Conformational Behavior and Magnetic Properties of Organic Radicals Derived from Amino Acid Residues. The Dipeptide Analog of Glycine Radical

Barone, Vincenzo; Adamo, Carlo; Grand, André; Brunel, Y.; Fontecave, M.; Subra, R.

doi:10.1021/ja00108a026

Cited by 33 publications

(41 citation statements)

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“…34,35 This model has been used to test the performances of a number of widely used exchange and correlation functionals in the evaluation of the hfc and g-tensor values, employing several popular basis sets. Next the effects both of solvent and vibrational averaging by low frequency motions at the radical center have been taken into the proper account.…”

Section: Complete Structural and Magnetic Characterization Of Biologimentioning

confidence: 99%

Complete structural and magnetic characterization of biological radicals in solution by an integrated quantum mechanical approach: Glycyl radical as a case study

Ciofini

Adamo²,

Barone³

2004

The Journal of Chemical Physics

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An integrated quantum mechanical approach for the structural and magnetic characterization of flexible free radicals in solution has been applied to a model of the glycyl radical engaged in peptidic chains. The hyperfine couplings computed using hybrid density functionals and purposely tailored basis sets are in good agreement with experiment when vibrational averaging effects from low frequency motions and solvent effects (both direct H bonding and bulk) are taken into the proper account. The g tensor shows a smaller dependence on the specific form of the density functional, the extension of the basis set over a standard double-zeta+polarization level, vibrational averaging, and bulk solvent effects. However, hydrogen bridges with solvent molecules belonging to the first solvation shell play a significant role. Together with their intrinsic interest, our results show that a comprehensive and reliable computational approach is becoming available for the complete characterization of open-shell systems of biological interest in their natural environment.

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Section: Complete Structural and Magnetic Characterization Of Biologimentioning

confidence: 99%

Complete structural and magnetic characterization of biological radicals in solution by an integrated quantum mechanical approach: Glycyl radical as a case study

Ciofini

Adamo²,

Barone³

2004

The Journal of Chemical Physics

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“…[19][20][21][22] While the nonradical form of a protein glycyl residue has access to a number of conformers, the conformational space of the radical was found to be restricted only to planar or quasi-planar conformations. [19][20][21][22] This is due to substantial delocalization of the unpaired π-electron over the whole structure. The fully extended conformer was proposed to be the best dipeptide model based on computed energies.…”

Section: Introductionmentioning

confidence: 99%

Understanding the Electon Paramagnetic Resonance Parameters of Protein-Bound Glycyl Radicals

2007

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The number of enzymes that require a glycyl-based radical for their function is growing. Here, we provide systematic quantum-chemical studies of spin-density distributions, electronic g-tensors, and hyperfine couplings of various models of protein-bound glycyl radicals. Similarly to what is found in a companion paper on N-acetylglycyl, the small g-anisotropy for this delocalized, unsymmetrical system presents appreciable challenges to state-of-the-art computational methodology. This pertains to the quality of structure optimization, as well as to the choice of the spin-orbit Hamiltonian and the gauge origin of the magnetic vector potential. Environmental effects due to hydrogen bonding are complicated and depend in a subtle fashion on the different intramolecular hydrogen bonding for different conformations of the radical. Indeed, the conformation has the largest overall effect on the computed g-tensors (less so on the hyperfine tensors). This is discussed in the context of different g-tensors obtained by recent high-field electron paramagnetic resonance (EPR) measurements for three different enzymes. On the basis of results of a parallel calibration study for N-acetylglycyl, it is suggested that the glycyl radical observed for E. coli anaerobic RNR may have a fully extended conformation, which differs from those of the corresponding radicals in pyruvate formate-lyase or benzylsuccinate synthase.

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“…9c Recent post-Hartree᎐Fock computations 11 showed that the radical obtained upon abstraction of the H ␣ atom from a glycine dipeptide analogue has a conformational behavior quite different from that of dipeptide analogues of natural amino acidic species. As a consequence, the onset of regular structures for polypeptides containing the glycine radical cannot be studied until a specifically tailored force field has been built from reliable quantum-mechanical results.…”

Section: Introduction Umerical Simulations Have Become In Recentmentioning

confidence: 99%

“…12 As a first step in this direction we considered the model systems shown in Figure 1, namely a simple dipeptide analogue, and the radical derived from it upon abstraction of the H ␣ atom, both of which have already been studied by quantum-mechanical methods. 11,13 We have performed some further computations to complete the quantum-mechanical results, which provide the basis for the fitting of molecular mechanics parameters. Among the various force fields available, the last version of AMBER 14 appears to model accurately conformational energies and intermolecular interactions involving proteins, nucleic acids, and other molecules with related functional groups, which are of interest in biological chemistry.…”

Section: Introduction Umerical Simulations Have Become In Recentmentioning

confidence: 99%

Development and validation of force-field parameters for molecular simulations of peptides and proteins containing open-shell residues

et al. 1997

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Conformational Behavior and Magnetic Properties of Organic Radicals Derived from Amino Acid Residues. The Dipeptide Analog of Glycine Radical

Cited by 33 publications

References 0 publications

Complete structural and magnetic characterization of biological radicals in solution by an integrated quantum mechanical approach: Glycyl radical as a case study

Complete structural and magnetic characterization of biological radicals in solution by an integrated quantum mechanical approach: Glycyl radical as a case study

Understanding the Electon Paramagnetic Resonance Parameters of Protein-Bound Glycyl Radicals

Development and validation of force-field parameters for molecular simulations of peptides and proteins containing open-shell residues

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