Multiple isotope effect study of the acid-catalyzed hydrolysis of methyl formate

Multiple isotope effects have been measured for the acid-catalyzed hydrolysis of methyl formate in 0.5 M HCl at 20 degrees C. The isotope effects in the present investigation include the carbonyl carbon (13k = 1.028 +/- 0.001), the carbonyl oxygen (18k = 0.9945 +/- 0.0009), the nucleophile oxygen (18k = 0.995 +/- 0.001), and the formyl hydrogen ((D)k = 0.81 +/- 0.02). Determination of the carbonyl carbon, carbonyl oxygen, and formyl hydrogen isotope effects was performed via isotopic analysis of residual substrate. However, determination of the oxygen nucleophile isotope effect required analysis of the oxygen atoms of the product (formic acid), which exchange with the solvent (water) under acid conditions. This necessitated measurement of the rate of exchange of these oxygen atoms under the conditions for hydrolysis (k(ex) = 0.0723 min(-1)) and correction of the raw isotope ratios measured during the nucleophile-O isotope effect experiment. These results, along with the previously reported isotope effect for the leaving oxygen (18k = 1.0009) and the ratio of the rate of hydrolysis to that of exchange of the carbonyl oxygen with water (k(h)/k(ex) = 11.3), give a detailed picture of the transition-state structure for the reaction.     

A theoretical study of the reaction between cyclopentadiene and protonated imine derivatives: a shift from a concerted to a stepwise molecular mechanism

The reaction between cyclopentadiene and protonated pyridine-2-carboxaldehyde imine derivatives has been studied by using Hartree-Fock (HF) and B3LYP methods together with the 6-31G basis set. The molecular mechanism is stepwise along an inverted energy profile. This results from the protonation on both nitrogen atoms of the imine group and the pyridine framework. The first step corresponds to the nucleophilic attack of cyclopentadiene on the electron-poor carbon atom of the iminium cation group to give an acyclic cation intermediate, and the second step is associated with the ring closure of this intermediate via the formation of a C-N single bond yielding the final cycloadduct. Two reactive channels have been characterized corresponding to the endo and exo approach modes of the cyclopentadiene to the iminium cation. The role of the pyridium cation substituent and the nitrogen position (ortho, meta, and para) along the reaction pathway has been also considered. Solvent effects (dichloromethane) by means of a continuum model have been taken into account to model the experimental environment.     

A theoretical analysis of the free-energy profile of the different pathways in the alkaline hydrolysis of methyl formate in aqueous solution

The free-energy profile for the different reaction pathways available to the hydroxide ion and methyl formate in aqueous solution is reported for the first time. The theoretical analysis was carried out by using the cluster-continuum method recently proposed by us for calculating the free energy of solvation of ions. Unlike the gas-phase reaction, our results are consistent with the fact that the reaction occurs mainly by nucleophilic attack of the hydroxide on the carbonyl carbon to yield a tetrahedral intermediate (B(AC)2 mechanism). However, an additional pathway, in which the hydroxide ion acts as a general base and a water molecule coordinated to this ion acts as the nucleophile, is also predicted to be important. The relative importance of these pathways is calculated to be 87 % and 13 %, respectively. The tetrahedral intermediate of the hydrolysis reaction has an estimated lifetime of 10 nanoseconds, and its conjugate acid has a pK(a) of 8.8. This tetrahedral intermediate is predicted to proceed to products by two pathways: elimination of methoxide ion (84 %) and by water catalyzed elimination of methanol (16 %). The less common reaction pathway, which involves attack of the hydroxide ion on the formyl hydrogen (decarbonylation mechanism) and leads to water, carbon monoxide, and methanol, is calculated to be only 3 kcal mol(-1) less favorable than the B(AC)2 mechanism. By comparison, direct attack of the hydroxide ion on the methyl group (B(AL)2 or S(N)2 mechanism) leading to an acyl-oxygen bond cleavage has a very high free energy of activation and is not expected to be important. The theoretically observed activation free energy at 298.15 K is calculated to be 15.5 kcal mol(-1), in excellent agreement with the experimentally measured value of 15.3 kcal mol(-1). This present model allows for a clear distinction between contributions due to solvation and those due to intrinsic (gas-phase) effects and proves to yield results in very good agreement with available experimental data.     

Analysis of linear free-energy relationships combined with activation parameters assigns a concerted mechanism to alkaline hydrolysis of x-substituted phenyl diphenylphosphinates

A kinetic study is reported for alkaline hydrolysis of X‐substituted phenyl diphenylphosphinates ( 1 a – i ). The Brønsted‐type plot for the reactions of 1 a – i is linear over 4.5 pK_a units with β_lg=?0.49, a typical β_lg value for reactions which proceed through a concerted mechanism. The Hammett plots correlated with σ^o and σ^? constants are linear but exhibit many scattered points, while the corresponding Yukawa–Tsuno plot results in excellent linear correlation with ρ=1.42 and r=0.35. The r value of 0.35 implies that leaving‐group departure is partially advanced at the rate‐determining step (RDS). A stepwise mechanism, in which departure of the leaving group from an addition intermediate occurs in the RDS, is excluded since the incoming HO^? ion is much more basic and a poorer nucleofuge than the leaving aryloxide. A dissociative (D_N + A_N) mechanism is also ruled out on the basis of the small β_lg value. As the substituent X in the leaving group changes from H to 4‐NO₂ and 3,4‐(NO₂)₂, ΔH ^≠ decreases from 11.3 kcal mol^?1 to 9.7 and 8.7 kcal mol^?1, respectively, while ΔS ^≠ varies from ?22.6 cal mol^?1 K^?1 to ?21.4 and ?20.2 cal mol^?1 K^?1, respectively. Analysis of LFERs combined with the activation parameters assigns a concerted mechanism to the current alkaline hydrolysis of 1 a – i .     

A change from stepwise to concerted mechanism in the acid-catalysed benzidine rearrangement: a theoretical study

The monoprotonated mechanism of the benzidine acid-catalysed rearrangement of hydrazobenzene (corresponding to a second order kinetics) is studied and compared with the diprotonated mechanism (corresponding to a third order reaction and previously studied). The nature of the two mechanisms is found to be completely different: a concerted closed-shell sigmatropic shift in the monoprotonated, a stepwise radical cation recoupling in the diprotonated. The activation energies, combined with the energetics of the protonation equilibria, are also very different: 35 kcal mol^?1 for the former and 26 kcal mol^?1 for the latter (in good agreement with the experimental data). These values make the third order diprotonated mechanism favoured with respect to the second order monoprotonated mechanism for the rearrangement of hydrazobenzene, as found at typical experimental acid concentrations.     

Theoretical study on the hydrolysis mechanism of N,N-dimethyl-N'-(2-oxo-1, 2-dihydro-pyrimidinyl)formamidine: water-assisted mechanism and cluster-continuum model

The hydrolysis reaction of N,N-dimethyl-N'-(2-oxo-1, 2-dihydro-pyrimidinyl)formamidine (DMPFA), a model compound of the antivirus drug amidine-3TC (3TC = 2', 3'-dideoxy-3'-thiacytidine), is investigated by the hybrid density functional theory B3LYP/6-31+G (d,p) method. The hydrolysis reaction of the title compound is predicted to undergo via two pathways, each of which is a stepwise process. Path A is the addition of H2O to the C=N double bond in the amidine group to form a tetrahedral structure in its first step, and then the transfer of the H atom of hydroxyl leads to the corresponding products via four possible channels. Path B simultaneously involves the nucleophilic attack of H2O to the C atom of the C=N bond and the proton transfer to the N atom of amino group leading to the cleavage of the C-N single bond in the amidine group. The results indicate that path A is more favorable than path B in the gas phase. Moreover, to simulate the title reaction in aqueous solution, water-assisted mechanism and the cluster-continuum model, based on the SCRF/CPCM model, are taken into account in our work. The results indicate that it is rational for two water molecules served as a bridge to assist in the first step of path A and that cytosine rather than the cytosine-substituted formamide should be released from the tetrahedral intermediate via s six-membered cycle transition state (channel 2). Our calculations exhibit that the process toward the tetrahedral intermediate is the rate-determining step both in the gas phase and in aqueous solution.     

Participation of molecular oxygen in the formation of complete oxidation products via a concerted mechanism

A comparison is given between the rate of catalytic reactions and that of decomposition of surface compounds under the influence of molecular oxygen of different isotopic composition in reactions of complete oxidation of n-butane and 1-hexene on zinc oxide and cuprous oxide. It has been shown that the rates of accumulation of products containing heavy oxygen are much smaller than those theoretically expected from the heavy isotope concentration in molecular oxygen. A conclusion is drawn that molecular oxygen is not directly incorporated into the reaction products but promotes decomposition of the surface compounds by oxidizing the surface sites where these compounds are stabilized.

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Minimum sequence requirements for selective RNA-ligand binding: a molecular mechanics algorithm using molecular dynamics and free-energy techniques

In vitro evolution techniques allow RNA molecules with unique functions to be developed. However, these techniques do not necessarily identify the simplest RNA structures for performing their functions. Determining the simplest RNA that binds to a particular ligand is currently limited to experimental protocols. Here, we introduce a molecular-mechanics based algorithm employing molecular dynamics simulations and free-energy methods to predict the minimum sequence requirements for selective ligand binding to RNA. The algorithm involves iteratively deleting nucleotides from an experimentally determined structure of an RNA-ligand complex, performing energy minimizations and molecular dynamics on each truncated structure, and assessing which truncations do not prohibit RNA binding to the ligand. The algorithm allows prediction of the effects of sequence modifications on RNA structural stability and ligand-binding energy. We have implemented the algorithm in the AMBER suite of programs, but it could be implemented in any molecular mechanics force field parameterized for nucleic acids. Test cases are presented to show the utility and accuracy of the methodology.     

Theoretical study of the scavenging mechanism to 1,4-dicarbonyls by pyridoxamine: The water-assisted reaction

A theoretical study for the water-assisted scavenging mechanism of pyridoxamine with 1,4-dicarbonyls was investigated by density functional theory (DFT) method at B3LYP/6-31G(d) basis set. Two scavenging pathways were examined: imine formation vs. pyrrole ring formation. In addition, solvent effect was performed using the Onsager model. Our calculations indicated that the pyrrole ring formation was the preferred pathway for the reaction, which results were consistent with experimental data. The participation of one water molecule in the reaction would reduce the active energy considerably and the energy barriers of all the transition states in the water-assisted reaction were much lower than those of the non-assisted reaction. The presence of a solvent in the continuum model disfavors the reaction. Hydrogen-bonding interactions and steric hindrance effect play an important role in the scavenging reaction.     

Theoretical study on the alkaline hydrolysis of methyl thioacetate in aqueous solution

A base-catalyzed hydrolysis reaction of thiolester has been studied in both gas and solution phases using two ab initio quantum mechanics calculations such as Gaussian09 and CPMD. The free-energy surface along the reaction path is also constructed using a configuration sampling technique, namely, the metadynamics method. While there are two different reaction paths obtained for the potential profile of the base-catalyzed hydrolysis reaction for thiolester in the gas phase, a triple-well reaction path is computed for the reaction in the solution phase by two quantum mechanics calculations. Unlike the S(N)2 mechanism (a concerted mechanism) found for the gas-phase reaction, a nucleophilic attack from the hydroxide ion on the carbonyl carbon to yield a tetrahedral intermediate (a stepwise mechanism) is observed for the solution-phase reaction. Moreover, the energy profiles computed by these two theoretical calculations are found to be very comparable with those determined experimentally.     

Characterization of the solvation dynamics of an ionic liquid via molecular dynamics simulation

The solvation dynamics of ionic liquids have been the subject of intense experimental study but remain poorly understood. We present the results of molecular dynamics simulations of the solvation dynamics of the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate in response to photoexcitation of the fluorescent dye coumarin-153. We reproduce the time-resolved fluorescence Stokes shift using linear response theory, then use novel statistical techniques to analyze cation and anion contributions to the signal. We find that the solvation dynamics are dominated by collective ionic motion and characterize the time scale for various features of the collective response. Further, we use the Steele analysis [Mol. Phys. 61, 1031 (1987)] to characterize the contributions to the observed Stokes shift made by translational and rovibrational degrees of freedom. Our results indicate that in contrast to molecular liquids, the rovibrational response is trivial and the observed fluorescence response arises almost entirely from ionic translation. Our results resolve previously open questions in the literature about the nature of the rapid dynamics in room-temperature ionic liquids and offer insight into the physical principles governing ionic liquid behavior on longer time scales.     

Theoretical mechanism study of UF6 hydrolysis in the gas phase

The mechanism of the gas-phase reaction UF 6 + H 2O --> UOF 4 + 2HF is explored using relativistic density functional theory calculations. Initially, H 2O coordinates with UF 6 to form a 1:1 complex UF 6.H 2O. Over an activation energy barrier of about 19 kcal/mol, H 2O transfers a H atom to a nearby ligand F, resulting in UF 5OH + HF. The eliminated HF or another H 2O molecule may form a hydrogen bond with UF 5OH. Starting from UF 5OH, the second HF elimination results in UOF 4. If UF 5OH is in the isolated form, UF 5OH --> UOF 4 + HF takes place over a barrier of 24 kcal/mol. If UF 5OH is hydrogen-bonded with H 2O or HF, the conversion barrier is less than 10 kcal/mol. Once formed, the unstable UOF 4 tends to associate with additional ligands and hydrogen-bonding donors. The calculated binding energies indicate the significance of such interactions, which may have profound impact on further HF eliminating reactions. The IR spectra features can be used to indicate the formation and interaction type of the intermediates and products.     

Ab initio molecular dynamics study of the hydrolysis reaction of diborane

The hydrolysis reaction of the diborane molecule in aqueous solution has been studied by a series of Car-Parrinello Molecular Dynamics simulations in the Blue Moon Ensemble. The total reaction has been divided into two parts: one dealing with the breaking of B(2)H(6) molecule and the formation of a BH(4)(-) ion, a H(2)BOH molecule and a H(+) ion; the second leads to the formation of two hydrogen molecules and another H(2)BOH molecule, starting from BH(4)(-), two water molecules and a H(+) ion. The total reaction studied in this work has been B(2)H(6) + 2H(2)O --> 2H(2)BOH + 2H(2). We have described both structurally and electronically the reagents and the products through the radial distribution functions and the Wannier Function Center positions calculations, with attention to the solvent effects on the compounds. The free energy barrier value for the first part of the reaction and a detailed mechanisms for both parts have been reported. An interesting behavior of BH(3) and H(2) molecules in solution has been observed. They form a quite stable three center bond between the electron pair of the hydrogen molecule and the empty orbital of the boron atom in BH(3), which has been described from both a structural and electronic point of view.     

Activation mechanism of the human histamine H4 receptor--an explicit membrane molecular dynamics simulation study

Molecular dynamics (MD) simulations in a membrane-embedded environment were carried out on the homology model of the human histamine H4 receptor (hH4R) alone and in complex with its endogenous activator histamine and with the first reported selective hH4R antagonist JNJ7777120. During the simulation of the histamine-hH4R complex, considerable changes occurred in the hH4R structure as well as in the interaction pattern of histamine at the binding site. These changes are in agreement with experimental data published on GPCR activation. In particular, the intracellular side of TM helix VI moved significantly away from TM helices III and VII. Moreover, histamine formed an interaction with Asn147 (4.57) that was previously proved to be important in hH4R activation. Results of the MD simulations of the native hH4R and the JNJ7777120-hH4R complex suggest that these models represent an inactive conformation of hH4R. MD simulation in the presence of JNJ7777120 resulted in the movement of the intracellular side of TM helix VI in the direction of TM helix III. Snapshots of the simulations may serve as functionally relevant models in the development of novel hH4R ligands in the future.     

Characterizing hydrophobicity at the nanoscale: a molecular dynamics simulation study

We use molecular dynamics (MD) simulations of water near nanoscopic surfaces to characterize hydrophobic solute-water interfaces. By using nanoscopic paraffin like plates as model solutes, MD simulations in isothermal-isobaric ensemble have been employed to identify characteristic features of such an interface. Enhanced water correlation, density fluctuations, and position dependent compressibility apart from surface specific hydrogen bond distribution and molecular orientations have been identified as characteristic features of such interfaces. Tetrahedral order parameter that quantifies the degree of tetrahedrality in the water structure and an orientational order parameter, which quantifies the orientational preferences of the second solvation shell water around a central water molecule, have also been calculated as a function of distance from the plate surface. In the vicinity of the surface these two order parameters too show considerable sensitivity to the surface hydrophobicity. The potential of mean force (PMF) between water and the surface as a function of the distance from the surface has also been analyzed in terms of direct interaction and induced contribution, which shows unusual effect of plate hydrophobicity on the solvent induced PMF. In order to investigate hydrophobic nature of these plates, we have also investigated interplate dewetting when two such plates are immersed in water.     

Theoretical study of the suicide inhibition mechanism of the enzyme pyruvate formate lyase by methacrylate

The determination of pyruvate formate lyase crystallographic structure brought new insights to its mechanism of reaction and presented the possibility of a direct attack to the substrate from cysteine 418 as opposed to the previously expected cysteine 419. An inhibition study performed by Knappe and co-workers, using substrate-analogue methacrylate, confirms that cysteine 418 is most likely to add directly to pyruvate, since an inhibition product has been found as a substituent in this residue. The work presented here consists of a study of the inhibition mechanism of pyruvate formate lyase by methacrylate, using density functional theory with the hybrid B3LYP functional. We were able to determine all pertinent structures, confirm the proposed experimental mechanism, and add important detail to the energy profile associated with the mechanism of inhibition. Additionally, the obtained results provide the energy values for both the chemical reaction and the stereochemical reorganization necessary in order for the thiol-methacrylate adduct to come within reactional reach of Cys419.     

Theoretical study on the role of cooperative solvent molecules in the neutral hydrolysis of ketene

The results of a theoretical study of the reaction mechanism for the neutral hydration of ketene, H₂C=C=O + (n + 1) H₂O → CH₃COOH + nH₂O (n = 0–4), in solution are presented. All structures were optimized and characterized at the MP2(fc)/6-31 + G* level of theory, and then re-optimized by MP2(fc)/6-311 ++G**, and the effect of the bulk solvent is taken into account according to the conductor-like polarized continuum model (CPCM) using the gas MP2(fc)/6-311 ++G** geometries. Energies were refined for five-water hydration at higher level of theory, QCISD(T)(fc)/6-311 ++G**//MP2(fc)/6-311 ++G**. In the combined supermolecular/continuum model, one water molecule directly attacks the central C-atom, and the other four explicit water molecules are divided into two groups, one acting as catalyst(s) by participating in the proton transfer to reduce the tension of proton transfer ring, and the other being placed near the non-reactive oxygen or carbon atom in order to catalyze the hydration by engaging in hydrogen-bonding to the substrate (the so-called cooperative effect). Between the two possible nucleophilic addition reactions of water molecule, across the C=O bond or the C=C bond, the former one is preferred. Our calculations suggest that the favorable hydrolysis mechanism of ketene involves a sort of eight-membered ring transition structure formed by a three-water proton transfer loop, and a cooperative dimeric water near the non-reactive carbon-atom. The best-estimated in the present paper for the rate-determining barrier in solution, $ \Updelta G_{\text{sol}}^{ \ne } $ (298 K), is about 58 kJ/mol, reasonably close to the available experimental result.     

Ab initio molecular dynamics free-energy study of microhydration effects on the neutral-zwitterion equilibrium of phenylalanine.

The structures and relative energies of the most stable conformers of both naked and microsolvated phenylalanine, Phe.(H(2)O)(n)(n=0-3), are calculated by density functional theory. For selected structures, coordination-constrained ab initio molecular dynamics simulations determine the proton-transfer mechanism connecting neutral and zwitterionic forms of Phe. The associated free-energy profiles are calculated by thermodynamic integration. While no zwitterionic free-energy minimum is found for naked Phe, microsolvation is found to stabilize the zwitterionic form. For cluster sizes n > or = 3, the proton-transfer equilibrium shifts towards the zwitterionic structure for specific proton-transfer pathways. The energetically most favourable interconversion path between the neutral and zwitterionic forms is through a H(2)O bridge with free-energy barriers as low as 14.4 kJ mol(-1) for Phe.(H(2)O)(3). The free energy required for breaking a carboxylic OH bond involved in intramolecular hydrogen bonding is typically lower than in the water-assisted case. However, the resulting zwitterion turns out to be unstable with respect to the backward proton-transfer reaction.     

Structure of proton disolvates formed in the acid hydrolysis of ethyl formate and methyl acetate

By the density functional method (B3LYP/6-31++G(d,p)) optimal structures of proton hetero and homo disolvates involving water molecules, ethyl formate, methyl acetate and products of their hydrolysis are calculated. The data on the structure of these ions and the strength of their H bonds are analyzed together with the results of a similar calculation previously performed for methyl formate. It is shown that in proton solvation by two molecules present in the solution during the hydrolysis of ethyl formate, methyl acetate, and methyl formate stable (X…H…X)⁺ or (X…H…Y)⁺ particles form. Structural and energy parameters of their O…H…O bridges obey the same regularities and are mainly determined by a difference in the proton affinity of X and Y molecules. Calculation results are compared to the data of a number of experimental studies of the acid hydrolysis of esters.