Solid state and dynamic solution structures of O-carbamidine amidoximes gives further insight into the mechanism of zinc(II)-mediated generation of 1,2,4-oxadiazoles

Synthesis, spectroscopic investigation, molecular docking, ADME/T toxicity predictions, and DFT study of two trendy ortho vanillin-based scaffolds

In this article, we have synthesized two contemporary ortho-vanillin-based Salen-type ligands (H₂L¹/H₂L²) characterized by modern spectroscopic tools. EDX analysis supports the elemental composition (C, N, O, and Br). SEM examined the morphology of the synthesized compounds. The molecular geometry was optimized in the gas phase using B3LYP-D3/6-311G (d, p) level. The global reactivity parameters, HOMO-LUMO energy gap (Δ), atomic properties, MESP, and ADME/T, vividly explore the chemical reactivity and toxicity of two Salen-type ligands. The DFT simulated IR/NMR characterized essential structural assignments, and UV-Visible spectra were employed to predict the optical properties. The article demonstrated in silico molecular docking against the Gm + ve Bacillus subtilis (6UF6), and Gm -ve Proteus Vulgaris establishes the ligand binding ability with essential amino acids through conventional H-bonding or other significant interactions. The docking simulation is compared for two compounds better than the control drugs and confirms the antimicrobial activity. The theoretical drug-like properties have been explored in-depth by ADME/T using the SWISSADME database. The analysis estimated the molecule's lipophilicity, the consensus P0/W, and water solubility. Thus, using various pharmaco-logical parameters, toxicity explains where the electron-withdrawing Br group plays a more toxic effect in H₂L² than in H₂L¹.

Interplay between the crystal stability and the energy of the molecular conformation

The lattice energy is the main factor in determining the structure even if the molecules adopt a less energetically favorable conformation.

A one-pot route to N-acyl ureas: a formal four-component hydrolytic reaction involving aminonitrones and isocyanide dibromides

A one-pot route to N-acyl ureas proceeds via generation of electrophilically activated 2-substituted 1,2,4-oxadiazolium salts. The conformation of the N-acyl ureas is stabilized via moderate strength (6.2–7.8 kcal mol⁻¹) resonance-assisted hydrogen bonds.

Correlations of NHN hydrogen bond energy with geometry and 1H NMR chemical shift difference of NH protons for aniline complexes

In this computational work, we propose to use the NMR chemical shift difference of NH₂ protons for 1:1 complexes formed by aniline and nitrogen-containing proton acceptors for the estimation of the hydrogen bond energy and geometry (N⋯H and N⋯N distances). The proposed correlations could be applied to other aromatic amines as well, in a gas phase, a solution, or a solid state, for both inter- and intramolecular hydrogen bonds. We considered a set of 21 complexes with the NHN hydrogen bond without proton transfer, including hydrogen bonds from weak to medium strong ones (2-21 kcal/mol), with neutral or anionic bases and with sp³ and sp² hybridized nitrogen proton acceptors. For each complex apart from direct hydrogen bond energy calculation, we have tested several other ways to estimate the energy: (a) using a correlation between NH stretching band intensity and hydrogen bond energy and (b) using correlations between electron density properties at (3, -1) bond critical point (quantum theory of atoms in molecules analysis) and hydrogen bond energy. Besides for the studied type of complexes, we obtained refined linear correlations linking the local electron kinetic (G) and potential (V) energy densities with the hydrogen bond energy.

Aminonitrones as highly reactive bifunctional synthons. An expedient one-pot route to 5-amino-1,2,4-triazoles and 5-amino-1,2,4-oxadiazoles – potential antimicrobials targeting multi-drug resistant bacteria

A four-component one-pot reaction proceeds very rapidly under mild conditions and gives the heterocyclic systems in good yields.

Intermolecular hydrogen bonding H···Cl in crystal structure of palladium(II)-bis(diaminocarbene) complex

The reaction of bis(isocyanide)palladium complex cis-[PdCl2(CNXyl)2] (Xyl=2,6-Me2C6H3) with excess of 4,5-dichlorobenzene-1,2-amine in a C2H4Cl2/MeOH mixture affords monocationic bis(diaminocarbene) complex cis-[PdClC{(NHXyl)=NHC6H2Cl2 NH2}{C(NHXyl)=NHC6H2Cl2NH2}]Cl (3) in moderate yield (42%). Complex 3 exists in the solid phase in the H-bonded dimeric associate of two single charged organometallic cations and two chloride anions according to X-ray diffraction data. The Hirshfeld surface analysis for the X-ray structure of 3 reveals that the crystal packing is determined primarily by intermolecular contacts H–Cl, H–H, and H–C. The intermolecular hydrogen bonds N–H···Cl and C–H···Cl in the H-bonded dimeric associate of 3 were studied by DFT calculations and topological analysis of the electron density distribution within the framework of QTAIM method, and estimated energies of these supramolecular contacts vary from 1.6 to 9.1 kcal/mol. Such non-covalent bonding means that complex 3 is an anionic receptor for the chloride anions.

Electrophilic-Nucleophilic Dualism of Nickel(II) toward Ni···I Noncovalent Interactions: Semicoordination of Iodine Centers via Electron Belt and Halogen Bonding via σ-Hole

The nitrosoguanidinate complex [Ni{NH═C(NMe₂)NN(O)}₂] (1) was cocrystallized with I₂ and sym-trifluorotriiodobenzene (FIB) to give associates 1·2I₂ and 1·2FIB. Structures of these solid species were studied by XRD followed by topological analysis of the electron density distribution within the framework of Bader's approach (QTAIM) at the M06/DZP-DKH level of theory and Hirshfeld surface analysis. Our results along with inspection of XRD (CCDC) data, accompanied by the theoretical calculations, allowed the identification of three types of Ni···I contacts. The Ni···I semicoordination of the electrophilic nickel(II) center with electron belt of I₂ was observed in 1·2I₂, the metal-involving halogen bonding between the nucleophilic nickel(II)-d_z² center and σ-hole of iodine center was recognized and confirmed theoretically in the structure of [FeNi(CN)₄(IPz)(H₂O)]_n (IPz = 4-N-coordinated 2-I-pyrazine), whereas the arrangement of FIB in 1·2FIB provides a boundary case between the semicoordination and the halogen Ni···I bondings. In 1·2I₂ and 1·2FIB, noncovalent interactions were studied by variable temperature XRD detecting the expansion of noncovalent contacts with preservation of covalent bond lengths upon the temperature increase from 100 to 300 K. The nature and energies of all identified types of the Ni···I noncovalent interactions in the obtained (1·2I₂ and 1·2FIB) and in the previously reported ([FeNi(CN)₄(IPz)(H₂O)]_n, [NiL₂](I₃)₂·2I₂ (L = o-phenylene-bis(dimethylphosphine), [NiL]I₂ (L = 1,4,8,11-tetra-azacyclotetradecane), Ni(en)₂]_n[AgI₂]_2n (en = ethylenediamine), and [NiL](ClO₄) (L = 4-iodo-2-((2-(2-(2-pyridyl)ethylsulfanyl)ethylimino)methyl)-phenolate)) structures were studied theoretically. The estimated strengths of these Ni···I noncovalent contacts vary from 1.6 to 4.1 kcal/mol and, as expected, become weaker on heating. This work is the first emphasizing electrophilic-nucleophilic dualism of any metal center toward noncovalent interactions.

Redox reactive (RNC)CuII species stabilized in the solid state via halogen bond with I2

The crystal structure of [Cu2(μ-O)(μ-I)2(CNXyl)4]·I2 (2·I2) was determined from single-crystal X-ray diffraction data. The adduct 2·I2 represents the first example of structurally characterized isocyanide-copper(II) complexes. In the structure of 2·I2, 2 forms independent chains connected through molecular iodine via I···I–I···I halogen bonding. The DFT calculations and topological analysis of the electron density distribution within the formalism of Bader’s theory (QTAIM method) were performed for model complex 2·I2 and the obtained results allowed the attribution of these contacts to moderate strength (3.8–5.3 kcal/mol) non-covalent contacts exhibiting some covalent character.

Mechanism of generation of closo-decaborato amidrazones. Intramolecular non-covalent B–H⋯π(Ph) interaction determines stabilization of the configuration around the amidrazone CN bond

Three types of N(H)-nucleophiles were used to study the nucleophilic addition to the CN group of the 2-propanenitrilium closo-decaborate cluster giving N-closo-decaborato amidrazones.

A novel family of homoleptic copper(i) complexes featuring disubstituted cyanamides: a combined synthetic, structural, and theoretical study

Homoleptic copper(i) complexes featuring disubstituted cyanamides were obtained and characterized using experimental methods and their properties were studied theoretically.

Trinuclear (aminonitrone)ZnII complexes as key intermediates in zinc(ii)-mediated generation of 1,2,4-oxadiazoles from amidoximes and nitriles

Amidoximes react with zinc salts in undried EtOAc furnishing the trinuclear species, where amidoximes are stabilized in the aminonitrone form.

Metal-mediated reactions between dialkylcyanamides and acetamidoxime generate unusual (nitrosoguanidinate)nickel(ii) complexes

Nitrosoguanidinate Ni^II complexes were generated via a hitherto unreported reaction between nickel(ii) salts, N,N-disubstituted cyanamides NCNR₂, and the amidoxime MeC(NOH)NH₂ in MeOH.

Halogen and hydrogen bonding in cis-dichlorobis(propionitrile)platinum(II) chloroform monosolvate

The weak intermolecular noncovalent interactions in the solvate cis-[PtCl2(C2H5CN)2]·CHCl3 were studied by XRD and DFT methods. Special attention was paid to a chloroform molecule as a potential donor of both hydrogen and halogen bonds. On the one hand, the H atom of chloroform links two Cl atoms of cis-[PtCl2(C2H5CN)2] (Hchloroform–Clcomplex (2.660 Å, 2.811 Å)), and on the other side, the weak Clchloroform–Clcomplex (3.247 and 3.497 Å) interactions were found. According to DFT calculation, only the Hchloroform–Clcomplex (2.660 and 2.811 Å) and Clchloroform–Clcomplex (3.247 Å) interactions can be classified as weak noncovalent bonds, whereas the contacts Clchloroform–Cnitrile (3.391 Å) and Clchloroform–Clcomplex (3.497 Å) are due to the crystal packing effect.

Hydrogen Bonding in Bis(6-amino-1,3-dimethyluracil-5-yl)-methane Derivatives: Dynamic NMR and DFT Evaluation

Three bis(6-amino-1,3-dimethyluracil-5-yl)-methane derivatives were studied experimentally by variable-temperature (1)H NMR in polar aprotic solutions (CD2Cl2, C5D5N, C2D2Cl4) and computationally by DFT. The unusual for diarylmethanes coplanar conformation of dimethyluracil rings of each molecule is held by a pair of unequal intramolecular N-H···O hydrogen bonds. We show the presence of two dynamic processes involving breakage/formation of these bonds. First, it is two independent NH2 group rotations, each coupled to nitrogen inversion. Second, it is uracil ring rotations (ring flips). The thermodynamic parameters (ΔH(‡), ΔS(‡), and ΔG(‡)) of both processes were estimated by the full line shape analysis of NMR signals and also by DFT calculations. We demonstrate that, though the ring flips exchange pairs of NH protons, the two processes are not coupled: during the ring flip NH2 groups do not rotate, and during the NH2 rotation the rings do not necessarily rotate. Unlike in many other diarylmethanes, the ring flips in the studied compounds are happening stepwise; i.e., the configuration when both rings are "in flight" at the same time is energetically unfavorable (small degree of "cog wheel effect"). The signs of the ΔS(‡) values indicate that the molecular flexibility increases during the NH2 rotations, but decreases during the ring flips.