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PubMed2006

Conformation effects on the electronic structures of beta-alanine.

Ten low-lying conformers of beta-alanine have been studied by the hybrid density functional B3LYP/aug-cc-pVDZ method. Energetic extrapolation calculations at the MP3 and MP4(SDQ) levels of theory and the theoretical photoelectron spectra simulated with the electron propagation theory demonstrate that there are at least three gauche conformers (G1, G2, and G3) in gas-phase experiments. The calculated ionization potentials are in good agreement with the experimental data available in the literature. Natural bond orbital and atoms-in-molecules analyses exhibit a remarkable influence on the molecular electronic structures by the strong intramolecular hydrogen bonding O-H...N in the neutral conformer G2. Remarkable internal rotations of the COOH group are found in the cationic G1+ and G3+ with respect to the neutral conformers. A distonic [NH3+-(CH2)2-COO*] radical can be formed through the spontaneous intramolecular proton transfer in G2+. A novel intramolecular hydrogen bonding, C-H...O, is found in the anti A1+ cation.

Computer Simulation↗
PubMed2002

Crystal and electronic structure of a new metallic modification of (ET)2[KHg(SCN)4].

A new room-temperature metallic modification of the well known radical cation salt (ET)(2)[KHg(SCN)(4)] has been prepared by electrochemical oxidation of ET. Its crystal and electronic structure have been examined at 110 K. The salt has a layered structure in which the conducting layers are characterized by the delta-type packing.

Journal Article↗
PubMed2005

Spectroscopy of non-heme iron thiolate complexes: insight into the electronic structure of the low-spin active site of nitrile hydratase.

Detailed spectroscopic and computational studies of the low-spin iron complexes [Fe(III)(S2(Me2)N3 (Pr,Pr))(N3)] (1) and [Fe(III)(S2(Me2)N3 (Pr,Pr))]1+ (2) were performed to investigate the unique electronic features of these species and their relation to the low-spin ferric active sites of nitrile hydratases. Low-temperature UV/vis/NIR and MCD spectra of 1 and 2 reflect electronic structures that are dominated by antibonding interactions of the Fe 3d manifold and the equatorial thiolate S 3p orbitals. The six-coordinate complex 1 exhibits a low-energy S(pi) --> Fe 3d(xy) (approximately 13,000 cm(-1)) charge-transfer transition that results predominantly from the low energy of the singly occupied Fe 3d(xy) orbital, due to pure pi interactions between this acceptor orbital and both thiolate donor ligands in the equatorial plane. The 3d(pi) --> 3d(sigma) ligand-field transitions in this species occur at higher energies (>15,000 cm(-1)), reflecting its near-octahedral symmetry. The Fe 3d(xz,yz) --> Fe 3d(xy) (d(pi) --> d(pi)) transition occurs in the near-IR and probes the Fe(III)-S pi-donor bond; this transition reveals vibronic structure that reflects the strength of this bond (nu(e) approximately 340 cm(-1)). In contrast, the ligand-field transitions of the five-coordinate complex 2 are generally at low energy, and the S(pi) --> Fe charge-transfer transitions occur at much higher energies relative to those in 1. This reflects changes in thiolate bonding in the equatorial plane involving the Fe 3d(xy) and Fe 3d(x2-y2) orbitals. The spectroscopic data lead to a simple bonding model that focuses on the sigma and pi interactions between the ferric ion and the equatorial thiolate ligands, which depend on the S-Fe-S bond angle in each of the complexes. These electronic descriptions provide insight into the unusual S = 1/2 ground spin state of these complexes: the orientation of the thiolate ligands in these complexes restricts their pi-donor interactions to the equatorial plane and enforces a low-spin state. These anisotropic orbital considerations provide some intriguing insights into the possible electronic interactions at the active site of nitrile hydratases and form the foundation for further studies into these low-spin ferric enzymes.

Binding Sites↗
PubMed1998

Influence of proximal side mutations on the molecular and electronic structure of cyanomet myoglobin: an 1H NMR study.

A series of proximal side mutants of sperm whale metmyoglobin (metMb) that involves residues which provide hydrogen bonds to the axial His and heme have been prepared, and the CO binding and solution molecular and electronic structure has been investigated by 1H NMR. These include Ser92(F7), whose O gamma serves as a hydrogen-bond acceptor to the axial His ring NdeltaH and whose O gamma H serves as hydrogen-bond donor to the 7-propionate carboxylate, and His97(FG3) whose ring provides the other hydrogen-bond donor to the 7-propionate carboxylate. 2D NMR data on the S92A-metMbCN, S92P-metMbCN and H97F-metMbCN show that the distal structure is completely conserved and that proximal side structural changes are highly localized. For the S92A-metMbCN, altered dipolar contacts to the F-helix backbone show that the axial His imidazole has rotated clockwise by approximately 10 degrees relative to a stationary heme, while in H97F-metMbCN, the altered heme-E helix backbone contacts reveal that the heme has rotated counterclockwise by approximately 3 degrees relative to a conserved axial His. The pattern of axial His rotation was qualitatively predicted by energy minimization calculations. The assignments and conserved structural elements allow the determination of a set of magnetic axes whose major magnetic axis is unchanged with respect to WT and confirms that local distal, and not proximal, interactions control the orientation of the major magnetic axis and, by inference, the degree and direction of tilt of the Fe-CN from the heme normal. The rhombic magnetic axes in S92A-metMbCN are rotated approximately 10 degrees in the opposite direction from the established approximately 10 degrees rotation for the axial His ring as expected. It is shown, moreover, that the pairwise alpha-, gamma-meso vs beta-, delta-meso-H hyperfine shift differences are well predicted by the change in the location of the rhombic magnetic axes. Carbon monoxide ligation rates experience minor but systematic perturbation for the S92A substitutions which confirms an influence (albeit very small) for axial His orientation on ligand affinity.

Animals↗
PubMed2005

Elucidation of the electronic structure of molecules with the help of NMR spin-spin coupling constants: the FH molecule.

It is demonstrated how the one-bond NMR spin-spin coupling constant (SSCC) (1)J(FH) can be used as a source of information on the electronic structure of the FH molecule. For this purpose, the best possible agreement between measured and calculated SSCC is achieved by large basis set coupled perturbed density functional theory calculations. Then, the calculated value is dissected into its four Ramsey terms: Fermi contact, the paramagnetic spin-orbit term, the diamagnetic spin-orbit term, and the spin dipole term, which in turn are decomposed into orbital contributions and then described by their spin densities and orbital current densities. In this way, the SSCC gives detailed information about the electronegativity of F, the bond polarity, the bond polarizability, the volume and the polarizability of sigma and pi lone pair orbitals, the s- or p-character of the bond orbital, the nature of the LUMO, and the density distribution around F.

Journal Article↗
PubMed2005

Electronic structure and intrinsic redox properties of [2Fe-2S]+ clusters with tri- and tetracoordinate iron sites.

Using potentially bidentate ligands (-SC2H4NH2), we produced [2Fe-2S]+ species of different coordination geometries by fission of [4Fe-4S]2+ complexes. Even though the ligands are monodentate in the cubane complexes, both mono- and bidentate complexes were observed in the [2Fe] fission products through self-assembly because of the high reactivity of the tricoordinate iron sites. The electronic structure of the [2Fe] species was probed using photoelectron spectroscopy and density functional calculations. It was found that tetracoordination significantly decreases the electron binding energies of the [2Fe] complexes, thus increasing the reducing capability of the [2Fe-2S]+ clusters.

Iron Compounds↗
PubMed2002

Electronic structure of the alpha and beta isomers of [Mo(8)O(26)](4-).

The structure and bonding in alpha and beta octamolybdate anions have been investigated using density functional methods. In general, good computational-experimental agreement for the geometrical parameters has been obtained. The electronic structure of the anions has been probed with molecular orbital and Mulliken-Mayer methods. All Mo-O interactions have been found to be predominantly d(Mo)-p(O) in character. Several multicentered molecular orbitals can be described as sigma or pi closed-loop structures, but the proposed connection with the stability of the polyanions is not completely supported by the calculations. Mayer indexes correspond to fractional multiple character for terminal bonds and approximately single or low-order character for bridging bonds, in accordance with structural and bond valence results. The valency analysis has yielded similar overall bonding capacity for the various oxygen atoms. A distribution of the negative charge over all types of oxygen sites and metal charges considerably smaller than the formal oxidation states have been obtained from the Mulliken analysis.

Journal Article↗
PubMed2001

Long-range magnetic order in Mn[N(CN)2]2(pyz) (pyz = pyrazine). Susceptibility, magnetization, specific heat, and neutron diffraction measurements and electronic structure calculations.

Using dc magnetization, ac susceptibility, specific heat, and neutron diffraction, we have studied the magnetic properties of Mn[N(CN)2]2(pyz) (pyz = pyrazine) in detail. The material crystallizes in the monoclinic space group P2(1)/n with a = 7.3248(2), b = 16.7369(4), and c = 8.7905 (2) A, beta = 89.596 (2) degrees, V = 1077.65(7) A(3), and Z = 4, as determined by Rietveld refinement of neutron powder diffraction data at 1.35 K. The 5 K neutron powder diffraction data reflect very little variation in the crystal structure. Interpenetrating ReO3-like networks are formed from axially elongated Mn(2+) octahedra and edges made up of mu-bonded [N(CN)2](-) anions and neutral pyz ligands. A three-dimensional antiferromagnetic ordering occurs below T(N) = 2.53(2) K. The magnetic unit cell is double the nuclear one along the a- and c-axes, giving the (1/2, 0, 1/2) superstructure. The crystallographic and antiferromagnetic structures are commensurate and consist of collinear Mn(2+) moments, each with a magnitude of 4.15(6) mu(B) aligned parallel to the a-direction (Mn-pyz-Mn chains). Electronic structure calculations indicate that the exchange interaction is much stronger along the Mn-pyz-Mn chain axis than along the Mn-NCNCN-Mn axes by a factor of approximately 40, giving rise to a predominantly one-dimensional magnetic system. Thus, the variable-temperature magnetic susceptibility data are well described by a Heisenberg antiferromagnetic chain model, giving g = 2.01(1) and J/k(B) = -0.27(1) K. Owing to single-ion anisotropy of the Mn(2+) ion, field-induced phenomena ascribed to spin-flop and paramagnetic transitions are observed at 0.43 and 2.83 T, respectively.

Journal Article↗
PubMed2000

Quantum mirages formed by coherent projection of electronic structure

Image projection relies on classical wave mechanics and the use of natural or engineered structures such as lenses or resonant cavities. Well-known examples include the bending of light to create mirages in the atmosphere, and the focusing of sound by whispering galleries. However, the observation of analogous phenomena in condensed matter systems is a more recent development, facilitated by advances in nanofabrication. Here we report the projection of the electronic structure surrounding a magnetic Co atom to a remote location on the surface of a Cu crystal; electron partial waves scattered from the real Co atom are coherently refocused to form a spectral image or 'quantum mirage'. The focusing device is an elliptical quantum corral, assembled on the Cu surface. The corral acts as a quantum mechanical resonator, while the two-dimensional Cu surface-state electrons form the projection medium. When placed on the surface, Co atoms display a distinctive spectroscopic signature, known as the many-particle Kondo resonance, which arises from their magnetic moment. By positioning a Co atom at one focus of the ellipse, we detect a strong Kondo signature not only at the atom, but also at the empty focus. This behaviour contrasts with the usual spatially-decreasing response of an electron gas to a localized perturbation.

Journal Article↗
PubMed1986

Nonequivalence in the electronic structure of the prosthetic groups between two alpha-subunits within deoxycobalthemoglobin as determined by single-crystal EPR spectroscopy.

An artificial hybrid hemoglobin, alpha(Co)2 beta(Fe)2, the alpha- and beta-subunits of which contain cobaltous and ferrous protoporphyrins IX, respectively, and its complementary hybrid, alpha(Fe)2 beta(Co)2, were prepared from human hemoglobin, crystallized in the deoxy state, and examined by electron paramagnetic resonance (EPR) spectroscopy. The orientations of the porphyrin normals in these deoxy Fe-Co hybrid hemoglobins in terms of the g parallel signals, were closely coincident with those of the heme normals of deoxyhemoglobin determined by x-ray crystallography. Two sets of axially symmetric EPR signals were found in the alpha(Co)-subunits, whereas only one set was observed in the beta(Co)-subunits. Nonequivalence in the electronic structures of the prosthetic groups between the two alpha(Co)-subunits, designated alpha I and alpha II, within deoxy-alpha(Co)2 beta(Fe)2 hybrid hemoglobin was correlated to these two distinct EPR signals. The interaction between the epsilon-nitrogen of the imidazole ring of the proximal histidine and the cobaltous ion in deoxy-alpha I(Co)-subunit is different from that in the deoxy-alpha II(Co)-subunit. The absence of a strict molecular dyad axis in the deoxy-alpha(Co)2 beta(Fe)2 hybrid hemoglobin suggests that the affinity state of the alpha(Co)-subunits may be partially switched to the R-state having a higher affinity for oxygen. Upon partial ligation of carbon monoxide to the beta(Fe)-subunits, the line width of the g parallel and perpendicular signals of the alpha II(Co)-subunit was found to become somewhat narrower without disruption of the crystal structure. This suggests that there may be very close contacts between the alpha- and beta-subunits of different hemoglobin molecules which appear to be responsible for stabilizing the deoxy crystal structure after partial ligation in the crystalline state.

Cobalt Radioisotopes↗
PubMed2006

Theoretical study of rhenium dinuclear complexes: Re-Re bonding nature and electronic structure.

Four dinuclear rhenium complexes, [Re2Cl8](2-) (1), [Re2(mu-Cl)3Cl6](2-) (2a), [Re2(mu-Cl)3Cl6](-) (2b), and [Re2(mu-Cl)2Cl8](2-) (3), were theoretically investigated by the CASSCF, MRMP2, SA-CASSCF, and MCQDPT methods. Interesting differences in electronic structure and Re-Re bonding nature among these complexes are clearly reported here, as follows: In 1, the ground state is the 1A1g state. The approximate stabilization energies by the sigma, pi, and delta bonding interactions are evaluated to be 4.36, 2.89, and 0.52 eV, respectively, by the MRMP2 method. In 2a, the ground state is the 2E" state. The approximate stabilization energy by two degenerate delta bonding interactions is estimated to be 0.36 eV by the MCQDPT method. One delta bonding interaction of 2a is much weaker than that of 1, which is discussed in terms of the Re-Re distance and the Re oxidation state. In 2b, the ground state is the 1A1' state, of which multiconfigurational nature is extremely large unlike that of the 2E" ground state of 2a despite similarities between 2a and 2b. In 3, the sigma, pi, and delta bonding interactions are not effectively formed between two Re centers. As a result, the 1Ag, 3B1u, 5Ag, and 7B1u states are in almost the same energy within 0.03 eV. This result is consistent with the paramagnetism of 3 experimentally reported.

Journal Article↗
PubMed2006

On the paucity of molecular actinide complexes with unsupported metal-metal bonds: a comparative investigation of the electronic structure and metal-metal bonding in U2X6 (X = Cl, F, OH, NH2, CH3) complexes and d-block analogues.

Density functional calculations have been performed on M2X6 complexes (where M = U, W, and Mo and X = Cl, F, OH, NH2, and CH3) to investigate general aspects of their electronic structures and explore the similarities and differences in metal-metal bonding between f-block and d-block elements. A detailed analysis of the metal-metal interactions has been conducted using molecular orbital theory and energy decomposition methods. Multiple (sigma and pi) bonding is predicted for all species investigated, with predominant f-f and d-d metal orbital character, respectively, for U and W or Mo complexes. The energy decomposition analysis involves contributions from orbital interactions (mixing of occupied and unoccupied orbitals), electrostatic effects (Coulombic attraction and repulsion), and Pauli repulsion (associated with four-electron two-orbital interactions). The general results suggest that the overall metal-metal interaction is stronger in the Mo and W species, relative to the U analogues, as a consequence of a significantly less destabilizing contribution from the combined Pauli and electrostatic ("pre-relaxation") effects. Although the orbital-mixing ("post-relaxation") contribution to the total bonding energy is predicted to have a larger magnitude in the U complexes, this is not sufficiently strong to compensate for the comparatively greater destabilization that originates from the Pauli-plus-electrostatic effects. Of the pre-relaxation terms, the Pauli repulsion is comparable in analogous U and d-block compounds, contrary to the electrostatic term, which is (much) less favorable in the U systems than in the W and Mo systems. This generally weak electrostatic stabilization accounts for the large pre-relaxation destabilization in the U complexes and, ultimately, for the relative weakness of the U-U bonds. The origin of the small electrostatic term in the U compounds is traced primarily to MX(3) fragment overlap effects.

Journal Article↗
PubMed2006

Ab initio investigations of the electric field dependence of the geometric and electronic structures of molecular wires.

Theoretical investigations on the typical molecular wire, polyacetylene, which bridges two chemically inert electrodes, have been carried out at the Hartree-Fock level by incorporating the external electric field into the calculations. The results demonstrate that both the geometric and the electronic structures of the conjugated molecular wires are sensitive to the electric field. When the electric field increases, the carbon-carbon single bonds become shorter and the double bonds become longer, leading to a higher conjugation. The electric field reduces the HOMO-LUMO gap and increases the dipole moment. The spatial distributions of the molecular orbitals are used to analyze the electrical properties of the molecular wire. All of these features are more pronounced with increasing conjugation chain length. Quantitative correlations between most of these features and the electric field have been discussed as well.

Journal Article↗
PubMed2006

Electronic structure, bonding, spectroscopy and energetics of Fe-dependent nitrile hydratase active-site models.

Fe-type nitrile hydratase (NHase) is a non-heme Fe(III)-dependent enzyme that catalyzes the hydration of nitriles to the corresponding amides. Despite experimental studies of the enzyme and model Fe(III)-containing complexes, many questions concerning the electronic structure and spectroscopic transitions of the metal center remain unanswered. In addition, the catalytic mechanism of nitrile hydration has not yet been determined. We now report density functional theory (B3LYP/6-31G) calculations on three models of the Fe(III) center in the active site of NHase corresponding to hypothetical intermediates in the enzyme-catalyzed hydration of acetonitrile. Together with natural bond orbital (NBO) analysis of the chemical bonding in these active-site models and INDO/S CIS calculations of their electronic spectra, this theoretical investigation gives new insight into the molecular origin of the unusual low-spin preference and spectroscopic properties of the Fe(III) center. In addition, the low-energy electronic transition observed for the active form of NHase is assigned to a dd transition that is coupled with charge-transfer transitions involving the metal and its sulfur ligands. Calculations of isodesmic ligand-exchange reaction energies provide support for coordination of the Fe(III) center in free NHase by a water molecule rather than a hydroxide ion and suggest that the activation of the nitrile substrate by binding to the metal in the sixth coordination site during catalytic turnover cannot yet be definitively ruled out.

Binding Sites↗
PubMed2006

Probing the electronic structure of platinum(II) chromophores: crystal structures, NMR structures, and photophysical properties of six new bis- and di- phenolate/thiolate Pt(II)diimine chromophores.

A general route for synthesis of six structurally similar Pt(II) diimine thiolate/phenolates chromophores possessing bulky phenolate or thiolate ligands is reported. The Pt chromophores were characterized using an array of techniques including 1H, 13C, and 195Pt NMR, absorption, emission, (spectro)electrochemistry, and EPR spectroscopy. Systematic variation of the electronic structure of the Pt(II) chromophores studied was achieved by (i) changing solvent polarity; (ii) substituting oxygen for sulfur in the donor ligand; (iii) alternating donor ligands from bis- to di-coordination; and (iv) changing the electron donating/withdrawing properties of the ligand(s). The lowest excited state in these new chromophores was assigned to a [charge-transfer-to-diimine] transition from the HOMO of mixed Pt/S (or Pt/O) character on the basis of absorption and emission spectroscopy, UV/vis (spectro)electrochemistry, and EPR spectroscopy. One of the chromophores, Pt(dpphen)(3,5-di-tert-butyl-catecholate) represents an example of a Pt(II) diimine phenolate chromophore that possesses a reversible oxidation centered predominantly on the donor ligand. Results from EPR spectroscopy indicate participation of the Pt(II) orbitals in the HOMO. There is a dramatic difference in the photophysical properties of carborane complexes compared to other mixed-ligand Pt(II) compounds, which includes room-temperature emission and photostability. The charge-transfer character of the lowest excited state in this series of chromophores is maintained throughout. Moreover, the absorption and emission energies and the redox properties of the excited state can be significantly tuned.

Crystallization↗
PubMed2005

Single crystal EPR study of electronic structure and exchange interactions for copper(II)(L-arginine)2(SO4).(H2O)6: a model system to study exchange interactions between unpaired spins in proteins.

We report EPR measurements at 9.77 and 34.1 GHz in powder and single crystal samples of the ternary copper amino acid complex Cu(L-arginine)(2)(SO(4)).(H(2)O)(6). The single crystal Electron Paramagnetic Resonance spectra display a single resonance for all magnetic field orientations in the ca and cb crystal planes. In the ab plane they display two resonances for most orientations of the magnetic field, and only one resonance for orientations close to the crystal axes. This behavior is a result of the selective collapse of the resonances corresponding to the four copper sites in the unit cell produced by the exchange interactions between copper ions. From the characteristics of the collapse and the angular dependences of the position and width of the resonances we evaluate the g-tensors of the copper molecules and estimate exchange interactions |J(1)/k(B)|=0.9 K and |J(2)/k(B)|=0.009 K between copper neighbors at 5.908 A and at 15.684 A, respectively. J(1) is assigned to a syn-anti equatorial-apical carboxylate bridge with a total bond length of 7.133 A. J(2) is assigned to a long bridge of 12 atoms with a total bond length of 19.789 A, that includes two hydrogen bonds. The results are discussed in terms of the crystal and electronic structure of Cu(L-arginine)(2)(SO(4)).(H(2)O)(6). We show that J(2) is in excellent agreement with the observed magnetic interaction between the reduced quinone acceptors in the photosynthetic reaction center protein of the bacterium Rb. sphaeroides, which is transmitted along a similar chemical path containing two hydrogen bonds. Our findings indicate that it is valid to estimate values for the exchange interactions between redox centers in proteins transmitted along long chemical paths containing sigma and H-bonds, from data obtained in model systems, and emphasize the importance of measuring exchange interactions in biologically relevant model systems.

Arginine↗
PubMed2006

Electronic structure and spectroscopic studies of D3d-C60Cl30, a chlorofullerene with a [18]trannulene ring, and its relation to other [18]trannulenes.

Detailed spectroscopic characterization of D3d-C60Cl30, including IR, Raman, UV-vis absorption, and fluorescence spectra, is presented for the first time. Assignment of the vibrational spectra is proposed on the basis of density functional theory computations. Electronic structure and excitations of C60Cl30 and other [18]trannulenes are studied theoretically with the use of time-dependent density functional theory and time-dependent Hartree-Fock approximation. Assignment of the low-energy part of electronic spectra of C60-based [18]trannulenes is given and importance of the interactions between trannulene moiety and remaining pi-subsystems in these molecules is established.

Journal Article↗
PubMed2001

Benzo[2,1-c:3,4-c']bis(1,2,3-thiaselenazole) (BSe) and its charge trasfer chemistry. Crystal and electronic structure of [BSe]3[ClO4]2.

The S-Se-N-based heterocycle benzo[2,1-c:3,4-c']bis(1,2,3-thiaselenazole) (BSe) can be prepared by the condensation of 1,4-diaminobenzene-2,3-dithiol with selenium tetrachloride. Crystals of this compound are not isomorphous with the related benzo[2,1-c:3,4-c']bis(1,2,3-dithiazole) (BT); a structure is adopted that allows for more extensive intermolecular Se- - -Se contacts. Electro-oxidation of BSe in the presence of [n-Bu4N][ClO4] affords metallic green needles of the charge transfer salt [BSe]3[ClO4]2, which exhibit a pressed pellet conductivity sigma(RT) = 10(-1) S cm(-1). The crystal structure of [BSe]3[ClO4]2 consists of slipped pi-stacks based on the triple-decker closed shell [BSe]3(2+) building block. The packing is analogous to that found for the charge transfer salt [BT]3[FSO3]2, for which sigma(RT) = 10(-2) S cm(-1). Extended Hückel band structure calculations on these two (sulfur- and selenium-based) 3:2 salts reveal more extensive intermolecular interactions in the selenium compound. As a result, the latter has a more two-dimensional electronic structure. Crystal data for Se2S2N2C6H2, a = 4.103(2) A, b = 12.159(2) A, c = 16.171(2) A, orthorhombic, Pbnm, Z = 4. Crystal data for Se6S6N6C18H6Cl2O4, a =17.00(1) A, b = 18.36(1) A, c = 10.679(4) A, 110.27(3), monoclinic, C2/c, Z = 4.

Journal Article↗