Origin of the Felkin-Anh(-Eisenstein) model: a quantitative rationalization of a seminal concept.

Quantum chemical calculations were carried out to quantitatively understand the origin of the Felkin-Anh(-Eisenstein) model, widely used to rationalize the π-facial stereoselectivity in the nucleophilic addition reaction to carbonyl groups directly attached to a stereogenic center. To this end, the possible approaches of cyanide to both ()-2-phenylpropanal and ()-3-phenylbutan-2-one have been explored in detail. With the help of the activation strain model of reactivity and the energy decomposition analysis method, it is found that the preference for the Felkin-Anh addition is mainly dictated by steric factors which manifest in a less destabilizing strain-energy rather than, as traditionally considered, in a lower Pauli repulsion.

Linear Mixed-Effects Models in chemistry: A tutorial.

A common goal in chemistry is to study the relationship between a measured signal and the variability of certain factors. To this end, researchers often use Design of Experiment to decide which experiments to conduct and (Multiple) Linear Regression, and/or Analysis of Variance to analyze the collected data. Among the assumptions to the very foundation of this strategy, all the experiments are independent, conditional on the settings of the factors.

Solvent-induced dual nucleophiles and the α-effect in the S2 E2 competition.

We have quantum chemically investigated how microsolvation affects the various E2 and S2 pathways, their mutual competition, and the α-effect of the model reaction system HOO(HO) + CHCHCl, at the CCSD(T) level. Interestingly, we identify the dual nature of the α-nucleophile HOO which, upon solvation, is in equilibrium with HO. This solvent-induced dual appearance gives rise to a rich network of competing reaction channels.

What defines electrophilicity in carbonyl compounds.

The origin of the electrophilicity of a series of cyclohexanones and benzaldehydes is investigated using the activation strain model and quantitative Kohn-Sham molecular orbital (MO) theory. We find that this electrophilicity is mainly determined by the electrostatic attractions between the carbonyl compound and the nucleophile (cyanide) along the entire reaction coordinate. Donor-acceptor frontier molecular orbital interactions, on which the current rationale behind electrophilicity trends is based, appear to have little or no significant influence on the reactivity of these carbonyl compounds.

Correction: Pericyclic reaction benchmarks: hierarchical computations targeting CCSDT(Q)/CBS and analysis of DFT performance.

Correction for 'Pericyclic reaction benchmarks: hierarchical computations targeting CCSDT(Q)/CBS and analysis of DFT performance' by Pascal Vermeeren , , 2022, , 18028-18042, https://doi.org/10.1039/D2CP02234F.

Dynamic hydrogen peroxide levels reveal a rate-dependent sensitivity in B-cell lymphoma signaling.

Although in vivo extracellular microenvironments are dynamic, most in vitro studies are conducted under static conditions. Here, we exposed diffuse large B-cell lymphoma (DLBCL) cells to gradient increases in the concentration of hydrogen peroxide (HO), thereby capturing some of the dynamics of the tumour microenvironment. Subsequently, we measured the phosphorylation response of B-cell receptor (BCR) signalling proteins CD79a, SYK and PLCγ2 at a high temporal resolution via single-cell phospho-specific flow cytometry.

Detection and Characterization of Rapidly Equilibrating Glycosylation Reaction Intermediates Using Exchange NMR.

The stereoselective introduction of glycosidic bonds (glycosylation) is one of the main challenges in the chemical synthesis of carbohydrates. Glycosylation reaction mechanisms are difficult to control because, in many cases, the exact reactive species driving product formation cannot be detected and the product outcome cannot be explained by the primary reaction intermediate observed. In these cases, reactions are expected to take place via other low-abundance reaction intermediates that are in rapid equilibrium with the primary reaction intermediate via a Curtin-Hammett scenario.

Unraveling the Bürgi-Dunitz Angle with Precision: The Power of a Two-Dimensional Energy Decomposition Analysis.

Understanding the geometrical preferences in chemical reactions is crucial for advancing the field of organic chemistry and improving synthetic strategies. One such preference, the Bürgi-Dunitz angle, is central to nucleophilic addition reactions involving carbonyl groups. This study successfully employs a novel two-dimensional Distortion-Interaction/Activation-Strain Model in combination with a two-dimensional Energy Decomposition Analysis to investigate the origins of the Bürgi-Dunitz angle in the addition reaction of CN to (CH)C═O.

S 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 S 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 , H CO , HS , H 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 S 2 pathway sharply decreases when the ring strain of the system is increased, thus on going from large to small cyclic ethers, the S 2 reactivity increases.

A Novel Method to Isolate RNase MRP Using RNA Streptavidin Aptamer Tags.

Interactions between RNA-binding proteins and RNA molecules are at the center of multiple biological processes. Therefore, accurate characterization of the composition of ribonucleoprotein complexes (RNPs) is crucial. Ribonuclease (RNase) for mitochondrial RNA processing (MRP) and RNase P are highly similar RNPs that play distinct roles at the cellular level; as a consequence, the specific isolation of either of these complexes is essential to study their biochemical function.

Multiple pkd and piezo gene family members are required for atrioventricular valve formation.

Cardiac valves ensure unidirectional blood flow through the heart, and altering their function can result in heart failure. Flow sensing via wall shear stress and wall stretching through the action of mechanosensors can modulate cardiac valve formation. However, the identity and precise role of the key mechanosensors and their effectors remain mostly unknown.

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 CO via a retro-DA reaction. Base catalysis, for example, by triethylamine, lowers the reaction barrier up to 10 kcal mol , causing the reaction to proceed smoothly at low temperature, which quenches the expulsion of CO , yielding efficient access to polyoxygenated natural compounds.

Stability of alkyl carbocations.

The traditional and widespread rationale behind the stability trend of alkyl-substituted carbocations is incomplete. Through state-of-the-art quantum chemical analyses, we quantitatively established a generally overlooked driving force behind the stability of carbocations, namely, that the parent substrates are substantially destabilized by the introduction of substituents, often playing a dominant role in solution. This stems from the repulsion between the substituents and the C-X bond.

Iodine Gauche Effect Induced by an Intramolecular Hydrogen Bond.

The conformer in 1-X,2-Y-disubstituted ethanes, that is, the staggered orientation in which X and Y are in closer contact, is only favored for relatively small substituents that do not give rise to large X···Y steric repulsion. For more diffuse substituents, weakly attractive orbital interactions between antiperiplanar bonds (i.e.

Pericyclic reaction benchmarks: hierarchical computations targeting CCSDT(Q)/CBS and analysis of DFT performance.

Hierarchical, convergent benchmark computations were performed followed by a systematic analysis of DFT performance for five pericyclic reactions comprising Diels-Alder, 1,3-dipolar cycloaddition, electrocyclic rearrangement, sigmatropic rearrangement, and double group transfer prototypes. Focal point analyses (FPA) extrapolating to the limit were executed explicit quantum chemical computations with electron correlation treatments through CCSDT(Q) and correlation-consistent Gaussian basis sets up to aug'-cc-pV5Z. Optimized geometric structures and vibrational frequencies of all stationary points were obtained at the CCSD(T)/cc-pVTZ level of theory.

S2 versus S2' Competition.

We have quantum chemically explored the competition between the S2 and S2' pathways for X + HC═CHCHY (X, Y = F, Cl, Br, I) using a combined relativistic density functional theory and coupled-cluster theory approach. Bimolecular nucleophilic substitution reactions at allylic systems, i.e.

Deterministic Generation and Guided Motion of Magnetic Skyrmions by Focused He-Ion Irradiation.

Magnetic skyrmions are quasiparticles with nontrivial topology, envisioned to play a key role in next-generation data technology while simultaneously attracting fundamental research interest due to their emerging topological charge. In chiral magnetic multilayers, current-generated spin-orbit torques or ultrafast laser excitation can be used to nucleate isolated skyrmions on a picosecond time scale. Both methods, however, produce randomly arranged skyrmions, which inherently limits the precision on the location at which the skyrmions are nucleated.

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°) = H C- (methyl, 0°), CH H C- (primary, 1°), (CH ) HC- (secondary, 2°), (CH ) 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.

Polycyclic Aromatic Hydrocarbons (PAHs) in Interstellar Ices: A Computational Study into How the Ice Matrix Influences the Ionic State of PAH Photoproducts.

It has been experimentally observed that water-ice-embedded polycyclic aromatic hydrocarbons (PAHs) form radical cations when exposed to vacuum UV irradiation, whereas ammonia-embedded PAHs lead to the formation of radical anions. In this study, we explain this phenomenon by investigating the fundamental electronic differences between water and ammonia, the implications of these differences on the PAH-water and PAH-ammonia interaction, and the possible ionization pathways in these complexes using density functional theory (DFT) computations. In the framework of the Kohn-Sham molecular orbital (MO) theory, we show that the ionic state of the PAH photoproducts results from the degree of occupied-occupied MO mixing between the PAHs and the matrix molecules.

Rational design of iron catalysts for C-X bond activation.

We have quantum chemically studied the iron-mediated CX bond activation (X = H, Cl, CH ) by d -FeL complexes using relativistic density functional theory at ZORA-OPBE/TZ2P. We find that by either modulating the electronic effects of a generic iron-catalyst by a set of ligands, that is, CO, BF, PH , BN(CH ) , or by manipulating structural effects through the introduction of bidentate ligands, that is, PH (CH ) PH with n = 6-1, one can significantly decrease the reaction barrier for the CX bond activation. The combination of both tuning handles causes a decrease of the CH activation barrier from 10.

A novel experimental approach for the selective isolation and characterization of human RNase MRP.

RNase MRP is a ribonucleoprotein complex involved in the endoribonucleolytic cleavage of different RNAs. Mutations in the RNA component of the RNP are the cause of cartilage hair hypoplasia. Patients with cartilage hair hypoplasia are characterized by skeletal dysplasia.

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

We have studied the palladium-mediated activation of C(sp )-X bonds (n = 1-3 and X = H, CH , Cl) in archetypal model substrates H C-CH -X, H C=CH-X and HC≡C-X by catalysts PdL with L = no ligand, Cl , and (PH ) , 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 )-X, to C(sp )-X, to C(sp)-X. Activation strain and matching energy decomposition analyses reveal that the decreased oxidative addition barrier going from sp , to sp , to sp, originates from a reduction in the destabilizing steric (Pauli) repulsion between catalyst and substrate.

How Solvation Influences the S2 versus E2 Competition.

We have quantum chemically investigated how solvation influences the competition between the S2 and E2 pathways of the model F + CHCl 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 S2 upon strong solvation of the Lewis base (i.

Radical Scavenging Potential of the Phenothiazine Scaffold: A Computational Analysis.

The reactivity of phenothiazine (PS), phenoselenazine (PSE), and phenotellurazine (PTE) with different reactive oxygen species (ROS) has been studied using density functional theory (DFT) in combination with the QM-ORSA (Quantum Mechanics-based Test for Overall Free Radical Scavenging Activity) protocol for an accurate kinetic rate calculation. Four radical scavenging mechanisms have been screened, namely hydrogen atom transfer (HAT), radical adduct formation (RAF), single electron transfer (SET), and the direct oxidation of the chalcogen atom. The chosen ROS are HO , HOO , and CH OO .