Comprehensive Analysis of Fragment Orbital Interactions to Build Highly π‐Conjugated Thienylene‐Substituted Phenylene Oligomers

π‐Conjugated thienylene? phenylene oligomers with fluorinated and dialkoxylated phenylene fragments have been designed and prepared to understand the interactions in fragment orbitals, the influence of the substituents (F, OMe) on the HOMO–LUMO gap, and the role of intramolecular non‐covalent cumulative interactions in the construction of π‐conjugated nanostructures. Their strong conjugation was also evidenced in the gas phase by UV photoelectron spectroscopy and theoretical calculations. These results can be explained by the crucial role of the relative energetic positions of the π orbitals of the dimethoxyphenylene, which was used to model the dialkoxyphenylene entity, in determining the π/π^* orbital levels of the fluorinated phenylene entity. Dialkoxyphenylenes raise the HOMO orbitals, whereas fluorinated phenylenes lower the LUMO orbitals in the oligomers. In addition, the presence of S???F and H???F interactions in the fluorinated phenylene? thienylene compounds add to the S???O interactions in the mixed targets and contribute to the full conjugation in the oligomer, inducing weak inter‐ring angles between the involved aromatic cycles. These results, which showed extended conjugation of the π system, were corroborated by a narrow HOMO–LUMO gap (according to DFT calculations) and by a relatively strong maximum wavelength (as obtained by TD‐DFT calculations and experimental UV/Vis measurements). The crystallographic data of two mixed thienylene? (fluorinated and dialkoxylated phenylene) five‐ring oligomers agree with the above results and show the formation of quasi‐planar conformations with non‐covalent S???O, H???F, and S???F interactions. These studies in the solid and gas phases show the relevance of associating dialkoxyphenylene and fluorinated phenylene fragments with thiophene to lead to oligomers with improved electronic delocalization for electronic or optoelectronic devices.     

Front Cover: Exploring Helical Folding in Oligomers of Cyclopentane‐Based ϵ‐Amino Acids: A Computational Study (ChemistryOpen 3/2022)

The Front Cover shows the preferred conformation of oligomers of the aminoacid Amc₅a. The backbone sequences were investigated using DFT methods in solution. More information can be found in the Research Article by Hae Sook Park et al.     

Theoretical Study on the Dual Behavior of XeO3 and XeF4 toward Aromatic Rings: Lone Pair–π versus Aerogen–π Interactions

In this study, several lone pair–π and aerogen–π complexes between XeO₃ and XeF₄ and aromatic rings with different electronic natures (benzene, trifluorobenzene, and hexafluorobenzene) are optimized at the RI‐MP2/aug‐cc‐pVTZ level of theory. All complexes are characterized as true minima by frequency analysis calculations. The donor/acceptor role of the ring in the complexes is analyzed using the natural bond orbital computational tool, showing a remarkable contribution of orbital interactions to the global stabilization of the aerogen–π complexes. Finally, Bader's AIM analysis of several complexes is performed to further characterize the lone pair–π and aerogen–π interactions.     

Intermolecular C—H...π interactions in 1,5‐diphenyl‐3‐(2‐pyridyl)‐2‐pyrazoline

The title compound, C₂₀H₁₇N₃, is a derivative of 1,3,5‐triaryl‐2‐pyrazoline and can act as an N,N′‐bidentate ligand. This molecule features strong fluorescence that can be explained by an extended pyridyl–C=N—N–phenyl system. The three‐dimensional structure is formed by means of an extended network of weak C—H...π hydrogen bonds supported by π–π interactions.     

A Study on the Intramolecular Mitsunobu Reaction of N6‐(ω‐Hydroxyalkyl)adenines

The cyclization of N ⁶‐(ω‐hydroxyalkyl)adenines with a N⁶H‐group leads to N⁶,N1 ring closure regardless of the method of the cyclization that was used. Five‐membered to eight‐membered rings were obtained using NBS/PPh₃; however, under Mitsunobu conditions, the eight‐membered fused purine was not formed. Surprisingly, the cyclization of N ⁶‐methyl‐N ⁶‐(4‐hydroxybutyl)adenine only leads to N⁶,N7 ring closure using both methods.     

Behavior of Halogen Bonds of the Y−X⋅⋅⋅π Type (X,Y=F,Cl, Br,I) in the Benzene π System,Elucidated by Using a Quantum Theory of Atoms in Molecules Dual‐Functional Analysis

The nature of halogen bonds of the Y?X‐?‐π(C₆H₆) type (X, Y=F, Cl, Br, and I) have been elucidated by using the quantum theory of atoms in molecules (QTAIM) dual‐functional analysis (QTAIM‐DFA), which we proposed recently. Asterisks (?) emphasize the presence of bond‐critical points (BCPs) in the interactions in question. Total electron energy densities, H_b( r _c), are plotted versus H_b( r _c)?V_b( r _c)/2 [=(?²/8m)?²ρ_b( r _c)] for the interactions in QTAIM‐DFA, in which V_b( r _c) are potential energy densities at the BCPs. Data for perturbed structures around fully optimized structures were used for the plots, in addition to those of the fully optimized ones. The plots were analyzed by using the polar (R, θ) coordinate for the data of fully optimized structures with (θ_p, κ_p) for those that contained the perturbed structures; θ_p corresponds to the tangent line of the plot and κ_p is the curvature. Whereas (R, θ) corresponds to the static nature, (θ_p, κ_p) represents the dynamic nature of the interactions. All interactions in Y?X‐?‐π(C₆H₆) are classified by pure closed‐shell interactions and characterized to have vdW nature, except for Y?I‐?‐π(C₆H₆) (Y=F, Cl, Br) and F?Br‐?‐π(C₆H₆), which have typical hydrogen‐bond nature without covalency. I?I‐?‐π(C₆H₆) has a borderline nature between the two. Y?F‐?‐π(C₆H₆) (Y=Br, I) were optimized as bent forms, in which Y‐?‐π interactions were detected. The Y‐?‐π interactions in the bent forms are predicted to be substantially weaker than those in the linear F?Y‐?‐π(C₆H₆) forms.     

Synthesis and Crystal Structure of [(1‐(Phenyltriazenido)‐2‐(phenyltriazeno)benzene)(nitrato)mercury(II)], {Hg[PhN3C6H4N3(H)Ph](NO3)}, a Complex with Weak Metal‐Arene π‐Interactions

The reaction of PhN₃(H)C₆H₄N₃(H)Ph with Hg(NO₃)₂ in THF in the presence of triethylamine yields {Hg[PhN₃C₆H₄N₃(H)Ph](NO₃)} as a yellow powder that can be recrystallized from THF/acetone. The crystals belong to the monoclinic system, space group P2₁ with the cell dimensions a = 9.639(2), b = 5.412(1), c = 19.675(4) Å, β= 97.47(3)°, V = 1017.7 (4) ų, Z = 2. The crystal structure determination (2668 unique reflections with [I>2σ(I)], 262 parameters, R₁ = 0.0393) shows that the structure consists of mononuclear complexes. Hg atoms are linearly coordinated by one N_α atom of the triazenide unit of the planar ligand [Hg‐N(1) = 2.101(8) Å] and an O atom of the NO₃^— ion [Hg‐O(1) = 2.11(1) Å]. Additional weak Hg‐N contacts [Hg‐N(4) = 2.662(9) and Hg‐N(3) = 2.851(9) Å] and an intramolecular hydrogen bond between the triazenide hydrogen and an O atom of the nitrate group are observed [N(6)‐H(6)···O(2) = 2.92(2) Å]. The complexes are stacked to infinite chains by metal‐arene π‐interactions. Each Hg atom is coordinated by the terminal phenyl rings of two neighboring complexes [Hg‐C from 3.40(1) to 4.10(1) Å] in a η² fashion.     

Density Functional Method Study on the Cooperativity of Intermolecular H-bonding and π-π+ Stacking Interactions in Thymine-[Cnmim]Br (n = 2, 4, 6, 8, 10) Microhydrates

The exploration of the ionic liquids’ mechanism of action on nucleobase’s structure and properties is still limited. In this work, the binding model of the 1-alkyl-3-methylimidazolium bromide ([C_nmim]Br, n = 2, 4, 6, 8, 10) ionic liquids to the thymine (T) was studied in a water environment (PCM) and a microhydrated surroundings (PCM + wH₂O). Geometries of the mono-, di-, tri-, and tetra-ionic thymine (T-wH₂O-y[C_nmim]⁺-xBr⁻, w = 5~1 and x + y = 0~4) complexes were optimized at the M06-2X/6-311++G(2d, p) level. The IR and UV-Vis spectra, QTAIM, and NBO analysis for the most stable T-4H₂O-Br⁻-1, T-3H₂O-[C_nmim]⁺-Br⁻-1, T-2H₂O-[C_nmim]⁺-2Br⁻-1, and T-1H₂O-2[C_nmim]⁺-2Br⁻-1 hydrates were presented in great detail. The results show that the order of the arrangement stability of thymine with the cations (T-[C_nmim]⁺) by PCM is stacking > perpendicular > coplanar, and with the anion (T-Br⁻) is front > top. The stability order for the different microhydrates is following T-5H₂O-1 < T-4H₂O-Br⁻-1 < T-3H₂O-[C_nmim]⁺-Br⁻-1 < T-2H₂O-[C_nmim]⁺-2Br⁻-1 < T-1H₂O-2[C_nmim]⁺-2Br⁻-1. A good linear relationship between binding E_B values and the increasing number (x + y) of ions has been found, which indicates that the cooperativity of interactions for the H-bonding and π-π⁺ stacking is varying incrementally in the growing ionic clusters. The stacking model between thymine and [C_nmim]⁺ cations is accompanied by weaker hydrogen bonds which are always much less favorable than those in T-xBr⁻ complexes; the same trend holds when the clusters in size grow and the length of alkyl chains in the imidazolium cations increase. QTAIM and NBO analytical methods support the existence of mutually reinforcing hydrogen bonds and π-π cooperativity in the systems.     

2‐tert‐Butyl‐5‐methyl‐7,8‐dihydro‐6H‐cyclopenta[e]pyrazolo[1,5‐a]pyrimidine: molecular stacks built from C—H...π(pyrazole) hydrogen bonds and π–π stacking interactions

In the title compound, C₁₄H₁₉N₃, the bond distances within the heterocyclic portion of the molecule indicate incomplete π delocalization. The molecules are linked into stacks by a combination of two C—H...π(pyrazole) hydrogen bonds and two independent π–π stacking interactions between inversion‐related pyrimidine rings. The significance of this study lies in its observation of significant differences in both molecular conformation and supramolecular aggregation between the title compound, an example of a 2‐alkylpyrazolo[1,5‐a]pyrimidine, and some analogous 2‐arylpyrazolo[1,5‐a]pyrimidines.     

Synthesis of Pyrano[3,2‐c]quinoline‐3‐carboxaldehyde and 3‐(Ethoxymethylene)‐pyrano[3,2‐c]quinolinone and Their Chemical Behavior toward Some Nitrogen and Carbon Nucleophiles

Synthesis of novel 3‐(ethoxymethylene)‐pyrano[3,2‐c]quinolinone and pyrano[3,2‐c]quinoline‐3‐carboxaldehyde was accomplished efficiently via a simple method. These two scaffolds were used as precursors to afford new biologically interesting products in good yield and short reaction times. The chemical reactivity of ethoxy methylene 2 and carboxaldehyde 3 toward different nucleophilic reagents was studied. Structures of the new synthesized compounds were elucidated by their analytical and spectral data.     

Structural and Spectral Studies on the Ni(II) Complexes of 1,5‐Diazacyclooctane (DACO) Bearing Heterocyclic Pendants: Formation of a Two‐dimensional Network via Hydrogen Bonds and π‐π Stacking Interactions

A penta‐coordinated Ni(II) complex with a 1,5‐diazacyclooctane (DACO) ligand functionalized by two imidazole donor pendants, [NiL¹Cl] (ClO₄) H₂O (1) (where L¹ = 1,5‐bis (imidazol‐4‐ylmethyl)‐l,5‐diazacyclooctane) has been synthesized and characterized by X‐ray diffraction, infrared spectra, elemental analyses, conductance, thermal analyses and UV‐Vis techniques. Complex 1 crystallizes in triclinic crystal system, P‐l space group with a = 0.74782(7), b = 1.15082 (10), c = 1.23781(11) nm, α = 82.090(2), β = 73.011(2), γ = 83.462(2)°, V = 1.00603(16) nm³, M, = 486.00, Z = 2, D_c = 1.604 g/cm³, final R = 0.0435, and wR = 0.1244. The structures of 1 and its related complexes show that in all the three mononuclear complexes, each Ni(II) center is penta‐coordinated with a near regular square pyramid (RSP) to distorted square‐pyramidal (DSP) coordination environment due to the boat/chair configuration of DACO ring in these complexes, and the degree of distortion increases with the augment of the size of the heterocyclic pendants. In addition, the most striking feature of complex 1 resides in the formation of a two‐dimensional network structure through hydrogen bonds and stabilized by π‐π stacking. The solution behaviors of the Ni(II) complexes are also discussed in detail.     

Ferromagnetic Interactions in a 1D Alternating Linear Chain of π‐Stacked 1,3‐Diphenyl‐7‐(thien‐2‐yl)‐1,4‐dihydro‐1,2,4‐benzotriazin‐4‐yl Radicals

X‐ray studies show that 1,3‐diphenyl‐7‐(thien‐2‐yl)‐1,4‐dihydro‐1,2,4‐benzotriazin‐4‐yl ( 6 ) adopts a distorted, slipped π‐stacked structure of centrosymmetric dimers with alternate short and long interplanar distances (3.48 and 3.52 Å). Cyclic voltammograms of 7‐(thien‐2‐yl)benzotriazin‐4‐yl 6 show two fully reversible waves that correspond to the ?1/0 and 0/+1 processes. EPR and DFT studies on radical 6 indicate that the spin density is mainly delocalized over the triazinyl fragment. Magnetic susceptibility measurements show that radical 6 obeys Curie–Weiss behavior in the 5–300 K region with C=0.378 emu K mol^?1 and θ=+4.72 K, which is consistent with ferromagnetic interactions between S=1/2 radicals. Fitting the magnetic susceptibility revealed the behavior is consistent with an alternating ferromagnetic chain (g=2.0071, J₁=+7.12 cm^?1, J₂=+1.28 cm^?1).     

[Na(DB18-C-6)(H2O)2][Na(DB18-C-6)(SCN)2]：Two-Di-mensional Network Complex Assembled by π-π Stacking Interactios,Hydrogen Bonds and Electrostatic Interactions

A novel two‐dimensional network dibenzo‐18‐crown‐6 (DB18‐C6) complex: [Na (DB18‐C‐6) (H₂O)₂] [Na (DB18‐C‐6) (SCN)₂] has been isolated and characterized by elemental, IR and X‐ray diffraction analysis. The crystal structure belongs to monoclinic, space group P2₁/c with cell dimensions a = 1.06178(7), b = 1.40243(8), c = 3.03496(19) nm, β = 90.4220(10)°, V = 4.5292(5) nm³, Z=4, D_calcd =1.351 g/ cm³, F(000) = 1936, R₁ = 0.0369, wR₂ = 0.0821. The most interesting feature in this structure is that complex cation and complex anion form a two‐dimensional network via τ‐τ stacking interactions, hydrogen bonds and electrostatic interactions.     

π‐Stacked dimers in 6‐methoxy‐3,3‐dimethyl‐3H‐benzo[f]chromene,and centrosymmetric dimers containing C—H...π(arene) hydrogen bonds in racemic 3‐bromo‐2,2,6,6‐tetramethyl‐3,4‐dihydro‐2H,6H‐1,5‐dioxatriphenylene

The title compounds, namely 6‐methoxy‐3,3‐dimethyl‐3H‐benzo[f]chromene, C₁₆H₁₆O₂, (III), and racemic 3‐bromo‐2,2,6,6‐tetramethyl‐3,4‐dihydro‐2H,6H‐1,5‐dioxatriphenylene, C₂₀H₂₁BrO₂, (IV), were both synthesized in one‐step regioselective Wittig reactions from substituted 1,2‐naphthoquinones. The new ring in both compounds adopts a screw‐boat conformation. A single π–π stacking interaction links the molecules of (III) into centrosymmetric dimeric aggregates, and a single C—H...π(arene) hydrogen bond links the molecules of (IV) into centrosymmetric dimers.     

Synthesis of 6‐(2‐hydroxybenzoyl)pyrazolo[1,5‐a]pyrimidines by reaction of 5‐amino‐1h‐pyrazoles and 3‐formylchromone

Reaction of 3‐formylchromone ( 1 ) with 5‐amino‐1H‐pyrazoles ( 2 ) in ethanol, afforded 6‐(2‐hydroxy‐benzoyl)pyrazolo[1,5‐a]pyrimidines ( 3a‐g ) in good yields. The structures and the regiospecificity of the reaction were established by nmr measurements and X‐ray analysis, in which soft intermolecular hydrogen‐bonded networks were found.     

The Analysis of Electronic Structures,NBO, EDA,and QTAIM of trans‐(H3P)2(η2‐BH4 )W(≡C‐para‐C6H4X)(CO) Complexes

In the present research, the impact of substitution on the dipole moment, electronic structure, and frontier orbital energy in trans ‐(H₃P )₂(η²‐BH₄ )W(≡C‐para ‐C₆H₄X )(CO ) complexes (X = H, F, SiH₃ , CN , NO₂ , SiMe₃ , CMe₃ , NH₂ , NMe₂ ) was studied with mpw1pw91 quantum chemical computations. The nature of the chemical bond between the trans‐[Cl(η²‐BH₄ )(H₃P ) ₂W ]⁻ and [C‐para ‐C₆H₄X ]⁺ fragments was demonstrated through energy decomposition analysis (EDA ). The percentage composition in terms of the specified groups of frontier orbitals was examined for these complexes to investigate the feature in metal–ligand bonds. Quantum theory of atoms in molecules (QTAIM ) and natural bond orbital (NBO ) analysis were applied to elucidate these complexes’ metal–ligand bonds.     

4‐(Allyl­amino)‐2‐amino‐6‐benzyl­oxy‐5‐nitro­so­pyrimidine from synchrotron data at 150 K: double chains built from N—H⋯N,N—H⋯O,N—H⋯π(arene) and aromatic π–π‐stacking interactions

In the title compound, C₁₄H₁₅N₅O₂, the intramolecular dimensions are consistent with a highly polarized electronic structure. The mol­ecules are linked into chains by a combination of N—H?N, N—H?O and N—H?π(arene) hydrogen bonds, and the chains are linked in pairs by aromatic π–π‐stacking interactions