Binding of O2 and NO to heme in heme-nitric oxide/oxygen-binding (H-NOX) proteins. A theoretical study.

The binding of O2 and NO to heme in heme-nitric oxide/oxygen-binding (H-NOX) proteins has been investigated with DFT as well as dispersion-corrected DFT methods. The local protein environment was accounted for by including the six nearest surrounding residues in the studied systems. Attention was also paid to the effects of the protein environment, particularly the distal Tyr140, on the proximal iron-histidine (Fe-His) binding.

Factors that distort the heme structure in Heme-Nitric Oxide/OXygen-Binding (H-NOX) protein domains. A theoretical study.

DFT and dispersion-corrected DFT calculations were carried out to probe the factors that distort the heme structure in Heme-Nitric oxide/OXygen-binding (H-NOX) protein domains. Various model systems that include heme, heme+surrounding residues, and heme+surrounding residues+additional protein environment were examined; the latter system was calculated with a quantum mechanics/molecular mechanics (QM/MM) method. The computations were extended to a myoglobin (Mb) protein, in which the heme structure is quite planar, in contrast to that in H-NOX.

FeP(Im)-AB Bonding Energies Evaluated with A Large Number of Density Functionals (P = porphine, Im = imidazole, AB = CO, NO, and O(2)).

Sixty-four (64) density functionals, ranging from GGA, meta-GGA, hybrid GGA to hybrid meta-GGA, were tested to evaluate the FeP(Im)-AB bonding energies (E(bond)) in the heme model complexes FeP(Im)(AB) (P = porphine, Im = imidazole, AB = CO, NO, and O(2)). The results indicate that an accurate prediction of E(bond) for the various ligands to heme is difficult with the DFT methods; usually a functional successful for one system does not perform equally well for the other system(s). Relatively satisfactory results for the various FeP(Im)-AB bonding energies are obtained with the meta-GGA funtionals BLAP3 and Bmτ1; they yield E(bond) values of ca.

Structure, bonding, and linear optical properties of a series of silver and gold nanorod clusters: DFT/TDDFT studies.

DFT/TDDFT calculations have been carried out for a series of silver and gold nanorod clusters (Ag(n), Au(n), n = 12-120) whose structures are of cigar-type. Pentagonal Ag(n) clusters with n = 49-121 and hexagonal Au(n) clusters with n = 14-74 were also calculated for comparison. Metal-metal distances, binding energies per atom, ionization potentials, and electron affinities were determined, and their trends with cluster size were examined.

Iron porphyrins with different imidazole ligands. A theoretical comparative study.

A theoretical comparative study of a series of five- and six-coordinate iron porphyrins, FeP(L) and FeP(L)(O(2)), has been carried out using DFT methods, where P = porphine and L = imidazole (Im), 1-methylimidazole (1-MeIm), 2-methylimidazole (2-MeIm), 1,2-dimethylimidazole (1,2-Me(2)Im), 4-ethylimidazole (4-EtIm), or histidine (His). Two ligated "picket-fence" iron porphyrins, FeTpivPP(2-MeIm) and FeTpivPP(2-MeIm)(O(2)), were also included in the study for comparison. A number of density functionals were employed in the computations to obtain reliable results.

Dispersion-corrected DFT calculations on C(60)-porphyrin complexes.

The quality of the newly added, empirical dispersion correction in density functional theory (DFT) calculations is examined for several supramolecular complexes of fullerene (C(60)) with free-base and metal porphyrins (Por). The benzene dimer (C(6)H(6))(2), naphthalene dimer (C(10)H(8))(2), and anthracene dimer (C(14)H(10))(2) were also included in the study for comparison. Three density functionals, two damping functions, and two types of basis sets were employed in the computations.

Electronic structure of some substituted iron(II) porphyrins. Are they intermediate or high spin?

The electronic structure of some substituted, four-coordinate iron(II) porphyrins has been investigated with DFT methods. These systems include iron tetraphenylporphine (FeTPP), iron octamethyltetrabenzporphine (FeOTBP), iron tetra(alpha,alpha,alpha,alpha-orthopivalamide)phenylporphine (FeTpivPP, also called "picket fence" porphyrin), halogenated iron porphyrins (FeTPPXn, X=F, Cl; n=20, 28), and iron octaethylporphine (FeOEP). A number of density functionals were used in the calculations.

DFT/TDDFT study of lanthanide(III) mono- and bisporphyrin complexes.

The electronic structure, molecular structure, and electronic spectra of lanthanide(III) mono- and bisporphyrin complexes are investigated using a DFT/TDDFT method. These complexes include YbP(acac), YbP(2), [YbP(2)](+), YbHP(2), and [YbP(2)](-) (where P = porphine and acac = acetylacetonate). To shed some light on the origin of the out-of-plane displacement of Yb in YbP(acac), unligated model systems, namely, planar D(4h) and distorted C(4nu) YbP, were calculated.

Assessment of the performance of density-functional methods for calculations on iron porphyrins and related compounds.

The behaviors of a large number of GGA, meta-GGA, and hybrid-GGA density functionals in describing the spin-state energetics of iron porphyrins and related compounds have been investigated. There is a large variation in performance between the various functionals for the calculations of the high-spin state relative energies. Most GGA and meta-GGA functionals are biased toward lower-spin states and so fail to give the correct ground state for the high-spin systems, for which the meta-GGA functionals show more or less improvement over the GGA ones.

Fe(II) in different macrocycles: electronic structures and properties.

A theoretical comparative study of complexes of porphyrin (P), porphyrazine (Pz), phthalocyanine (Pc), porphycene (Pn), dibenzoporphycene (DBPn), and hemiporphyrazine (HPz) with iron (Fe) has been carried out using a density functional theory (DFT) method. The difference in the core size and shape of the macrocycle has a substantial effect on the electronic structure and properties of the overall system. The ground states of FeP and FePc were identified to be the 3A2g [(d(xy))2(d(z)2)2(d(pi))2] state, followed by 3E(g) [(d(xy))2(d(z)2)1(d(pi))3].

Spectroscopy, crystal structure, valance molecular orbital energy level diagram and DFT study of cis-[Cr(2,2'-bipy)2Cl2](Cl)0.38(PF6)0.62.

A new octahedral chromium(III) complex having 2,2'-bipyridine as ligand system was synthesized in methanol. Single crystal X-ray diffraction analysis shows that it possesses non-stoichiometry in its anionic primary covalency. It has also been studied by elemental analyses, optical spectroscopy (UV-vis, IR) and magnetic susceptibility data.

Effects of peripheral substituents and axial ligands on the electronic structure and properties of cobalt porphyrins.

The effects of peripheral substituents and axial ligands (L) on the electronic structure and properties of cobalt tetraphenylporphyrin (CoTPP) have been studied using DFT methods. Various density functionals were tested, and the ground state of each system was determined by considering several possible low-lying states. The ground states of the fully fluorinated CoTPPF28(L)2 complexes with L = THF, Py, and Im were identified to be high-spin (4E(g)) by the meta-GGA functional tau-HCTH, which contains the kinetic energy density tau, in agreement with experimental measurements.

Effects of Peripheral Substituents on the Electronic Structure and Properties of Unligated and Ligated Metal Phthalocyanines, Metal = Fe, Co, Zn.

The effects of peripheral, multiple -F as well as -C2F5 substituents, on the electronic structure and properties of unligated and ligated metal phthalocyanines, PcM, PcM(acetone)2 (M = Fe, Co, Zn), PcZn(Cl), and PcZn(Cl(-)), have been investigated using a DFT method. The calculations provide a clear explanation for the changes in the ground state, molecular orbital (MO) energy levels, ionization potentials (IP), electron affinities (EA), charge distribution on the metal (QM), axial binding energies, and in electronic spectra. While the strongly electron-withdrawing -C2F5 groups on the Pc ring change the ground state of PcFe, they do not influence the ground state of PcCo.

DFT study of unligated and ligated manganese(II) porphyrins and phthalocyanines.

A theoretical study of the electronic structure, bonding, and properties of unligated and ligated manganese(II) porphyrins and phthalocyanines has been carried out "in detail" using a density functional theory (DFT) method. While manganese tetraphenylporphine (MnTPP) in the crystal is high spin (S = 5/2) with the Mn(II) atom out of the porphyrin plane, the present calculations find that the free manganese porphine (MnP) molecule has no obvious tendency to distort from planarity even in the high-spin state. The ground state of the planar structure is found to be intermediate spin (S = 3/2).

Effects of peripheral substituents and axial ligands on the electronic structure and properties of iron phthalocyanine.

The effects of peripheral substituents and axial ligands on the electronic structure and properties of iron phthalocyanine, H(16)PcFe, have been investigated using a DFT method. Substitution by electron-withdrawing fluorinated groups alters the ground state of H(16)PcFe and gives rise to large changes in the ionization potentials and electron affinity. For the six-coordinate adducts with acetone, H(2)O, and pyridine, the axial coordination of two weak-field ligands leads to an intermediate-spin ground state, while the strong-field ligands make the system diamagnetic.

Performance assessment of density-functional methods for study of charge-transfer complexes.

Various density functionals are applied to a number of weakly bound intermolecular pi-pi charge-transfer (CT) complexes. Most functionals, including the recently developed mPWPW91 and mPW1PW91, grossly underestimate experimental excitation energies; good agreement is obtained only with the half-and-half hybrid BH&HLYP functional. PW91PW91 provides the best agreement with intermolecular distances measured in crystal, while the BH&HLYP values are about 0.

Comparative study of metal-porphyrins, -porphyrazines, and -phthalocyanines.

A theoretical comparative study of complexes of porphyrin (P), porphyrazine (Pz), and phthalocyanine (Pc) with metal (M) = Fe, Co, Ni, Cu, and Zn has been carried out using a DFT method. The calculations provide a clear elucidation of the ground states for the MP/Pz/Pc molecules and for a series of [MP/Pz/Pc](x-) and [MP/Pz/Pc](y+) ions (x = 1, 2, 3, 4; y = 1, 2). There are significant differences among MP, MPz, and MPc in the electronic structure and other calculated properties.