Mechanism of the S-->N isomerization and aquation of the thiocyanato pentaammine cobalt(III) ion

All of the stationary points on the potential energy surface of the S-->N isomerization and aquation of the Co(NH3)5SCN2+ ion have been investigated with ab initio quantum chemical methods. Also the corresponding anations of the Co(NH3)5OH2(3+) ion by the N and S ends of SCN- and the substitution of thiocyanate via the D mechanism have been studied. All calculations have been performed by taking into account hydration. The most favorable reaction of Co(NH3)5SCN2+ is the isomerization. It is concerted, follows the I or Id mechanism, depending on the applied criteria, and proceeds via a T-shaped transition state. The aquations of Co(NH3)5SCN2+ and Co-(NH3)5NCS2+ and the corresponding inverse reactions, the anations, all proceed via the Id mechanism. The activation energies, calculated for the isomerization and aquation, agree with experiment, and so does the difference of the activation energies for the anations by the two donors of SCN-. This energy difference reflects the disparate nucleophilicities of the N and S ends of SCN- and shows that bond making in the transition state is significant for the Id mechanism. Isomerization and aquation are two parallel reactions which proceed via two disparate transition states. The computed activation energy for the SCN- substitution via the D mechanism is the highest, and therefore, this pathway is unlikely to operate for the isomerization and aquation of Co(NH3)5SCN2+. The S-->N isomerization and the SCN- substitution via the D mechanism were furthermore computed for the free ions in the gas phase: the isomerization would require a higher activation energy and follow the Ia mechanism. The activation energy for the SCN- substitution via the D mechanism would be very high, because of the large electrostatic work which is required for the removal of an anion from a (formally) 3+ charged cation.     

Aquation of the ruthenium-based anticancer drug NAMI-A: a density functional study

We carried out density functional theory (DFT) calculations to investigate the thermodynamics and the kinetics of the double aquation reaction of the anticancer drug NAMI-A. Three explicit water molecules were included in the calculations to improve the PB solvation energies. Our calculations show that the chloride substitution reactions on the considered Ru(III) octahedral complex follow a dissociative interchange mechanism, I(d), passing through a loose heptacoordinate transition state. We calculated an activation enthalpy and free energy for the first aquation step of 101.5 and 103.7 kJ mol(-1), respectively, values that are in good agreement with the available experimental results. The activation enthalpy and free energy for the second aquation step were found significantly higher, 118.7 and 125.0 kJ mol(-1), again in agreement with the experimental evidence indicating a slower rate for the second aquation.     

Photoinduced electron transfer reactions by SmI2 in THF: luminescence quenching studies and mechanistic investigations

Photoluminescence quenching studies of SmI2 in dry THF were carried out in the presence of five different classes of compounds: ketone, alkyl chloride, nitrile, alkene and imine. The free energy change (DeltaG0) of the photoinduced electron transfer (PET) reactions was calculated from the redox potentials of the donor (SmI2) and acceptors. The bimolecular quenching constants (k(q)) derived from the Stern-Volmer experiments parallel the free energy changes of the PET processes. The observed quenching constants were compared with the theoretically derived electron transfer rate constants (k(et)) from Marcus theory and found to be in good agreement when a value of lambda = 167 kJ mol(-1) (40 kcal mol(-1)) was used for the reorganization energy of the system. A careful comparison of the excited state dynamics of SmII in the solid state to the results obtained in solution (THF) provides new insight in to the excited states of SmII in THF. The activation parameters determined for the PET reactions in SmI2/1-chlorobutane system are consistent with a less ordered transition state and high degree of bond reorganization in the activated complex compared to similar ground state reactions. Irradiation studies clearly show that SmI2 acts as a better reductant in the excited state and provides an alternative pathway for rate enhancement in known and novel functional group reductions.     

Correlating DFT-Calculated Energy Barriers to Experiments in Nonheme Octahedral Fe(IV) O Species

The experimentally measured bimolecular reaction rate constant, k(2) , should in principle correlate with the theoretically calculated rate-limiting free energy barrier, ΔG(≠) , through the Eyring equation, but it fails quite often to do so due to the inability of current computational methods to account in a precise manner for all the factors contributing to ΔG(≠) . This is further aggravated by the exponential sensitivity of the Eyring equation to these factors. We have taken herein a pragmatic approach for C?H activation reactions of 1,4-cyclohexadiene with a variety of octahedral nonheme Fe(IV) O complexes. The approach consists of empirically determining two constants that would aid in predicting experimental k(2) values uniformly from theoretically calculated electronic energy (ΔE(≠) ) values. Shown in this study is the predictive power as well as insights into energy relationships in Fe(IV) O C?H activation reactions. We also find that the difference between ΔG(≠) and ΔE(≠) converges at slow reactions, in a manner suggestive of changes in the importance of the triplet spin state weight in the overall reaction.     

A comparison of acetyl- and methoxycarbonylnitrenes by computational methods and a laser flash photolysis study of benzoylnitrene

Density functional theory (DFT), CCSD(T), and CBS-QB3 calculations were performed to understand the chemical and reactivity differences between acetylnitrene (CH(3)C(=O)N) and methoxycarbonylnitrene (CH(3)OC(=O)N) and related compounds. CBS-QB3 theory alone correctly predicts that acetylnitrene has a singlet ground state. We agree with previous studies that there is a substantial N-O interaction in singlet acetylnitrene and find a corresponding but weaker interaction in methoxycarbonylnitrene. Methoxycarbonylnitrene has a triplet ground state because the oxygen atom stabilizes the triplet state of the carbonyl nitrene more than the corresponding singlet state. The oxygen atom also stabilizes the transition state of the Curtius rearrangement and accelerates the isomerization of methoxycarbonylnitrene relative to acetylnitrene. Acetyl azide is calculated to decompose by concerted migration of the methyl group along with nitrogen extrusion; the free energy of activation for this concerted process is only 27 kcal/mol, and a free nitrene is not produced upon pyrolysis of acetyl azide. Methoxycarbonyl azide, on the other hand, does have a preference for stepwise Curtius rearrangement via the free nitrene. The bimolecular reactions of acetylnitrene and methoxycarbonylnitrene with propane, ethylene, and methanol were calculated and found to have enthalpic barriers that are near zero and free energy barriers that are controlled by entropy. These predictions were tested by laser flash photolysis studies of benzoyl azide. The absolute bimolecular reaction rate constants of benzoylnitrene were measured with the following substrates: acetonitrile (k = 3.4 x 10(5) M(-1) (s-1)), methanol (6.5 x 10(6) M(-1) s(-1)), water (4.0 x 10(6) M(-1) s(-1)), cyclohexane (1.8 x 10(5) M(-1) s(-1)), and several representative alkenes. The activation energy for the reaction of benzoylnitrene with 1-hexene is -0.06 +/- 0.001 kcal/mol. The activation energy for the decay of benzoylnitrene in pentane is -3.20 +/- 0.02 kcal/mol. The latter results indicate that the rates of reactions of benzoylnitrene are controlled by entropic factors in a manner reminiscent of singlet carbene processes.     

Analyzing Reaction Rates with the Distortion/Interaction‐Activation Strain Model

The activation strain or distortion/interaction model is a tool to analyze activation barriers that determine reaction rates. For bimolecular reactions, the activation energies are the sum of the energies to distort the reactants into geometries they have in transition states plus the interaction energies between the two distorted molecules. The energy required to distort the molecules is called the activation strain or distortion energy. This energy is the principal contributor to the activation barrier. The transition state occurs when this activation strain is overcome by the stabilizing interaction energy. Following the changes in these energies along the reaction coordinate gives insights into the factors controlling reactivity. This model has been applied to reactions of all types in both organic and inorganic chemistry, including substitutions and eliminations, cycloadditions, and several types of organometallic reactions.     

Computational study of the Curtius-like rearrangements of phosphoryl, phosphinyl, and phosphinoyl azides and their corresponding nitrenes

The free energies of reaction (DeltaG) and activation (DeltaG) were determined for the Curtius-like rearrangement of dimethylphosphinoyl, dimethylphosphinyl, and dimethylphosphoryl azides as well as the corresponding singlet and triplet nitrenes by CBS-QB3 and B3LYP computational methods. From CASSCF calculations, it was established that the closed-shell configuration was the lower energy singlet state for each of these nitrenes. The triplet states of dimethylphosphinyl- and dimethylphosphorylnitrene are the preferred ground states. However, the closed-shell singlet state is the ground state for dimethylphosphinoylnitrene. The CBS-QB3 DeltaG values for the Curtius-like rearrangements of dimethylphosphinyl and dimethylphosphoryl azides were 45.4 and 47.0 kcal mol-1, respectively. For the closed-shell singlet dimethylphosphinyl- and dimethylphosphorylnitrene, the CBS-QB3 DeltaG values for the rate-limiting step of the Curtius-like rearrangement were 22.9 and 18.0 kcal mol-1, respectively. It is unlikely that the nitrenes will undergo a Curtius-like rearrangement because of competing bimolecular reactions that have lower activation barriers. The pharmacology of weaponized organophosphorus compounds can be investigated using phosphorylnitrenes as photoaffinity labels. Dominant bimolecular reactivity is a desirable quality for a photoaffinity label to possess, and thus, the resistance of phosphorylnitrenes to intramolecular Curtius-like rearrangements increases their usefulness as photoaffinity labels.     

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.     

A Theoretical Study of Ene Reactions in Solution: A Solution‐Phase Translational Entropy Model

Several density functional theory (DFT) methods, such as CAM‐B3LYP, M06, ωB97x, and ωB97xD, are used to characterize a range of ene reactions. The Gibbs free energy, activation enthalpy, and entropy are calculated with both the gas‐ and solution‐phase translational entropy; the results obtained from the solution‐phase translational entropies are quite close to the experimental measurements, whereas the gas‐phase translational entropies do not perform well. For ene reactions between the enophile propanedioic acid (2‐oxo‐1,3‐dimethyl ester) and π donors, the two‐solvent‐involved explicit+implicit model can be employed to obtain accurate activation entropies and free‐energy barriers, because the interaction between the carbonyl oxygen atom and the solvent in the transition state is strengthened with the formation of C?C and O?H bonds. In contrast, an implicit solvent model is adequate to calculate activation entropies and free‐energy barriers for the corresponding reactions of the enophile 4‐phenyl‐1,2,4‐triazoline‐3,5‐dione.     

Ab initio study of the SN1Ar and SN2Ar reactions of benzenediazonium ion with water. On the conception of "unimolecular dediazoniation" in solvolysis reactions

The nucleophilic substitution of N2 in benzenediazonium ion 1 by one H2O molecule to form protonated phenol 2 has been studied with ab initio (RHF, MP2, QCISD(T)//MP2) and hybrid density functional (B3LYP) methods. Three mechanisms were considered: (a) the unimolecular process SN1Ar with steps 1 --> Ph+ + N2 and Ph+ + H2O --> 2, (b) the bimolecular process SN2Ar with precoordination 1 + H2O --> 1 x H2O, SN reaction 1 x H2O --> [TS]++ --> 2 x N2 and dissociation of the postcoordination complex 2 x N2 --> 2 + N2, and (c) the direct bimolecular process SN2Ar that bypasses precoordination and involves just the SN reaction 1 + H2O --> [TS]++ --> 2 + N2. The SN2Ar reactions proceed by way of a Cs symmetric SN2Ar transition state structure that is rather loose, contains essentially a phenyl cation weakly bound to N2 and OH2, and is analogous to the transition state structures of front-side nucleophilic replacement at saturated centers. In solvolysis reactions, all of these processes follow first-order kinetics, and the electronic relaxation is essentially the same. It is argued that "unimolecular dediazoniations" have to proceed by way of SN2Ar transition state structures because strict SN1Ar reactions cannot be realized in solvolyses, despite the fact that the Gibbs free energy profile favors the strict SN1Ar process over the SN2Ar reaction by 6.7 kcal/mol. It is further argued that the direct SN2Ar process is the best model for the solvolysis reaction for dynamic reasons, and its Gibbs free energy of activation is 19.3 kcal/mol and remains higher than the SN1Ar value. Even though the SN1Ar and SN2Ar models provide activation enthalpies and SKIE values that closely match the experimental data, the analysis leads us to the unavoidable conclusion that this agreement is fortuitous. While the experiments do show that the solvent effect on the activation energy is about the same for all solvents, they do not show the absence of a solvent effect. The ab initio results presented here suggest that the solvent effect on the direct SN2Ar dediazoniation is approximately 12 kcal/mol, and computation of solvent effects with the isodensity polarized continuum model (IPCM) support this conclusion.     

Thermolysis of polyethylene hydroperoxides in the melt, Part 11: Relative yields of thermolysis products

The experimental ratios of the main products from polyethylene hydroperoxide thermolysis are examined. Comparison with the corresponding theoretical ratios calculated for different hydroperoxide decomposition reactions allows discriminating between the main hydroperoxide decomposition reactions. The experimental values can usually be explained best by the true bimolecular reaction involving two hydroperoxide groups. Mostly these values are significantly different from the theoretical ratios calculated for the bimolecular reaction with an alcohol group and for the pseudo-monomolecular reaction with a segment of the polymer. The bulk of the results points unequivocally to true bimolecular hydroperoxide decomposition for explaining thermolysis of polyethylene hydroperoxides.     

The Impact of Resonance Stabilization on the Intramolecular Hydrogen‐Atom Shift Reactions of Hydrocarbon Radicals

A series of intramolecular H‐atom shift reactions of both alkenyl and allylic radicals were investigated by using CBS‐QB3 electronic structure calculations. In the first set of reactions, an alkyl radical site was converted into an allylic radical site. In the second set, an allylic radical was converted into another allylic radical. The results are discussed in the context of a Benson‐type model to examine the impact of the transition‐state partial resonance stabilization on both the activation energies and the pre‐exponential factors. In most cases, the differences in the activation energies relative to those for the analogous alkyl radicals are primarily due to the barriers of the bimolecular reaction component of the activation energy. For the first set of reactions, there is additional entropy loss relative to the alkyl radical analogues. This additional loss of entropy may be smaller than some previous estimates. The pre‐exponential factors for the second set of reactions are generally similar to those of the analogous alkyl radical reactions (once the double bond in the transition state is accounted for).     

Ab initio molecular orbital calculations on the transition state for the addition of a methyl radical to vinyl monomers

Ab initio molecular orbital calculations have been performed on the transition state for the addition of methyl radical to twelve vinyl monomers using the SV 3–21G basis set. A linear relationship has been found between the calculated energies of activation and previously calculated energies of reaction. This supports the assumption of an Evans-Polanyi type rule in previous work which attempted to correlate reactivity with calculated energies of reaction. The activation energies obtained for methyl addition to butadiene and styrene were calculated to be negative. This is caused by errors introduced by a number of sources, viz. basis set superposition error, spin contamination and zero point energy. These errors are discussed. Previous authors have reported reasonable agreement between calculated activation energies at SV3–21G and experimental values for methyl addition to ethylene, this work suggests that this agreement was coincidental and results from the fortuitous cancellation of errors. The nature of the transition state for these radical addition reactions is discussed and the limitations of the SV3–21G basis set are highlighted. The theoretical prediction of activation energies for radical addition reactions would require much larger calculations, beyond the computational means of most research laboratories.     

An analysis of the interaction energy in some SN2 reactions

The interaction energy between an incoming group X^– and the substrate CRH₂Y at the geometry of the transition state (TS) for bimolecular nucleophilic substitution reactions (with X, Y, and R equal to H and F) has been subjected to decomposition according to the Morokuma scheme. The influence of the basis set and of the geometry chosen for the TS is examined. The results bring out regular trends in the different terms of the decomposition along the whole set of reactions, but they are not sufficient to give a rationale of the energetic factors involved in these reactions.     

Stereochemistry of transition states and mechanisms of chemical reactions on silica surface

The activation energy of substitution and bond cleavage reactions of siloxane derivatives on silica surfaces is discussed considering the stereochemistry of the transition state. General concepts are developed and utilized in predicting reactivity trends for reactions occurring on the silica surface.     

A microscopic view of substitution reactions solvated by ionic liquids

The solvation effect of the ionic liquid 1-N-butyl-3-methylimidazolium hexafluorophosphate on nucleophilic substitution reactions of halides toward the aliphatic carbon of methyl p-nitrobenzenesulfonate (pNBS) was investigated by computer simulations. The calculations were performed by using a hybrid quantum-mechanical/molecular-mechanical (QM/MM) methodology. A semiempirical Hamiltonian was first parametrized on the basis of comparison with ab initio calculations for Cl(-) and Br(-) reaction with pNBS at gas phase. In condensed phase, free energy profiles were obtained for both reactions. The calculated reaction barriers are in agreement with experiment. The structure of species solvated by the ionic liquid was followed along the reaction progress from the reagents, through the transition state, to the final products. The simulations indicate that this substitution reaction in the ionic liquid is slower than in nonpolar molecular solvents proper to significant stabilization of the halide anion by the ionic liquid in comparison with the transition state with delocalized charge. Solute-solvent interactions in the first solvation shell contain several hydrogen bonds that are formed or broken in response to charge density variation along the reaction coordinate. The detailed structural analysis can be used to rationalize the design of new ionic liquids with tailored solvation properties.     

Cl_2 2HI=2HCl I_2反应机理的理论研究

分别在MP2/3-21G!!、CCSD(T)/3-21G!!//MP2/3-21G!!和B3LYP/3-21G!!3种水平上,计算研究了气相反应Cl2 2HI=2HCl I2的机理,求得一系列四中心和三中心的过渡态.通过比较六种反应通道的活化能大小,得到了相同的结论:双分子基元反应Cl2 HI"HCl ICl和ICl HI"I2 HCl的最小活化能小于Cl2、HI和ICl的解离能,从理论上证明了反应Cl2 2HI=2HCl I2将优先以分子与分子作用形式分两步完成.用内禀反应坐标(IRC)验证了MP2/3-21G!!方法计算得到的过渡态.     

Hybrid Solvation Model with First Solvation Shell for Calculation of Solvation Free Energy

We present a hybrid solvation model with first solvation shell to calculate solvation free energies. This hybrid model combines the quantum mechanics and molecular mechanics methods with the analytical expression based on the Born solvation model to calculate solvation free energies. Based on calculated free energies of solvation and reaction profiles in gas phase, we set up a unified scheme to predict reaction profiles in solution. The predicted solvation free energies and reaction barriers are compared with experimental results for twenty bimolecular nucleophilic substitution reactions. These comparisons show that our hybrid solvation model can predict reliable solvation free energies and reaction barriers for chemical reactions of small molecules in aqueous solution.     

Relationship between bond dissociation energies and activation energies for bond scission reactions

Bond dissociation energies are frequently derived from values of the high pressure activation energy for bond scission reactions. The value derived depends on the transition state structure chosen for the reaction. We consider several models of the transition state and show that the variation in derived BDE values can be quite substantial, 3 to 6 kcal/mol at the high temperatures of pyrolysis kinetics. Application of the restricted Gorin model of the transition state results in BDE values in good agreement with current thermochemistry, while the other models tested result in lower to much lower values. © 1994 John Wiley & Sons, Inc.     

变分过渡态理论对H＋H2及其同位素选态反应的研究

将选态速度常数的计算推广到任意指定反应物、过渡态的振动激发态.用此法计算了H+H_2(v)及其同位素经不同振动激发过渡态时的速度常数,发现弯曲振动模激发所得结果与实验值更符合,并且在给定能量下,过渡态的弯曲振动模激发比其对称伸缩模激发更有利于反应进行.