The structures of 5-methyl-5-phenyl-5H-dibenzo[b,f] silepin and its saturated analog

The structures of 5-methyl-5-phenyl-5H-dibenzo[b,f] silepin (I) and 5-methyl- 5-phenyl-1O,11-dihydro-5H-dibenzo [b,f] silepin (II) have been determined from three-dimensional X-ray data collected by counter methods. I crystallizes in the orthorhombic space group Pnam with a 7.596(3), b 18.102(5) and c 12.190(2) Å; observed and calculated densities (Z = 4) are 1.17 and 1.18 g cm^?3, respectively. II crystallizes in the monoclinic space group $\text{P}\text{2}{}_1\text{c}$ with a 11.115(3), b 7.920(3), c 20.765(5) Å and β 111.71(2)°; observed and calculated densities (Z = 4) are 1.17 g cm^?3. Anisotropic refinement of nonhydrogen atoms, with hydrogen atoms included at fixed ideal locations, gave conventional R-factors of 4.5% (I) and 5.0% (II). Compound I exhibits the boat conformation for the tricyclic framework and is located on a crystallographically required mirror plane. Com- pound II has the expected folded boat conformation. The torsion angle about the 10,11-bond is 0.0° for I, a crystallographic symmetry requirement, and 89.9° for II. Mean SiC bond distances are 1.863 Å(I) and 1.875 Å(II). The dihedral angles between the planar benzo groups are 129.7° (I) and 137.2° (II); introduc- tion of unsaturation at the 10,11-position decreases the dihedral angle in the tri- cyclic system, i.e., the tricyclic system is more bent.     

Ab initio MRD-CI calculations for breaking a chemical bond in a molecule in a crystal or other solid environment. III. Me2N?NO2 decomposition of dimethylnitramine in a large crystalline environment

Recently we extended our strategy for MRD-CI (multireference double excitation-configuration interaction) calculations, based on localized/local orbitals and an “effective” CI Hamiltonian, for molecular decompositions of large molecules to breaking a chemical bond in a molecule in a crystalline or other solid environment. Our technique begins with an explicit quantum chemical SCF calculation for a reference molecule surrounded by a number of other molecules in the multipole environment of more distant neighbors. The resulting canonical molecular orbitals are then localized, and the localized occupied and virtual orbitals in the region of interest are included explicitly in the MRD-CI with the remainder of the occupied localized orbitals being folded into an “effective” CI Hamiltonian. The MRD-CI calculations are then carried out for breaking a bond in the reference molecule. This method is completely general in that the space treated explicitly, as well as the surrounding space, may contain voids, defects, deformations, dislocations, impurities, dopants, edges and surfaces, boundaries, etc. Dimethylnitramine is the smallest prototype of the energetic R₂N—NO₂ nitramines, such as the 6-member ring RDX or the 8-member ring HMX. Decomposition of energetic compounds is initiated in the solid by a breaking of the target bond. Thus, it is crucial to know the difference in energy between breaking a bond in an isolated energetic molecule versus in the molecule in a solid. In the present study, we have carried out MRD-CI calculations for the Me₂N—NO₂ dissociation of dimethylnitramine in a dimethylnitramine crystal. The cases we investigated were one dimethylnitramine molecule (surrounded by 53 and 685 neighboring dimethylnitramine molecules represented by multipoles), three dimethylnitramine molecules, and three dimethylnitramine molecules (surrounded by 683 neighbors). All multipoles were cumulative atomic multipoles up through quadrupoles. The MRD-CI calculations on dimethylnitramine required large numbers of reference configurations from which were allowed all single and double excitations.     

Variability in the Chemical Composition of Myrcia sylvatica (G. Mey) DC. Essential Oils Growing in the Brazilian Amazon

Myrcia sylvatica (G. Mey) DC. is known as “insulin plant” because local communities use the infusions of various organs empirically to treat diabetes. The leaves of seven specimens of Myrcia sylvatica (Msy-01 to Msy-07) were collected in the Brazilian Amazon. Furthermore, the essential oils were extracted by hydrodistillation and analyzed by gas chromatography coupled to mass spectrometry, and their chemical compositions were submitted to multivariate analysis (Principal Component Analysis and Hierarchical Cluster Analysis). The multivariate analysis displayed the formation of four chemical profiles (chemotypes), described for the first time as follows: chemotype I (specimen Msy-01) was characterized by germacrene B (24.5%), γ-elemene (12.5%), and β-caryophyllene (10.0%); chemotype II (specimens Msy-03, -06 and -07) by spathulenol (11.1–16.0%), germacrene B (7.8–20.7%), and γ-elemene (2.9–7.6%); chemotype III (Msy-04 and -05) by spathulenol (9.8–10.1%), β-caryophyllene (2.5–10.1%), and δ-cadinene (4.8-5.6%); and chemotype IV, (Msy-02) by spathulenol (13.4%), caryophyllene oxide (15.0%), and α-cadinol (8.9%). There is a chemical variability in the essential oils of Myrcia sylvatica occurring in the Amazon region.     

Seasonal Variability of a Caryophyllane Chemotype Essential Oil of Eugenia patrisii Vahl Occurring in the Brazilian Amazon

Eugenia patrisii Vahl is a native and non-endemic myrtaceous species of the Brazilian Amazon. Due to few botanical and phytochemical reports of this species, the objective of the present work was to evaluate the seasonal variability of their leaf essential oils, performed by GC and GC-MS and chemometric analysis. The results indicated that the variation in oil yields (0.7 ± 0.1%) could be correlated with climatic conditions and rainy (R) and dry seasons (D). (E)-caryophyllene (R = 17.1% ± 16.0, D = 20.2% ± 17.7) and caryophyllene oxide (R = 30.1% ± 18.4, D = 14.1% ± 19.3) are the major constituents and did not display significant differences between the two seasons. However, statistically, a potential correlation between the main constituents of E. patrisii essential oil and the climatic parameters is possible. It was observed that the higher temperature and insolation rates and the lower humidity rate, which are characteristics of the dry season, lead to an increase in the (E)-caryophyllene contents, while lower temperature and insolation and higher humidity, which occur in the rainy season, lead to an increase in the caryophyllene oxide content. The knowledge of variations in the E. patrisii essential oil composition could help choose the best plant chemical profile for medicinal purposes.     

An Integrated Mass Spectrometry-Based Glycomics-Driven Glycoproteomics Analytical Platform to Functionally Characterize Glycosylation Inhibitors

Cancer progression is linked to aberrant protein glycosylation due to the overexpression of several glycosylation enzymes. These enzymes are underexploited as potential anticancer drug targets and the development of rapid-screening methods and identification of glycosylation inhibitors are highly sought. An integrated bioinformatics and mass spectrometry-based glycomics-driven glycoproteomics analysis pipeline was performed to identify an N-glycan inhibitor against lung cancer cells. Combined network pharmacology and in silico screening approaches were used to identify a potential inhibitor, pictilisib, against several glycosylation-related proteins, such as Alpha1-6FucT, GlcNAcT-V, and Alpha2,6-ST-I. A glycomics assay of lung cancer cells treated with pictilisib showed a significant reduction in the fucosylation and sialylation of N-glycans, with an increase in high mannose-type glycans. Proteomics analysis and in vitro assays also showed significant upregulation of the proteins involved in apoptosis and cell adhesion, and the downregulation of proteins involved in cell cycle regulation, mRNA processing, and protein translation. Site-specific glycoproteomics analysis further showed that glycoproteins with reduced fucosylation and sialylation were involved in apoptosis, cell adhesion, DNA damage repair, and chemical response processes. To determine how the alterations in N-glycosylation impact glycoprotein dynamics, modeling of changes in glycan interactions of the ITGA5–ITGB1 (Integrin alpha 5-Integrin beta-1) complex revealed specific glycosites at the interface of these proteins that, when highly fucosylated and sialylated, such as in untreated A549 cells, form greater hydrogen bonding interactions compared to the high mannose-types in pictilisib-treated A549 cells. This study highlights the use of mass spectrometry to identify a potential glycosylation inhibitor and assessment of its impact on cell surface glycoprotein abundance and protein–protein interaction.     

Macrocyclic thioether design by molecular modelling

Abstract

Two trithiamacrocycles have been designed by molecular modelling to have preorganised endodentate sulfur donor atoms. These new macrocycles have five- and six-membered saturated heterocycles inserted into 2,5,8-trithia[9]-m-benzenophane; molecular dynamics simulations suggest that the endo forms will be rigid on a nanosecond timescale. Optimum metal-sulfur distances which the new ligands will accommodate lie between 2.76 Å and 2.95 Å, suggesting they will be particularly suitable for a large soft metal ion such as silver(I).