Low-Bias Conductance Mechanism of Diarylethene Isomers:a First-Principle Study

The structure-property relationship of diarylethene (DAE)-derivative molecular isomers, which involve ring-closed and ring-open forms, is investigated by employing the non-equilibrium Green's function formalism combined with density functional theory. Molecular junctions are formed by the isomers connecting to Au(111) electrodes through flanked pyridine groups. The difference in electronic structures caused by different geometry structures for the two isomers, particularly the interatomic alternative single bond and double bond of the ring-closed molecule, contributes to the vastly different low-bias conductance values. The lowest unoccupied molecular orbital (LUMO) of the isomers is the main channel for electron transport. In addition, more electrons transferred to the ring-closed molecular junction in the equilibrium condition, thereby decreasing the LUMO energy to near the Fermi energy, which may contribute to a larger conductance value at the Fermi level. Our findings are helpful for understanding the mechanism of low-bias conductance and are conducive to the design of high-performance molecular switching based on diarylethene or diarylethene-derivative molecules.     

Bond characterization on a Cr-Cr quintuple bond: a combined experimental and theoretical study

A combined experimental and theoretical charge density study on a quintuply bonded dichromium complex, Cr(2)(dipp)(2) (dipp = (Ar)NC(H)N(Ar) and Ar = 2,6-i-Pr(2)-C(6)H(3)), is performed. Two dipp ligands are bridged between two Cr ions; each Cr atom is coordinated to two N atoms of the ligands in a linear fashion. The Cr atom is in a low oxidation state, Cr(I), and in low coordination number condition, which stabilizes a metal-metal multiple bond, in this case, a quintuple bond. Indeed, it gives an ultrashort Cr-Cr bond distance of 1.7492(1) ? in the complex. The bond characterization of such a quintuple bond is undertaken both experimentally by high-resolution single-crystal X-ray diffraction and theoretically by density functional calculation (DFT). Electron densities are depicted via deformation density and Laplacian distributions. Bond characterizations of the complex are presented in terms of topological properties, Fermi hole function, source function (SF), and natural bonding orbital (NBO) analysis. The electron density at the Cr-Cr bond critical point (BCP) is 1.70 e/?(3), quite a high value for metal-metal bonding and mainly contributed from the metal ion itself. The quintuple bond is confirmed with one σ, two π, and two δ interactions by NBO analysis and Fermi hole function. The molecular orbitals (MOs) illustrate that five bonding orbitals are predominantly contributed from the 3d orbitals of the Cr(I) ion. The effective bond order from NBO analysis is 4.60. The detail comparison between experiment and theory will be given. Additionally, three closely related complexes are calculated for systematic comparison.     

Heterobismetal complexes of [26]hexaphyrin(1.1.1.1.1.1)

Au(III)Cu(III) and Au(III)Rh(I) heterobismetal complexes of meso-aryl-substituted [26]hexaphyrin were rationally prepared from a monometal Au(III) complex. The Au(III)Cu(III) complex is an aromatic molecule with a rectangular shape, while Au(III)Rh(I) complexes are out-of-plane macrocycles, being either aromatic or antiaromatic depending upon the number of conjugated pi electrons. The 26pi Au(III)Rh(I) complex was converted into an aromatic and planar 26pi Au(III)Rh(III) complex via double C-H bond activation upon refluxing in pyridine.     

Electron spin resonance studies of the anaerobic and aerobic photolysis of alkylcobaloximes

Aerobic and anaerobic photolysis of methyl(pyridine)cobaloxime, benzyl(pyridine)cobaloxime and analogous compounds in CHCl₃ results only in an electron transfer reaction from an equatorial ligand producing photo-reduction of Co^III to Co^II, the complex retaining its axial ligands.If after the anaerobic photolysis of benzyl(pyridine)cobaloxime the oxygen is introduced without any further photolysis we obtain an ESR spectrum of nitroxide, arising from the attack of a benzyl radical on the dimethylglyoxime equatorial ligand.For the other complexes, homolytic cleavage of the CoC bond occurs and in the presence of oxygen gives rise to the superoxide cobalt complex adduct Py(Co^IIIO₂^?.During photolysis of methyl(pyridine)cobaloxime in isopropanol homolytic cleavage of the CoC bond occurs in preference to electron transfer reaction from the equatorial ligands.The anaerobic photolysis of benzyl(pyridine)cobaloxime in isopropanol or in water at 113–133 K results in an electron transfer reaction. However, at 170 K we observe the formation of the Co^II complex arising from CoC bond cleavage.A mechanism for photo-induced insertion of oxygen in the CoC bond is proposed.     

Electron-transfer oxidation of coenzyme B12 model compounds and facile cleavage of the cobalt(IV)-carbon bond via charge-transfer complexes with bases. A negative temperature dependence of the rates

The electron-transfer oxidation and subsequent cobalt-carbon bond cleavage of vitamin B12 model complexes were investigated using cobaloximes, (DH)2Co(III)(R)(L), where DH- = the anion of dimethylglyoxime, R = Me, Et, Ph, PhCH2, and PhCH(CH3), and L = a substituted pyridine, as coenzyme B12 model complexes and [Fe(bpy)3](PF6)3 or [Ru(bpy)3](PF6)3 (bpy = 2,2'-bipyridine) as a one-electron oxidant. The rapid one-electron oxidation of (DH)2Co(III)(Me)(py) (py = pyridine) with the oxidant gives the corresponding Co(IV) complexes, [(DH)2Co(IV)(Me)(py)]+, which were well identified by the ESR spectra. The reorganization energy (lambda) for the electron-transfer oxidation of (DH)2Co(Me)(py) was determined from the ESR line broadening of [(DH)2Co(Me)(py)]+ caused by the electron exchange with (DH)2Co(Me)(py). The lambda value is applied to evaluate the rate constants of photoinduced electron transfer from (DH)2Co(Me)(py) to photosensitizers in light of the Marcus theory of electron transfer. The Co(IV)-C bond cleavage of [(DH)2Co(Me)(py)]+ is accelerated significantly by the reaction with a base. The overall activation energy for the second-order rate constants of Co(IV)-C bond cleavage of [(DH)2Co(IV)(Me)(py)]+ in the presence of a base is decreased by charge-transfer complex formation with a base, which leads to a negative activation energy for the Co(IV)-C cleavage when either 2-methoxypyridine or 2,6-dimethoxypyridine is used as the base.     

Binding characteristics of pyridine on Ag(110)

A combination of low-temperature scanning tunneling microscopy and density functional theory calculations was used to determine the binding characteristics of single pyridine molecules at a low coverage on a silver surface. The results indicated that pyridine binds to silver through the nitrogen atom in either a perpendicular or a parallel configuration with the latter structure being more prevalent. Both configurations are produced predominantly through electrostatic interaction between nitrogen and silver atoms. This is induced by charge redistribution in the pyridine molecule and nearby silver atoms upon pyridine adsorption.     

Dual fluorescence of ellipticine: excited state proton transfer from solvent versus solvent mediated intramolecular proton transfer

Photophysical properties of a natural plant alkaloid, ellipticine (5,11-dimethyl-6H-pyrido[4,3-b]carbazole), which comprises both proton donating and accepting sites, have been studied in different solvents using steady state and time-resolved fluorescence techniques primarily to understand the origin of dual fluorescence that this molecule exhibits in some specific alcoholic solvents. Ground and excited state calculations based on density functional theory have also been carried out to help interpretation of the experimental data. It is shown that the long-wavelength emission of the molecule is dependent on the hydrogen bond donating ability of the solvent, and in methanol, this emission band arises solely from an excited state reaction. However, in ethylene glycol, both ground and excited state reactions contribute to the long wavelength emission. The time-resolved fluorescence data of the system in methanol and ethylene glycol indicates the presence of two different hydrogen bonded species of ellipticine of which only one participates in the excited state reaction. The rate constant of the excited state reaction in these solvents is estimated to be around 4.2-8.0 × 10(8) s(-1). It appears that the present results are better understood in terms of solvent-mediated excited state intramolecular proton transfer reaction from the pyrrole nitrogen to the pyridine nitrogen leading to the formation of the tautomeric form of the molecule rather than excited state proton transfer from the solvents leading to the formation of the protonated form of ellipticine.     

Single molecule electron transport junctions: charging and geometric effects on conductance

A p-benzenedithiolate (BDT) molecule covalently bonded between two gold electrodes has become one of the model systems utilized for investigating molecular transport junctions. The plethora of papers published on the BDT system has led to varying conclusions with respect to both the mechanism and the magnitude of transport. Conductance variations have been attributed to difficulty in calculating charge transfer to the molecule, inability to locate the Fermi energy accurately, geometric dispersion, and stochastic switching. Here we compare results obtained using two transport codes, TRANSIESTA-C and HUCKEL-IV, to show that upon Au-S bond lengthening, the calculated low bias conductance initially increases by up to a factor of 30. This increase in highest occupied molecular orbital (HOMO) mediated conductance is attributed to charging of the terminal sulfur atom and a corresponding decrease in the energy gap between the Fermi level and the HOMO. Addition of a single Au atom to each terminal of the extended BDT molecule is shown to add four molecular states near the Fermi energy, which may explain the varying results reported in the literature.     

Stabilization of a subvalent oxidation state of bismuth in N,N-dimethylthioformamide solution: an EXAFS, UV-Vis, IR, and cyclic voltammetry study

At the dissolution of anhydrous bismuth(III) trifluoromethanesulfonate in N,N-dimethylthioformamide (DMTF) a deep red-orange complex, lambda(max) = 457 nm, is formed. Bismuth(III) is reduced by the solvent to a low-valent oxidation state stabilized by the sulfur-coordinating solvent DMTF. The obtained complex is weakly solvated seen by a low EXAFS amplitude and a slightly higher absorption energy of the L(III) edge than of the DMTF-solvated bismuth(III) ion. The EXAFS data reveal a dimeric bismuth complex solvated by a single DMTF molecule, which sulfur atom bridges the bismuth atoms. The Bi-S bond distance is 2.543(2) A, and the Bi...Bi distance is 3.929(7) A giving a Bi-S-Bi angle of 101.2(4) degrees. The very low number of coordinated solvent molecule shows that the lone electron pairs of the reduced bismuth ions are stereochemically active. Cyclic voltammetry investigations provide evidence that at least one bismuth atom in the dimer exists in an oxidation state lower than +III, seen by two peaks at approximately -0.36 and -0.57 V in the reduction half-cycle. The absence of EPR signals excludes the presence of bismuth(II) radicals.     

Continuous-wave and pulse EPR study of the copper(II) complex of N-confused tetraphenylporphyrin: direct observation of a sigma metal-carbon bond

N-confused or inverted porphyrins, a family of porphyrin isomers that contain a confused pyrrole ring connected through its alpha and beta' positions in the macrocycle, exhibit unique physical and chemical properties, like, for instance, the ability to stabilize unusual oxidation states of metals due to the reactivity of the inverted pyrrole. In this Article, a combined multifrequency continuous-wave and pulse electron paramagnetic resonance (EPR) study of the copper(II) complex of N-confused tetraphenylporphyrin (TPP) is presented. By use of pulse EPR methods like ENDOR and HYSCORE, the magnetic interactions between the unpaired electron of the compound and the surrounding nitrogen nuclei were revealed. Through 13C labeling of the macrocycle, a detailed study of the carbon hyperfine interaction became possible and provided further insight into the character of the metal-carbon bond. The observed hyperfine couplings of the ligand atoms in the first coordination sphere showed the presence of a remarkably strong sigma Cu-C bond and allowed for a detailed analysis of the spin delocalization over the porphyrin macrocycle. Interestingly, it was found that the observed delocalization is approximately 11% larger than the corresponding one for CuTPP.     

Controlling Metalation Reaction of Phthalocyanine with Cobalt at Single-Molecule Level on Au(111) Surface

Metalation reaction of metal-free phthalocyanine molecule with Co atom adsorbed on Au(111) surface has been studied in situ at single atom/molecule scale by low-temperature scanning tunneling microscopy (STM) experiment combined with simulations based on density function theory calculations. Through manipulations using STM tip, we showed a controlled manner to have a single metal-free phthalocyanine molecule react with a Co atom to form Co phthalocyanine molecule. In this reaction process, an intermediate state originating from $\pi$-d interaction between the metal-free phthalocyanine molecule and Co atom has been identified. Moreover, we also revealed that the redox reaction represented as bond breaking and bond forming relative to the Co and pyrrolic N atoms, not pyrrolic H atoms, is a key process for dehydrogenation and metalation reaction. Our DFT calculations provided theoretical supporting for the above conclusions, and further understanding of the related mechanisms.     

Topological analysis and charge density studies of an alpha-diimine macrocyclic complex of cobalt(II)--a combined experimental and theoretical study

A combined experimental and theoretical study of the paramagnetic [Co(II)(C12H20N8)(H2O)2] x 2 ClO4 complex was made on the basis of the electron density distribution and topological analysis. Accurate single-crystal diffraction data were measured on a suitable crystal with Mo(K alpha) radiation at 125 K. The CoII ion is coordinated in a square bipyramidal fashion with four imino nitrogen atoms at the equatorial plane and two water molecules at the axial positions. The hydrogen-bonding interaction at 125 K between the coordinated water molecule and the ClO(4)(-) ion makes the space group different from that at 298 K. Parallel MO calculations were made at UHF and DFT/UB3LYP. The agreement between experiment and theory is reasonably good. The chemical bonding characterization is presented in terms of the topological properties associated with bond critical points and the natural bond orbital (NBO) analysis as well. The Co-N(imino) and Co-O(water) bonds are dative bonds, where the lone-pair electrons of N or O serve as a -donor; however, a certain covalent character is identified in the Co-N(imino) bond. A delocalized C-N, N-N pi-bond model is proposed. The d-orbital energies of Co in this complex are such that E(d(xz)) is approximately equal to E(d(yz)) is approximately equal to E(dx(2-y2)) < E(d(z2)) < E(d(xy)); notice that d(xy) and d(z2) are d(sigma) orbitals in this case. The Co(II) ion is in a low-spin d7 state with the singly occupied d(z2) orbital. The asphericity in electron density at Co and Cl nuclei is nicely demonstrated by the Laplacian of electron density. The envelope plot of the isovalue Laplacian surface around the nucleus gives the exact shape of such asphericity. The isovalue Laplacian surfaces of these two nuclei show significantly different VSCC character in both experimental and theoretical results.     

Structure and stability of Co(n)(pyridine)(m)- clusters: absence of metal inserted structures

A synergistic approach combining the experimental photoelectron spectroscopy and theoretical electronic structure studies is used to probe the geometrical structure and the spin magnetic moment of Co(n)(pyridine)(m) (-) clusters. It is predicted that the ground state of Co(pyridine)(-) is a structure where the Co atom is inserted in a CH bond. However, the insertion is marked by a barrier of 0.33 eV that is not overcome under the existing experimental conditions resulting in the formation of a structure where Co occupies a site above the pyridine plane. For Co(2)(pyridine)(-), a ground-state structure is predicted in which the Co(2) diametric moiety is inserted in one of the CH bonds, but again because of a barrier, the structure which matches the photoelectron spectrum is a higher-energy isomer in which the Co(2) moiety is bonded directly to nitrogen on the pyridine ring. In all cases, the Co sites have finite magnetic moments suggesting that the complexes may provide ways of making cluster-based magnetic materials.     

Structural Transformation of Surface-Confined Porphyrin Networks by Addition of Co Atoms

The self-assembly of a nickel-porphyrin derivative (Ni-DPPyP) containing two pyridyl coordinating sites and two pentyl chains at trans meso positions was studied with scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS) and low energy electron diffraction (LEED) on Au(111). Deposition of Ni-DPPyP onto Au(111) gave rise to a close-packed network for coverages smaller or equal to one monolayer as revealed by STM and LEED. The molecular arrangement of this two-dimensional network is stabilized via hydrogen bonds formed between the pyridyl's nitrogen and hydrogen atoms from the pyrrole groups of neighboring molecules. Subsequent deposition of cobalt atoms onto the close-packed network and post-deposition annealing at 423 K led to the formation of a Co-coordinated hexagonal porous network. As confirmed by XPS measurements, the porous network is stabilized by metal-ligand interactions between one cobalt atom and three pyridyl ligands, each pyridyl ligand coming from a different Ni-DPPyP molecule.     

Electron interaction in molecules

An idea of electron interaction in molecule has been applied to the SCF MO calculations of theπ-electronic structure of some complex aromatic hydrocarbons and their derivatives. The theoretical results for singlet and triplet transition energies, first ionization potentials and bond lengths agree fairly well with the experimental data. A correlation equation between the valence state ionization potential and the one center electron repulsion integral has been proposed. It has been shown that the electron repulsion in molecule is considerably smaller than in free atom. The present calculation shows that we can treat sulphur as a normal heteroatom analogous to oxygen and nitrogen.     

Oxidation and oxygenation of iron complexes of 2-aza-21-carbaporphyrin

Oxidation and oxygenation of (HCTPPH)Fe(II)Br an iron(II) complex of 2-aza-5,10,15,20-tetraphenyl-21-carbaporphyrin (CTPPH)H2 have been followed by 1H and 2H NMR spectroscopy. Addition of I2 or Br2 to the solution of (HCTPPH)Fe(II)Br in the absence of dioxygen results in one-electron oxidation yielding [(HCTPPH)Fe(III)Br]+. One electron oxidation with dioxygen, accompanied by deprotonation of a C(21)H fragment and formation of an Fe-C(21) bond, produces an intermediate-spin, five-coordinate iron(III) complex (HCTPP)Fe(III)Br. In the subsequent step an insertion of the oxygen atom into the preformed Fe(III)-C(21) bond has been detected to produce [(CTPPO)Fe(III)Br]-. Protonation at the N2 atom affords (HCTPPO)Fe(III)Br. The considered mechanism of (HCTPPH)Fe(II)Br oxygenation involves the insertion of dioxygen into the Fe-C bond. The 1H NMR and 2H NMR spectra of paramagnetic iron(III) complexes were examined. Functional group assignments have been made with use of selective deuteration. The characteristic patterns of pyrrole and 2-NH resonances have been found diagnostic of the ground electronic state of iron and the donor nature localized at C(21) center as exemplified by the 1H NMR spectrum of intermediate-spin (HCTPP)Fe(III)Br: beta-H 7.2, -10.6, -19.2, -20.6, -23.2, -24.9, -43.2; 2-NH -76.6 (ppm, 298 K). The structures of two compounds (HCTPP)Fe(III)Br and (HCTPPO)Fe(III)Br, were determined by X-ray diffraction studies. In the first case, the iron(III) is five-coordinate with bonds to three pyrrole nitrogen atoms (Fe-N distances: 1.985(8), 2.045(7), 2.023(8) A), and the pyrrolic trigonal carbon (Fe-C: 1.981(8) A). The iron(III) of (HCTPPO)Fe(III)Br forms bonds to three pyrrole nitrogen atoms (Fe-N distances 2.104(5), 2.046(5), 2.102(5) A). The Fe-O 2.041(5) A and Fe-C(21) 2.192(5) A distances suggests a direct interaction between the iron center and the pi electron density on the carbonyl group in a eta2 fashion.     

Hydrogen bonding. Part 75. Infrared, titrametric and molecular orbital study of the structure, solubility and reaction with fluoride ion of 2,3-dicarboxypyrazine

2,3-Dicarboxypyrazine (2,3-H₂DCPz), unlike 2,3-dicarboxypyridine (2,3-H₂DCPy), does not exist as a zwitterion in the solid state. This is due to the remarkably low base strength of nitrogen in the pyrazine ring relative to that of pyridine. The decrease in the base strength of pyrazine relative to pyridine may result from greater disruption of the aromatic π-system of pyrazine on protonation than is the case with pyridine. We propose that 2,3-H₂DCPz has a structure of C_s symmetry in the solid state in which one carboxyl group forms an internal hydrogen bond to carbonyl of adjacent carboxyl in the same molecule, and the second carboxyl forms an intermolecular hydrogen bond to carbonyl in an adjacent molecule. The monoanion in 2,3-NaHDCPz has a strong O–H–O covalent three-center hydrogen bond between carboxylate groups. When saturated solutions of 2,3-H₂DCPz are treated with F⁻, one additional diacid molecule is taken into solution for each 1.5 F⁻ added. As is the case with 2,3-H₂DCPy, the high solubility and acid strength of 2,3-H₂DCPz (pK_a=2.87) leads to formation of the hydrogen-rich H₂F₃⁻ ion instead of HF₂⁻.     

Anodic Processes Involving Trifluoromethyl Cobaloxime and Nucleophiles

Anodic oxidation of trifluoromethyl cobaloxime (CF₃)Co(DH)₂Py in the presence of such nucleophiles as pyridine or NO^– ₃ and C₆F₁₃COO^– anions is studied. A controlled-potential electrolysis and ¹⁹F NMR spectroscopy show the anodic reaction products to contain compounds with the bond >N–CF₃. A mechanism for the reaction between a labile Co(+4) complex and pyridine is offered. At potentials more positive than that of the Co(+3) Co(+4) oxidation, secondary products of electrochemical reaction form and are revealed by a cathodic reduction peak.     

Application of the Mössbauer spectroscopy to the study of the oxidation state of azaferrocene derivatives

Azaferrocene has two active sites of iron and nitrogen atoms. Drastic change of the oxidation state in iodine oxidation of azaferrocene is observed by introducing the methyl substituents into the pyrrole ring, while all the N-methylates show a similar electronic state. It was revealed that an introduction of methyl substituent to the pyrrole ring promotes the oxidation of nitrogen atom in pyrrole ring more than the central iron atom.     

How do azoles inhibit cytochrome P450 enzymes? A density functional study

To examine how azole inhibitors interact with the heme active site of the cytochrome P450 enzymes, we have performed a series of density functional theory studies on azole binding. These are the first density functional studies on azole interactions with a heme center and give fundamental insight into how azoles inhibit the catalytic function of P450 enzymes. Since azoles come in many varieties, we tested three typical azole motifs representing a broad range of azole and azole-type inhibitors: methylimidazolate, methyltriazolate, and pyridine. These structural motifs represent typical azoles, such as econazole, fluconazole, and metyrapone. The calculations show that azole binding is a stepwise mechanism whereby first the water molecule from the resting state of P450 is released from the sixth binding site of the heme to create a pentacoordinated active site followed by coordination of the azole nitrogen to the heme iron. This process leads to the breaking of a hydrogen bond between the resting state water molecule and the approaching inhibitor molecule. Although, formally, the water molecule is released in the first step of the reaction mechanism and a pentacoordinated heme is created, this does not lead to an observed spin state crossing. Thus, we show that release of a water molecule from the resting state of P450 enzymes to create a pentacoordinated heme will lead to a doublet to quartet spin state crossing at an Fe-OH(2) distance of approximately 3.0 A, while the azole substitution process takes place at shorter distances. Azoles bind heme with significantly stronger binding energies than a water molecule, so that these inhibitors block the catalytic cycle of the enzyme and prevent oxygen binding and the catalysis of substrate oxidation. Perturbations within the active site (e.g., a polarized environment) have little effect on the relative energies of azole binding. Studies with an extra hydrogen-bonded ethanol molecule in the model, mimicking the active site of the CYP121 P450, show that the resting state and azole binding structures are close in energy, which may lead to chemical equilibrium between the two structures, as indeed observed with recent protein structural studies that have demonstrated two distinct azole binding mechanisms to P450 heme.