Garth A. Jones

Chemically modulating the photophysics of the GFP chromophore.

There is growing interest in engineering the properties of fluorescent proteins through modifications to the chromophore structure utilizing mutagenesis with either natural or unnatural amino acids. This entails an understanding of the photophysical and photochemical properties of the modified chromophore. In this work, a range of GFP chromophores with different alkyl substituents are synthesized and their electronic spectra, pH dependence, and ultrafast fluorescence decay kinetics are investigated. The weakly electron donating character of the alkyl substituents leads to dramatic red shifts in the electronic spectra of the anions, which are accompanied by increased fluorescence decay times. This high sensitivity of electronic structure to substitution is also characteristic of some fluorescent proteins. The solvent viscosity dependence of the decay kinetics are investigated, and found to be consistent with a bimodal radiationless relaxation coordinate. Some substituents are shown to distort the planar structure of the chromophore, which results in a blue shift in the electronic spectra and a strong enhancement of the radiationless decay. The significance of these data for the rational design of novel fluorescent proteins is discussed.

What Is Adenine Doing in Photolyase

The short answer to the title question is that it acts as an electrostatic bouncer that shoves the charge flow from flavin toward the DNA lesion that photolyase repairs. This explanation is provided by an explicit time-dependent quantum mechanical approach, which is used to investigate the electron transfer process that triggers the repair mechanism. The transfer occurs from the flavin photolyase cofactor to the cyclobutane ring of DNA, previously formed by light-induced cycloaddition of adjacent pyrimidine bases. The electron wave function dynamics accurately accounts for the previously proposed mechanism of transfer via the terminal methyl group of the flavin moiety present in the catalytic electron-donor cofactor, FADH(-), which also contains adenine. This latter moiety, which has often been assumed to be present mainly for structural reasons, instantaneously modifies the interaction between acceptor and donor by a variation of the electrostatic interactions so that the presence of its local atomic charges is necessary to trigger the transfer. In principle, knowledge of the details of the electron transfer dynamics and of the important role of polarization effects can be exploited to improve the efficiency of the repair mechanism in artificial systems.

On-the-Fly, Electric-Field-Driven, Coupled Electron-Nuclear Dynamics

An on-the-fly, electric field driven, coupled electron-nuclear dynamics approach is developed and applied to model the photodissociation of water in the A((1)B1) excited state. In this method, a quantum propagator evolves the photon-induced electronic dynamics in the ultrafast time scale, and a quasi-classical surface hopping approach describes the nuclear dynamics in the slower time scale. In addition, strong system-field interactions are explicitly included in the electronic propagator. This theoretical development enables us to study rapid photon-induced bond dissociation dynamics and demonstrates the partial breakdown of electronic coherence as well as electronic population trapping in the excited state when the molecular vibrations detune the system with respect to the applied field. The method offers a practical way to use on-the-fly dynamics for modeling light-molecule interactions that lead to interesting photochemical events.

Tyrosyl radicals in proteins: a comparison of empirical and density functional calculated EPR parameters.

Finding the exact location of a tyrosyl radical in an enzyme is an important step in elucidating the enzymes mechanism. Although the electron paramagnetic resonance (EPR) spectrum of a tyrosyl radical strongly depends on the radicals conformation and environment, no methodology is available for locating the tyrosine residue responsible for the spectrum solely on the basis of the crystal structure of an enzyme. A method of predicting tyrosyl radical EPR spectra from first principles should encompass a computational methodology that yields a close correlation between the calculated and empirically obtained EPR parameters. An approach is developed that allows a clear comparison of these two groups of parameters on an array of different tyrosyl radicals. The B3LYP density functional method is used to calculate the EPR parameters (spin densities and g- and A-tensors) for tyrosyl radicals of four different enzymes. The calculated EPR parameters are compared to those derived from empirical data by an algorithm. The results of the DFT calculations are found to be in good agreement with the principal dependences employed by the algorithm. However, the calculated EPR parameters do not correlate with empirical data on the whole set of the four radicals studied. The correlation is significantly improved when hydrogen bonds to the radical are formed, both in the case of the protein radicals and in a radical model, when hydrogen bonds to the radical are formed. Therefore, it is suggested that a full correlation between the calculated and the algorithm-derived empirical EPR parameters might be achieved when water molecules are included in the calculation model.

Ultrafast Dynamics in Light-Driven Molecular Rotary Motors Probed by Femtosecond Stimulated Raman Spectroscopy

Photochemical isomerization in sterically crowded chiral alkenes is the driving force for molecular rotary motors in nanoscale machines. Here the excited-state dynamics and structural evolution of the prototypical light-driven rotary motor are followed on the ultrafast time scale by femtosecond stimulated Raman spectroscopy (FSRS) and transient absorption (TA). TA reveals a sub-100-fs blue shift and decay of the Franck-Condon bright state arising from relaxation along the reactive potential energy surface. The decay is accompanied by coherently excited vibrational dynamics which survive the excited-state structural evolution. The ultrafast Franck-Condon bright state relaxes to a dark excited state, which FSRS reveals to have a rich spectrum compared to the electronic ground state, with the most intense Raman-active modes shifted to significantly lower wavenumber. This is discussed in terms of a reduced bond order of the central bridging bond and overall weakening of bonds in the dark state, which is supported by electronic structure calculations. The observed evolution in the FSRS spectrum is assigned to vibrational cooling accompanied by partitioning of the dark state between the product isomer and the original ground state. Formation of the product isomer is observed in real time by FSRS. It is formed vibrationally hot and cools over several picoseconds, completing the characterization of the light-driven half of the photocycle.

Excitation Energy Transfer and Low-Efficiency Photolytic Splitting of Water Ice by Vacuum UV Light

Experimental estimates of photolytic efficiency (yield per photon) for photodissociation and photodesorption from water ice range from about 10(-3) to 10(-1). However, in the case of photodissociation of water in the gas phase, it is close to unity. Exciton dynamics carried out by a quantum mechanical time-dependent propagator shows that in the eight most stable water hexamers, the excitation diffuses away from the initially excited molecule within a few femtoseconds. On the basis of these quantum dynamics simulations, it is hypothesized that the ultrafast exciton energy transfer process, which in general gives rise to a delocalized exciton within these clusters, may contribute to the low efficiency of photolytic processes in water ice. It is proposed that exciton diffusion inherently competes with the nuclear dynamics that drives the photodissociation process in the repulsive S1 state on the sub-10 fs time scale.

Perspective: Quantum Hamiltonians for optical interactions

The multipolar Hamiltonian of quantum electrodynamics is extensively employed in chemical and optical physics to treat rigorously the interaction of electromagnetic fields with matter. It is also widely used to evaluate intermolecular interactions. The multipolar version of the Hamiltonian is commonly obtained by carrying out a unitary transformation of the Coulomb gauge Hamiltonian that goes by the name of Power-Zienau-Woolley (PZW). Not only does the formulation provide excellent agreement with experiment, and versatility in its predictive ability, but also superior physical insight. Recently, the foundations and validity of the PZW Hamiltonian have been questioned, raising a concern over issues of gauge transformation and invariance, and whether observable quantities obtained from unitarily equivalent Hamiltonians are identical. Here, an in-depth analysis of theoretical foundations clarifies the issues and enables misconceptions to be identified. Claims of non-physicality are refuted: the PZW transformation and ensuing Hamiltonian are shown to rest on solid physical principles and secure theoretical ground.

On the nature of long range electronic coupling in a medium: Distance and orientational dependence for chromophores in molecular aggregates

The electronic coupling that mediates energy transfer in molecular aggregates is theoretically investigated using the principles of quantum electrodynamics (QED). In this context, both the electromagnetic tensor and rate equation relating to these couplings are re-examined with a focus on the role of the relative distance and orientation of transition dipole moment pairs, considering near-, intermediate-, and far-zone contributions to the coupling. The QED based coupling terms are investigated both analytically and numerically, and they are physically interpreted in terms of the character of the mediating (virtual) photons. The spatial dependence of the couplings for a two-dimensional molecular aggregate of ordered and isotropic transition dipole moments is numerically calculated. Further, Pauli Master Equations are employed for a one-dimensional chain of molecules and donor-acceptor pairs, to investigate the importance of intermediate- and far-zone contributions to the electronic coupling on electronic energy transfer dynamics. The results indicate that although Förster theory is often qualitatively and quantitatively correct for describing electronic energy transfer (EET) processes, intermediate- and far-zone coupling terms could sometimes be non-negligible for correctly describing EET in natural and artificial, mesoscopic, solar energy harvesting systems. In particular, the results indicate that these terms are non-negligible when using Förster resonance energy transfer spectroscopic ruler techniques for distances >10 nm.

A quantum dynamical comparison of the electronic couplings derived from quantum electrodynamics and Förster theory: application to 2D molecular aggregates

The objective of this study is to investigate under what circumstances Forster theory of electronic (resonance) energy transfer breaks down in molecular aggregates. This is achieved by simulating the dynamics of exciton diffusion, on the femtosecond timescale, in molecular aggregates using the Liouville–von Neumann equation of motion. Specifically the focus of this work is the investigation of both spatial and temporal deviations between exciton dynamics driven by electronic couplings calculated from Forster theory and those calculated from quantum electrodynamics. The quantum electrodynamics (QED) derived couplings contain medium- and far-zone terms that do not exist in Forster theory. The results of the simulations indicate that Forster coupling is valid when the dipole centres are within a few nanometres of one another. However, as the distance between the dipole centres increases from 2 nm to 10 nm, the intermediate- and far-zone coupling terms play non-negligible roles and Forster theory begins to break down. Interestingly, the simulations illustrate how contributions to the exciton dynamics from the intermediate- and far-zone coupling terms of QED are quickly washed-out by the near-zone mechanism of Forster theory for lattices comprising closely packed molecules. On the other hand, in the case of sparsely packed arrays, the exciton dynamics resulting from the different theories diverge within the 100 fs lifetime of the trajectories. These results could have implications for the application of spectroscopic ruler techniques as well as design principles relating to energy harvesting materials.

Resonance energy transfer: The unified theory via vector spherical harmonics

In this work, we derive the well-established expression for the quantum amplitude associated with the resonance energy transfer (RET) process between a pair of molecules that are beyond wavefunction overlap. The novelty of this work is that the field of the mediating photon is described in terms of a spherical wave rather than a plane wave. The angular components of the field are constructed in terms of vector spherical harmonics while Hankel functions are used to define the radial component. This approach alleviates the problem of having to select physically correct solution from non-physical solutions, which seems to be inherent in plane wave derivations. The spherical coordinate system allows one to easily decompose the photons fields into longitudinal and transverse components and offers a natural way to analyse near-, intermediate-, and far-zone RET within the context of the relative orientation of the transition dipole moments for the two molecules.