We have performed density functional theory (DFT) calculations of
iron−porphyrin (FeP) and its complexes
with O2, CO, NO, and imidazole (Im). Our fully
optimized structures agree well with the available
experimental
data for synthetic heme models. Comparison with crystallographic
data for proteins highlights interesting
features of carbon monoxymyoglobin. The diatomic molecule induces
a 0.3−0.4 Å displacement of the Fe
atom out of the porphyrin nitrogen (Np) plane and a doming
of the overall porphyrin ring. The energy of the
iron−diatomic bond increases in the order Fe−O2 (9
kcal/mol) < Fe−CO (26 kcal/mol) < Fe−NO (35
kcal/mol). The ground state of FeP(O2) is an open
shell singlet. The bent Fe−O2 bond can be
formally
described as FeIII−O2
-, and it
is characterized by the anti-ferromagnetic coupling between one of the
d electrons
of Fe and one of the π* electrons of O2.
FeP(CO) is a closed shell singlet, with a linear Fe−C−O
bond.
The complex with NO has a doublet ground state and a Fe−NO
geometry intermediate between that of
FeP(CO) and FeP(O2). The bending of the
Fe−(diatomic) angle requires a rather low energy for these
three
complexes, resulting in large-amplitude oscillations of the ligand even
at room temperature. The addition of
an imidazole ligand to FeP moves the Fe atom out of the porphyrin plane
toward the imidazole and decreases
significantly the energy differences among the spin states.
Moreover, our calculations underline the potential
role of the imidazole ligand in controlling the electronic structure of
FeP by changing the out-of-planarity of
the Fe atom. The presence of the imidazole increases the strength
of the Fe−O2 and Fe−CO bonds (15 and
35 kcal/mol, respectively), but does not affect the energy of the
Fe−NO bond, while the resulting FeP(Im)(NO) complex exhibits a longer and weaker Fe−Im bond.
The effect of pressure on optical phonon frequencies of MgB2 has been calculated using the frozenphonon approach based on a pseudopotential method. Grüneisen parameters of the harmonic mode frequencies are reported for the high-frequency zone-center E2g and B1g and the zone-boundary E2u and B2u modes at A. Anharmonic effects of phonon frequencies and the implications of the calculated phonon frequency shifts for the pressure dependence of the superconducting transition temperature of MgB2 are discussed. Also reported are Raman and optical reflectance spectra of MgB2 measured at high pressures. The experimental observations in combination with calculated results indicate that broad spectral features we observed in the Raman spectra at frequencies between 500 and 900 cm −1 cannot be attributed to first-order scattering by zone-center modes, but originate in part from a chemical species other than MgB2 at the sample surface and in part from a maximum in the MgB2 phonon density of states. Low-temperature Raman spectra taken at ambient pressure showed increased scattering intensity in the region below 300 cm −1 .
The effect of pressure on the zone-center optical phonon modes of antimony in the A7 structure has been investigated by Raman spectroscopy. The Ag and Eg frequencies exhibit a pronounced softening with increasing pressure, the effect being related to a gradual suppression of the Peierls-like distortion of the A7 phase relative to a cubic primitive lattice. Also, both Raman modes broaden significantly under pressure. Spectra taken at low temperature indicate that the broadening is at least partly caused by phonon-phonon interactions. We also report results of ab initio frozenphonon calculations of the Ag and Eg mode frequencies. Presence of strong anharmonicity is clearly apparent in calculated total energy versus atom displacement relations. Pronounced nonlinearities in the force versus displacement relations are observed. Structural instabilities of the Sb-A7 phase are briefly addressed in the Appendix.
First-principles calculations are employed to study SrTiO 3 (001) (1ϫ1) surfaces with both SrO and TiO 2 termination. A detailed geometry of the relaxed systems, surface energy, and the individual relaxation energies of the two types of surface are obtained. The longitudinal surface dipole moments are derived from variation of the macroscopic electrostatic potential along the surface normal direction. Pseudopotential-plane-wave calculations are performed in the slab geometry, on both symmetric and asymmetric slabs; the merits and the limits of the latter geometry are discussed. PRB 62 C. CHENG, K. KUNC, AND M. H. LEE
A quantitative study of the structure and electronic properties of Co-corrole, Co-corrin, and Co-porphyrin, using density functional theory, is reported. The structure of each macrocycle is optimized, with no symmetry constraints, by considering different spin states. The ground-state structures and spin states (S = 1 for Co-corrole, S = 0 for Co-corrin and S = 1/2 for Co-porphyrin) are in good agreement with the experimental data available. The trends in the sizes of the coordination cavities upon varying the inner metal atom and/or the macrocycle are analyzed and compared with those for the Fe-porphyrin we studied previously. Our results reveal that most of the distortion of the Co-corrin core in the B12 coenzyme is due to the inherent properties of Co-corrin. Quite different behaviors are found between corrinoids and porphyrins upon varying the spin state. While an increase in the metal-nitrogen (M-N) distance with spin state occurs in the porphyrins, the corrinoids show little variation in the M-N distance and, in some cases, undergo small structural changes in the ring structure. These results aid in understanding the often discussed question of why nature has chosen corrin/porphyrin for carrying out the particular biological functions identified in the B12 coenzyme.
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