Quantum Chemical Study of the Thermodynamic and Kinetic Aspects of the SN2 Reaction in Gas Phase and Solution Using a DFT Interpretation

3D Information-Theoretic Analysis of the Simplest Hydrogen Abstraction Reaction

We investigate the course of an elementary chemical reaction from the perspective of information theory in 3D space through the hypersurface of several information-theoretic (IT) functionals such as disequilibrium (D), Shannon entropy (S), Fisher information (I), and the complexity measures of Fisher-Shannon (FS) and López-Mancini-Calbet (LMC). The probe for the study is the hydrogenic identity abstraction reaction. In order to perform the analysis, the reactivity pattern of the reaction is examined by use of the aforementioned functionals of the single-particle density, which is analyzed in position (r) and momentum (p) spaces. The 3D analyses revealed interesting reactivity patterns in the neighborhood of the intrinsic reaction coordinate (IRC) path, which allow to interpret the reaction mechanism for this reaction in a novel manner. In addition, the chemically interesting regions that have been characterized through the information functionals and their complexity measures are depicted and analyzed in the framework of the three-dimensional structure of the information-theoretical data of a chemical reaction, that is, the reactant/product (R/P) complexes, the transition state (TS), and the ones that are only revealed through IT measures such as the bond-cleavage energy region (BCER), the bond-breaking/forming (B-B/F) region, and the spin-coupling (SC) process. Furthermore, focus has been placed on the diagonal part of the hypersurface of the IT functionals, aside from the IRC path itself, with the purpose of analyzing the dissociation process of the triatomic transition-state complex that has revealed other interesting features of the bond-breaking (B-B) process. In other respects, it is shown throughout the combined analyses of the 3D structure of the IT functionals in conjugated spaces that the chemically significant regions occurring at the onset of the TS are completely characterized by information-theoretic aspects of localizability (S), uniformity (D), and disorder. Further, novel regions of low complexity seem to indicate new boundaries for chemically stable complex molecules. Finally, the study reveals that the chemical reaction occurs at low-complexity regions, where the concurrent phenomena take place: bond-breaking/forming (B-B/F), bond-cleavage energy reservoirs (BCER), spin-coupling (SC), and transition state (TS).

The Reactivity of Ambident Nucleophiles: Marcus Theory or Hard and Soft Acids and Bases Principle?

The model reactions CH₃ X + (NH-CH=O)M ➔ CH₃ -NH-NH═O or NH═CH-O-CH₃  + MX (M = none, Li, Na, K, Ag, Cu; X = F, Cl, Br) are investigated to demonstrate the feasibility of Marcus theory and the hard and soft acids and bases (HSAB) principle in predicting the reactivity of ambident nucleophiles. The delocalization indices (DI) are defined in the framework of the quantum theory of atoms in molecules (QT-AIM), and are used as the scale of softness in the HSAB principle. To react with the ambident nucleophile NH═CH-O^- , the carbocation H₃ C⁺ from CH₃ X (F, Cl, Br) is actually a borderline acid according to the DI values of the forming C…N and C…O bonds in the transition states (between 0.25 and 0.49), while the counter ions are divided into three groups according to the DI values of weak interactions involving M (M…X, M…N, and M…O): group I (M = none, and Me₄ N) basically show zero DI values; group II species (M = Li, Na, and K) have noticeable DI values but the magnitudes are usually less than 0.15; and group III species (M = Ag and Cu(I)) have significant DI values (0.30-0.61). On a relative basis, H₃ C⁺ is a soft acid with respect to group I and group II counter ions, and a hard acid with respect to group III counter ions. Therefore, N-regioselectivity is found in the presence of group I and group II counter ions (M = Me₄ N, Li, Na, K), while O-regioselectivity is observed in the presence of the group III counter ions (M = Ag, and Cu(I)). The hardness of atoms, groups, and molecules is also calculated with new functions that depend on ionization potential (I) and electron affinity (A) and use the atomic charges obtained from localization indices (LI), so that the regioselectivity is explained by the atomic hardness of reactive nitrogen atoms in the transition states according to the maximum hardness principle (MHP). The exact Marcus equation is derived from the simple harmonic potential energy parabola, so that the concepts of activation free energy, intrinsic activation barrier, and reaction energy are completely connected. The required intrinsic activation barriers can be either estimated from ab initio calculations on reactant, transition state, and product of the model reactions, or calculated from identity reactions. The counter ions stabilize the reactant through bridging N- and O-site of reactant of identity reactions, so that the intrinsic barriers for the salts are higher than those for free ambident anions, which is explained by the increased reorganization parameter Δr. The proper application of Marcus theory should quantitatively consider all three terms of Marcus equation, and reliably represent the results with potential energy parabolas for reactants and all products. For the model reactions, both Marcus theory and HSAB principle/MHP principle predict the N-regioselectivity when M = none, Me₄ N, Li, Na, K, and the O-regioselectivity when M = Ag and Cu(I). © 2019 Wiley Periodicals, Inc.

Catalytic Effect of Aqueous Solution in Water-Assisted Proton-Transfer Mechanism of 8-Hydroxy Guanine Radical

Water-assisted proton-transfer process is a key step in guanine damage reaction by hydroxyl radical in aqueous solution. In this article, we quantitatively determine the solvent effect in water-assisted proton-transfer mechanism of 8-hydroxy guanine radical using combined quantum mechanics and molecular mechanism with an explicit solvation model. Atomic-level reaction pathway was mapped, which shows a synchronized two-proton-transfer mechanism between the assistant water molecule and 8-hydroxy guanine radical. The transition-state dipole moment is the largest along the reaction pathway, which electrostatically stabilizes the proton-transfer transition-state complex. The free-energy reaction barrier for this water-assisted proton-transfer reaction was calculated at 19.2 kcal/mol with the density functional theory/M08-SO/cc-pVTZ+/molecular mechanics level of theory. The solvent effect not only has a big impact on geometries, but also dramatically changes the energetics along the reaction pathway. Among the solvent effect contributions to the transition state, the solvent energy contribution is -28.5 kcal/mol and the polarization effect contribution is 19.9 kcal/mol. In total, the solvent effect contributes -8.6 kcal/mol to the free-energy barrier height, which means that the presence of aqueous solution has a catalytic effect on the reaction mechanism and enhances the proton-transfer reactivity in aqueous solution.

A new, double-inversion mechanism of the F- + CH3Cl SN2 reaction in aqueous solution

Atomic-level, bimolecular nucleophilic substitution reaction mechanisms have been studied mostly in the gas phase, but the gas-phase results cannot be expected to reliably describe condensed-phase chemistry. As a novel, double-inversion mechanism has just been found for the F^- + CH₃Cl S_N2 reaction in the gas phase [Nat. Commun., 2015, 6, 5972], here, using multi-level quantum mechanics methods combined with the molecular mechanics method, we discovered a new, double-inversion mechanism for this reaction in aqueous solution. However, the structures of the stationary points along the reaction path show significant differences from those in the gas phase due to the strong influence of solvent and solute interactions, especially due to the hydrogen bonds formed between the solute and the solvent. More importantly, the relationship between the two double-inversion transition states is not clear in the gas phase, but, here we revealed a novel intermediate complex serving as a "connecting link" between the two transition states of the abstraction-induced inversion and the Walden-inversion mechanisms. A detailed reaction path was constructed to show the atomic-level evolution of this novel double reaction mechanism in aqueous solution. The potentials of mean force were calculated and the obtained Walden-inversion barrier height agrees well with the available experimental value.

Multilevel Quantum Mechanics Theories and Molecular Mechanics Calculations of the Cl- + CH3I Reaction in Water

The Cl^- + CH₃I → CH₃Cl + I^- reaction in water was studied using combined multilevel quantum mechanism theories and molecular mechanics with an explicit water solvent model. The study shows a significant influence of aqueous solution on the structures of the stationary points along the reaction pathway. A detailed, atomic-level evolution of the reaction mechanism shows a concerted one-bond-broken and one-bond-formed mechanism, as well as a synchronized charge-transfer process. The potentials of mean force calculated with the CCSD(T) and DFT treatments of the solute produce a free activation barrier at 24.5 and 19.0 kcal/mol, respectively, which agrees with the experimental one at 22.0 kcal/mol. The solvent effects have also been quantitatively analyzed: in total, the solvent effects raise the activation energy by 20.2 kcal/mol, which shows a significant impact on this reaction in water.

A Benchmark Study of Kinetic Isotope Effects and Barrier Heights for the Finkelstein Reaction

Herein, we present a combined (experimental and computational) study of the Finkelstein reaction in condensed phase, where bromine is substituted by iodine in 2-bromoethylbenzene, in the presence of either acetone or acetonitrile as a solvent. Performance of various density functional theory and ab initio methods were tested for reaction barrier heights as well as for bromine and carbon kinetic isotope effects (KIEs). Two different implicit solvation models were examined (PCM and SMD). Theoretically predicted KIEs were compared with experimental values, while reaction barrier heights were assessed using the CCSD(T)-level and experimental energies as reference. In general, although the tested parameters (energies and KIEs) do not exhibit any substantial difference upon a change of the solvent, the different behavior of the theoretical methods was observed depending on the solvent. With respect to isotope effects, both PCM and SMD seem to perform very similarly, though results obtained with PCM are slightly closer to the experimental values. For predicting reaction barriers, utilization of either PCM or SMD solvation models yielded different results. Functionals from the ωB97 family: ωB97, ωB97X, and ωB97X-D provide the most accurate results for the studied system.

Investigation of the CH3Cl + CN(-) reaction in water: Multilevel quantum mechanics/molecular mechanics study

The CH3Cl + CN(-) reaction in water was studied using a multilevel quantum mechanics/molecular mechanics (MM) method with the multilevels, electrostatic potential, density functional theory (DFT) and coupled-cluster single double triple (CCSD(T)), for the solute region. The detailed, back-side attack SN2 reaction mechanism was mapped along the reaction pathway. The potentials of mean force were calculated under both the DFT and CCSD(T) levels for the reaction region. The CCSD(T)/MM level of theory presents a free energy activation barrier height at 20.3 kcal/mol, which agrees very well with the experiment value at 21.6 kcal/mol. The results show that the aqueous solution has a dominant role in shaping the potential of mean force. The solvation effect and the polarization effect together increase the activation barrier height by ∼11.4 kcal/mol: the solvation effect plays a major role by providing about 75% of the contribution, while polarization effect only contributes 25% to the activation barrier height. Our calculated potential of mean force under the CCSD(T)/MM also has a good agreement with the one estimated using data from previous gas-phase studies.

Combined Electrostatically Embedded Multiconfiguration Molecular Mechanics and Molecular Mechanical Method: Application to Molecular Dynamics Simulation of a Chemical Reaction in Aqueous Solution with Hybrid Density Functional Theory

We here combine the electrostatically embedded multiconfiguration molecular mechanics (EE-MCMM) method for generating global potential energy surfaces in the presence of an electrostatic potential with molecular mechanics (MM). The resulting EE-MCMM/MM method is illustrated by applying it to carry out a molecular dynamics simulation for the symmetric bimolecular reaction Cl(-) + CH3Cl' → ClCH3 + Cl'(-) in aqueous solution with hybrid density functional theory as the quantum mechanical level. The potential of mean force is calculated, and the free energy barrier is found to be 25.3 kcal/mol, which is in good agreement with previous work. The advantage of the combined EE-MCMM and MM method is that the number of quantum mechanical calculations required for the active subsystem is very small compared to straight direct dynamics.

A multilayered-representation, quantum mechanical/molecular mechanics study of the CH3Cl + F− reaction in aqueous solution: the reaction mechanism, solvent effects and potential of mean force

A multi-layered representation, hybrid quantum mechanical and molecular mechanics method study of the CH₃Cl + F⁻ → CH₃F + Cl⁻ reaction in water.

Solvent effects and potential of mean force: a multilayered-representation quantum mechanical/molecular mechanics study of the CH3Br + CN− reaction in aqueous solution

The potential of mean force for the CH₃Br + CN⁻ reaction was obtained at the CCSD(T)/MM level of theory using a multilayered-representation quantum mechanical/molecular mechanics approach, as well as the reactant, transition state and product complexes along the reaction pathway in aqueous solution.

Should negative electron affinities be used for evaluating the chemical hardness?

Despite recent advances in computing negative electron affinities using density-functional theory, it is an open issue as to whether it is appropriate to use negative electron affinities, instead of zero electron affinity, to compute the chemical hardness of atoms and molecules with metastable anions. We seek to answer this question using the accepted empirical rules linking the chemical hardness to the atomic size and the polarizability; we also propose a new correlation with the C6 London dispersion coefficient. For chemical reactivity in the gas phase, it seems to make no difference whether negative, or zero, electron affinities are used for systems with metastable anions. For reactions in solution the evidence that is presently available is insufficient to establish a preference. In addressing this issue, we noted that electron affinity data from which atomic chemical hardness values are computed are out of date; an update to Pearson's classic 1988 table [Inorg. Chem., 1988, 27, 734-740] is thus provided.

Efficiency of bulky protic solvent for SN2 reaction

We calculate and compare the effects of aprotic vs protic solvent on the rate of SN2 reaction [F- + C3H7OMs--> C3H7F + OMs-]. We find that aprotic solvent acetonitrile is more efficient than a small protic solvent such as methanol. Bulky protic solvent (tert-butyl alcohol) is predicted to be quite efficient, giving the rate constant that is similar to that in CH3CN. Our calculated relative activation barriers of the SN2 reaction in methanol, tert-butyl alcohol, and CH3CN are in good agreement with experimental observations.

Facile SN2 Reaction in Protic Solvent: Quantum Chemical Analysis

We study the effects of protic solvent (water, methanol, ethanol, and tert-butyl alcohol) and cation (Na+, K+, Cs+) on the unsymmetrical SN2 reaction X- + RY --> RX + Y- (X = F, Br; R = CH3,C3H7;Y = Cl, OMs). We describe a series of calculations for the S(N)2 reaction mechanism under the influence of cation and protic solvent, presenting the structures of pre- and postreaction complexes and transition states and the magnitude of the activation barrier. An interesting mechanism is proposed, in which the protic solvent molecules that are shielded from the nucleophile by the intervening cation act as a Lewis base to reduce the unfavorable Coulombic influence of the cation on the nucleophile. We predict that the reaction barrier for the S(N)2 reaction is significantly lowered by the cooperative effects of cation and protic solvent. We show that the cation and protic solvent, each of which has been considered to retard the SN2 reactivity of the nucleophile, can accelerate the reaction tremendously when they interact with the fluoride ion in an intricate, combined fashion. This alternative S(N)2 mechanism is discussed in relation to the recently observed phenomenal efficiency of fluorination in tert-alcohol media [Kim, D. W.; et al. J. Am. Chem. Soc. 2006, 128, 16394].

Gas Phase SN2 Reactions of Halide Ions with Trifluoromethyl Halides: Front- and Back-Side Attack vs. Complex Formation

Density functional theory computations and pulsed-ionization high-pressure mass spectrometry experiments have been used to explore the potential energy surfaces for gas-phase S(N)2 reactions between halide ions and trifluoromethyl halides, X(-) + CF(3)Y --> Y(-) + CF(3)X. Structures of neutrals, ion-molecule complexes, and transition states show the possibility of two mechanisms: back- and front-side attack. From pulsed-ionization high-pressure mass spectrometry, enthalpy and entropy changes for the equilibrium clustering reactions for the formation of Cl(-)(BrCF(3)) (-16.5 +/- 0.2 kcal mol(-1) and -24.5 +/- 1 cal mol(-1) K(-1)), Cl(-)(ICF(3)) (-23.6 +/- 0.2 kcal mol(-1)), and Br(-)(BrCF(3)) (-13.9 +/- 0.2 kcal mol(-1) and -22.2 +/- 1 cal mol(-1) K(-1)) have been determined. These are in good to excellent agreement with computations at the B3LYP/6-311+G(3df)//B3LYP/6-311+G(d) level of theory. It is shown that complex formation takes place by a front-side attack complex, while the lowest energy S(N)2 reaction proceeds through a back-side attack transition state. This latter mechanism involves a potential energy profile which closely resembles a condensed phase S(N)2 reaction energy profile. It is also shown that the Cl(-) + CF(3)Br --> Br(-) + CF(3)Cl S(N)2 reaction can be interpreted using Marcus theory, in which case the reaction is described as being initiated by electron transfer. A potential energy surface at the B3LYP/6-311+G(d) level of theory confirms that the F(-) + CF(3)Br --> Br(-) + CF(4) S(N)2 reaction proceeds through a Walden inversion transition state.

Relative Gibbs Energies in Solution through Continuum Models: Effect of the Loss of Translational Degrees of Freedom in Bimolecular Reactions on Gibbs Energy Barriers

We present here a cell model for evaluating Gibbs energy barriers corresponding to bimolecular reactions (or processes of larger molecularity) in which a loss of translational degrees of freedom takes place along the reaction coordinate. With this model, we have studied the Walden inversion processes: Xa- + H3CXb --> XaCH3 + Xb- (X = F, Cl, Br, and I). In these processes, our model yields an increase of about 2.3-3.4 kcal/mol in Gibbs energy in solution corresponding to the loss of the translational degrees of freedom when passing from separate reactants to the TS in good agreement with experimental data. The corresponding value in the gas phase is about 6.7-7.1 kcal/mol. When the difference between these two figures is used to correct the results obtained by the standard UAHF implementation of the continuum model, the theoretical results are brought significantly closer to the experimental ones. This seems to indicate that for these reactions the parametrization used does not adequately introduce the increase in Gibbs energy corresponding to the constriction of the translational motion of the species along the reaction coordinate when passing from the gas phase to solution. Therefore, we believe that continuum models could perform much better if we released the parametrization process from the task of taking into account the constriction in translation motion in solution, which could be more adequately evaluated using the cell model proposed here, thus allowing it to focus on better reproducing all the remaining solvation effects.

The Importance of the External Potential on Group Electronegativity

The electronegativity of groups placed in a molecular environment is obtained using CCSD calculations of the electron affinity and ionization energy. A point charge model is used as an approximation of the molecular environment. The electronegativity values obtained in the presence of a point charge model are compared to the isolated group property to estimate the importance of the external potential on the group's electronegativity. The validity of the "group in molecule" electronegativities is verified by comparing EEM (electronegativity equalization method) charge transfer values to the explicitly calculated natural population analysis (NPA) ones, as well as by comparing the variation in electronegativity between the isolated functional group and the functional group in the presence of a modeled environment with the variation based on a perturbation expansion of the chemical potential.

A Coupled Reference Interaction Site Model/Molecular Dynamics Study of the Potential of Mean Force Curve of the SN2 Cl- + CH3Cl Reaction in Water

An application of the coupled reference interaction site model (RISM)/simulation methodology to the calculation of the potential of mean force (PMF) curve in aqueous solution for the identity nucleophilic substitution reaction Cl(-) + CH(3)Cl is performed. The free energy of activation is calculated to be 27.1 kcal/mol which compares very well with the experimentally determined barrier height of 26.6 kcal/mol. Furthermore, the calculated PMF is almost superimposed with that previously calculated using the computationally rigorous Monte Carlo with importance sampling method (Chandrasekhar, J.; Smith, S. F.; Jorgensen, W. L. J. Am. Chem. Soc. 1985, 107, 154). Using the calculated PMF, a crude estimate of the solvated kinetic transmission coefficient also compares well with that of previous more accurate simulations. These results indicate that the coupled RISM/simulation method provides a cost-effective methodology for studying reactions in solution.

A G2(+) level investigation of the gas-phase non-identity SN2 reactions of halides with halodimethylamine

The gas-phase non-identity S(N)2 reactions on nitrogen Y(-) + NMe(2)X --> NMe(2)Y + X(-) (Y, X = F, Cl, Br, and I) were evaluated at the G2(+) level. The reactions are exothermic only when the nucleophile is the lighter halide. The complexation enthalpies for complexes Y(-) em leader Me(2)NX are found to correlate with electronegativity of X. Both central and overall barriers can be interpreted with the aid of Marcus equation. Kinetic and thermodynamic investigations predict that the nucleophilicity of X(-) decreases in the order: F(-) > Cl(-) > Br(-) > I(-) and the leaving-group ability increases in the order: F < Cl < Br < I.

Chlorine kinetic isotope effects on the haloalkane dehalogenase reaction

We have found chlorine kinetic isotope effects on the dehalogenation catalyzed by haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 to be 1.0045 +/- 0.0004 for 1,2-dichloroethane and 1.0066 +/- 0.0004 for 1-chlorobutane. The latter isotope effect approaches the intrinsic chlorine kinetic isotope effect for the dehalogenation step. The intrinsic isotope effect has been modeled using semiempirical and DFT theory levels using the ONIOM QM/QM scheme. Our results indicate that the dehalogenation step is reversible; the overall irreversibility of the enzyme-catalyzed reaction is brought about by a step following the dehalogenation.