A multistate empirical valence bond description of protonatable amino acids

The multistate empirical valence bond (MS-EVB) model, which was developed for molecular dynamics simulations of proton transport in water and biomolecular systems, is extended for the modeling of protonatable amino acid residues in aqueous environments, specifically histidine and glutamic acid. The parameters of the MS-EVB force field are first determined to reproduce the geometries and energetics of the gas phase amino acid-water clusters. These parameters are then optimized to reproduce experimental pK(a) values. The free energy profiles for acid ionization and the corresponding pK(a) values are calculated by MS-EVB molecular dynamics simulations utilizing the umbrella sampling technique, with the center of excess charge coordinate chosen as the dissociation reaction coordinate. A general procedure for fitting the MS-EVB parameters is formulated, which allows for the parametrization of other amino acid residues with protonatable groups and the subsequent use of the MS-EVB approach for molecular dynamics simulations of proton transfer processes in proteins involving protonation/deprotonation of the protonatable amino acid groups.     

Deprotonation of a histidine residue in aqueous solution using constrained ab initio molecular dynamics

The dissociation of a weak acid - a histidine residue - in water was investigated by means of constrained Car-Parrinello ab initio molecular dynamics. Both linear and coordination constraints were employed, and the structural, electronic, and dynamical transformations along the respective reaction coordinates were analyzed. The calculated potentials of mean force for the dissociation of a hydrogen atom from the Nepsilon and Ndelta positions of the imidazole ring reveal that protonated forms are approximately 9.0-9.5 kcal/mol more stable than the deprotonated. This result seems to agree well with the experimental estimate based on pKa. A possible transition state for the deprotonation has also been identified. Analysis of the electron localization function indicates that the proton transfer along the selected reaction path is not a fully concerted process.     

The oxidation of tyrosine and tryptophan studied by a molecular dynamics normal hydrogen electrode

The thermochemical constants for the oxidation of tyrosine and tryptophan through proton coupled electron transfer in aqueous solution have been computed applying a recently developed density functional theory (DFT) based molecular dynamics method for reversible elimination of protons and electrons. This method enables us to estimate the solvation free energy of a proton (H(+)) in a periodic model system from the free energy for the deprotonation of an aqueous hydronium ion (H(3)O(+)). Using the computed solvation free energy of H(+) as reference, the deprotonation and oxidation free energies of an aqueous species can be converted to pK(a) and normal hydrogen electrode (NHE) potentials. This conversion requires certain thermochemical corrections which were first presented in a similar study of the oxidation of hydrobenzoquinone [J. Cheng, M. Sulpizi, and M. Sprik, J. Chem. Phys. 131, 154504 (2009)]. Taking a different view of the thermodynamic status of the hydronium ion, these thermochemical corrections are revised in the present work. The key difference with the previous scheme is that the hydronium is now treated as an intermediate in the transfer of the proton from solution to the gas-phase. The accuracy of the method is assessed by a detailed comparison of the computed pK(a), NHE potentials and dehydrogenation free energies to experiment. As a further application of the technique, we have analyzed the role of the solvent in the oxidation of tyrosine by the tryptophan radical. The free energy change computed for this hydrogen atom transfer reaction is very similar to the gas-phase value, in agreement with experiment. The molecular dynamics results however, show that the minimal solvent effect on the reaction free energy is accompanied by a significant reorganization of the solvent.     

Acidity constants from vertical energy gaps: density functional theory based molecular dynamics implementation

The question of how to compute acidity constants (pK(a)) treating solvent and solute at the same level of theory remains of some interest, for example in the case of high or low pH conditions. We have developed a density functional theory based molecular dynamics implementation of such a method. The method is based on a half reaction scheme computing free energies of dissociation from the vertical energy gaps for insertion or removal of protons. Finite system size effects are important, but largely cancel when half reactions are combined to full reactions. We verified the method by investigating a series of organic and inorganic acids and bases spanning a wide range of pK(a) values (20 units). We find that the response of the aqueous solvent to vertical protonation/deprotonation is almost always asymmetric and correlated with the strength of the hydrogen bonding of the deprotonated base. We interpret these observations in analogy with the picture of solvent response to electronic ionization.     

Hydrolysis of Al3+ from constrained molecular dynamics

We investigated the hydrolysis reactions of Al(3+) in AlCl(3) aqueous solution using the constrained molecular dynamics based on the Car-Parrinello molecular-dynamics method. By employing the proton-aluminum coordination number as a reaction coordinate in the constrained molecular dynamics the deprotonation as well as dehydration processes are successfully realized. From our free-energy difference of DeltaG(0) approximately 8.0 kcal mol(-1) the hydrolysis constant pK(a1) is roughly estimated as 5.8, comparable to the literature value of 5.07. We show that the free-energy difference for the hydrolysis of Al(3+) in acidic conditions is at least 4 kcal mol(-1) higher than that in neutral condition, indicating that the hydrolysis reaction is inhibited by the presence of excess protons located around the hydrated ion, in agreement with the change of the predominant species by pH.     

Acido-base behavior of hydroxamic acids: experimental and ab initio studies on hydroxyureas

The values of Ka, DeltaSa, and DeltaHa for deprotonation of hydroxyurea (HU) and N-methylhydroxyurea (NMHU), as targeted compounds, and for betainohydroxamic acid, were potentiometrically determined. Although NMHU has two and HU even three deprotonation sites, the measurements confirm that they behave as weak acids with a single pK a approximately 10. Comparison with analogous thermodynamic parameters previously determined for series of monohydroxamic acids reveals deviations from a DeltaSa, vs DeltaHa plot for HU and NMHU, raising the question of the dissociation site of hydroxureas in water. In addition to the deprotonation of the hydroxyl oxygen, ab initio calculations performed at the MP2/6-311++G(d,p) level of theory for these two compounds indicate a notable participation of the nitrogen deprotonation site in HU. The calculations for the isolated, monohydrate, trihydrate, and decahydrate molecular and anionic forms of hydroxyureas support the importance of hydrogen bonding in the gas and aqueous phases. The hydroxylamino nitrogen in HU is the most acidic site in water, contributing approximately 94% to the overall deprotonation process at 25 degrees C. On the contrary, the hydroxylamino oxygen is by far the most favored deprotonation site in NMHU, contributing almost 100% in aqueous medium. The predicted participations of two deprotonation sites in HU, calculated at the MP2/6-311++G(d,p) level of theory, combined with the calculated relative reaction enthalpy and entropy for the deprotonation, satisfactorily explain the observed deviation from linearity of DeltaHa vs DeltaSa, plot. There is no such a simple explanation for acid-base behavior of NMHU.     

Theoretical study on reaction scheme of silver(I) containing 5-substituted uracils bridge formation

We present a reaction scheme of silver containing 5-substituted uracils (N) bridge formation with two silver ions to a silver-mediated base pair [N-Ag(2)-N] by using the conductor-like polarizable continuum model (CPCM)-B3LYP/aug-cc-pVDZ level of theory. The whole reaction scheme is divided into the following three steps: (1) silver ion binding and deprotonation, (2) silver ion transfer, and (3) dimer formation and structural fluctuation. With a new pK(a) computing scheme proposed in our previous studies, it is found that a silver coordination decreases the pK(a) of N by 2.5-3.0 pK(a) units, which is an important clue for silver-ion selectivity by N. Judging from the calculation, we revealed that the silver ion transfer reaction and the dimerization reaction occur spontaneously. Moreover, both reactions are independent of the C5 ligand in N so that the deprotonation reaction, which is the first step of this scheme, plays a key role in forming the [N-Ag(2)-N] pairing.     

The sorption of divalent metal ions on AlPO4

The sorption of Cu(2+), Pb(2+), Ni(2+), and Cd(2+) ions on the aluminum(III) phosphate was observed to increase with increases in the concentration, temperature, and pH of the system. The apparent dissociation (pK(a)), binding (pK(b)) and exchange (pK(ex)) constants of aluminum(III) phosphate were evaluated and found to be dependent upon the temperature and nature of the metal cations. The values of the dissociation constants (pK(a)) followed the order Pb(2+)相似文献   

Probing pH-dependent dissociation of HdeA dimers

HdeA protein is a small, ATP-independent, acid stress chaperone that undergoes a dimer-to-monomer transition in acidic environments. The HdeA monomer binds a broad range of proteins to prevent their acid-induced aggregation. To understand better HdeA's function and mechanism, we perform constant-pH molecular dynamics simulations (CPHMD) to elucidate the details of the HdeA dimer dissociation process. First the pK(a) values of all the acidic titratable groups in HdeA are obtained and reveal a large pK(a) shift only for Glu(37). However, the pH-dependent monomer charge exhibits a large shift from -4 at pH > 6 to +6 at pH = 2.5, suggesting that the dramatic change in charge on each monomer may drive dissociation. By combining the CPHMD approach with umbrella sampling, we demonstrate a significant stability decrease of the HdeA dimer when the environmental pH changes from 4.0 to 3.5 and identify the key acidic residue-lysine interactions responsible for the observed pH sensing in HdeA chaperon activity function.     

Protonation processes and electronic spectra of histidine and related ions

A full structural assignment of the neutral, protonated, and deprotonated histidine conformers in the gas phase is presented. A total of 3024 unique trial structures were generated by all combinations of internal single-bond rotamers of these species and optimized at the B3LYP/6-311G* level and further optimized at the B3LYP/6-311++G** level. A set of unique conformers is found, and their relative energies, free energies, dipole moments, rotational constants, electron affinities, ionization energies, and harmonic frequencies are determined. The population ratio of histidine and its tautomer is 1:0.16 at 298 K. Massive conformational changes are observed due to protonation and deprotonation, and the intramolecular H-bonds are characterized with the atoms in molecules theory. The calculated proton dissociation energy, gas-phase acidity, proton affinity, and gas-phase basicity are in excellent agreement with the experiments. The deprotonation and protonation of gaseous histidine both occur on the imidazole ring, explaining the versatile biofunctions of histidine in large biomolecules. The UV spectra of neutral and singly and doubly protonated histidine are investigated with the TDDFT/B3LYP/6-311+G(2df,p) calculations. The S0-S1, S0-S2, and S0-S3 excitations of histidine are mixed pipi*/npi* transitions at 5.37, 5.44, and 5.69 eV, respectively. The three excitation energies for histidine tautomer are 4.85, 5.47, and 5.52 eV, respectively. The three excitations for protonated histidine are mainly npi* transitions at 5.45, 5.67, and 5.82 eV, respectively. The S0-S1 excitation of protonated histidine produces ImH-CbetaH2-CalphaH(COOH)-NH2+, while the S0-S2 and S0-S3 transitions produce ImH-CbetaH2-CalphaH(NH2)-(COOH)+. These data may help to understand the mechanisms of the UV fragmentation of biomolecules.     

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.     

Applications of quantum-classical and quantum-stochastic molecular dynamics simulations for proton transfer processes

Quantum-classical and quantum-stochastic molecular dynamics models (QCMD/QSMD) are formulated and applied to describe proton transfer processes in three model systems - the proton bound ammonia-ammonia dimer in an external electrostatic field; malonaldehyde, which undergoes a quantum tautomeric rearrangement; and phospholipase A₂, an enzyme which induces a water dissociation process in its active site followed by proton hopping to a histidine imidazole ring. The proton dynamics are described by the time-dependent Schrödinger equation. The dynamics of the classical atoms are described using classical molecular dynamics. Coupling between the quantum proton (s) and the classical atoms is accomplished via conventional or extended Hellmann-Feynman forces, as well as the time-dependence of the potential energy function in the Schrödinger equation. The interaction of the system with its environment is described by stochastic forces. Possible extensions of the models as well as future applications in molecular structure and dynamics analysis will be briefly discussed.     

Deprotonation sites of acetohydroxamic acid isomers. A theoretical and experimental study

Theoretical (ab initio calculations) and experimental (NMR, spectrophotometric, and potentiometric measurements) investigations of the isomers of acetohydroxamic acid (AHA) and their deprotonation processes have been performed. Calculations with the Gaussian 98 package, refined at the MP2(FC)/AUG-cc-pVDZ level considering the molecule isolated, indicate that the Z(cis) amide is the most stable form of the neutral molecule. This species and the less stable (Z)-imide form undergo deprotonation, giving rise to two stable anions. Upon deprotonation, the E(trans) forms give three stable anions. The ab initio calculations were performed in solution as well, regarding water as a continuous dielectric; on the basis of the relative energies of the most stable anion and neutral forms, calculated with MP2/PCM/AUG-cc-pVDZ, N-deprotonation of the amide (Z or E) structure appeared to be the most likely process in solution. NMR measurements provided evidence for the existence of (Z)- and (E)-isomers of both the neutral and anion forms in solution. Comparisons of the dynamic NMR and NOESY (one-dimensional) results obtained for the neutral species and their anions were consistent with N-deprotonation, which occurred preferentially to O-deprotonation. The (microscopic) acid dissociation constants of the two isomers determined at 25 degrees C from the pH dependence of the relevant chemical shifts, pK(E) = 9.01 and pK(Z) = 9.35, were consistent with the spectrophotometric and potentiometric evaluations (pK(HA) = 9.31).     

Mechanism of C-terminal intein cleavage in protein splicing from QM/MM molecular dynamics simulations

Protein splicing is a post-translational process in which a biologically inactive protein is activated by the release of a segment denoted as an intein. The process involves four steps. In the third, the scission of the intein takes place after the cyclization of the last amino acid of the segment, an asparagine. Little is known about the chemical reaction necessary for this cyclization. Experiments demonstrate that two histidines (the penultimate amino acid of the intein, and a histidine located 10 amino acids upstream) are relevant in the cyclization of the asparagine. We have investigated the mechanism and determinants of reaction in the GyrA intein focusing on the requirements for asparagine activation for its cyclization. First, the influence that the protonation states of these two histidines have on the orientation of the asparagine side chain is investigated by means of molecular dynamics simulation. Molecular dynamics simulations using the CHARMM27 force field were carried out on the three possible protonation states for each of these two histidines. The results indicate that the only protonation state in which the conformation of the system is suitable for cyclization is when the penultimate histidine is fully protonated (positively charged), and the upstream histidine is in the His(ε) neutral tautomeric form. The free energy profile for the reaction in which the asparagine is activated by a proton transfer to the upstream histidine is presented, computed by hybrid quantum mechanics/molecular mechanics (QM/MM) umbrella sampling molecular dynamics at the SCCDFTB/CHARMM27 level of theory. The calculated free energy barrier for the reaction is 19.0 kcal mol(-1). B3LYP/6-31+G(d) QM/MM single-point calculations give a qualitatively a similar energy profile, although with somewhat higher energy barriers, in good agreement with the value derived from experiment of 25 kcal mol(-1) at 60 °C. QM/MM molecular dynamics simulations of the reactant, activated reactant and intermediate states highlight the importance of the Arg181-Val182-Asp183 segment in catalysing the reaction. Overall, the results indicate that nucleophilic activation of the asparagine for its cyclization by the upstream histidine acting as the base is a plausible mechanism for the C-terminal cleavage in protein splicing.     

Substituent effects on electrophilic catalysis by the carbonyl group: anatomy of the rate acceleration for PLP-catalyzed deprotonation of glycine

First-order rate constants, determined by (1)H NMR, are reported for deuterium exchange between solvent D(2)O and the α-amino carbon of glycine in the presence of increasing concentrations of carbonyl compounds (acetone, benzaldehyde, and salicylaldehyde) and at different pD and buffer concentrations. These rate data were combined with (1)H NMR data that define the position of the equilibrium for formation of imines/iminium ions from addition of glycine to the respective carbonyl compounds, to give second-order rate constants k(DO) for deprotonation of α-imino carbon by DO(-). The assumption that these second-order rate constants lie on linear structure-reactivity correlations between log k(OL) and pK(a) was made in estimating the following pK(a)'s for deprotonation of α-imino carbon: pK(a) = 22, glycine-acetone iminium ion; pK(a) = 27, glycine-benzaldehyde imine; pK(a) ≈ 23, glycine-benzaldehyde iminium ion; and, pK(a) = 25, glycine-salicylaldehyde iminium ion. The much lower pK(a) of 17 [Toth, K.; Richard, J. P. J. Am. Chem. Soc. 2007, 129, 3013-3021] for carbon deprotonation of the adduct between 5'-deoxypyridoxal (DPL) and glycine shows that the strongly electron-withdrawing pyridinium ion is unique in driving the extended delocalization of negative charge from the α-iminium to the α-pyridinium carbon. This favors carbanion protonation at the α-pyridinium carbon, and catalysis of the 1,3-aza-allylic isomerization reaction that is a step in enzyme-catalyzed transamination reactions. An analysis of the effect of incremental changes in structure on the activity of benzaldehyde in catalysis of deprotonation of glycine shows the carbonyl group electrophile, the 2-O(-) ring substituent and the cation pyridinium nitrogen of DPL each make a significant contribution to the catalytic activity of this cofactor analogue. The extraordinary activity of DPL in catalysis of deprotonation of α-amino carbon results from the summation of these three smaller effects.     

Isolation and crystal structure of a water-soluble iridium hydride: a robust and highly active catalyst for acid-catalyzed transfer hydrogenations of carbonyl compounds in acidic media

This paper reports the isolation and structural determination of a water-soluble hydride complex [Cp*Ir(III)(bpy)H](+) (1, Cp* = eta(5)-C(5)Me(5), bpy = 2,2'-bipyridine) that serves as a robust and highly active catalyst for acid-catalyzed transfer hydrogenations of carbonyl compounds at pH 2.0-3.0 at 70 degrees C. The catalyst 1 was synthesized from the reaction of a precatalyst [Cp*Ir(III)(bpy)(OH(2))](2+) (2) with hydrogen donors HCOOX (X = H or Na) in H(2)O under controlled conditions (2.0 < pH < 6.0, 25 degrees C) which avoid protonation of the hydrido ligand of 1 below pH ca. 1.0 and deprotonation of the aqua ligand of 2 above pH ca. 6.0 (pK(a) value of 2 = 6.6). X-ray analysis shows that complex 1 adopts a distorted octahedral geometry with the Ir atom coordinated by one eta(5)-Cp*, one bidentate bpy, and one terminal hydrido ligand that occupies a bond position. The isolation of 1 allowed us to investigate the robust ability of 1 in acidic media and reducing ability of 1 in the reaction with carbonyl compounds under both stoichiometric and catalytic conditions. The rate of the acid-catalyzed transfer hydrogenation is drastically dependent on pH of the solution, reaction temperature, and concentration of HCOOH. The effect of pH on the rate of the transfer hydrogenation is rationalized by the pH-dependent formation of 1 and activation process of the carbonyl compounds by protons. High turnover frequencies of the acid-catalyzed transfer hydrogenations at pH 2.0-3.0 are ascribed not only to nucleophilicity of 1 toward the carbonyl groups activated by protons but also to a protonic character of the hydrido ligand of 1 that inhibits the protonation of the hydrido ligand.     

Thermodynamic, kinetic and pH studies on the reactions of NCS-, N3-, and CH3CO2- with Fusarium galactose oxidase

Thermodynamic and kinetic studies on the X- = NCS-, N3-, and CH3CO2- replacement of H2O/OH- at the CuII exogenous site of the tyrosyl-radical-containing enzyme galactose oxidase (GOaseox) from Fusarium (NRR 2903), have been studied by methods involving UV-vis spectrophotometry (25 degrees C), pH range 5.5-8.7, I = 0.100 M (NaCl). In the case of N3- and CH3CO2- previous X-ray structures have confirmed coordination at the exogenous H2O/OH- site. From the effect of pH on the UV-vis spectrum of GOaseox under buffer-free conditions, acid dissociation constants of 5.7 (pK1a; coordinated H2O) and 7.0 (pK2a; H+Tyr-495) have been determined. At pH 7.0 formation constants K(25 degrees C)/M-1 are NCS- (480), N3- (1.98 x 10(4)), and CH3CO2- (104), and from the variations in K with pH the same two pKa values are seen to apply. No pK1a is observed when X- is coordinated. From equilibration stopped-flow studies rate constants at pH 7.0 for the formation reaction kf(25 degrees C)/M-1 s-1 are NCS- (1.13 x 10(4)) and N3- (5.2 x 10(5)). Both K and kf decrease with increasing pH, consistent with the electrostatic effect of replacing H2O by OH-. In the case of the GOaseox Tyr495Phe variant pK1a is again 5.7, but no pK2a is observed, confirming the latter as acid dissociation of protonated Tyr-495. At pH 7.0, K for the reaction of four-coordinate GOaseox Tyr495Phe with NCS- (1.02 x 10(5) M-1) is more favorable than the value for GOaseox. Effects of H+Tyr-495 deprotonation on K are smaller than those for the H2O/OH- change. The pK1a for GOasesemi is very similar (5.6) to that for GOaseox (both at CuII), but pK2a is 8.0. At pH 7.0 values of K for GOasesemi are NCS- (270 M-1), N3- (4.9 x 10(3)), and CH3CO2- (107).     

H-abstraction is more efficient than cis-trans isomerization in (4-methylcyclohexylidene) fluoromethane. An ab initio molecular dynamics study

Non-adiabatic molecular dynamics simulations have been performed in the fluoro-olefin (4-methylcyclohexylidene) fluoromethane (4MCF) using multiconfigurational CASSCF (complete active space self-consistent field) on-the-fly calculations. As an olefin containing a C[double bond, length as m-dash]C double bond, 4MCF is expected to undergo cis-trans isomerization after light irradiation. However, ab initio molecular dynamics shows that a preferential dissociation of atomic hydrogen is taking place after population transfer to the bright ππ* state. This state is strongly mixed with πσ* states allowing dissociation in the electronic excited state before deactivation to the ground state occurs. A minor amount of trajectories experiences F-dissociation, followed by pyramidalization at the sp(2) carbons and CHF dissociation. In contrast, the amount of trajectories undergoing torsion around the double bond, and therefore cis-trans isomerization, is marginal. The H-abstraction reaction is ultrafast, taking place in less than 60 fs.     

Solvent polarization and kinetic isotope effects in nitroethane deprotonation and implications to the nitroalkane oxidase reaction

We have carried out a mixed molecular dynamics and centroid path integral simulation using a combined quantum mechanical and molecular mechanical (QM/MM) potential to study the anomalous Br?nsted relationship between rates and equilibria for deprotonation of nitroalkanes in water, which is known as the nitroalkane anomaly. The deprotonation process is catalyzed by nitroalkane oxidase. Our results show that the difference in solvent polarization effects for the TS and products is a major factor for the differential solvent effects on rate and equilibrium of nitroalkane deprotonation. This is due to poor charge delocalization as a result of slow rehybridization compared to bond breaking. Although solvent effects do not affect significantly the computed kinetic isotope effects in comparison with the gas-phase value, there is slight solvent-induced increase in tunneling. The present results suggest that an effective means by which the transition state can be stabilized in the enzyme nitroalkane oxidase is to facilitate the Calpha rehybridization.     

Formation and stability of peptide enolates in aqueous solution

Second-order rate constants k(DO) (M(-1) s(-1)) were determined in D(2)O for deprotonation of the N-terminal alpha-amino carbon of glycylglycine and glycylglycylglycine zwitterions, the internal alpha-amino carbon of the glycylglycylglycine anion, and the acetyl methyl group and the alpha-amino carbon of the N-acetylglycine anion and N-acetylglycinamide by deuterioxide ion. The data were used to estimate values of k(HO) (M(-1) s(-1)) for proton transfer from these carbon acids to hydroxide ion in H(2)O. Values of the pK(a) for these carbon acids ranging from 23.9 to 30.8 were obtained by interpolation or extrapolation of good linear correlations between log k(HO) and carbon acid pK(a) established in earlier work for deprotonation of related neutral and cationic alpha-carbonyl carbon acids. The alpha-amino carbon at a N-protonated N-terminus of a peptide or protein is estimated to undergo deprotonation about 130-fold faster than the alpha-amino carbon at the corresponding internal amino acid residue. The value of k(HO) for deprotonation of the N-terminal alpha-amino carbon of the glycylglycylglycine zwitterion (pK(a) = 25.1) is similar to that for deprotonation of the more acidic ketone acetone (pK(a) = 19.3), as a result of a lower Marcus intrinsic barrier to deprotonation of cationic alpha-carbonyl carbon acids. The cationic NH(3)(+) group is generally more strongly electron-withdrawing than the neutral NHAc group, but the alpha-NH(3)(+) and the alpha-NHAc substituents result in very similar decreases in the pK(a) of several alpha-carbonyl carbon acids.