Not Carbon s-p Hybridization, but Coordination Number Determines C-H and C-C Bond Length

Backside versus Frontside SN2 Reactions of Alkyl Triflates and Alcohols

Nucleophilic substitution reactions are elementary reactions in organic chemistry that are used in many synthetic routes. By quantum chemical methods, we have investigated the intrinsic competition between the backside SN2 (SN2-b) and frontside SN2 (SN2-f) pathways using a set of simple alkyl triflates as the electrophile in combination with a systematic series of phenols and partially fluorinated ethanol nucleophiles. It is revealed how and why the well-established mechanistic preference for the SN2-b pathway slowly erodes and can even be overruled by the unusual SN2-f substitution mechanism going from strong to weak alcohol nucleophiles. Activation strain analyses disclose that the SN2-b pathway is favored for strong alcohol nucleophiles because of the well-known intrinsically more efficient approach to the electrophile resulting in a more stabilizing nucleophile-electrophile interaction. In contrast, the preference of weaker alcohol nucleophiles shifts to the SN2-f pathway, benefiting from a stabilizing hydrogen bond interaction between the incoming alcohol and the leaving group. This hydrogen bond interaction is strengthened by the increased acidity of the weaker alcohol nucleophiles, thereby steering the mechanistic preference toward the frontside SN2 pathway.

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.

Combined NMR and molecular dynamics conformational filter identifies unambiguously dynamic ensembles of Dengue protease NS2B/NS3pro

The dengue protease NS2B/NS3pro has been reported to adopt either an 'open' or a 'closed' conformation. We have developed a conformational filter that combines NMR with MD simulations to identify conformational ensembles that dominate in solution. Experimental values derived from relaxation parameters for the backbone and methyl side chains were compared with the corresponding back-calculated relaxation parameters of different conformational ensembles obtained from free MD simulations. Our results demonstrate a high prevalence for the 'closed' conformational ensemble while the 'open' conformation is absent, indicating that the latter conformation is most probably due to crystal contacts. Conversely, conformational ensembles in which the positioning of the co-factor NS2B results in a 'partially' open conformation, previously described in both MD simulations and X-ray studies, were identified by our conformational filter. Altogether, we believe that our approach allows for unambiguous identification of true conformational ensembles, an essential step for reliable drug discovery.

Lewis Structures and the Bonding Classification of End-on Bridging Dinitrogen Transition Metal Complexes

The activation of dinitrogen by coordination to transition metal ions is a widely used and promising approach to the utilization of Earth's most abundant nitrogen source for chemical synthesis. End-on bridging N₂ complexes (μ-η¹:η¹-N₂) are key species in nitrogen fixation chemistry, but a lack of consensus on the seemingly simple task of assigning a Lewis structure for such complexes has prevented application of valence electron counting and other tools for understanding and predicting reactivity trends. The Lewis structures of bridging N₂ complexes have traditionally been determined by comparing the experimentally observed NN distance to the bond lengths of free N₂, diazene, and hydrazine. We introduce an alternative approach here and argue that the Lewis structure should be assigned based on the total π-bond order in the MNNM core (number of π-bonds), which derives from the character (bonding or antibonding) and occupancy of the delocalized π-symmetry molecular orbitals (π-MOs) in MNNM. To illustrate this approach, the complexes cis,cis-[(^iPr4PONOP)MCl₂]₂(μ-N₂) (M = W, Re, and Os) are examined in detail. Each complex is shown to have a different number of nitrogen-nitrogen and metal-nitrogen π-bonds, indicated as, respectively: W≡N-N≡W, Re═N═N═Re, and Os-N≡N-Os. It follows that each of these Lewis structures represents a distinct class of complexes (diazanyl, diazenyl, and dinitrogen, respectively), in which the μ-N₂ ligand has a different electron donor number (total of 8e^-, 6e^-, or 4e^-, respectively). We show how this classification can greatly aid in understanding and predicting the properties and reactivity patterns of μ-N₂ complexes.

Methyl Substitution Destabilizes Alkyl Radicals

We have quantum chemically investigated how methyl substituents affect the stability of alkyl radicals Me_mH_3−mC⋅ and the corresponding Me_mH_3−mC−X bonds (X = H, CH₃, OH; m = 0 – 3) using density functional theory at M06‐2X/TZ2P. The state‐of‐the‐art in physical organic chemistry is that alkyl radicals are stabilized upon an increase in their degree of substitution from methyl<primary<secondary<tertiary, and that this is the underlying cause for the decrease in C−H bond strength along this series. Here, we provide evidence that falsifies this model and show that, on the contrary, the Me_mH_3−mC⋅ radical is destabilized with increasing substitution. The reason that the corresponding C−H bond nevertheless becomes weaker is that substitution destabilizes the sterically more congested Me_mH_3−mC−H molecule even more.

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.

Clarifying notes on the bonding analysis adopted by the energy decomposition analysis

We discuss the fundamental aspects of the EDA-NOCV method and address some critical comments that have been made recently. The EDA-NOCV method unlike most other methods focuses on the process of bond formation between the interacting species and not just only on the analysis of the finally formed bond. This is demonstrated using LiF as an example. There is a difference between the interactions between the initial species which form the bond and are also the final product of bond cleavage, and the interactions between the fragments in the eventually formed molecule. The flexibility of the method allows the choice of the interacting fragments which helps to identify the charge and electron configuration of the fragments which describe the bond. This is very helpful in cases where the bond may be described with several Lewis structures. We reject the idea that it would be a disadvantage to have "bond path functions" as the energy components in the EDA, which actually indicate the variability of the method. The bonding analysis in a different sequence of the bond formation gives important results for the various questions that can be asked. This is demonstrated by using CH₂, CO₂ and the formation of a guanine quartet as examples. The fact that a bond is always defined by the bound molecule, the fragments, and their states is universal and deeply physical, as we show here again for various examples. The results of the EDA-NOCV method are in full accordance with the physical mechanism of the chemical bond as revealed by Ruedenberg.

Offsets between hyperconjugations, p→d donations and Pauli repulsions impact the bonding of E-O-E systems. Case study on elements of Group 14

The nature of the E-O chemical bond (E = C, Si, Ge, Sn) is investigated in a wide range of model derivatives, such as oxonium cations, hydrogenated/methylated/fluorinated/chlorinated ethers and acyclic oligomers incorporating the E-O-E moiety. By means of density functional theory (DFT) calculations and natural bond orbital (NBO) techniques, we propose a bonding mechanism that explains the structural contrast between the organic and the inorganic counterparts of all these derivatives: the interplay between stabilizing interactions like LP(O)→σ*(E-X) hyperconjugations and LP(O)→d(E) donations with LP(O)⋯σ(E-X) vicinal Pauli repulsions (X = H, C, O, F, Cl) dictates the equilibrium structures in terms of E-O-E angles and E-O bond lengths. In addition, the present work represents the first study of oxonium ions that describes the structural discrepancies among organic derivatives and their heavier analogues. Another novel outcome for ethers and oligomers is that the two non-equivalent lone pair electrons (LPs) at the oxygen atoms impact in different manners the geometries of such derivatives, i.e. the s/p LP is correlated with the bending behaviour of the E-O-E units, while the pure p LP mainly dictates the short E-O bond distances of inorganic derivatives. Lastly, we evaluate the impact of the number of electronegative substituents, e.g. F, Cl or OEH₃ groups, on the bond patterns developed for hydrogenated or methylated ethers.

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

We have studied the palladium-mediated activation of C(spn )-X bonds (n = 1-3 and X = H, CH3 , Cl) in archetypal model substrates H3 C-CH2 -X, H2 C=CH-X and HC≡C-X by catalysts PdLn with Ln = 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(sp3 )-X, to C(sp2 )-X, to C(sp)-X. Activation strain and matching energy decomposition analyses reveal that the decreased oxidative addition barrier going from sp3 , to sp2 , 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(spn )-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(sp3 )-X to C(sp)-X.

Delta Variant with P681R Critical Mutation Revealed by Ultra-Large Atomic-Scale Ab Initio Simulation: Implications for the Fundamentals of Biomolecular Interactions

The SARS-CoV-2 Delta variant is emerging as a globally dominant strain. Its rapid spread and high infection rate are attributed to a mutation in the spike protein of SARS-CoV-2 allowing for the virus to invade human cells much faster and with an increased efficiency. In particular, an especially dangerous mutation P681R close to the furin cleavage site has been identified as responsible for increasing the infection rate. Together with the earlier reported mutation D614G in the same domain, it offers an excellent instance to investigate the nature of mutations and how they affect the interatomic interactions in the spike protein. Here, using ultra large-scale ab initio computational modeling, we study the P681R and D614G mutations in the SD2-FP domain, including the effect of double mutation, and compare the results with the wild type. We have recently developed a method of calculating the amino-acid-amino-acid bond pairs (AABP) to quantitatively characterize the details of the interatomic interactions, enabling us to explain the nature of mutation at the atomic resolution. Our most significant finding is that the mutations reduce the AABP value, implying a reduced bonding cohesion between interacting residues and increasing the flexibility of these amino acids to cause the damage. The possibility of using this unique mutation quantifiers in a machine learning protocol could lead to the prediction of emerging mutations.

The inversion of tetrahedral p-block element compounds: general trends and the relation to the second-order Jahn-Teller effect

The tetrahedron is the primary structural motif among the p-block elements and determines the architecture of our bio- and geosphere. However, a broad understanding of the configurational inversion of tetrahedral compounds is missing. Here, we report over 250 energies (DLPNO-CCSD(T)) for square planar inversion of third- and fourth-period element species of groups 13, 14, and 15. Surprisingly low inversion barriers are identified for compounds of industrial relevance (e.g., ≈100 kJ mol-1 for Al(OH)4 -). More fundamentally, the second-order Jahn-Teller theorem is disclosed as suitable to rationalize substituent and central element effects. Bond analysis tools give further insights into the preference of eight valence electron systems with four substituents to be tetrahedral. Hence, this study develops a model to understand, memorize, and predict the angular flexibility of tetrahedral species. Perceiving the tetrahedron not as forcingly rigid but as a dynamic structural entity might leverage new approaches and visions for adaptive matter.

Acid and base strength variations: rationalization for cyclic amine bases and acidic aqua cations

This perspective highlights and evaluates recent key developments in the thermodynamic approach used to analyze trends in acid and base strength variation. According to this approach, acid and base strength ranking can be interpreted by using thermodynamic or thermochemical cycles. Each cycle generally consists of three independent but well-defined steps. The modus operandi described here entails the identification of the dominant step and the rationalization of its free energy/enthalpy/energy change along a selected series in terms of known structural chemical concepts. Developments in this approach are described by focusing on two related series of bases and two series of acids. In the case of the former the protonation of a series of N-heterocyclic amine bases together with their methyl-substituted analogs receives particular attention while in the case of acids, the acidic properties of aqua dications of elements in period 4 and group 2 are probed. It is illustrated how significant progress in computational chemistry and mass spectrometric techniques can be employed to compare 'inherent' basicity or acidity in the selected families of compounds by using simple gas-phase energy cycles. Unique, dual functions for both electronegativity (element and orbital) and charge density (for aqua cations) indicators are identified and used to evaluate these cycles. Solvent effects (in aqueous solution) are accommodated by including dehydration and hydration changes in appropriately-extended, three-step free energy cycles. It is further suggested that the dominant step in the extended thermodynamic cycle for monomeric aqua cations is the transfer of M(H₂O)_n²⁺ complex hydrates from the gas-phase to bulk water. Charge density of the aqua cations again features prominently in proposed rationalizations. Finally, this article also sheds light on salient relationships that exist between empirically and quantum-chemically estimated enthalpy and entropy changes for the aforementioned transfer process.

Not Carbon s-p Hybridization, but Coordination Number Determines C-H and C-C Bond Length

A fundamental and ubiquitous phenomenon in chemistry is the contraction of both C−H and C−C bonds as the carbon atoms involved vary, in s–p hybridization, along sp³ to sp² to sp. Our quantum chemical bonding analyses based on Kohn–Sham molecular orbital theory show that the generally accepted rationale behind this trend is incorrect. Inspection of the molecular orbitals and their corresponding orbital overlaps reveals that the above‐mentioned shortening in C−H and C−C bonds is not determined by an increasing amount of s‐character at the carbon atom in these bonds. Instead, we establish that this structural trend is caused by a diminishing steric (Pauli) repulsion between substituents around the pertinent carbon atom, as the coordination number decreases along sp³ to sp² to sp.

Origins of Lewis acid acceleration in nickel-catalysed C–H, C–C and C–O bond cleavage

The effects of charge transfer, Pauli repulsion and electrostatics/polarization are identified as dominant factors for Lewis acid accelerations in Ni-catalyzed C–X (X = H, C and O) bond cleavages.