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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.

Dedicated with best wishes to Prof. Edgar Heilbronner on the occasion of his 80th birthdayThe photochemistry of several 2-(2-nitrophenyl)ethyl-caged compounds including caged thymidine nucleosides was studied by nanosecond laser flash photolysis and stationary illumination experiments with quantitative HPLC analysis for quantum yields and product distribution. Effects of solvent basicity and acidity were investigated by varying the H 2 O content and HCl concentration, respectively, in MeCN/H 2 O mixtures. For all compounds 1 ± 7 investigated, intramolecular H abstraction by the nitro group from the exocyclic a-position with respect to the aryl moiety was found to be the primary process. The protolytic dissociation equilibrium of the resulting aci-nitro compound was kinetically characterized in the 0.1 ± 10 ms time region. In general, two reaction channels compete for the aci-nitro compound and its anion: b-elimination of the caged compound occurs from the anion, while from the undissociated aci-nitro compound, a nitrosobenzene derivative is formed with no release of the caged compound. The yield ratio of these two reaction channels can be controlled through shifts in the protolytic dissociation equilibrium of the aci-nitro compound. In solutions with either low basicity (H 2 O-free MeCN) or high acidity (higher concentration of HCl in H 2 O/MeCN), two as yet unidentified products are formed, each one specifically for one of the mentioned conditions. Introduction. ± Photolabile protecting groups play an important role in synthetic organic chemistry [1], for caging of biologically active molecules [2], and for lightdirected, combinatorial solid-phase syntheses of biopolymers [3]. A particularly attractive application is the generation of so-called high-density DNA chips [4] [5] which are needed in various types to perform the sequencing by hybridisation (SBH) method for oligonucleotide and gene sequencing [6]. The o-nitrobenzyl (oNB) type of protecting groups has been commonly used since 1901 when the photoreaction was discovered [7], and its reaction mechanism has been investigated in detail [8]. So far, the [(a-methyl-2-nitropiperonyl)oxy]carbonyl ([1-(6-nitro-1,3-benzodioxol-5-yl)-ethoxy]carbonyl; MeNPOC) group has been the preferred choice in DNA-chip production [4].The photochemical cleavage mechanism of the (o-nitrobenzyl)oxy function is triggered by the abstraction of a benzylic H-atom by the excited nitro group [9]. Recently, a new type of photolabile protecting group was developed on the basis of the [2-(2-nitrophenyl)ethoxy]carbonyl functionality [10] [11] which is cleaved by a lightinduced b-elimination process with formation of o-nitrostyrene, CO 2 , and the corresponding alcohol. It was suggested [10] that, in analogy to the o-nitrobenzyl groups, the cleavage of the [2-(2-nitrophenyl)ethoxy]carbonyl moiety, too, should start with the formation of an aci-nitro intermediate, through H abstraction by the nitro group at the exocyclic a-position with respect to the aryl moiety. Based on results from laser f...

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 ≥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 ≥72% of the correct extension product in all cases, and ≥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.

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.