Structural Chemistry最新文献

In 2023, a themed collection on “Emerging frontiers in aromaticity” was published in Chemical Science. The collection included a Perspective Essay entitled “Aromaticity – Quo Vadis”, which presents a wealth of viewpoints on the multiple definitions of aromaticity. The present Prefatory Review revives the viewpoint that aromaticity is a theoretical notion and as such, its meaning is theory dependent. Therefore, when aromaticity is made to correspond to two or more ‘experimental’ ideas, e.g., energetic, structural, electronic, magnetic, it would be absurd to maintain that aromaticity is explicitly defined by each of these ideas in turn. The Review emphasizes that the descriptor ‘theoretical’ in general, including in the context of aromaticity does not mean ‘computational’. The theoretical notion of aromaticity is illustrated by Craig’s rules of aromaticity and by Craig’s second type of aromaticity based on symmetry and delocalization in pπ-dπ bonds, recently highlighted as ‘Craig-Type Möbius aromaticity’.

The homogeneous phase reaction of [Ru(η²-RL)(PPh₃)₂(CO)(Cl)] (1) [η²-RL is C₆H₂O-2-CHNHC₆H₄R(p)-3-Me-5 and R is OMe, Cl] with the sodium salts of p-nitrobenzoic acid [NaPNB] and m-nitrobenzoic acid [NaMNB] afforded the complexes of the type [Ru(η¹-RL)(PPh₃)₂(CO)(PNB)] (2(R)) and [Ru(η¹-RL)(PPh₃)₂(CO)(MNB)] (3(R)) respectively in excellent yield [η¹-RL is C₆H₂OH-2-CHNC₆H₄R(p)-3-Me-5]. When 1 was reacted with the nitrobenzoic acid instead of their sodium salt, the Ru─C(aryl) bond cleavage products [Ru(PPh₃)₂(CO)(Cl)(PNB)] (4) and [Ru(PPh₃)₂(CO)(Cl)(MNB)] (5) were obtained. The spectral (UV–vis, IR, NMR) and electrochemical data of the complexes are reported. In dichloromethane solution the type 2(R) and 3(R) complexes display two successive quasi-reversible one electron oxidation processes whereas the complexes 4 and 5 display only one oxidation process. The crystal structures of [Ru(η¹-ClL)(PPh₃)₂(CO)(MNB)] (3(Cl)) and [Ru(PPh₃)₂(CO)(Cl)(MNB)] (5) are reported, which revealed a distorted octahedral RuP₂C₂O₂ coordination sphere for 3(Cl) and RuP₂CO₂Cl coordination sphere for 5. The electronic structure and absorption spectra of the complexes are scrutinized by DFT and TD-DFT analyses. The complex 3(Cl) was tested for its ability to exhibit DNA-binding activity.

Ab initio investigation of the spectroscopic constants, bond dissociation energies of germanium monohalides, germanium dihalides and their ionic systems, viz. GeX, GeX⁻, GeX⁺, GeX₂, GeX₂⁻ and GeX₂⁺ (X = F, Cl, Br and I) have been carried out using correlation consistent triple-zeta basis sets for F and Cl and similar triple-zeta basis sets with RECPs for Ge, Br and I atoms. Geometry and frequency of all the neutral and ionic systems of germanium halides are obtained using MP2, CCSD(T) and QCISD(T) methods. The energetics are obtained at the CCSD(T)//MP2, QCISD(T)//MP2, CCSD(T) and QCISD(T) levels. Electron affinity (EA) and ionization potential (IP) of the monohalides and dihalides are reported to be consistent with the data available in literature. The bond dissociation energies (BDEs) to various dissociation asymptotes for most of the ionic systems are to be reported new in literature. The BDEs of the neutral germanium dihalides GeX₂ are calculated by using the BDEs of GeX₂⁻ and GeX₂⁺ ions and EA and IP of the associated neutral systems. A good agreement is found between the calculated values and the data wherever available. The BDEs of GeX₂ for higher halogen member are reported to be new in literature. The enthalpies of formation for atomization and ionization of the neutral GeX₂ dihalides are also reported here. The enthalpies of ionization are reported first time in literature and found consistent with other group IV dihalides. The reported molecular properties may be helpful to understand the chemistry involved in the plasma-assisted fabrication process of the Ge-based modern microelectronic devices, as well as will serve as a future reference.

Smoking is the g`reatest preventable cause of mortality all over the world as it causes lung cancer, vascular disease, peptic ulcers, coronary heart disease, stroke and harm to the developing fetal brain, and numerous respiratory issues, such as chronic bronchitis, emphysema, pulmonary hypertension, obstruction of tiny airways, and chronic obstructive pulmonary diseases. These diseases are mainly caused by smoking of tobacco products, including pipe tobacco, snuff, cigars, and cigarettes. To overcome the dangerous and adverse effects of tobacco alkaloids, the utilization of novel class of quantum dots, the graphene quantum dot (GQD) has not yet been thoroughly investigated. To fill this gap, the mechanistic sensing capability of the tetragonal graphene quantum dot towards tobacco alkaloids including anabasine (Anab), anatabine (Anat), myosmine (Myos), nitrosoanabasine (NAB), nitrosoanatabine (NAT), and nornicotine (NOR) has been investigated by employing first-principles DFT and TD-DFT computations. The computational tools have been utilized to investigate the interaction energies, the energy gap (FMO analysis), non-covalent interactions (NCI analysis), transfer of charges (QNBO), and the nature and strength of intermolecular interactions (QTAIM analysis). The NOR@T-GQD complex has the greatest interaction energy (− 20.1051 kcal/mol) among all the studied complexes. Also, the complex NOR@T-GQD has the lowest energy gap (1.072 eV) and chemical hardness (0.536 eV) which indicates the highest conductivity (2.486 × 10⁹), shortest recovery time (3.005 × 10⁻¹⁶), and highest sensing response (2.326). UV–Vis analysis explored the maximum absorbance wavelength, excitation energy, and oscillator strength for the studied system and the thermodynamic analysis explored the spontaneity of the interaction process of the studied complexes. So, all the investigation parameters have proved that the tetragonal graphene quantum dot-based sensor is an influential sensing material towards all studied tobacco alkaloids especially for the tobacco alkaloid nornicotine.

We have investigated the basic mechanism of carbon nanotube (CNT) interactions with various room-temperature ionic liquids (RTILs) using molecular dynamics (MD) simulations. To understand the effects of the cation molecular geometry on the properties of the interface structure in the RTIL systems, we have studied a set of three RTILs with the same [BF₄]^- (tetrafluoroborate) anion but with different cations, namely, [EMIM]⁺ (1-ethyl-3-methylimidazolium), [BMIM]⁺ (1-butyl-3-methylimidazolium), [HMIM]⁺ (1-hexyl-3-methylimidazolium), and [OMIM]⁺ (1-octyl-3-methylimidazolium) ions. The simulation results showed that the imidazolium cations exhibit two distinct orientations (perpendicular and parallel to the CNTs surface) at the interface irrespective of the alkyl chain length of the cations. The average number of hydrogen bonds per cations inside the CNT was found to be higher for [OMIM][BF₄] (1.01), which suggests that [OMIM]⁺ imidazolium rings to be concentrated at the center of the CNT, which favors hydrogen bond. The reported results show the diffusion coefficients of ions in confinement are much lower in comparison to the bulk region. The interaction energy between [OMIM][BF₄] (-8.75 kcal.mol⁻¹.ion⁻¹) and CNT was found to be higher as compared to other ILs. The cations paralleling the CNT surface are thermodynamically significantly more stable because of the substantial interfacial π-π stacking interactions, as shown by a comparison with the calculated interaction energies between cations and the CNTs. Our simulation results provide a molecular-level understanding of the stabilization and dispersion of CNT bundles in ILs.

The recent global pandemic by the outbreak of the SARS-CoV-2 virus caused about seven million deaths worldwide. The WHO approved the repurposing of antiviral drugs as the treatment protocol for COVID-19. Yet, it was insufficient to stop the outbreak of COVID-19. By virtue of a broad spectrum of variable oxidation numbers, geometries, tuneable redox, and kinetic and thermodynamic properties, transition metal complexes offer themselves as a viable alternative to the antiviral drugs against SARS-CoV-2. The computational methods in biology and chemistry are a promising starting point in this regard. Here, we present the synthesis, crystal structure, docking study with SARS-CoV-2 receptors, and potential drug property of two tetrahedral Zn(II) complexes, viz. [Zn(µ₂-Bz)₃]_n (1) and [Zn(Phen)Cl₂]₂ (2) (Bz = benzoate ion, Phen = 1,10-phenanthroline). They were synthesized at room temperature and characterized by elemental analyses, FT-IR spectroscopy, thermal analysis (TGA/DTG), powder X-ray diffraction (PXRD), and single crystal X-ray diffraction. Complex 1 is a coordination polymer with unusual triply-bridged triangular secondary building unit (SBU), whereas complex 2 is a novel supramolecular dimer. The crystal structures of 1 and 2 are stabilized by a number of supramolecular interactions, which ultimately lead to a 3D architecture for each of them. Their crystal packing is discussed in details, with inputs from energy calculations, by the analysis of electrostatic potential mapped on the Hirshfeld surface and two-dimensional (2D)-fingerprint plot by CrystalExplorer. A molecular docking study of the synthesized complexes was performed against seven important proteins of SARS-CoV-2. ADMET calculations were used to evaluate their drug potential.

A novel (Z)-10-(bromoiodomethylene)phenanthren-9(10H)-one crystal structure is reported herein. Its synthetic formation arising from the phenyl shift during the electrophilic iodination of the alkynol of fluorenone provides proof of the early proposed mechanism of the McNelis rearrangement. The implication of the Z-geometry in the mechanism is discussed. Single crystal X-ray diffraction studies on the title compound show the β-vinyl bromine and the β-iodine atoms trans and syn, respectively, to the C = O in the molecule establishing the configuration of the dihaloenone about the alkenyl motif as Z-geometry. The intermolecular interactions primarily involve the iodine and oxygen atoms with a C-I…O = C distance of 3.110 (1) Ả, which describes an I…O halogen bond since the I···O distance is less than the sums of the respective van der Waals radii, 3.50 Å. In this interaction, the iodine acts as a Lewis acid, and the carbonyl oxygen serves as the Lewis base electron donor moiety. Consistent with the strong directional polarization of halogen bonds, the C-I···O angle = 167°. There is an additional intramolecular C-I ∙∙∙O = C distance of 3.147 (1) Å and I∙∙∙I distance of 3.956 (1) Å along the c-axis. These interactions form a one-dimensional, non-planar infinite network along the c-axis.

The first representative of 3-nitro-4-aminobenzoic acid (3N-4ABA) monoligand metal complexes has been obtained on an example of the Cu(II) complex. The structure of the compound was studied using element analysis, IR- and UV-spectroscopy, and Hirshfeld surface analysis while bioactivity is assessed by molecular docking. Cu(II) ions coordinate two 3N-4ABA molecules bidentately through the oxygen atoms of the carboxylate group, and there are water molecules in the other two positions of the coordination sphere, i.e., all coordinated atoms are only oxygen ones which leads to the formation of the essentially distorted octahedron due to the Janh-Teller effect. Moreover, there is one water molecule in the outer sphere, making this compound a crystal hydrate with the formula of [Cu(3N-4ABA)₂(H₂O)₂]·H₂O. The complicated system of the intermolecular H-bonds and π···π staking interactions incorporate complex molecules into the 3D network. In silico studies of the 3N-4ABA ligand and Cu-complex attested that antimicrobial and antitumor activities indicate a higher affinity of the complex for some key binding sites especially relatively to S. aureus and KDM4 with binding energies of − 9.6 and − 9.2 kcal/mol, respectively.

The effects of planar biaxial strain on the stability, electronic structure, and magnetic properties of monolayer CrS₂ systems doped with nitrogen group elements have been investigated based on first principles. Calculations of energy differences, formation energies, bond population, and binding energies indicate the relative stability of the system. Calculations of the electronic structure (energy band structure, density of states, and differential charge density distribution) and magnetic parameters (spin density profiles, single-atom magnetic moments, and total magnetic moments of the system) show that atomic doping in conjunction with strain induces several excellent electronic properties of the system, such as magnetic semiconductors and semimetals. The bandgap of the spin-down channel increases with tensile strain and decreases with compressive strain. In addition, we note that the total magnetic moments of the monolayer CrS₂ system and the N atom-doped system decrease with tensile strain and show an increase with compressive strain. The above results provide a reference for further investigation of this material and its application in nanospin devices.

Due to different solvent conditions, double helix DNA exists in various conformations, such as B-DNA, A-DNA, C-DNA, and Z-DNA. Studies have found that A-DNA is present in complexes with proteins and has an important biological role in the context of cellular defense mechanisms under harsh conditions. In this study, the well-tempered meta-dynamics (WTM-eABF) were used to explore the free energy barriers for base flipping of the four natural bases, adenine, guanine, cytosine, and thymine, in both A-form and B-form DNA duplex. The results show that the free energy barriers for base flipping were lower in A-DNA than that in B-DNA for all of the four natural bases. We analyzed the factors that may affect base flipping, such as π-π stacking, SASA, H-bonding, and conformational changes, and concluded that conformational changes and π-π stacking are the most important factors affecting base flipping.