Role of charge transfer interaction and conjugation length on electrical polarizability of doped trans-polyacetylene oligomers

The effects of charge transfer and molecular chain length on the electrical polarizability of doped trans-polyacetylene oligomers have been investigated using a series of quantum chemical methods ranging from Hartree-Fock to current density functional theory. Polarizability tensors of pristine and metal-doped trans-polyacetylene oligomers have been estimated. The nature of variations of polarizability tensor components are quite different for pristine and doped oligomers. For doped samples, distinct minima in the average static polarizabilities per acetylene unit have been observed. The results suggest that the competitive role of charge-transfer interaction and oligomer chain length are responsible for the observed minima. To simulate the ab initio results on polarizability variation, we propose a mathematical model that describes the minima quite satisfactorily.     

Electronic coherence effects in photosynthetic light harvesting

Photosynthetic light harvesting is a paradigmatic example for quantum effects in biology. In this work, we review studies on quantum coherence effects in the LH2 antenna complex from purple bacteria to demonstrate how quantum mechanical rules play important roles in the speedup of excitation energy transfer, the stabilization of electronic excitations, and the robustness of light harvesting in photosynthesis. Subsequently, we present our recent theoretical studies on exciton dynamical localization and excitonic coherence generation in photosynthetic systems. We apply a variational-polaron approach to investigate decoherence of exciton states induced by dynamical fluctuations due to system-environment interactions. The results indicate that the dynamical localization of photoexcitations in photosynthetic complexes is significant and imperative for a complete understanding of coherence and excitation dynamics in photosynthesis. Moreover, we use a simple model to investigate quantum coherence effects in intercomplex excitation energy transfer in natural photosynthesis, with a focus on the likelihoods of generating excitonic coherences during the process. Our model simulations reveal that excitonic coherence between acceptor exciton states and transient nonlocal quantum correlation between distant pairs of chromophores can be generated through intercomplex energy transfer. Finally, we discuss the implications of these theoretical works and important open questions that remain to be answered.     

Simulation of tethered oligomers in nanochannels using multi-particle collision dynamics

The effect of a high Reynold's number, pressure-driven flow of a compressible gas on the conformation of an oligomer tethered to the wall of a square channel is studied under both ideal solvent and poor solvent conditions using a hybrid multiparticle collision dynamics and molecular dynamics algorithm. Unlike previous studies, the flow field contains an elongational component in addition to a shear component as well as fluid slip near the walls and results in a Schmidt number for the polymer beads that is less than unity. In both solvent regimes the oligomer is found to extend in the direction of flow. Under the ideal solvent conditions, torsional twisting of the chain and aperiodic cyclical dynamics are observed for the end of the oligomer. Under poor solvent conditions, a metastable helix forms in the end of the chain despite the lack of any attractive potential between beads in the oligomeric chain. The formation of the helix is postulated to be the result of a solvent induced chain collapse that has been confined to a single dimension by a strong flow field.     

Ultrafast vibrational dynamics of adenine-thymine base pairs in DNA oligomers

N-H stretching excitations of DNA oligomers containing 23 alternating adenine-thymine base pairs are studied in femtosecond two-color pump-probe experiments. For a DNA film in a zero relative humidity atmosphere, transient vibrational spectra and their time evolution up to 10 ps demonstrate negligible spectral diffusion and allow for discerning different N-H stretching bands and the O-H stretching absorption of residual water molecules. Lifetimes on the order of 0.5 ps are found for both N-H and O-H stretching modes. The time-dependent pump-probe anisotropies of the different N-H excitations point to a pronounced coupling among them, whereas the O-H stretching anisotropy remains essentially constant.     

Mesoscopic simulation of self-assembly in surfactant oligomers by dissipative particle dynamics

Self-assembling properties of surfactant oligomers in an aqueous medium is simulated by dissipative particle dynamics (DPD). The critical micellar concentration (CMC) of dimeric (oligomerization = 2) and trimeric (oligomerization = 3) surfactant is much lower than their single-chain counterpart. All surfactants form spherical micelles at the concentration not far above their CMC. The transition from spherical to cylindrical micelles exhibits with increasing surfactant concentration. Lamellar micelles will appear with further increasing the surfactant concentration. For dimeric and trimeric surfactants, cylindrical micelles transform into extremely long “wormlike” or “threadlike” micelles before the transition to lamellar micelles. These results are in qualitative agreement with laboratory experiment. Average aggregation numbers (AN) of micelles increase with a power law of AN  c when the surfactant concentration c CMC. The self-diffusion coefficients will drop with a power law of D  c⁻ when wormlike micelles are formed.     

Population and coherence dynamics in large conjugated porphyrin nanorings

In photosynthesis, nature exploits the distinctive electronic properties of chromophores arranged in supramolecular rings for efficient light harvesting. Among synthetic supramolecular cyclic structures, porphyrin nanorings have attracted considerable attention as they have a resemblance to naturally occurring light-harvesting structures but offer the ability to control ring size and the level of disorder. Here, broadband femtosecond transient absorption spectroscopy, with pump pulses in resonance with either the high or the low energy sides of the inhomogeneously broadened absorption spectrum, is used to study the population dynamics and ground and excited state vibrational coherence in large porphyrin nanorings. A series of fully conjugated, alkyne bridged, nanorings constituted of between ten and forty porphyrin units is studied. Pump-wavelength dependent fast spectral evolution is found. A fast rise or decay of the stimulated emission is found when large porphyrin nanorings are excited on, respectively, the high or low energy side of the absorption spectrum. Such dynamics are consistent with the hypothesis of a variation in transition dipole moment across the inhomogeneously broadened ground state ensemble. The observed dynamics indicate the interplay of nanoring conformation and oscillator strength. Oscillatory dynamics on the sub-ps time domain are observed in both pumping conditions. A combined analysis of the excitation wavelength-dependent transient spectra along with the amplitude and phase evolution of the oscillations allows assignment to vibrational wavepackets evolving on either ground or excited states electronic potential energy surfaces. Even though porphyrin nanorings support highly delocalized electronic wavefunctions, with coherence length spanning tens of chromophores, the measured vibrational coherences remain localised on the monomers. The main contributions to the beatings are assigned to two vibrational modes localised on the porphyrin cores: a Zn–N stretching mode and a skeletal methinic/pyrrolic C–C stretching and in-plane bending mode.

Pump wavelength-dependent, ultrafast excited state dynamics arising from inhomogeneous broadening and ground and excited state nuclear wavepackets were observed for a series of Zn porphyrin nanorings made of 10 to 40 repeating units.     

Electronic coupling between base pair dimers of LNA:DNA oligomers

We calculated ab initio electronic coupling elements between neighboring base-pair dimers in a set of LNA:DNA oligomers with different numbers of locked nucleotides and compared them by averaging the values over ensembles of snapshots from molecular dynamics trajectories. Averaging was based on coupling elements for various ensembles comprising of 33,000 structures. The known pronounced variations of coupling elements on the nanosecond timescale due to thermal fluctuations of the DNA structure were confirmed. We found significant differences in electronic coupling at the dimer level between a non-modified DNA:DNA duplex and the corresponding duplex containing one fully LNA-substituted strand. We rationalized these differences by very dissimilar overlap in the pi-stack as a consequence of the LNA-modified system approximating an A-DNA-type helix. The calculated coupling elements for the non-modified reference duplex were similar to those of standard B-DNA and those for the fully modified oligomer resembled the matrix elements estimated for standard A-DNA.     

Electronic properties of thienylene vinylene oligomers: synthesis and theoretical study

(E)-1,2-bis(2-thienyl)vinylene (TV), (E)-1,2-bis(3-octyl-2-thienyl)vinylene (TOV), (E)-1,2-bis(3-(2-ethylhexyl)-2-thienyl)vinylene (T2EHV), and (E)-1,2-bis-[2,2??-bithienyl] vinylene (BTV) have been synthesized by a combination of formylation reaction and Mc Murry dimerization. UV?CVis spectra of BTV showed the longest wavelength absorption, TOV and T2EHV showed a bathochromic shift to the red compared with TV, due to an increment of delocalization of the conjugated ??-system as the result of the weakening of the carbon?Ccarbon double bonds of the thienyl rings due to the substitution of one hydrogen by the alkyl group. Based on optical data, the effect of linear and branched alkyl chain and extension of conjugation length on the electronic properties is discussed. ¹H, ¹³C-NMR, UV?CVisible, Fluorescence data are discussed and theoretical DFT and TD-DFT calculations of ground state and excited states have been also considered in the analysis and explanation of results.     

Solvation dynamics by coherence period resolved transient grating

We report a third-order nonlinear time-domain method, coherence period (τ) resolved transient grating (TRTG), that gives accurate solvation dynamics free from population relaxation in a short data acquisition time. The validity of TRTG is established by theory and experiment. The TRTG signal is shown to follow the transition frequency correlation function by an analytic expression based on the response function theory for delta function pulses and by model numerical calculations including finite pulse durations. TRTG is demonstrated for two cyanine dyes IR144 and IR125 in methanol by using a diffractive-optics based four wave mixing apparatus. Solvation dynamics in methanol obtained from the TRTG are consistent with those reported previously confirming the validity of TRTG.     

Structural properties of polystyrene oligomers in different environments: a molecular dynamics study

We have performed detailed molecular dynamics simulations to investigate the effects of solvation and confinement on the structure of polystyrene (PS) oligomers in four different environments, melt, concentrated solution, dilute solution and confined concentrated solution at 450 K and 1 bar, respectively. Local packing of the monomers and the solvent (toluene, good solvent) molecules were monitored by means of radial distribution functions (RDFs). We have also investigated bond, angle, and dihedral angle distributions of the monomers. End-to-end distances, radii of gyration and persistence lengths were calculated to characterize the static properties. The chain in the dilute solution was found to exhibit more stretched conformations. Dilution effect of the solvent was observed in the RDFs between the monomer centers. Only slight conformational changes in the polymers were observed by solvation. The effect of confinement was mainly seen in the density profiles, which showed an oscillatory behavior in the confined system.     

Electronic currents and Born-Oppenheimer molecular dynamics

Born-Oppenheimer variable separation is the mainstay of studies of chemical reactivity and dynamics. A long-standing problem of this ansatz is the absence of electronic currents in a system undergoing dynamics. I analyze the physical origin of the "missing" electronic currents in Born-Oppenheimer wavefunctions. By examining the problem within the multi-state Born-Huang ansatz, I demonstrate that electronic currents arise from the first-order non-adiabatic coupling to electronically excited states. I derive two expressions for the electronic currents induced by nuclear motion. The sum-over-the-states formula, identical to the result of "complete adiabatic" treatment of Nafie [J. Chem. Phys. 79, 4950 (1983)] leads to a transparent and intuitive physical picture of the induced currents, but is unsuitable for practical implementation in all but the simplest systems. The equivalent expression in terms of the electronic energy derivatives is straightforward to implement numerically. I present first applications of this approach to small systems of potential chemical interest.     

Electronic properties and reactivity of short-chain oligomers of 3,4-phenylenedioxythiophene (PheDOT)

The dimer and trimer of 3,4-phenylenedioxythiophene (PheDOT) have been synthesized. Unlike the parent systems based on 3,4-ethylenedioxythiophene (EDOT), these compounds are quite stable under atmospheric conditions. The electronic absorption spectra of di- and tri-PheDOT exhibit a well-resolved vibronic fine structure indicative of self-rigidification of the conjugated structure by noncovalent intramolecular sulfur-oxygen interactions. Comparison of UV-visible data for the PheDOT oligomers with those of the corresponding EDOT oligomers reveals a faster decrease of the HOMO-LUMO gap with chain length for the former. Cyclic voltammetric data show that whereas PheDOT oxidizes at a lower potential than EDOT, the PheDOT dimer and trimer exhibit much higher oxidation potentials than their EDOT-based analogues. A comparative analysis of the electropolymerization of the three PheDOT-based systems shows that although PheDOT is very difficult to polymerize, its dimer and trimer can be readily electropolymerized. This unexpected increase of reactivity with chain extension is discussed with the aid of theoretical calculations.     

Excited-State dynamics of conjugated polycarbosilane oligomers with branched dimethyl or diphenyl group

Dimethyl or diphenyl branched conjugated polycarbosilane oligomers in solutions, including poly[[1,4-bis(thiophenyl)buta-1,3-diyne]-alt-(dimethylsilane)], poly[[1,4-bis(thiophenyl)buta-1,3-diyne]-alt-(diphenylsilane)], poly[[1,4-bis(phenyl)buta-1,3-diyne]-alt-(dimethylsilane)], and poly[[1,4-bis(phenyl)buta-1,3-diyne]-alt-(diphenylsilane)], were investigated by steady-state and picosecond time-resolved spectroscopies to elucidate the effect of silicon-atom introduction into the π-conjugated copolymer backbone and the substitution of the aromatic phenyl group on the silicon atom. The introduction of silicon atoms into π-conjugated copolymer backbones induces slow decay emission components with lifetimes of about 450 ps in addition to π–π* local excited-state relaxations in the time-resolved fluorescence decay profiles. The diphenyls, which are branched in the silicon atoms, bring about broad, structureless emission bands in the low-frequency region of the steady-state fluorescence spectra. However, such broad bands do not occur in the case of dimethyl branched conjugated polycarbosilane oligomers. The time-resolved and solvent-dependent studies of these bands imply that the excited-state dynamics of diphenyl branched conjugated polycarbosilane oligomers can be related to an intramolecular charge-transfer dynamics through an inductive and (d-p) π-conjugation effect between the π-conjugated backbone and the branched phenyl ring. © 1999 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 37: 2901–2908, 1999     

Temperature-dependent tail-tail dynamics of pyrene-labeled poly(dimethylsiloxane) oligomers dissolved in ethyl acetate

We have determined the tail-tail dynamics and energetics of linear poly(dimethylsiloxane) (PDMS) polymers (M(n) = 3100; M(w)/M(n) = 1.07) that have been terminally labeled with pyrene (Py-PDMS-Py) in ethyl acetate between 255 and 323 K. The upper critical solution temperature (theta(u)) for the PDMS/ethyl acetate system is 278 K. The Py-PDMS-Py photophysics follow the Birks model at all of the temperatures studied. However, there is evidence for an increase in the local composition of PDMS surrounding the Py- residues in Py-PDMS-Py below the theta temperature. The recovered activation energy for Py-PDMS-Py tail-tail cyclization is the same as the activation energy for diffusion in ethyl acetate. The activation energy for cyclization is about fourfold larger in comparison to the barrier for PDMS internal backbone rotations. The estimated internal activation barrier for Py-PDMS-Py in ethyl acetate is in line with the internal barrier rotation for PDMS backbone rotation. The intramolecular excimer binding energy for Py-PDMS-Py in ethyl acetate is similar to the intermolecular pyrene excimer. In the ground state, the mean distance between the Py-PDMS-Py tail segments does not change over the temperature range studied. A comparison of these temperature-dependent Py-PDMS-Py/ethyl acetate results with previous results on Py-PDMS-Py in pure supercritical CO2 and CO2-dilated liquids shows that the addition of CO2 to the liquid phase offers the way to tune to Py-PDMS-Py tail-tail dynamics over the greatest range.     

Topological nature of intrinsic structural defects in a trans-polyacetylene chain

Using a topological approach, we consider the nature of intrinsic structural defects in a real trans-polyacetylene chain. We show that remnant cis segments are internal diaclination loops having two components: a wedge loop of strength ±/3 and a twist loop of strength , while defects of the soliton type are a combination of a point dislocation and an external twist disclination loop of strength .Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 25, No. 1, pp. 71–74, January–February, 1989.