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DOTA (1,4,7,10‐tetraazacyclododecane‐1,4,7,10‐tetraacetic acid)‐based chelates that give only a single isomer in solution when complexed with lanthanide (Ln3+) ions is of value for studying protein dynamics and interactions via NMR. Herein, we have investigated the geometries, energetics, and electrostatic potentials of Lu complexed with DOTA (1), ring methylated M4DOTA (2), and arm methylated R‐DOTMA (3) and S‐DOTMA (4), as well as, both ring and arm methylated 4S‐4S‐M4DOTMA (5) and 4S‐4R‐M4DOTMA (6) at the level of M06‐L/6‐31+G(d)‐SDD, to elucidate the origin of the isomer stability. These analyses indicate that the electrostatic repulsion between the arm methyl and the neighboring carboxylate significantly destabilizes the square antiprism (SAP) isomer of Lu‐5 and the twisted square antiprism (TSAP) isomer of Lu‐6, while the steric repulsion between the ring and arm methyl groups attenuates the stability of both TSAP of Lu‐5 and SAP of Lu‐6. To rationalize the variable temperature proton NMR spectra, the energy barriers for the inter‐conversion in Lu‐5 and Lu‐6 via arm rotation were also calculated. The modulation of the stability and rigidity of Ln complexes via a modification of DOTA is also discussed. Our investigation will aid to design better chelates for the Ln3+ ions for its use in molecular medicine. [ABSTRACT FROM AUTHOR]

Predicting the range of substrates accepted by an enzyme from its amino acid sequence is challenging. Although sequence‐ and structure‐based annotation approaches are often accurate for predicting broad categories of substrate specificity, they generally cannot predict which specific molecules will be accepted as substrates for a given enzyme, particularly within a class of closely related molecules. Combining targeted experimental activity data with structural modeling, ligand docking, and physicochemical properties of proteins and ligands with various machine learning models provides complementary information that can lead to accurate predictions of substrate scope for related enzymes. Here we describe such an approach that can predict the substrate scope of bacterial nitrilases, which catalyze the hydrolysis of nitrile compounds to the corresponding carboxylic acids and ammonia. Each of the four machine learning models (logistic regression, random forest, gradient‐boosted decision trees, and support vector machines) performed similarly (average ROC = 0.9, average accuracy = ~82%) for predicting substrate scope for this dataset, although random forest offers some advantages. This approach is intended to be highly modular with respect to physicochemical property calculations and software used for structural modeling and docking. [ABSTRACT FROM AUTHOR]

Abstract: The crystal structure of [4‐damp])2[Cl4Q]3 (4‐damp=4‐dimethylamino‐N‐methylpyridinium, Cl4Q=tetrachloroquinone) salt is built up from slipped columnar stacks of quinoid rings composed of closely bound trimers with the intra‐trimer separation distance of 2.84 Å and total charge of −2 whereas the inter‐trimer distance is 3.59 Å. The individual rings exhibit partial negative charges that are distributed unevenly among the three Cl4Qs in the trimer. The strong interactions within a trimer (Cl4Q)32− have a partially covalent character with two‐electron/multicentered bonding, that is extended over three rings, plausibly termed as “pancake bonding”. The electron pairing within this multicentre bond leads to the fact that the crystals are diamagnetic and act as insulators. The studies of the structure and nature of bonding are based on X‐ray charge density analysis and density functional theory. [ABSTRACT FROM AUTHOR]

Abstract: We show that the diradicaloid triangulene, a graphene nano‐flake molecule, can aggregate in a variety of dimerization modes. We found by density functional theory modeling a number of triangulene dimers including six doubly bonded σ‐dimers in addition to the previously reported six pancake bonded π‐dimer isomers. The σ‐dimers display a wide range of stabilities: the interaction energy of the most stable σ‐dimer is −25.17 kcal mol−1. Besides the doubly bonded σ‐dimers with closed shell ground states, we also found an open‐shell singly σ‐bonded diradicaloid dimer. We found an interesting isomerization route between a doubly bonded σ‐dimer, a singly bonded σ‐dimer with a low‐lying triplet state and two π‐bonded dimers with low‐lying quintet states. Derivatives of triangulene, trioxo‐triangulenes (TOTs) have been previously characterized experimentally. Here, we show the reasons why so far only the π‐dimer but not the σ‐dimer was experimentally observed for all TOTs. [ABSTRACT FROM AUTHOR]

The structural parameters and semiconductivity of crystals with stacked 5,6-dichloro-2,3-dicyanosemiquinone (DDQ) radicals were studied for a series of the first nine salts of DDQ with substituted N-ethyl- and N-methylpyridinium cations. Structures with stacks of equidistant radicals (interplanar separation ＜3.3 Å) are fairly good semiconductors (10−9 S cm−1), while those with Peierls-distorted stacks comprising diamagnetic dimers of radicals (interplanar separations are ＜3.1 Å within the dimers and ＞3.4 Å between the dimers) are insulators. DFT calculations indicate the covalent character (pancake bonding) of the interactions between the DDQ radical anions. The inductive effects of electronegative substituents (halogeno and cyano) on the quinoid ring stabilise the radicals, but also increase the HOMO–LUMO gap, resulting in lower electrical conductivity. [ABSTRACT FROM AUTHOR]

π-Stacking pancake bonding between radicals poses special challenges to density functional theories (DFTs) due to their shorter than van der Waals contact distances, their multireference singlet ground states and the concurrently important dispersion interactions. We examined over 50 DFTs including 22 with dispersion corrections on four different π-dimerized pancake-bonded systems exploring the performances of these DFTs in the very short intermolecular contact regime. We examined crucial energetic as well as geometric parameters against available high-level multireference average quadratic coupled cluster (MR-AQCC) results. Overall we did not find an omnipotent DFT applicable for all four pancake-bonded π-dimers. However, some DFTs were found to perform well for each individual system: M05-2X and PBE0-MBD are the only DFTs that work well for the phenalenyl π-dimer; BLYP is the only appropriate DFT for the 1,2,4,6-thiatriazine π-dimer; O3LYP works best on the double pancake-bonded 1,3,2,4,6-dithiatriazine π-dimer with a few acceptable ones and MN15L is the best method for K+TCNE−π-dimer in addition to a few acceptable ones. We believe our findings can deliver insights towards the design and characterization of the pancake-bond based materials and the development of new DFTs. [ABSTRACT FROM AUTHOR]

Conjugated radicals are capable of forming π-stacking 'pancake-bonded' dimers. Members of the family of triangulene hydrocarbons, non-Kekulé neutral multiradicals, can utilize more than one singly occupied molecular orbital (SOMO) to form multiple pancake-bonded dimers with formal bond orders of up to five. The resulting dimer binding energies can be quite high and the intermolecular contacts rather small compared to the respective van der Waals values. The preferred configurations are driven by the large stabilization energy of overlapping SOMOs. [ABSTRACT FROM AUTHOR]

Homogeneous π-stacking dimers of phenalenyl and its derivatives have gained tremendous interest as components of conducting organic materials. For the first time, we investigate theoretically heterogeneous phenalenyl π-dimers. Key parameters, including charge transfer, interaction energy, singly occupied molecular orbital (SOMO) energy, and spin density, are studied with the help of density functional theory. We find that the amount of charge transfer between the two monomers in phenalenyl π-dimers correlates with the difference in the SOMO energies of the constituent monomers, where the SOMO energy plays the role of a monomer (group) electronegativity index. Charge transfer plays an important role in stabilizing the heterodimers while maintaining a significant diradicaloid character. For five heterodimers the interaction energy is found to be as large as −30 to −50 kcal mol−1. The presented correlation between the monomer SOMO energy levels and their stability can provide a simple predictive tool to design new highly stable π-stacking heterodimers. [ABSTRACT FROM AUTHOR]

3D Fe3O4–graphene nanocomposites were conveniently prepared via a direct hydrothermal grafting method. On the basis of the unique properties of both single-crystalline Fe3O4 and 3D chemically reduced graphene oxide, with characteristics such as ultralow density and high surface area, the as-prepared graphene–Fe3O4 nanocomposites showed high-performance microwave absorption ability and have the potential for application as advanced microwave absorbers. [ABSTRACT FROM AUTHOR]

Front Cover: Origin of the Isomer Stability of Polymethylated DOTA Chelates Complexed with Ln3+ Ions (Eur. J. Inorg. Density functional calculations, Electrostatic repulsion, Isomers, Lanthanide complexes, Polymethylated DOTA chelates To understand the origin of the stability of one isomer over the other, the structures and energetics of DOTA-like chelates complexed with Lu ions were investigated with DFT calculations. [Extracted from the article]