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Room-temperature ionic liquids are an exciting group of materials with the potential to revolutionize energy storage. Due to their chemical structure and means of interaction, they are challenging to study computationally. Classical descriptions of their inter- and intra-molecular interactions require time intensive parametrization of force-fields which is prone to assumptions. While ab initio molecular dynamics approaches can capture all necessary interactions, they are too slow to achieve the time and length scales required. In this work, we take a step towards addressing these challenges by applying state-of-the-art machine-learned potentials to the simulation of 1-butyl-3-methylimidazolium tetrafluoroborate. We demonstrate a learning-on-the-fly procedure to train machine-learned potentials from single-point density functional theory calculations before performing production molecular dynamics simulations. Obtained structural and dynamical properties are in good agreement with computational and experimental references. Furthermore, our results show that hybrid machine-learned potentials can contribute to an improved prediction accuracy by mitigating the inherent shortsightedness of the models. Given that room-temperature ionic liquids necessitate long simulations to address their slow dynamics, achieving an optimal balance between accuracy and computational cost becomes imperative. To facilitate further investigation of these materials, we have made our IPSuite-based training and simulation workflow publicly accessible, enabling easy replication or adaptation to similar systems.

Chemical processes taking place on ice-grain mantles are pivotal to the complex chemistry of interstellar environments. In this study, we conducted a comprehensive analysis of the catalytic effects of an amorphous solid water (ASW) surface on the reaction between ammonia (NH 3 ) and formaldehyde (H 2 CO) to form aminomethanol (NH 2 CH 2 OH) using density functional theory. We identified potential catalytic sites based on the binding energy distribution of NH 3 and H 2 CO reactants, on a set-of-clusters surface model composed of 22 water molecules and found a total of 14 reaction paths. Our results indicate that the catalytic sites can be categorized into four groups, depending on the interactions of the carbonyl oxygen and the amino group with the ice surface in the reactant complex. A detailed analysis of the reaction mechanism using Intrinsic Reaction Coordinate and reaction force analysis, revealed three distinct chemical events for this reaction: formation of the C-N bond, breaking of the N-H bond, and formation of the O-H hydroxyl bond. Depending on the type of catalytic site, these events can occur within a single, concerted, albeit asynchronous, step, or can be isolated in a step-wise mechanism, with the lowest overall transition state energy observed at 1.3 kcal mol -1 . A key requirement for the low-energy mechanism is the presence of a pair of dangling OH bonds on the surface, found at 5% of the potential catalytic sites on an ASW porous surface.

Covalent organic frameworks (COFs) are a class of porous materials whose sorption properties have so far been studied primarily by physisorption. Quantifying the self-diffusion of guest molecules inside their nanometer-sized pores allows for a better understanding of confinement effects or transport limitations and is thus essential for various applications ranging from molecular separation to catalysis. Using a combination of pulsed field gradient nuclear magnetic resonance measurements and molecular dynamics simulations, we have studied the self-diffusion of acetonitrile and chloroform in the 1D pore channels of two imine-linked COFs (PI-3-COF) with different levels of crystallinity and porosity. The higher crystallinity and porosity sample exhibited anisotropic diffusion for MeCN parallel to the pore direction, with a diffusion coefficient of D par = 6.1(3) × 10 -10 m 2 s -1 at 300 K, indicating 1D transport and a 7.4-fold reduction in self-diffusion compared to the bulk liquid. This finding aligns with molecular dynamics simulations predicting 5.4-fold reduction, assuming an offset-stacked COF layer arrangement. In the low-porosity sample, more frequent diffusion barriers result in isotropic, yet significantly reduced diffusivities ( D B = 1.4(1) × 10 -11 m 2 s -1 ). Diffusion coefficients for chloroform at 300 K in the pores of the high- ( D par = 1.1(2) × 10 -10 m 2 s -1 ) and low-porosity ( D B = 4.5(1) × 10 -12 m 2 s -1 ) samples reproduce these trends. Our multimodal study thus highlights the significant influence of real structure effects such as stacking faults and grain boundaries on the long-range diffusivity of molecular guest species while suggesting efficient intracrystalline transport at short diffusion times.

The field of machine learning potentials has experienced a rapid surge in progress, thanks to advances in machine learning theory, algorithms, and hardware capabilities. While the underlying methods are continuously evolving, the infrastructure for their deployment has lagged. The community, due to these rapid developments, frequently finds itself split into groups built around different implementations of machine-learned potentials. In this work, we introduce IPSuite , a Python-driven software package designed to connect different methods and algorithms from the comprehensive field of machine-learned potentials into a single platform while also providing a collaborative infrastructure, helping ensure reproducibility. Furthermore, the data management infrastructure of the IPSuite code enables simple model sharing and deployment in simulations. Currently, IPSuite supports six state-of-the-art machine learning approaches for the fitting of interatomic potentials as well as a variety of methods for the selection of training data, running of ab initio calculations, learning-on-the-fly strategies, model evaluation, and simulation deployment.

Molybdenum alkylidyne N -heterocyclic carbene (NHC) complexes of the type [Mo(C- p -C 6 H 4 Y)(OC(R)(CF 3 ) 2 ) 2 (L)(NHC)][B(Ar F ) 4 ] (Y = OMe, NO 2 ; R = CH 3 , CF 3 ; L = none, pivalonitrile, tetrahydrofuran; NHC = 1,3-dimesitylimidazol-2-ylidene (IMes), 1,3-dimesityl-3,4-dihydroimidazol-2-ylidene (IMesH 2 ), 1,3-dimesityl-3,4-dichloroimidazol-2-ylidene (IMesCl 2 ), 1,3-diisopropylimidazol-2-ylidene (I i Pr); B(Ar F ) 4 - = tetrakis(3,5-bis(trifluoromethyl)phen-1-yl)borate) were used in the ring expansion metathesis polymerization (REMP) of cyclic olefins. With cis -cyclooctene ( c COE) cyclic, low molecular weight oligomers were obtained at low monomer concentrations and the cyclic nature of the polymer was confirmed by MALDI-TOF measurements. High-molecular weight cyclic poly( c COE) became available at high monomer concentrations. Also, post-REMP allowed for converting low-molecular-weight cyclic poly(cCOE) into high-molecular-weight cyclic poly(cCOE). Tailored catalysts together with suitable additives offered access to the stereoselective REMP of functional norbornenes providing functional cis -isotactic ( cis-it ), cis -syndiotactic ( cis-st ) and trans-it poly(norbornene)s with up to 99% stereoselectivity. Mechanistic details supported by density functional theory (DFT) calculations are outlined.

The discovery of C 60 , C 60 + , and C 70 in the interstellar medium has ignited a profound interest in the astrochemistry of fullerene and related systems. In particular, the presence of diffuse interstellar bands and their association with C 60 + has led to the hypothesis that hydrogenated derivatives, known as fulleranes, may also exist in the interstellar medium and contribute to these bands. In this study, we systematically investigated the structural and spectroscopic properties of C 60 H n + q ( n = 0-4, q = 0,1) using an automated global minimum search and density functional theory calculations. Our results revealed novel global minimum structures for C 60 H 2 and C 60 H 4 , distinct from previous reports. Notably, all hydrogenated fullerenes exhibited lower ionization potentials and higher proton affinities compared to C 60 . From an astrochemical perspective, our results exposed the challenges in establishing definitive spectroscopic criteria for detecting fulleranes using mid-infrared and UV-Vis spectroscopies. However, we successfully identified distinct electronic transitions in the near-infrared range that serve as distinctive signatures of cationic fulleranes. We strongly advocate for further high-resolution experimental studies to fully explore the potential of these transitions for the interstellar detection of fulleranes.

The first neutral and cationic Mo imido alkylidene cyclic alkyl amino carbene (CAAC) complexes of the general formulae [Mo(N-Ar)(CHCMe 2 Ph)(X) 2 (CAAC)] and [Mo(N-Ar)(CHCMe 2 Ph)(X)(CAAC)][B(Ar F ) 4 ] (X=Br, Cl, OTf, OC 6 F 5 ; CAAC=1-(2,6-iPr 2 -C 6 H 3 )-3,3,5,5-tetramethyltetrahydropyrrol-2-ylidene) have been synthesized from molybdenum imido bishalide alkylidene DME precursors. Different combinations of the imido and "X" ligands have been employed to understand synthetic peculiarities. Selected complexes have been characterized by single-crystal X-ray analysis. Due to the pronounced σ-donor/π-acceptor characteristics of CAACs, the corresponding neutral and cationic molybdenum imido alkylidene CAAC complexes do not require the presence of stabilizing donor ligands such as nitriles. Calculations on the PBE0-D3BJ/def2-TZVP level for PBE0-D3BJ/def2-SVP optimized geometries revealed partial charges at molybdenum similar to the corresponding molybdenum imido alkylidene N-heterocyclic carbene (NHC) complexes with a slightly higher polarization of the molybdenum alkylidene bond in the CAAC complexes. All cationic complexes have been tested in olefin metathesis reactions and showed improved activity compared to the analogous NHC complexes for hydrocarbon-based substrates, allowing for turnover numbers (TONs) up to 9500 even at room temperature. Some Mo imido alkylidene CAAC complexes are tolerant towards functional groups like thioethers and sulfonamides., (© 2023 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)

Pyrazolones represent an important structural motif in active pharmaceutical ingredients. Their asymmetric synthesis is thus widely studied. Still, a generally highly enantio- and diastereoselective 1,4-addition to nitroolefins providing products with adjacent stereocenters is elusive. In this article, a new polyfunctional Cu II -1,2,3-triazolium-aryloxide catalyst is presented which enables this reaction type with high stereocontrol. DFT studies revealed that the triazolium stabilizes the transition state by hydrogen bonding between C(5)-H and the nitroolefin and verify a cooperative mode of activation. Moreover, they show that the catalyst adopts a rigid chiral cage/pore structure by intramolecular hydrogen bonding, by which stereocontrol is achieved. Control catalyst systems confirm the crucial role of the triazolium, aryloxide and Cu II , requiring a sophisticated structural orchestration for high efficiency. The addition products were used to form pyrazolidinones by chemoselective C=N reduction. These heterocycles are shown to be valuable precursors toward β,γ'-diaminoamides by chemoselective nitro and N-N bond reductions. Morphological profiling using the Cell painting assay identified biological activities for the pyrazolidinones and suggest modulation of DNA synthesis as a potential mode of action. One product showed biological similarity to Camptothecin, a lead structure for cancer therapy., (© 2023 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

In the interstellar medium, six molecules have been conclusively detected in the solid state in interstellar ices, and a few dozen have been hypothesized and modeled to be present in the solid state as well. The icy mantles covering micrometer-sized dust grains are, in fact, thought to be at the core of complex molecule formation as a consequence of the local high density of molecules that are simultaneously adsorbed. From a structural perspective, the icy mantle is considered to be layered, with an amorphous water-rich inner layer surrounding the dust grain, covered by an amorphous CO-rich outer layer. Moreover, recent studies have suggested that the CO-rich layer might be crystalline and possibly even be segregated as a single crystal atop the ice mantle. If so, there are far-reaching consequences for the formation of more complex organic molecules, such as methanol and sugars, that use CO as a backbone. Validation of these claims requires further investigation, in particular on acquiring atomistic insight into surface processes, such as adsorption, diffusion, and reactivity on CO ices. Here, we present the first detailed computational study toward treating the weak interaction of (pure) CO ices. We provide a benchmark of the performance of various density functional theory methods in treating the binding of pure CO ices. Furthermore, we perform an atomistic and in-depth study of the binding energy of CO on amorphous and crystalline CO ices using a pair-potential-based force field. We find that CO adsorption is represented by a large distribution of binding energies (200-1600 K) on amorphous CO, including a significant amount of weak binding sites (<350 K). Increasing both the cluster size and the number of neighbors increases the mean of the observed binding energy distribution. Finally, we find that CO binding energies are dominated by dispersion and, as such, exchange-correlation functionals need to include a treatment of dispersion to accurately simulate surface processes on CO ices. In particular, we find the ωB97M-V functional to be a strong candidate for such simulations., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

For decades there were many attempts to dispense with stoichiometric amounts of metal reagents for the synthesis of secondary alcohols. In 2021, the synthetic results of Newman and collaborators pioneered a synthesis still with metals, but not as reactants. Instead, they serverd as catalytic engines. Here we present a description by means of Density Functional Theory calculations of how this process can occur, and an attempt is made to shed light on the mechanism that facilitates the attainment of secondary alcohols, emphasizing the eternal cross-coupling debate of whether the catalytically active species is Ni(0) or they are really taking shortcuts following the course of Ni(II). Effective Orbital analyses give a clear picture. Furthermore, this paper provides insight not only into the nature of the ligands of the metal catalyst but also the role of the base., (© 2023 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)

Organometallic complexes are frequently deposited on solid surfaces, but little is known about how the resulting complex-solid interactions alter their properties. Here, a series of complexes of the type Cu(dppf)(L x ) + (dppf = 1,1'-bis(diphenylphosphino)ferrocene, L x = mono- and bidentate ligands) were synthesized, physisorbed, ion-exchanged, or covalently immobilized on solid surfaces and investigated by 31 P MAS NMR spectroscopy. Complexes adsorbed on silica interacted weakly and were stable, while adsorption on acidic γ-Al 2 O 3 resulted in slow complex decomposition. Ion exchange into mesoporous Na-[Al]SBA-15 resulted in magnetic inequivalence of 31 P nuclei verified by 31 P- 31 P RFDR and 1 H- 31 P FSLG HETCOR. DFT calculations verified that a MeCN ligand dissociates upon ion exchange. Covalent immobilization via organic linkers as well as ion exchange with bidentate ligands both lead to rigidly bound complexes that cause broad 31 P CSA tensors. We thus demonstrate how the interactions between complexes and functional surfaces determine and alter the stability of complexes. The applied Cu(dppf)(L x ) + complex family members are identified as suitable solid-state NMR probes for investigating the influence of support surfaces on deposited inorganic complexes.

The positions of grid points for representing a multidimensional potential energy surface (PES) have a non-negligible impact on its accuracy and the associated computational effort for its generation. Six different positioning schemes were studied for PESs represented by n-mode expansions as needed for the accurate calculation of anharmonic vibrational frequencies by means of vibrational configuration interaction theory. A static approach, which has successfully been used in many applications, and five adaptive schemes based on Gaussian process regression have been investigated with respect to the number of necessary grid points and the accuracy of the fundamental modes for a small set of test molecules. A comparison with a related, more sophisticated, and consistent approach by Christiansen et al. is provided. The impact of the positions of the ab initio grid points is discussed for multilevel PESs, for which the computational effort of the individual electronic structure calculations decreases for increasing orders of the n-mode expansion. As a result of that, the ultimate goal is not the maximal reduction of grid points but rather the computational cost, which is not directly related.

A catalyst type is disclosed allowing for exceptional efficiency in direct 1,4-additions. The catalyst is a zwitterionic entity, in which acetate binds to Cu II , which is formally negatively charged and serving as counterion for benzimidazolium. All 3 functionalities are involved in the catalytic activation. For maleimides productivity was increased by a factor >300 compared to literature (TONs up to 6700). High stereoselectivity and productivity was attained for a broad range of other Michael acceptors as well. The polyfunctional catalyst is accessible in only 4 steps from N-Ph-benzimidazole with an overall yield of 96 % and robust during catalysis. This allowed to reuse the same catalyst multiple times with nearly constant efficiency. Mechanistic studies, in particular by DFT, give a detailed picture how the catalyst operates. The benzimidazolium unit stabilizes the coordinated enolate nucleophile and prevents that acetate/acetic acid dissociate from the catalyst., (© 2023 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

Developing machine learning-based interatomic potentials from ab initio electronic structure methods remains a challenging task for computational chemistry and materials science. This work studies the capability of transfer learning, in particular discriminative fine-tuning, for efficiently generating chemically accurate interatomic neural network potentials on organic molecules from the MD17 and ANI data sets. We show that pre-training the network parameters on data obtained from density functional calculations considerably improves the sample efficiency of models trained on more accurate ab initio data. Additionally, we show that fine-tuning with energy labels alone can suffice to obtain accurate atomic forces and run large-scale atomistic simulations, provided a well-designed fine-tuning data set. We also investigate possible limitations of transfer learning, especially regarding the design and size of the pre-training and fine-tuning data sets. Finally, we provide GM-NN potentials pre-trained and fine-tuned on the ANI-1x and ANI-1ccx data sets, which can easily be fine-tuned on and applied to organic molecules.

Aiming at merocyanine dyes with good linear optical and self-assembly properties, a series of rigid mono-, bi- and tricyclic merocyanines with O - and N -donor units as well as keto or malodinitrile acceptor units was prepared by a convergent approach. With particular focus on tailoring the donor unit, a selection of appropriate derivatives was investigated with respect to their dye properties in solution and in the bulk (UV/Vis, fluorescence, temperature-dependent fluorescence, lifetime). Determination of fluorescence quantum yields revealed the importance of the donor unit and the chromophore size. Larger chromophores and N -donors were beneficial for strong emission in solution, whereas small chromophores and O -donors favored emission in the solid state. To rationalize the different optical properties depending on their donor unit, density functional theory (DFT) calculations were performed. Liquid crystalline derivatives were additionally studied by optical polarization microscopy, differential scanning calorimetry, and X-ray diffraction experiments. For merocyanines with O -donor, fluorinated side chains were mandatory to get stable enantiotropic SmA phases regardless of chromophore size, side chain lengths or acceptor unit. Increased mesophase widths (up to 134 K) were observed upon increasing the chromophore lengths, chain lengths (up to C 12 ) and F/C ratio in the side chain. On the other hand, merocyanines with N -donor and keto acceptor showed enantiotropic SmA phases in the presence of simple alkoxy side chains. The tricyclic merocyanine with N -donor shows an additional SmE phase at lower temperatures. The results revealed the importance of the donor unit to balance optical and mesomorphic properties in merocynanines.

MLL3, also known as KMT2C, is a lysine mono-methyltransferase in charge of the writing of an epigenetic mark on lysine 4 from histone 3. The catalytic site of MLL3 is composed of four tyrosines, namely, Y44, Y69, Y128, and Y130. Tyrosine residues are highly conserved among lysine methyltransferases' catalytic sites, although their complete function is still unclear. The exploration of how modifications on these residues from the enzymatic machinery impact the enzymatic activity of MLL3 could shed light transversally into the inner functioning of enzymes with similar characteristics. Through the use of QMMM calculations, we focus on the effect of the mutation of each tyrosine from the catalytic site on the enzymatic activity and the product specificity in the current study. While we found that the mutations of Y44 and Y128 by phenylalanine inactivated the enzyme, the mutation of Y128 by alanine reactivated the enzymatic activity of MLL3. Moreover, according to our models, the Y128A mutant was even found to be capable of di- and tri-methylate lysine 4 from histone 3, what would represent a gain of function mutation, and could be responsible for the development of diseases. Finally, we were able to establish the inactivation mechanism, which involved the use of Y130 as a water occlusion structure, whose conformation, once perturbed by its mutation or Y128 mutant, allows the access of water molecules that sequester the electron pair from lysine 4 avoiding its methylation process and, thus, increasing the barrier height.

We investigated the field evaporation process of frozen water in atom probe tomography (APT) by density functional simulations. In previous experiments, a strong tailing effect was observed for peaks caused by the molecular structure (H 2 O) n H + , in contrast to other peaks. In purely field-induced and thermally assisted evaporation simulations, we found that chains of protonated water molecules were pulled out of the dielectric surface by up to 6 Å, which are stable over a wide range of field strengths. Therefore, the resulting water clusters experience only part of the acceleration after evaporation compared to molecules evaporating directly from the surface and, thus, exhibit an energy deficit, which explains the tailing effect. Our simulations provide new insight into the complex evaporation behavior of water in high electrical fields and reveal possibilities for adapting the existing reconstruction algorithms.

Recently, searches were made for H 2 CCS and HCCSH in a variety of interstellar environments─all of them resulted in nondetections of these two species. Recent findings have indicated the importance of destruction pathways, e.g., with atomic hydrogen, in explaining the consistent nondetection of other species, such as the H 2 C 3 O family of isomers. We have thus performed ab initio calculations looking at reactions of H 2 CCS, HCCSH, and related species with atomic hydrogen. Our results show that H 2 CCS and HCCSH are both destroyed barrierlessly by atomic hydrogen, thus providing a plausible explanation for the nondetections. We further find that subsequent reactions with atomic hydrogen can barrierlessly lead to CH 3 CH 2 SH, which has been detected. Astrochemical simulations including these reactions result not only in reproducing the observed abundance of H 2 CCS in TMC-1 but also show that CH 3 CH 2 SH, produced via our H-addition pathways and subsequently trapped on grains, can desorb in warmer sources up to abundances that match previous observations of CH 3 CH 2 SH in Orion KL. These results, taken together, point to the importance of grain-surface H-atom addition reactions and highlight the chemical links between cold prestellar cores and their subsequent, warmer evolutionary stages.

The accuracy of the training data limits the accuracy of bulk properties from machine-learned potentials. For example, hybrid functionals or wave-function-based quantum chemical methods are readily available for cluster data but effectively out of scope for periodic structures. We show that local, atom-centered descriptors for machine-learned potentials enable the prediction of bulk properties from cluster model training data, agreeing reasonably well with predictions from bulk training data. We demonstrate such transferability by studying structural and dynamical properties of bulk liquid water with density functional theory and have found an excellent agreement with experimental and theoretical counterparts.

Imaging of liquids and cryogenic biological materials by electron microscopy has been recently enabled by innovative approaches for specimen preparation and the fast development of optimized instruments for cryo-enabled electron microscopy (cryo-EM). Yet, cryo-EM typically lacks advanced analytical capabilities, in particular for light elements. With the development of protocols for frozen wet specimen preparation, atom probe tomography (APT) could advantageously complement insights gained by cryo-EM. Here, we report on different approaches that have been recently proposed to enable the analysis of relatively large volumes of frozen liquids from either a flat substrate or the fractured surface of a wire. Both allowed for analyzing water ice layers which are several micrometers thick consisting of pure water, pure heavy water, and aqueous solutions. We discuss the merits of both approaches and prospects for further developments in this area. Preliminary results raise numerous questions, in part concerning the physics underpinning field evaporation. We discuss these aspects and lay out some of the challenges regarding the APT analysis of frozen liquids.

We propose a machine learning method to model molecular tensorial quantities, namely, the magnetic anisotropy tensor, based on the Gaussian moment neural network approach. We demonstrate that the proposed methodology can achieve an accuracy of 0.3-0.4 cm -1 and has excellent generalization capability for out-of-sample configurations. Moreover, in combination with machine-learned interatomic potential energies based on Gaussian moments, our approach can be applied to study the dynamic behavior of magnetic anisotropy tensors and provide a unique insight into spin-phonon relaxation.

Microemulsions provide a unique opportunity to tailor the polarity and liquid confinement in asymmetric catalysis via nanoscale polar and nonpolar domains separated by a surfactant film. For chiral diene Rh complexes, the influence of counterion and surfactant film on the catalytic activity and enantioselectivity remained elusive. To explore this issue chiral norbornadiene Rh(X) complexes (X=OTf, OTs, OAc, PO 2 F 2 ) were synthesized and characterized by X-ray crystallography and theoretical calculations. These complexes were used in Rh-catalyzed 1,2-additions of phenylboroxine to N-tosylimine in microemulsions stabilized either exclusively by n-octyl-β-D-glucopyranoside (C 8 G 1 ) or a C 8 G 1 -film doped with anionic or cationic surfactants (AOT, SDS and DTAB). The Rh(OAc) complex showed the largest dependence on the composition of the microemulsion, yielding up to 59 % (90 %ee) for the surfactant film doped with 5 wt% of AOT as compared to 52 % (58 %ee) for neat C 8 G 1 at constant surfactant concentration. Larger domains, determined by SAXS analysis, enabled further increase in yield and selectivity while the reaction rate almost remained constant according to kinetic studies., (© 2021 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)

We compare three methods for quantitatively distinguishing the location of noble metal (NM) particles in mesopores from those found on the external support surface. MCM-41 and SBA-15 with NM located in mesopores or on the external surface were prepared and characterized by TEM. 31 P MAS NMR spectroscopy was used to quantify arylphosphines in complexes with NM. Phosphine/NM ratios drop from 2.0 to 0.2 when increasing the probe diameter from 1.08 to 1.54 nm. The reaction between NM and triphenylphosphine (TPP) within 3.0 nm MCM-41 pores takes due to confinement effects multiple weeks. In contrast, external NM react with TPP instantly. A promising method is filling the pores by using the pore volume impregnation technique with tetraethylorthosilicate (TEOS). TPP loading revealed that 66 % of NMs are located on the external surface of MCM-41. The pore filling method can be used in association with any probe molecule, also for the quantification of acid sites., (© 2021 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)

We report new computational and experimental evidence of an efficient and astrochemically relevant formation route to formaldehyde (H 2 CO). This simplest carbonylic compound is central to the formation of complex organics in cold interstellar clouds and is generally regarded to be formed by the hydrogenation of solid-state carbon monoxide. We demonstrate H 2 CO formation via the reaction of carbon atoms with amorphous solid water. Crucial to our proposed mechanism is a concerted proton transfer catalyzed by the water hydrogen bonding network. Consequently, the reactions 3 C + H 2 O → 3 HCOH and 1 HCOH → 1 H 2 CO can take place with low or without barriers, contrary to the high-barrier traditional internal hydrogen migration. These low barriers (or the absence thereof) explain the very small kinetic isotope effect in our experiments when comparing the formation of H 2 CO to D 2 CO. Our results reconcile the disagreement found in the literature on the reaction route C + H 2 O → H 2 CO.

Artificial neural networks (NNs) are one of the most frequently used machine learning approaches to construct interatomic potentials and enable efficient large-scale atomistic simulations with almost ab initio accuracy. However, the simultaneous training of NNs on energies and forces, which are a prerequisite for, e.g., molecular dynamics simulations, can be demanding. In this work, we present an improved NN architecture based on the previous GM-NN model [Zaverkin V.; Kästner, J. J. Chem. Theory Comput . 2020, 16, 5410-5421], which shows an improved prediction accuracy and considerably reduced training times. Moreover, we extend the applicability of Gaussian moment-based interatomic potentials to periodic systems and demonstrate the overall excellent transferability and robustness of the respective models. The fast training by the improved methodology is a prerequisite for training-heavy workflows such as active learning or learning-on-the-fly.

Covalent organic frameworks (COFs) with a pore size beyond 5 nm are still rarely seen in this emerging field. Besides obvious complications such as the elaborated synthesis of large linkers with sufficient solubility, more subtle challenges regarding large-pore COF synthesis, including pore occlusion and collapse, prevail. Here we present two isoreticular series of large-pore imine COFs with pore sizes up to 5.8 nm and correlate the interlayer interactions with the structure and thermal behavior of the COFs. By adjusting interlayer interactions through the incorporation of methoxy groups acting as pore-directing "anchors", different stacking modes can be accessed, resulting in modified stacking polytypes and, hence, effective pore sizes. A strong correlation between stacking energy toward highly ordered, nearly eclipsed structures, higher structural integrity during thermal stress, and a novel, thermally induced phase transition of stacking modes in COFs was found, which sheds light on viable design strategies for increased structural control and stability in large-pore COFs.

Geometry optimization based on Gaussian process regression (GPR) was extended to internal coordinates. We used delocalized internal coordinates composed of distances and several types of angles and compared two methods of including them. In both cases, the GPR surrogate surface is trained on geometries in internal coordinates. In one case, it predicts the gradient in Cartesian coordinates and in the other, in internal coordinates. We tested both methods on a set of 30 small molecules and one larger Rh complex taken from the study of a catalytic mechanism. The former method is slightly more efficient, while the latter method is somewhat more robust. Both methods reduce the number of required optimization steps compared to GPR in Cartesian coordinates or the standard L-BFGS optimizer. We found it advantageous to use automatically adjusted hyperparameters to optimize them.

The mixed lineage leukemia 3 or MLL3 is the enzyme in charge of the writing of an epigenetic mark through the methylation of lysine 4 from the N-terminal domain of histone 3 and its deregulation has been related to several cancer lines. An interesting feature of this enzyme comes from its regulation mechanism, which involves its binding to an activating dimer before it can be catalytically functional. Once the trimer is formed, the reaction mechanism proceeds through the deprotonation of the lysine followed by the methyl-transfer reaction. Here we present a detailed exploration of the activation mechanism through a QM/MM approach focusing on both steps of the reaction, aiming to provide new insights into the deprotonation process and the role of the catalytic machinery in the methyl-transfer reaction. Our finding suggests that the source of the activation mechanism comes from conformational restriction mediated by the formation of a network of salt-bridges between MLL3 and one of the activating subunits, which restricts and stabilizes the positioning of several residues relevant for the catalysis. New insights into the deprotonation mechanism of lysine are provided, identifying a valine residue as crucial in the positioning of the water molecule in charge of the process. Finally, a tyrosine residue was found to assist the methyl transfer from SAM to the target lysine.

Enantiopure secondary alcohols are fundamental high-value synthetic building blocks. One of the most attractive ways to get access to this compound class is the catalytic hydroboration. We describe a new concept for this reaction type that allowed for exceptional catalytic turnover numbers (up to 15 400), which were increased by around 1.5-3 orders of magnitude compared to the most active catalysts previously reported. In our concept an aprotic ammonium halide moiety cooperates with an oxophilic Lewis acid within the same catalyst molecule. Control experiments reveal that both catalytic centers are essential for the observed activity. Kinetic, spectroscopic and computational studies show that the hydride transfer is rate limiting and proceeds via a concerted mechanism, in which hydride at Boron is continuously displaced by iodide, reminiscent to an S N 2 reaction. The catalyst, which is accessible in high yields in few steps, was found to be stable during catalysis, readily recyclable and could be reused 10 times still efficiently working., (© 2020 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

Atom probe tomography allows us to measure the three-dimensional composition of materials with up to atomic resolution by evaporating the material using high electric fields. Initially developed for metals, it is increasingly used for covalently bound structures. To aid the interpretation of the obtained fragmentation pattern, we modeled the fragmentation and desorption of self-assembled monolayers of thiolate molecules on a gold surface in strong electrostatic fields using density functional theory. We used a cluster model and a periodic model of amino-undecanethiolate, NH 2 (CH 2 ) 11 S, and fluoro-decanethiolate, CF 3 (CF 2 ) 7 (CH 2 ) 2 S. In the former molecule, the fragment CH 2 NH 2 + was found to evaporate at fields of 5.4-7.7 V/nm. It was followed by different hydrocarbon fragments. Fluoro-decanethiolate evaporates CF 3 + at fields of 5.7-6.7 V/nm in the cluster model and at 15.4-23.1 V/nm in the periodic model, followed by CF 2 + and C 2 F 4 2+ . Detailed analysis of the electronic structure during the evaporation process revealed a stepwise accumulation of the charge in the head groups exposed to the strongest fields, followed by dissociation of covalent bonds. These observations will facilitate the analysis of atom probe experiments of covalently bound structures.

We show how Gaussian process regression can be used to update Hessian matrices using gradient-based information in the course of an optimization procedure. This is done by building a Gaussian process with at least one initial Hessian and some further energies and gradients from electronic structure calculations and evaluating the desired second derivative of the resulting Gaussian process. To a certain extent, we can overcome the significant scaling problems that occur when training a Gaussian process with Hessian information. We demonstrate in benchmark runs using the partitioned rational function optimization (P-RFO) that this new update method can outperform classical Hessian update methods for small systems.

We investigated the behavior of H2, the main constituent of the gas phase in dense clouds, after collision with amorphous solid water (ASW) surfaces, one of the most abundant chemical species of interstellar ices. We developed a general framework to study the adsorption dynamics of light species on interstellar ices. We provide binding energies and their distribution, sticking probabilities for incident energies between 1 meV and 60 meV, and thermal sticking coefficients between 10 and 300 K for surface temperatures from 10 to 110 K. We found that the sticking probability depends strongly on the adsorbate kinetic energy and the surface temperature, but hardly on the angle of incidence. We observed finite sticking probabilities above the thermal desorption temperature. Adsorption and thermal desorption should be considered as separate events with separate time scales. Laboratory results for these species have shown a gap in the trends attributed to the differently utilized experimental techniques. Our results complement observations and extend them, increasing the range of gas temperatures under consideration. We plan to use our method to study a variety of adsorbates, including radicals and charged species.

We implemented a gradient-based algorithm for finding minimum energy paths (MEPs) using Gaussian process regression (GPR). A subsequent search for transition states can be performed very fast. We describe the algorithm in detail and compare its performance to the nudged elastic band (NEB) method in 27 test systems. Additionally, three different possibilities for an initial guess of the path are evaluated. We found the new optimizer to considerably decrease the number of required energy and gradient evaluations.

We calculated reaction rate constants including atom tunneling for the hydrogen abstraction reaction CH 3 OH + H → CH 2 OH + H 2 with the instanton method. The potential energy was fitted by a neural network that was trained to UCCSD(T)-F12/VTZ-F12 data. Bimolecular gas-phase rate constants were calculated using microcanonic instanton theory. All H/D isotope patterns on the CH 3 group and the incoming H atom are studied. Unimolecular reaction rate constants, representing the reaction on a surface, down to 30 K, are presented for all isotope patterns. At 30 K, they range from 4100 for the replacement of the abstracted H by D to ∼8 for the replacement of the abstracting H to ∼2 to 6 for secondary KIEs. The 12 C/ 13 C kinetic isotope effect is 1.08 at 30 K, while the 16 O/ 18 O kinetic isotope effect is extremely small. A simple kinetic surface model using these data predicts high abundances of the deuterated forms of methanol.

Water is one of the most abundant molecules in the form of solid ice phase in the different regions of the interstellar medium (ISM). This large abundance cannot be properly explained by using only traditional low temperature gas-phase reactions. Thus, surface chemical reactions are believed to be major synthetic channels for the formation of interstellar water ice. Among the different proposals, hydrogenation of atomic O ( i.e. , 2H + O → H 2 O) is a chemically "simple" and plausible reaction toward water formation occurring on the surfaces of interstellar grains. Here, novel theoretical results concerning the formation of water adopting this mechanism on the crystalline (010) Mg 2 SiO 4 surface (a unequivocally identified interstellar silicate) are presented. The investigated reaction aims to simulate the formation of the first water ice layer covering the silicate core of dust grains. Adsorption of the atomic O as a first step of the reaction has been computed, results indicating that a peroxo ( O 2 2 - ) group is formed. The following steps involve the adsorption, diffusion and reaction of two successive H atoms with the adsorbed O atom. Results indicate that H diffusion on the surface has barriers of 4-6 kcal mol -1 , while actual formation of OH and H 2 O present energy barriers of 22-23 kcal mol -1 . Kinetic study results show that tunneling is crucial for the occurrence of the reactions and that formation of OH and H 2 O are the bottlenecks of the overall process. Several astrophysical implications derived from the theoretical results are provided as concluding remarks.

A trivial flaw in the utilization of artificial neural networks in interpolating chemical potential energy surfaces (PES) whose descriptors are Cartesian coordinates is their dependence on simple translations and rotations of the molecule under consideration. A different set of descriptors can be chosen to circumvent this problem, internuclear distances, inverse internuclear distances or z-matrix coordinates are three such descriptors. The objective is to use an interpolated PES in instanton rate constant calculations, hence information on the energy, gradient, and Hessian is required at coordinates in the vicinity of the tunneling path. Instanton theory relies on smoothly fitted Hessians, therefore we use energy, gradients, and Hessians in the training procedure. A major challenge is presented in the proper back-transformation of the output gradients and Hessians from internal coordinates to Cartesian coordinates. We perform comparisons between our method, a previous approach and on-the-fly rate constant calcuations on the hydrogen abstraction from methanol and on the hydrogen addition to isocyanic acid. © 2018Wiley Periodicals, Inc., (© 2018 Wiley Periodicals, Inc.)

The vibrational spectra of simple CH 3 + -Rg (Rg = He, Ne, Ar, Kr) complexes have been studied by vibrational configuration interaction theory relying on multidimensional potential energy surfaces (PESs) obtained from explicitly correlated coupled cluster calculations, CCSD(T)-F12a. In agreement with experimental results, the series of rare gas atoms leads to rather unsystematic results and indicates huge zero point vibrational energy effects for the helium complex. In order to study these sensitive complexes more consistently, we also introduce configuration averaged vibrational self-consistent field theory, which is a generalization of standard vibrational self-consistent field theory to several configurations. The vibrational spectra of the complexes are compared to that of the methyl cation, for which corrections due to scalar-relativistic effects, high-order coupled-cluster terms, e.g., quadruple excitations, and core-valence correlation have explicitly been accounted for. The occurrence of tunneling splittings for the vibrational ground-state of CH 3 + -He has been investigated on the basis of semiclassical instanton theory. These calculations and a direct comparison of the energy profiles along the intrinsic reaction coordinates with that of the hydronium cation, H 3 O + , suggest that tunneling effects for vibrationally excited states should be very small.

The proton affinity (PA) of a range of structurally different N-heterocycles with an exocyclic double bond (= N-heterocyclic olefins, NHOs) has been determined using DFT calculations on the BLYP/def2-TZVPP level. It was found that NHOs belong to the upper end of the superbasicity scale, covering PA values from 262 to 296 kcal/mol. Different types of NHOs are compared with each other and with frequently employed organocatalysts. To boost PA, (a) the ability to delocalize the positive charge and (b) steric pressure/ring strain which can be relieved after protonation were identified as key tuning parameters. Importantly, by analyzing PA alongside partial charges and molecular electrostatic potentials, it is shown that an increase of double bond polarization is not a necessary prerequisite for high PA. In contrast, the more basic, more sterically congested NHOs minimize unfavorable interactions by partly pyramidalyzing the nitrogen atoms, rendering the olefinic bond less electron rich and less polarized. These findings are in excellent agreement with experimental evidence on NHO catalysis, not only providing guidelines for a more rational design regarding PA/basicity but also suggesting that NHOs could be specifically tailored toward either nucleophilic or base-type reaction pathways.

Asymmetric 1,2-additions of cyanide yield enantioenriched cyanohydrins as versatile chiral building blocks. Next to HCN, volatile organic cyanide sources are usually used. Among them, cyanoformates are more attractive on technical scale than TMSCN for cost reasons, but catalytic productivity is usually lower. Here, the development of a new strategy for cyanations is described, in which this activity disadvantage is overcome. A Lewis acidic Al center cooperates with an aprotic onium moiety within a remarkably robust bifunctional Al-F-salen complex. This allowed for unprecedented turnover numbers of up to 10 4 . DFT studies suggest an unexpected unique trimolecular pathway in which the ammonium bound cyanide attacks the aldehyde, which itself is activated by the carbonyl group of the cyanoformate binding to the Al center. In addition, a novel practical carboxycyanation method was developed that makes use of KCN as the sole cyanide source. The use of a pyrocarbonate as carboxylating reagent provided the best results., (© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Canonical instanton theory is a widespread approach to describe the dynamics of chemical reactions in low temperature environments when tunneling effects become dominant. It is a semiclassical theory which requires locating classical periodic orbits on the upside-down potential energy surface, so-called instantons, and the computation of second order quantum corrections. The calculation of these corrections usually involves a matrix diagonalization. In this paper we present an alternative approach, which requires to solve only linear systems of equations involving sparse matrices. Furthermore, the proposed method provides a reliable and numerically stable way to obtain stability parameters in multidimensional systems, which are of particular interest in the context of microcanonical instanton theory.

We implemented a gradient-based algorithm for transition state search which uses Gaussian process regression. Besides a description of the algorithm, we provide a method to find the starting point for the optimization if only the reactant and product minima are known. We perform benchmarks on 27 test systems against the dimer method and partitioned rational function optimization as implemented in the DL-FIND library. We found the new optimizer to significantly decrease the number of required energy and gradient evaluations.

Instanton theory is an established method to calculate rate constants of chemical reactions including atom tunneling. Technical and methodological improvements increased its applicability. Still, a large number of energy and gradient calculations is necessary to optimize the instanton tunneling path, and second derivatives of the potential energy along the tunneling path have to be evaluated, restricting the range of suitable electronic structure methods. To enhance the applicability of instanton theory, we present a dual-level approach in which instanton optimizations and Hessian calculations are performed using an efficient but approximate electronic structure method, and the potential energy along the tunneling path is recalculated using a more accurate method. This procedure extends the applicability of instanton theory to high-level electronic structure methods for which analytic gradients may not be available, like local linear-scaling approaches. We demonstrate for the analytical Eckart barrier and three molecular systems how the dual-level instanton approach corrects for the largest part of the error caused by the inaccuracy of the efficient electronic structure method. This reduces the error of the calculated rate constants significantly.

Lewis pair polymerization employing N -Heterocyclic olefins (NHOs) and simple metal halides as co-catalysts has emerged as a useful tool to polymerize diverse lactones. To elucidate some of the mechanistic aspects that remain unclear to date and to better understand the impact of the metal species, computational methods have been applied. Several key aspects have been considered: (1) the formation of NHO-metal halide adducts has been evaluated for eight different NHOs and three different Lewis acids, (2) the coordination of four lactones to MgCl₂ was studied and (3) the deprotonation of an initiator (butanol) was investigated in the presence and absence of metal halide for one specific Lewis pair. It was found that the propensity for adduct formation can be influenced, perhaps even designed, by varying both organic and metallic components. Apart from the NHO backbone, the substituents on the exocyclic, olefinic carbon have emerged as interesting tuning site. The tendency to form adducts is ZnCl₂ > MgCl₂ > LiCl. If lactones coordinate to MgCl₂, the most likely binding mode is via the carbonyl oxygen. A chelating coordination cannot be ruled out and seems to gain importance upon increasing ring-size of the lactone. For a representative NHO, it is demonstrated that in a metal-free setting an initiating alcohol cannot be deprotonated, while in the presence of MgCl₂ the same process is exothermic with a low barrier., Competing Interests: The authors declare no conflict of interest.

Isoxazolinones are biologically and synthetically interesting densely functionalized heterocycles, which for a long time were not accessible in enantioenriched form by asymmetric catalysis. Next to the deficit of enantioselective methods, the functionalization of isoxazolinones is often plagued by regioselectivity issues due to the competition of various nucleophilic centers within the heterocycles. We report the first regio- and enantioselective C-allylations of isoxazolinones. These occur with high regioselectivity in favor of the linear allylation products, although Ir phosphoramidite catalysts were used, which commonly results in branched isomers. Our studies suggest that this outcome is the result of a reaction cascade via an initial regio- and enantioselective N-allylation to provide a branched allyl intermediate, followed by a spontaneous [3,3]-rearrangement resulting in chirality transfer., (© 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The hydrogen abstraction reaction between H and H 2 S, yielding HS and H 2 as products, has been studied within the framework of interstellar surface chemistry. High-temperature rate constants below 2000 K are calculated in the gas phase and are in agreement with previously reported values. Subsequently, low-temperature rate constants down to 55 K are presented for the first time that are of interest to astrochemistry, i.e., covering both bimolecular and unimolecular reaction mechanisms. For this, a so-called implicit surface model is used. In strict terms, this is a structural gas-phase model in which the restriction of the rotation in the solid state is taken into account. The calculated kinetic isotope effects are explained in terms of the difference in activation and delocalization. All rate constants are calculated at the UCCSD(T)-F12/cc-VTZ-F12 level of theory. Finally, we show that the energetics of the reaction is affected to an only small extent by the presence of H 2 O or H 2 S molecular clusters that simulate an ice surface, calculated at the MPWB1K/def2-TZVP level of theory.

Canonical instanton theory is known to overestimate the rate constant close to a system-dependent crossover temperature and is inapplicable above that temperature. We compare the accuracy of the reaction rate constants calculated using recent semi-classical rate expressions to those from canonical instanton theory. We show that rate constants calculated purely from solving the stability matrix for the action in degrees of freedom orthogonal to the instanton path is not applicable at arbitrarily low temperatures and use two methods to overcome this. Furthermore, as a by-product of the developed methods, we derive a simple correction to canonical instanton theory that can alleviate this known overestimation of rate constants close to the crossover temperature. The combined methods accurately reproduce the rate constants of the canonical theory along the whole temperature range without the spurious overestimation near the crossover temperature. We calculate and compare rate constants on three different reactions: H in the Müller-Brown potential, methylhydroxycarbene → acetaldehyde and H 2  + OH → H + H 2 O. © 2017 Wiley Periodicals, Inc., (© 2017 Wiley Periodicals, Inc.)

A detailed analysis of the C(sp 3 )-H activation process by vinylidene Au I complexes is described based on an intrinsic bond orbital analysis. Based on our analysis this event can be divided into three phases: (i) hydride transfer, (ii) C-C bond formation, and (iii) σ to π rearrangement of the lone pair coordinated to Au. Small perturbations of the system lead to either a concerted asynchronous reaction, or a stepwise reaction featuring an intermediate with a C-H-C three-centre two-electron (3c-2e) bond. The role of π-donating substituents is highlighted and provides a way of controlling reactions of this type in future experimental studies., (© 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The first synthetic protocol to high oxidation state molybdenum(VI) N-heterocyclic carbene (NHC) alkylidyne complexes (NHC=1,3-diisopropylimidazol-2-ylidene, 1,3-dimethyl-4,5-R 2 -imidazol-2-ylidene, R 2 =H, Cl, CN) is reported. Steric limitations of the NHCs and the benzylidyne are described. All novel complexes were characterized by single crystal X-ray diffraction and solution NMR techniques. It was shown that all complexes presented here show activity in the self-metathesis of 1-phenyl-1-propyne at room temperature. To identify mechanistic differences, an experimental sequence to detect dissociation of ligands was developed. Results reveal dissociation of less electron-donating NHCs in course of the reaction. Mechanistic and reactivity differences were attributed to electronic and steric effects through Tolman's electronic parameter and the percentage of buried volume. Furthermore, Mo-1 containing the 1,3-dimethylimidazol-2-ylidene ligand showed good activity in self-metathesis reactions of p-substituted 1-phenyl-1-propynes with electron-donating moieties at room temperature., (© 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Atom tunneling in the hydrogen atom transfer reaction of the 2,4,6-tri-tert-butylphenyl radical to 3,5-di-tert-butylneophyl, which has a short but strongly curved reaction path, was investigated using instanton theory. We found the tunneling path to deviate qualitatively from the classical intrinsic reaction coordinate, the steepest-descent path in mass-weighted Cartesian coordinates. To perform that comparison, we implemented a new variant of the predictor-corrector algorithm for the calculation of the intrinsic reaction coordinate. We used the reaction force analysis method as a means to decompose the reaction barrier into structural and electronic components. Due to the narrow energy barrier, atom tunneling is important in the abovementioned reaction, even above room temperature. Our calculated rate constants between 350 K and 100 K agree well with experimental values. We found a H/D kinetic isotope effect of almost 10 6 at 100 K. Tunneling dominates the protium transfer below 400 K and the deuterium transfer below 300 K. We compared the lengths of the tunneling path and the classical path for the hydrogen atom transfer in the reaction HCl + Cl and quantified the corner cutting in this reaction. At low temperature, the tunneling path is about 40% shorter than the classical path.