Molecular structures of (555)macrotricyclic chelates appearing in 3d-element(ii) ion-hydrazinomethanethioamide-ethanedial systems according to density functional theory calculations

Thermodynamic and geometric parameters have been calculated using the hybrid density functional theory method B3LYP with the 6-31G(d) basis set and the Gaussian03 program for the macrotricyclic complexes of Mn(II), Fe(II), Co(II), Ni(II), Cu(II), and Zn(II) with an (NSSN)-coordinated ligand that can result from the complexation of metal hexacyanoferrates(II) with hydrazinomethanethioamide H₂N-HN-C(=S)-NH₂ and ethanedial HC(=O)-CH(=O) in gelatin-immobilized matrix implants. Bond lengths and valence and torsion angles in these complexes are reported. The Ni(II) and Cu(II) complexes are practically planar. The Mn(II), Fe(II), and Co(II) complexes are characterized by a small deviation from coplanarity, and the Zn(II) complex is noticeably noncoplanar. The additional five-membered metallacycle resulting from template ??joining?? is nearly planar in all complexes.     

Quantum-chemical simulation of structure of isomeric asymmetric (555)macrotricyclic chelates of 3d elements arising via self-assembly in quaternary systems metal(II)-ethanedithioamide-hydrazinomethanethioamide-ethanedial

We utilized the OPBE/TZVP (GAUSSIAN-09) hybrid density functional method to compute thermodynamic (full energy; standard enthalpy, entropy, and Gibbs energy of formation) and geometry (bond lengths, bond angles, and torsion angles) parameters of (555)macrotricyclic complexes of Mn(II), Fe(II), Co(II), Ni(II), Cu(II), and Zn(II) with (NSSN) coordination of the ligand donor centers. Such complexes can be formed upon interaction of hexacyanoferrate(II) of the listed metals, ethanedithioamide, hydrazinomethanethioamide, and ethanedial in gelatin-immobilized matrix implants. Complexes of Cu(II) and Zn(II) are slightly nonplanar, the other complexes are almost flat. In all cases the additionally formed five-membered cycle is practically flat.     

Specifics of molecular structures of (565)macrotricyclic 3d-Metal chelates in the ternary systems M(II)-hydrazinecarbothioamide-2,4-Pentanedione according to DFT calculations

The geometric parameters of the molecular structures and thermodynamic parameters of formation of macrotricyclic M(II) complexes (M = Mn, Fe, Co, Ni, Cu, and Zn) with the MN₂S₂ coordination core formed by the reactions of corresponding hexacyanoferrates(II) with hydrazinecarbothioamide H₂N-HN-C(=S)-NH₂ and 2,4-pentanedione H₃C-C(=O)-CH₂-C(=O)-CH₃ in gelatin-immobilized matrix implants have been calculated by the B3LYP hybrid density functional theory method with the use of the 6-31G(d) basis set and the Gaussian 09 program package. The bond lengths and bond and torsion angles in these chelates have been reported. It has been shown that the Fe(II) and Ni(II) complexes are strictly planar, whereas the Mn(II), Co(II), and Cu(II) complexes are quasi-planar with a rather small deviation of the MN₂S₂ chelate core from coplanarity, and only the Zn(II) complex is pseudotetrahedral. The additional sixmembered chelate rings resulting from the above processes are almost planar in all chelates.     

Quantum chemical calculation of the molecular structures of (666)macrotricyclic chelates of 3D elements in the M(II)-propanedithioamide-formaldehyde systems by the density functional theory method

The nonhybrid OPBE/TZVP density functional theory (DFT) method and the Gaussian09 program package were used to calculate the thermodynamic and geometric parameters of asymmetric macrocyclic M(II) complexes with three six-membered metal rings and (NNNN)-coordination of the donor sites of the ligand. The complexes are formed upon self-assembly (template synthesis) of hexacyanoferrates(II) of the corresponding M(II), propanedithioamide H₂N-C(=S)-CH₂-C(=S)-NH₂, and formaldehyde H₂C(=O) in gelatin-immobilized matrix implants. Note that complexes of this type are formed only for M = Ni, Cu, and Zn, while for M = Mn, Co, and Fe, these compounds are unstable. Bond lengths and bond and torsion angles are presented. In each of these complexes, both the MN₄ chelate units and the N₄ units and all sixmembered metal rings were found to be non-coplanar.     

Comparative stability of isomeric (565)macrotricyclic chelates of 3d-elements formed in the systems M(II)-thiosemicarbazide-formaldehyde according to DFT B3LYP data

Comparative stability of three types of (565)macrotricyclic chelates of Mn(II), Fe(II), Co(II), Ni(II), Cu(II), and Zn(II) with chelate nodes MN₂S₂ and MN₄ have been analyzed by means of hybrid density functional method B3LYP with the 6-31G(d) basis set using GAUSSIAN-09 software. These chelates may potentially be formed in template interaction between gelatin-immobilized hexacyanoferrate(II) of respective metal ions M(II), thiosemicarbazide H₂N-HN-C(=S)-NH₂, and formaldehyde H₂C=O. It has been demonstrated that for all M(II) considered, the complex with chelate nodes MN₂S₂ is more stable. Key structural parameters of the complexes (bond lengths, bond and torsion angles) are presented. It is noted that pseudotetrahedral coordination of ligand donor centers around M(II) is typical for Mn(II), Co(II), Cu(II), and Zn(II), whereas for Fe(II) and Ni(II) it is almost planar. Values of standard enthalpy ΔH _f,298 ⁰ and standard Gibbs energy ΔG _f,298 ⁰ are positive for nearly all the complexes studied.     

On the molecular structures of (545)macrotricyclic chelates in the M(II) ion-2,3-butanedione-aminomethanamidine ternary systems

The geometric parameters of the molecular structures of macrotricyclic M(II) complexes with a tetradentate chelating ligand with the (NOON) coordination of donor sites formed by the template reactions in the M(II)-2,3-butanedione (H₃C-C(=O)-C(=O)-CH₃)-aminomethanamidine (H₂N-C(=NH)-NH₂) systems have been calculated by the OPBE/TZVP density functional theory (DFT) method. The bond lengths and bond and torsion angles in the resulting complexes have been reported. The enthalpies and Gibbs energies for the reaction of their formation have also been calculated. A conclusion has been drawn that template synthesis in these systems can be realized only upon complex formation in a gelatin-immobilized matrix.     

Molecular structures of metalmacrocyclic chelates of 3d-elements formed at template synthesis in the ion M(II)- thiooxamide-guanidine-formaldehyde quaternary systems

Using density functional theory (DFT) at the OPBE/TZP level, the calculation of the geometric parameters of the molecular structures of M(II) (5456)macrotetracyclic complexes with a tetradentate macrocyclic ligand with (NNNN)-coordination of donor centers, resulting from template reactions in M(II)- thiooxamide- guanidine-formaldehyde quaternary systems, where M= Mn, Fe, Co, Ni, Cu, Zn was performed. The calculation of the molecular structure of this “template” ligand itself was also carried out. The values of the bond lengths, bond and torsion angles in the resulting complexes are presented. The values of the standard enthalpy, entropy and Gibbs free energy of formation of these compounds were also calculated.      

Molecular structures of macrotricyclic 4<Emphasis Type="Italic">d</Emphasis> M(II) chelates with the (NNNN)-donor ligand 2,7-dithio-3,6-diazaoctadiene-3,5-dithioamide-1,8 according to quantum-chemical density functional theory calculations

The thermodynamic and geometric parameters of the molecular structures of macrotricyclic Mo(II), Ru(II), Rh(II), Pd(II), Ag(II), and Cd(II) complexes with the tetradentate ligand 2,7-dithio-3,6-diazaoctadiene-3,5-dithioamide-1,8 with the (NNNN) coordination of the donor centers have been calculated by the hybrid density functional theory (DFT) method in the OPBE/TZVPQZP approximation with the use of the Gaussian09 program package. The Pd(II), Ag(II), and Cd(II) complexes are exactly planar, the Tc(II) and Rh(II) complexes exhibit slight deviations from coplanarity, while the Mo(II) and Ru(II) complexes have rather significant deviations. The five-membered chelate rings in the complexes are either strictly planar or deviate slightly (no more than by 5°) from coplanarity.     

(5656)Macrotetracyclic chelates of doubly charged 3d-element ions with 1,4,8,11-tetraazacyclotetradecane-2,3,9,10-tetrathione and their molecular structures according to density functional theory data

The OPBE/TZVP density functional theory (DFT) calculations were performed to study the molecular structures of (5656)macrotetracyclic M(II) complexes with a tetradentate ligand with (NNNN)-coordination of the donor sites formed upon template reactions in the M(II)-dithiooxamide-propane-1,3-diol ternary systems (M = Mn, Fe, Co, Ni, Cu, Zn). The bond lengths and bond angles for the resulting complexes are presented. The standard enthalpy, entropy, and Gibbs energy of formation of these compounds were calculated.     

Density functional theory calculations on the molecular structures and vibration spectra of platinum(II) antitumor drugs

A comparison of six density functional theory (DFT) methods and six basis sets for predicting the molecular structures and vibration spectra of cisplatin is reported. The theoretical results are discussed and compared with the experimental data. It is remarkable that LSDA/SDD level is clearly superior to all the remaining density functional methods (including mPW1PW) in predicting the structures of cisplatin. Mean deviation between the calculated harmonic and observed fundamental vibration frequencies for each method is also calculated. The results indicate that PBE1PBE/SDD is the best method to predict all frequencies on average for cisplatin molecule in DFT methods.     

Quantum-chemical calculation of the molecular structures of 3d metal chelates with ligands self-assembled in the M(II)-hydrazinomethane thiohydrazide-acetone systems

The geometric parameters of M(II) complexes (M = Mn, Fe, Co, Ni, Cu, and Zn) with chelating ligands 1-hydrazino-4,6,6,12-tetramethyl-2,3,7,8,10,11-hexaazatridecatetraene-1,3,8,11-dithiol-1,9 and 2,8,8,10,16-pentamethyl-3,4,6,7,11,12,14,15-octaazaheptadecapentaene-2,5,10,12,15-dithiol-5,13 with the NNSS coordination self-assembled in the M(II)-hydrazinomethane thiohydrazide-acetone systems have been calculated by the hybrid B3LYP density functional theory method with the use of the 6-31G(d) basis set and the Gaussian 03 program package. The bond lengths and bond and torsion angles in these complexes have been reported. It has been stated that, in the complexes formed by the same M(II) ion, these characteristics are close to each other. For all M(II) ions under consideration, an additional six-membered chelate ring resulting from template cross-linking is turned to the two five-membered rings and is nonplanar as distinct from the latter.     

The relative stability of macrotricyclic metal complexes in M(II)-thiocarbohydrazide-acetone (M = Mn, Fe, Co, Ni, Cu, Zn) ternary systems according to the data of quantum-chemical calculations

The B3LYP hybrid method of density functional theory with the 6–31G(d) basis set was used to calculate the optimum geometry and standard thermodynamic parameters of Mn(II), Fe(II), Co(II), Ni(II), Cu(II), and Zn(II) macrotricyclic complexes with MN₂S₂ and MN₄ chelate nodes. The calculations were performed using the Gaussian 98 package. Such complexes could in principle appear because of temperature processes between gelatin-immobilized hexacyanoferrates(II) of the corresponding M(II) metal ions, thiocarbohydrazide, and acetone. For all the M(II) metals considered, complexes with MN₂S₂ chelate nodes were stablest. The standard Gibbs energies Δ_f G ₂₉₈^° values were positive for all the complexes specified.     

Molecular structures of (5454) macrotetracyclic chelates of 3d M(II) ions with 4,5,9,10-tetramethyl-1,3,6,8-tetraaza-5,8-cyclodecadiene-2,7-diimine according to DFT quantum-chemical calculations

The molecular structures of (5454)macrotetracyclic M(II) complexes with the tetradentate ligand with the (NNNN)-coordination of donor sites formed by the template reactions in the ternary systems M(II)-aminomethanamidine (H₂N-C(=NH)-NH₂)-3-hydroxy-2-butanone H₃C-C(=O)-C(OH)-CH₃), where M = Mn, Fe, Co, Ni, Cu, and Zn, have been calculated by the OPBE/TZVP density functional theory (DFT) method. The bond lengths and bond and torsion angles in the complexes, as well as the standard enthalpies, entropies, and Gibbs energies of formation of these compounds, are reported.     

Factors influencing Al(3+)-dimer speciation and stability from density functional theory calculations

We have investigated aqueous Al-dimer complexes using density functional theory methods (e.g. the B3LYP exchange-correlation functional and the 6-311++G(d,p) basis set). In these calculations interactions between the Al(3+) cations and the H(2)O or OH(-) coordinating ligands are considered explicitly while the second hydration shell and remaining solvent are treated as a continuum under the IEF-PCM formalism. The Al-dimer chemical reactivity is discussed by analysis of changes in geometry, electronic structure and Gibbs free energy of formation, relative to two independent Al(H(2)O) monomers, as a function of water and hydroxide coordination. Our results indicate that the mechanism of cooperativity, i.e. decreased Al-water bond stability with increasing OH(-) coordination and increased water ligand hydrolysis as complex CN decreases, is operating on the dimer species and that, therefore, a wide variety of dimer species are available. While the stability of these species is observed to be dependent on the number of water and hydroxide ligands, the hydroxide bridging structure (singly, doubly and triply bridged species are considered) does not appear to correlate with dimer stability. Interestingly, intra-molecular H-bonds (in the form of the well known H(3)O bridge as well as two bridging structures, H(4)O(2) and H(2)O, that have not, to our knowledge, been previously considered) are observed to influence dimer stability. The evaluation of the equilibrium mole fraction of the dimer species in equilibrium with the aqueous Al(3+) monomer species of our previous study displays the qualitatively correct trend of solution composition as pH increases, namely monomeric aqueous Al(3+) and Al(OH) complexes dominate at low and high pH, respectively, and all remaining monomer and dimer species exist at intermediate pH. Further refinement of our data set by eliminating dimer complexes with OH/Al ratios greater than 2.6 brings our predicted equilibrium mole fraction distributions into excellent agreement with experimental observations. The triply bridged dimer is observed in low amounts while the singly and doubly bridged dimers dominate our model system at pH = ～4-7.     

The molecular structures of tris(dipivaloylmethanato)chromium and tris(dipivaloylmethanato)cobalt determined by gas electron diffraction and density functional theory calculations

The molecular structures of tris(dipivaloylmethanato)chromium and tris(dipivaloylmethanato)cobalt have been determined by quantum chemical calculations and gas electron diffraction. Both the experimental data and the theoretical results are consistent with molecular structures having D ₃ symmetry which is in agreement with the Kepert model. The experimental bond distances, r _h1(Å), and bond angles, ∠ _h1(°), are: Cr–O = 1.976(5), C–O = 1.287(3), C–C_r = 1.392(6), C–C_t = 1.547(3), OCrO = 90.1(0.9), CC_rC = 122.3(0.9), OCC_t = 114.7(0.9) and Co–O = 1.891(4), C–O = 1.269(3), C–C_r = 1.411(5), C–C_t = 1.546(3), OCoO = 95.2(0.5), CC_rC = 122.5(0.9), OCC_t = 115.1(0.8).     

Calculation of geometric parameters of macrocyclic metal chelates formed by template synthesis in tertiary systems M(II) ion-ethanedithioamide-formaldehyde-ammonia

The geometric parameters of macrotricyclic Mn(II), Fe(II), Co(II), Ni(II), Cu(II), and Zn(II) complexes with 2,8-dithio-3,5,7-triazanonanedithioamide-1,9 with the (N,N,S,S) coordination of the chelant donor centers (formed by template synthesis in the M(II)-ethanedithioamide-formaldehyde-ammonia system) have been calculated by the hybrid B3LYP density functional theory method with the use of the 6-31G(d) basis set and the Gaussian 98 program package. The bond lengths and bond angles in the complexes with the MN₂S₂ coordination core have been reported. Calculations demonstrated that in none of the complexes are the five-membered chelate rings planar and that these rings in the Zn(II) complex are significantly different. For all M(II) ions under consideration, an additional six-membered chelate ring resulting from template cross-linking is turned at a rather large angle to the two five-membered rings and this ring itself is nonplanar.     

Geometric parameters and energies of molecular structures of macrocyclic metal chelates in the ternary 3<Emphasis Type="Italic">d</Emphasis> M(II) ion-ethanedithioamide-ethanedial systems according to quantum-chemical DFT B3LYP calculations

The thermodynamic and geometric parameters of isomeric macrotricyclic Mn(II), Fe(II), Co(II), Ni(II), Cu(II), and Zn(II) complexes with the (NSSN) coordination of the ligand donor centers formed in the reaction of corresponding hexacyanoferrates(II) with ethanedithioamide H₂N-C(=S)-C(=S)-NH₂ and ethanedial HC(=O)-CH(=O) in gelatin-immobilized matrix implants have been calculated by the hybrid B3LYP density functional theory method with the use of the 6–31G(d) basis set and the Gaussian 03 program package. The bond lengths and bond and torsion angles in these complexes have been reported, and it has been stated that the Mn(II), Co(II), and Cu(II) complexes are nearly planar, the Fe(II) and Ni(II) complexes are slightly nonplanar, while the Zn(II) complex exhibits a rather considerable deviation from coplanarity. The additional five-membered chelate ring resulting from template cross-linking is almost planar in all cases.     

Molecular structure and thermodynamic parameters of (5656)macrotetracyclic chelates in the 3d-element(ii) ion-hydrazinomethanethiohydrazide-2,3-butanedione ternary system according to density functional quantum-chemical calculations

The thermodynamic and geometric parameters of the macrocyclic chelates of Mn(II), Fe(II), Co(II), Ni(II), Cu(II), and Zn(II) with the (NNNN) coordination of the ligand donor centers formed upon complexation between the above metal ions, hydrazinomethanethiohydrazide (H₂N-HN-C(=S)-NH-NH₂), and 2,3-butanedione (H₃C-C(=O)-C(=O)-CH₃) in gelatin-immobilized matrix implants were calculated by the B3LYP 6–31G(d) density functional theory method with the use of the Gaussian 09 program package. The bond lengths, valence angles, and torsion angles were reported, and it was noted that the complexes of Fe(II), Co(II), Ni(II), and Cu(II) are almost planar, whereas the complexes of Mn(II) and Zn(II) have a quasi-pyramidal structure of the chelate unit. The additional six-membered metallocycles resulting from template cross-linking, as well as five-membered rings, are almost planar.     

Structure of (5656)macrotetracyclic chelates in the ternary systems M(II)-ethanedithioamide-acetone (M = Mn, Fe, Co, Ni, Cu, Zn) according to DFT calculations

The thermodynamic and geometric parameters of M(II) macrotetracyclic chelates (M = Mn, Fe, Co, Ni, Cu, and Zn) with the (NNNN) coordination of the donor ligand sites, formed by the complexation reactions of corresponding M(II) compounds, ethanedithioamide H₂N-C(=S)-C(=S)-NH₂, and acetone H₃C-C(=O)-CH₃ in gelatin-immobilized matrix implants have been calculated by the OPBE/TZVP density functional theory method with the use of the Gaussian 09 program package. The bond lengths and bond and torsion angles in these complexes have been reported. It has been shown that despite the fact that the MN₄ chelate core in them is almost planar, the five- and six-membered chelate rings are pronouncedly non-coplanar. In the Mn(II), Fe(II), Co(II), and Ni(II) complexes, these chelate rings are pairwise identical, whereas in the Cu(II) and Zn(II) complexes, they are noticeably different.     

Ab initio benchmark calculations on Ca(II) complexes and assessment of density functional theory methodologies

A set of benchmark results for the geometries, binding energies, and protonation affinities of 24 complexes of small organic ligands with Ca(II) is provided. The chosen level of theory is CCSD(T)/CBS obtained by means of a composite procedure. The performance of four density functionals, namely, PW91, PBE, B3LYP, and TPSS and several Pople-type basis sets, namely, 6-31G(d), 6-31+G(d), 6-31+G(2d,p) and 6-311+G(d) have been assessed. Additionally, the nature of the metal ligand bonding has been analyzed by means of the Symmetry Adapted Perturbation Theory (SAPT). We have found that the B3LYP hybrid functional, in conjunction with either the polarized double-ζ 6-31+G(2d,p) or the triple-ζ 6-311+G(d) basis sets, yields the closest results compared to the benchmark data. The SAPT analysis stresses the importance of induction effects in the binding of these complexes and suggests that consideration of classical electrostatic contributions alone may not be reliable enough for the prediction of relative binding energies for Ca(II) complexes.