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PubMed1999

The Electronic Structure and Spectrum of RhC: New Bands in the 400-500 nm Region, Interacting (2)Sigma(+) and (2)Pi States, and Deperturbation.

Rhodium monocarbide (RhC) molecules were generated using a laser ablation/supersonic molecular beam source. Laser-induced and dispersed-fluorescence (DF) techniques were used to study the visible spectrum between 400 and 530 nm. Rh(12)C/Rh(13)C isotope shifts, DF, and excited level lifetime measurements assisted in classifying the observed bands into three series: the known C(2)Sigma(+) <-- X(2)Sigma(+) system (short excited state lifetimes) and the two spin subsystems of a (2)Pi(i) <-- X(2)Sigma(+) transition (long excited state lifetimes). A time-filtering technique was employed to separate effectively emission from close-lying (2)Pi and C(2)Sigma levels. The C-X system is inherently strong; the (2)Pi(i) <-- (2)Sigma(+) system very weak. The (2)Pi(1/2) <-- (2)Sigma component is identified with the B-X system, previously taken to be of (2)Sigma(+) <-- (2)Sigma(+) symmetry. The (2)Pi(3/2) component gives rise to local perturbations in the C state. Many new bands in the (2)Pi(i) <-- X(2)Sigma(+) transition were recorded and analyzed and the interactions/perturbations among the (2)Sigma(+) and the newly established (2)Pi(i) states were examined in detail. We calculated many spectroscopic constants and other properties associated with the perturbed (mixed) levels of the (2)Pi(1/2) and (2)Sigma(+) states and compared them with the experimental data. In most of the comparisons, the calculated values are in quantitative agreement with the experimental ones. Calculations of the spin-rotation constants of the (2)Sigma(+) and the Lambda-doubling constants of the (2)Pi(1/2) suggest the involvement of remote perturbers. Theory and experiment suggest that the electronic state labels of Scullman and Kaving [J. Mol. Spectrosc. 32, 475 (1969)], i.e., A(2)Pi(r), B(2)Sigma(+), C(2)Sigma(+), and D(2)Sigma(-), should be relabeled B(2)Pi(r), D(2)Pi(3/2), E(2)Sigma(+), and D(2)Pi(1/2), respectively. Copyright 1999 Academic Press.

Journal Article↗
PubMed2005

Systematic sparse matrix error control for linear scaling electronic structure calculations.

Efficient truncation criteria used in multiatom blocked sparse matrix operations for ab initio calculations are proposed. As system size increases, so does the need to stay on top of errors and still achieve high performance. A variant of a blocked sparse matrix algebra to achieve strict error control with good performance is proposed. The presented idea is that the condition to drop a certain submatrix should depend not only on the magnitude of that particular submatrix, but also on which other submatrices that are dropped. The decision to remove a certain submatrix is based on the contribution the removal would cause to the error in the chosen norm. We study the effect of an accumulated truncation error in iterative algorithms like trace correcting density matrix purification. One way to reduce the initial exponential growth of this error is presented. The presented error control for a sparse blocked matrix toolbox allows for achieving optimal performance by performing only necessary operations needed to maintain the requested level of accuracy.

Algorithms↗
PubMed2006

Multilevel and density functional electronic structure calculations of proton affinities and gas-phase basicities involved in biological phosphoryl transfer.

Five multilevel model chemistries (CBS-QB3, G3B3, G3MP2B3, MCG3/3, and MC-QCISD/3) and seven hybrid density functional methods (PBE0, B1B95, B3LYP, MPW1KCIS, PBE1KCIS, and MPW1B95) have been applied to the calculation of gas-phase basicity and proton affinity values for a series of 17 molecules relevant to the study of biological phosphoryl transfer. In addition, W1 calculations were performed on a subset of molecules. The accuracy of the methods was assessed and the nature of systematic errors was explored, leading to the introduction of a set of effective bond enthalpy and entropy correction terms. The multicoefficient correlation methods (MCG3/3 and MC-QCISD), with inclusion of specific zero-point scale factors, slightly outperform the other multilevel methods tested (CBS-QB3, G3B3, and G3MP2B3), with significantly less computational cost, and in the case of MC-QCISD, slightly less severe scaling. Four density functional methods, PBE1KCIS, MPW1B95, PBE0, and B1B95 perform nearly as well as the multilevel methods. These results provide an important set of benchmarks relevant to biological phosphoryl transfer reactions.

Electrons↗
PubMed2006

A fast correlated electronic structure method for computing interaction energies of large van der Waals complexes applied to the fullerene-porphyrin dimer.

A new implementation of the scaled opposite spin Møller-Plesset (SOS-MP2) method is briefly described, which exploits the locality and sparsity of expansion coefficients and as a result has computational costs that increase approximately quadratically with molecular size. The performance of SOS-MP2 for describing stacked pi-complexes is carefully investigated using the benzene, ethylene, uracil, and naphthalene dimers as model systems. It is demonstrated that counterpoise-corrected SOS-MP2 results, extrapolated towards the complete basis set (CBS) limit using a two-point extrapolation scheme, can yield association energies that are reasonably close to the best available numbers, when the single scale factor is chosen as 1.55 for extrapolating results at the cc-pVDZ and cc-pVTZ levels. This methodology yields an interaction energy for the fullerene-tetraphenylporphyrin dimer of -31.47 kcal mol(-1) while Hartree-Fock (HF) with the cc-pVTZ basis finds the dimer at the same geometry is unbound by +10.83 kcal mol(-1). This implies that the net binding is a result of substantial correlation effects, presumably long-range London dispersions.

Chemical Phenomena↗
PubMed2005

Mechanistic insights into the Bazarov synthesis of urea from NH3 and CO2 using electronic structure calculation methods.

The mechanism of the noncatalyzed and reagent-catalyzed Bazarov synthesis of urea has extensively been investigated in the gas phase by means of density functional (B3LYP/6-31G(d,p)) and high quality ab initio (CBS-QB3) computational techniques. It was found that the first step of urea formation from NH3(g) and CO2(g) corresponds to a simple addition reaction leading to the carbamic acid intermediate, a process being slightly endothermic. Among the three possible reaction mechanisms considered, the addition-elimination-addition (AEA) and the double addition-elimination (DAE) mechanisms are almost equally favored, while the concerted (C) one was predicted kinetically forbidden. The second step involves the formation of loose adducts between NH3 and carbamic acid corresponding to an ammonium carbamate intermediate, which subsequently dehydrates to urea. The formation of "ammonium carbamate" corresponds to an almost thermoneutral process, whereas its dehydration, which is the rate-determining step, is highly endothermic. The Bazarov synthesis of urea is strongly assisted by the active participation of extra NH3 or H2O molecules (autocatalysis). For all reaction pathways studied the entire geometric and energetic profiles were computed and thoroughly analyzed. The reaction scheme described herein can be related with the formation of both isocyanic acid, H-N=C=O, and carbamic acid, H2N-COOH, as key intermediates in the initial formation of organic molecules, such as urea, under prebiotic conditions.

Ammonia↗
PubMed1980

The electronic structure of platinum-guanine complexes.

Molecular orbital calculations using the SC-MEH method have been carried out on guanine and its mode of interaction with the anti cancer drug,cis-diamminodichloroplatinum(II) (DDP), in various geometrical bonding conformations. It is shown that if indeed a monomeric complex between DDP and guanine is formed, the N-7 and O-6 positions of guanine bond most strongly with DDP in both monodentate and bidentate chelation models. The influence of this bonding on the N-1--H-1 bond is studied in terms of atomic charge variations and orbital overlap population densities to determine if miss-pairing in DNA might occur via the loss of the guanine H-1 proton, as proposed in the mechanism of O-6 methylation. Preliminary findings do not support one of the proposed mechanisms for miss-pairing in DNA if a bidentated N-7, O-6 DNA-DDP chelate is formed. Interest in the cellular effects of square-planar platinum complexes began with Rosenberg's discovery in 1965 that DDP, inhibited cell division with inhibiting growth rate in Escherichia coli bacteria [u]. Shortly thereafter, the anti-cancer activity of DDP and a number of related platinum complexes was demonstrated [2]. Since then, DDP has been used effectively for a number of types of cancers including lung, head and neck, prostate, bladder, ovaran, and testicular cancers [3], and has recently been released in the United States for distribution as a prescribed drug in chemotherapy.

Chemical Phenomena↗
PubMedDate not supplied

[Electron structure of the active center of paramagnetic hemoproteins from the data of low-temperature magnetic circular dichroism. High-spin ferric derivatives].

The temperature dependences of magnetic circular dichroism (MCD) spectra of the high-spin fluoride complexes of metmyoglobin, methemoglobin and horse-radish ferriperoxidase have been studied and analysed in spectral region 250-1100 nm at temperatures from 2 to 300 K. Upon lowering of the temperature the increase of the MCD intensity was observed over all spectral regions studied, indicating the presence of the so called C-type effects. In contrast to other paramagnetic hemoproteins studied previously the significant changes of the shape of MCD spectra of fluoride complexes in the near UV B (pi--pi*)-band (Soret band) was observed at the lowest temperatures. The changes are explained by the superposition of effects of two types: the usual C-type effects which have the shape of absorption dispersion and of the derivative shape CA-type effects. The CA-type effects in the Soret band were analysed in terms of the theoretical model suggested previously. The data are in qualitative agreement with the prediction of the model. New information on the energies of the 4E and 4A2 excited states of the heme iron, on the orbital contribution into ground state paramagnetism and on the value of the pi--d pi-splitting, typical for B(pi--pi*)-state and ground Kramers doublet, were obtained on the basis of quantitative analysis of the MCD temperature dependences. The parameter D of zero-field splitting was estimated from MCD spectra and its value (6 cm-1) agrees well with that obtained by other methods.

Animals↗
PubMed2006

Geometries and electronic structures of cyanide adducts of the non-heme iron active site of superoxide reductases: vibrational and ENDOR studies.

We have added cyanide to oxidized 1Fe and 2Fe superoxide reductase (SOR) as a surrogate for the putative ferric-(hydro)peroxo intermediate in the reaction of the enzymes with superoxide and have used vibrational and ENDOR spectroscopies to study the properties of the active site paramagnetic iron center. Addition of cyanide changes the active site iron center in oxidized SOR from rhombic high-spin ferric (S = 5/2) to axial-like low-spin ferric (S = 1/2). Low-temperature resonance Raman and ENDOR data show that the bound cyanide adopts three distinct conformations in Fe(III)-CN SOR. On the basis of 13CN, C15N, and 13C15N isotope shifts of the Fe-CN stretching/Fe-C-N bending modes, resonance Raman studies of 1Fe-SOR indicate one near-linear conformation (Fe-C-N angle approximately 175 degrees) and two distinct bent conformations (Fe-C-N angles <140 degrees). FTIR studies of 1Fe-SOR at ambient temperatures reveals three bound C-N stretching frequencies in the oxidized (ferric) state and one in the reduced (ferrous) state, indicating that the conformational heterogeneity in cyanide binding is a characteristic of the ferric state and is not caused by freezing-in of conformational substates at low temperature. 13C-ENDOR spectra for the 13CN-bound ferric active sites in both 1Fe- and 2Fe-SORs also show three well-resolved Fe-C-N conformations. Analysis of the 13C hyperfine tensors for the three substates of the 2Fe-SOR within a simple heuristic model for the Fe-C bonding gives values for the Fe-C-N angles in the three substates of ca. 123 degrees (C3) and 133 degrees (C2), taking a reference value from vibrational studies of 175 degrees (C1 species). Resonance Raman and ENDOR studies of SOR variants, in which the conserved glutamate and lysine residues in a flexible loop above the substrate binding pocket have been individually replaced by alanine, indicate that the side chains of these two residues are not involved in direct interaction with bound cyanide. The implications of these results for understanding the mechanism of SOR are discussed.

Binding Sites↗
PubMed2003

Assignment of heme resonances and determination of the electronic structures of high- and low-spin nitrophorin 2 by 1H and 13C NMR spectroscopy: an explanation of the order of heme methyl resonances in high-spin ferriheme proteins.

The (1)H NMR resonances of the heme substituents of the low-spin Fe(III) form of nitrophorin 2, as its complexes with N-methylimidazole (NP2-NMeIm) and imidazole (NP2-ImH), have been assigned by a combination of (1)H homonuclear two-dimensional NMR techniques and (1)H-(13)C HMQC. Complete assignment of the proton and partial assignment of the (13)C resonances of the heme of these complexes has been achieved. Due to favorable rates of ligand exchange, it was also possible to assign part of the (1)H resonances of the high-spin heme via saturation transfer between high- and low-spin protein forms in a partially liganded NP2-NMeIm sample; additional resonances (vinyl and propionate) were assigned by NOESY techniques. The order of heme methyl resonances in the high-spin form of the protein over the temperature range of 10-37 degrees C is 8 = 5 > 1 > 3; the NMeIm complex has 5 > 1 > 3 > 8 as the order of heme methyl resonances at <30 degrees C, while above that temperature, the order is 5 > 3 > 1 > 8, due to crossover of the closely spaced 3- and 1-methyl resonances of the low-spin complex at higher temperatures. This crossover defines the nodal plane of the heme orbital used for spin delocalization as being oriented 162 +/- 2 degrees clockwise from the heme N(II)-Fe-N(IV) axis for the heme in the B orientation. For the NP2-ImH complex, the order of heme methyl resonances is 3 > 5 > 1 > 8, which defines the orientation of the nodal plane of the heme orbital used for spin delocalization as being oriented approximately 150-155 degrees clockwise from the heme N(II)-Fe-N(IV) axis. In both low-spin complexes, the results are most consistent with the exogenous planar ligand controlling the orientation of the nodal plane of the heme orbital. In the high-spin form of NP2, the proximal histidine plane is shown to be oriented 135 degrees clockwise from the heme N(II)-Fe-N(IV) axis, again for the B heme orientation. A correlation between the order of heme methyl resonances in the high-spin form of NP2 and several other ferriheme proteins and an apparent 90 degrees shift in the nodal plane of the orbital involved in spin delocalization from that expected on the basis of the orientation of the axial histidine imidazole nodal plane have been explained in terms of bonding interactions between Fe(III), the axial histidine imidazole nitrogen, and the porphyrin pi orbitals of the high-spin protein.

Animals↗
PubMed2002

Planar three-coordinate high-spin Fe(II) complexes with large orbital angular momentum: Mössbauer, electron paramagnetic resonance, and electronic structure studies.

Mössbauer spectra of [LFe(II)X](0) (L = beta-diketiminate; X = Cl(-), CH(3)(-), NHTol(-), NHtBu(-)), 1.X, were recorded between 4.2 and 200 K in applied magnetic fields up to 8.0 T. A spin Hamiltonian analysis of these data revealed a spin S = 2 system with uniaxial magnetization properties, arising from a quasi-degenerate M(S) = +/-2 doublet that is separated from the next magnetic sublevels by very large zero-field splittings (3/D/ > 150 cm(-1)). The ground levels give rise to positive magnetic hyperfine fields of unprecedented magnitudes, B(int) = +82, +78, +72, and +62 T for 1.CH(3), 1.NHTol, 1.NHtBu, and 1.Cl, respectively. Parallel-mode EPR measurements at X-band gave effective g values that are considerably larger than the spin-only value 8, namely g(eff) = 10.9 (1.Cl) and 11.4 (1.CH(3)), suggesting the presence of unquenched orbital angular momenta. A qualitative crystal field analysis of g(eff) shows that these momenta originate from spin-orbit coupling between energetically closely spaced yz and z(2) 3d-orbital states at iron and that the spin of the M(S) = +/-2 doublet is quantized along x, where x is along the Fe-X vector and z is normal to the molecular plane. A quantitative analysis of g(eff) provides the magnitude of the crystal field splitting of the lowest two orbitals, /epsilon(yz) - epsilon(2)(z)/ = 452 (1.Cl) and 135 cm(-1) (1.CH(3)). A determination of the sign of the crystal field splitting was attempted by analyzing the electric field gradient (EFG) at the (57)Fe nuclei, taking into account explicitly the influence of spin-orbit coupling on the valence term and ligand contributions. This analysis, however, led to ambiguous results for the sign of epsilon(yz) - epsilon(2)(z). The ambiguity was resolved by analyzing the splitting Delta of the M(S) = +/-2 doublet; Delta = 0.3 cm(-1) for 1.Cl and Delta = 0.03 cm(-)(1) for 1.CH(3). This approach showed that z(2) is the ground state in both complexes and that epsilon(yz) - epsilon(2)(z) approximately 3500 cm(-1) for 1.Cl and 6000 cm(-1) for 1.CH(3). The crystal field states and energies were compared with the results obtained from time-dependent density functional theory (TD-DFT). The isomer shifts and electric field gradients in 1.X exhibit a remarkably strong dependence on ligand X. The ligand contributions to the EFG, denoted W, were expressed by assigning ligand-specific parameters: W(X) to ligands X and W(N) to the diketiminate nitrogens. The additivity and transferability hypotheses underlying this model were confirmed by DFT calculations. The analysis of the EFG data for 1.X yields the ordering W(N(diketiminate)) < W(Cl) < W(N'HR), W(CH(3)) and indicates that the diketiminate nitrogens perturb the iron wave function to a considerably lesser extent than the monodentate nitrogen donors do. Finally, our study of these synthetic model complexes suggests an explanation for the unusual values for the electric hyperfine parameters of the iron sites in the Fe-Mo cofactor of nitrogenase in the M(N) state.

Electron Spin Resonance Spectroscopy↗