A Click Chemistry Approach to Targeted DNA Crosslinking with cis-Platinum(II)-Modified Triplex-Forming Oligonucleotides.

Limitations of clinical platinum(II) therapeutics include systemic toxicity and inherent resistance. Modern approaches, therefore, seek new ways to deliver active platinum(II) to discrete nucleic acid targets. In the field of antigene therapy, triplex-forming oligonucleotides (TFOs) have attracted interest for their ability to specifically recognise extended duplex DNA targets. Here, we report a click chemistry based approach that combines alkyne-modified TFOs with azide-bearing cis-platinum(II) complexes-based on cisplatin, oxaliplatin, and carboplatin motifs-to generate a library of PtII -TFO hybrids. These constructs can be assembled modularly and enable directed platinum(II) crosslinking to purine nucleobases on the target sequence under the guidance of the TFO. By covalently incorporating modifications of thiazole orange-a known DNA-intercalating fluorophore-into PtII -TFOs constructs, enhanced target binding and discrimination between target and off-target sequences was achieved.

Isotope Effects and the Mechanism of Photoredox-Promoted [2 + 2] Cycloadditions of Enones.

13C kinetic isotope effects (KIEs) for the photoredox-promoted [2 + 2] cycloaddition of enones were determined in homocoupling and heterocoupling examples. The only significant KIEs were observed at the ß carbon, indicating that Cß-Cß bond formation is irreversible. However, these KIEs were much lower than computational predictions, suggesting that product selectivity is determined in part by a step prior to Cß-Cß bond formation. The results are explained as arising from a competition between C-C bond formation and electron exchange between substrate alkenes. This idea is supported by a relatively small substituent effect on substrate selectivity. The possible rates for electron transfer and bond-forming steps are analyzed, and the competition appears plausible, particularly if the mechanism involves a complex between reduced and neutral enone molecules.

Vibrationally Hot and Cold Triplets. Sensitizer-Dependent Dynamics and Localized Vibrational Promotion of a Di-π-methane Rearrangement.

Large intramolecular 13C kinetic isotope effects (KIEs) for the di-π-methane rearrangement of benzobarrelene fit with statistical expectations from heavy-atom tunneling when a low-energy sensitizer is employed, but much lower KIEs are observed with higher-energy sensitizers. These results in combination with trajectory studies suggest that the excess vibrational energy available from triplet energy transfer leads to hot and nonstatistical dynamics in the rearrangement.

Solvation Dynamics and the Nature of Reaction Barriers and Ion-Pair Intermediates in Carbocation Reactions.

Additions of acids to 1,3-dienes are conventionally understood as involving discrete intermediates that undergo an ordinary competition between subsequent pathways to form the observed products. The combined experimental, computational, and dynamic trajectory study here suggests that this view is incorrect, and that solvation dynamics plays a critical role in the mechanism. While implicit solvent models were inadequate, QM/QM' trajectories in explicit solvent provide an accurate prediction of the experimental selectivity in the addition of HCl to 1,3-pentadiene. Trajectories initiated from a protonation saddle point on the potential of mean force surface are predominantly unproductive due to a gating effect of solvation that allows diene protonation only when the incipient ion pair is neither too solvent-stabilized nor too little. Protonation then leads to relatively unsolvated ion pairs, and a majority of these collapse rapidly to the 1,2-product, without barrier and without achieving equilibrium solvation as intermediates. The remainder decay slowly, at a rate consistent with equilibrium solvation as true intermediates, affording a mixture of addition products. Overall, an accurate description of the nature and pathway selectivity of the ion pair intermediates in carbocation reactions must allow for species lacking equilibrium solvation. Potential reinterpretations of a series of historically notable observations in carbocation reactions are discussed.

AT-CuAAC Synthesis of Mechanically Interlocked Oligonucleotides.

We present a simple strategy for the synthesis of main chain oligonucleotide rotaxanes with precise control over the position of the macrocycle. The novel DNA-based rotaxanes were analyzed to assess the effect of the mechanical bond on their properties.

Bond Memory in Dynamically Determined Stereoselectivity.

The carboborative ring contraction of cyclohexenes exhibits an abnormal selectivity pattern in which a formally concerted double migration gives rise to predominant but not exclusive inversion products. In dynamic trajectories, the inversion and retention products are formed from the same transition state, and the trajectories accurately account for the experimental product ratios. The unusual origin of the selectivity is the dynamically retained non-equivalence of newly formed versus pre-existing bonds after the first bond migration.

Development of Gene-Targeted Polypyridyl Triplex-Forming Oligonucleotide Hybrids.

In the field of nucleic acid therapy there is major interest in the development of libraries of DNA-reactive small molecules which are tethered to vectors that recognize and bind specific genes. This approach mimics enzymatic gene editors, such as ZFNs, TALENs and CRISPR-Cas, but overcomes the limitations imposed by the delivery of a large protein endonuclease which is required for DNA cleavage. Here, we introduce a chemistry-based DNA-cleavage system comprising an artificial metallo-nuclease (AMN) that oxidatively cuts DNA, and a triplex-forming oligonucleotide (TFO) that sequence-specifically recognises duplex DNA. The AMN-TFO hybrids coordinate CuII ions to form chimeric catalytic complexes that are programmable - based on the TFO sequence employed - to bind and cut specific DNA sequences. Use of the alkyne-azide cycloaddition click reaction allows scalable and high-throughput generation of hybrid libraries that can be tuned for specific reactivity and gene-of-interest knockout. As a first approach, we demonstrate targeted cleavage of purine-rich sequences, optimisation of the hybrid system to enhance stability, and discrimination between target and off-target sequences. Our results highlight the potential of this approach where the cutting unit, which mimics the endonuclease cleavage machinery, is directly bound to a TFO guide by click chemistry.

Design of thiazole orange oligonucleotide probes for detection of DNA and RNA by fluorescence and duplex melting.

We have synthesised a range of thiazole orange (TO) functionalised oligonucleotides for nucleic acid detection in which TO is attached to the nucleobase or sugar of thymidine. The properties of duplexes between TO-probes and their DNA and RNA targets strongly depend on the length of the linker between TO and the oligonucleotide, the position of attachment of TO to the nucleotide (major or minor groove) and the mode of attachment of thiazole orange (via benzothiazole or quinoline moiety). This information can be used to design probes for detection of target nucleic acids by fluorescence or duplex melting. With cellular imaging in mind we show that 2'-OMe RNA probes with TO at the 5-position of uracil or the 2'-position of the ribose sugar are particularly effective, exhibiting up to 44-fold fluorescence enhancement against DNA and RNA, and high duplex stability. Excellent mismatch discrimination is achieved when the mispaired base is located adjacent to the TO-modified nucleotide rather than opposite to it. The simple design, ease of synthesis and favourable properties of these TO probes suggest applications in fluorescent imaging of DNA and RNA in a cellular context.

Failure and Redemption of Statistical and Nonstatistical Rate Theories in the Hydroboration of Alkenes.

Our previous work found that canonical forms of transition state theory incorrectly predict the regioselectivity of the hydroboration of propene with BH3 in solution. In response, it has been suggested that alternative statistical and nonstatistical rate theories can adequately account for the selectivity. This paper uses a combination of experimental and theoretical studies to critically evaluate the ability of these rate theories, as well as dynamic trajectories and newly developed localized statistical models, to predict quantitative selectivities and qualitative trends in hydroborations on a broader scale. The hydroboration of a series of terminally substituted alkenes with BH3 was examined experimentally, and a classically unexpected trend is that the selectivity increases as the alkyl chain is lengthened far from the reactive centers. Conventional and variational transition state theories can predict neither the selectivities nor the trends. The canonical competitive nonstatistical model makes somewhat better predictions for some alkenes but fails to predict trends, and it performs poorly with an alkene chosen to test a specific prediction of the model. Added nonstatistical corrections to this model make the predictions worse. Parametrized Rice-Ramsperger-Kassel-Marcus (RRKM)-master equation calculations correctly predict the direction of the trend in selectivity versus alkene size but overpredict its magnitude, and the selectivity with large alkenes remains unpredictable with any parametrization. Trajectory studies in explicit solvent can predict selectivities without parametrization but are impractical for predicting small changes in selectivity. From a lifetime and energy analysis of the trajectories, "localized RRKM-ME" and "competitive localized noncanonical" rate models are suggested as steps toward a general model. These provide the best predictions of the experimental observations and insight into the selectivities.

Concert along the Edge: Dynamics and the Nature of the Border between General and Specific Acid-Base Catalysis.

Reactions that involve a combination of proton transfer and heavy-atom bonding changes are normally categorized by whether the proton transfer is occurring during the rate-limiting step, as in the distinction between general and specific acid-base catalysis. The experimental and computational study here of a ß-ketoacid decarboxylation shows how the distinction between the two mechanisms breaks down near its border due to the differing time scales for proton versus heavy-atom motion. Isotope effects in the decarboxylation of benzoylacetic acid support a transition state in which the proton transfer is complete. In quasiclassical trajectories passing through this transition state, the new O-H bond after proton transfer undergoes several vibrations before heavy-atom motion completes the reaction. The bonding changes are thus temporally separated at a "dynamic intermediate" structure that acts equivalently to an ordinary intermediate in the trajectories, including the reversal of trajectories at the intermediate when the second "step" fails, but the structure is not an energy minimum. The results define a border between mechanisms where the usual energetic definition of intermediates is not meaningful.

Ir-Catalyzed ortho-Borylation of Phenols Directed by Substrate-Ligand Electrostatic Interactions: A Combined Experimental/in Silico Strategy for Optimizing Weak Interactions.

A strategy for affecting ortho versus meta/para selectivity in Ir-catalyzed C-H borylations (CHBs) of phenols is described. From selectivity observations with ArylOBpin (pin = pinacolate), it is hypothesized that an electrostatic interaction between the partial negatively charged OBpin group and the partial positively charged bipyridine ligand of the catalyst favors ortho selectivity. Experimental and computational studies designed to test this hypothesis support it. From further computational work a second generation, in silico designed catalyst emerged, where replacing Bpin with Beg (eg = ethylene glycolate) was predicted to significantly improve ortho selectivity. Experimentally, reactions employing B2eg2 gave ortho selectivities > 99%. Adding triethylamine significantly improved conversions. This ligand-substrate electrostatic interaction provides a unique control element for selective C-H functionalization.

Mechanistic Studies of Formal Thioboration Reactions of Alkynes.

Several formal heteroborylative cyclization reactions have been recently reported, but little physical-organic and mechanistic data are known. We now investigate the catalyst-free formal thioboration reaction of alkynes to gain mechanistic insight into B-chlorocatecholborane (ClBcat) in its new role as an alkynophilic Lewis acid in electrophilic cyclization/dealkylation reactions. In kinetic studies, the reaction is second-order globally and first-order with respect to both the 2-alkynylthioanisole substrate and the ClBcat electrophile, with activation parameters of ΔG‡ = 27.1 ± 0.1 kcal mol-1 at 90 °C, ΔH‡ = 13.8 ± 1.0 kcal mol-1, and ΔS‡ = -37 ± 3 cal mol-1 K-1, measured over the range 70-90 °C. Carbon kinetic isotope effects supported a rate-determining AdE3 mechanism wherein alkyne activation by neutral ClBcat is concerted with cyclative attack by nucleophilic sulfur. A Hammett study found a ρ+ of -1.7, suggesting cationic charge buildup during the cyclization and supporting rate-determining concerted cyclization. Studies of the reaction with tris(pentafluorophenyl)borane (B(C6F5)3), an activating agent capable of cyclization but not dealkylation, resulted in the isolation of a postcyclization zwitterionic intermediate. Kinetic studies via UV-vis spectroscopy with this boron reagent found second-order kinetics, supporting the likely relevancy of intermediates in this system to the ClBcat system. Computational studies comparing ClBcat with BCl3 as an activating agent showed why BCl3, in contrast to ClBcat, failed to mediate the complete the cyclization/demethylation reaction sequence by itself. Overall, the results support a mechanism in which the ClBcat reagent serves a bifunctional role by sequentially activating the alkyne, despite being less electrophilic than other known alkyne-activating reagents and then providing chloride for post-rate-determining demethylation/neutralization of the resulting zwitterionic intermediate.

Dynamics and the Regiochemistry of Nitration of Toluene.

The regiochemistry of the nitration of toluene by NO2+BF4- in dichloromethane is accurately predicted from trajectories in explicit solvent. Simpler models and approaches based on transition state theory fail to account for the selectivity. Potential of mean force calculations find no free-energy barrier for reaction of the toluene/NO2+BF4- encounter complex, yet the trajectories require an extraordinary 3 ps to descend an exergonic slope. The selectivity is decided late in long trajectories because their completion requires solvent and counterion reorganization. The normal descriptive understanding of the regiochemistry based on transition-state energies is unsupported.

Controlling Selectivity by Controlling Energy Partitioning in a Thermal Reaction in Solution.

The comparison of experimental and predicted kinetic isotope effects in the α-cleavage of alkoxy radicals is used here to judge the applicability of statistical rate theories. It is found that the governing rate theory and the statistical versus nonstatistical nature of the cleavage depend on the cleavage barrier and how much energy is imparted to the radical. The latter can then be controlled by changing the size of substituents in the system. With a large alkyl group substituent, the vibrational energy of the alkoxy radical is increased, but this energy is not statistically distributed, leading to a lower isotope effect than predicted by statistical theories. The observed isotope effect can be approximately rationalized using a semistatistical localized RRKM model.

Dynamically Complex [6+4] and [4+2] Cycloadditions in the Biosynthesis of Spinosyn A.

SpnF, an enzyme involved in the biosynthesis of spinosyn A, catalyzes a transannular Diels-Alder reaction. Quantum mechanical computations and dynamic simulations now show that this cycloaddition is not well described as either a concerted or stepwise process, and dynamical effects influence the identity and timing of bond formation. The transition state for the reaction is ambimodal and leads directly to both the observed Diels-Alder and an unobserved [6+4] cycloadduct. The potential energy surface bifurcates and the cycloadditions occur by dynamically stepwise modes featuring an "entropic intermediate". A rapid Cope rearrangement converts the [6+4] adduct into the observed [4+2] adduct. Control of nonstatistical dynamical effects may serve as another way by which enzymes control reactions.

Increased duplex stabilization in porphyrin-LNA zipper arrays with structure dependent exciton coupling.

Porphyrins were attached to LNA uridine building blocks via rigid 5-acetylene or more flexible propargyl-amide linkers and incorporated into DNA strands. The systems show a greatly increased thermodynamic stability when using as little as three porphyrins in a zipper arrangement. Thermodynamic analysis reveals clustering of the strands into more ordered duplexes with both greater negative ΔΔS and ΔΔH values, and less ordered duplexes with small positive ΔΔS differences, depending on the combination of linkers used. The exciton coupling between the porphyrins is dependent on the flanking DNA sequence in the single stranded form, and on the nature of the linker between the nucleobase and the porphyrin in the double stranded form; it is, however, also strongly influenced by intermolecular interactions. This system is suitable for the formation of stable helical chromophore arrays with sequence and structure dependent exciton coupling.

Controlling Selectivity by Controlling the Path of Trajectories.

Consideration of the role of dynamic trajectories in [1,2]- and [2,3]-sigmatropic rearrangements suggests a counterintuitive approach to controlling the selectivity. In our hypothesis, [2,3] selectivity can be promoted by reaction conditions that thermodynamically disfavor the [2,3] rearrangement step and thereby make the transition state later. The application of this idea has led to a successful prescription for dictating the selectivity in Stevens/Sommelet-Hauser rearrangements of ammonium ylides. A combination of kinetic isotope effects, crossover experiments, and computational dynamic trajectories support the idea that the selectivity is controlled through control of the path of trajectories.

A case study of the mechanism of alcohol-mediated Morita Baylis-Hillman reactions. The importance of experimental observations.

The mechanism of the Morita Baylis-Hillman reaction has been heavily studied in the literature, and a long series of computational studies have defined complete theoretical energy profiles in these reactions. We employ here a combination of mechanistic probes, including the observation of intermediates, the independent generation and partitioning of intermediates, thermodynamic and kinetic measurements on the main reaction and side reactions, isotopic incorporation from solvent, and kinetic isotope effects, to define the mechanism and an experimental mechanistic free-energy profile for a prototypical Morita Baylis-Hillman reaction in methanol. The results are then used to critically evaluate the ability of computations to predict the mechanism. The most notable prediction of the many computational studies, that of a proton-shuttle pathway, is refuted in favor of a simple but computationally intractable acid-base mechanism. Computational predictions vary vastly, and it is not clear that any significant accurate information that was not already apparent from experiment could have been garnered from computations. With care, entropy calculations are only a minor contributor to the larger computational error, while literature entropy-correction processes lead to absurd free-energy predictions. The computations aid in interpreting observations but fail utterly as a replacement for experiment.

Dynamics and a unified understanding of competitive [2,3]- and [1,2]-sigmatropic rearrangements based on a study of ammonium ylides.

The [2,3]- and [1,2]-sigmatropic rearrangements of ammonium ylides are studied by a combination of experimental, standard computational, and dynamic trajectory methods. The mixture of concerted [2,3] rearrangement and bond cleavage observed experimentally is accounted for by the outcome of trajectories passing through the formal [2,3] rearrangement transition state. In this way the bond cleavage is promoted by the pericyclic stabilization of the [2,3] transition state. It is proposed that this dynamic effect is responsible for the pervasive co-occurrence of the two rearrangements.

Isotope effects, dynamic matching, and solvent dynamics in a Wittig reaction. Betaines as bypassed intermediates.

The mechanism of the Wittig reaction of anisaldehyde with a stabilized ylide was studied by a combination of (13)C kinetic isotope effects, conventional calculations, and molecular dynamics calculations in a cluster of 53 THF molecules. The isotope effects support a cycloaddition mechanism involving two sequential transition states associated with separate C-C and P-O bond formations. However, the betaine structure in between the two transition states is bypassed as an equilibrated intermediate in most trajectories. The role of the dynamics of solvent equilibration in the nature of mechanistic intermediates is discussed.