Bridging Proton Research Articles

Synthesis and Properties of 3,2’-Polymethylene-2-phenylbenzo[b]-1,10-phenanthrolines

Reactions of 4-aminoacridine-3-carbaldehyde with benzo[b]cyclo-alkanones and 3,4-dihydro-1 (2H) -anthracenone afforded a series of corresponding 3,2'-polymethylene-2-phenylbenzo[b ]-1,10 -phenanthrolines and 3,3'-dimethylene-2-(naphth-2'-yl)benzo[b ]-1,10 -phenanthroline, respectively, as new N,N,C-terdentates. Dehydrogenation of dimethylene-bridged systems afforded the corresponding fully aromatized systems. Flexibility of annulated bridges is highly dependent on the length of the carbon chain, where tetramethylene-bridge is rigid enough to differentiate eight bridge protons in 1 H NMR time scale at room temperature.

IR Spectrum of the H5O2+ Cation in the Context of Proton Disolvates L−H+−L

The H(5)O(2)(+) ion has been studied in chlorocarbon, benzene, and weakly coordinating anion environments to bridge the gap between the gas-phase and traditional condensed-phase investigations. Symmetrical cations of the type [H(5)O(2)(+) x 4Solv] are formed via H-bonding with the terminal O-H groups. In the infrared spectrum, the nu(s)OH and nu(as)OH vibrations behave in a manner similar to those of common water molecules: the stronger is the H-bonding interaction with the surroundings, the lower is the frequency shift. A consistent pattern of IR bands from the central O-H(+)-O group is identified, regardless of the strength of the interaction of H(5)O(2)(+) with its environment. Three intense bands develop: a (860-995 cm-1), b (1045-1101 cm(-1)), and c (1672-1700 cm(-1)), as well as two weak bands, d ( approximately 1300 cm(-1)) and e ( approximately 1400-1500 cm(-1)). These fingerprint bands are highly characteristic for vibrations of O-H-O group irrespective of formal charge. They are seen in symmetrical proton disolvates of the type L-H(+)-L, where L is an O-atom donor (alcohol, ether, ketone, phosphate, etc.), and in [A-H-A](-) acid salts (A(-) = oxyanion). The commonality is equivalency of the two O-atoms, a short O...O distance (ca. 2.40 Angstrom), and a flat-bottomed potential well for the bridging proton, that is, a short, strong, low-barrier H-bond. Assignments for bands a-e are suggested in an attempt to resolve inconsistencies between experimental and calculated data.

The first-order molecular hyperpolarizability and thermal stability of charge-transfer azo diol and azo aldimine

Nonlinear optical chromophores with nitro acceptors have been designed and synthesized. The first-order hyperpolarizability of the chromophores was determined using hyper-Rayleigh scattering; the decomposition temperature was determined using DSC and the absorption spectra of the compounds were measured. The nonlinear optical properties of the chromophores were discussed; the first-order hyperpolarizabilities of chromophores 3 and 4 come from their two-dimensional structure, the length of the conjugation bridge and intramolecular proton transfer. The strong dihydroxyl donor of chromophores 1 and 2 expanded the first-order hyperpolarizabilities, the measured β HRS values of chromophores 1 and 2 at 1064 nm are 211 × 10 −30 esu and 177 × 10 −30 esu, respectively. These NLO-chromophores exhibit higher decomposition temperature in the range of 290–330 °C.

Study of Chemical Shift Variations in Tricyclic Urazoles with a Norbornane Skeleton

Molecules related to norbornane commonly serve as useful models for stereochemical and conformational analysis, as well as for elucidation of steric and electronic substituent effects. Chemical shifts of their bridge protons are well tabulated and follow clear, easily predictable patterns. For example, the exo protons on a two‐carbon bridge of these molecules are typically deshielded relative to the endo protons. Previously, some exceptions to this rule were noted and satisfactorily explained. In tricyclic urazoles, common precursors to cyclic diazenes, the order of chemical shifts of exo and endo bridge protons is reversed. In this paper, we use aromatic solvent induced shifts (ASIS) and homodecoupling experiments to assign 1H‐NMR signals in these urazoles and bridge proton signals in model molecules, and we discuss analysis of factors that influence chemical shifts in this polycyclic system.

Concerted transfer and transfer direction of three protons in the protonated amino-acid dimers

Several dimers involving two molecule species, which are linked by a proton bridge, are discussed at the B3LYP/6-311++G(3df,3pd)//B3LYP/6-31++G∗∗ level. These molecule species include glycine(s), an alanine, a glyglycine peptide, and a water molecule. Results reveal that the most stable protonated glycine can stabilize a zwitterionic glycine (ZW) in the gas phase, but their complex (dimer) would degenerate into the most stable structure, in which two neutral glycines (NE) are linked by a proton, barrierlessly if the zero point vibrational energies are included. In the degeneration process, three intramolecular proton (hydrogen) transfers are involved and concerted, and the transfer directions of two protons (hydrogens) respective at the two amino terminals of two ZW species point to the corresponding carboxyl oxygens. The bridge proton locates at the middle site of two carboxyl oxygens of two NE species in the most stable dimer. If the two reactant species linked by the bridge proton are unequal, then the bridge proton would transfer to the larger species with small energy barrier. The induced proton (hydrogen) transfers or excursions would also be concerted. The dipole interaction from a water molecule is less than from a glycine for a protonated glyglycine, but enough to induce the hydrogen (proton) at amine terminal nitrogen of the glyglycine transferring to the opposite carboxyl oxygen.

Effect of metal ions and length of alkylene bridge on the strength of hydrogen bonds in diiminedioxime cobalt(III) and nickel(II) complexes

Both octahedral dinitro and dichloro cobalt(III) complexes of 3,3′-(1,4 butanediyldinitrilo)bis(2-butanone)dioxime, complexes 1 and 2, respectively, crystallized in the orthorhombic system with space group P2 12 12 1. Their average O O distances are 2.434(5) and 2.419(4) Å, respectively. The trans-dichloro[3,3′-(1,2-ethanediyldinitrilo)bis(2-butanonedioximato)cobalt(III)] complex 3 crystallized in the monoclinic system with space group P2 1/ c. Its long O O distance of 2.708(2) Å indicates that no hydrogen bond between the two cis oximes occured. It is because the ethylene bridge between the two imine nitrogens imposes more constraints on the ligand than the butylene bridge does. The square planar nickel(II) complex of 3,3′-(1,4-butanediyldinitrilo)bis(2-butanone)dioximato, complex 4, crystallized in the triclinic system with space group P1. The average O O distance is 2.432(9) Å, which is comparable to that of the corresponding cobalt complexes. The ν OHO vibration occurs in the region 1700–1800 cm −1 and varies inversely as the O O distance. The hydrogen bridge proton resonances for complexes 1, 2 and 4 appear downfield (18–20 ppm). For complex 3 no such resonance was observed.

A Stacking Interaction between a Bridging Hydrogen Atom and Aromatic π Density in the n‐B18H22–Benzene System

The structures of n-B18H22 and of n-B18H22 x C6H6 were determined by single-crystal X-ray analysis at -60 degrees C. The geometry of the boron cluster itself does not seem to be appreciably affected by solvation. There does, however, appear to be an unusual interaction of a polyborane bridging hydrogen atom with the benzene pi system, giving rise to an extended stacked structure. The 1H{11B} spectrum of n-B18H22 in [D6]benzene differs from that in [D12]cyclohexane most noticeably in the bridging proton region. Upon moving from the aliphatic to the aromatic solvent, the greatest increase in shielding was for the signal corresponding to the bridge hydrogen atom that interacts with the pi system of benzene; the signal was shifted upfield by 0.49 ppm. Density functional theory calculations were performed on 1:1 and 2:1 complexes of the n-B18H22 unit with benzene.

The Structure of the Strongest Brønsted Acid: The Carborane Acid H(CHB11Cl11)

The strongest and most robust carborane acid, H(CHB11Cl11), has a monomeric structure in the gas phase. IR spectra show two nuH-Cl bands at 2357(br) and 2066(br) cm-1 which, together with DFT calculations, indicate the coexistence of at least two isomers. The acidic proton bridges adjacent chlorine atoms with asymmetric Cl-H...Cl hydrogen bonding. The 12,7 isomer is more stable than the 7,8 isomer. These monomers can be condensed into an amorphous solid phase but are metastable. They quickly decay, first to an amorphous dimeric structure, then to a crystalline polymeric phase that has been characterized by X-ray crystallography. In the polymeric structure, the acidic proton bridges chlorine atoms from the 7-11 positions of carborane anions in linear chains. The dimeric phase (nuCl-H...Cl = 1100-2200 cm-1) and polymeric phase (nuasClHCl ca. 1100 cm-1, v broad) have more nearly symmetrical, low-barrier H-bonding. These findings have implications for the dependency of acid strength upon phase.

The first member of the eleven-vertex azadicarbaborane series, 1,6,9-NC2B8H13, and its N-alkyl derivatives

Reactions between closo-1,2-C(2)B(8)H(10) (1) and amines of general formulation R(1)R(2)NH (where R(1), R(2) = H, H; Me, H; t-Bu, H and Et, Et) resulted in a straightforward cluster expansion and formation of the 11-vertex arachno-azadicarbaboranes of the 1,1-R(1),R(2-)1,6,9-NC(2)B(8)H(11) (2) cluster constitution (where R(1), R(2) = H, H 2a; Me, H 2b; t-Bu, H 2c and Et, Et 2d) in yields 10-75%, depending on the nature of the amine used. The reactions are the first example of a direct closo to arachno transformation in the area of cluster-boron compounds. Compounds 2b and 2c were isolated in two isomeric forms anti- and syn- that differ in the positioning of the t-Bu substituent with respect to the bridging hydrogen site. Deprotonation of compounds 2 generally leads to removal of the bridging proton and formation of the [1,1-R(1),R(2-)1,6,9-NC(2)B(8)H(11)](-) (2-) anions that, in the case of the monoalkylated Me and t-Bu derivatives, adopt only an anti configuration. The structure of anti-2c was determined by X-ray diffraction analysis and the geometries of the parent compound and the corresponding syn and anti isomers were optimised at the RMP2/6-31G* level. The composition of all compounds is consistent with the results of mass spectrometry and multinuclear ((1)H and (11)B) spectroscopy complemented by two-dimensional [(11)B-(11)B]-COSY and (1)H{(11)B(selective)} NMR measurements. Experimental (11)B chemical shifts generally show acceptable agreement with theoretical values calculated by GIAO methods, in particular at GIAO-MP2/II, where possible.

Partial incorporation of a cyclopentadienyl ligand into a molybdaborane to form a molybdacarbaborane

Reaction of the molybdaborane arachno-2-[Mo(η-C 5H 5)(η 5:η 1-C 5H 4)B 4H 7] ( I) with NEt 3 in toluene at 120 °C for 7 days gives a 90% yield of the molybdacarbaborane nido-1-[Mo(η-C 5H 5)(η 3:η 2-C 3H 3)C 2B 3H 5] ( II). Two of the carbon atoms in the substituted cyclopentadienyl ring in I are incorporated into the metallacarbaborane cluster II. The carbaborane {C 2B 3H 5} fragment in II is attached to an allylic {C 3H 3} group and can be thought of as a new non-planar {C 5B 3H 8} ligand providing seven electrons to the molybdenum atom. Reaction of I with KH in thf at 20 °C gives the anion [ nido - 1 - Mo ( η - C 5 H 5 ) ( η 3 : η 2 - C 3 H 3 ) C 2 B 3 H 4 - ] ( III ) via deprotonation of a B–H–B bridging proton.

A study of the isomerization and dissociation of formal [acetone–methanol]+· ion–molecule complexes

The energy barrier for the keto–enol isomerization of the isolated acetone ion to its distonic (enol) isomer lies above its lowest dissociation limit and so the spontaneous isomerization can never be observed. Keto–enol isomerizations can be catalyzed within appropriate ion–molecule complexes. The present study involved two systems, [(CH3)2C=O···H+···O(H)CH2·] (ion 1) and [(CH3)2C=O···H+····OCH3] (ion 2), in both stable and metastable adducts. When acetone is bound to ·CH2OH though a proton bridge, shown as ion 1, an enol acetone ion is produced. This reaction results from a proton attaching to the acetone, which then gives an H· atom back to the radical site by a 1,6-H transfer, involving a transition state of low energy requirement. In contrast, when the acetone is protonated and bound to the radical CH3O· (ion 2), the above rearrangement does not take place. The metastable complex ion 2 loses a methyl radical, producing a new [C3H7O2]+ isomer of structure [CH3C+(O)···(H)OCH3]. Tandem mass spectrometry combined with ab initio calculations were used to investigate the two systems. Potential energy surface diagrams were obtained by calculations at the MP2/6-31+G(d) level of theory to aid further elucidation of the reaction mechanisms. Key words: ion–molecule complexes, keto–enol mechanisms, ion rearrangements and structures.

Strong Electronic Coupling between Mo2n+ Units: The Oxidation Products of [Mo2(DAniF)3]2(μ−H)2 and Mo2(DAniF)4

AbstractThe two compounds [[Mo2(DAniF)3]2(μ−H)2]PF6 (2), and [Mo2(DAniF)4]TFPB (3), (DAniF represents (p−MeOC6H4N)2CH, and TFPB tetra–3,5–bis(trifluoromethyl)phenylborate) have been prepared and characterized structurally by X‐ray crystallography, and by cyclic voltammetry and EPR spectroscopy. DFT calculations have been performed on 2. This is a fully delocalized system in which the two Mo2 units have essentially identical Mo–Mo distances, 2.115(1) Å and 2.116(1) Å, that are 0.017(1) Å longer than those in the neutral precursor. Delocalization over four molybdenum atoms is confirmed by the hyperfine structure observed in the EPR spectrum. No coupling of the delocalized electron to the bridging protons is observed, and this is consistent with the electronic structure calculated by DFT. The cation in 3, which is commonly a contaminant of 2, shows exactly the structural and EPR characteristics expected.

Gas‐Phase Infrared Spectrum of the Protonated Water Dimer: Molecular Dynamics Simulation and Accuracy of the Potential Energy Surface

Ab initio molecular dynamics simulations show that the gas-phase infrared spectra of H5O2+ (blue line) and the H5O2+⋅Ar complex (black line) are very similar. The broad band between 800 and 1300 cm−1 is due to motions of the bridging proton in the OO direction coupled to torsion and wagging of the bridged water molecules. The bending motions of the proton perpendicular to the OO direction are not seen in the IR spectrum.

Protonation of the Binuclear Metal Center within the Active Site of Phosphotriesterase

Phosphotriesterase (PTE) is a binuclear metalloenzyme that catalyzes the hydrolysis of organophosphates, including pesticides and chemical warfare agents, at rates approaching the diffusion controlled limit. The catalytic mechanism of this enzyme features a bridging solvent molecule that is proposed to initiate nucleophilic attack at the phosphorus center of the substrate. X-band EPR spectroscopy is utilized to investigate the active site of Mn/Mn-substituted PTE. Simulation of the dominant EPR spectrum from the coupled binuclear center of Mn/Mn-PTE requires slightly rhombic zero-field splitting parameters. Assuming that the signal arises from the S = 2 manifold, an exchange coupling constant of J = -2.7 +/- 0.2 cm(-)(1) (H(ex) = -2JS(1) x S(2)) is calculated. A kinetic pK(a) of 7.1 +/- 0.1 associated with loss in activity at low pH indicates that a protonation event is responsible for inhibition of catalysis. Analysis of changes in the EPR spectrum as a function of pH provides a pK(a) of 7.3 +/- 0.1 that is assigned as the protonation of the hydroxyl bridge. From the comparison of kinetic and spectral pK(a) values, it is concluded that the loss of catalytic activity at acidic pH results from the protonation of the hydroxide that bridges the binuclear metal center.

Effect of Solvent upon CH···O Hydrogen Bonds with Implications for Protein Folding

The series of CH...O bonds formed between CF(n)H(4-n) (n = 0-3) and water are studied by quantum calculations under vacuum and in various solvents, including aqueous environment. The results are compared with the OH...O bond of the water dimer in the same solvents. Increasing polarity of the solvent leads in all cases to a lessening of the H-bond interaction energy, in a uniform fashion such that the CH...O bonds all remain weaker than OH...O in any solvent. These H-bond weakenings are coupled to a shortening of the inter-subunit separation. The contraction of the covalent CH bond to the bridging proton is reduced as the solvent becomes more polar, and the blue shift of its stretching vibration is likewise diminished. A process is considered that simulates protein folding by starting from a pair of noninteracting subunits in aqueous solvent and then goes to a H-bonded pair within the confines of a protein environment. This process is found to be energetically more favorable for some of the CH...O H-bonds than for the nominally stronger conventional OH...O H-bond. This finding suggests that CH...O bonds can make important energetic contributions to protein folding, on par with those made by traditional H-bonds.

Gold(0) and Gold(III) Reactivity towards the Tetraphenyldithioimidodiphosphinic Acid, [Ph2P(S)NHP(S)Ph2

AbstractThe reaction of gold powder with the iodine adduct of Ph2P(S)NHP(S)Ph2 (HL) in Et2O gave the complex [Au(L)I2] under mild reaction conditions. Its crystal structure is comprised of discrete, monomeric molecules with a central AuIII ion bonded to two sulfur atoms by an anionic ligand L and two iodide anions in a slightly distorted square‐planar coordination geometry. From the reaction of [AuCl3(tht)] with HL in CH2Cl2 it is possible, besides the main complex [Au(L)]2, to separate the neutral AuI complex [Au(L′2H)], L′ = [Ph2P(S)NP(O)Ph2]−, the crystal structure of which features a AuI ion linearly coordinated to two sulfur atoms and a proton bridging two oxygen atoms of the PO groups. 31P NMR CP MAS spectroscopy is in accordance with the nature of the ligands in the complex. The reaction chemistry of [Au(L′2H)] in CH2Cl2 towards the acid CF3COOH and the organic base 1,8‐bis(dimethylamino)naphthalene is reported. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)

Potential construction via charge perturbation: HCN protonation

Ab initio calculations have been performed for proton attachment to HCN to form the ion HCNH +. The potential for the proton attachment is well reproduced at the level of third order perturbation theory taking the proton's charge as the perturbation. This can be analyzed in terms of electrical properties, e.g. a first-order response with the permanent charge field (moments) of HCN, a second-order response from polarization, and a third-order response from hyperpolarization. The calculations show the expected dominance of these effects at long range and the importance, with each perturbative order of energy correction, of other effects closer in. Then, starting from the electrical analysis, a concise model potential was constructed basically by finding that a relatively simple functional form was needed for the low-order, close-in effects. The utility of this modeling scheme is shown here in the building of a proton bridging potential for HCN–H +–NCH starting from simply combining HCN–H + and H +–NCH potentials.

Toluene disproportionation and coking on zeolites Y modified with Lewis-connected InO+ acid sites

Abstract The effect of introduction of Lewis acid sites on the reactions of toluene transformation and catalysts coking has been studied over parent (Si/Al = 2.5) and dealuminated (Si/Al = 3.7) Y zeolites modified with Lewis connected InO+ cationic acid sites. The catalysts with prevalent amount of Bronsted acid sites (less than 40% of protons exchanged by InO+) possess the typical for the proton directed reaction of methyl transfer upon toluene disproportionation long period of activation, the longer the higher the concentration of bridging protons. In contrast, at predominant Lewis sites concentration, the activation period disappear, an enhanced initial activity is observed, followed by deactivation on the expense of a rapid process of accumulation of strongly held reaction products and intermediates. Their further condensation leads to catalysts aging, the faster the higher the concentration of electron acceptor Lewis acid sites. A relation has been found between the initially accelerated processes of alkyl transfer and the reinforced formation of carbonaceous deposits over the In-modified catalysts.

Dimer-of-dimers model for the oxygen-evolving complex of photosystem II. Synthesis and properties of [MnIV4O5(terpy)4(H2O)2](ClO4)6.

A dimer-of-dimers model compound for the oxygen-evolving complex of photosystem II, [[(H(2)O)(terpy)Mn(IV)(micro-O)(2)Mn(IV)(terpy)](2)(micro-O)](ClO(4))(6) (terpy = 2,2':6',2' '-terpyridine), has been prepared and characterized by X-ray crystallography and ESI-MS. Low pH was found to promote the disproportionation of [Mn(III/IV)(2)O(2)(terpy)(2)(OH(2))(2)](3+) to Mn(2+) and a Mn(IV/IV)(2)O(2)(terpy)(2) species; the latter complex slowly dimerizes to form the title complex. Protonation of a micro-oxo bridge is proposed to initiate the disproportionation, based on analogy with the [Mn(III/)(IV)(2)O(2)(bpy)(4)](3+) system.

Proton inventory studies of alpha-thrombin-catalyzed reactions of substrates with selected P and P' sites.

Deuterium kinetic solvent isotope effects for the human alpha-thrombin-catalyzed hydrolysis of (1) substrates with selected P(1)-P(3) sites, Z-Pro-Arg-7-amido-4-methylcoumarin (7-AMC), N-t-Boc-Val-Pro-Arg-7-AMC, Bz-Phe-Val-Arg-4-nitroanilide (pNA), and H-D-Phe-L-Pip-Arg-pNA, are (DOD)k(cat) = (2.8-3.3) +/- 0.1 and (DOD)(k(cat)/K(m)) = (0.8-2.1) +/- 0.1 and (2) internally fluorescence-quenched substrates (a) (AB)Val-Phe-Pro-Arg-Ser-Phe-Arg-Leu-Lys(DNP)-Asp-OH, an optimal sequence, and (b) (AB)Val-Ser-Pro-Arg-Ser-Phe-Gln-Lys(DNP)-Asp-OH, recognition sequence for factor VIII, are (DOD)k(cat) = 2.2 +/- 0.2 and (DOD)(k(cat)/K(m)) = (0.8-0.9) +/- 0.1, at the pL (L = H, D) maximum, 8.4-9.0, and (25.0-26.0) +/- 0.1 degrees C. The most plausible models fitting the partial isotope effect (proton inventory) data have been selected on the basis of lowest values of the reduced chi squared and consistency of fractionation factors at all substrate concentrations, assuming rate-determining acylation. The data for Z-Pro-Arg-7-AMC are consistent with a single-proton bridge at the transition state phi(TS) = 0.39 +/- 0.05 and components for solvent reorganization phi(S) = 0.8 +/- 0.1 and phi(S) = 1.22 for k(cat) and k(cat)/K(m), respectively. The data for tripeptide amides fit bowl-shaped curves; an example is N-t-Boc-Val-Pro-Arg-7-AMC: phi(TS)(1) = phi(TS)(2) = 0.57 +/- 0.01 and phi(S) = 1 for k(cat) and 1.6 +/- 0.1 for k(cat)/K(m). Proton inventories for the nonapeptide (2b) are linear. The data for k(cat) for H-D-Phe-L-Pip-Arg-pNA and the decapeptide (2a) are most consistent with two identical fractionation factors for catalytic proton bridging, phi(TS)(1) = phi(TS)(2) = 0.68 +/- 0.02 and a large inverse component (phi(S) = 3.1 +/- 0.5) for the latter, indicative of substantial solvent reorganization upon leaving group departure. Proton inventory curves for k(cat)/K(m) for nearly all substrates are dome-shaped with an inverse isotope effect component (phi(S) = 1.2-2.4) originating from solvent reorganization during association of thrombin with substrate. These large contributions from medium effects are in full accord with the conformational adjustments required for the fulfillment of the dual, hemostatic and thrombolytic, functions of thrombin.