Chemical bonding, electron-phonon coupling, and structural transformations in high-pressure phases of Si

The nature of chemical bonding of the stable phases of Si at high pressure was analyzed. The effect of pressure is to promote sp electrons into the d orbitals, thus increasing the metallic character and reducing the dimensionality of covalent bonding. Localized covalent bonds, however, persist up to approximately 40 GPa (Si-VI, Cmca) and help to stabilize directional framework structures. At high pressures, Si becomes a metal, and the usual dense packed structures prevail. The existence of conducting and localized electrons gives rise to a combination of "steep and flat bands" near the Fermi level in Si-V. This peculiar electron topology in conjunction with low-frequency vibrations contributes to the relatively high superconducting temperature in Si-V and VI.     

Controllable propagation of light pulses in Er-doped fibers with saturable absorption

We report controllable (slow or fast) propagation of low-intensity probe-light pulses through erbium-doped fiber periodically saturated by the synchronized master-pulse sequence. These two pulse sequences could have significantly different carrier wavelengths within the fundamental absorption spectrum 1470-1570 nm of Er(+3) ions. The effect of fractional delay or advancement grew with the fiber optical absorption at the probe wavelength and could be significantly stronger than that at the saturating wavelength. The probe-pulse advancement was observed in the case when the saturating and probe waves were modulated approximately in antiphase. The observed effects are explained in the framework of a simple model of a periodically saturated homogeneously broadened absorption line.     

Supersymmetry and cohomology of graph complexes

Letters in Mathematical Physics - I describe a combinatorial construction of the cohomology classes in compactified moduli spaces of curves $$\widehat{Z}_{I}\in H^{*}\left( \bar{\mathcal...     

New insights into the transition pathway from nonspecific to specific complex of DNA with Escherichia coli integration host factor

To elucidate the nature of the transition-state ensemble along the reaction pathway from a nonspecific protein-DNA complex to the specific complex, we have carried out measurements of DNA bending/unbending dynamics on a cognate DNA substrate in complex with integration host factor (IHF), an architectural protein from E. coli that bends its cognate site by approximately 180 degrees . We use a laser temperature jump to perturb the IHF-DNA complex and monitor the relaxation kinetics with time-resolved FRET measurements on DNA substrates end-labeled with a FRET pair. Previously, we showed that spontaneous bending/kinking of DNA, from thermal disruption of base-pairing/-stacking interactions, may be the rate-limiting step in the formation of the specific complex (Kuznetsov, S. V.; Sugimura, S.; Vivas, P.; Crothers, D. M.; Ansari, A. Proc. Natl. Acad. Sci. USA 2006, 103, 18515). Here, we probe the effect of varying [KCl], which affects the stability of the complex, on this rate-limiting step. We find that below approximately 250 mM KCl, the observed relaxation kinetics are from the unimolecular bending/unbending of DNA, and the relaxation rate kr is independent of [KCl]. Above approximately 300 mM KCl, dissociation of the IHF-DNA complex becomes significant, and the observed relaxation process includes contributions from the association/dissociation step, with kr decreasing with increasing [KCl]. The DNA bending step occurs with a positive activation enthalpy, despite the large negative enthalpy change reported for the specific IHF-DNA complex (Holbrook, J. A.; Tsodikov, O. V.; Saecker, R. M.; Record, M. T., Jr. J. Mol. Biol. 2001, 310, 379). Our conclusion from these studies is that in the uphill climb to the transition state, the DNA is kinked, but with no release of ions, as indicated by the salt-independent behavior of k(r) at low [KCl]. Any release of ions in the unimolecular process, together with conformational changes in the protein-DNA complex that facilitate favorable interactions and that contribute to the negative enthalpy change, must occur as the system leaves the transition state, downhill to the final complex.     

Tubular aggregates of cyclic oligothiophenes. A theoretical study

The geometries of neutral, mono-, and dioxidized tubular aggregates of cyclo[8]thiophenes containing up to 5 repeating units were fully optimized at the MPWB1K/3-21G* level of theory. Calculated interplane distances between macrocycles were found to be close to 3.1 A for neutral and charged aggregates. The binding energies between macrocycles in neutral intermediates were in the range of 40-45 kcal/mol, increasing for monocations and dropping strongly for dicationic species due to electrostatic repulsion between polarons. It was established that there exists a noticeable interaction between pi-orbitals of individual macrocycles in tubular aggregates as follows from decreasing of the band gap with a number of repeating units in aggregates and the polaron delocalization toward tube axes in oxidized species. A polaron pair is the most stable dicationic state for all studied molecules according to the calculations. A singlet polaron pair is more stable than a triplet one. The energy difference between singlet and triplet states is growing smaller with the size of the system, becoming zero for the pentamer corresponding to a completely dissociated bipolaron.     

Oligothiophene catenanes and knots. Part II. Mono and dications. A theoretical study

Mono- and dications of catenanes and knots containing 16, 22, and 28 thiophene units have been studied at the BHandHLYP/3-21G* level of theory. The polaron localization and relaxation energies of monoionized molecules increase with dihedral angle between thiophene fragments, being higher for catenanes and knots compared to linear oligomers. Monoionization of catenanes results in the polaron localization at one macrocycle leaving another one intact. In all diionized oligomers, polaron pairs were found to be more stable than corresponding bipolarons. The energy difference between bipolaron and polaron pairs increases with the number of repeating units in oligomers for all studied molecular architectures. Singlet polaron pairs are more stable than triplet ones. The energy difference between triplet and singlet states does not exceed 7-8 kcal/mol and decreases with the number of thiophene units in oligomers. Two different singlet minima were found for diionized catenanes. In the first one (the most stable), each macrocycle loses one electron, and in the other one, the polaron pairs are located at one macrocycle, leaving another intact. The energy difference between two minima decreases with the number of repeating units in catenanes.     

Open tube combustion method of organic samples for stable carbon isotope analysis

A simple and effective method for the conversion of organic carbon into carbon dioxide for analysis of stable carbon isotopes (delta(13)C) in samples of various organic substances, soils, sedimentary rocks, oils and volatile organic liquids is presented. The conversion of organic carbon of the samples is carried out in a quartz reactor connected to a vacuum line for CO(2) freezing and purification. A solid organic sample mixed with CuO is placed at the reactor bottom and the reactor is subsequently filled with granular CuO. One end of the CuO column is preheated to 850 degrees C while the other end of the column in contact with the sample is kept at ambient temperature. Heating of the sample (850 degrees C) and the remainder of the column is then performed. The preheated part of the column provides efficient conversion of carbon into CO(2). The reactor for the conversion of volatile liquid organic compounds is filled with granular CuO. The column of CuO is heated to 850 degrees C. Samples of volatile liquids are introduced into the reactor through a septum using a microsyringe. Complete conversion takes 10 min for solid samples and 3 min for volatile liquids. The precision of the delta(13)C analysis for solid and volatile liquid organic substances is +/-0.1 per thousand and +/-0.04 per thousand, respectively.     

Prussian blue analogue CsFe[Cr(CN)(6)] as a matrix for the Fe(II) spin-crossover

The origin of the intriguing spin-transition behavior of the Prussian blue analogue cesium iron hexacyanochromate CsFe[Cr(CN)6] has been investigated by means of correlated ab initio CASPT2 calculations. Using the smallest transiting core [Fe(NC)6]4-, the relative importance of the local ligand field and the Madelung field generated by the rest of the crystal was estimated. It is shown that in the presence of a frozen-charge environment, the high-spin state lies lower in energy than the low-spin state, thus excluding the possibility of observing a spin transition. In contrast, the charge reorganization in the environment evaluated from unrestricted periodic Hartree-Fock calculations creates a prerequisite for the spin-transition phenomenon. The influence of the disorder in the cesium ions' positions on the spin transition has been examined as a possible stabilizing factor of the low-spin state of [Fe(NC)6]4-. It is concluded that this experimentally observed disorder cannot account solely for the unprecedented behavior of the CsFe[Cr(CN)6] compound.     

Superelectrophilic Activation of N‐Substituted Isatins: Implications for Polymer Synthesis,a Theoretical Study

The stability and reactivity of mono‐ and multi‐protonatred N‐substituted isatin derivatives were studied at PBE0/aug‐cc‐pvtz//PBE0/6‐31+G** level of theory in triflic acid (TFSA) solution. Calculations showed that the monocationic intermediates are the principal reactive species in the reaction of hydroxyalkylation of isatin derivatives in TFSA media. Electron‐withdrawing substituents on the nitrogen atom increase the reactivity of isatin‐containing electrophiles towards aromatic hydrocarbons, in accordance with their expected electronic influence. Steric factors also play an important role in the reactivity of isatin‐containing electrophiles, especially in the second reaction step, due to their more sterically hindered reactive center.