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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 (Ln(3+)) 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 Ln(3+) ions for its use in molecular medicine.

Mercury (Hg) pollution is a global environmental problem. The abiotic formation of dimethylmercury (DMeHg) from monomethylmercury (MMeHg) may account for a large portion of DMeHg in oceans. Previous experimental work has shown that abiotic formation of DMeHg from MMeHg can be facilitated by reduced sulfur groups on sulfide mineral surfaces. In that work, a mechanism was proposed in which neighboring MMeHg moieties bound to sulfide sites on a mineral surface react through an SN2-type mechanism to form DMeHg and incorporate the remaining Hg atoms into the mineral surface. Here, we perform density functional theory calculations to explore the mechanisms of DMeHg formation on the 110 surface of a CdS(s) (hawleyite) nanoparticle. We show that coordination of MMeHg substituents to adjacent reduced sulfur groups protruding from the surface indeed facilitates DMeHg formation and that the reaction proceeds through direct transmethylation from one MMeHg substituent to another. Coordination of Hg by multiple S atoms provides a transition-state stabilization and activates a C-Hg bond for methyl transfer. In addition, solvation effects play an important role in the surface reconstruction of the nanoparticle and in decreasing the energetic barrier for DMeHg formation relative to the corresponding reaction in vacuo.

SARS-CoV and SARS-CoV-2 bind to the human ACE2 receptor in practically identical conformations, although several residues of the receptor-binding domain (RBD) differ between them. Herein, we have used molecular dynamics (MD) simulations, machine learning (ML), and free-energy perturbation (FEP) calculations to elucidate the differences in binding by the two viruses. Although only subtle differences were observed from the initial MD simulations of the two RBD–ACE2 complexes, ML identified the individual residues with the most distinctive ACE2 interactions, many of which have been highlighted in previous experimental studies. FEP calculations quantified the corresponding differences in binding free energies to ACE2, and examination of MD trajectories provided structural explanations for these differences. Lastly, the energetics of emerging SARS-CoV-2 mutations were studied, showing that the affinity of the RBD for ACE2 is increased by N501Y and E484K mutations but is slightly decreased by K417N.

Lignin is a highly abundant polyphenolic polymer that imparts mechanical strength to plant biomass. Transition-metal complexes can catalyze lignin oxidation to produce value-added products, but low...

Both SARS-CoV and SARS-CoV-2 bind to the human ACE2 receptor. Based on high-resolution structures, the two viruses bind in practically identical conformations, although several residues of the receptor-binding domain (RBD) differ between them. Here we have used molecular dynamics (MD) simulations, machine learning (ML), and free energy perturbation (FEP) calculations to elucidate the differences in RBD binding by the two viruses. Although only subtle differences were observed from the initial MD simulations of the two RBD-ACE2 complexes, ML identified the individual residues with the most distinctive ACE2 interactions, many of which have been highlighted in previous experimental studies. FEP calculations quantified the corresponding differences in binding free energies to ACE2, and examination of MD trajectories provided structural explanations for these differences. Lastly, the energetics of emerging SARS-CoV-2 mutations were studied, showing that the affinity of the RBD for ACE2 is increased by N501Y and E484K mutations but is slightly decreased by K417N.

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.

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 A and total charge of -2 whereas the inter-trimer distance is 3.59 A. 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-electrons / multi-centered 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.

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.

We demonstrate that the electrocyclic (EC) ring-closure of cethrene in solution proceeds in a conrotatory mode both thermally and photochemically. The facile photochemical EC process promises that cethrene can serve as an efficient chiroptical switch operated solely by light. As for the thermally activated EC reaction, a low reaction barrier and a solvation effect on the EC rate indicate that the C2-symmetric pathway predicted by DFT calculations might not be the correct mechanism. Instead, we argue that the molecular symmetry decreases along the reaction coordinate as a consequence of the low-energy singlet excited state in this diradicaloid molecule, which might lead to a lower activation energy in accord with that determined through kinetic studies. Cethrene, therefore, represents a thought-provoking molecular chameleon of the Woodward–Hoffmann rules that puts our chemical concepts and intuition to test.