO(OR) 2 and 1 H atoms with the active nuclear spin is 99.985% 24 ) in water molecules and the ribose hydroxyls. In our computations the HFC for the named atoms includes the both isotropic and anisotropic terms; their analytical expressions might be found elsewhere [20][21][22]. The RP term includes the spin-spin electron coupling terms [22,23,[26][27][28] arising from the interaction between the AMP -, OH and hydrogens of water molecules and ribose hydroxyls.…”

Section: Geometry Parameters and Computationsmentioning

confidence: 99%

“…The gradient-corrected BLYP functional [30] is used with a plane-wave basis (cutoff: 70.0 Ry) and norm-conserving pseudopotentials of Troullier-Martins type [20][21][22]. The temperature of the simulation is set to 310 K. For the solvated system like ours the thermostatting is accomplished by rescaling the kinetic energy of the nuclei whenever the temperature is deviated more than a specific tolerance [30] (±10 K) from the desired 310 K temperature.…”

Section: Geometry Parameters and Computationsmentioning

confidence: 99%

“…The Zundel cation, located at the interface of i and ii regions, is introduced into the subvolume to give a chance for the O -radical, see below, to interact with the proton and to imitate the acidic properties of living cell media. The distances between the water molecules in the periodic box, including The spin effects in the nucleotide polymerization initially assumed, the standard energy functional requires its enlargement by adding two specific terms: the hyperfine coupling (HFC) term and the radical pair RP term [20][21][22][23]. The inclusion of the HFC term is highly considerable, specifically for the phosphorus atoms, which active spin nuclei show a 100% natural abundance [24] and strongly affect the behavior of unpaired electrons in the PO(OR) 2 and 1 H atoms with the active nuclear spin is 99.985% 24 ) in water molecules and the ribose hydroxyls.…”

Section: Geometry Parameters and Computationsmentioning

confidence: 99%

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Spin effects govern DNA/RNA nucleotide polymerization

Tulub¹

2011

JBPC

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A new radical mechanism of nucleotide polymerization is found. The finding is based on the Car-Parrinello molecular dynamics computations at 310 K with an additional spin-spin coupling term for 31P and 1H atoms and a radical pair spin term included. The mechanism is initiated by a creation of a high-energy spin-separated Mg-ATP complex in a triplet state in which the Mg prefers an uncommon chelation to the O2-O3 oxygens of the ATP. The cleavage of the complex produces the AMP-and O-radicals. The latter captures a proton from acidic solution (the Zundel cation) that converts it into the OH radical. The process agrees with the protoncoupled electron transfer (PCET) mechanism. Through interacting with the HO-C3' group of the deoxyribose/ribose the OH radical captures its hydrogen atom. The process is accompanied by producing water and the AMP radical. The AMP-and AMP radicals then interact yielding a dimer. The described mechanism is easily generalized for a bigger number of adjoining nucleotides and their type. The radical mechanism is highly sensitive to the AMP-OH radical pair spin symmetry and the radius of the OH diffusion. This confines the operation of the radical mechanism: it is applicable to nucleotide polymerization through the HO-C3' group of deoxyribose/ribose (DNA/RNA polymerization) and inapplicable through the HO-C2' group of ribose (RNA)-a result that nature has developed over evolution.

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Hyperfine Coupling Tensors of the Benzosemiquinone Radical Anion from Car–Parrinello Molecular Dynamics

Cited by 22 publications

References 50 publications

Density functional theory and ab initio studies on hyperfine coupling constants of phosphinyl radicals

Density functional theory and ab initio studies on hyperfine coupling constants of phosphinyl radicals

Toward an Understanding of the Ambiguous Electron Paramagnetic Resonance Spectra of the Iminoxy Radical from o-Fluorobenzaldehyde Oxime: Density Functional Theory and ab Initio Studies

Spin effects govern DNA/RNA nucleotide polymerization

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