Calculating the geometry and Raman spectrum of physiological bis(l-histidinato)copper(II): an assessment of DFT functionals for aqueous and isolated systems

Abstract

Reliable density functional theory (DFT) calculations can be performed in conjuction with spectroscopic measurements to elucidate the structural properties of physiologically important bis(amino acidato)copper(II) compounds in solutions. They can provide insight into the influence of intermolecular interactions on the molecular geometry in the crystal lattice or solution when compared with a DFT gas-phase minimum. Our previous paper [Marković et al. (2014) Eur J Inorg Chem 198] reported the DFT-determined geometries and Raman spectra for different conformers of physiological bis(L-histidinato)copper(II) with 20 explicit water molecules, as calculated using the B3LYP functional. The present study examined the reliability of those B3LYP results by applying the M06 functional instead, as it should better account for noncovalent interactions. The water molecules were positioned more compactly around the complex by M06 than by B3LYP. The accuracies of the two functionals when compared to relevant experimental data showed that M06 was better at reproducing in-plane Cu-N bond lengths but B3LYP gave more accurate axial Cu-O distances. Both functionals reproduced the experimental Raman spectrum at pH 8 to similar levels of accuracy and provided precise information on the Cu(II) coordination mode and conformation in aqueous solution. Additionally, we assessed several DFT and DFT-D functionals (BP86, B3LYP, B3LYP-D, M06, M06 L, wB97XD, mPW2PLYPD) by using them to model the geometries of experimental bis(L-histidinato)copper(II) crystalline conformations as isolated systems, and then benchmarking the results against those from high-level second-order pertubation Møller-Plesset (MP2) calculations. Although this assessment resulted in an equivocal conclusion because the MP2 results for the isolated complex were inconsistent with the corresponding DFT outcomes, it does provide new information on future benchmark options.

Conformational Analyses of Physiological Binary and Ternary Copper(II) Complexes with l‐Asparagine and l‐Histidine; Study of Tridentate Binding of Copper(II) in Aqueous Solution

“…Such an axial coordination was achieved in only one NONo conformer in the gas phase (Table ), for cNONo1 (Figure S1), in which an inter‐ligand C β −H⋅⋅⋅O interaction is formed. A similar result was obtained by the B3LYP calculations of isolated and aqueous Cu( l ‐His) 2 , and Cu( l ‐His)( l ‐Thr) conformers, that the axial coordination of carboxylato O atom(s) can be stabilized only by intramolecular and/or intermolecular noncovalent interactions.…”

“…The nonrelativistic effective‐core potentials of Hay and Wadt were used to describe the shielding effects of electrons in the copper inner shells. The suitability of the method/basis set for the conformational analyses of Cu(aa) 2 complexes was extensively evaluated elsewhere . Besides, the application of this combination of functional and basis set, which was previously applied for the conformational analyses of physiological Cu( l ‐His) 2 , Cu( l ‐Thr) 2 , and Cu( l ‐His)( l ‐Thr), allows a comparison of the new results estimated for the title complexes with the previously studied systems at a consistent level.…”

“…Cu( l ‐His)( l ‐Asn) . l ‐His has three possible donor atoms: amino group N am , imidazole N π (N im ), and carboxylate O, which can form three different in‐plane binding modes as described in details elsewhere: G, H, and I for glycine‐like (N am and O bind to the copper), histamine‐like (N am and N im are the donor atoms), and imidazole–propionic acid (impa)‐like mode (O and N im are the chelating atoms), respectively. These modes are illustrated in Scheme .…”

“…For Cu( l ‐His) 2 , the experimental studies at physiological pH as well as the computational studies with explicit water molecules suggested an equilibrium of a histamine‐histamine (HH) and a histamine‐glycine (HG) bonding type in a cis ‐configuration with carboxylato O atom(s) in the axial position(s), while a glycine‐glycine mode was considered improbable. Such a fluctuating type of coordination could be maintained by changing a local water molecule environment around Cu( l ‐His) 2 , as suggested by the DFT calculations .…”

Disorder at the Chiral Cα Center and Room-Temperature Solid-State cis–trans Isomerization; Synthesis and Structural Characterization of Copper(II) Complexes with d-allo,l-Isoleucine

“…The minimum structures were optimized using the unrestricted DFT/B3LYP method and the LanL2DZ double-ζ basis set, augmented by a set of polarization and diffuse functions on N, O, and C, and Los Alamos effective core potentials − for the copper. The choice of this functional/basis set combination was shown suitable for the conformational analyses of Cu­(aa) 2 complexes in our previous studies. − The equilibrium geometries were computed for the conformers in the gas phase and using implicit solvent effects (the dielectric constant used for water, methanol, and ethanol was 78.355, 32.613, and 24.852, respectively) modeled with the integral equation formalism of polarization continuum model (PCM) , as it is implemented in Gaussian 09 suite of programs and detailed elsewhere . The thermal correction to the Gibbs free energy was calculated at a temperature of 298.15 K in the standard way…”