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We have quantum chemically investigated how microsolvation affects the various E2 and SN2 pathways, their mutual competition, and the α-effect of the model reaction system HOO−(H2O)n + CH3CH2Cl, 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. Among both nucleophiles, SN2 is always favored over E2, and this preference increases upon increasing microsolvation. Furthermore, we found a pronounced α-effect, not only for SN2 substitution but also for E2 elimination, i.e., HOO− is more reactive than HO− in both cases. Our activation strain and quantitative molecular orbital analyses reveal the physical mechanisms behind the various computed trends. In particular, we demonstrate that two recently proposed criteria, required for solvent-free nucleophiles to display the α-effect, must also be satisfied by microsolvated HOO−(H2O)n nucleophiles. [ABSTRACT FROM AUTHOR]

The demand for electric vehicles with extended ranges has created a renaissance of interest in replacing the common metal-ion with higher energy-density metal-anode batteries. However, the potential battery safety issues associated with lithium metal must be addressed to enable lithium metal battery chemistries. A considerable performance gap between lithium (Li) symmetric cells and practical Li batteries motivated us to explore the correlation between the shape of voltage traces and degradation. We coupled impedance spectroscopy and operando NMR and used the new approach to show that transient (i.e., soft) shorts form in realistic conditions for battery applications; however, they are typically overlooked, as their electrochemical signatures are often not distinct. The typical rectangular-shaped voltage trace, widely considered ideal, was proven, under the conditions studied here, to be a result of soft shorts. Recoverable soft-shorted cells were demonstrated during a symmetric cell polarisation experiment, defining a new type of critical current density: the current density at which the soft shorts are not reversible. Moreover, we demonstrated that soft shorts, detected via electrochemical impedance spectroscopy (EIS) and validated via operando NMR, are predictive towards the formation of hard shorts, showing the potential use of EIS as a relatively low-cost and non-destructive method for early detection of catastrophic shorts and battery failure while demonstrating the strength of operando NMR as a research tool for metal plating in lithium batteries. [ABSTRACT FROM AUTHOR]

The group of Costa Figueiredo reported Cu-based catalysts for the electrosynthesis of ammonia from nitrate, and X-ray photoelectron spectroscopy demonstrated that Cu(0) is the active phase during catalysis. The Hamlin and Bickelhaupt group performed high level quantum chemical analysis, showing that C(spn)-halogen bonds are easier to activate by a palladium catalyst when the halogen is larger, due to a difference in activation strain and a more favorable electrostatic attraction between the palladium catalyst and the substrate. The importance of catalysis has been recognized a long time ago and the first industrial application stems from the early nineteenth century. We develop new catalytic processes based on 1) rational ligand design in transition metal catalysis 2) Supramolecular catalysis 3) Bio-inspired catalysis. [Extracted from the article]

Non‐hydrogenative Para‐Hydrogen Induced Hyperpolarization (nhPHIP) is a Nuclear Magnetic Resonance (NMR) hyperpolarization technique which has experimentally been used to analyze complex biological samples containing amino acids using the Ir‐IMes hyperpolarization transfer catalyst. A computational study based on Density Function Theory (DFT) was performed on all relevant stereoisomers of [Ir(H)2(IMes)(AA)(Py)] (with AA=glycine, alanine, valine; Py=pyridine), for which R/S chirality and orientation of the amino acid chelation (C/A) were considered. A total of 30 structures were calculated comprising of 6 stereoisomers for achiral glycine, and 12 stereoisomers for each of the chiral amino acids. The abundances derived from the DFT energies confirmed the trends observed in thermal (non‐hyperpolarized) NMR experiments. Additionally, theoretical calculations of electronic (Wiberg bond indices, Natural Bond Orders, Frontier Orbital Analysis), bond dissociation energies, transition states, and activation energies related to interconversion between binding modes, and steric factors (Solid angle) were performed to provide detailed explanations for NMR experimental observations. [ABSTRACT FROM AUTHOR]

Solid-to-solid polymorphic transitions are a common phenomenon in organic crystals. The different interactions that play a role in these transitions are however far from understood. In this computational study, we aim to quantify the interactions that play a role in these transitions using the α ↔ β phase transition of DL -methionine as a model system. DL -Methionine has a layered structure and its phase transition occurs via shifting of the bilayers parallel to the b and c lattice vectors and the rotation of the side chains, which mostly affects the layers along the c lattice vector. We obtained two "order parameters" to describe the changes along b and c, respectively and that can be used to quantify the phase transition in terms of its thermodynamic parameters. The potential energy landscape is an interplay between van der Waals energy and configurational energy, where α is stabilized by configurational energy and destabilized by van der Waals energy as compared to β. The entropic contribution to the free energy difference between α and β is found to be in good agreement with experiments and completely dominated by configurational entropy. [ABSTRACT FROM AUTHOR]

The blood coagulation cascade is a complex physiological process involving the action of multiple coupled enzymes, cofactors, and substrates, ultimately leading to clot formation. Serine proteases have a crucial role, and aberrations in their activity can lead to life‐threatening bleeding disorders and thrombosis. This review summarizes the essential proteases involved in blood coagulation and fibrinolysis, the endogenous peptide sequences they recognize and hydrolyze, and synthetic peptide probes based on these sequences to measure their activity. The information in this review can contribute to developing novel anticoagulant therapies and specific substrates for point‐of‐care diagnosis of coagulation pathologies. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Hierarchical, convergent ab initio 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 ab initio limit were executed via 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. The FPA reaction barriers and energies exhibit convergence to within a few tenths of a kcal mol−1. The FPA benchmarks were used to evaluate the performance of 60 density functionals (eight dispersion-corrected), covering the local-density approximation (LDA), generalized gradient approximations (GGAs), meta-GGAs, hybrids, meta-hybrids, double-hybrids, and range-separated hybrids. The meta-hybrid M06-2X functional provided the best overall performance [mean absolute error (MAE) of 1.1 kcal mol−1] followed closely by the double-hybrids B2K-PLYP, mPW2K-PLYP, and revDSD-PBEP86 [MAE of 1.4–1.5 kcal mol−1]. The regularly used GGA functional BP86 gave a higher MAE of 5.8 kcal mol−1, but it qualitatively described the trends in reaction barriers and energies. Importantly, we established that accurate yet efficient meta-hybrid or double-hybrid DFT potential energy surfaces can be acquired based on geometries from the computationally efficient and robust BP86/DZP level. [ABSTRACT FROM AUTHOR]

In this article, the idea of essential information‐based compression is extended to trilinear datasets. This basically boils down to identifying and labelling the essential rows (ERs), columns (ECs) and tubes (ETs) of such three‐dimensional datasets that allow by themselves to reconstruct in a linear way the entire space of the original measurements. ERs, ECs and ETs can be determined by exploiting convex geometry computational approaches such as convex hull or convex polytope estimations and can be used to generate a reduced version of the data at hand. These compressed data and their uncompressed counterpart share the same multilinear properties and their factorisation (carried out by means of, for example, parallel factor analysis–alternating least squares [PARAFAC‐ALS]) yield, in principle, indistinguishable results. More in detail, an algorithm for the assessment and extraction of the essential information encoded in trilinear data structures is here proposed. Its performance was evaluated in both real‐world and simulated scenarios which permitted to highlight the benefits that this novel data reduction strategy can bring in domains like multiway fluorescence spectroscopy and imaging. [ABSTRACT FROM AUTHOR]

Context. Interstellar ices and their energetic processing play an important role in advancing the chemical complexity in space. Interstellar ices covering dust grains are intrinsically mixed, and it is assumed that physicochemical changes induced by energetic processing – triggered by photons, electrons, and ions – strongly depend on the content of the ice. Yet, the modelling of these complex mixed systems in experiments and theory is complicated. Aims. In this paper, we investigate the effect of infrared irradiation on a series of different molecules mixed with porous amorphous solid water (pASW) to study the release of vibrational energy in the hydrogen-bonding network of water as a function of mixing ratio and ice content. Particularly, we select mixtures of 20:1 H2O:X and 5:1 H2O:X with X=CO2, NH3, or CH4. Methods. Infrared radiation was supplied by the intense and tunable free electron laser (FEL) 2 at the HFML-FELIX facility. We monitored the structural changes in the interstellar ice analogue after resonant infrared excitation using Fourier-transform reflection absorption infrared (FT-RAIR) spectroscopy. Results. We observed that on-resonance irradiation at the OH-stretching vibration of pASW results in quantitatively identical changes compared to pure pASW for all investigated mixtures. The structural changes we observed closely resemble the previously reported local reordering. The 5:1 mixtures show weaker changes compared to pure pASW, with a decrease in strength from NH3 to CO2. Conclusions. Since the hydrogen-bonding network of pASW restructures similarly upon FEL irradiation, regardless of the mixing component, treating ice layers in models that simulate energy dissipation in the hydrogen-bonding network as pure H2O ice layers can be a justified approximation. Hence, complex systems might not always be necessary to describe the infrared energetic processing of ices. [ABSTRACT FROM AUTHOR]

We have quantum chemically studied the influence of ring strain on the competition between the two mechanistically different SN2 and E2 pathways using a series of archetypal ethers as substrate in combination with a diverse set of Lewis bases (F−, Cl−, Br−, HO−, H3CO−, HS−, H3CS−), 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 SN2 pathway sharply decreases when the ring strain of the system is increased, thus on going from large to small cyclic ethers, the SN2 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 SN2, 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 SN2 reaction. [ABSTRACT FROM AUTHOR]

Biochemical reactions occurring in highly crowded cellular environments require different means of control to ensure productivity and specificity. Compartmentalization of reagents by liquid‐liquid phase separation is one of these means. However, extremely high local protein concentrations of up to 400 mg/ml can result in pathological aggregation into fibrillar amyloid structures, a phenomenon that has been linked to various neurodegenerative diseases. Despite its relevance, the process of liquid‐to‐solid transition inside condensates is still not well understood at the molecular level. We thus herein use small peptide derivatives that can undergo both liquid‐liquid and subsequent liquid‐to‐solid phase transition as model systems to study both processes. Using solid‐state nuclear magnetic resonance (NMR) and transmission electron microscopy (TEM), we compare the structure of condensed states of leucine, tryptophan and phenylalanine containing derivatives, distinguishing between liquid‐like condensates, amorphous aggregates and fibrils, respectively. A structural model for the fibrils formed by the phenylalanine derivative was obtained by an NMR‐based structure calculation. The fibrils are stabilised by hydrogen bonds and side‐chain π‐π interactions, which are likely much less pronounced or absent in the liquid and amorphous state. Such noncovalent interactions are equally important for the liquid‐to‐solid transition of proteins, particularly those related to neurodegenerative diseases. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

We have quantum chemically studied the iron‐mediated CX bond activation (X = H, Cl, CH3) by d8‐FeL4 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, PH3, BN(CH3)2, or by manipulating structural effects through the introduction of bidentate ligands, that is, PH2(CH2)nPH2 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 10.4 to 4.6 kcal mol−1. Our activation strain and Kohn‐Sham molecular orbital analyses reveal that the electronic tuning works via optimizing the catalyst–substrate interaction by introducing a strong second backdonation interaction (i.e., "ligand‐assisted" interaction), while the mechanism for structural tuning is mainly caused by the reduction of the required activation strain because of the pre‐distortion of the catalyst. In all, we present design principles for iron‐based catalysts that mimic the favorable behavior of their well‐known palladium analogs in the bond‐activation step of cross‐coupling reactions. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The iron‐catalyzed oxidative addition of C(spn)−X bonds (n=1–3 and X=H, CH3, Cl) in archetypal model substrates H3C−CH2−X, H2C=CH−X and HC≡C−X to Fe(CO)4 was investigated using relativistic density functional theory at ZORA‐OPBE/TZ2P. The C(spn)−X bonds become substantially stronger going from C(sp3)−X to C(sp2)−X to C(sp)−X, whereas the oxidative addition reaction barrier decreases along this series. Our activation strain and energy decomposition analyses expose that the decreased reaction barrier for the oxidative addition going from sp3 to sp2 to sp stems from a relief of the destabilizing (steric) Pauli repulsion between the catalyst and substrate. This originates from the decreasing coordination number of the carbon atom that goes from four in C(sp3)−X to three in C(sp2)−X to two in C(sp)−X. In analogy with our previous results on palladium‐catalyzed oxidative additions, this enhances the stabilizing catalyst–substrate interaction, which is able to overcome the more destabilizing strain associated with the stronger C(spn)−X bonds. This work again demonstrates that iron‐based catalysts can resemble the behavior of their well‐known palladium analogs in the oxidative addition step of cross‐coupling reactions. [ABSTRACT FROM AUTHOR]

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°) = H3C− (methyl, 0°), CH3H2C− (primary, 1°), (CH3)2HC− (secondary, 2°), (CH3)3C− (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. [ABSTRACT FROM AUTHOR]

We have quantum chemically studied the palladium‐mediated activation of C(spn)−X bonds (n=1–3; X=F, Cl, Br, I) in the archetypal model substrates H3C−CH2−X, H2C=CH−X, and HC≡C−X by a model bare palladium catalyst, using relativistic density functional theory at ZORA‐BLYP/TZ2P. The bond activation reaction barrier decreases, for all sp‐hybridized carbon centers, when the substituent X of the substrate is changed from X=F to I. Activation strain and energy decomposition analyses reveal that the enhanced reactivity along this series originates from (i) a less destabilizing activation strain due to an intrinsically weaker C(spn)−X bond; and (ii) an increasingly more stabilizing electrostatic interaction between the catalyst and the substrate. The latter is a direct consequence of the more diffuse electron density and higher nuclear charge of the X atom in the C(spn)−X bond when going from X=F to I, which, in turn, engages in a more favorable electrostatic attraction with the nucleus and electrons, respectively, of the palladium catalyst. [ABSTRACT FROM AUTHOR]

We have studied the palladium‐mediated activation of C(spn)−X bonds (n = 1–3 and X = H, CH3, Cl) in archetypal model substrates H3C−CH2−X, H2C=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. [ABSTRACT FROM AUTHOR]

Finding ways to achieve switching between magnetic states at the fastest possible timescale that simultaneously dissipates the least amount of energy is one of the main challenges in magnetism. Antiferromagnets exhibit intrinsic dynamics in the THz regime, the highest among all magnets, and are, therefore, ideal candidates to address this energy-time dilemma. Here, we study theoretically the THz-driven parametric excitation of antiferromagnetic magnon-pairs at the edge of the Brillouin zone and explore the potential for switching between two stable oscillation states. Using a semi-classical theory, we predict that switching can occur at the femtosecond timescale with an energy dissipation down to a few zepto Joule. This result touches the thermodynamical bound of the Landauer principle and approaches the quantum speed limit up to 5 orders of magnitude closer than demonstrated with magnetic systems so far. [ABSTRACT FROM AUTHOR]

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 ( S )-2-phenylpropanal and ( S )-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. In addition, other factors such as the more favorable electrostatic interactions also contribute to the preferred approach of the nucleophile. Our work, therefore, provides a different, more complete rationalization, based on quantitative analyses, of the origin of this seminal and highly useful concept in organic chemistry., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

We have quantum chemically investigated how microsolvation affects the various E2 and S N 2 pathways, their mutual competition, and the α-effect of the model reaction system HOO - (H 2 O) n + CH 3 CH 2 Cl, 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. Among both nucleophiles, S N 2 is always favored over E2, and this preference increases upon increasing microsolvation. Furthermore, we found a pronounced α-effect, not only for S N 2 substitution but also for E2 elimination, i.e. , HOO - is more reactive than HO - in both cases. Our activation strain and quantitative molecular orbital analyses reveal the physical mechanisms behind the various computed trends. In particular, we demonstrate that two recently proposed criteria, required for solvent-free nucleophiles to display the α-effect, must also be satisfied by microsolvated HOO - (H 2 O) n nucleophiles.

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., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

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. Despite this principle being well-known in organic synthesis, mechanistic studies investigating this model in glycosylation reactions are complicated by the challenge of detecting the extremely short-lived reactive species responsible for product formation. Herein, we report the utilization of the chemical equilibrium between low-abundance reaction intermediates and the stable, readily observed α-glycosyl triflate intermediate in order to infer the structure of the former species by employing exchange NMR. Using this technique, we enabled the detection of reaction intermediates such as β-glycosyl triflates and glycosyl dioxanium ions. This demonstrates the power of exchange NMR to unravel reaction mechanisms as we aim to build a catalog of kinetic parameters, allowing for the understanding and eventual prediction of glycosylation reactions.

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 3 ) 2 C═O. We constructed a 2D potential energy surface defined by the distance between the nucleophile and carbonylic carbon atom and by the attack angle, followed by an in-depth exploration of energy components, including strain and interaction energy. Our analysis reveals that the Bürgi-Dunitz angle emerges from a delicate balance between two key factors: strain energy and interaction energy. High strain energy, as a result of the carbonyl compound distorting to avoid Pauli repulsion, is encountered at high angles, thus setting the upper bound. On the other hand, interaction energy is shaped by a dominant Pauli repulsion when the angles are lower. This work emphasizes the value of the 2D Energy Decomposition Analysis as a refined tool, offering both quantitative and qualitative insights into chemical reactivity and selectivity.

The Bürgi-Dunitz (BD) angle plays a pivotal role in organic chemistry to rationalize the nucleophilic addition to carbonyl groups. Yet, the origin of the obtuse trajectory of the nucleophile remains incompletely understood. Herein, we quantify the importance of the underlying physical factors quantum chemically. The obtuse BD angle appears to originate from the concerted action of a reduced Pauli repulsion between the nucleophile HOMO and carbonyl π bond, a more stabilizing HOMO-π*-LUMO(C=O) interaction, as well as a more favorable electrostatic attraction., (© 2023 The Authors. ChemPhysChem published by Wiley-VCH GmbH.)

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. Since their protein components are nearly identical, purification of these endoribonucleases using protein-centric methods is not feasible. Here, we describe a procedure employing an optimized high-affinity streptavidin-binding RNA aptamer, termed S1m, to purify RNase MRP free of RNase P. This report details all steps from the RNA tagging to the characterization of the purified material. We show that using the S1m tag allows efficient isolation of active RNase MRP., Competing Interests: Competing interests The authors declare no conflict of interest., (Copyright © 2023 The Authors; exclusive licensee Bio-protocol LLC.)

Simple mathematical models can serve to reveal the essence of experimental phenomena and scientific concepts. The particle in a box (PIB), for example, is widely used in undergraduate programs to teach the quantum mechanical principles behind the UV-vis spectra of conjugated polyenes and polyynes. In this work, the particle on a ring (POR) and the PIB models are used to elucidate the concept of aromaticity in Introductory Chemistry courses. Thus, we explain the origin of the aromatic stabilization energy, Hückel's rule, and Baird's rule. Besides applications, the limitations of the POR and PIB models are also discussed., Competing Interests: The authors declare no competing financial interest., (© 2022 The Authors. Published by American Chemical Society and Division of Chemical Education, Inc.)

The gauche 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., hyperconjugation) cannot overrule the repulsive forces between X and Y. Our quantum chemical analyses of the rotational isomerism of XCH 2 CH 2 Y (X = F, OH; Y = I) at ZORA-BP86-D3(BJ)/QZ4P reveal that indeed the anti conformer is generally favored due to a less destabilizing I···F and I···O-H steric repulsion. The only case when the gauche conformer is preferred is when the hydroxyl hydrogen is oriented toward the iodine atom in the 2-iodoethanol. This is because of the significantly stabilizing covalent component of the I···H-O intramolecular hydrogen bond. Therefore, we show that strong intramolecular interactions can overcome the steric repulsion between bulky substituents in 1,2-disubstituted ethanes and cause the gauche effect. Our quantum chemical computations have guided nuclear magnetic resonance experiments that confirm the increase in the gauche population as X goes from F to OH.

We have quantum chemically explored the competition between the S N 2 and S N 2' pathways for X - + H 2 C═CHCH 2 Y (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., C γ ═C β -C α -Y, bearing a leaving-group at the α-position, proceed either via a direct attack at the α-carbon (S N 2) or via an attack at the γ-carbon, involving a concerted allylic rearrangement (S N 2'), in both cases leading to the expulsion of the leaving-group. Herein, we provide a physically sound model to rationalize under which circumstances a nucleophile will follow either the aliphatic S N 2 or allylic S N 2' pathway. Our activation strain analyses expose the underlying physical factors that steer the S N 2/S N 2' competition and, again, demonstrate that the concepts of a reaction's "characteristic distortivity" and "transition state acidity" provide explanations and design tools for understanding and predicting reactivity trends in organic synthesis.

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. Here, we show that nanopatterning of the anisotropy landscape with a He + -ion beam creates well-defined skyrmion nucleation sites, thereby transforming the skyrmion localization into a deterministic process. This approach allows control of individual skyrmion nucleation as well as guided skyrmion motion with nanometer-scale precision, which is pivotal for both future fundamental studies of skyrmion dynamics and applications.

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. When interacting with the PAH, the lone pair-type highest occupied molecular orbital (HOMO) of water has poor orbital overlap and is too low in energy to mix with the filled π-orbitals of the PAH. As the lone-pair HOMO of ammonia is significantly higher in energy and has better overlap with filled π-orbitals of the PAH, the subsequent Pauli repulsion leads to mixed MOs with both PAH and ammonia character. By time-dependent DFT calculations, we demonstrate that the formation of mixed PAH-ammonia MOs opens alternative charge-transfer excitation pathways as now electronic density from ammonia can be transferred to unoccupied PAH levels, yielding anionic PAHs. As this pathway is much less available for water-embedded PAHs, charge transfer mainly occurs from localized PAH MOs to mixed PAH-water virtual levels, leading to cationic PAHs., Competing Interests: The authors declare no competing financial interest., (© 2022 The Authors. Published by American Chemical Society.)

We have quantum chemically investigated how solvation influences the competition between the S N 2 and E2 pathways of the model F - + C 2 H 5 Cl 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.