How solvation influences the S(N)2 versus E2 competition

We have quantum chemically investigated how solvation influences the competition between the S(N)2 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(N)2 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(N)2 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(N)2 pathway becomes viable.Bio-organic Synthesi

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

Bio-organic Synthesi

Rational tuning of the reactivity of three-membered heterocycle ring-openings via SN2 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 for 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. We here investigate the intrinsic reactivity of substrates containing a class of widely used electrophilic traps, the three-membered heterocycles with an N- (aziridine), P- (phosphirane), O- (epoxide) and S-atom (thiirane) as heteroatom. Using quantum chemical approaches, we studied the conformational flexibility and nucleophilic ring-opening reaction of a series of model substrates, in which these electrophilic traps are mounted on a cyclohexene scaffold (C6H10Y with Y = NH, PH, O, S). It is revealed that the activation energy of the ring-opening reaction does not necessarily follow the trend that is expected from C-Y leaving-group bond strength, but steeply decreases from NH, to PH, to O, to S. We illustrate that the HOMONu-LUMOSubstrate 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.NWONWO-Rekentijd grant 17569 and 11116Bio-organic Synthesi

A unified framework for understanding nucleophilicity and protophilicity in the SN2/E2 competition

The concepts of nucleophilicity and protophilicity are fundamental and ubiquitous in chemistry. A case in point is bimolecular nucleophilic substitution (S(N)2) and base-induced elimination (E2). A Lewis base acting as a strong nucleophile is needed for S(N)2 reactions, whereas a Lewis base acting as a strong protophile (i.e., base) is required for E2 reactions. A complicating factor is, however, the fact that a good nucleophile is often a strong protophile. Nevertheless, a sound, physical model that explains, in a transparent manner, when an electron-rich Lewis base acts as a protophile or a nucleophile, which is not just phenomenological, is currently lacking in the literature. To address this fundamental question, the potential energy surfaces of the S(N)2 and E2 reactions of X-+C2H5Y model systems with X, Y = F, Cl, Br, I, and At, are explored by using relativistic density functional theory at ZORA-OLYP/TZ2P. These explorations have yielded a consistent overview of reactivity trends over a wide range in reactivity and pathways. Activation strain analyses of these reactions reveal the factors that determine the shape of the potential energy surfaces and hence govern the propensity of the Lewis base to act as a nucleophile or protophile. The concepts of "characteristic distortivity" and "transition state acidity" of a reaction are introduced, which have the potential to enable chemists to better understand and design reactions for synthesis.Bio-organic Synthesi

Dipolar repulsion in alpha-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.Theoretical Chemistr

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.Theoretical Chemistr

How divalent cations interact with the internal channel site of guanine quadruplexes

The formation of guanine quadruplexes (GQ) in DNA is crucial in telomere homeostasis and regulation of gene expression. Pollution metals can interfere with these DNA superstructures upon coordination. In this work, we study the affinity of the internal GQ channel site towards alkaline earth metal (Mg2+, Ca2+, Sr2+, and Ba2+), and (post-)transition metal (Zn2+, Cd2+, Hg2+, and Pb2+) cations using density functional theory computations. We find that divalent cations generally bind to the GQ cavity with a higher affinity than conventional monovalent cations (e. g. K+). Importantly, we establish the nature of the cation-GQ interaction and highlight the relationship between ionic and nuclear charge, and the electrostatic and covalent interactions. The covalent interaction strength plays an important role in the cation affinity and can be traced back to the relative stabilization of cations' unoccupied atomic orbitals. Overall, our findings contribute to a deeper understanding of how pollution metals could induce genomic instability.Theoretical Chemistr

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, CH3, Cl) in archetypal model substrates H3C-CH2-X, H2C=CH-X and HC equivalent to C-X by catalysts PdLn with L-n = no ligand, Cl-, and (PH3)(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.Bio-organic Synthesi

Regioselectivity of Epoxide Ring-Openings via S(N)2 Reactions Under Basic and Acidic Conditions

We have quantum chemically analyzed the ring-opening reaction of the model non-symmetrical epoxide 2,2-dimethyloxirane under basic and acidic conditions using density functional theory at OLYP/TZ2P. For the first time, our combined activation strain and Kohn-Sham molecular orbital analysis approach have revealed the interplay of physical factors that control the regioselectivity of these chemical reactions. Ring-opening under basic conditions occurs in a regime of strong interaction between the nucleophile (OH-) and the epoxide and the interaction is governed by the steric (Pauli) repulsion. The latter steers the attack preferentially towards the sterically less encumbered C-beta. Under acidic conditions, the interaction between the nucleophile (H2O) and the epoxide is weak and, now, the regioselectivity is governed by the activation strain. Protonation of the epoxide induces elongation of the weaker (CH3)(2)C-alpha-O bond, and effectively predistorts the substrate for the attack at the sterically more hindered side, which goes with a less destabilizing overall strain energy. Our quantitative analysis significantly builds on the widely accepted rationales behind the regioselectivity of these ring-opening reactions and provide a concrete framework for understanding these indispensable textbook reactions.Bio-organic Synthesi

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.Bio-organic Synthesi