Theoretical investigation of the mechanism of DMAP-promoted [4 + 2]-annulation of prop-2-ynylsulfonium with isatoic anhydride

The mechanism for DMAP-promoted [4 + 2]-annulation of prop-2-ynylsulfonium with isatoic anhydride is investigated using the M06-2X functional. The reaction comprises isomerization of prop-2-ynylsulfonium in stage 1. Stage 2 includes DMAP-promoted deprotonation, nucleophilic addition, ring opening, and decarboxylation. Three steps of intramolecular cycloaddition, DMAP-promoted protonation, and dealkylation occur in stage 3, generating methylated DMAP and neutral thioether, which undergo double-bond isomerization to yield 3-methylthio-4-quinolone. The ability of DMAP to promote the reaction lies in the barrier decrease for alkyne isomerization, deprotonation/protonation of allenes, and dealkylation as effective bases for transferring protons and methyl groups. The roles of prop-2-ynylsulfonium and isatoic anhydride were demonstrated to be C2 and C4 synthons via Multiwfn analysis on the frontier molecular orbital. An alternative path was also confirmed by the Mayer bond order of the vital transition states.

Theoretical investigation of Fe–Rh binary nanoalloys: Chemical ordering and magnetic behavior

Gupta and Density Functional Theory (DFT) calculations were performed to investigate of structural and magnetic behaviors of 19 atom FenRh[Formula: see text] ([Formula: see text]–19) nanoalloys. A double icosahedron structure was considered for FenRh[Formula: see text] ([Formula: see text]–19) nanoalloys. Significantly, the effects of Fe atom addition on the chemical ordering, stability and total magnetic moments of the nanoalloys were investigated. Local optimization results at the Gupta level show that the Fe atoms are located in the center of the double icosahedron structure and finally in the equatorial region on the surface. The mixing energy analysis obtained that Fe[Formula: see text]Rh7 and Fe4Rh[Formula: see text] nanoalloys are the most stable compositions at Gupta and DFT levels, respectively. It was found that FenRh[Formula: see text] ([Formula: see text]–19) nanoalloys are energetically suitable for mixing at both Gupta and DFT levels. Also, the bond order parameter result is compatible with the mixing energy analysis result. The total magnetic moments of the FenRh[Formula: see text] ([Formula: see text]–19) nanoalloys increase with the addition of the Fe atom, which is a ferromagnetic metal.

Perspective/Discussion on “Quantum Mechanical Metric for Internal Cohesion in Cement Crystals” by C. C. Dharmawardhana, A. Misra and Wai-Yim Ching

The single most important structural material, and the major Portland cement binding phase in application globally, is calcium silicate hydrate (C-S-H). The concentration has increasingly changed due to its atomic level comprehension because of the chemistry and complex structures of internal C-S-H cohesion in cement crystals at different lengths. This perspective aimed at describing on calcium-silicate-hydrates (C-S-H) structures with differing contents of Ca/Si ratio based on the report entitled “Quantum mechanical metric for internal cohesion in cement crystals” published by C. C. Dharmawardhana, A. Misra and Wai-Yim Ching. Crystal structural and bond behaviors in synthesized C-S-H were also discussed. The investigator studied large subset electronic structures and bonding of the common C-S-H minerals. From each bonding type, the results and findings show a wide variety of contributions, particularly hydrogen bonding, that allow critical analyses of spectroscopic measurement and constructions of practical C-S-H models. The investigator found that the perfect overall measurement for examining crystal cohesions of the complex substances is the total bond density (TBOD), which needs to be substituted for traditional metrics such as calcium to silicon ratios. In comparison to Tobermorite and Jennite, hardly known orthorhombic phased Suolunites were revealed to have greater cohesion and total order distribution density than those of the hydrated Portland cement backbone. The findings of the perspective showed that utilizing quantum mechanical metrics, the total bond orders and total bond order distributions are the most vital criteria for assessing the crystalline cohesions in C-S-H crystals. These metrics encompass effects of both interatomic interactions and geometric elements. Thus, the total bond order distribution and bond order offer comprehensive and in-depth measures for the overall behaviors of these diverse groups of substances. The total bond order distributions must clearly be substituted for the conventional and longstanding Ca/Si ratios applied in categorizing the cement substances. The inconspicuous Suolunite crystals were found to have the greatest total bond order distributions and the perfect bonding characteristics, compositions, and structures for cement hydrates.

Synthesis and Crystal Structure of Benzyl 4-(2-fluoro-4-(trifluoromethyl)phenyl)- 2,6,6-trimethyl-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate and Its DFT Analysis Combined with Bond Order Modeling in Terms of The Bond Critical Point Quantities

Inflammation is the underlying cause of many diseases such as cardiovascular diseases, cancer and autoimmune diseases. Recently 1,4-dihydropyridine (1,4-DHP) compounds were found effective to reduce inflammation which contributes to development of inflammation associated diseases. Based on these data we synthesized to investigate this type of action of annulated 1,4-DHP molecule, benzyl 4-(2-fluoro-4-(trifluoromethyl)phenyl)-2,6,6-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate and proved the structure of this molecule by IR, 1H-NMR, 13C-NMR, HMRS and X-ray crystallography.X-ray analyses were conducted to find out the exact 3D structure of the mentioned molecule. The molecular structure crystallizes in triclinic space group, P-1, with a = 7.0889(11) Å, b = 12.4861(18) Å, c = 14.338(2) Å, α = 66.899(4)°, β = 89.025(4)°, γ = 85.101(4)° and V = 1162.9(3) Å3. In the title molecule, C27H25F4NO3, the cyclohexene ring is in a sofa conformation and the 1,4-dihydropyridine ring is in a slight boat conformation. In the 2-fluoro phenyl and benzyl rings form a dihedral angle of 13.6(1)°. In the crystal structure stabilized by the intra- and intermolecular N—H···O, C—H···O and C—H···F interactions. The molecules are linked together to form a dimer by N(1)—H(1N) ···O(1)i and C(2)—H(2A) ···O(1)i hydrogen bonds [symmetry code: (i) x+1,y,z ], producing two R12(6) rings.Natural charge, QTAIM, bond order, molecular planarity and molecular surface analyses have been performed on the optimized geometry by DFT. Considering the quantities obtained at the bond critical poins, the chemical bonds are discussed for classification. The correlation between bond critical point quantities and the bond orders based on different definitions have been explored considering different bond order models from the literature. The Laplacian Bond Order (LBO) gives best correlation for four of five bond order models. All the bond order models with an exception of the model with parameter G have approximately same correlation degree for C-C bonds. For C-H bonds, only bond model with parameters of electron density and the principle curvatures for LBO gives relatively good correlation with R2 value of 0.943. The two phenyl rings of the structure have aromaticity comparable to benzene as deduced from QTAIM quantities and molecular planarity metrics. As a result of molecular surface analysis, the mass density, molecular polarity index, v (the measure of charge balance), σ2tot .v (measure of intermolecular interactions) were calculated and compared with literature values.

Crystal Structure and Solid-State Packing of 4-Chloro-5H-1,2,3-dithiazol-5-one and 4-Chloro-5H-1,2,3-dithiazole-5-thione

The crystal structure and solid-state packing of 4-chloro-5H-1,2,3-dithiazol-5-one and two polymorphs of 4-chloro-5H-1,2,3-dithiazole-5-thione were analyzed and compared to structural data of similar systems. These five-membered S,N-rich heterocycles are planar with considerable bond localization. All three structures demonstrate tight solid-state packing without voids which is attributed to a rich network of short intermolecular electrostatic contacts. These include Sδ+…Nδ−, Sδ+…Oδ−, Sδ+…Clδ− and Sδ+…Sδ− interactions that are well within the sum of their van der Waals radii (∑VDW). B3LYP, BLYP, M06, mPW1PW, PBE and MP2 were employed to calculate their intramolecular geometrical parameters, the Fukui condensed functions to probe their reactivity, the bond order, Bird Index and NICS(1) to establish their aromaticity.

Bonding features in Appel's salt from the orbital-free quantum crystallographic perspective

Bonding properties in the crystal of 4,5-dichloro-l,2,3-dithiazolium chloride (Appel's salt) were studied using a combination of single-crystal high-resolution X-ray diffraction data and the orbital-free quantum crystallography approach. A QTAIM-based topological model shows the proximity of S—C and S—N bonds to the sesquialteral type and establishes the low S—S bond order in the l,2,3-dithiazolium heterocycle. It is found that the electrostatic potential carries the traces of a common positive area on the junction of interatomic zero-flux surfaces of S1 and S2 atomic basins; meanwhile the exchange energy density per particle shows perfectly here two separate minima through which the two bond paths run. Thus, the pair intermolecular interactions Cl−...S1 and Cl−...S2 formed by the common chloride anion placed near the center of the S—S bond are categorized as chalcogen bonds.

Measuring Shared Electrons in Extended Molecular Systems: Covalent Bonds from Plane-Wave Representation of Wave Function

In the study of materials and macromolecules by first-principle methods, the bond order is a useful tool to represent molecules, bulk materials and interfaces in terms of simple chemical concepts. Despite the availability of several methods to compute the bond order, most applications have been limited to small systems because a high spatial resolution of the wave function and an all-electron representation of the electron density are typically required. Both limitations are critical for large-scale atomistic calculations, even within approximate density-functional theory (DFT) approaches. In this work, we describe our methodology to quickly compute delocalization indices for all atomic pairs, while keeping the same representation of the wave function used in most compute-intensive DFT calculations on high-performance computing equipment. We describe our implementation into a post-processing tool, designed to work with Quantum ESPRESSO, a popular open-source DFT package. In this way, we recover a description in terms of covalent bonds from a representation of wave function containing no explicit information about atomic types and positions.