The condensation of 1,3-diketones with hydrazine to access 4-pyrazoles is a well-established synthetic route that travels through a 4-pyrazol-1-ium intermediate. In the route to a 3,5-diphenyl-4-pyrazole containing a cyclobutane spirocycle, density functional theory calculations predict and experiments show that the protonated intermediate undergoes a rapid 1,5-sigmatropic shift to form a tetrahydrocyclopenta[]pyrazole. Replacing the 3,5-diphenyl groups with 2-furanyl groups decreases the calculated rate of the 1,5-sigmatropic shift by 6.2 × 10-fold and enables the isolation of new spirocyclic 4-pyrazoles for click chemistry.

Rate and product data are reported for the solvolysis reactions of twenty-seven mono, di (3,4) and tri (3,4,5) ring-substituted benzyl chlorides. The first order rate constant for solvolysis in 20% acetonitrile in water decrease from = 2.2 s for 4-methoxybenzyl chloride to 1.1 x 10 s for 3,4-dinitrobenzyl chloride. The product rate constant ratios / for solvolysis in 70/27/3 (v/v/v) HOH/TFE/MeOH range from a minimum of / = 8 to a maximum of 110. The rate data were fit to a four-parameter Hammett equation that separates the resonance and polar effects of the aromatic ring substituents on the reaction rate. Increases in the values of the Hammett reaction constants and are observed as the substituent constants or are increased. A sharp decrease in the product selectivity / = 26 for stepwise solvolysis of 4-methoxybenzyl chloride is observed as electron-withdrawing substituents are added to 4-methoxybenzyl ring due to a Hammond-effect on the position of the transition state for solvent addition to the substituted 4-methoxybenzyl carbocation reaction intermediates. Sharp increases in the selectivity / are observed with decreasing reactivity of other 3,4,5-subsituted benzyl chlorides due to anti-Hammond shifts on a two-dimensional More-O'Ferrall reaction coordinate diagram in the position of the transition state for a concerted solvolysis reaction.

The Diels-Alder reactivity of 5-membered dienes is tunable through spirocyclization at the saturated center. As the size of the spirocycle decreases, the Diels-Alder reactivity increases with the cyclobutane spirocycle, spiro[3.4]octa-5,7-diene, being the most reactive. Density functional theory calculations suggest that spiro[3.4]octa-5,7-diene dimerizes 220,000-fold faster than 5,5-dimethylcyclopentadiene and undergoes a Diels-Alder reaction with ethylene 1,200-fold faster than 5,5-dimethylcyclopentadiene. These findings show that spirocyclization is an effective way to enhance the Diels-Alder reactivity of geminally substituted 5-membered dienes.

In this perspective, we highlight the recent progress in utilizing Baird aromatic species to improve fluorophore performance in microscopy and imaging applications. We specifically focus on the origins of the use of Baird aromaticity in fluorescence applications, the development of “self‐healing” fluorophores leveraging cyclooctatetraene’ Baird aromaticity, and where developments need to occur to optimize this technology.

Fluorescent dyes are routinely used to visualize DNA or RNA in various experiments, and some dyes also act as photosensitizers capable of catalyzing oxidation reactions. The present studies explored whether the common labeling dyes fluorescein, rhodamine, BODIPY, or cyanine3 (Cy3) can function as photosensitizers to oxidize nucleic acid polymers. Photoirradiation of each dye in the presence of the guanine (G) heterocycle, which is the most sensitive toward oxidation, identified slow rates of nucleobase oxidation in the nucleoside and DNA contexts. For all four fluorophores studied, the only product detected was spiroiminodihydantoin (Sp) suggesting the dyes functioned as Type II photosensitizers and generate singlet oxygen (O). The nucleoside reactions were then conducted in DO solutions, known to increase the lifetime of O which resulted in a ~6-fold increase in the Sp yield, further supporting the classification of these dyes as Type II photosensitizers. Lastly, we inspected the pattern of G reactivity with the dyes upon photoirradiation in the context of a parallel-stranded G-quadruplex. The G nucleotides in the two exterior G-tetrads were found to be oxidation prone, providing the third line of evidence that the dyes are Type II photooxidants. The present work found that the common dyes fluorescein, rhodamine, BODIPY, or Cy3 can drive G oxidation but with a slow rate and low overall yield. This will likely not impact many experiments using dyes to study nucleic acids except for those that have long exposures with high-intensity lights, such as sequencing-by-synthesis experiments using fluorescence as the readout.

The glutamine transporter ASCT2 is highly overexpressed in cancer cells. Block of glutamine uptake by ASCT2 is a potential strategy to inhibit growth of cancer cells. However, pharmacology of the ASCT2 binding site is not well established. In this work, we report the computational docking to the binding site, and the synthesis of a new class of ASCT2 inhibitors based on the novel L-hydroxyhomoserine scaffold. While these compounds inhibit the ASCT2 leak anion conductance, as expected for competitive inhibitors, they did not block leak conductance in glutamate transporters (EAAT1-3 and EAAT5). They were also ineffective with respect to subtype ASCT1, which has >57% amino acid sequence similarity to ASCT2. Molecular docking studies agree very well with the experimental results and suggest specific polar interactions in the ASCT2 binding site. Our findings add to the repertoire of ASCT2 inhibitors and will aid in further studies of ASCT2 pharmacology.

Organic light-emitting diodes (OLED) have considerable advantages over the conventional counterpart. Molecular design by simulations is important for the discovery of new material candidate to improve the performance of OLED. Recently, thermally assisted delayed fluorescence OLED based on DMAC (9,9-dimethyl-9,10-dihydroacridine)-related molecules have been found to have superior performance. In this work, a series of first-principles calculations are performed on DMAC-DPS (diphenylsulfone, emission of blue-color light), DMAC-BP (benzophenone, green), DMAC-DCPP (dicyclohexylphosphonium, red), and the newly designed DMAC-BF (enaminone difluoroboron complexes, red) molecules, based on time-dependent density-functional theory, the hybrid-exchange density functional, and the long-range corrected hybrid-exchange density functional. By varying the percentage of Hartree-Fock (HF) exchange in the hybrid-exchange functional, the emission spectra can be over 97% fitted to the experimental results. We found that the fitted proportion of HF will increase as the wavelengths of the molecules decrease (30% for DPS, 20% for BP, and 10% for DCPP). By contrast, the long-range corrected hybrid-exchange density functional can lead to a good estimate on the absorption spectra. In addition, we have also applied our fitting computational procedure to the newly designed molecule. The molecular orbitals involved in the related excited states have also been investigated for these molecules, which show a common charge-transfer characteristic between the acceptor part (DPS/BP/DCPP/BF) and the donor (DMAC).

Hormones like testosterone and progesterone in the humans play significant role in the regulation of various biological processes like the body growth, reproduction, and others. In last two decades, researchers are using ionic liquids (ILs) extensively in different areas of sciences, and they are a novel class of compounds as well as their polarity can be tuned. ILs are multidisciplinary in nature and can be used in chemistry, materials science, chemical engineering, and environmental science. Further, ILs are being explored to increase the solubility of drugs or biological potential molecules. Testosterone and progesterone are found to be not very polar in nature; therefore, the authors attempt to increase the solubility of testosterone and progesterone via interaction with ILs. It was studied with density functional theory calculations using Gaussian, and an increase in the value of dipole moment is observed for the complex of testosterone/progesterone with the ILs in comparison of individual one. The optimization energy and other thermodynamic energies of the ILs (IL1-IL3), testosterone (T), testosterone-IL (T-IL1 to T-IL3), progesterone (P), and progesterone-ILs (P-IL1 to P-IL3) are found to be negative. Further, the change in free energy for the formation of complexes at room temperature is calculated. Further, the authors have investigated the synergistic effect of testosterone and progesterone against the main protease of new coronavirus using molecular docking. It is observed that the testosterone- {IL1-3-(2-hydroxyethyl)-1-methyl-1H-imidazol-3-ium 2,4,6-trinitrophenolate} is found to be prominent against the main protease of SARS-CoV-2.

Self-propagating cascade reactions are a recent development for chemo-sensing protocols. These cascade reactions, in principle, offer low limits of detection by virtue of exponential signal amplification, and are initiated by a specific, pre-planned molecular detection event. This combination of selectivity for a detection event followed by in situ signal amplification is achieved by exploitation of mechanistic organic chemistry, and thus has resulted in various chemo-sensing protocols that employ one or more reagents to achieve the desired selectivity and sensitivity for an assay. Species such as hydrogen peroxide, thiols, and fluoride, have been used as active reagents to initiate the first examples of self-propagating signal amplification reactions, although many other active reagents should be compatible with the approaches. A common feature of the reagents that support the self-propagating signal amplification reactions is the involvement of quinonemethide intermediates resulting from elimination of optical reporters and/or active reagents, where the latter propagates the signal amplification reaction. The early examples of these amplification sequences, however, are slow to reach full signal, thus leaving time for background reactions to generate non-specific signals. This issue of background has limited practical applications of these self-propagating signal amplification reactions, as has challenging synthetic routes to the reagents, as well as the potential for other chemical species to interfere with the detection and signal amplification processes. Thus, the goal of this review is to summarize the progress of self-propagating signal amplification technology, identify the pitfalls of current designs, and by doing so, to stimulate future studies in this growing and promising research area.

Acridonylalanine (Acd) is a useful fluorophore for studying proteins by fluorescence spectroscopy, but it can potentially be improved by being made longer wavelength or brighter. Here, we report the synthesis of Acd core derivatives and their photophysical characterization. We also performed calculations of the absorption and emission spectra of Acd derivatives, which agree well with experimental measurements. The amino acid aminoacridonylalanine (Aad) was synthesized in forms appropriate for genetic incorporation and peptide synthesis. We show that Aad is a superior FRET acceptor to Acd in a peptide cleavage assay, and that Aad can be activated by an aminoacyl tRNA synthetase for genetic incorporation. Together, these results show that we can use computation to design enhanced Acd derivatives which can be used in peptides and proteins.

The results of studies on the structure and reactivity of spiro[5.2]oct-5,7-diene-4yl carbocation [phenonium ion] have had a significant impact on the course of discussion about the distinction between classical and nonclassical carbocations. This minireview will present a brief overview of the structure, bonding and reactivity of ring substituted phenonium ions (), with an emphasis on work completed since 2004. The discussion will focus on the development of new experimental protocol for determination of the selectivity for addition of nucleophilic anions to in aqueous solution. The existing relationships between carbocation lifetime and nucleophilic selectivity, and the known lifetime of 140 sec for [2.5]oct-4,7-diene-6-one provide rough estimates of the lifetimes for and in aqueous solution. Evidence is presented that nucleophile addition to proceeds through an "exploded" transition state, with relatively weak bonding the nucleophile and leaving group, and the development of significant positive charge at the reacting primary cyclopropyl carbon.

The Kemp elimination is prototypical reaction used to study proton abstraction from carbon. Several hydrophobic systems are known to accelerate this reaction, including two classes of computationally-designed enzymes. However, it is unclear whether these computationally-designed enzymes establish specific interactions with their substrates, as natural enzymes do, or if most of the rate acceleration is due to the hydrophobicity of the substrate. We used a simple system composed of cationic micelles and a long chain base (such as lauryl phosphate or lauric acid) to measure the rate acceleration for the Kemp elimination. Remarkably, we found that this simple system can accelerate the reaction by 4 orders of magnitude, approaching the rates of more complex designed systems. Use of different substrates suggests that the reaction takes place at the interface between the micellar head and water (the Stern layer) with the long-chain base embedded in the micelle and the substrate in the aqueous solution. Thus, we suggest that significant rate accelerations can be achieved regardless of the precise positioning of substrates. Because natural enzymes use specific interactions to position their substrates, we propose that acceleration of the Kemp elimination is not a suitable benchmark for the success of the design process, and we suggest that more complex reactions should be used.

Nature's selection of the contemporary nucleobases in RNA and DNA continues to intrigue the origin of life community. While the prebiotic synthesis of the -glycosyl bond has historically been a central area of investigation, variations in hydrolytic stabilities among the -glycosyl bonds may have presented an additional selection pressure that contributed to nucleobase and nucleoside evolution. To experimentally probe this hypothesis, a systematic kinetic analysis of the hydrolytic deglycosylation reactions of modified, alternative and native nucleosides was undertaken. Rate constants were measured as a function of temperature (at pH 1) to produce Arrhenius and Eyring plots for extrapolation to 37°C and determination of thermodynamic activation parameters. Rate enhancements based on the differences in reaction rates of deoxyribo- and ribo-glycosidic bonds were found to vary under the same conditions. Rate constants of deoxynucleosides were also measured across the pH range of 1 - 3 (at 50°C), which highlighted how simple changes to the heterocycle alone can lead to significant variation in deglycosylation rates. The contemporary nucleosides exhibited the slowest deglycosylation rates in comparison to the non-native/alternative nucleosides, which we suggest as experimental support for nature's selection of the fittest -glycosyl bonds.

The mechanistic imperatives for catalysis of deprotonation of α-carbonyl carbon by triosephosphate isomerase (TIM) are discussed. There is a strong imperative to reduce the large thermodynamic barrier for deprotonation of carbon to form an enediolate reaction intermediate; and, a strong imperative for specificity in the expression of the intrinsic phosphodianion binding energy at the transition state for the enzyme-catalyzed reaction. Binding energies of 2 and 6 kcal/mol, respectively, have been determined for formation of phosphite dianion complexes to TIM and to the transition state for TIM-catalyzed deprotonation of the truncated substrate glycolaldehyde [T. L. Amyes, J. P. Richard, , , 5841]. We propose that the phosphite dianion binding energy, which is specifically expressed at the transition state complex, is utilized to stabilize a rare catalytically active loop-closed form of TIM. The results of experiments to probe the role of the side chains of Ile172 and Leu232 in activating the loop-closed form of TIM for catalysis of substrate deprotonation are discussed. Evidence is presented that the hydrophobic side chain of Ile172 assists in activating TIM for catalysis of substrate deprotonation through an enhancement of the basicity of the carboxylate side-chain of Glu167. Our experiments link the two imperatives for TIM-catalyzed deprotonation of carbon by providing evidence that the phosphodianion binding energy is utilized to drive an enzyme conformational change, which results in a reduction in the thermodynamic barrier to deprotonation of the carbon acid substrate at TIM compared with the barrier for deprotonation in water. The effects of a P168A mutation on the kinetic parameters for the reactions of whole and truncated substrates are discussed.

The capability to identify and sequence DNA damage within the context of the genome is an important goal for medical diagnostics. However, currently available methods are not suitable for this purpose. Ion channel nanopore analysis shows promise as a potential single-molecule method to sequence genomic DNA in such a way that also allows detection of base or backbone modifications. Recent studies in human cell lines demonstrated the occurrence of a new DNA cross-link between guanine(C8) and thymine(N3) (5'-G*CT*-3'). The current work presents immobilization and translocation studies of the 5'-G*CT*-3' cross-link in a single-stranded oligodeoxynucleotide using the α-hemolysin (α-HL) ion channel. A 3'-biotinylated DNA strand containing the 5'-G*CT*-3' cross-link was incubated with streptavidin that allowed immobilization of the DNA in the β-barrel of α-HL. In this experiment, the 5'-G*CT*-3' cross-link was placed near the sensitive constriction zone of α-HL, yielding a 2.5% deeper blockage to the ion current level when compared to the unmodified strand. Next, free translocation of a cross-link-containing strand was studied, and an inverse relationship of the time constant with respect to an increase in the applied voltage was found, indicating that the cross-link can easily fit into the β-barrel and traverse through the ion channel. However, a modulation in the ion current level was not observed. These studies suggest that higher resolution ion channels or mechanisms to slow the translocation process, or both, might ultimately provide a mechanism for single-molecule sequencing for G-T cross-links.

The glucose dehydrogenase of the mesophilic bacterium (optimal growth around 35 °C) exhibits non-linear Eyring temperature dependences from 25 to 55 °C in its catalysis of the oxidation by hydride-transfer to NAD of the β-anomers of 1--D-glucose and 1--D-glucose (rate constant k/K). A break around 300K separates a high-T region from a low-T region. In the high-T region, isotopic enthalpies of activation within a considerable experimental error are equal to zero. In the low-T region, the enthalpies of activation are roughly equal for the isotopic substrates but are different from zero. An alternative treatment with Eyring plots taken as effectively linear produces enthalpies of activation having the unusual feature of being larger for the H-substrate (26 kJ/mol) than for the D-substrate (21 kJ/mol). Compensation of the enthalpic effect by a more positive entropy for the H-substrate then reproduces the isotope effects. For oxidation by NADP of the same pair of isotopic glucose substrates, catalysis by the glucose dehydrogenase of , a thermophilic archaeon, leads to temperature dependences characterized by a high-T region and a low-T region separated by a gentle thermal transition (K. Anandarajah, K.B. Schowen, and R.L. Schowen, 2008, 1333-1347). Tentative approaches to a mechanistic interpretation of both cases rely on models featuring configurational searches of the enzyme for tunneling states, followed by hydrogen-transfer tunneling, although explanations can be constructed also on the basis of simple transition-state stabilization without tunnelling.

The reaction of 2-(4-methyphenyl)ethyl tosylate () in 50/50 (v/v) trifluoroethanol/water at 25 °C is first-order in the concentration of azide anion nucleophile. A carbon-13 NMR analysis of the products of the reactions of in 50/50 (v/v) trifluoroethanol/water at 25 °C shows the formation of , and from the trapping of a symmetrical 4-methylphenonium ion reaction intermediate . The formation of by concerted bimolecular displacement of azide ion at ( = 3.8 × 10 M s) and of and by concerted bimolecular displacement of solvent ( = 1.8 × 10 s) is also observed. An analysis of the rate and product data provides a value of / = 32 M for partitioning of between addition of azide ion and solvent that is nearly 3-fold smaller than / = 83 M reported in an earlier study on the partitioning of [, , 9568]. This change is attributed to a decrease in nucleophile selectivity with increasing electrophile reactivity for the activation-limited addition of solvent and azide anion to . These data set a limit of 1/ ≥ 10 s for the lifetime of in aqueous solution.

Reactive intermediates are key species involved in many chemical and biochemical processes. For example, carbon-centered aromatic σ,σ-biradicals formed in biological systems from naturally occurring enediyne antitumor antibiotics are responsible for the irreversible cleavage of double-stranded DNA caused by these prodrugs. However, because of their high reactivity, it is very difficult or impossible to isolate and investigate these biradicals. The aromatic σ,σ-biradical, 2,6-didehydropyridine, has been speculated for many years to be formed in certain organic reactions; however, no definitive proof of its generation has been obtained. We report here the successful generation of protonated 2,6-didehydropyridine and the examination of its chemical properties in the gas phase by using a Fourier transform ion cyclotron resonance mass spectrometer. The results suggest that a mixture of singlet (ground) state and triplet (excited) state 2,6-didehydropyridinium cations was generated. The two different states show qualitatively different reactivity, with the triplet state showing greater Brønsted acidity than that of the singlet state. The triplet state also shows much greater radical reactivity than that of the singlet state, as expected because of the coupling of the nonbonding electrons in the singlet state.

We have performed high level quantum mechanical calculations for aminoethene and the three isomeric 1,1- ()- or ()-1,2-diaminoethenes as well as their singly and doubly charged cations derived by loss of electrons and/or upon protonation. Gas phase molecular structures were computed at the MP2/6-311+G(3df,2p) level. Standard molar enthalpies of formation in the gas phase, at = 298.15 K were estimated using the G3 composite method and atomization, isodesmic and homodesmotic reactions. Other energetic parameters were also calculated at the G3 level: proton affinities, basicities and adiabatic ionization enthalpies. Theoretical and experimental data are compared. The reported experimental data refer only to aminoethene wherein the standard molar enthalpy of formation has a considerable uncertainty, although the molecular structure is well-established. There are no such data, neither structural nor thermochemical, for any of the three isomeric diaminoethenes. Isoelectronic comparisons are made. For example, the diprotonated diaminoethenes are isoelectronic to isobutene and ()- and ()-butene, while the doubly ionized diaminoethenes are likewise related to trimethylenemethane and 1,3-butadiene.

We designed, synthesized and screened a library of analogs of the organophosphate pesticide metabolite paraoxon against a recombinant variant of human serum paraoxonase-1. Alterations of both the aryloxy leaving group and the retained alkyl chains of paraoxon analogs resulted in substantial changes to binding and hydrolysis, as measured directly by spectrophotometric methods or in competition experiments with paraoxon. Increases or decreases in the steric bulk of the retained groups generally reduced the rate of hydrolysis, while modifications of the leaving group modulated both binding and turnover. Studies on the hydrolysis of phosphoryl azide analogs as well as amino-modified paraoxon analogs, the former being developed as photo-affinity labels, found enhanced tolerance of structural modifications, when compared with -alkyl substituted molecules. Results from computational modeling predict a predominant active site binding mode for these molecules which is consistent with several proposed catalytic mechanisms in the literature, and from which a molecular-level explanation of the experimental trends is attempted. Overall, the results of this study suggest that while paraoxonase-1 is a promiscuous enzyme, there are substantial constraints in the active site pocket, which may relate to both the leaving group and the retained portion of paraoxon analogs.

The base-induced rearrangement of aziridines has been examined using a combination of calculations and experiment. The calculations show that the substituent on nitrogen is a critical feature that greatly affects the favorability of both α-deprotonation, and β-elimination to form an allylic amine. Experiments were carried out to determine whether E2-like rearrangement to the allylic amine with lithium diisopropyl amide (LDA) is possible. N-Tosyl aziridines were found to deprotonate on the tosyl group, preventing further reaction. A variety of N-benzenesulfonyl aziridines having both α- and β-protons decomposed when treated with LDA in either tetrahydrofuran or hexamethylphosphoramide. However, when α-protons were not present, allylic amine was formed, presumably via β-elimination.