Structure and ESR Features of Glycine Radical

Barone, Vincenzo; Adamo, Carlo; Grand, André; Jolibois, Frank; Brunel, Y.; Subra, R.

doi:10.1021/ja00155a026

Cited by 37 publications

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“…Next the effects both of solvent and vibrational averaging by low frequency motions at the radical center have been taken into the proper account. 36 Our aim is to show that a single integrated computational approach based on last generation hybrid density functionals and including environmental and vibrational averaging effects is able to provide not only accurate values for the spectroscopic parameters under investigation ͑hfc and g tensors͒, but also insights on the nature of the fine tuning of these observables by structural, dynamic, and environmental effects.…”

Section: Complete Structural and Magnetic Characterization Of Biologimentioning

confidence: 99%

“…21,34,36 Next, the mass weighted Cartesian coordinates of successive points on the original path are translated and rotated in order to minimize the angular moment connected to the motion. 21,48 The distance between the reoriented structures represents the progress variable for an effective onedimensional Hamiltonian, whose vibrational levels are obtained by a numerical procedure based on a discrete variational ͑DVR͒ approach.…”

Section: Computational Detailsmentioning

confidence: 99%

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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%

Section: Computational Detailsmentioning

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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“…The situation is very different in solution, where the conformer 1 is the most stable structure for the zwitterionic form, though remaining less stable than the neutral radical. 75 The solvent induces noticeable geometry rearrangements in this system, in particular concern- ing the planarity of the radical center; it is noteworthy that this geometrical change has a negligible effect on the solvation energy but significantly affects the values of electronic properties such as Ž . the isotropic hyperfine couplings hfc .…”

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confidence: 95%

Geometry optimization of molecular structures in solution by the polarizable continuum model

1998

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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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Structure and ESR Features of Glycine Radical

Cited by 37 publications

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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

Geometry optimization of molecular structures in solution by the polarizable continuum model

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

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