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PubMed2006

Density functional theory investigation of the geometric and electronic structures of [UO2(H2O)m(OH)n](2 - n) (n + m = 5).

Gradient corrected density functional theory has been used to calculate the geometric and electronic structures of the family of molecules [UO2(H2O)m(OH)n](2 - n) (n + m = 5). Comparisons are made with previous experimental and theoretical structural and spectroscopic data. r(U-O(yl)) is found to lengthen as water molecules are replaced by hydroxides in the equatorial plane, and the nu(sym) and nu(asym) uranyl vibrational wavenumbers decrease correspondingly. GGA functionals (BP86, PW91 and PBE) are generally found to perform better for the cationic complexes than for the anions. The inclusion of solvent effects using continuum models leads to spurious low frequency imaginary vibrational modes and overall poorer agreement with experimental data for nu(sym) and nu(asym). Analysis of the molecular orbital structure is performed in order to trace the origin of the lengthening and weakening of the U-O(yl) bond as waters are replaced by hydroxides. No evidence is found to support previous suggestions of a competition for U 6d atomic orbitals in U-O(yl) and U-O(hydroxide)pi bonding. Rather, the lengthening and weakening of U-O(yl) is attributed to reduced ionic bonding generated in part by the sigma-donating ability of the hydroxide ligands.

Journal Article↗
PubMed2006

The molecular, electronic structures and vibrational spectra of metal-free, N,N'-dideuterio and magnesium tetra-2,3-pyridino-porphyrazines: Density functional calculations.

A theoretical investigation of the fully optimized geometries and electronic structures of the metal-free (TPdPzH(2)), N,N'-dideuterio (TPdPzD(2)), and magnesium (TPdPzMg) tetra-2,3-pyridino-porphyrazine has been conducted based on density functional theory. The optimized geometries at density functional theory level for these compounds are reported here for the first time. A comparison between the different molecules for the geometry, molecular orbital, and atomic charge is made. The substituent effect of the N atoms on the molecular structures of these compounds is discussed. The IR and Raman spectra for these three compounds have also been calculated at density functional B3LYP level using the 6-31G(d) basis set. Detailed assignments of the NH, NM, and pyridine ring vibrational bands in the IR and Raman spectra have been made based on assistance of animated pictures. The simulated IR spectra of TPdPzH(2) are compared with the experimental absorption spectra, and very good consistency has been found. The isotope effect on the IR and Raman spectra is also discussed.

Chemical Phenomena↗
PubMed2000

Computational method for general multicenter electronic structure calculations.

Here a three-dimensional fully numerical (i.e., chemical basis-set free) method [P. F. Batcho, Phys. Rev. A 57, 6 (1998)], is formulated and applied to the calculation of the electronic structure of general multicenter Hamiltonian systems. The numerical method is presented and applied to the solution of Schrödinger-type operators, where a given number of nuclei point singularities is present in the potential field. The numerical method combines the rapid "exponential" convergence rates of modern spectral methods with the multiresolution flexibility of finite element methods, and can be viewed as an extension of the spectral element method. The approximation of cusps in the wave function and the formulation of multicenter nuclei singularities are efficiently dealt with by the combination of a coordinate transformation and a piecewise variational spectral approximation. The complete system can be efficiently inverted by established iterative methods for elliptical partial differential equations; an application of the method is presented for atomic, diatomic, and triatomic systems, and comparisons are made to the literature when possible. In particular, local density approximations are studied within the context of Kohn-Sham density functional theory, and are presented for selected subsets of atomic and diatomic molecules as well as the ozone molecule.

Computer Simulation↗
PubMed2003

Spectroscopic and electronic structure studies of the diamagnetic side-on CuII-superoxo complex Cu(O2)[HB(3-R-5-iPrpz)3]: antiferromagnetic coupling versus covalent delocalization.

Magnetic, vibrational, and optical techniques are combined with density functional calculations to elucidate the electronic structure of the diamagnetic mononuclear side-on CuII-superoxo complex. The electronic nature of its lowest singlet/triplet states and the ground-state diamagnetism are explored. The triplet state is found to involve the interaction between the Cu xy and the superoxide pi v * orbitals, which are orthogonal to each other. The singlet ground state involves the interaction between the Cu xy and the in-plane superoxide pi v * orbitals, which have a large overlap and thus strong bonding. The ground-state singlet/triplet states are therefore fundamentally different in orbital origin and not appropriately described by an exchange model. The ground-state singlet is highly delocalized with no spin polarization.

Copper↗
PubMed2005

Electronic structure and properties of isoreticular metal-organic frameworks: the case of M-IRMOF1 (M = Zn, Cd, Be, Mg, and Ca).

We investigate the possibility of tailoring the electronic properties of isoreticular metal-organic materials by replacing the metal atom in the metal-organic cluster and by doping. The electronic structure of M-IRMOF1, where IRMOF1 stands for isoreticular metal-organic framework 1 and M = Be, Mg, Ca, Zn, and Cd, was examined using density-functional theory. The results show that these materials have similar band gaps (ca. 3.5 eV) and a conduction band that is split into two bands, the lower of which has a width that varies with metal substitution. This variation prompted us to investigate whether doping with Al or Li could be used to tailor the electronic properties of the Zn-IRMOF1 and Be-IRMOF1 materials. It is shown that replacing one metal atom with Al can effectively be used to create IRMOFs with different metallic properties. On the other hand, adding Li produces structural changes that render this approach less suitable.

Journal Article↗
PubMed2004

The electronic structure of nitrilimines revisited.

A combination of density-functional theory and natural resonance theory has been used to show that a complete description of the electronic structure of nitrilimines, R(1)CNNR(2), requires four resonance structures (propargylic, allenic, 1,3-dipolar and carbenic); appropriate substituents were shown to enhance the carbene character of nitrilimines to the point where they may be considered stable carbenes.

Journal Article↗
PubMed2005

Spin-unrestricted linear-scaling electronic structure theory and its application to magnetic carbon-doped boron nitride nanotubes.

We present an extension of the density-matrix-based linear-scaling electronic structure theory to incorporate spin degrees of freedom. When the spin multiplicity of the system can be predetermined, the generalization of the existing linear-scaling methods to spin-unrestricted cases is straightforward. However, without calculations it is hard to determine the spin multiplicity of some complex systems, such as many magnetic nanostuctures and some inorganic or bioinorganic molecules. Here we give a general prescription to obtain the spin-unrestricted ground state of open-shell systems. Our methods are implemented into the linear-scaling trace-correcting density-matrix purification algorithm. The numerical atomic-orbital basis, rather than the commonly adopted Gaussian basis functions, is used. The test systems include O2 molecule and magnetic carbon-doped boron nitride (BN)(5,5) and BN(7,6) nanotubes. Using the newly developed method, we find that the magnetic moments in carbon-doped BN nanotubes couple antiferromagnetically with each other. Our results suggest that the linear-scaling spin-unrestricted trace-correcting purification method is very powerful to treat large magnetic systems.

Journal Article↗
PubMed2006

Structural, electronic, and magnetic properties of manganese-doped Zn12O12 clusters: a first-principles study.

A first-principles study has been performed to evaluate the structural, electronic, and magnetic properties of Zn(12)O(12) clusters doped with one or two Mn atoms. The substitutional, exohedral, and endohedral dopings are taken into account. For the monodoped clusters, the substitutional isomer is most energetically favorable, and an exohedral isomer may appear as a low-lying metastable state. All isomers present 5 mu(B) magnetic moment that is mainly contributed by the Mn-3d component. For the bidoped clusters, the antiferromagnetic state is degenerate with the ferromagnetic state at larger Mn-Mn distance (>5 A), while it is more energetically favorable at smaller Mn-Mn distance. Thus, the cohesion of bidoped isomer is sensitive to the magnetic coupling or chemical bonding. The endohedral bidoped isomer is found to be a stable local minimum, and the direct Mn-Mn interaction causes the reduction of local magnetic moment of Mn to about 4 mu(B).

Journal Article↗
PubMed2000

STM studies of the electronic structure of vortex cores in Bi(2)Sr(2)CaCu(2)O(8+delta)

We report on low temperature scanning tunneling microscopy (STM) studies of the electronic structure of vortex cores in Bi 2Sr 2CaCu 2O (8+delta). At the vortex core center, an enhanced density of states is observed at energies near Omega = +/-7 meV. Spectroscopic imaging at these energies reveals an exponential decay of these "core states" with a decay length of 22+/-3 A. The fourfold symmetry sometimes predicted for d-wave vortices is not seen in spectroscopic vortex images. A locally nodeless order parameter induced by the magnetic field may be consistent with these measurements.

Journal Article↗
PubMed2006

Electronic structure of metal/molecule//metal junctions: a density functional theory study of the influence of the molecular terminal group.

We report on density functional theory calculations of the electronic structure of Au(111)/molecule//Au(111) junctions in which thiol molecules are chemically bound at one end to a gold electrode (the "substrate"), while the other end has a separation of a few to several angstroms from a second gold electrode (the "tip"). Our goal is to investigate the role of different molecular terminal groups and of the tip-molecule distance either on the spatial dependence of the local density of states (LDOS) at the Fermi energy E(f) or on the energy dependence of the projected density of states onto different molecular subunits. We consider conjugated diphenylthiol (SPh2R) molecules with terminal groups R = H, SH, CH3, or CF3 as well as "mixed" conjugated-saturated phenylthiol-pentane (SPhC4CH3) and butanethiol-toluene (SC4PhCH3) molecules. For SPh2R molecules, the LDOS at E(f) exhibits an oscillatory exponential decay along the molecule, with an average decay constant that depends weakly on the R terminal group. For the mixed aromatic-aliphatic molecules instead, there are large differences in the LDOS at E(f), with SC4PhCH3 showing a much larger LDOS in the proximity of the terminal CH3 group than SPhC4CH3.

Journal Article↗
PubMedDate not supplied

[Relationship between the electron structure of phosphates and the problem of ATP synthesis and utilization].

The nature of macroergic bonds and some problems of ATP formation and utilization are considered in terms of electron structure of phosphates. The main acting compound in the ATP synthesis and in the reactions of transfer and utilization of the energy of macroergic bonds as well, is ATP terminal phosphate or phosphoryl group which in the free state is a monomeric methaphosphate-ion. High reactive ability of monomeric methaphosphate-ion, its affinity of lown electrom pairs is conditioned by the presence of a vacant sp3-orbitals in phosphor atom of methaphosphate-ion. Therefore in the reactions with ATP participation the phosphoryl group plays the role of electrophilic agent. Formation of intermediate methaphosphate-ion preceding the synthesis of ATP from ADP during substrate phosphorylation results from the breakage of O--P bond, during which both electrons which form the bond stay in the oxygen atom. Another possible pathway of methaphosphate-ion formation is the ejaction of the electron from ortophosphate dianion with the help of suitable acceptor of the electrons, by light-stimulated pigment system of chloroplasts or chromatophores or singlet oxygen liberated during the decomposition of hydrogen peroxide with catalase. Due to the redistribution of electron density in the phosphate radical the latter turns into the monomeric methaphosphate-ion bound to ADP with the formation of ATP.

Adenosine Triphosphate↗
PubMed1999

Experimental and Theoretical Investigation of the Molecular and Electronic Structure of [Zn(4)(&mgr;(4)-S){&mgr;-S(2)As(CH(3))(2)}(6)] and [Cd(4)(&mgr;(4)-S){&mgr;-S(2)As(CH(3))(2)}(6)]: Two Possible Molecular Models of Extended Metal Chalcogenide Semiconductors.

The molecular and electronic structure of hexakis[&mgr;-(dimethylarsinodithioate-S:S')]-&mgr;(4)-thioxotetrazinc has been investigated by combining X-ray diffraction measurements, electrospray mass spectrometry (ESI), UV absorption spectroscopy, and density functional calculations. The polynuclear zinc complex consists of discrete "tetrazinc sulfide" moieties held together by van der Waals interactions. The unit cell contains four independent molecules and four solvent molecules. Each independent unit is characterized by a central &mgr;(4)-S coordinated to four Zn ions, each of them at the center of an irregular tetrahedron of S atoms. ESI measurements point out that the synthesis of the analogous Cd derivative was successful. Crystal data are as follows: chemical formula, C(12)H(36)As(6)Cl(1.5)S(13)Zn(4); monoclinic space group P2(1)/n (no. 14); a = 30.4228(7) Å, b = 18.3720(5) Å, c = 32.3758(8) Å, beta = 95.857(1) degrees; Z = 16. Theoretical calculations indicate that, despite their structural arrangement, neither the Zn nor the Cd complex can be considered molecular models of the extended ZnS and CdS. Nevertheless, the electronic transitions localized in the Zn(4)(&mgr;(4)-S) and Cd(4)(&mgr;(4)-S) inner cores of the title compounds have the same nature as those giving rise to the maxima in the excitation spectra of the extended Zn(4)S(BO(2))(6) and Cd(4)S(AlO(2))(6) [Blasse, G.; Dirksen, G. J.; Brenchley, M. E.; Weller, M. T. Chem. Phys. Lett. 1995, 234, 177].

Journal Article↗
PubMedDate not supplied

Electronic structure calculations as a tool for investigating acyl migrations in ester saponins.

The possibility of acyl migrations in ester saponins from Maesa lanceolata was investigated by molecular mechanics and electronic structure calculations carried out on the major constituent maesasaponin IV3 (3beta-O-[[alpha-L-rhamnopyranosyl-(1-->2)-[beta-D-galactopyranosyl-(1-->3)]-[beta-D-galactopyranosyl-(1-->2)]-beta-D-gluco-pyranuronyl]-21beta-angeloyloxy-22alpha-propanoyloxy-13beta,28-oxido-olean-16alpha, 28alpha-diol). It was confirmed that acyl migrations could occur in rings D and E of maesasaponins.

Esters↗
PubMed2003

Solution NMR characterization of the electronic structure and magnetic properties of high-spin ferrous heme in deoxy myoglobin from Aplysia limacina.

Solution (1)H NMR has been used to elucidate the magnetic properties and electronic structure of the prosthetic group in high-spin, ferrous deoxy myoglobin from the sea hare Aplysia limacina. A sufficient number of dipolar shifted residue signals were assigned to allow the robust determination of the orientation and anisotropy of the paramagnetic susceptibility tensor, chi. The resulting quantitative description of dipolar shifts allows a determination of the contact shifts for the heme. Chi was found to be axial, with Deltachi(ax) = -2.07 x 10(-8) m(3)/mol, with the major axis tilted (approximately 76 degrees) almost into the heme plane and in the general direction of the orientation of the axial HisF8 imidazole plane which coincides approximately with the beta-,delta-meso axis. The factored contact shifts for the heme are shown to be consistent with the transfer of positive pi spin density into one of the two components of the highest filled pi molecular orbital, 3e(pi), and the transfer of negative pi-spin density, via spin-spin correlation, into the orthogonal excited-state component of the 3e(pi) molecular orbital. The thermal population of the excited state leads to strong deviation from the Curie law for the heme substituents experiencing primarily the negative pi-spin density. The much larger transfer of negative spin density via the spin-paired dpi orbital into the excited state 3e(pi) in high-spin iron(II) than in low-spin iron(III) hemoproteins is attributed to the much stronger correlation exerted by the four unpaired spin on the iron in the former, as compared to the single unpaired spins on iron in the latter.

Animals↗
PubMed2005

Electronic structure, reactivity, and spectroscopy of dihydrides of group-IB metals.

Atomic pseudopotentials and highly correlated wave functions, including spin-orbit interactions, have been used to evaluate the electronic structure, stability, and spectroscopy of triatomic molecule MH(2), with a metal M belonging to group IB (Cu, Ag, and Au). CuH(2) and AuH(2) have been recently observed by IR spectroscopy in solid hydrogen and bending anharmonic wave numbers have been assigned to these two systems. The AgH(2) molecule has not been detected nor experimentally characterized, despite several theoretical works arguing on its stability. Our results confirm that the MH(2) radicals have a metastable bent ground state separated from the dissociation into [M+H(2)] ground state by barriers which have been evaluated to 1.43, 0.78, and 0.80 eV, for Cu, Ag, and Au compounds, respectively. These barriers are calculated smaller than in previous determinations but still large enough to stabilize the MH(2) systems. Spectroscopic data are calculated for these radicals.

Journal Article↗
PubMed2006

Electronic structures and spectroscopic properties of nitrido-osmium(VI) complexes with acetylide ligands [OsN(C[Triple Bond]CR)4]- R=H, CH3, and Ph by density functional theory calculation.

Electronic structures and spectroscopic properties of a series of nitrido-osmium (VI) complex ions with acetylide ligands, [OsN(C[Triple Bond]CR)(4)](-) (R[Double Bond]H, (1), CH(3) (2), and Ph (3)) were investigated theoretically. The structures of the complexes were fully optimized at the B3LYP and CIS level for the ground states and excited states, respectively. The calculated bond lengths of Os[Triple Bond]N (1.639 A in 1, 1.642 A in 2, and 1.643 A in 3) and Os-C (2.040 A in 1, 2.043 A in 2, and 2.042 A in 3) in ground state agree well with the experimental results. The bond length of Os[Triple Bond]N bond is lengthened by ca. 0.13 A in the A (3)B(2) excited state compared to the (1)A(1) ground state, which is consistent with the lower vibration frequency of nu(Os-N) ( approximately 780 cm(-1)) in the excited state than that ( approximately 1175 cm(-1)) in the ground state. Among the calculated dipole-allowed absorptions at lambda>250 nm, the intense absorption at 261 nm for 1, 266 nm for 2, and 300 nm for 3 were attributed to the (1)[pi(C[Triple Bond]C)]-->(1)[pi(*)(N[Triple Bond]Os)+pi(*)(C[Triple Bond]C)], (1)[pi(C[Triple Bond]C)]-->(1)[pi(*)(N[Triple Bond]Os)+pi(*)(C[Triple Bond]C)], and (1)[pi(C[Triple Bond]CPh)]-->(1)[pi(*)(N[Triple Bond]Os)+pi(*)(C[Triple Bond]CPh)], respectively. The lowest energy absorption at lambda(max)=393 nm for 1, 400 nm for 2, and 400 nm for 3 were assigned as (1)[d(xy)(Os)+pi(C[Triple Bond]C)]-->(1)[pi(*)(N[Triple Bond]Os)+pi(*)(C[Triple Bond]C)], (1)[d(xy)(Os)+pi(C[Triple Bond]C)]-->(1)[pi(*)(N[Triple Bond]Os)+pi(*)(C[Triple Bond]C)], and (1)[d(xy)(Os)+pi(C[Triple Bond]CPh)]-->(1)[pi(*)(N[Triple Bond]Os)+pi(*)(C[Triple Bond]CPh)], respectively. The calculated phosphorescence emission at lambda(max)=581 nm for 1, 588 nm for 2, and 609 nm for 3 were originated from (3)[(pi(*)(N[Triple Bond]Os)+pi(*)(C[Triple Bond]C))(1)(d(xy)(Os)+pi(C[Triple Bond]C))(1)], (3)[(pi(*)(N[Triple Bond]Os)+pi(*)(C[Triple Bond]C))(1)(d(xy)(Os)+pi(C[Triple Bond]C))(1)], and (3)[(pi(*)(N[Triple Bond]Os)+pi(*)(C[Triple Bond]CPh))(1)(d(xy)(Os)+pi(C[Triple Bond]CPh))(1)] excited state, respectively.

Journal Article↗
PubMed2005

Photoelectron spectroscopy and electronic structures of fullerene oxides: C60Ox- (x = 1-3).

We report a photoelectron spectroscopy (PES) study on a series of fullerene oxides, C60Ox- (x = 1-3). The PES spectra reveal one isomer for C60O-, two isomers for C60O2, and multiple isomers for C60O3-. Compared to C60, the electronic structures of C60Ox are only slightly perturbed, resulting in similar anion photoelectron spectra. The electron affinity of C60Ox was observed to increase only marginally with the number of oxygen atoms, x, from 2.683 eV for C60, to 2.745 eV for C60O, and 2.785 eV/2.820 eV for C60O2 (two isomers). We also carried out theoretical calculations, which confirmed the observed isomers and showed that all the fullerene oxides are in the form of epoxide. The PES and theoretical calculations, as well as molecular orbital analysis, indicate that addition of oxygen atoms to the C60 cage only modifies the local carbon network and leave the rest of the fullerene cage largely intact geometrically and electronically.

Journal Article↗
PubMed2002

Electronic structure, electrical and magnetic properties of RMo(8)O(14) compounds (R = La, Ce, Pr, Nd, Sm) containing bicapped Mo(8) clusters.

Magnetic and electrical resistivity properties of RMo(8)O(14) (R = La, Ce, Pr, Nd, Sm) compounds containing different bicapped-octahedral Mo(8) clusters are discussed. Extended Hückel (EH) molecular calculations were carried out in order to study the influence of the position of metal capping atoms on the electronic structure of different Mo(8) isomers. Different optimal metal electron counts are possible for these clusters. Periodic density functional calculations confirm the molecular character of these compounds and allow the understanding of their semiconducting and magnetic properties.

Journal Article↗