Best-Practice DFT Protocols for Basic Molecular Computational Chemistry

Indenoannulated Tridecacyclene: An All-Carbon Seven-Stage Redox-Amphoter

We disclose an indenoannulated tridecacyclene comprising a central cyclooctatetraene moiety with multiple adjacent pentagonal rings which is accessible in a concise synthetic sequence. The saddle-shaped geometry of the non-benzenoid polycyclic scaffold and its unique packing behavior in the solid state were characterized by X-ray crystallography. In electrochemical studies, the compound undergoes seven reversible redox events comprising five reductions and two oxidations. The dicationic and dianionic species obtained by chemical oxidation and reduction, respectively, were characterized spectroscopically in solution. Density functional theory calculations were applied to provide insights into aromaticity evolution in the respective charged species, highlighting the beneficial effect of the non-benzenoid moieties on charge stabilization.

The Fe-MAN Challenge: Ferrates-Microkinetic Assessment of Numerical Quantum Chemistry

Organometallic species, such as organoferrate ions, are prototypical nucleophiles prone to reacting with a wide range of electrophiles, including proton donors. In solution, the operation of dynamic equilibria and the simultaneous presence of several organometallic species severely complicate the analysis of these fundamentally important reactions. This can be overcome by gas-phase experiments on mass-selected ions, which allow for the determination of the microscopic reactivity of the target species. In this contribution, we focus on the reactivity of a series of trisarylferrate complexes toward 2,2,2-trifluoroethanol and 2,2-difluoroethanol. By means of mass-spectrometric measurements, we determined the experimental bimolecular rate constants kexp of the gas-phase protolysis reactions of the trisarylferrate anions FePh3- and FeMes3- with the aforementioned acids. Based on these experiments, we carried out a dual blind challenge, inviting theoretical groups to submit their best predictions for the activation barriers and/or theoretical rate constants ktheo. This provides a unique opportunity to evaluate different computational protocols under minimal bias and sets the stage for further benchmarking of quantum chemical methods and data-driven approaches in the future.

Possibilities and Limitations of Kinetic Studies in On-Surface Synthesis by Real Time X-ray Photoelectron Spectroscopy

The kinetics of coupling reactions on surfaces can be quantitatively studied in real time by X-ray Photoelectron Spectroscopy (XPS). From fitting experimental data, kinetic reaction parameters such as the rate constant's pre-exponential and activation energy can be deduced and compared to quantum chemical simulations. To elucidate the possibilities and limitations of this approach, we propose studies in which experimental data are first simulated and subsequently fitted. Knowing the exact kinetic parameters used in the simulation allows one to evaluate the accuracy of the fit result. Here, several experimental influences, such as the data point density and the addition of noise, are explored for a model reaction with first-order kinetics. The proposed procedure sheds light on the accuracy with which kinetic parameters can be derived and may also help in the design of future experiments.

Recent advances in computational and experimental protein-ligand affinity determination techniques

INTRODUCTION

Modern drug discovery revolves around designing ligands that target the chosen biomolecule, typically proteins. For this, the evaluation of affinities of putative ligands is crucial. This has given rise to a multitude of dedicated computational and experimental methods that are constantly being developed and improved.

AREAS COVERED

In this review, the authors reassess both the industry mainstays and the newest trends among the methods for protein - small-molecule affinity determination. They discuss both computational affinity predictions and experimental techniques, describing their basic principles, main limitations, and advantages. Together, this serves as initial guide to the currently most popular and cutting-edge ligand-binding assays employed in rational drug design.

EXPERT OPINION

The affinity determination methods continue to develop toward miniaturization, high-throughput, and in-cell application. Moreover, the availability of data analysis tools has been constantly increasing. Nevertheless, cross-verification of data using at least two different techniques and careful result interpretation remain of utmost importance.

Encapsulation of charged halogens by the 512 water cage

This study focuses on the encapsulation of the entire series of halides by the 512 cage of twenty water molecules and on the characterization of water to water and water to anion interactions. State-of-the-art computations are used to determine equilibrium geometries, energy related quantities, and thermal stability towards dissociation and to dissect the nature and strength of intermolecular interactions holding the clusters as stable units. Two types of structures are revealed: heavily deformed cages for F- indicating a preference for microsolvation, and slightly deformed cages for the remaining anions indicating a preference for encapsulation. The primary variable dictating the properties of the clusters is the charge density of the central halide, with the most severe effects observed for the F- case. For the remaining halides, the anion may be safely viewed as a sort of "big electron" with little local disruptive power, enough to affect the network of non-covalent hydrogen bonds in the cage, but not enough to break it. Gibbs energies for dissociation either into cavity and halide or into water molecules and halide suggest that, in a similar way as to methane clathrate, a more weakly bonded complex that has been detected in the gas phase, all halide containing clathrate-like structures should be amenable to experimental detection in the gas phase at moderate temperature and pressure conditions.

Scaffold-Oriented Asymmetric Catalysis: Conformational Modulation of Transition State Multivalency during a Catalyst-Controlled Assembly of a Pharmaceutically Relevant Atropisomer

A new class of superbasic, bifunctional peptidyl guanidine catalysts is presented, which enables the organocatalytic, atroposelective synthesis of axially chiral quinazolinediones. Computational modeling unveiled the conformational modulation of the catalyst by a novel phenyl urea N-cap, that preorganizes the structure into the active, folded state. A previously unanticipated noncovalent interaction involving a difluoroacetamide acting as a hybrid mono- or bidentate hydrogen bond donor emerged as a decisive control element inducing atroposelectivity. These discoveries spurred from a scaffold-oriented project inspired from a fascinating investigational BTK inhibitor featuring two stable chiral axes and relies on a mechanistic framework that was foreign to the extant lexicon of asymmetric catalysis.

Reply to the Comments on Planar Tetracoordinate Hydrogen: Pushing the Limit of Multicentre Bonding

Recently, Huo et al. has commented on our communication (Angew. Chem. Int. Ed. 2024, 63, e202317312, DOI: 10.1002/anie.202317312), regarding the multireference character (MRC) of our proposed cluster. Their argument is based on small HOMO-LUMO gap, fractional occupation density (FOD) and CASPT2(12,13) calculations. They also proposed that the singlet planar In4H+ cluster cannot be observed. We present our calculations which reveals that some of their arguments are based on wrong interpretation of data and inadequate use of methodology. While we certainly agree with the strong physical ground of FOD, CASSF and CASPT2 methodology, we believe that such analysis for clusters is not adequate.

Electronic properties and collision cross sections of AgOkHm± (k, m = 1-4) aerosol ionic clusters

Experimental evidence shows that hydroxylated metal ions are often produced during cluster synthesis by atmospheric pressure spark ablation. In this work, we predict the ground state equilibrium structures of AgOkHm± clusters (k and m = 1-4), which are readily produced when spark ablating Ag, using the coupled cluster with singles and doubles (CCSD) method. The stabilization energy of these clusters is calculated with respect to the dissociation channel having the lowest energy, by accounting perturbative triples corrections to the CCSD method. The interatomic interactions in each of the systems have been investigated using the frontier molecular orbital (FMO), natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) methods. Many of the ground states of these ionic clusters are found to be stable, corroborating experimental observations. We find that clusters having singlet spin states are more stable in terms of dissociation than the clusters that have doublet or triplet spin states. Our calculations also indicate a strong affinity of the ionic and neutral Ag atom towards water and hydroxyl radicals or ions. Many 3-center, 4-electron (3c/4e) hyperbonds giving rise to more than one resonance structure are identified primarily for the anionic clusters. The QTAIM analysis shows that the O-H and O-Ag bonds in the clusters of both polarities are respectively covalent and ionic. The FMO analysis indicates that the anionic clusters are more reactive than the cationic ones. Using the cluster structures predicted by the CCSD method, we calculate the collision cross sections of the AgOkHm± family, with k and m ranging from 1 to 4, by the trajectory method. In turn, we predict the electrical mobilities of these clusters when suspended in helium at atmospheric pressure and compare them with experimental measurements.

Evaluation of DFT methods for predicting geometries and NMR spectra of Bi(III) dithiocarbamate complexes with antitumor properties

CONTEXT

Bismuth complexes with dithiocarbamate ligands have attracted attention because of their biological applications, such as antimicrobial, antileishmanial, and anticancer properties. These complexes have high cytotoxic activity against cancer cells, being more active than the standard drugs cisplatin, doxorubicin, and tamoxifen. In the present study, we investigated the ability of some DFT methods to reproduce the geometries and NMR spectra of the Bi(III) dithiocarbamate complexes, selected based on their proven antitumor activity. Our investigation revealed that the M06-L/def2-TZVP/ECP/CPCM method presented good accuracy in predicting geometries, while the TPSSh/def2-SVP/ECP/CPCM method proved effective in analyzing the 13C NMR spectra of these molecules. In general, all examined methods exhibited comparable performance in predicting 1H NMR signals.

METHODS

Calculations were performed with the Gaussian 09 program using the def2-SVP and def2-TZVP basis sets, employing relativistic effective core potential (ECP) for Bi and using the CPCM solvent model. The exchange-correlation functionals BP86, PBE, OLYP, M06-L, B3LYP, B3LYP-D3, M06-2X, TPSSh, CAM-B3LYP, and ωB97XD were used in the study. Geometry optimizations were started from crystallographic structures available at the Cambridge Structural Database. The theoretical results were compared with experimental data using the mean root-mean-square deviation (RMSD), mean absolute deviations (MAD), and linear correlation coefficient (R2).

Asymmetric Pd/Organoboron-Catalyzed Site-Selective Carbohydrate Functionalization with Alkoxyallenes Involving Noncovalent Stereocontrol

Herein, we demonstrate the robustness of a synergistic chiral Pd/organoboron system in tackling a challenging suite of site-, regio-, enantio- and diastereoselectivity issues across a considerable palette of biologically relevant carbohydrate polyols, when prochiral alkoxyallenes were employed as electrophiles. In view of the burgeoning role of noncovalent interactions (NCIs) in stereoselective carbohydrate synthesis, our mechanistic experiments and DFT modeling of the reaction path unexpectedly revealed that NCIs such as hydrogen bonding and CH-π interactions between the resting states of the Pd-π-allyl complex and the borinate saccharide are critically involved in the stereoselectivity control. Our strategy thus illuminates the untapped potential of harnessing NCIs in the context of transition metal catalysis to tackle stereoselectivity challenges in carbohydrate functionalization.

Antifungal Potential of Secondary Metabolites Derived from Arcangelisia flava (L.) Merr.: An Analysis of In Silico Enzymatic Inhibition and In Vitro Efficacy against Candida Species

Considering the escalating resistance to conventional antifungal medications, it is critical to identify novel compounds that can efficiently counteract this challenge. The purpose of this research was to elucidate the fungicidal properties of secondary metabolites derived from Arcangelisia flava, with a specific focus on their efficacy against Candida species. This study utilized a combination approach comprising laboratory simulations and experiments to discern and evaluate the biologically active constituents present in the dichloromethane extract of A. flava. The in vitro experiments demonstrated that compounds 1 (palmatine) and 2 (fibraurin) exhibited antifungal properties. The compounds exhibited minimum inhibitory concentrations (MICs) ranging from 15.62 to 62.5 µg/mL against Candida sp. Moreover, compound 1 demonstrated a minimum fungicidal concentration (MFC) of 62.5 µg/mL against Candida glabrata and C. krusei. In contrast, compound 2 exhibited an MFC of 125 µg/mL against both Candida species. Based on a molecular docking study, it was shown that compounds 1 and 2 have a binding free energy of -6.6377 and -6.7075 kcal/mol, respectively, which indicates a strong affinity and specificity for fungal enzymatic targets. This study utilized pharmacophore modeling and Density Functional Theory (DFT) simulations to better understand the interaction dynamics and structural properties crucial for antifungal activity. The findings underscore the potential of secondary metabolites derived from A. flava to act as a foundation for creating novel and highly efficient antifungal treatments, specifically targeting fungal diseases resistant to existing treatment methods. Thus, the results regarding these compounds can provide references for the next stage in antifungal drug design. Further investigation is necessary to thoroughly evaluate these natural substances' clinical feasibility and safety characteristics, which show great potential as antifungal agents.

Reinvestigation of the internal glycan rearrangement of Lewis a and blood group type H1 epitopes

Protonated ions of fucose-containing oligosaccharides are prone to undergo internal glycan rearrangement which results in chimeric fragments that obfuscate mass-spectrometric analysis. Lack of accessible tools that would facilitate systematic analysis of glycans in the gas phase limits our understanding of this phenomenon. In this work, we use density functional theory modeling to interpret cryogenic IR spectra of Lewis a and blood group type H1 trisaccharides and to establish whether these trisaccharides undergo the rearrangement during gas-phase analysis. Structurally unconstrained search reveals that none of the parent ions constitute a thermodynamic global minimum. In contrast, predicted collision cross sections and anharmonic IR spectra provide a good match to available experimental data which allowed us to conclude that fucose migration does not occur in these antigens. By comparing the predicted structures with those obtained for Lewis x and blood group type H2 epitopes, we demonstrate that the availability of the mobile proton and a large difference in the relative stability of the parent ions and rearrangement products constitute the prerequisites for the rearrangement reaction.

EnTdecker - A Machine Learning-Based Platform for Guiding Substrate Discovery in Energy Transfer Catalysis

Due to the magnitude of chemical space, the discovery of novel substrates in energy transfer (EnT) catalysis remains a daunting task. Experimental and computational strategies to identify compounds that successfully undergo EnT-mediated reactions are limited by their time and cost efficiency. To accelerate the discovery process in EnT catalysis, we herein present the EnTdecker platform, which facilitates the large-scale virtual screening of potential substrates using machine-learning (ML) based predictions of their excited state properties. To achieve this, a data set is created containing more than 34,000 molecules aiming to cover a vast fraction of synthetically relevant compound space for EnT catalysis. Using this data predictive models are trained, and their aptitude for an in-lab application is demonstrated by rediscovering successful substrates from literature as well as experimental validation through luminescence-based screening. By reducing the computational effort needed to obtain excited state properties, the EnTdecker platform represents a tool to efficiently guide substrate selection and increase the experimental success rate for EnT catalysis. Moreover, through an easy-to-use web application, EnTdecker is made publicly accessible under entdecker.uni-muenster.de.

XMECP: Reaching State-of-the-Art MECP Optimization in Multiscale Complex Systems

The Python-based program, XMECP, is developed for realizing robust, efficient, and state-of-the-art minimum energy crossing point (MECP) optimization in multiscale complex systems. This article introduces the basic capabilities of the XMECP program by theoretically investigating the MECP mechanism of several example systems including (1) the photosensitization mechanism of benzophenone, (2) photoinduced proton-coupled electron transfer in the cytosine-guanine base pair in DNA, (3) the spin-flip process in oxygen activation catalyzed by an iron-containing 2-oxoglutarate-dependent oxygenase (Fe/2OGX), and (4) the photochemical pathway of flavoprotein adjusted by the intensity of an external electric field. MECPs related to multistate reaction and multistate reactivity in large-scale complex biochemical systems can be well-treated by workflows suggested by the XMECP program. The branching plane updating the MECP optimization algorithm is strongly recommended as it provides derivative coupling vector (DCV) with explicit calculation and can equivalently evaluate contributions from non-QM residues to DCV, which can be nonadiabatic coupling or spin-orbit coupling in different cases. In the discussed QM/MM examples, we also found that the influence on the QM region by DCV can occur through noncovalent interactions and decay with distance. In the example of DNA base pairs, the nonadiabatic coupling occurs across the π-π stacking structure formed in the double-helix system. In contrast to general intuition, in the example of Fe/2OGX, the central ferrous and oxygen part contribute little to the spin-orbit coupling; however, a nearby arginine residue, which is treated by molecular mechanics in the QM/MM method, contributes significantly via two hydrogen bonds formed with α-ketoglutarate (α-KG). This indicates that the arginine residue plays a significant role in oxygen activation, driving the initial triplet state toward the productive quintet state, which is more than the previous knowledge that the arginine residue can bind α-KG at the reaction site by hydrogen bonds.

Influence of acid-base equilibrium on interactions of some monofunctional coumarin Pd(II) complexes with biologically relevant nucleophiles-comprehensive kinetic study

This aimed to develop a comprehensive theoretical protocol for examining substitution reaction processes. The researchers used a theoretical quantum-mechanical protocol based on the QM-ORSA approach, which estimates the kinetic parameters of thermodynamically favourable reaction pathways. This theoretical protocol was validated by experimentally investigating substitution mechanisms in two previously synthesised Pd(II) complexes: chlorido-[(3-(1-(2-hydroxypropylamino)ethylidene)chroman-2,4-dione)]palladium(II) (C1) and chlorido-[(3-(1-(2-mercaptoethylamino)-ethylidene)-chroman-2,4dione)]palladium(II) (C2), along with biologically relevant nucleophiles, namely L-cysteine (l-Cys), L-methionine (l-Met), and guanosine-5'-monophosphate (5'-GMP). Reactions were investigated under pseudo-first-order conditions, monitoring nucleophile concentration and temperature changes using stopped-flow UV-vis spectrophotometry. All reactions were conducted under physiological conditions (pH = 7.2) at 37 °C. The reactivity of the studied nucleophiles follows the order: l-Cys > l-Met > 5'-GMP, and the reaction mechanism is associative based on the activation parameters. The experimental and theoretical data showed that C2 is more reactive than C1, confirming that the complexes' structural and electronic properties greatly affect their reactivity with selected nucleophiles. The study's findings have confirmed that the primary interaction occurs with the acid-base species L-Cys, mostly through the involvement of the partially negative sulfur atom (87.2%). On the other hand, C2 has a higher propensity for reacting with L-Cys-, primarily through the partially negative oxygen atom (92.6%). The implementation of this theoretical framework will significantly restrict the utilization of chemical substances, hence facilitating cost reduction and environmental protection.

NBN- and BNB-Phenalenyls: the Yin and Yang of Heteroatom-doped π Systems

NBN- and BNB-doped phenalenyls are isoelectronic to phenalenyl anions and cations, respectively. They represent a pair of complementary molecules that have essentially identical structures but opposite properties as electron donors and acceptors. The NBN-phenalenyls 1-4 considered here were prepared from N,N'-dimethyl-1,8-diaminonaphthalene and readily available boron-containing building blocks (i. e., BH3⋅SMe2 (1), p-CF3-C6H4B(OH)2 (2), C6H5B(OH)2 (3), or MesBCl2/iPr2NEt (4)). Treatment of 1 with 4-Me2N-2,6-Me2-C6H2Li gave the corresponding NBN derivative 5. The BNB-phenalenyl 6 was synthesized from 1,8-naphthalenediyl-bridged diborane(6), PhNH2, and MesMgBr. A computational study reveals that the photoemission of 1, 4, and 5 originates from locally excited (LE) states at the NBN-phenalenyl fragments, while that of 2 is dominated by charge transfer (CT) from the NBN-phenalenyl to the p-CF3-C6H4 fragment. Depending on the dihedral angle θ between its Ph and NBN planes, compound 3 emits mainly from a less polar LE (θ >55°) or more polar CT state (θ <55°). In turn, the energetic preference for either state is governed by the polarity of the solvent used. An equimolar aggregate of the NBN- and BNB-phenalenyls 3 and 6 (in THF/H2O) shows a distinct red-shifted emission compared to that of the individual components, which originates from an intermolecular CT state.

Dimerization of Fe(III) Ion in an Aqueous Medium: Mechanistic Modelling and Effects of Ligands

Aqueous iron solutions generally undergo spontaneous hydrolysis followed by aggregation resulting in the precipitation of nanocrystalline oxyhydroxide minerals. The mechanism of nucleation of such multinuclear oxyhydroxide clusters are unclear due to limited experimental evidence. Here, we investigate the mechanistic pathway of dimerization of Fe(III) ions using density functional theory (DFT) in aqueous medium considering effects of other ligands. Two hydrolyzed monomeric Fe(III) ions in aqueous medium may react to form two closely related binuclear products, the μ-oxo and the dihydroxo Fe2 dimer. Our studies indicate that the water molecules in the second coordination sphere and those co-ordinated to the Fe(III) ion, both participate in the dimerization process. The proposed mechanism effectively explains the formation of dihydroxo and μ-oxo Fe2 dimers with interconversion possibilities, for the first time. Results show, with only water molecules present in the second co-ordination sphere, dihydroxo Fe2 dimer is the thermodynamically and kinetically favored product with a low activation free energy. We calculated the step-wise reaction free energies of dimerization in the presence of nitrate ions in the first and second coordination sphere of Fe(III) ion separately, which shows that with nitrate ions in the second co-ordination sphere, the μ-oxo Fe2 dimer is the kinetically favored product.

Amino Group-Driven Adsorption of Sodium p-Perfluorous Nonenoxybenzene Sulfonate in Water by the Modified Graphene Oxide

Sodium p-perfluorous nonenoxybenzene sulfonate (OBS) is one of the key alternatives to perfluoroalkyl substances (PFASs). Its widespread tendency has increased extensive contamination in the aquatic environment. However, the present treatment technology for OBS exhibited insignificant adsorption capacity and long adsorption time. In this study, three proportions (1:5, 3:5, and 10:1) of chitosan-modified amino-driven graphene oxide (CS-GO) were innovated to strengthen the OBS adsorption capacity, compared with graphene oxide (GO) and graphene (GH). Through the characterization of SEM, BET, and FTIR, it was discovered that CS was synthetized on GO surfaces successfully with a low specific surface area. Subsequently, batch single influence factor studies on OBS removal from simulated wastewater were investigated. The optimum removal efficiency of OBS could be achieved up to 95.4% within 2 h when the adsorbent was selected as CS-GO (10:1), the dosage was 2 mg, and the pH was 3. The addition of inorganic ions could promote the adsorption efficiency of OBS. In addition, CS-GO presented the maximum adsorption energy due to additional functional groups of -NH3, and electrostatic interaction was the foremost motive for improving the adsorption efficiency of OBS. Moreover, OBS exhibited the fastest diffusion coefficient in the CS-GO-OBS solution, which is consistent with the fitting results of adsorption kinetics.

Robust vibrational coherence protected by a core-shell structure in silver nanoclusters

Vibrational coherence has attracted considerable research interests because of its potential functions in light harvesting systems. Although positive signs of vibrational coherence in metal nanoclusters have been observed, the underlying mechanism remains to be verified. Here, we demonstrate that robust vibrational coherence with a lifetime of 1 ps can be clearly identified in Ag44(SR)30 core-shell nanoclusters, in which an icosahedral Ag12 core is well protected by a dodecahedral Ag20 cage. Ultrafast spectroscopy reveals that two vibrational modes at around 2.4 THz and 1.6 THz, corresponding to the breathing mode and quadrupolar-like mode of the icosahedral Ag12 core, respectively, are responsible for the generation of vibrational coherence. In addition, the vibrational coherence of Ag44 has an additional high frequency mode (2.4 THz) when compared with that of Ag29, in which there is only one low frequency vibration mode (1.6 THz), and the relatively faster dephasing in two-layer Ag29 relative to that in Ag44 further supports the fact that the robust vibrational coherence in Ag44 is ascribed to its unique matryoshka-like core-shell structure. Our findings not only present unambiguous experimental evidence for a multi-layer core-shell structure protected vibrational coherence under ambient conditions but also offers a practical strategy for the design of highly efficient quantum optoelectronic devices.

From a humorous post to a detailed quantum-chemical study: isocyanate synthesis revisited

Isocyanates play an essential role in modern manufacturing processes, especially in polyurethane production. There are numerous synthesis strategies for isocyanates both under industrial and laboratory conditions, which do not prevent searching for alternative highly efficient synthetic protocols. Here, we report a detailed theoretical investigation of the mechanism of sulfur dioxide-catalyzed rearrangement of phenylnitrile oxide into phenyl isocyanate, which was first reported in 1977. The DLPNO-CCSD(T) method and up-to-date DFT protocols were used to perform a highly accurate quantum-chemical study of the rearrangement mechanism. An overview of various organic and inorganic catalysts has revealed other potential catalysts, such as sulfur trioxide and selenium dioxide. Furthermore, the present study elucidated how substituents in phenylnitrile oxide influence reaction kinetics. This study was performed by a self-organized collaboration of scientists initiated by a humorous post on the VK social network.

Aluminagerma[5]pyramidanes-Formation and Skeletal Rearrangement

The salt metathesis reaction of dipotassium germacyclopentadienediide with aluminum(III) dichlorides provides either half-sandwich alumole complexes of germanium(II) or aluminylene germole complexes. Their molecular structure and the delocalized bonding situation, revealed by density functional theory (DFT) calculations, are equally described as isomeric aluminagerma[5]pyramidanes with either the germanium or the aluminum atom in the apical position of the pentagonal pyramid. The product formation and the selectivity of the reaction depends on the third substituent of the aluminum dichloride. Aryl-substituents favor the formation of alumole complexes and Cp*-substituents that of the isomeric germole complexes. With amino-substituents at the aluminum atom mixtures of both isomers are formed and the positional exchange of the two heteroatoms is shown by NMR spectroscopy. The alumole complexes of germanium(II) undergo facile reductive elimination of germanium and form the corresponding alumoles.

Argentophilic Interactions, Flexibility, and Dynamics of Pyrrole Cages Encapsulating Silver(I) Clusters

Recently, pyrrole cages have been synthesized that encapsulate ion pairs and silver(I) clusters to form intricate supramolecular capsules. We report here a computational analysis of these structures using density functional theory combined with a semiempirical tight-binding approach. We find that for neutral pyrrole cages, the Gibbs free energies of formation provide reliable predictions for the ratio of bound ions. For charged pyrrole cages, we find strong argentophilic interactions between Ag ions on the basis of the calculated bond indices and molecular orbitals. For the cage with the Ag4 cluster, we find two minimum-geometry conformations that differ by only 6.5 kcal/mol, with an energy barrier <1 kcal/mol, suggesting a very flexible structure as indicated by molecular dynamics. The predicted energies of formation of [Agn⊂1]n-3+ (n = 1-5) cryptands provide low energy barriers of formation of 5-20 kcal/mol for all cases, which is consistent with the experimental data. Furthermore, we also examined the structural variability of mixed-valence silver clusters to test whether additional geometrical conformations inside the organic cage are thermodynamically accessible. In this context, we show that the time-dependent density functional theory UV-vis spectra may potentially serve as a diagnostic probe to characterize mixed-valence and geometrical configurations of silver clusters encapsulated into cryptands.

Using atomic clustering based on structural and electronic descriptors that consider surrounding environment to evaluate local properties of DFT functionals

We developed a method for evaluating the accuracies of the local properties of DFT functionals in detail using a clustering method based on machine learning and structural/electronic descriptors. We generated 36 clusters consistent with human intuition using 30,436 carbon atoms from the QM9 dataset. The results were used to evaluate 13C NMR chemical shifts calculated using 84 DFT functionals. Carbon atoms were grouped based on their similar environments, reducing errors within these groups. This enables more accurate assessment of the accuracy using a specific DFT functional. Therefore, the present atomic clustering provides more detailed insight into accuracy verification.

Carbon-Rich Plasma-Deposited Silicon Oxycarbonitride Films Derived from 4-(Trimethylsilyl)morpholine as a Novel Single-Source Precursor

4-(trimethylsilyl)morpholine O(CH2CH2)2NSi(CH3)3 (TMSM) was investigated as a single-source precursor for SiCNO films synthesis. Optical emission spectroscopy of plasma generated from TMSM/He, TMSM/H2, and TMSM/NH3 gas mixtures revealed the presence of N2, CH, H, CN, and CO species. The last two are suggested to be responsible for the lowering of carbon concentration in the films in comparison with the precursor. The refractive index ranged from 1.5 to 2.0, and bandgap varied from 2.0 to 4.6 eV, which pointed that some of the films can be used as antireflective coatings in silicon photovoltaic cell technologies and dielectric layers in electronic devices.

An Update in Computational Methods for Environmental Monitoring: Theoretical Evaluation of the Molecular and Electronic Structures of Natural Pigment-Metal Complexes

Metals are beneficial to life, but the presence of these elements in excessive amounts can harm both organisms and the environment; therefore, detecting the presence of metals is essential. Currently, metal detection methods employ powerful instrumental techniques that require a lot of time and money. Hence, the development of efficient and effective metal indicators is essential. Several synthetic metal detectors have been made, but due to their risk of harm, the use of natural pigments is considered a potential alternative. Experiments are needed for their development, but they are expensive and time-consuming. This review explores various computational methods and approaches that can be used to investigate metal-pigment interactions because choosing the right methods and approaches will affect the reliability of the results. The results show that quantum mechanical methods (ab initio, density functional theory, and semiempirical approaches) and molecular dynamics simulations have been used. Among the available methods, the density functional theory approach with the B3LYP functional and the LANL2DZ ECP and basis set is the most promising combination due to its good accuracy and cost-effectiveness. Various experimental studies were also in good agreement with the results of computational methods. However, deeper analysis still needs to be carried out to find the best combination of functions and basis sets.

Differentiation of solvatomorphs of active pharmaceutical ingredients (API) by solid-state vibrational circular dichroism (VCD)

Here, we present the new application of solid-state Vibrational Circular Dichroism (VCD) spectroscopy to differentiate several dutasteride (DS) solvatomorphs - the model active pharmaceutical ingredient (API). Several crystalline DS hydrochloride hydrates solvated with methanol, ethanol, acetonitrile, acetone, and acetic acid were prepared. In contrast to almost identical IR spectra, the VCD ones were very sensitive to changes in the sample composition. We marked significant differences in the shape of VCD spectra of studied DS solvatomorphs, DS hydrates, and DS polymorphic forms. Our findings, supported by DFT calculations, show that VCD spectroscopy has the pronounced ability to distinguish their crystal arrangements. We believe that this contribution will extend the use of VCD in the pharmaceutical industry for developing and designing new chiral drug products for the identification, description, and in-depth probing of several pharmaceutical solvatomorphs in the future.

Multilevel Framework for Analysis of Protein Folding Involving Disulfide Bond Formation

In this study, a three-layered multicenter ONIOM approach is implemented to characterize the naive folding pathway of bovine pancreatic trypsin inhibitor (BPTI). Each layer represents a distinct level of theory, where the initial layer, encompassing the entire protein, is modeled by a general all-atom force-field GFN-FF. An intermediate electronic structure layer consisting of three multicenter fragments is introduced with the state-of-the-art semiempirical tight-binding method GFN2-xTB. Higher accuracy, specifically addressing the breaking and formation of the three disulfide bonds, is achieved at the innermost layer using the composite DFT method r2SCAN-3c. Our analysis sheds light on the structural stability of BPTI, particularly the significance of interlinking disulfide bonds. The accuracy and efficiency of the multicenter QM/SQM/MM approach are benchmarked using the oxidative formation of cystine. For the folding pathway of BPTI, relative stabilities are investigated through the calculation of free energy contributions for selected intermediates, focusing on the impact of the disulfide bond. Our results highlight the intricate trade-off between accuracy and computational cost, demonstrating that the multicenter ONIOM approach provides a well-balanced and comprehensive solution to describe electronic structure effects in biomolecular systems. We conclude that multiscale energy landscape exploration provides a robust methodology for the study of intriguing biological targets.

Formoxyboranes as hydroborane surrogates for the catalytic reduction of carbonyls through transfer hydroboration

A new class of Lewis base stabilized formoxyboranes demonstrates the feasibility of catalytic transfer hydroboration. In the presence of a ruthenium catalyst, they have shown broad applicability for reducing carbonyl compounds. Various borylated alcohols are obtained in high selectivity and yields up to 99%, tolerating several functional groups. Computational studies enabled to propose a mechanism for this transformation, revealing the role of the ruthenium catalyst and the absence of hydroborane intermediates.

A Novel Abiotic Pathway for Phosphine Synthesis over Acidic Dust in Venus' Atmosphere

Recent ground-based observations of Venus have detected a single spectral feature consistent with phosphine (PH3) in the middle atmosphere, a gas which has been suggested as a biosignature on rocky planets. The presence of PH3 in the oxidized atmosphere of Venus has not yet been explained by any abiotic process. However, state-of-the-art experimental and theoretical research published in previous works demonstrated a photochemical origin of another potential biosignature-the hydride methane-from carbon dioxide over acidic mineral surfaces on Mars. The production of methane includes formation of the HC · O radical. Our density functional theory (DFT) calculations predict an energetically plausible reaction network leading to PH3, involving either HC · O or H· radicals. We suggest that, similarly to the photochemical formation of methane over acidic minerals already discussed for Mars, the origin of PH3 in Venus' atmosphere could be explained by radical chemistry starting with the reaction of ·PO with HC·O, the latter being produced by reduction of CO2 over acidic dust in upper atmospheric layers of Venus by ultraviolet radiation. HPO, H2P·O, and H3P·OH have been identified as key intermediate species in our model pathway for phosphine synthesis.

Systematic QM/MM Study for Predicting 31P NMR Chemical Shifts of Adenosine Nucleotides in Solution and Stages of ATP Hydrolysis in a Protein Environment

NMR (nuclear magnetic resonance) spectroscopy allows for important atomistic insights into the structure and dynamics of biological macromolecules; however, reliable assignments of experimental spectra are often difficult. Herein, quantum mechanical/molecular mechanical (QM/MM) calculations can provide crucial support. A major problem for the simulations is that experimental NMR signals are time-averaged over much longer time scales, and since computed chemical shifts are highly sensitive to local changes in the electronic and structural environment, sufficiently large averages over representative structural ensembles are essential. This entails high computational demands for reliable simulations. For NMR measurements in biological systems, a nucleus of major interest is 31P since it is both highly present (e.g., in nucleic acids) and easily observable. The focus of our present study is to develop a robust and computationally cost-efficient framework for simulating 31P NMR chemical shifts of nucleotides. We apply this scheme to study the different stages of the ATP hydrolysis reaction catalyzed by p97. Our methodology is based on MM molecular dynamics (MM-MD) sampling, followed by QM/MM structure optimizations and NMR calculations. Overall, our study is one of the most comprehensive QM-based 31P studies in a protein environment and the first to provide computed NMR chemical shifts for multiple nucleotide states in a protein environment. This study sheds light on a process that is challenging to probe experimentally and aims to bridge the gap between measured and calculated NMR spectroscopic properties.

The Importance of Reaction Energy in Predicting Chemical Reaction Barriers with Machine Learning Models

Improving our fundamental understanding of complex heterocatalytic processes increasingly relies on electronic structure simulations and microkinetic models based on calculated energy differences. In particular, calculation of activation barriers, usually achieved through compute-intensive saddle point search routines, remains a serious bottleneck in understanding trends in catalytic activity for highly branched reaction networks. Although the well-known Brønsted-Evans-Polyani (BEP) scaling - a one-feature linear regression model - has been widely applied in such microkinetic models, they still rely on calculated reaction energies and may not generalize beyond a single facet on a single class of materials, e. g., a terrace sites on transition metals. For highly branched and energetically shallow reaction networks, such as electrochemical CO2 reduction or wastewater remediation, calculating even reaction energies on many surfaces can become computationally intractable due to the combinatorial explosion of states that must be considered. Here, we investigate the feasibility of activation barrier prediction without knowledge of the reaction energy using linear and nonlinear machine learning (ML) models trained on a new database of over 500 dehydrogenation activation barriers. We also find that inclusion of the reaction energy significantly improves both classes of ML models, but complex nonlinear models can achieve performance similar to the simplest BEP scaling when predicting activation barriers on new systems. Additionally, inclusion of the reaction energy significantly improves generalizability to new systems beyond the training set. Our results suggest that the reaction energy is a critical feature to consider when building models to predict activation barriers, indicating that efforts to reliably predict reaction energies through, e. g., the Open Catalyst Project and others, will be an important route to effective model development for more complex systems.

CREST-A program for the exploration of low-energy molecular chemical space

Conformer-rotamer sampling tool (CREST) is an open-source program for the efficient and automated exploration of molecular chemical space. Originally developed in Pracht et al. [Phys. Chem. Chem. Phys. 22, 7169 (2020)] as an automated driver for calculations at the extended tight-binding level (xTB), it offers a variety of molecular- and metadynamics simulations, geometry optimization, and molecular structure analysis capabilities. Implemented algorithms include automated procedures for conformational sampling, explicit solvation studies, the calculation of absolute molecular entropy, and the identification of molecular protonation and deprotonation sites. Calculations are set up to run concurrently, providing efficient single-node parallelization. CREST is designed to require minimal user input and comes with an implementation of the GFNn-xTB Hamiltonians and the GFN-FF force-field. Furthermore, interfaces to any quantum chemistry and force-field software can easily be created. In this article, we present recent developments in the CREST code and show a selection of applications for the most important features of the program. An important novelty is the refactored calculation backend, which provides significant speed-up for sampling of small or medium-sized drug molecules and allows for more sophisticated setups, for example, quantum mechanics/molecular mechanics and minimum energy crossing point calculations.

DELFI: a computer oracle for recommending density functionals for excited states calculations

Density functional theory (DFT) is the workhorse of computational quantum chemistry. One of its main limitations is that choosing the right functional is a non-trivial task left for human experts. The choice is particularly hard for excited state calculations when using its time-dependent formulation (TD-DFT). This is due to the approximations of the method, but also because the photophysical properties of a molecule are defined by a manifold of states that all need to be properly described. This includes not only the relative energy of the states, but also capturing the correct character, order, and intensity of the transitions. In this work, we developed a neural network to recommend functionals to be used on molecules for TD-DFT calculations, by simultaneously considering all these properties for a manifold of states. This was possible by developing a scoring system to define the accuracy of an excited state's calculation against a higher-accuracy reference. The scoring system is generalizable to any level of theory; we here applied it to evaluate the performance of common functionals of different rungs against a higher accuracy method on a large set of organic molecules. The results are collected in a database that we released and made open, providing four million data points to the community for future applications. The scoring system assigns a value between zero and one hundred to each functional for each molecule, transforming the complicated task of learning photophysical properties into a simpler regression task. We used the dataset to train a graph attention neural network to predict the scores for unseen molecules. We call this oracle DELFI (Data-driven EvaLuation of Functionals by Inference), which can be used to quickly screen and predict the ranking of functionals to calculate the optical properties of organic molecules. We validated DELFI in two in silico experiments: choosing a common functional for a series of spiropyran-merocyanine isomers and a unique functional to screen a large dataset of over 50 000 organic photovoltaic molecules, for which an extensive benchmark would be unfeasible. A corresponding web application allows DELFI to be easily run and the results to be analyzed, alleviating the hurdle of choosing the right functional for TD-DFT calculations.

Reversible Thiyl Radical Addition-Fragmentation Chain Transfer Polymerization

Developing reversible-deactivation radical polymerization (RDRP) methods that could directly control the thiyl radical propagation is highly desirable yet remains challenging in modern polymer chemistry. Here, we reported the first reversible thiyl radical addition-fragmentation chain transfer (SRAFT) polymerization strategy, which utilizes allyl sulfides as chain transfer agents for reversibly deactivating the propagating thiyl radicals, thus allowing us to directly control a challenging thiyl radical chain polymerization to afford polymers with well-defined architectures. A linear dependence of molecular weight on conversion, high chain-end fidelity, and efficient chain extension proved good controllability of the polymerization. In addition, density functional theory calculations provided insight into the reversible deactivation ability of allyl sulfides. The SRAFT strategy developed in this work represents a promising platform for discovering new controlled polymerizations based on thiyl radical chemistry.

Improving Quantum Chemical Solvation Models by Dynamic Radii Adjustment for Continuum Solvation (DRACO)

We present the Dynamic Radii Adjustment for COntinuum solvation (DRACO) approach, which employs precomputed atomic partial charges and coordination numbers of the solute atoms to improve the solute cavity. As such, DRACO is compatible with major solvation models, improving their performance significantly and robustly at virtually no extra cost, especially for charged solutes. Combined with the purely electrostatic CPCM and COSMO models, DRACO reduces the mean absolute deviation (MAD) of the solvation free energy by up to 4.5 kcal mol-1 (67%) for a large data set of polar and ionic solutes. Even in combination with the highly empirical universal solvation model (SMD), DRACO substantially reduces the MAD for charged solutes by up to 1.5 kcal mol-1 (39%), while neutral solutes are slightly improved (0.2 kcal mol-1 or 16%). We present an interface of DRACO with two computationally efficient atomic charge models that enables fully automated, out-of-the-box calculations with the widely used program packages Orca and TurboMole.

Density functional theory methods applied to homogeneous and heterogeneous catalysis: a short review and a practical user guide

The application of density functional theory (DFT) methods in catalysis has been growing fast in the last few decades thanks to both the availability of more powerful high computing resources and the development of new efficient approximations and approaches. DFT calculations allow for the understanding of crucial catalytic aspects that are difficult or even impossible to access by experiments, thus contributing to faster development of more efficient and selective catalysts. Depending on the catalytic system and properties under investigation, different approaches should be used. Moreover, the reliability of the obtained results deeply depends on the approximations involved in both the selected method and model. This review addresses chemists, physicists and materials scientists whose interest deals with the application of DFT-based computational tools in both homogeneous catalysis and heterogeneous catalysis. First, a brief introduction to DFT is presented. Then, the main approaches based on atomic centered basis sets and plane waves are discussed, underlining the main differences, advantages and limitations. Eventually, guidance towards the selection of the catalytic model is given, with a final focus on the evaluation of the energy barriers, which represents a crucial step in all catalytic processes. Overall, the review represents a rational and practical guide for both beginners and more experienced users involved in the wide field of catalysis.

Mechanism and Origin of Stereoselectivity for the NHC-Catalyzed Desymmetrization Reaction for the Synthesis of Axially Chiral Biaryl Aldehydes

Organocatalytic desymmetrization reaction is a powerful tool for constructing axial chirality, but the theoretical study on the origin of stereoselectivity still lags behind even now. In this work, the N-heterocyclic carbene (NHC)-catalyzed desymmetrization reaction of biaryl frameworks for the synthesis of axially chiral aldehydes has been selected and theoretically investigated by using density functional theory (DFT). The fundamental pathway involves several steps, i.e., desymmetrization, formation of Breslow oxidation, esterification, and NHC regeneration. The desymmetrization and formation of Breslow processes have been identified as stereoselectivity-determining and rate-determining steps. Further weak interaction analyses proved that the C-H···O hydrogen bond and C-H···π interactions are responsible for the stability of the key stereoselective desymmetrization transition states. This research contributes to understanding the nature of NHC-catalyzed desymmetrization reactions for the synthesis of axially chiral compounds.

Integrating multiscale and machine learning approaches towards the SAMPL9 log P challenge

The partition coefficient (log P) is an important physicochemical property that provides information regarding a molecule's pharmacokinetics, toxicity, and bioavailability. Methods to accurately predict the partition coefficient have the potential to accelerate drug design. In an effort to test current methods and explore new computational techniques, the statistical assessment of the modeling of proteins and ligands (SAMPL) has established a blind prediction challenge. The ninth iteration challenge was to predict the toluene-water partition coefficient (log Ptol/w) of sixteen drug molecules. Herein, three approaches are reported broadly under the categories of quantum mechanics (QM), molecular mechanics (MM), and data-driven machine learning (ML). The three blind submissions yield mean unsigned errors (MUE) ranging from 1.53-2.93 log Ptol/w units. The MUEs were reduced to 1.00 log Ptol/w for the QM methods. While MM and ML methods outperformed DFT approaches for challenge molecules with fewer rotational degrees of freedom, they suffered for the larger molecules in this dataset. Overall, DFT functionals paired with a triple-ζ basis set were the simplest and most effective tool to obtain quantitatively accurate partition coefficients.

Scalar Relativistic All-Electron and Pseudopotential Ab Initio Study of a Minimal Nitrogenase [Fe(SH)4H]- Model Employing Coupled-Cluster and Auxiliary-Field Quantum Monte Carlo Many-Body Methods

Nitrogenase is the only enzyme that can cleave the triple bond in N2, making nitrogen available to organisms. The detailed mechanism of this enzyme is currently not known, and computational studies are complicated by the fact that different density functional theory (DFT) methods give very different energetic results for calculations involving nitrogenase models. Recently, we designed a [Fe(SH)4H]- model with the fifth proton binding either to Fe or S to mimic different possible protonation states of the nitrogenase active site. We showed that the energy difference between these two isomers (ΔE) is hard to estimate with quantum-mechanical methods. Based on nonrelativistic single-reference coupled-cluster (CC) calculations, we estimated that the ΔE is 101 kJ/mol. In this study, we demonstrate that scalar relativistic effects play an important role and significantly affect ΔE. Our best revised single-reference CC estimates for ΔE are 85-91 kJ/mol, including energy corrections to account for contributions beyond triples, core-valence correlation, and basis-set incompleteness error. Among coupled-cluster approaches with approximate triples, the canonical CCSD(T) exhibits the largest error for this problem. Complementary to CC, we also used phaseless auxiliary-field quantum Monte Carlo calculations (ph-AFQMC). We show that with a Hartree-Fock (HF) trial wave function, ph-AFQMC reproduces the CC results within 5 ± 1 kJ/mol. With multi-Slater-determinant (MSD) trials, the results are 82-84 ± 2 kJ/mol, indicating that multireference effects may be rather modest. Among the DFT methods tested, τ-HCTH, r2SCAN with 10-13% HF exchange with and without dispersion, and O3LYP/O3LYP-D4, and B3LYP*/B3LYP*-D4 generally perform the best. The r2SCAN12 (with 12% HF exchange) functional mimics both the best reference MSD ph-AFQMC and CC ΔE results within 2 kJ/mol.

Thermochemistry of Species in Gas-Phase Thermal Oxidation of C2 to C8 Perfluorinated Carboxylic Acids

New thermochemical properties, Cp°(T), H°(T), S°(T), and G°(T), are predicted for 123 species involved in the thermal destruction of perfluorinated carboxylic acids (PFCAs) using computational quantum chemistry and ideal-gas statistical mechanics. Relevant species were identified from the development of mechanisms for the pyrolysis and oxidation of PFCAs of C2 to C8 in length. Partition functions were obtained from the results of calculations at the G4 level for species up to C4 in length and M06-2X-D3(0)/def2-QZVPP for species C5 to C8 in length. The 1D hindered-rotor approximation was used to correct for torsional modes in the larger species. Ideal-gas thermochemistry was computed and fitted to 7-parameter NASA polynomials over a 200-2500 K temperature range, and the data are provided in standardized format. To gauge the effects of both method and basis set choice, enthalpies of formation at 0 K are calculated from various other density functionals (including B3LYP and ωB97XD), basis sets, and composite model chemistries (CBS-QB3). They are benchmarked against data from the Active Thermochemical Tables, high-level ANL0 calculations from the literature, and G4 calculations from this work. The effects of internal rotations and other anharmonicities are discussed, and bond dissociation energies and reaction equilibria provide mechanistic insights.

Studying the adsorption of emerging organic contaminants in zeolites with dispersion-corrected density functional theory calculations: From numbers to recommendations

Adsorption energies obtained from dispersion-corrected density functional theory (DFT) calculations show a considerable dependence on the choice of exchange-correlation functional and dispersion correction. A number of investigations have employed different approaches to compute adsorption energies of small molecules in zeolites, using reference values from high-level calculations and/or experiments. Such comparative studies are lacking for larger functional organic molecules such as pharmaceuticals or personal care products, despite their potential relevance for applications, e. g., in contaminant removal or drug delivery. The present study aims to fill this gap by comparing adsorption energies and, for selected cases, equilibrium structures of emerging organic contaminants adsorbed in MOR- and FAU-type all-silica zeolites. A total of 13 dispersion-corrected DFT approaches are compared, including methods using a pairwise dispersion correction as well as non-local van der Waals density functionals. While absolute values of adsorption energies vary widely, qualitative trends across the set of zeolite-guest combinations are not strongly dependent on the choice of functional. For selected cluster models, DFT adsorption energies are compared to reference values from coupled cluster (DLPNO-CCSD(T)) calculations. Although all DFT approaches deliver systematically more negative adsorption energies than the coupled cluster reference, this tendency is least pronounced for the rev-vdW-DF2 functional.

Development of a universal method for vibrational analysis of the terminal alkyne C≡C stretch

The terminal alkyne C≡C stretch has a large Raman scattering cross section in the "silent" region for biomolecules. This has led to many Raman tag and probe studies using this moiety to study biomolecular systems. A computational investigation of these systems is vital to aid in the interpretation of these results. In this work, we develop a method for computing terminal alkyne vibrational frequencies and isotropic transition polarizabilities that can easily and accurately be applied to any terminal alkyne molecule. We apply the discrete variable representation method to a localized version of the C≡C stretch normal mode. The errors of (1) vibrational localization to the terminal alkyne moiety, (2) anharmonic normal mode isolation, and (3) discretization of the Born-Oppenheimer potential energy surface are quantified and found to be generally small and cancel each other. This results in a method with low error compared to other anharmonic vibrational methods like second-order vibrational perturbation theory and to experiments. Several density functionals are tested using the method, and TPSS-D3, an inexpensive nonempirical density functional with dispersion corrections, is found to perform surprisingly well. Diffuse basis functions are found to be important for the accuracy of computed frequencies. Finally, the computation of vibrational properties like isotropic transition polarizabilities and the universality of the localized normal mode for terminal alkynes are demonstrated.

Predicting the Decomposition Mechanism of the Serine α-Amino Acid in the Gas Phase and Condensed Media

Comprehending the nitrogen combustion chemistry during the thermal treatment of biomass demands acquiring a detailed mechanism for reaction pathways that dictate the degradation of amino acids. Serine (Ser) is an important α-amino acid that invariably exists in various categories of biomass, most notably algae. Based on density functional theory (DFT) coupled with kinetic modeling, this study presents a mechanistic overview of reactions that govern the fragmentation of the Ser compound in the gas phase as well as in the crystalline form. Thermokinetic parameters are computed for a large set of reactions and involved species. The initial decomposition of Ser is solely controlled by a dehydration channel that leads to the formation of a 2-aminoacrylic acid molecule. Decarboxylation and deamination routes are likely to be of negligible importance. The falloff window of the dehydration channel extends until the atmospheric pressure. Bimolecular reactions between two Ser compounds simulate the widely discussed cross-linking reactions that prevail in the condensed medium. It is demonstrated that the formation of the key experimentally observed products (NH3, CO2, and CO) may originate from direct bond fissions in the melted phase of Ser prior to evaporation. A constructed kinetic model (with 24 reactions) accounts for the primary steps in the degradation of the Ser molecule in the gas phase. These steps include dehydration, decarboxylation, deamination, and others. The kinetic model presents an onset decomposition temperature of 700 K with the complete conversion attained at ∼1090 K. Likewise, the model portrays the temperature-dependent increasing yields of CO2 and NH3. The results presented in this work offer a detailed analysis of the intricate chemical processes involved in nitrogen transformations, specifically in relation to amino acids. Amino acids play a crucial role as the primary nitrogen carriers in biomass, such as microalgae and protein-rich biomass.

A Linear Two-Coordinate Cr(II) Complex: Synthesis, Characterization, and Reactivity

The synthesis and characterization of a linear two-coordinate Cr(II) amido complex, Cr{N(t Bu)Dipp}2 (Dipp=2,6-diisopropylphenyl), from the reaction of 1 molar equivalent (equiv) of CrCl2 and 2 equiv. of LiN(t Bu)Dipp is reported. Single-crystal X-ray diffractometry (SC-XRD) analysis revealed that it has a short Cr-N bond distance of 1.8878(9) Å, which could be attributed to the relatively less bulky nature of the amido ligand compared with reported systems. Furthermore, the oxidation reaction of the two-coordinate Cr(II) complex was explored. The oxidation reaction of Cr{N(t Bu)Dipp}2 with the one-electron oxidants AgOTf and [FeCp2 ][BArF 4 ] (BArF 4 - =[B{C6 H3 -3,5-(CF3 )2 }4 ]- ) afforded the trigonal planar three- and bent two-coordinate Cr(III) complexes Cr{N(t Bu)Dipp}2 (OTf) and [Cr{N(t Bu)Dipp}2 ][BArF 4 ], respectively. The reaction of Cr{N(t Bu)Dipp}2 with 1 equiv. of the organic azides AdN3 (Ad=1-adamantyl) and PhN3 afforded the three-coordinate Cr(IV) imido complexes Cr{N(t Bu)Dipp}2 (NAd) and Cr{N(t Bu)Dipp}2 (NPh), respectively. The reaction of Cr{N(t Bu)Dipp}2 and two equiv. of Me3 NO afforded the Cr(VI) dioxo complex Cr{N(t Bu)Dipp}2 (O)2 . The reaction of Cr{N(t Bu)Dipp}2 with 1 equiv. of CyN=C=NCy resulted in the insertion of the carbodiimide into the Cr-N bond, with the formation of a three-coordinate Cr(II) complex. Finally, density functional theory (DFT) calculations were used to elucidate the electronic structure of these complexes.

Theoretical Prediction of the Reaction Probabilities of H, O, and OH Radicals on the Polypropylene Surface

To determine the H-abstraction reaction probabilities of H/O/OH radicals with a polypropylene (PP) surface, a first-principles calculation was performed based on the DLPNO-CCSD(T)/CBS//M06-2X-D3/def-TZVP theory level. The PP chain model used in this study was 2,4,6-trimethylheptane. The rate constants of the H/O/OH radicals with the isolated PP chain model were calculated based on the conventional transition-state theory. By comparing the experimental values and considering the error factors and their compensation, it was concluded that the orders of magnitude of the predicted rate constants were accurate. The resulting rate constants were converted to reaction probabilities between the H/O/OH radicals and the PP surface. The method used in this study is applicable for obtaining theoretical values of surface reaction probabilities based on first-principles calculations. The calculation at the DLPNO-CCSD(T)/CBS theory level has high accuracy but consumes a large amount of computational resources. The study also demonstrated that the double-hybrid functionals, wB97x-2-D3(BJ) and rev-DSD-PBEP86-D3(BJ), with a 3-ζ or 4-ζ basis set, could reproduce the electronic energy values obtained from DLPNO-CCSD(T)/CBS while using only approximately 1/100 of the computational resources required by the latter under our computer configuration.

UV Laser-Induced Photodecomposition of Matrix-Isolated Salicylhydroxamic Acid: Identification of New Isocyanate Complexes

Photochemical reactions of salicylhydroxamic acid were induced using tunable UV laser radiation followed by FTIR spectroscopy. Four pairs of co-products were experimentally found to appear in the photolysis: C6H4(OH)NCO⋯H2O (1), C6H4(OH)C(O)N⋯H2O (2), C6H4(OH)2⋯HNCO (3), and C6H4(OH)NHOH⋯CO (4). The comparison of the theoretical spectra with the experimental ones allowed us to determine the structures of the complexes formed in the matrices. The mechanisms of the reaction channels leading to the formation of the photoproducts were proposed. It was concluded that the first step in the formation of the complexes (1), (2), and (3) was the scission of the N-O bond, whereas the creation of complex (4) was due to cleavage of the C-N bond.

DFT-Enabled Development of Hemilabile (P∧N) Ligands for Gold(I/III) RedOx Catalysis: Application to the Thiotosylation of Aryl Iodides

Ligand-enabled oxidative addition of Csp2-X bonds to Au(I) centers has recently appeared as a valuable strategy for the development of catalytic RedOx processes. Several cross-coupling reactions that were previously considered difficult to achieve were reported lately, thus expanding the synthetic potential of gold(I) complexes beyond the traditional nucleophilic functionalization of π-systems. MeDalPhos has played an important role in this development and, despite several studies on alternative structures, remains, so far, the only general ligand for such process. We report herein the discovery and DFT-enabled structural optimization of a new family of hemilabile (P∧N) ligands that can promote the oxidative addition of aryl iodides to gold(I). These flexible ligands, which possess a common 2-methylamino heteroaromatic N-donor motif, are structurally and electronically tunable, beyond being easily accessible and affordable. The corresponding Au(I) complexes were shown to outperform the reactivity of (MeDalPhos)Au(I) in a series of alkoxy- and amidoarylations of alkenes. Their synthetic potential and comparatively higher reactivity were further highlighted in the thiotosylation of aryl iodides, a challenging unreported C-S cross-coupling reaction that could not be achieved under classical Pd(0/II) catalysis and that allows for general and divergent access to aryl sulfur derivatives.

Molecular Gas-Phase Conformational Ensembles

Accurately determining the global minima of a molecular structure is important in diverse scientific fields, including drug design, materials science, and chemical synthesis. Conformational search engines serve as valuable tools for exploring the extensive conformational space of molecules and for identifying energetically favorable conformations. In this study, we present a comparison of Auto3D, CREST, Balloon, and ETKDG (from RDKit), which are freely available conformational search engines, to evaluate their effectiveness in locating global minima. These engines employ distinct methodologies, including machine learning (ML) potential-based, semiempirical, and force field-based approaches. To validate these methods, we propose the use of collisional cross-section (CCS) values obtained from ion mobility-mass spectrometry studies. We hypothesize that experimental gas-phase CCS values can provide experimental evidence that we likely have the global minimum for a given molecule. To facilitate this effort, we used our gas-phase conformation library (GPCL) which currently consists of the full ensembles of 20 small molecules and can be used by the community to validate any conformational search engine. Further members of the GPCL can be readily created for any molecule of interest using our standard workflow used to compute CCS values, expanding the ability of the GPCL in validation exercises. These innovative validation techniques enhance our understanding of the conformational landscape and provide valuable insights into the performance of conformational generation engines. Our findings shed light on the strengths and limitations of each search engine, enabling informed decisions for their utilization in various scientific fields, where accurate molecular structure determination is crucial for understanding biological activity and designing targeted interventions. By facilitating the identification of reliable conformations, this study significantly contributes to enhancing the efficiency and accuracy of molecular structure determination, with particular focus on metabolite structure elucidation. The findings of this research also provide valuable insights for developing effective workflows for predicting the structures of unknown compounds with high precision.

Hybrid DFT Geometries and Properties for 17k Lanthanoid Complexes─The LnQM Data Set

The unique properties of lanthanoids and their diverse applications make them an indispensable part of modern research and industry. While the field has garnered attention, there remains a gap in available molecule data sets that facilitate both classical quantum chemistry calculations and the burgeoning field of machine learning in data science applications. This research addresses the need for a comprehensive data set that allows for a comparative analysis of various lanthanoids. The herein presented, curated data set includes 17269 monolanthanoid complexes derived from 1205 distinct ligand motifs. Structures encompass all 15 lanthanoids in the +3 oxidation state and exhibit molecular charges ranging from -1 to +3, including structures with a high spin multiplicity up to 8. Starting from lanthanum complexes, samples were processed with a permutation of the central lanthanoid atom, resulting in highly comparable subsets, facilitating comparative studies in which the influence of the lanthanoid can be investigated independently of ligand effects. The data set provides a broad range of features such as PBE0-D4/def2-SVP optimized geometries and optimization trajectories, while also covering ωB97M-V/def2-SVPD energies, rotational constants, dipole moments, highest occupied molecular orbital-lowest-unoccupied molecular orbital (HOMO-LUMO) energies, and Mulliken, Löwdin, and Hirshfeld population analyses. Additionally, coordination numbers, polarizabilities, and partial charges from D4, electronegativity equilibration (EEQ), GFN2-xTB, and charge extended Hückel (CEH) calculations are included. The data set is openly accessible and may serve as a basis for further investigations into the properties of lanthanoids.

Amidinatotetrylenes Donor Functionalized on Both N Atoms: Structures and Coordination Chemistry

E(hmds)(bqfam) (E = Ge (1a), Sn (1b); hmds = N(SiMe3)2, bqfam = N,N'-bis(quinol-8-yl)formamidinate), which are amidinatotetrylenes equipped with quinol-8-yl fragments on the amidinate N atoms, have been synthesized from the formamidine Hbqfam and Ge(hmds)2 or SnCl(hmds). Both 1a and 1b are fluxional in solution at room temperature, as the E atom oscillates from being attached to the two amidinate N atoms to being chelated by an amidinate N atom and its closest quinolyl N atom (both situations are similarly stable according to density functional theory calculations). The hmds group of 1a and 1b is still reactive and the deprotonation of another equivalent of Hbqfam can be achieved, allowing the formation of the homoleptic derivatives E(bqfam)2 (E = Ge, Sn). The reactions of 1a and 1b with [AuCl(tht)] (tht = tetrahydrothiophene), [PdCl2(MeCN)2], [PtCl2(cod)] (cod = cycloocta-1,5-diene), [Ru3(CO)12] and [Co2(CO)8] have been investigated. The gold(I) complexes [AuCl{κE-E(hmds)(bqfam)}] (E = Ge, Sn) have a monodentate κE-tetrylene ligand and display fluxional behavior in solution the same as that of 1a and 1b. However, the palladium(II) and platinum(II) complexes [MCl{κ3E,N,N'-ECl(hmds)(bqfam)}] (M = Pd, Pt; E = Ge, Sn) contain a κ3E,N,N'-chloridotetryl ligand that arises from the insertion of the tetrylene E atom into an M-Cl bond and the coordination of an amidinate N atom and its closest quinolyl N atom to the metal center. Finally, the binuclear ruthenium(0) and cobalt(0) complexes [Ru2{μE-κ3E,N,N'-E(hmds)(bqfam)}(CO)6] and [Co2{μE-κ3E,N,N'-E(hmds)(bqfam)}(μ-CO)(CO)4] (E = Ge, Sn) have a related κ3E,N,N'-tetrylene ligand that bridges two metal atoms through the E atom. For the κ3E,N,N'-metal complexes, the quinolyl fragment not attached to the metal is pendant in all the germanium compounds but, for the tin derivatives, is attached to (in the Pd and Pt complexes) or may interact with (in the Ru2 and Co2 complexes) the tin atom.