Computational mutation analysis of hydrogen abstraction and radical rearrangement steps in the catalysis of coenzyme B12-dependent diol dehydratase

A mutation analysis of the catalytic functions of active-site residues of coenzyme B(12)-dependent diol dehydratase in the conversion of 1,2-propanediol to 1,1-propanediol has been carried out by using QM/MM computations. Mutants His143Ala, Glu170Gln, Glu170Ala, and Glu170Ala/Glu221Ala were considered to estimate the impact of the mutations of His143 and Glu170. In the His143Ala mutant the activation energy for OH migration increased to 16.4 from 11.5 kcal mol(-1) in the wild-type enzyme. The highest activation energy, 19.6 kcal mol(-1), was measured for hydrogen back-abstraction in this reaction. The transition state for OH migration is not sufficiently stabilized by the hydrogen-bonding interaction formed between the spectator OH group and Gln170 in the Glu170Gln mutant, which demonstrates that a strong proton acceptor is required to promote OH migration. In the Glu170Ala mutant, a new strong hydrogen bond is formed between the spectator OH group and Glu221. A computed activation energy of 13.6 kcal mol(-1) for OH migration in the Glu170Ala mutant is only 2.1 kcal mol(-1) higher than the corresponding barrier in the wild-type enzyme. Despite the low activation barrier, the Glu170Ala mutant is inactive because the subsequent hydrogen back-abstraction is energetically demanding in this mutant. OH migration is not feasible in the Glu170Ala/Glu221Ala mutant because the activation barrier for OH migration is greatly increased by the loss of COO(-) groups near the spectator OH group. This result indicates that the effect of partial deprotonation of the spectator OH group is the most important factor in reducing the activation barrier for OH migration in the conversion of 1,2-propanediol to 1,1-propanediol catalyzed by diol dehydratase.     

Can hydridic-to-protonic hydrogen bonds catalyze hydride transfers in biological systems?

Catalysis of hydride transfer by hydridic-to-protonic hydrogen (HHH) bonding in α-hydroxy carbonyl isomerization reactions was examined computationally in the lithium salts of 7-substituted endo-3-hydroxybicyclo[2.2.1]hept-5-en-2-ones. The barrier for intramolecular hydride transfer in the parent system was calculated to be 17.2 kcal/mol. Traditional proton donors, such as OH and NH(3)(+), stabilized the metal cation-bridged transition state by 1.4 and 3.3 kcal/mol, respectively. Moreover, among the conformers of the OH systems, the one in which the proton donor is able to interact with the migrating hydride (H(m)) has an activation barrier lower by 1.3 and 1.7 kcal/mol than the other possible OH conformers. By contrast, the presence of an electronegative group such as F, which disfavors the migration electronically by opposing development of hydridic charge, destabilizes the hydride migration by 1.5 kcal/mol relative to the epimeric exo system. In both ground and transition states the H(m)···H distance decreased with increasing acidity of the proton donor, reaching a minimum of 1.58 ? at the transition state for NH(3)(+). Both Mulliken and NPA charges show enhancement of negative character of the migrating hydride in the cases in which HHH bonding is possible.     

Computational investigation of hydrogen abstraction from 2-aminoethanol by the 1,5-dideoxyribose-5-yl radical: a model study of a reaction occurring in the active site of ethanolamine ammonia lyase

Hydrogen abstraction from 2-aminoethanol by the 5'-deoxyadenosyl radical, which is formed upon Co--C bond homolysis in coenzyme B(12), was investigated by theoretical means with employment of the DFT (B3LYP) and ab initio (MP2) approaches. As a model system for the 5'-deoxyadenosyl moiety the computationally less demanding 1,5-dideoxyribose was employed; two conformers, which differ in ring conformation (C2- and C3-endo), were considered. If hydrogen is abstracted from "free" substrate by the C2-endo conformer of the 1,5-dideoxyribose-5-yl radical, the activation enthalpy is 16.7 kcal mol(-1); with the C3-endo counterpart, the value is 17.3 kcal mol(-1). These energetic requirements are slightly above the activation enthalpy limit (15 kcal mol(-1)) determined experimentally for the rate-determining step of the sequence, that is, hydrogen delivery from 5'-deoxyadenosine to the product radical. The activation enthalpy is lower when the substrate interacts with at least one amino acid from the active site. According to the computations, when a His model system partially protonates the substrate the activation enthalpy is 4.5 kcal mol(-1) for the C3-endo conformer and 5.8 kcal mol(-1) for the C2-endo counterpart. As hydrogen abstraction from the fully as well as the partially protonated substrate is preceded by the formation of quite stable encounter complexes, the actual activation barriers are around 13-15 kcal mol(-1). A synergistic interaction of 2-aminoethanol with two amino acids where His partially protonates the NH(2) group and Asp partially deprotonates the OH group of the substrate results in an activation enthalpy of 12.4 kcal mol(-1) for the C3-endo conformer and 13.2 kcal mol(-1) for the C2-endo counterpart. However, if encounter complexes exist in the active site, the actual activation barriers are much higher (>25 kcal mol(-1)) than that reported for the rate-determining step. These findings together with previous computations suggest that the energetics of the initial hydrogen abstraction decrease with an interaction of the substrate with only a protonating auxiliary, but for the rearrangement of the radical the synergistic effects of two auxiliaries are essential to pull the barrier below the limit of 15 kcal mol(-1).     

Retro-[3 + 2]-cycloaddition reactions in the decomposition of five-membered nitrogen-containing heterocycles

Nitrogen-containing heterocycles form the basis for a new generation of high-energy density materials, and they serve as model compounds for nitrogen-containing fuels, such as coal and biomass, and they form the backbone of ionic liquids. A novel retro-[3 + 2]-cycloaddition to a three-membered diene and a two-membered dienophile, analogous to a retro-Diels-Alder reaction, may constitute an important initial reaction step in the thermal decomposition of these heterocyclic compounds. We investigate the kinetics and thermodynamics of these reactions for the heterocycles pyrrole, pyrazole, imidazole, 1,2,3-triazole, 1,2,4-triazole, 1,2,5-triazole, 1,3,4,-triazole, 1H-tetrazole, and 2H-tetrazole, using theoretical computational chemistry. The retro-cycloadditions are shown to form one of the three-membered products: hydrazoic acid (NH=N=N), nitrilimine (NH=N=CH), carbodiimide (NH=C=NH), or ketenimine (NH=C=CH2) plus one of the two-membered products acetylene, hydrogen cyanide, or N2. Accurate enthalpies of formation are calculated for the reaction products using the high-level W1 computational protocol, providing the previously undetermined enthalpy values of 70.09, 88.75, 35.03, and 44.28 kcal mol(-1) for hydrazoic acid, nitrilimine, carbodiimide, and ketenimine, respectively. We apply a variable-order form of the Marcus equation to the dissociation reactions in correlating the enthalpy of reaction with the activation enthalpy. Typical molecular elimination reactions from the heterocycles proceed with an intrinsic activation enthalpy of 36.8 kcal mol(-1) and intrinsic activation free energy of 42.1 kcal mol(-1). However, dissociation reactions resulting in the formation of either NH=C=NH or NH=C=CH2 demonstrate intrinsic barriers ca. 30 kcal mol(-1) higher, as a result of a concerted intramolecular hydrogen shift. Rate constants calculated between 300 and 3000 K indicate that the proposed dissociation reactions should be important in the decomposition of tetrazole and 1,2,3-triazole. This is confirmed by comparison with available experimental data. Decomposition of 1,2,4-triazole to HCN + nitrilimine may also be important at high temperatures. From extrapolation of our Marcus equation relationship, we predict pentazole to decompose to N2 + NHNN with an activation enthalpy of 19.5 kcal mol-1 and a half-life of only 14 s at 298 K.     

Polar group enhanced gas-phase acidities of carboxylic acids: an investigation of intramolecular electrostatic interaction

We studied the effects of polar groups on the gas-phase acidities of carboxylic acids experimentally and computationally. In this connection, the gas-phase acidities (DeltaH(acid), the enthalpy of deprotonation, and DeltaG(acid), the deprotonation free energy) of borane-complexed methylaminoacetic acid ((CH(3))2N(BH(3))CH(2)CO(2)H) and methylthioacetic acid (CH(3)S(BH(3))CH(2)CO(2)H) were measured using the kinetic method in a flowing afterglow-triple quadrupole mass spectrometer. The values of DeltaH(acid) and DeltaG(acid) of (CH(3))2N(BH(3))CH(2)CO(2)H were determined to be 328.8 +/- 1.9 and 322.1 +/- 1.9 kcal/mol, and those of CH(3)S(BH(3))CH(2)CO(2)H were determined to be 325.8 +/- 1.9 and 319.2 +/- 1.9 kcal/mol, respectively. The theoretical enthalpies of deprotonation of (CH(3))2N(BH(3))CH(2)CO(2)H (329.2 kcal/mol) and CH(3)S(BH(3))CH(2)CO(2)H (325.5 kcal/mol) were calculated at the B3LYP/6-31+G(d) level of theory. The calculated enthalpies of deprotonation of N-oxide-acetic acid (CH(3)NOCH(2)CO(2)H, 329.4 kcal/mol) and S-oxide-acetic acid (CH(3)SOCH(2)CO(2)H, 328.6 kcal/mol) are comparable to the experimental results for borane-complexed methylamino- and methylthioacetic acids. The enthalpy of deprotonation of sulfone-acetic acid (CH(3)SO2CH(2)CO(2)H, 326.1 kcal/mol) is about 2 kcal/mol lower than the S-oxide-acetic acid. The calculated enthalpy of deprotonation of sulfoniumacetic acid, (CH(3))2S+CH(2)CO(2)H, is 243.0 kcal/mol. Compared to the corresponding reference molecules, CH(3)NHCH(2)CO(2)H and CH(3)SCH(2)CO(2)H, the dipolar group and the monopolar group substituted carboxylic acids are stronger acids by 11-14 and 97 kcal/mol, respectively. We correlated the changes of the acidity upon a polar group substitution to the electrostatic free energy within the carboxylate anion. The acidity enhancements in polar group substituted carboxylic acids are the results of the favorable electrostatic interactions between the polar group and the developing charge at the carboxyl group.     

Catalytic roles of the metal ion in the substrate-binding site of coenzyme B12-dependent diol dehydratase

Functions of the metal ion in the substrate-binding site of diol dehydratase are studied on the basis of quantum mechanical/molecular mechanical (QM/MM) calculations. The metal ion directly coordinates to substrate and is essential for structural retention and substrate binding. The metal ion has been originally assigned to the K(+) ion; however, QM/MM computations indicate that Ca(2+) ion is more reasonable as the metal ion because calculated Ca-O distances better fit to the coordination distances in X-ray crystal structures rather than calculated K-O distances. The activation energy for the OH group migration, which is essential in the conversion of diols to corresponding aldehydes, is sensitive to the identity of the metal ion. For example, the spectator OH group of substrate is fully deprotonated by Glu170 in the transition state for the OH group migration in the Ca-contained QM/MM model, and therefore the barrier height is significantly decreased in the model having Ca(2+) ion. On the other hand, the deprotonation of the spectator OH group cannot effectively be triggered by the K(+) ion. Moreover, in the hydrogen recombination, the most energy-demanding step is more favorable in the Ca-contained model. The proposal that the Ca(2+) ion should be involved in the substrate-binding site is consistent with an observed large deuterium kinetic isotope effect of 10, which indicates that C-H bond activation is involved in the rate-determining step. Asp335 is found to have a strong anticatalytic effect on the OH group migration despite its important role in substrate binding. The synergistic interplay of the O-C bond cleavage by Ca(2+) ion and the deprotonation of the spectator OH group by Glu170 is required to overcome the anticatalytic effect of Asp335.     

The cysteine radical cation: structures and fragmentation pathways

A theoretical study on the structures, relative energies, isomerization reactions and fragmentation pathways of the cysteine radical cation, [NH(2)CH(CH(2)SH)COOH].+, is reported. Hybrid density functional theory (B3LYP) has been used in conjunction with the 6-311++G(d,p) basis set. The isomer at the global minimum, Captodative-1, has the structure NH(2)C.(CH(2)SH)C(OH)(2)+; the stability of this ion is attributed to the captodative effect in which the NH(2) functions as a powerful pi-electron donor and C(OH)(2)+ as a powerful pi-electron acceptor. Ion Distonic-S-1, H(3)N(+)CH(CH(2)S.)COOH, in which the radical is formally situated on the S atom, is higher in enthalpy (DeltaH degrees (0)) than Captodative-1 by 6.1 kcal mol(-1), but is lower in enthalpy than another isomer Distonic-C-1, H(3)N(+)C.(CH(2)SH)COOH, by 8.2 kcal mol(-1). Isomerization of the canonical radical cation of cysteine, [H(2)NCH(CH(2)SH)COOH].+, (Canonical-1), to Captodative-1 has an enthalpy of activation of 25.8 kcal mol(-1), while the barrier against isomerization of Canonical-1 to Distonic-S-1 is only 9.6 kcal mol(-1). Two additional transient tautomers, one with the radical located at C(alpha) and the charge on SH(2), and the other a carboxy radical with the charge on NH(3), are reported. Plausible fragmentation pathways (losses of small molecules, CO(2), CH(2)S, H(2)S and NH(3), and neutral radicals COOH. , HSCH(2). and NH(2).) from Canonical-1 are examined.     

Substituent effects on the bond dissociation enthalpies of aromatic amines

Bond dissociation enthalpy differences, Z-X DeltaBDE = BDE(4-YC(6)H(4)Z-X) - BDE(C(6)H(5)Z-X), for Z = CH(2) and O are largely independent of X and are determined mainly by the stabilization/destabilization effect of Y on the 4-YC(6)H(4)Z(*) radicals. The effects of Y are small (< or =2 kcal/mol for all Y) for Z = CH(2), but they are large for Z = O, where good correlations with sigma(p)(+)(Y) yield rho(+) = 6.5 kcal/mol. For Z = NH, two sets of electrochemically measured N-H DeltaBDEs correlate with sigma(p)(+)(Y), yielding rho(+) = 3.9 and 3.0 kcal/mol. However, in contrast to the situation with phenols, these data indicate that the strengthening effect on N-H BDEs of electron-withdrawing (EW) Y's is greater than the weakening effect of electron-donating (ED) Y's. Attempts to measure N-H DeltaBDEs in anilines using two nonelectrochemical techniques were unsuccessful; therefore, we turned to density functional theory. Calculations on 15 4-YC(6)H(4)NH(2) gave N-H DeltaBDEs correlating with sigma(p)(+) (rho(+) = 4.6 kcal/mol) and indicated that EW and ED Y's had comparable strengthening and weakening effects, respectively, on the N-H bonds. To validate theory by connecting it to experiment, the N-H DeltaBDEs of four 4,4'-disubstituted diphenylamines and five 3,7-disubstituted phenothiazines were both calculated and measured by the radical equilibration EPR technique. For all compounds, theory and experiment agreed to better than 1 kcal/mol. Dissection of N-H DeltaBDEs in 4-substituted anilines and O-H DeltaBDEs in 4-substituted phenols into interaction enthalpies between Y and NH(2)/OH (molecule stabilization/destabilization enthalpy, MSE) and NH*/O* (radical stabilization/destabilization enthalpy, RSE) reveals that for both groups of compounds, ED Y's destabilize the molecule and stabilize the radical, while the opposite holds true for EW Y's. However, in the phenols the effects of substituents on the radical are roughly 3 times as great as those in the molecule, whereas in the anilines the two effects are of comparable magnitudes. These differences arise from the stronger ED character of NH(2) vs OH and the weaker EW character of NH* vs O*. The relatively large contributions to N-H BDEs in anilines arising from interactions in the molecules suggested that N-X DeltaBDEs in 4-YC(6)H(4)NH-X would depend on X, in contrast to the lack of effect of X on O-X and CH(2)-X DeltaBDEs in 4-YC(6)H(4)O-X and 4-YC(6)H(4)CH(2)-X. This suggestion was confirmed for X = CH(3), H, OH, and F, for which the calculated NH-X DeltaBDEs yielded rho(+) = 5.0, 4.6, 4.0, and 3.0 kcal/mol, respectively.     

Active Thermochemical Tables: accurate enthalpy of formation of hydroperoxyl radical, HO2

Through the use of the Active Thermochemical Tables approach, the best currently available enthalpy of formation of HO2 has been obtained as delta(f)H(o)298 (HO2) = 2.94 +/- 0.06 kcal mol(-1) (3.64 +/- 0.06 kcal mol(-1) at 0 K). The related enthalpy of formation of the positive ion, HO2+, within the stationary electron convention is delta(f)H(o)298 (HO2+) = 264.71 +/- 0.14 kcal mol(-1) (265.41 +/- 0.14 kcal mol(-1) at 0 K), while that for the negative ion, HO2- (within the same convention), is delta(f)H(o)298 (HO2-) = -21.86 +/- 0.11 kcal mol(-1) (-21.22 +/- 0.11 kcal mol(-1) at 0 K). The related proton affinity of molecular oxygen is PA298(O2) = 100.98 +/- 0.14 kcal mol(-1) (99.81 +/- 0.14 kcal mol(-1) at 0 K), while the gas-phase acidity of H2O2 is delta(acid)G(o)298 (H2O2) = 369.08 +/- 0.11 kcal mol(-1), with the corresponding enthalpy of deprotonation of H2O2 of delta(acid)H(o)298 (H2O2) = 376.27 +/- 0.11 kcal mol(-1) (375.02 +/- 0.11 kcal mol(-1) at 0 K). In addition, a further improved enthalpy of formation of OH is briefly outlined, delta(f)H(o)298 (OH) = 8.93 +/- 0.03 kcal mol(-1) (8.87 +/- 0.03 kcal mol(-1) at 0 K), together with new and more accurate enthalpies of formation of NO, delta(f)H(o)298 (NO) = 21.76 +/- 0.02 kcal mol(-1) (21.64 +/- 0.02 kcal mol(-1) at 0 K) and NO2, delta(f)H(o)298 (NO2) = 8.12 +/- 0.02 kcal mol(-1) (8.79 +/- 0.02 kcal mol(-1) at 0 K), as well as H(2)O(2) in the gas phase, delta(f)H(o)298 (H2O2) = -32.45 +/- 0.04 kcal mol(-1) (-31.01 +/- 0.04 kcal mol(-1) at 0 K). The new thermochemistry of HO2, together with other arguments given in the present work, suggests that the previous equilibrium constant for NO + HO2 --> OH + NO2 was underestimated by a factor of approximately 2, implicating that the OH + NO2 rate was overestimated by the same factor. This point is experimentally explored in the companion paper of Srinivasan et al. (next paper in this issue).     

Dimesitylketone O-oxide: spectroscopic characterization, conformation, and reaction modes: OH formation and OH capture.

Dimesitylketone O-oxide 1b was synthesized by photolysis of dimesityldiazomethane dissolved in an oxygen saturated CCl3F solution at 140 K. Conformation and geometry of 1b were determined by comparing measured NMR chemical shifts with the corresponding chemical shifts calculated at the DFT-IGLO level of theory where it had to be considered that the molecule exists in two enantiomeric forms. Measured and calculated 1H chemical shifts agree within 0.1 ppm while the calculated 13C shift of the COO carbon (210.6 ppm) differs by only 0.4 ppm from the measured shift of 211.0 ppm. The two mesityl rings are perpendicular to each other and enclose angles of 40 and 57 degrees with the COO plane. The preferred rearrangement process of 1b is an H migration from one of the ortho-methyl groups to the terminal O atom of the COO unit. The calculated activation enthalpy of this process is 12.7 kcal/mol (B3LYP/cc-pVTZ). In contrast, the activation enthalpy for isomerization to dioxirane is 5 kcal/mol higher. In CCl3F, the activation barrier for the thermal decay was determined to be 13.8 +/- 0.2 kcal/mol and in acetonitrile 13.1 +/- 0.4 kcal/mol. H migration initiates cleavage of the OO bond and the production of an OH and a benzyl radical. Recombination of the latter in the solvent cage leads to the formation of 2-methylhydroxy-pentamethylbenzophenone, while escape of the OH radical from the solvent cage yields a ketone. These results confirm the possibility of OH production from carbonyl oxides in the solution phase.     

Reaction mechanism and tautomeric equilibrium of 2-mercaptopyrimidine in the gas phase and in aqueous solution: a combined Monte Carlo and quantum mechanics study

A combined Monte Carlo and quantum mechanical study was carried out to analyze the tautomeric equilibrium of 2-mercaptopyrimidine in the gas phase and in aqueous solution. Second- and fourth-order M?ller-Plesset perturbation theory calculations indicate that in the gas phase thiol (Pym-SH) is more stable than the thione (Pym-NH) by ca. 8 kcal/mol. In aqueous solution, thermodynamic perturbation theory implemented on a Monte Carlo NpT simulation indicates that both the differential enthalpy and Gibbs free energy favor the thione form. The calculated differential enthalpy is DeltaH(SH)(-->)(NH)(solv) = -1.7 kcal/mol and the differential Gibbs free energy is DeltaG(SH)(-->)(NH)(solv) = -1.9 kcal/mol. Analysis is made of the contribution of the solute-solvent hydrogen bonds and it is noted that the SH group in the thiol and NH group in the thione tautomers act exclusively as a hydrogen bond donor in aqueous solution. The proton transfer reaction between the tautomeric forms was also investigated in the gas phase and in aqueous solution. Two distinct mechanisms were considered: a direct intramolecular transfer and a water-assisted mechanism. In the gas phase, the intramolecular transfer leads to a large energy barrier of 34.4 kcal/mol, passing through a three-center transition state. The proton transfer with the assistance of one water molecule decreases the energy barrier to 17.2 kcal/mol. In solution, these calculated activation barriers are, respectively, 32.0 and 14.8 kcal/mol. The solvent effect is found to be sizable but it is considerably more important as a participant in the water-assisted mechanism than the solvent field of the solute-solvent interaction. Finally, the calculated total Gibbs free energy is used to estimate the equilibrium constant.     

Computational exploration of rearrangements related to the vitamin B12-dependent ethanolamine ammonia lyase catalyzed transformation

DFT (B3LYP/6-31G) and ab initio molecular orbital theory (QCISD/cc-pVDZ) are used to investigate several possible mechanisms involving free radical intermediates as well as their protonated forms for processes related to the coenzyme B(12)-dependent rearrangement catalyzed by ethanolamine ammonia lyase. Two major types of rearrangements are discussed in detail, intramolecular migration and dissociation of the amine/ammonia groups, for both of which several scenarios are considered. According to the calculations, the complete dissociation of the migrating group and its subsequent association constitute an unlikely route for both the protonated and the unprotonated reactant because of the high-energy barriers (more than 23 kcal/mol) involved in these steps. Direct migration of the protonated amine group is far more favorable (10.4 kcal/mol) and therefore presents the most likely candidate for the actual enzymatic reaction. The calculations further imply that the direct loss of an ammonium cation (10.6 kcal/mol) represents a feasible pathway as well. Comparing the rearrangements for the aminoethanol radical and its protonated counterpart, in line with previous findings reported by Golding, Radom, and co-workers, we find that the migration of a protonated group is in general associated with lower energy barriers, suggesting that the actual enzyme substrate quite likely corresponds to (partially) protonated aminoethanol. As the extent of the substrate protonation/deprotonation by the active site of the enzyme may vary, the actual energy barriers are expected to range between the values calculated for the two extreme cases of a substrate, that is, the aminoethanol radical 2 and its fully protonated form 6.     

Gas-phase acid-base properties of melamine and cyanuric acid

The thermochemical properties of melamine and cyanuric acid were characterized using mass spectrometry measurements along with computational studies. A triple-quadrupole mass spectrometer was employed with the application of the extended Cooks kinetic method. The proton affinity (PA), gas-phase basicity (GB), and protonation entropy (Δ_pS) of melamine were determined to be 226.2 ± 2.0 kcal/mol, 218.4 ± 2.0 kcal/mol, and 26.2 ± 2.0 cal/mol K, respectively. The deprotonation enthalpy (Δ_acidH), gas-phase acidity (Δ_acidG), and deprotonation entropy (Δ_acidS) of cyanuric acid were determined to be 330.7 ± 2.0 kcal/mol, 322.9 ± 2.0 kcal/mol, and 26.1 ± 2.0 cal/mol K, respectively. The geometries and energetics of melamine, cyanuric acid, and related ionic species were calculated at the B3LYP/6-31+G(d) level of theory. The computationally predicted proton affinity of melamine (225.9 kcal/mol) and gas-phase deprotonation enthalpy of cyanuric acid (328.4 kcal/mol) agree well with the experimental results. Melamine is best represented as the imide-like triazine-triamine form and the triazine nitrogen is more basic than the amino group nitrogen. Cyanuric acid is best represented as the keto-like tautomer and the N-H group is the most probable proton donor.     

Bridging QTAIM with vibrational spectroscopy: the energy of intramolecular hydrogen bonds in DNA-related biomolecules

Physical properties of over 8000 intramolecular hydrogen bonds (iHBs), including 2901 ones of the types OH···O, OH···N, NH···O and OH···C, in 4244 conformers of the DNA-related molecules (four canonical 2'-deoxyribonucleotides, 1,2-dideoxyribose-5-phosphate, and 2-deoxy-D-ribose in its furanose, pyranose and linear forms) have been investigated using quantum theory of atoms in molecules (QTAIM) and vibrational analysis. It has been found that for all iHBs with positive red-shift of the proton donating group stretching frequency the shift value correlates with ρ(cp)-the electron charge density at the (3,-1)-type bond critical point. Combining QTAIM and spectroscopic data new relationships for estimation of OH···O, OH···N, NH···O and OH···C iHB enthalpy of formation (kcal mol(-1)) with RMS error below 0.8 kcal mol(-1) have been established: E(OH···O) = -3.09 + 239·ρ(cp), E(OH···N) = 1.72 + 142·ρ(cp), E(NH···O) = -2.03 + 225·ρ(cp), E(OH···C) = -0.29 + 288·ρ(cp), where ρ(cp) is in e a(0)(-3) (a(0)- the Bohr radius). It has been shown that XHY iHBs with red-shift values over 40 cm(-1) are characterized by the following minimal values of the XHY angle, ρ(cp) and nubla(2)ρ(cp): 112°, 0.005 e a(0)(-3) and 0.016 e a(0)(-5), respectively. New relationships have been used to reveal the strongest iHBs in canonical 2'-deoxy- and ribonucleosides and the O(5')H···N(3) H-bond in ribonucleoside guanosine was found to have the maximum energy (8.1 kcal mol(-1)).     

DNA polymerase beta catalysis: are different mechanisms possible?

DNA polymerases are crucial constituents of the complex cellular machinery for replicating and repairing DNA. Discerning mechanistic pathways of DNA polymerase on the atomic level is important for revealing the origin of fidelity discrimination. Mammalian DNA polymerase beta (pol beta), a small (39 kDa) member of the X-family, represents an excellent model system to investigate polymerase mechanisms. Here, we explore several feasible low-energy pathways of the nucleotide transfer reaction of pol beta for correct (according to Watson-Crick hydrogen bonding) G:C basepairing versus the incorrect G:G case within a consistent theoretical framework. We use mixed quantum mechanics/molecular mechanics (QM/MM) techniques in a constrained energy minimization protocol to effectively model not only the reactive core but also the influence of the rest of the enzymatic environment and explicit solvent on the reaction. The postulated pathways involve initial proton abstraction from the terminal DNA primer O3'H group, nucleophilic attack that extends the DNA primer chain, and elimination of pyrophosphate. In particular, we analyze several possible routes for the initial deprotonation step: (i) direct transfer to a phosphate oxygen O(Palpha) of the incoming nucleotide, (ii) direct transfer to an active site Asp group, and (iii) transfer to explicit water molecules. We find that the most probable initial step corresponds to step (iii), involving initial deprotonation to water, which is followed by proton migration to active site Asp residues, and finally to the leaving pyrophosphate group, with an activation energy of about 15 kcal/mol. We argue that initial deprotonation steps (i) and (ii) are less likely as they are at least 7 and 11 kcal/mol, respectively, higher in energy. Overall, the rate-determining step for both the correct and the incorrect nucleotide cases is the initial deprotonation in concert with nucleophilic attack at the phosphate center; however, the activation energy we obtain for the mismatched G:G case is 5 kcal/mol higher than that of the matched G:C complex, due to active site structural distortions. Taken together, our results support other reported mechanisms and help define a framework for interpreting nucleotide specificity differences across polymerase families, in terms of the concept of active site preorganization or the so-called "pre-chemistry avenue".     

Ab initio and density functional theory studies of the catalytic mechanism for ester hydrolysis in serine hydrolases

We present results from ab initio and density functional theory studies of the mechanism for serine hydrolase catalyzed ester hydrolysis. A model system containing both the catalytic triad and the oxyanion hole was studied. The catalytic triad was represented by formate anion, imidazole, and methanol. The oxyanion hole was represented by two water molecules. Methyl formate was used as the substrate. In the acylation step, our computations show that the cooperation of the Asp group and oxyanion hydrogen bonds is capable of lowering the activation barrier by about 15 kcal/mol. The transition state leading to the first tetrahedral intermediate in the acylation step is rate limiting with an activation barrier (ΔE₀) of 13.4 kcal/mol. The activation barrier in the deacylation step is smaller. The double-proton-transfer mechanism is energetically unfavorable by about 2 kcal/mol. The bonds between the Asp group and the His group, and the hydrogen bonds in the oxyanion hole, increase in strength going from the Michaelis complex toward the transition state and the tetrahedral intermediate. In the acylation step, the tetrahedral intermediate is a very shallow minimum on the energy surface and is not viable when molecular vibrations are included. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 69: 89–103, 1998     

Acid-base chemistry of a carbenium ion in a zeolite under equilibrium conditions: verification of a theoretical explanation of carbenium ion stability

The 1,3-dimethylcyclopentenyl carbenium ion (C7H11(+)) was reproducibly prepared on zeolite HZSM-5 using a pulse-quench reactor, and then each of a number of bases was coadsorbed into the catalyst channels to either compete with the cation for protonation or to possibly react with it as a nucleophile. For seven bases with proton affinities (PA) between 142 and 212.1 kcal/mol, there was no reaction with C7H11(+). Coadsorption of smaller amounts of dimethylacetamide (PA = 217 kcal/mol) also produced no reaction, but with a higher loading, a proton was transferred from the carbenium ion to the base to leave 1,3-dimethylcyclopenta-1,3-diene in the zeolite as a neutral olefin. Deprotonation was the primary reaction with coadsorption of either pyridine (PA = 222 kcal/mol) or trimethylphosphine (PA = 229.2 kcal/mol). The estimated experimental deprotonation enthalpy for C7H11(+), approximately 217 kcal/mol in the zeolite, is in excellent agreement with MP4/6-311G gas-phase value of 215.6 kcal/mol. Coadsorption of either NH3 (PA = 204.0 kcal/mol) or PH3 (PA = 188 kcal/mol) does not deprotonate the carbenium ion, but these species do react as nucleophiles to form onium ion derivatives of C7H11(+). Analogous onium complexes with pyridine or trimethylphosphine formed in lower yields due to steric constraints in the zeolite channels. The essential experimental observations were all predicted and explained by density functional calculations (B3LYP/6-311G) and extensions of our recently developed theory of carbenium ion stability in zeolites. In addition, we report theoretical geometries for several complexes which contain unusual C-H- - -X hydrogen bonds.     

Polarization Effects for Hydrogen-Bonded Complexes of Substituted Phenols with Water and Chloride Ion

Variations in hydrogen-bond strengths are investigated for complexes of nine para-substituted phenols (XPhOH) with a water molecule and chloride ion. Results from ab initio HF/6-311+G(d, p) and MP2/6-311+G(d, p)//HF/6-311+G(d, p) calculations are compared with those from the OPLS-AA and OPLS/CM1A force fields. In the OPLS-AA model, the partial charges on the hydroxyl group of phenol are not affected by the choice of para substituent, while the use of CM1A charges in the OPLS/CM1A approach does provide charge redistribution. The ab initio calculations reveal a 2.0-kcal/mol range in hydrogen-bond strengths for the XPhOH?OH(2) complexes in the order X = NO(2) > CN > CF(3) > Cl > F > H >OH >CH(3) > NH(2). The pattern is not well-reproduced with OPLS-AA, which also compresses the variation to 0.7 kcal/mol. However, the OPLS/CM1A results are in good accord with the ab initio findings for both the ordering and range, 2.3 kcal/mol. The hydrogen bonding is, of course, weaker with XPhOH as acceptor, the order for X is largely inverted, and the range is reduced to ca. 1.0 kcal/mol. The substituent effects are found to be much greater for the chloride ion complexes with a range of 11 kcal/mol. For quantitative treatment of such strong ion-molecule interactions the need for fully polarizable force fields is demonstrated.     

Density functional calculations of ATP systems. 2. ATP hydrolysis at the active site of actin

The hydrolysis of adenosine 5'-triphosphate (ATP) at the active site of actin has been studied using density functional calculations. The active site is modeled by the triphosphate tail of ATP, an Mg cation, surrounding water molecules, and the nearby protein residues. Four reaction paths have been followed by constraining coordinates that allow phosphate stretching, nucleophilic attack of the catalytic water, and OH(-) formation via water deprotonation. The lowest-energy barrier (21.0 kcal/mol) is obtained for a dissociative reaction where the terminal phosphate breaks on approaching the catalytic water, followed by proton release via a proton wire mechanism. A higher barrier (39.6 kcal/mol) results for an associative reaction path where OH(-) is formed first, with a pentacoordinated phosphorus atom (P-O distances 2.1 A). Stretching the terminal bridging P-O bond results in bond rupture at 2.8 A with an energy barrier of 28.8 kcal/mol. The residues Gln137 and His161 are not important in the reactions, but insight into their roles in vivo has been obtained. The favored coordination of the end products H(2)PO(4)(-) and ADP(3-) includes a hydrogen bond and an O-Mg-O bridge between the phosphates as well as a hydrogen bond between H(2)PO(4)(-) and the Ser14 side chain. The total energy is 2.1 kcal/mol lower than in the initial reactants. Classical simulations of ATP- and ADP.P(i)-actin show few hydrolysis-induced differences in the protein structure, indicating that phosphate migration is necessary for a change in conformation.     

Model of uptake of OH radicals on nonreactive solids

A model of adsorption and recombination of OH radicals was developed for nonreactive solid surfaces of atmospheric interest. A parametrization of this heterogeneous mechanism was carried out to determine the role of the catalytic properties of these solid surfaces, taking into account the adsorption energy, defects, surface diffusion, and chemical reactions in the gas-solid interface. The uptake process was simulated for diffusion-controlled chemical reactions on the surface on the basis of Langmuir-Hinshelwood and Eley-Rideal mechanisms. Using an analytical approach and the Monte Carlo technique, we show the dependencies of the uptake probability of the heterogeneous reactions on the OH concentration and adsorption energy. The model is employed in the analysis of the empirically derived uptake coefficient for water ice, Al(2)O(3), NaCl, NH(4)NO(3), NH(4)HSO(4), and (NH(4))(2)SO(4). We found the following values for the free energy of adsorption of OH radicals: E(ice) = 7.3-7.6 kcal/mol, E(Al)(2)(O)(3) = 11-11.7 kcal/mol, E(NH)(4)(NO)(3) = 10.2 kcal/mol, E(NaCl) = 10.2 kcal/mol, E(NH)(4)(HSO)(4) = 9.8 kcal/mol, and E((NH)(4))(2)(SO)(4) = 9.8 kcal/mol. The atmospheric implications of the catalytic reactions of OH with adsorbed reactive molecules are discussed. The results of the modeling of the uptake process showed that the heterogeneous decay rate can exceed the corresponding gas-phase reaction rate under atmospheric conditions.