Charge-transfer as a mechanism for controlling molecular fragmentation

We investigate control over molecular fragmentation in the halogen substituted acetone 1,1-dibromo-3,3,3-trifluoroacetone using shaped ultrafast laser pulses. Following insight gained from closed-loop learning control experiments, further tests reveal that control over the CF₃⁺/CHBr₂⁺ ratio exploits a charge-transfer mechanism. We interpret the control in terms of adiabatic rapid passage.     

Life as a nanoscale phenomenon

The nanoscale is not just the middle ground between molecular and macroscopic but a dimension that is specifically geared to the gathering, processing, and transmission of chemical-based information. Herein we consider the living cell as an integrated self-regulating complex chemical system run principally by nanoscale miniaturization, and propose that this specific level of dimensional constraint is critical for the emergence and sustainability of cellular life in its minimal form. We address key aspects of the structure and function of the cell interface and internal metabolic processing that are coextensive with the up-scaling of molecular components to globular nanoobjects (integral membrane proteins, enzymes, and receptors, etc) and higher-order architectures such as microtubules, ribosomes, and molecular motors. Future developments in nanoscience could provide the basis for artificial life.     

Vertical excitation as a transient phenomenon

For a particular model with two electronic states, each with two vibrations, the dipole correlation function governing electronic absorption is e ^?iωOt cosγt with spectrum ω ₀±γ. The function starts as e ^?iωOt (γ?ω ₀), with Fourier transform peaking around ω ₀ instead of ω ₀±γ, and this is associated with vertical excitation. After a time t～2/γ the spectrum goes over into the normal one. As a generalization, a procedure is outlined for characterizing the state reached first after interaction with light is initiated. Finally it is suggested that one can understand aspects of internal conversion by analogy with the case of vertical excitation.     

Charge-transfer and spin dynamics in DNA hairpin conjugates with perylenediimide as a base-pair surrogate

A perylenediimide chromophore (P) was incorporated into DNA hairpins as a base-pair surrogate to prevent the self-aggregation of P that is typical when it is used as the hairpin linker. The photoinduced charge-transfer and spin dynamics of these hairpins were studied using femtosecond transient absorption spectroscopy and time-resolved EPR spectroscopy (TREPR). P is a photooxidant that is sufficiently powerful to quantitatively inject holes into adjacent adenine (A) and guanine (G) nucleobases. The charge-transfer dynamics observed following hole injection from P into the A-tract of the DNA hairpins is consistent with formation of a polaron involving an estimated 3-4 A bases. Trapping of the (A 3-4) (+*) polaron by a G base at the opposite end of the A-tract from P is competitive with charge recombination of the polaron and P (-*) only at short P-G distances. In a hairpin having 3 A-T base pairs between P and G ( 4G), the radical ion pair that results from trapping of the hole by G is spin-correlated and displays TREPR spectra at 295 and 85 K that are consistent with its formation from (1*)P by the radical-pair intersystem crossing mechanism. Charge recombination is spin-selective and produces (3*)P, which at 85 K exhibits a spin-polarized TREPR spectrum that is diagnostic of its origin from the spin-correlated radical ion pair. Interestingly, in a hairpin having no G bases ( 0G), TREPR spectra at 85 K revealed a spin-correlated radical pair with a dipolar interaction identical to that of 4G, implying that the A-base in the fourth A-T base pair away from the P chromophore serves as a hole trap. Our data suggest that hole injection and transport in these hairpins is completely dominated by polaron generation and movement to a trap site rather than by superexchange. On the other hand, the barrier for charge injection from G (+*) back onto the A-T base pairs is strongly activated, so charge recombination from G (or even A trap sites at 85 K) most likely proceeds by a superexchange mechanism.     

Diverse polymorphism of G-quadruplexes as a kinetic phenomenon

Knowledge of forces that drive conformational transitions of G-quadruplexes is crucial for understanding the molecular basis of several key cellular processes. It can only be acquired by combining structural, thermodynamic and kinetic information. Existing biophysical and structural evidences on polymorphism of intermolecular G-quadruplexes have shown that the formation of a number of these structures is a kinetically controlled process. Reported kinetic models that have been used to describe the association of single strands into quadruplex structures seem to be inappropriate since the corresponding model-predicted activation energies turn out to be negative. By contrast, we propose here a novel kinetic model that successfully describes experimentally monitored folding/unfolding transitions of G-quadruplexes and gives positive activation energies for all elementary steps, including those describing association of two single strands into bimolecular quadruplex structures. It is based on a combined thermodynamic and kinetic investigation of polymorphic behavior of bimolecular G-quadruplexes formed from d(G4T4G4) and d(G4T4G3) strands in the presence of Na(+) ions, monitored by spectroscopic (UV, CD) and calorimetric (DSC) techniques. According to our experiment and model analysis the topology of the measured G-quadruplexes is clearly flexible with the conformational forms that respond to the rate of temperature change at which global unfolding/folding transitions occur.     

Cyclodextrin complexation as a probe of molecular photophys1cs

Three examples are described in which complexation of organic guests by a cyclodextrin (CD) alters the photophysical paths for excited state decay of the host-guest complex. The fluorescence properties ol the complexes between β- and γ-CD and the bichromophoric molecule 1.1'-bis-(α-naphthylmethyl) dithiane are presented to illustrate how complexation alters the dynamics of conformational interconversion. The complexation of β-naphthol by β-CD is shown by time-correlated emission spectroscopy to prevent the adiabatic deprotonation of the excited alcohol normally observed in aqueous solution. Lastly, solid complexes of CD's and aromatic donor-acceptor molecules such as p-nitroaniline (PNA) are shown to be active for generation of second harmonic radiation (SHG) when irradiated by 1.06 μ light from a Nd-YAG laser. Since PNA itself crystallizes in a centrosymmetric space group incapable of producing SHG, the complexation method effectively induces SHG activity in this polarizable, but nonpolar material.     

Substitution with retention in organoboranes and utilization of the phenomenon for a general synthesis of pure enantiomers

Organoboranes, readily available via the hydroboration of unsaturated organic compounds, exhibit a remarkable versatility in their reactions. The boron atom in these organoboranes can be readily converted into a wide variety of organic groups under very mild conditions, providing simple versatile syntheses of organic compounds. Exploration of these substitution reactions reveal that, with rare exceptions, the organoboranes transfer the alkyl group to other elements of synthetic interest with complete retention of stereochemistry. Recently we have discovered a method of synthesizing essentially optically pure organoborane intermediates. These optically active alkyl groups attached to boron can also be transferred with complete retention of optical activity. Consequently, it is now possible to achieve by a rational synthesis the preparation of almost any optically active compound with a chiral center, either R- or S-, in essentially 100% enantiomeric excess.     

Self-assembly of electrospun polymer nanofibers: a general phenomenon generating honeycomb-patterned nanofibrous structures

A general phenomenon that electrospun polymer nanofibers self-assemble into honeycomb-patterned nanofibrous structures (HNFSs) is reported. We used electrospinning to produce charged polymer nanofibers, which were kept in liquid state (wet) on landing on the substrates by appropriately controlling the electrospinning conditions. Driven by the competitive actions of surface tension and electrostatic repulsion, these charged wet nanofibers self-assemble into the HNFSs. Fabrication of the well-defined three-dimensional HNFSs was successfully demonstrated for three different polymers, that is, polyacrylonitrile, polyvinyl alcohol, and polyethylene oxide. The pore diameter of the obtained honeycomb structures spans a wide range from micrometers to over 200 μm with depths as large as over 150 μm. The pore walls are composed of uniaxially aligned polymer nanofibers.     

Charge-transfer excited states in a pi-stacked adenine dimer, as predicted using long-range-corrected time-dependent density functional theory

The lowest few electronic excitations of a pi-stacked adenine dimer in its B-DNA geometry are investigated, in the gas phase and in a water cluster, using a long-range-corrected version of time-dependent density functional theory (TD-DFT) that asymptotically incorporates Hartree-Fock exchange. Long-range correction is shown to eliminate the catastrophic underestimation of charge-transfer (CT) excitation energies that plagues conventional TD-DFT, at the expense of introducing one adjustable parameter, mu, that determines the length scale on which Hartree-Fock exchange is turned on. This parameter allows us to interpolate smoothly between hybrid density functionals and time-dependent Hartree-Fock theory. Excitation energies for CT states (in which an electron is transferred from one adenine molecule to the other) are found to increase dramatically as a function of mu. Uncorrected hybrid functionals underestimate the CT excitation energies, placing them well below the valence excitations, while time-dependent Hartree-Fock calculations place these states well above the valence states. Values for mu determined from certain benchmark calculations place the CT states well above the valence pipi* and npi* states at the Franck-Condon point.     

Charge-transfer interactions in a multichromophoric hexaarylbenzene containing pyrene and triarylamines

Two different hexaarylbenzenes with three pyrene and three triarylamine substituents in different positions (trigonal symmetric and asymmetric arrangement) were synthesized, and their charge-transfer states were investigated by optical spectroscopy. In these multichromophoric systems triarylamine acts as the electron donor and pyrene as the electron acceptor. A reference chromophore with only one donor-acceptor pair was also investigated. All these chromophores form charge-transfer states upon photoexcitation which relax with a moderate fluorescence quantum yield to the ground state. The compounds do not differ significantly concerning most of their fluorescence properties, which shows that the fluorescent charge-transfer state is very similar in all chromophores. This observation indicates symmetry breaking for the symmetric chromophore within fluorescence lifetime of several tens of ns. This interpretation was substantiated by fluorescence excitation anisotropy measurements in a sucrose octaacetate matrix.     

Disconnected lamellar phases (Lalpha) in pseudobinary water-non-ionic surfactant systems: a general phenomenon

This study provides new experimental evidence for the disconnection of the lamellar phase (L(alpha)) in pseudobinary water-non-ionic surfactant systems. To prove that the disconnection is indeed a general phenomenon the phase behavior of the pseudobinary system water-pentaethylene glycol dodecyl ether/hexaethylene glycol dodecyl ether (H(2)O-C(12)E(5)/C(12)E(6)) was investigated as a function of the surfactant composition delta and the total surfactant concentration gamma. At a fixed gamma of 0.10 the extension of the highly diluted L(alpha) phase shrank continuously with increasing amount of C(12)E(6), i.e., increasing delta, until it disappeared at delta=0.60. The gamma-T phase diagram of this particular surfactant mixture was found to have a disconnected L(alpha) phase. For the first time, SAXS measurements were carried out to monitor structural changes related to the disconnection. For this purpose the interlayer spacing d and the effective cross-sectional area a(s) were determined from the SAXS data along characteristic paths through the L(alpha) phase.     

Charge-transfer controlled exchange interaction in radical-triplet encounter pairs as studied by FT-EPR spectroscopy

The exchange interaction, J, producing quartet and doublet energy separation in radical-triplet excited molecule encounter pairs, was investigated in solution by measuring chemically induced dynamic electron polarization (CIDEP) created through the radical-triplet pair mechanism. A time-resolved FT-EPR method was utilized to measure CIDEP of galvinoxyl radical by recording FID signals and an absolute magnitude of CIDEP, P(n), was determined for each radical-triplet system by detailed analysis of the time evolution curves of CIDEP. A transient FT-EPR signal phase remarkably depends on the triplet molecule. The signal phase is related to the sign of J value, which is responsible for the radical-triplet pair interaction. Most of galvinoxyl-triplet systems showed normal negative sign. An unusual positive sign was found in some systems characterized by a small energy gap, DeltaG, between the radical-triplet pair and intermolecular charge transfer (CT) states. A theoretical calculation of J value for radical-triplet encounter pairs was carried out by considering exchange integral and intermolecular CT interaction. According to the calculated J value and the diffusion theory for CIDEP magnitude, experimental Pn values were theoretically reproduced as a function of DeltaG. The present results confirm our previously reported CT model explaining the complicated nature of the sign of J value in the galvinoxyl-triplet encounter pairs. According to the proposed model for CT effect on J value and CIDEP results, nature of J value in radical-triplet pairs is discussed.     

The measure cone: Irreversibility as a geometrical phenomenon

The statistical state space is discussed in terms of the geometry of normed real vector spaces with particular reference to the novel concept of direction distance. Specialization to the geometry of the measure cone and the correspondingly specialized concept of mixing distance suggest strong mutual relationship as is shown subsequently in physically required generality. Thereby, the phenomenon of irreversibility attains an interpretation that seems to be the canonical mathematical background for classical and nonclassical statistical physics.     

Tetraiodophenolsulfonphthalein as a spectral substitute to characterize the complexation between cationic and anionic surfactant

The complexation of cetyltrimethylammonium bromide (CTAB) with sodium dodecyl sulfate (SDS) with sodium dodecyl benzene sulfonate (SDBS), with tetraiodophenolsulfonphthalein (TIPST) as a spectral substitute was investigated at pH 5.89 and 8.30 by the microsurface adsorption--spectral correction (MSASC) technique. The aggregations of TIPST, SDS, and SDBS on CTAB obeyed the Langmuir isothermal adsorption. The aggregates TIPST-CTAB, TIPST2-CTAB3, SDS3-CTAB2, and SDBS3-CTAB2 were formed at 20 degrees C and the binding constants of all the aggregates were determined. The replacement of TIPST-binding CTAB monomer with SDS or SDBS at pH 5.89 was applied to the quantitative determination of anionic detergent (AD) in water with satisfactory recovery.     

Charge-transfer properties of the hydrogen bond: Part 6. Charge-transfer theory and dipole moments of hydrogen-bonded complexes

The enhancement of the dipole moments of hydrogen-bonded complexes are discussed using Mulliken's charge-transfer theory.A linear relation is found between the ratio a/b and the ionization potential of the donor, I^V_D. This behaviour is similar to that previously found for halogen charge-transfer complexes [6].     

Charge-transfer transitions in the vacuum-ultraviolet of protein circular dichroism spectra

Circular dichroism (CD) is widely used in the structural characterization and secondary structure determination of proteins. The vacuum UV region (below 190 nm), where charge-transfer transitions have an influence on the CD spectra, can be accessed using synchrotron radiation circular dichroism (SRCD) spectroscopy. Recently, charge-transfer transitions in a conformationally diverse set of dipeptides have been characterized ab initio using complete active space self-consistent field calculations, and the relevant charge distributions have been parametrized for use in the matrix method for calculations of protein CD. Here, we present calculations of the vacuum UV CD spectra of 71 proteins, for which experimental SRCD spectra and X-ray crystal structures are available. The theoretical spectra are calculated considering charge-transfer and side chain transitions. This significantly improves the agreement with experiment, raising the Spearman correlation coefficient between the calculated and the experimental intensity at 175 nm from 0.12 to 0.79. The influence of the conformation on charge-transfer transitions is analyzed in detail, showing that the n --> pi* charge-transfer transitions are most important in alpha-helical proteins, whereas in beta strand proteins the pi --> pi* charge-transfer transition along the chain in the amino- to carboxy-end direction is most dominant.     

Pyrogallarenes as alkali metal receptors: the role of cation-pi interactions in complexation

Crystallization studies of C-methyl pyrogallarene with potassium, rubidium and caesium bromides or chlorides resulted in a hydrogen bonded molecular cage in which the alkali metal cations are eta6 coordinated to aromatic rings via strong cation-pi interactions.     

The overshoot phenomenon as a function of internal resistance in microbial fuel cells

A method for assessing the performance of microbial fuel cells (MFCs) is the polarisation sweep where different external resistances are applied at set intervals (sample rates). The resulting power curves often exhibit an overshoot where both power and current decrease concomitantly. To investigate these phenomena, small-scale (1 mL volume) MFCs operated in continuous flow were subjected to polarisation sweeps under various conditions. At shorter sample rates the overshoot was more exaggerated and power generation was overestimated; sampling at 30 s produced 23% higher maximum power than at 3 min. MFCs with an immature anodic biofilm (5 days) exhibited a double overshoot effect, which disappeared after a sufficient adjustment period (5 weeks). Mature MFCs were subject to overshoot when the anode was fed weak (1 mM acetate) feedstock with low conductivity (<100 μS) but not when fed with a higher concentration (20 mM acetate) feedstock with high conductivity (>1500 μS). MFCs developed in a pH neutral environment produced overshoot after the anode had been exposed to acidic (pH 3) conditions for 24 h. In contrast, changes to the cathode both in terms of pH and varying catholyte conductivity, although affecting power output did not result in overshoot suggesting that this is an anodic phenomenon.     

Diphenic acid as a general conformational lock in the design of bihelical structures

The bihelical (figure of "infinity") topology was examined from vantages of design, crystal structures, chirality, circular dichroism (CD) studies and molecular-orbital calculations. The minimalistic design envisaged the sequential linking of cystine to the anchor diphenic acid, which proved to be a general conformational lock. The bihelical compound 4 was obtained in two steps from diphenic anhydride 1 and cystine di-OMe. The chirality of 4 arises largely from the L-cystine. The bihelical compound 5 obtained from D-cystine di-OMe was found, by X-ray crystallography, CD studies, and optical rotation, to be the perfect mirror image of 4 prepared from L-cystine. The crystal structure of prototype 8, prepared by protocols used for 4 from the achiral cystine analogue cystamine, had a "U"-shaped conformation held together by intramolecular hydrogen bonds. Analysis of 4 and 5 show that the pairs of nine-membered beta-turn-like constructs made compact through hydrogen bonding with DMSO hold the key for the bihelical conformation. Another factor is the need for the presence of a ligand at the Calpha position. The absence of this, as in 8, allows major flexibility in the torsional angles around this critical region, promoting flexible alternatives. The CD analysis of 4, confirmed to be bihelical by X-ray crystallography, showed a typical negative band at about 210 A attributed to the beta-turn-like motif, and in the positive-band region a peak at about 227 A, generally related to the twist of the biphenyl unit. The cystamine analogue 8, which showed a "U"-type structure, presented a CD spectrum with no typical features. The total energy, derived from theoretical calculations by using the X-ray structure data, support the bihelical structure for 4 and a "U"-shaped one for 8. The limited utility of such calculations was tested with composite 9. Composite 9, in which the anchor diphenic acid is linked to cystamine on the one hand and to cystine on the other, showed a CD spectrum similar to that of 4, and this coupled with molecular-orbital calculations, using data from 4 and 8, predict a bihelical structure for this compound.