Coherent dynamics of photoexcited green fluorescent proteins

The coherent dynamics of vibronic wave packets in the green fluorescent protein is reported. At room temperature the nonstationary dynamics following impulsive photoexcitation displays an oscillating optical transmissivity pattern with components at 67 fs (497 cm(-1)) and 59 fs (593 cm(-1)). Our results are complemented by ab initio calculations of the vibrational spectrum of the chromophore. This analysis shows the interplay between the dynamics of the aminoacidic structure and the electronic excitation in the primary optical events of green fluorescent proteins.     

Fine-structure fluorescence of conjugated chain molecules

The fine-structure fluorescence spectra of conjugated chain compounds—distyrylbenzene (DSB), its fluorine-substituted derivative (FDSB), 1,4-bis-(5-phenyl-2-oxazolyl) benzene (POPOP), and 1,4-bis-(5-phenyl-2-oxadiazolyl) benzene (PDPDP)—are obtained at 4.2 K using the Shpolskii method. The multiplicity of the spectra is revealed and their vibrational analysis is performed involving Raman scattering data. It is shown that some vibrational frequencies of the fluorescence spectra are common for all the molecules under study, while other frequencies are specific for the spectra of the pairs DSB-FDSB and POPOP-PDPDP. The relation between the spectra of the molecules and their structure is considered.     

Third-order optical polarizability of conjugated organic molecules

We present a theoretical investigation of the π-electron contribution to linear and non-linear polarizabilities of conjugated chains. Using simple models the respective influence of chain length and bond alternation on optical non-linearities are analyzed. The results are applied to symmetrical cyanines and polyenes.     

On the magnetic properties of conjugated molecules

Recent criticisms of the gauge factors usually employed in the ‘test-dipole’ method for the calculation of ‘ring current’ chemical shifts in conjugated molecules, are discussed. It is shown that, in a simple semi-empirical scheme of the London-McWeeny type, insertion of a dipole contribution into the vector potential appearing in the gauge factor, whilst having no effect on the calculated ‘ring current’ intensities, is algebraically analogous (and, at large distances from ring centres, numerically equivalent) to estimating the secondary field at the origin due to a set of classical line currents, as discussed originally by Salem; these ‘line currents’ are of the same magnitude as the quantum-mechanical ‘bond currents’ implicit in the ‘ring currents’ calculated using the simpler gauge factors originally due to London, but their contributions to the secondary magnetic field experienced by the peripheral protons, are estimated classically. Extensive numerical comparison is made between experimentally-observed proton chemical shifts in some conjugated hydrocarbons, and secondary fields estimated by this semi-classical formalism, and its predictions are found to correlate as well with experiment as do those of the original McWeeny approach. It is concluded that any further illegitimacy involved in the procedure of inserting a dipole contribution into the gauge factor, is evidently quite simply compensated for, numerically, by an appropriate empirical parametrization. Such empirical parametrizations are also thought to absorb errors due to all the other various approximations of the ‘ring current’ theories (with apparently unwarranted efficiency), and they should, therefore, be treated with more scepticism than has previously been thought necessary.     

On conjugated molecules with identical topological spectra

Properties of molecular graphs having identical topological spectra are investigated in some detail. It has been established that whole families of isospectral graphs can be derived from a molecular skeleton of vinyl benzene. A pair of isospectral graphs are obtained by an exchange of two non-equivalent residuals attached to particular sites of the skeleton. Additional pairs of isospectral graphs can be derived from related skeletons in which ortho positions of vinyl benzene are occupied by substituents. No constraints have to be imposed on the nature and form of the residuals or the substituting groups. This allows construction of larger isospectral systems including polymeric species. The theoretical foundation for the construction of isospectral graphs described in this work rests on the factorization of the eigenvalue problem of the adjacency matrix associated with molecular graphs which is analogous to a fragmentation of a secular determinant of a Hückel MO problem as outlined some time ago by Heilbronner. A formal proof of the procedure, expressed in a symbolic form, is presented in the Appendix. A discussion of some interesting features of isospectral systems reflected in special properties of topological eigenfunctions is presented.     

Geometry-dependent electronic properties of highly fluorescent conjugated molecules

We present a combined experimental/theoretical study of the electronic properties of conjugated para-phenylene type molecules under high pressure up to 80 kbar. Pressure is used as a tool to vary the molecular geometry and intermolecular interaction. The influence of the latter two on singlet and triplet excitons as well as polarons is monitored via optical spectroscopy. We have performed band structure calculations for the planar poly(para-phenylene) and calculated the dielectric function. By varying the intermolecular distances and the length of the polymer repeat unit the observed pressure effects can be explained.     

The calculation of chemical shifts in conjugated molecules

Within the context of pi-electron theory an expression for the proton chemical shifts in conjugated molecules is derived via a current density approach. Using London integral approximations the method is applied to benzene and naphthalene. Provided a particular form of the London Approximation is used, theoretical values in good agreement with experiment are obtained.     

Properties of the self-consistent field treatment of conjugated molecules

The polarizability properties of π electron systems are treated by the self-consistent field method, as modified by Pople for application to conjugated molecules. An analytical treatment of the π electron configuration of substituted hydrocarbons deduces certain universal symmetry properties of this method, and contains the Hückel treatment of inductive substituents as a simplified special case. Whereas the usual Hückel theory derives results by approximate perturbation methods, the treatment given here is formally exact. In a later section s.c.f. polarizability coefficients, as calculated on an Elliott 402 digital computer, are given for benzene, naphthalene, anthracene and phenanthrene, and the predictions of chemical properties are shown to be in better agreement with experiment than predictions derived from Hückel theory.     

Conformational dynamics of some short-chain biradicals in solutions

Intramolecular electron spin exchange, as a function of temperature and the solvent nature, has been studied by X-band electron paramagnetic resonance (EPR) spectroscopy in five short-chain flexible nitroxide biradicals. Certain thermodynamic parameters of the conformational rearrangements were calculated from the EPR spectra. The process of spin exchange in short flexible biradicals has some peculiarities in comparison with that in long-chain molecules.     

Exciton coherence and electron energy loss spectroscopy of conjugated molecules

Signatures of the exciton coherence size, which controls the nonlinear optical response and luminescence of conjugated systems, in the electronic dynamic structure factor S(q,omega) are calculated. We find that for small molecules the momentum dependence of the lowest exciton resonance is purely geometric, reflecting the molecular size rather than a universal exciton size, as suggested recently. For long chains the q dependence is determined by the interplay of the exciton size and the bond-alternation length scales.     

Orbital-dependent charge transfer dynamics in conjugated self-assembled monolayers

Femtosecond charge transfer (CT) dynamics in a series of self-assembled monolayers with an oligo(phenylenethynylene) and oligo(phenyl) backbone is addressed by resonant Auger spectroscopy using the core hole clock method. The characteristic CT times are found to depend strongly on the character of the molecular orbital (MO) which mediates the CT process. This demonstrates that the efficiency and rate of CT through molecular frameworks can be controlled by resonant injection of the charge carriers into specific MOs.     

Single- and multigrain nanojunctions with a self-assembled monolayer of conjugated molecules

Systematic conductivity measurements in nanoscale junctions containing a self-assembled monolayer of conjugated molecules are reported. Different conductivity mechanisms are identified depending on the granularity of the metal used as a substrate for assembling the monolayer. Unexpectedly, the energy scale controlling the dominant conductance channels is quite low in comparison with the molecular level spacing. In single-grain junctions, the dominant conductance mechanism is hopping with an energy scale of the order of 10-100 meV determined by the nature of the metal contacts. In the case of multigrain junctions, additional tunnel conductance is observed with low-energy Coulomb-blockade features.     

Conformational dynamics of triradical nitroxides as studied by EPR

The EPR spectra of a flexible nitroxide triradical are recorded in a large temperature range. A detailed analysis of the spectral features is performed and the spectra are compared with computer simulations. An excellent agreement with the experimental spectra is obtained by using a dynamic model based on the conformation interconversion of different molecular structures, characterized by the electron exchange interactions between pairs of free radicals. The energy barrier for the interconversion process and the temperature variation of the constant for the equilibrium among the conformations have been obtained. The results show that EPR spectra of nitroxide triradicals spin labelled polymers could be of valuable use for studying subtle details of molecular dynamics.     

A new class of conjugated molecules with large second order polarizability

We report measurements of the second order polarizability β in a new class of conjugated molecules. A representative member of this class is H₃C-NC₅H₄-CH-CH-C₆H₄-O. The measured value of β, 10^-27 esu, for this molecule is larger than any other known value for molecules with the same length and number of π-electrons. We present a discussion of this high value in terms of resonating chemical structures and hyperconjugation.     

Preparation and medical application of magnetic beads conjugated with bioactive molecules

Ferrite nanobeads were synthesized from an aqueous solution utilizing Fe²⁺ to Fe³⁺ oxidation for use as magnetic carriers in bioscreening, bio-molecular recognition and anti-cancer diagnosis and therapy. The beads had a crystal structure that was intermediate between Fe₃O₄ and γ-Fe₂O₃. Functional biomolecules were strongly conjugated onto the surfaces of the ferrite beads via COOH and SH groups. The addition of ferrite seed crystals (3-8 nm in size) together with a disaccharide enabled the synthesis of monodisperse, spherical ferrite beads with average diameters (d¯) between 50 and 150 nm and relative deviation Δd/d¯=9-16%. Hollow ferrite nano-spheres (d¯=150-450 nm, Δd/d¯≈10%) were prepared using silica spheres as templates, which were dissolved in NaOH solution. Ferrite beads 40 nm in size were encapsulated in polymer spheres of styrene and polymerized glycidyl methacrylate (poly-GMA), 184±9 nm in diameter. They were used for high throughput bioscreening system for affinity purification of target proteins which make specific bindings to anti-cancer drugs, porphyrins, environment hormones, etc.     

Conformational dependence of tag induced intramolecular STM contrast in hexaphenylbenzene molecules

Chemically tagged hexaphenylbenzene molecules physisorbed on Au(1 1 1) surface display their tag differently under STM as compared to their physisorption on a Cu(1 1 1) surface. Our STM findings complemented by First Principles and Quantum Chemistry calculations have attributed this difference to two different conformations adopted by these molecules on Au(1 1 1) in comparison to its one conformation on Cu(1 1 1). The demonstration of the sensitivity of the tag to its electronic or chemical environment would have important implications in designing single molecule machinery where the motion of the molecule is to be discerned by tracking its tag induced intramolecular STM contrast.