Mechanism Underlying the Nucleobase-Distinguishing Ability of Benzopyridopyrimidine (BPP).

Benzopyridopyrimidine (BPP) is a fluorescent nucleobase analogue capable of forming base pairs with adenine (A) and guanine (G) at different sites. When incorporated into oligodeoxynucleotides, it is capable of differentiating between the two purine nucleobases by virtue of the fact that its fluorescence is largely quenched when it is base-paired to guanine, whereas base-pairing to adenine causes only a slight reduction of the fluorescence quantum yield. In the present article, the photophysics of BPP is investigated through computer simulations. BPP is found to be a good charge acceptor, as demonstrated by its positive and appreciably large electron affinity. The selective quenching process is attributed to charge transfer (CT) from the purine nucleobase, which is predicted to be efficient in the BPP-G base pair, but essentially inoperative in the BPP-A base pair. The CT process owes its high selectivity to a combination of two factors: the ionization potential of guanine is lower than that of adenine, and less obviously, the site occupied by guanine enables a greater stabilization of the CT state through electrostatic interactions than the one occupied by adenine. The case of BPP illustrates that molecular recognition via hydrogen bonding can enhance the selectivity of photoinduced CT processes.

Theoretical Study of the Photophysics of 8-Vinylguanine, an Isomorphic Fluorescent Analogue of Guanine.

Paving the way for the application of the algebraic-diagrammatic construction scheme of second-order (ADC(2)) to systems based on the guanine chromophore, we demonstrate the this excited-state electronic structure method provides a realistic description of the photochemistry of 9H-guanine, in close agreement with the benchmark provided by the CASPT2 method. We then proceed to apply the ADC(2) method to the photochemistry of 8-vinylguanine (8vG), a minimally modified analogue of guanine which, unlike the naturally occurring nucleobase, displays intense fluorescence, indicative of a much longer-lived excited electronic state. The emissive electronic state of 8vG is identified as an ππ*-type intramolecular charge transfer (ICT) state, in which a charge of roughly -0.2 e is transferred from the guanine moiety onto the vinyl substituent. The main radiationless deactivation pathway competing with fluorescence is predicted to involve the molecule leaving the minimum on the ICT ππ* state, and reaching a region of the S1 adiabatic state where it resembles the La ππ* state of unmodified 9H-guanine. The topology of the La ππ* region of the S1 state favors subsequent internal conversion at a crossing seam with the ground electronic state. The sensitivity of this process to environment polarity may explain the experimentally observed fluorescence quenching of 8vG upon incorporation in single- and double-stranded DNA.

Hybrid QM/QM simulations of photochemical reactions in the molecular crystal N-salicylidene-2-chloroaniline.

In this paper, we report the application of the QM/QM hybrid simulation technique to the photoisomerisation reactions of anils (i.e., Schiff bases of salicylaldehyde with aniline derivatives) in the solid state, on the example of the photochromic polymorph of N-salicylidene-2-chloroaniline. By propagating molecular dynamics on a potential energy surface constructed using a combination of time-dependent DFT and ground-state DFT calculations, two reaction pathways of the cis-enol isomer were observed, which occur with approximately equal probability. In the first pathway, the photoexcited molecule undergoes an intramolecular proton transfer reaction on average 25 fs after photoexcitation. It then persists in the cis-keto form for a few hundred femtoseconds before undergoing a pedal motion through which it reaches an S1/S0 conical intersection. This pathway, whose existence has previously been proposed in the literature to rationalize the feasibility of the photoisomerisation reaction in the confined environment of the crystal lattice, is predicted to lead to the formation of the trans-keto form. The second pathway is nonreactive and is analogous to a previously characterised radiationless de-excitation pathway of the isolated molecule. The cis-enol to trans-keto photoisomerisation is reversible. Following the photoexcitation of a trans-keto molecule, it persists in a largely unchanged geometry for a period of time ranging from a few hundred femtoseconds to over a picosecond, and subsequently undergoes a pedal motion in the same direction as the one involved in the cis-enol to trans-keto photoisomerisation, leading to the cis-keto isomer through another S1/S0 conical intersection.

Linear conjugated polymer photocatalysts with various linker units for photocatalytic hydrogen evolution from water.

Polymer photocatalysts have shown potential for light-driven hydrogen evolution from water. Here we studied the relative importance of the linker type in two series of conjugated polymers based on dibenzo[b,d]thiophene sulfone and dimethyl-9H-fluorene. The alkenyl-linked polymers were found to be more active photocatalysts than their alkyl and alkyne-linked counterparts. The co-polymer of dibenzo[b,d]thiophene sulfone and 1,2-diphenylethene has a hydrogen evolution rate of 3334 µmol g-1 h-1 and an external quantum efficiency of 5.6% at 420 nm.

Femtosecond dynamics of the ring closing process of diarylethene: a case study of electrocyclic reactions in photochromic single crystals.

The cyclization reaction of the photochromic diarylethene derivative 1,2-bis(2,4-dimethyl-5-phenyl-3-thienyl)perfluorocyclopentene was studied in its single crystal phase with femtosecond transient absorption spectroscopy. The transient absorption measurements were performed with a robust acquisition scheme that explicitly exploits the photoreversibility of the molecular system and monitors the reversibility conditions. The crystalline system demonstrated 3 × 10(4) repeatable cycles before significant degradation was observed. Immediately following photoexcitation, the excited state absorption associated with the open-ring conformation undergoes a large spectral shift with a time constant of approximately 200 fs. Following this evolution on the excited state potential energy surface, the ring closure occurs with a time constant of 5.3 ps, which is significantly slower than previously reported measurements for similar derivatives in the solution phase. Time resolved electron diffraction studies were used to further demonstrate the assignment of the transient absorption dynamics to the ring closing reaction. The mechanistic details of the ring closing are discussed in the context of prior computational work along with a vibrational mode analysis using density functional theory to give some insight into the primary motions involved in the ring closing reaction.

Early Events in the Nonadiabatic Relaxation Dynamics of 4-(N,N-Dimethylamino)benzonitrile.

4-(N,N-Dimethylamino)benzonitrile (DMABN) is the archetypal system for dual fluorescence. Several past studies, both experimental and theoretical, have examined the mechanism of its relaxation in the gas phase following photoexcitation to the S2 state, without converging to a single description. In this contribution, we report first-principles simulations of the early events involved in this process performed using the nonadiabatic trajectory surface hopping (TSH) approach in combination with the ADC(2) electronic structure method. ADC(2) is verified to reproduce the ground- and excited-state structures of DMABN in reasonably close agreement with previous theoretical benchmarks. The TSH simulations predict that internal conversion from the S2 state to the S1 takes place as early as 8.5 fs, on average, after the initial photoexcitation, and with no significant torsion of the dimethylamino group relative to the aromatic ring. As evidenced by supporting EOM-CCSD calculations, the population transfer from S2 to S1 can be attributed to the skeletal deformation modes of the aromatic ring and the stretching of the ring-dimethylamino nitrogen bond. The non- or slightly twisted locally excited structure is the predominant product of the internal conversion, and the twisted intramolecular charge transfer structure is formed through equilibration with the locally excited structure with no change of adiabatic state. These findings point toward a new interpretation of data from previous time-resolved experiments.

Cold ablation driven by localized forces in alkali halides.

Laser ablation has been widely used for a variety of applications. Since the mechanisms for ablation are strongly dependent on the photoexcitation level, so called cold material processing has relied on the use of high-peak-power laser fluences for which nonthermal processes become dominant; often reaching the universal threshold for plasma formation of ~1 J cm(-2) in most solids. Here we show single-shot time-resolved femtosecond electron diffraction, femtosecond optical reflectivity and ion detection experiments to study the evolution of the ablation process that follows femtosecond 400 nm laser excitation in crystalline sodium chloride, caesium iodide and potassium iodide. The phenomenon in this class of materials occurs well below the threshold for plasma formation and even below the melting point. The results reveal fast electronic and localized structural changes that lead to the ejection of particulates and the formation of micron-deep craters, reflecting the very nature of the strong repulsive forces at play.

Hybrid QM/QM Simulations of Excited-State Intramolecular Proton Transfer in the Molecular Crystal 7-(2-Pyridyl)-indole.

A subtractive implementation of the QM/QM hybrid method for the description of photochemical reactions occurring in molecular crystals is presented and tested by applying it in a simulation study of the ultrafast intramolecular excited-state proton transfer reaction in the crystal form of 7-(2-pyridyl)-indole, an organic compound featuring an intramolecular hydrogen bond within a six-membered ring. By propagating molecular dynamics on the excited-state potential energy surface, a mean proton transfer time was calculated as 80 fs. The reaction mechanism is discussed in terms of three-dimensional reaction coordinate diagrams. Proton transfer was found to be barrierless and to be strongly coupled to vibrational modes of the photoexcited molecule that modulate the proton donor-acceptor distance. Some 300 fs after the initial photoexcitation, the excited state molecule reached an S1/S0 conical intersection through the mutual twist of the pyridyl and indolyl moieties.

Ring-closing reaction in diarylethene captured by femtosecond electron crystallography.

The photoinduced ring-closing reaction in diarylethene, which serves as a model system for understanding reactive crossings through conical intersections, was directly observed with atomic resolution using femtosecond electron diffraction. Complementary ab initio calculations were also performed. Immediately following photoexcitation, subpicosecond structural changes associated with the formation of an open-ring excited-state intermediate were resolved. The key motion is the rotation of the thiophene rings, which significantly decreases the distance between the reactive carbon atoms prior to ring closing. Subsequently, on the few picosecond time scale, localized torsional motions of the carbon atoms lead to the formation of the closed-ring photoproduct. These direct observations of the molecular motions driving an organic chemical reaction were only made possible through the development of an ultrabright electron source to capture the atomic motions within the limited number of sampling frames and the low data acquisition rate dictated by the intrinsically poor thermal conductivity and limited photoreversibility of organic materials.