Solvent effects on the reaction coordinate of the hydrolysis of phosphates and sulfates: application of Hammond and anti-Hammond postulates to understand hydrolysis in solution.

The mechanism of the alkaline hydrolysis of phosphate and sulfate esters is of great interest. Ab initio quantum mechanical calculations and dielectric continuum methods are used to investigate the effect of the solvent on the associative/dissociative and the in-line/sideways character of the hydrolysis reaction of ethylene sulfate (ES) and ethylene phosphate (EP(-)), and their acyclic counterparts, dimethyl sulfate (DMS) and dimethyl phosphate (DMP(-)). The gas-phase reaction coordinates are determined by Hartree-Fock and density functional theory. For ES, the reaction coordinate in solution is determined; for the other three reactions only the transition state in solution is obtained. The alterations in the reaction induced by solvent are interpreted by use of the Hammond and anti-Hammond postulates.     

Hsc70 ATPase: an insight into water dissociation and joint catalytic role of K+ and Mg2+ metal cations in the hydrolysis reaction

Hybrid quantum mechanics/molecular mechanics simulations, coupled to the recently introduced metadynamics method, performed on the adenosine triphosphate (ATP) of the bovine Hsc70 ATPase protein, show which specific water molecule of the solvation shell of the Mg2+ metal cation acts as a trigger in the initial phase of the ATP hydrolysis reaction in ATP synthase. Furthermore, we provide a detailed picture of the reaction mechanism, not accessible to experimental probes, that allows us to address two important issues not yet unraveled: (i) the pathway followed by a proton and a hydroxyl anion, produced upon dissociation of a putative catalytic H2O molecule, that is crucial in the selection of the reaction channel leading to the hydrolysis; (ii) the unique and cooperative role of K+ and Mg2+ metal ions in the reaction, acting as co-catalysts and promoting the release of the inorganic phosphate via an exchange of the OH- hydroxyl anion between their respective solvation shells. This is deeply different from the proton wire mechanism evidenced, for instance, in actin and lowers significantly the free energy barrier of the reaction.     

磷酸二甲酯阴离子与二价金属离子相互作用的研究

在B3LYP/6-31G(d, p)水平上,用全电子分别研究了Mg2+、Ca2+、Mn2+、Co2+、Ni2+、Cu2+和Zn2+与磷酸二甲酯(DMP-)“双齿”配位模式下的相互作用,且由4个水分子((H2O)4)“饱和”各金属离子六配位模式下的其它位点。结果表明:这种配位模式下,DMP-对上述金属离子的选择性顺序为:Cu2+>Ni2+>Zn2+>Co2+>Mg2+>Mn2+>Ca2+,和Irving-Williams序列基本一致。且具有未充满d层轨道的金属对配体的变化“响应”明显。通过NBO(自然键轨道)方法对配合物电荷布居分析可得出主族金属离子与配体间以静电相互作用为主,非主族金属离子配合物中存在一定的共价作用的结论,同时关于配合物各部分间键轨道相互作用的分析部分的反映了金属离子与配体的作用实质。     

Thiolysis and alcoholysis of phosphate tri- and monoesters with alkyl and aryl leaving groups. An ab initio study in the gas phase

Phosphate esters are important compounds in living systems. Their biological reactions with alcohol and thiol nucleophiles are catalyzed by a large superfamily of phosphatase enzymes. However, very little is known about the intrinsic reactivity of these nucleophiles with phosphorus centers. We have performed ab initio calculations on the thiolysis and alcoholysis at phosphorus of trimethyl phosphate, dimethyl phenyl phosphate, methyl phosphate, and phenyl phosphate. Results in the gas phase are a reference for the study of the intrinsic reactivity of these compounds. Thiolysis of triesters was much slower and less favorable than the corresponding alcoholysis. Triesters reacted through an associative mechanism. Monoesters can react by both associative and dissociative mechanisms. The basicity of the attacking and leaving groups and the possibility of proton transfers can modulate the reaction mechanisms. Intermediates formed along associative reactions did not follow empirically proposed rules for ligand positioning. Our calculations also allow re-interpretation of some experimental results, and new experiments are proposed to trace reactions that are normally not observed, both in the gas phase and in solution.     

Mechanism of SN2 disulfide bond cleavage by phosphorus nucleophiles. Implications for biochemical disulfide reducing agents

The B3LYP variant of DFT has been used to study the mechanism of S-S bond scission in dimethyl disulfide by a phosphorus nucleophile, trimethylphospine (TMP). The reaction is highly endothermic in the gas phase and requires significant external stabilization of the charged products. DFT calculations (B3LYP) were performed with explicit (water molecules added) and implicit solvent corrections (COSMO model). The transition structures for this SN2 displacement reaction in a number of model systems have been located and fully characterized. The reaction barriers calculated with different approaches for different systems are quite close (around 11 kcal/mol). Remarkably, the calculations suggest that the reaction is almost barrierless with respect to the preorganized reaction complex and that most of the activation energy is required to rearrange the disulfide and TMP to its most effective orientation for the SMe group transfer way. Different reactivities of different phosphorus nucleophiles were suggested to be the result of steric effects, as manifested largely by varying amounts of hindrance to solvation of the initial product phosphonium ion. These data indicate that the gas-phase addition of a phosphine to the disulfide moiety will most likely form a phosphonium cation-thiolate anion salt, in the presence of four or more water molecules, that provide sufficient H-bonding stabilization to allow displacement of the thiolate anion, a normal uncomplicated SN2 transition state is to be expected.     

On the role of the conserved aspartate in the hydrolysis of the phosphocysteine intermediate of the low molecular weight tyrosine phosphatase

The usual rate-determining step in the catalytic mechanism of the low molecular weight tyrosine phosphatases involves the hydrolysis of a phosphocysteine intermediate. To explain this hydrolysis, general base-catalyzed attack of water by the anion of a conserved aspartic acid has sometimes been invoked. However, experimental measurements of solvent deuterium kinetic isotope effects for this enzyme do not reveal a rate-limiting proton transfer accompanying dephosphorylation. Moreover, base activation of water is difficult to reconcile with the known gas-phase proton affinities and solution phase pK(a)'s of aspartic acid and water. Alternatively, hydrolysis could proceed by a direct nucleophilic attack by a water molecule. To understand the hydrolysis mechanism, we have used high-level density functional methods of quantum chemistry combined with continuum electrostatics models of the protein and the solvent. Our calculations do not support a catalytic activation of water by the aspartate. Instead, they indicate that the water oxygen directly attacks the phosphorus, with the aspartate residue acting as a H-bond acceptor. In the transition state, the water protons are still bound to the oxygen. Beyond the transition state, the barrier to proton transfer to the base is greatly diminished; the aspartate can abstract a proton only after the transition state, a result consistent with experimental solvent isotope effects for this enzyme and with established precedents for phosphomonoester hydrolysis.     

Theoretical studies on the hydrolysis of phosphate diesters in the gas phase,solution, and RNase A

Density functional theory, polarizable continuum models and semiempirical hybrid quantum mechanical/molecular mechanical (QM/MM) calculations were applied to the hydrolysis of phosphate diesters in the gas phase, in solution, and in the enzyme RNase A. Neutralization of the negative charge of the pentacovalent phosphorane intermediates provides a substantial stabilization of the transition‐state structures in the gas phase. Inclusion of solvent effects on the phosphate/phosphorane species was critical to reproducing the trends in reactivity observed experimentally. Finally, the catalytic mechanism for the hydrolysis of uridine 2′,3′‐cyclic phosphate by RNase A was studied by QM/MM calculations. Our results suggest that the rate‐limiting transition state of the reaction corresponds to the approach of a water molecule to the phosphate and its activation by His119. Thus, His119 acts as a generalized base for the reaction. The water attack leads to a pentacovalent phosphorane transition state of formal charge ?2; this excess of negative charge in the transition state is stabilized by a number of positively charged residues including His12 and Lys41. In the second stage of the reaction, the phosphorane is converted into products. This part of the reaction proceeds without a detectable barrier, and it is facilitated by a proton transfer from Lys41 to the departing O_2′. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Alkaline hydrolysis of ethylene phosphate: an ab initio study by supermolecule model and polarizable continuum approach

The alkaline hydrolysis reaction of ethylene phosphate (EP) has been investigated using a supermolecule model, in which several explicit water molecules are included. The structures and single-point energies for all of the stationary points are calculated in the gas phase and in solution at the B3LYP/6-31++G(df,p) and MP2/6-311++G(df,2p) levels. The effect of water bulk solvent is introduced by the polarizable continuum model (PCM). Water attack and hydroxide attack pathways are taken into account for the alkaline hydrolysis of EP. An associative mechanism is observed for both of the two pathways with a kinetically insignificant intermediate. The water attack pathway involves a water molecule attacking and a proton transfer from the attacking water to the hydroxide in the first step, followed by an endocyclic bond cleavage to the leaving group. While in the first step of the hydroxide attack pathway the nucleophile is the hydroxide anion. The calculated barriers in aqueous solution for the water attack and hydroxide attack pathways are all about 22 kcal/mol. The excellent agreement between the calculated and observed values demonstrates that both of the two pathways are possible for the alkaline hydrolysis of EP.     

Interaction of dimethyl carbonate with anilines in the presence of potassium methylate: Kinetics and the role of the base

The kinetic patterns of the reaction between dimethyl carbonate and anilines in the presence of a potassium methylate as a catalyst were studied. The mechanism of aminolysis was clarified, which includes the detachment of the proton from the amino group of aniline and the subsequent attack of the resulting anion on the carbonyl group of dimethyl carbonate. It is shown that when the reaction occurs in the dimethyl carbonate-methanol 3:1 system, the process can be described as an irreversible first-order reaction in the aniline though the target reaction is complicated by side interaction between potassium methylate and dimethyl carbonate. The rate constants of the target reaction with substituted anilines and of the side reaction in the temperature range of 70-90°C were determined. It is shown that the influence of the substituent on the reaction rate is described by the Hammett equation, with the constant of the reaction series being positive and the best correlation being achieved for σ-scale. The results obtained are consistent with the proposed mechanism of the reaction and are explained by the facilitation of the aniline deprotonation with increasing acceptor properties of the substituent. Effective activation energies for the reaction of various anilines with dimethyl carbonate are found.     

Hydrolytic reactions of diadenosine 5',5'-triphosphate

The hydrolysis of diadenosine 5',5'-triphosphate to AMP and ADP has been studied over a wide pH-range. Under acidic conditions the reaction shows a first-order dependence on the hydronium ion concentration. Below pH 3 the rate-increase begins to level off. From pH 6 to 9 the hydrolysis is slow and pH-independent. Base-catalysed hydrolysis is observed in NaOH-solutions. Under alkaline conditions an intramolecular nucleophilic attack on the phosphate producing 3',5'-cAMP is also observed, but it is slower than the intermolecular reaction. Depurination of the adenosine moieties competes with the hydrolysis both under acidic and alkaline conditions, but the mechanisms are different. The temperature-dependence of the hydrolysis of Ap(3)A and the depurination of adenosine moieties were studied under acidic conditions, and the activation parameters of the reactions were calculated. The results of the work reflect the fact that the negatively charged polyphosphate group is very resistant towards nucleophilic attack. An efficient catalysis is only observed under acidic conditions, where the phosphate group becomes protonated. General acids or bases did not catalyse the hydrolysis. Furthermore, hydroxide ion catalysed cleavage is only observed at high base concentrations and other negatively charged nucleophiles did not attack the phosphate groups of diadenosine polyphosphates.     

The gas-phase reaction between hydroxide ion and methyl formate: a theoretical analysis of the energy surface and product distribution

The potential energy surface for the prototype solvent-free ester hydrolysis reaction: OH- +HCOOCH3 --> products has been characterized by high level ab initio calculations of MP4/6-311 + G(2df,2p)//MP2/6-31 + G(d) quality. These calculations reveal that the approach of an OH- ion leads to the formation of two distinct ion-molecule complexes: 1) the MS1 species with the hydroxide ion hydrogen bonded to the methyl group of the ester, and 2) the MS4 moiety resulting from proton abstraction of the formyl hydrogen by the hydroxide ion and formation of a three-body complex of water, methoxide ion and carbon monoxide. The first complex reacts to generate formate anion and methanol products through the well known B(AC)2 and S(N)2 mechanisms. RRKM calculations predict that these pathways will occur with a relative contribution of 85% and 15% at 298.15 K, in excellent agreement with experimentally measured values of 87% and 13%, respectively. The second complex reacts by loss of carbon monoxide to yield the water-methoxide complex through a single minimum potential surface and is the preferred pathway in the gas-phase. This water-methoxide adduct can further dissociate if the reactants have excess energy. These results provide clear evidence that the preferred pathways for ester hydrolysis in solution are dictated by solvation of the hydroxide ion.     

Structure and stability of solvation complexes of trimethyl phosphate and dimethyl methyl phosphonate

The presently used electrolytes in Lithium ion batteries, dimethyl carbonate (DMC), and ethylene carbonate are flammable. Trimethyl phosphate (TMP) and dimethyl methyl phosphonate (DMMP) have been shown to be potential nonflammable electrolytes. Density functional theory is used to calculate the structure and stability of the solvation complexes of TMP and DMMP. The calculations indicate that TMP and DMMP can form a solvation complex of the form Li⁺(X)₄ where X is the TMP or DMMP molecule. Calculations of the solvation energy and bond dissociation energies to remove one TMP and DMMP from the solvation complexes are compared with the same calculations on DMC. The results indicate that TMP and DMMP are considerably more stable than DMC.     

Efficient intramolecular general acid catalysis of nucleophilic attack on a phosphodiester

The hydrolysis of methyl 8-dimethylamino-1-naphthyl phosphate 4 and its reactions with a representative range of nucleophiles are catalyzed by the dimethylammonium group at acidic pH with rate accelerations of the order of 106. The reaction persists up to pH 7 because the strong intramolecular hydrogen bond, which is the key to efficient general acid catalysis, is present also in the reactant. The sensitivity to the basicity of the nucleophile (Br?nsted beta(nuc) = 0.29) lies between values measured previously for mono- and triesters. The comparisons suggest that general acid catalyzed reactions of phosphate mono- or diesters with strongly basic oxyanion nucleophiles (like those derived from a serine oxygen or a bound water molecule in an enzyme active site) will be fastest when their negative charges are neutralized by protonation. Reactions with NH2OH and its N-methylated derivatives show an apparent alpha-effect, but NH2OMe reacts no faster than a primary amine of similar basicity. It is suggested that the reaction involving NH2OH as an oxygen nucleophile proceeds through the pre-equilibrium formation of the tautomer H3N+-O- as the active nucleophile: ab initio calculations support this idea.     

Theoretical evaluation of the substrate-assisted catalysis mechanism for the hydrolysis of phosphate monoester dianions

Quantum chemistry methods coupled with a continuum solvation model have been applied to evaluate the substrate-assisted catalysis (SAC) mechanism recently proposed for the hydrolysis of phosphate monoester dianions. The SAC mechanism, in which a proton from the nucleophile is transferred to a nonbridging phosphoryl oxygen atom of the substrate prior to attack, has been proposed in opposition to the widely accepted mechanism of direct nucleophilic reaction. We have assessed the SAC proposal for the hydrolysis of three representative phosphate monoester dianions (2,4-dinitrophenyl phosphate, phenyl phosphate, and methyl phosphate) by considering the reactivity of the hydroxide ion toward the phosphorus center of the corresponding singly protonated monoesters. The reliability of the calculations was verified by comparing the calculated and the observed values of the activation free energies for the analogous S_N2(P) reactions of F⁻ with the monoanion of the monoester 2,4-dinitrophenyl phosphate and its diester analogue, methyl 2,4-dinitrophenyl phosphate. It was found that the orientation of the phosphate hydrogen atom has important implications with regard to the nature of the transition state. Hard nucleophiles such as OH⁻ and F⁻ can attack the phosphorus atom of a singly protonated phosphate monoester only if the phosphate hydrogen atom is oriented toward the leaving-group oxygen atom. As a result of this proton orientation, the SAC mechanism in solution is characterized by a small Brønsted coefficient value (β_lg=−0.25). This mechanism is unlikely to apply to aryl phosphates, but becomes a likely possibility for alkyl phosphate esters. If oxyanionic nucleophiles of pK_a<11 are involved, as in alkaline phosphatase, then the S_N2(P) reaction may proceed with the phosphate hydrogen atom oriented toward the nucleophile. In this situation, a large negative value of β_lg (−0.95) is predicted for the substrate-assisted catalysis mechanism.     

A FMO-controlled reaction path in the benzil-benzilic acid rearrangement

Reaction paths for the title rearrangement along with its methyl analogue were investigated by density functional theory calculations. The reaction model is R-CO-CO-R + OH(-)(H2O)4 --> R2C(OH)-COO- + (H2O)4 (R = Me and Ph), where the water tetramer is employed both for solvation to OH- and for the proton relay along hydrogen bonds. The reaction is composed of OH- addition, C-C rotation, carbanion [1,2] migration, and proton relay toward the product anions. The rate-determining step was calculated to be the carbanion migration. Apparently, carbanion [1,2] migration is unlikely relative to the carbonium ion one. However, LUMOs of the 1,2-diketones have large and nodeless lobes at the reaction center, the C1-C2 bond. The specific LUMO character is reflected both in the [2+1]-like one-center nucleophilic addition and in the carbanion [1,2] shift. The proton relay involved in the isomerization from the oxo intermediate to the carboxylate was calculated to take place via the water tetramer.     

Theoretical study of the importance of the spectator groups on the hydrolysis of phosphate triesters

The spontaneous hydrolysis of a series of five triaryl and two dialkyl aryl phosphate triesters, previously studied experimentally, is examined theoretically using two different hybrid density functional methods, B3LYP and M06; two basic sets, 6-31+G(d) and 6-311++G(d,p); and the Gaussian 09 program. The B3LYP/6-31+G(d) methodology combined excellent accuracy with minor computational cost. The calculations show excellent quantitative agreement with experiment, which is best in the presence of three discrete water molecules. The results support a two-step mechanism involving a pentacovalent addition intermediate, with a lifetime of tenths of a millisecond. The rate-determining formation of this intermediate involves general base catalysis, defined by concerted proton transfers in a six-membered cyclic activated complex (TS1), which involves two hydrogen-bonded water molecules supporting a well-developed H(2)O···P bond (mean % evolution 77.83 ± 0.97). The third water molecule is hydrogen-bonded to P═O and subsequently involved in product formation via TS2. The effects on reactivity of all the groups attached to phosphorus in TS1 are examined in detail: the two non-leaving groups in particular are found to play an important role, accounting for the substantial difference in reactivity between triaryl and dialkyl aryl phosphate triesters.     

Ring Strain VS. Solvent Effects in Phosphate Base Hydrolysis

To determine the factors governing the enhanced reactivity of 5-membered ring phosphates, the lowest activation free-energy profiles for the alkaline hydrolyses of methyl ethylene phosphate (5-MEP), its acyclic analog, trimethyl phosphate (a-TMP), and its 6-membered ring analog, methyl propylene phosphate (6-MPP), have been computed using ab initio and continuum dielectric methods. The calculations yield product distributions and activation free energy differences in accord with experiment. They show that solvent stabilization of the 5-membered ring transition state plays a key role in the million-fold enhanced rates of alkaline hydrolysis of 5-MEP relative to its acyclic or 6-membered ring analogs. Furthermore, strain energy calculations show that ring strain contributes partly to the observed rate enhancement of 5-MEP relative to 6-MPP but not to that of 5-MEP relative to a-TMP.     

Mechanisms of amine-catalyzed organosilicate hydrolysis at circum-neutral pH

Mono- and polyamines can catalyze the hydrolysis and condensation of organosilicate starting materials in biomimetic silica synthesis pathways at circum-neutral pHs and room temperature. Our study is focused on understanding the mechanistic role of amines in catalyzing the hydrolysis process that precedes condensation. We have conducted (29)Si NMR experimental studies over a range of temperature and pHs for the hydrolysis rates of trimethylethoxysilane (TMES), a model compound with only one hydrolyzable bond, combined with quantum mechanical hybrid density functional theory calculations of putative intermediate and transition-state structures for TMES and tetramethyl orthosilicate (TMOS). Comparison of calculated energies with experimentally determined activation energies indicates that amine catalysis of TMES is primarily a consequence of the amine's acidity at neutral pH. The proton released by the amine is transferred to the organosilicate, producing a protonated ethoxy leaving group that can be displaced by water in an S(N)2 reaction. For TMOS, the activation energy of proton-transfer coupled with S(N)2 substitution is comparable to that for Corriu's nucleophile-activated nucleophilic displacement, such that the mechanism of amine-catalyzed hydrolysis is dependent mostly on the ambient pH conditions as well as the type of amine. The relevance of our results to biological silica precipitation is discussed.     

Reactions of the hydroperoxide anion with dimethyl methylphosphonate in an ion trap mass spectrometer: evidence for a gas phase alpha-effect

The gas phase degradation reactions of the chemical warfare agent (CWA) simulant, dimethyl methylphosphonate (DMMP), with the hydroperoxide anion (HOO(-)) were investigated using a modified quadrupole ion trap mass spectrometer. The HOO(-) anion reacts readily with neutral DMMP forming two significant product ions at m/z 109 and m/z 123. The major reaction pathways correspond to (i) the nucleophilic substitution at carbon to form [CH(3)P(O)(OCH(3))O](-) (m/z 109) in a highly exothermic process and (ii) exothermic proton transfer. The branching ratios of the two reaction pathways, 89% and 11% respectively, indicate that the former reaction is significantly faster than the latter. This is in contrast to the trend for the methoxide anion with DMMP, where proton transfer dominates. The difference in the observed reactivities of the HOO(-) and CH(3)O(-) anions can be considered as evidence for an alpha-effect in the gas phase and is supported by electronic structure calculations at the B3LYP/aug-cc-pVTZ//B3LYP/6-31+G(d) level of theory that indicate the S(N)2(carbon) process has an activation energy 7.8 kJ mol(-1) lower for HOO(-) as compared to CH(3)O(-). A similar alpha-effect was calculated for nucleophilic addition-elimination at phosphorus, but this process--an important step in the perhydrolysis degradation of CWAs in solution--was not observed to occur with DMMP in the gas phase. A theoretical investigation revealed that all processes are energetically accessible with negative activation energies. However, comparison of the relative Arrhenius pre-exponential factors indicate that substitution at phosphorus is not kinetically competitive with respect to the S(N)2(carbon) and deprotonation processes.