The influence of hindered rotation on electron transfer and exchange interaction in triarylamine-triptycene-perylene diimide triads.

Stretched electron-donor-bridge-acceptor triads that exhibit intramolecular twisting degrees of freedom are capable of modulating exchange interaction (J) as well as electronic couplings through variable π-overlap at the linear bond links, affecting the rate constants of photoinduced charge separation and recombination. Here we present an in-depth investigation of such effects induced by methyl substituents leading to controlled steric hindrance of intramolecular twisting around biaryl axes. Starting from the parent structure, consisting of a triphenyl amine donor, a triptycene (TTC) bridge and a phenylene-perylene diimide acceptor (Me0), one of the two phenylene linkers attached to the TTC was ortho-substituted by two methyl groups (Me2, Me3), or both such phenylene linkers by two pairs of methyl groups (Me23). Photoinduced charge separation (kCS) leading to a charge-separated (CS) state was studied by fs-laser spectroscopy, charge recombination to either singlet ground state (kS) or to the first excited local triplet state of the acceptor (kT) by ns-laser spectroscopy, whereby kinetic magnetic field effects in an external magnetic field were recorded and analysed using quantum dynamic simulations of the spin dependent kinetics of the CS state. Kinetic spectra of the initial first order rate constants of charge recombination (k(B)) exhibited characteristic J-resonances progressing to lower fields in the series Me0, Me2, Me3, Me23. From the quantum simulations, the values of the parameters J, kS, kT and kSTD, the singlet/triplet dephasing constant, were obtained. They were analysed in terms of molecular dynamics simulations of the intramolecular twisting dynamics based on potentials calculated by density functional theory. Apart from kT, all of the parameters exhibit a clear correlation with the averaged cosine square products of the biaryl angles.

Mapping 13C hyperfine couplings and exchange interactions in short-lived charge separated states of rigid donor-bridge-acceptor dyads.

A detailed experimental study on reversible photo-induced intramolecular charge separation is presented based on nuclear magnetic resonance detection of chemically induced dynamic nuclear polarization. From variation of such polarization with the external magnetic field, the coupling constants of isotropic and anisotropic hyperfine interactions at individual 13C sites are measured in the short-lived charge separated state of dyad molecules composed of donor-bridge-acceptor parts. The objects of study were rigid donor-bridge-acceptor dyads, consisting of triarylamine as a donor, naphthalene diimide as an acceptor, and a meta-conjugated diethynylbenzene fragment as a bridge. By systematic variation of side groups in the bridging moiety, their influence on the electron withdrawing strength is traced. In combination with similar data for the 1H positions obtained previously for the same compounds [I. Zhukov et al., J. Chem. Phys. 152, 014203 (2020)], our results provide a reliable basis for the determination of the spin density distribution in the charge separated state of such dyads.

Giant magnetic field effects in donor-acceptor triads: On the charge separation and recombination dynamics in triarylamine-naphthalenediimide triads with bis-diyprrinato-palladium(II), porphodimethenato-palladium(II), and palladium(II)-porphyrin photosensitizers.

A series of triads consisting of a triarylamine donor, a naphthalenediimide acceptor, and a palladium photosensitizer bridge was investigated for the photoinduced electron transfer processes and the spin chemistry involved. In this series, the ligand in the palladium photosensitizer was varied from bis-dipyrrinato to porphodimethenato and to a porphyrin. With the porphyrin photosensitizer, no charge separated state could be reached. This is caused by the direct relaxation of the excited photosensitizer to the ground state by intersystem crossing. The bis-dipyrrinato-palladium photosensitizer gave only a little yield (7%) of the charge separated state, which is due to the population of a metal centered triplet state and a concomitant geometrical rearrangement to a disphenoidal coordination sphere. This state relaxes rapidly to the ground state. In contrast, in the porphodimethenato-palladium triads, a long lived (µs to ms) charge separated state could be generated in high quantum yields (66%-74%) because, here, the population of a triplet metal centered state is inhibited by geometrical constraints. The magnetic field dependent transient absorption measurement of one of the porphodimethenato triads revealed a giant magnetic field effect by a factor of 26 on the signal amplitude of the charge separated state. This is the consequence of a magnetic field dependent triplet-singlet interconversion that inhibits the fast decay of the charge separated triplet state through the singlet recombination channel. A systematic comparative analysis of the spin-dependent kinetics in terms of three classical and one fully quantum theoretical methods is provided, shedding light on the pros and cons of each of them.

Magnetic field effects in rigidly linked D-A dyads: Extreme on-resonance quantum coherence effect on charge recombination.

Charge recombination in the photoinduced charge separated (CS) state of a rigidly linked donor/bridge/acceptor triad with a triarylamine (TAA) donor, a 1,3-diethynyl-2,5-dimethoxy benzene bridge (OMe), and a perylenediimide (PDI) unit as an acceptor, represents a spin chemical paradigm case of a rigid radical ion pair formed with singlet spin and recombining almost exclusively to the locally excited PDI triplet state (3PDI). The magnetic field dependence of the CS state decay and 3PDI formation kinetics are investigated from 0 to 1800 mT by nanosecond laser flash spectroscopy. The time-resolved magnetic field affected reaction yields spectra of the CS state population and 3PDI population exhibit a sharp and deep resonance at 18.9 mT, indicating level crossing of the S and T+ levels separated by an exchange interaction of J = 18.9/2 mT at zero field. The kinetics are biexponential around the resonance field and monoexponential outside that range. The monoexponential behavior can be simulated by a classical kinetic model assuming a single field dependent double Lorentzian function for the energy gap dependence of all spin conversion processes. The full field dependence of the kinetics has been simulated quantum theoretically. It has been shown that incoherent and coherent hyperfine coupling contribute to S/T+ spin conversion at all fields and that the biexponentiality of the kinetics at resonance is due to a partitioning of the overall kinetics into 2/3 of the singlet hyperfine states exhibiting strong isotropic coupling to T+ and 1/3 of the singlet hyperfine states that do not or only weakly couple isotropically to T+.

How Small Heterocycles Make a Reaction Network of Amino Acids and Nucleotides Efficient in Water.

Organisms use enzymes to ensure a flow of substrates through biosynthetic pathways. How the earliest form of life established biosynthetic networks and prevented hydrolysis of intermediates without enzymes is unclear. Organocatalysts may have played the role of enzymes. Quantitative analysis of reactions of adenosine 5'-monophosphate and glycine that produce peptides, pyrophosphates, and RNA chains reveals that organocapture by heterocycles gives hydrolytically stabilized intermediates with balanced reactivity. We determined rate constants for 20 reactions in aqueous solutions containing a carbodiimide and measured product formation with cyanamide as a condensing agent. Organocapture favors reactions that are kinetically slow but productive, and networks, over single transformations. Heterocycles can increase the metabolic efficiency more than two-fold, with up to 0.6 useful bonds per fuel molecule spent, boosting the efficiency of life-like reaction systems in the absence of enzymes.

Fine tuning of electron transfer and spin chemistry parameters in triarylamine-bridge-naphthalene diimide dyads by bridge substituents.

The photoinduced charge separation and charge recombination in a set of four molecular dyads consisting of a triarylamine donor and a naphthalene diimide acceptor were investigated by time resolved transient absorption spectroscopy with fs and ns time resolution. In these dyads the donor and acceptor are bridged by a meta-conjugated diethynylbenzene bridge whose electronic nature was tuned by small electron donating (OMe, Me) or electron withdrawing (Cl, CN) substituents. While the formation of the transient charge separated states is complete within tens of ps, charge recombination is biphasic with a shorter component of several hundred ns and a longer component of several microseconds. This behaviour could be rationalized by assuming an equilibrium of singlet and triplet charge separated states. Magnetic field dependent measurements showed a strong influence on the biphasic decay kinetics and also a pronounced level crossing effect in the magnetic field affected reaction yield (MARY) spectra caused by a significant exchange coupling. An analysis of the observed kinetics using classical kinetic rate equations yields rate constants for charge separation and charge recombination as well as the exchange interaction splitting in the radical ion pair, all of them showing a delicate dependence on the bridge substituents.

Photoexcited Triplet State Kinetics Studied by Electron Paramagnetic Resonance Spectroscopy.

Following the first evidence of the triplet character of the optically excited phosphorescent state of naphthalene by Hutchison and Mangum in 1958, electron paramagnetic resonance (EPR) spectroscopy has become widely used to study and understand the properties and kinetic characteristics of excited triplet states. This minireview gives an overview over EPR techniques based on continuous microwave methods using lock-in or direct detection as well as pulsed EPR methods with respect to their suitability for kinetic studies of excited triplet states. A short historical overview of the experimental and theoretical developments in this field of research as well as of the triplet systems studied, with a final focus on fullerenes, is given. This may help newcomers to the field as a guide to the relevant literature.

Optical Detection of Photorelease Kinetics on Gold and Glass Surfaces using Streptavidin-Coupled Biotinylated Photolabile Protecting Groups for Nucleosides.

Five biotinylated photolabile compounds of the general structure Bt-L1 -NPPOC-X-L2 were synthesized, in which Bt represents a biotin unit, L1 is a 3,6-dioxa-n-octane or an n-hexane spacer, NPPOC is the photolabile protecting group 2-(2-nitrophenyl)propoxycarbonyl, and X is a thymidine unit as a representative nucleoside or a direct linkage to L2 , an ω-mercapto- or ω-aminohexoyl linker, for coupling to a substrate surface. These compounds served for testing the photocleavage kinetics in self-assembled monolayers on gold or glass by using surface plasmon resonance (SPR) on gold or reflectometric interference spectroscopy (RIfS) on glass, whereby the biotin moiety offered the possibility to increase the bulkiness of the leaving group by binding to streptavidin, which thereby largely enhanced the SPR or RIfS signals. The photokinetics, found to consist in a dominating fast stage and a less contributing slow stage, were quantitatively analyzed, and the quantum yield of the fast part reached values up to almost 1 in favorable cases. A direct comparison of the results from SPR and RIfS yielded almost identical results. The present investigations pave the way to in situ monitoring of the photolithographic synthesis of DNA chips.

Ribonucleotides and RNA Promote Peptide Chain Growth.

All known forms of life use RNA-mediated polypeptide synthesis to produce the proteins encoded in their genes. Because the principal parts of the translational machinery consist of RNA, it is likely that peptide synthesis was achieved early in the prebiotic evolution of an RNA-dominated molecular world. How RNA attracted amino acids and then induced peptide formation in the absence of enzymes has been unclear. Herein, we show that covalent capture of an amino acid as a phosphoramidate favors peptide formation. Peptide coupling is a robust process that occurs with different condensation agents. Kinetics show that covalent capture can accelerate chain growth over oligomerization of the free amino acid by at least one order of magnitude, so that there is no need for enzymatic catalysis for peptide synthesis to begin. Peptide chain growth was also observed on phosphate-terminated RNA strands. Peptide coupling promoted by ribonucleotides or ribonucleotide residues may have been an important transitional form of peptide synthesis that set in when amino acids were first captured by RNA.

The strength of the template effect attracting nucleotides to naked DNA.

The transmission of genetic information relies on Watson-Crick base pairing between nucleoside phosphates and template bases in template-primer complexes. Enzyme-free primer extension is the purest form of the transmission process, without any chaperon-like effect of polymerases. This simple form of copying of sequences is intimately linked to the origin of life and provides new opportunities for reading genetic information. Here, we report the dissociation constants for complexes between (deoxy)nucleotides and template-primer complexes, as determined by nuclear magnetic resonance and the inhibitory effect of unactivated nucleotides on enzyme-free primer extension. Depending on the sequence context, Kd's range from 280 mM for thymidine monophosphate binding to a terminal adenine of a hairpin to 2 mM for a deoxyguanosine monophosphate binding in the interior of a sequence with a neighboring strand. Combined with rate constants for the chemical step of extension and hydrolytic inactivation, our quantitative theory explains why some enzyme-free copying reactions are incomplete while others are not. For example, for GMP binding to ribonucleic acid, inhibition is a significant factor in low-yielding reactions, whereas for amino-terminal DNA hydrolysis of monomers is critical. Our results thus provide a quantitative basis for enzyme-free copying.

Complete Monitoring of Coherent and Incoherent Spin Flip Domains in the Recombination of Charge-Separated States of Donor-Iridium Complex-Acceptor Triads.

The spin chemistry of photoinduced charge-separated (CS) states of three triads comprising one or two triarylamine donors, a cyclometalated iridium complex sensitizer and a naphthalene diimide (NDI) acceptor, was investigated by transient absorption spectroscopy in the ns-µs time regime. Strong magnetic-field effects (MFE) were observed for two triads with a phenylene bridge between iridium complex sensitizer and NDI acceptor. For these triads, the lifetimes of the CS states increased from 0.6 µs at zero field to 40 µs at about 2 T. Substituting the phenylene by a biphenyl bridge causes the lifetime of the CS state at zero field to increase by more than 2 orders of magnitude (τ = 79 µs) and the MFE to disappear almost completely. The kinetic MFE was analyzed in the framework of a generalized Hayashi-Nagakura scheme describing coherent (S, T0 ↔ T±) as well as incoherent (S, T0 ⇌ T±) processes by a single rate constant k±. The magnetic-field dependence of k± of the triads with phenylene bridge spans 2 orders of magnitude and exhibits a biphasic behavior characterized by a superposition of two Lorentzians. This biphasic MFE is observed for the first time and is clearly attributable to the coherent (B < 10 mT) and incoherent (10 mT < B < 2 T) domains of spin motion induced by isotropic and anisotropic hyperfine coupling. The parameters of both domains are well understood in terms of the structural properties of the two triads, including the effect of electron hopping in the triad with two donor moieties. The kinetic model also accounts for the reduction of the MFE on reducing the rate constant of charge recombination in the triad with the biphenyl bridge.

Large protonation-gated photochromism of an OPE-embedded difurylperfluorocyclopentene.

A recently reported protolytic gating effect on the ring closing reaction of an oligo(phenylene ethynylene) (OPE) embedded difurylperfluorocyclopentene (S) with a dimethylaminophenyl chain link in each of the side arms, was quantitatively analyzed in detail. The reaction system (So, SoH(+), SoH2(2+), Sc, ScH(+), ScH2(2+)) comprising three protolytic forms in both open and closed configuration, is characterized by four protolytic equilibrium constants and six photochemical quantum yields of ring closing and ring opening. The absorption spectra, conductivity, and effective photochemical quantum yields were measured in acetonitrile as functions of solvent acidity varied by addition of trifluoroacetic acid and triethylamine and characterized by an effective pHnon-aq. Based on the derivation of a rigorous method for assessing the individual quantum yields of ring closure and ring opening of the six species, it was shown that it is specifically the second protonation step that is responsible for a more than 10-fold increase in the quantum yield of ring closure.

Optical switching of radical pair conformation enhances magnetic sensitivity.

The yield of radical pair reactions is influenced by magnetic fields well beyond the levels expected from energy considerations. This dependence can be traced back to the microscopic dynamics of electron spins and constitutes the basis of chemical compasses. Here we propose a new experimental approach based on molecular photoswitches to achieve additional control on the chemical reaction and allow short-time resolution of the spin dynamics. Our proposal enables experiments to test some of the standard assumptions of the radical pair model and improves the sensitivity of a paradigmatic model of chemical magnetometer by up to two orders of magnitude.

Templating efficiency of naked DNA.

Template-directed synthesis of complementary strands is pivotal for life. Nature employs polymerases for this reaction, leaving the ability of DNA itself to direct the incorporation of individual nucleotides at the end of a growing primer difficult to assess. Using 64 sequences, we now find that any of the four nucleobases, in combination with any neighboring residue, support enzyme-free primer extension when primer and mononucleotide are sufficiently reactive, with >or=93% primer extension for all sequences. Between the 64 possible base triplets, the rate of extension for the poorest template, CAG, with A as templating base, and the most efficient template, TCT, with C as templating base, differs by less than two orders of magnitude. Further, primer extension with a balanced mixture of monomers shows >or=72% of the correct extension product in all cases, and >or=90% incorporation of the correct base for 46 out of 64 triplets in the presence of a downstream-binding strand. A mechanism is proposed with a binding equilibrium for the monomer, deprotonation of the primer, and two chemical steps, the first of which is most strongly modulated by the sequence. Overall, rates show a surprisingly smooth reactivity landscape, with similar incorporation on strongly and weakly templating sequences. These results help to clarify the substrate contribution to copying, as found in polymerase-catalyzed replication, and show an important feature of DNA as genetic material.

Charge transport characteristics of diarylethene photoswitching single-molecule junctions.

We report on the experimental analysis of the charge transport through single-molecule junctions of the open and closed isomers of photoswitching molecules. Sulfur-free diarylethene molecules are developed and studied via electrical and optical measurements as well as density functional theory calculations. The single-molecule conductance and the current-voltage characteristics are measured in a mechanically controlled break-junction system at low temperatures. Comparing the results with the single-level transport model, we find an unexpected behavior of the current-dominating molecular orbital upon isomerization. We show that both the side chains and end groups of the molecules are crucial to understand the charge transport mechanism of photoswitching molecular junctions.

Diffusion-controlled sensitization of photocleavage reactions on surfaces.

The kinetic rate equation for the photosensitized cleavage reaction of surface-bound photolabile chromophores with free diffusion of sensitizer molecules from the bulk of a solution to the surface is derived by determining the stationary solution of a diffusion equation with suitable boundary conditions. The relation between the phenomenological rate constant for the photosensitized reaction at the surface and in the bulk is established. Applying the result to the analysis of an experimental example, the origin of the quasi zeroth-order kinetics of the sensitized reaction is revealed. A theoretical comparison of intramolecular sensitization in photocleavable protecting groups with a molecular antenna and sensitization with the freely diffusing sensitizer shows that in a typical case sensitization with free diffusion is more effective than intramolecular sensitization for sensitizer concentrations higher than 5 mM.

Synthesis and photoswitching studies of difurylperfluorocyclopentenes with extended π-systems.

In an attempt to design molecular optoelectronic switches functioning in molecular junctions between two metal tips, we synthesized a set of photochromic compounds by extending the π-system of 1,2-bis-(2-methyl-5-formylfuran-3-yl)perfluorocyclopentene through suitable coupling reactions involving the formyl functions, thereby also introducing terminal groups with a binding capacity to gold. Avoiding the presence of gold-binding sulphur atoms in the photoreactive centre, as they are present in the frequently used analogous thienyl compounds, the newly synthesized compounds should be more suitable for the purpose indicated. The kinetics of reversible photoswitching of the new compounds by UV and visible light was quantitatively investigated in solution. The role of conformational flexibility of the π-system for the width of the UV/Vis spectra was clarified by using quantum chemical calculations with time-dependent (TD)-DFT. As a preliminary test of the potential of the new compounds to serve as optoelectronic molecular switches, monolayer formation and photochemical switching on gold surfaces was observed by using surface plasmon resonance.

Kinetic magnetic-field effect involving the small biologically relevant inorganic radicals NO and O2(·-).

Oxidation of dihydrorhodamine 123 (DHR) to rhodamine 123 (RH) by oxoperoxonitrite (ONOO(-)), formed through recombination of NO and O(2)(·-) radicals resulting from thermal decomposition of 3-morpholinosydnonimine (SIN-1) in buffered aerated aqueous solution at pH 7.6, represents a kinetic model system of the reactivity of NO and O(2)(·-) in biochemical systems. A magnetic-field effect (MFE) on the yield of RH detected in this system is explored in the full range of fields between 0 and 18 T. It is found to increase in a nearly linear fashion up to a value of 5.5±1.6 % at 18 T and 23 °C (3.1±0.7 % at 40 °C). A theoretical framework to analyze the MFE in terms of the magnetic-field-enhanced recombination rate constant k(rec) of NO and O(2)(·-) due to magnetic mixing of T(0) and S spin states of the radical pair by the Δg mechanism is developed, including estimation of magnetic properties (g tensor and spin relaxation times) of NO and O(2)(·-) in aqueous solution, and calculation of the MFE on k(rec) using the theoretical formalism of Gorelik at al. The factor with which the MFE on k(rec) is translated to the MFE on the yield of ONOO(-) and RH is derived for various kinetic scenarios representing possible sink channels for NO and O(2)(·-). With reasonable assumptions for the values of some unknown kinetic parameters, the theoretical predictions account well for the observed MFE.

Rapid glycoconjugation with glycosyl amines.

Conjugation of unprotected carbohydrates to surfaces or probes by chemoselective ligation reactions is indispensable for the elucidation of their numerous biological functions. In particular, the reaction with oxyamines leading to the formation of carbohydrate oximes which are in equilibrium with cyclic N-glycosides (oxyamine ligation) has an enormous impact in the field. Although highly chemoselective, the reaction is rather slow. Here, we report that the oxyamine ligation is significantly accelerated without the need for a catalyst when starting with glycosyl amines. Reaction rates are increased up to 500-fold compared to the reaction of the reducing carbohydrate. For comparison, aniline-catalyzed oxyamine ligation is only increased 3.8-fold under the same conditions. Glycosyl amines from mono- and oligosaccharides are easily accessible from reducing carbohydrates via the corresponding azides by using Shoda's reagent (2-chloro-1,3-dimethylimidazolinium chloride, DMC) and subsequent reduction. Furthermore, glycosyl amines are readily obtained by enzymatic release from N-glycoproteins making the method suited for glycomic analysis of these glycoconjugates which we demonstrate employing RNase B. Oxyamine ligation of glycosyl amines can be carried out at close to neutral conditions which makes the procedure especially valuable for acid-sensitive oligosaccharides.

Readout of spin quantum beats in a charge-separated radical pair by pump-push spectroscopy.

Spin quantum beats prove the quantum nature of reactions involving radical pairs, the key species of spin chemistry. However, such quantum beats remain hidden to transient absorption­based optical observation because the spin hardly affects the absorption properties of the radical pairs. We succeed in demonstrating such quantum beats in the photoinduced charge-separated state (CSS) of an electron donor­acceptor dyad by using two laser pulses­one for pumping the sample and another one, with variable delay, for further exciting the CSS to a higher electronic state, wherein ultrafast recombination to distinct, optically detectable products of singlet or triplet multiplicity occurs. This represents a spin quantum measurement of the spin state of the CSS at the time instant of the second (push) pulse.