Protonated benzofuran,anthracene, naphthalene,benzene, ethene,and ethyne: measurements and estimates of pK(a) and pK(R)

Aqueous solvolyses of acyl derivatives of hydrates (water adducts) of anthracene and benzofuran yield carbocations which undergo competitive deprotonation to form the aromatic molecules and nucleophilic reaction with water to give the aromatic hydrates. Trapping experiments with azide ions yield rate constants k(p) for the deprotonation and k(H2O) for the nucleophilic reaction based on the "azide clock". Combining these with rate constants for (a) the H(+)-catalyzed reaction of the hydrate to form the carbocation and (b) hydrogen isotope exchange of the aromatic molecule (from the literature) yields pK(R) = -6.0 and -9.4 and pK(a) = -13.5 and -16.3 for the protonated anthracene and protonated benzofuran, respectively. These pK values may be compared with pK(R) = -6.7 for naphthalene hydrate (1-hydroxy-1,2-dihydronaphthalene), extrapolated to water from measurements by Pirinccioglu and Thibblin for acetonitrile-water mixtures, and pK(a) = -20.4 for the 2-protonated naphthalene from combining k(p) with an exchange rate constant. The differences between pK(R) and pK(a) correspond to pK(H2O), the equilibrium constant for hydration of the aromatic molecule (pK(H2O) = pK(R) - pK(a)). For naphthalene and anthracene values of pK(H2O) = +13.7 and +7.5 compare with independent estimates of +14.2 and +7.4. For benzene, pK(a) = -24.3 is derived from an exchange rate constant and an assigned value for the reverse rate constant close to the limit for solvent relaxation. Combining this pK(a) with calculated values of pK(H2O) gives pK(R) = -2.4 and -2.1 for protonated benzenes forming 1,2- and 1,4-hydrates, respectively. Coincidentally, the rate constant for protonation of benzene is similar to those for protonation of ethylene and acetylene (Lucchini, V.; Modena, G. J. Am. Chem Soc. 1990, 112, 6291). Values of pK(a) for the ethyl and vinyl cations (-24.8) may thus be derived in the same way as that for the benzenonium ion. Combining these with appropriate values of pK(H2O) then yields pK(R) = -39.8 and -29.6 for the vinyl and ethyl cations, respectively.     

Modeling Pb(II) adsorption onto sandy loam soil

The adsorption of Pb(II) onto hydrous sandy loam soil was investigated with batch equilibrium adsorption experiments. Results show that the amount of Pb(II) adsorbed increases with increasing pH and surface loading. It was demonstrated that the surface acidity of the soil could be determined using electrophoretic mobility measurements. The surface acidity constants, pK(a1)(int) and pK(a2)(int), were 1.57 and 3.43, respectively. A surface complex formation model (SCFM) was employed to describe the adsorption. The intrinsic stability constants, pK(i)(s), for the surface reaction between the Pb species and the ionized soil surface hydroxyl groups were determined from SCFM fitting. The adsorption free energy of Pb2+ and Pb(OH)+ ions ranges from -5.74 to -6.48 kcal/mol and from -9.68 to -10.00 kcal/mol, respectively, for surface loadings between 1.21 x 10(-5) and 2.41 x 10(-4) mol/g. The adsorption binding calculation indicated that the specific chemical interaction is the major mechanism responsible for the adsorption process.     

Sequential hydration energies of the sulfate ion, from determinations of the equilibrium constants for the gas-phase reactions: SO4(H2O)(n)2- = SO4(H2O)(n-1)2- + H2O

Sequential hydration energies of SO4(H2O)(n)2- were obtained from determinations of the equilibrium constants of the following reactions: SO4(H2O)(n)2- = SO4(H2O)(n-1)2- + H2O. The SO4(2-) ions were produced by electrospray and the equilibrium constants Kn,n-1 were determined with a reaction chamber attached to a mass spectrometer. Determinations of Kn,n-1 at different temperatures were used to obtain DeltaG0n,n-1, DeltaH0 n,n-1, and DeltaS0n,n-1 for n = 7 to 19. Interference of the charge separation reaction SO4(H2O)(n)2- = HSO4(H2O)(n-k)- + OH(H2O)(k-1)- at higher temperatures prevented determinations for n < 7. The DeltaS0n,n-1 values obtained are unusually low and this indicates very loose, disordered structures for the n > or = 7 hydrates. The DeltaH0n,n-1 values are compared with theoretical values DeltaEn,n-1, obtained by Wang, Nicholas, and Wang. Rate constant determinations of the dissociation reactions n,n - 1, obtained with the BIRD method by Wong and Williams, showed relatively lower rates for n = 6 and 12, which indicate that these hydrates are more stable. No discontinuities of the DeltaG0n,n-1 values indicating an unusually stable n = 12 hydrate were observed in the present work. Rate constants evaluated from the DeltaG0n,n-1 results also fail to indicate a lower rate for n = 12. An analysis of the conditions used in the two types of experiments indicates that the different results reflect the different energy distributions expected at the dissociation threshold. Higher internal energies prevail in the equilibrium measurements and allow the participation of more disordered transition states in the reaction.     

Rate and driving force for protonation of aryl radical anions in ethanol

Aryl radical anions created in liquid alcohols decay on the microsecond time scale by transfer of protons from the solvent. This paper reports a 4.5 decade range of rate constants for proton transfer from a single weak acid, ethanol, to a series of unsubstituted aryl radical anions, Ar-*. The rate constants correlate with free energy change, DeltaG(o), despite wide variations in the two factors that contribute to DeltaG(o): (a) the reduction potentials of the aryls and (b) the Ar-H* bond strengths in the product radicals. For aryl radical anions containing CH2OH substituents, such as 2,2'-biphenyldimethanol*- which is protonated with a rate constant of 3x10(9) s(-1), the faster rates do not fit well in the free energy correlation, suggesting a change in mechanism.     

Improved modification for the density-functional theory calculation of thermodynamic properties for C-H-O composite compounds

A three-parametric modification equation and the least-squares approach are adopted to calibrating hybrid density-functional theory energies of C(1)-C(10) straight-chain aldehydes, alcohols, and alkoxides to accurate enthalpies of formation DeltaH(f) and Gibbs free energies of formation DeltaG(f), respectively. All calculated energies of the C-H-O composite compounds were obtained based on B3LYP6-311++G(3df,2pd) single-point energies and the related thermal corrections of B3LYP6-31G(d,p) optimized geometries. This investigation revealed that all compounds had 0.05% average absolute relative error (ARE) for the atomization energies, with mean value of absolute error (MAE) of just 2.1 kJ/mol (0.5 kcal/mol) for the DeltaH(f) and 2.4 kJ/mol (0.6 kcal/mol) for the DeltaG(f) of formation.     

An important role of intramolecular free radical reactions in antimalarial activity of artemisinin and its analogs

The kinetic schemes of intramolecular reactions of five analogs of artemisinin were built. The method of intersecting parabolas was used for the calculation of activation energies and rate constants of each elementary step of these schemes. The competition between monomolecular and bimolecular free radicals was taken into account. It was evidenced that the intramolecular oxidation of these compounds proceeds as a cascade of consecutive free radical reactions with the formation of hydroperoxide groups. The latter decompose via reactions with the Fe(II) complexes generating free radicals. Among the radicals formed, the hydroxyl radical was proved to play the key role. A correlation between the yield of hydroxyl radicals n(OH) and antimalarial activity of compounds (IC(50)) was observed. The dependence of index IC(50) on n(OH) is linear in the logarithmic coordinates: ln[IC(50)(Artemisinin)/IC(50)(Compound)] = -14.10 + 3.85 ×n(OH). The proposed scheme explains and demonstrates a strong dependence of the antimalarial effectiveness of a drug on the chemical structure.     

Aerobic oxidation of benzyl alcohols catalyzed by aryl substituted N-hydroxyphthalimides. Possible involvement of a charge-transfer complex

A series of aryl-substituted N-hydroxyphthalimides (X-NHPIs) containing either electron-withdrawing groups (4-CH(3)OCO, 3-F) or electron-donating groups (4-CH(3), 4-CH(3)O, 3-CH(3)O, 3,6-(CH(3)O)(2)) have been used as catalysts in the aerobic oxidation of primary and secondary benzylic alcohols. The selective formation of aromatic aldehydes was observed in the oxidation of primary alcohols; aromatic ketones were the exclusive products in the oxidation of secondary alcohols. O-H bond dissociation enthalpies (BDEs) of X-NHPIs have been determined by using the EPR radical equilibration technique. BDEs increase with increasing the electron-withdrawing properties of the aryl substituent. Kinetic isotope effect studies and the increase of the substrate oxidation rate by increasing the electron-withdrawing power of the NHPI aryl substituent indicate a rate-determining benzylic hydrogen atom transfer (HAT) from the alcohol to the aryl-substituted phthalimide-N-oxyl radical (X-PINO). Besides enthalpic effects, polar effects also play a role in the HAT process, as shown by the negative rho values of the Hammett correlation with sigma(+) and by the decrease of the rho values (from -0.54 to -0.70) by increasing the electron-withdrawing properties of the NHPI aryl substituent. The relative reactivity of 3-CH(3)O-C(6)H(4)CH(2)OH and 3,4-(CH(3)O)(2)-C(6)H(3)CH(2)OH, which is higher than expected on the basis of the sigma(+) values, the small values of relative reactivity of primary vs secondary benzylic alcohols, and the decrease of the rho values by increasing the electron-withdrawing properties of the NHPI aryl substituent, suggest that the HAT process takes place inside a charge-transfer (CT) complex formed by the X-PINO and the benzylic alcohol.     

Aromaticity and antiaromaticity in fulvenes, ketocyclopolyenes, fulvenones, and diazocyclopolyenes

The structures, energies, natural charges, and magnetic properties of 3-, 5-, 7-, and 9-membered cyclic polyenes 1-4, respectively, with exocyclic methylene, keto, ketenyl, and diazo substituents (a-d, respectively) were computed at the B3LYP/6-311G+ **//B3LYP/6-311+G** level to elucidate their aromatic and antiaromatic properties. The corresponding conjugated cyclic cations le and 3e were also studied. The criteria used are isomerization energies (ISE), magnetic susceptibility exaltations (lambda), aromatic stabilization energies (ASE), nucleus independent chemical shifts (NICS), and bond length alternation (deltaR). Planar C2v structures were found to be the lowest energy minima with the exceptions of diazocyclopropene (1d), cycloheptafulvenone (3c), diazocycloheptatriene (3d), and all of the cyclononatetraene derivatives (4). The fulvenes (1a-4a) have modest aromatic or antiaromatic character, and are used as standards for comparison. By these criteria the ketenylidene and diazo cyclopropenes and cycloheptatrienes 1,3-c,d and oxo cyclopentadiene and cyclononatetraene 2,4b are antiaromatic, while the 5- and 9-ring ketenyl and diazo compounds and 3- and 7-ring ketones are aromatic. The degree of aromatic/antiaromatic character decreases with ring size. The consistent agreement with Hückel rule predictions for all the criteria shows their utility for the evaluation of the elusive properties of aromaticity and antiaromaticity.     

Potentiometric studies of ternary complex formation Cu(II), Ni, Zn or Cd iminodiacetic acid/amino-acid complexes

The formation constants, log K(mab), for the reactions MA + B right harpoon over left harpoon MAB [where M = Cu(II), Ni, Zn or Cd, A = terdentate ligand and B = bidentate or terdentate ligand] have been determined. Potentiometric evidence is presented for the stepwise addition of the secondary ligand B to the 1:1 metal iminodiacetate (MA). The formation constants and the free energies of formation (DeltaG) have been calculated at 25 +/- 1 degrees and mu = 0.10. The order in terms of secondary ligands has been found to be ASPA > Gly > Aln and Gly > Aln > ASPA with iminodiacetic and nitrilotriacetic acid as primary ligands respectively (ASPA = aspartic acid, Gly = glycine, Aln = dl-alanine). The plot of log K(mab) against log k(mb)(2) shows a linear relationship between the formation constants of the ternary and 1:2 M(II)secondary ligand complexes.     

Accurate pK(a) calculations for carboxylic acids using complete basis set and Gaussian-n models combined with CPCM continuum solvation methods

Complete Basis Set and Gaussian-n methods were combined with CPCM continuum solvation methods to calculate pK(a) values for six carboxylic acids. An experimental value of -264.61 kcal/mol for the free energy of solvation of H(+), DeltaG(s)(H(+)), was combined with a value for G(gas)(H(+)) of -6.28 kcal/mol to calculate pK(a) values with Cycle 1. The Complete Basis Set gas-phase methods used to calculate gas-phase free energies are very accurate, with mean unsigned errors of 0.3 kcal/mol and standard deviations of 0.4 kcal/mol. The CPCM solvation calculations used to calculate condensed-phase free energies are slightly less accurate than the gas-phase models, and the best method has a mean unsigned error and standard deviation of 0.4 and 0.5 kcal/mol, respectively. The use of Cycle 1 and the Complete Basis Set models combined with the CPCM solvation methods yielded pK(a) values accurate to less than half a pK(a) unit.     

Higher alcohol synthesis over Cu-Fe composite oxides with high selectivity to C2+OH

Cu-Fe composite oxides were prepared by co-precipitation method and tested for higher alcohol synthesis from syngas. The selectivity to C₂₊OH and C₆₊OH in alcohol distribution was very high while the methane product fraction in hydrocarbon distribution was rather low, demonstrating a promising potential in higher alcohols synthesis from syngas. The distribution of alcohols and hydrocarbons approximately obeyed Anderson-Schulz-Flory distribution with similar chain growth probability, indicating alcohols and hydrocarbons derived from the same intermediates. The effects of Cu/Fe molar ratio, reaction temperature and gas hourly space velocity (GHSV) on catalytic performance were studied in detail. The sample with a Cu/Fe molar ratio of 10/1 exhibited the best catalytic performance. Higher reaction temperature accelerated water-gas-shift reaction and led to lower total alcohols selectivity. GHSV showed great effect on catalytic performance and higher GHSV increased the total alcohol selectivity, indicating there existed visible dehydration reaction of alcohol into hydrocarbon.     

Accurate prediction of basicity in aqueous solution with COSMO-RS

The COSMO-RS method, a combination of the quantum chemical dielectric continuum solvation model COSMO with a statistical thermodynamics treatment for realistic solvation simulations, has been used for the prediction of base pK(a) constants. For a variety of 43 organic bases the directly calculated values of the free energies of dissociation in water showed a very good correlation with experimental base pK(a) values (r2 = 0.98), corresponding to a standard deviation of 0.56 pK(a) units. Thus, we have an a priori prediction method for base pK(a) with the regression constant and the slope as only adjusted parameters. In accord with recent findings for pK(a) acidity predictions, the slope of pK(a) vs. DeltaG(diss) was significantly smaller than the theoretically expected value of 1/RTln(10). The predictivity of the presented method is general and not restricted to certain compound classes, but systematic corrections of 1 and 2 pKa units for secondary and tertiary aliphatic amines are required, respectively. The pK(a) prediction method was validated on a set of 58 complex multifunctional drug-like compounds, yielding an RMS accuracy of 0.66 pK(a) units.     

Just a near attack conformer for catalysis (chorismate to prephenate rearrangements in water,antibody, enzymes,and their mutants)

Standard free energies for formation of ground-state reactive conformers (DeltaGN degrees ) and transition states (DeltaG) in the conversion of chorismate to prephenate in water, B. subtilis mutase, E. coli mutase, and their mutants, as well as a catalytic antibody, are related by DeltaG = DeltaGN degrees + 16 kcal/mol. Thus, the differences in the rate constants for the water reaction and catalysts reactions reside in the mole fraction of substrate present as reactive conformers (NACs). These results, and knowledge of the importance of transition state stabilization in other cases, suggest a proposal that enzymes utilize both NAC and transition state stabilization in the mix required for the most efficient catalysis.     

Rates and equilibria of the reactions of tertiary phosphanes and phosphites with benzhydrylium ions

The kinetics of the reactions of benzhydrylium ions and quinone methides with eight tertiary phosphanes and two phosphites were investigated photometrically. The nucleophilicity parameters N and slope parameters s of these nucleophiles were derived according to the equation log k(20 degrees C) = s(N + E). Correlations of the nucleophilicity parameters N with pK(Ha) and sigma(p) values as well as with the rate constants of reactions with other electrophiles are discussed. In some cases, equilibrium constants for the formation of phosphonium ions were measured, which allow one to determine the Marcus intrinsic barriers of DeltaG(0) (not equal) = 58 kJ mol(-1) for the reactions of triarylphosphanes with benzhydrylium ions. The N parameters [5.51 for P(OPh)3, 10.36 for P(OBu)3, 14.33 for PPh3, 15.49 for PBu3, 18.39 for P(4-Me2NC6H4)3] are compared with the reactivities of other classes of nucleophiles (see, www.cup. uni-muenchen.de/oc/mayr).     

Molecular dynamics simulation of the reaction of hydration of formaldehyde using a potential based on solute-solvent interaction energy components

Molecular dynamics simulations of aqueous solutions at infinite dilution of the reaction of water with formaldehyde, H(2)O + H(2)CO --> H(2)C(OH)(2), were performed using Lennard-Jones 12-6-1 potentials to describe the solute-solvent interactions, and TIP3P to describe the water-water interactions. The Morokuma decomposition scheme of ab initio interaction energies at the SCF level and the dispersion component at MP2 level were used to reproduce the molecular parameters of the solute-water interaction potential. The results show that the functions that use the EX-PL-DIS-ES interaction model to describe the solvation of the reactant and product systems lead to good values of the reaction (DeltaG) and activation (DeltaG(#)) free energy as compared with those from using AMBER-derived parameters, and with the available theoretical and experimental data.     

Calculations of pH-dependent binding of proteins to biological membranes

Binding of proteins to membranes is often accompanied by titration of ionizable residues and is, therefore, dependent on pH. We present a theoretical treatment and computational approach for predicting absolute, pH-dependent membrane binding free energies. The standard free energy of binding, DeltaG, is defined as -RTln(P(b)/P(f)), where P(b) and P(f) are the amounts of bound and free protein. The apparent pK(a) of binding is the pH value at which P(b) and P(f) are equal. Proteins bind to the membrane in the pH range where DeltaG is negative. The components of the binding free energy are (a) the free energy cost of ionization state changes (DeltaG(ion)), (b) the effective energy of transfer from solvent to the membrane surface, (c) the translational/rotational entropy cost of binding, and (d) an ideal entropy term that depends on the relative volume of the bound and free state and therefore depends on lipid concentration. Calculation of the first term requires determination of pK(a) values in solvent and on the membrane surface. All energies required by the method are obtained from molecular dynamics trajectories on an implicit membrane (IMM1-GC). The method is tested on pentalysine and the helical peptide VEEKS, derived from the membrane-binding domain of phosphocholine cytidylyltransferase. The agreement between the measured and the calculated free energies of binding of pentalysine is good. The extent of membrane binding of VEEKS is, however, underestimated compared to experiment. Calculations of the interaction energy between two VEEKS helices on the membrane suggest that the discrepancy is mainly due to the neglect of protein-protein interactions on the membrane surface.     

Prediction of the dissociation constant pKa of organic acids from local molecular parameters of their electronic ground state

A quantum chemical method has been developed to estimate the dissociation constant pK(a) of organic acids from their neutral molecular structures by employing electronic structure properties. The data set covers 219 phenols (including 29 phenols with intramolecular H-bonding), 150 aromatic carboxylic acids, 190 aliphatic carboxylic acids, and 138 alcohols, with pK(a) varying by 16 units (0.38-16.80). Optimized ground-state geometries employing the semiempirical AM1 Hamiltonian have been used to quantify the site-specific molecular readiness to donate or accept electron charge in terms of both charge-associated energies and energy-associated charges, augmented by an ortho substitution indicator for aromatic compounds. The resultant regression models yield squared correlation coefficients (r(2)) from 0.82 to 0.90 and root-mean-square errors (rms) from 0.39 to 0.70 pK(a) units, corresponding to an overall (subset-weighted) r(2) of 0.86. Simulated external validation, leave-10%-out cross-validation and target value scrambling demonstrate the statistical robustness and prediction power of the derived model suite. The low intercorrelation with prediction errors from the commercial ACD package provides opportunity for a consensus model approach, offering a pragmatic way for further increasing the confidence in prediction significantly. Interestingly, inclusion of calculated free energies of aqueous solvation does not improve the prediction performance, probably because of the limited precision provided by available continuum-solvation models.     

High-load, soluble oligomeric carbodiimide: synthesis and application in coupling reactions

A facile preparation of a high-load, soluble oligomeric alkyl cyclohexylcarbodiimide (OACC) reagent via ROM polymerization from commercially available starting materials is described. This reagent is exploited as a coupling reagent for esterification, amidation, and dehydration of carboxylic acids (aliphatic and aromatic) with an assortment of alcohols (aliphatic primary, secondary, and benzylic), thiols, phenols, and amines (aliphatic primary, secondary, benzylic, and aromatic/anilines), respectively. Following the coupling event, precipitation with an appropriate solvent (Et(2)O, MeOH, or EtOAc), followed by filtration through a SPE provides the products in good to excellent yield and purity.     

Three empirical correlations connecting gaseous cluster energies and solvation energies of alkali metal and halide ions.

This paper gives two empirical correlations of formation Gibbs energies of gaseous clusters DeltaG(f)n as function of number of solvent molecules attached to the ion, n, and one correlation connecting the DeltaG(f)n for each individual cluster with the total DeltaG(o)hydr value. The experimental ratios of DeltaG(f)2/DeltaG(f)1 and DeltaG(f)3/DeltaG(f)1 for both alkali metal and halide ions are on average equal to 0.75 and 0.5, respectively. DeltaG(f)n values for n > or = 4 are correlated with n as DeltaG(f)n = [a/(n - 1)] DeltaG(f)1 + b DeltaG(f)1. For all available data on cluster energies and each individual cluster, the DeltaG(f)n's are straight-line functions of DeltaG(o)hydr. This well corresponds to another empirical rule stating that the Gibbs energies of transfer of ions between two solvents are often as well straight-line functions of DeltaG(o)(hydr) [J. Rais and T. Okada, J. Phys. Chem. A, 2000, 104, 7314]. Tentative models of the found behavior are proposed. A full data set of the gaseous cluster energies of formation based on inclusion of new, usually not used entries from the literature is provided.     

Theoretical study of the enol imine <--> enaminone tautomeric equilibrium in organic solvents

The tautomeric enol imine <--> enaminone (phenol <--> quinone) equilibrium of the 1-hydroxy-2-naphthaldehyde Schiff base (2-phenyliminomethyl-naphthalen-1-ol) was investigated by density functional theory (B3LYP) and ab initio (MP2) methods in the IEF-PCM polarizable continuum dielectric solvent approximation and by a combined ab initio + FEP/MC study by considering an explicit solvent model. Special emphasis was put on the effect of solvation on this equilibrium by using an apolar (CCl4), polar aprotic (CH3CN), and polar protic (CH3OH) solvent. Compared with experimental tautomerization Gibbs free energies, the IEF-PCM/B3LYP calculations apparently overestimate the stability of the quinone form both when the 6-31G(d,p) and the 6-311++G(d,p) basis sets are applied. IEF-PCM/MP2 studies with the above basis sets predict the preference of the aromatic phenol tautomer, in contrast to the experiment in methanol and acetonitrile solvent. Calculation of the total relative free energy as DeltaG(tot) = DeltaE(int)(IEF-PCM/QCISD(T)/6-31G(d)) + DeltaG(solv, FEP/MC) + DeltaG(thermal) provided agreement with the experimental values up to 0.6 kcal/mol in the three solvents, and the predominant tautomer was always correctly predicted. In-solution relevant atomic charges, derived by a fit to the molecular electrostatic potential generated by the IEF-PCM/B3LYP/6-31G(d,p) wave function, show strong dependence on the fitting procedure (CHELPG or RESP) and are fairly insensitive to the chemical nature of the actual solvent. Use of the CHELPG charges in FEP/MC simulations revealed to be superior in comparison with the use of the RESP charge set.