C-X Bond Activation by Palladium: Steric Shielding versus Steric Attraction.

The C-X bond activation (X = H, C) of a series of substituted C(n°)-H and C(n°)-C(m°) bonds with C(n°) and C(m°) = H3 C- (methyl, 0°), CH3 H2 C- (primary, 1°), (CH3 )2 HC- (secondary, 2°), (CH3 )3 C- (tertiary, 3°) by palladium were investigated using relativistic dispersion-corrected density functional theory at ZORA-BLYP-D3(BJ)/TZ2P. The effect of the stepwise introduction of substituents was pinpointed at the C-X bond on the bond activation process. The C(n°)-X bonds become substantially weaker going from C(0°)-X, to C(1°)-X, to C(2°)-X, to C(3°)-X because of the increasing steric repulsion between the C(n°)- and X-group. Interestingly, this often does not lead to a lower barrier for the C(n°)-X bond activation. The C-H activation barrier, for example, decreases from C(0°)-X, to C(1°)-X, to C(2°)-X and then increases again for the very crowded C(3°)-X bond. For the more congested C-C bond, in contrast, the activation barrier always increases as the degree of substitution is increased. Our activation strain and matching energy decomposition analyses reveal that these differences in C-H and C-C bond activation can be traced back to the opposing interplay between steric repulsion across the C-X bond versus that between the catalyst and substrate.

Cooperative Self-Assembly in Linear Chains Based on Halogen Bonds.

Cooperative properties of halogen bonds were investigated with computational experiments based on dispersion-corrected relativistic density functional theory. The bonding mechanism in linear chains of cyanogen halide (X-CN), halocyanoacetylene (X-CC-CN), and 4-halobenzonitrile (X-C6 H4 -CN) were examined for X = H, Cl, Br, and I. Our energy decomposition and Kohn-Sham molecular-orbital analyses revealed the bonding mechanism of the studied systems. Cyanogen halide and halocyanoacetylene chains possess an extra stabilizing effect with increasing chain size, whereas the 4-halobenzonitrile chains do not. This cooperativity can be traced back to charge separation within the σ-electronic system by charge-transfer between the lone-pair orbital of the nitrogen (σHOMO ) on one unit and the acceptor orbital of the C-X (σ*LUMO ) on the adjacent unit. As such, the HOMO-LUMO gap in the σ-system decreases, and the cooperativity increases with chain length revealing the similarity in the bonding mechanisms of hydrogen and halogen bonds.

Nucleophilic Substitution in Solution: Activation Strain Analysis of Weak and Strong Solvent Effects.

We have quantum chemically studied the effect of various polar and apolar solvents on the shape of the potential energy surface (PES) of a diverse collection of archetypal nucleophilic substitution reactions at carbon, silicon, phosphorus, and arsenic by using density functional theory at the OLYP/TZ2P level. In the gas phase, all our model SN 2 reactions have single-well PESs, except for the nucleophilic substitution reaction at carbon (SN 2@C), which has a double-well energy profile. The presence of the solvent can have a significant effect on the shape of the PES and, thus, on the nature of the SN 2 process. Solvation energies, charges on the nucleophile or leaving group, and structural features are compared for the various SN 2 reactions in a spectrum of solvents. We demonstrate how solvation can change the shape of the PES, depending not only on the polarity of the solvent, but also on how the charge is distributed over the interacting molecular moieties during different stages of the reaction. In the case of a nucleophilic substitution at three-coordinate phosphorus, the reaction can be made to proceed through a single-well [no transition state (TS)], bimodal barrier (two TSs), and then through a unimodal transition state (one TS) simply by increasing the polarity of the solvent.

Mechanistic Insight into the Oxidation of Organic Phenylselenides by H2 O2.

The oxidation of organic phenylselenides by H2 O2 is investigated in model compounds, namely, n-butyl phenyl selenide (PhSe(nBu)), bis(phenylselanyl)methane (PhSeMeSePh), diphenyl diselenide (PhSeSePh), and 1,2-bis(phenylselanyl)ethane (PhSeEtSePh). Through a combined experimental (1 H and 77 Se NMR) and computational approach, we characterize the direct oxidation of monoselenide to selenoxide, the stepwise double oxidation of PhSeMeSePh that leads to different diastereomeric diselenoxides, the complete oxidation of the diphenyldiselenide that leads to selenium-selenium bond cleavage, and the subsequent formation of the phenylseleninic product. The oxidation of PhSeEtSePh also results in the formation of phenylseleninic acid along with 1-(vinylseleninyl)benzene, which is derived from a side elimination reaction. The evidence of a direct mechanism, in addition to an autocatalytic mechanism that emerges from kinetic studies, is discussed. By considering our observations of diselenides with chalcogen atoms that are separated by alkyl spacers of different length, a rationale for the advantage of diselenide versus monoselenide catalysts is presented.

Enhanced π-Back-Donation as a Way to Higher Coordination Numbers in d10 [M(NHC)n ] Complexes: A DFT Study.

We aim to understand the electronic factors determining the stability and coordination number of d10 transition-metal complexes bearing N-heterocyclic carbene (NHC) ligands, with a particular emphasis on higher coordinated species. In this DFT study on the formation and bonding of Group 9-12 d10 [M(NHC)n ] (n=1-4) complexes, we found that all metals form very stable [M(NHC)2 ] complexes, but further coordination depends on the specific interplay of 1) the interaction energy (ΔEint ) between the [M(NHC)n-1 ] (n=2-4) fragment and the incoming NHC ligand, and 2) the strain energy (ΔEstrain ) associated with bending of the linear NHC-M-NHC arrangement. The key observation is that ΔEstrain , which is an antagonist for higher coordination numbers, can significantly be lowered by M→NHC π*-back-donation. This leads to favorable thermodynamics for n=3-4 for highly electrophilic metals in our study, and thus presents a general design motif to achieve coordination numbers beyond two. The scope of our findings extends beyond the NHC model systems and has wider implications for the synthesis of d10 [MLn ] complexes and their catalytic activity.

General AMBER Force Field Parameters for Diphenyl Diselenides and Diphenyl Ditellurides.

The General AMBER Force Field (GAFF) has been extended to describe a series of selenium and tellurium diphenyl dichalcogenides. These compounds, besides being eco-friendly catalysts for numerous oxidations in organic chemistry, display peroxidase activity, i.e., can reduce hydrogen peroxide and harmful organic hydroperoxides to water/alcohols and as such are very promising antioxidant drugs. The novel GAFF parameters are tested in MD simulations in different solvents and the (77)Se NMR chemical shift of diphenyl diselenide is computed using structures extracted from MD snapshots and found in nice agreement with the measured value in CDCl3. The whole computational protocol is described in detail and integrated with in-house code to allow easy derivation of the force field parameters for analogous compounds as well as for Se/Te organocompounds in general.

Addition-Elimination or Nucleophilic Substitution? Understanding the Energy Profiles for the Reaction of Chalcogenolates with Dichalcogenides.

We have quantum chemically explored the mechanism of the substitution reaction between CH3X(-) and the homo- and heterodichalcogenides CH3X'X″CH3 (X, X', X″ = S, Se, Te) using relativistic density functional theory at ZORA-OLYP/TZ2P and COSMO for simulating the effect of aqueous solvation. In the gas phase, all substitution reactions proceed via a triple-well addition-elimination mechanism that involves a stable three-center intermediate. Aqueous solvation, in some cases, switches the character of the mechanism to double-well SN2 in which the stable three-center intermediate has become a labile transition state. We rationalize reactivity trends and some puzzling aspects of these elementary reactions, in particular, vanishing activation energies and ghost three-center intermediates, using the activation strain model (ASM).

Insights on selenium and tellurium diaryldichalcogenides: A benchmark DFT study.

Selenium based diaryl dichalcogenides are compounds that are receiving attention in organic synthesis as eco-friendly oxidation agents as well as in pharmaceutical chemistry, where, together with tellurium-based derivatives, are appealing drugs mainly for their antioxidant properties. A benchmark study to establish optimal density functional theory (DFT) methods for the description of their molecular and electronic structure as well as for their energetics is presented here. Structural features, such as the orientation of the phenyl rings, as well as energetic aspects, i.e., the chalcogen-chalcogen bond strength, are discussed, with the aim of applying the novel insights to quantum mechanics-based investigations of their reactivity and to facilitate drug design. © 2016 Wiley Periodicals, Inc.

Selective C-H and C-C Bond Activation: Electronic Regimes as a Tool for Designing d(10) MLn Catalysts.

We wish to understand how a transition-metal catalyst can be rationally designed so as to selectively activate one particular bond in a substrate, herein, C-H and C-C bonds in ethane. To this end, we quantum chemically analyzed the activity and selectivity of a large series of model catalysts towards ethane and, for comparison, methane, by using the activation strain model and quantitative molecular orbital theory. The model catalysts comprise d(10) MLn complexes with coordination numbers n=0, 1, and 2; metal centers M=Co(-), Rh(-), Ir(-), Ni, Pd, Pt, Cu(+), Ag(+), and Au(+); and ligands L=NH3, PH3, and CO. Our analyses reveal that rather subtle electronic differences between bonds can be exploited to induce a lower barrier for activating one or the other, depending, among other factors, on the catalysts electronic regime (i.e., s-regime versus d-regime catalysts). Interestingly, the concepts and design principles emerging from this work can also be applied to the more challenging problem of differentiating between activation of the C-H bonds in ethane versus those in methane.

The activation strain model and molecular orbital theory.

The activation strain model is a powerful tool for understanding reactivity, or inertness, of molecular species. This is done by relating the relative energy of a molecular complex along the reaction energy profile to the structural rigidity of the reactants and the strength of their mutual interactions: ΔE(ζ) = ΔEstrain(ζ) + ΔEint(ζ). We provide a detailed discussion of the model, and elaborate on its strong connection with molecular orbital theory. Using these approaches, a causal relationship is revealed between the properties of the reactants and their reactivity, e.g., reaction barriers and plausible reaction mechanisms. This methodology may reveal intriguing parallels between completely different types of chemical transformations. Thus, the activation strain model constitutes a unifying framework that furthers the development of cross-disciplinary concepts throughout various fields of chemistry. We illustrate the activation strain model in action with selected examples from literature. These examples demonstrate how the methodology is applied to different research questions, how results are interpreted, and how insights into one chemical phenomenon can lead to an improved understanding of another, seemingly completely different chemical process. WIREs Comput Mol Sci 2015, 5:324-343. doi: 10.1002/wcms.1221.

Covalency in resonance-assisted halogen bonds demonstrated with cooperativity in N-halo-guanine quartets.

Halogen bonds are shown to possess the same characteristics as hydrogen bonds: charge transfer, resonance assistance and cooperativity. This follows from the computational analyses of the structure and bonding in N-halo-base pairs and quartets. The objective was to achieve an understanding of the nature of resonance-assisted halogen bonds (RAXB): how they resemble or differ from the better understood resonance-assisted hydrogen bonds (RAHB) in DNA. We present an accurate physical model of the RAXB based on the molecular orbital theory, which is derived from the corresponding energy decomposition analyses and study of the charge distribution. We show that the RAXB arise from classical electrostatic interaction and also receive strengthening from donor-acceptor interactions within the σ-electron system. Similar to RAHB, there is also a small stabilization by π-electron delocalization. This resemblance leads to prove cooperativity in N-halo-guanine quartets, which originates from the charge separation that occurs with donor-acceptor orbital interactions in the σ-electron system.

Controlling the oxidative addition of aryl halides to Au(I).

By means of density functional theory calculations, we computationally analyze the physical factors governing the oxidative addition of aryl halides to gold(I) complexes. Using the activation strain model of chemical reactivity, it is found that the strain energy associated with the bending of the gold(I) complex plays a key role in controlling the activation barrier of the process. A systematic study on how the reaction barrier depends on the nature of the aryl halide, ligand, and counteranion allows us to identify the best combination of gold(I) complex and aryl halide to achieve a feasible (i.e., low barrier) oxidative addition to gold(I), a process considered as kinetically sluggish so far.

New concepts for designing d10 -M(L)n catalysts: d regime, s regime and intrinsic bite-angle flexibility.

Our aim is to understand the electronic and steric factors that determine the activity and selectivity of transition-metal catalysts for cross-coupling reactions. To this end, we have used the activation strain model to quantum-chemically analyze the activity of catalyst complexes d(10) -M(L)n toward methane C-H oxidative addition. We studied the effect of varying the metal center M along the nine d(10) metal centers of Groups 9, 10, and 11 (M=Co(-), Rh(-), Ir(-), Ni, Pd, Pt, Cu(+), Ag(+), Au(+)), and, for completeness, included variation from uncoordinated to mono- to bisligated systems (n=0, 1, 2), for the ligands L=NH(3), PH(3), and CO. Three concepts emerge from our activation strain analyses: 1) bite-angle flexibility, 2) d-regime catalysts, and 3) s-regime catalysts. These concepts reveal new ways of tuning a catalyst's activity. Interestingly, the flexibility of a catalyst complex, that is, its ability to adopt a bent L-M-L geometry, is shown to be decisive for its activity, not the bite angle as such. Furthermore, the effect of ligands on the catalyst's activity is totally different, sometimes even opposite, depending on the electronic regime (d or s) of the d(10) -M(L)n complex. Our findings therefore constitute new tools for a more rational design of catalysts.

Understanding E2 versus SN2 Competition under Acidic and Basic Conditions.

Our purpose is to understand the mechanism through which pH affects the competition between base-induced elimination and substitution. To this end, we have quantum chemically investigated the competition between elimination and substitution pathways in H2O+C2H5OH2 (+) and OH(-)+C2H5OH, that is, two related model systems that represent, in a generic manner, the same reaction under acidic and basic conditions, respectively. We find that substitution is favored in the acidic case while elimination prevails under basic conditions. Activation-strain analyses of the reaction profiles reveal that the switch in preferred reactivity from substitution to elimination, if one goes from acidic to basic catalysis, is related to (1) the higher basicity of the deprotonated base, and (2) the change in character of the substrates LUMO from C(ß)-H bonding in C2H5OH2 (+) to C(ß)-H antibonding in C2H5OH.

In silico design of heteroaromatic half-sandwich RhI catalysts for acetylene [2+2+2] cyclotrimerization: evidence of a reverse indenyl effect.

A mechanistic density functional theory study of acetylene [2+2+2] cyclotrimerization to benzene catalyzed by Rh(I) half metallocenes is presented. The catalyst fragment contains a heteroaromatic ligand, that is, the 1,2-azaborolyl (Ab) or the 3a,7a-azaborindenyl (Abi) anions, which are isostructural and isoelectronic to the hydrocarbon cyclopentadienyl (Cp) and indenyl (Ind) anions, respectively, but differ from the last ones on having two adjacent carbon atoms replaced with a boron and a nitrogen atom. The better performance of either the classic hydrocarbon or the heteroaromatic catalysts is found to depend on the different mechanistic paths that can be envisioned for the process. The present analyses uncover and explain general structure-reactivity relationships that may serve as rational design principles. In particular, we provide evidence of a reverse indenyl effect.

Nonlinear d(10)-ML2 Transition-Metal Complexes.

We have investigated the molecular geometries of a series of dicoordinated d(10)-transition-metal complexes ML2 (M=Co(-), Rh(-), Ir(-), Ni, Pd, Pt, Cu(+), Ag(+), Au(+); L=NH3, PH3, CO) using relativistic density functional theory (DFT) at ZORA-BLYP/TZ2P. Not all complexes have the expected linear ligand-metal-ligand (L-M-L) angle: this angle varies from 180° to 128.6° as a function of the metal as well as the ligands. Our main objective is to present a detailed explanation why ML2 complexes can become bent. To this end, we have analyzed the bonding mechanism in ML2 as a function of the L-M-L angle using quantitative Kohn-Sham molecular orbital (MO) theory in combination with an energy decomposition analysis (EDA) scheme. The origin of bent L-M-L structures is π backdonation. In situations of strong π backdonation, smaller angles increase the overlap of the ligand's acceptor orbital with a higher-energy donor orbital on the metal-ligand fragment, and therefore favor π backdonation, resulting in additional stabilization. The angle of the complexes thus depends on the balance between this additional stabilization and increased steric repulsion that occurs as the complexes are bent.

Halogen Bonding versus Hydrogen Bonding: A Molecular Orbital Perspective.

We have carried out extensive computational analyses of the structure and bonding mechanism in trihalides DX⋅⋅⋅A(-) and the analogous hydrogen-bonded complexes DH⋅⋅⋅A(-) (D, X, A=F, Cl, Br, I) using relativistic density functional theory (DFT) at zeroth-order regular approximation ZORA-BP86/TZ2P. One purpose was to obtain a set of consistent data from which reliable trends in structure and stability can be inferred over a large range of systems. The main objective was to achieve a detailed understanding of the nature of halogen bonds, how they resemble, and also how they differ from, the better understood hydrogen bonds. Thus, we present an accurate physical model of the halogen bond based on quantitative Kohn-Sham molecular orbital (MO) theory, energy decomposition analyses (EDA) and Voronoi deformation density (VDD) analyses of the charge distribution. It appears that the halogen bond in DX⋅⋅⋅A(-) arises not only from classical electrostatic attraction but also receives substantial stabilization from HOMO-LUMO interactions between the lone pair of A(-) and the σ* orbital of D-X.

Alkali-metal-supported bismuth polyhedra-principles and theoretical studies.

We have quantum chemically investigated the structure, stability, and bonding mechanism in highly aggregated alkali-metal salts of bismuthanediide anions [RBi](2-) using relativistic density functional theory (DFT, at ZORA-BP86/TZ2P) in combination with a quantitative energy decomposition analysis (EDA). Our model systems are alkali-metal-supported bismuth polyhedra [(RBi)(n)M(2n-4)](4-) with unique interpenetrating shells of a bismuth polyhedron and an alkali-metal superpolyhedron. Furthermore, we have analyzed the trianionic inclusion complexes [M'@{(RBi)(n)M(2n-4)}](3-) involving an additional endohedral alkali-metal ion M'. The main objective is to assist the further development of synthetic approaches toward this class of compounds. Our analyses led to electron-counting rules relating, for example, the number of bonding orbitals (N(bond)) of the cage molecules [(RBi)(n)M(2n+Q)](Q) to the number of bismuth atoms (n(Bi)), alkali-metal atoms (n(M)), and net charge Q as N(bond) = n(Bi) + n(M) - Q (R = one-electron donor ligand; M = alkali metal; n = 4-12; Q = -4, -6, -8). Finally, on the basis of our findings, we predict the next members in the 5-fold symmetrical row of alkali-metallobismaspheres with a macroicosahedral arrangement.

Reaction Coordinates and the Transition-Vector Approximation to the IRC.

The appearance of a reaction profile or potential energy surface (PES) associated with the reaction path (defined as the path of steepest descent from the saddle point) depends on the choice of reaction coordinate onto which the intrinsic reaction coordinate is projected. This provides one with the freedom, but also the problem, of choosing the optimal perspective (i.e., the optimal reaction coordinate) for revealing what is essential for understanding the reaction. Here, we address this issue by analyzing a number of different reaction coordinates for the same set of model reactions, namely, prototypical oxidative addition reactions of C-X bonds to palladium. We show how different choices affect the appearance of the PES, and we discuss which qualities make a particular reaction coordinate most suitable for comparing and analyzing the reactions. Furthermore, we show how the transition vector (i.e., the normal mode associated with a negative force constant that leads from the saddle point to the steepest descent paths) can serve as a useful and computationally much more efficient approximation (designated TV-IRC) for full IRC computations, in the decisive region around the transition state.