Interaction of aromatic units of amino acids with guanidinium cation: The interplay of π···π, XH···π, and M+···π contacts

Complexes formed by guanidinium cation and a pair of aromatic molecules among benzene, phenol, or indole have been computationally studied to determine the characteristics of the cation···π interaction in ternary systems modeling amino acid side chains. Guanidinium coordinates to the aromatic units preferentially in the following order: indole, phenol, and benzene. Complexes containing two different aromatic units show an intermediate behavior between that observed for complexes with only one kind of aromatic unit. Most stable structures correspond to doubly‐T shaped arrangements with the two aromatic units coordinating guanidinium by its NH₂ groups. Other structures with only one aromatic unit coordinated to guanidinium, such as T‐shaped or parallel‐stacked ones, are less favorable but still showing significant stabilization. In indole and phenol complexes, the formation of hydrogen bonds between the aromatic molecules introduces extra stabilization in T‐shaped structures. Three body effects are small and repulsive in doubly T‐shaped minima. Only when hydrogen bonds involving the aromatic molecules are formed in T‐shaped structures a cooperative effect can be observed. In most complexes the interaction is controlled by electrostatics, with induction and dispersion also contributing significantly depending on the nature and orientation of the aromatic species forming the complex. Although the stability in these systems is mainly controlled by the intensity of the interaction between guanidinium and the aromatic molecules coordinated to it, interactions between aromatic molecules can modulate the characteristics of the complex, especially when hydrogen bonds are formed. © 2014 Wiley Periodicals, Inc.     

The O–H···O, O–H···N and C–H···O hydrogen bonds in 1,4-dimethylpiperazine mono-betaine monohydrate

1,4-Dimethylpiperazine mono-betaine (1-carboxymethyl-1,4-dimethylpiperazinium inner salt, MBPZ) crystallizes as monohydrate. The crystals are orthorhombic, space group Pccn. Two MBPZ molecules and two water molecules form a cyclic oligomer, (MBPZ·H₂O)₂. The O–H···O and O–H···N hydrogen bonds are of 2.769(1) and 2.902(1) Å, respectively. The dimers interact with the neighboring molecules through the C–H···O hydrogen bonds of 3.234(1) Å. The piperazine ring assumes a chair conformation with the N(4)–CH₃ and N⁺(1)–CH₂COO⁻ groups in the equatorial position and the N⁺(1)–CH₃ group in the axial one. The FTIR spectrum is compared with that calculated by the B3LYP/6-31G(d,p) level of theory.     

Experimental and theoretical study of the intramolecular C–H···N and C–H···S hydrogen bonding effects in the 1H and 13C NMR spectra of the 2‐(alkylsulfanyl)‐5‐amino‐1‐vinylpyrroles: a particular state of amine nitrogen

In the ¹H NMR spectra of the 1‐vinylpyrroles with amino‐ and alkylsulfanyl groups in 5 and 2 positions, an extraordinarily large difference between resonance positions of the H_A and H_B terminal methylene protons of the vinyl group is discovered. Also, the one‐bond ¹J(C_β,H_B) coupling constant is surprisingly greater than the ¹J(C_β,H_A) coupling constant in pyrroles under investigation, while in all known cases, there was a reverse relationship between these coupling constants. These spectral anomalies are substantiated by quantum chemical calculations. The calculations show that the amine nitrogen lone pair is removed from the conjugation with the π‐system of the pyrrole ring so that it is directed toward the H_B hydrogen. These factors are favorable to the emergence of the intramolecular C–H_B???N hydrogen bonding in the s‐cis(N) conformation. On the other hand, the spatial proximity of the sulfur to the H_B hydrogen provides an opportunity of the intramolecular C–H_B???S hydrogen bonding in the s‐cis(S) conformation. Presence of the hydrogen bond critical points as well as ring critical point for corresponding chelate ring revealed by a quantum theory of atoms in molecules (QTAIM) approach confirms the existence of the weak intramolecular C–H???N and C–H???S hydrogen bonding. Therefore, an unusual high‐frequency shift of the H_B signal and the increase in the ¹J(C_β,H_B) coupling constant can be explained by the effects of hydrogen bonding. Copyright © 2013 John Wiley & Sons, Ltd.     

Van Der Waals heterogeneous layer‐layer carbon nanostructures involving π···H‐C‐C‐H···π···H‐C‐C‐H stacking based on graphene and graphane sheets

Noncovalent interactions involving aromatic rings, such as π···π stacking, CH···π are very essential for supramolecular carbon nanostructures. Graphite is a typical homogenous carbon matter based on π···π stacking of graphene sheets. Even in systems not involving aromatic groups, the stability of diamondoid dimer and layer‐layer graphane dimer originates from C − H···H − C noncovalent interaction. In this article, the structures and properties of novel heterogeneous layer‐layer carbon‐nanostructures involving π···H‐C‐C‐H···π···H‐C‐C‐H stacking based on [n ]‐graphane and [n ]‐graphene and their derivatives are theoretically investigated for n = 16–54 using dispersion corrected density functional theory B3LYP‐D3 method. Energy decomposition analysis shows that dispersion interaction is the most important for the stabilization of both double‐ and multi‐layer‐layer [n ]‐graphane@graphene. Binding energy between graphane and graphene sheets shows that there is a distinct additive nature of CH···π interaction. For comparison and simplicity, the concept of H‐H bond energy equivalent number of carbon atoms (noted as NHEQ), is used to describe the strength of these noncovalent interactions. The NHEQ of the graphene dimers, graphane dimers, and double‐layered graphane@graphene are 103, 143, and 110, indicating that the strength of C‐H···π interaction is close to that of π···π and much stronger than that of C‐H···H‐C in large size systems. Additionally, frontier molecular orbital, electron density difference and visualized noncovalent interaction regions are discussed for deeply understanding the nature of the C‐H···π stacking interaction in construction of heterogeneous layer‐layer graphane@graphene structures. We hope that the present study would be helpful for creations of new functional supramolecular materials based on graphane and graphene carbon nano‐structures. © 2017 Wiley Periodicals, Inc.     

π–π Stacking‐Interlinked Molecular Squares with Hepta‐Coordinated Cadmium(II) Corners, [Cd(DMAP)3(NO2)2]·0.5H2O

The single crystal X‐ray analysis data of the new hepta‐coordinate cadmium(II) complex of N,N‐dimethyl‐N‐(4‐pyridyl)amine (DMPA), [Cd(DMPA)₃(NO₂)₂]·0.5H₂O, shows that the coordination environment around the Cd^II is pentagonal bipyramidal. Furthermore, self‐assembly of this complex as molecular squares that interlink via π–π stacking interactions is observed. This network contains voids that are filled by water molecules.     

Theoretical study of metal ligand aromatic cation–π interactions of [Co(NH3)6]3+ with benzene

In this work, density functional theory calculations on geometries and energies of all possible conformers of the [Co(NH₃)₆]³⁺–C₆H₆ cation–π complex are described. The calculations show that stationary points are several η₂ and the η₃ structures. The most stable η₃ structure has bonding energy, after basis set superposition error correction, of 32.18 kcal/mol. The energies of η₃ structures are similar; also, the energies of η₂ structures are similar while the difference in energy between η₃ and the η₂ structures is about 2 kcal/mol. This indicates a possibility for various orientations of the benzene ring with respect to interacting ligands in the case of metal ligand aromatic cation–π (MLACπ) interactions and a possibility for the existence of these interactions in different molecular systems. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

A 2D Supramolecular Network Based on Aromatic π···π Stacking Interactions

Using ferrocenecarboxylic acid (FcCOOH) as organometallic ligand in the synthesis of heterometallic complexes led to the isolation of the compound [(FcCOO)Cu(bpy)₂](BF₄) · bpy · CH₃OH. It was characterized by IR spectroscopy, EA, powder XRD, UV, and TGA measurements. Single‐crystal X‐ray structural analysis revealed that a unique 2D supramolecular network purely formed by aromatic π ··· π stacking interactions was observed, namely, {[(FcCOO)Cu(bpy)₂](BF₄) · bpy · CH₃OH}_∞ ( 1 ). The solid UV/Vis diffuse reflectance spectrum revealed the optical energy gap of 1 to be 3.54 eV, which is dramatically blue shifted compared with the value of ferrocene. Experimental results of thermal analysis and electrochemical analysis show that 1 has good thermal and better electrochemical stability.     

Dissecting the concave–convex π‐π interaction in corannulene and sumanene dimers: SAPT(DFT) analysis and performance of DFT dispersion‐corrected methods

The characteristics of the concave–convex π‐π interactions are evaluated in 32 buckybowl dimers formed by corannulene, sumanene, and two substituted sumanenes (with S and CO groups), using symmetry‐adapted perturbation theory [SAPT(DFT)] and density functional theory (DFT). According to our results, the main stabilizing contribution is dispersion, followed by electrostatics. Regarding the ability of DFT methods to reproduce the results obtained with the most expensive and rigorous methods, TPSS‐D seems to be the best option overall, although its results slightly tend to underestimate the interaction energies and to overestimate the equilibrium distances. The other two tested DFT‐D methods, B97‐D2 and B3LYP‐D, supply rather reasonable results as well. M06‐2X, although it is a good option from a geometrical point of view, leads to too weak interactions, with differences with respect to the reference values amounting to about 4 kcal/mol (25% of the total interaction energy). © 2017 Wiley Periodicals, Inc.     

Orbital Effect‐Induced Anomalous Anion–π Interactions between Electron‐Rich Aromatic Hydrocarbons and Fluoride

Anion–π interactions generally exist between an anion and an electron‐deficient π‐ring because of the electron‐accepting character of the ring. In this paper, we report orbital effect‐induced anomalous binding between electron‐rich π systems and F^? through anion–π interactions calculated at the MP2/6‐31+G(d,p) and ωB97X‐D/6‐31+G(d,p) levels of theory. We find that anion–π interactions between F^? and electron‐rich π rings increase markedly with increasing number of π electrons and size of the π rings. This is contrary to intuition because anion–π interactions would be expected to gradually decrease because of gradually increasing Coulombic repulsion between the negative charge of the anions and gradually increasing number of π electrons of the aromatic surfaces. Energy decomposition analysis showed that the key to this anomalous effect is the more effective delocalization of negative charge to the unoccupied π* orbitals of larger π rings, which is termed an “orbital effect”.     

DFT studies on hydrogen‐bonding,Stacking, and XH···π‐Bonded systems in presence of external electric field

Effect of external electric field on interaction energy as well as stability of the hydrogen‐bonding, stacking, and O? H π‐bonded systems are analyzed in the light of density functional theory (DFT) and conceptual DFT. Interaction energy and stability measured in terms of global hardness and highest occupied molecular orbital energy of the considered systems are observed to be sensitive toward the strength and direction of the applied external electric field. The curvature of the potential energy surfaces gets changed in presence of an external electric field. © 2015 Wiley Periodicals, Inc.     

Structure determination of three furan‐substituted benzimidazoles and calculation of π–π and C—H...π interaction energies

The synthesis and structural characterization of 2‐(furan‐2‐yl)‐1‐(furan‐2‐ylmethyl)‐1H‐benzimidazole [C₁₆H₁₂N₂O₂, (I)], 2‐(furan‐2‐yl)‐1‐(furan‐2‐ylmethyl)‐1H‐benzimidazol‐3‐ium chloride monohydrate [C₁₆H₁₃N₂O₂⁺·Cl⁻·H₂O, (II)] and the hydrobromide salt 5,6‐dimethyl‐2‐(furan‐2‐yl)‐1‐(furan‐2‐ylmethyl)‐1H‐benzimidazol‐3‐ium bromide [C₁₈H₁₇N₂O₂⁺·Br⁻, (III)] are described. Benzimidazole (I) displays two sets of aromatic interactions, each of which involves pairs of molecules in a head‐to‐tail arrangement. The first, denoted set (Ia), exhibits both intermolecular C—H...π interactions between the 2‐(furan‐2‐yl) (abbreviated as Fn) and 1‐(furan‐2‐ylmethyl) (abbreviated as MeFn) substituents, and π–π interactions involving the Fn substituents between inversion‐center‐related molecules. The second, denoted set (Ib), involves π–π interactions involving both the benzene ring (Bz) and the imidazole ring (Im) of benzimidazole. Hydrated salt (II) exhibits N—H...OH₂...Cl hydrogen bonding that results in chains of molecules parallel to the a axis. There is also a head‐to‐head aromatic stacking of the protonated benzimidazole cations in which the Bz and Im rings of one molecule interact with the Im and Fn rings of adjacent molecules in the chain. Salt (III) displays N—H...Br hydrogen bonding and π–π interactions involving inversion‐center‐related benzimidazole rings in a head‐to‐tail arrangement. In all of the π–π interactions observed, the interacting moieties are shifted with respect to each other along the major molecular axis. Basis set superposition energy‐corrected (counterpoise method) interaction energies were calculated for each interaction [DFT, M06‐2X/6‐31+G(d)] employing atomic coordinates obtained in the crystallographic analyses for heavy atoms and optimized H‐atom coordinates. The calculated interaction energies are −43.0, −39.8, −48.5, and −55.0 kJ mol⁻¹ for (Ia), (Ib), (II), and (III), respectively. For (Ia), the analysis was used to partition the interaction energies into the C—H...π and π–π components, which are 9.4 and 24.1 kJ mol⁻¹, respectively. Energy‐minimized structures were used to determine the optimal interplanar spacing, the slip distance along the major molecular axis, and the slip distance along the minor molecular axis for 2‐(furan‐2‐yl)‐1H‐benzimidazole.     

A Platinum(II) Terpyridine Metallogel with an L‐Valine‐Modified Alkynyl Ligand: Interplay of Pt⋅⋅⋅Pt, π–π and Hydrogen‐Bonding Interactions

A series of platinum(II) terpyridine complexes with L ‐valine‐modified alkynyl ligands has been synthesized. A complex with an unsubstituted terpyridine and one valine unit on the alkynyl is shown to be capable of gel formation, which is in sharp contrast to the gelation properties of the corresponding organic counterparts. Upon sol–gel transition, a drastic color change from yellow to red is observed, which is indicative of the involvement of Pt ??? Pt interactions. Through the concentration‐ and temperature‐dependent UV/Vis absorption, emission, circular dichroism, and ¹H NMR studies, the contribution of hydrogen bonding, Pt ??? Pt and π–π stacking interactions as driving forces for gelation have been established, and the importance of maintaining a delicate balance between different intermolecular forces has also been illustrated.     

Synthesis and Structural Characterization of Several Ytterbium Bis(trimethylsilyl)amides Including Base‐free [Yb{N(SiMe3)2}2(μ‐Cl)]2 — A Coordinatively Unsaturated Complex with Additional Agostic Yb···(H3C—Si) Interactions

The reaction of YbCl₃ with two equivalents of NaN‐(SiMe₃)₂ has afforded a mixture of several ytterbium bis(trimethylsilyl) amides with the known complexes [Yb{N(SiMe₃)₂}2(μ‐Cl)(thf)]₂ ( 1 ) and [Yb{N(SiMe₃)₂}₃]( 4 ) as the main products and the cluster compound [Yb₃Cl₄O{N(SiMe₃)₂}₃(thf)₃]( 2 ) as a minor product. Treatment of 1 and 2 with hot n‐heptane gave the basefree complex [Yb{N(SiMe₃)₂}₂(μ‐Cl)]₂ ( 3 ) in small yield. The structures of compounds 1—4 and the related peroxo complex [Yb₂{N(SiMe₃)₂}₄(μ‐O₂)(thf)₂]( 5 ) have been investigated by single crystal X‐ray diffraction. In the solid‐state, 3 shows chlorobridged dimers with terminal amido ligands (av. Yb—Cl = 262.3 pm, av. Yb—N = 214.4 pm). Additional agostic interactions are observed from the ytterbium atoms to four methyl carbon atoms of the bis(trimethylsilyl)amido groups (Yb···C = 284—320 pm). DFT calculations have been performed on suitable model systems ([Yb₂(NH₂)₄(μ‐Cl)₂(OMe₂)₂]( 1m ), [Yb₂(NH₂)₄(μ‐Cl)₂]( 3m ), [Yb‐(NH₂)₃]( 4m ), [Yb₂(NH2₄(μ‐O₂)(OMe₂)₂]( 5m ), [Yb{N‐(SiMe₃)₂}₂Cl] ( 3m/2 ) and Ln(NH₂)₂NHSiMe₃ (Ln = Yb ( 6m ), Y ( 7m )) in order to rationalize the different experimentally observed Yb—N distances, to support the assignment of the O—O stretching vibration (775 cm ^‐1) in the Raman spectrum of complex 5 and to examine the nature of the agostic‐type interactions in σ‐donorfree 3 .     

(2‐Aminopyrimidine‐κN1)aqua(pyridine‐2,6‐dicarboxylato‐κ3O2,N,O6)copper(II): X‐ray and DFT calculated structure

In the title compound, [Cu(C₇H₃N₂O₄)(C₄H₅N₂)(H₂O)], (I), pyridine‐2,6‐dicarboxylate (pydc²⁻), 2‐aminopyrimidine and aqua ligands coordinate the Cu^II centre through two N atoms, two carboxylate O atoms and one water O atom, respectively, to give a nominally distorted square‐pyramidal coordination geometry, a common arrangement for copper complexes containing the pydc²⁻ ligand. Because of the presence of Cu...X_bridged contacts (X = N or O) between adjacent molecules in the crystal structures of (I) and three analogous previously reported compounds, and the corresponding uncertainty about the effective coordination number of the Cu^II centre, density functional theory (DFT) calculations were used to elucidate the degree of covalency in these contacts. The calculated Wiberg and Mayer bond‐order indices reveal that the Cu...O contact can be considered as a coordination bond, whereas the amine group forming a Cu...N contact is not an effective participant in the coordination environment.     

Competition Between π–π and CH/π Interactions: A Comparison of the Structural and Electronic Properties of Alkoxy‐Substituted 1,8‐Bis((propyloxyphenyl)ethynyl)naphthalenes

The structural and electronic consequences of π–π and C?H/π interactions in two alkoxy‐substituted 1,8‐bis‐ ((propyloxyphenyl)ethynyl)naphthalenes are explored by using X‐ray crystallography and electronic structure computations. The crystal structure of analogue 4 , bearing an alkoxy side chain in the 4‐position of each of the phenyl rings, adopts a π‐stacked geometry, whereas analogue 8 , bearing alkoxy groups at both the 2‐ and the 5‐positions of each ring, has a geometry in which the rings are splayed away from a π‐stacked arrangement. Symmetry‐adapted perturbation theory analysis was performed on the two analogues to evaluate the interactions between the phenylethynyl arms in each molecule in terms of electrostatic, steric, polarization, and London dispersion components. The computations support the expectation that the π‐stacked geometry of the alkoxyphenyl units in 4 is simply a consequence of maximizing π–π interactions. However, the splayed geometry of 8 results from a more subtle competition between different noncovalent interactions: this geometry provides a favorable anti‐alignment of C?O bond dipoles, and two C?H/π interactions in which hydrogen atoms of the alkyl side chains interact favorably with the π electrons of the other phenyl ring. These favorable interactions overcome competing π–π interactions to give rise to a geometry in which the phenylethynyl substituents are in an offset, unstacked arrangement.     

A comparative experimental and theoretical investigation of hydrogen‐bond,halogen‐bond and π–π interactions in the solid‐state supramolecular assembly of 2‐ and 4‐formylphenyl arylsulfonates

To explore the operational role of noncovalent interactions in supramolecular architectures with designed topologies, a series of solid‐state structures of 2‐ and 4‐formylphenyl 4‐substituted benzenesulfonates was investigated. The compounds are 2‐formylphenyl 4‐methylbenzenesulfonate, C₁₄H₁₂O₄S, 3a , 2‐formylphenyl 4‐chlorobenzenesulfonate, C₁₃H₉ClO₄S, 3b , 2‐formylphenyl 4‐bromobenzenesulfonate, C₁₃H₉BrO₄S, 3c , 4‐formylphenyl 4‐methylbenzenesulfonate, C₁₄H₁₂O₄S, 4a , 4‐formylphenyl 4‐chlorobenzenesulfonate, 4b , C₁₃H₉ClO₄S, and 4‐formylphenyl 4‐bromobenzenesulfonate, C₁₃H₉BrO₄S, 4c . The title compounds were synthesized under basic conditions from salicylaldehyde/4‐hydroxybenzaldehydes and various aryl sulfonyl chlorides. Remarkably, halogen‐bonding interactions are found to be important to rationalize the solid‐state crystal structures. In particular, the formation of O…X (X = Cl and Br) and type I X…X halogen‐bonding interactions have been analyzed by means of density functional theory (DFT) calculations and characterized using Bader's theory of `atoms in molecules' and molecular electrostatic potential (MEP) surfaces, confirming the relevance and stabilizing nature of these interactions. They have been compared to antiparallel π‐stacking interactions that are formed between the arylsulfonates.     

Insight into the π‐hole···π‐electrons tetrel bonds between F2ZO (Z = C,Si, Ge) and unsaturated hydrocarbons

The intermolecular π‐hole···π‐electrons interactions between F₂ZO (Z = C, Si, Ge) molecules and unsaturated hydrocarbons including acetylene, ethylene, 1,3‐butadiene and benzene were constructed to reveal the differences of tetrel bonds forming by carbon and heavier tetrel atoms. The ab initio computation in association with topological analysis of electron density, natural bond orbital, and energy decomposition analysis demonstrate that the strength of Si···π and Ge···π tetrel bonds is much stronger than that of C···π tetrel bonds. The Si···π and Ge···π tetrel bonds exhibit covalent or partially covalent interaction nature, while the weak C···π tetrel bonds display the hallmarks of noncovalent interaction, the electrostatic interaction is the primary influencing factor. The Si···π and Ge···π interactions are determined by both the σ‐ and π‐electron densities, while the C···π interactions are dominated mainly by the π‐electron densities. The π‐hole···π‐electrons tetrel bonds are dominated by electrostatic interaction, and polarization has a comparable contribution in the Si···π and Ge···π tetrel bonds.     

Construction of a Hexameric Zn(II)‐metallomacrocycle and its Photo‐ and Electroluminescence Properties: [Zn6(O‐hexyl‐3,5‐bis(2,2′:6′,2″‐terpyridine)phenol)6(BF4)12]

Summary: An O‐hexyl‐3,5‐bis(terpyridine)phenol ligand has been synthesized and transformed into a hexagonal Zn(II)‐metallomacrocycle by a facile self‐assembly procedure capitalizing on terpyridine‐Zn(II)‐terpyridine connectivity. The structural composition was confirmed by NMR and mass spectral techniques; photo‐ and electroluminescence properties were also investigated. The OLED device shows green electroluminescent emission at 515 nm with a maximum luminance of 39 cd · m⁻² and maximum efficiency of 0.16 cd · A⁻¹.

Structure and electroluminescent properties of the metallomacrocycle investigated.     

CH–π and CF–π Interactions Lead to Structural Changes of N‐Heterocyclic Carbene Palladium Complexes

The role of CH–π and CF–π interactions in determining the structure of N‐heterocyclic carbene (NHC) palladium complexes were studied using ¹H NMR spectroscopy, X‐ray crystallography, and DFT calculations. The CH–π interactions led to the formation of the cis‐anti isomers in 1‐aryl‐3‐isopropylimidazol‐2‐ylidene‐based [(NHC)₂PdX₂] complexes, while CF–π interactions led to the exclusive formation of the cis‐syn isomer of diiodobis(3‐isopropyl‐1‐pentafluorophenylimidazol‐2‐ylidene) palladium(II).