The taxonomic distribution of histamine-secreting bacteria in the human gut microbiome.

Background: Biogenic histamine plays an important role in immune response, neurotransmission, and allergic response. Although endogenous histamine production has been extensively studied, the contributions of histamine produced by the human gut microbiota have not been explored due to the absence of a systematic annotation of histamine-secreting bacteria.

Results: To identify the histamine-secreting bacteria from in the human gut microbiome, we conducted a systematic search for putative histamine-secreting bacteria in 36,554 genomes from the Genome Taxonomy Database and Unified Human Gastrointestinal Genome catalog.

Mechanistic Investigation of Dimethylmercury Formation Mediated by a Sulfide Mineral Surface.

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.

Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2.

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.

Origin of the Isomer Stability of Polymethylated DOTA Chelates Complexed with Ln ions.

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) 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 (), ring methylated M4DOTA (), and arm methylated -DOTMA () and -DOTMA (), as well as, both ring and arm methylated 4-4-M4DOTMA ( and 4-4-M4DOTMA () 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- and the twisted square antiprism (TSAP) isomer of Lu-, while the steric repulsion between the ring and arm methyl groups attenuates the stability of both TSAP of Lu- and SAP of Lu-.

Machine learning-based prediction of enzyme substrate scope: Application to bacterial nitrilases.

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.

Pancake Bonding in π-Stacked Trimers in a Salt of Tetrachloroquinone Anion.

The crystal structure of [4-damp]) [Cl Q] (4-damp=4-dimethylamino-N-methylpyridinium, Cl Q=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.

Cethrene: The Chameleon of Woodward-Hoffmann Rules.

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 C-symmetric pathway predicted by DFT calculations might not be the correct mechanism.

Sigma- versus Pi-Dimerization Modes of Triangulene.

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.

Validation of density functionals for pancake-bonded π-dimers; dispersion is not enough.

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.

Pancake Bond Orders of a Series of π-Stacked Triangulene Radicals.

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.

Fluxional σ-Bonds of the 2,5,8-Trimethylphenalenyl Dimer: Direct Observation of the Sixfold σ-Bond Shift via a π-Dimer.

Direct evidence for σ-bond fluxionality in a phenalenyl σ-dimer was successfully obtained by a detailed investigation of the solution-state dynamics of 2,5,8-trimethylphenalenyl (TMPLY) using both experimental and theoretical approaches. TMPLY formed three diamagnetic dimers, namely, the σ-dimer (RR/SS), σ-dimer (RS), and π-dimer, which were fully characterized by (1)H NMR spectroscopy and electronic absorption measurements. The experimental findings gave the first quantitative insights into the essential preference of these competitive and unusual dimerization modes.

Hetero-π-Dimers of Phenalenyls.

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.

Evidence of σ- and π-dimerization in a series of phenalenyls.

Phenalenyl and a wide variety of its derivatives form stable radicals, which often associate in various aggregates with interesting properties that include magnetism and high electrical conductivity. The two main modes of aggregation involve π-stacking pancake multicenter bond formation and σ-bond formation. We explore the energetics of the various σ- and π-dimers for six phenalenyl derivatives with both computational and experimental methods.

3D graphene-Fe3O4 nanocomposites with high-performance microwave absorption.

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.