Proton Attack Research Articles

The kinetics of the dissolution of chlorite as a function of pH and at 25°C

Abstract Far from equilibrium, quasi-steady state dissolution rates of an iron rich chlorite (Mg2.76Fe2+1.90Fe3+0.07Al0.97)[Si2.48Al1.52O10](OH)8, have been measured as a function of H+ concentration for the pH range 3 to 10.5 and at 25°C. The rates were determined using a single pass flow through cell and with a time frame for observing the steady state condition of between 10 to 50 days. Rates are independent of the buffers used to control the pH, sample preparation, experimental methodology and chlorite composition. The results were collated with literature values allowing the rate to be expressed as a function of H+ as; log R = − [ 9.79 a H 0.49 + 13.00 + 16.79 / a H 0.43 ] where R stands for the dissolution rate in mol m−2 s−1 and ai refers to the activity of the subscripted aqueous species. When the data for the Al3+ concentration at the outlet was incorporated into the analysis it was found that the rate could also be described by the relationship R = 10 − 10.46 ( a H + 3 a Al 3 + ) 0.27 which suggests the rate controlling complex is formed via a proton attack of the lattice aluminium.

Mevalonolactone-d9; A Versatile Tool for Biosynthetic Study of Isoprenoids. Synthesis and Its Application

A new practical approach to the preparation of highly and multiply deuterated isoprenoids, archaeal membrane lipid, diterpene antibiotic terpentecin, and carotenoids as examples, and its potential for analyzing the biosynthetic mechanism of isoprenoids are described by using fully deuterated mevalonolactone (MVL-d9). Racemic MVL-d9 was successfully synthesized starting from deuterated dimethoxyphenyl-acetone and trimethyl phosphonoacetate in gram scale. Enantiomerically pure (R) -MVL-d9 was also synthesized using Sharpless asymmetric epoxidation. The methodology for biosynthetic studies using MVL-d9 is meritorious for mechanistic enzymology, particularly, the key transformation involving proton attack and/or proton quench as observed in isoprenoids biosynthesis.

Regioselectivity in the Chemical Reactions between Molecules and Protons: A Quantum Fluid Density Functional Study

Proton−molecule collisions mimicking various chemical reactions are studied within a quantum fluid density functional framework. The regioselectivity of a proton attack is clearly delineated through the dynamic hardness and polarizability profiles. A time-dependent version of the HSAB principle is found to be operative.

The dehydrogenation and cracking reactions of isobutane over the ZSM-5 zeolite

Abstract The dehydrogenation and cracking reactions of isobutane over zeolite HZMS-5 were studied at the DFT/B3LYP level of calculation. The zeolite was represented by the‘double-ring’ 20T cluster. The activation energies for the reactions were 9–12 kcal/mol lower than those obtained with the linear 5T cluster. In both cases the attack of the acid site proton was directly on a carbon atom of the substrate, and not on the C–H and C–C bonds, evidencing carbonium-ion-type transition states. The results suggest that the reactions should be competitive, although the more hindered acid sites should favor the dehydrogenation over the cracking reaction.

Chemically modified smectites

AbstractThis paper summarizes recent results obtained on chemical modifications of smectites. These include replacement of exchangeable cations with protons, a process connected with smectite autotransformation – attack of protons on the layers and liberation of central atoms from the octahedral and tetrahedral sheets, causing modification of the acid sites on the particles. More severe modifications occur during dissolution in inorganic acids, when the layers are dissolved and threedimensional amorphous silica is formed. The negative charge on the smectite layers can be increased via reduction of structural Fe(III) to Fe(II) or decreased via fixation of small exchangeable cations, such as Li+, upon treatment at elevated temperatures. Heating for 24 h at different temperatures between 100 and 300ºC leads to a series of chemically similar materials of different charge, prepared from the same parent mineral. Such series are suitable for investigation of the effect of the layer charge on selected properties of smectites. Fe(II) can be partly stabilized in reduced smectites by Li fixation upon heating.

HSAB principle applied to the time evolution of chemical reactions.

Time evolution of various reactivity parameters such as electronegativity, hardness, and polarizability associated with a collision process between a proton and an X- atom/ion (X = He, Li(+), Be(2+), B(3+), C(4+)) in its ground ((1)S) and excited((1)P,(1)D,(1)F) electronic states as well as various complexions of a two-state ensemble is studied using time-dependent and excited-state density functional theory. This collision process may be considered to be a model mimicking the actual chemical reaction between an X-atom/ion and a proton to give rise to an XH(+) molecule. A favorable dynamical process is characterized by maximum hardness and minimum polarizability values according to the dynamical variants of the principles of maximum hardness and minimum polarizability. An electronic excitation or an increase in the excited-state contribution in a two-state ensemble makes the system softer and more polarizable, and the proton, being a hard acid, gradually prefers less to interact with X as has been discerned through the drop in maximum hardness value and the increase in the minimum polarizability value when the actual chemical process occurs. Among the noble gas elements, Xe is the most reactive. During the reaction: H(2) + H(+) --> H(3)(+) hardness maximizes and polarizability minimizes and H(2) is more reactive in its excited state. Regioselectivity of proton attack in the O-site of CO is clearly delineated wherein HOC(+) may eventually rearrange itself to go to the thermodynamically more stable HCO(+).

Proton affinities and N-glycosidic bond stabilities of hydroxyl radical modified adenosine

The stabilities of the N-glycosidic bonds of three adenosine analogs were studied by means of ab inito quantum chemistry methods. The N9-methoxymethyl derivatives were studied as model compounds representing nucleosides. The Gibbs free energies were estimated for all possible mono- and double-protonated tautomers of 2-OH-adenosine (2a), 2-oxo-adenosine (2b), 8-OH-adenosine (3a), 8-oxo-adenosine (3b) and fapy-adenosine (4). The solvent effect was estimated based on an SCI-PCM model. The presented results suggest that for C2 modified adenosine analogs the most basic atom is the N3 centre of 2-oxo-adenosine followed by the N1 atom of 2-OH-adenosine. Adenosine modified at C8 is mostly protonated on N1, irrespective of the tautomeric form, but the keto form is much more likely than 8-enol one. In the case of fapy-adenosine protonation takes place mainly on N3. The rest of the electronegative centres of all studied compounds are in practice not protonated. At very low pH, 2-OH-Ade is mostly represented by N3 and N7 double protonated forms. In the case of 8-oxo-adenosine and fapy-adenosine in the second protonation reaction O8 may be the active centre. For 8-oxo-adenosine there are mainly two products of double protonation: [dAB2-HO8N1]2+ and [dAB2-HO8N3]2+. Fapy-adenosine is also protonated at O8, which led to the [dAC-HN3O8]2+ cation with 99.9% probability. Mutual proton attack on N1 and O8 centres is much less probable (0.1%).

Enzymatic formation of an unnatural hexacyclic C35 polyprenoid by bacterial squalene cyclase.

A C35 polyprene in which a farnesyl C15 unit is connected in a head-to-head fashion to a geranylgeranyl C20 unit was enzymatically converted to an unnatural hexacyclic polyprenoid by squalene:hopene cyclase from Alicyclobacillus acidocaldarius. This is the first demonstration of the remarkable ability of the squalene cyclizing enzyme to perform construction of unnatural hexacyclic skeleton. The cyclization of the C35 polyprene was initiated by a proton attack on the terminal double bond of the C15 unit and proceeded without rearrangement of carbon and hydrogen. The substrate should be folded in chair-chair-chair-chair-boat-boat conformation to achieve the stereochemistry of the cyclization product.

Ab initio study of structure, protonation and complex formation of novel pyrazolone-5 derivatives

Abstract The protonation of two novel pyrazolone-5 derivatives and their complex formation with rare-earth metals have been studied by ab initio methods at HF level of theory. The full geometry optimization of the ligands, their protonated forms and model fragments of the complexes with Pr3+ and Sc3+ ions was carried out. The carbonyl group of the pyrazolone cycle is the most preferable site to the proton attack that is indicated by the analysis of the relative stability of the different protonated forms, composition of the frontier molecular orbitals and the electrostatic potential (ESP) calculations. In contrast, the bidentate type of coordination via both carbonyl groups is realized at the complex formation with transition metals. The protonation and complex formation are accompanied by significant conformational changes of the substituent at fourth position of the pyrazolone cycle (R) in spite of the existence of the high potential barrier (ca. 2–2.5 eV) for the rotation of R.

(Bio)chemistry of bacterial leaching—direct vs. indirect bioleaching

Abstract Bioleaching of metal sulfides is effected by bacteria, like Thiobacillus ferrooxidans , Leptospirillum ferrooxidans , Sulfolobus/Acidianus , etc., via the (re)generation of iron(III) ions and sulfuric acid. According to the new integral model for bioleaching presented here, metal sulfides are degraded by a chemical attack of iron(III) ions and/or protons on the crystal lattice. The primary iron(III) ions are supplied by the bacterial extracellular polymeric substances, where they are complexed to glucuronic acid residues. The mechanism and chemistry of the degradation is determined by the mineral structure. The disulfides pyrite (FeS 2 ), molybdenite (MoS 2 ), and tungstenite (WS 2 ) are degraded via the main intermediate thiosulfate. Exclusively iron(III) ions are the oxidizing agents for the dissolution. Thiosulfate is, consequently, degraded in a cyclic process to sulfate, with elemental sulfur being a side product. This explains, why only iron(II) ion-oxidizing bacteria are able to oxidize these metal sulfides. The metal sulfides galena (PbS), sphalerite (ZnS), chalcopyrite (CuFeS 2 ), hauerite (MnS 2 ), orpiment (As 2 S 3 ), and realgar (As 4 S 4 ) are degradable by iron(III) ion and proton attack. Consequently, the main intermediates are polysulfides and elemental sulfur (thiosulfate is only a by-product of further degradation steps). The dissolution proceeds via a H 2 S* + -radical and polysulfides to elemental sulfur. Thus, these metal sulfides are degradable by all bacteria able to oxidize sulfur compounds (like T. thiooxidans , etc.). The kinetics of these processes are dependent on the concentration of the iron(III) ions and, in the latter case, on the solubility product of the metal sulfide.

Dissolution and structural alteration of phlogopite mediated by proton attack and bacterial oxidation of ferrous iron

Microbiological weathering of a research-grade mica mineral, phlogopite, was studied using ferrous sulfate media that were inoculated with an acidophilic iron-oxidizing bacterium, Thiobacillus ferrooxidans. Weathering due to dissolution was monitored by analysis of Si, Al, Fe, K, Na, Mg, and Ca in the leach solutions and in chemical controls at pH 1.0, 1.5 and 2.0. Structural alterations of phlogopite were analyzed by X-ray diffraction. At pH 2, the oxidation of Fe(II) by T. ferrooxidans was accompanied by the formation of jarosite within 7 days of incubation at 22°C. The precipitation of jarosite was coupled with partial alteration of phlogopite to vermiculite and an interstratified (mixed-layer) phlogopite/vermiculite. Similar results were obtained with chemical controls containing 120 mM ferric sulfate. The data suggested that K incorporated into jarosite was released from interlayer positions in phlogopite; thus, jarosite constituted a sink for K. The formation of jarosite and expansible layer silicate phases was pH-dependent. At pH<1.5, jarosite was not formed and phlogopite weathering was due to chemical dissolution without detectable structural alteration.

Quantum-chemical study of the protonation of pyrrolo[2,1-b]thiazole and its selenium and tellurium analogs

The possibility of proton attack on various centers in pyrrolo[2,1-b]thiazole (1) has been evaluated. The results of semiempirical (MNDO, AM1, and PM3) andab initio (6-31G*) calculations were compared. The MNDO and 6-31G* methods give “chemically proper” and qualitatively coincident results. Analysis of the intramolecular (geometric and electronic) reorganization of molecule1, depending on the protonation center, has been carried out. The most probable attack centers, depending on the mechanism of electrophilic reaction, have been recognized. The energy parameters of intramolecular prototropic rearrangements in cation1 and the “blocking” factor value of methyl groups reducting the corresponding complex stability have been evaluated. It has been established that the relative stability of the protonated forms does not change on going to pyrrolo[2,1-b]selenium- and telluriumazoles, but the range of variations is considerably narrowed in the series S>Se>Te.

Hydrolysis mechanisms for the acetylpyridinephenylhydrazone ligand in sulfuric acid

The excess acidity method was applied to rate data obtained for 2-acetylpyridinephenylhydrazone hydrolysis in strong acid media using various aqueous/organic solvents, and it was observed that the reaction rate decreases with increasing permittivity of the medium. Two hydrolysis mechanisms are indicated. Below 0.6 M H(2)SO(4), no hydrolysis was observed; between 0.6 and 6.0 M H(2)SO(4), the substrate hydrolyzes by an A-S(E)2 mechanism and switches to an A-2 mechanism at higher acidity. This change of mechanism was justified on the basis of the syn and anti rotational conformers of the diene -N((1))=C-C=N((2))- group; the greater stability of the former can be explained by the formation of hydrogen bonds between the proton and the N((1)) and N((2)) nitrogen atoms, giving rise to a very stable five-membered ring. If the syn conformer is predominant, then no hydrolysis is observed; above 0.6 M, the attack of a second proton gives rise to a balance between the syn and anti forms, the latter being responsible for the hydrolysis of the hydrazone group.

Absolute proton affinity of some polyguanides

The problem of the absolute proton affinity (APA) of some polyguanides is addressed by the MP2(fc)/6-311+G//HF/6-31G theoretical model. It is shown that the linear chain polyguanides exhibit increased basicity as a function of the number of guanide subunits. However, the saturation effect yields an asymptotic APA value of 254 kcal/mol. Branched polyguanides on the other hand have higher APAs than their linear counterparts. The largest proton affinity is found in a doubly bifurcated heptaguanide, being as high as 285 kcal/mol, thus potentially representing one of the strongest organic bases. Finally, it is found that all polyguanides protonate at imino nitrogen atoms, since they are apparently susceptible the most to the proton attack. The origin of their very high intrinsic basicity is traced down to a dramatic increase in the resonance interaction of the corresponding conjugate bases. For instance, the increase in the resonance energy in the protonated guanidine is estimated to be in a range of 24-27 kcal/mol, which is higher than the aromatic stabilization in benzene. The proton affinity of some polycyclic guanides including Schwesinger proton sponge and porphine is briefly discussed.

Microelectrochemical measurements at expanding droplets (MEMED): investigation of cupric ion stripping kinetics in a two-phase oil/water system

Microelectrochemical measurements at expanding droplets (MEMED) are used as a new approach for investigating the stripping kinetics of metals ions between an organic phase containing an extractant ligand, which complexes the metal ion of interest, and an aqueous acid solution. The approach is illustrated with measurements of the stripping of cupric ion from 1,2-dichloroethane (DCE) droplets containing CuL2 (where L is the oxime ligand, Acorga P50) that are formed periodically through a capillary tip submerged in an aqueous receptor phase containing HCl. First-order dependences of the stripping rate constants on the bulk concentration of CuL2 in the DCE phase (5–20 mmol dm−3) and HCl in the aqueous phase (0.25–2.0 mol dm−3) were found, with an effective bimolecular rate constant of (6.2±1.0)×10−5 cm s−1 M−1. The results obtained demonstrate that the cupric ion stripping process is likely to be heterogeneous, occurring at the immiscible liquid/liquid interface, with the first attack of protons on CuL2 as the rate-limiting step. The prospects for using MEMED more generally to investigate metal extraction/stripping kinetics are discussed.

ZSM-5 zeolite with enhanced acidic properties

ZSM-5 zeolite, when doped with fluorine species in relatively low concentration using ammonium fluoride as precursor, and subsequently activated stepwise at high temperature, shows an enhanced surface acidity because of: (i) the formation of new Bronsted acid sites; and (ii) the strengthening of some acid sites of the parent zeolite. This is ascribed to the proton attack of the zeolite surface by the chemisorbed H+F− ion pair. Under these preparation conditions, the zeolite structure is fully preserved. Such enhanced acid properties are traduced by a significant increase in the yield of methyl tert-butyl ether (gas phase reaction).

Adsorbed carbocations as transition states in heterogeneous acid catalyzed transformations of hydrocarbons

Abstract Ab initio quantum chemical calculations indicated that adsorbed carbenium and carbonium ion active intermediates of acid-catalyzed transformations of hydrocarbons on zeolites are not the really existing highly reactive species but the transition states of the corresponding elementary steps. Adsorbed carbenium ion-like activated complexes can be formed both via proton addition to the double bonds of olefins or as energetically excited unstable ion pairs resulting from partial dissociation of the carbonyl bonds in more stable alkoxy species. In contrast, the highly energetically excited adsorbed carbonium ion-like transition states result only from proton attack at the C–C or C–H bonds of paraffins. The quantum chemical calculations provided the information on geometry and electronic structure of these activated complexes which depend on the elementary reactions in which these transition states are involved. The calculated heat effects and activation energies for the main elementary steps in acid catalyzed transformations of hydrocarbons on zeolites, i.e. of double bond shift, skeletal isomerization and cracking of olefins or protolytic dehydrogenation, protolytic cracking of paraffins and hydride transfer from isoparaffins to carbenium ions are in a reasonable agreement with the experiment.

Protonation Reactions on the Binuclear Complexes [W2Cp2(CO)n(μ-L2)] [L2 = Ph2PCH2PPh2, Me2PCH2PMe2; n = 2, 4]. Chemical Behavior of Their Hydrido and Hydroxycarbyne Derivatives

Reaction of the triply bonded dimers [W2Cp2(CO)2(μ-L2)] (L2 = Ph2PCH2PPh2, Me2PCH2PMe2) with HBF4·OEt2 and other strong acids leads to the unsaturated cationic hydrides [W2Cp2(μ-H)(CO)2(μ-L2)]+. In contrast with this, reaction of HBF4·OEt2 with the singly bonded dimers [W2Cp2(CO)4(μ-L2)] leads, depending on L2 and reaction conditions, to either hydroxycarbyne cations [W2(μ-COH)Cp2(CO)2(μ-L2)]+ or hydridoderivatives [W2Cp2(μ-H)(CO)n(μ-L2)]+ (n = 2 or 4). The relative amounts of the above products in the reaction mixtures depend both on the nature of L2 and reaction conditions. From these data and the results of additional experiments it is concluded that, when L2 = Ph2PCH2PPh2, protonation gives initially the hydroxycarbyne complex, which can experience afterward a solvent-assisted transformation into the corresponding hydrido derivatives, possibly through an H−C(cyclopentadienyl) activation step. When L2 = Me2PCH2PMe2, the above O-protonation competes with direct proton attack at the intermetallic bond, t...

Functional analysis of the DXDDTA motif in squalene-hopene cyclase by site-directed mutagenesis experiments: initiation site of the polycyclization reaction and stabilization site of the carbocation intermediate of the initially cyclized A-ring.

In order to clarify the function of the DXDDTA motif in squalene-hopene cyclase and to identify the acidic amino acid residues crucial for the catalysis, site-directed mutagenesis experiments were carried out. The following results were found: (1) residues D374 and D376 work for the initiation of polyolefin cyclization which arises from the proton attack on the terminal double bond; (2) residue D377 stabilizes C-10 carbocation of the initially cyclized A-ring intermediate, leading to subsequent B-ring closure, which was further verified by isolating the partially cyclized monocyclic product; (3) residues D313 and D447 outside the DXDDTA motif were identified as new active sites; (4) the H451 residue is likely to work in the protonated form to enhance the acidity of the carboxyl groups of D374 and/or D376.

The effect of water vapour atmospheres on the thermal transformation of kaolinite investigated by XRD, FTIR and solid state MAS NMR

Abstract The dehydroxylation of kaolinite and its subsequent transformation to cubic Al-spinel and mullite has been studied under water vapour atmospheres up to 0·8 atm pressure. Dehydroxylation, as determined by XRD, FTIR and solid state MAS NMR, can be accomplished at low temperatures (ca 500°C) under water vapour atmospheres, the efficiency increasing with increasing water vapour pressure. The subsequent thermal transformations to crystalline products are also facilitated by water vapour atmospheres, which also enhance the mechanical properties of the fired kaolinite (crushing strength and softening coefficient) by 3–4 times. These effects are discussed in terms of proton attack on the Si–O bonds followed by polycondensation of the resulting silanol groups to siloxane, facilitating the nucleation of mullite from amorphous aluminosilicate and strengthening the chemical bonds between the grains.