Preparation of polyetherol-appended sulfur porphyrazines and investigations of peripheral metal ion binding in polar solvents

We describe the complete synthesis and characterization of a new family of peripherally functionalized porphyrazines (pz's) with four, three, or two (in a trans conformation) bis[thioethoxy(ethoxy)ethanol] moieties appended at the pyrroles. These "polyetherol" groups serve as weak exocyclic binding sites for a number of metal ions and also provide solubility of the pz's in low molecular-weight alcohols and water. Electronic spectra of the modified porphyrazines exhibit distinct changes in the visible region (both absorbance and fluorescence) in response to treatment with Ag+, Pb2+, Cd2+, Cs+, and Ni2+ in solution. Such properties make these compounds intriguing candidates for incorporation into the transducer layers in optically based chemical sensors.     

Rigid Arrangements of Ionic Charge in Zeolite Frameworks Conferred by Specific Aluminum Distributions Preferentially Stabilize Alkanol Dehydration Transition States

Zeolite reactivity depends on the solvating environments of their micropores and the proximity of their Brønsted acid sites. Turnover rates (per H⁺) for methanol and ethanol dehydration increase with the fraction of H⁺ sites sharing six-membered rings of chabazite (CHA) zeolites. Density functional theory (DFT) shows that activation barriers vary widely with the number and arrangement of Al (1–5 per 36 T-site unit cell), but cannot be described solely by Al–Al distance or density. Certain Al distributions yield rigid arrangements of anionic charge that stabilize cationic intermediates and transition states via H-bonding to decrease barriers. This is a key feature of acid catalysis in zeolite solvents, which lack the isotropy of liquid solvents. The sensitivity of polar transition states to specific arrangements of charge in their solvating environments and the ability to position such charges in zeolite lattices with increasing precision herald rich catalytic diversity among zeolites of varying Al arrangement.     

Testing if the interstitial atom, X, of the nitrogenase molybdenum-iron cofactor is N or C: ENDOR, ESEEM, and DFT studies of the S = 3/2 resting state in multiple environments

A high-resolution (1.16 A) X-ray structure of the nitrogenase molybdenum-iron (MoFe) protein revealed electron density from a single N, O, or C atom (denoted X) inside the central iron prismane ([6Fe]) of the [MoFe7S9:homocitrate] FeMo-cofactor (FeMo-co). We here extend earlier efforts to determine the identity of X through detailed tests of whether X = N or C by interlocking and mutually supportive 9 GHz electron spin echo envelope modulation (ESEEM) and 35 GHz electron-nuclear double resonance (ENDOR) measurements on 14/15N and 12/13C isotopomers of FeMo-co in three environments: (i) incorporated into the native MoFe protein environment; (ii) extracted into N-methyl formamide solution; and (iii) incorporated into the NifX protein, which acts as a chaperone during FeMo-co biosynthesis. These measurements provide powerful evidence that X not equal N/C, unless X in effect is magnetically decoupled from the S = 3/2 electron spin system of resting FeMo-co. They reveal no signals from FeMo-co in any of the three environments that can be assigned to X from either 14/15N or 13C: If X were either element, its maximum observed hyperfine coupling at all fields of measurement is estimated to be A(14/15NX) < 0.07/0.1 MHz, A(13CX) < 0.1 MHz, corresponding to intrinsic couplings of about half these values. In parallel, we have explicitly calculated the hyperfine tensors for X = 14/15N/13C/17O, nuclear quadrupole coupling constant e2qQ for X = 14N, and hyperfine constants for the Fe sites of S = 3/2 FeMo-co using density functional theory (DFT) in conjunction with the broken-symmetry (BS) approach for spin coupling. If X = C/N, then the decoupling required by experiment strongly supports the "BS7" spin coupling of the FeMo-co iron sites, in which a small X hyperfine coupling is the result of a precise balance of spin density contributions from three spin-up and three spin-down (3 upward arrow:3 downward arrow) iron atoms of the [6Fe] prismane "waist" of FeMo-co; this would rule out the "BS6" assignment (4 upward arrow:2 downward arrow for [6Fe]) suggested in earlier calculations. However, even with the BS7 scheme, the hyperfine couplings that would be observed for X near g2 are sufficiently large that they should have been detected: we suggest that the experimental results are compatible with X = N only if aiso(14/15NX) < 0.03-0.07/0.05-0.1 MHz and aiso(13CX) < 0.05-0.1 MHz, compared with calculated values of aiso(14/15NX) = 0.3/0.4 MHz and aiso(13CX) = 1 MHz. However, the DFT uncertainties are large enough that the very small hyperfine couplings required by experiment do not necessarily rule out X = N/C.     

Renner-Teller/Jahn-Teller intersections along the collinear axes of polyatomic molecules: C2H2 + as a case study

Recently we discussed the Renner-Teller effect in triatomic molecules [J. Chem. Phys. 125, 094102 (2006)]. In that article the main message is that the Renner-Teller phenomenon, just like the Jahn-Teller phenomenon, is a topological effect. Now we extend this study to a tetra-atomic system, namely, the C(2)H(2) (+) ion, for which topological effects are revealed when one atom surrounds the triatom axis or when two atoms surround (at a time) the two-atom axis. The present study not only supports the findings of the previous study, in particular, the crucial role played by the topological D matrix for diabatization, but it also reveals new features which are expected to be more and more pronounced the larger the original collinear molecule. As already implied, shifting away two atoms from the collinear molecular axis does not necessarily abolish the ability of the remaining two atoms to form topological effects. Moreover, the study indicates that when the two hydrogens are shifted away, the CC axis produces two kinds of topological effects: (1) a Renner-Teller effect (characterized by a topological phase of 2pi) which is revealed when the two hydrogens surround, rigidly, this axis (as mentioned above), and (2) a Jahn-Teller effect (characterized by a topological phase of pi) which is revealed when one of the hydrogens surrounds this axis while the other hydrogen is clamped to its position.     

Dynamic docking of cytochrome b5 with myoglobin and alpha-hemoglobin: heme-neutralization "squares" and the binding of electron-transfer-reactive configurations

Intracomplex electron transfer (ET) occurs most often in intrinsically transient, low affinity complexes. As a result, the means by which adequate specificity and reactivity are obtained to support effective ET is still poorly understood. We report here on two such ET complexes: cytochrome b5 (cyt b5) in reaction with its physiological partners, myoglobin (Mb) and hemoglobin (Hb). These complexes obey the Dynamic Docking (DD) paradigm: a large ensemble of weakly bound protein-protein configurations contribute to binding in the rapid-exchange limit, but only a few are ET-active. We report the ionic-strength dependence of the second-order rate constant, k2, for photoinitiated ET from within all four combinations of heme-neutralized Zn deuteroporphyrin-substituted Mb/alphaHb undergoing ET with cyt b5, the four "corners" of a "heme-neutralization square". These experiments provide insights into the relative importance of both global and local electrostatic contributions to the binding of reactive configurations, which are too few to be observed directly. To interpret the variations of k2 arising from heme neutralization, we have developed a procedure by which comparisons of the ET rate constants for a heme-neutralization square permit us to decompose the free energy of reactive binding into individual local electrostatic contributions associated with interactions between (i) the propionates of the two hemes and (ii) the heme of each protein with the polypeptide of its partner. Most notably, we find the contribution from the repulsion between propionates of partner hemes to the reactive binding free energy to be surprisingly small, DeltaG(Hb) approximately +1 kcal/mol at ambient temperature, 18 mM ionic strength, and we speculate about possible causes of this observation. To confirm the fundamental assumption of these studies, that the structure of a heme-neutralized protein is unaltered either by substitution of Zn or by heme neutralization, we have obtained the X-ray structure of ZnMb prepared with the porphyrin dimethyl ester and find it to be nearly isostructural with the native protein.     

Structural characterization of a rigidified threading bisintercalator

NMR spectroscopy was used to explore the sequence-specific interaction of DNA with a new threading bisintercalator (C1) consisting of two intercalating 1,4,5,8-naphthalenetetracarboxylic diimide (NDI) units connected by a rigid, tricyclic spiro linker. A structural model of C1 complexed to d(CGGTACCG)(2) was calculated using distance constraints obtained from solution NMR data. The model was also supported by the results from residual dipolar coupling (RDC) measurements obtained using Pf1-phage as a cosolvent. According to the model, the central cyclohexane ring of the linker connecting the two NDI units lies flat in the minor groove of DNA. Linker length, hydrogen bonding, steric, and hydrophobic factors all appear to contribute to the observed sequence specificity of binding. These results serve to illustrate the versatility of threading polyintercalation given that, in a previous study, a ligand consisiting of two NDI units joined by a flexible peptide linker was shown to bind sequence specifically within the major groove of this same sequence of DNA.     

Dispersive photon blockade in a superconducting circuit

Mediated photon-photon interactions are realized in a superconducting coplanar waveguide cavity coupled to a superconducting charge qubit. These nonresonant interactions blockade the transmission of photons through the cavity. This so-called dispersive photon blockade is characterized by measuring the total transmitted power while varying the energy spectrum of the photons incident on the cavity. A staircase with four distinct steps is observed and can be understood in an analogy with electron transport and the Coulomb blockade in quantum dots. This work differs from previous efforts in that the cavity-qubit excitations retain a photonic nature rather than a hybridization of qubit and photon and provides the needed tolerance to disorder for future condensed matter experiments.     

Dynamic evanescent phonon coupling across the La(1-x)Sr(x)MnO3/SrTiO3 interface

The transport and magnetic properties of correlated La0.53Sr0.47MnO3 ultrathin films, grown epitaxially on SrTiO3, show a sharp cusp at the structural transition temperature of the substrate. Using a combination of experiment and first principles theory we show that the cusp is a result of evanescent cross-interface coupling between the charge carriers in the film and a soft phonon mode in the SrTiO3, mediated through linked oxygen octahedral motions. The amplitude of the mode diverges at the transition temperature, and phonons are launched into the first few atomic layers of the film, affecting its electronic state.