Simulating the active sites of copper-trafficking proteins. Density functional structural and spectroscopy studies on copper(I) complexes with thiols, carboxylato, amide and phenol ligands
Creators: name: Tamasi, Gabriella
name: Bonechi, Claudia
name: Rossi, Claudio
name: Cini, Renzo
name: Magnani, Agnese
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: FOS: Physical sciences
subject: Cell Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Hematology

description: A series of mononuclear binary and ternary Cu(I) complexes with formato, formamide, methylphenol, and methanethiolato ligands were optimized at DFT-B3LYP/6-31G** (BS1) and DFT-B3LYP/6-311++G** (BS2) levels of theory. The solvent effect was taken into account via PCM method (BS1W and BS2W, respectively). The coordination arrangement for [Cu<sup>I</sup>(SCH<sub>3</sub>/S(H)CH<sub>3</sub>)(OOCH)]<sup>−/0</sup> and [Cu<sup>I</sup>(SCH<sub>3</sub>/S(H)CH<sub>3</sub>)(O(H)(C<sub>6</sub>H<sub>4</sub>)CH<sub>3</sub>)]<sup>0/+</sup> was <i>pseudo</i>-linear and for [Cu<sup>I</sup>(SCH<sub>3</sub>/S(H)CH<sub>3</sub>)(OOCH)(OC(H)NH<sub>2</sub>)]<sup>−/0</sup> was <i>pseudo</i>-trigonal. The [Cu<sup>I</sup>(<i>S</i>-S(H)CH<sub>3</sub>/Cu<sup>I</sup>(<i>S</i>-SCH<sub>3</sub>)]<sup>+/0</sup> link even to amide carbonyl and to general O(H)R residues (R=C<sub>6</sub>H<sub>5</sub>CH<sub>3</sub>). [Cu<sup>I</sup>(SCH<sub>3</sub>)<sub>2</sub>(O(H)(C<sub>6</sub>H<sub>4</sub>)CH<sub>3</sub>)]<sup>−</sup> went towards dissociation of the O(H)(C<sub>6</sub>H<sub>4</sub>)CH<sub>3</sub> ligand, whereas [Cu<sup>I</sup>(S(H)CH<sub>3</sub>)<sub>2</sub>(O(H)(C<sub>6</sub>H<sub>4</sub>)CH<sub>3</sub>)]<sup>+</sup> converged nicely, maintaining the hydroxy function linked to the metal. The trends of total electronic energies seemed to be significant, suggesting that linear Cu<sup>I</sup>S<sub>2</sub> coordination is more suitable than Cu<sup>I</sup>S, Cu<sup>I</sup>S<sub>3</sub> and Cu<sup>I</sup>S<sub>4</sub> arrangements. The formation energies of [Cu<sup>I</sup>(S(H)CH<sub>3</sub>/SCH<sub>3</sub>)(OOCH)]<sup>0/−1</sup> were higher than those of [Cu<sup>I</sup>(S(H)CH<sub>3</sub>/SCH<sub>3</sub>)<sub>2</sub>]<sup>+/−</sup> on starting from [Cu<sup>I</sup>(S(H)CH<sub>3</sub>/Cu<sup>I</sup>(SCH<sub>3</sub>)]<sup>+/0</sup> by <i>ca.</i> 11–9 kcal mol<sup>−1</sup> (BS2W). The structural arrangements, bond distances, and angles as well as computed spectroscopic parameters resulted in good agreement with experimental data for corresponding synthetic complexes and with metal site regions of several copper(I)-proteins. These data help in interpreting structural data of complex biological systems and in constructing reliable force fields for molecular mechanics computations.