Intramolecular H···H Interactions for the Crystal Structures of [4-((E)-But-1-enyl)-2,6-dimethoxyphenyl]pyridine-3-carboxylate and [4-((E)-Pent-1-enyl)-2,6-dimethoxyphenyl]pyridine-3-carboxylate; DFT Calculations on Modeled Styrene Derivatives

Synthesis and Structure Elucidation of Novel Spirooxindole Linked to Ferrocene and Triazole Systems via [3 + 2] Cycloaddition Reaction

In the present work, a novel heterocyclic hybrid of a spirooxindole system was synthesized via the attachment of ferrocene and triazole motifs into an azomethine ylide by [3 + 2] cycloaddition reaction protocol. The X-ray structure of the heterocyclic hybrid (1″R,2″S,3R)-2″-(1-(3-chloro-4-fluorophenyl)-5-methyl-1H-1,2,3-triazole-4-carbonyl)-5-methyl-1″-(ferrocin-2-yl)-1″,2″,5″,6″,7″,7a″-hexahydrospiro[indoline-3,3″-pyrrolizin]-2-one revealed very well the expected structure, by using different analytical tools (FTIR and NMR spectroscopy). It crystallized in the triclinic-crystal system and the P-1-space group. The unit cell parameters are a = 9.1442(2) Å, b = 12.0872(3) Å, c = 14.1223(4) Å, α = 102.1700(10)°, β = 97.4190(10)°, γ = 99.1600(10)°, and V = 1484.81(7) ų. There are two molecules per unit cell and one formula unit per asymmetric unit. Hirshfeld analysis was used to study the molecular packing of the heterocyclic hybrid. H···H (50.8%), H···C (14.2%), Cl···H (8.9%), O···H (7.3%), and N···H (5.1%) are the most dominant intermolecular contacts in the crystal structure. O···H, N···H, H···C, F···H, F···C, and O···O are the only contacts that have the characteristic features of short and significant interactions. AIM study indicated predominant covalent characters for the Fe–C interactions. Also, the electron density (ρ(r)) at the bond critical point correlated inversely with the Fe–C distances.

Synthesis, X-ray, Hirshfeld, and AIM Studies on Zn(II) and Cd(II) Complexes with Pyridine Ligands

The synthesis and crystal structures of three heteroleptic complexes of Zn(II) and Cd(II) with pyridine ligands (ethyl nicotinate (EtNic), N,N-diethylnicotinamide (DiEtNA), and 2-amino-5-picoline (2Ampic) are presented. The complex [Zn(EtNic)2Cl2] (1) showed a distorted tetrahedral coordination geometry with two EtNic ligand units and two chloride ions as monodentate ligands. Complexes [Zn(DiEtNA)(H2O)4(SO4)]·H2O (2) and [Cd(OAc)2(2Ampic)2] (3) had hexa-coordinated Zn(II) and Cd(II) centers. In the former, the Zn(II) was coordinated with three different monodentate ligands, which were DiEtNA, H2O, and SO42−. In 3, the Cd(II) ion was coordinated with two bidentate acetate ions and two monodentate 2Ampic ligand units. The supramolecular structures of the three complexes were elucidated using Hirshfeld analysis. In 1, the most important interactions that governed the molecular packing were O···H (15.5–15.6%), Cl···H (13.6–13.8%), Cl···C (6.3%), and C···H (10.3–10.6%) contacts. For complexes 2 and 3, the H···H, O···H, and C···H contacts dominated. Their percentages were 50.2%, 41.2%, and 7.1%, respectively, for 2 and 57.1%, 19.6%, and 15.2%, respectively, for 3. Only in complex 3, weak π-π stacking interactions between the stacked pyridines were found. The Zn(II) natural charges were calculated using the DFT method to be 0.8775, 1.0559, and 1.2193 for complexes 1–3, respectively. A predominant closed-shell character for the Zn–Cl, Zn–N, Zn–O, Cd–O, and Cd–N bonds was also concluded from an atoms in molecules (AIM) study.

Molecular, Supramolecular Structures Combined with Hirshfeld and DFT Studies of Centrosymmetric M(II)-azido {M=Ni(II), Fe(II) or Zn(II)} Complexes of 4-Benzoylpyridine

The supramolecular structures of the three metal (II) azido complexes [Fe(4bzpy)4(N3)2]; 1, [Ni(4bzpy)4(N3)2]; 2 and [Zn(4bzpy)2(N3)2]n; 3 with 4-benzoylpyridine (4bzpy) were presented. All complexes contain hexa-coordinated divalent metal ions with a slightly distorted octahedral MN6 coordination sphere. Complexes 1 and 2 are monomeric with terminal azido groups while 3 is one-dimensional coordination polymer containing azido groups with μ(1,1) and μ(1,3) bridging modes of bonding. Hirshfeld analysis was used to quantitatively determine the different contacts affecting the molecular packing in the studied complexes. The most common interactions are the polar O…H and N…H interactions and the hydrophobic C…H contacts. The charges at the M(II) sites are calculated to be 1.004, 0.847, and 1.147 e for complexes 1–3, respectively. The degree of asymmetry is the highest in the case of the terminal azide in complexes 1 and 2 while was found the lowest in the μ(1,1) and μ(1,3) azide bonding modes in the Zn(II) complex 3. These facts were further explained in terms of atoms in molecules (AIM) topological parameters.

Predicted structure and selectivity of 3d transition metal complexes with glutamic N,N-bis(carboxymethyl) acid

Structure and selectivity of 3d transition metal complexes with glutamic N,N-bis(carboxymethyl) acid are analyzed and predicted from DFT calculations.

Experimental and theoretical investigation of conformational states and noncovalent interactions in crystalline sulfonamides with a methoxyphenyl moiety

The conformational and noncovalent interaction properties of sulfonamides with a methoxyphenyl moiety were examined by both experimental and theoretical methods.

Synthesis, X-ray Crystal Structure and Antimicrobial Activity of Unexpected Trinuclear Cu(II) Complex from s-Triazine-Based Di-Compartmental Ligand via Self-Assembly

The synthesis and X-ray crystal structure of the trinuclear [Cu3(HL)(Cl)2(NO3)(H2O)5](NO3)2 complex of the s-triazine-based di-compartmental ligand, 2-methoxy-4,6-bis(2-(pyridin-2-ylmsethylene)hydrazinyl)-1,3,5-triazine (H2L), are presented. The Cu1 and Cu2 are penta-coordinated with CuN3ClO coordination environment, distorted square pyramidal coordination geometry while Cu3 is hexa-coordinated with CuN2O4 coordination sphere, and distorted octahedral geometry. The complex crystallized in the primitive P-1 triclinic crystal system with two molecular units per unit cell. Its packing is dominated by the O–H (35.5%) and Cl–H (8.8%) hydrogen bonding interactions as well as the π–π stacking (2.3%) and anion–π-stacking interactions (3.7%). The different coordination interactions were analyzed using atoms in molecules (AIM) theory, and the number of charge transferences from the ligand group to Cu(II) were determined using natural bond orbital calculations. The effect of the free ligand and its Cu(II) complex on the tested pathogenic microbes (Staphylococcus aureus, S. epidermidis, Enterococcus faecalis, Escherichia coli, Salmonella typhi and Pseudomonas aeruginosa) and one fungal isolate (Candida albicans) is presented. Both have wide spectrum antimicrobial activity against the selected microorganism. It is observed that the free ligand at 180 µg/mL was more effective than its Cu(II) complex and showed close results compared to the positive control gentamicin. At higher concentrations (1 mg/mL), the Cu(II) complex was found to be more active against S. epidermidis, E. coli and C. albicans than the lower concentration. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values are also lower for the Cu(II) complex than the free ligand.

Synthesis, Molecular and Supramolecular Structures of New Cd(II) Pincer-Type Complexes with s-TriazineCore Ligand

The manuscript described the synthesis and characterization of the new [Cd(BDMPT)2](ClO4)2; 1 and [Cd2(MBPT)2(H2O)2Cl](ClO4)3.4H2O ; 2s-triazine pincer-type complexes, where BDMPT and MBPT are 2,4-bis(3,5-dimethyl-1H-pyrazol-1-yl)-6-methoxy-1,3,5-triazine and 2-methoxy-4,6-bis(2-(pyridin-2-ylmsethylene)hydrazinyl)-1,3,5-triazinerespectively.The synthesized complexes were characterized using Fourier-transform infrared spectroscopy (FTIR), 1H and 13C NMR spectroscopy, and the single-crystal X-ray diffraction technique.The homoleptic mononuclear complex (1)contains a hexa-coordinated Cd(II) center with two tridentate N-pincer ligand (BDMPT) with a highly distorted octahedral coordination environment located as an intermediate case between the octahedron and trigonal prism. The heteroleptic dinuclear complex (2) contains two hepta-coordinated Cd(II) coordination spheres where each Cd(II) is coordinated with one pentadentate pincer N-chelate (MBPT), one water, and one bridged chloride ligand connecting the two metal ions. The different intermolecular interactions in the studied complexes were quantified using Hirshfeld analysis. Their thermal stabilities and FTIR spectra were compared with the corresponding free ligands. The strength and nature of Cd–N, Cd–O, and Cd–Cl coordination interactions were discussed in light of atoms in molecules calculations (AIM). The M(II)–BDMPT and M(II)–MBPT interaction energies revealed that such sterically hindered ligands have higher affinity toward large-size metal ions (M =Cd) compared to smaller ones (M= Ni or Mn).

Combined QTAIM and ETS-NOCV investigation of the interactions in ClnM[PhB(NtBu)2] complexes with M = Si & Ge (n = 0), As & Sb (n = 1), Te & Po (n = 2)

In this work, the nature of the chemical interactions between the metalloid atom (M = Si, Ge, As, Sb, Te, Po) and the nitrogen atoms in the bora-amidinate (bam) complexes (Cl_nM[PhB(N^tBu)₂]) are investigated, mainly via density-based indices. The descriptors used are derived using the quantum theory of atoms in molecules and natural orbitals for chemical valence approaches. It is shown that the strongest interaction is achieved with silicon. Indeed, it is generally the lightest metalloid in a particular group of the periodic table (i.e., Si, As, and Te for groups 14-16, respectively) that exhibits the strongest bond in the bam complex. This suggests that the atomic radius of the metalloid is a useful parameter for predicting the bonding strength. Extended transition state (ETS) decomposition results indicate that the interactions are more electrostatic than due to orbital interactions.

Revealing Factors Influencing the Fluorine-Centered Non-Covalent Interactions in Some Fluorine-Substituted Molecular Complexes: Insights from First-Principles Studies

We examine the equilibrium structure and properties of six fully or partially fluorinated hydrocarbons and several of their binary complexes using computational methods. In the monomers, the electrostatic surface of the fluorine is predicted to be either entirely negative or weakly positive. However, its lateral sites are always negative. This enables the fluorine to display an anisotropic distribution of charge density on its electrostatic surface. While this is the electrostatic surface scenario of the fluorine atom, its negative sites in some of these monomers are shown to have the potential to engage in attractive engagements with the negative site(s) on the same atom in another molecule of the same type, or a molecule of a different type, to form bimolecular complexes. This is revealed by analyzing the results of current state-of-the-art computational approaches such as DFT, together with those obtained from the quantum theory of atoms in molecules, molecular electrostatic surface potential and symmetry adapted perturbation theories. We demonstrate that the intermolecular interaction energy arising in part from the universal London dispersion, which has been underappreciated for decades, is an essential factor in explaining the attraction between the negative sites, although energy arising from polarization strengthens the extent of the intermolecular interactions in these complexes.

The nature of NO-bonding in N-oxide group

The nature of the NO-bond in the N-oxide group was investigated by means of combined theoretical calculations (including QTAIM and NBO approaches) and statistical analyses of the contents of crystal structure databases. The N-O bond in the N-oxide group should be classified as the NO donating bond with an important contribution of ON back-donation (of the π-electron type, when available). The visualization of the Laplacian of electron density in the region of an oxygen valence sphere suggests the presence of two lone pairs for the imine-N-oxide group (characterized by effective ON back-donation). A detailed bonding analysis performed by means of natural resonance theory indicates that the N→O bond is of an order of magnitude clearly greater than 1. In addition, the stability of the N→O bond in various N-oxides was estimated. The analyses of the hydrogen- and halogen-bonded complexes of the N-oxides reveal strong Lewis basicity of the N-oxide group. The formation of H- and X-bonding leads to N→O bond elongation due to its structural, topological and spectroscopic characteristics. Moreover, in pyridine-N-oxide, the electron-withdrawing -NO2 group additionally stabilizes the N→O bond, whereas the opposite effect can be observed for the electron-donating-NH2 substituent. This is due to a substituent effect on the π-type ON back-donation. As a result, the oxygen atom in pyridine-N-oxide may change its availability during intermolecular interaction formation, as revealed in the interaction energy, which changes by about half of the estimated total interaction energy.

Hydrogen-hydrogen bonds in highly branched alkanes and in alkane complexes: A DFT, ab initio, QTAIM, and ELF study

The hydrogen-hydrogen (H-H) bond or hydrogen-hydrogen bonding is formed by the interaction between a pair of identical or similar hydrogen atoms that are close to electrical neutrality and it yields a stabilizing contribution to the overall molecular energy. This work provides new, important information regarding hydrogen-hydrogen bonds. We report that stability of alkane complexes and boiling point of alkanes are directly related to H-H bond, which means that intermolecular interactions between alkane chains are directional H-H bond, not nondirectional induced dipole-induced dipole. Moreover, we show the existence of intramolecular H-H bonds in highly branched alkanes playing a secondary role in their increased stabilities in comparison with linear or less branched isomers. These results were accomplished by different approaches: density functional theory (DFT), ab initio, quantum theory of atoms in molecules (QTAIM), and electron localization function (ELF).

The influence of H-bonding on the ‘ambidentate’ coordination behaviour of the thiocyanate ion to Cd(ii): a combined experimental and theoretical study

The importance of H-bonding in stabilizing the unusual S-coordination of the thiocyanate ion to Cd(ii) in hetero-metallic Cu₂Cd compounds has been established by structural analyses and DFT studies.

Anion induced formation of supramolecular associations involving lone pair-π and anion-π interactions in Co(II) malonate complexes: experimental observations, Hirshfeld surface analyses and DFT studies

Three Co(II)-malonate complexes, namely, (C(5)H(7)N(2))(4)[Co(C(3)H(2)O(4))(2)(H(2)O)(2)](NO(3))(2) (1), (C(5)H(7)N(2))(4)[Co(C(3)H(2)O(4))(2)(H(2)O)(2)](ClO(4))(2) (2), and (C(5)H(7)N(2))(4)[Co(C(3)H(2)O(4))(2)(H(2)O)(2)](PF(6))(2) (3) [C(5)H(7)N(2) = protonated 2-aminopyridine, C(3)H(4)O(4) = malonic acid, NO(3)(-) = nitrate, ClO(4)(-) = perchlorate, PF(6)(-) = hexafluorophosphate], have been synthesized from purely aqueous media, and their crystal structures have been determined by single crystal X-ray diffraction. A thorough analysis of Hirshfeld surfaces and fingerprint plots facilitates a comparison of intermolecular interactions in 1-3, which are crucial in building supramolecular architectures. When these complexes are structurally compared with their previously reported analogous Ni(II) or Mg(II) compounds, a very interesting feature regarding the role of counteranions has emerged. This phenomenon can be best described as anion-induced formation of extended supramolecular networks of the type lone pair-π/π-π/π-anion-π/π-lone pair and lone pair-π/π-π/π-anion involving various weak forces like lone pair-π, π-π, and anion-π interactions. The strength of these π contacts has been estimated using DFT calculations (M06/6-31+G*), and the formation energy of the supramolecular networks has been also evaluated. The influence of the anion (NO(3)(-), ClO(4)(-), and PF(6)(-)) on the total interaction energy of the assembly is also studied.

Dihydrogen contacts in alkanes are subtle but not faint

Alkane molecules are held together in the crystal state by purportedly weak homonuclear R-H···H-R dihydrogen interactions. In an apparent contradiction, the high melting points and vaporization enthalpies of polyhedranes in condensed phases require quite strong intermolecular interactions. Two questions arise: 'How strong can a weak C-H···H-C bond be?' and 'How do the size and topology of the carbon skeleton affect these bonding interactions?' A systematic computational study of intermolecular interactions in dimers of n-alkanes and polyhedranes, such as tetrahedrane, cubane, octahedrane or dodecahedrane, showed that attractive C-H···H-C interactions are stronger than usually thought. We identified factors that account for the strength of these interactions, including the tertiary nature of the carbon atoms and their low pyramidality. An alkane with a bowl shape was designed in the search for stronger dihydrogen intermolecular bonding, and a dissociation energy as high as 12 kJ mol⁻¹ is predicted by our calculations.