PyFrag 2019-Automating the exploration and analysis of reaction mechanisms

Computational Organic Chemistry: The Frontier for Understanding and Designing Bioorthogonal Cycloadditions

Computational organic chemistry has become a valuable tool in the field of bioorthogonal chemistry, offering insights and aiding in the progression of this branch of chemistry. In this review, I present an overview of computational work in this field, including an exploration of both the primary computational analysis methods used and their application in the main areas of bioorthogonal chemistry: (3 + 2) and [4 + 2] cycloadditions. In the context of (3 + 2) cycloadditions, detailed studies of electronic effects have informed the evolution of cycloalkyne/1,3-dipole cycloadditions. Through computational techniques, researchers have found ways to adjust the electronic structure via hyperconjugation to enhance reactions without compromising stability. For [4 + 2] cycloadditions, methods such as distortion/interaction analysis and energy decomposition analysis have been beneficial, leading to the development of bioorthogonal reactants with improved reactivity and the creation of orthogonal reaction pairs. To conclude, I touch upon the emerging fields of cheminformatics and machine learning, which promise to play a role in future reaction discovery and optimization.

Multiple hydrogen-bonded dimers: are only the frontier atoms relevant?

Non-frontier atom exchanges in hydrogen-bonded aromatic dimers can induce significant interaction energy changes (up to 6.5 kcal mol-1). Our quantum-chemical analyses reveal that the relative hydrogen-bond strengths of N-edited guanine-cytosine base pair isosteres, which cannot be explained from the frontier atoms, follow from the charge accumulation in the monomers.

Effect of electric fields on tungsten distribution in Na2WO4-WO3 molten salt

Tungsten coatings have unique properties such as high melting points and hardness and are widely used in the nuclear fusion and aviation fields. In experiments, compared to pure Na2WO4 molten salt, electrolysis with Na2WO4-WO3 molten salt results in a lower deposition voltage. Herein, an investigation combining experimental and computational approaches was conducted, involving molecular dynamics simulations with deep learning, high-temperature in situ Raman spectroscopy and activation strain model analysis. The results indicated that the molten salt system's behaviour, influenced by migration and polarization effects, led to increased formation of Na2W2O7 in the Na2WO4-WO3 molten salt, which has a lower decomposition voltage and subsequently accelerated the cathodic deposition of tungsten. We analyzed the mechanism of the effect of the electric field on the Na2W2O7 structure based on the bond strength and electron density. This research provides crucial theoretical support for the effect of electric field on tungsten in molten salt and demonstrates the feasibility of using machine learning-based DPMD methods in simulating tungsten-containing molten salt systems.

Stabilization of Diborynes versus Destabilization of Diborenes by Coordination of Lewis Bases: Unravelling the Dichotomy

We have quantum chemically investigated the boron-boron bonds in B2 , diborynes B2 L2 , and diborenes B2 H2 L2 (L=none, OH2 , NH3 ) using dispersion-corrected relativistic density functional theory at ZORA-BLYP-D3(BJ)/TZ2P. B2 has effectively a single B-B bond provided by two half π bonds, whereas B2 H2 has effectively a double B=B bond provided by two half π bonds and one σ 2p-2p bond. This different electronic structure causes B2 and B2 H2 to react differently to the addition of ligands. Thus, in B2 L2 , electron-donating ligands shorten and strengthen the boron-boron bond whereas, in B2 H2 L2 , they lengthen and weaken the boron-boron bond. The aforementioned variations in boron-boron bond length and strength become more pronounced as the Lewis basicity of the ligands L increases.

Nature and strength of group-14 A-A' bonds

We have quantum chemically investigated the nature and stability of C-C and Si-Si bonds in R3A-AR3 (A = C, Si; R3 = H3, Me3, Me2Ph, MePh2, Ph3, t-Bu3) using density functional theory (DFT). Systematic increase of steric bulk of the substituents R has opposite effects on C-C and Si-Si bonds: the former becomes weaker whereas the latter becomes stronger. Only upon going further, from R = Ph to the bulkiest R = t-Bu, the R3Si-SiR3 bond begins to weaken. Our bonding analyses show how different behavior upon increasing the steric bulk of the substituents stems from the interplay of (Pauli) repulsive and (dispersion) attractive steric mechanisms. Extension of our analyses to other model systems shows that C-Si bonds display behavior that is in between that of C-C and Si-Si bonds. Further increasing the size of the group-14 atoms from C-C and Si-Si to Ge-Ge, Sn-Sn and Pb-Pb leads to a further decrease in the sensitivity of the bond strength with respect to the substituents' bulkiness. Our findings can be used as design principles for tuning A-A and A-A' bond strengths.

Exploring borderline SN1-SN2 mechanisms: the role of explicit solvation protocols in the DFT investigation of isopropyl chloride

Nucleophilic substitution at saturated carbon is a crucial class of organic reactions, playing a pivotal role in various chemical transformations that yield valuable compounds for society. Despite the well-established SN1 and SN2 mechanisms, secondary substrates, particularly in solvolysis reactions, often exhibit a borderline pathway. A molecular-level understanding of these processes is fundamental for developing more efficient chemical transformations. Typically, quantum-chemical simulations of the solvent medium combine explicit and implicit solvation methods. The configuration of explicit molecules can be defined through top-down approaches, such as Monte Carlo (MC) calculations for generating initial configurations, and bottom-up methods that involve user-dependent protocols to add solvent molecules around the substrate. Herein, we investigated the borderline mechanism of the hydrolysis of a secondary substrate, isopropyl chloride (iPrCl), at DFT-M06-2X/aug-cc-pVDZ level, employing explicit and explicit + implicit protocols. Top-down and bottom-up approaches were employed to generate substrate-solvent complexes of varying number (n = 1, 3, 5, 7, 9, and 12) and configurations of H2O molecules. Our findings consistently reveal that regardless of the solvation approach, the hydrolysis of iPrCl follows a loose-SN2-like mechanism with nucleophilic solvent assistance. Increasing the water cluster around the substrate in most cases led to reaction barriers of ΔH‡ ≈ 21 kcal mol-1, with nine water molecules from MC configurations sufficient to describe the reaction. The More O'Ferrall-Jencks plot demonstrates an SN1-like character for all transition state structures, showing a clear merged profile. The fragmentation activation strain analyses indicate that energy barriers are predominantly controlled by solvent-substrate interactions, supported by the leaving group stabilization assessed through CHELPG atomic charges.

Blueshift in Trifurcated Hydrogen Bonds: A Tradeoff between Tetrel Bonding and Steric Repulsion

We have quantum chemically investigated the origin of the atypical blueshift of the H-C bond stretching frequency in the hydrogen-bonded complex X- •••H3 C-Y (X, Y=F, Cl, Br, I), as compared to the corresponding redshift occurring in Cl- •••H3 N and Cl- •••H3 C-H, using relativistic density functional theory (DFT) at ZORA-BLYP-D3(BJ)/QZ4P. Previously, this blueshift was attributed, among others, to the contraction of the H-C bonds as the H3 C moiety becomes less pyramidal. Herein, we provide quantitative evidence that, instead, the blueshift arises from a direct and strong X- •••C interaction of the HOMO of A- with the backside lobe on carbon of the low-lying C-Y antibonding σ* LUMO of the H3 C-Y fragment. This X- •••C bond, in essence a tetrel bond, pushes the H atoms towards a shorter H-C distance and makes the H3 C moiety more planar. The blueshift may, therefore, serve as a diagnostic for tetrel bonding.

SN 2 versus E2 Competition of Cyclic Ethers

We have quantum chemically studied the influence of ring strain on the competition between the two mechanistically different SN 2 and E2 pathways using a series of archetypal ethers as substrate in combination with a diverse set of Lewis bases (F- , Cl- , Br- , HO- , H3 CO- , HS- , H3 CS- ), using relativistic density functional theory at ZORA-OLYP/QZ4P. The ring strain in the substrate is systematically increased on going from a model acyclic ether to a 6- to 5- to 4- to 3-membered ether ring. We have found that the activation energy of the SN 2 pathway sharply decreases when the ring strain of the system is increased, thus on going from large to small cyclic ethers, the SN 2 reactivity increases. In contrast, the activation energy of the E2 pathway generally rises along this same series, that is, from large to small cyclic ethers. The opposing reactivity trends induce a mechanistic switch in the preferred reaction pathway for strong Lewis bases from E2, for large cyclic substrates, to SN 2, for small cyclic substrates. Weak Lewis bases are unable to overcome the higher intrinsic distortivity of the E2 pathway and, therefore, always favor the less distortive SN 2 reaction.

Exact decompositions of the total KS-DFT exchange-correlation energy into one- and two-center terms

In the so-called Interacting Quantum Atoms (IQA) approach, the molecular energy is numerically decomposed as a sum of atomic and diatomic contributions. While proper formulations have been put forward for both Hartree-Fock and post-Hartree-Fock wavefunctions, this is not the case for the Kohn-Sham density functional theory (KS-DFT). In this work, we critically analyze the performance of two fully additive approaches for the IQA decomposition of the KS-DFT energy, namely, the one from Francisco et al., which uses atomic scaling factors, and that from Salvador and Mayer based upon the bond order density (SM-IQA). Atomic and diatomic exchange-correlation (xc) energy components are obtained for a molecular test set comprising different bond types and multiplicities and along the reaction coordinate of a Diels-Alder reaction. Both methodologies behave similarly for all systems considered. In general, the SM-IQA diatomic xc components are less negative than the Hartree-Fock ones, which is in good agreement with the known effect of electron correlation upon (most) covalent bonds. In addition, a new general scheme to minimize the numerical error of the sum of two-electron energy contributions (i.e., Coulomb and exact exchange) in the framework of overlapping atoms is described in detail.

Substituent Effects in Bioorthogonal Diels-Alder Reactions of 1,2,4,5-Tetrazines

1,2,4,5-Tetrazines are increasingly used as reactants in bioorthogonal chemistry due to their high reactivity in Diels-Alder reactions with various dienophiles. Substituents in the 3- and 6-positions of the tetrazine scaffold are known to have a significant impact on the rate of cycloadditions; this is commonly explained on the basis of frontier molecular orbital theory. In contrast, we show that reactivity differences between commonly used classes of tetrazines are not controlled by frontier molecular orbital interactions. In particular, we demonstrate that mono-substituted tetrazines show high reactivity due to decreased Pauli repulsion, which leads to a more asynchronous approach associated with reduced distortion energy. This follows the recent Vermeeren-Hamlin-Bickelhaupt model of reactivity increase in asymmetric Diels-Alder reactions. In addition, we reveal that ethylene is not a good model compound for other alkenes in Diels-Alder reactions.

The Key Role of Chalcogenurane Intermediates in the Reduction Mechanism of Sulfoxides and Selenoxides by Thiols Explored In Silico

Sulfoxides and selenoxides oxidize thiols to disulfides while being reduced back to sulfides and selenides. While the reduction mechanism of sulfoxides to sulfides has been thoroughly explored experimentally as well as computationally, less attention has been devoted to the heavier selenoxides. In this work, we explore the reductive mechanism of dimethyl selenoxide, as an archetypal selenoxide and, for the sake of comparison, the reductive mechanism of dimethyl sulfoxide to gain insight into the role of the chalcogen on the reaction substrate. Particular attention is devoted to the key role of sulfurane and selenurane intermediates. Moreover, the capacity of these system to oxidize selenols rather than thiols, leading to the formation of selenyl sulfide bridges, is explored in silico. Notably, this analysis provides molecular insight into the role of selenocysteine in methionine sulfoxide reductase selenoenzyme. The activation strain model of chemical reactivity is employed in the studied reactions as an intuitive tool to bridge the computationally predicted effect of the chalcogen on the chalcogenoxide as well as on the chalcogenol.

Not antiaromaticity gain, but increased asynchronicity enhances the Diels-Alder reactivity of tropone

Tropone is an unreactive diene in normal electron demand Diels-Alder reactions, but it can be activated via carbonyl umpolung by using hydrazone ion analogs. Recently, the higher reactivity of hydrazone ion analogs was ascribed to a raised HOMO energy induced by antiaromaticity (L. J. Karas, A. T. Campbell, I. V. Alabugin and J. I. Wu, Org. Lett., 2020, 22, 7083). We show that this is incorrect, and that the activation barrier is lowered by increased asynchronicity.

Unravelling the Mechanism and Governing Factors in Lewis Acid and Non-Covalent Diels-Alder Catalysis: Different Perspectives

In the current literature, many non-covalent interaction (NCI) donors have been proposed that can potentially catalyze Diels-Alder (DA) reactions. In this study, a detailed analysis of the governing factors in Lewis acid and non-covalent catalysis of three types of DA reactions was carried out, for which we selected a set of hydrogen-, halogen-, chalcogen-, and pnictogen-bond donors. We found that the more stable the NCI donor-dienophile complex, the larger the reduction in DA activation energy. We also showed that for active catalysts, a significant part of the stabilization was caused by orbital interactions, though electrostatic interactions dominated. Traditionally, DA catalysis was attributed to improved orbital interactions between the diene and dienophile. Recently, Vermeeren and co-workers applied the activation strain model (ASM) of reactivity, combined with the Ziegler-Rauk-type energy decomposition analysis (EDA), to catalyzed DA reactions in which energy contributions for the uncatalyzed and catalyzed reaction were compared at a consistent geometry. They concluded that reduced Pauli repulsion energy, and not enhanced orbital interaction energy, was responsible for the catalysis. However, when the degree of asynchronicity of the reaction is altered to a large extent, as is the case for our studied hetero-DA reactions, the ASM should be employed with caution. We therefore proposed an alternative and complementary approach, in which EDA values for the catalyzed transition-state geometry, with the catalyst present or deleted, can be compared one to one, directly measuring the effect of the catalyst on the physical factors governing the DA catalysis. We discovered that enhanced orbital interactions are often the main driver for catalysis and that Pauli repulsion plays a varying role.

Palladium-catalyzed activation of HnA–AHn bonds (AHn = CH3, NH2, OH, F)

We have quantum chemically studied activation of HnA–AHn bonds (AHn = CH3, NH2, OH, F) by PdLn catalysts with Ln = no ligand, PH3, (PH3)2, using relativistic density functional theory at ZORA-BLYP/TZ2P. The activation energy associated with the oxidative addition step decreases from H3C–CH3 to H2N–NH2 to HO–OH to F–F, where the activation of the F–F bond is barrierless. Activation strain and Kohn–Sham molecular orbital analyses reveal that the enhanced reactivity along this series of substrates originates from a combination of (i) reduced activation strain due to a weaker HnA–AHn bond; (ii) decreased Pauli repulsion as a result of a difference in steric shielding of the HnA–AHn bond; and (iii) enhanced backbonding interaction between the occupied 4d atomic orbitals of the palladium catalyst and σ* acceptor orbital of the substrate.

How Bases Catalyze Diels-Alder Reactions

We have quantum chemically studied the base-catalyzed Diels-Alder (DA) reaction between 3-hydroxy-2-pyrone and N-methylmaleimide using dispersion-corrected density functional theory. The uncatalyzed reaction is slow and is preceded by the extrusion of CO₂ via a retro-DA reaction. Base catalysis, for example, by triethylamine, lowers the reaction barrier up to 10 kcal mol^-1 , causing the reaction to proceed smoothly at low temperature, which quenches the expulsion of CO₂ , yielding efficient access to polyoxygenated natural compounds. Our activation strain analyses reveal that the base accelerates the DA reaction via two distinct electronic mechanisms: i) by the HOMO-raising effect, which enhances the normal electron demand orbital interaction; and ii) by donating charge into 3-hydroxy-2-pyrone which accumulates in its reactive region and promotes strongly stabilizing secondary electrostatic interactions with N-methylmaleimide.

Rational Tuning of the Reactivity of Three-Membered Heterocycle Ring Openings via SN 2 Reactions

The development of small-molecule covalent inhibitors and probes continuously pushes the rapidly evolving field of chemical biology forward. A key element in these molecular tool compounds is the "electrophilic trap" that allows a covalent linkage with the target enzyme. The reactivity of this entity needs to be well balanced to effectively trap the desired enzyme, while not being attacked by off-target nucleophiles. Here we investigate the intrinsic reactivity of substrates containing a class of widely used electrophilic traps, the three-membered heterocycles with a nitrogen (aziridine), phosphorus (phosphirane), oxygen (epoxide) or sulfur atom (thiirane) as heteroatom. Using quantum chemical approaches, we studied the conformational flexibility and nucleophilic ring opening of a series of model substrates, in which these electrophilic traps are mounted on a cyclohexene scaffold (C₆ H₁₀ Y with Y=NH, PH, O, S). It was revealed that the activation energy of the ring opening does not necessarily follow the trend that is expected from C-Y leaving-group bond strength, but steeply decreases from Y=NH, to PH, to O, to S. We illustrate that the HOMO_Nu -LUMO_Substrate interaction is an all-important factor for the observed reactivity. In addition, we show that the activation energy of aziridines and phosphiranes can be tuned far below that of the corresponding epoxides and thiiranes by the addition of proper electron-withdrawing ring substituents. Our results provide mechanistic insights to rationally tune the reactivity of this class of popular electrophilic traps and can guide the experimental design of covalent inhibitors and probes for enzymatic activity.

A Quantum Chemical Deep-Dive into the π-π Interactions of 3-Methylindole and Its Halogenated Derivatives—Towards an Improved Ligand Design and Tryptophan Stacking

Non-covalent π-π stacking interactions often play a key role in the stability of the secondary and tertiary structures of peptides and proteins, respectively, and can be a means of ensuring the binding of ligands within protein and enzyme binding sites. It is generally accepted that minor structural changes to the aromatic ring, such as substitution, can have a large influence on these interactions. Nevertheless, a thorough understanding of underpinning phenomena guiding these key interactions is still limited. This is especially true for larger aromatic structures. To expand upon this knowledge, elaborate ab initio calculations were performed to investigate the effect of halogenation on the stability of 3-methylindole stacking. 3-Methylindole served as a representation of the tryptophan side chain, and is a frequently used motif in drug design and development. Moreover, an expression is derived that is able to accurately predict the interaction stability of stacked halogenated 3-methylindole dimers as well as halogenated toluene dimers, based on monomer level calculated DFT descriptors. We aim for this expression to provide the field with a straightforward and reliable method to assess the effect of halogenation on the π-π stacking interactions between aromatic scaffolds.

How Ionization Catalyzes Diels‐Alder Reactions

The catalytic effect of ionization on the Diels‐Alder reaction between 1,3‐butadiene and acrylaldehyde has been studied using relativistic density functional theory (DFT). Removal of an electron from the dienophile, acrylaldehyde, significantly accelerates the Diels‐Alder reaction and shifts the reaction mechanism from concerted asynchronous for the neutral Diels‐Alder reaction to stepwise for the radical‐cation Diels‐Alder reaction. Our detailed activation strain and Kohn‐Sham molecular orbital analyses reveal how ionization of the dienophile enhances the Diels‐Alder reactivity via two mechanisms: (i) by amplifying the asymmetry in the dienophile's occupied π‐orbitals to such an extent that the reaction goes from concerted asynchronous to stepwise and thus with substantially less steric (Pauli) repulsion per reaction step; (ii) by enhancing the stabilizing orbital interactions that result from the ability of the singly occupied molecular orbital of the radical‐cation dienophile to engage in an additional three‐electron bonding interaction with the highest occupied molecular orbital of the diene.

CalcUS: An Open-Source Quantum Chemistry Web Platform

Computational chemistry is an increasingly active field due to the improvement of computing resources and theoretical tools. However, its use remains usually limited to technically inclined users due to the technical challenges of preparing, launching, and analyzing calculations. In this context, we have developed CalcUS, an open-source platform to streamline quantum chemistry studies. Its objective is to democratize access to computational chemistry by providing a user-friendly web interface to simplify running and analyzing quantum mechanical calculations. It is freely available, expandable, and customizable. It promotes connectivity to multiple software packages and algorithms, thus providing state-of-the-art techniques to all practitioners. We propose CalcUS as a standalone tool and infrastructure to support other open-source packages.

C(spn)-X (n = 1-3) Bond Activation by Palladium

We have studied the palladium-mediated activation of C( sp n )-X bonds (n = 1-3 and X = H, CH 3 , Cl) in archetypal model substrates H 3 C-CH 2 -X, H 2 C=CH-X and HC≡C-X by catalysts PdL n  with L n  = no ligand, Cl - , and (PH 3 ) 2 , using relativistic density functional theory at ZORA-BLYP/TZ2P. The oxidative addition barrier decreases along this series, even though the strength of the bonds increases going from C( sp 3 )-X, to C( sp 2 )-X, to C( sp )-X. Activation strain and matching energy decomposition analyses reveal that the decreased oxidative addition barrier going from  sp 3  to  sp 2  to  sp , originates from a reduction in the destabilizing steric (Pauli) repulsion between catalyst and substrate. This is the direct consequence of the decreasing coordination number of the carbon atom in C( sp n )-X, which goes from four, to three, to two along this series. The associated net stabilization of the catalyst-substrate interaction dominates the trend in strain energy which indeed becomes more destabilizing along this same series as the bond becomes stronger from C( sp 3 )-X to C( sp )-X.

How Solvation Influences the SN2 versus E2 Competition

We have quantum chemically investigated how solvation influences the competition between the S_N2 and E2 pathways of the model F^– + C₂H₅Cl reaction. The system is solvated in a stepwise manner by going from the gas phase, then via microsolvation of one to three explicit solvent molecules, then last to bulk solvation using relativistic density functional theory at (COSMO)-ZORA-OLYP/QZ4P. We explain how and why the mechanistic pathway of the system shifts from E2 in the gas phase to S_N2 upon strong solvation of the Lewis base (i.e., nucleophile/protophile). The E2 pathway is preferred under weak solvation of the system by dichloromethane, whereas a switch in reactivity from E2 to S_N2 is observed under strong solvation by water. Our activation strain and Kohn–Sham molecular orbital analyses reveal that solvation of the Lewis base has a significant impact on the strength of the Lewis base. We show how strong solvation furnishes a weaker Lewis base that is unable to overcome the high characteristic distortivity associated with the E2 pathway, and thus the S_N2 pathway becomes viable.

The Chemical Bond: When Atom Size Instead of Electronegativity Difference Determines Trend in Bond Strength

We have quantum chemically analyzed element−element bonds of archetypal H_nX−YH_n molecules (X, Y=C, N, O, F, Si, P, S, Cl, Br, I), using density functional theory. One purpose is to obtain a set of consistent homolytic bond dissociation energies (BDE) for establishing accurate trends across the periodic table. The main objective is to elucidate the underlying physical factors behind these chemical bonding trends. On one hand, we confirm that, along a period (e. g., from C−C to C−F), bonds strengthen because the electronegativity difference across the bond increases. But, down a period, our findings constitute a paradigm shift. From C−F to C−I, for example, bonds do become weaker, however, not because of the decreasing electronegativity difference. Instead, we show that the effective atom size (via steric Pauli repulsion) is the causal factor behind bond weakening in this series, and behind the weakening in orbital interactions at the equilibrium distance. We discuss the actual bonding mechanism and the importance of analyzing this mechanism as a function of the bond distance.

σ-Electrons Responsible for Cooperativity and Ring Equalization in Hydrogen-Bonded Supramolecular Polymers

We have quantum chemically analyzed the cooperative effects and structural deformations of hydrogen-bonded urea, deltamide, and squaramide linear chains using dispersion-corrected density functional theory at BLYP-D3(BJ)/TZ2P level of theory. Our purpose is twofold: (i) reveal the bonding mechanism of the studied systems that lead to their self-assembly in linear chains; and (ii) rationalize the C-C bond equalization in the ring moieties of deltamide and squaramide upon polymerization. Our energy decomposition and Kohn-Sham molecular orbital analyses reveal cooperativity in all studied systems, stemming from the charge separation within the σ-electronic system by charge transfer from the carbonyl oxygen lone pair donor orbital of one monomer towards the σ* N-H antibonding acceptor orbital of the neighboring monomer. This key orbital interaction causes the C=O bonds to elongate, which, in turn, results in the contraction of the adjacent C-C single bonds that, ultimately, makes the ring moieties of deltamide and squaramide to become more regular. Notably, the π-electron delocalization plays a much smaller role in the total interaction between the monomers in the chain.

Dipolar repulsion in α-halocarbonyl compounds revisited

The concept of dipolar repulsion has been widely used to explain several phenomena in organic chemistry, including the conformational preferences of carbonyl compounds. This model, in which atoms and bonds are viewed as point charges and dipole moment vectors, respectively, is however oversimplified. To provide a causal model rooted in quantitative molecular orbital theory, we have analyzed the rotational isomerism of haloacetaldehydes OHC–CH₂X (X = F, Cl, Br, I), using relativistic density functional theory. We have found that the overall trend in the rotational energy profiles is set by the combined effects of Pauli repulsion (introducing a barrier around gauche that separates minima at syn and anti), orbital interactions (which can pull the anti minimum towards anticlinal to maximize hyperconjugation), and electrostatic interactions. Only for X = F, not for X = Cl–I, electrostatic interactions push the preference from syn to anti. Our bonding analyses show how this trend is related to the compact nature of F versus the more diffuse nature of the heavier halogens.

Beyond point charges! The point charge concept within dipolar repulsion model is valid for compact atoms like fluorine. This model breaks down for larger halogens, for which the electrostatic attraction between nuclei and charge densities dominates.

Origin of asynchronicity in Diels-Alder reactions

Asynchronicity in Diels-Alder reactions plays a crucial role in determining the height of the reaction barrier. Currently, the origin of asynchronicity is ascribed to the stronger orbital interaction between the diene and the terminal carbon of an asymmetric dienophile, which shortens the corresponding newly formed C-C bond and hence induces asynchronicity in the reaction. Here, we show, using the activation strain model and Kohn-Sham molecular orbital theory at ZORA-BP86/TZ2P, that this rationale behind asynchronicity is incorrect. We, in fact, found that following a more asynchronous reaction mode costs favorable HOMO-LUMO orbital overlap and, therefore, weakens (not strengthens) these orbital interactions. Instead, it is the Pauli repulsion that induces asynchronicity in Diels-Alder reactions. An asynchronous reaction pathway also lowers repulsive occupied-occupied orbital overlap which, therefore, reduces the unfavorable Pauli repulsion. As soon as this mechanism of reducing Pauli repulsion dominates, the reaction begins to deviate from synchronicity and adopts an asynchronous mode. The eventual degree of asynchronicity, as observed in the transition state of a Diels-Alder reaction, is ultimately achieved when the gain in stability, as a response to the reduced Pauli repulsion, balances with the loss of favorable orbital interactions.

Origin of Increased Reactivity in Rhenium-Mediated Cycloadditions of Tetrazines

Pyridyl tetrazines coordinated to metals like rhenium have been shown to be more reactive in [4 + 2] cycloadditions than their uncomplexed counterparts. Using density functional theory calculations, we found a more favorable interaction energy caused by stronger orbital interactions as the origin of this increased reactivity. Additionally, the high regioselectivity is due to a greater degree of charge stabilization in the transition state, leading to the major product.

Lewis Acid-Catalyzed Diels-Alder Reactions: Reactivity Trends across the Periodic Table

The catalytic effect of various weakly interacting Lewis acids (LAs) across the periodic table, based on hydrogen (Group 1), pnictogen (Group 15), chalcogen (Group 16), and halogen (Group 17) bonds, on the Diels-Alder cycloaddition reaction between 1,3-butadiene and methyl acrylate was studied quantum chemically by using relativistic density functional theory. Weakly interacting LAs accelerate the Diels-Alder reaction by lowering the reaction barrier up to 3 kcal mol-1 compared to the uncatalyzed reaction. The reaction barriers systematically increase from halogen Collapse

Key Words

• Diels-Alder reaction
• Lewis acids
• activation strain model
• density functional calculations
• reactivity

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MESH Headings Collapse

Grants

• Netherlands Organization for Scientific Research (NWO)
• Dutch Astrochemistry Network (DAN)
• PID2019-106184GB-I00 Spanish MICIIN
• RED2018-102387-T Spanish MICIIN
• Nederlandse Organisatie voor Wetenschappelijk Onderzoek
• Dutch Astrochemistry Network
• Nederlandse Organisatie voor Wetenschappelijk Onderzoek

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Affiliation(s)

Pascal Vermeeren Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdam (TheNetherlands
Marco Dalla Tiezza Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdam (TheNetherlands
Michelle van Dongen Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdam (TheNetherlands
Israel Fernández Departamento de Química Orgánica I and Centro de Innovación en Química Avanzada (ORFEO-CINQA)Facultad de Ciencias QuímicasUniversidad Complutense de Madrid28040MadridSpain
F. Matthias Bickelhaupt Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdam (TheNetherlands Institute for Molecules and MaterialsRadboud UniversityHeyendaalseweg 1356525 AJNijmegen (TheNetherlands
Trevor A. Hamlin Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdam (TheNetherlands

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Boron Tunneling in the "Weak" Bond-Stretch Isomerization of N-B Lewis Adducts

Some nitrile-boron halide adducts exhibit a double-well potential energy surface with two distinct minima: a "long bond" geometry (LB, a van der Waals interaction mostly based on electrostatics, but including a residual charge transfer component) and a "short bond" structure (SB, a covalent dative bond). This behavior can be considered as a "weak" form of bond stretch isomerism. Our computations reveal that complexes RCN-BX₃ (R=CH₃ , FCH₂ , BrCH₂ , and X=Cl, Br) exhibit a fast interconversion from LB to SB geometries even close to the absolute zero thanks to a boron atom tunneling mechanism. The computed half-lives of the meta-stable LB compounds vary between minutes to nanoseconds at cryogenic conditions. Accordingly, we predict that the long bond structures are practically impossible to isolate or characterize, which agrees with previous matrix-isolation experiments.

The pnictogen bond: a quantitative molecular orbital picture

We have analyzed the structure and stability of archetypal pnictogen-bonded model complexes D3PnA- (Pn = N, P, As, Sb; D, A = F, Cl, Br) using state-of-the-art relativistic density functional calculations at the ZORA-M06/QZ4P level. We have accomplished two tasks: (i) to compute accurate trends in pnictogen-bond strength based on a set of consistent data; and (ii) to rationalize these trends in terms of detailed analyses of the bonding mechanism based on quantitative Kohn-Sham molecular orbital (KS-MO) theory in combination with a canonical energy decomposition analysis (EDA) and Voronoi deformation density (VDD) analyses of the charge distribution. We have found that pnictogen bonds have a significant covalent character stemming from strong HOMO-LUMO interactions between the lone pair of A- and σ* of D3Pn. As such, the underlying mechanism of the pnictogen bond is similar to that of hydrogen, halogen, and chalcogen bonds.

Chemical reactivity from an activation strain perspective

Chemical reactions are ubiquitous in the universe, they are at the core of life, and they are essential for industrial processes. The drive for a deep understanding of how something occurs, in this case, the mechanism of a chemical reaction and the factors controlling its reactivity, is intrinsically valuable and an innate quality of humans. The level of insight and degree of understanding afforded by computational chemistry cannot be understated. The activation strain model is one of the most powerful tools in our arsenal to obtain unparalleled insight into reactivity. The relative energy of interacting reactants is evaluated along a reaction energy profile and related to the rigidity of the reactants' molecular structure and the strength of the stabilizing interactions between the deformed reactants: ΔE(ζ) = ΔEstrain(ζ) + ΔEint(ζ). Owing to the connectedness between the activation strain model and Kohn-Sham molecular orbital theory, one is able to obtain a causal relationship between both the sterics and electronics of the reactants and their mutual reactivity. Only when this is accomplished one can eclipse the phenomenological explanations that are commonplace in the literature and textbooks and begin to rationally tune and optimize chemical transformations. We showcase how the activation strain model is the ideal tool to elucidate fundamental organic reactions, the activation of small molecules by metallylenes, and the cycloaddition reactivity of cyclic diene- and dipolarophiles.

On the Role of Hydrogen Bonding in Gas-Phase SN2 Reactions at Silicon

The shape of the potential energy surface (PES) of gas-phase S_N2 reactions at silicon is determined by the type of nucleophile, the leaving group, and substituents which remain bonded to silicon. In this study, we present PES scans along the reaction coordinate of six symmetrical S_N2 reactions: X^- + SiR₃X → XSiR₃ + X^-, where X = Cl or F and R = H, Me, or OMe. While the fluorine systems and the ClSiH₃Cl system only give single-well PESs, ClSiMe₃Cl and ClSi(OMe)₃Cl give triple- and double-well PESs with stable pre- and post-reaction complexes. A complementary bonding analysis (energy decomposition analysis, quantum theory of atoms in molecules, and natural bond orbitals) reveals that the leaving group (X^-) is stabilized by hydrogen bonding in the XSiMe₃X and XSi(OMe)₃X systems. It is shown that this so far neglected stabilizing contribution, along with σ-hole bonding, is responsible for the shapes of the PESs of ClSiMe₃Cl and ClSi(OMe)₃Cl in the gas phase.

The Gauche Effect in XCH2 CH2 X Revisited

We have quantum chemically investigated the rotational isomerism of 1,2-dihaloethanes XCH2 CH2 X (X = F, Cl, Br, I) at ZORA-BP86-D3(BJ)/QZ4P. Our Kohn-Sham molecular orbital (KS-MO) analyses reveal that hyperconjugative orbital interactions favor the gauche conformation in all cases (X = F-I), not only for X = F as in the current model of this so-called gauche effect. We show that, instead, it is the interplay of hyperconjugation with Pauli repulsion between lone-pair-type orbitals on the halogen substituents that constitutes the causal mechanism for the gauche effect. Thus, only in the case of the relatively small fluorine atoms, steric Pauli repulsion is too weak to overrule the gauche preference of the hyperconjugative orbital interactions. For the larger halogens, X⋅⋅⋅X steric Pauli repulsion becomes sufficiently destabilizing to shift the energetic preference from gauche to anti, despite the opposite preference of hyperconjugation.

A Quantitative Molecular Orbital Perspective of the Chalcogen Bond

We have quantum chemically analyzed the structure and stability of archetypal chalcogen-bonded model complexes D2 Ch⋅⋅⋅A- (Ch = O, S, Se, Te; D, A = F, Cl, Br) using relativistic density functional theory at ZORA-M06/QZ4P. Our purpose is twofold: (i) to compute accurate trends in chalcogen-bond strength based on a set of consistent data; and (ii) to rationalize these trends in terms of detailed analyses of the bonding mechanism based on quantitative Kohn-Sham molecular orbital (KS-MO) theory in combination with a canonical energy decomposition analysis (EDA). At odds with the commonly accepted view of chalcogen bonding as a predominantly electrostatic phenomenon, we find that chalcogen bonds, just as hydrogen and halogen bonds, have a significant covalent character stemming from strong HOMO-LUMO interactions. Besides providing significantly to the bond strength, these orbital interactions are also manifested by the structural distortions they induce as well as the associated charge transfer from A- to D2 Ch.

How Oriented External Electric Fields Modulate Reactivity

A judiciously oriented external electric field (OEEF) can catalyze a wide range of reactions and can even induce endo/exo stereoselectivity of cycloaddition reactions. The Diels-Alder reaction between cyclopentadiene and maleic anhydride is studied by using quantitative activation strain and Kohn-Sham molecular orbital theory to pinpoint the origin of these catalytic and stereoselective effects. Our quantitative model reveals that an OEEF along the reaction axis induces an enhanced electrostatic and orbital interaction between the reactants, which in turn lowers the reaction barrier. The stronger electrostatic interaction originates from an increased electron density difference between the reactants at the reactive center, and the enhanced orbital interaction arises from the promoted normal electron demand donor-acceptor interaction driven by the OEEF. An OEEF perpendicular to the plane of the reaction axis solely stabilizes the exo pathway of this reaction, whereas the endo pathway remains unaltered and efficiently steers the endo/exo stereoselectivity. The influence of the OEEF on the inverse electron demand Diels-Alder reaction is also investigated; unexpectedly, it inhibits the reaction, as the electric field now suppresses the critical inverse electron demand donor-acceptor interaction.

Computational Exploration of Ambiphilic Reactivity of Azides and Sustmann's Paradigmatic Parabola

We examine the theoretical underpinnings of the seminal discoveries by Reiner Sustmann about the ambiphilic nature of Huisgen’s phenyl azide cycloadditions. Density functional calculations with ωB97X-D and B2PLYP-D3 reproduce the experimental data and provide insights into ambiphilic control of reactivity. Distortion/interaction-activation strain and energy decomposition analyses show why Sustmann’s use of dipolarophile ionization potential is such a powerful predictor of reactivity. We add to Sustmann’s data set several modern distortion-accelerated dipolarophiles used in bioorthogonal chemistry to show how these fit into the orbital energy criteria that are often used to understand cycloaddition reactivity. We show why such a simple indicator of reactivity is a powerful predictor of reaction rates that are actually controlled by a combination of distortion energies, charge transfer, closed-shell repulsion, polarization, and electrostatic effects.

Bifunctional Hydrogen Bond Donor-Catalyzed Diels-Alder Reactions: Origin of Stereoselectivity and Rate Enhancement

The selectivity and rate enhancement of bifunctional hydrogen bond donor-catalyzed Diels-Alder reactions between cyclopentadiene and acrolein were quantum chemically studied using density functional theory in combination with coupled-cluster theory. (Thio)ureas render the studied Diels-Alder cycloaddition reactions exo selective and induce a significant acceleration of this process by lowering the reaction barrier by up to 7 kcal mol-1 . Our activation strain and Kohn-Sham molecular orbital analyses uncover that these organocatalysts enhance the Diels-Alder reactivity by reducing the Pauli repulsion between the closed-shell filled π-orbitals of the diene and dienophile, by polarizing the π-orbitals away from the reactive center and not by making the orbital interactions between the reactants stronger. In addition, we establish that the unprecedented exo selectivity of the hydrogen bond donor-catalyzed Diels-Alder reactions is directly related to the larger degree of asynchronicity along this reaction pathway, which is manifested in a relief of destabilizing activation strain and Pauli repulsion.

How Lewis Acids Catalyze Ring-Openings of Cyclohexene Oxide

We have quantum chemically studied the Lewis acid-catalyzed epoxide ring-opening reaction of cyclohexene epoxide by MeZH (Z = O, S, and NH) using relativistic dispersion-corrected density functional theory. We found that the reaction barrier of the Lewis acid-catalyzed epoxide ring-opening reactions decreases upon ascending in group 1 along the series Cs+ > Rb+ > K+ > Na+ > Li+ > H+. Our activation strain and Kohn-Sham molecular orbital analyses reveal that the enhanced reactivity of the Lewis acid-catalyzed ring-opening reaction is caused by the reduced steric (Pauli) repulsion between the filled orbitals of the epoxide and the nucleophile, as the Lewis acid polarizes the filled orbitals of the epoxide more efficiently away from the incoming nucleophile. Furthermore, we established that the regioselectivity of these ring-opening reactions is, aside from the "classical" strain control, also dictated by a hitherto unknown mechanism, namely, the steric (Pauli) repulsion between the nucleophile and the substrate, which could be traced back to the asymmetric orbital density on the epoxide. In all, this work again demonstrates that the concept of Pauli-lowering catalysis is a general phenomenon.

How the Lewis Base F- Catalyzes the 1,3-Dipolar Cycloaddition between Carbon Dioxide and Nitrilimines

The mechanism of the Lewis base F^– catalyzed 1,3-dipolar cycloaddition between CO₂ and nitrilimines is interrogated using DFT calculations. F^– activates the nitrilimine, not CO₂ as proposed in the literature, and imparts a significant rate enhancement for the cycloaddition. The origin of this catalysis is in the strength of the primary orbital interactions between the reactants. The Lewis base activated nitrilimine–F^– has high-lying filled FMOs. The smaller FMO-LUMO gap promotes a rapid nucleophilic attack and overall cycloaddition with CO₂.

Nature and Strength of Lewis Acid/Base Interaction in Boron and Nitrogen Trihalides

We have quantum chemically investigated the bonding between archetypical Lewis acids and bases. Our state-of-the-art computations on the X3 B-NY3 Lewis pairs have revealed the origin behind the systematic increase in B-N bond strength as X and Y are varied from F to Cl, Br, I, H. For H3 B-NY3 , the bonding trend is driven by the commonly accepted mechanism of donor-acceptor [HOMO(base)-LUMO(acid)] interaction. Interestingly, for X3 B-NH3 , the bonding mechanism is determined by the energy required to deform the BX3 to the pyramidal geometry it adopts in the adduct. Thus, Lewis acids that can more easily pyramidalize form stronger bonds with Lewis bases. The decrease in the strain energy of pyramidalization on going from BF3 to BI3 is directly caused by the weakening of the B-X bond strength, which stems primarily from the bonding in the plane of the molecule (σ-like) and not in the π system, at variance with the currently accepted mechanism.

SN2 versus E2 Competition of F- and PH2- Revisited

We have quantum chemically analyzed the competition between the bimolecular nucleophilic substitution (S_N2) and base-induced elimination (E2) pathways for F^- + CH₃CH₂Cl and PH₂^- + CH₃CH₂Cl using the activation strain model and Kohn-Sham molecular orbital theory at ZORA-OLYP/QZ4P. Herein, we correct an earlier study that intuitively attributed the mechanistic preferences of F^- and PH₂^-, i.e., E2 and S_N2, respectively, to a supposedly unfavorable shift in the polarity of the abstracted β-proton along the PH₂^--induced E2 pathway while claiming that ″...no correlation between the thermodynamic basicity and E2 rate should be expected.″ Our analyses, however, unequivocally show that it is simply the 6 kcal mol^-1 higher proton affinity of F^- that enables this base to engage in a more stabilizing orbital interaction with CH₃CH₂Cl and hence to preferentially react via the E2 pathway, despite the higher characteristic distortivity (more destabilizing activation strain) associated with this pathway. On the other hand, the less basic PH₂^- has a weaker stabilizing interaction with CH₃CH₂Cl and is, therefore, unable to overcome the characteristic distortivity of the E2 pathway. Therefore, the mechanistic preference of PH₂^- is steered to the S_N2 reaction channel (less-destabilizing activation strain).

Understanding the 1,3-Dipolar Cycloadditions of Allenes

We have quantum chemically studied the reactivity, site-, and regioselectivity of the 1,3-dipolar cycloaddition between methyl azide and various allenes, including the archetypal allene propadiene, heteroallenes, and cyclic allenes, by using density functional theory (DFT). The 1,3-dipolar cycloaddition reactivity of linear (hetero)allenes decreases as the number of heteroatoms in the allene increases, and formation of the 1,5-adduct is, in all cases, favored over the 1,4-adduct. Both effects find their origin in the strength of the primary orbital interactions. The cycloaddition reactivity of cyclic allenes was also investigated, and the increased predistortion of allenes, that results upon cyclization, leads to systematically lower activation barriers not due to the expected variations in the strain energy, but instead from the differences in the interaction energy. The geometric predistortion of cyclic allenes enhances the reactivity compared to linear allenes through a unique mechanism that involves a smaller HOMO-LUMO gap, which manifests as more stabilizing orbital interactions.

Diastereoselective Synthesis of β-Lactams by Ligand-Controlled Stereodivergent Intramolecular Tsuji-Trost Allylation

The diastereoselective synthesis of highly substituted β-lactams by intramolecular Tsuji–Trost allylation is reported. Judicious selection of the ligand on palladium allows selective access to either the trans isomer (in generally good to excellent yield with very high diastereomeric excess) or cis isomer (with yields and diastereoselectivity ranging from modest to excellent depending on the substrate). The reaction proceeds under exceedingly mild conditions (rt, no additives) with a broad range of substrates, which are readily accessible by the Ugi reaction.

How Alkali Cations Catalyze Aromatic Diels-Alder Reactions

We have quantum chemically studied alkali cation-catalyzed aromatic Diels-Alder reactions between benzene and acetylene forming barrelene using relativistic, dispersion-corrected density functional theory. The alkali cation-catalyzed aromatic Diels-Alder reactions are accelerated by up to 5 orders of magnitude relative to the uncatalyzed reaction and the reaction barrier increases along the series Li+ < Na+ < K+ < Rb+ < Cs+ < none. Our detailed activation strain and molecular-orbital bonding analyses reveal that the alkali cations lower the aromatic Diels-Alder reaction barrier by reducing the Pauli repulsion between the closed-shell filled orbitals of the dienophile and the aromatic diene. We argue that such Pauli mechanism behind Lewis-acid catalysis is a more general phenomenon. Also, our results may be of direct importance for a more complete understanding of the network of competing mechanisms towards the formation of polycyclic aromatic hydrocarbons (PAHs) in an astrochemical context.

Ligand-Mediated Regioselective Rhodium-Catalyzed Benzotriazole-Allene Coupling: Mechanistic Exploration and Quantum Chemical Analysis

The ligand‐controlled rhodium‐catalyzed regioselective coupling of 1,2,3‐benzotriazoles and allenes was investigated by DFT calculations. Because allylation can occur at either the N1 or N2 position of the 1,2,3‐benzotriazole, the complete Gibbs free energy profiles for both pathways were computed. A kinetic preference emerged for the experimentally observed N1 allylation with the JoSPOphos ligand, whereas N2 allylation was favored with DPEphos. Analysis of the regiodetermining oxidative addition step by using the activation strain model in conjunction with a matching energy decomposition analysis has revealed that the unprecedented N2 reaction regioselectivity is dictated by the strength of the electrostatic interactions between the 1,2,3‐benzotriazole and the rhodium catalyst. The nature of the electrostatic interaction was rationalized by analysis of the electrostatic potential maps and Hirshfeld charges: a stabilizing electrostatic interaction was found between the key atoms involved in the oxidative addition for the N2 pathway, analogous interactions are weaker in the N1 case.

Halogen Bonds in Ligand-Protein Systems: Molecular Orbital Theory for Drug Design

Halogen bonds are highly important in medicinal chemistry as halogenation of drugs, generally, improves both selectivity and efficacy toward protein active sites. However, accurate modeling of halogen bond interactions remains a challenge, since a thorough theoretical investigation of the bonding mechanism, focusing on the realistic complexity of drug–receptor systems, is lacking. Our systematic quantum-chemical study on ligand/peptide-like systems reveals that halogen bonding is driven by the same bonding interactions as hydrogen bonding. Besides the electrostatic and the dispersion interactions, our bonding analyses, based on quantitative Kohn–Sham molecular orbital theory together with energy decomposition analysis, reveal that donor–acceptor interactions and steric repulsion between the occupied orbitals of the halogenated ligand and the protein need to be considered more carefully within the drug design process.

Understanding chemical reactivity using the activation strain model

Understanding chemical reactivity through the use of state-of-the-art computational techniques enables chemists to both predict reactivity and rationally design novel reactions. This protocol aims to provide chemists with the tools to implement a powerful and robust method for analyzing and understanding any chemical reaction using PyFrag 2019. The approach is based on the so-called activation strain model (ASM) of reactivity, which relates the relative energy of a molecular system to the sum of the energies required to distort the reactants into the geometries required to react plus the strength of their mutual interactions. Other available methods analyze only a stationary point on the potential energy surface, but our methodology analyzes the change in energy along a reaction coordinate. The use of this methodology has been proven to be critical to the understanding of reactions, spanning the realms of the inorganic and organic, as well as the supramolecular and biochemical, fields. This protocol provides step-by-step instructions-starting from the optimization of the stationary points and extending through calculation of the potential energy surface and analysis of the trend-decisive energy terms-that can serve as a guide for carrying out the analysis of any given reaction of interest within hours to days, depending on the size of the molecular system.

PyFrag 2019-Automating the exploration and analysis of reaction mechanisms

We present a substantial update to the PyFrag 2008 program, which was originally designed to perform a fragment-based activation strain analysis along a provided potential energy surface. The original PyFrag 2008 workflow facilitated the characterization of reaction mechanisms in terms of the intrinsic properties, such as strain and interaction, of the reactants. The new PyFrag 2019 program has automated and reduced the time-consuming and laborious task of setting up, running, analyzing, and visualizing computational data from reaction mechanism studies to a single job. PyFrag 2019 resolves three main challenges associated with the automated computational exploration of reaction mechanisms: it (1) computes the reaction path by carrying out multiple parallel calculations using initial coordinates provided by the user; (2) monitors the entire workflow process; and (3) tabulates and visualizes the final data in a clear way. The activation strain and canonical energy decomposition results that are generated relate the characteristics of the reaction profile in terms of intrinsic properties (strain, interaction, orbital overlaps, orbital energies, populations) of the reactant species. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.