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1.
High-level electronic structure calculations have been used to construct portions of the potential energy surfaces related to the reaction of diborane with ammonia and ammonia borane (B2H6 + NH3 and B2H6 + BH3NH3)to probe the molecular mechanism of H2 release. Geometries of stationary points were optimized at the MP2/aug-cc-pVTZ level. Total energies were computed at the coupled-cluster CCSD(T) theory level with the correlation-consistent basis sets. The results show a wide range of reaction pathways for H2 elimination. The initial interaction of B2H6 + NH3 leads to a weak preassociation complex, from which a B-H-B bridge bond is broken giving rise to a more stable H3BHBH2NH3 adduct. This intermediate, which is also formed from BH3NH3 + BH3, is connected with at least six transition states for H2 release with energies 18-93 kal/mol above the separated reactants. The lowest-lying transition state is a six-member cycle, in which BH3exerts a bifunctional catalytic effect accelerating H2 generation within a B-H-H-N framework. Diborane also induces a catalytic effect for H2 elimination from BH3NH3 via a three-step pathway with cyclic transition states. Following conformational changes, the rate-determining transition state for H2 release is approximately 27 kcal/mol above the B2H6 + BH3NH3 reactants, as compared with an energy barrier of approximately 37 kcal/mol for H2 release from BH3NH3. The behavior of two separated BH3 molecules is more complex and involves multiple reaction pathways. Channels from diborane or borane initially converge to a complex comprising the H3BHBH2NH3adduct plus BH3. The interaction of free BH3 with the BH3 moiety of BH3NH3 via a six-member transition state with diborane type of bonding leads to a lower-energy transition state. The corresponding energy barrier is approximately 8 kcal/mol, relative to the reference point H3BHBH2NH3 adduct + BH3. These transition states are 27-36 kcal/mol above BH3NH3 + B2H6, but 1-9 kcal/mol below the separated reactants BH3NH3 + 2 BH3. Upon chemical activation of B2H6 by forming 2 BH3, there should be sufficient internal energy to undergo spontaneous H2 release. Proceeding in the opposite direction, the H2 regeneration of the products of the B2H6 + BH3NH3reaction should be a feasible process under mild thermal conditions.  相似文献   

2.
Hypertension is a chronic condition that affects nearly 25% of adults worldwide. As the Renin-Angiotensin-Aldosterone System is implicated in the control of blood pressure and body fluid homeostasis, its combined blockage is an attractive therapeutic strategy currently in use for the treatment of several cardiovascular conditions. We have performed QM/MM calculations to study the mouse renin catalytic mechanism in atomistic detail, using the N-terminal His6-Asn14 segment of angiotensinogen as substrate. The enzymatic reaction (hydrolysis of the peptidic bond between residues in the 10th and 11th positions) occurs through a general acid/base mechanism and, surprisingly, it is characterized by three mechanistic steps: it begins with the creation of a first very stable tetrahedral gem-diol intermediate, followed by protonation of the peptidic bond nitrogen, giving rise to a second intermediate. In a final step the peptidic bond is completely cleaved and both gem-diol hydroxyl protons are transferred to the catalytic dyad (Asp32 and Asp215). The final reaction products are two separate peptides with carboxylic acid and amine extremities. The activation energy for the formation of the gem-diol intermediate was calculated as 23.68 kcal mol(-1), whereas for the other steps the values were 15.51 kcal mol(-1) and 14.40 kcal mol(-1), respectively. The rate limiting states were the reactants and the first transition state. The associated barrier (23.68 kcal mol(-1)) is close to the experimental values for the angiotensinogen substrate (19.6 kcal mol(-1)). We have also tested the influence of the density functional on the activation and reaction energies. All eight density functionals tested (B3LYP, B3LYP-D3, X3LYP, M06, B1B95, BMK, mPWB1K and B2PLYP) gave very similar results.  相似文献   

3.
Hydrogen abstraction reaction, H C2H4 --H2 C2H2 was studied by using A initio SCF method. Ge-ometries were fully optimized at SCF level and energies were computed at STO-3G basis set for reactants and transition state. Vibrational analysis was performed thereupon. Finally, the rate constant calculations were carried out at different temperatures for all range of reaction temperature according to Eyring's sbwlute reaction rate theory. The calculated activation energy is 12. 68 kcal/mol, lower than observed value (H. S kcal/mol) by 1. 82 kcal/mol only. The agreement of the calculated rate constants with the experiments is satisfactory.  相似文献   

4.
To elucidate enzyme catalysis through computer simulation, a prerequisite is to reliably compute free energy barriers for both enzyme and solution reactions. By employing on-the-fly Born-Oppenheimer molecular dynamics simulations with the ab initio quantum mechanical/molecular mechanical approach and the umbrella sampling method, we have determined free energy profiles for the methyl-transfer reaction catalyzed by the histone lysine methyltransferase SET7/9 and its corresponding uncatalyzed reaction in aqueous solution, respectively. Our calculated activation free energy barrier for the enzyme catalyzed reaction is 22.5 kcal/mol, which agrees very well with the experimental value of 20.9 kcal/mol. The difference in potential of mean force between a corresponding prereaction state and the transition state for the solution reaction is computed to be 30.9 kcal/mol. Thus, our simulations indicate that the enzyme SET7/9 plays an essential catalytic role in significantly lowering the barrier for the methyl-transfer reaction step. For the reaction in solution, it is found that the hydrogen bond network near the reaction center undergoes a significant change, and there is a strong shift in electrostatic field from the prereaction state to the transition state, whereas for the enzyme reaction, such an effect is much smaller and the enzyme SET7/9 is found to provide a preorganized electrostatic environment to facilitate the methyl-transfer reaction. Meanwhile, we find that the transition state in the enzyme reaction is a little more dissociative than that in solution.  相似文献   

5.
The reaction mechanism for imine hydrosilylation in the presence of an iron methyl complex and hydrosilane was studied using density functional theory at the M06/6-311G(d,p) level of theory. Benzylidenemethylamine (PhCH = NMe) and trimethylhydrosilane (HSiMe3) were employed as the model imine and hydrosilane, respectively. Hydrosilylation has been experimentally proposed to occur in two stages. In the first stage, the active catalyst (CpFe(CO)SiMe3, 1 ) is formed from the reaction of pre-catalyst, CpFe(CO)2Me, and hydrosilane through CO migratory insertion into the Fe Me bond and the reaction of the resulting acetyl complex intermediate with hydrosilane. In the second stage, 1 catalyzes the reaction of imine with hydrosilane. Calculations for the first stage showed that the most favorable pathway for CO insertion involved a spin state change, that is, two-state reactivity mechanism through a triplet state intermediate, and the acetyl complex reaction with HSiMe3 follows a σ-bond metathesis pathway. The calculations also showed that, in the catalytic cycle, the imine coordinates to 1 to form an Fe C N three-membered ring intermediate accompanied by silyl group migration. This intermediate then reacts with HSiMe3 to yield the hydrosilylated product through a σ-bond metathesis and regenerate 1 . The rate-determining step in the catalytic cycle was the coordination of HSiMe3 to the three-membered ring intermediate, with an activation energy of 23.1 kcal/mol. Imine hydrosilylation in the absence of an iron complex through a [2 + 2] cycloaddition mechanism requires much higher activation energies. © 2018 Wiley Periodicals, Inc.  相似文献   

6.
7.
Recently we reported Pd-catalyzed decarboxylative cross-coupling of cyanoacetate salts with aryl halides and triflates. This reaction shows good functional group tolerance and is useful for the synthesis of-aryl nitriles. To elucidate the mechanism for this reaction, we now carry out a density functional theory study on the cross-coupling of potassium cyanoacetate with bromobenzene. Our results show that the decarboxylation transition state involving the interaction of Pd with the-carbon atom has a very high energy barrier of +34.5 kcal/mol and therefore, must be excluded. Decarboxylation of free ion (or tight-ion-pair) also causes a high energy increase and should be ruled out. Thus the most favored decarboxylation mechanism corresponds to a transition state in which Pd interacts with the cyano nitrogen. The energy profile of the whole catalytic cycle shows that decarboxylation is the rate-determining step. The total energy barrier is +27.5 kcal/mol, which is comprised of two parts, i.e. the energy barrier for decarboxylation and the energy cost for transmetallation.  相似文献   

8.
The isomerization reaction from c-OSiH2O to t-OSiHOH, a vital reaction to understand the spontaneous ignition of silane, has been reinvestigated with Gaussian-2 theory and the CASSCF(6,6) method. It has been found that the reaction proceeds through two consecutive steps; i.e., c-OSiH2O undergoes isomerization to yield w-OSiH2O, and then the latter is converted to t-OSiHOH. The G-2 energy of the transition state of the latter process is 4.3 kcal/mol higher than that of the former. However, the G-2 energy of this higher transition state plus H atom is still 4.8 kcal/mol lower than that of the original reactants of SiH3 + O2.  相似文献   

9.
Molecular dynamics simulations using a combined QM/MM potential have been performed to study the catalytic mechanism of human cathepsin K, a member of the papain family of cysteine proteases. We have determined the two-dimensional free energy surfaces of both acylation and deacylation steps to characterize the reaction mechanism. These free energy profiles show that the acylation step is rate limiting with a barrier height of 19.8 kcal/mol in human cathepsin K and of 29.3 kcal/mol in aqueous solution. The free energy of activation for the deacylation step is 16.7 kcal/mol in cathepsin K and 17.8 kcal/mol in aqueous solution. The reduction of free energy barrier is achieved by stabilization of the oxyanion in the transition state. Interestingly, although the "oxyanion hole" has been formed in the Michaelis complex, the amide units do not donate hydrogen bonds directly to the carbonyl oxygen of the substrate, but they stabilize the thiolate anion nucleophile. Hydrogen-bonding interactions are induced as the substrate amide group approaches the nucleophile, moving more than 2 A and placing the oxyanion in contact with Gln19 and the backbone amide of Cys25. The hydrolysis of peptide substrate shares a common mechanism both for the catalyzed reaction in human cathepsin K and for the uncatalyzed reaction in water. Overall, the nucleophilic attack by Cys25 thiolate and the proton-transfer reaction from His162 to the amide nitrogen are highly coupled, whereas a tetrahedral intermediate is formed along the nucleophilic reaction pathway.  相似文献   

10.
The stereocontrol steps of the (S)-proline catalyzed Mannich reaction of cyclohexanone, formaldehyde, and aniline were theoretically investigated. The geometries of reactants, products, and transition states were optimized using density functional theory using the B3LYP functional with the 6-31++G(d,p) basis set. The energies of these compounds were then more accurately determined at the MP2 level, and the effect of DMSO as the solvent was included using a polarizable continuum model (PCM). The reaction was modeled from the previously proposed mechanism that cyclohexanone reacts with (S)-proline to generate an enamine, while formaldehyde reacts with aniline to produce an imine, and that the conformation around the C-N bond of the enamine 1 is crucial for the further enantioselective step. The formation of two conformations of the enamine via a proton transfer process was examined, revealing activation barriers for syn- and anti-enamine proton transfer of 10.2 and 17.9 kcal/mol, respectively. The transformation of syn- to anti-enamine through C-N bond rotation, however, was predicted to require only 4.2 kcal/mol, while the (S)- and (R)-intermediates could be obtained from subsequent reactions between enamine and imine with energy barriers of 8.5 and 12.4 kcal/mol, respectively. The difference between these barriers, but not the C-N rotation energy, becomes larger at the MP2 level and when DMSO as a solvent is included. This predicted enantioselective reaction, through the kinetic and thermodynamic favoring of the (S)-pathway, is in agreement with experimental results, which have reported the (S)-configuration as the major product.  相似文献   

11.
Density functional (B3LYP) calculations, using the 6-31G basis set, have been employed to study the title reactions. For the model reaction (H(2)C=C-NH(+)=CH(2) + H(2)C=CH(2)), a complex has been formed with 6.2 kcal/mol of stabilization energy and the transition state is 4.0 kcal/mol above this complex, but 2.1 kcal/mol below the reactants. However, the substituent effects are quite remarkable. When ethene is substituted by electron-withdrawing group CN, the reaction could also yield six-membered-ring products, but the energy barriers are all more than 7 kcal/mol, which shows that CN group unfavors the reaction. The other substituents, such as CH(3)O and CH(3) groups, have also been considered in the present work, and the results show that they are favorable for the formation of six-membered-ring adducts. The calculated results have been rationalized with frontier orbital interaction and topological analysis.  相似文献   

12.
The kinetics of the thermal decomposition and rearrangement of benzoyl azide into phenyl isocyanate was studied in n-heptane in the presence of boron trifluoride etherate as the catalyst. The apparent activation energy of the noncatalytic reaction is 28.0 kcal/mol, and that of the catalytic reaction is 11.0 kcal/mol. The electronic structure and geometry of various complexes between benzoyl azide and BF3 were studied using the PBE/TZ2P density functional method, and fragments of the potential energy surface were calculated for the catalytic rearrangement. Comparatively stable 1: 1 and 1: 2 complexes between the syn conformer of benzoyl azide and the catalyst can form in the system by coordination to the oxygen and nitrogen atoms of the acyl azide group. The heats of formation of these complexes are between ?1.7 and ?6.4 kcal/mol. The main consequence of the formation of these complexes is that the acyl azide group comes out of the benzene ring plane and thus becomes more reactive. The effective activation energies calculated for the catalytic rearrangement involving complexes of different compositions are 12–15 kcal/mol lower the effective activation energy of the noncatalytic reaction. Information has been obtained about the structure of the transition state of the catalytic reaction, in which a nitrogen molecule is abstracted from benzoyl azide with a synchronous rearrangement of other atoms, resulting in the formation of the ultimate product.  相似文献   

13.
Thermochemical parameters of carbonic acid and the stationary points on the neutral hydration pathways of carbon dioxide, CO 2 + nH 2O --> H 2CO 3 + ( n - 1)H 2O, with n = 1, 2, 3, and 4, were calculated using geometries optimized at the MP2/aug-cc-pVTZ level. Coupled-cluster theory (CCSD(T)) energies were extrapolated to the complete basis set limit in most cases and then used to evaluate heats of formation. A high energy barrier of approximately 50 kcal/mol was predicted for the addition of one water molecule to CO 2 ( n = 1). This barrier is lowered in cyclic H-bonded systems of CO 2 with water dimer and water trimer in which preassociation complexes are formed with binding energies of approximately 7 and 15 kcal/mol, respectively. For n = 2, a trimeric six-member cyclic transition state has an energy barrier of approximately 33 (gas phase) and a free energy barrier of approximately 31 (in a continuum solvent model of water at 298 K) kcal/mol, relative to the precomplex. For n = 3, two reactive pathways are possible with the first having all three water molecules involved in hydrogen transfer via an eight-member cycle, and in the second, the third water molecule is not directly involved in the hydrogen transfer but solvates the n = 2 transition state. In the gas phase, the two transition states have comparable energies of approximately 15 kcal/mol relative to separated reactants. The first path is favored over in aqueous solution by approximately 5 kcal/mol in free energy due to the formation of a structure resembling a (HCO 3 (-)/H 3OH 2O (+)) ion pair. Bulk solvation reduces the free energy barrier of the first path by approximately 10 kcal/mol for a free energy barrier of approximately 22 kcal/mol for the (CO 2 + 3H 2O) aq reaction. For n = 4, the transition state, in which a three-water chain takes part in the hydrogen transfer while the fourth water microsolvates the cluster, is energetically more favored than transition states incorporating two or four active water molecules. An energy barrier of approximately 20 (gas phase) and a free energy barrier of approximately 19 (in water) kcal/mol were derived for the CO 2 + 4H 2O reaction, and again formation of an ion pair is important. The calculated results confirm the crucial role of direct participation of three water molecules ( n = 3) in the eight-member cyclic TS for the CO 2 hydration reaction. Carbonic acid and its water complexes are consistently higher in energy (by approximately 6-7 kcal/mol) than the corresponding CO 2 complexes and can undergo more facile water-assisted dehydration processes.  相似文献   

14.
A previously unreported channel in the spin-allowed reaction path for the CH+N2 reaction that involves the HNNC radical is presented. The structures and energetics of the HNNC radical and its isomers HCNN and HNCN and the relevant intermediates and transition states that are involved in the proposed mechanism are obtained at the coupled cluster singles and doubles level of theory with noniterative triples correction (CCSD(T)) using a converging series of basis sets aug-cc-pVDZ, aug-cc-pVTZ, and aug-cc-pVQZ. The aug-cc-pVQZ basis is used for all the final single point energy calculations using the CCSD(T)/aug-cc-pVTZ optimized geometries. We find the HNNC radical to have a heat of formation of DeltafH0 (HNNC)=116.5 kcal mol(-1). An assessment of the quality of computed data of the radical species HNCN and HCNN is presented by comparison with the available experimental data. We find that HNNC can convert to HNCN, the highest barrier in this path being 14.5 kcal mol(-1) above the energy of the CH+N2 reactants. Thus, HNNC can play a role in the high-temperature spin-allowed mechanism for the reaction of CH+N2 proposed by Moskaleva, Xia, and Lin (Chem. Phys. Lett. 2000, 331, 269).  相似文献   

15.
Accurate calculations are presented on the mechanism of the MBH reaction, focusing on the reaction between methyl acrylate and benzaldehyde, catalyzed by a tertiary amine. We address the mechanism under protic solvent-free conditions, but also consider how the mechanism and rate-limiting step change in the presence of alcohols. We have carefully calibrated the DFT method used in the calculations by carrying out high-level G3MP2 calculations on a model system. All of our calculations also treat the effect of solvent, described as a dielectric continuum. In the absence of protic solvent, we predict that deprotonation of the alpha-position is the rate-determining step and occurs through a cyclic transition state, with proton transfer to a hemiacetal alkoxide formed by addition of a second equivalent of aldehyde to the intermediate alkoxide. As first suggested by McQuade, this mechanism explains the observed second-order kinetics with respect to aldehyde concentration in the absence of protic solvent. In contrast, in the presence of methanol, we find a slightly lower energy pathway, in which the alcohol serves as a shuttle to transfer the proton from carbon to oxygen. Overall, the barrier to reaction for the latter mechanism is of 24.6 kcal/mol with respect to reactants at the B3LYP level of theory. The relative energy for the addition transition state of the amine-acrylate betaine adduct to the aldehyde is much lower, at 16.0 kcal/mol relative to reactants, so C-C bond formation should not be rate-limiting, except perhaps for some aliphatic aldehydes or imines. We discuss the implications of this mechanism for the design of asymmetric versions of the MBH reaction, given the overwhelming importance of the proton-transfer step.  相似文献   

16.
Mechanistic and energetic aspects for the conversion of camphor to 5-exo-hydroxycamphor by the compound I iron-oxo species of cytochrome P450 are discussed from B3LYP DFT calculations. This reaction occurs in a two-step manner along the lines that the oxygen rebound mechanism suggests. The activation energy for the first transition state of the H atom abstraction at the C5 atom of camphor is computed to be more than 20 kcal/mol. This H atom abstraction is the rate-determining step in this hydroxylation reaction, leading to a reaction intermediate that involves a carbon radical species and the iron-hydroxo species. The second transition state of the rebound step that connects the reaction intermediate and the product alcohol complex lies a few kcal/mol below that for the H atom abstraction on the doublet and quartet potential energy surfaces. This energetic feature allows the virtually barrierless recombination in both spin states, being consistent with experimentally observed high stereoselectivity and brief lifetimes of the reaction intermediate. The overall energetic profile of the catalytic mechanism of camphor hydroxylation particularly with respect to why the high activation energy for the H atom abstraction is accessible under physiological conditions is also considered and calculated. According to a proton source model involving Thr252, Asp251, and two solvent water molecules (Biochemistry 1998, 37, 9211), the energetics for the conversion of the iron-peroxo species to compound I is studied. A significant energy over 50 kcal/mol is released in the course of this dioxygen activation process. The energy released in this chemical process is an important driving force in alkane hydroxylation by cytochrome P450. This energy is used for the access to the high activation energy for the H atom abstraction.  相似文献   

17.
The energy required to activate the H--H bond in the entire series of Cp(2)LnH complexes has been calculated by DFT (B3PW91) methods. The activation energies have been calculated to vary from 0.5 to 8.0 kcal x mol(-1), indicating an overall facile reaction. The electronegativity of the lanthanide in its most stable oxidation state is suggested to be a leading factor for interpreting the trends in activation energy. The geometry of the transition state is best viewed as an almost linear H(3)(-) ligand with short H--H distances and strong M--H interaction, through the wingtip H centers, with Ln. The exchange reaction is thus established to be a sigma bond metathesis reaction.  相似文献   

18.
The dehydrogenation reaction of H2S by the 3∑- ground state of VS+: VS+ + H2S → VS2+ + H2 has been studied by using Density Functional Theory (DFT) at the B3LYP/DZVP level. It is found that the reaction proceeds along two possible pathways (A and B) yielding two isomer dehydrogenation products VS2+-1 (3B2) and VS2+-2 (3A1), respectively. For both pathways,the reaction has a two-step-reaction mechanism that involves the migration of two hydrogen atoms from S2 to V+, respectively. The migration of the second hydrogen via TS3 and that of the first via TS4 are the rate-determining steps for pathways A and B, respectively. The activation energy is 17.4 kcal/mol for pathway A and 22.8 kcal/mol for pathway B relative to the reactants. The calculated reaction heat of 9.9 kcal/mol indicates the endothermicity of pathway A and that of -11.9 kcal/mol suggests the exothermicity of pathway B.  相似文献   

19.
The reaction mechanism of carbonyl oxide with hydroxyl radical was investigated by using CASSCF, B3LYP, QCISD, CASPT2, and CCSD(T) theoretical approaches with the 6-311+G(d,p), 6-311+G(2df, 2p), and aug-cc-pVTZ basis sets. This reaction involves the formation of H2CO + HO2 radical in a process that is computed to be exothermic by 57 kcal/mol. However, the reaction mechanism is very complex and begins with the formation of a pre-reactive hydrogen-bonded complex and follows by the addition of HO radical to the carbon atom of H2COO, forming the intermediate peroxy-radical H2C(OO)OH before producing formaldehyde and hydroperoxy radical. Our calculations predict that both the pre-reactive hydrogen-bonded complex and the transition state of the addition process lie energetically below the enthalpy of the separate reactants (DeltaH(298K) = -6.1 and -2.5 kcal/mol, respectively) and the formation of the H2C(OO)OH adduct is exothermic by about 74 kcal/mol. Beyond this addition process, further reaction mechanisms have also been investigated, which involve the abstraction of a hydrogen of carbonyl oxide by HO radical, but the computed activation barriers suggest that they will not contribute to the gas-phase reaction of H2COO + HO.  相似文献   

20.
Electronic energies, geometries, and harmonic vibration frequencies for the reactants, products, and transition state for the Cl(3P)+C2H6→C2H5+HCl abstraction reaction were evaluated at the HF and MP2 levels using several correlation consistent polarized-valence basis sets. Single-point calculations at PMP2, MP4, QCISD(T), and CCSD(T) levels were also carried out. The values of the forward activation energies obtained at the MP4/cc-pVTZ, QCISD(T)/cc-pVTZ, and CCSD(T)/cc-pVTZ levels using the MP2/cc-pVTZ structures are equal to −0.1, −0.4, and −0.3 kcal/mol, respectively. The experimental value is equal to 0.3±0.2 kcal/mol. We found that the MP2/aug-cc-pVTZ adiabatic vibration energy for the reaction (−2.4 kcal/mol) agrees well with the experimental value −(2.2–2.6) kcal/mol. Rate constants calculated with the zeroth-order interpolated variational transition state (IVTST-0) method are in good agreement with experiment. In general, the theoretical rate constants differ from experiment by, at most, a factor of 2.6.  相似文献   

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