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Ion-pair interactions between a cationic ruthenium complex, [Ru(dtb)2(dea)][PF6]2, C1 2+ where deais 4,4′-diethanolamide-2,2′-bipyridine and dtbis 4,4′-di-tert-butyl-2,2′-bipyridine, and chloride, bromide, and iodide are reported. A remarkable result is that a 1:1 iodide:excited-state ion-pair, [ C1 2+ , I – ]+*, underwent diffusional electron-transfer oxidation of iodide that did not occur when ion-pairing was absent. The ion-pair equilibrium constants ranged 104–106M–1in CH3CN and decreased in the order Cl–> Br–> I–. The ion-pairs had longer-lived excited states, were brighter emitters, and stored more free energy than did the non-ion-paired states. The1H NMR spectra revealed that the halides formed tight ion-pairs with the amide and alcohol groups of the dealigand. Electron-transfer reactivity of the ion-paired excited state was not simply due to it being a stronger photooxidant than the non-ion-paired excited state. Instead, work term, ΔG wwas the predominant contributor to the driving force for the reaction. Natural bond order calculations provided natural atomic charges that enabled quantification of ΔG wfor all the atoms in C1 2+ and [ C1 2+ , I – ]+*presented herein as contour diagrams that show the most favorable electrostatic positions for halide interactions. The results were most consistent with a model wherein the non-ion-paired C1 2+* excited state traps the halide and prevents its oxidation, but allows for dynamic oxidation of a second iodide ion. [ABSTRACT FROM AUTHOR]

The homotetrameric M2 proton channel of influenza A plays a crucial role in the viral life cycle and is thus an important therapeutic target. It selectively conducts protons against a background of other competing cations whose concentrations are up to a million times greater than the proton concentration. Its selectivity is largely determined by a constricted region of its open pore known as the selectivity filter, which is lined by four absolutely conserved histidines. While the mechanism of proton transport through the channel has been studied, the physical principles underlying the selectivity for protons over other cations in the channel's His4 selectivity filter remain elusive. Furthermore, it is not known if proton selectivity absolutely requires all four histidines with two of the four histidines protonated and if other titratable amino acid residues in lieu of the histidines could bind protons and how they affect proton selectivity. Here, we elucidate how the competition between protons and rival cations such as Na+ depends on the selectivity filter's (1) histidine protonation state, (2) solvent exposure, (3) oligomeric state (the number of protein chains and thus the number of His ligands), and (4) ligand composition by evaluating the free energies for replacing monovalent Na+ with H3O+ in various model selectivity filters. We show that tetrameric His4 filters are more proton-selective than their trimeric His3 counterparts, and a dicationic His4 filter where two of the four histidines are protonated is more proton-selective than tetrameric filters with other charge states/composition (different combinations of His protonation states or different metal-ligating ligands). The [His4]2+ filter achieves proton selectivity by providing suboptimal binding conditions for rival cations such as Na+, which prefers a neutral or negatively charged filter instead of a dicationic one, and three rather than four ligands with oxygen-ligating atoms. [ABSTRACT FROM AUTHOR]

The protonation–reduction of a dioxygen adduct with [LCuI][B(C6F5)4], cupric superoxo complex [LCuII(O2•–)]+ (1) (L = TMG3tren (1,1,1-tris[2-[N2-(1,1,3,3-tetramethylguanidino)]ethyl]amine)) has been investigated. Trifluoroacetic acid (HOAcF) reversibly associates with the superoxo ligand in ([LCuII(O2•–)]+) in a 1:1 adduct [LCuII(O2•–)(HOAcF)]+ (2), as characterized by UV–visible, resonance Raman (rR), nuclear magnetic resonance (NMR), and X-ray absorption (XAS) spectroscopies, along with density functional theory (DFT) calculations. Chemical studies reveal that for the binding of HOAcF with 1 to give 2, Keq = 1.2 × 105 M–1 (−130 °C) and ΔHo = −6.9(7) kcal/mol, ΔSo = −26(4) cal mol–1 K–1). Vibrational (rR) data reveal a significant increase (29 cm–1) in vO–O (= 1149 cm–1) compared to that known for [LCuII(O2•–)]+ (1). Along with results obtained from XAS and DFT calculations, hydrogen bonding of HOAcF to a superoxo O-atom in 2 is established. Results from NMR spectroscopy of 2 at −120 °C in 2-methyltetrahydrofuran are also consistent with 1/HOAcF = 1:1 formulation of 2 and with this complex possessing a triplet (S = 1) ground state electronic configuration, as previously determined for 1. The pre-equilibrium acid association to 1 is followed by outer-sphere electron-transfer reduction of 2 by decamethylferrocene (Me10Fc) or octamethylferrocene (Me8Fc), leading to the products H2O2, the corresponding ferrocenium salt, and [LCuII(OAcF)]+. Second-order rate constants for electron transfer (ket) were determined to be 1365 M–1 s–1 (Me10Fc) and 225 M–1 s–1 (Me8Fc) at −80 °C. The (bio)chemical relevance of the proton-triggered reduction of the metal-bound dioxygen-derived fragment is discussed. [ABSTRACT FROM AUTHOR]

G protein-coupled receptors exhibit a wide variety of signaling behaviors in response to different ligands. When a small label was incorporated on the cytosolic interface of transmembrane helix 6 (Cys-265), 19F NMR spectra of the β2 adrenergic receptor (β2AR) reconstituted in maltose/neopentyl glycol detergent micelles revealed two distinct inactive states, an activation intermediate state en route to activation, and, in the presence of a G protein mimic, a predominant active state. Analysis of the spectra as a function of temperature revealed that for all ligands, the activation intermediate is entropically favored and enthalpically disfavored. β2AR enthalpy changes toward activation are notably lower than those observed with rhodopsin, a likely consequence of basal activity and the fact that the ionic lock and other interactions stabilizing the inactive state of β2AR are weaker. Positive entropy changes toward activation likely reflect greater mobility (configurational entropy) in the cytoplasmic domain, as confirmed through an order parameter analysis. Ligands greatly influence the overall changes in enthalpy and entropy of the system and the corresponding changes in population and amplitude of motion of given states, suggesting a complex landscape of states and substates. [ABSTRACT FROM AUTHOR]

Raman spectroscopy is combined with multivariate curve resolution to quantify interactions between ions and molecular hydrophobic groups in water. The molecular solutes in this study all have similar structures, with a trimethyl hydrophobic domain and a polar or charged headgroup. Our results imply that aqueous sodium and fluoride ions are strongly expelled from the first hydration shells of the hydrophobic (methyl) groups, while iodide ions are found to enter the hydrophobic hydration shell, to an extent that depends on the methyl group partial charge. However, our quantitative estimates of the corresponding ion binding equilibrium constants indicate that the iodide concentration in the first hydrophobic hydration shell is generally lower than that in the surrounding bulk water, and so an iodide ion cannot be viewed as having a true affinity for the molecular hydrophobic interface, but rather is less strongly expelled from such an interface than fluoride. [ABSTRACT FROM AUTHOR]

Apart from a few compounds under heavy use in organic chemistry, diboranes are relatively exotic and poorly understood. Recently, interest in these molecules has intensified with the advent of so-called "sp²-sp³" diboranes which exhibit useful reactivity toward organic substrates. In our hands, addition of Lewis bases to dihalodiorganyl diboranes(4) has previously shown some very surprising reactivity, including a substituent exchange between the boron atoms, and diboranes in which halide atoms bridge the B-B bond. Herein we have expanded the range of diborane(4) and Lewis base reaction partners, in the process uncovering three new reactivity patterns as well as some cases where mixtures are obtained. Trends are established for the preferential formation of certain products which rationalize the results based on electronic and steric effects. The substituent exchange, clearly based on an inorganic version of the well-known Wagner–Meerwein rearrangement, was also found to be an equilibrium reaction with the halide-bridged Lewis adducts on the other side. [ABSTRACT FROM AUTHOR]

The ability to perturb large ensembles of molecules from equilibrium led to major advances in understanding reaction mechanisms in chemistry and biology. Here, we demonstrate the ability to control, measure, and make use of rapid temperature changes in fluid volumes that are commensurate with the size of single molecules. The method is based on attaching gold nanoparticles to a single nanometer-scale pore formed by a protein ion channel. Visible laser light incident on the nanoparticles causes a rapid and large increase of the adjacent solution temperature, which is estimated from the change in the nanopore ionic conductance. The temperature shift also affects the ability of individual molecules to enter into and interact with the nanopore. This technique could significantly improve sensor systems and force measurements based on single nanopores, thereby enabling a method for single molecule thermodynamics and kinetics. [ABSTRACT FROM AUTHOR]

A detailed stereomechanistic analysis has led to the design of a new tetradentate ligand for the enantioselective Ti(IV)-catalyzed oxidation of unsymmetrical sulfides to sulfoxides with high selectivity. The pathway of this oxidation and the closely related and long-known Kagan—Modena oxidation have been clarified to identify the likely origin of the enantioselectivity. [ABSTRACT FROM AUTHOR]

Structural plasticity is often required for distinct microscopic steps during enzymatic reaction cycles. Adenylate kinase from Escherichia coli (AKeco) populates two major conformations in solution; the open (inactive) and closed (active) state, and the overall turnover rate is inversely proportional to the lifetime of the active conformation. Therefore, structural plasticity is intimately coupled to enzymatic turnover in AKeco. Here, we probe the open to closed conformational equilibrium in the absence of bound substrate with NMR spectroscopy and molecular dynamics simulations. The conformational equilibrium in absence of substrate and, in turn, the turnover number can be modulated with mutational- and osmolyte-driven perturbations. Removal of one hydrogen bond between the ATP and AMP binding subdomains results in a population shift toward the open conformation and a resulting increase of kcat. Addition of the osmolyte TMAO to AKeco results in population shift toward the closed conformation and a significant reduction of kcat. The Michaelis constants (KM) scale with the change in kcat, which follows from the influence of the population of the closed conformation for substrate binding affinity. Hence, kcat and KM are mutually dependent, and in the case of AKeco, any perturbation that modulates kcat is mirrored with a proportional response in KM. Thus, our results demonstrate that the equilibrium constant of a pre-existing conformational equilibrium directly affects enzymatic catalysis. From an evolutionary perspective, our findings suggest that, for AKeco, there exists ample flexibility to obtain a specificity constant (kcat/KM) that commensurate with the exerted cellular selective pressure. [ABSTRACT FROM AUTHOR]

Electrostatic interactions are a critical factor in the adsorption of quadrupolar species such as CO2 and N2 in metal-organic frameworks (MOFs) and other nanoporous materials. We show how a version of the semiempirical charge equilibration method suitable for periodic materials can be used to efficiently assign charges and allow molecular simulations for a large number of MOFs. This approach is illustrated by simulating CO2 and N2 adsorption in ∼500 MOFs; this is the largest set of structures for which this information has been reported to date. For materials predicted by our calculations to have promising adsorption selectivities, we performed more detailed calculations in which accurate quantum chemistry methods were used to assign atomic point charges, and molecular simulations were used to assess molecular diffusivities and binary adsorption isotherms. Our results identify two MOFs, experimentally known to be stable upon solvent removal, that are predicted to show no diffusion limitations for adsorbed molecules and extremely high CO2/N2 adsorption selectivities for CO2 adsorption from dry air and from gas mixtures typical of dry flue gas. [ABSTRACT FROM AUTHOR]

Hydrogen bond interactions in small covalent model compounds (i.e., deprotonated polyhydroxy alcohols) were measured by negative ion photoelectron spectroscopy. The experimentally determined vertical and adiabatic electron detachment energies for (HOCH2CH2)2CHO-(2a), (HOCH2CH2)3CO- (3a), and (HOCH2CH2CH(OH)CH2)3CO- (4a)reveal that hydrogen-bonded networks can provide enormous stabilizations and that a single charge center not only can be stabilized by up to three hydrogen bonds but also can increase the interaction energy between noncharged OH groups by 5.8 kcal mol-1 or more per hydrogen bond. This can lead to pKa values that are very different from those in water and can provide some of the impetus for catalytic processes. [ABSTRACT FROM AUTHOR]

Measurements of pKR show that the cycloheptadienyl cation is less stable than the cyclohexadienyl (benzenium) cation by 18 kcal mol-1. This difference is ascribed here to "hyperaromaticity" of the latter. For the cycloheptadienyl cation a value of KR = [ROH][H+]/[R+] is assigned by combining a rate constant for reaction of the cation with water based on the azide clock with a rate constant for the acid-catalyzed formation of the cation accompanying equilibration of cycloheptadienol with its trifluoroethyl ether in TFE-water mixtures. Comparison of pKR = -16.1 with pKR = -2.6 for the cyclohexadienyl cation yields the difference in stabilities of the two ions. Interpretation of this difference in terms of hyperconjugative aromaticity is supported by the effect of benzannelation in reducing pKR for the benzenium ion: from -2.6 down to -3.5 for the 1H-naphthalenium and -6.0 for the 9H-anthracenium ions, respectively. MP2/6-311+G** and G3MP2 calculations of hydride ion affinities of benzenium ions show an order of stabilities for substituents at the methylene group consistent with their hyperconjugative abilities, i.e., (H3Si)2 > cyclopropyl > H2 > Me2> (HO)2 > F2. Calculations of ring currents show a similar ordering. No conventional ring current is seen for the cycloheptadienyl cation, whereas currents in the F2-substituted benzenium ion are consistent with antiaromaticity. Arenium ions where the methylene group is substituted with a single OH group show characteristic energy differences between conformations, with C-H or C-OH bonds respectively occupying or constrained to axial positions favorable to hyperconjugation. The differences were found to be 8.8, 6.3, 2.4, and 0.4 kcal mol-1 for benzenium, naphthalenium, phenanthrenium, and cyclohexenyl cations, respectively. [ABSTRACT FROM AUTHOR]

Kinetic and isotopic data and density functional theory treatments provide evidence for the elementary steps and the active site requirements involved in the four distinct kinetic regimes observed during CH4 oxidation reactions using O2, H2O, or CO2 as oxidants on Pt clusters. These four regimes exhibit distinct rate equations because of the involvement of different kinetically relevant steps, predominant adsorbed species, and rate and equilibrium constants for different elementary steps. Transitions among regimes occur as chemisorbed oxygen (O*) coverages change on Pt clusters. O* coverages are given, in turn, by a virtual O2 pressure, which represents the pressure that would give the prevalent steady-state O* coverages if their adsorption-desorption equilibrium was maintained. The virtual O2 pressure acts as a surrogate for oxygen chemical potentials at catalytic surfaces and reflects the kinetic coupling between C-H and O═O activation steps. O* coverages and virtual pressures depend on O2 pressure when O2 activation is equilibrated and on O2/CH4 ratios when this step becomes irreversible as a result of fast scavenging of O* by CH4-derived intermediates. In three of these kinetic regimes, C-H bond activation is the sole kinetically relevant step, but occurs on different active sites, which evolve from oxygen-oxygen (O*-O*), to oxygen-oxygen vacancy (O*-*), and to vacancy-vacancy (*-*) site pairs as O* coverages decrease. On O*-saturated cluster surfaces, O*-O* site pairs activate C-H bonds in CH4 via homolytic hydrogen abstraction steps that form CH3 groups with significant radical character and weak interactions with the surface at the transition state. In this regime, rates depend linearly on CH4 pressure but are independent of O2 pressure. The observed normal CH4/CD4 kinetic isotope effects are consistent with the kinetic-relevance of C-H bond activation; identical 16O2-18O2 isotopic exchange rates in the presence or absence of CH4 show that O2 activation steps are quasi-equilibrated during catalysis. Measured and DFT-derived C-H bond activation barriers are large, because of the weak stabilization of the CH3 fragments at transition states, but are compensated by the high entropy of these radical-like species. Turnover rates in this regime decrease with increasing Pt dispersion, because low-coordination exposed Pt atoms on small clusters bind O* more strongly than those that reside at low-index facets on large clusters, thus making O* less effective in H-abstraction. As vacancies (*, also exposed Pt atoms) become available on O*-covered surfaces, O*-* site pairs activate C-H bonds via concerted oxidative addition and H-abstraction in transition states effectively stabilized by CH3 interactions with the vacancies, which lead to much higher turnover rates than on O*-O* pairs. In this regime, O2 activation becomes irreversible, because fast C-H bond activation steps scavenge O* as it forms. Thus, O* coverages are set by the prevalent O2/CH4 ratios instead of the O2 pressures. CH4/CD4 kinetic isotope effects are much larger for turnovers mediated by O*-* than by O*-O* site pairs, because C-H (and C-D) activation steps are required to form the * sites involved in C-H bond activation. Turnover rates for CH4-O2 reactions mediated by O*-* pairs decrease with increasing Pt dispersion, as in the case of O*-O* active structures, because stronger O* binding on small clusters leads not only to less reactive O* atoms, but also to lower vacancy concentrations at cluster surfaces. As O2/CH4 ratios and O* coverages become smaller, O2 activation on bare Pt clusters becomes the sole kinetically relevant step; turnover rates are proportional to O2 pressures and independent of CH4 pressure and no CH4/CD4 kinetic isotope effects are observed. In this regime, turnover rates become nearly independent of Pt dispersion, because the O2 activation step is essentially barrierless. In the absence of O2, alternate weaker oxidants, such as H2O or CO2, lead to a final kinetc regime in which C-H bond dissociation on *-* pairs at bare cluster surfaces limit CH4 conversion rates. Rates become first-order in CH4 and independent of coreactant and normal CH4/CD4 kinetic isotope effects are observed. In this case, turnover rates increase with increasing dispersion, because low-coordination Pt atoms stabilize the C-H bond activation transition states more effectively via stronger binding to CH3 and H fragments. These findings and their mechanistic interpretations are consistent with all rate and isotopic data and with theoretical estimates of activation barriers and of cluster size effects on transition states. They serve to demonstrate the essential role of the coverage and reactivity of chemisorbed oxygen in determining the type and effectiveness of surface structures in CH4 oxidation reactions using O2, H2O, or CO2 as oxidants, as well as the diversity of rate dependencies, activation energies and entropies, and cluster size effects that prevail in these reactions. These results also show how theory and experiments can unravel complex surface chemistries on realistic catalysts under practical conditions and provide through the resulting mechanistic insights specific predictions for the effects of cluster size and surface coordination on turnover rates, the trends and magnitude of which depend sensitively on the nature of the predominant adsorbed intermediates and the kinetically relevant steps. [ABSTRACT FROM AUTHOR]

Equilibria between phenylhalocarbenes, halide ions, and phenyldihalomethide carbanions have been spectroscopically characterized and computationally investigated for the halogens Cl and Br. Equilibrium constants, forward and reverse rate constants, and associated thermodynamic parameters are reported. [ABSTRACT FROM AUTHOR]