Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes

A systematic DFT study of structure and electronic properties of titanium dioxide

DFT functionals are of paramount importance for an accurate electronic and structural description of transition metal systems. In this work, a systematic analysis using some well-known and commonly used DFT functionals is performed. A comparison of the structural and energetic parameters calculated with the available experimental data is made in order to find the adequate functional for an accurate description of the TiO2 bulk and surface of both anatase and rutile structures. In the absence of experimental data on the surface energy, the theoretical predictions obtained using the high-accuracy HSE06 functional were used as a reference to compare against the surface energy values calculated with the other DFT functionals. A clear improvement in the electronic description of both anatase and rutile was observed by introducing the Hubbard U correction term to PBE, PW91, and OptPBE functionals. The OptPBE-U4 functional was found to offer a good compromise between accurately describing the structural and electronic properties of titania.

A detailed theoretical investigation to unravel the molecular mechanism of the ligand-free copper-catalyzed Suzuki cross-coupling reaction

The Suzuki-Miyaura coupling (SMC) represents a very efficacious method for constructing C-C bonds in organic synthesis. The ligand-free variants of SMC have been grabbing attention these days. Despite this momentousness, the mechanistic details of the ligand-free variants are scant in the literature. Herein, we have carried out a detailed mechanistic investigation into the ligand-free Cu-catalyzed SMC of unsaturated organic halides with aryl boronic acid with the aid of density functional theory (DFT) calculations employing the conductor-like polarizable continuum model (CPCM) method. The present study elucidates that in the absence of ancillary ligands on the metal, the substrates, base, and solvent molecules could act as pseudo-ancillary ligands to facilitate the cross-coupling reaction. The investigation further revealed that unsaturated halides like alkynyl halides/vinyl halides could act as good ancillary ligands for copper by forming a Cu-π intermediate and promoting a facile transmetalation process. However, regarding the oxidative addition and reductive elimination steps, a concerted pathway is observed contrary to Pd catalyzed Suzuki coupling, owing to the instability of Cu(III) species and the favourability of Csp²-Csp bond formation. In the whole set of mechanisms explored, oxidative addition/oxidative nucleophilic substitution was the rate-determining step in all the cases. A thermodynamically stable π-coordinated intermediate species where the substrate and base molecule are coordinated to the metal center is identified as the rate-determining species for the ligand-free Suzuki cross-coupling reaction. The presence of the aforesaid intermediate increases the energy span and consequently the activation barrier for the rate-determining step. This study unveiled a theoretical rationale for the high-temperature requirement in the ligand-free Cu-catalyzed SMC reaction.

Reliability of computed molecular structures

When the structures of 1342 molecules are optimized by 30 methods and 7 basis sets, there appear 289 (21.54%) problematic molecules and 112 (8.35%) failed ones. When 278 problematic molecules are compared, the best methods are BHandH and LC-wPBE, while B97D, BP86, HFS, VSXC, and HCTH are very unreliable. When 179 problematic molecules are computed with larger basis sets, the smallest mean absolute deviation (MAD) of bond angle (2.3°) is shown by QCISD(T)/cc-pVTZ, while the smallest MAD of bond length (0.021 Å), the best SUM1 (4.9 unit), and the best SUM2 (2.4 unit) are shown by DSDPBEP86(Full), DSDPBEP86, PBE1PBE-D3, MP2, and MP2(Full) in combination with aug-cc-pVQZ, cc-pVQZ, Def2QZVP, Def2TZVPP, and/or 6-311++G(3df,3pd). Very large basis sets, for example, larger than cc-pVTZ usually have to be used to obtain very good structures and the performances of many density-functional theory methods are encouraging. The best results may be the limit of modern computational chemistry.

Unraveling the Mechanism of Aerobic Alcohol Oxidation by a Cu/pytl-β-Cyclodextrin/TEMPO Catalytic System under Air in Neat Water

The mechanism for the oxidation of p-tolylmethanol to p-tolualdehyde catalyzed by a Cu/pytl-β-cyclodextrin/TEMPO (TEMPO = 2,2,6,6-tetramethylpiperidinyl-1-oxy) catalytic system under air in neat water is fully investigated by density functional theory (DFT). Four possible pathways (paths A → D) are presented. The calculated TOF = 0.67 h^-1 for path A is consistent with the experimental TOF = 1.9 h^-1 but much lower than that for path D (TOF = 1.1 × 10⁵ h^-1). The results demonstrate that path A is the dominant pathway under the optimal experimental conditions, even though path D is more kinetically favorable. This is because the concentration of precatalyst 11 [(pytl-β-CD)Cu^II(OH)] in path D is too low to start path D, so p-tolylmethanol oxidation can only proceed via path A. This finding implies that the relative concentration of precatalysts in a one-pot synthesis experiment plays a vital role in the aerobic alcohol oxidation reaction. Based on this finding, we speculate that the direct use of the presynthesized precatalyst 11 or addition of an appropriate amount of NaOH to the reaction solution, but with the total amount of the base added unchanged, is a good way to improve its catalytic activity. Meanwhile, the solvent water was not found to directly participate in the catalytic active sites for the oxidation of alcohols but rather inhibited it by forming the hydrogen-bonded network.

Structure prediction of neutral physiological copper(II) compounds with l-cysteine and l-histidine

Bis(aminoacidato)copper(II) [Cu^II(aa)₂] coordination compounds are the physiological species of copper(II) amino acid compounds in blood plasma. Since there are no experimental data in the literature about the geometries that physiological Cu^II(aa)₂ could form with l-cysteine (Cys), that is, for bis(l-cysteinato)copper(II) [Cu(Cys)₂] and the ternary (l-histidinato)(l-cysteinato)copper(II) [Cu(His)(Cys)], this paper computationally examines the possible conformations that the two compounds could form with the Cys ligand having a protonated sulfur, as in the conventional zwitterion, which was determined to be prevailing in aqueous solution. These two amino acids can bind metals in a tridentate fashion and thus form many possible coordination patterns. Density functional calculations were performed for the conformational analyses in the gas phase and in implicitly modeled aqueous solution using a polarizable continuum model. Additionally, we examine which coordination mode, with thiol or thiolate group, is more stable. The Cys coordination via the amino N and carboxylato O atoms (a glycinato mode) is obtained as the most stable one in aqueous Cu(Cys)₂, and also in Cu(His)(Cys) when the His glycinato or histaminato mode combines with the intact thiol group. Whereas the conformers with N and thiol S as the copper(II) donor atoms are predicted to be the least stable, those with the Cu-N and Cu-S(thiolate) bonding (and protonated carboxylato group) are the most stable. The differences are explained by different covalent and ionic contributions of Cu-S(thiol) vs. Cu-S(thiolate). The study can contribute to the insight into formation and reactivity of the copper(II) cysteinato complexes in solution.

Cu(I) Controls Conformational States in Human Atox1 Metallochaperone: An EPR and Multiscale Simulation Study

Atox1 is a human copper metallochaperone that is responsible for transferring copper ions from the main human copper transporter, hCtr1, to ATP7A/B in the Golgi apparatus. Atox1 interacts with the Ctr1 C-terminal domain as a dimer, although it transfers the copper ions to ATP7A/B in a monomeric form. The copper binding site in the Atox1 dimer involves Cys12 and Cys15, while Lys60 was also suggested to play a role in the copper binding. We recently showed that Atox1 can adopt various conformational states, depending on the interacting protein. In the current study, we apply EPR experiments together with hybrid quantum mechanics–molecular mechanics molecular dynamics simulations using a recently developed semiempirical density functional theory approach, to better understand the effect of Atox1’s conformational states on copper coordination. We propose that the flexibility of Atox1 occurs owing to protonation of one or more of the cysteine residues, and that Cys15 is an important residue for Atox1 dimerization, while Cys12 is a critical residue for Cu(I) binding. We also show that Lys60 electrostatically stabilizes the Cu(I)–Atox1 dimer.

Modeling σ-Bond Activations by Nickel(0) Beyond Common Approximations: How Accurately Can We Describe Closed-Shell Oxidative Addition Reactions Mediated by Low-Valent Late 3d Transition Metal?

Accurate modelings of reactions involving 3d transition metals (TMs) are very challenging to both ab initio and DFT approaches. To gain more knowledge in this field, we herein explored typical σ-bond activations of H-H, C-H, C-Cl, and C-C bonds promoted by nickel(0), a low-valent late 3d TM. For the key parameters of activation energy (ΔE^‡) and reaction energy (ΔE_R) for these reactions, various issues related to the computational accuracy were systematically investigated. From the scrutiny of convergence issue with one-electron basis set, augmented (A) basis functions are found to be important, and the CCSD(T)/CBS level with complete basis set (CBS) limit extrapolation based on augmented double-ζ and triple-ζ basis pair (ADZ and ATZ), which produces deviations below 1 kcal/mol from the reference, is recommended for larger systems. As an alternative, the explicitly correlated F12 method can accelerate the basis set convergence further, especially after its CBS extrapolations. Thus, the CCSD(T)-F12/CBS(ADZ-ATZ) level with computational cost comparable to the conventional CCSD(T)/CBS(ADZ-ATZ) level, is found to reach the accuracy of the conventional CCSD(T)/A5Z level, which produces deviations below 0.5 kcal/mol from the reference, and is also highly recommendable. Scalar relativistic effects and 3s3p core-valence correlation are non-negligible for achieving chemical accuracy of around 1 kcal/mol. From the scrutiny of convergence issue with the N-electron basis set, in comparison with the reference CCSDTQ result, CCSD(T) is found to be able to calculate ΔE^‡ quite accurately, which is not true for the ΔE_R calculations. Using highest-level CCSD(T) results of ΔE^‡ in this work as references, we tested 18 DFT methods and found that PBE0 and CAM-B3LYP are among the three best performing functionals, irrespective of DFT empirical dispersion correction. With empirical dispersion correction included, ωB97XD is also recommendable due to its improved performance.

Luminescent Cyclometalated Platinum Complexes with π-Bonded Catecholate Organometallic Ligands

A series of cyclometalated platinum(II) complexes of the type [(ppy)Pt(L_M)]ⁿ⁺ (n = 0, 1) with π-bonded catecholates acting as organometallic ligands (L_M) have been prepared and characterized by analytical techniques. In addition, the structures of two complexes of the series were determined by single-crystal X-ray diffraction. The packing shows the formation of a 1D supramolecular assembly generated by d_Pt-π_Cp* interactions among individual units. All complexes are luminescent in the solid state and in solution media. The results of photophysics have been rationalized by means of density functional theory (DFT) and time-dependent DFT investigations.

A density functional theory protocol for the calculation of redox potentials of copper complexes

The calculated redox potentials of copper complexes agree nicely with their corresponding experimental redox potentials.

Benchmarking of Density Functionals for the Accurate Description of Thiol-Disulfide Exchange

A set of 92 density functionals was employed to accurately characterize thiol-disulfide exchange. The properties we have benchmarked throughout the study include the geometry of a 15 atoms model system, the potential energy surface, the activation barrier, and the energy of reaction for thiol-disulfide exchange. Reference energies were determined at the CCSD(T)/CBS//MP2/aug-cc-pVDZ level of theory, and reference geometries were calculated at the MP2/aug-cc-pVTZ level. M11-L, M06-2X, M06-HF, N12-SX, PBE1PBE, PBEh1PBE, and OHSE2PBE described better the geometry of the model system, with average deviations of 0.06 Å in bond lengths (0.06 Å in bond-breaking lengths) and 1.9° in bond angles. On the other hand, the potential energy surface and its gradient were more accurately described by the hybrid density functional BHandH, closely followed by mPW1N, mPW1K, and mPWB1K. The barrier height and energy of reaction were better reproduced by the BMK and M06-2X functionals (deviations of 0.17 and 0.07 kcal·mol(-1), respectively) for a set of 10 Pople's basis sets. MN12-SX and M11-L showed very good results for the widely used 6-311++G(2d,2p) basis set, with deviations of 0.02 and 0.05 kcal·mol(-1), respectively. We studied the effect of the split-valence, diffuse, and polarized functions in the activation barrier of thiol-disulfide exchange, for a set of 10 Pople's basis sets. While increasing the splitting and polarization may increase the activation barrier in approximately 1 kcal·mol(-1), diffuse functions generally contribute to decreasing it no more than 0.10 kcal·mol(-1). In general, 13 functionals provided energies within 1 kcal·mol(-1) of the reference value. The BB1K density functional is one of the best density functionals to characterize thiol-disulfide exchange reactions; however, several density functionals with modified Perdew-Wang exchange and about 40% Hartree-Fock exchange, such as mPW1K, mPW1N, and mPWB1K, show a good performance, too.

Geometrical and optical benchmarking of copper(II) guanidine-quinoline complexes: insights from TD-DFT and many-body perturbation theory (part II)

Ground- and excited-state properties of copper(II) charge-transfer systems have been investigated starting from density-functional calculations with particular emphasis on the role of (i) the exchange and correlation functional, (ii) the basis set, (iii) solvent effects, and (iv) the treatment of dispersive interactions. Furthermore (v), the applicability of TD-DFT to excitations of copper(II) bis(chelate) charge-transfer systems is explored by performing many-body perturbation theory (GW + BSE), independent-particle approximation and ΔSCF calculations for a small model system that contains simple guanidine and imine groups. These results show that DFT and TD-DFT in particular in combination with hybrid functionals are well suited for the description of the structural and optical properties, respectively, of copper(II) bis(chelate) complexes. Furthermore, it is found an accurate theoretical geometrical description requires the use of dispersion correction with Becke-Johnson damping and triple-zeta basis sets while solvent effects are small. The hybrid functionals B3LYP and TPSSh yielded best performance. The optical description is best with B3LYP, whereby heavily mixed molecular transitions of MLCT and LLCT character are obtained which can be more easily understood using natural transition orbitals. An natural bond orbital analysis sheds light on the donor properties of the different donor functions and the intraguanidine stabilization during coordination to copper(I) and (II).

The glycation site specificity of human serum transferrin is a determinant for transferrin's functional impairment under elevated glycaemic conditions

Human serum transferrin is susceptible to modification under elevated glycaemic conditions, such as those encountered in diabetes mellitus. The study of transferrin glycation shows that key amino acid residues undergo glycation, inducing structural alterations that compromise its function as an iron-binding protein.

DFT/TDDFT insights into the chemistry, biochemistry and photophysics of copper coordination compounds

Highlighting the recent progress in DFT/TDDFT application to coordination chemistry of copper.