Atomic Spin Densities Research Articles

Oxophlorin and metallooxophlorin radicals--DFT studies.

A flexible oxophlorin macrocycle, which allows the location of labile hydrogen atoms alternatively at the pyrrole nitrogen, oxygen, or meso-carbon atoms, has been studied by density functional theory (DFT). DFT calculations were carried out on oxophlorin 1, 5-hydroxyporphyrin 2, and two isomers of oxophlorin 3 and 4 (the proton added at the tetrahedral C(15) or the C(10) meso-carbon, respectively). The oxophlorin-hydroxyporphyrin structural changes are appropriately reflected by the significant changes of the meso carbon-oxygen bond lengths, which are in the limits of typical C=O and C-O distances. The rearrangement that creates the iso-oxophlorin macrocycle 3 (4) results in near tetrahedral geometry around the C(15) (C(10)) carbon atom, with the C(14)-C(15) and C(15)-C(16) (C(9)-C(10) and C(10)-C(11)) bond lengths corresponding to a single C-C bond. 5-Hydroxyporphyrin 2 is aromatic and has a bond pattern resembling that of regular porphyrin. In 1, 3, and 4, a localization of single and double bonds was seen, which agrees with the nonaromatic nature of oxophlorin, or isooxophlorin. The relative stability decreases in the order: 2 (0) > 3 (4.85) > 1 (5.11) > 4 (10.04) > 3-cis (12.89) (the number in parentheses is the relative energy, in kcal mol-1). The energy difference between the NH-cis and NH-trans tautomers, which is 8.04 kcal mol-1 for 3, results from a destabilizing NH-NH cis-interaction. DFT calculations were performed on the oxophlorin dianion radical (OP.)2- and a series of metallooxophlorin radicals ([(OP.)LiI]-, [(OP.)ZnII], [(OP.)GaIII]+, and (OP.)GaIIIF, in order to assess their electronic structures. Typically, the largest atomic spin density was found at the C(10) (C(20)) and C(15) meso positions, with the spin density at C(15) being twice as large as that at C(10). The spin density at the C(5) atom is negligible. A large spin density was found at the O(5) oxygen atom. The amount of spin density at the meso positions decreased as the cationic charge increased. When considering the absolute values of the spin densities, the opposite trend was observed at the pyrrolic carbon atoms. The spin density at the nucleus (Fermi contact terms) has also been analyzed. The spin distributions of iron oxophlorins determined by NMR were attributed to an oxophlorin radical electronic structure. The calculated spin density maps accounted for the essential NMR spectroscopic features of important intermediates in the heme degradation process--iron oxophlorin complexes. The DFT calculations reproduced the following spectroscopic patterns: a) |delta H(15)|>|delta H(10)|>>|delta (beta-H)|, b) a sign alteration of the contact shifts for identical substituents located on the same pyrrole ring.

High‐spin silicon fullerene Si60 and its oligomers

AbstractHigh‐spin states of the Si60 fullerene and its oligomers are considered semiempirically by using sequential and parallel implementations of the AM1 codes. The states are energetically favorable and nearly degenerated over triplet, quintet, and septet spins. All atoms of the Si60 fullerene are in sp3‐configuration, which is supported by atomic spin density in addition to electron density, the latter to be responsible for the formation of chemical bonds. Spotted distribution of spin density over atoms provides molecular magnetism of the molecule. A similar picture is disclosed for oligomers {Si60}n with n up to 8, which according to computational results should be magnetic with a fractal‐like distribution of spin density over atoms. Opposite the latter, composites Si60C60 and Si60H60 behave conventionally and are nonmagnetic. A way of the Si60 fullerene synthesizing is suggested via the above composite product as intermediates. The considered oligomers are proposed as a model of silicon nanofibers observed recently. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002

Density functional theory of spin-coupled models for diiron-oxo proteins: Effects of oxo and hydroxo bridging on geometry, electronic structure, and magnetism

We have performed a comprehensive study of the electronic structure and magnetic properties of structurally characterized models for diiron-oxo proteins. Results from Kohn–Sham density functional theory show that two complexes, with formula Fe2(μ-O)(μ-O2CCH3)2(HBpz3)2 and [Fe2(μ-OH)(μ-O2CCH3)2(HBpz3)2]+, are strongly and weakly antiferromagnetically coupled, respectively, in agreement with experiment. The physical origin of the stronger and weaker exchange typically measured for oxo- and hydroxo-bridged diiron complexes, respectively, has been elucidated. The main superexchange pathways giving rise to molecular antiferromagnetism in both complexes have been identified. The dominant pathway in the oxo-bridged complex, Fe1(dxz):μ-O(px):Fe2(dxz), was formed by π interactions whereas that of the hydroxo-bridged, Fe1(dz2):μ-OH(p∥):Fe2(dz2), was formed by σ interactions. We also found a pathway mediated by the bridging acetates, Fe1(dx2−y2):bis(μ-acetato):Fe2(dx2−y2), which induces weak antiferromagnetism in the oxo-bridged complex but is significantly more important in the hydroxo-bridged complex. The antiferromagnetic exchange constants that parameterize the Heisenberg Hamiltonian H=JS1⋅S2 have been predicted for both, strongly and weakly, coupled complexes. Overall, the signs, trends, and magnitudes of the theoretical values (Jμ-Ocalc=+152.7 cm−1, Jμ-OHcalc=+23.3 cm−1) were in excellent agreement with experiment. The geometries of the complete molecular structures have been optimized in C2v symmetry and used to calculate molecular properties such as atomic charges and spin densities. The electronic configurations (Fe:4s0.293d5.93,μ-O:2s1.922p4.99;Fe:4s0.303d5.82,μ-OH:2s1.822p5.25,H:1s0.51) of the respective binuclear cores revealed relatively high occupancies for the nominally ferric ions, thus reflecting a donating character of their immediate N3O3 coordination. In addition, the diiron-oxo protein hemerythrin has been discussed. Theoretical and structural considerations indicated that the oxo-bridged diferric complex considered herein models extremely well the antiferromagnetic behavior of azidomet- and azidometmyo-hemerythrin. Finally, the magnetic behavior of closely related oxo-bridged diferric and hydroxo-bridged diferrous complexes containing Me3TACN capping ligands has been explained in light of the results presented in this work.

Electronic structure of an isolated oxygen vacancy at the TiO 2(1 1 0) surface

The electronic structure of the rutile(1 1 0) surface after formation of an isolated oxygen vacancy has been studied with density functional (DF) calculations and TiO 2 embedded clusters. Restricted and unrestricted open shell wave functions have been analyzed in terms of atomic spin densities and Ti core level shifts. The removal of a neutral oxygen atom from the bridging oxygens of the TiO 2(1 1 0) surface results in two unpaired electrons localized at the 3d orbitals of neighboring 5-coordinated Ti atoms. The electronic structure of an O vacancy on the surface of TiO 2 is compared with that of the same defect in MgO and SiO 2.

The molecular configuration of bis(trifluoromethyl)nitroxide (CF 3) 2NO [rad

Anisotropic 14 N couplings have been determined using electron paramagnetic resonance spectroscopy for the radicals, bis(trifluoromethyl)nitroxide and di- tert-butylnitroxide as isolated in a polycrystalline fluorotrichloromethane matrix at 77 K. The results show that the nitrogen 2p z orbital spin-population in bis(trifluoromethyl)nitroxide is 26%, as compared with 48% in di- tert-butylnitroxide, which is due mainly to the importance of the oxygen-localised canonical structure (CF 3) 2N–O and to spin-delocalisation onto the CF 3 groups: it is the large oxygen atom spin density of 0.63 that determines the relatively high reactivity of bis(trifluoromethyl)nitroxide in hydrogen-atom transfer reactions. On the basis of their anisotropic and isotropic 14 N couplings (measured in liquid fluorotrichloromethane), it is concluded that the configuration at the nitrogen centre is near-planar in both nitroxides. This result is supported by molecular orbital calculations made on these, and related molecules in order to evaluate some of the theoretical methods available to organic chemists.

Cleavage of cyclopropyl ketones mediated by alkylmercury(ii) hydridesA preliminary account of part of this work was presented at the 12th National Symposium of Organic Chemistry (XII SINAQO), Córdoba, Argentina, November 1999. Abstract published in Molecules (online computer file), 2000, 5, 447.Electronic supplementary information (ESI) available: UHF/6-31G**-calculated structures, spin-density surfaces, cartesian coordinates, total atomic spin densities and Fermi-contact data for simplified

Cyclopropyl ketones are converted into their hydrazones which react with mercury(II) oxide and mercury(II) acetate to give α-(acetoxymercurio)alkyl acetates. These are reduced in situ to the corresponding α-acetoxyalkylmercury(II) hydrides which rearrange spontaneously with cleavage of the cyclopropane ring. The procedure is used to obtain D-homo- and 17(13→18)-abeo-pregnanes.

Molecular geometry and electronic structure of molecules in free‐radical copolymerization of styrene and methyl methacrylate derived from density functional calculations

AbstractThe molecular geometry and electronic structure of styrene and methyl methacrylate as well as corresponding radicals formed by the addition of a methyl radical to the β‐carbon of the monomer were determined using the density functional theory at the B3LYP/6‐311+G** level. Results were in good agreement with the theoretical and experimental data available in the literature. Full optimized molecular geometry of methyl methacrylate showed the trans form of the molecule. Monomers transformed into corresponding radicals preserved the main structural parameters of substituents whereas bonds between substituents and adjacent radical carbon atoms shortened. It was found that the correlation of the theoretically calculated electronic parameters for monomers and the corresponding radicals with the Q and e parameters from the Alfrey–Price scheme strongly depends on the level of calculations. Application of the higher level of theory including the correlation effect changes the relationship discussed in the literature between energy (EY) of formation of a radical from the monomer, the experimental e parameter, and the Q parameter and monomer/average electronegativity, respectively. The total atomic spin density at the radical carbon atom correlated with the radical parameter P in the Alfrey–Price scheme was computed to be higher for the methoxycarbonyl‐1‐methyl‐ethyl radical when compared with the 1‐phenyl‐propyl radical. These values are in good agreement with the localization energies and the P values determined from the kinetic measurements for macroradicals ending with styrene and methyl methacrylate monomer units. © 2001 John Wiley & Sons, Inc. J Polym Sci Part A: Polym Chem 39: 3761–3769, 2001

DFT calculations of the electronic structure of the paramagnetic states Ni-A, Ni-B and Ni-C of [NiFe] hydrogenase

Structural parameters and atomic spin densities of the active centre of [NiFe] hydrogenases in the paramagnetic states Ni-A, Ni-B and Ni-C are reported. The DFT (BLYP/DZVP) calculated spin density distribution is found to be in good agreement with experimental data when the bridging ligand is OH− in the Ni-B and O2− in the Ni-A states of the enzyme. For the reduced enzyme (Ni-C) it is postulated that a hydride ligand bridges the Ni and Fe atoms. The atomic spin densities for the proposed paramagnetic states are in good agreement with experimental electron magnetic resonance data. Based on the deduced composition of the states Ni-A, Ni-B and Ni-C a model for the reaction mechanism is proposed.

Electron transfer from phenolic compounds to parent n-butyl chloride radical cations—a quantum chemical study of product transient formation and stability

The Density Functional Theory (DFT) B3LYP and the semiempirical PM3 quantum chemical methods were used to describe the mechanism of electron transfer from aromatic solutes to n-butyl chloride radical cations. The influence of the electronic parameters, the distribution of the Mulliken charges for the radical cations, and the equilibrium geometries of the ground state and the radical cation on the chemical reactivity were analyzed. Pulse radiolysis experiments had shown that phenol radical cations and phenoxyl radicals appear as direct products of the electron transfer, indicating a product distribution determined by encounter geometry. The quantum chemical approaches introduced enabled both the geometry, the energy and the molecular orbitals of an encounter complex to be calculated, explaining the rapid phenoxyl radical formation by a second reaction channel. The experimentally observed lifetimes of the phenol radical cations were correlated with quantum chemical calculated spin and Mulliken charge distributions. It was found that the influence of the solvent type approximated by the Onsager reaction field model and the DFT method showed no essential differences in the atomic spin and Mulliken charge distributions. The semiempirical PM3-calculated parameters tally well with those observed at the B3LYP/6-31G(d) level. Furthermore, a reliable trend correlation between the atomic spin density on the oxygen atom and the lifetime of the radical cations was found. The configuration interaction with single excitation approximation at the semiempirical PM3 level was applied to calculate the low-energy electronic transitions of the aromatic transients. Finally, the electronic transitions are calculated for both the radical cations and the deprotonated neutral radicals.

Photoinduced electron-transfer reactions with quinolinic and trimellitic acid imides: experiments and spin density calculations(1)

The regioselectivity of photoinduced electron-transfer (PET) reactions of unsymmetrical phthalimides is controlled by the spin density distribution of the intermediate radical anions. ROHF ab initio calculations were found to be most suitable for atomic spin density analysis. Intramolecular PET reactions of quinolinic acid imides were studied with the potassium butyrate and hexanoate 1a,b and a cysteine derivative 3. The photocyclizations products 2a,b and 4 were formed with moderate regioselectivities (68:32, 57:43, and 81:19) showing preferential ortho cyclization. The intermolecular reaction of potassium propionate and potassium isobutyrate with N-methylquinolinic acid imide (5) yielded as addition products the dihydropyrrolo[3,4-b]pyridines 6a,b with slight ortho regioselectivity (55:45). In contrast to these low regioselectivities, the PET reaction of potassium propionate with the methyl ester of N-methyltrimellitic acid imide (9) yielded solely the para addition product 10. Likewise, the intramolecular photoreaction of the cysteine derivative 7 gave a 75:25 (para/meta) mixture of regioisomeric cyclization products 8. The regioselectivity originates from donor-acceptor interactions prior to electron transfer and differences in spin densities in the corresponding imide radical anions. The results of DFT and ab initio calculations for the radical anions of the quinolinic acid imide (11(*)(-)) and the methyl ester of trimellitic acid imide (12(*)(-))( )()were in agreement with the latter assumption: spin densities in 11(*)(-) were higher for the imido ortho carbon atoms (indicating preferential ortho coupling); for 12(*)(-) the spin densities were higher for the imido para carbon atoms (indicating preferential para coupling). These correlations became more significant when the additional spin densities at the carbonyl oxygen and the adjacent carbon atoms were taken into account. The cyclization selectivities for 2, 4, and 8 deviate from the intermolecular examples probably because of ground-state and solvent effects.

Full configuration interaction and multiconfigurational spin density in boron and carbon atoms

The reliability of spin polarization method results for atomic spin densities, obtained with several widely used Gaussian basis sets, is examined by comparison with the results of full configuration interaction (FCI) calculations. The spin densities obtained with these basis sets using the spin polarization model and some other methods disagree with the FCI treatment. Since the FCI wave function is exact for a given basis, it is not clear that the spin polarization model will be generally reliable. A large active space multiconfigurational (CASSCF) calculation is shown to be inadequate as an alternative to FCI treatment. The importance of accounting at least to some extent for excitations to all orbitals in the complete space of basis functions is illustrated by very slow convergence of CASSCF results with increasing size of active space. The FCI results reported here can be used as benchmarks to test various approaches to spin density calculation.

A Parametrized Valence-Bond Study of the Origin of the Long, Weak N−N Bond of asym-N2O3

The results of an all-electron STO-6G valence-bond study of the origin of the long, weak N−N bond of asym-N2O3 are reported. Attention is given to the valence-bond structures which differ in the locations of eight electrons among five overlapping nitrogen and oxygen atomic orbitals, designated as π̄1, h2, and π̄3 for NO2, and h4 and π̄5 for NO. These orbitals accommodate the electrons of the N−N σ-bond and oxygen lone-pair electrons prior to any delocalization of the latter electrons. The calculations are parametrized so that UHF/cc-pVQZ estimates of the atomic spin densities for NO2 and NO are approximately reproduced when their odd electrons are assumed to occupy these overlapping atomic orbitals. The origin of the N−N bond lengthening is thereby shown to be associated with (a) the orientation of the h4 atomic orbital, and (b) some delocalization of oxygen π̄ electrons into the nitrogen h2 and h4 atomic orbitals when the latter orbitals are initially singly occupied. Covalent−ionic resonance (O2N−NO ↔ O2N-NO+ ↔ O2N+NO-) is calculated to be needed in order to stabilize the N2O3 relative to the NO2 and NO dissociation products.

Structure of isolated and solvated peroxyl radicals

We have investigated the structure of HO2 and a series of alkyl peroxyl radicals ROO using a variety of quantum mechanical methods. We first compute the geometries, vibrational frequencies, electronic charge distributions, and spin densities for the series of radicals considered in the gas phase. Significant differences with respect to previous calculations have been pointed out in a few cases. In particular, we show the fundamental importance of electronic correlation when computing net atomic charges and spin densities, which have generally been estimated in the litterature by means of Hartree–Fock SCF electronic densities. Solvation effects on the geometry and electronic structure have been estimated by carrying out self-consistent reaction field computations in a polarizable continuum environment with relative dielectric permittivity equal to that of liquid water. Large electronic polarization is predicted in such conditions. This may be important in order to understand reactive properties of the radicals in different media. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1039–1048, 1999

Triplet State Characteristics of Higher Fullerenes

A theoretical study on the energetics and the structures of lowest triplets of C60, C70, C76, C78, C82, and C84 is reported. Excited state geometries, and excitation and phosphorescence energies, as well as Jahn−Teller distortions for degenerate levels were determined. Zero-field splittings of various triplets were evaluated; the signs and magnitudes of the resulting D and E parameters are quite sensitive to the system and to the symmetry of the particular excited state. Atomic spin density distributions are determined for the lowest triplet states.

Atomic Spin Densities from Correlation-Consistent Basis Sets

Recently introduced correlation-consistent (cc-) basis sets are used together with the quadratic configuration interaction (QCISD) correlation recovery technique and a hybrid density functional met...

Density-Functional-Derived Structures, Spin Properties, and Vibrations for Phenol Radical Cation

Phenol radical cation (PhOH•+) structures, proton hyperfine coupling constants, atomic spin densities, vibrational frequencies, and deuterium isotopic vibrational frequency shifts were calculated by using spin-unrestricted Hartree−Fock (UHF), second-order Møller−Plesset perturbation (UMP2), as well as density-functional (DF) and hybrid Hartree−Fock/density-functional (HF/DF) methods. Of the methods tested, the three-parameter, hybrid HF/DF method incorporating the gradient-corrected correlation functional of Lee, Yang, and Parr (B3LYP) appears to yield the most accurate overall results. Calculated CC bond distances for PhOH•+ display pronounced quinoidal features, and the CO bond distance (1.313 Å) implies significant double-bond character. Unscaled vibrational frequencies calculated by using the B3LYP method differ from experiment by an average absolute magnitude of only 15 cm-1 and are therefore more accurate than uniformly scaled UMP2-derived frequencies. Our assignment of the CO stretching mode to a calculated frequency of 1522 cm-1 and the strong mixing between the CO stretching mode 7a and a CH bending mode at lower frequency (19a) suggests that isotopic frequency shifts be measured to distinguish clearly the CO stretching and CH bending modes in radicals related to PhOH•+. PhOH•+ displays a spin density distribution reminiscent of an odd-alternant hydrocarbon, but with large spin density on its oxygen-bearing C1 atom. Of the methods tested, the gradient-corrected BP86 and BLYP and hybrid B3LYP methods yield the most accurate proton hyperfine coupling constants for PhOH•+, whereas calculated spin densities on the carbon and oxygen atoms are much less sensitive to the particular DF method used. The B3LYP method also gives an accurate proton affinity for PhO• (208.5 kcal/mol), within 2.9 kcal/mol of experiment (205.6 ± 0.3 kcal/mol).

Simplified Non-Empirical Unrestricted Hartree-Fock Approximation (SUHF) for the Calculation of Electronic Ground State Properties of Molecules with Closed and Open Valence Shells. II. Diatomic Molecules

Abstract A comparison of numerical Simplified Unrestricted Hartree-Fock (SUHF) results (electronic ground state configurations, total energies, first ionization potentials, atomic charges, atomic spin densities of diatomic molecules) with those of equivalent standard calculations suggests the applicability of the non-empirical but drastically simplified procedure. SUHF may even approach ab initio quality obtained with simple (STO-3G) contracted Gaussian basis sets.

Chemical bonds and electronic configurations of Cu-O clusters in the Y-Ba-Cu-O system

Discrete variational DV-Xα calculations were carried out on the Cu 3O 15− 10, Cu 3O 17− 12 and Cu 4O 17− 14 clusters as models of Y-Ba-Cu-O superconductors. The calculated results reveal that the valence levels consist mainly of Cu d and O p orbitals, with strong covalent hybridization. The unpaired spins are mostly localized on the planar Cu2 sites, while the spin densities of the other atoms are very small compared with the experimental results. The charge distributions obtained support the absence of Cu 3+ and the presence of Cu +, Cu 2+, O − and O 2− electronic configurations due to the covalent interaction.

A selection rule in SiHn(n=1–4)+F reactions: An ab initio molecular orbital study

Reactions of SiHn(n=1–4) with a fluorine atom were studied by using an ab initio molecular orbital method [fourth-order Mo/ller–Plesset (MP4/6-21G**//second-order Mo/ller–Plesset MP2/6-21G**)]. Structures of the transition states were determined. In the cases of SiH3+F and SiH+F, fluorine atom addition to a silicon atom was a favorable reaction at the singlet state and abstraction of a hydrogen by a fluorine atom was a favorable route at the triplet state. Abstraction of a hydrogen was also favorable at the doublet state in the case of SiH2+F. A selection rule of these reactions on the basis of the atomic spin density on each atom was proposed. The selection rule proposed was proved to also be applicable to the reaction CH3+F.

ATOMIC SHORT RANGE ORDER AND SPIN DENSITY WAVE PROPAGATION IN CuMn

Neutron scattering studies of the atomic short range order (ASRO) and spin density waves (SDW) were carried out for a Cu-35% Mn sample with an unusually high degree of ASRO that develops mostly in a single tetragonal domain. The SDW peaks show a distinctly non-cubic distribution that is readily correlated with the ASRO and which corresponds to the propagation of SDW only in the c plane of the tetragonally based ASRO. The high degree of ASRO and single domain character of this carefully heat-treated sample produces an unusually stable SDW with a higher transition temperature and a larger correlation length than is observed for quenched alloys of the same Mn content. Since SDW stability depends on structural features in the conduction electron susceptibility and on flat, parallel sections of the Fermi surface, these observations suggest that the degree of ASRO and/or the presence of single domain ASRO influences the sharpness of the relevant Fermi surface features in these alloys.