Ab initio studies of parts of the potential surface for the system C3H6 + HO2

The addition reactions between HO₂ and propene leading to the radical intermediates CH₃CHCH₂OOH and CH₃CHOHCH₂ have been studied by ab initio molecular orbital calculations using a 6-31G * basis set and including electron correlation through fourth-order Møller–Plesset calculations. The intermediates are predicted to have energies of about 5 kcal/mol below the total reactant energies, the complex resulting from the HO₂ attack on the central carbon of propene being slightly preferred. The activation energies for the addition to the terminal carbon and the central carbon are predicted to be 8.5 and 8.0 kcal/mol, respectively, at the highest level of calculation [MP 4(SDTQ )] with corrections for spin contamination. Spin contamination corrections are found to be very important in the calculation of these values. Referring to previous calculations at the same level for the addition of HO₂ to ethylene [12], we assume that the addition step is the rate-determining one in the reaction leading to HO and propene oxide. The observed activation energy for this reaction, 14.2 kcal/mol [2], is significantly higher than the predicted one for the addition step. The discrepancy found, 6.2 kcal/mol, is virtually the same as the one encountered in the ethylene case, 6.6 kcal/mol [12]. The barrier to intramolecular hydrogen migration leading to the intermediate radical CH₂CH₂CH₂OOH is found to be 42.6 kcal/mol at the highest level of calculation. Spin contaminiation corrections are not important for this energy.     

Direct ab initio MD study on the hydrogen abstraction reaction of triplet state acetone from methanol molecule

Solvent re-orientation process of triplet acetone/methanol complex and intermolecular hydrogen atom abstraction reaction on the triplet state energy surface, (CH₃)₂C=O (T₁) + CH₃OH → (CH₃)₂C–OH + CH₂OH in gas phase, have been investigated by means of density functional theory (DFT) and direct ab initio molecular dynamics (MD) methods. The static DFT calculation of hydrogen abstraction reaction at the T₁ state showed that the transition state is 16.4 and 30.9 kcal/mol lower than the energy levels of S₁ and S₂ states, respectively, and 9.2 kcal/mol higher than the bottom of T₁ state. The product state, (CH₃)₂C–OH⋯CH₂OH, is 8.4 kcal/mol lower in energy than the level of T₁ state. The direct ab initio MD calculation showed that the product is rapidly formed within 150 fs and the separated products (CH₃)₂C–OH + CH₂OH were formed. The mechanism of reaction dynamics of the triplet acetone/methanol complex was discussed on the basis of theoretical results.     

Identification of decomposition reactions for HMDSO organosilicon using quantum chemical calculations

Hexamethyldisiloxane [HMDSO, (CH₃)₃-SiOSi-(CH₃)₃] is an important precursor for SiO₂ formation during flame-based silica material synthesis. As a result, HMDSO reactions in flame have been widely investigated experimentally, and many results have indicated that HMDSO decomposition reactions occur very early in this process. In this paper, quantum chemical calculations are performed to identify the initial decomposition of HMDSO and its subsequent reactions using the density functional theory at the level of B3LYP/6-311+G (d, p). Four reaction pathways—(a) Si O bond dissociation of HMDSO, (b) Si C bond dissociation of HMDSO, (c) dissociation and recombination of Si O and Si C bonds, and (d) elimination of a methane molecule from HMDSO—have been examined and identified. From the results, it is found that the barrier of 84.38 kcal/mol and Si O bond dissociation energy of 21.55 kcal/mol are required for the initial decomposition reaction of HMDSO in the first pathway, but the highest free energy barrier (100.69 kcal/mol) is found in the third reaction pathway. By comparing the free energy barriers and reaction rate constants, it is concluded that the most possible initial decomposition reaction of HMDSO is to eliminate the CH₃ radical by Si C bond dissociation.     

Ab initio studies of isomerization and dissociation reactions of methyl peroxynitrate

Using the CCSD(T)/cc-pVDZ//B3LYP/6-311G(2d,2p) method, we calculated the detailed potential energy surfaces (PESs) for the unimolecular isomerization and decomposition of methyl peroxynitrate (CH₃O₂NO₂). The results show that there are the two most stable isomers, IS1a and IS1b, which are a pair of mirror image isomers. From IS1a and IS1b, different isomerization and unimolecular decomposition reaction channels have been studied and discussed. Among them, the predominant thermal decomposition pathways are those leading to CH₃O₂ + NO₂ and cis-CH₃ONO + O₂. The former is the lowest-energy path through the direct O–N bond rupture in IS1a or IS1b. The PES along the O–N bond in IS1a has been scanned, where the energy of IS1a reaches maximum value of 23.5 kcal/mol when the O–N bond is stretched to about 2.8 Å. This energy is 2.7 kcal/mol larger than the O–N bond dissociation energy (BDE) and 2.8 kcal/mol larger than the experimental active energy. In addition, because the energy barriers of IS1a isomerization to IS2a are 23.8 kcal/mol, close to the 20.8 kcal/mol O–N BDE in IS1a or IS1b, the isomerization reaction may compete with the direct bond rupture dissociation reaction.     

Energetics of proton transfer between carbon atoms (H3CH ? CH3)−

Ab initio calculations were carried out to study the potential energy surface of (H₃C? H? CH₃)^?. The 6–31G* basis set is supplemented by a set of diffuse p functions on both C and H (with a range of exponents for the latter). The binding energy of CH₄ and CH₃^? to form the (H₃CH? CH₃)^? complex is about 2 kcal/mol, much smaller than for comparable ionic H-bonded systems involving O or N atoms. Nearly half of this interaction energy is due to correlation effects, computed at second and third orders of Møller-Plesset perturbation theory. Correlation is also responsible for substantial reductions in the energy barrier to proton transfer within the complex. This barrier is computed to be 13?15 kcal/mol at the MP3 level, depending upon the exponent used for the H p functions.     

Iodo-methyl ligand exchange reaction in platinum complexes: A density functional study

A theoretical investigation at the gradient-corrected density functional (BP86) level of theory on the iodo-methyl ligand exchange reaction in platinum-diphosphine complexes is discussed. The reaction consists of two elementary steps: the oxidative addition of methyl-iodide, and reductive elimination of ethane from the intermediate Pt(bdpp)(CH₃)₃I complex which is the rate determining step with a free energy of activation of 19.5 kcal/mol in acetonitrile phase. The oxidative addition step takes place with S_N2 mechanism via a transition state with a collinear arrangement of the I-CH₃-Pt moiety.     

A multilayered representation,quantum mechanical and molecular mechanics study of the CH3F + OH− reaction in water

The bimolecular nucleophilic substitution (S_N2) reaction of CH₃F + OH^? in aqueous solution was investigated using a combined quantum mechanical and molecular mechanics approach. Reactant complex, transition state, and product complex along the reaction pathway were analyzed in water. The potentials of mean force were calculated using a multilayered representation with the DFT and CCSD(T) level of theory for the reactive region. The obtained free energy activation barrier for this reaction at the CCSD(T)/MM representation is 18.3 kcal/mol which agrees well with the experimental value at ～21.6 kcal/mol. Both the solvation effect and solute polarization effect play key roles on raising the activation barrier height in aqueous solution, with the former raising the barrier height by 3.1 kcal/mol, the latter 1.5 kcal/mol. © 2013 Wiley Periodicals, Inc.     

Ethylene addition to group-6 transition metal oxo complexes - A theoretical study

Quantum chemical calculations using density functional theory (B3LYP) were carried out to elucidate the reaction pathways for ethylene addition to the chromium and molybdenum complexes CrO(CH₃)₂(CH₂) (Cr1) and MoO(CH₃)₂(CH₂) (Mo1). The results are compared with previously published results of the analogous tungsten system WO(CH₃)₂(CH₂) (W1). The comparison of the group-6 elements shows that the molybdenum and tungsten compounds Mo1 and W1 have a similar reactivity while the chromium compound has a more complex reactivity pattern. The kinetically most favorable reaction pathway for ethylene addition to Mo1 is the [2+2]_Mo,C addition across the MoCH₂ double bond which has an activation barrier of only 8.4 kcal/mol. The reaction is slightly exothermic with ΔE_R = −0.6 kcal/mol. The [2+2]_Mo,O addition across the MoO double bond and the [3+2]_C,O addition have much higher barriers and are strongly endothermic. The thermodynamically mostly favored reaction is the [1+2]_Mo addition of ethylene to the metal atom which takes place after prior rearrangement of the Mo(VI) compound Mo1 to the Mo(IV) isomer Mo1g. The reaction is −19.2 kcal/mol exothermic but it has a large barrier of 34.5 kcal/mol. The kinetically and thermodynamically most favorable reaction pathway for ethylene addition to the chromium homologue Cr1 is the multiple-step process with initial rearrangements Cr1 → Cr1c → Cr1g which are followed by a [1+2]_Cr addition yielding an ethylene π complex Cr1g + C₂H₄ → Cr1g-1. The highest barrier comes from the first step Cr1 → Cr1c which has an activation energy of 14.2 kcal/mol. The overall reaction is exothermic by −26.3 kcal/mol.     

Theoretical study of model elementary reactions of dissociative addition of light hydrocarbons to the Ti-doped aluminide cluster Al<Subscript>12</Subscript>Ti

The potential energy surfaces (PES), energies E, and activation barriers h of elementary reactions of dissociative addition of CH₄ and C₂H₆ molecules to the Al₁₂Ti cluster with a marquee structure in the singlet and triplet states were calculated within the B3LYP approximation of the density functional theory using the 6-31G* basis set. The first stage of the reaction Al₁₂Ti + CH₄ leads to the adsorption complex CH₄ · Al₁₂Ti with the R(TiC) distance of ～2.4 Å. The methane molecule is coordinated as a tridentate ligand the singlet state and as a bidentate ligand in the triplet state, although both coordination modes are close in energy. In the transition state, the CH₄ molecule is coordinated through its active C-H bond to an inclined Ti-Al edge of the cluster, and the C-H bond is significantly elongated and weakened. The activation barrier height h referenced to the CH₄ complex is ～9 and ～19 kcal/mol for the singlet and triplet, respectively, and that referenced to the primary products Al₁₂Ti(CH₃)(H) is ～21 kcal/mol. The barrier to migration of the CH₃ group around the metal cluster is estimated at ～10 kcal/mol. At the initial stage of the reaction Al₁₂Ti + C₂H₆, two types of C₂H₆ · Al₁₂Ti adsorption complexes are formed. In one of them, the ethane molecule is coordinated through a methyl group (as the methane molecule); and in the other type, the coordination is through the C-C bond. This reaction can proceed through two paths by means of insertion into C-H or C-C bonds to give Al₁₂Ti(C₂H₅)(H) or Al₁₂Ti(CH₃)₂, respectively. The second path is impeded by a high barrier (～30 kcal/mol) and is possible, if at all, only at high temperatures. Conversely, the insertion into a C-H bond in ethane is somewhat more favorable than in methane. Analogously, the PES of addition of the second methane molecule to Al₁₂Ti(CH₃)(H) was calculated. The second molecule is adsorbed and dissociates by the same mechanism as the first CH₄ molecule, but with somewhat lower barriers and energy effect of formation of Al₁₂Ti(CH₃)₂(H)₂. The addition of propane and longer hydrocarbons is briefly considered. The results are compared with the results of previous analogous calculations of the PES of related reactions of dissociative adsorption of dihydrogen on the Al₁₂Ti cluster, which are more exothermic, have lower barriers, and can occur under milder conditions.     

Quantum mechanical and molecular mechanics approach with a multilayered-quantum representation study of solvent effects and potentials of mean force for the CH<Subscript>3</Subscript>CH<Subscript>2</Subscript>Cl + ClO<Superscript>−</Superscript> S<Subscript>N</Subscript>2 reaction in aqueous solution

The bimolecular nucleophilic substitution reaction of CH₃CH₂Cl + ClO^? in aqueous solution was investigated using a multilayered-quantum representation, quantum mechanical and molecular mechanics approach with an explicit water model. Ten configurations along the reaction pathway including reactant complex, transition state and product complex were analyzed in the presence of the aqueous solution. The obtained free energy activation barrier under the CCSD(T)/MM representation is 13.2 kcal/mol, while it is 11.7 kcal/mol under the DFT/MM representation which agrees very well with the DFT calculation, at 11.0 kcal/mol, with a polarizable continuum solvent model. The solvent effects including the solvation free energy contribution and the polarization effect raise the free activation barrier by 9.8 kcal/mol. The rate constant, at 298 K, is 5.27 × 10^?17 cm³/molecule/s which is about seven orders of magnitude smaller than that in the gas phase (1.10 × 10^?10 cm³/molecule/s). All in all, the aqueous solution plays an essential role in shaping the reaction pathway for this reaction in water.     

Binding of anticancer drug Ru(η 6 -C6H5(CH2)2OH)Cl2(DAPTA) to DNA purine bases and amino acid residues: a theoretical study

The hydrolyzed Ru(η ⁶ -C₆H₅(CH₂)₂OH)Cl₂(DAPTA) (DAPTA = 3,7-diacetyl-1,3,7-triaza-5-phosphabicyclo[3.3.1]nonane) binding to guanine(G), adenine (A), cytosine(C), cysteine (Cys), and histidine (His) residues were explored using the B3LYP hybrid functional and IEF-PCM solvation models. The computed activation barriers for the reactions of diaqua complex were lower than those of chloroaqua complex except for binding to cytosine. For the chloroaqua complex, the activation free energy was lowest when binding to cytosine (10.5 kcal/mol). Whereas, the substitution reaction of diaqua complex binding to cysteine showed the lowest activation free energy with 10.1 kcal/mol, closely followed by histidine (15.8 kcal/mol), adenine (20.1 kcal/mol), cytosine (20.7 kcal/mol), and guanine (24.4 kcal/mol) by turns. It could be deduced that the completely hydrolyzed Ru(η ⁶ -C₆H₅(CH₂)₂OH)Cl₂(DAPTA) compounds might preferentially bind to amino acids residues in vivo. In addition, to simulate the protein and DNA environment in vivo, a detailed investigation of the activation free energies for the substitution reactions in dependence of the dielectric constant ε (4, 24, and 78.39) was systematically performed as well. The calculated results demonstrated that the environmental effect had a little impact on these substitution reactions.     

Theoretical study of the [1,3]-prototropic rearrangements of oximes and their ethers

In the framework of the MP2/6-311++G**//RHF/6-31G* ab initio approach we investigated the structure and relative stability of the imine (-CHR-CH=N-) and enamine (-CR=CH-NH-) forms of the simplest imines, oximes, and their ethers. Although the enamine form is unstable, double bond migration R₂CH-CH=N-→ R₂C=CH-NH-is often regarded as one of the stages of a series of reactions that take place in superbasic media, in particular, synthesis of pyrroles from ketoximes and acetylene. For isomerization of E-ethaneimine CH₃-CH=NH to vinylamine CH₂=CH-NH₂, calculations predict an increase of 4.3 kcal/mol in energy. A close value (4.8 kcal/mol) was obtained for the energy of isomerization of ketimine (CH₃)₂C=NH to 2-aminopropene. The methyl group in CH₃-CH=CH-NH₂ stabilizes the neighboring double bond, and the transformation of E-propane-1-imine into E-and Z-aminoprop-1-ene is accompanied by an increase of 2.8 kcal/mol in energy. After the transition from imines to oximes, the enamine form is drastically destabilized. The highly endothermal character of the CH₃-CH=NOH → CH₂=CH-NHOH rearrangement (16.4 kcal/mol) is retained from acetaldoxime to its methyl ether and decreases by only 1.0 kcal/mol for the isomerization reaction of the vinyl ether of acetaldoxime to N,O-divinylhydroxylamine. These rearrangements are thermodynamically unfavorable probably because of the increased negative charge on the nitrogen atom and, as a consequence, destabilization of the N-O bond.     

Structure and fluxional behavior of pentamethoxycarbonylcyclopentadiene

Quantum-chemical calculations by the density functional theory method at the B3LYP/6- 311++G** level have shown that the fulvene form of pentamethoxycarbonylcyclopentadiene 1 in the gas phase is more favorable in energy than cyclopentadiene form 2 by ΔE_ZPE = 7.8 kcal/mol. The fluxional behavior of fulvene 1, detected by dynamic NMR can be explained by the mechanism of circular low-barrier 1,9-O,O'-H shifts accompanied by rotations of the hydroxymethoxymethylene substituent about the С=С bond with the activation barrier ΔE_ZPE= 23.5 (gas) and 20.9 (CH₂Cl₂) kcal/mol. This reaction path is 18.6 kcal/mol more favorable in energy than transition of fulvene 1 to cyclopentadiene 2 with subsequent 1,5- sigmatropic hydrogen shifts in the five-membered ring.     

Ab initio MO study of ethylene insertion into the Sm–C bond of H2SiCp2SmCH3

Ethylene insertion into the Sm–C bond of H₂SiCp₂SmCH₃, a model reaction of an olefin polymerization propagation step, has been studied by ab initio molecular orbital methods. The small electronegativity of the Sm atom makes the Sm–C bond ionic, the methyl group being negatively charged by −0.75. The reaction passes through a loose ethylene complex with a binding energy of 15 kcal/mol and then a tight four-centered transition state with an agostic interaction between the Sm atom and one of the methyl CH bonds. A small activation energy of 14 kcal/mol is required to pass through this transition state, indicating that this is an easy reaction. Compared with the reactions with group 4 cationic silylene-bridged metallocenes the activation energy is higher and the reaction is less exothermic. The origin of these differences is discussed. The results of molecular mechanics calculations on regio- and stereoselectivities in the insertion reaction of propylene are also reported. Received: 13 July 1998 / Accepted: 28 August 1998 / Published online: 2 November 1998     

Ab initioMO calculations on the acidities of water and methanol,and hydrogen bond energies of the conjugate ions with a water molecule

The acidities, deprotonation energies, of water and methanol were calculated by the use of the ab initio self-consistent-field (SCF ) molecular orbital (MO ) method with electron correlation computed by the thirdorder Møller–Plesset perturbation method and configuration interaction with double excitations. Zero-point vibrational energy correction translational energy change, and the PV work term were included to evaluate the accurate acidities. The calculated acidity difference including these corrections was 7 kcal/mol, which is somewhat smaller than the experimental ones (9.5–12.5 kcal/mol) recently determined. The hydrogen bond energies of the conjugate ions (OH^? and CH₃O^?) with a water molecule were calculated to be 2.3 kcal/mol near the Hartree–Fock limit; this energy only amounts to 25% of the (total) hydration energy difference between the two negative ions. The aqueous solvation effect on the acidity scale was discussed.     

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     

Preliminary attempt to follow the enthalpy of an enzymatic reaction by ab initio computations: Catalytic action of papain

A new theoretical approach to study the enthalpy variations occurring during an enzymatic reaction is presented. The structural modifications of the enzyme–substrate complex along the reaction path are distinguished as macro- and microdeformations. Macrodeformations, which concern primarily the approach of the substrate to the enzyme and the release of the reaction products and arise from nonbonded interactions, are treated with an empirical method for computing the energy of a macromolecule. Microdeformations, which are local displacements driven by variations of the electronic structure and its energy and involve only a limited portion of the complex, are treated with the ab initio SCF-LCAO-MO method. The reaction path is idealized as a sequence of major steps: at each step, first the empirical program REFINE is used to calculate the geometry of the system for that step, then the energy of an appropriate subsystem is computed ab initio with the program IBMOL, using the geometry provided by REFINE and applying small concerted atomic displacements. Thus along the entire reaction path one can obtain an energy profile computed with the ab initio method and compatible with the structure of the whole complex. This approach was applied here to the first steps of the reaction of proteolysis catalyzed by papain. The formation of an ion pair ImH⁺ …S^? between the side chains of residues His-159 and Cys-25 was examined in detail. The results show that the instability of the ion pair decreases by ? 11.5 kcal/mol when the interactions with residues Asn-175 and Ala- 160 are taken into account; the instability is further decreased by ?2 kcal/mol after a partial geometry optimization. The energies of the noncovalent enzyme–substrate complex and of the tetrahedral intermediate were computed, considering N-methyl acetamide (NMA) as model substrate and representing papain with the residues Cys-25, His-159, Gln-19, and Ala-160. The interaction energy of the noncovalent complex is -3.8 kcal/mol, compared to the value of +7.4 kcal/mol for the CH₃S^? -NMA complex. The tetrahedral intermediate is found to be less stable than the noncovalent complex by 27 and 38.5 kcal/mol, respectively, for the papain–NMA and the CH₃S^? -NMA systems. While these rather large energy differences are possibly due to the incorrect geometry of the tetrahedral intermediate and optimization of the structure is required, it appears that the interactions with the various protein residues represent a very important stabilization factor, which lowers the onthalpy variations during the reaction.     

Carbonyl insertion reaction into the Pt?C bond in heterobimetallic Pt(SnCl3)(PH3)2(CO)(CH3) compound: Theoretical study

Quantum‐mechanical calculations were carried out at the MP4(SDQ)//MP2 level of theory to determine the energies and reaction mechanism for the carbonyl insertion reaction (second step in the olefin hydroformylation catalytic cycle), using a heterobimetallic Pt(SnCl₃)(PH₃)₂(CO)(CH₃) compound as a model catalytic species. The results show that this reaction proceeds through a three‐center transition state, with an activation energy of 26.4 kcal/mol, followed by an intramolecular rearrangement to the square‐planar cis‐Pt(SnCl₃)(PH₃)₂(MeCO) metal–acyl product. Analysis of the nature of the bonds shows that there is a negligible participation of the tin d‐orbitals in the formation of the Pt Sn bond. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 668–674, 2000     

Reaction mechanisms of methanol oxidation by FeIVO biomimetic complex

Density functional theory calculations were carried out to investigate the reaction mechanism of methanol oxidation mediated by [(bpg)Fe^IVO]⁺ ( A ). Two models (CH₃CN‐bound ferryl model B and CH₃OH‐bound ferryl model C ) were also studied in this work to probe ligand effect. Mechanistically, both direct and concerted hydrogen transfer (DHT and CHT) pathways were explored. It is found that the initial step of methanol oxidation by A is C? H bond activation via a DHT pathway. Addition of different equatorial ligands has considerable influence on the reaction mechanisms. Methanol oxidation mediated by B commences via O? H bond activation; in sharp contrast, the oxidation mediated by C stems from C? H bond activation. Frontier molecular orbital analysis showed that the initial C? H bond activation by all these model complexes follows a hydrogen atom transfer (HAT) mechanism, whereas O? H bond activation proceeds via an HAT or proton transfer. © 2016 Wiley Periodicals, Inc.     

Density functional theory study of the oxidative dehydrogenation of propane on the (001) surface of V2O5

The density functional theory using a plane‐waves basis set and pseudopotential has been used to study the reaction pathways for ODH of propane on the V₂O₅(001) surface. The calculations indicated that propane adsoprtion step was initiated by the insertion of vanadyl oxygen O (1) into methylene C? H bond forming an iso‐propanol structure. This step is the rate‐determining step with an activation energy of 23.3 kcal/mol. The subsequent step involved the abstraction of the second hydrogen by O (1) site leading the formation of propene. This process had an activation energy of 22.5 kcal/mol. The elimination of surface bound water molecule at the O (1) was a barrierless process. The energy required for this process was compensated from O2 dissociative adsorption. Finally, the electronic density of state has been applied to prove the reality of the calculated results. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010