NMR exchange dynamics studies of metal-capped cyclodextrins reveal multiple populations of host-guest complexes in solution.

Metal-capped molecular hosts are unique in supramolecular chemistry, benefitting from the inner cavity's hydrophobic nature and the metal center's electrochemical properties. It is shown here that the paramagnetic properties of the metals in lanthanide-capped cyclodextrins (Ln-α-CDs and Ln-ß-CDs) are a convenient NMR indicator for different populations of host-guest complexes in a given solution. The paramagnetic guest exchange saturation transfer (paraGEST) method was used to study the exchange dynamics in systems composed of Ln-α-CDs or Ln-ß-CDs with fluorinated guests, revealing multiple co-existing populations of host-guest complexes exclusively in solutions containing Ln-ß-CDs. The enhanced spectral resolution of paraGEST, achieved by a strong pseudo contact shift induction, revealed that different molecular guests can adopt multiple orientations within Ln-ß-CDs' cavities and, in contrast, only a single orientation inside Ln-α-CDs. Thus, paraGEST, which can significantly improve NMR detectability and spectral resolution of host-guest systems that experience fast exchange dynamics, is a convenient tool for studying supramolecular systems of metal-capped molecular hosts.

Measurement of Water Saturation in Soybean Oil.

In a previous study, it was observed that survivability was low when attempting to cryopreserve sperm cells in a nanoliter-sized droplet protected under soybean oil, in stark contrast to the high survival rates in milliliter-sized droplets. In this study, infrared spectroscopy was used to provide an estimate of the saturation concentration of water in soybean oil. By following the time evolution of the infrared absorption spectrum of water-oil mixtures, the saturation of water in soybean oil was found to reach equilibrium after 1 h. From the absorption spectra of neat water and neat soybean oil and the application of the Beer-Lambert law to an estimation of the absorption of a mixture from its individual components, it was estimated that the saturation concentration of water is 0.010 M. This estimate was supported by molecular modeling using the latest semiempirical methods (in particular, GFN2-xTB). While for most applications the very low solubility has little impact, the implications in those exceptions were discussed.

Fluorophore spectroscopy in aqueous glycerol solution: the interactions of glycerol with the fluorophore.

A common perception exists that glycerol provides an inert-like environment modifying viscosity and index of refraction by its various concentrations in aqueous solution. Said perception is herein challenged by investigating the effects of the glycerol environment on the spectroscopic properties of fluorescein, as a representative fluorophore, using steady-state and time-resolved techniques and computational chemistry. Results strongly suggest that the fluorescence quantum yield, measured fluorescence lifetime (FLT), natural lifetime and calculated fluorescence lifetime are all highly sensitive to the presence of glycerol. Glycerol was found to impact both the ground and first excited states of fluorescein, quenching and modifying both absorption and emission spectra, affecting the fundamental electrical dipoles of the ground and first excited singlet states, and lowering FLT and quantum yield. Furthermore, the Stern-Volmer, Lippert-Mataga, Perrin and Strickler-Berg relations indicate that glycerol acts upon fluorescein in aqueous solution as a quencher and alters the fluorescein geometry. Predictions made by computational chemistry impressively correspond to experimental results, both indicating changes in the properties of fluorescein at around 35% v/v aqueous glycerol, a clear indication that glycerol is not an innocent medium. This study proposes the Strickler-Berg relation as a means of detecting non-negligible effects of a hosting medium on its host fluorophore. These new insights on the molecular structures, the interactions between glycerol and its host fluorophore, and the effects of one on the other may be essential for understanding fundamental phenomena in chemistry and related fields.

Noncovalent Bonding Caught in Action: From Amorphous to Cocrystalline Molecular Thin Films.

We demonstrate the solvent-free amorphous-to-cocrystalline transformations of nanoscale molecular films. Exposing amorphous films to vapors of a haloarene results in the formation of a cocrystalline coating. This transformation proceeds by gradual strengthening of halogen-bonding interactions as a result of the crystallization process. The gas-solid diffusion mechanism involves formation of an amorphous metastable phase prior to crystallization of the films. In situ optical microscopy shows mass transport during this process, which is confirmed by cross-section analysis of the final structures using focused ion beam milling combined with scanning electron microscopy. Nanomechanical measurements show that the rigidity of the amorphous films influences the crystallization process. This surface transformation results in molecular arrangements that are not readily obtained through other means. Cocrystals grown in solution crystallize in a monoclinic centrosymmetric space group, whereas the on-surface halogen-bonded assembly crystallizes into a noncentrosymmetric material with a bulk second-order nonlinear optical response.

The formyloxyl radical: electrophilicity, C-H bond activation and anti-Markovnikov selectivity in the oxidation of aliphatic alkenes.

In the past the formyloxyl radical, HC(O)O˙, had only been rarely experimentally observed, and those studies were theoretical-spectroscopic in the context of electronic structure. The absence of a convenient method for the preparation of the formyloxyl radical has precluded investigations into its reactivity towards organic substrates. Very recently, we discovered that HC(O)O˙ is formed in the anodic electrochemical oxidation of formic acid/lithium formate. Using a [CoIIIW12O40]5- polyanion catalyst, this led to the formation of phenyl formate from benzene. Here, we present our studies into the reactivity of electrochemically in situ generated HC(O)O˙ with organic substrates. Reactions with benzene and a selection of substituted derivatives showed that HC(O)O˙ is mildly electrophilic according to both experimentally and computationally derived Hammett linear free energy relationships. The reactions of HC(O)O˙ with terminal alkenes significantly favor anti-Markovnikov oxidations yielding the corresponding aldehyde as the major product as well as further oxidation products. Analysis of plausible reaction pathways using 1-hexene as a representative substrate favored the likelihood of hydrogen abstraction from the allylic C-H bond forming a hexallyl radical followed by strongly preferred further attack of a second HC(O)O˙ radical at the C1 position. Further oxidation products are surmised to be mostly a result of two consecutive addition reactions of HC(O)O˙ to the C[double bond, length as m-dash]C double bond. An outer-sphere electron transfer between the formyloxyl radical donor and the [CoIIIW12O40]5- polyanion acceptor forming a donor-acceptor [D+-A-] complex is proposed to induce the observed anti-Markovnikov selectivity. Finally, the overall reactivity of HC(O)O˙ towards hydrogen abstraction was evaluated using additional substrates. Alkanes were only slightly reactive, while the reactions of alkylarenes showed that aromatic substitution on the ring competes with C-H bond activation at the benzylic position. C-H bonds with bond dissociation energies (BDE) ≤ 85 kcal mol-1 are easily attacked by HC(O)O˙ and reactivity appears to be significant for C-H bonds with a BDE of up to 90 kcal mol-1. In summary, this research identifies the reactivity of HC(O)O˙ towards radical electrophilic substitution of arenes, anti-Markovnikov type oxidation of terminal alkenes, and indirectly defines the activity of HC(O)O˙ towards C-H bond activation.

Manganese Catalyzed Hydrogenation of Carbamates and Urea Derivatives.

We report the hydrogenation of carbamates and urea derivatives, two of the most challenging carbonyl compounds to be hydrogenated, catalyzed for the first time by a complex of an earth-abundant metal. The hydrogenation reaction of these CO2-derived compounds, catalyzed by a manganese pincer complex, yields methanol in addition to amine and alcohol, which makes this methodology a sustainable alternative route for the conversion of CO2 to methanol, involving a base-metal catalyst. Moreover, the hydrogenation proceeds under mild pressure (20 bar). Our observations support a hydrogenation mechanism involving the Mn-H complex. A plausible catalytic cycle is proposed based on informative mechanistic experiments.

Cost-effective density functional theory (DFT) calculations of equilibrium isotopic fractionation in large organic molecules.

The application of stable isotopes to address a wide range of biochemical, microbiological and environmental problems is hindered by the experimental difficulty and the computational cost of determining equilibrium isotopic fractionations (EIF) of large organic molecules. Here, we evaluate the factors that impact the accuracy of computed EIFs and develop a framework for cost-effective and accurate computation of EIFs by density functional theory (DFT). We generated two benchmark databases of experimentally determined EIFs, one for H isotopes and another for the isotopes of the heavy atoms C, N and O. The accuracy of several DFT exchange-correlation functionals in calculating EIFs was then evaluated by comparing the computational results to these experimental datasets. We find that with the def2-TZVP basis set, O3LYP had the lowest mean absolute deviation (21‰ and 3.9‰ for the isotopic fractionation of H and the heavier atoms, respectively), but the GGA/meta-GGA functionals τHCTHD3BJ, τHCTH and HCTH have similar performances (22‰ and 4.1‰, respectively, for τHCTHD3BJ). Leveraging the good performance of computationally efficient functionals, we provide a robust, practical, experimentally validated framework for using DFT to accurately predict EIFs of large organic molecules, including uncertainty estimates.

Evaluating Transition Metal Barrier Heights with the Latest Density Functional Theory Exchange-Correlation Functionals: The MOBH35 Benchmark Database.

A new database of transition metal reaction barrier heights (MOBH35) is presented. Benchmark energies (forward and reverse barriers and reaction energy) are calculated using DLPNO-CCSD(T) extrapolated to the complete basis set limit using a Weizmann-1-like scheme. Using these benchmark energies, the performance of a wide selection of density functional theory (DFT) exchange-correlation functionals, including the latest from the Martin, Truhlar, and Head-Gordon groups, is evaluated. It was found, using the def2-TZVPP basis set, that the ωB97M-V (MAD 1.7 kcal/mol), ωB97M-D3BJ (MAD 1.9 kcal/mol), ωB97X-V (MAD 2.0 kcal/mol), and revTPSS0-D4 (MAD 2.2 kcal/mol) hybrid functionals are recommended. The double-hybrid functionals B2K-PLYP (MAD 1.7 kcal/mol) and revDOD-PBEP86-D4 (MAD 1.8 kcal/mol) also performed well, but this has to be balanced by their increased computational cost.

Dynamic Interactions in Synthetic Receptors: A Guest Exchange Saturation Transfer Study.

The accumulated knowledge regarding molecular architectures is based on established, reliable, and accessible analytical tools that provide robust structural and functional information on assemblies. However, both the dynamicity and low population of noncovalently interacting moieties within studied molecular systems limit the efficiency and accuracy of traditional methods. Herein, the use of a saturation transfer-based NMR approach to study the dynamic binding characteristics of an anion to a series of synthetic receptors derived from bambusuril macrocycles is demonstrated. The exchange rates of BF4 - are mediated by the side chains on the receptor (100 s-1

The cationic dye basic orange 21 (BO21) as a potential fluorescent sensor.

The present study investigates the fluorescence properties of BO21 and their dependence on various intracellular conditions. The results obtained with cell-free solutions indicate that the influences of pH and temperature on the fluorescence spectra are negligible, while viscosity, various proteins and heparin have significant influence. In the presence of heparin, a red shift of the emission spectrum (from 515 to 550 nm) is observed, suggesting that this shift cannot simply be attributed to electrostatic interaction between BO21 and the polyanionic heparin, but rather to aggregation of BO21 on the polyanion. In water, the quantum yield of BO21 was found to be 1000 times lower than that of fluorescein, yet surprisingly its fluorescence polarization (FP) was found to be about 40 times higher (FP = 0.470), even though both have similar structures and molecular weights. A thorough analytical and experimental investigation of these phenomena indicates that the very high FP of BO21 in water is a consequence of its very short lifetime. However, upon the addition of heparin to aqueous BO21, the fluorescence lifetime (FLT) of BO21 increases from τ = 10.35 to 56.5 ps, with a consequent dramatic drop in its fluorescence polarization from 0.470 to 0.230. From its behavior in aqueous glycerol solution, it is hypothesized, with support from theoretical calculations, that BO21 is a molecular rotor. Using these properties, BO21 may be a good candidate as a sensor, for example, of heparin levels in blood or of intracellular viscosity.

Self-Assembled Hybrid Materials Based on Organic Nanocrystals and Carbon Nanotubes.

Organic crystalline materials are used as dyes/pigments, pharmaceuticals, and active components of photonic and electronic devices. There is great interest in integrating organic crystals with inorganic and carbon nanomaterials to create nanocomposites with enhanced properties. Such efforts are hampered by the difficulties in interfacing organic crystals with dissimilar materials. Here, an approach that employs organic nanocrystallization is presented to fabricate solution-processed organic nanocrystal/carbon nanotube (ONC/CNT) hybrid materials based on readily available organic dyes (perylene diimides (PDIs)) and carbon nanotubes. The hybrids are prepared by self-assembly in aqueous media to afford free-standing films with tunable CNT content. These exhibit excellent conductivities (as high as 5.78 ± 0.56 S m-1 ), and high thermal stability that are superior to common polymer/CNT hybrids. The color of the hybrids can be tuned by adding various PDI derivatives. ONC/CNT hybrids represent a novel class of nanocomposites, applicable as optoelectronic and conductive colorant materials.

Evaluation of the Factors Impacting the Accuracy of 13C NMR Chemical Shift Predictions using Density Functional Theory-The Advantage of Long-Range Corrected Functionals.

The various factors influencing the accuracy of 13C NMR calculations using density functional theory (DFT), including the basis set, exchange-correlation (XC) functional, and isotropic shielding calculation method, are evaluated. A wide selection of XC functionals (over 70) were considered, and it was found that long-range corrected functionals offer a significant improvement over the other classes of functionals. Based on a thorough study, it is recommended that for calculating NMR chemical shifts (δ) one should use the CSGT method, the COSMO solvation model, and the LC-TPSSTPSS exchange-correlation functional in conjunction with the cc-pVTZ basis set. A selection of problems in natural product identification are considered in light of the newly recommended level of theory.

Enolonium Species-Umpoled Enolates.

Enolonium species/iodo(III)enolates of carbonyl compounds have been suggested to be intermediates in a wide variety of hypervalent iodine induced chemical transformations of ketones, including α-C-O, α-C-N, α-C-C, and α-carbon-halide bond formation, but they have never been characterized. We report that these elusive umpoled enolates may be made as discrete species that are stable for several minutes at -78 °C, and report the first spectroscopic identification of such species. It is shown that enolonium species are direct intermediates in C-O, C-N, C-Cl, and C-C bond forming reactions. Our results open up chemical space for designing a variety of new transformations. We showcase the ability of enolonium species to react with prenyl, crotyl, cinnamyl, and allyl silanes with absolute regioselectivity in up to 92 % yield.

Mechanism of the Copper/TEMPO-Catalyzed Aerobic Oxidation of Alcohols.

Identifying the mechanism of a catalytic reaction is paramount for designing new and improved catalysts. Several alternative catalytic cycles for the copper/2,2,6,6-tetramethylpiperidine-N-oxyl (TEMPO)-catalyzed aerobic oxidation of alcohols to the corresponding aldehydes or ketones were examined using DFT at the SMD(CH3 CN)-RIJCOSX-DSD-PBEB95/def2-TZVP//DF-PBED3BJ /def2-SVP level of theory. A catalytic cycle in which TEMPO remains coordinated to copper throughout was identified as the most likely mechanism. There are three components to the catalytic cycle: 1) hydrogen transfer from the alkoxyl ligand to coordinated TEMPO, 2) oxygen activation with formation of a peroxo complex, and 3) alcohol activation with transfer of the OH proton to the peroxo ligand. The oxidation takes place via a six-membered intramolecular hydrogen-transfer transition state. Importantly, this is not the rate-determining step, which instead involves oxygen activation and/or the initial alcohol activation.

Overcoming artificial broadening in Gd(3+)-Gd(3+) distance distributions arising from dipolar pseudo-secular terms in DEER experiments.

By providing accurate distance measurements between spin labels site-specifically attached to bio-macromolecules, double electron-electron resonance (DEER) spectroscopy provides a unique tool to probe the structural and conformational changes in these molecules. Gd(3+)-tags present an important family of spin-labels for such purposes, as they feature high chemical stability and high sensitivity in high-field DEER measurements. The high sensitivity of the Gd(3+) ion is associated with its high spin (S = 7/2) and small zero field splitting (ZFS), resulting in a narrow spectral width of its central transition at high fields. However, under the conditions of short distances and exceptionally small ZFS, the weak coupling approximation, which is essential for straightforward DEER data analysis, becomes invalid and the pseudo-secular terms of the dipolar Hamiltonian can no longer be ignored. This work further explores the effects of pseudo-secular terms on Gd(3+)-Gd(3+) DEER measurements using a specifically designed ruler molecule; a rigid bis-Gd(3+)-DOTA model compound with an expected Gd(3+)-Gd(3+) distance of 2.35 nm and a very narrow central transition at the W-band (95 GHz). We show that the DEER dipolar modulations are damped under the standard W-band DEER measurement conditions with a frequency separation, Δν, of 100 MHz between the pump and observe pulses. Consequently, the DEER spectrum deviates considerably from the expected Pake pattern. We show that the Pake pattern and the associated dipolar modulations can be restored with the aid of a dual mode cavity by increasing Δν from 100 MHz to 1.09 GHz, allowing for a straightforward measurement of a Gd(3+)-Gd(3+) distance of 2.35 nm. The increase in Δν increases the contribution of the |-5/2〉→|-3/2〉 and |-7/2〉→|-5/2〉 transitions to the signal at the expense of the |-3/2 〉→|-1/2〉 transition, thus minimizing the effect of dipolar pseudo-secular terms and restoring the validity of the weak coupling approximation. We apply this approach to the A93C/N140C mutant of T4 lysozyme labeled with two different Gd(3+) tags that have narrow central transitions and show that even for a distance of 4 nm there is still a significant (about two-fold) broadening that is removed by increasing Δν to 636 MHz and 898 MHz.

Amplifying undetectable NMR signals to study host-guest interactions and exchange.

The characteristics of host-guest systems, such as molecular recognition, complexation, encapsulation, guest composition, and dynamic exchange, are manifested by changes in the chemical shifts (Δω) in the NMR spectrum. However, in cases where NMR signals cannot be detected, due to low concentrations, poor solubility, or relatively fast exchange, an alternative is needed. Here, we show that by using the magnetization transfer (MT) method, the undetectable NMR signals of host-guest assemblies can be amplified by two orders of magnitude. It is shown that the binding kinetics characteristics of a fluorinated guest and cucurbit[n]uril (CB[n]) hosts in aqueous solutions determine the NMR signal amplification of host-guest assemblies. In addition, by using the MT technique within the 19F-NMR framework, one can detect µM concentrations of the complex and study the effect of different solutes on the resulting host-guest system. The results expand the "NMR toolbox" available to explore a wider range of dynamic host-guest systems in which NMR signals cannot be detected.

Synthesis and stability of cyclic α-hydrogen nitroxides.

Nitroxides (nitroxyl radicals) hold a unique place in science due to their stable radical nature. We have recently reported the first design concept providing a general solution to the problem of designing and preparing monocyclic α-hydrogen nitroxides. The initial studies were limited to aryl derivatives. We now report a wider study showing that alkyl substituents may be employed as well. In addition, we report several additional examples of aryl substituents and reveal some of the structural limitations with regard to nitroxide stability as a function of the α-carbon substituent.

Mechanistic Aspects of Aryl-Halide Oxidative Addition, Coordination Chemistry, and Ring-Walking by Palladium.

This contribution describes the reactivity of a zero-valent palladium phosphine complex with substrates that contain both an aryl halide moiety and an unsaturated carbon-carbon bond. Although η(2) -coordination of the metal center to a C=C or C≡C unit is kinetically favored, aryl halide bond activation is favored thermodynamically. These quantitative transformations proceed under mild reaction conditions in solution or in the solid state. Kinetic measurements indicate that formation of η(2) -coordination complexes are not nonproductive side-equilibria, but observable (and in several cases even isolated) intermediates en route to aryl halide bond cleavage. At the same time, DFT calculations show that the reaction with palladium may proceed through a dissociation-oxidative addition mechanism rather than through a haptotropic intramolecular process (i.e., ring walking). Furthermore, the transition state involves coordination of a third phosphine to the palladium center, which is lost during the oxidative addition as the C-halide bond is being broken. Interestingly, selective activation of aryl halides has been demonstrated by adding reactive aryl halides to the η(2) -coordination complexes. The product distribution can be controlled by the concentration of the reactants and/or the presence of excess phosphine.

A novel liquid organic hydrogen carrier system based on catalytic peptide formation and hydrogenation.

Hydrogen is an efficient green fuel, but its low energy density when stored under high pressure or cryogenically, and safety issues, presents significant disadvantages; hence finding efficient and safe hydrogen carriers is a major challenge. Of special interest are liquid organic hydrogen carriers (LOHCs), which can be readily loaded and unloaded with considerable amounts of hydrogen. However, disadvantages include high hydrogen pressure requirements, high reaction temperatures for both hydrogenation and dehydrogenation steps, which require different catalysts, and high LOHC cost. Here we present a readily reversible LOHC system based on catalytic peptide formation and hydrogenation, using an inexpensive, safe and abundant organic compound with high potential capacity to store and release hydrogen, applying the same catalyst for loading and unloading hydrogen under relatively mild conditions. Mechanistic insight of the catalytic reaction is provided. We believe that these findings may lead to the development of an inexpensive, safe and clean liquid hydrogen carrier system.