Rationally seeded computational protein design of ɑ-helical barrels.

Computational protein design is advancing rapidly. Here we describe efficient routes starting from validated parallel and antiparallel peptide assemblies to design two families of α-helical barrel proteins with central channels that bind small molecules. Computational designs are seeded by the sequences and structures of defined de novo oligomeric barrel-forming peptides, and adjacent helices are connected by loop building. For targets with antiparallel helices, short loops are sufficient. However, targets with parallel helices require longer connectors; namely, an outer layer of helix-turn-helix-turn-helix motifs that are packed onto the barrels. Throughout these computational pipelines, residues that define open states of the barrels are maintained. This minimizes sequence sampling, accelerating the design process. For each of six targets, just two to six synthetic genes are made for expression in Escherichia coli. On average, 70% of these genes express to give soluble monomeric proteins that are fully characterized, including high-resolution structures for most targets that match the design models with high accuracy.

An expandable, modular de novo protein platform for precision redox engineering.

The electron-conducting circuitry of life represents an as-yet untapped resource of exquisite, nanoscale biomolecular engineering. Here, we report the characterization and structure of a de novo diheme "maquette" protein, 4D2, which we subsequently use to create an expanded, modular platform for heme protein design. A well-folded monoheme variant was created by computational redesign, which was then utilized for the experimental validation of continuum electrostatic redox potential calculations. This demonstrates how fundamental biophysical properties can be predicted and fine-tuned. 4D2 was then extended into a tetraheme helical bundle, representing a 7 nm molecular wire. Despite a molecular weight of only 24 kDa, electron cryomicroscopy illustrated a remarkable level of detail, indicating the positioning of the secondary structure and the heme cofactors. This robust, expressible, highly thermostable and readily designable modular platform presents a valuable resource for redox protein design and the future construction of artificial electron-conducting circuitry.

Probing the electronic structure and photophysics of thiophene-diketopyrrolopyrrole derivatives in solution.

Diketopyrrolopyrroles are a popular class of electron-withdrawing unit in optoelectronic materials. When combined with electron donating side-chain functional groups such as thiophenes, they form a very broad class of donor-acceptor molecules: thiophene-diketopyrrolopyrroles (TDPPs). Despite their widescale use in biosensors and photovoltaic materials, studies have yet to establish the important link between the electronic structure of the specific TDPP and the critical optical properties. To bridge this gap, ultrafast transient absorption with 22 fs time resolution has been used to explore the photophysics of three prototypical TDPP molecules: a monomer, dimer and polymer in solution. Interpretation of experimental data was assisted by a recent high-level theoretical study, and additional density functional theory calculations. These studies show that the photophysics of these molecular prototypes under visible photoexcitation are determined by just two excited electronic states, having very different electronic characters (one is optically bright, the other dark), their relative energetic ordering and the timescales for internal conversion from one to the other and/or to the ground state. The underlying difference in electronic structure alters the branching between these excited states and their associated dynamics. In turn, these factors dictate the fluorescence quantum yields, which are shown to vary by ∼1-2 orders of magnitude across the TDPP prototypes investigated here. The fast non-radiative transfer of molecules from the bright to dark states is mediated by conical intersections. Remarkably, wavepacket signals in the measured transient absorption data carry signatures of the nuclear motions that enable mixing of the electronic-nuclear wavefunction and facilitate non-adiabatic coupling between the bright and dark states.

Singlet and Triplet Contributions to the Excited-State Activities of Dihydrophenazine, Phenoxazine, and Phenothiazine Organocatalysts Used in Atom Transfer Radical Polymerization.

The photochemical dynamics of three classes of organic photoredox catalysts employed in organocatalyzed atom-transfer radical polymerization (O-ATRP) are studied using time-resolved optical transient absorption and fluorescence spectroscopy. The nine catalysts selected for study are examples of N-aryl and core-substituted dihydrophenazine, phenoxazine and phenothiazine compounds with varying propensities for control of polymerization outcomes. Excited singlet-state lifetimes extracted from the spectroscopic measurements are reported in N,N-dimethylformamide (DMF), dichloromethane (DCM), and toluene. Ultrafast (<200 fs to 3 ps) electronic relaxation of the photocatalysts after photoexcitation at near-UV wavelengths (318-390 nm) populates the first singlet excited state (S1). The S1-state lifetimes range from 130 ps to 40 ns with a considerable dependence on the photocatalyst structure and the solvent. The competition between ground electronic state recovery and intersystem crossing controls triplet state populations and is a minor pathway in the dihydrophenazine derivatives but is of greater importance for phenoxazine and phenothiazine catalysts. A comparison of our results with previously reported O-ATRP performances of the various photoredox catalysts shows that high triplet-state quantum yields are not a prerequisite for controlling polymer dispersity. For example, the photocatalyst 5,10-bis(4-cyanophenyl)-5,10-dihydrophenazine, shown previously to exert good polymerization control, possesses the shortest S1-state lifetime (135 ps in DMF and 180 ps in N,N-dimethylacetamide) among the nine examples reported here and a negligible triplet-state quantum yield. The results call for a re-evaluation of the excited-state properties of most significance in governing the photocatalytic behavior of organic photoredox catalysts in O-ATRP reactions.

Photosynthesis and crop productivity are enhanced by glucose-functionalised carbon dots.

From global food security to textile production and biofuels, the demands currently made on plant photosynthetic productivity will continue to increase. Enhancing photosynthesis using designer, green and sustainable materials offers an attractive alternative to current genetic-based strategies and promising work with nanomaterials has recently started to emerge. Here we describe the in planta use of carbon-based nanoparticles produced by low-cost renewable routes that are bioavailable to mature plants. Uptake of these functionalised nanoparticles directly from the soil improves photosynthesis and also increases crop production. We show for the first time that glucose functionalisation enhances nanoparticle uptake, photoprotection and pigment production, unlocking enhanced yields. This was demonstrated in Triticum aestivum 'Apogee' (dwarf bread wheat) and resulted in an 18% increase in grain yield. This establishes the viability of a functional nanomaterial to augment photosynthesis as a route to increased crop productivity.

Exploring ultraviolet photoinduced charge-transfer dynamics in a model dinucleotide of guanine and thymine.

An understanding of the initial photoexcited states of DNA is essential to unravelling deleterious photoinduced chemical reactions and the intrinsic ultrafast photoprotection of the genetic code for all life. In our combined experimental and theoretical study, we have elucidated the primary non-radiative relaxation dynamics of a model nucleotide of guanine and thymine (2'-deoxyguanosine 3'-monophosphate 5'-thymidine, d(GpT)) in buffered aqueous solution. Experimentally, we unequivocally demonstrate that the Franck-Condon excited states of d(GpT) are significantly delocalised across both nucleobases, and mediate d(G+pT-) exciplex product formation on an ultrafast (<350 fs) timescale. Theoretical studies show that the nature of the vertical excited states is very dependent on the specific geometry of the dinucleotide, and dictate the degree of delocalised, charge-transfer or localised character. Our mechanism for prompt exciplex formation involves a rapid change in electronic structure and includes a diabatic surface crossing very close to the Franck-Condon region mediating fast d(G+pT-) formation. Exciplexes are quickly converted back to neutral ground state molecules on a ∼10 ps timescale with a high quantum yield, ensuring the photostability of the nucleotide sequence.

A Photoresponsive Stiff-Stilbene Ligand Fuels the Reversible Unfolding of G-Quadruplex DNA.

The polymorphic nature of G-quadruplex (G4) DNA structures points to a range of potential applications in nanodevices and an opportunity to control G4 in biological settings. Light is an attractive means for the regulation of oligonucleotide structure as it can be delivered with high spatiotemporal precision. However, surprisingly little attention has been devoted towards the development of ligands for G4 that allow photoregulation of G4 folding. We report a novel G4-binding chemotype derived from stiff-stilbene. Surprisingly however, whilst the ligand induces high stabilization in the potassium form of human telomeric DNA, it causes the unfolding of the same G4 sequence in sodium buffer. This effect can be reversed on demand by irradiation with 400 nm light through deactivation of the ligand by photo-oxidation. By fuelling the system with the photolabile ligand, the conformation of G4 DNA was switched five times.

Molecular Photofragmentation Dynamics in the Gas and Condensed Phases.

Exciting a molecule with an ultraviolet photon often leads to bond fission, but the final outcome of the bond cleavage is typically both molecule and phase dependent. The photodissociation of an isolated gas-phase molecule can be viewed as a closed system: Energy and momentum are conserved, and the fragmentation is irreversible. The same is not true in a solution-phase photodissociation process. Solvent interactions may dissipate some of the photoexcitation energy prior to bond fission and will dissipate any excess energy partitioned into the dissociation products. Products that have no analog in the corresponding gas-phase study may arise by, for example, geminate recombination. Here, we illustrate the extent to which dynamical insights from gas-phase studies can inform our understanding of the corresponding solution-phase photochemistry and how, in the specific case of photoinduced ring-opening reactions, solution-phase studies can in some cases reveal dynamical insights more clearly than the corresponding gas-phase study.

Correlating the motion of electrons and nuclei with two-dimensional electronic-vibrational spectroscopy.

Multidimensional nonlinear spectroscopy, in the electronic and vibrational regimes, has reached maturity. To date, no experimental technique has combined the advantages of 2D electronic spectroscopy and 2D infrared spectroscopy, monitoring the evolution of the electronic and nuclear degrees of freedom simultaneously. The interplay and coupling between the electronic state and vibrational manifold is fundamental to understanding ensuing nonradiative pathways, especially those that involve conical intersections. We have developed a new experimental technique that is capable of correlating the electronic and vibrational degrees of freedom: 2D electronic-vibrational spectroscopy (2D-EV). We apply this new technique to the study of the 4-(di-cyanomethylene)-2-methyl-6-p-(dimethylamino)styryl-4H-pyran (DCM) laser dye in deuterated dimethyl sulfoxide and its excited state relaxation pathways. From 2D-EV spectra, we elucidate a ballistic mechanism on the excited state potential energy surface whereby molecules are almost instantaneously projected uphill in energy toward a transition state between locally excited and charge-transfer states, as evidenced by a rapid blue shift on the electronic axis of our 2D-EV spectra. The change in minimum energy structure in this excited state nonradiative crossing is evident as the central frequency of a specific vibrational mode changes on a many-picoseconds timescale. The underlying electronic dynamics, which occur on the hundreds of femtoseconds timescale, drive the far slower ensuing nuclear motions on the excited state potential surface, and serve as a excellent illustration for the unprecedented detail that 2D-EV will afford to photochemical reaction dynamics.

A method for the direct measurement of electronic site populations in a molecular aggregate using two-dimensional electronic-vibrational spectroscopy.

Two dimensional electronic spectroscopy has proved to be a valuable experimental technique to reveal electronic excitation dynamics in photosynthetic pigment-protein complexes, nanoscale semiconductors, organic photovoltaic materials, and many other types of systems. It does not, however, provide direct information concerning the spatial structure and dynamics of excitons. 2D infrared spectroscopy has become a widely used tool for studying structural dynamics but is incapable of directly providing information concerning electronic excited states. 2D electronic-vibrational (2DEV) spectroscopy provides a link between these domains, directly connecting the electronic excitation with the vibrational structure of the system under study. In this work, we derive response functions for the 2DEV spectrum of a molecular dimer and propose a method by which 2DEV spectra could be used to directly measure the electronic site populations as a function of time following the initial electronic excitation. We present results from the response function simulations which show that our proposed approach is substantially valid. This method provides, to our knowledge, the first direct experimental method for measuring the electronic excited state dynamics in the spatial domain, on the molecular scale.

Determining the static electronic and vibrational energy correlations via two-dimensional electronic-vibrational spectroscopy.

Changes in the electronic structure of pigments in protein environments and of polar molecules in solution inevitably induce a re-adaption of molecular nuclear structure. Both changes of electronic and vibrational energies can be probed with visible or infrared lasers, such as two-dimensional electronic spectroscopy or vibrational spectroscopy. The extent to which the two changes are correlated remains elusive. The recent demonstration of two-dimensional electronic-vibrational (2DEV) spectroscopy potentially enables a direct measurement of this correlation experimentally. However, it has hitherto been unclear how to characterize the correlation from the spectra. In this paper, we present a theoretical formalism to demonstrate the slope of the nodal line between the excited state absorption and ground state bleach peaks in the spectra as a characterization of the correlation between electronic and vibrational transition energies. We also show the dynamics of the nodal line slope is correlated to the vibrational spectral dynamics. Additionally, we demonstrate the fundamental 2DEV spectral line-shape of a monomer with newly developed response functions.

Measuring correlated electronic and vibrational spectral dynamics using line shapes in two-dimensional electronic-vibrational spectroscopy.

Two-dimensional electronic-vibrational (2DEV) spectroscopy is an experimental technique that shows great promise in its ability to provide detailed information concerning the interactions between the electronic and vibrational degrees of freedom in molecular systems. The physical quantities 2DEV is particularly suited for measuring have not yet been fully determined, nor how these effects manifest in the spectra. In this work, we investigate the use of the center line slope of a peak in a 2DEV spectrum as a measure of both the dynamic and static correlations between the electronic and vibrational states of a dye molecule in solution. We show how this center line slope is directly related to the solvation correlation function for the vibrational degrees of freedom. We also demonstrate how the strength with which the vibration on the electronic excited state couples to its bath can be extracted from a set of 2DEV spectra. These analytical techniques are then applied to experimental data from the laser dye 3,3'-diethylthiatricarbocyanine iodide in deuterated chloroform, where we determine the lifetime of the correlation between the electronic transition frequency and the transition frequency for the backbone C = C stretch mode to be ∼1.7 ps. Furthermore, we find that on the electronic excited state, this mode couples to the bath ∼1.5 times more strongly than on the electronic ground state.

Unraveling the Photoionization Dynamics of Indole in Aqueous and Ethanol Solutions.

The photoionization dynamics of indole, the ultraviolet-B chromophore of tryptophan, were explored in water and ethanol using ultrafast transient absorption spectroscopy with 292, 268, and 200 nm excitation. By studying the femtosecond-to-nanosecond dynamics of indole in two different solvents, a new photophysical model has been generated that explains many previously unsolved facets of indole's complex solution phase photochemistry. Photoionization is only an active pathway for indole in aqueous solution, leading to a reduction in the fluorescence quantum yield in water-rich environments, which is frequently used in biophysical experiments as a key signature of the protein-folded state. Photoionization of indole in aqueous solution was observed for all three pump wavelengths but via two different mechanisms. For 200 nm excitation, electrons are ballistically ejected directly into the bulk solvent. Conversely, 292 and 268 nm excitation populates an admixture of two 1ππ* states, which form a dynamic equilibrium with a tightly bound indole cation and electron-ion pair. The ion pair dissociates on a nanosecond time scale, generating separated solvated electrons and indole cations. The charged species serve as important precursors to triplet indole production and greatly enhance the overall intersystem crossing rate. Our proposed photophysical model for indole in aqueous solution is the most appropriate for describing photoinduced dynamics of tryptophan in polypeptide sequences; tryptophan in aqueous pH 7 solution is zwitterionic, unlike in peptides, and resultantly has a competitive excited state proton transfer pathway that quenches the tryptophan fluorescence.

Comparing molecular photofragmentation dynamics in the gas and liquid phases.

This article explores the extent to which insights gleaned from detailed studies of molecular photodissociations in the gas phase (i.e. under isolated molecule conditions) can inform our understanding of the corresponding photofragmentation processes in solution. Systems selected for comparison include a thiophenol (p-methylthiophenol), a thioanisole (p-methylthioanisole) and phenol, in vacuum and in cyclohexane solution. UV excitation in the gas phase results in RX-Y (X = O, S; Y = H, CH3) bond fission in all cases, but over timescales that vary by ~4 orders of magnitude - all of which behaviours can be rationalised on the basis of the relevant bound and dissociative excited state potential energy surfaces (PESs) accessed by UV photoexcitation, and of the conical intersections that facilitate radiationless transfer between these PESs. Time-resolved UV pump-broadband UV/visible probe and/or UV pump-broadband IR probe studies of the corresponding systems in cyclohexane solution reveal additional processes that are unique to the condensed phase. Thus, for example, the data clearly reveal evidence of (i) vibrational relaxation of the photoexcited molecules prior to their dissociation and of the radical fragments formed upon X-Y bond fission, and (ii) geminate recombination of the RX and Y products (leading to reformation of the ground state parent and/or isomeric adducts). Nonetheless, the data also show that, in each case, the characteristics (and the timescale) of the initial bond fission process that occurs under isolated molecule conditions are barely changed by the presence of a weakly interacting solvent like cyclohexane. These condensed phase studies are then extended to an ether analogue of phenol (allyl phenyl ether), wherein UV photo-induced RO-allyl bond fission constitutes the first step of a photo-Claisen rearrangement.

Exploring the energy disposal immediately after bond-breaking in solution: the wavelength-dependent excited state dissociation pathways of para-methylthiophenol.

A wavelength-resolved (λpump = 295, 285, 270, and 267 nm) photodissociation study of para-methylthiophenol (p-MePhSH) in ethanol solution has been performed using femtosecond transient absorption (TA) spectroscopy, and the results compared with those from studies of the corresponding photodissociation in cyclohexane solution at 270 nm. Anisotropy spectra are used to identify the electronic character of the initially populated excited state(s). S-H bond fission is found to occur via the dissociative S2(1(1)πσ*) state, which can be populated directly, or by ultrafast nonradiative transitions from the S3(2(1)ππ*) state, or by very efficient tunneling from the S1(1(1)ππ*) state, depending on the excitation wavelength, in line with conclusions from previous gas-phase studies of this same molecular photodissociation (Oliver, T. A. A.; King, G. A.; Tew, D. P.; Dixon R. N.; Ashfold, M. N. R. J. Phys. Chem. A 2012, 116, 12444). p-MePhS radicals are observed on a time scale faster than the instrument response at all wavelengths, but the available time resolution affords a rare opportunity to explore the branching between different electronic states of a product (the à and X̃ states of the p-MePhS radical in this case). The present study provides estimates of this branching in the products formed immediately after the first pass through the conical intersection (CI) between the S2 and S0 states. At 270 nm, for example, we identify a marked population inversion in the radical products, in contrast to the reported gas phase behavior. The finding that the contrast in branching ratio is largest between cyclohexane solution and the gas phase, with ethanol being intermediate, can be rationalized by recognizing the differing distributions of the S-H torsion angle (relative to the ring plane) in a room temperature solution compared with those in a jet-cooled molecular beam. The available time resolution also allows exploration of the electronic quenching of nascent à state radicals as solvent motion encourages recrossing of the S2/S0 CI. The average separation distance, , between the H + p-MePhS products arising in successful dissociation events is seen to increase with decreasing photolysis wavelength. This finding accords with the previous gas phase results, which determined that most of the excess energy following population of the dissociative S2 state (directly, or by ultrafast coupling from the S3 state) is released as product translation, and the expectation that should scale with the total kinetic energy release. The present work also confirms that geminate recombination of the H + p-MePhS products leads not just to reformation of parent p-MePhSH molecules but also to alternative adducts wherein the H atom bonds to the benzene ring. Analysis of the present data and results of high level ab initio calculations together with recent UV-IR pump-probe measurements (Murdock, D.; Harris, S. J.; Karsili, T. N. V.; Greetham, G. M.; Clark, I. P.; Towrie, M.; Orr-Ewing, A. J.; Ashfold, M. N. R. J. Phys. Chem. Lett. 2012, 3, 3715) allows identification of the likely adduct structures.

Vibronically induced decay paths from the C̃1B1-state of water and its isotopomers.

The photochemistry of the water molecule has revealed a wealth of quantum phenomena, which arise from the involvement of several coupled electronic states with very different potential energy surfaces. Most recently, dissociation from single rotational levels of its C̃(1)B1 state near 124 nm has been attributed to a vibronically coupled decay via the lower Ã-state surface, despite a large vertical energy gap of 2.8 eV. Similar conclusions have been reached for subsequent experimental data for D2O. The present paper presents further experimental data for HOD and for both the H+OD(X) and D+OH(X) products. Unlike the cases for H2O and D2O, the vibrational populations for hydroxyl products do not follow a smooth distribution with v(OH∕OD). In particular, for OH there is a clear alternation in population for all the strong peaks, with odd v favoured over even v. These experimental data are analysed using new MRCI+Q calculations, which have been used to generate potential surfaces and associated non-adiabatic matrix elements for transition from the adiabatic C̃-state to lower unbound potential surfaces; and hence, to guide dynamical calculations using time-dependent wavepackets. It is concluded that although there is a minor contribution from the C̃→ à decay route, the major route follows C̃→ (1)A2 → Ã. This is mediated through two regions of near degeneracy of the elusive (1)A2 surface with C̃ for short bonds ca. 0.8 Å; and between (1)A2 and à with long bonds ≥2 Å, thereby bridging the vertical energy gap. The striking population alternation for the D+OH(X) products is attributed to dynamic symmetry breaking on the (1)A2 surface.