Differentiation of Cation−π Bonding from Cation−π Intermolecular Interactions: A Quantum Chemistry Study Using Density-Functional Theory and Morokuma Decomposition Methods

Formation of Eigen or Zundel Features at Protonated Water Cluster-Aromatic Interfaces

Interfacial interactions of protonated water clusters adsorbed at aromatic surfaces play an important role in biology, and in atmospheric, chemical and materials sciences. Here, we investigate the interaction of protonated water clusters ((H+ H2 O)n (where n=1-3)) with benzene (Bz), coronene (Cor) and dodecabenzocoronene (Dbc)). To study the structure, stability and spectral features of these complexes, computations are done using DFT-PBE0(+D3) and SAPT0 methods. These interactions are probed by AIM electron density topography and non-covalent interactions index (NCI) analyses. We suggest that the excess proton plays a crucial role in the stability of these model interfaces through strong inductive effects and the formation of Eigen or Zundel features. Also, computations reveal that the extension of the π-aromatic system and the increase of the number of water molecules in the H-bounded water network led to a strengthening of the interactions between the corresponding aromatic compound and protonated water molecules, except when a Zundel ion is formed. The present findings may serve to understand in-depth the role of proton localized at aqueous medium interacting with large aromatic surfaces such as graphene interacting with acidic liquid water. Besides, we give the IR and UV-Vis spectra of these complexes, which may help for their identification in laboratory.

Application of biogenic iron precipitation by strain H117 for tetracycline removal: mechanism of adsorption and activation

To date, biogenic metals have opened up a window for new applications in adsorption of contaminants. But there is still little attention to be paid in the removal of tetracycline (TC) by biogenic iron precipitation (BIP). In this paper, the BIP, from iron-based mixotrophic denitrification batch reactor, was estimated for its adsorption property of TC under various parameters to simulate the behavior in aquatic environment. The maximum adsorption capacity for TC was 195.336 mg g^-1. Analyses of spectrum verified the existence of Fe₃O₄ and FeOOH in BIP, which was the main reason for the removal of TC. The adsorption kinetic and isotherm of TC were well fitted to Elovich and Langmuir isotherm models, respectively, indicating that the adsorption process was mainly controlled by chemical adsorption. Furthermore, we proposed a potential mechanism of adsorption: a combination of cation-π, hydrogen bonding (H-bonding), and electrostatic interaction. Additionally, the activation experiment showed that BIP could enhance the degradation of TC (more than 98.00% removal within 1.0 h) by advanced oxidation process (AOP), due to the existence of FeOOH and Fe₃O₄. Considering its effectiveness in both adsorption and activation performance, BIP is highlighted as an economical and eco-friendly material for TC removal and offers a promising method to resolve sludge disposal in biological treatment of iron-rich groundwater.

Alkali and Alkaline-Earth Cations in Complexes with Small Bioorganic Ligands: Ab Initio Benchmark Calculations and Bond Energy Decomposition

Herein, we report a computational database for the complexes of alkali [Li(I), Na(I), K(I)] and alkaline-earth [Be(II), Mg(II) and Ca(II)] cations with 25 small ligands with varying charge and donor atoms ("O", "N", and "S") that provides geometries and accurate bond energies useful to analyze metal-ligand interactions in proteins and nucleic acids. The role of the ligand→metal charge transfer, the equilibrium bond distance, the electronegativity of the donor atom, the ligand polarizability, and the relative stability of the complexes are discussed in detail. The interacting quantum atoms (IQA) method is used to decompose the binding energy into electrostatic and quantum mechanical contributions. In addition, bond energies are also estimated by means of multipolar electrostatic calculations. No simple correlation exists between bond energies and structural/electronic descriptors unless the data are segregated by the type of ligand or metal. The electrostatic attraction of some molecules (H₂ O, NH₃ , CH₃ OH) towards the metal cations is well reproduced using their (unrelaxed) atomic multipoles, but the same comparison is much less satisfactory for other ligands (e. g. benzene, thiol/thiolate groups, etc.). Besides providing reference structures and bond energies, the database can contribute to validate molecular mechanics potentials capable of yielding a balanced description of alkali and alkaline-earth metals binding to biomolecules.

A molecular tailoring approach – a new guide to quantify the energy of push–pull effects: a case study on (E)-3-(1H-pyrrol-2-yl)prop-2-enones

We report a new approach to quantify the push–pull effect in molecules with internal charge transfer.

Transformation of tetracyclines induced by Fe(III)-bearing smectite clays under anoxic dark conditions

Smectite clays are widely found in subsurface soils and waters. Although they strongly sequester tetracyclines (TCs), little is known about their reactions with these antibiotics under dark anoxic conditions. This study investigated the interactions between TCs and Fe-bearing smectite clays and the influences of environmental factors. Fe-bearing smectite clays were shown to significantly induce the transformation of TCs, including tautomerization, dechlorination, and dehydration. Moreover, the adsorbed TCs reduced the structural Fe(III) in clay particles to structural Fe(II) through electron transfer. The transformation of TCs was more readily induced by smectite clays with a higher rather than a lower Fe content. Tetrahedral Fe(III), and distorted cis- or trans-octahedral Fe(III), were more reactive as an electron acceptor than cis-octahedral Fe(III), as observed on the Mössbauer and FTIR spectra. A lower pH facilitated the adsorption of TCs through dimethyl-amino, amide, and conjugated -OH functional groups and induced a higher rate of TCs transformation. The transformation of chlortetracycline (CTC) was faster than that of oxytetracycline or tetracycline (TTC) due to -Cl substitution. The major transformation CTC products included keto-CTC, epi-CTC, iso-CTC, anhydro-CTC and TTC. Mixtures of these transformed products were found to have a higher acute toxicity than their parent compounds to Photobacterium phosphoreum T3. Our study revealed several previously overlooked interactions between TCs and clay particles that could cause these antibiotics to become unstable in the subsurface environment, with negative effects on the soil-borne microbial community.

The effects of Fe-bearing smectite clays on OH formation and diethyl phthalate degradation with polyphenols and H2O2

The natural formation of hydroxyl radicals (OH) is important for the attenuation of organic contaminants. In this study, seven model polyphenols were selected to react with four types of smectite clays with varied Fe contents in the presence of H₂O₂. Diethyl phthalate (DEP) was selected as a model organic contaminant due to its wide distribution in environment. The results show the appearance of Fe-bearing smectite clays can significantly promote ·OH formation with polyphenols and H₂O₂ under anoxic conditions; clay particle size, the content and location of lattice Fe in smectite clays greatly affect OH formation. Hydrogen bond between phenolic group and smectite surfaces, and cation assisted hydrogen bond between carboxylic group and clay surfaces are important types of complexation. Electrons can be transferred from coordinated polyphenols to structural Fe(III) atoms in tetrahedral layers or at broken edges to form structural Fe(II) and/or semiquinone radicals, both of which can induce H₂O₂ decomposition to OH. DEP can be degraded by OH attack, and the main products are proposed as phthalic acid, monomethyl phthalate, hydroxyl-diethyl phthalates. Our findings suggest that Fe(III)-bearing smectite clay can be reduced by polyphenol and produce OH in anoxic environments, which can induce organic contaminants transformation.

Steel slag as low-cost adsorbent for the removal of phenanthrene and naphthalene

This study investigates the removal effectiveness and characteristics of phenanthrene and naphthalene using low-cost steel slag with batch experiments. The adsorption characteristics of steel slag were measured and analysed using X-ray fluorescence, X-ray diffraction, and Fourier transform infrared spectroscopy. The batch experiments investigated the effect of the time gradient, pH, and steel slag dosage gradient on the adsorption of the steel slag. The results show that with time and dosage of steel slag increased, the adsorption capacity of phenanthrene and naphthalene increased and gradually became balanced, but pH had no obvious effect on the adsorption of phenanthrene and naphthalene. The Langmuir isotherm model best describes the phenanthrene and naphthalene removal by the steel slag, which shows the adsorption occurring in a monolayer. The maximum adsorption capacity of the steel slag to phenanthrene and naphthalene is 0.043 and 0.041 mg/g, respectively. A pseudo-first-order kinetic model can better represent the adsorption of phenanthrene and naphthalene by steel slag. The research demonstrates that the steel slag has a certain adsorption capacity for phenanthrene and naphthalene.

Effect of the cation on the stability of cation–glyme complexes and their interactions with the [TFSA]− anion

The interactions of glymes with alkali or alkaline earth metal cations depend strongly on the metal cations.

Effect of substituent and solvent on cation-π interactions in benzene and borazine: a computational study

A DFT and ab initio quantum chemical study has been carried out at different theoretical levels to delve into the role of the cation-π interaction within the main group metal cations (Li(+), Na(+) and K(+)), substituted benzene and borazine. The effects of electron withdrawing and electron donating groups on these non-covalent forces of interaction were also studied. The excellent correlation between Hammett constants and binding energy values indicates that the cation-π interaction is influenced by both inductive and resonance effects. Electron donating groups (EDG) such as -CH3 and -NH2 attached to benzene at the 1, 3 and 5 position and the three boron atoms of borazine were found to strengthen these interactions, while electron withdrawing groups (EWG) such as -NO2 did the reverse. These results were further substantiated by topological analysis using the quantum theory of atoms in molecules (QTAIM). The polarized continuum model (PCM) and the discrete solvation model were used to elucidate the effect of solvation on the cation-π interaction. The size of the cations and the nature of the substituents were found to influence the enthalpy and binding energy of the systems (or complex). In the gas phase, the cation-π interaction was found to be exothermic, whereas in the presence of a polar solvent the interaction was highly endothermic. Thermochemical analysis predicts the presence of thermodynamic driving forces for borazine and benzene substituted with EDG. DFT based reactivity descriptors, such as global hardness (η), chemical potential (μ) and the electrophilicity index (ω) were used to elucidate the effect of the substituent on the reactivity of the cation-π complexes.

Predicting the cation–π binding of substituted benzenes: energy decomposition calculations and the development of a cation–π substituent constant

This work proposes a new substituent constant,Π⁺, to describe cation–π binding using computational methods at the MP2(full)/6-311++G** level of theory with Symmetry Adapted Perturbation Theory (SAPT) calculations on selected cation–π complexes.

Effects of the aromatic substitution pattern in cation-π sandwich complexes

A computational study investigating the effects of the aromatic substitution pattern on the structure and binding energies of cation-π sandwich complexes is reported. The correlation between the binding energies (Ebind) and Hammett substituent constants is approximately the same as what is observed for cation-π half-sandwich complexes. For cation-π sandwich complexes where both aromatics contain substituents the issue of relative conformation is a possible factor in the strength of the binding; however, the work presented here shows the Ebind values are approximately the same regardless of the relative conformation of the two substituted aromatics. Finally, recent computational work has shown conflicting results on whether cation-π sandwich Ebind values (Ebind,S) are approximately equal to twice the respective half-sandwich Ebind values (Ebind,HS), or if cation-π sandwich Ebind,S values are less than double the respective half-sandwich Ebind,HS values. The work presented here shows that for cation-π sandwich complexes involving substituted aromatics the Ebind,S values are less than twice the respective half-sandwich Ebind,HS values, and this is termed nonadditive. The extent to which the cation-π sandwich complexes investigated here are nonadditive is greater for B3LYP calculated values than for MP2 calculated values and for sandwich complexes with electron-donating substituents than those with electron-withdrawing groups.

Parallel stacking interactions in square-planar transition-metal complexes containing fused chelate and C6-aromatic rings

Stacking interactions in the crystal structures of square-planar transition metal complexes from the Cambridge Structural Database with five- and six-membered chelate rings fused with C6-arom rings (arom = aromatic) were analyzed. The distribution of distances between the closest C6-arom–C6-arom and C6-arom–chelate contacts shows that in a large fraction of the intermolecular interactions the C6-arom ring of one molecule is closer to the chelate than to the C6-arom ring of the other molecule. These results indicate a possible preference of the C6-arom ring to form stacking contacts with the chelate rings. The preference is ubiquitous and does not depend on the metal type.

The use of hammett constants to understand the non-covalent binding of aromatics

Non-covalent interactions of aromatics are important in a wide range of chemical and biological applications. The past two decades have seen numerous reports of arene-arene binding being understood in terms Hammett substituent constants, and similar analyses have recently been extended to cation-arene and anion-arene binding. It is not immediately clear why electrostatic Hammett parameters should work so well in predicting the binding for all three interactions, given that different intermolecular forces dominate each interaction. This review explores such anomalies, and summarizes how Hammett substituent constants have been employed to understand the non-covalent binding in arene-arene, cation-arene and anion-arene interactions.

Reassessment of Hammett σ as an effective parameter representing intermolecular interaction energy-links between traditional and modern QSAR approaches

The Hammett σ constant has for a long time been known to be one of most important linear free-energy related parameters that correlate with biological activity. It is a conventionally used electronic parameter in studies of enzymatic quantitative structure-activity relationships (QSAR). However, it is not necessarily obvious why σ represents variations in the free-energy change associated with the complex formation between a congeneric series of ligands with their target protein. So far, several powerful molecular calculations, such as the ab initio fragment molecular orbital (FMO) one, that are directly applicable to ligand-protein complexes have emerged. In this study, we comprehensively reevaluate experimentally derived parameter σ confirming it represents intermolecular interaction energy terms, by applying molecular orbital (MO) calculations to a simple ligand-protein complex model. The current results provide a rational and quantitative basis for bridging the gap between the traditional QSAR approach and 'the modern QSAR one', which involves the molecular calculations to evaluate the overall free-energy change for complex formation.

A MP2 and DFT study of the influence of complexation on the aromatic character of phosphole

This work is focused in three topical subjects: intermolecular interactions, metal ions, and aromaticity. A comprehensive MP2/6-31 + G and B3LYP/6-31 + G study of the influence of cation-π interactions on the aromatic character of phosphole was conducted. For this purpose, the structures of complexes were optimized at both theoretical level and different magnetic properties were evaluated. The main conclusion is the increase of the aromatic character of the phosphole when complexes with Li(+), Be(2+), and Al(3+) are formed.

Can lone pair-π and cation-π interactions coexist? A theoretical study

The interplay between two important noncovalent interactions involving different aromatic rings is studied by means of ab initio calculations (MP2/6-31++G**) computing the non-additivity energies. In this study we demonstrate the existence of cooperativity effects when cation-π and lone pair-π interactions coexist in the same system. These effects are studied theoretically using energetic and geometric features of the complexes. In addition we use Bader’s theory of atoms-in-molecules and Molecular Interaction Potential with polarization (MIPp) partition scheme to characterize the interactions. Experimental evidence for this combination of interactions has been obtained from the Cambridge Structural Database.

Exploring the size dependence of cyclic and acyclic pi-systems on cation-pi binding

MP2(FULL)/6-311++G** calculations are performed on the cation-pi complexes of Li+ and Mg2+ with the pi-face of linear (ethylene, butadiene, hexatriene, and octatetraene) and cyclic (benzene, naphthalene, anthracene, phenanthrene and naphthacene) unsaturated hydrocarbons. The interaction energy is found to increase systematically as the size of the pi-system increases. The higher interaction energy is in good correlation with the extent of charge transfer. The increase in the interaction energy is more dramatic in the case of acyclic systems. The computations reveal that larger pi-systems tend to have higher complexation energy with the metal ions, which will have important implications in our understanding of the structural and functional aspects of metal binding.

Organometallic Polymers Assembled from Cation–π Interactions: Use of Ferrocene as a Ditopic Linker Within the Homologous Series [{(Me3Si)2NM}2⋅(Cp2Fe)]∞ (M=Na, K, Rb, Cs; Cp=cyclopentadienyl)

Addition of ferrocene to solutions of alkali metal hexamethyldisilazides M(HMDS) in arenes (in which M=Na, K, Rb, Cs) allows the subsequent crystallization of the homologous series of compounds [{(Me(3)Si)(2)NM}(2) (Cp(2)Fe)](infinity) (1-4). Similar reactions using LiHMDS led to the recrystallization of the starting materials. The crystal structures of 1-4 reveal the formation of one-dimensional chains composed of dimeric [{M(HMDS)}(2)] aggregates, which are bridged through neutral ferrocene molecules by eta(5)-cation-pi interactions. In addition, compounds 3 and 4 also contain interchain agostic M--C interactions, producing two-dimensional 4(4)-nets. Whereas 1 and 2 were prepared from toluene, the syntheses of 3 and 4 required the use of tert-butylbenzene as the reaction media. The attempted crystallization of 3 and 4 from toluene resulted in formation of the mixed toluene/ferrocene solvated complexes [{(Me(3)Si)(2)NM)(2)}(2) (Cp(2)Fe)(x)(Tol)(y)](infinity) (in which M=Rb, x=0.6, y=0.8, 5; M=Cs, x=0.5, y=1, 6). The extended solid-state structures of 5 and 6 are closely related to the 4(4)-sheets 3 and 4, but are now assembled from a combination of cation-pi, agostic, and pi-pi interactions. The charge-separated complex [K{(C(6)H(6))(2)Cr}(1.5)(Mes)][Mg(HMDS)(3)] (15) was also structurally characterized and found to adopt an anionic two-dimensional 6(3)-network through doubly eta(3)-coordinated bis(benzene)chromium molecules. DFT calculations at the B3 LYP/6-31G* level of theory indicate that the binding energies of both ferrocene and toluene to the M(HMDS) dimers increases in the sequence Li<Na<K. This pattern is a consequence of the larger metals allowing more open coordination spheres to support cation-pi contacts. By comparison, binding of the isolated metal cations to the aromatic groups follow the reverse order K<Na<Li. A combined analysis of theoretical and experimental data suggest that ferrocene is a stronger cation-pi donor than toluene for the lighter metals, but that this difference is eliminated on descending the group.

Effects of bridge ions, DNA species, and developing temperature on flat-lying DNA monolayers

Recently, we have successfully constructed flat-lying DNA monolayers on a mica surface (J. Phys. Chem. B 2006, 110, 10792-10798). In this work, the effects of various factors including bridge ions, DNA species, and developing temperature on the configuration of DNA monolayers have been investigated by atomic force microscopy (AFM) in detail. AFM results show that the species of bridge ions and developing temperature play a crucial role during the formation process. For example, the divalent cation Zn2+ resulted in many DNA chains stuck side by side in the monolayers due to the strong interactions between it and DNA's bases or the mica surface. Most DNA chain's conglutinations disappeared when the developing temperature was higher than 40 degrees C. Cd2+ and Ca2+ produced more compact DNA monolayers with some obvious aggregations, especially for the DNA monolayers constructed by using Ca2+ as the bridge ion. Co2+ produced well-ordered, flat-lying DNA monolayers similar to that of Mg2+. Furthermore, it was found that the flat-lying DNA monolayers could still form on a mica surface when plasmid DNA pBR 322 and linear DNA pBR 322/Pst I were used as the DNA source. Whereas, it was hard to form DNA monolayers on a (3-aminopropyl)triethoxysilane-mica surface because the strong interactions between DNA and substrate prevented the lateral movement of DNA molecules. These results suggested that the appropriate interactions between divalent cations and DNA or mica surface were important for the formation of flat-lying DNA monolayers. The obtained information is a necessary supplement to our previous studies on the formation kinetics of such monolayers and may be useful for practical application of the monolayers and further theoretical studies.

Electrochemical detection of single-nucleotide mismatches using an electrode microarray

Gold electrode arrays with electrode diameters of 10 mum were used for the detection of eight single-nucleotide mismatches in unlabeled and prehybridized DNA by electrochemical impedance spectroscopy (EIS). Because of the differences in the electrical properties of films of duplex DNA (normal duplex DNA in B-form) in the presence and absence of Zn(2+) at pH > or = 8.6, Randles equivalent circuits were employed to evaluate the EIS results. The difference in the charge-transfer resistance (DeltaR(CT)) between B-DNA (absence of Zn2+ at pH > or = 8.6) and M-DNA (presence of Zn2+ at pH > or = 8.6) allows unequivocal detection of all eight single-nucleotide mismatches within a 20-mer DNA sequence. After dehybridization/rehybridization with target DNA, DeltaR(CT) allows the discrimination of single-nucleotide mismatches with concentrations of the target strand as low as 10 fM. Although the presence of protein impurities (bovine serum albumin, 10 microg/mL) interferes with the detection of the target strand (1 pM detection limit), the presence of nontarget DNA (calf thymus DNA, 10(-8) M) does not interfere, and the detection limit for recognition of the target strand remains at 10 fM.

Chip-based microelectrodes for detection of single-nucleotide mismatch

Microelectrode arrays having eight 10-microm-diameter gold microelectrodes arranged on a gold-covered Si chip were designed and characterized. The chips prove useful for the detection of single-nucleotide mismatches in unlabeled and prehybridized DNA by electrochemical impedance spectroscopy.

Influence of metal and ligand types on stacking interactions of phenyl rings with square-planar transition metal complexes

In order to find out whether metal type influences the stacking interactions of phenyl rings in square-planar complexes, geometrical parameters for Cu, Ni, Pd and Pt complexes, with and without chelate rings, were analyzed and compared. By searching the Cambridge Structural Database, 220 structures with Cu complexes, 211 with Ni complexes, 285 with Pd complexes, and 220 with Pt complexes were found. The results show that the chelate ring has a tendency to make the stacking interaction with the phenyl ring independent of metal type in the chelate ring. However, there are some differences among metals for complexes without a chelate ring. There are a number of structures containing Pd and Pt complexes, without chelate rings, that have short carbon-metal distances and parallel orientations of the phenyl ring with respect to the coordination plane. It was found that some of these complexes have a common fragment, CN, as a part of the ligands. This indicates that the CN supports stacking interactions of square planar complexes with the phenyl ring.